source stringlengths 52 77 | text stringlengths 9 32.2k |
|---|---|
https://openstax.org/books/biology/pages/1-chapter-summary | Biology is the science that studies living organisms and their interactions with one another and their environments. Science attempts to describe and understand the nature of the universe in whole or in part by rational means. Science has many fields; those fields related to the physical world and its phenomena are considered natural sciences.
Science can be basic or applied. The main goal of basic science is to expand knowledge without any expectation of short-term practical application of that knowledge. The primary goal of applied research, however, is to solve practical problems.
Two types of logical reasoning are used in science. Inductive reasoning uses particular results to produce general scientific principles. Deductive reasoning is a form of logical thinking that predicts results by applying general principles. The common thread throughout scientific research is the use of the scientific method, a step-based process that consists of making observations, defining a problem, posing hypotheses, testing these hypotheses, and drawing one or more conclusions. The testing uses proper controls. Scientists present their results in peer-reviewed scientific papers published in scientific journals. A scientific research paper consists of several well-defined sections: introduction, materials and methods, results, and, finally, a concluding discussion. Review papers summarize the research done in a particular field over a period of time.
Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized parts of a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere. The great diversity of life today evolved from less-diverse ancestral organisms over billions of years. A diagram called a phylogenetic tree can be used to show evolutionary relationships among organisms.
Biology is very broad and includes many branches and subdisciplines. Examples include molecular biology, microbiology, neurobiology, zoology, and botany, among others. |
https://openstax.org/books/biology/pages/1-key-terms | abstract : opening section of a scientific paper that summarizes the research and conclusions
applied science : form of science that aims to solve real-world problems
atom : smallest and most fundamental unit of matter
basic science : science that seeks to expand knowledge and understanding regardless of the short-term application of that knowledge
biochemistry : study of the chemistry of biological organisms
biology : the study of living organisms and their interactions with one another and their environments
biosphere : collection of all the ecosystems on Earth
botany : study of plants
cell : smallest fundamental unit of structure and function in living things
community : set of populations inhabiting a particular area
conclusion : section of a scientific paper that summarizes the importance of the experimental findings
control : part of an experiment that does not change during the experiment
deductive reasoning : form of logical thinking that uses a general inclusive statement to forecast specific results
descriptive science : (also, discovery science) form of science that aims to observe, explore, and investigate
discussion : section of a scientific paper in which the author interprets experimental results, describes how variables may be related, and attempts to explain the phenomenon in question
ecosystem : all the living things in a particular area together with the abiotic, nonliving parts of that environment
eukaryote : organism with cells that have nuclei and membrane-bound organelles
evolution : process of gradual change during which new species arise from older species and some species become extinct
falsifiable : able to be disproven by experimental results
homeostasis : ability of an organism to maintain constant internal conditions
hypothesis : suggested explanation for an observation, which can be tested
hypothesis-based science : form of science that begins with a specific question and potential testable answers
inductive reasoning : form of logical thinking that uses related observations to arrive at a general conclusion
introduction : opening section of a scientific paper, which provides background information about what was known in the field prior to the research reported in the paper
life science : field of science, such as biology, that studies living things
macromolecule : large molecule, typically formed by the joining of smaller molecules
materials and methods : section of a scientific paper that includes a complete description of the substances, methods, and techniques used by the researchers to gather data
microbiology : study of the structure and function of microorganisms
molecular biology : study of biological processes and their regulation at the molecular level, including interactions among molecules such as DNA, RNA, and proteins
molecule : chemical structure consisting of at least two atoms held together by one or more chemical bonds
natural science : field of science that is related to the physical world and its phenomena and processes
neurobiology : study of the biology of the nervous system
organ : collection of related tissues grouped together performing a common function
organ system : level of organization that consists of functionally related interacting organs
organelle : small structures that exist within cells and carry out cellular functions
organism : individual living entity
paleontology : study of lifeâs history by means of fossils
peer-reviewed manuscript : scientific paper that is reviewed by a scientistâs colleagues who are experts in the field of study
phylogenetic tree : diagram showing the evolutionary relationships among various biological species based on similarities and differences in genetic or physical traits or both; in essence, a hypothesis concerning evolutionary connections
physical science : field of science, such as geology, astronomy, physics, and chemistry, that studies nonliving matter
plagiarism : using other peopleâs work or ideas without proper citation, creating the false impression that those are the authorâs original ideas
population : all of the individuals of a species living within a specific area
prokaryote : single-celled organism that lacks organelles and does not have nuclei surrounded by a nuclear membrane
results : section of a scientific paper in which the author narrates the experimental findings and presents relevant figures, pictures, diagrams, graphs, and tables, without any further interpretation
review article : paper that summarizes and comments on findings that were published as primary literature
science : knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method
scientific method : method of research with defined steps that include observation, formulation of a hypothesis, testing, and confirming or falsifying the hypothesis
serendipity : fortunate accident or a lucky surprise
theory : tested and confirmed explanation for observations or
phenomena
tissue : group of similar cells carrying out related functions
variable : part of an experiment that the experimenter can vary or
change
zoology : study of animals |
https://openstax.org/books/biology/pages/2-chapter-summary | Matter is anything that occupies space and has mass. It is made up of elements. All of the 92 elements that occur naturally have unique qualities that allow them to combine in various ways to create molecules, which in turn combine to form cells, tissues, organ systems, and organisms. Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can be transferred, shared, or cause charge disparities between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.
Water has many properties that are critical to maintaining life. It is a polar molecule, allowing for the formation of hydrogen bonds. Hydrogen bonds allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent. The hydrogen bonds between water molecules cause the water to have a high heat capacity, meaning it takes a lot of added heat to raise its temperature. As the temperature rises, the hydrogen bonds between water continually break and form anew. This allows for the overall temperature to remain stable, although energy is added to the system. Water also exhibits a high heat of vaporization, which is key to how organisms cool themselves by the evaporation of sweat. Waterâs cohesive forces allow for the property of surface tension, whereas its adhesive properties are seen as water rises inside capillary tubes. The pH value is a measure of hydrogen ion concentration in a solution and is one of many chemical characteristics that is highly regulated in living organisms through homeostasis. Acids and bases can change pH values, but buffers tend to moderate the changes they cause. These properties of water are intimately connected to the biochemical and physical processes performed by living organisms, and life would be very different if these properties were altered, if it could exist at all.
The unique properties of carbon make it a central part of biological molecules. Carbon binds to oxygen, hydrogen, and nitrogen covalently to form the many molecules important for cellular function. Carbon has four electrons in its outermost shell and can form four bonds. Carbon and hydrogen can form hydrocarbon chains or rings. Functional groups are groups of atoms that confer specific properties to hydrocarbon (or substituted hydrocarbon) chains or rings that define their overall chemical characteristics and function. |
https://openstax.org/books/biology/pages/2-key-terms | acid : molecule that donates hydrogen ions and increases the concentration of hydrogen ions in a solution
adhesion : attraction between water molecules and other molecules
aliphatic hydrocarbon : hydrocarbon consisting of a linear chain of carbon atoms
anion : negative ion that is formed by an atom gaining one or more electrons
aromatic hydrocarbon : hydrocarbon consisting of closed rings of carbon atoms
atom : the smallest unit of matter that retains all of the chemical properties of an element
atomic mass : calculated mean of the mass number for an elementâs isotopes
atomic number : total number of protons in an atom
balanced chemical equation : statement of a chemical reaction with the number of each type of atom equalized for both the products and reactants
base : molecule that donates hydroxide ions or otherwise binds excess hydrogen ions and decreases the concentration of hydrogen ions in a solution
buffer : substance that prevents a change in pH by absorbing or releasing hydrogen or hydroxide ions
calorie : amount of heat required to change the temperature of one gram of water by one degree Celsius
capillary action : occurs because water molecules are attracted to charges on the inner surfaces of narrow tubular structures such as glass tubes, drawing the water molecules to the sides of the tubes
cation : positive ion that is formed by an atom losing one or more electrons
chemical bond : interaction between two or more of the same or different atoms that results in the formation of molecules
chemical reaction : process leading to the rearrangement of atoms in molecules
chemical reactivity : the ability to combine and to chemically bond with each other
cohesion : intermolecular forces between water molecules caused by the polar nature of water; responsible for surface tension
compound : substance composed of molecules consisting of atoms of at least two different elements
covalent bond : type of strong bond formed between two of the same or different elements; forms when electrons are shared between atoms
dissociation : release of an ion from a molecule such that the original molecule now consists of an ion and the charged remains of the original, such as when water dissociates into H+and OH-
electrolyte : ion necessary for nerve impulse conduction, muscle contractions and water balance
electron : negatively charged subatomic particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a negative charge of â1 unit
electron configuration : arrangement of electrons in an atomâs electron shell (for example, 1s22s22p6)
electron orbital : how electrons are spatially distributed surrounding the nucleus; the area where an electron is most likely to be found
electron transfer : movement of electrons from one element to another; important in creation of ionic bonds
electronegativity : ability of some elements to attract electrons (often of hydrogen atoms), acquiring partial negative charges in molecules and creating partial positive charges on the hydrogen atoms
element : one of 118 unique substances that cannot be broken down into smaller substances; each element has unique properties and a specified number of protons
enantiomers : molecules that share overall structure and bonding patterns, but differ in how the atoms are three dimensionally placed such that they are mirror images of each other
equilibrium : steady state of relative reactant and product concentration in reversible chemical reactions in a closed system
evaporation : separation of individual molecules from the surface of a body of water, leaves of a plant, or the skin of an organism
functional group : group of atoms that provides or imparts a specific function to a carbon skeleton
geometric isomer : isomer with similar bonding patterns differing in the placement of atoms alongside a double covalent bond
heat of vaporization of water : high amount of energy required for liquid water to turn into water vapor
hydrocarbon : molecule that consists only of carbon and hydrogen
hydrogen bond : weak bond between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules
hydrophilic : describes ions or polar molecules that interact well with other polar molecules such as water
hydrophobic : describes uncharged non-polar molecules that do not interact well with polar molecules such as water
inert gas : (also, noble gas) element with filled outer electron shell that is unreactive with other atoms
ion : atom or chemical group that does not contain equal numbers of protons and electrons
ionic bond : chemical bond that forms between ions with opposite charges (cations and anions)
irreversible chemical reaction : chemical reaction where reactants proceed uni-directionally to form products
isomers : molecules that differ from one another even though they share the same chemical formula
isotope : one or more forms of an element that have different numbers of neutrons
law of mass action : chemical law stating that the rate of a reaction is proportional to the concentration of the reacting substances
litmus paper : (also, pH paper) filter paper that has been treated with a natural water-soluble dye that changes its color as the pH of the environment changes so it can be used as a pH indicator
mass number : total number of protons and neutrons in an atom
matter : anything that has mass and occupies space
molecule : two or more atoms chemically bonded together
neutron : uncharged particle that resides in the nucleus of an atom; has a mass of one amu
noble gas : see inert gas
nonpolar covalent bond : type of covalent bond that forms between atoms when electrons are shared equally between them
nucleus : core of an atom; contains protons and neutrons
octet rule : rule that atoms are most stable when they hold eight electrons in their outermost shells
orbital : region surrounding the nucleus; contains electrons
organic molecule : any molecule containing carbon (except carbon dioxide)
periodic table : organizational chart of elements indicating the atomic number and atomic mass of each element; provides key information about the properties of the elements
pH paper : see litmus paper
pH scale : scale ranging from zero to 14 that is inversely proportional to the concentration of hydrogen ions in a solution
polar covalent bond : type of covalent bond that forms as a result of unequal sharing of electrons, resulting in the creation of slightly positive and slightly negative charged regions of the molecule
product : molecule found on the right side of a chemical equation
proton : positively charged particle that resides in the nucleus of an atom; has a mass of one amu and a charge of +1
radioisotope : isotope that emits radiation composed of subatomic particles to form more stable elements
reactant : molecule found on the left side of a chemical equation
reversible chemical reaction : chemical reaction that functions bi-directionally, where products may turn into reactants if their concentration is great enough
solvent : substance capable of dissolving another substance
specific heat capacity : the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius
sphere of hydration : when a polar water molecule surrounds charged or polar molecules thus keeping them dissolved and in solution
structural isomers : molecules that share a chemical formula but differ in the placement of their chemical bonds
substituted hydrocarbon : hydrocarbon chain or ring containing an atom of another element in place of one of the backbone carbons
surface tension : tension at the surface of a body of liquid that prevents the molecules from separating; created by the attractive cohesive forces between the molecules of the liquid
valence shell : outermost shell of an atom
van der Waals interaction : very weak interaction between molecules due to temporary charges attracting atoms that are very close together |
https://openstax.org/books/biology/pages/3-chapter-summary | Proteins, carbohydrates, nucleic acids, and lipids are the four major classes of biological macromoleculesâlarge molecules necessary for life that are built from smaller organic molecules. Macromolecules are made up of single units known as monomers that are joined by covalent bonds to form larger polymers. The polymer is more than the sum of its parts: it acquires new characteristics, and leads to an osmotic pressure that is much lower than that formed by its ingredients; this is an important advantage in the maintenance of cellular osmotic conditions. A monomer joins with another monomer with the release of a water molecule, leading to the formation of a covalent bond. These types of reactions are known as dehydration or condensation reactions. When polymers are broken down into smaller units (monomers), a molecule of water is used for each bond broken by these reactions; such reactions are known as hydrolysis reactions. Dehydration and hydrolysis reactions are similar for all macromolecules, but each monomer and polymer reaction is specific to its class. Dehydration reactions typically require an investment of energy for new bond formation, while hydrolysis reactions typically release energy by breaking bonds.
Carbohydrates are a group of macromolecules that are a vital energy source for the cell and provide structural support to plant cells, fungi, and all of the arthropods that include lobsters, crabs, shrimp, insects, and spiders. Carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides depending on the number of monomers in the molecule. Monosaccharides are linked by glycosidic bonds that are formed as a result of dehydration reactions, forming disaccharides and polysaccharides with the elimination of a water molecule for each bond formed. Glucose, galactose, and fructose are common monosaccharides, whereas common disaccharides include lactose, maltose, and sucrose. Starch and glycogen, examples of polysaccharides, are the storage forms of glucose in plants and animals, respectively. The long polysaccharide chains may be branched or unbranched. Cellulose is an example of an unbranched polysaccharide, whereas amylopectin, a constituent of starch, is a highly branched molecule. Storage of glucose, in the form of polymers like starch of glycogen, makes it slightly less accessible for metabolism; however, this prevents it from leaking out of the cell or creating a high osmotic pressure that could cause excessive water uptake by the cell.
Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, waxes, phospholipids, and steroids. Fats are a stored form of energy and are also known as triacylglycerols or triglycerides. Fats are made up of fatty acids and either glycerol or sphingosine. Fatty acids may be unsaturated or saturated, depending on the presence or absence of double bonds in the hydrocarbon chain. If only single bonds are present, they are known as saturated fatty acids. Unsaturated fatty acids may have one or more double bonds in the hydrocarbon chain. Phospholipids make up the matrix of membranes. They have a glycerol or sphingosine backbone to which two fatty acid chains and a phosphate-containing group are attached. Steroids are another class of lipids. Their basic structure has four fused carbon rings. Cholesterol is a type of steroid and is an important constituent of the plasma membrane, where it helps to maintain the fluid nature of the membrane. It is also the precursor of steroid hormones such as testosterone.
Proteins are a class of macromolecules that perform a diverse range of functions for the cell. They help in metabolism by providing structural support and by acting as enzymes, carriers, or hormones. The building blocks of proteins (monomers) are amino acids. Each amino acid has a central carbon that is linked to an amino group, a carboxyl group, a hydrogen atom, and an R group or side chain. There are 20 commonly occurring amino acids, each of which differs in the R group. Each amino acid is linked to its neighbors by a peptide bond. A long chain of amino acids is known as a polypeptide.
Proteins are organized at four levels: primary, secondary, tertiary, and (optional) quaternary. The primary structure is the unique sequence of amino acids. The local folding of the polypeptide to form structures such as theαhelix andβ-pleated sheet constitutes the secondary structure. The overall three-dimensional structure is the tertiary structure. When two or more polypeptides combine to form the complete protein structure, the configuration is known as the quaternary structure of a protein. Protein shape and function are intricately linked; any change in shape caused by changes in temperature or pH may lead to protein denaturation and a loss in function.
Nucleic acids are molecules made up of nucleotides that direct cellular activities such as cell division and protein synthesis. Each nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic acids: DNA and RNA. DNA carries the genetic blueprint of the cell and is passed on from parents to offspring (in the form of chromosomes). It has a double-helical structure with the two strands running in opposite directions, connected by hydrogen bonds, and complementary to each other. RNA is single-stranded and is made of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is involved in protein synthesis and its regulation. Messenger RNA (mRNA) is copied from the DNA, is exported from the nucleus to the cytoplasm, and contains information for the construction of proteins. Ribosomal RNA (rRNA) is a part of the ribosomes at the site of protein synthesis, whereas transfer RNA (tRNA) carries the amino acid to the site of protein synthesis. microRNA regulates the use of mRNA for protein synthesis. |
https://openstax.org/books/biology/pages/3-key-terms | alpha-helix structure (α-helix) : type of secondary structure of proteins formed by folding of the polypeptide into a helix shape with hydrogen bonds stabilizing the structure
amino acid : monomer of a protein; has a central carbon or alpha carbon to which an amino group, a carboxyl group, a hydrogen, and an R group or side chain is attached; the R group is different for all 20 amino acids
beta-pleated sheet (β-pleated) : secondary structure found in proteins in which âpleatsâ are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain
biological macromolecule : large molecule necessary for life that is built from smaller organic molecules
carbohydrate : biological macromolecule in which the ratio of carbon to hydrogen and to oxygen is 1:2:1; carbohydrates serve as energy sources and structural support in cells and form the a cellular exoskeleton of arthropods
cellulose : polysaccharide that makes up the cell wall of plants; provides structural support to the cell
chaperone : (also, chaperonin) protein that helps nascent protein in the folding process
chitin : type of carbohydrate that forms the outer skeleton of all arthropods that include crustaceans and insects; it also forms the cell walls of fungi
dehydration synthesis : (also, condensation) reaction that links monomer molecules together, releasing a molecule of water for each bond formed
denaturation : loss of shape in a protein as a result of changes in temperature, pH, or exposure to chemicals
deoxyribonucleic acid (DNA) : double-helical molecule that carries the hereditary information of the cell
disaccharide : two sugar monomers that are linked together by a glycosidic bond
enzyme : catalyst in a biochemical reaction that is usually a complex or conjugated protein
glycogen : storage carbohydrate in animals
glycosidic bond : bond formed by a dehydration reaction between two monosaccharides with the elimination of a water molecule
hormone : chemical signaling molecule, usually protein or steroid, secreted by endocrine cells that act to control or regulate specific physiological processes
hydrolysis : reaction causes breakdown of larger molecules into smaller molecules with the utilization of water
lipid : macromolecule that is nonpolar and insoluble in water
messenger RNA (mRNA) : RNA that carries information from DNA to ribosomes during protein synthesis
monomer : smallest unit of larger molecules called polymers
monosaccharide : single unit or monomer of carbohydrates
nucleic acid : biological macromolecule that carries the genetic blueprint of a cell and carries instructions for the functioning of the cell
nucleotide : monomer of nucleic acids; contains a pentose sugar, one or more phosphate groups, and a nitrogenous base
omega fat : type of polyunsaturated fat that is required by the body; the numbering of the carbon omega starts from the methyl end or the end that is farthest from the carboxylic end
peptide bond : bond formed between two amino acids by a dehydration reaction
phosphodiester : linkage covalent chemical bond that holds together the polynucleotide chains with a phosphate group linking two pentose sugars of neighboring nucleotides
phospholipid : major constituent of the membranes; composed of two fatty acids and a phosphate-containing group attached to a glycerol backbone
polymer : chain of monomer residues that is linked by covalent bonds; polymerization is the process of polymer formation from monomers by condensation
polynucleotide : long chain of nucleotides
polypeptide : long chain of amino acids linked by peptide bonds
polysaccharide : long chain of monosaccharides; may be branched or unbranched
primary structure : linear sequence of amino acids in a protein
protein : biological macromolecule composed of one or more chains of amino acids
purine : type of nitrogenous base in DNA and RNA; adenine and guanine are purines
pyrimidine : type of nitrogenous base in DNA and RNA; cytosine, thymine, and uracil are pyrimidines
quaternary structure : association of discrete polypeptide subunits in a protein
ribonucleic acid (RNA) : single-stranded, often internally base paired, molecule that is involved in protein synthesis
ribosomal RNA (rRNA) : RNA that ensures the proper alignment of the mRNA and the ribosomes during protein synthesis and catalyzes the formation of the peptide linkage
saturated fatty acid : long-chain of hydrocarbon with single covalent bonds in the carbon chain; the number of hydrogen atoms attached to the carbon skeleton is maximized
secondary structure : regular structure formed by proteins by intramolecular hydrogen bonding between the oxygen atom of one amino acid residue and the hydrogen attached to the nitrogen atom of another amino acid residue
starch : storage carbohydrate in plants
steroid : type of lipid composed of four fused hydrocarbon rings forming a planar structure
tertiary structure : three-dimensional conformation of a protein, including interactions between secondary structural elements; formed from interactions between amino acid side chains
trans fat : fat formed artificially by hydrogenating oils, leading to a different arrangement of double bond(s) than those found in naturally occurring lipids
transcription : process through which messenger RNA forms on a template of DNA
transfer RNA (tRNA) : RNA that carries activated amino acids to the site of protein synthesis on the ribosome
translation : process through which RNA directs the formation of protein
triacylglycerol (also, triglyceride) : fat molecule; consists of three fatty acids linked to a glycerol molecule
unsaturated fatty acid : long-chain hydrocarbon that has one or more double bonds in the hydrocarbon chain
wax : lipid made of a long-chain fatty acid that is esterified to a long-chain alcohol; serves as a protective coating on some feathers, aquatic mammal fur, and leaves |
https://openstax.org/books/biology/pages/4-chapter-summary | A cell is the smallest unit of life. Most cells are so tiny that they cannot be seen with the naked eye. Therefore, scientists use microscopes to study cells. Electron microscopes provide higher magnification, higher resolution, and more detail than light microscopes. The unified cell theory states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells.
Prokaryotes are predominantly single-celled organisms of the domains Bacteria and Archaea. All prokaryotes have plasma membranes, cytoplasm, ribosomes, and DNA that is not membrane-bound. Most have peptidoglycan cell walls and many have polysaccharide capsules. Prokaryotic cells range in diameter from 0.1 to 5.0 μm.
As a cell increases in size, its surface area-to-volume ratio decreases. If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume.
Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleusâs nucleolus is the site of ribosome assembly. Ribosomes are either found in the cytoplasm or attached to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria participate in cellular respiration; they are responsible for the majority of ATP produced in the cell. Peroxisomes hydrolyze fatty acids, amino acids, and some toxins. Vesicles and vacuoles are storage and transport compartments. In plant cells, vacuoles also help break down macromolecules.
Animal cells also have a centrosome and lysosomes. The centrosome has two bodies perpendicular to each other, the centrioles, and has an unknown purpose in cell division. Lysosomes are the digestive organelles of animal cells.
Plant cells and plant-like cells each have a cell wall, chloroplasts, and a central vacuole. The plant cell wall, whose primary component is cellulose, protects the cell, provides structural support, and gives shape to the cell. Photosynthesis takes place in chloroplasts. The central vacuole can expand without having to produce more cytoplasm.
The endomembrane system includes the nuclear envelope, lysosomes, vesicles, the ER, and Golgi apparatus, as well as the plasma membrane. These cellular components work together to modify, package, tag, and transport proteins and lipids that form the membranes.
The RER modifies proteins and synthesizes phospholipids used in cell membranes. The SER synthesizes carbohydrates, lipids, and steroid hormones; engages in the detoxification of medications and poisons; and stores calcium ions. Sorting, tagging, packaging, and distribution of lipids and proteins take place in the Golgi apparatus. Lysosomes are created by the budding of the membranes of the RER and Golgi. Lysosomes digest macromolecules, recycle worn-out organelles, and destroy pathogens.
The cytoskeleton has three different types of protein elements. From narrowest to widest, they are the microfilaments (actin filaments), intermediate filaments, and microtubules. Microfilaments are often associated with myosin. They provide rigidity and shape to the cell and facilitate cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. They are also the structural element of centrioles, flagella, and cilia.
Animal cells communicate via their extracellular matrices and are connected to each other via tight junctions, desmosomes, and gap junctions. Plant cells are connected and communicate with each other via plasmodesmata.
When protein receptors on the surface of the plasma membrane of an animal cell bind to a substance in the extracellular matrix, a chain of reactions begins that changes activities taking place within the cell. Plasmodesmata are channels between adjacent plant cells, while gap junctions are channels between adjacent animal cells. However, their structures are quite different. A tight junction is a watertight seal between two adjacent cells, while a desmosome acts like a spot weld. |
https://openstax.org/books/biology/pages/4-key-terms | cell theory : see unified cell theory
cell wall : rigid cell covering made of various molecules that protects the cell, provides structural support, and gives shape to the cell
central vacuole : large plant cell organelle that regulates the cellâs storage compartment, holds water, and plays a significant role in cell growth as the site of macromolecule degradation
centrosome : region in animal cells made of two centrioles
chlorophyll : green pigment that captures the light energy that drives the light reactions of photosynthesis
chloroplast : plant cell organelle that carries out photosynthesis
chromatin : protein-DNA complex that serves as the building material of chromosomes
chromosome : structure within the nucleus that is made up of chromatin that contains DNA, the hereditary material
cilium : (plural = cilia) short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire cell or move substances along the outer surface of the cell
cytoplasm : entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals
cytoskeleton : network of protein fibers that collectively maintain the shape of the cell, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable unicellular organisms to move independently
cytosol : gel-like material of the cytoplasm in which cell structures are suspended
desmosome : linkages between adjacent epithelial cells that form when cadherins in the plasma membrane attach to intermediate filaments
electron microscope : an instrument that magnifies an object using a beam of electrons passed and bent through a lens system to visualize a specimen
endomembrane system : group of organelles and membranes in eukaryotic cells that work together modifying, packaging, and transporting lipids and proteins
endoplasmic reticulum (ER) : series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids
eukaryotic cell : cell that has a membrane-bound nucleus and several other membrane-bound compartments or sacs
extracellular matrix : material (primarily collagen, glycoproteins, and proteoglycans) secreted from animal cells that provides mechanical protection and anchoring for the cells in the tissue
flagellum : (plural = flagella) long, hair-like structure that extends from the plasma membrane and is used to move the cell
gap junction : channel between two adjacent animal cells that allows ions, nutrients, and low molecular weight substances to pass between cells, enabling the cells to communicate
Golgi apparatus : eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution
intermediate filament : cytoskeletal component, composed of several intertwined strands of fibrous protein, that bears tension, supports cell-cell junctions, and anchors cells to extracellular structures
light microscope : an instrument that magnifies an object using a beam visible light passed and bent through a lens system to visualize a specimen
lysosome : organelle in an animal cell that functions as the cellâs digestive component; it breaks down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles
microfilament : narrowest element of the cytoskeleton system; it provides rigidity and shape to the cell and enables cellular movements
microscope : an instrument that magnifies an object
microtubule : widest element of the cytoskeleton system; it helps the cell resist compression, provides a track along which vesicles move through the cell, pulls replicated chromosomes to opposite ends of a dividing cell, and is the structural element of centrioles, flagella, and cilia
mitochondria : (singular = mitochondrion) cellular organelles responsible for carrying out cellular respiration, resulting in the production of ATP, the cellâs main energy-carrying molecule
nuclear envelope : double-membrane structure that constitutes the outermost portion of the nucleus
nucleoid : central part of a prokaryotic cell in which the chromosome is found
nucleolus : darkly staining body within the nucleus that is responsible for assembling the subunits of the ribosomes
nucleoplasm : semi-solid fluid inside the nucleus that contains the chromatin and nucleolus
nucleus : cell organelle that houses the cellâs DNA and directs the synthesis of ribosomes and proteins
organelle : compartment or sac within a cell
peroxisome : small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons
plasma membrane : phospholipid bilayer with embedded (integral) or attached (peripheral) proteins, and separates the internal content of the cell from its surrounding environment
plasmodesma : (plural = plasmodesmata) channel that passes between the cell walls of adjacent plant cells, connects their cytoplasm, and allows materials to be transported from cell to cell
prokaryote : unicellular organism that lacks a nucleus or any other membrane-bound organelle
ribosome : cellular structure that carries out protein synthesis
rough endoplasmic reticulum (RER) : region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification and phospholipid synthesis
smooth endoplasmic reticulum (SER) : region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies certain chemicals (like pesticides, preservatives, medications, and environmental pollutants), and stores calcium ions
tight junction : firm seal between two adjacent animal cells created by protein adherence
unified cell theory : a biological concept that states that all organisms are composed of one or more cells; the cell is the basic unit of life; and new cells arise from existing cells
vacuole : membrane-bound sac, somewhat larger than a vesicle, which functions in cellular storage and transport
vesicle : small, membrane-bound sac that functions in cellular storage and transport; its membrane is capable of fusing with the plasma membrane and the membranes of the endoplasmic reticulum and Golgi apparatus |
https://openstax.org/books/biology/pages/5-chapter-summary | The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of which span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some of the proteins and lipids on the outward-facing surface of the membrane, forming complexes that function to identify the cell to other cells. The fluid nature of the membrane is due to temperature, the configuration of the fatty acid tails (some kinked by double bonds), the presence of cholesterol embedded in the membrane, and the mosaic nature of the proteins and protein-carbohydrate combinations, which are not firmly fixed in place. Plasma membranes enclose and define the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux.
The passive forms of transport, diffusion and osmosis, move materials of small molecular weight across membranes. Substances diffuse from areas of high concentration to areas of lower concentration, and this process continues until the substance is evenly distributed in a system. In solutions containing more than one substance, each type of molecule diffuses according to its own concentration gradient, independent of the diffusion of other substances. Many factors can affect the rate of diffusion, including concentration gradient, size of the particles that are diffusing, temperature of the system, and so on.
In living systems, diffusion of substances into and out of cells is mediated by the plasma membrane. Some materials diffuse readily through the membrane, but others are hindered, and their passage is made possible by specialized proteins, such as channels and transporters. The chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem. In living systems, diffusion of some substances would be slow or difficult without membrane proteins that facilitate transport.
The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. A positive ion, for example, might tend to diffuse into a new area, down its concentration gradient, but if it is diffusing into an area of net positive charge, its diffusion will be hampered by its electrical gradient. When dealing with ions in aqueous solutions, a combination of the electrochemical and concentration gradients, rather than just the concentration gradient alone, must be considered. Living cells need certain substances that exist inside the cell in concentrations greater than they exist in the extracellular space. Moving substances up their electrochemical gradients requires energy from the cell. Active transport uses energy stored in ATP to fuel this transport. Active transport of small molecular-sized materials uses integral proteins in the cell membrane to move the materials: These proteins are analogous to pumps. Some pumps, which carry out primary active transport, couple directly with ATP to drive their action. In co-transport (or secondary active transport), energy from primary transport can be used to move another substance into the cell and up its concentration gradient.
Active transport methods require the direct use of ATP to fuel the transport. Large particles, such as macromolecules, parts of cells, or whole cells, can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle entirely enclosed by an envelope of plasma membrane. Vesicle contents are broken down by the cell, with the particles either used as food or dispatched. Pinocytosis is a similar process on a smaller scale. The plasma membrane invaginates and pinches off, producing a small envelope of fluid from outside the cell. Pinocytosis imports substances that the cell needs from the extracellular fluid. The cell expels waste in a similar but reverse manner: it pushes a membranous vacuole to the plasma membrane, allowing the vacuole to fuse with the membrane and incorporate itself into the membrane structure, releasing its contents to the exterior. |
https://openstax.org/books/biology/pages/5-key-terms | active transport : method of transporting material that requires energy
amphiphilic : molecule possessing a polar or charged area and a nonpolar or uncharged area capable of interacting with both hydrophilic and hydrophobic environments
antiporter : transporter that carries two ions or small molecules in different directions
aquaporin : channel protein that allows water through the membrane at a very high rate
carrier protein : membrane protein that moves a substance across the plasma membrane by changing its own shape
caveolin : protein that coats the cytoplasmic side of the plasma membrane and participates in the process of liquid update by potocytosis
channel protein : membrane protein that allows a substance to pass through its hollow core across the plasma membrane
clathrin : protein that coats the inward-facing surface of the plasma membrane and assists in the formation of specialized structures, like coated pits, for phagocytosis
concentration gradient : area of high concentration adjacent to an area of low concentration
diffusion : passive process of transport of low-molecular weight material according to its concentration gradient
electrochemical gradient : gradient produced by the combined forces of an electrical gradient and a chemical gradient
electrogenic pump : pump that creates a charge imbalance
endocytosis : type of active transport that moves substances, including fluids and particles, into a cell
exocytosis : process of passing bulk material out of a cell
facilitated transport : process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins
fluid mosaic model : describes the structure of the plasma membrane as a mosaic of components including phospholipids, cholesterol, proteins, glycoproteins, and glycolipids (sugar chains attached to proteins or lipids, respectively), resulting in a fluid character (fluidity)
glycolipid : combination of carbohydrates and lipids
glycoprotein : combination of carbohydrates and proteins
hydrophilic : molecule with the ability to bond with water; âwater-lovingâ
hydrophobic : molecule that does not have the ability to bond with water; âwater-hatingâ
hypertonic : situation in which extracellular fluid has a higher osmolarity than the fluid inside the cell, resulting in water moving out of the cell
hypotonic : situation in which extracellular fluid has a lower osmolarity than the fluid inside the cell, resulting in water moving into the cell
integral protein : protein integrated into the membrane structure that interacts extensively with the hydrocarbon chains of membrane lipids and often spans the membrane; these proteins can be removed only by the disruption of the membrane by detergents
isotonic : situation in which the extracellular fluid has the same osmolarity as the fluid inside the cell, resulting in no net movement of water into or out of the cell
osmolarity : total amount of substances dissolved in a specific amount of solution
osmosis : transport of water through a semipermeable membrane according to the concentration gradient of water across the membrane that results from the presence of solute that cannot pass through the membrane
passive transport : method of transporting material through a membrane that does not require energy
peripheral protein : protein found at the surface of a plasma membrane either on its exterior or interior side; these proteins can be removed (washed off of the membrane) by a high-salt wash
pinocytosis : a variation of endocytosis that imports macromolecules that the cell needs from the extracellular fluid
plasmolysis : detaching of the cell membrane from the cell wall and constriction of the cell membrane when a plant cell is in a hypertonic solution
potocytosis : variation of pinocytosis that uses a different coating protein (caveolin) on the cytoplasmic side of the plasma membrane
primary active transport : active transport that moves ions or small molecules across a membrane and may create a difference in charge across that membrane
pump : active transport mechanism that works against electrochemical gradients
receptor-mediated endocytosis : variation of endocytosis that involves the use of specific binding proteins in the plasma membrane for specific molecules or particles, and clathrin-coated pits that become clathrin-coated vesicles
secondary active transport : movement of material that is due to the electrochemical gradient established by primary active transport
selectively permeable : characteristic of a membrane that allows some substances through but not others
solute : substance dissolved in a liquid to form a solution
symporter : transporter that carries two different ions or small molecules, both in the same direction
tonicity : amount of solute in a solution
transport protein : membrane protein that facilitates passage of a substance across a membrane by binding it
transporter : specific carrier proteins or pumps that facilitate movement
uniporter : transporter that carries one specific ion or molecule |
https://openstax.org/books/biology/pages/6-chapter-summary | Cells perform the functions of life through various chemical reactions. A cellâs metabolism refers to the chemical reactions that take place within it. There are metabolic reactions that involve the breaking down of complex chemicals into simpler ones, such as the breakdown of large macromolecules. This process is referred to as catabolism, and such reactions are associated with a release of energy. On the other end of the spectrum, anabolism refers to metabolic processes that build complex molecules out of simpler ones, such as the synthesis of macromolecules. Anabolic processes require energy. Glucose synthesis and glucose breakdown are examples of anabolic and catabolic pathways, respectively.
Energy comes in many different forms. Objects in motion do physical work, and kinetic energy is the energy of objects in motion. Objects that are not in motion may have the potential to do work, and thus, have potential energy. Molecules also have potential energy because the breaking of molecular bonds has the potential to release energy. Living cells depend on the harvesting of potential energy from molecular bonds to perform work. Free energy is a measure of energy that is available to do work. The free energy of a system changes during energy transfers such as chemical reactions, and this change is referred to as âG.
The âG of a reaction can be negative or positive, meaning that the reaction releases energy or consumes energy, respectively. A reaction with a negative âG that gives off energy is called an exergonic reaction. One with a positive âG that requires energy input is called an endergonic reaction. Exergonic reactions are said to be spontaneous, because their products have less energy than their reactants. The products of endergonic reactions have a higher energy state than the reactants, and so these are nonspontaneous reactions. However, all reactions (including spontaneous -âG reactions) require an initial input of energy in order to reach the transition state, at which theyâll proceed. This initial input of energy is called the activation energy.
In studying energy, scientists use the term âsystemâ to refer to the matter and its environment involved in energy transfers. Everything outside of the system is called the surroundings. Single cells are biological systems. Systems can be thought of as having a certain amount of order. It takes energy to make a system more ordered. The more ordered a system is, the lower its entropy. Entropy is a measure of the disorder of a system. As a system becomes more disordered, the lower its energy and the higher its entropy become.
A series of laws, called the laws of thermodynamics, describe the properties and processes of energy transfer. The first law states that the total amount of energy in the universe is constant. This means that energy canât be created or destroyed, only transferred or transformed. The second law of thermodynamics states that every energy transfer involves some loss of energy in an unusable form, such as heat energy, resulting in a more disordered system. In other words, no energy transfer is completely efficient and tends toward disorder.
ATP is the primary energy-supplying molecule for living cells. ATP is made up of a nucleotide, a five-carbon sugar, and three phosphate groups. The bonds that connect the phosphates (phosphoanhydride bonds) have high-energy content. The energy released from the hydrolysis of ATP into ADP + Piis used to perform cellular work. Cells use ATP to perform work by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions. ATP donates its phosphate group to another molecule via a process known as phosphorylation. The phosphorylated molecule is at a higher-energy state and is less stable than its unphosphorylated form, and this added energy from the addition of the phosphate allows the molecule to undergo its endergonic reaction.
Enzymes are chemical catalysts that accelerate chemical reactions at physiological temperatures by lowering their activation energy. Enzymes are usually proteins consisting of one or more polypeptide chains. Enzymes have an active site that provides a unique chemical environment, made up of certain amino acid R groups (residues). This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, called substrates, into unstable intermediates called transition states. Enzymes and substrates are thought to bind with an induced fit, which means that enzymes undergo slight conformational adjustments upon substrate contact, leading to full, optimal binding. Enzymes bind to substrates and catalyze reactions in four different ways: bringing substrates together in an optimal orientation, compromising the bond structures of substrates so that bonds can be more easily broken, providing optimal environmental conditions for a reaction to occur, or participating directly in their chemical reaction by forming transient covalent bonds with the substrates.
Enzyme action must be regulated so that in a given cell at a given time, the desired reactions are being catalyzed and the undesired reactions are not. Enzymes are regulated by cellular conditions, such as temperature and pH. They are also regulated through their location within a cell, sometimes being compartmentalized so that they can only catalyze reactions under certain circumstances. Inhibition and activation of enzymes via other molecules are other important ways that enzymes are regulated. Inhibitors can act competitively, noncompetitively, or allosterically; noncompetitive inhibitors are usually allosteric. Activators can also enhance the function of enzymes allosterically. The most common method by which cells regulate the enzymes in metabolic pathways is through feedback inhibition. During feedback inhibition, the products of a metabolic pathway serve as inhibitors (usually allosteric) of one or more of the enzymes (usually the first committed enzyme of the pathway) involved in the pathway that produces them. |
https://openstax.org/books/biology/pages/6-key-terms | activation energy : energy necessary for reactions to occur
active site : specific region of the enzyme to which the substrate binds
allosteric inhibition : inhibition by a binding event at a site different from the active site, which induces a conformational change and reduces the affinity of the enzyme for its substrate
anabolic : (also, anabolism) pathways that require an input of energy to synthesize complex molecules from simpler ones
ATP : adenosine triphosphate, the cellâs energy currency
bioenergetics : study of energy flowing through living systems
catabolic : (also, catabolism) pathways in which complex molecules are broken down into simpler ones
chemical energy : potential energy in chemical bonds that is released when those bonds are broken
coenzyme : small organic molecule, such as a vitamin or its derivative, which is required to enhance the activity of an enzyme
cofactor : inorganic ion, such as iron and magnesium ions, required for optimal regulation of enzyme activity
competitive inhibition : type of inhibition in which the inhibitor competes with the substrate molecule by binding to the active site of the enzyme
denature : process that changes the natural properties of a substance
endergonic : describes chemical reactions that require energy input
enthalpy : total energy of a system
entropy (S) : measure of randomness or disorder within a system
exergonic : describes chemical reactions that release free energy
feedback inhibition : effect of a product of a reaction sequence to decrease its further production by inhibiting the activity of the first enzyme in the pathway that produces it
free energy : Gibbs free energy is the usable energy, or energy that is available to do work.
heat : energy energy transferred from one system to another that is not work (energy of the motion of molecules or particles)
heat energy : total bond energy of reactants or products in a chemical reaction
induced fit : dynamic fit between the enzyme and its substrate, in which both components modify their structures to allow for ideal binding
kinetic energy : type of energy associated with objects or particles in motion
metabolism : all the chemical reactions that take place inside cells, including anabolism and catabolism
phosphoanhydride bond : bond that connects phosphates in an ATP molecule
potential energy : type of energy that has the potential to do work; stored energy
substrate : molecule on which the enzyme acts
thermodynamics : study of energy and energy transfer involving physical matter
transition state : high-energy, unstable state (an intermediate form between the substrate and the product) occurring during a chemical reaction |
https://openstax.org/books/biology/pages/7-chapter-summary | ATP functions as the energy currency for cells. It allows the cell to store energy briefly and transport it within the cell to support endergonic chemical reactions. The structure of ATP is that of an RNA nucleotide with three phosphates attached. As ATP is used for energy, a phosphate group or two are detached, and either ADP or AMP is produced. Energy derived from glucose catabolism is used to convert ADP into ATP. When ATP is used in a reaction, the third phosphate is temporarily attached to a substrate in a process called phosphorylation. The two processes of ATP regeneration that are used in conjunction with glucose catabolism are substrate-level phosphorylation and oxidative phosphorylation through the process of chemiosmosis.
Glycolysis is the first pathway used in the breakdown of glucose to extract energy. It was probably one of the earliest metabolic pathways to evolve and is used by nearly all of the organisms on earth. Glycolysis consists of two parts: The first part prepares the six-carbon ring of glucose for cleavage into two three-carbon sugars. ATP is invested in the process during this half to energize the separation. The second half of glycolysis extracts ATP and high-energy electrons from hydrogen atoms and attaches them to NAD+. Two ATP molecules are invested in the first half and four ATP molecules are formed by substrate phosphorylation during the second half. This produces a net gain of two ATP and two NADH molecules for the cell.
In the presence of oxygen, pyruvate is transformed into an acetyl group attached to a carrier molecule of coenzyme A. The resulting acetyl CoA can enter several pathways, but most often, the acetyl group is delivered to the citric acid cycle for further catabolism. During the conversion of pyruvate into the acetyl group, a molecule of carbon dioxide and two high-energy electrons are removed. The carbon dioxide accounts for two (conversion of two pyruvate molecules) of the six carbons of the original glucose molecule. The electrons are picked up by NAD+, and the NADH carries the electrons to a later pathway for ATP production. At this point, the glucose molecule that originally entered cellular respiration has been completely oxidized. Chemical potential energy stored within the glucose molecule has been transferred to electron carriers or has been used to synthesize a few ATPs.
The citric acid cycle is a series of redox and decarboxylation reactions that remove high-energy electrons and carbon dioxide. The electrons temporarily stored in molecules of NADH and FADH2are used to generate ATP in a subsequent pathway. One molecule of either GTP or ATP is produced by substrate-level phosphorylation on each turn of the cycle. There is no comparison of the cyclic pathway with a linear one.
The electron transport chain is the portion of aerobic respiration that uses free oxygen as the final electron acceptor of the electrons removed from the intermediate compounds in glucose catabolism. The electron transport chain is composed of four large, multiprotein complexes embedded in the inner mitochondrial membrane and two small diffusible electron carriers shuttling electrons between them. The electrons are passed through a series of redox reactions, with a small amount of free energy used at three points to transport hydrogen ions across a membrane. This process contributes to the gradient used in chemiosmosis. The electrons passing through the electron transport chain gradually lose energy, High-energy electrons donated to the chain by either NADH or FADH2complete the chain, as low-energy electrons reduce oxygen molecules and form water. The level of free energy of the electrons drops from about 60 kcal/mol in NADH or 45 kcal/mol in FADH2to about 0 kcal/mol in water. The end products of the electron transport chain are water and ATP. A number of intermediate compounds of the citric acid cycle can be diverted into the anabolism of other biochemical molecules, such as nonessential amino acids, sugars, and lipids. These same molecules can serve as energy sources for the glucose pathways.
If NADH cannot be oxidized through aerobic respiration, another electron acceptor is used. Most organisms will use some form of fermentation to accomplish the regeneration of NAD+, ensuring the continuation of glycolysis. The regeneration of NAD+in fermentation is not accompanied by ATP production; therefore, the potential of NADH to produce ATP using an electron transport chain is not utilized.
The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism. The simple sugars are galactose, fructose, glycogen, and pentose. These are catabolized during glycolysis. The amino acids from proteins connect with glucose catabolism through pyruvate, acetyl CoA, and components of the citric acid cycle. Cholesterol synthesis starts with acetyl groups, and the components of triglycerides come from glycerol-3-phosphate from glycolysis and acetyl groups produced in the mitochondria from pyruvate.
Cellular respiration is controlled by a variety of means. The entry of glucose into a cell is controlled by the transport proteins that aid glucose passage through the cell membrane. Most of the control of the respiration processes is accomplished through the control of specific enzymes in the pathways. This is a type of negative feedback, turning the enzymes off. The enzymes respond most often to the levels of the available nucleosides ATP, ADP, AMP, NAD+, and FAD. Other intermediates of the pathway also affect certain enzymes in the systems. |
https://openstax.org/books/biology/pages/7-key-terms | acetyl CoA : combination of an acetyl group derived from pyruvic acid and coenzyme A, which is made from pantothenic acid (a B-group vitamin)
aerobic respiration : process in which organisms convert energy in the presence of oxygen
anaerobic : process that does not use oxygen
anaerobic cellular respiration : process in which organisms convert energy for their use in the absence of oxygen
ATP synthase : (also, F1F0 ATP synthase) membrane-embedded protein complex that adds a phosphate to ADP with energy from protons diffusing through it
chemiosmosis : process in which there is a production of adenosine triphosphate (ATP) in cellular metabolism by the involvement of a proton gradient across a membrane
citric acid cycle : (also, Krebs cycle) series of enzyme-catalyzed chemical reactions of central importance in all living cells
dephosphorylation : removal of a phosphate group from a molecule
fermentation : process of regenerating NAD+with either an inorganic or organic compound serving as the final electron acceptor, occurs in the absence; occurs in the absence of oxygen
GLUT protein : integral membrane protein that transports glucose
glycolysis : process of breaking glucose into two three-carbon molecules with the production of ATP and NADH
isomerase : enzyme that converts a molecule into its isomer
Krebs cycle : (also, citric acid cycle) alternate name for the citric acid cycle, named after Hans Krebs who first identified the steps in the pathway in the 1930s in pigeon flight muscles; see citric acid cycle
oxidative phosphorylation : production of ATP using the process of chemiosmosis and oxygen
phosphorylation : addition of a high-energy phosphate to a compound, usually a metabolic intermediate, a protein, or ADP
prosthetic group : (also, prosthetic cofactor) molecule bound to a protein that facilitates the function of the protein
pyruvate : three-carbon sugar that can be decarboxylated and oxidized to make acetyl CoA, which enters the citric acid cycle under aerobic conditions; the end product of glycolysis
redox reaction : chemical reaction that consists of the coupling of an oxidation reaction and a reduction reaction
substrate-level phosphorylation : production of ATP from ADP using the excess energy from a chemical reaction and a phosphate group from a reactant
TCA cycle : (also, citric acid cycle) alternate name for the citric acid cycle, named after the group name for citric acid, tricarboxylic acid (TCA); see citric acid cycle
ubiquinone : soluble electron transporter in the electron transport chain that connects the first or second complex to the third |
https://openstax.org/books/biology/pages/8-chapter-summary | The process of photosynthesis transformed life on Earth. By harnessing energy from the sun, photosynthesis evolved to allow living things access to enormous amounts of energy. Because of photosynthesis, living things gained access to sufficient energy that allowed them to build new structures and achieve the biodiversity evident today.
Only certain organisms, called photoautotrophs, can perform photosynthesis; they require the presence of chlorophyll, a specialized pigment that absorbs certain portions of the visible spectrum and can capture energy from sunlight. Photosynthesis uses carbon dioxide and water to assemble carbohydrate molecules and release oxygen as a waste product into the atmosphere. Eukaryotic autotrophs, such as plants and algae, have organelles called chloroplasts in which photosynthesis takes place, and starch accumulates. In prokaryotes, such as cyanobacteria, the process is less localized and occurs within folded membranes, extensions of the plasma membrane, and in the cytoplasm.
The pigments of the first part of photosynthesis, the light-dependent reactions, absorb energy from sunlight. A photon strikes the antenna pigments of photosystem II to initiate photosynthesis. The energy travels to the reaction center that contains chlorophyllato the electron transport chain, which pumps hydrogen ions into the thylakoid interior. This action builds up a high concentration of ions. The ions flow through ATP synthase via chemiosmosis to form molecules of ATP, which are used for the formation of sugar molecules in the second stage of photosynthesis. Photosystem I absorbs a second photon, which results in the formation of an NADPH molecule, another energy and reducing power carrier for the light-independent reactions.
Using the energy carriers formed in the first steps of photosynthesis, the light-independent reactions, or the Calvin cycle, take in CO2from the environment. An enzyme, RuBisCO, catalyzes a reaction with CO2and another molecule, RuBP. After three cycles, a three-carbon molecule of G3P leaves the cycle to become part of a carbohydrate molecule. The remaining G3P molecules stay in the cycle to be regenerated into RuBP, which is then ready to react with more CO2. Photosynthesis forms an energy cycle with the process of cellular respiration. Plants need both photosynthesis and respiration for their ability to function in both the light and dark, and to be able to interconvert essential metabolites. Therefore, plants contain both chloroplasts and mitochondria. |
https://openstax.org/books/biology/pages/8-key-terms | absorption spectrum : range of wavelengths of electromagnetic radiation absorbed by a given substance
antenna protein : pigment molecule that directly absorbs light and transfers the energy absorbed to other pigment molecules
Calvin cycle : light-independent reactions of photosynthesis that convert carbon dioxide from the atmosphere into carbohydrates using the energy and reducing power of ATP and NADPH
carbon fixation : process of converting inorganic CO2gas into organic compounds
carotenoid : photosynthetic pigment that functions to dispose of excess energy
chemoautotroph : organism that can build organic molecules using energy derived from inorganic chemicals instead of sunlight
chlorophylla : form of chlorophyll that absorbs violet-blue and red light and consequently has a bluish-green color; the only pigment molecule that performs the photochemistry by getting excited and losing an electron to the electron transport chain
chlorophyllb : accessory pigment that absorbs blue and red-orange light and consequently has a yellowish-green tint
chloroplast : organelle in which photosynthesis takes place
cytochrome complex : group of reversibly oxidizable and reducible proteins that forms part of the electron transport chain between photosystem II and photosystem I
electromagnetic spectrum : range of all possible frequencies of radiation
electron transport chain : group of proteins between PSII and PSI that pass energized electrons and use the energy released by the electrons to move hydrogen ions against their concentration gradient into the thylakoid lumen
granum : stack of thylakoids located inside a chloroplast
heterotroph : organism that consumes organic substances or other organisms for food
light harvesting complex : complex that passes energy from sunlight to the reaction center in each photosystem; it consists of multiple antenna proteins that contain a mixture of 300â400 chlorophyllaandbmolecules as well as other pigments like carotenoids
light-dependent reaction : first stage of photosynthesis where certain wavelengths of the visible light are absorbed to form two energy-carrying molecules (ATP and NADPH)
light-independent reaction : second stage of photosynthesis, though which carbon dioxide is used to build carbohydrate molecules using energy from ATP and NADPH
mesophyll : middle layer of chlorophyll-rich cells in a leaf
P680 : reaction center of photosystem II
P700 : reaction center of photosystem I
photoact : ejection of an electron from a reaction center using the energy of an absorbed photon
photoautotroph : organism capable of producing its own organic compounds from sunlight
photon : distinct quantity or âpacketâ of light energy
photosystem : group of proteins, chlorophyll, and other pigments that are used in the light-dependent reactions of photosynthesis to absorb light energy and convert it into chemical energy
photosystem I : integral pigment and protein complex in thylakoid membranes that uses light energy to transport electrons from plastocyanin to NADP+(which becomes reduced to NADPH in the process)
photosystem II : integral protein and pigment complex in thylakoid membranes that transports electrons from water to the electron transport chain; oxygen is a product of PSII
pigment : molecule that is capable of absorbing certain wavelengths of light and reflecting others (which accounts for its color)
primary electron acceptor : pigment or other organic molecule in the reaction center that accepts an energized electron from the reaction center
reaction center : complex of chlorophyll molecules and other organic molecules that is assembled around a special pair of chlorophyll molecules and a primary electron acceptor; capable of undergoing oxidation and reduction
reduction : gain of electron(s) by an atom or molecule
spectrophotometer : instrument that can measure transmitted light and compute the absorption
stoma : opening that regulates gas exchange and water evaporation between leaves and the environment, typically situated on the underside of leaves
stroma : fluid-filled space surrounding the grana inside a chloroplast where the light-independent reactions of photosynthesis take place
thylakoid : disc-shaped, membrane-bound structure inside a chloroplast where the light-dependent reactions of photosynthesis take place; stacks of thylakoids are called grana
thylakoid lumen : aqueous space bound by a thylakoid membrane where protons accumulate during light-driven electron transport
wavelength : distance between consecutive points of equal position (two crests or two troughs) of a wave in a graphic representation; inversely proportional to the energy of the radiation |
https://openstax.org/books/biology/pages/9-chapter-summary | Cells communicate by both inter- and intracellular signaling. Signaling cells secrete ligands that bind to target cells and initiate a chain of events within the target cell. The four categories of signaling in multicellular organisms are paracrine signaling, endocrine signaling, autocrine signaling, and direct signaling across gap junctions. Paracrine signaling takes place over short distances. Endocrine signals are carried long distances through the bloodstream by hormones, and autocrine signals are received by the same cell that sent the signal or other nearby cells of the same kind. Gap junctions allow small molecules, including signaling molecules, to flow between neighboring cells.
Internal receptors are found in the cell cytoplasm. Here, they bind ligand molecules that cross the plasma membrane; these receptor-ligand complexes move to the nucleus and interact directly with cellular DNA. Cell-surface receptors transmit a signal from outside the cell to the cytoplasm. Ion channel-linked receptors, when bound to their ligands, form a pore through the plasma membrane through which certain ions can pass. G-protein-linked receptors interact with a G-protein on the cytoplasmic side of the plasma membrane, promoting the exchange of bound GDP for GTP and interacting with other enzymes or ion channels to transmit a signal. Enzyme-linked receptors transmit a signal from outside the cell to an intracellular domain of a membrane-bound enzyme. Ligand binding causes activation of the enzyme. Small hydrophobic ligands (like steroids) are able to penetrate the plasma membrane and bind to internal receptors. Water-soluble hydrophilic ligands are unable to pass through the membrane; instead, they bind to cell-surface receptors, which transmit the signal to the inside of the cell.
Ligand binding to the receptor allows for signal transduction through the cell. The chain of events that conveys the signal through the cell is called a signaling pathway or cascade. Signaling pathways are often very complex because of the interplay between different proteins. A major component of cell signaling cascades is the phosphorylation of molecules by enzymes known as kinases. Phosphorylation adds a phosphate group to serine, threonine, and tyrosine residues in a protein, changing their shapes, and activating or inactivating the protein. Small molecules like nucleotides can also be phosphorylated. Second messengers are small, non-protein molecules that are used to transmit a signal within a cell. Some examples of second messengers are calcium ions (Ca2+), cyclic AMP (cAMP), diacylglycerol (DAG), and inositol triphosphate (IP3).
The initiation of a signaling pathway is a response to external stimuli. This response can take many different forms, including protein synthesis, a change in the cellâs metabolism, cell growth, or even cell death. Many pathways influence the cell by initiating gene expression, and the methods utilized are quite numerous. Some pathways activate enzymes that interact with DNA transcription factors. Others modify proteins and induce them to change their location in the cell. Depending on the status of the organism, cells can respond by storing energy as glycogen or fat, or making it available in the form of glucose. A signal transduction pathway allows muscle cells to respond to immediate requirements for energy in the form of glucose. Cell growth is almost always stimulated by external signals called growth factors. Uncontrolled cell growth leads to cancer, and mutations in the genes encoding protein components of signaling pathways are often found in tumor cells. Programmed cell death, or apoptosis, is important for removing damaged or unnecessary cells. The use of cellular signaling to organize the dismantling of a cell ensures that harmful molecules from the cytoplasm are not released into the spaces between cells, as they are in uncontrolled death, necrosis. Apoptosis also ensures the efficient recycling of the components of the dead cell. Termination of the cellular signaling cascade is very important so that the response to a signal is appropriate in both timing and intensity. Degradation of signaling molecules and dephosphorylation of phosphorylated intermediates of the pathway by phosphatases are two ways to terminate signals within the cell.
Yeasts and multicellular organisms have similar signaling mechanisms. Yeasts use cell-surface receptors and signaling cascades to communicate information on mating with other yeast cells. The signaling molecule secreted by yeasts is called mating factor.
Bacterial signaling is called quorum sensing. Bacteria secrete signaling molecules called autoinducers that are either small, hydrophobic molecules or peptide-based signals. The hydrophobic autoinducers, such as AHL, bind transcription factors and directly affect gene expression. The peptide-based molecules bind kinases and initiate signaling cascades in the cells. |
https://openstax.org/books/biology/pages/9-key-terms | apoptosis : programmed cell death
autocrine signal : signal that is sent and received by the same or similar nearby cells
autoinducer : signaling molecule secreted by bacteria to communicate with other bacteria of its kind and others
cell-surface receptor : cell-surface protein that transmits a signal from the exterior of the cell to the interior, even though the ligand does not enter the cell
chemical synapse : small space between axon terminals and dendrites of nerve cells where neurotransmitters function
cyclic AMP (cAMP) : second messenger that is derived from ATP
cyclic AMP-dependent kinase : (also, protein kinase A, or PKA) kinase that is activated by binding to cAMP
diacylglycerol (DAG) : cleavage product of PIP2that is used for signaling within the plasma membrane
dimer : chemical compound formed when two molecules join together
dimerization : (of receptor proteins) interaction of two receptor proteins to form a functional complex called a dimer
endocrine cell : cell that releases ligands involved in endocrine signaling (hormones)
endocrine signal : long-distance signal that is delivered by ligands (hormones) traveling through an organisms circulatory system from the signaling cell to the target cell
enzyme-linked receptor : cell-surface receptor with intracellular domains that are associated with membrane-bound enzymes
extracellular domain : region of a cell-surface receptor that is located on the cell surface
G-protein-linked receptor : cell-surface receptor that activates membrane-bound G-proteins to transmit a signal from the receptor to nearby membrane components
growth factor : ligand that binds to cell-surface receptors and stimulates cell growth
inhibitor : molecule that binds to a protein (usually an enzyme) and keeps it from functioning
inositol phospholipid : lipid present at small concentrations in the plasma membrane that is converted into a second messenger; it has inositol (a carbohydrate) as its hydrophilic head group
inositol triphosphate (IP3) : cleavage product of PIP2that is used for signaling within the cell
intercellular signaling : communication between cells
internal receptor : (also, intracellular receptor) receptor protein that is located in the cytosol of a cell and binds to ligands that pass through the plasma membrane
intracellular mediator : (also, second messenger) small molecule that transmits signals within a cell
intracellular signaling : communication within cells
ion channel-linked receptor : cell-surface receptor that forms a plasma membrane channel, which opens when a ligand binds to the extracellular domain (ligand-gated channels)
kinase : enzyme that catalyzes the transfer of a phosphate group from ATP to another molecule
ligand : molecule produced by a signaling cell that binds with a specific receptor, delivering a signal in the process
mating factor : signaling molecule secreted by yeast cells to communicate to nearby yeast cells that they are available to mate and communicating their mating orientation
neurotransmitter : chemical ligand that carries a signal from one nerve cell to the next
paracrine signal : signal between nearby cells that is delivered by ligands traveling in the liquid medium in the space between the cells
phosphatase : enzyme that removes the phosphate group from a molecule that has been previously phosphorylated
phosphodiesterase : enzyme that degrades cAMP, producing AMP, to terminate signaling
quorum sensing : method of cellular communication used by bacteria that informs them of the abundance of similar (or different) bacteria in the environment
receptor : protein in or on a target cell that bind to ligands
second messenger : small, non-protein molecule that propagates a signal within the cell after activation of a receptor causes its release
signal integration : interaction of signals from two or more different cell-surface receptors that merge to activate the same response in the cell
signal transduction : propagation of the signal through the cytoplasm (and sometimes also the nucleus) of the cell
signaling cell : cell that releases signal molecules that allow communication with another cell
signaling pathway : (also signaling cascade) chain of events that occurs in the cytoplasm of the cell to propagate the signal from the plasma membrane to produce a response
synaptic signal : chemical signal (neurotransmitter) that travels between nerve cells
target cell : cell that has a receptor for a signal or ligand from a signaling cell |
https://openstax.org/books/biology/pages/10-chapter-summary | Prokaryotes have a single circular chromosome composed of double-stranded DNA, whereas eukaryotes have multiple, linear chromosomes composed of chromatin surrounded by a nuclear membrane. The 46 chromosomes of human somatic cells are composed of 22 pairs of autosomes (matched pairs) and a pair of sex chromosomes, which may or may not be matched. This is the 2nor diploid state. Human gametes have 23 chromosomes or one complete set of chromosomes; a set of chromosomes is complete with either one of the sex chromosomes. This is thenor haploid state. Genes are segments of DNA
that code for a specific protein. An organismâs traits are determined by the genes inherited from each parent. Duplicated chromosomes are composed of two sister chromatids. Chromosomes are compacted using a variety of mechanisms during certain stages of the cell cycle. Several classes of protein are involved in the organization and packing of the chromosomal DNA into a highly condensed structure. The condensing complex compacts chromosomes, and the resulting condensed structure is necessary for chromosomal segregation during mitosis.
The cell cycle is an orderly sequence of events. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages. In eukaryotes, the cell cycle consists of a long preparatory period, called interphase. Interphase is divided into G1, S, and G2phases. The mitotic phase begins with karyokinesis (mitosis), which consists of five stages: prophase, prometaphase, metaphase, anaphase, and telophase. The final stage of the mitotic phase is cytokinesis, during which the cytoplasmic components of the daughter cells are separated either by an actin ring (animal cells) or by cell plate formation (plant cells).
Each step of the cell cycle is monitored by internal controls called checkpoints. There are three major checkpoints in the cell cycle: one near the end of G1, a second at the G2/M transition, and the third during metaphase. Positive regulator molecules allow the cell cycle to advance to the next stage. Negative regulator molecules monitor cellular conditions and can halt the cycle until specific requirements are met.
Cancer is the result of unchecked cell division caused by a breakdown of the mechanisms that regulate the cell cycle. The loss of control begins with a change in the DNA sequence of a gene that codes for one of the regulatory molecules. Faulty instructions lead to a protein that does not function as it should. Any disruption of the monitoring system can allow other mistakes to be passed on to the daughter cells. Each successive cell division will give rise to daughter cells with even more accumulated damage. Eventually, all checkpoints become nonfunctional, and rapidly reproducing cells crowd out normal cells, resulting in a tumor or leukemia (blood cancer).
In both prokaryotic and eukaryotic cell division, the genomic DNA is replicated and then each copy is allocated into a daughter cell. In addition, the cytoplasmic contents are divided evenly and distributed to the new cells. However, there are many differences between prokaryotic and eukaryotic cell division. Bacteria have a single, circular DNA chromosome but no nucleus. Therefore, mitosis is not necessary in bacterial cell division. Bacterial cytokinesis is directed by a ring composed of a protein called FtsZ. Ingrowth of membrane and cell wall material from the periphery of the cells results in the formation of a septum that eventually constructs the separate cell walls of the daughter cells. |
https://openstax.org/books/biology/pages/10-key-terms | anaphase : stage of mitosis during which sister chromatids are separated from each other
binary fission : prokaryotic cell division process
cell cycle : ordered sequence of events that a cell passes through between one cell division and the next
cell cycle : ordered series of events involving cell growth and cell division that produces two new daughter cells
cell cycle checkpoint : mechanism that monitors the preparedness of a eukaryotic cell to advance through the various cell cycle stages
cell plate : structure formed during plant cell cytokinesis by Golgi vesicles, forming a temporary structure (phragmoplast) and fusing at the metaphase plate; ultimately leads to the formation of cell walls that separate the two daughter cells
centriole : rod-like structure constructed of microtubules at the center of each animal cell centrosome
centromere : region at which sister chromatids are bound together; a constricted area in condensed chromosomes
chromatid : single DNA molecule of two strands of duplicated DNA and associated proteins held together at the centromere
cleavage furrow : constriction formed by an actin ring during cytokinesis in animal cells that leads to cytoplasmic division
condensin : proteins that help sister chromatids coil during prophase
cyclin : one of a group of proteins that act in conjunction with cyclin-dependent kinases to help regulate the cell cycle by phosphorylating key proteins; the concentrations of cyclins fluctuate throughout the cell cycle
cyclin-dependent kinase : one of a group of protein kinases that helps to regulate the cell cycle when bound to cyclin; it functions to phosphorylate other proteins that are either activated or inactivated by phosphorylation
cytokinesis : division of the cytoplasm following mitosis that forms two daughter cells.
diploid : cell, nucleus, or organism containing two sets of chromosomes (2n)
FtsZ : tubulin-like protein component of the prokaryotic cytoskeleton that is important in prokaryotic cytokinesis (name origin:Filamentingtemperature-sensitive mutantZ)
G0phase : distinct from the G1phase of interphase; a cell in G0is not preparing to divide
G1phase : (also, first gap) first phase of interphase centered on cell growth during mitosis
G2phase : (also, second gap) third phase of interphase during which the cell undergoes final preparations for mitosis
gamete : haploid reproductive cell or sex cell (sperm, pollen grain, or egg)
gene : physical and functional unit of heredity, a sequence of DNA that codes for a protein.
genome : total genetic information of a cell or organism
haploid : cell, nucleus, or organism containing one set of chromosomes (n)
histone : one of several similar, highly conserved, low molecular weight, basic proteins found in the chromatin of all eukaryotic cells; associates with DNA to form nucleosomes
homologous chromosomes : chromosomes of the same morphology with genes in the same location; diploid organisms have pairs of homologous chromosomes (homologs), with each homolog derived from a different parent
interphase : period of the cell cycle leading up to mitosis; includes G1, S, and G2phases (the interim period between two consecutive cell divisions
karyokinesis : mitotic nuclear division
kinetochore : protein structure associated with the centromere of each sister chromatid that attracts and binds spindle microtubules during prometaphase
locus : position of a gene on a chromosome
metaphase : stage of mitosis during which chromosomes are aligned at the metaphase plate
metaphase plate : equatorial plane midway between the two poles of a cell where the chromosomes align during metaphase
mitosis : (also, karyokinesis) period of the cell cycle during which the duplicated chromosomes are separated into identical nuclei; includes prophase, prometaphase, metaphase, anaphase, and telophase
mitotic phase : period of the cell cycle during which duplicated chromosomes are distributed into two nuclei and cytoplasmic contents are divided; includes karyokinesis (mitosis) and cytokinesis
mitotic spindle : apparatus composed of microtubules that orchestrates the movement of chromosomes during mitosis
nucleosome : subunit of chromatin composed of a short length of DNA wrapped around a core of histone proteins
oncogene : mutated version of a normal gene involved in the positive regulation of the cell cycle
origin : (also, ORI) region of the prokaryotic chromosome where replication begins (origin of replication)
p21 : cell cycle regulatory protein that inhibits the cell cycle; its levels are controlled by p53
p53 : cell cycle regulatory protein that regulates cell growth and monitors DNA damage; it halts the progression of the cell cycle in cases of DNA damage and may induce apoptosis
prometaphase : stage of mitosis during which the nuclear membrane breaks down and mitotic spindle fibers attach to kinetochores
prophase : stage of mitosis during which chromosomes condense and the mitotic spindle begins to form
proto-oncogene : normal gene that when mutated becomes an oncogene
quiescent : refers to a cell that is performing normal cell functions and has not initiated preparations for cell division
retinoblastoma protein (Rb) : regulatory molecule that exhibits negative effects on the cell cycle by interacting with a transcription factor (E2F)
S phase : second, or synthesis, stage of interphase during which DNA replication occurs
septum : structure formed in a bacterial cell as a precursor to the separation of the cell into two daughter cells
telophase : stage of mitosis during which chromosomes arrive at opposite poles, decondense, and are surrounded by a new nuclear envelope
tumor suppressor gene : segment of DNA that codes for regulator proteins that prevent the cell from undergoing uncontrolled division |
https://openstax.org/books/biology/pages/11-chapter-summary | Sexual reproduction requires that diploid organisms produce haploid cells that can fuse during fertilization to form diploid offspring. As with mitosis, DNA replication occurs prior to meiosis during the S-phase of the cell cycle. Meiosis is a series of events that arrange and separate chromosomes and chromatids into daughter cells. During the interphases of meiosis, each chromosome is duplicated. In meiosis, there are two rounds of nuclear division resulting in four nuclei and usually four daughter cells, each with half the number of chromosomes as the parent cell. The first separates homologs, and the secondâlike mitosisâseparates chromatids into individual chromosomes. During meiosis, variation in the daughter nuclei is introduced because of crossover in prophase I and random alignment of tetrads at metaphase I. The cells that are produced by meiosis are genetically unique.
Meiosis and mitosis share similarities, but have distinct outcomes. Mitotic divisions are single nuclear divisions that produce daughter nuclei that are genetically identical and have the same number of chromosome sets as the original cell. Meiotic divisions include two nuclear divisions that produce four daughter nuclei that are genetically different and have one chromosome set instead of the two sets of chromosomes in the parent cell. The main differences between the processes occur in the first division of meiosis, in which homologous chromosomes are paired and exchange non-sister chromatid segments. The homologous chromosomes separate into different nuclei during meiosis I, causing a reduction of ploidy level in the first division. The second division of meiosis is more similar to a mitotic division, except that the daughter cells do not contain identical genomes because of crossover.
Nearly all eukaryotes undergo sexual reproduction. The variation introduced into the reproductive cells by meiosis appears to be one of the advantages of sexual reproduction that has made it so successful. Meiosis and fertilization alternate in sexual life cycles. The process of meiosis produces unique reproductive cells called gametes, which have half the number of chromosomes as the parent cell. Fertilization, the fusion of haploid gametes from two individuals, restores the diploid condition. Thus, sexually reproducing organisms alternate between haploid and diploid stages. However, the ways in which reproductive cells are produced and the timing between meiosis and fertilization vary greatly. There are three main categories of life cycles: diploid-dominant, demonstrated by most animals; haploid-dominant, demonstrated by all fungi and some algae; and the alternation of generations, demonstrated by plants and some algae. |
https://openstax.org/books/biology/pages/11-key-terms | alternation of generations : life-cycle type in which the diploid and haploid stages alternate
chiasmata : (singular,chiasma) the structure that forms at the crossover points after genetic material is exchanged
cohesin : proteins that form a complex that seals sister chromatids together at their centromeres until anaphase II of meiosis
crossover : exchange of genetic material between non-sister chromatids resulting in chromosomes that incorporate genes from both parents of the organism
diploid-dominant : life-cycle type in which the multicellular diploid stage is prevalent
fertilization : union of two haploid cells from two individual organisms
gametophyte : a multicellular haploid life-cycle stage that produces gametes
germ cells : specialized cell line that produces gametes, such as eggs or sperm
haploid-dominant : life-cycle type in which the multicellular haploid stage is prevalent
interkinesis : (also,interphase II) brief period of rest between meiosis I and meiosis II
life cycle : the sequence of events in the development of an organism and the production of cells that produce offspring
meiosis : a nuclear division process that results in four haploid cells
meiosis I : first round of meiotic cell division; referred to as reduction division because the ploidy level is reduced from diploid to haploid
meiosis II : second round of meiotic cell division following meiosis I; sister chromatids are separated into individual chromosomes, and the result is four unique haploid cells
recombination nodules : protein assemblies formed on the synaptonemal complex that mark the points of crossover events and mediate the multistep process of genetic recombination between non-sister chromatids
reduction division : nuclear division that produces daughter nuclei each having one-half as many chromosome sets as the parental nucleus; meiosis I is a reduction division
somatic cell : all the cells of a multicellular organism except the gametes or reproductive cells
spore : haploid cell that can produce a haploid multicellular organism or can fuse with another spore to form a diploid cell
sporophyte : a multicellular diploid life-cycle stage that produces haploid spores by meiosis
synapsis : formation of a close association between homologous chromosomes during prophase I
synaptonemal complex : protein lattice that forms between homologous chromosomes during prophase I, supporting crossover
tetrad : two duplicated homologous chromosomes (four chromatids) bound together by chiasmata during prophase I |
https://openstax.org/books/biology/pages/12-chapter-summary | Working with garden pea plants, Mendel found that crosses between parents that differed by one trait produced F1offspring that all expressed the traits of one parent. Observable traits are referred to as dominant, and non-expressed traits are described as recessive. When the offspring in Mendelâs experiment were self-crossed, the F2offspring exhibited the dominant trait or the recessive trait in a 3:1 ratio, confirming that the recessive trait had been transmitted faithfully from the original P0parent. Reciprocal crosses generated identical F1and F2offspring ratios. By examining sample sizes, Mendel showed that his crosses behaved reproducibly according to the laws of probability, and that the traits were inherited as independent events.
Two rules in probability can be used to find the expected proportions of offspring of different traits from different crosses. To find the probability of two or more independent events occurring together, apply the product rule and multiply the probabilities of the individual events. The use of the word âandâ suggests the appropriate application of the product rule. To find the probability of two or more events occurring in combination, apply the sum rule and add their individual probabilities together. The use of the word âorâ suggests the appropriate application of the sum rule.
When true-breeding or homozygous individuals that differ for a certain trait are crossed, all of the offspring will be heterozygotes for that trait. If the traits are inherited as dominant and recessive, the F1offspring will all exhibit the same phenotype as the parent homozygous for the dominant trait. If these heterozygous offspring are self-crossed, the resulting F2offspring will be equally likely to inherit gametes carrying the dominant or recessive trait, giving rise to offspring of which one quarter are homozygous dominant, half are heterozygous, and one quarter are homozygous recessive. Because homozygous dominant and heterozygous individuals are phenotypically identical, the observed traits in the F2offspring will exhibit a ratio of three dominant to one recessive.
Alleles do not always behave in dominant and recessive patterns. Incomplete dominance describes situations in which the heterozygote exhibits a phenotype that is intermediate between the homozygous phenotypes. Codominance describes the simultaneous expression of both of the alleles in the heterozygote. Although diploid organisms can only have two alleles for any given gene, it is common for more than two alleles of a gene to exist in a population. In humans, as in many animals and some plants, females have two X chromosomes and males have one X and one Y chromosome. Genes that are present on the X but not the Y chromosome are said to be X-linked, such that males only inherit one allele for the gene, and females inherit two. Finally, some alleles can be lethal. Recessive lethal alleles are only lethal in homozygotes, but dominant lethal alleles are fatal in heterozygotes as well.
Mendel postulated that genes (characteristics) are inherited as pairs of alleles (traits) that behave in a dominant and recessive pattern. Alleles segregate into gametes such that each gamete is equally likely to receive either one of the two alleles present in a diploid individual. In addition, genes are assorted into gametes independently of one another. That is, alleles are generally not more likely to segregate into a gamete with a particular allele of another gene. A dihybrid cross demonstrates independent assortment when the genes in question are on different chromosomes or distant from each other on the same chromosome. For crosses involving more than two genes, use the forked line or probability methods to predict offspring genotypes and phenotypes rather than a Punnett square.
Although chromosomes sort independently into gametes during meiosis, Mendelâs law of independent assortment refers to genes, not chromosomes, and a single chromosome may carry more than 1,000 genes. When genes are located in close proximity on the same chromosome, their alleles tend to be inherited together. This results in offspring ratios that violate Mendel's law of independent assortment. However, recombination serves to exchange genetic material on homologous chromosomes such that maternal and paternal alleles may be recombined on the same chromosome. This is why alleles on a given chromosome are not always inherited together. Recombination is a random event occurring anywhere on a chromosome. Therefore, genes that are far apart on the same chromosome are likely to still assort independently because of recombination events that occurred in the intervening chromosomal space.
Whether or not they are sorting independently, genes may interact at the level of gene products such that the expression of an allele for one gene masks or modifies the expression of an allele for a different gene. This is called epistasis. |
https://openstax.org/books/biology/pages/12-key-terms | allele : gene variations that arise by mutation and exist at the same relative locations on homologous chromosomes
autosomes : any of the non-sex chromosomes
blending theory of inheritance : hypothetical inheritance pattern in which parental traits are blended together in the offspring to produce an intermediate physical appearance
codominance : in a heterozygote, complete and simultaneous expression of both alleles for the same characteristic
continuous variation : inheritance pattern in which a character shows a range of trait values with small gradations rather than large gaps between them
dihybrid : result of a cross between two true-breeding parents that express different traits for two characteristics
discontinuous variation : inheritance pattern in which traits are distinct and are transmitted independently of one another
dominant : trait which confers the same physical appearance whether an individual has two copies of the trait or one copy of the dominant trait and one copy of the recessive trait
dominant lethal : inheritance pattern in which an allele is lethal both in the homozygote and the heterozygote; this allele can only be transmitted if the lethality phenotype occurs after reproductive age
epistasis : antagonistic interaction between genes such that one gene masks or interferes with the expression of another
F1 : first filial generation in a cross; the offspring of the parental generation
F2 : second filial generation produced when F1individuals are self-crossed or fertilized with each other
genotype : underlying genetic makeup, consisting of both physically visible and non-expressed alleles, of an organism
hemizygous : presence of only one allele for a characteristic, as in X-linkage; hemizygosity makes descriptions of dominance and recessiveness irrelevant
heterozygous : having two different alleles for a given gene on the homologous chromosome
homozygous : having two identical alleles for a given gene on the homologous chromosome
hybridization : process of mating two individuals that differ with the goal of achieving a certain characteristic in their offspring
incomplete dominance : in a heterozygote, expression of two contrasting alleles such that the individual displays an intermediate phenotype
law of dominance : in a heterozygote, one trait will conceal the presence of another trait for the same characteristic
law of independent assortment : genes do not influence each other with regard to sorting of alleles into gametes; every possible combination of alleles is equally likely to occur
law of segregation : paired unit factors (i.e., genes) segregate equally into gametes such that offspring have an equal likelihood of inheriting any combination of factors
linkage : phenomenon in which alleles that are located in close proximity to each other on the same chromosome are more likely to be inherited together
model system : species or biological system used to study a specific biological phenomenon to be applied to other different species
monohybrid : result of a cross between two true-breeding parents that express different traits for only one characteristic
P0 : parental generation in a cross
phenotype : observable traits expressed by an organism
product rule : probability of two independent events occurring simultaneously can be calculated by multiplying the individual probabilities of each event occurring alone
Punnett square : visual representation of a cross between two individuals in which the gametes of each individual are denoted along the top and side of a grid, respectively, and the possible zygotic genotypes are recombined at each box in the grid
recessive : trait that appears âlatentâ or non-expressed when the individual also carries a dominant trait for that same characteristic; when present as two identical copies, the recessive trait is expressed
recessive lethal : inheritance pattern in which an allele is only lethal in the homozygous form; the heterozygote may be normal or have some altered, non-lethal phenotype
reciprocal cross : paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross
sex-linked : any gene on a sex chromosome
sum rule : probability of the occurrence of at least one of two mutually exclusive events is the sum of their individual probabilities
test cross : cross between a dominant expressing individual with an unknown genotype and a homozygous recessive individual; the offspring phenotypes indicate whether the unknown parent is heterozygous or homozygous for the dominant trait
trait : variation in the physical appearance of a heritable characteristic
X-linked : gene present on the X, but not the Y chromosome |
https://openstax.org/books/biology/pages/13-chapter-summary | The Chromosomal Theory of inheritance, proposed by Sutton and Boveri, states that chromosomes are the vehicles of genetic heredity. Neither Mendelian genetics nor gene linkage is perfectly accurate; instead, chromosome behavior involves segregation, independent assortment, and occasionally, linkage. Sturtevant devised a method to assess recombination frequency and infer the relative positions and distances of linked genes on a chromosome on the basis of the average number of crossovers in the intervening region between the genes. Sturtevant correctly presumed that genes are arranged in serial order on chromosomes and that recombination between homologs can occur anywhere on a chromosome with equal likelihood. Whereas linkage causes alleles on the same chromosome to be inherited together, homologous recombination biases alleles toward an inheritance pattern of independent assortment.
The number, size, shape, and banding pattern of chromosomes make them easily identifiable in a karyogram and allows for the assessment of many chromosomal abnormalities. Disorders in chromosome number, or aneuploidies, are typically lethal to the embryo, although a few trisomic genotypes are viable. Because of X inactivation, aberrations in sex chromosomes typically have milder phenotypic effects. Aneuploidies also include instances in which segments of a chromosome are duplicated or deleted. Chromosome structures may also be rearranged, for example by inversion or translocation. Both of these aberrations can result in problematic phenotypic effects. Because they force chromosomes to assume unnatural topologies during meiosis, inversions and translocations are often associated with reduced fertility because of the likelihood of nondisjunction. |
https://openstax.org/books/biology/pages/13-key-terms | aneuploid : individual with an error in chromosome number; includes deletions and duplications of chromosome segments
autosome : any of the non-sex chromosomes
centimorgan (cM) : (also, map unit) relative distance that corresponds to a recombination frequency of 0.01
Chromosomal Theory of Inheritance : theory proposing that chromosomes are the vehicles of genes and that their behavior during meiosis is the physical basis of the inheritance patterns that Mendel observed
chromosome inversion : detachment, 180° rotation, and reinsertion of a chromosome arm
euploid : individual with the appropriate number of chromosomes for their species
homologous recombination : process by which homologous chromosomes undergo reciprocal physical exchanges at their arms, also known as crossing over
karyogram : photographic image of a karyotype
karyotype : number and appearance of an individuals chromosomes; includes the size, banding patterns, and centromere position
monosomy : otherwise diploid genotype in which one chromosome is missing
nondisjunction : failure of synapsed homologs to completely separate and migrate to separate poles during the first cell division of meiosis
nonparental (recombinant) type : progeny resulting from homologous recombination that exhibits a different allele combination compared with its parents
paracentric : inversion that occurs outside of the centromere
parental types : progeny that exhibits the same allelic combination as its parents
pericentric : inversion that involves the centromere
polyploid : individual with an incorrect number of chromosome sets
recombination frequency : average number of crossovers between two alleles; observed as the number of nonparental types in a population of progeny
translocation : process by which one segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome
trisomy : otherwise diploid genotype in which one entire chromosome is duplicated
X inactivation : condensation of X chromosomes into Barr bodies during embryonic development in females to compensate for the double genetic dose |
https://openstax.org/books/biology/pages/14-chapter-summary | DNA was first isolated from white blood cells by Friedrich Miescher, who called it nuclein because it was isolated from nuclei. Frederick Griffith's experiments with strains ofStreptococcus pneumoniaeprovided the first hint that DNA may be the transforming principle. Avery, MacLeod, and McCarty proved that DNA is required for the transformation of bacteria. Later experiments by Hershey and Chase using bacteriophage T2 proved that DNA is the genetic material. Chargaff found that the ratio of A = T and C = G, and that the percentage content of A, T, G, and C is different for different species.
The currently accepted model of the double-helix structure of DNA was proposed by Watson and Crick. Some of the salient features are that the two strands that make up the double helix are complementary and anti-parallel in nature. Deoxyribose sugars and phosphates form the backbone of the structure, and the nitrogenous bases are stacked inside. The diameter of the double helix, 2 nm, is uniform throughout. A purine always pairs with a pyrimidine; A pairs with T, and G pairs with C. One turn of the helix has ten base pairs. During cell division, each daughter cell receives a copy of the DNA by a process known as DNA replication. Prokaryotes are much simpler than eukaryotes in many of their features. Most prokaryotes contain a single, circular chromosome. In general, eukaryotic chromosomes contain a linear DNA molecule packaged into nucleosomes, and have two distinct regions that can be distinguished by staining, reflecting different states of packaging and compaction.
The model for DNA replication suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. In conservative replication, the parental DNA is conserved, and the daughter DNA is newly synthesized. The semi-conservative method suggests that each of the two parental DNA strands acts as template for new DNA to be synthesized; after replication, each double-stranded DNA includes one parental or âoldâ strand and one ânewâ strand. The dispersive mode suggested that the two copies of the DNA would have segments of parental DNA and newly synthesized DNA.
Replication in prokaryotes starts from a sequence found on the chromosome called the origin of replicationâthe point at which the DNA opens up. Helicase opens up the DNA double helix, resulting in the formation of the replication fork. Single-strand binding proteins bind to the single-stranded DNA near the replication fork to keep the fork open. Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides only in the 5' to 3' direction. One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand. Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase, which creates phosphodiester bonds between the 3'-OH of one end and the 5' phosphate of the other strand.
Replication in eukaryotes starts at multiple origins of replication. The mechanism is quite similar to prokaryotes. A primer is required to initiate synthesis, which is then extended by DNA polymerase as it adds nucleotides one by one to the growing chain. The leading strand is synthesized continuously, whereas the lagging strand is synthesized in short stretches called Okazaki fragments. The RNA primers are replaced with DNA nucleotides; the DNA remains one continuous strand by linking the DNA fragments with DNA ligase. The ends of the chromosomes pose a problem as polymerase is unable to extend them without a primer. Telomerase, an enzyme with an inbuilt RNA template, extends the ends by copying the RNA template and extending one end of the chromosome. DNA polymerase can then extend the DNA using the primer. In this way, the ends of the chromosomes are protected.
DNA polymerase can make mistakes while adding nucleotides. It edits the DNA by proofreading every newly added base. Incorrect bases are removed and replaced by the correct base, and then a new base is added. Most mistakes are corrected during replication, although when this does not happen, the mismatch repair mechanism is employed. Mismatch repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base. In yet another type of repair, nucleotide excision repair, the incorrect base is removed along with a few bases on the 5' and 3' end, and these are replaced by copying the template with the help of DNA polymerase. The ends of the newly synthesized fragment are attached to the rest of the DNA using DNA ligase, which creates a phosphodiester bond.
Most mistakes are corrected, and if they are not, they may result in a mutation defined as a permanent change in the DNA sequence. Mutations can be of many types, such as substitution, deletion, insertion, and translocation. Mutations in repair genes may lead to serious consequences such as cancer. Mutations can be induced or may occur spontaneously. |
https://openstax.org/books/biology/pages/14-key-terms | electrophoresis : technique used to separate DNA fragments according to size
helicase : during replication, this enzyme helps to open up the DNA helix by breaking the hydrogen bonds
induced mutation : mutation that results from exposure to chemicals or environmental agents
lagging strand : during replication, the strand that is replicated in short fragments and away from the replication fork
leading strand : strand that is synthesized continuously in the 5'-3' direction which is synthesized in the direction of the replication fork
ligase : enzyme that catalyzes the formation of a phosphodiester linkage between the 3' OH and 5' phosphate ends of the DNA
mismatch repair : type of repair mechanism in which mismatched bases are removed after replication
mutation : variation in the nucleotide sequence of a genome
nucleotide excision repair : type of DNA repair mechanism in which the wrong base, along with a few nucleotides upstream or downstream, are removed
Okazaki fragment : DNA fragment that is synthesized in short stretches on the lagging strand
point mutation : mutation that affects a single base
primase : enzyme that synthesizes the RNA primer; the primer is needed for DNA pol to start synthesis of a new DNA strand
primer : short stretch of nucleotides that is required to initiate replication; in the case of replication, the primer has RNA nucleotides
proofreading : function of DNA pol in which it reads the newly added base before adding the next one
replication fork : Y-shaped structure formed during initiation of replication
silent mutation : mutation that is not expressed
single-strand binding protein : during replication, protein that binds to the single-stranded DNA; this helps in keeping the two strands of DNA apart so that they may serve as templates
sliding clamp : ring-shaped protein that holds the DNA pol on the DNA strand
spontaneous mutation : mutation that takes place in the cells as a result of chemical reactions taking place naturally without exposure to any external agent
telomerase : enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends
telomere : DNA at the end of linear chromosomes
topoisomerase : enzyme that causes underwinding or overwinding of DNA when DNA replication is taking place
transformation : process in which external DNA is taken up by a cell
transition substitution : when a purine is replaced with a purine or a pyrimidine is replaced with another pyrimidine
transversion substitution : when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine |
https://openstax.org/books/biology/pages/15-chapter-summary | The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet (20 amino acids). The Central Dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three nonsense codons. Almost every species on the planet uses the same genetic code.
In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus sequences that recruit RNA polymerase. The prokaryotic polymerase consists of a core enzyme of four protein subunits and aÏprotein that assists only with initiation. Elongation synthesizes mRNA in the 5' to 3' direction at a rate of 40 nucleotides per second. Termination liberates the mRNA and occurs either by rho protein interaction or by the formation of an mRNA hairpin.
Transcription in eukaryotes involves one of three types of polymerases, depending on the gene being transcribed. RNA polymerase II transcribes all of the protein-coding genes, whereas RNA polymerase I transcribes rRNA genes, and RNA polymerase III transcribes rRNA, tRNA, and small nuclear RNA genes. The initiation of transcription in eukaryotes involves the binding of several transcription factors to complex promoter sequences that are usually located upstream of the gene being copied. The mRNA is synthesized in the 5' to 3' direction, and the FACT complex moves and reassembles nucleosomes as the polymerase passes by. Whereas RNA polymerases I and III terminate transcription by protein- or RNA hairpin-dependent methods, RNA polymerase II transcribes for 1,000 or more nucleotides beyond the gene template and cleaves the excess during pre-mRNA processing.
Eukaryotic pre-mRNAs are modified with a 5' methylguanosine cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Pre-mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs that have undergone 5' capping, 3' polyadenylation, and intron splicing are exported from the nucleus to the cytoplasm. Pre-rRNAs and pre-tRNAs may be processed by intramolecular cleavage, splicing, methylation, and chemical conversion of nucleotides. Rarely, RNA editing is also performed to insert missing bases after an mRNA has been synthesized.
The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit forms on the mRNA template either at the Shine-Dalgarno sequence (prokaryotes) or the 5' cap (eukaryotes). Translation begins at the initiating AUG on the mRNA, specifying methionine. The formation of peptide bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. Charged tRNAs enter the ribosomal A site, and their amino acid bonds with the amino acid at the P site. The entire mRNA is translated in three-nucleotide âstepsâ of the ribosome. When a nonsense codon is encountered, a release factor binds and dissociates the components and frees the new protein. Folding of the protein occurs during and after translation. |
https://openstax.org/books/biology/pages/15-key-terms | 7-methylguanosine cap : modification added to the 5' end of pre-mRNAs to protect mRNA from degradation and assist translation
aminoacyl tRNA synthetase : enzyme that âchargesâ tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid
anticodon : three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon
CAAT box : (GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors
Central Dogma : states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins
codon : three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation
colinear : in terms of RNA and protein, three âunitsâ of RNA (nucleotides) specify one âunitâ of protein (amino acid) in a consecutive fashion
consensus : DNA sequence that is used by many species to perform the same or similar functions
core enzyme : prokaryotic RNA polymerase consisting ofα,α,β, andβ' but missingÏ; this complex performs elongation
degeneracy : (of the genetic code) describes that a given amino acid can be encoded by more than one nucleotide triplet; the code is degenerate, but not ambiguous
downstream : nucleotides following the initiation site in the direction of mRNA transcription; in general, sequences that are toward the 3' end relative to a site on the mRNA
exon : sequence present in protein-coding mRNA after completion of pre-mRNA splicing
FACT : complex that âfacilitates chromatin transcriptionâ by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by
GC-rich box : (GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter
hairpin : structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides
holoenzyme : prokaryotic RNA polymerase consisting ofα,α,β,β', andÏ; this complex is responsible for transcription initiation
initiation site : nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a â+1â
initiator tRNA : in prokaryotes, calledtRNAfMettRNAfMet; in eukaryotes, called tRNAi; a tRNA that interacts with a start codon, binds directly to the ribosome P site, and links to a special methionine to begin a polypeptide chain
intron : nonâprotein-coding intervening sequences that are spliced from mRNA during processing
Kozakâs rules : determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must appear around the AUG: 5â-GCC(purine)CCunderlineAUGend underlineG-3â; the bolded bases are most important
nonsense codon : one of the three mRNA codons that specifies termination of translation
nontemplate strand : strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA
Octamer box : (ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter
peptidyl transferase : RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation of peptide bonds
plasmid : extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common in prokaryotes
poly-A tail : modification added to the 3' end of pre-mRNAs to protect mRNA from degradation and assist mRNA export from the nucleus
polysome : mRNA molecule simultaneously being translated by many ribosomes all going in the same direction
preinitiation complex : cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template
promoter : DNA sequence to which RNA polymerase and associated factors bind and initiate transcription
reading frame : sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that protein
Rho-dependent termination : in prokaryotes, termination of transcription by an interaction between RNA polymerase and the rho protein at a run of G nucleotides on the DNA template
Rho-independent : termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin formation in the mRNA that stalls the polymerase
RNA editing : direct alteration of one or more nucleotides in an mRNA that has already been synthesized
Shine-Dalgarno sequence : (AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules comprising the 30S ribosome
signal sequence : short tail of amino acids that directs a protein to a specific cellular compartment
small nuclear RNA : molecules synthesized by RNA polymerase III that have a variety of functions, including splicing pre-mRNAs and regulating transcription factors
splicing : process of removing introns and reconnecting exons in a pre-mRNA
start codon : AUG (or rarely, GUG) on an mRNA from which translation begins; always specifies methionine
TATA box : conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for transcription
template strand : strand of DNA that specifies the complementary mRNA molecule
transcription bubble : region of locally unwound DNA that allows for transcription of mRNA
upstream : nucleotides preceding the initiation site; in general, sequences toward the 5' end relative to a site on the mRNA |
https://openstax.org/books/biology/pages/16-chapter-summary | While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is mostly regulated at the transcriptional level (some epigenetic and post-translational regulation is also present), whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels.
The regulation of gene expression in prokaryotic cells occurs at the transcriptional level. There are three ways to control the transcription of an operon: repressive control, activator control, and inducible control. Repressive control, typified by thetrpoperon, uses proteins bound to the operator sequence to physically prevent the binding of RNA polymerase and the activation of transcription. Therefore, if tryptophan is not needed, the repressor is bound to the operator and transcription remains off. Activator control, typified by the action of CAP, increases the binding ability of RNA polymerase to the promoter when CAP is bound. In this case, low levels of glucose result in the binding of cAMP to CAP. CAP then binds the promoter, which allows RNA polymerase to bind to the promoter better. In the last exampleâthelacoperonâtwo conditions must be met to initiate transcription. Glucose must not be present, and lactose must be available for thelacoperon to be transcribed. If glucose is absent, CAP binds to the operator. If lactose is present, the repressor protein does not bind to its operator. Only when both conditions are met will RNA polymerase bind to the promoter to induce transcription.
In eukaryotic cells, the first stage of gene expression control occurs at the epigenetic level. Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription.
To start transcription, general transcription factors, such as TFIID, TFIIH, and others, must first bind to the TATA box and recruit RNA polymerase to that location. The binding of additional regulatory transcription factors tocis-acting elements will either increase or prevent transcription. In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription.
Post-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex. Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. The RNA stability can be increased, leading to longer residency time in the cytoplasm, or decreased, leading to shortened time and less protein synthesis. RNA stability is controlled by RNA-binding proteins (RPBs) and microRNAs (miRNAs). These RPBs and miRNAs bind to the 5' UTR or the 3' UTR of the RNA to increase or decrease RNA stability. Depending on the RBP, the stability can be increased or decreased significantly; however, miRNAs always decrease stability and promote decay.
Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell. To translate the protein, a protein initiator complex must assemble on the RNA. Modifications (such as phosphorylation) of proteins in this complex can prevent proper translation from occurring. Once a protein has been synthesized, it can be modified (phosphorylated, acetylated, methylated, or ubiquitinated). These post-translational modifications can greatly impact the stability, degradation, or function of the protein.
Cancer can be described as a disease of altered gene expression. Changes at every level of eukaryotic gene expression can be detected in some form of cancer at some point in time. In order to understand how changes to gene expression can cause cancer, it is critical to understand how each stage of gene regulation works in normal cells. By understanding the mechanisms of control in normal, non-diseased cells, it will be easier for scientists to understand what goes wrong in disease states including complex ones like cancer. |
https://openstax.org/books/biology/pages/16-key-terms | 3' UTR : 3' untranslated region; region just downstream of the protein-coding region in an RNA molecule that is not translated
5' cap : a methylated guanosine triphosphate (GTP) molecule that is attached to the 5' end of a messenger RNA to protect the end from degradation
5' UTR : 5' untranslated region; region just upstream of the protein-coding region in an RNA molecule that is not translated
activator : protein that binds to prokaryotic operators to increase transcription
catabolite activator protein (CAP) : protein that complexes with cAMP to bind to the promoter sequences of operons that control sugar processing when glucose is not available
cis-acting element : transcription factor binding sites within the promoter that regulate the transcription of a gene adjacent to it
dicer : enzyme that chops the pre-miRNA into the mature form of the miRNA
DNA methylation : epigenetic modification that leads to gene silencing; commonly found in cancer cells
enhancer : segment of DNA that is upstream, downstream, perhaps thousands of nucleotides away, or on another chromosome that influence the transcription of a specific gene
epigenetic : heritable changes that do not involve changes in the DNA sequence
eukaryotic initiation factor-2 (eIF-2) : protein that binds first to an mRNA to initiate translation
gene expression : processes that control the turning on or turning off of a gene
guanine diphosphate (GDP) : molecule that is left after the energy is used to start translation
guanine triphosphate (GTP) : energy-providing molecule that binds to eIF-2 and is needed for translation
histone acetylation : epigenetic modification that leads to gene silencing; commonly found in cancer cells
inducible operon : operon that can be activated or repressed depending on cellular needs and the surrounding environment
initiation complex : protein complex containing eIF2-2 that starts translation
lac operon : operon in prokaryotic cells that encodes genes required for processing and intake of lactose
large 60S ribosomal subunit : second, larger ribosomal subunit that binds to the RNA to translate it into protein
microRNA (miRNA) : small RNA molecules (approximately 21 nucleotides in length) that bind to RNA molecules to degrade them
myc : oncogene that causes cancer in many cancer cells
negative regulator : protein that prevents transcription
operator : region of DNA outside of the promoter region that binds activators or repressors that control gene expression in prokaryotic cells
operon : collection of genes involved in a pathway that are transcribed together as a single mRNA in prokaryotic cells
poly-A tail : a series of adenine nucleotides that are attached to the 3' end of an mRNA to protect the end from degradation
positive regulator : protein that increases transcription
post-transcriptional : control of gene expression after the RNA molecule has been created but before it is translated into protein
post-translational : control of gene expression after a protein has been created
proteasome : organelle that degrades proteins
repressor : protein that binds to the operator of prokaryotic genes to prevent transcription
RISC : protein complex that binds along with the miRNA to the RNA to degrade it
RNA stability : how long an RNA molecule will remain intact in the cytoplasm
RNA-binding protein (RBP) : protein that binds to the 3' or 5' UTR to increase or decrease the RNA stability
small 40S ribosomal subunit : ribosomal subunit that binds to the RNA to translate it into protein
trans-acting element : transcription factor binding site found outside the promoter or on another chromosome that influences the transcription of a particular gene
transcription factor : protein that binds to the DNA at the promoter or enhancer region and that influences transcription of a gene
transcription factor binding site : sequence of DNA to which a transcription factor binds
transcriptional start site : site at which transcription begins
trp operon : series of genes necessary to synthesize tryptophan in prokaryotic cells
tryptophan : amino acid that can be synthesized by prokaryotic cells when necessary
untranslated region : segment of the RNA molecule that are not translated into protein. These regions lie before (upstream or 5') and after (downstream or 3') the protein-coding region |
https://openstax.org/books/biology/pages/17-chapter-summary | Nucleic acids can be isolated from cells for the purposes of further analysis by breaking open the cells and enzymatically destroying all other major macromolecules. Fragmented or whole chromosomes can be separated on the basis of size by gel electrophoresis. Short stretches of DNA or RNA can be amplified by PCR. Southern and northern blotting can be used to detect the presence of specific short sequences in a DNA or RNA sample. The term âcloningâ may refer to cloning small DNA fragments (molecular cloning), cloning cell populations (cellular cloning), or cloning entire organisms (reproductive cloning). Genetic testing is performed to identify disease-causing genes, and gene therapy is used to cure an inheritable disease.
Transgenic organisms possess DNA from a different species, usually generated by molecular cloning techniques. Vaccines, antibiotics, and hormones are examples of products obtained by recombinant DNA technology. Transgenic plants are usually created to improve characteristics of crop plants.
Genome mapping is similar to solving a big, complicated puzzle with pieces of information coming from laboratories all over the world. Genetic maps provide an outline for the location of genes within a genome, and they estimate the distance between genes and genetic markers on the basis of recombination frequencies during meiosis. Physical maps provide detailed information about the physical distance between the genes. The most detailed information is available through sequence mapping. Information from all mapping and sequencing sources is combined to study an entire genome.
Whole-genome sequencing is the latest available resource to treat genetic diseases. Some doctors are using whole-genome sequencing to save lives. Genomics has many industrial applications including biofuel development, agriculture, pharmaceuticals, and pollution control. The basic principle of all modern-day sequencing strategies involves the chain termination method of sequencing.
Although the human genome sequences provide key insights to medical professionals, researchers use whole-genome sequences of model organisms to better understand the genome of the species. Automation and the decreased cost of whole-genome sequencing may lead to personalized medicine in the future.
Imagination is the only barrier to the applicability of genomics. Genomics is being applied to most fields of biology; it is being used for personalized medicine, prediction of disease risks at an individual level, the study of drug interactions before the conduct of clinical trials, and the study of microorganisms in the environment as opposed to the laboratory. It is also being applied to developments such as the generation of new biofuels, genealogical assessment using mitochondria, advances in forensic science, and improvements in agriculture.
Proteomics is the study of the entire set of proteins expressed by a given type of cell under certain environmental conditions. In a multicellular organism, different cell types will have different proteomes, and these will vary with changes in the environment. Unlike a genome, a proteome is dynamic and in constant flux, which makes it both more complicated and more useful than the knowledge of genomes alone.
Proteomics approaches rely on protein analysis; these techniques are constantly being upgraded. Proteomics has been used to study different types of cancer. Different biomarkers and protein signatures are being used to analyze each type of cancer. The future goal is to have a personalized treatment plan for each individual. |
https://openstax.org/books/biology/pages/17-key-terms | antibiotic resistance : ability of an organism to be unaffected by the actions of an antibiotic
biomarker : individual protein that is uniquely produced in a diseased state
biotechnology : use of biological agents for technological advancement
cDNA library : collection of cloned cDNA sequences
cellular cloning : production of identical cell populations by binary fission
chain termination method : method of DNA sequencing using labeled dideoxynucleotides to terminate DNA replication; it is also called the dideoxy method or the Sanger method
clone : exact replica
contig : larger sequence of DNA assembled from overlapping shorter sequences
cytogenetic mapping : technique that uses a microscope to create a map from stained chromosomes
deoxynucleotide : individual monomer (single unit) of DNA
dideoxynucleotide : individual monomer of DNA that is missing a hydroxyl group (âOH)
DNA microarray : method used to detect gene expression by analyzing an array of DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and identify sequences
expressed sequence tag (EST) : short STS that is identified with cDNA
false negative : incorrect test result that should have been positive
foreign DNA : DNA that belongs to a different species or DNA that is artificially synthesized
gel electrophoresis : technique used to separate molecules on the basis of size using electric charge
gene targeting : method for altering the sequence of a specific gene by introducing the modified version on a vector
gene therapy : technique used to cure inheritable diseases by replacing mutant genes with good genes
genetic diagnosis : diagnosis of the potential for disease development by analyzing disease-causing genes
genetic engineering : alteration of the genetic makeup of an organism
genetic map : outline of genes and their location on a chromosome
genetic marker : gene or sequence on a chromosome with a known location that is associated with a specific trait
genetic recombination : exchange of DNA between homologous pairs of chromosomes
genetic testing : process of testing for the presence of disease-causing genes
genetically modified organism (GMO) : organism whose genome has been artificially changed
genome annotation : process of attaching biological information to gene sequences
genome mapping : process of finding the location of genes on each chromosome
genomic library : collection of cloned DNA which represents all of the sequences and fragments from a genome
genomics : study of entire genomes including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species
host DNA : DNA that is present in the genome of the organism of interest
linkage analysis : procedure that analyzes the recombination of genes to determine if they are linked
lysis buffer : solution used to break the cell membrane and release cell contents
metabolome : complete set of metabolites which are related to the genetic makeup of an organism
metabolomics : study of small molecule metabolites found in an organism
metagenomics : study of the collective genomes of multiple species that grow and interact in an environmental niche
microsatellite polymorphism : variation between individuals in the sequence and number of repeats of microsatellite DNA
model organism : species that is studied and used as a model to understand the biological processes in other species represented by the model organism
molecular cloning : cloning of DNA fragments
multiple cloning site (MCS) : site that can be recognized by multiple restriction endonucleases
next-generation sequencing : group of automated techniques used for rapid DNA sequencing
northern blotting : transfer of RNA from a gel to a nylon membrane
pharmacogenomics : study of drug interactions with the genome or proteome; also called toxicogenomics
physical map : representation of the physical distance between genes or genetic markers
polygenic : phenotypic characteristic caused by two or more genes
polymerase chain reaction (PCR) : technique used to amplify DNA
probe : small DNA fragment used to determine if the complementary sequence is present in a DNA sample
protease : enzyme that breaks down proteins
protein signature : set of uniquely expressed proteins in the diseased state
proteome : entire set of proteins produced by a cell type
proteomics : study of the function of proteomes
pure culture : growth of a single type of cell in the laboratory
radiation hybrid mapping : information obtained by fragmenting the chromosome with x-rays
recombinant DNA : combination of DNA fragments generated by molecular cloning that does not exist in nature; also known as a chimeric molecule
recombinant protein : protein product of a gene derived by molecular cloning
reproductive cloning : cloning of entire organisms
restriction endonuclease : enzyme that can recognize and cleave specific DNA sequences
restriction fragment length polymorphism (RFLP) : variation between individuals in the length of DNA fragments generated by restriction endonucleases
reverse genetics : method of determining the function of a gene by starting with the gene itself instead of starting with the gene product
reverse transcriptase PCR (RT-PCR) : PCR technique that involves converting RNA to DNA by reverse transcriptase
ribonuclease : enzyme that breaks down RNA
sequence mapping : mapping information obtained after DNA sequencing
shotgun sequencing : method used to sequence multiple DNA fragments to generate the sequence of a large piece of DNA
single nucleotide polymorphism (SNP) : variation between individuals in a single nucleotide
Southern blotting : transfer of DNA from a gel to a nylon membrane
systems biology : study of whole biological systems (genomes and proteomes) based on interactions within the system
Ti plasmid : plasmid system derived fromAgrobacterium tumifaciensthat has been used by scientists to introduce foreign DNA into plant cells
transgenic : organism that receives DNA from a different species
variable number of tandem repeats (VNTRs) : variation in the number of tandem repeats between individuals in the population
whole-genome sequencing : process that determines the DNA sequence of an entire genome |
https://openstax.org/books/biology/pages/18-chapter-summary | Evolution is the process of adaptation through mutation which allows more desirable characteristics to be passed to the next generation. Over time, organisms evolve more characteristics that are beneficial to their survival. For living organisms to adapt and change to environmental pressures, genetic variation must be present. With genetic variation, individuals have differences in form and function that allow some to survive certain conditions better than others. These organisms pass their favorable traits to their offspring. Eventually, environments change, and what was once a desirable, advantageous trait may become an undesirable trait and organisms may further evolve. Evolution may be convergent with similar traits evolving in multiple species or divergent with diverse traits evolving in multiple species that came from a common ancestor. Evidence of evolution can be observed by means of DNA code and the fossil record, and also by the existence of homologous and vestigial structures.
Speciation occurs along two main pathways: geographic separation (allopatric speciation) and through mechanisms that occur within a shared habitat (sympatric speciation). Both pathways isolate a population reproductively in some form. Mechanisms of reproductive isolation act as barriers between closely related species, enabling them to diverge and exist as genetically independent species. Prezygotic barriers block reproduction prior to formation of a zygote, whereas postzygotic barriers block reproduction after fertilization occurs. For a new species to develop, something must cause a breach in the reproductive barriers. Sympatric speciation can occur through errors in meiosis that form gametes with extra chromosomes (polyploidy). Autopolyploidy occurs within a single species, whereas allopolyploidy occurs between closely related species.
Speciation is not a precise division: overlap between closely related species can occur in areas called hybrid zones. Organisms reproduce with other similar organisms. The fitness of these hybrid offspring can affect the evolutionary path of the two species. Scientists propose two models for the rate of speciation: one model illustrates how a species can change slowly over time; the other model demonstrates how change can occur quickly from a parent generation to a new species. Both models continue to follow the patterns of natural selection. |
https://openstax.org/books/biology/pages/18-key-terms | adaptation : heritable trait or behavior in an organism that aids in its survival and reproduction in its present environment
adaptive radiation : speciation when one species radiates out to form several other species
allopatric speciation : speciation that occurs via geographic separation
allopolyploid : polyploidy formed between two related, but separate species
aneuploidy : condition of a cell having an extra chromosome or missing a chromosome for its species
autopolyploid : polyploidy formed within a single species
behavioral isolation : type of reproductive isolation that occurs when a specific behavior or lack of one prevents reproduction from taking place
convergent evolution : process by which groups of organisms independently evolve to similar forms
dispersal : allopatric speciation that occurs when a few members of a species move to a new geographical area
divergent evolution : process by which groups of organisms evolve in diverse directions from a common point
gametic barrier : prezygotic barrier occurring when closely related individuals of different species mate, but differences in their gamete cells (eggs and sperm) prevent fertilization from taking place
gradual speciation model : model that shows how species diverge gradually over time in small steps
habitat isolation : reproductive isolation resulting when populations of a species move or are moved to a new habitat, taking up residence in a place that no longer overlaps with the other populations of the same species
homologous structures : parallel structures in diverse organisms that have a common ancestor
hybrid : offspring of two closely related individuals, not of the same species
hybrid zone : area where two closely related species continue to interact and reproduce, forming hybrids
natural selection : reproduction of individuals with favorable genetic traits that survive environmental change because of those traits, leading to evolutionary change
postzygotic barrier : reproductive isolation mechanism that occurs after zygote formation
prezygotic barrier : reproductive isolation mechanism that occurs before zygote formation
punctuated equilibrium : model for rapid speciation that can occur when an event causes a small portion of a population to be cut off from the rest of the population
reinforcement : continued speciation divergence between two related species due to low fitness of hybrids between them
reproductive isolation : situation that occurs when a species is reproductively independent from other species; this may be brought about by behavior, location, or reproductive barriers
speciation : formation of a new species
species : group of populations that interbreed and produce fertile offspring
sympatric speciation : speciation that occurs in the same geographic space
temporal isolation : differences in breeding schedules that can act as a form of prezygotic barrier leading to reproductive isolation
variation : genetic differences among individuals in a population
vestigial structure : physical structure present in an organism but that has no apparent function and appears to be from a functional structure in a distant ancestor
vicariance : allopatric speciation that occurs when something in the environment separates organisms of the same species into separate groups |
https://openstax.org/books/biology/pages/19-chapter-summary | The modern synthesis of evolutionary theory grew out of the cohesion of Darwinâs, Wallaceâs, and Mendelâs thoughts on evolution and heredity, along with the more modern study of population genetics. It describes the evolution of populations and species, from small-scale changes among individuals to large-scale changes over paleontological time periods. To understand how organisms evolve, scientists can track populationsâ allele frequencies over time. If they differ from generation to generation, scientists can conclude that the population is not in Hardy-Weinberg equilibrium, and is thus evolving.
Both genetic and environmental factors can cause phenotypic variation in a population. Different alleles can confer different phenotypes, and different environments can also cause individuals to look or act differently. Only those differences encoded in an individualâs genes, however, can be passed to its offspring and, thus, be a target of natural selection. Natural selection works by selecting for alleles that confer beneficial traits or behaviors, while selecting against those for deleterious qualities. Genetic drift stems from the chance occurrence that some individuals in the germ line have more offspring than others. When individuals leave or join the population, allele frequencies can change as a result of gene flow. Mutations to an individualâs DNA may introduce new variation into a population. Allele frequencies can also be altered when individuals do not randomly mate with others in the group.
Because natural selection acts to increase the frequency of beneficial alleles and traits while decreasing the frequency of deleterious qualities, it is adaptive evolution. Natural selection acts at the level of the individual, selecting for those that have a higher overall fitness compared to the rest of the population. If the fit phenotypes are those that are similar, natural selection will result in stabilizing selection, and an overall decrease in the populationâs variation. Directional selection works to shift a populationâs variance toward a new, fit phenotype, as environmental conditions change. In contrast, diversifying selection results in increased genetic variance by selecting for two or more distinct phenotypes.
Other types of selection include frequency-dependent selection, in which individuals with either common (positive frequency-dependent selection) or rare (negative frequency-dependent selection) are selected for. Finally, sexual selection results from the fact that one sex has more variance in the reproductive success than the other. As a result, males and females experience different selective pressures, which can often lead to the evolution of phenotypic differences, or sexual dimorphisms, between the two. |
https://openstax.org/books/biology/pages/19-key-terms | adaptive evolution : increase in frequency of beneficial alleles and decrease in deleterious alleles due to selection
allele frequency : (also, gene frequency) rate at which a specific allele appears within a population
assortative mating : when individuals tend to mate with those who are phenotypically similar to themselves
bottleneck effect : magnification of genetic drift as a result of natural events or catastrophes
cline : gradual geographic variation across an ecological gradient
directional selection : selection that favors phenotypes at one end of the spectrum of existing variation
diversifying selection : selection that favors two or more distinct phenotypes
evolutionary fitness : (also, Darwinian fitness) individualâs ability to survive and reproduce
founder effect : event that initiates an allele frequency change in part of the population, which is not typical of the original population
frequency-dependent selection : selection that favors phenotypes that are either common (positive frequency-dependent selection) or rare (negative frequency-dependent selection)
gene flow : flow of alleles in and out of a population due to the migration of individuals or gametes
gene pool : all of the alleles carried by all of the individuals in the population
genetic drift : effect of chance on a populationâs gene pool
genetic structure : distribution of the different possible genotypes in a population
genetic variance : diversity of alleles and genotypes in a population
geographical variation : differences in the phenotypic variation between populations that are separated geographically
good genes hypothesis : theory of sexual selection that argues individuals develop impressive ornaments to show off their efficient metabolism or ability to fight disease
handicap principle : theory of sexual selection that argues only the fittest individuals can afford costly traits
heritability : fraction of population variation that can be attributed to its genetic variance
honest signal : trait that gives a truthful impression of an individualâs fitness
inbreeding : mating of closely related individuals
inbreeding depression : increase in abnormalities and disease in inbreeding populations
macroevolution : broader scale evolutionary changes seen over paleontological time
microevolution : changes in a populationâs genetic structure
modern synthesis : overarching evolutionary paradigm that took shape by the 1940s and is generally accepted today
nonrandom mating : changes in a populationâs gene pool due to mate choice or other forces that cause individuals to mate with certain phenotypes more than others
population genetics : study of how selective forces change the allele frequencies in a population over time
population variation : distribution of phenotypes in a population
relative fitness : individualâs ability to survive and reproduce relative to the rest of the population
selective pressure : environmental factor that causes one phenotype to be better than another
sexual dimorphism : phenotypic difference between the males and females of a population
stabilizing selection : selection that favors average phenotypes |
https://openstax.org/books/biology/pages/20-chapter-summary | Scientists continually gain new information that helps understand the evolutionary history of life on Earth. Each group of organisms went through its own evolutionary journey, called its phylogeny. Each organism shares relatedness with others, and based on morphologic and genetic evidence, scientists attempt to map the evolutionary pathways of all life on Earth. Historically, organisms were organized into a taxonomic classification system. However, today many scientists build phylogenetic trees to illustrate evolutionary relationships.
To build phylogenetic trees, scientists must collect accurate information that allows them to make evolutionary connections between organisms. Using morphologic and molecular data, scientists work to identify homologous characteristics and genes. Similarities between organisms can stem either from shared evolutionary history (homologies) or from separate evolutionary paths (analogies). Newer technologies can be used to help distinguish homologies from analogies. After homologous information is identified, scientists use cladistics to organize these events as a means to determine an evolutionary timeline. Scientists apply the concept of maximum parsimony, which states that the order of events probably occurred in the most obvious and simple way with the least amount of steps. For evolutionary events, this would be the path with the least number of major divergences that correlate with the evidence.
The phylogenetic tree, first used by Darwin, is the classic âtree of lifeâ model describing phylogenetic relationships among species, and the most common model used today. New ideas about HGT and genome fusion have caused some to suggest revising the model to resemble webs or rings. |
https://openstax.org/books/biology/pages/20-key-terms | analogy : (also, homoplasy) characteristic that is similar between organisms by convergent evolution, not due to the same evolutionary path
basal taxon : branch on a phylogenetic tree that has not diverged significantly from the root ancestor
binomial nomenclature : system of two-part scientific names for an organism, which includes genus and species names
branch point : node on a phylogenetic tree where a single lineage splits into distinct new ones
cladistics : system used to organize homologous traits to describe phylogenies
class : division of phylum in the taxonomic classification system
eukaryote-first hypothesis : proposal that prokaryotes evolved from eukaryotes
family : division of order in the taxonomic classification system
gene transfer agent (GTA) : bacteriophage-like particle that transfers random genomic segments from one species of prokaryote to another
genome fusion : fusion of two prokaryotic genomes, presumably by endosymbiosis
genus : division of family in the taxonomic classification system; the first part of the binomial scientific name
horizontal gene transfer (HGT) : (also, lateral gene transfer) transfer of genes between unrelated species
kingdom : division of domain in the taxonomic classification system
maximum parsimony : applying the simplest, most obvious way with the least number of steps
mitochondria-first hypothesis : proposal that prokaryotes acquired a mitochondrion first, followed by nuclear development
molecular systematics : technique using molecular evidence to identify phylogenetic relationships
monophyletic group : (also, clade) organisms that share a single ancestor
nucleus-first hypothesis : proposal that prokaryotes acquired a nucleus first, and then the mitochondrion
order : division of class in the taxonomic classification system
phylogenetic tree : diagram used to reflect the evolutionary relationships among organisms or groups of organisms
phylogeny : evolutionary history and relationship of an organism or group of organisms
phylum : (plural: phyla) division of kingdom in the taxonomic classification system
polytomy : branch on a phylogenetic tree with more than two groups or taxa
ring of life : phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes
rooted : single ancestral lineage on a phylogenetic tree to which all organisms represented in the diagram relate
shared ancestral character : describes a characteristic on a phylogenetic tree that is shared by all organisms on the tree
shared derived character : describes a characteristic on a phylogenetic tree that is shared only by a certain clade of organisms
sister taxa : two lineages that diverged from the same branch point
systematics : field of organizing and classifying organisms based on evolutionary relationships
taxon : (plural: taxa) single level in the taxonomic classification system
taxonomy : science of classifying organisms
web of life : phylogenetic model that attempts to incorporate the effects of horizontal gene transfer on evolution |
https://openstax.org/books/biology/pages/21-chapter-summary | Viruses are tiny, acellular entities that can usually only be seen with an electron microscope. Their genomes contain either DNA or RNAânever bothâand they replicate using the replication proteins of a host cell. Viruses are diverse, infecting archaea, bacteria, fungi, plants, and animals. Viruses consist of a nucleic acid core surrounded by a protein capsid with or without an outer lipid envelope. The capsid shape, presence of an envelope, and core composition dictate some elements of the classification of viruses. The most commonly used classification method, the Baltimore classification, categorizes viruses based on how they produce their mRNA.
Viral replication within a living cell always produces changes in the cell, sometimes resulting in cell death and sometimes slowly killing the infected cells. There are six basic stages in the virus replication cycle: attachment, penetration, uncoating, replication, assembly, and release. A viral infection may be productive, resulting in new virions, or nonproductive, which means that the virus remains inside the cell without producing new virions. Bacteriophages are viruses that infect bacteria. They have two different modes of replication: the lytic cycle, where the virus replicates and bursts out of the bacteria, and the lysogenic cycle, which involves the incorporation of the viral genome into the bacterial host genome. Animal viruses cause a variety of infections, with some causing chronic symptoms (hepatitis C), some intermittent symptoms (latent viruses such a herpes simplex virus 1), and others that cause very few symptoms, if any (human herpesviruses 6 and 7). Oncogenic viruses in animals have the ability to cause cancer by interfering with the regulation of the host cell cycle. Viruses of plants are responsible for significant economic damage in both agriculture and plants used for ornamentation.
Viruses cause a variety of diseases in humans. Many of these diseases can be prevented by the use of viral vaccines, which stimulate protective immunity against the virus without causing major disease. Viral vaccines may also be used in active viral infections, boosting the ability of the immune system to control or destroy the virus. A series of antiviral drugs that target enzymes and other protein products of viral genes have been developed and used with mixed success. Combinations of anti-HIV drugs have been used to effectively control the virus, extending the lifespans of infected individuals. Viruses have many uses in medicines, such as in the treatment of genetic disorders, cancer, and bacterial infections.
Prions are infectious agents that consist of protein, but no DNA or RNA, and seem to produce their deadly effects by duplicating their shapes and accumulating in tissues. They are thought to contribute to several progressive brain disorders, including mad cow disease and Creutzfeldt-Jakob disease. Viroids are single-stranded RNA pathogens that infect plants. Their presence can have a severe impact on the agriculture industry. |
https://openstax.org/books/biology/pages/21-key-terms | acellular : lacking cells
acute disease : disease where the symptoms rise and fall within a short period of time
asymptomatic disease : disease where there are no symptoms and the individual is unaware of being infected unless lab tests are performed
attenuation : weakening of a virus during vaccine development
AZT : anti-HIV drug that inhibits the viral enzyme reverse transcriptase
back mutation : when a live virus vaccine reverts back to it disease-causing phenotype
bacteriophage : virus that infects bacteria
budding : method of exit from the cell used in certain animal viruses, where virions leave the cell individually by capturing a piece of the host plasma membrane
capsid : protein coating of the viral core
capsomere : protein subunit that makes up the capsid
cell necrosis : cell death
chronic infection : describes when the virus persists in the body for a long period of time
cytopathic : causing cell damage
envelope : lipid bilayer that envelopes some viruses
fusion : method of entry by some enveloped viruses, where the viral envelope fuses with the plasma membrane of the host cell
gall : appearance of a plant tumor
gene therapy : treatment of genetic disease by adding genes, using viruses to carry the new genes inside the cell
group I virus : virus with a dsDNA genome
group II virus : virus with a ssDNA genome
group III virus : virus with a dsRNA genome
group IV virus : virus with a ssRNA genome with positive polarity
group V virus : virus with a ssRNA genome with negative polarity
group VI virus : virus with a ssRNA genomes converted into dsDNA by reverse transcriptase
group VII virus : virus with a single-stranded mRNA converted into dsDNA for genome replication
horizontal transmission : transmission of a disease between unrelated individuals
hyperplasia : abnormally high cell growth and division
hypoplasia : abnormally low cell growth and division
intermittent symptom : symptom that occurs periodically
latency : virus that remains in the body for a long period of time but only causes intermittent symptoms
lysis : bursting of a cell
lysogenic cycle : type of virus replication in which the viral genome is incorporated into the genome of the host cell
lytic cycle : type of virus replication in which virions are released through lysis, or bursting, of the cell
matrix protein : envelope protein that stabilizes the envelope and often plays a role in the assembly of progeny virions
negative polarity : ssRNA viruses with genomes complimentary to their mRNA
oncogenic virus : virus that has the ability to cause cancer
oncolytic virus : virus engineered to specifically infect and kill cancer cells
pathogen : agent with the ability to cause disease
permissive : cell type that is able to support productive replication of a virus
phage therapy : treatment of bacterial diseases using bacteriophages specific to a particular bacterium
positive polarity : ssRNA virus with a genome that contains the same base sequences and codons found in their mRNA
prion : infectious particle that consists of proteins that replicate without DNA or RNA
productive : viral infection that leads to the production of new virions
prophage : phage DNA that is incorporated into the host cell genome
PrPc : normal prion protein
PrPsc : infectious form of a prion protein
replicative intermediate : dsRNA intermediate made in the process of copying genomic RNA
reverse transcriptase : enzyme found in Baltimore groups VI and VII that converts single-stranded RNA into double-stranded DNA
vaccine : weakened solution of virus components, viruses, or other agents that produce an immune response
vertical transmission : transmission of disease from parent to offspring
viral receptor : glycoprotein used to attach a virus to host cells via molecules on the cell
virion : individual virus particle outside a host cell
viroid : plant pathogen that produces only a single, specific RNA
virus core : contains the virus genome |
https://openstax.org/books/biology/pages/22-chapter-summary | Prokaryotes existed for billions of years before plants and animals appeared. Hot springs and hydrothermal vents may have been the environments in which life began. Microbial mats are thought to represent the earliest forms of life on Earth, and there is fossil evidence of their presence about 3.5 billion years ago. A microbial mat is a multi-layered sheet of prokaryotes that grows at interfaces between different types of material, mostly on moist surfaces. During the first 2 billion years, the atmosphere was anoxic and only anaerobic organisms were able to live. Cyanobacteria evolved from early phototrophs and began the oxygenation of the atmosphere. The increase in oxygen concentration allowed the evolution of other life forms. Fossilized microbial mats are called stromatolites and consist of laminated organo-sedimentary structures formed by precipitation of minerals by prokaryotes. They represent the earliest fossil record of life on Earth.
Bacteria and archaea grow in virtually every environment. Those that survive under extreme conditions are called extremophiles (extreme lovers). Some prokaryotes cannot grow in a laboratory setting, but they are not dead. They are in the viable-but-non-culturable (VBNC) state. The VBNC state occurs when prokaryotes enter a dormant state in response to environmental stressors. Most prokaryotes are social and prefer to live in communities where interactions take place. A biofilm is a microbial community held together in a gummy-textured matrix.
Prokaryotes (domains Archaea and Bacteria) are single-celled organisms lacking a nucleus. They have a single piece of circular DNA in the nucleoid area of the cell. Most prokaryotes have a cell wall that lies outside the boundary of the plasma membrane. Some prokaryotes may have additional structures such as a capsule, flagella, and pili. Bacteria and Archaea differ in the lipid composition of their cell membranes and the characteristics of the cell wall. In archaeal membranes, phytanyl units, rather than fatty acids, are linked to glycerol. Some archaeal membranes are lipid monolayers instead of bilayers.
The cell wall is located outside the cell membrane and prevents osmotic lysis. The chemical composition of cell walls varies between species. Bacterial cell walls contain peptidoglycan. Archaean cell walls do not have peptidoglycan, but they may have pseudopeptidoglycan, polysaccharides, glycoproteins, or protein-based cell walls. Bacteria can be divided into two major groups: Gram positive and Gram negative, based on the Gram stain reaction. Gram-positive organisms have a thick cell wall, together with teichoic acids. Gram-negative organisms have a thin cell wall and an outer envelope containing lipopolysaccharides and lipoproteins.
Prokaryotes are the most metabolically diverse organisms; they flourish in many different environments with various carbon energy and carbon sources, variable temperature, pH, pressure, and water availability. Nutrients required in large amounts are called macronutrients, whereas those required in trace amounts are called micronutrients or trace elements. Macronutrients include C, H, O, N, P, S, K, Mg, Ca, and Na. In addition to these macronutrients, prokaryotes require various metallic elements for growth and enzyme function. Prokaryotes use different sources of energy to assemble macromolecules from smaller molecules. Phototrophs obtain their energy from sunlight, whereas chemotrophs obtain energy from chemical compounds.
Prokaryotes play roles in the carbon and nitrogen cycles. Carbon is returned to the atmosphere by the respiration of animals and other chemoorganotrophic organisms. Consumers use organic compounds generated by producers and release carbon dioxide into the atmosphere. The most important contributor of carbon dioxide to the atmosphere is microbial decomposition of dead material. Nitrogen is recycled in nature from organic compounds to ammonia, ammonium ions, nitrite, nitrate, and nitrogen gas. Gaseous nitrogen is transformed into ammonia through nitrogen fixation. Ammonia is anaerobically catabolized by some prokaryotes, yielding N2as the final product. Nitrification is the conversion of ammonium into nitrite. Nitrification in soils is carried out by bacteria. Denitrification is also performed by bacteria and transforms nitrate from soils into gaseous nitrogen compounds, such as N2O, NO, and N2.
Devastating diseases and plagues have been among us since early times. There are records about microbial diseases as far back as 3000 B.C. Infectious diseases remain among the leading causes of death worldwide. Emerging diseases are those rapidly increasing in incidence or geographic range. They can be new or re-emerging diseases (previously under control). Many emerging diseases affecting humans, such as brucellosis, are zoonoses. The WHO has identified a group of diseases whose re-emergence should be monitored: Those caused by bacteria include bubonic plague, diphtheria, and cholera.
Biofilms are considered responsible for diseases such as bacterial infections in patients with cystic fibrosis, Legionnairesâ disease, and otitis media. They produce dental plaque; colonize catheters, prostheses, transcutaneous, and orthopedic devices; and infect contact lenses, open wounds, and burned tissue. Biofilms also produce foodborne diseases because they colonize the surfaces of food and food-processing equipment. Biofilms are resistant to most of the methods used to control microbial growth. The excessive use of antibiotics has resulted in a major global problem, since resistant forms of bacteria have been selected over time. A very dangerous strain, methicillin-resistantStaphylococcus aureus(MRSA), has wreaked havoc recently. Foodborne diseases result from the consumption of contaminated food, pathogenic bacteria, viruses, or parasites that contaminate food.
Pathogens are only a small percentage of all prokaryotes. In fact, our life would not be possible without prokaryotes. Nitrogen is usually the most limiting element in terrestrial ecosystems; atmospheric nitrogen, the largest pool of available nitrogen, is unavailable to eukaryotes. Nitrogen can be âfixed,â or converted into ammonia (NH3) either biologically or abiotically. Biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes. After photosynthesis, BNF is the second most important biological process on Earth. The most important source of BNF is the symbiotic interaction between soil bacteria and legume plants.
Microbial bioremediation is the use of microbial metabolism to remove pollutants. Bioremediation has been used to remove agricultural chemicals that leach from soil into groundwater and the subsurface. Toxic metals and oxides, such as selenium and arsenic compounds, can also be removed by bioremediation. Probably one of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills.
Human life is only possible due to the action of microbes, both those in the environment and those species that call us home. Internally, they help us digest our food, produce crucial nutrients for us, protect us from pathogenic microbes, and help train our immune systems to function correctly. |
https://openstax.org/books/biology/pages/22-key-terms | acidophile : organism with optimal growth pH of three or below
alkaliphile : organism with optimal growth pH of nine or above
ammonification : process by which ammonia is released during the decomposition of nitrogen-containing organic compounds
anaerobic : refers to organisms that grow without oxygen
anoxic : without oxygen
antibiotic : biological substance that, in low concentration, is antagonistic to the growth of prokaryotes
biofilm : a microbial community growing together on a surface, often held together with a gummy matrix
biological nitrogen fixation : conversion of atmospheric nitrogen into ammonia exclusively carried out by prokaryotes
bioremediation : use of microbial metabolism to remove pollutants
biotechnology : any technological application that uses living organisms, biological systems, or their derivatives to produce or modify other products
Black Death : devastating pandemic that is believed to have been an outbreak of bubonic plague caused by the bacteriumYersinia pestis
botulism : disease produced by the toxin of the anaerobic bacteriumClostridium botulinum
CA-MRSA : MRSA acquired in the community rather than in a hospital setting
capsule : external structure that enables a prokaryote to attach to surfaces and protects it from dehydration
chemotroph : organism that obtains energy from chemical compounds
conjugation : process by which prokaryotes move DNA from one individual to another using a pilus
cyanobacteria : bacteria that evolved from early phototrophs and oxygenated the atmosphere; also known as blue-green algae
decomposer : organism that carries out the decomposition of dead organisms
denitrification : transformation of nitrate from soil to gaseous nitrogen compounds such as N2O, NO and N2
emerging disease : disease making an initial appearance in a population or that is increasing in incidence or geographic range
endemic disease : disease that is constantly present, usually at low incidence, in a population
epidemic : disease that occurs in an unusually high number of individuals in a population at the same time
extremophile : organism that grows under extreme or harsh conditions
foodborne disease : any illness resulting from the consumption of contaminated food, or of the pathogenic bacteria, viruses, or other parasites that contaminate food
Gram negative : bacterium whose cell wall contains little peptidoglycan but has an outer membrane
Gram positive : bacterium that contains mainly peptidoglycan in its cell walls
halophile : organism that require a salt concentration of at least 0.2 M
hydrothermal vent : fissure in Earthâs surface that releases geothermally heated water
hyperthermophile : organism that grows at temperatures between 80â122 °C
microbial mat : multi-layered sheet of prokaryotes that may include bacteria and archaea
MRSA : (methicillin-resistantStaphylococcus aureus) very dangerousStaphylococcusaureusstrain resistant to multiple antibiotics
nitrification : conversion of ammonium into nitrite and nitrate in soils
nitrogen fixation : process by which gaseous nitrogen is transformed, or âfixedâ into more readily available forms such as ammonia
nodule : novel structure on the roots of certain plants (legumes) that results from the symbiotic interaction between the plant and soil bacteria, is the site of nitrogen fixation
nutrient : essential substances for growth, such as carbon and nitrogen
osmophile : organism that grows in a high sugar concentration
pandemic : widespread, usually worldwide, epidemic disease
peptidoglycan : material composed of polysaccharide chains cross-linked to unusual peptides
phototroph : organism that is able to make its own food by converting solar energy to chemical energy
pilus : surface appendage of some prokaryotes used for attachment to surfaces including other prokaryotes
pseudopeptidoglycan : component of archaea cell walls that is similar to peptidoglycan in morphology but contains different sugars
psychrophile : organism that grows at temperatures of -15 °C or lower
radioresistant : organism that grows in high levels of radiation
resuscitation : process by which prokaryotes that are in the VBNC state return to viability
S-layer : surface-layer protein present on the outside of cell walls of archaea and bacteria
serotype : strain of bacteria that carries a set of similar antigens on its cell surface, often many in a bacterial species
stromatolite : layered sedimentary structure formed by precipitation of minerals by prokaryotes in microbial mats
teichoic acid : polymer associated with the cell wall of Gram-positive bacteria
thermophile : organism that lives at temperatures between 60â80 °C
transduction : process by which a bacteriophage moves DNA from one prokaryote to another
transformation : process by which a prokaryote takes in DNA found in its environment that is shed by other prokaryotes
viable-but-non-culturable (VBNC) state : survival mechanism of bacteria facing environmental stress conditions
zoonosis : disease that primarily infects animals that is transmitted to humans |
https://openstax.org/books/biology/pages/23-chapter-summary | The oldest fossil evidence of eukaryotes is about 2 billion years old. Fossils older than this all appear to be prokaryotes. It is probable that todayâs eukaryotes are descended from an ancestor that had a prokaryotic organization. The last common ancestor of todayâs Eukarya had several characteristics, including cells with nuclei that divided mitotically and contained linear chromosomes where the DNA was associated with histones, a cytoskeleton and endomembrane system, and the ability to make cilia/flagella during at least part of its life cycle. It was aerobic because it had mitochondria that were the result of an aerobic alpha-proteobacterium that lived inside a host cell. Whether this host had a nucleus at the time of the initial symbiosis remains unknown. The last common ancestor may have had a cell wall for at least part of its life cycle, but more data are needed to confirm this hypothesis. Todayâs eukaryotes are very diverse in their shapes, organization, life cycles, and number of cells per individual.
Protists are extremely diverse in terms of their biological and ecological characteristics, partly because they are an artificial assemblage of phylogenetically unrelated groups. Protists display highly varied cell structures, several types of reproductive strategies, virtually every possible type of nutrition, and varied habitats. Most single-celled protists are motile, but these organisms use diverse structures for transportation.
The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified many relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into six supergroups: Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The goal of this classification scheme is to create clusters of species that all are derived from a common ancestor. At present, the monophyly of some of the supergroups are better supported by genetic data than others. Although tremendous variation exists within the supergroups, commonalities at the morphological, physiological, and ecological levels can be identified.
Protists function at several levels of the ecological food web: as primary producers, as direct food sources, and as decomposers. In addition, many protists are parasites of plants and animals that can cause deadly human diseases or destroy valuable crops. |
https://openstax.org/books/biology/pages/23-key-terms | biological carbon pump : process by which inorganic carbon is fixed by photosynthetic species that then die and fall to the sea floor where they cannot be reached by saprobes and their carbon dioxide consumption cannot be returned to the atmosphere
bioluminescence : generation and emission of light by an organism, as in dinoflagellates
contractile vacuole : vesicle that fills with water (as it enters the cell by osmosis) and then contracts to squeeze water from the cell; an osmoregulatory vesicle
cytoplasmic streaming : movement of cytoplasm into an extended pseudopod such that the entire cell is transported to the site of the pseudopod
endosymbiosis : engulfment of one cell within another such that the engulfed cell survives, and both cells benefit; the process responsible for the evolution of mitochondria and chloroplasts in eukaryotes
endosymbiotic theory : theory that states that eukaryotes may have been a product of one cell engulfing another, one living within another, and evolving over time until the separate cells were no longer recognizable as such
hydrogenosome : organelle carried by parabasalids (Excavata) that functions anaerobically and outputs hydrogen gas as a byproduct; likely evolved from mitochondria
kinetoplast : mass of DNA carried within the single, oversized mitochondrion, characteristic of kinetoplastids (phylum: Euglenozoa)
mitosome : nonfunctional organelle carried in the cells of diplomonads (Excavata) that likely evolved from a mitochondrion
mixotroph : organism that can obtain nutrition by autotrophic or heterotrophic means, usually facultatively
pellicle : outer cell covering composed of interlocking protein strips that function like a flexible coat of armor, preventing cells from being torn or pierced without compromising their range of motion
phagolysosome : cellular body formed by the union of a phagosome containing the ingested particle with a lysosome that contains hydrolytic enzymes
plankton : diverse group of mostly microscopic organisms that drift in marine and freshwater systems and serve as a food source for larger aquatic organisms
plastid : one of a group of related organelles in plant cells that are involved in the storage of starches, fats, proteins, and pigments
raphe : slit in the silica shell of diatoms through which the protist secretes a stream of mucopolysaccharides for locomotion and attachment to substrates
test : porous shell of a foram that is built from various organic materials and typically hardened with calcium carbonate |
https://openstax.org/books/biology/pages/24-chapter-summary | Fungi are eukaryotic organisms that appeared on land more than 450 million years ago. They are heterotrophs and contain neither photosynthetic pigments such as chlorophyll, nor organelles such as chloroplasts. Because fungi feed on decaying and dead matter, they are saprobes. Fungi are important decomposers that release essential elements into the environment. External enzymes digest nutrients that are absorbed by the body of the fungus, which is called a thallus. A thick cell wall made of chitin surrounds the cell. Fungi can be unicellular as yeasts, or develop a network of filaments called a mycelium, which is often described as mold. Most species multiply by asexual and sexual reproductive cycles and display an alternation of generations. Another group of fungi do not have a sexual cycle. Sexual reproduction involves plasmogamy (the fusion of the cytoplasm), followed by karyogamy (the fusion of nuclei). Meiosis regenerates haploid individuals, resulting in haploid spores.
Chytridiomycota (chytrids) are considered the most primitive group of fungi. They are mostly aquatic, and their gametes are the only fungal cells known to have flagella. They reproduce both sexually and asexually; the asexual spores are called zoospores. Zygomycota (conjugated fungi) produce non-septated hyphae with many nuclei. Their hyphae fuse during sexual reproduction to produce a zygospore in a zygosporangium. Ascomycota (sac fungi) form spores in sacs called asci during sexual reproduction. Asexual reproduction is their most common form of reproduction. Basidiomycota (club fungi) produce showy fruiting bodies that contain basidia in the form of clubs. Spores are stored in the basidia. Most familiar mushrooms belong to this division. Fungi that have no known sexual cycle were classified in the form phylum Deuteromycota, which the present classification puts in the phyla Ascomycota and Basidiomycota. Glomeromycota form tight associations (called mycorrhizae) with the roots of plants.
Fungi have colonized nearly all environments on Earth, but are frequently found in cool, dark, moist places with a supply of decaying material. Fungi are saprobes that decompose organic matter. Many successful mutualistic relationships involve a fungus and another organism. Many fungi establish complex mycorrhizal associations with the roots of plants. Some ants farm fungi as a supply of food. Lichens are a symbiotic relationship between a fungus and a photosynthetic organism, usually an alga or cyanobacterium. The photosynthetic organism provides energy derived from light and carbohydrates, while the fungus supplies minerals and protection. Some animals that consume fungi help disseminate spores over long distances.
Fungi establish parasitic relationships with plants and animals. Fungal diseases can decimate crops and spoil food during storage. Compounds produced by fungi can be toxic to humans and other animals. Mycoses are infections caused by fungi. Superficial mycoses affect the skin, whereas systemic mycoses spread through the body. Fungal infections are difficult to cure.
Fungi are important to everyday human life. Fungi are important decomposers in most ecosystems. Mycorrhizal fungi are essential for the growth of most plants. Fungi, as food, play a role in human nutrition in the form of mushrooms, and also as agents of fermentation in the production of bread, cheeses, alcoholic beverages, and numerous other food preparations. Secondary metabolites of fungi are used as medicines, such as antibiotics and anticoagulants. Fungi are model organisms for the study of eukaryotic genetics and metabolism. |
https://openstax.org/books/biology/pages/24-key-terms | arbuscular mycorrhiza : mycorrhizal association in which the fungal hyphae enter the root cells and form extensive networks
Arbuscular mycorrhizae : mycorrhizae commonly involving Glomeromycetes in which the fungal hyphae penetrate the cell walls of the plant root cells (but not the cell membranes)
ascocarp : fruiting body of ascomycetes
Ascomycota : (also, sac fungi) phylum of fungi that store spores in a sac called ascus
basidiocarp : fruiting body that protrudes from the ground and bears the basidia
Basidiomycota : (also, club fungi) phylum of fungi that produce club-shaped structures (basidia) that contain spores
basidium : club-shaped fruiting body of basidiomycetes
Chytridiomycota : (also, chytrids) primitive phylum of fungi that live in water and produce gametes with flagella
coenocytic hypha : single hypha that lacks septa and contains many nuclei
commensalism : symbiotic relationship in which one member benefits while the other member is not affected
Deuteromycota : former form phylum of fungi that do not have a known sexual reproductive cycle (presently members of two phyla: Ascomycota and Basidiomycota)
ectomycorrhiza : mycorrhizal fungi that surround the roots with a mantle and have a Hartig net that extends into the roots between cells
Ectomycorrhizae : mycorrhizae in which the fungal hyphae do not penetrate the root cells of the plant
faculative anaerobes : organisms that can perform both aerobic and anaerobic respiration and can survive in oxygen-rich and oxygen-poor environment
Glomeromycota : phylum of fungi that form symbiotic relationships with the roots of trees
haustoria : modified hyphae on many parasitic fungi that penetrate the tissues of their hosts, release digestive enzymes, and/or absorb nutrients from the host
heterothallic : describes when only one mating type is present in an individual mycelium
homothallic : describes when both mating types are present in mycelium
hypha : fungal filament composed of one or more cells
karyogamy : fusion of nuclei
lichen : close association of a fungus with a photosynthetic alga or bacterium that benefits both partners
mold : tangle of visible mycelia with a fuzzy appearance
mycelium : mass of fungal hyphae
mycetismus : ingestion of toxins in poisonous mushrooms
mycology : scientific study of fungi
mycorrhiza : mutualistic association between fungi and vascular plant roots
mycorrhizae : a mutualistic relationship between a plant and a fungus. Mycorrhizae are connections between fungal hyphae, which provide soil minerals to the plant, and plant roots, which provide carbohydrates to the fungus
mycosis : fungal infection
mycotoxicosis : poisoning by a fungal toxin released in food
obligate aerobes : organisms, such as humans, that must perform aerobic respiration to survive
obligate anaerobes : organisms that only perform anaerobic respiration and often cannot survive in the presence of oxygen
parasitism : symbiotic relationship in which one member of the association benefits at the expense of the other
plasmogamy : fusion of cytoplasm
saprobe : organism that derives nutrients from decaying organic matter; also saprophyte
septa : cell wall division between hyphae
soredia : clusters of algal cells and mycelia that allow lichens to propagate
sporangium : reproductive sac that contains spores
spore : a haploid cell that can undergo mitosis to form a multicellular, haploid individua
thallus : vegetative body of a fungus
yeast : general term used to describe unicellular fungi
Zygomycota : (also, conjugated fungi) phylum of fungi that form a zygote contained in a zygospore
zygospore : structure with thick cell wall that contains the zygote in zygomycetes |
https://openstax.org/books/biology/pages/25-chapter-summary | Land plants acquired traits that made it possible to colonize land and survive out of the water. All land plants share the following characteristics: alternation of generations, with the haploid plant called a gametophyte, and the diploid plant called a sporophyte; protection of the embryo, formation of haploid spores in a sporangium, formation of gametes in a gametangium, and an apical meristem. Vascular tissues, roots, leaves, cuticle cover, and a tough outer layer that protects the spores contributed to the adaptation of plants to dry land. Land plants appeared about 500 million years ago in the Ordovician period.
Green algae share more traits with land plants than other algae, according to structure and DNA analysis. Charales form sporopollenin and precursors of lignin, phragmoplasts, and have flagellated sperm. They do not exhibit alternation of generations.
Seedless nonvascular plants are small, having the gametophyte as the dominant stage of the lifecycle. Without a vascular system and roots, they absorb water and nutrients on all their exposed surfaces. Collectively known as bryophytes, the three main groups include the liverworts, the hornworts, and the mosses. Liverworts are the most primitive plants and are closely related to the first land plants. Hornworts developed stomata and possess a single chloroplast per cell. Mosses have simple conductive cells and are attached to the substrate by rhizoids. They colonize harsh habitats and can regain moisture after drying out. The moss sporangium is a complex structure that allows release of spores away from the parent plant.
Vascular systems consist of xylem tissue, which transports water and minerals, and phloem tissue, which transports sugars and proteins. With the development of the vascular system, there appeared leaves to act as large photosynthetic organs, and roots to access water from the ground. Small uncomplicated leaves are microphylls. Large leaves with vein patterns are megaphylls. Modified leaves that bear sporangia are sporophylls. Some sporophylls are arranged in cone structures called strobili.
The seedless vascular plants include club mosses, which are the most primitive; whisk ferns, which lost leaves and roots by reductive evolution; and horsetails and ferns. Ferns are the most advanced group of seedless vascular plants. They are distinguished by large leaves called fronds and small sporangia-containing structures called sori, which are found on the underside of the fronds.
Mosses play an essential role in the balance of the ecosystems; they are pioneering species that colonize bare or devastated environments and make it possible for a succession to occur. They contribute to the enrichment of the soil and provide shelter and nutrients for animals in hostile environments. Mosses and ferns can be used as fuels and serve culinary, medical, and decorative purposes. |
https://openstax.org/books/biology/pages/25-key-terms | adventitious : describes an organ that grows in an unusual place, such as a roots growing from the side of a stem
antheridium : male gametangium
archegonium : female gametangium
capsule : case of the sporangium in mosses
charophyte : other term for green algae; considered the closest relative of land plants
club mosses : earliest group of seedless vascular plants
diplontic : diploid stage is the dominant stage
embryophyte : other name for land plant; embryo is protected and nourished by the sporophyte
extant : still-living species
extinct : no longer existing species
fern : seedless vascular plant that produces large fronds; the most advanced group of seedless vascular plants
gametangium : structure on the gametophyte in which gametes are produced
gemma : (plural, gemmae) leaf fragment that spreads for asexual reproduction
haplodiplodontic : haploid and diploid stages alternate
haplontic : haploid stage is the dominant stage
heterosporous : produces two types of spores
homosporous : produces one type of spore
hornworts : group of non-vascular plants in which stomata appear
horsetail : seedless vascular plant characterized by joints
lignin : complex polymer impermeable to water
liverworts : most primitive group of the non-vascular plants
lycophyte : club moss
megaphyll : larger leaves with a pattern of branching veins
megaspore : female spore
microphyll : small size and simple vascular system with a single unbranched vein
microspore : male spore
mosses : group of bryophytes in which a primitive conductive system appears
non-vascular plant : plant that lacks vascular tissue, which is formed of specialized cells for the transport of water and nutrients
peat moss : Sphagnum
peristome : tissue that surrounds the opening of the capsule and allows periodic release of spores
phloem : tissue responsible for transport of sugars, proteins, and other solutes
protonema : tangle of single celled filaments that forms from the haploid spore
rhizoids : thin filaments that anchor the plant to the substrate
seedless vascular plant : plant that does not produce seeds
seta : stalk that supports the capsule in mosses
sporocyte : diploid cell that produces spores by meiosis
sporophyll : leaf modified structurally to bear sporangia
sporopollenin : tough polymer surrounding the spore
streptophytes : group that includes green algae and land plants
strobili : cone-like structures that contain the sporangia
tracheophyte : vascular plant
vascular plant : plant containing a network of cells that conducts water and solutes through the organism
vein : bundle of vascular tissue made of xylem and phloem
whisk fern : seedless vascular plant that lost roots and leaves by reduction
xylem : tissue responsible for long-distance transport of water and nutrients |
https://openstax.org/books/biology/pages/26-chapter-summary | Seed plants appeared about one million years ago, during the Carboniferous period. Two major innovationsâseed and pollenâallowed seed plants to reproduce in the absence of water. The gametophytes of seed plants shrank, while the sporophytes became prominent structures and the diploid stage became the longest phase of the lifecycle. Gymnosperms became the dominant group during the Triassic. In these, pollen grains and seeds protect against desiccation. The seed, unlike a spore, is a diploid embryo surrounded by storage tissue and protective layers. It is equipped to delay germination until growth conditions are optimal. Angiosperms bear both flowers and fruit. The structures protect the gametes and the embryo during its development. Angiosperms appeared during the Mesozoic era and have become the dominant plant life in terrestrial habitats.
Gymnosperms are heterosporous seed plants that produce naked seeds. They appeared in the Paleozoic period and were the dominant plant life during the Mesozoic. Modern-day gymnosperms belong to four phyla. The largest phylum, Coniferophyta, is represented by conifers, the predominant plants at high altitude and latitude. Cycads (phylum Cycadophyta) resemble palm trees and grow in tropical climates.Gingko bilobais the only representative of the phylum Gingkophyta. The last phylum, Gnetophyta, is a diverse group of shrubs that produce vessel elements in their wood.
Angiosperms are the dominant form of plant life in most terrestrial ecosystems, comprising about 90 percent of all plant species. Most crops and ornamental plants are angiosperms. Their success comes from two innovative structures that protect reproduction from variability in the environment: the flower and the fruit. Flowers were derived from modified leaves. The main parts of a flower are the sepals and petals, which protect the reproductive parts: the stamens and the carpels. The stamens produce the male gametes in pollen grains. The carpels contain the female gametes (the eggs inside the ovules), which are within the ovary of a carpel. The walls of the ovary thicken after fertilization, ripening into fruit that ensures dispersal by wind, water, or animals.
The angiosperm life cycle is dominated by the sporophyte stage. Double fertilization is an event unique to angiosperms. One sperm in the pollen fertilizes the egg, forming a diploid zygote, while the other combines with the two polar nuclei, forming a triploid cell that develops into a food storage tissue called the endosperm. Flowering plants are divided into two main groups, the monocots and eudicots, according to the number of cotyledons in the seedlings. Basal angiosperms belong to an older lineage than monocots and eudicots.
Angiosperm diversity is due in part to multiple interactions with animals. Herbivory has favored the development of defense mechanisms in plants, and avoidance of those defense mechanism in animals. Pollination (the transfer of pollen to a carpel) is mainly carried out by wind and animals, and angiosperms have evolved numerous adaptations to capture the wind or attract specific classes of animals.
Plants play a key role in ecosystems. They are a source of food and medicinal compounds, and provide raw materials for many industries. Rapid deforestation and industrialization, however, threaten plant biodiversity. In turn, this threatens the ecosystem. |
https://openstax.org/books/biology/pages/26-key-terms | anther : sac-like structure at the tip of the stamen in which pollen grains are produced
Anthophyta : phylum to which angiosperms belong
barcoding : molecular biology technique in which one or more short gene sequences taken from a well-characterized portion of the genome is used to identify a species
basal angiosperms : a group of plants that probably branched off before the separation of monocots and eudicots
calyx : whorl of sepals
carpel : single unit of the pistil
conifer : dominant phylum of gymnosperms with the most variety of trees
corolla : collection of petals
cotyledon : primitive leaf that develop in the zygote; monocots have one cotyledon, and dicots have two cotyledons
crop : cultivated plant
cycad : gymnosperm that grows in tropical climates and resembles a palm tree; member of the phylum Cycadophyta
dicot : (also, eudicot) related group of angiosperms whose embryos possess two cotyledons
dioecious : describes a species in which the male and female reproductive organs are carried on separate specimens
filament : thin stalk that links the anther to the base of the flower
flower : branches specialized for reproduction found in some seed-bearing plants, containing either specialized male or female organs or both male and female organs
fruit : thickened tissue derived from ovary wall that protects the embryo after fertilization and facilitates seed dispersal
gingkophyte : gymnosperm with one extant species, theGingko biloba: a tree with fan-shaped leaves
gnetophyte : gymnosperm shrub with varied morphological features that produces vessel elements in its woody tissues; the phylum includes the generaEphedra, GnetumandWelwitschia
gymnosperm : seed plant with naked seeds (seeds exposed on modified leaves or in cones)
gynoecium : (also, carpel) structure that constitute the female reproductive organ
heirloom seed : seed from a plant that was grown historically, but has not been used in modern agriculture on a large scale
herbaceous : grass-like plant noticeable by the absence of woody tissue
herbivory : consumption of plants by insects and other animals
integument : layer of sporophyte tissue that surrounds the megasporangium, and later, the embryo
megasporocyte : megaspore mother cell; larger spore that germinates into a female gametophyte in a heterosporous plant
microsporocyte : smaller spore that produces a male gametophyte in a heterosporous plant
monocot : related group of angiosperms that produce embryos with one cotyledon and pollen with a single ridge
monoecious : describes a species in which the male and female reproductive organs are on the same plant
nectar : liquid rich in sugars produced by flowers to attract animal pollinators
ovary : chamber that contains and protects the ovule or female megasporangium
ovulate cone : cone containing two ovules per scale
ovule : female gametophyte
perianth : part of the plant consisting of the calyx (sepals) and corolla (petals)
petal : modified leaf interior to the sepals; colorful petals attract animal pollinators
pistil : fused group of carpels
pollen grain : structure containing the male gametophyte of the plant
pollen tube : extension from the pollen grain that delivers sperm to the egg cell
pollination : transfer of pollen from the anther to the stigma
progymnosperm : transitional group of plants that resembled conifers because they produced wood, yet still reproduced like ferns
seed : structure containing the embryo, storage tissue and protective coat
sepal : modified leaf that encloses the bud; outermost structure of a flower
spermatophyte : seed plant; from the Greeksperm(seed) andphyte(plant)
stamen : structure that contains the male reproductive organs
stigma : uppermost structure of the carpel where pollen is deposited
strobilus : plant structure with a tight arrangement of sporophylls around a central stalk, as seen in cones or flowers; the male strobilus produces pollen, and the female strobilus produces eggs
style : long, thin structure that links the stigma to the ovary |
https://openstax.org/books/biology/pages/27-chapter-summary | Animals constitute an incredibly diverse kingdom of organisms. Although animals range in complexity from simple sea sponges to human beings, most members of the animal kingdom share certain features. Animals are eukaryotic, multicellular, heterotrophic organisms that ingest their food and usually develop into motile creatures with a fixed body plan. A major characteristic unique to the animal kingdom is the presence of differentiated tissues, such as nerve, muscle, and connective tissues, which are specialized to perform specific functions. Most animals undergo sexual reproduction, leading to a series of developmental embryonic stages that are relatively similar across the animal kingdom. A class of transcriptional control genes calledHoxgenes directs the organization of the major animal body plans, and these genes are strongly homologous across the animal kingdom.
Organisms in the animal kingdom are classified based on their body morphology and development. True animals are divided into those with radial versus bilateral symmetry. Generally, the simpler and often non-motile animals display radial symmetry. Animals with radial symmetry are also generally characterized by the development of two embryological germ layers, the endoderm and ectoderm, whereas animals with bilateral symmetry are generally characterized by the development of a third embryological germ layer, the mesoderm. Animals with three germ layers, called triploblasts, are further characterized by the presence or absence of an internal body cavity called a coelom. The presence of a coelom affords many advantages, and animals with a coelom may be termed true coelomates or pseudocoelomates, depending on which tissue gives rise to the coelom. Coelomates are further divided into one of two groups called protostomes and deuterostomes, based on a number of developmental characteristics, including differences in zygote cleavage and method of coelom formation.
Scientists are interested in the evolutionary history of animals and the evolutionary relationships among them. There are three main sources of data that scientists use to create phylogenetic evolutionary tree diagrams that illustrate such relationships: morphological information (which includes developmental morphologies), fossil record data, and, most recently, molecular data. The details of the modern phylogenetic tree change frequently as new data are gathered, and molecular data has recently contributed to many substantial modifications of the understanding of relationships between animal phyla.
The most rapid diversification and evolution of animal species in all of history occurred during the Cambrian period of the Paleozoic Era, a phenomenon known as the Cambrian explosion. Until recently, scientists believed that there were only very few tiny and simplistic animal species in existence before this period. However, recent fossil discoveries have revealed that additional, larger, and more complex animals existed during the Ediacaran period, and even possibly earlier, during the Cryogenian period. Still, the Cambrian period undoubtedly witnessed the emergence of the majority of animal phyla that we know today, although many questions remain unresolved about this historical phenomenon.
The remainder of the Paleozoic Era is marked by the growing appearance of new classes, families, and species, and the early colonization of land by certain marine animals. The evolutionary history of animals is also marked by numerous major extinction events, each of which wiped out a majority of extant species. Some species of most animal phyla survived these extinctions, allowing the phyla to persist and continue to evolve into species that we see today. |
https://openstax.org/books/biology/pages/27-key-terms | acoelomate : animal without a body cavity
bilateral symmetry : type of symmetry in which there is only one plane of symmetry, so the left and right halves of an animal are mirror images
blastopore : indentation formed during gastrulation, evident in the gastrula stage
blastula : 16â32 cell stage of development of an animal embryo
body plan : morphology or constant shape of an organism
Cambrian explosion : time during the Cambrian period (542â488 million years ago) when most of the animal phyla in existence today evolved
cleavage : cell division of a fertilized egg (zygote) to form a multicellular embryo
coelom : lined body cavity
Cryogenian period : geologic period (850â630 million years ago) characterized by a very cold global climate
determinate cleavage : developmental tissue fate of each embryonic cell is already determined
deuterostome : blastopore develops into the anus, with the second opening developing into the mouth
diploblast : animal that develops from two germ layers
Ecdysozoa : clade of protostomes that exhibit exoskeletal molting (ecdysis)
Ediacaran period : geological period (630â542 million years ago) when the oldest definite multicellular organisms with tissues evolved
enterocoely : mesoderm of deuterostomes develops as pouches that are pinched off from endodermal tissue, cavity contained within the pouches becomes coelom
eucoelomate : animal with a body cavity completely lined with mesodermal tissue
Eumetazoa : group of animals with true differentiated tissues
gastrula : stage of animal development characterized by the formation of the digestive cavity
germ layer : collection of cells formed during embryogenesis that will give rise to future body tissues, more pronounced in vertebrate embryogenesis
Hox gene : (also, homeobox gene) master control gene that can turn on or off large numbers of other genes during embryogenesis
indeterminate cleavage : early stage of development when germ cells or âstem cellsâ are not yet pre-determined to develop into specific cell types
Lophotrochozoa : clade of protostomes that exhibit a trochophore larvae stage or a lophophore feeding structure
mass extinction : event that wipes out the majority of species within a relatively short geological time period
Metazoa : group containing all animals
organogenesis : formation of organs in animal embryogenesis
Parazoa : group of animals without true differentiated tissues
protostome : blastopore develops into the mouth of protostomes, with the second opening developing into the anus
pseudocoelomate : animal with a body cavity located between the mesoderm and endoderm
radial cleavage : cleavage axes are parallel or perpendicular to the polar axis, resulting in the alignment of cells between the two poles
radial symmetry : type of symmetry with multiple planes of symmetry, with body parts (rays) arranged around a central disk
schizocoely : during development of protostomes, a solid mass of mesoderm splits apart and forms the hollow opening of the coelom
spiral cleavage : cells of one pole of the embryo are rotated or misaligned with respect to the cells of the opposite pole
triploblast : animal that develops from three germ layers |
https://openstax.org/books/biology/pages/28-chapter-summary | Animals included in phylum Porifera are Parazoans because they do not show the formation of true tissues (except in class Hexactinellida). These organisms show very simple organization, with a rudimentary endoskeleton. Sponges have multiple cell types that are geared toward executing various metabolic functions. Although these animals are very simple, they perform several complex physiological functions.
Cnidarians represent a more complex level of organization than Porifera. They possess outer and inner tissue layers that sandwich a noncellular mesoglea. Cnidarians possess a well-formed digestive system and carry out extracellular digestion. The cnidocyte is a specialized cell for delivering toxins to prey as well as warning off predators. Cnidarians have separate sexes and have a lifecycle that involves morphologically distinct forms. These animals also show two distinct morphological formsâmedusoid and polypoidâat various stages in their lifecycle.
Phylum Annelida includes vermiform, segmented animals. Segmentation is seen in internal anatomy as well, which is called metamerism. Annelids are protostomes. These animals have well-developed neuronal and digestive systems. Some species bear a specialized band of segments known as a clitellum. Annelids show the presence numerous chitinous projections termed chaetae, and polychaetes possess parapodia. Suckers are seen in order Hirudinea. Reproductive strategies include sexual dimorphism, hermaphroditism, and serial hermaphroditism. Internal segmentation is absent in class Hirudinea.
Flatworms are acoelomate, triploblastic animals. They lack circulatory and respiratory systems, and have a rudimentary excretory system. This digestive system is incomplete in most species. There are four traditional classes of flatworms, the largely free-living turbellarians, the ectoparasitic monogeneans, and the endoparasitic trematodes and cestodes. Trematodes have complex lifecycles involving a molluscan secondary host and a primary host in which sexual reproduction takes place. Cestodes, or tapeworms, infect the digestive systems of primary vertebrate hosts.
The rotifers are microscopic, multicellular, mostly aquatic organisms that are currently under taxonomic revision. The group is characterized by the rotating, ciliated, wheel-like structure, the corona, on their head. The mastax or jawed pharynx is another structure unique to this group of organisms.
The nemertini are the simplest eucoelomates. These ribbon-shaped animals bear a specialized proboscis enclosed within a rhynchocoel. The development of a closed circulatory system derived from the coelom is a significant difference seen in this species compared to other pseudocoelomate phyla. Alimentary, nervous, and excretory systems are more developed in the nemertini than in less advanced phyla. Embryonic development of nemertine worms proceeds via a planuliform larval stage.
Phylum Mollusca is a large, marine group of invertebrates. Mollusks show a variety of morphological variations within the phylum. This phylum is also distinct in that some members exhibit a calcareous shell as an external means of protection. Some mollusks have evolved a reduced shell. Mollusks are protostomes. The dorsal epidermis in mollusks is modified to form the mantle, which encloses the mantle cavity and visceral organs. This cavity is quite distinct from the coelomic cavity, which in the adult animal surrounds the heart. Respiration is facilitated by gills known as ctenidia. A chitinous-toothed tongue called the radula is present in most mollusks. Early development in some species occurs via two larval stages: trochophore and veliger. Sexual dimorphism is the predominant sexual strategy in this phylum. Mollusks can be divided into seven classes, each with distinct morphological characteristics.
Nematodes are pseudocoelomate animals akin to flatworms, yet display more advanced neuronal development, a complete digestive system, and a body cavity. This phylum includes free-living as well as parasitic organisms likeCaenorhabditis elegansandAscarisspp., respectively. They include dioeceous as well as hermaphroditic species. Nematodes also possess an excretory system that is not quite well developed. Embryonic development is external and proceeds via three larval stages. A peculiar feature of nematodes is the secretion of a collagenous/chitinous cuticle outside the body.
Arthropods represent the most successful phylum of animal on Earth, in terms of the number of species as well as the number of individuals. These animals are characterized by a segmented body as well as the presence of jointed appendages. In the basic body plan, a pair of appendages is present per body segment. Within the phylum, traditional classification is based on mouthparts, number of appendages, and modifications of appendages present. Arthropods bear a chitinous exoskeleton. Gills, trachea, and book lungs facilitate respiration. Sexual dimorphism is seen in this phylum, and embryonic development includes multiple larval stages.
Echinoderms are deuterostomic marine organisms. This phylum of animals bears a calcareous endoskeleton composed of ossicles. These animals also have spiny skin. Echinoderms possess water-based circulatory systems. A pore termed the madreporite is the point of entry and exit for water into the water vascular system. Osmoregulation is carried out by specialized cells known as podocytes.
The characteristic features of Chordata are a notochord, a dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail. Chordata contains two clades of invertebrates: Urochordata (tunicates) and Cephalochordata (lancelets), together with the vertebrates in Vertebrata. Most tunicates live on the ocean floor and are suspension feeders. Lancelets are suspension feeders that feed on phytoplankton and other microorganisms. |
https://openstax.org/books/biology/pages/28-key-terms | amoebocyte : sponge cell with multiple functions, including nutrient delivery, egg formation, sperm delivery, and cell differentiation
Annelida : phylum of vermiform animals with metamerism
archenteron : primitive gut cavity within the gastrula that opens outwards via the blastopore
Arthropoda : phylum of animals with jointed appendages
biramous : referring to two branches per appendage
captacula : tentacle-like projection that is present in tusks shells to catch prey
cephalothorax : fused head and thorax in some species
chelicera : modified first pair of appendages in subphylum Chelicerata
choanocyte : (also, collar cell) sponge cell that functions to generate a water current and to trap and ingest food particles via phagocytosis
Chordata : phylum of animals distinguished by their possession of a notochord, a dorsal, hollow nerve cord, pharyngeal slits, and a post-anal tail at some point in their development
clitellum : specialized band of fused segments, which aids in reproduction
Cnidaria : phylum of animals that are diploblastic and have radial symmetry
cnidocyte : specialized stinging cell found in Cnidaria
conispiral : shell shape coiled around a horizontal axis
corona : wheel-like structure on the anterior portion of the rotifer that contains cilia and moves food and water toward the mouth
ctenidium : specialized gill structure in mollusks
cuticle (animal) : the tough, external layer possessed by members of the invertebrate class Ecdysozoa that is periodically molted and replaced
cypris : larval stage in the early development of crustaceans
Echinodermata : phylum of deuterostomes with spiny skin; exclusively marine organisms
enterocoelom : coelom formed by fusion of coelomic pouches budded from the endodermal lining of the archenteron
epidermis : outer layer (from ectoderm) that lines the outside of the animal
extracellular digestion : food is taken into the gastrovascular cavity, enzymes are secreted into the cavity, and the cells lining the cavity absorb nutrients
gastrodermis : inner layer (from endoderm) that lines the digestive cavity
gastrovascular cavity : opening that serves as both a mouth and an anus, which is termed an incomplete digestive system
gemmule : structure produced by asexual reproduction in freshwater sponges where the morphology is inverted
hemocoel : internal body cavity seen in arthropods
hermaphrodite : referring to an animal where both male and female gonads are present in the same individual
invertebrata : (also, invertebrates) category of animals that do not possess a cranium or vertebral column
madreporite : pore for regulating entry and exit of water into the water vascular system
mantle : (also, pallium) specialized epidermis that encloses all visceral organs and secretes shells
mastax : jawed pharynx unique to the rotifers
medusa : free-floating cnidarian body plan with mouth on underside and tentacles hanging down from a bell
mesoglea : non-living, gel-like matrix present between ectoderm and endoderm in cnidarians
mesohyl : collagen-like gel containing suspended cells that perform various functions in the sponge
metamerism : series of body structures that are similar internally and externally, such as segments
Mollusca : phylum of protostomes with soft bodies and no segmentation
nacre : calcareous secretion produced by bivalves to line the inner side of shells as well as to coat intruding particulate matter
nauplius : larval stage in the early development of crustaceans
nematocyst : harpoon-like organelle within cnidocyte with pointed projectile and poison to stun and entangle prey
Nematoda : phylum of worm-like animals that are triploblastic, pseudocoelomates that can be free-living or parasitic
Nemertea : phylum of dorsoventrally flattened protostomes known as ribbon worms
osculum : large opening in the spongeâs body through which water leaves
ostium : pore present on the spongeâs body through which water enters
oviger : additional pair of appendages present on some arthropods between the chelicerae and pedipalps
parapodium : fleshy, flat, appendage that protrudes in pairs from each segment of polychaetes
pedipalp : second pair of appendages in Chelicerata
pilidium : larval form found in some nemertine species
pinacocyte : epithelial-like cell that forms the outermost layer of sponges and encloses a jelly-like substance called mesohyl
planospiral : shell shape coiled around a vertical axis
planuliform : larval form found in phylum Nemertea
polymorphic : possessing multiple body plans within the lifecycle of a group of organisms
polyp : stalk-like sessile life form of a cnidarians with mouth and tentacles facing upward, usually sessile but may be able to glide along surface
Porifera : phylum of animals with no true tissues, but a porous body with rudimentary endoskeleton
radula : tongue-like organ with chitinous ornamentation
rhynchocoel : cavity present above the mouth that houses the proboscis
schizocoelom : coelom formed by groups of cells that split from the endodermal layer
sclerocyte : cell that secretes silica spicules into the mesohyl
seta/chaeta : chitinous projection from the cuticle
siphonophore : tubular structure that serves as an inlet for water into the mantle cavity
spicule : structure made of silica or calcium carbonate that provides structural support for sponges
spongocoel : central cavity within the body of some sponges
trochophore : first of the two larval stages in mollusks
uniramous : referring to one branch per appendage
veliger : second of the two larval stages in mollusks
water vascular system : system in echinoderms where water is the circulatory fluid
zoea : larval stage in the early development of crustaceans |
https://openstax.org/books/biology/pages/29-chapter-summary | The characteristic features of Chordata are a notochord, a dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail. Chordata contains two clades of invertebrates: Urochordata (tunicates) and Cephalochordata (lancelets), together with the vertebrates in Vertebrata. Most tunicates live on the ocean floor and are suspension feeders. Lancelets are suspension feeders that feed on phytoplankton and other microorganisms. Vertebrata is named for the vertebral column, which is a feature of almost all members of this clade.
The earliest vertebrates that diverged from the invertebrate chordates were the jawless fishes. Fishes with jaws (gnathostomes) evolved later. Jaws allowed early gnathostomes to exploit new food sources. Agnathans include the hagfishes and lampreys. Hagfishes are eel-like scavengers that feed on dead invertebrates and other fishes. Lampreys are characterized by a toothed, funnel-like sucking mouth, and most species are parasitic on other fishes. Gnathostomes include the cartilaginous fishes and the bony fishes, as well as all other tetrapods. Cartilaginous fishes include sharks, rays, skates, and ghost sharks. Most cartilaginous fishes live in marine habitats, with a few species living in fresh water for part or all of their lives. The vast majority of present-day fishes belong to the clade Osteichthyes, which consists of approximately 30,000 species. Bony fishes can be divided into two clades: Actinopterygii (ray-finned fishes, virtually all extant species) and Sarcopterygii (lobe-finned fishes, comprising fewer than 10 extant species but which are the ancestors of tetrapods).
As tetrapods, most amphibians are characterized by four well-developed limbs, although some species of salamanders and all caecilians are limbless. The most important characteristic of extant amphibians is a moist, permeable skin used for cutaneous respiration. The fossil record provides evidence of amphibian species, now extinct, that arose over 400 million years ago as the first tetrapods. Amphibia can be divided into three clades: salamanders (Urodela), frogs (Anura), and caecilians (Apoda). The life cycle of frogs, like the majority of amphibians, consists of two distinct stages: the larval stage and metamorphosis to an adult stage. Some species in all orders bypass a free-living larval stage.
The amniotes are distinguished from amphibians by the presence of a terrestrially adapted egg protected by amniotic membranes. The amniotes include reptiles, birds, and mammals. The early amniotes diverged into two main lines soon after the first amniotes arose. The initial split was into synapsids (mammals) and sauropsids. Sauropsids can be further divided into anapsids (turtles) and diapsids (birds and reptiles). Reptiles are tetrapods either having four limbs or descending from such. Limbless reptiles (snakes) are classified as tetrapods, as they are descended from four-limbed organisms. One of the key adaptations that permitted reptiles to live on land was the development of scaly skin containing the protein keratin, which prevented water loss from the skin. Reptilia includes four living clades: Crocodilia (crocodiles and alligators), Sphenodontia (tuataras), Squamata (lizards and snakes), and Testudines (turtles).
Birds are endothermic, meaning they produce their own body heat and regulate their internal temperature independently of the external temperature. Feathers not only act as insulation but also allow for flight, providing lift with secondary feathers and thrust with primary feathers. Pneumatic bones are bones that are hollow rather than filled with tissue, containing air spaces that are sometimes connected to air sacs. Airflow through bird lungs travels in one direction, creating a cross-current exchange with the blood. Birds are diapsids and belong to a group called the archosaurs. Birds are thought to have evolved from theropod dinosaurs. The oldest known fossil of a bird is that ofArchaeopteryx, which is from the Jurassic period. Modern birds are now classified into two groups, Paleognathae and Neognathae.
Mammals in general are vertebrates that possess hair and mammary glands. The mammalian integument includes various secretory glands, including sebaceous glands, eccrine glands, apocrine glands, and mammary glands. Mammals are synapsids, meaning that they have a single opening in the skull. A key characteristic of synapsids is endothermy rather than the ectothermy seen in other vertebrates. Mammals probably evolved from therapsids in the late Triassic period, as the earliest known mammal fossils are from the early Jurassic period. There are three groups of mammals living today: monotremes, marsupials, and eutherians. Monotremes are unique among mammals as they lay eggs, rather than giving birth to young. Eutherian mammals are sometimes called placental mammals, because all species possess a complex placenta that connects a fetus to the mother, allowing for gas, fluid, and nutrient exchange.
All primate species possess adaptations for climbing trees, as they all probably descended from tree-dwellers, although not all species are arboreal. Other characteristics of primates are brains that are larger than those of other mammals, claws that have been modified into flattened nails, typically only one young per pregnancy, stereoscopic vision, and a trend toward holding the body upright. Primates are divided into two groups: prosimians and anthropoids. Monkeys evolved from prosimians during the Oligocene Epoch. Apes evolved from catarrhines in Africa during the Miocene Epoch. Apes are divided into the lesser apes and the greater apes. Hominins include those groups that gave rise to our species, such asAustralopithecusandH.erectus, and those groups that can be considered âcousinsâ of humans, such as Neanderthals. Fossil evidence shows that hominins at the time ofAustralopithecuswere walking upright, the first evidence of bipedal hominins. A number of species, sometimes called archaicH.sapiens, evolved fromH.erectusapproximately 500,000 years ago. There is considerable debate about the origins of anatomically modern humans orH.sapiens sapiens. |
https://openstax.org/books/biology/pages/29-key-terms | Acanthostega : one of the earliest known tetrapods
Actinopterygii : ray-finned fishes
allantois : membrane of the egg that stores nitrogenous wastes produced by the embryo; also facilitates respiration
amnion : membrane of the egg that protects the embryo from mechanical shock and prevents dehydration
amniote : animal that produces a terrestrially adapted egg protected by amniotic membranes
Amphibia : frogs, salamanders, and caecilians
ampulla of Lorenzini : sensory organ that allows sharks to detect electromagnetic fields produced by living things
anapsid : animal having no temporal fenestrae in the cranium
anthropoid : monkeys, apes, and humans
Anura : frogs
apocrine gland : scent gland that secretes substances that are used for chemical communication
Apoda : caecilians
Archaeopteryx : transition species from dinosaur to bird from the Jurassic period
archosaur : modern crocodilian or bird, or an extinct pterosaur or dinosaur
Australopithecus : genus of hominins that evolved in eastern Africa approximately 4 million years ago
brachiation : movement through trees branches via suspension from the arms
brumation : period of much reduced metabolism and torpor that occurs in any ectotherm in cold weather
caecilian : legless amphibian that belongs to the clade Apoda
Casineria : one of the oldest known amniotes; had both amphibian and reptilian characteristics
Catarrhini : clade of Old World monkeys
Cephalochordata : chordate clade whose members possess a notochord, dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail in the adult stage
Chondrichthyes : jawed fish with paired fins and a skeleton made of cartilage
Chordata : phylum of animals distinguished by their possession of a notochord, a dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail at some point during their development
chorion : membrane of the egg that surrounds the embryo and yolk sac
contour feather : feather that creates an aerodynamic surface for efficient flight
Craniata : clade composed of chordates that possess a cranium; includes Vertebrata together with hagfishes
cranium : bony, cartilaginous, or fibrous structure surrounding the brain, jaw, and facial bones
Crocodilia : crocodiles and alligators
cutaneous respiration : gas exchange through the skin
dentary : single bone that comprises the lower jaw of mammals
diapsid : animal having two temporal fenestrae in the cranium
diphyodont : refers to the possession of two sets of teeth in a lifetime
dorsal hollow nerve cord : hollow, tubular structure derived from ectoderm, which is located dorsal to the notochord in chordates
down feather : feather specialized for insulation
eccrine gland : sweat gland
Enantiornithes : dominant bird group during the Cretaceous period
eutherian mammal : mammal that possesses a complex placenta, which connects a fetus to the mother; sometimes called placental mammals
flight feather : feather specialized for flight
frog : tail-less amphibian that belongs to the clade Anura
furcula : wishbone formed by the fusing of the clavicles
gnathostome : jawed fish
Gorilla : genus of gorillas
hagfish : eel-like jawless fish that live on the ocean floor and are scavengers
heterodont tooth : different types of teeth that are modified for different purposes
hominin : species that are more closely related to humans than chimpanzees
hominoid : pertaining to great apes and humans
Homo : genus of humans
Homo sapiens sapiens : anatomically modern humans
Hylobatidae : family of gibbons
Hylonomus : one of the earliest reptiles
lamprey : jawless fish characterized by a toothed, funnel-like, sucking mouth
lancelet : member of Cephalochordata; named for its blade-like shape
lateral line : sense organ that runs the length of a fishâs body; used to detect vibration in the water
lepidosaur : modern lizards, snakes, and tuataras
mammal : one of the groups of endothermic vertebrates that possesses hair and mammary glands
mammary gland : in female mammals, a gland that produces milk for newborns
marsupial : one of the groups of mammals that includes the kangaroo, koala, bandicoot, Tasmanian devil, and several other species; young develop within a pouch
monotreme : egg-laying mammal
Myxini : hagfishes
Neognathae : birds other than the Paleognathae
Neornithes : modern birds
notochord : flexible, rod-shaped support structure that is found in the embryonic stage of all chordates and in the adult stage of some chordates
Ornithorhynchidae : clade that includes the duck-billed platypus
Osteichthyes : bony fish
ostracoderm : one of the earliest jawless fish covered in bone
Paleognathae : ratites; flightless birds, including ostriches and emus
Pan : genus of chimpanzees and bonobos
Petromyzontidae : clade of lampreys
pharyngeal slit : opening in the pharynx
Platyrrhini : clade of New World monkeys
Plesiadapis : oldest known primate-like mammal
pneumatic bone : air-filled bone
Pongo : genus of orangutans
post-anal tail : muscular, posterior elongation of the body extending beyond the anus in chordates
primary feather : feather located at the tip of the wing that provides thrust
Primates : order of lemurs, tarsiers, monkeys, apes, and humans
prognathic jaw : long jaw
prosimian : division of primates that includes bush babies of Africa, lemurs of Madagascar, and lorises, pottos, and tarsiers of Southeast Asia
salamander : tailed amphibian that belongs to the clade Urodela
Sarcopterygii : lobe-finned fish
sauropsid : reptile or bird
sebaceous gland : in mammals, a skin gland that produce a lipid mixture calledsebum
secondary feather : feather located at the base of the wing that provides lift
Sphenodontia : clade of tuataras
Squamata : clade of lizards and snakes
stereoscopic vision : two overlapping fields of vision from the eyes that produces depth perception
swim bladder : in fishes, a gas filled organ that helps to control the buoyancy of the fish
synapsid : mammal having one temporal fenestra
Tachyglossidae : clade that includes the echidna or spiny anteater
tadpole : larval stage of a frog
temporal fenestra : non-orbital opening in the skull that may allow muscles to expand and lengthen
Testudines : order of turtles
tetrapod : phylogenetic reference to an organism with a four-footed evolutionary history; includes amphibians, reptiles, birds, and mammals
theropod : dinosaur group ancestral to birds
tunicate : sessile chordate that is a member of Urochordata
Urochordata : clade composed of tunicates
Urodela : salamanders
vertebral column : series of separate bones joined together as a backbone
Vertebrata : members of the phylum Chordata that possess a backbone |
https://openstax.org/books/biology/pages/30-chapter-summary | A vascular plant consists of two organ systems: the shoot system and the root system. The shoot system includes the aboveground vegetative portions (stems and leaves) and reproductive parts (flowers and fruits). The root system supports the plant and is usually underground. A plant is composed of two main types of tissue: meristematic tissue and permanent tissue. Meristematic tissue consists of actively dividing cells found in root and shoot tips. As growth occurs, meristematic tissue differentiates into permanent tissue, which is categorized as either simple or complex. Simple tissues are made up of similar cell types; examples include dermal tissue and ground tissue. Dermal tissue provides the outer covering of the plant. Ground tissue is responsible for photosynthesis; it also supports vascular tissue and may store water and sugars. Complex tissues are made up of different cell types. Vascular tissue, for example, is made up of xylem and phloem cells.
The stem of a plant bears the leaves, flowers, and fruits. Stems are characterized by the presence of nodes (the points of attachment for leaves or branches) and internodes (regions between nodes).
Plant organs are made up of simple and complex tissues. The stem has three tissue systems: dermal, vascular, and ground tissue. Dermal tissue is the outer covering of the plant. It contains epidermal cells, stomata, guard cells, and trichomes. Vascular tissue is made up of xylem and phloem tissues and conducts water, minerals, and photosynthetic products. Ground tissue is responsible for photosynthesis and support and is composed of parenchyma, collenchyma, and sclerenchyma cells.
Primary growth occurs at the tips of roots and shoots, causing an increase in length. Woody plants may also exhibit secondary growth, or increase in thickness. In woody plants, especially trees, annual rings may form as growth slows at the end of each season. Some plant species have modified stems that help to store food, propagate new plants, or discourage predators. Rhizomes, corms, stolons, runners, tubers, bulbs, tendrils, and thorns are examples of modified stems.
Roots help to anchor a plant, absorb water and minerals, and serve as storage sites for food. Taproots and fibrous roots are the two main types of root systems. In a taproot system, a main root grows vertically downward with a few lateral roots. Fibrous root systems arise at the base of the stem, where a cluster of roots forms a dense network that is shallower than a taproot. The growing root tip is protected by a root cap. The root tip has three main zones: a zone of cell division (cells are actively dividing), a zone of elongation (cells increase in length), and a zone of maturation (cells differentiate to form different kinds of cells). Root vascular tissue conducts water, minerals, and sugars. In some habitats, the roots of certain plants may be modified to form aerial roots or epiphytic roots.
Leaves are the main site of photosynthesis. A typical leaf consists of a lamina (the broad part of the leaf, also called the blade) and a petiole (the stalk that attaches the leaf to a stem). The arrangement of leaves on a stem, known as phyllotaxy, enables maximum exposure to sunlight. Each plant species has a characteristic leaf arrangement and form. The pattern of leaf arrangement may be alternate, opposite, or spiral, while leaf form may be simple or compound. Leaf tissue consists of the epidermis, which forms the outermost cell layer, and mesophyll and vascular tissue, which make up the inner portion of the leaf. In some plant species, leaf form is modified to form structures such as tendrils, spines, bud scales, and needles.
Water potential (Ψ) is a measure of the difference in potential energy between a water sample and pure water. The water potential in plant solutions is influenced by solute concentration, pressure, gravity, and matric potential. Water potential and transpiration influence how water is transported through the xylem in plants. These processes are regulated by stomatal opening and closing. Photosynthates (mainly sucrose) move from sources to sinks through the plantâs phloem. Sucrose is actively loaded into the sieve-tube elements of the phloem. The increased solute concentration causes water to move by osmosis from the xylem into the phloem. The positive pressure that is produced pushes water and solutes down the pressure gradient. The sucrose is unloaded into the sink, and the water returns to the xylem vessels.
Plants respond to light by changes in morphology and activity. Irradiation by red light converts the photoreceptor phytochrome to its far-red light-absorbing formâPfr. This form controls germination and flowering in response to length of day, as well as triggers photosynthesis in dormant plants or those that just emerged from the soil. Blue-light receptors, cryptochromes, and phototropins are responsible for phototropism. Amyloplasts, which contain heavy starch granules, sense gravity. Shoots exhibit negative gravitropism, whereas roots exhibit positive gravitropism. Plant hormonesânaturally occurring compounds synthesized in small amountsâcan act both in the cells that produce them and in distant tissues and organs. Auxins are responsible for apical dominance, root growth, directional growth toward light, and many other growth responses. Cytokinins stimulate cell division and counter apical dominance in shoots. Gibberellins inhibit dormancy of seeds and promote stem growth. Abscisic acid induces dormancy in seeds and buds, and protects plants from excessive water loss by promoting stomatal closure. Ethylene gas speeds up fruit ripening and dropping of leaves. Plants respond to touch by rapid movements (thigmotropy and thigmonasty) and slow differential growth (thigmomorphogenesis). Plants have evolved defense mechanisms against predators and pathogens. Physical barriers like bark and spines protect tender tissues. Plants also have chemical defenses, including toxic secondary metabolites and hormones, which elicit additional defense mechanisms. |
https://openstax.org/books/biology/pages/30-key-terms | abscisic acid (ABA) : plant hormone that induces dormancy in seeds and other organs
abscission : physiological process that leads to the fall of a plant organ (such as leaf or petal drop)
adventitious root : aboveground root that arises from a plant part other than the radicle of the plant embryo
apical bud : bud formed at the tip of the shoot
apical meristem : meristematic tissue located at the tips of stems and roots; enables a plant to extend in length
auxin : plant hormone that influences cell elongation (in phototropism), gravitropism, apical dominance and root growth
axillary bud : bud located in the axil: the stem area where the petiole connects to the stem
bark : tough, waterproof, outer epidermal layer of cork cells
bulb : modified underground stem that consists of a large bud surrounded by numerous leaf scales
Casparian strip : waxy coating that forces water to cross endodermal plasma membranes before entering the vascular cylinder, instead of moving between endodermal cells
chromophore : molecule that absorbs light
collenchyma cell : elongated plant cell with unevenly thickened walls; provides structural support to the stem and leaves
companion cell : phloem cell that is connected to sieve-tube cells; has large amounts of ribosomes and mitochondrion
compound leaf : leaf in which the leaf blade is subdivided to form leaflets, all attached to the midrib
corm : rounded, fleshy underground stem that contains stored food
cortex : ground tissue found between the vascular tissue and the epidermis in a stem or root
cryptochrome : protein that absorbs light in the blue and ultraviolet regions of the light spectrum
cuticle : waxy covering on the outside of the leaf and stem that prevents the loss of water
cuticle : waxy protective layer on the leaf surface
cytokinin : plant hormone that promotes cell division
dermal tissue : protective plant tissue covering the outermost part of the plant; controls gas exchange
endodermis : layer of cells in the root that forms a selective barrier between the ground tissue and the vascular tissue, allowing water and minerals to enter the root while excluding toxins and pathogens
epidermis : single layer of cells found in plant dermal tissue; covers and protects underlying tissue
ethylene : volatile plant hormone that is associated with fruit ripening, flower wilting, and leaf fall
fibrous root system : type of root system in which the roots arise from the base of the stem in a cluster, forming a dense network of roots; found in monocots
gibberellin (GA) : plant hormone that stimulates shoot elongation, seed germination, and the maturation and dropping of fruit and flowers
ground tissue : plant tissue involved in photosynthesis; provides support, and stores water and sugars
guard cells : paired cells on either side of a stoma that control stomatal opening and thereby regulate the movement of gases and water vapor
intercalary meristem : meristematic tissue located at nodes and the bases of leaf blades; found only in monocots
internode : region between nodes on the stem
jasmonates : small family of compounds derived from the fatty acid linoleic acid
lamina : leaf blade
lateral meristem : meristematic tissue that enables a plant to increase in thickness or girth
lenticel : opening on the surface of mature woody stems that facilitates gas exchange
megapascal (MPa) : pressure units that measure water potential
meristem : plant region of continuous growth
meristematic tissue : tissue containing cells that constantly divide; contributes to plant growth
negative gravitropism : growth away from Earthâs gravity
node : point along the stem at which leaves, flowers, or aerial roots originate
oligosaccharin : hormone important in plant defenses against bacterial and fungal infections
palmately compound leaf : leaf type with leaflets that emerge from a point, resembling the palm of a hand
parenchyma cell : most common type of plant cell; found in the stem, root, leaf, and in fruit pulp; site of photosynthesis and starch storage
pericycle : outer boundary of the stele from which lateral roots can arise
periderm : outermost covering of woody stems; consists of the cork cambium, cork cells, and the phelloderm
permanent tissue : plant tissue composed of cells that are no longer actively dividing
petiole : stalk of the leaf
photomorphogenesis : growth and development of plants in response to light
photoperiodism : occurrence of plant processes, such as germination and flowering, according to the time of year
phototropin : blue-light receptor that promotes phototropism, stomatal opening and closing, and other responses that promote photosynthesis
phototropism : directional bending of a plant toward a light source
phyllotaxy : arrangement of leaves on a stem
phytochrome : plant pigment protein that exists in two reversible forms (Pr and Pfr) and mediates morphologic changes in response to red light
pinnately compound leaf : leaf type with a divided leaf blade consisting of leaflets arranged on both sides of the midrib
pith : ground tissue found towards the interior of the vascular tissue in a stem or root
positive gravitropism : growth toward Earthâs gravitational center
primary growth : growth resulting in an increase in length of the stem and the root; caused by cell division in the shoot or root apical meristem
rhizome : modified underground stem that grows horizontally to the soil surface and has nodes and internodes
root cap : protective cells covering the tip of the growing root
root hair : hair-like structure that is an extension of epidermal cells; increases the root surface area and aids in absorption of water and minerals
root system : belowground portion of the plant that supports the plant and absorbs water and minerals
runner : stolon that runs above the ground and produces new clone plants at nodes
sclerenchyma cell : plant cell that has thick secondary walls and provides structural support; usually dead at maturity
secondary growth : growth resulting in an increase in thickness or girth; caused by the lateral meristem and cork cambium
sessile : leaf without a petiole that is attached directly to the plant stem
shoot system : aboveground portion of the plant; consists of non-reproductive plant parts, such as leaves and stems, and reproductive parts, such as flowers and fruits
sieve-tube cell : phloem cell arranged end to end to form a sieve tube that transports organic substances such as sugars and amino acids
simple leaf : leaf type in which the lamina is completely undivided or merely lobed
sink : growing parts of a plant, such as roots and young leaves, which require photosynthate
source : organ that produces photosynthate for a plant
statolith : (also,amyloplast) plant organelle that contains heavy starch granules
stele : inner portion of the root containing the vascular tissue; surrounded by the endodermis
stipule : small green structure found on either side of the leaf stalk or petiole
stolon : modified stem that runs parallel to the ground and can give rise to new plants at the nodes
strigolactone : hormone that promotes seed germination in some species and inhibits lateral apical development in the absence of auxins
tap root system : type of root system with a main root that grows vertically with few lateral roots; found in dicots
tendril : modified stem consisting of slender, twining strands used for support or climbing
thigmomorphogenesis : developmental response to touch
thigmonastic : directional growth of a plant independent of the direction in which contact is applied
thigmotropism : directional growth of a plant in response to constant contact
thorn : modified stem branch appearing as a sharp outgrowth that protects the plant
tracheid : xylem cell with thick secondary walls that helps transport water
translocation : mass transport of photosynthates from source to sink in vascular plants
transpiration : loss of water vapor to the atmosphere through stomata
trichome : hair-like structure on the epidermal surface
tuber : modified underground stem adapted for starch storage; has many adventitious buds
vascular bundle : strands of stem tissue made up of xylem and phloem
vascular stele : strands of root tissue made up of xylem and phloem
vascular tissue : tissue made up of xylem and phloem that transports food and water throughout the plant
venation : pattern of veins in a leaf; may be parallel (as in monocots), reticulate (as in dicots), or dichotomous (as inGingko biloba)
vessel element : xylem cell that is shorter than a tracheid and has thinner walls
water potential (Ψw) : the potential energy of a water solution per unit volume in relation to pure water at atmospheric pressure and ambient temperature
whorled : pattern of leaf arrangement in which three or more leaves are connected at a node |
https://openstax.org/books/biology/pages/31-chapter-summary | Plants can absorb inorganic nutrients and water through their root system, and carbon dioxide from the environment. The combination of organic compounds, along with water, carbon dioxide, and sunlight, produce the energy that allows plants to grow. Inorganic compounds form the majority of the soil solution. Plants access water though the soil. Water is absorbed by the plant root, transports nutrients throughout the plant, and maintains the structure of the plant. Essential elements are indispensable elements for plant growth. They are divided into macronutrients and micronutrients. The macronutrients plants require are carbon, nitrogen, hydrogen, oxygen, phosphorus, potassium, calcium, magnesium, and sulfur. Important micronutrients include iron, manganese, boron, molybdenum, copper, zinc, chlorine, nickel, cobalt, silicon and sodium.
Plants obtain mineral nutrients from the soil. Soil is the outer loose layer that covers the surface of Earth. Soil quality depends on the chemical composition of the soil, the topography, the presence of living organisms, the climate, and time. Agricultural practice and history may also modify the characteristics and fertility of soil. Soil consists of four major components: 1) inorganic mineral matter, 2) organic matter, 3) water and air, and 4) living matter. The organic material of soil is made of humus, which improves soil structure and provides water and minerals. Soil inorganic material consists of rock slowly broken down into smaller particles that vary in size, such as sand, silt, and loam.
Soil formation results from a combination of biological, physical, and chemical processes. Soil is not homogenous because its formation results in the production of layers called a soil profile. Factors that affect soil formation include: parent material, climate, topography, biological factors, and time. Soils are classified based on their horizons, soil particle size, and proportions. Most soils have four distinct horizons: O, A, B, and C.
Atmospheric nitrogen is the largest pool of available nitrogen in terrestrial ecosystems. However, plants cannot use this nitrogen because they do not have the necessary enzymes. Biological nitrogen fixation (BNF) is the conversion of atmospheric nitrogen to ammonia. The most important source of BNF is the symbiotic interaction between soil bacteria and legumes. The bacteria form nodules on the legumeâs roots in which nitrogen fixation takes place. Fungi form symbiotic associations (mycorrhizae) with plants, becoming integrated into the physical structure of the root. Through mycorrhization, the plant obtains minerals from the soil and the fungus obtains photosynthate from the plant root. Ectomycorrhizae form an extensive dense sheath around the root, while endomycorrhizae are embedded within the root tissue. Some plantsâparasites, saprophytes, symbionts, epiphytes, and insectivoresâhave evolved adaptations to obtain their organic or mineral nutrition from various sources. |
https://openstax.org/books/biology/pages/31-key-terms | A horizon : consists of a mixture of organic material with inorganic products of weathering
B horizon : soil layer that is an accumulation of mostly fine material that has moved downward
bedrock : solid rock that lies beneath the soil
C horizon : layer of soil that contains the parent material, and the organic and inorganic material that is broken down to form soil; also known as the soil base
clay : soil particles that are less than 0.002 mm in diameter
epiphyte : plant that grows on other plants but is not dependent upon other plants for nutrition
horizon : soil layer with distinct physical and chemical properties, which differs from other layers depending on how and when it was formed
humus : organic material of soil; made up of microorganisms, dead animals and plants in varying stages of decay
inorganic compound : chemical compound that does not contain carbon; it is not part of or produced by a living organism
insectivorous plant : plant that has specialized leaves to attract and digest insects
loam : soil that has no dominant particle size
macronutrient : nutrient that is required in large amounts for plant growth; carbon, hydrogen, oxygen, nitrogen, phosphorus, potassium, calcium, magnesium, and sulfur
micronutrient : nutrient required in small amounts; also called trace element
mineral soil : type of soil that is formed from the weathering of rocks and inorganic material; composed primarily of sand, silt, and clay
nitrogenase : enzyme that is responsible for the reduction of atmospheric nitrogen to ammonia
nodules : specialized structures that containRhizobiabacteria where nitrogen fixation takes place
O horizon : layer of soil with humus at the surface and decomposed vegetation at the base
organic compound : chemical compound that contains carbon
organic soil : type of soil that is formed from sedimentation; composed primarily of organic material
parasitic plant : plant that is dependent on its host for survival
parent material : organic and inorganic material in which soils form
rhizobia : soil bacteria that symbiotically interact with legume roots to form nodules and fix nitrogen
rhizosphere : area of soil affected by root secretions and microorganisms
sand : soil particles between 0.1â2 mm in diameter
saprophyte : plant that does not have chlorophyll and gets its food from dead matter
silt : soil particles between 0.002 and 0.1 mm in diameter
soil : outer loose layer that covers the surface of Earth
soil profile : vertical section of a soil
symbiont : plant in a symbiotic relationship with bacteria or fungi |
https://openstax.org/books/biology/pages/32-chapter-summary | The flower contains the reproductive structures of a plant. All complete flowers contain four whorls: the calyx, corolla, androecium, and gynoecium. The stamens are made up of anthers, in which pollen grains are produced, and a supportive strand called the filament. The pollen contains two cellsâ a generative cell and a tube cellâand is covered by two layers called the intine and the exine. The carpels, which are the female reproductive structures, consist of the stigma, style, and ovary. The female gametophyte is formed from mitotic divisions of the megaspore, forming an eight-nuclei ovule sac. This is covered by a layer known as the integument. The integument contains an opening called the micropyle, through which the pollen tube enters the embryo sac.
The diploid sporophyte of angiosperms and gymnosperms is the conspicuous and long-lived stage of the life cycle. The sporophytes differentiate specialized reproductive structures called sporangia, which are dedicated to the production of spores. The microsporangium contains microspore mother cells, which divide by meiosis to produce haploid microspores. The microspores develop into male gametophytes that are released as pollen. The megasporangium contains megaspore mother cells, which divide by meiosis to produce haploid megaspores. A megaspore develops into a female gametophyte containing a haploid egg. A new diploid sporophyte is formed when a male gamete from a pollen grain enters the ovule sac and fertilizes this egg.
For fertilization to occur in angiosperms, pollen has to be transferred to the stigma of a flower: a process known as pollination. Gymnosperm pollination involves the transfer of pollen from a male cone to a female cone. When the pollen of the flower is transferred to the stigma of the same flower, it is called self-pollination. Cross-pollination occurs when pollen is transferred from one flower to another flower on the same plant, or another plant. Cross-pollination requires pollinating agents such as water, wind, or animals, and increases genetic diversity. After the pollen lands on the stigma, the tube cell gives rise to the pollen tube, through which the generative nucleus migrates. The pollen tube gains entry through the micropyle on the ovule sac. The generative cell divides to form two sperm cells: one fuses with the egg to form the diploid zygote, and the other fuses with the polar nuclei to form the endosperm, which is triploid in nature. This is known as double fertilization. After fertilization, the zygote divides to form the embryo and the fertilized ovule forms the seed. The walls of the ovary form the fruit in which the seeds develop. The seed, when mature, will germinate under favorable conditions and give rise to the diploid sporophyte.
Many plants reproduce asexually as well as sexually. In asexual reproduction, part of the parent plant is used to generate a new plant. Grafting, layering, and micropropagation are some methods used for artificial asexual reproduction. The new plant is genetically identical to the parent plant from which the stock has been taken. Asexually reproducing plants thrive well in stable environments.
Plants have different life spans, dependent on species, genotype, and environmental conditions. Parts of the plant, such as regions containing meristematic tissue, continue to grow, while other parts experience programmed cell death. Leaves that are no longer photosynthetically active are shed from the plant as part of senescence, and the nutrients from these leaves are recycled by the plant. Other factors, including the presence of hormones, are known to play a role in delaying senescence. |
https://openstax.org/books/biology/pages/32-key-terms | accessory fruit : fruit derived from tissues other than the ovary
aggregate fruit : fruit that develops from multiple carpels in the same flower
aleurone : single layer of cells just inside the seed coat that secretes enzymes upon germination
androecium : sum of all the stamens in a flower
antipodals : the three cells away from the micropyle
apomixis : process by which seeds are produced without fertilization of sperm and egg
coleoptile : covering of the shoot tip, found in germinating monocot seeds
coleorhiza : covering of the root tip, found in germinating monocot seeds
cotyledon : fleshy part of seed that provides nutrition to the seed
cross-pollination : transfer of pollen from the anther of one flower to the stigma of a different flower
cutting : method of asexual reproduction where a portion of the stem contains notes and internodes is placed in moist soil and allowed to root
dormancy : period of no growth and very slow metabolic processes
double fertilization : two fertilization events in angiosperms; one sperm fuses with the egg, forming the zygote, whereas the other sperm fuses with the polar nuclei, forming endosperm
endocarp : innermost part of fruit
endosperm : triploid structure resulting from fusion of a sperm with polar nuclei, which serves as a nutritive tissue for embryo
endospermic dicot : dicot that stores food reserves in the endosperm
epicotyl : embryonic shoot above the cotyledons
exine : outermost covering of pollen
exocarp : outermost covering of a fruit
gametophyte : multicellular stage of the plant that gives rise to haploid gametes or spores
grafting : method of asexual reproduction where the stem from one plant species is spliced to a different plant
gravitropism : response of a plant growth in the same direction as gravity
gynoecium : the sum of all the carpels in a flower
hypocotyl : embryonic axis above the cotyledons
intine : inner lining of the pollen
layering : method of propagating plants by bending a stem under the soil
megagametogenesis : second phase of female gametophyte development, during which the surviving haploid megaspore undergoes mitosis to produce an eight-nucleate, seven-cell female gametophyte, also known as the megagametophyte or embryo sac.
megasporangium : tissue found in the ovary that gives rise to the female gamete or egg
megasporogenesis : first phase of female gametophyte development, during which a single cell in the diploid megasporangium undergoes meiosis to produce four megaspores, only one of which survives
megasporophyll : bract (a type of modified leaf) on the central axis of a female gametophyte
mesocarp : middle part of a fruit
micropropagation : propagation of desirable plants from a plant part; carried out in a laboratory
micropyle : opening on the ovule sac through which the pollen tube can gain entry
microsporangium : tissue that gives rise to the microspores or the pollen grain
microsporophyll : central axis of a male cone on which bracts (a type of modified leaf) are attached
monocarpic : plants that flower once in their lifetime
multiple fruit : fruit that develops from multiple flowers on an inflorescence
nectar guide : pigment pattern on a flower that guides an insect to the nectaries
non-endospermic dicot : dicot that stores food reserves in the developing cotyledon
perianth : (also, petal or sepal) part of the flower consisting of the calyx and/or corolla; forms the outer envelope of the flower
pericarp : collective term describing the exocarp, mesocarp, and endocarp; the structure that encloses the seed and is a part of the fruit
plumule : shoot that develops from the germinating seed
polar nuclei : found in the ovule sac; fusion with one sperm cell forms the endosperm
pollination : transfer of pollen to the stigma
polycarpic : plants that flower several times in their lifetime
radicle : original root that develops from the germinating seed
scarification : mechanical or chemical processes to soften the seed coat
scion : the part of a plant that is grafted onto the root stock of another plant
scutellum : type of cotyledon found in monocots, as in grass seeds
self-pollination : transfer of pollen from the anther to the stigma of same flower
senescence : process that describes aging in plant tissues
simple fruit : fruit that develops from a single carpel or fused carpels
sporophyte : multicellular diploid stage in plants that is formed after the fusion of male and female gametes
suspensor : part of the growing embryo that makes connection with the maternal tissues
synergid : type of cell found in the ovule sac that secretes chemicals to guide the pollen tube towards the egg
tegmen : inner layer of the seed coat
testa : outer layer of the seed coat
vernalization : exposure to cold required by some seeds before they can germinate |
https://openstax.org/books/biology/pages/33-chapter-summary | Animal bodies come in a variety of sizes and shapes. Limits on animal size and shape include impacts to their movement. Diffusion affects their size and development. Bioenergetics describes how animals use and obtain energy in relation to their body size, activity level, and environment.
The basic building blocks of complex animals are four primary tissues. These are combined to form organs, which have a specific, specialized function within the body, such as the skin or kidney. Organs are organized together to perform common functions in the form of systems. The four primary tissues are epithelia, connective tissues, muscle tissues, and nervous tissues.
Homeostasis is a dynamic equilibrium that is maintained in body tissues and organs. It is dynamic because it is constantly adjusting to the changes that the systems encounter. It is in equilibrium because body functions are kept within a normal range, with some fluctuations around a set point for the processes. |
https://openstax.org/books/biology/pages/33-key-terms | acclimatization : alteration in a body system in response to environmental change
alteration : change of the set point in a homeostatic system
apodeme : ingrowth of an animalâs exoskeleton that functions as an attachment site for muscles
asymmetrical : describes animals with no axis of symmetry in their body pattern
basal metabolic rate (BMR) : metabolic rate at rest in endothermic animals
canaliculus : microchannel that connects the lacunae and aids diffusion between cells
cartilage : type of connective tissue with a large amount of ground substance matrix, cells called chondrocytes, and some amount of fibers
chondrocyte : cell found in cartilage
columnar epithelia : epithelia made of cells taller than they are wide, specialized in absorption
connective tissue : type of tissue made of cells, ground substance matrix, and fibers
cuboidal epithelia : epithelia made of cube-shaped cells, specialized in glandular functions
dorsal cavity : body cavity on the posterior or back portion of an animal; includes the cranial and vertebral cavities
ectotherm : animal incapable of maintaining a relatively constant internal body temperature
endotherm : animal capable of maintaining a relatively constant internal body temperature
epithelial tissue : tissue that either lines or covers organs or other tissues
estivation : torpor in response to extremely high temperatures and low water availability
fibrous connective tissue : type of connective tissue with a high concentration of fibers
frontal (coronal) plane : plane cutting through an animal separating the individual into front and back portions
fusiform : animal body shape that is tubular and tapered at both ends
hibernation : torpor over a long period of time, such as a winter
homeostasis : dynamic equilibrium maintaining appropriate body functions
lacuna : space in cartilage and bone that contains living cells
loose (areolar) connective tissue : type of connective tissue with small amounts of cells, matrix, and fibers; found around blood vessels
matrix : component of connective tissue made of both living and non-living (ground substances) cells
midsagittal plane : plane cutting through an animal separating the individual into even right and left sides
negative feedback loop : feedback to a control mechanism that increases or decreases a stimulus instead of maintaining it
osteon : subunit of compact bone
positive feedback loop : feedback to a control mechanism that continues the direction of a stimulus
pseudostratified : layer of epithelia that appears multilayered, but is a simple covering
sagittal plane : plane cutting through an animal separating the individual into right and left sides
set point : midpoint or target point in homeostasis
simple epithelia : single layer of epithelial cells
squamous epithelia : type of epithelia made of flat cells, specialized in aiding diffusion or preventing abrasion
standard metabolic rate (SMR) : metabolic rate at rest in ectothermic animals
stratified epithelia : multiple layers of epithelial cells
thermoregulation : regulation of body temperature
torpor : decrease in activity and metabolism that allows an animal to survive adverse conditions
trabecula : tiny plate that makes up spongy bone and gives it strength
transitional epithelia : epithelia that can transition for appearing multilayered to simple; also called uroepithelial
transverse (horizontal) plane : plane cutting through an animal separating the individual into upper and lower portions
ventral cavity : body cavity on the anterior or front portion of an animal that includes the thoracic cavities and the abdominopelvic cavities |
https://openstax.org/books/biology/pages/34-chapter-summary | Different animals have evolved different types of digestive systems specialized to meet their dietary needs. Humans and many other animals have monogastric digestive systems with a single-chambered stomach. Birds have evolved a digestive system that includes a gizzard where the food is crushed into smaller pieces. This compensates for their inability to masticate. Ruminants that consume large amounts of plant material have a multi-chambered stomach that digests roughage. Pseudo-ruminants have similar digestive processes as ruminants but do not have the four-compartment stomach. Processing food involves ingestion (eating), digestion (mechanical and enzymatic breakdown of large molecules), absorption (cellular uptake of nutrients), and elimination (removal of undigested waste as feces).
Many organs work together to digest food and absorb nutrients. The mouth is the point of ingestion and the location where both mechanical and chemical breakdown of food begins. Saliva contains an enzyme called amylase that breaks down carbohydrates. The food bolus travels through the esophagus by peristaltic movements to the stomach. The stomach has an extremely acidic environment. An enzyme called pepsin digests protein in the stomach. Further digestion and absorption take place in the small intestine. The large intestine reabsorbs water from the undigested food and stores waste until elimination.
Animal diet should be balanced and meet the needs of the body. Carbohydrates, proteins, and fats are the primary components of food. Some essential nutrients are required for cellular function but cannot be produced by the animal body. These include vitamins, minerals, some fatty acids, and some amino acids. Food intake in more than necessary amounts is stored as glycogen in the liver and muscle cells, and in fat cells. Excess adipose storage can lead to obesity and serious health problems. ATP is the energy currency of the cell and is obtained from the metabolic pathways. Excess carbohydrates and energy are stored as glycogen in the body.
Digestion begins with ingestion, where the food is taken in the mouth. Digestion and absorption take place in a series of steps with special enzymes playing important roles in digesting carbohydrates, proteins, and lipids. Elimination describes removal of undigested food contents and waste products from the body. While most absorption occurs in the small intestines, the large intestine is responsible for the final removal of water that remains after the absorptive process of the small intestines. The cells that line the large intestine absorb some vitamins as well as any leftover salts and water. The large intestine (colon) is also where feces is formed.
The brain and the endocrine system control digestive processes. The brain controls the responses of hunger and satiety. The endocrine system controls the release of hormones and enzymes required for digestion of food in the digestive tract. |
https://openstax.org/books/biology/pages/34-key-terms | alimentary canal : tubular digestive system with a mouth and anus
aminopeptidase : protease that breaks down peptides to single amino acids; secreted by the brush border of small intestine
anus : exit point for waste material
bile : digestive juice produced by the liver; important for digestion of lipids
bolus : mass of food resulting from chewing action and wetting by saliva
carboxypeptidase : protease that breaks down peptides to single amino acids; secreted by the brush border of the small intestine
carnivore : animal that consumes animal flesh
cephalic phase : first phase of digestion, controlled by the neural response to the stimulus provided by food
cholecystokinin : hormone that stimulates the contraction of the gallbladder to release bile
chylomicron : small lipid globule
chyme : mixture of partially digested food and stomach juices
chymotrypsin : pancreatic protease
digestion : mechanical and chemical break down of food into small organic fragments
dipeptidase : protease that breaks down peptides to single amino acids; secreted by the brush border of small intestine
duodenum : first part of the small intestine where a large part of digestion of carbohydrates and fats occurs
elastase : pancreatic protease
endocrine system : system that controls the response of the various glands in the body and the release of hormones at the appropriate times
esophagus : tubular organ that connects the mouth to the stomach
essential nutrient : nutrient that cannot be synthesized by the body; it must be obtained from food
gallbladder : organ that stores and concentrates bile
gastric inhibitory peptide : hormone secreted by the small intestine in the presence of fatty acids and sugars; it also inhibits acid production and peristalsis in order to slow down the rate at which food enters the small intestine
gastric phase : digestive phase beginning once food enters the stomach; gastric acids and enzymes process the ingested materials
gastrin : hormone which stimulates hydrochloric acid secretion in the stomach
gastrovascular cavity : digestive system consisting of a single opening
gizzard : muscular organ that grinds food
herbivore : animal that consumes strictly plant diet
ileum : last part of the small intestine; connects the small intestine to the large intestine; important for absorption of B-12
ingestion : act of taking in food
intestinal phase : third digestive phase; begins when chyme enters the small intestine triggering digestive secretions and controlling the rate of gastric emptying
jejunum : second part of the small intestine
lactase : enzyme that breaks down lactose into glucose and galactose
large intestine : digestive system organ that reabsorbs water from undigested material and processes waste matter
lipase : enzyme that chemically breaks down lipids
liver : organ that produces bile for digestion and processes vitamins and lipids
maltase : enzyme that breaks down maltose into glucose
mineral : inorganic, elemental molecule that carries out important roles in the body
monogastric : digestive system that consists of a single-chambered stomach
omnivore : animal that consumes both plants and animals
pancreas : gland that secretes digestive juices
pepsin : enzyme found in the stomach whose main role is protein digestion
pepsinogen : inactive form of pepsin
peristalsis : wave-like movements of muscle tissue
proventriculus : glandular part of a birdâs stomach
rectum : area of the body where feces is stored until elimination
roughage : component of food that is low in energy and high in fiber
ruminant : animal with a stomach divided into four compartments
salivary amylase : enzyme found in saliva, which converts carbohydrates to maltose
secretin : hormone which stimulates sodium bicarbonate secretion in the small intestine
small intestine : organ where digestion of protein, fats, and carbohydrates is completed
somatostatin : hormone released to stop acid secretion when the stomach is empty
sphincter : band of muscle that controls movement of materials throughout the digestive tract
stomach : saclike organ containing acidic digestive juices
sucrase : enzyme that breaks down sucrose into glucose and fructose
trypsin : pancreatic protease that breaks down protein
villi : folds on the inner surface of the small intestine whose role is to increase absorption area
vitamin : organic substance necessary in small amounts to sustain life |
https://openstax.org/books/biology/pages/35-chapter-summary | The nervous system is made up of neurons and glia. Neurons are specialized cells that are capable of sending electrical as well as chemical signals. Most neurons contain dendrites, which receive these signals, and axons that send signals to other neurons or tissues. There are four main types of neurons: unipolar, bipolar, multipolar, and pseudounipolar neurons. Glia are non-neuronal cells in the nervous system that support neuronal development and signaling. There are several types of glia that serve different functions.
Neurons have charged membranes because there are different concentrations of ions inside and outside of the cell. Voltage-gated ion channels control the movement of ions into and out of a neuron. When a neuronal membrane is depolarized to at least the threshold of excitation, an action potential is fired. The action potential is then propagated along a myelinated axon to the axon terminals. In a chemical synapse, the action potential causes release of neurotransmitter molecules into the synaptic cleft. Through binding to postsynaptic receptors, the neurotransmitter can cause excitatory or inhibitory postsynaptic potentials by depolarizing or hyperpolarizing, respectively, the postsynaptic membrane. In electrical synapses, the action potential is directly communicated to the postsynaptic cell through gap junctionsâlarge channel proteins that connect the pre-and postsynaptic membranes. Synapses are not static structures and can be strengthened and weakened. Two mechanisms of synaptic plasticity are long-term potentiation and long-term depression.
The vertebrate central nervous system contains the brain and the spinal cord, which are covered and protected by three meninges. The brain contains structurally and functionally defined regions. In mammals, these include the cortex (which can be broken down into four primary functional lobes: frontal, temporal, occipital, and parietal), basal ganglia, thalamus, hypothalamus, limbic system, cerebellum, and brainstemâalthough structures in some of these designations overlap. While functions may be primarily localized to one structure in the brain, most complex functions, like language and sleep, involve neurons in multiple brain regions. The spinal cord is the information superhighway that connects the brain with the rest of the body through its connections with peripheral nerves. It transmits sensory and motor input and also controls motor reflexes.
The peripheral nervous system contains both the autonomic and sensory-somatic nervous systems. The autonomic nervous system provides unconscious control over visceral functions and has two divisions: the sympathetic and parasympathetic nervous systems. The sympathetic nervous system is activated in stressful situations to prepare the animal for a âfight or flightâ response. The parasympathetic nervous system is active during restful periods. The sensory-somatic nervous system is made of cranial and spinal nerves that transmit sensory information from skin and muscle to the CNS and motor commands from the CNS to the muscles.
Some general themes emerge from the sampling of nervous system disorders presented above. The causes for most disorders are not fully understoodâat least not for all patientsâand likely involve a combination of nature (genetic mutations that become risk factors) and nurture (emotional trauma, stress, hazardous chemical exposure). Because the causes have yet to be fully determined, treatment options are often lacking and only address symptoms. |
https://openstax.org/books/biology/pages/35-key-terms | acetylcholine : neurotransmitter released by neurons in the central nervous system and peripheral nervous system
action potential : self-propagating momentary change in the electrical potential of a neuron (or muscle) membrane
Alzheimerâs disease : neurodegenerative disorder characterized by problems with memory and thinking
amygdala : structure within the limbic system that processes fear
arachnoid mater : spiderweb-like middle layer of the meninges that cover the central nervous system
astrocyte : glial cell in the central nervous system that provide nutrients, extracellular buffering, and structural support for neurons; also makes up the blood-brain barrier
attention deficit hyperactivity disorder (ADHD) : neurodevelopmental disorder characterized by difficulty maintaining attention and controlling impulses
autism spectrum disorder (ASD) : neurodevelopmental disorder characterized by impaired social interaction and communication abilities
autonomic nervous system : part of the peripheral nervous system that controls bodily functions
axon : tube-like structure that propagates a signal from a neuronâs cell body to axon terminals
axon hillock : electrically sensitive structure on the cell body of a neuron that integrates signals from multiple neuronal connections
axon terminal : structure on the end of an axon that can form a synapse with another neuron
basal ganglia : interconnected collections of cells in the brain that are involved in movement and motivation; also known as basal nuclei
basal nuclei : see basal ganglia
brainstem : portion of the brain that connects with the spinal cord; controls basic nervous system functions like breathing, heart rate, and swallowing
cerebellum : brain structure involved in posture, motor coordination, and learning new motor actions
cerebral cortex : outermost sheet of brain tissue; involved in many higher-order functions
cerebrospinal fluid (CSF) : clear liquid that surrounds the brain and spinal cord and fills the ventricles and central canal; acts as a shock absorber and circulates material throughout the brain and spinal cord.
choroid plexus : spongy tissue within ventricles that produces cerebrospinal fluid
cingulate gyrus : helps regulate emotions and pain; thought to directly drive the bodyâs conscious response to unpleasant experiences
corpus callosum : thick fiber bundle that connects the cerebral hemispheres
cranial nerve : sensory and/or motor nerve that emanates from the brain
dendrite : structure that extends away from the cell body to receive messages from other neurons
depolarization : change in the membrane potential to a less negative value
dura mater : tough outermost layer that covers the central nervous system
ependymal : cell that lines fluid-filled ventricles of the brain and the central canal of the spinal cord; involved in production of cerebrospinal fluid
epilepsy : neurological disorder characterized by recurrent seizures
excitatory postsynaptic potential (EPSP) : depolarization of a postsynaptic membrane caused by neurotransmitter molecules released from a presynaptic cell
frontal lobe : part of the cerebral cortex that contains the motor cortex and areas involved in planning, attention, and language
glia : (also, glial cells) cells that provide support functions for neurons
gyrus : (plural: gyri) ridged protrusions in the cortex
hippocampus : brain structure in the temporal lobe involved in processing memories
hyperpolarization : change in the membrane potential to a more negative value
hypothalamus : brain structure that controls hormone release and body homeostasis
inhibitory postsynaptic potential (IPSP) : hyperpolarization of a postsynaptic membrane caused by neurotransmitter molecules released from a presynaptic cell
limbic system : connected brain areas that process emotion and motivation
long-term depression (LTD) : prolonged decrease in synaptic coupling between a pre- and postsynaptic cell
long-term potentiation (LTP) : prolonged increase in synaptic coupling between a pre-and postsynaptic cell
major depression : mental illness characterized by prolonged periods of sadness
membrane potential : difference in electrical potential between the inside and outside of a cell
meninge : membrane that covers and protects the central nervous system
microglia : glia that scavenge and degrade dead cells and protect the brain from invading microorganisms
myelin : fatty substance produced by glia that insulates axons
neurodegenerative disorder : nervous system disorder characterized by the progressive loss of neurological functioning, usually caused by neuron death
neuron : specialized cell that can receive and transmit electrical and chemical signals
nodes of Ranvier : gaps in the myelin sheath where the signal is recharged
norepinephrine : neurotransmitter and hormone released by activation of the sympathetic nervous system
occipital lobe : part of the cerebral cortex that contains visual cortex and processes visual stimuli
oligodendrocyte : glial cell that myelinates central nervous system neuron axons
parasympathetic nervous system : division of autonomic nervous system that regulates visceral functions during rest and digestion
parietal lobe : part of the cerebral cortex involved in processing touch and the sense of the body in space
Parkinsonâs disease : neurodegenerative disorder that affects the control of movement
pia mater : thin membrane layer directly covering the brain and spinal cord
proprioception : sense about how parts of the body are oriented in space
radial glia : glia that serve as scaffolds for developing neurons as they migrate to their final destinations
refractory period : period after an action potential when it is more difficult or impossible for an action potential to be fired; caused by inactivation of sodium channels and activation of additional potassium channels of the membrane
saltatory conduction : âjumpingâ of an action potential along an axon from one node of Ranvier to the next
satellite glia : glial cell that provides nutrients and structural support for neurons in the peripheral nervous system
schizophrenia : mental disorder characterized by the inability to accurately perceive reality; patients often have difficulty thinking clearly and can suffer from delusions
Schwann cell : glial cell that creates myelin sheath around a peripheral nervous system neuron axon
sensory-somatic nervous system : system of sensory and motor nerves
somatosensation : sense of touch
spinal cord : thick fiber bundle that connects the brain with peripheral nerves; transmits sensory and motor information; contains neurons that control motor reflexes
spinal nerve : nerve projecting between skin or muscle and spinal cord
sulcus : (plural: sulci) indents or âvalleysâ in the cortex
summation : process of multiple presynaptic inputs creating EPSPs around the same time for the postsynaptic neuron to be sufficiently depolarized to fire an action potential
sympathetic nervous system : division of autonomic nervous system activated during stressful âfight or flightâ situations
synapse : junction between two neurons where neuronal signals are communicated
synaptic cleft : space between the presynaptic and postsynaptic membranes
synaptic vesicle : spherical structure that contains a neurotransmitter
temporal lobe : part of the cerebral cortex that processes auditory input; parts of the temporal lobe are involved in speech, memory, and emotion processing
thalamus : brain area that relays sensory information to the cortex
threshold of excitation : level of depolarization needed for an action potential to fire
ventricle : cavity within brain that contains cerebrospinal fluid |
https://openstax.org/books/biology/pages/36-chapter-summary | A sensory activation occurs when a physical or chemical stimulus is processed into a neural signal (sensory transduction) by a sensory receptor. Perception is an individual interpretation of a sensation and is a brain function. Humans have special senses: olfaction, gustation, equilibrium, and hearing, plus the general senses of somatosensation.
Sensory receptors are either specialized cells associated with sensory neurons or the specialized ends of sensory neurons that are a part of the peripheral nervous system, and they are used to receive information about the environment (internal or external). Each sensory receptor is modified for the type of stimulus it detects. For example, neither gustatory receptors nor auditory receptors are sensitive to light. Each sensory receptor is responsive to stimuli within a specific region in space, which is known as that receptorâs receptive field. The most fundamental function of a sensory system is the translation of a sensory signal to an electrical signal in the nervous system.
All sensory signals, except those from the olfactory system, enter the central nervous system and are routed to the thalamus. When the sensory signal exits the thalamus, it is conducted to the specific area of the cortex dedicated to processing that particular sense.
Somatosensation includes all sensation received from the skin and mucous membranes, as well as from the limbs and joints. Somatosensation occurs all over the exterior of the body and at some interior locations as well, and a variety of receptor types, embedded in the skin and mucous membranes, play a role.
There are several types of specialized sensory receptors. Rapidly adapting free nerve endings detect nociception, hot and cold, and light touch. Slowly adapting, encapsulated Merkelâs disks are found in fingertips and lips, and respond to light touch. Meissnerâs corpuscles, found in glabrous skin, are rapidly adapting, encapsulated receptors that detect touch, low-frequency vibration, and flutter. Ruffini endings are slowly adapting, encapsulated receptors that detect skin stretch, joint activity, and warmth. Hair receptors are rapidly adapting nerve endings wrapped around the base of hair follicles that detect hair movement and skin deflection. Finally, Pacinian corpuscles are encapsulated, rapidly adapting receptors that detect transient pressure and high-frequency vibration.
There are five primary tastes in humans: sweet, sour, bitter, salty, and umami. Each taste has its own receptor type that responds only to that taste. Tastants enter the body and are dissolved in saliva. Taste cells are located within taste buds, which are found on three of the four types of papillae in the mouth.
Regarding olfaction, there are many thousands of odorants, but humans detect only about 10,000. Like taste receptors, olfactory receptors are each responsive to only one odorant. Odorants dissolve in nasal mucosa, where they excite their corresponding olfactory sensory cells. When these cells detect an odorant, they send their signals to the main olfactory bulb and then to other locations in the brain, including the olfactory cortex.
Audition is important for territory defense, predation, predator defense, and communal exchanges. The vestibular system, which is not auditory, detects linear acceleration and angular acceleration and deceleration. Both the auditory system and vestibular system use hair cells as their receptors.
Auditory stimuli are sound waves. The sound wave energy reaches the outer ear (pinna, canal, tympanum), and vibrations of the tympanum send the energy to the middle ear. The middle ear bones shift and the stapes transfers mechanical energy to the oval window of the fluid-filled inner ear cochlea. Once in the cochlea, the energy causes the basilar membrane to flex, thereby bending the stereocilia on receptor hair cells. This activates the receptors, which send their auditory neural signals to the brain.
The vestibular system has five parts that work together to provide the sense of direction, thus helping to maintain balance. The utricle and saccule measure head orientation: their calcium carbonate crystals shift when the head is tilted, thereby activating hair cells. The semicircular canals work similarly, such that when the head is turned, the fluid in the canals bends stereocilia on hair cells. The vestibular hair cells also send signals to the thalamus and to somatosensory cortex, but also to the cerebellum, the structure above the brainstem that plays a large role in timing and coordination of movement.
Vision is the only photo responsive sense. Visible light travels in waves and is a very small slice of the electromagnetic radiation spectrum. Light waves differ based on their frequency (wavelength = hue) and amplitude (intensity = brightness).
In the vertebrate retina, there are two types of light receptors (photoreceptors): cones and rods. Cones, which are the source of color vision, exist in three formsâL, M, and Sâand they are differentially sensitive to different wavelengths. Cones are located in the retina, along with the dim-light, achromatic receptors (rods). Cones are found in the fovea, the central region of the retina, whereas rods are found in the peripheral regions of the retina.
Visual signals travel from the eye over the axons of retinal ganglion cells, which make up the optic nerves. Ganglion cells come in several versions. Some ganglion cell axons carry information on form, movement, depth, and brightness, while other axons carry information on color and fine detail. Visual information is sent to the superior colliculi in the midbrain, where coordination of eye movements and integration of auditory information takes place. Visual information is also sent to the suprachiasmatic nucleus (SCN) of the hypothalamus, which plays a role in the circadian cycle. |
https://openstax.org/books/biology/pages/36-key-terms | audition : sense of hearing
basilar membrane : stiff structure in the cochlea that indirectly anchors auditory receptors
bipolar neuron : neuron with two processes from the cell body, typically in opposite directions
candela : (cd) unit of measurement of luminous intensity (brightness)
circadian : describes a time cycle about one day in length
cochlea : whorled structure that contains receptors for transduction of the mechanical wave into an electrical signal
cone : weakly photosensitive, chromatic, cone-shaped neuron in the fovea of the retina that detects bright light and is used in daytime color vision
cornea : transparent layer over the front of the eye that helps focus light waves
fovea : region in the center of the retina with a high density of photoreceptors and which is responsible for acute vision
free nerve ending : ending of an afferent neuron that lacks a specialized structure for detection of sensory stimuli; some respond to touch, pain, or temperature
glabrous : describes the non-hairy skin found on palms and fingers, soles of feet, and lips of humans and other primates
glomerulus : in the olfactory bulb, one of the two neural clusters that receives signals from one type of olfactory receptor
Golgi tendon organ : muscular proprioceptive tension receptor that provides the sensory component of the Golgi tendon reflex
gustation : sense of taste
hyperopia : (also, farsightedness) visual defect in which the image focus falls behind the retina, thereby making images in the distance clear, but close-up images blurry
incus : (also, anvil) second of the three bones of the middle ear
inner ear : innermost part of the ear; consists of the cochlea and the vestibular system
iris : pigmented, circular muscle at the front of the eye that regulates the amount of light entering the eye
kinesthesia : sense of body movement
labyrinth : bony, hollow structure that is the most internal part of the ear; contains the sites of transduction of auditory and vestibular information
lens : transparent, convex structure behind the cornea that helps focus light waves on the retina
malleus : (also, hammer) first of the three bones of the middle ear
mechanoreceptor : sensory receptor modified to respond to mechanical disturbance such as being bent, touch, pressure, motion, and sound
Meissnerâs corpuscle : (also, tactile corpuscle) encapsulated, rapidly-adapting mechanoreceptor in the skin that responds to light touch
Merkel's disc : unencapsulated, slowly-adapting mechanoreceptor in the skin that responds to touch
middle ear : part of the hearing apparatus that functions to transfer energy from the tympanum to the oval window of the inner ear
muscle spindle : proprioceptive stretch receptor that lies within a muscle and that shortens the muscle to an optimal length for efficient contraction
myopia : (also, nearsightedness) visual defect in which the image focus falls in front of the retina, thereby making images in the distance blurry, but close-up images clear
nociception : neural processing of noxious (such as damaging) stimuli
odorant : airborne molecule that stimulates an olfactory receptor
olfaction : sense of smell
olfactory bulb : neural structure in the vertebrate brain that receives signals from olfactory receptors
olfactory epithelium : specialized tissue in the nasal cavity where olfactory receptors are located
olfactory receptor : dendrite of a specialized neuron
organ of Corti : in the basilar membrane, the site of the transduction of sound, a mechanical wave, to a neural signal
ossicle : one of the three bones of the middle ear
outer ear : part of the ear that consists of the pinna, ear canal, and tympanum and which conducts sound waves into the middle ear
oval window : thin diaphragm between the middle and inner ears that receives sound waves from contact with the stapes bone of the middle ear
Pacinian corpuscle : encapsulated mechanoreceptor in the skin that responds to deep pressure and vibration
papilla : one of the small bump-like projections from the tongue
perception : individual interpretation of a sensation; a brain function
pheromone : substance released by an animal that can affect the physiology or behavior of other animals
pinna : cartilaginous outer ear
presbyopia : visual defect in which the image focus falls behind the retina, thereby making images in the distance clear, but close-up images blurry; caused by age-based changes in the lens
proprioception : sense of limb position; used to track kinesthesia
pupil : small opening though which light enters
reception : receipt of a signal (such as light or sound) by sensory receptors
receptive field : region in space in which a stimulus can activate a given sensory receptor
receptor potential : membrane potential in a sensory receptor in response to detection of a stimulus
retina : layer of photoreceptive and supporting cells on the inner surface of the back of the eye
rhodopsin : main photopigment in vertebrates
rod : strongly photosensitive, achromatic, cylindrical neuron in the outer edges of the retina that detects dim light and is used in peripheral and nighttime vision
Ruffini ending : (also, bulbous corpuscle) slowly-adapting mechanoreceptor in the skin that responds to skin stretch and joint position
semicircular canal : one of three half-circular, fluid-filled tubes in the vestibular labyrinth that monitors angular acceleration and deceleration
sensory receptor : specialized neuron or other cells associated with a neuron that is modified to receive specific sensory input
sensory transduction : conversion of a sensory stimulus into electrical energy in the nervous system by a change in the membrane potential
stapes : (also, stirrup) third of the three bones of the middle ear
stereocilia : in the auditory system, hair-like projections from hair cells that help detect sound waves
superior colliculus : paired structure in the top of the midbrain, which manages eye movements and auditory integration
suprachiasmatic nucleus : cluster of cells in the hypothalamus that plays a role in the circadian cycle
tastant : food molecule that stimulates gustatory receptors
taste bud : clusters of taste cells
tectorial membrane : cochlear structure that lies above the hair cells and participates in the transduction of sound at the hair cells
tonic activity : in a neuron, slight continuous activity while at rest
tympanum : (also, tympanic membrane or ear drum) thin diaphragm between the outer and middle ears
ultrasound : sound frequencies above the human detectable ceiling of approximately 20,000 Hz
umami : one of the five basic tastes, which is described as âsavoryâ and which may be largely the taste of L-glutamate
vestibular sense : sense of spatial orientation and balance
vision : sense of sight |
https://openstax.org/books/biology/pages/37-chapter-summary | There are three basic types of hormones: lipid-derived, amino acid-derived, and peptide. Lipid-derived hormones are structurally similar to cholesterol and include steroid hormones such as estradiol and testosterone. Amino acid-derived hormones are relatively small molecules and include the adrenal hormones epinephrine and norepinephrine. Peptide hormones are polypeptide chains or proteins and include the pituitary hormones, antidiuretic hormone (vasopressin), and oxytocin.
Hormones cause cellular changes by binding to receptors on target cells. The number of receptors on a target cell can increase or decrease in response to hormone activity. Hormones can affect cells directly through intracellular hormone receptors or indirectly through plasma membrane hormone receptors.
Lipid-derived (soluble) hormones can enter the cell by diffusing across the plasma membrane and binding to DNA to regulate gene transcription and to change the cellâs activities by inducing production of proteins that affect, in general, the long-term structure and function of the cell. Lipid insoluble hormones bind to receptors on the plasma membrane surface and trigger a signaling pathway to change the cellâs activities by inducing production of various cell products that affect the cell in the short-term. The hormone is called a first messenger and the cellular component is called a second messenger. G-proteins activate the second messenger (cyclic AMP), triggering the cellular response. Response to hormone binding is amplified as the signaling pathway progresses. Cellular responses to hormones include the production of proteins and enzymes and altered membrane permeability.
Water levels in the body are controlled by antidiuretic hormone (ADH), which is produced in the hypothalamus and triggers the reabsorption of water by the kidneys. Underproduction of ADH can cause diabetes insipidus. Aldosterone, a hormone produced by the adrenal cortex of the kidneys, enhances Na+reabsorption from the extracellular fluids and subsequent water reabsorption by diffusion. The renin-angiotensin-aldosterone system is one way that aldosterone release is controlled.
The reproductive system is controlled by the gonadotropins follicle-stimulating hormone (FSH) and luteinizing hormone (LH), which are produced by the pituitary gland. Gonadotropin release is controlled by the hypothalamic hormone gonadotropin-releasing hormone (GnRH). FSH stimulates the maturation of sperm cells in males and is inhibited by the hormone inhibin, while LH stimulates the production of the androgen testosterone. FSH stimulates egg maturation in females, while LH stimulates the production of estrogens and progesterone.Estrogensare a group of steroid hormones produced by the ovaries that trigger the development of secondary sex characteristics in females as well as control the maturation of the ova. In females, the pituitary also produces prolactin, which stimulates milk production after childbirth, and oxytocin, which stimulates uterine contraction during childbirth and milk let-down during suckling.
Insulin is produced by the pancreas in response to rising blood glucose levels and allows cells to utilize blood glucose and store excess glucose for later use. Diabetes mellitus is caused by reduced insulin activity and causes high blood glucose levels, or hyperglycemia. Glucagon is released by the pancreas in response to low blood glucose levels and stimulates the breakdown of glycogen into glucose, which can be used by the body. The bodyâs basal metabolic rate is controlled by the thyroid hormones thyroxine (T4) and triiodothyronine (T3). The anterior pituitary produces thyroid stimulating hormone (TSH), which controls the release of T3and T4from the thyroid gland. Iodine is necessary in the production of thyroid hormone, and the lack of iodine can lead to a condition called goiter.
Parathyroid hormone (PTH) is produced by the parathyroid glands in response to low blood Ca2+levels. The parafollicular cells of the thyroid produce calcitonin, which reduces blood Ca2+levels. Growth hormone (GH) is produced by the anterior pituitary and controls the growth rate of muscle and bone. GH action is indirectly mediated by insulin-like growth factors (IGFs). Short-term stress causes the hypothalamus to trigger the adrenal medulla to release epinephrine and norepinephrine, which trigger the fight or flight response. Long-term stress causes the hypothalamus to trigger the anterior pituitary to release adrenocorticotropic hormone (ACTH), which causes the release of corticosteroids, glucocorticoids, and mineralocorticoids, from the adrenal cortex.
Hormone levels are primarily controlled through negative feedback, in which rising levels of a hormone inhibit its further release. The three mechanisms of hormonal release are humoral stimuli, hormonal stimuli, and neural stimuli. Humoral stimuli refers to the control of hormonal release in response to changes in extracellular fluid levels or ion levels. Hormonal stimuli refers to the release of hormones in response to hormones released by other endocrine glands. Neural stimuli refers to the release of hormones in response to neural stimulation.
The pituitary gland is located at the base of the brain and is attached to the hypothalamus by the infundibulum. The anterior pituitary receives products from the hypothalamus by the hypophyseal portal system and produces six hormones. The posterior pituitary is an extension of the brain and releases hormones (antidiuretic hormone and oxytocin) produced by the hypothalamus.
The thyroid gland is located in the neck and is composed of two lobes connected by the isthmus. The thyroid is made up of follicle cells that produce the hormones thyroxine and triiodothyronine. Parafollicular cells of the thyroid produce calcitonin. The parathyroid glands lie on the posterior surface of the thyroid gland and produce parathyroid hormone.
The adrenal glands are located on top of the kidneys and consist of the renal cortex and renal medulla. The adrenal cortex is the outer part of the adrenal gland and produces the corticosteroids, glucocorticoids, and mineralocorticoids. The adrenal medulla is the inner part of the adrenal gland and produces the catecholamines epinephrine and norepinephrine.
The pancreas lies in the abdomen between the stomach and the small intestine. Clusters of endocrine cells in the pancreas form the islets of Langerhans, which are composed of alpha cells that release glucagon and beta cells that release insulin.
Some organs possess endocrine activity as a secondary function but have another primary function. The heart produces the hormone atrial natriuretic peptide, which functions to reduce blood volume, pressure, and Na+concentration. The gastrointestinal tract produces various hormones that aid in digestion. The kidneys produce renin, calcitriol, and erythropoietin. Adipose tissue produces leptin, which promotes satiety signals in the brain. |
https://openstax.org/books/biology/pages/37-key-terms | acromegaly : condition caused by overproduction of GH in adults
Addisonâs disease : disorder caused by the hyposecretion of corticosteroids
adenylate cyclase : an enzyme that catalyzes the conversion of ATP to cyclic AMP
adrenal cortex : outer portion of adrenal glands that produces corticosteroids
adrenal gland : endocrine glands associated with the kidneys
adrenal medulla : inner portion of adrenal glands that produces epinephrine and norepinephrine
adrenocorticotropic hormone (ACTH) : hormone released by the anterior pituitary, which stimulates the adrenal cortex to release corticosteroids during the long-term stress response
aldosterone : steroid hormone produced by the adrenal cortex that stimulates the reabsorption of Na+from extracellular fluids and secretion of K+.
alpha cell : endocrine cell of the pancreatic islets that produces the hormone glucagon
amino acid-derived hormone : hormone derived from amino acids
androgen : male sex hormone such as testosterone
anterior pituitary : portion of the pituitary gland that produces six hormones; also called adenohypophysis
antidiuretic hormone (ADH) : hormone produced by the hypothalamus and released by the posterior pituitary that increases water reabsorption by the kidneys
atrial natriuretic peptide (ANP) : hormone produced by the heart to reduce blood volume, pressure, and Na+concentration
beta cell : endocrine cell of the pancreatic islets that produces the hormone insulin
calcitonin : hormone produced by the parafollicular cells of the thyroid gland that functions to lower blood Ca2+levels and promote bone growth
colloid : fluid inside the thyroid gland that contains the glycoprotein thyroglobulin
corticosteroid : hormone released by the adrenal cortex in response to long-term stress
cortisol : glucocorticoid produced in response to stress
Cushingâs disease : disorder caused by the hypersecretion of glucocorticoids
diabetes insipidus : disorder caused by underproduction of ADH
diabetes mellitus : disorder caused by low levels of insulin activity
diabetogenic effect : effect of GH that causes blood glucose levels to rise similar to diabetes mellitus
down-regulation : a decrease in the number of hormone receptors in response to increased hormone levels
endocrine gland : gland that secretes hormones into the surrounding interstitial fluid, which then diffuse into blood and are carried to various organs and tissues within the body
epinephrine : hormone released by the adrenal medulla in response to a short term stress
erythropoietin (EPO) : hormone produced by the kidneys to stimulate red blood cell production in the bone marrow
estrogens : - a group of steroid hormones, including estradiol and several others, that are produced by the ovaries and elicit
secondary sex characteristics in females as well as control the maturation of the ova
first messenger : the hormone that binds to a plasma membrane hormone receptor to trigger a signal transduction pathway
follicle-stimulating hormone (FSH) : hormone produced by the anterior pituitary that stimulates gamete production
G-protein : a membrane protein activated by the hormone first messenger to activate formation of cyclic AMP
gigantism : condition caused by overproduction of GH in children
glucagon : hormone produced by the alpha cells of the pancreas in response to low blood sugar; functions to raise blood sugar levels
glucocorticoid : corticosteroid that affects glucose metabolism
gluconeogenesis : synthesis of glucose from amino acids
glucose-sparing effect : effect of GH that causes tissues to use fatty acids instead of glucose as an energy source
glycogenolysis : breakdown of glycogen into glucose
goiter : enlargement of the thyroid gland caused by insufficient dietary iodine levels
gonadotropin : hormone that regulates the gonads, including FSH and LH
growth hormone (GH) : hormone produced by the anterior pituitary that promotes protein synthesis and body growth
growth hormone-inhibiting hormone (GHIH) : hormone produced by the hypothalamus that inhibits growth hormone production, also called somatostatin
growth hormone-releasing hormone (GHRH) : hormone released by the hypothalamus that triggers the release of GH
hormonal stimuli : release of a hormone in response to another hormone
hormone receptor : the cellular protein that binds to a hormone
humoral stimuli : control of hormone release in response to changes in extracellular fluids such as blood or the ion concentration in the blood
hyperglycemia : high blood sugar level
hyperthyroidism : overactivity of the thyroid gland
hypoglycemia : low blood sugar level
hypophyseal portal system : system of blood vessels that carries hormones from the hypothalamus to the anterior pituitary
hypothyroidism : underactivity of the thyroid gland
insulin : hormone produced by the beta cells of the pancreas in response to high blood glucose levels; functions to lower blood glucose levels
insulin-like growth factor (IGF) : growth-promoting protein produced by the liver
intracellular hormone receptor : a hormone receptor in the cytoplasm or nucleus of a cell
islets of Langerhans (pancreatic islets) : endocrine cells of the pancreas
isthmus : tissue mass that connects the two lobes of the thyroid gland
leptin : hormone produced by adipose tissue that promotes feelings of satiety and reduces hunger
lipid-derived hormone : hormone derived mostly from cholesterol
mineralocorticoid : corticosteroid that affects ion and water balance
neural stimuli : stimulation of endocrine glands by the nervous system
norepinephrine : hormone released by the adrenal medulla in response to a short-term stress hormone production by the gonads
osmoreceptor : receptor in the hypothalamus that monitors the concentration of electrolytes in the blood
oxytocin : hormone released by the posterior pituitary to stimulate uterine contractions during childbirth and milk let-down in the mammary glands
pancreas : organ located between the stomach and the small intestine that contains exocrine and endocrine cells
parafollicular cell : thyroid cell that produces the hormone calcitonin
parathyroid gland : gland located on the surface of the thyroid that produces parathyroid hormone
parathyroid hormone (PTH) : hormone produced by the parathyroid glands in response to low blood Ca2+levels; functions to raise blood Ca2+levels
peptide hormone : hormone composed of a polypeptide chain
phosphodiesterase (PDE) : enzyme that deactivates cAMP, stopping hormone activity
pituitary dwarfism : condition caused by underproduction of GH in children
pituitary gland : endocrine gland located at the base of the brain composed of an anterior and posterior region; also called hypophysis
pituitary stalk : (also, infundibulum) stalk that connects the pituitary gland to the hypothalamus
plasma membrane hormone receptor : a hormone receptor on the surface of the plasma membrane of a cell
posterior pituitary : extension of the brain that releases hormones produced by the hypothalamus; along with the infundibulum, it is also referred to as the neurohypophysis
prolactin (PRL) : hormone produced by the anterior pituitary that stimulates milk production
prolactin-inhibiting hormone : hormone produced by the hypothalamus that inhibits the release of prolactin
prolactin-releasing hormone : hormone produced by the hypothalamus that stimulates the release of prolactin
renin : enzyme produced by the juxtaglomerular apparatus of the kidneys that reacts with angiotensinogen to cause the release of aldosterone
thymus : gland located behind the sternum that produces thymosin hormones that contribute to the development of the immune system
thyroglobulin : glycoprotein found in the thyroid that is converted into thyroid hormone
thyroid gland : endocrine gland located in the neck that produces thyroid hormones thyroxine and triiodothyronine
thyroid-stimulating hormone (TSH) : hormone produced by the anterior pituitary that controls the release of T3and T4from the thyroid gland
thyroxine (tetraiodothyronine, T4) : thyroid hormone containing 4 iodines that controls the basal metabolic rate
triiodothyronine (T3) : thyroid hormone containing 3 iodines that controls the basal metabolic rate
up-regulation : an increase in the number of hormone receptors in response to increased hormone levels |
https://openstax.org/books/biology/pages/38-chapter-summary | The three types of skeleton designs are hydrostatic skeletons, exoskeletons, and endoskeletons. A hydrostatic skeleton is formed by a fluid-filled compartment held under hydrostatic pressure; movement is created by the muscles producing pressure on the fluid. An exoskeleton is a hard external skeleton that protects the outer surface of an organism and enables movement through muscles attached on the inside. An endoskeleton is an internal skeleton composed of hard, mineralized tissue that also enables movement by attachment to muscles. The human skeleton is an endoskeleton that is composed of the axial and appendicular skeleton. The axial skeleton is composed of the bones of the skull, ossicles of the ear, hyoid bone, vertebral column, and ribcage. The skull consists of eight cranial bones and 14 facial bones. Six bones make up the ossicles of the middle ear, while the hyoid bone is located in the neck under the mandible. The vertebral column contains 26 bones, and it surrounds and protects the spinal cord. The thoracic cage consists of the sternum, ribs, thoracic vertebrae, and costal cartilages. The appendicular skeleton is made up of the limbs of the upper and lower limbs. The pectoral girdle is composed of the clavicles and the scapulae. The upper limb contains 30 bones in the arm, the forearm, and the hand. The pelvic girdle attaches the lower limbs to the axial skeleton. The lower limb includes the bones of the thigh, the leg, and the foot.
Bone, or osseous tissue, is connective tissue that includes specialized cells, mineral salts, and collagen fibers. The human skeleton can be divided into long bones, short bones, flat bones, and irregular bones. Compact bone tissue is composed of osteons and forms the external layer of all bones. Spongy bone tissue is composed of trabeculae and forms the inner part of all bones. Four types of cells compose bony tissue: osteocytes, osteoclasts, osteoprogenitor cells, and osteoblasts. Ossification is the process of bone formation by osteoblasts. Intramembranous ossification is the process of bone development from fibrous membranes. Endochondral ossification is the process of bone development from hyaline cartilage. Long bones lengthen as chondrocytes divide and secrete hyaline cartilage. Osteoblasts replace cartilage with bone. Appositional growth is the increase in the diameter of bones by the addition of bone tissue at the surface of bones. Bone remodeling involves the processes of bone deposition by osteoblasts and bone resorption by osteoclasts. Bone repair occurs in four stages and can take several months.
The structural classification of joints divides them into bony, fibrous, cartilaginous, and synovial joints. The bones of fibrous joints are held together by fibrous connective tissue; the three types of fibrous joints are sutures, syndesomes, and gomphoses. Cartilaginous joints are joints in which the bones are connected by cartilage; the two types of cartilaginous joints are synchondroses and symphyses. Synovial joints are joints that have a space between the adjoining bones. The functional classification divides joints into three categories: synarthroses, amphiarthroses, and diarthroses. The movement of synovial joints can be classified as one of four different types: gliding, angular, rotational, or special movement. Gliding movements occur as relatively flat bone surfaces move past each other. Angular movements are produced when the angle between the bones of a joint changes. Rotational movement is the movement of a bone as it rotates around its own longitudinal axis. Special movements include inversion, eversion, protraction, retraction, elevation, depression, dorsiflexion, plantar flexion, supination, pronation, and opposition. Synovial joints are also classified into six different categories on the basis of the shape and structure of the joint: planar, hinge, pivot, condyloid, saddle, and ball-and-socket.
The body contains three types of muscle tissue: skeletal muscle, cardiac muscle, and smooth muscle. Skeleton muscle tissue is composed of sarcomeres, the functional units of muscle tissue. Muscle contraction occurs when sarcomeres shorten, as thick and thin filaments slide past each other, which is called the sliding filament model of muscle contraction. ATP provides the energy for cross-bridge formation and filament sliding. Regulatory proteins, such as troponin and tropomyosin, control cross-bridge formation. Excitationâcontraction coupling transduces the electrical signal of the neuron, via acetylcholine, to an electrical signal on the muscle membrane, which initiates force production. The number of muscle fibers contracting determines how much force the whole muscle produces. |
https://openstax.org/books/biology/pages/38-key-terms | abduction : when a bone moves away from the midline of the body
acetylcholinesterase : (AChE) enzyme that breaks down ACh into acetyl and choline
actin : globular contractile protein that interacts with myosin for muscle contraction
adduction : movement of the limbs inward after abduction
amphiarthrosis : joint that allows slight movement; includes syndesmoses and symphyses
angular movement : produced when the angle between the bones of a joint changes
appendicular skeleton : composed of the bones of the upper limbs, which function to grasp and manipulate objects, and the lower limbs, which permit locomotion
appositional growth : increase in the diameter of bones by the addition of bone tissue at the surface of bones
articulation : any place where two bones are joined
auditory ossicle : (also, middle ear) transduces sounds from the air into vibrations in the fluid-filled cochlea
axial skeleton : forms the central axis of the body and includes the bones of the skull, the ossicles of the middle ear, the hyoid bone of the throat, the vertebral column, and the thoracic cage (ribcage)
ball-and-socket joint : joint with a rounded, ball-like end of one bone fitting into a cuplike socket of another bone
bone : (also, osseous tissue) connective tissue that constitutes the endoskeleton
bone remodeling : replacement of old bone tissue by new bone tissue
calcification : process of deposition of mineral salts in the collagen fiber matrix that crystallizes and hardens the tissue
cardiac muscle : tissue muscle tissue found only in the heart; cardiac contractions pump blood throughout the body and maintain blood pressure
carpus : eight bones that comprise the wrist
cartilaginous joint : joint in which the bones are connected by cartilage
circumduction : movement of a limb in a circular motion.
clavicle : S-shaped bone that positions the arms laterally
compact bone : forms the hard external layer of all bones
condyloid joint : oval-shaped end of one bone fitting into a similarly oval-shaped hollow of another bone
coxal bone : hip bone
cranial bone : one of eight bones that form the cranial cavity that encloses the brain and serves as an attachment site for the muscles of the head and neck
depression : movement downward of a bone, such as after the shoulders are shrugged and the scapulae return to their normal position from an elevated position; opposite of elevation
diaphysis : central shaft of bone, contains bone marrow in a marrow cavity
diarthrosis : joint that allows for free movement of the joint; found in synovial joints
dorsiflexion : bending at the ankle such that the toes are lifted toward the knee
elevation : movement of a bone upward, such as when the shoulders are shrugged, lifting the scapulae
endochondral ossification : process of bone development from hyaline cartilage
endoskeleton : skeleton of living cells that produce a hard, mineralized tissue located within the soft tissue of organisms
epiphyseal plate : region between the diaphysis and epiphysis that is responsible for the lengthwise growth of long bones
epiphysis : rounded end of bone, covered with articular cartilage and filled with red bone marrow, which produces blood cells
eversion : movement of the sole of the foot outward, away from the midline of the body; opposite of inversion
exoskeleton : a secreted cellular product external skeleton that consists of a hard encasement on the surface of an organism
extension : movement in which the angle between the bones of a joint increases; opposite of flexion
facial bone : one of the 14 bones that form the face; provides cavities for the sense organs (eyes, mouth, and nose) and attachment points for facial muscles
femur : (also, thighbone) longest, heaviest, and strongest bone in the body
fibrous joint : joint held together by fibrous connective tissue
fibula : (also, calf bone) parallels and articulates with the tibia
flat bone : thin and relatively broad bone found where extensive protection of organs is required or where broad surfaces of muscle attachment are required
flexion : movement in which the angle between the bones decreases; opposite of extension
forearm : extends from the elbow to the wrist and consists of two bones: the ulna and the radius
gliding movement : when relatively flat bone surfaces move past each other
gomphosis : the joint in which the tooth fits into the socket like a peg
Haversian canal : contains the boneâs blood vessels and nerve fibers
hinge joint : slightly rounded end of one bone fits into the slightly hollow end of the other bone
humerus : only bone of the arm
hydrostatic skeleton : skeleton that consists of aqueous fluid held under pressure in a closed body compartment
hyoid bone : lies below the mandible in the front of the neck
hyperextension : extension past the regular anatomical position
intervertebral disc : composed of fibrous cartilage; lies between adjacent vertebrae from the second cervical vertebra to the sacrum
intramembranous ossification : process of bone development from fibrous membranes
inversion : soles of the feet moving inward, toward the midline of the body
irregular bone : bone with complex shapes; examples include vertebrae and hip bones
joint : point at which two or more bones meet
lamella : layer of compact tissue that surrounds a central canal called the Haversian canal
lateral rotation : rotation away from the midline of the body
long bone : bone that is longer than wide, and has a shaft and two ends
lower limb : consists of the thigh, the leg, and the foot
medial rotation : rotation toward the midline of the body
metacarpus : five bones that comprise the palm
metatarsal : one of the five bones of the foot
motor end plate : sarcolemma of the muscle fiber that interacts with the neuron
myofibril : long cylindrical structures that lie parallel to the muscle fiber
myofilament : small structures that make up myofibrils
myosin : contractile protein that interacts with actin for muscle contraction
opposition : movement of the thumb toward the fingers of the same hand, making it possible to grasp and hold objects
osseous tissue : connective tissue that constitutes the endoskeleton
ossification : (also, osteogenesis) process of bone formation by osteoblasts
osteoblast : bone cell responsible for bone formation
osteoclast : large bone cells with up to 50 nuclei, responsible for bone remodeling
osteocyte : mature bone cells and the main cell in bone tissue
osteon : cylindrical structure aligned parallel to the long axis of the bone
patella : (also, kneecap) triangular bone that lies anterior to the knee joint
pectoral girdle : bones that transmit the force generated by the upper limbs to the axial skeleton
pelvic girdle : bones that transmit the force generated by the lower limbs to the axial skeleton
phalange : one of the bones of the fingers or toes
pivot joint : joint with the rounded end of one bone fitting into a ring formed by the other bone
planar joint : joint with bones whose articulating surfaces are flat
plantar flexion : bending at the ankle such that the heel is lifted, such as when standing on the toes
pronation : movement in which the palm faces backward
protraction : anterior movement of a bone in the horizontal plane
radius : bone located along the lateral (thumb) side of the forearm; articulates with the humerus at the elbow
resorption : process by which osteoclasts release minerals stored in bones
retraction : movement in which a joint moves back into position after protraction
rib : one of 12 pairs of long, curved bones that attach to the thoracic vertebrae and curve toward the front of the body to form the ribcage
rotational movement : movement of a bone as it rotates around its own longitudinal axis
saddle joint : joint with concave and convex portions that fit together; named because the ends of each bone resemble a saddle
sarcolemma : plasma membrane of a skeletal muscle fiber
sarcomere : functional unit of skeletal muscle
scapula : flat, triangular bone located at the posterior pectoral girdle
sesamoid bone : small, flat bone shaped like a sesame seed; develops inside tendons
short bone : bone that has the same width and length, giving it a cube-like shape
skeletal muscle tissue : forms skeletal muscles, which attach to bones and control locomotion and any movement that can be consciously controlled
skull : bone that supports the structures of the face and protects the brain
smooth muscle : tissue occurs in the walls of hollow organs such as the intestines, stomach, and urinary bladder, and around passages such as the respiratory tract and blood vessels
spongy bone tissue : forms the inner layer of all bones
sternum : (also, breastbone) long, flat bone located at the front of the chest
supination : movement of the radius and ulna bones of the forearm so that the palm faces forward
suture : short fiber of connective tissue that holds the skull bones tightly in place; found only in the skull
suture bone : small, flat, irregularly shaped bone that forms between the flat bones of the cranium
symphysis : hyaline cartilage covers the end of the bone, but the connection between bones occurs through fibrocartilage; symphyses are found at the joints between vertebrae
synarthrosis : joint that is immovable
synchondrosis : bones joined by hyaline cartilage; synchondroses are found in the epiphyseal plates of growing bones in children
syndesmosis : joint in which the bones are connected by a band of connective tissue, allowing for more movement than in a suture
synovial joint : only joint that has a space between the adjoining bones
tarsal : one of the seven bones of the ankle
thick filament : a group of myosin molecules
thin filament : two polymers of actin wound together along with tropomyosin and troponin
thoracic cage : (also, ribcage) skeleton of the chest, which consists of the ribs, thoracic vertebrae, sternum, and costal cartilages
tibia : (also, shinbone) large bone of the leg that is located directly below the knee
trabeculae : lamellae that are arranged as rods or plates
tropomyosin : acts to block myosin binding sites on actin molecules, preventing cross-bridge formation and preventing contraction until a muscle receives a neuron signal
troponin : binds to tropomyosin and helps to position it on the actin molecule, and also binds calcium ions
ulna : bone located on the medial aspect (pinky-finger side) of the forearm
vertebral column : (also, spine) surrounds and protects the spinal cord, supports the head, and acts as an attachment point for ribs and muscles of the back and neck |
https://openstax.org/books/biology/pages/39-chapter-summary | Animal respiratory systems are designed to facilitate gas exchange. In mammals, air is warmed and humidified in the nasal cavity. Air then travels down the pharynx, through the trachea, and into the lungs. In the lungs, air passes through the branching bronchi, reaching the respiratory bronchioles, which house the first site of gas exchange. The respiratory bronchioles open into the alveolar ducts, alveolar sacs, and alveoli. Because there are so many alveoli and alveolar sacs in the lung, the surface area for gas exchange is very large. Several protective mechanisms are in place to prevent damage or infection. These include the hair and mucus in the nasal cavity that trap dust, dirt, and other particulate matter before they can enter the system. In the lungs, particles are trapped in a mucus layer and transported via cilia up to the esophageal opening at the top of the trachea to be swallowed.
The lungs can hold a large volume of air, but they are not usually filled to maximal capacity. Lung volume measurements include tidal volume, expiratory reserve volume, inspiratory reserve volume, and residual volume. The sum of these equals the total lung capacity. Gas movement into or out of the lungs is dependent on the pressure of the gas. Air is a mixture of gases; therefore, the partial pressure of each gas can be calculated to determine how the gas will flow in the lung. The difference between the partial pressure of the gas in the air drives oxygen into the tissues and carbon dioxide out of the body.
The structure of the lungs and thoracic cavity control the mechanics of breathing. Upon inspiration, the diaphragm contracts and lowers. The intercostal muscles contract and expand the chest wall outward. The intrapleural pressure drops, the lungs expand, and air is drawn into the airways. When exhaling, the intercostal muscles and diaphragm relax, returning the intrapleural pressure back to the resting state. The lungs recoil and airways close. The air passively exits the lung. There is high surface tension at the air-airway interface in the lung. Surfactant, a mixture of phospholipids and lipoproteins, acts like a detergent in the airways to reduce surface tension and allow for opening of the alveoli.
Breathing and gas exchange are both altered by changes in the compliance and resistance of the lung. If the compliance of the lung decreases, as occurs in restrictive diseases like fibrosis, the airways stiffen and collapse upon exhalation. Air becomes trapped in the lungs, making breathing more difficult. If resistance increases, as happens with asthma or emphysema, the airways become obstructed, trapping air in the lungs and causing breathing to become difficult. Alterations in the ventilation of the airways or perfusion of the arteries can affect gas exchange. These changes in ventilation and perfusion, called V/Q mismatch, can arise from anatomical or physiological changes.
Hemoglobin is a protein found in red blood cells that is comprised of two alpha and two beta subunits that surround an iron-containing heme group. Oxygen readily binds this heme group. The ability of oxygen to bind increases as more oxygen molecules are bound to heme. Disease states and altered conditions in the body can affect the binding ability of oxygen, and increase or decrease its ability to dissociate from hemoglobin.
Carbon dioxide can be transported through the blood via three methods. It is dissolved directly in the blood, bound to plasma proteins or hemoglobin, or converted into bicarbonate. The majority of carbon dioxide is transported as part of the bicarbonate system. Carbon dioxide diffuses into red blood cells. Inside, carbonic anhydrase converts carbon dioxide into carbonic acid (H2CO3), which is subsequently hydrolyzed into bicarbonate(HCO3â)(HCO3â)and H+. The H+ion binds to hemoglobin in red blood cells, and bicarbonate is transported out of the red blood cells in exchange for a chloride ion. This is called the chloride shift. Bicarbonate leaves the red blood cells and enters the blood plasma. In the lungs, bicarbonate is transported back into the red blood cells in exchange for chloride. The H+dissociates from hemoglobin and combines with bicarbonate to form carbonic acid with the help of carbonic anhydrase, which further catalyzes the reaction to convert carbonic acid back into carbon dioxide and water. The carbon dioxide is then expelled from the lungs. |
https://openstax.org/books/biology/pages/39-key-terms | alveolarPO2PO2 : partial pressure of oxygen in the alveoli (usually around 100 mmHg)
alveolar duct : duct that extends from the terminal bronchiole to the alveolar sac
alveolar sac : structure consisting of two or more alveoli that share a common opening
alveolar ventilation : how much air is in the alveoli
alveolus : (plural: alveoli) (also, air sac) terminal region of the lung where gas exchange occurs
anatomical dead space : (also, anatomical shunt) region of the lung that lacks proper ventilation/perfusion due to an anatomical block
bicarbonate(HCO3â)(HCO3â)ion : ion created when carbonic acid dissociates into H+and(HCO3â)(HCO3â)
bicarbonate buffer system : system in the blood that absorbs carbon dioxide and regulates pH levels
bronchiole : airway that extends from the main tertiary bronchi to the alveolar sac
bronchus : (plural: bronchi) smaller branch of cartilaginous tissue that stems off of the trachea; air is funneled through the bronchi to the region where gas exchange occurs in alveoli
carbaminohemoglobin : molecule that forms when carbon dioxide binds to hemoglobin
carbonic anhydrase (CA) : enzyme that catalyzes carbon dioxide and water into carbonic acid
chloride shift : chloride shift exchange of chloride for bicarbonate into or out of the red blood cell
compliance : measurement of the elasticity of the lung
dead space : area in the lung that lacks proper ventilation or perfusion
diaphragm : domed-shaped skeletal muscle located under lungs that separates the thoracic cavity from the abdominal cavity
elastic recoil : property of the lung that drives the lung tissue inward
elastic work : work conducted by the intercostal muscles, chest wall, and diaphragm
expiratory reserve volume (ERV) : amount of additional air that can be exhaled after a normal exhalation
FEV1/FVC ratio : ratio of how much air can be forced out of the lung in one second to the total amount that is forced out of the lung; a measurement of lung function that can be used to detect disease states
flow-resistive : work of breathing performed by the alveoli and tissues in the lung
forced expiratory volume (FEV) : (also, forced vital capacity) measure of how much air can be forced out of the lung from maximal inspiration over a specific amount of time
functional residual capacity (FRC) : expiratory reserve volume plus residual volume
functional vital capacity (FVC) : amount of air that can be forcibly exhaled after taking the deepest breath possible
heme group : centralized iron-containing group that is surrounded by the alpha and beta subunits of hemoglobin
hemoglobin : molecule in red blood cells that can bind oxygen, carbon dioxide, and carbon monoxide
inspiratory capacity (IC) : tidal volume plus inspiratory reserve volume
inspiratory reserve volume (IRV) : amount of additional air that can be inspired after a normal inhalation
intercostal muscle : muscle connected to the rib cage that contracts upon inspiration
intrapleural space : space between the layers of pleura
larynx : voice box, a short passageway connecting the pharynx and the trachea
lung capacity : measurement of two or more lung volumes (how much air can be inhaled from the end of an expiration to maximal capacity)
lung volume : measurement of air for one lung function (normal inhalation or exhalation)
mucin : complex glycoprotein found in mucus
mucus : sticky protein-containing fluid secretion in the lung that traps particulate matter to be expelled from the body
nasal cavity : opening of the respiratory system to the outside environment
obstructive disease : disease (such as emphysema and asthma) that arises from obstruction of the airways; compliance increases in these diseases
oxygen dissociation curve : curve depicting the affinity of oxygen for hemoglobin
oxygen-carrying capacity : amount of oxygen that can be transported in the blood
partial pressure : amount of pressure exerted by one gas within a mixture of gases
particulate matter : small particle such as dust, dirt, viral particles, and bacteria that are in the air
pharynx : throat; a tube that starts in the internal nares and runs partway down the neck, where it opens into the esophagus and the larynx
physiological dead space : (also, physiological shunt) region of the lung that lacks proper ventilation/perfusion due to a physiological change in the lung (like inflammation or edema)
pleura : tissue layer that surrounds the lungs and lines the interior of the thoracic cavity
pleurisy : painful inflammation of the pleural tissue layers
primary bronchus : (also, main bronchus) region of the airway within the lung that attaches to the trachea and bifurcates to each lung where it branches into secondary bronchi
recruitment : process of opening airways that normally remain closed when the cardiac output increases
residual volume (RV) : amount of air remaining in the lung after a maximal expiration
resistance : measurement of lung obstruction
respiratory bronchiole : terminal portion of the bronchiole tree that is attached to the terminal bronchioles and alveoli ducts, alveolar sacs, and alveoli
respiratory distress syndrome : disease that arises from a deficient amount of surfactant
respiratory quotient (RQ) : ratio of carbon dioxide production to each oxygen molecule consumed
respiratory rate : number of breaths per minute
restrictive disease : disease that results from a restriction and decreased compliance of the alveoli; respiratory distress syndrome and pulmonary fibrosis are examples
sickle cell anemia : genetic disorder that affects the shape of red blood cells, and their ability to transport oxygen and move through capillaries
spirometry : method to measure lung volumes and to diagnose lung diseases
surfactant : detergent-like liquid in the airways that lowers the surface tension of the alveoli to allow for expansion
terminal bronchiole : region of bronchiole that attaches to the respiratory bronchioles
thalassemia : rare genetic disorder that results in mutation of the alpha or beta subunits of hemoglobin, creating smaller red blood cells with less hemoglobin
tidal volume (TV) : amount of air that is inspired and expired during normal breathing
total lung capacity (TLC) : sum of the residual volume, expiratory reserve volume, tidal volume, and inspiratory reserve volume
trachea : cartilaginous tube that transports air from the larynx to the primary bronchi
venousPCO2PCO2 : partial pressure of carbon dioxide in the veins (40 mm Hg in the pulmonary veins)
venousPO2PO2 : partial pressure of oxygen in the veins (100 mm Hg in the pulmonary veins)
ventilation/perfusion (V/Q) mismatch : region of the lung that lacks proper alveolar ventilation (V) and/or arterial perfusion (Q)
vital capacity (VC) : sum of the expiratory reserve volume, tidal volume, and inspiratory reserve volume |
https://openstax.org/books/biology/pages/40-chapter-summary | In most animals, the circulatory system is used to transport blood through the body. Some primitive animals use diffusion for the exchange of water, nutrients, and gases. However, complex organisms use the circulatory system to carry gases, nutrients, and waste through the body. Circulatory systems may be open (mixed with the interstitial fluid) or closed (separated from the interstitial fluid). Closed circulatory systems are a characteristic of vertebrates; however, there are significant differences in the structure of the heart and the circulation of blood between the different vertebrate groups due to adaptions during evolution and associated differences in anatomy. Fish have a two-chambered heart with unidirectional circulation. Amphibians have a three-chambered heart, which has some mixing of the blood, and they have double circulation. Most non-avian reptiles have a three-chambered heart, but have little mixing of the blood; they have double circulation. Mammals and birds have a four-chambered heart with no mixing of the blood and double circulation.
Specific components of the blood include red blood cells, white blood cells, platelets, and the plasma, which contains coagulation factors and serum. Blood is important for regulation of the bodyâs pH, temperature, osmotic pressure, the circulation of nutrients and removal of waste, the distribution of hormones from endocrine glands, and the elimination of excess heat; it also contains components for blood clotting. Red blood cells are specialized cells that contain hemoglobin and circulate through the body delivering oxygen to cells. White blood cells are involved in the immune response to identify and target invading bacteria, viruses, and other foreign organisms; they also recycle waste components, such as old red blood cells. Platelets and blood clotting factors cause the change of the soluble protein fibrinogen to the insoluble protein fibrin at a wound site forming a plug. Plasma consists of 90 percent water along with various substances, such as coagulation factors and antibodies. The serum is the plasma component of the blood without the coagulation factors.
The heart muscle pumps blood through three divisions of the circulatory system: coronary, pulmonary, and systemic. There is one atrium and one ventricle on the right side and one atrium and one ventricle on the left side. The pumping of the heart is a function of cardiomyocytes, distinctive muscle cells that are striated like skeletal muscle but pump rhythmically and involuntarily like smooth muscle. The internal pacemaker starts at the sinoatrial node, which is located near the wall of the right atrium. Electrical charges pulse from the SA node causing the two atria to contract in unison; then the pulse reaches the atrioventricular node between the right atrium and right ventricle. A pause in the electric signal allows the atria to empty completely into the ventricles before the ventricles pump out the blood. The blood from the heart is carried through the body by a complex network of blood vessels; arteries take blood away from the heart, and veins bring blood back to the heart.
Blood primarily moves through the body by the rhythmic movement of smooth muscle in the vessel wall and by the action of the skeletal muscle as the body moves. Blood is prevented from flowing backward in the veins by one-way valves. Blood flow through the capillary beds is controlled by precapillary sphincters to increase and decrease flow depending on the bodyâs needs and is directed by nerve and hormone signals. Lymph vessels take fluid that has leaked out of the blood to the lymph nodes where it is cleaned before returning to the heart. During systole, blood enters the arteries, and the artery walls stretch to accommodate the extra blood. During diastole, the artery walls return to normal. The blood pressure of the systole phase and the diastole phase gives the two pressure readings for blood pressure. |
https://openstax.org/books/biology/pages/40-key-terms | angina : pain caused by partial blockage of the coronary arteries by the buildup of plaque and lack of oxygen to the heart muscle
aorta : major artery of the body that takes blood away from the heart
arteriole : small vessel that connects an artery to a capillary bed
artery : blood vessel that takes blood away from the heart
atherosclerosis : buildup of fatty plaques in the coronary arteries in the heart
atrioventricular valve : one-way membranous flap of connective tissue between the atrium and the ventricle in the right side of the heart; also known as tricuspid valve
atrium : (plural: atria) chamber of the heart that receives blood from the veins and sends blood to the ventricles
bicuspid valve : (also, mitral valve; left atrioventricular valve) one-way membranous flap between the atrium and the ventricle in the left side of the heart
blood pressure (BP) : pressure of blood in the arteries that helps to push blood through the body
capillary : smallest blood vessel that allows the passage of individual blood cells and the site of diffusion of oxygen and nutrient exchange
capillary bed : large number of capillaries that converge to take blood to a particular organ or tissue
cardiac cycle : filling and emptying the heart of blood by electrical signals that cause the heart muscles to contract and relax
cardiac output : the volume of blood pumped by the heart in one minute as a product of heart rate multiplied by stroke volume
cardiomyocyte : specialized heart muscle cell that is striated but contracts involuntarily like smooth muscle
closed circulatory system : system in which the blood is separated from the bodily interstitial fluid and contained in blood vessels
coronary artery : vessel that supplies the heart tissue with blood
coronary vein : vessel that takes blood away from the heart tissue back to the chambers in the heart
diastole : relaxation phase of the cardiac cycle when the heart is relaxed and the ventricles are filling with blood
double circulation : flow of blood in two circuits: the pulmonary circuit through the lungs and the systemic circuit through the organs and body
electrocardiogram (ECG) : recording of the electrical impulses of the cardiac muscle
endocardium : innermost layer of tissue in the heart
epicardium : outermost tissue layer of the heart
gill circulation : circulatory system that is specific to animals with gills for gas exchange; the blood flows through the gills for oxygenation
hemocoel : cavity into which blood is pumped in an open circulatory system
hemolymph : mixture of blood and interstitial fluid that is found in insects and other arthropods as well as most mollusks
inferior vena cava : drains blood from the veins that come from the lower organs and the legs
interstitial fluid : fluid between cells
lymph node : specialized organ that contains a large number of macrophages that clean the lymph before the fluid is returned to the heart
myocardial infarction : (also, heart attack) complete blockage of the coronary arteries and death of the cardiac muscle tissue
myocardium : heart muscle cells that make up the middle layer and the bulk of the heart wall
open circulatory system : system in which the blood is mixed with interstitial fluid and directly covers the organs
ostium : (plural: ostia) holes between blood vessels that allow the movement of hemolymph through the body of insects, arthropods, and mollusks with open circulatory systems
pericardium : membrane layer protecting the heart; also part of the epicardium
peripheral resistance : resistance of the artery and blood vessel walls to the pressure placed on them by the force of the heart pumping
plasma : liquid component of blood that is left after the cells are removed
platelet : (also, thrombocyte) small cellular fragment that collects at wounds, cross-reacts with clotting factors, and forms a plug to prevent blood loss
precapillary sphincter : small muscle that controls blood circulation in the capillary beds
pulmocutaneous circulation : circulatory system in amphibians; the flow of blood to the lungs and the moist skin for gas exchange
pulmonary circulation : flow of blood away from the heart through the lungs where oxygenation occurs and then returns to the heart again
red blood cell : small (7â8 μm) biconcave cell without mitochondria (and in mammals without nuclei) that is packed with hemoglobin, giving the cell its red color; transports oxygen through the body
semilunar valve : membranous flap of connective tissue between the aorta and a ventricle of the heart (the aortic or pulmonary semilunar valves)
serum : plasma without the coagulation factors
sinoatrial (SA) node : the heartâs internal pacemaker; located near the wall of the right atrium
stroke volume> : - the volume of blood pumped into the aorta per contraction of the left ventricle
superior vena cava : drains blood from the jugular vein that comes from the brain and from the veins that come from the arms
systemic circulation : flow of blood away from the heart to the brain, liver, kidneys, stomach, and other organs, the limbs, and the muscles of the body, and then the return of this blood to the heart
systole : contraction phase of cardiac cycle when the ventricles are pumping blood into the arteries
tricuspid valve : one-way membranous flap of connective tissue between the atrium and the ventricle in the right side of the heart; also known as atrioventricular valve
unidirectional circulation : flow of blood in a single circuit; occurs in fish where the blood flows through the gills, then past the organs and the rest of the body, before returning to the heart
vasoconstriction : narrowing of a blood vessel
vasodilation : widening of a blood vessel
vein : blood vessel that brings blood back to the heart
vena cava : major vein of the body returning blood from the upper and lower parts of the body; see the superior vena cava and inferior vena cava
ventricle : (heart) large inferior chamber of the heart that pumps blood into arteries
venule : blood vessel that connects a capillary bed to a vein
white blood cell : large (30 μm) cell with nuclei of which there are many types with different roles including the protection of the body from viruses and bacteria, and cleaning up dead cells and other waste |
https://openstax.org/books/biology/pages/41-chapter-summary | Solute concentrations across a semi-permeable membranes influence the movement of water and solutes across the membrane. It is the number of solute molecules and not the molecular size that is important in osmosis. Osmoregulation and osmotic balance are important bodily functions, resulting in water and salt balance. Not all solutes can pass through a semi-permeable membrane. Osmosis is the movement of water across the membrane. Osmosis occurs to equalize the number of solute molecules across a semi-permeable membrane by the movement of water to the side of higher solute concentration. Facilitated diffusion utilizes protein channels to move solute molecules from areas of higher to lower concentration while active transport mechanisms are required to move solutes against concentration gradients. Osmolarity is measured in units of milliequivalents or milliosmoles, both of which take into consideration the number of solute particles and the charge on them. Fish that live in fresh water or saltwater adapt by being osmoregulators or osmoconformers.
The kidneys are the main osmoregulatory organs in mammalian systems; they function to filter blood and maintain the osmolarity of body fluids at 300 mOsm. They are surrounded by three layers and are made up internally of three distinct regionsâthe cortex, medulla, and pelvis.
The blood vessels that transport blood into and out of the kidneys arise from and merge with the aorta and inferior vena cava, respectively. The renal arteries branch out from the aorta and enter the kidney where they further divide into segmental, interlobar, arcuate, and cortical radiate arteries.
The nephron is the functional unit of the kidney, which actively filters blood and generates urine. The nephron is made up of the renal corpuscle and renal tubule. Cortical nephrons are found in the renal cortex, while juxtamedullary nephrons are found in the renal cortex close to the renal medulla. The nephron filters and exchanges water and solutes with two sets of blood vessels and the tissue fluid in the kidneys.
There are three steps in the formation of urine: glomerular filtration, which occurs in the glomerulus; tubular reabsorption, which occurs in the renal tubules; and tubular secretion, which also occurs in the renal tubules.
Many systems have evolved for excreting wastes that are simpler than the kidney and urinary systems of vertebrate animals. The simplest system is that of contractile vacuoles present in microorganisms. Flame cells and nephridia in worms perform excretory functions and maintain osmotic balance. Some insects have evolved Malpighian tubules to excrete wastes and maintain osmotic balance.
Ammonia is the waste produced by metabolism of nitrogen-containing compounds like proteins and nucleic acids. While aquatic animals can easily excrete ammonia into their watery surroundings, terrestrial animals have evolved special mechanisms to eliminate the toxic ammonia from their systems. Urea is the major byproduct of ammonia metabolism in vertebrate animals. Uric acid is the major byproduct of ammonia metabolism in birds, terrestrial arthropods, and reptiles.
Hormonal cues help the kidneys synchronize the osmotic needs of the body. Hormones like epinephrine, norepinephrine, renin-angiotensin, aldosterone, anti-diuretic hormone, and atrial natriuretic peptide help regulate the needs of the body as well as the communication between the different organ systems. |
https://openstax.org/books/biology/pages/41-key-terms | afferent arteriole : arteriole that branches from the cortical radiate artery and enters the glomerulus
ammonia : compound made of one nitrogen atom and three hydrogen atoms
ammonotelic : describes an animal that excretes ammonia as the primary waste material
angiotensin converting enzyme (ACE) : enzyme that converts angiotensin I to angiotensin II
angiotensin I : product in the renin-angiotensin-aldosterone pathway
angiotensin II : molecule that affects different organs to increase blood pressure
anti-diuretic hormone (ADH) : hormone that prevents the loss of water
antioxidant : agent that prevents cell destruction by reactive oxygen species
arcuate artery : artery that branches from the interlobar artery and arches over the base of the renal pyramids
ascending limb : part of the loop of Henle that ascends from the renal medulla to the renal cortex
blood urea nitrogen (BUN) : estimate of urea in the blood and an indicator of kidney function
Bowman's capsule : structure that encloses the glomerulus
calyx : structure that connects the renal pelvis to the renal medulla
cortex (animal) : outer layer of an organ like the kidney or adrenal gland
cortical nephron : nephron that lies in the renal cortex
cortical radiate artery : artery that radiates from the arcuate arteries into the renal cortex
countercurrent exchanger : peritubular capillary network that allows exchange of solutes and water from the renal tubules
countercurrent multiplier : osmotic gradient in the renal medulla that is responsible for concentration of urine
descending limb : part of the loop of Henle that descends from the renal cortex into the renal medulla
distal convoluted tubule (DCT) : part of the renal tubule that is the most distant from the glomerulus
efferent arteriole : arteriole that exits from the glomerulus
electrolyte : solute that breaks down into ions when dissolved in water
flame cell : (also, protonephridia) excretory cell found in flatworms
glomerular filtration : filtration of blood in the glomerular capillary network into the glomerulus
glomerular filtration rate (GFR) : amount of filtrate formed by the glomerulus per minute
glomerulus (renal) : part of the renal corpuscle that contains the capillary network
hilum : region in the renal pelvis where blood vessels, nerves, and ureters bunch before entering or exiting the kidney
inferior vena cava : one of the main veins in the human body
interlobar artery : artery that branches from the segmental artery and travels in between the renal lobes
juxtaglomerular cell : cell in the afferent and efferent arterioles that responds to stimuli from the macula densa
juxtamedullary nephron : nephron that lies in the cortex but close to the renal medulla
kidney : organ that performs excretory and osmoregulatory functions
lobes of the kidney : renal pyramid along with the adjoining cortical region
loop of Henle : part of the renal tubule that loops into the renal medulla
macula densa : group of cells that senses changes in sodium ion concentration; present in parts of the renal tubule and collecting ducts
Malpighian tubule : excretory tubules found in arthropods
medulla : middle layer of an organ like the kidney or adrenal gland
microvilli : cellular processes that increase the surface area of cells
molality : number of moles of solute per kilogram of solvent
molarity : number of moles of solute per liter of solution
mole : gram equivalent of the molecular weight of a substance
nephridia : excretory structures found in annelids
nephridiopore : pore found at the end of nephridia
nephron : functional unit of the kidney
non-electrolyte : solute that does not break down into ions when dissolved in water
osmoconformer : organism that changes its tonicity based on its environment
osmoregulation : mechanism by which water and solute concentrations are maintained at desired levels
osmoregulator : organism that maintains its tonicity irrespective of its environment
osmotic balance : balance of the amount of water and salt input and output to and from a biological system without disturbing the desired osmotic pressure and solute concentration in every compartment
osmotic pressure : pressure exerted on a membrane to equalize solute concentration on either side
perirenal fat capsule : fat layer that suspends the kidneys
peritubular capillary network : capillary network that surrounds the renal tubule after the efferent artery exits the glomerulus
proximal convoluted tubule (PCT) : part of the renal tubule that lies close to the glomerulus
renal artery : branch of the artery that enters the kidney
renal capsule : layer that encapsulates the kidneys
renal column : area of the kidney through which the interlobar arteries travel in the process of supplying blood to the renal lobes
renal corpuscle : glomerulus and the Bowman's capsule together
renal fascia : connective tissue that supports the kidneys
renal pelvis : region in the kidney where the calyces join the ureters
renal pyramid : conical structure in the renal medulla
renal tubule : tubule of the nephron that arises from the glomerulus
renal vein : branch of a vein that exits the kidney and joins the inferior vena cava
renin-angiotensin-aldosterone : biochemical pathway that activates angiotensin II, which increases blood pressure
segmental artery : artery that branches from the renal artery
semi-permeable membrane : membrane that allows only certain solutes to pass through
transport maximum : maximum amount of solute that can be transported out of the renal tubules during reabsorption
tubular reabsorption : reclamation of water and solutes that got filtered out in the glomerulus
tubular secretion : process of secretion of wastes that do not get reabsorbed
urea cycle : pathway by which ammonia is converted to urea
ureotelic : describes animals that secrete urea as the primary nitrogenous waste material
ureter : urine-bearing tube coming out of the kidney; carries urine to the bladder
uric acid : byproduct of ammonia metabolism in birds, insects, and reptiles
urinary bladder : structure that the ureters empty the urine into; stores urine
urine : filtrate produced by kidneys that gets excreted out of the body
vasa recta : peritubular network that surrounds the loop of Henle of the juxtamedullary nephrons
vasodilator : compound that increases the diameter of blood vessels
vasopressin : another name for anti-diuretic hormone |
https://openstax.org/books/biology/pages/42-chapter-summary | The innate immune system serves as a first responder to pathogenic threats that bypass natural physical and chemical barriers of the body. Using a combination of cellular and molecular attacks, the innate immune system identifies the nature of a pathogen and responds with inflammation, phagocytosis, cytokine release, destruction by NK cells, and/or a complement system. When innate mechanisms are insufficient to clear an infection, the adaptive immune response is informed and mobilized.
The adaptive immune response is a slower-acting, longer-lasting, and more specific response than the innate response. However, the adaptive response requires information from the innate immune system to function. APCs display antigens via MHC molecules to complementary naïve T cells. In response, the T cells differentiate and proliferate, becoming THcells or CTLs. THcells stimulate B cells that have engulfed and presented pathogen-derived antigens. B cells differentiate into plasma cells that secrete antibodies, whereas CTLs induce apoptosis in intracellularly infected or cancerous cells. Memory cells persist after a primary exposure to a pathogen. If re-exposure occurs, memory cells differentiate into effector cells without input from the innate immune system. The mucosal immune system is largely independent from the systemic immune system but functions in a parallel fashion to protect the extensive mucosal surfaces of the body.
Antibodies (immunoglobulins) are the molecules secreted from plasma cells that mediate the humoral immune response. There are five antibody classes; an antibody's class determines its mechanism of action and production site but does not control its binding specificity. Antibodies bind antigens via variable domains and can either neutralize pathogens or mark them for phagocytosis or activate the complement cascade.
Immune disruptions may involve insufficient immune responses or inappropriate immune targets. Immunodeficiency increases an individual's susceptibility to infections and cancers. Hypersensitivities are misdirected responses either to harmless foreign particles, as in the case of allergies, or to host factors, as in the case of autoimmunity. Reactions to self components may be the result of molecular mimicry. |
https://openstax.org/books/biology/pages/42-key-terms | adaptive immunity : immunity that has memory and occurs after exposure to an antigen either from a pathogen or a vaccination
affinity : attraction of molecular complementarity between antigen and antibody molecules
allergy : immune reaction that results from immediate hypersensitivities in which an antibody-mediated immune response occurs within minutes of exposure to a harmless antigen
antibody : protein that is produced by plasma cells after stimulation by an antigen; also known as an immunoglobulin
antigen : foreign or ânon-selfâ protein that triggers the immune response
antigen-presenting cell (APC) : immune cell that detects, engulfs, and informs the adaptive immune response about an infection by presenting the processed antigen on the cell surface
autoantibody : antibody that incorrectly marks âselfâ components as foreign and stimulates the immune response
autoimmune response : inappropriate immune response to host cells or self-antigens
autoimmunity : type of hypersensitivity to self antigens
avidity : total binding strength of a multivalent antibody with antigen
B cell : lymphocyte that matures in the bone marrow and differentiates into antibody-secreting plasma cells
basophil : leukocyte that releases chemicals usually involved in the inflammatory response
cell-mediated immune response : adaptive immune response that is carried out by T cells
clonal selection : activation of B cells corresponding to one specific BCR variant and the dramatic proliferation of that variant
complement system : array of approximately 20 soluble proteins of the innate immune system that enhance phagocytosis, bore holes in pathogens, and recruit lymphocytes; enhances the adaptive response when antibodies are produced
cross reactivity : binding of an antibody to an epitope corresponding to an antigen that is different from the one the antibody was raised against
cytokine : chemical messenger that regulates cell differentiation, proliferation, gene expression, and cell trafficking to effect immune responses
cytotoxic T lymphocyte (CTL) : adaptive immune cell that directly kills infected cells via perforin and granzymes, and releases cytokines to enhance the immune response
dendritic cell : immune cell that processes antigen material and presents it on the surface of other cells to induce an immune response
effector cell : lymphocyte that has differentiated, such as a B cell, plasma cell, or cytotoxic T lymphocyte
eosinophil : leukocyte that responds to parasites and is involved in the allergic response
epitope : small component of an antigen that is specifically recognized by antibodies, B cells, and T cells; the antigenic determinant
granzyme : protease that enters target cells through perforin and induces apoptosis in the target cells; used by NK cells and killer T cells
helper T lymphocyte (TH) : cell of the adaptive immune system that binds APCs via MHC II molecules and stimulates B cells or secretes cytokines to initiate the immune response
host : an organism that is invaded by a pathogen or parasite
humoral immune response : adaptive immune response that is controlled by activated B cells and antibodies
hypersensitivities : spectrum of maladaptive immune responses toward harmless foreign particles or self antigens; occurs after tissue sensitization and includes immediate-type (allergy), delayed-type, and autoimmunity
immune tolerance : acquired ability to prevent an unnecessary or harmful immune response to a detected foreign body known not to cause disease or to self-antigens
immunodeficiency : failure, insufficiency, or delay at any level of the immune system, which may be acquired or inherited
inflammation : localized redness, swelling, heat, and pain that results from the movement of leukocytes and fluid through opened capillaries to a site of infection
innate immunity : immunity that occurs naturally because of genetic factors or physiology, and is not induced by infection or vaccination
interferon : cytokine that inhibits viral replication and modulates the immune response
lymph : watery fluid that bathes tissues and organs with protective white blood cells and does not contain erythrocytes
lymphocyte : leukocyte that is histologically identifiable by its large nuclei; it is a small cell with very little cytoplasm
macrophage : large phagocytic cell that engulfs foreign particles and pathogens
major histocompatibility class (MHC) I/II molecule : protein found on the surface of all nucleated cells (I) or specifically on antigen-presenting cells (II) that signals to immune cells whether the cell is healthy/normal or is infected/cancerous; it provides the appropriate template into which antigens can be loaded for recognition by lymphocytes
mast cell : leukocyte that produces inflammatory molecules, such as histamine, in response to large pathogens and allergens
memory cell : antigen-specific B or T lymphocyte that does not differentiate into effector cells during the primary immune response but that can immediately become an effector cell upon re-exposure to the same pathogen
monocyte : type of white blood cell that circulates in the blood and lymph and differentiates into macrophages after it moves into infected tissue
mucosa-associated lymphoid tissue (MALT) : collection of lymphatic tissue that combines with epithelial tissue lining the mucosa throughout the body
natural killer (NK) cell : lymphocyte that can kill cells infected with viruses or tumor cells
neutrophil : phagocytic leukocyte that engulfs and digests pathogens
opsonization : process that enhances phagocytosis using proteins to indicate the presence of a pathogen to phagocytic cells
passive immunity : transfer of antibodies from one individual to another to provide temporary protection against pathogens
pathogen : an agent, usually a microorganism, that causes disease in the organisms that they invade
pathogen-associated molecular pattern (PAMP) : carbohydrate, polypeptide, and nucleic acid âsignatureâ that is expressed by viruses, bacteria, and parasites but differs from molecules on host cells
pattern recognition receptor (PRR) : molecule on macrophages and dendritic cells that binds molecular signatures of pathogens and promotes pathogen engulfment and destruction
perforin : destructive protein that creates a pore in the target cell; used by NK cells and killer T cells
plasma cell : immune cell that secrets antibodies; these cells arise from B cells that were stimulated by antigens
regulatory T (Treg) cell : specialized lymphocyte that suppresses local inflammation and inhibits the secretion of cytokines, antibodies, and other stimulatory immune factors; involved in immune tolerance
T cell : lymphocyte that matures in the thymus gland; one of the main cells involved in the adaptive immune system |
https://openstax.org/books/biology/pages/43-chapter-summary | Reproduction may be asexual when one individual produces genetically identical offspring, or sexual when the genetic material from two individuals is combined to produce genetically diverse offspring. Asexual reproduction occurs through fission, budding, and fragmentation. Sexual reproduction may mean the joining of sperm and eggs within animalsâ bodies or it may mean the release of sperm and eggs into the environment. An individual may be one sex, or both; it may start out as one sex and switch during its life, or it may stay male or female.
Sexual reproduction starts with the combination of a sperm and an egg in a process called fertilization. This can occur either outside the bodies or inside the female. Both methods have advantages and disadvantages. Once fertilized, the eggs can develop inside the female or outside. If the egg develops outside the body, it usually has a protective covering over it. Animal anatomy evolved various ways to fertilize, hold, or expel the egg. The method of fertilization varies among animals. Some species release the egg and sperm into the environment, some species retain the egg and receive the sperm into the female body and then expel the developing embryo covered with shell, while still other species retain the developing offspring through the gestation period.
As animals became more complex, specific organs and organ systems developed to support specific functions for the organism. The reproductive structures that evolved in land animals allow males and females to mate, fertilize internally, and support the growth and development of offspring. Processes developed to produce reproductive cells that had exactly half the number of chromosomes of each parent so that new combinations would have the appropriate amount of genetic material. Gametogenesis, the production of sperm (spermatogenesis) and eggs (oogenesis), takes place through the process of meiosis.
The male and female reproductive cycles are controlled by hormones released from the hypothalamus and anterior pituitary as well as hormones from reproductive tissues and organs. The hypothalamus monitors the need for the FSH and LH hormones made and released from the anterior pituitary. FSH and LH affect reproductive structures to cause the formation of sperm and the preparation of eggs for release and possible fertilization. In the male, FSH and LH stimulate Sertoli cells and interstitial cells of Leydig in the testes to facilitate sperm production. The Leydig cells produce testosterone, which also is responsible for the secondary sexual characteristics of males. In females, FSH and LH cause estrogen and progesterone to be produced. They regulate the female reproductive system which is divided into the ovarian cycle and the menstrual cycle. Menopause occurs when the ovaries lose their sensitivity to FSH and LH and the female reproductive cycles slow to a stop.
Human pregnancy begins with fertilization of an egg and proceeds through the three trimesters of gestation. The labor process has three stages (contractions, delivery of the fetus, expulsion of the placenta), each propelled by hormones. The first trimester lays down the basic structures of the body, including the limb buds, heart, eyes, and the liver. The second trimester continues the development of all of the organs and systems. The third trimester exhibits the greatest growth of the fetus and culminates in labor and delivery. Prevention of a pregnancy can be accomplished through a variety of methods including barriers, hormones, or other means. Assisted reproductive technologies may help individuals who have infertility problems.
The early stages of embryonic development begin with fertilization. The process of fertilization is tightly controlled to ensure that only one sperm fuses with one egg. After fertilization, the zygote undergoes cleavage to form the blastula. The blastula, which in some species is a hollow ball of cells, undergoes a process called gastrulation, in which the three germ layers form. The ectoderm gives rise to the nervous system and the epidermal skin cells, the mesoderm gives rise to the muscle cells and connective tissue in the body, and the endoderm gives rise to columnar cells and internal organs.
Organogenesis is the formation of organs from the germ layers. Each germ layer gives rise to specific tissue types. The first stage is the formation of the neural system in the ectoderm. The mesoderm gives rise to somites and the notochord. Formation of vertebrate axis is another important developmental stage. |
https://openstax.org/books/biology/pages/43-key-terms | acrosomal reaction : series of biochemical reactions that the sperm uses to break through the zona pellucida
asexual reproduction : form of reproduction that produces offspring that are genetically identical to the parent
blastocyst : structure formed when cells in the mammalian blastula separate into an inner and outer layer
budding : form of asexual reproduction that results from the outgrowth of a part of a cell leading to a separation from the original animal into two individuals
bulbourethral gland : secretion that cleanses the urethra prior to ejaculation
clitoris : sensory structure in females; stimulated during sexual arousal
cloaca : common body opening for the digestive, excretory, and reproductive systems found in non-mammals, such as birds
contraception : (also, birth control) various means used to prevent pregnancy
estrogen : reproductive hormone in females that assists in endometrial regrowth, ovulation, and calcium absorption
external fertilization : fertilization of egg by sperm outside animal body, often during spawning
fission : (also, binary fission) method by which multicellular organisms increase in size or asexual reproduction in which a unicellular organism splits into two separate organisms by mitosis
follicle stimulating hormone (FSH) : reproductive hormone that causes sperm production in men and follicle development in women
fragmentation : cutting or fragmenting of the original animal into parts and the growth of a separate animal from each part
gastrulation : process in which the blastula folds over itself to form the three germ layers
gestation : length of time for fetal development to birth
gonadotropin-releasing hormone (GnRH) : hormone from the hypothalamus that causes the release of FSH and LH from the anterior pituitary
hermaphroditism : state of having both male and female reproductive parts within the same individual
holoblastic : complete cleavage; takes place in cells with a small amount of yolk
human beta chorionic gonadotropin (β-HCG) : hormone produced by the chorion of the zygote that helps to maintain the corpus luteum and elevated levels of progesterone
infertility : inability to conceive, carry, and deliver children
inhibin : hormone made by Sertoli cells; provides negative feedback to hypothalamus in control of FSH and GnRH release
inner cell mass : inner layer of cells in the blastocyst
internal fertilization : fertilization of egg by sperm inside the body of the female
interstitial cell of Leydig : cell in seminiferous tubules that makes testosterone
labia majora : large folds of tissue covering the inguinal area
labia minora : smaller folds of tissue within the labia majora
luteinizing hormone (LH) : reproductive hormone in both men and women, causes testosterone production in men and ovulation and lactation in women
menopause : loss of reproductive capacity in women due to decreased sensitivity of the ovaries to FSH and LH
menstrual cycle : cycle of the degradation and re-growth of the endometrium
meroblastic : partial cleavage; takes place in cells with a large amount of yolk
morning sickness : condition in the mother during the first trimester; includes feelings of nausea
neural tube : tube-like structure that forms from the ectoderm and gives rise to the brain and spinal cord
oogenesis : process of producing haploid eggs
organogenesis : process of organ formation
ovarian cycle : cycle of preparation of egg for ovulation and the conversion of the follicle to the corpus luteum
oviduct : (also, fallopian tube) muscular tube connecting the uterus with the ovary area
oviparity : process by which fertilized eggs are laid outside the femaleâs body and develop there, receiving nourishment from the yolk that is a part of the egg
ovoviparity : process by which fertilized eggs are retained within the female; the embryo obtains its nourishment from the eggâs yolk and the young are fully developed when they are hatched
ovulation : release of the egg by the most mature follicle
parthenogenesis : form of asexual reproduction where an egg develops into a complete individual without being fertilized
penis : male reproductive structure for urine elimination and copulation
placenta : organ that supports the diffusion of nutrients and waste between the motherâs and fetusâ blood
polyspermy : condition in which one egg is fertilized by multiple sperm
progesterone : reproductive hormone in women; assists in endometrial re-growth and inhibition of FSH and LH release
prostate gland : structure that is a mixture of smooth muscle and glandular material and that contributes to semen
scrotum : sac containing testes; exterior to the body
semen : fluid mixture of sperm and supporting materials
seminal vesicle : secretory accessory gland in males; contributes to semen
seminiferous tubule : site of sperm production in testes
Sertoli cell : cell in seminiferous tubules that assists developing sperm and makes inhibin
sexual reproduction : mixing of genetic material from two individuals to produce genetically unique offspring
somite : group of cells separated by small spaces that form from the mesoderm and give rise to connective tissue
spermatheca : specialized sac that stores sperm for later use
spermatogenesis : process of producing haploid sperm
testes : pair of reproductive organs in males
testosterone : reproductive hormone in men that assists in sperm production and promoting secondary sexual characteristics
trophoblast : outer layer of cells in the blastocyst
uterus : environment for developing embryo and fetus
vagina : muscular tube for the passage of menstrual flow, copulation, and birth of offspring
viviparity : process in which the young develop within the female, receiving nourishment from the motherâs blood through a placenta
zona pellucida : protective layer of glycoproteins on the mammalian egg |
https://openstax.org/books/biology/pages/44-chapter-summary | Ecology is the study of the interactions of living things with their environment. Ecologists ask questions across four levels of biological organizationâorganismal, population, community, and ecosystem. At the organismal level, ecologists study individual organisms and how they interact with their environments. At the population and community levels, ecologists explore, respectively, how a population of organisms changes over time and the ways in which that population interacts with other species in the community. Ecologists studying an ecosystem examine the living species (the biotic components) of the ecosystem as well as the nonliving portions (the abiotic components), such as air, water, and soil, of the environment.
Biogeography is the study of the geographic distribution of living things and the abiotic factors that affect their distribution. Endemic species are species that are naturally found only in a specific geographic area. The distribution of living things is influenced by several environmental factors that are, in part, controlled by the latitude or elevation at which an organism is found. Ocean upwelling and spring and fall turnovers are important processes regulating the distribution of nutrients and other abiotic factors important in aquatic ecosystems. Energy sources, temperature, water, inorganic nutrients, and soil are factors limiting the distribution of living things in terrestrial systems. Net primary productivity is a measure of the amount of biomass produced by a biome.
The Earth has terrestrial biomes and aquatic biomes. Aquatic biomes include both freshwater and marine environments. There are eight major terrestrial biomes: tropical wet forests, savannas, subtropical deserts, chaparral, temperate grasslands, temperate forests, boreal forests, and Arctic tundra. The same biome can occur in different geographic locations with similar climates. Temperature and precipitation, and variations in both, are key abiotic factors that shape the composition of animal and plant communities in terrestrial biomes. Some biomes, such as temperate grasslands and temperate forests, have distinct seasons, with cold weather and hot weather alternating throughout the year. In warm, moist biomes, such as the tropical wet forest, net primary productivity is high, as warm temperatures, abundant water, and a year-round growing season fuel plant growth. Other biomes, such as deserts and tundra, have low primary productivity due to extreme temperatures and a shortage of available water.
Aquatic ecosystems include both saltwater and freshwater biomes. The abiotic factors important for the structuring of aquatic ecosystems can be different than those seen in terrestrial systems. Sunlight is a driving force behind the structure of forests and also is an important factor in bodies of water, especially those that are very deep, because of the role of photosynthesis in sustaining certain organisms. Density and temperature shape the structure of aquatic systems. Oceans may be thought of as consisting of different zones based on water depth and distance from the shoreline and light penetrance. Different kinds of organisms are adapted to the conditions found in each zone. Coral reefs are unique marine ecosystems that are home to a wide variety of species. Estuaries are found where rivers meet the ocean; their shallow waters provide nourishment and shelter for young crustaceans, mollusks, fishes, and many other species. Freshwater biomes include lakes, ponds, rivers, streams, and wetlands. Bogs are an interesting type of wetland characterized by standing water, lower pH, and a lack of nitrogen.
The Earth has gone through periodic cycles of increases and decreases in temperature. During the past 2000 years, the Medieval Climate Anomaly was a warmer period, while the Little Ice Age was unusually cool. Both of these irregularities can be explained by natural causes of changes in climate, and, although the temperature changes were small, they had significant effects. Natural drivers of climate change include Milankovitch cycles, changes in solar activity, and volcanic eruptions. None of these factors, however, leads to rapid increases in global temperature or sustained increases in carbon dioxide. The burning of fossil fuels is an important source of greenhouse gases, which plays a major role in the greenhouse effect. Long ago, global warming resulted in the Permian extinction: a large-scale extinction event that is documented in the fossil record. Currently, modern-day climate change is associated with the increased melting of glaciers and polar ice sheets, resulting in a gradual increase in sea level. Plants and animals can also be affected by global climate change when the timing of seasonal events, such as flowering or pollination, is affected by global warming. |
https://openstax.org/books/biology/pages/44-key-terms | abiotic : nonliving components of the environment
aboveground biomass : total mass of aboveground living plants per area
abyssal zone : deepest part of the ocean at depths of 4000 m or greater
algal bloom : rapid increase of algae in an aquatic system
aphotic zone : part of the ocean where no light penetrates
benthic realm : (also, benthic zone) part of the ocean that extends along the ocean bottom from the shoreline to the deepest parts of the ocean floor
biogeography : study of the geographic distribution of living things and the abiotic factors that affect their distribution
biome : ecological community of plants, animals, and other organisms that is adapted to a characteristic set of environmental conditions
biotic : living components of the environment
canopy : branches and foliage of trees that form a layer of overhead coverage in a forest
channel : width of a river or stream from one bank to the other bank
clathrates : frozen chunks of ice and methane found at the bottom of the ocean
climate : long-term, predictable atmospheric conditions present in a specific area
conspecifics : individuals that are members of the same species
coral reef : ocean ridges formed by marine invertebrates living in warm, shallow waters within the photic zone
cryptofauna : invertebrates found within the calcium carbonate substrate of coral reefs
ecology : study of interaction between living things and their environment
ecosystem services : human benefits and services provided by natural ecosystems
emergent vegetation : wetland plants that are rooted in the soil but have portions of leaves, stems, and flowers extending above the waterâs surface
endemic : species found only in a specific geographic area that is usually restricted in size
estuary : biomes where a source of fresh water, such as a river, meets the ocean
fall and spring turnover : seasonal process that recycles nutrients and oxygen from the bottom of a freshwater ecosystem to the top
global climate change : altered global weather patterns, including a worldwide increase in temperature, due largely to rising levels of atmospheric carbon dioxide
greenhouse effect : warming of Earth due to carbon dioxide and other greenhouse gases in the atmosphere
greenhouse gases : atmospheric gases such as carbon dioxide and methane that absorb and emit radiation, thus trapping heat in Earthâs atmosphere
haze-effect cooling : effect of the gases and solids from a volcanic eruption on global climate
heterospecifics : individuals that are members of different species
intertidal zone : part of the ocean that is closest to land; parts extend above the water at low tide
Milankovitch cycles : cyclic changes in the Earth's orbit that may affect climate
neritic zone : part of the ocean that extends from low tide to the edge of the continental shelf
net primary productivity : measurement of the energy accumulation within an ecosystem, calculated as the total amount of carbon fixed per year minus the amount that is oxidized during cellular respiration
ocean upwelling : rising of deep ocean waters that occurs when prevailing winds blow along surface waters near a coastline
oceanic zone : part of the ocean that begins offshore where the water measures 200 m deep or deeper
pelagic realm : (also, pelagic zone) open ocean waters that are not close to the bottom or near the shore
permafrost : perennially frozen portion of the Arctic tundra soil
photic zone : portion of the ocean that light can penetrate
planktivore : animal species that eats plankton
predator : animal species that hunt and are carnivores or âflesh eatersâ
Sargassum : type of free-floating marine seaweed
solar intensity : amount of solar power energy the sun emits in a given amount of time
source water : point of origin of a river or stream
thermocline : layer of water with a temperature that is significantly different from that of the surrounding layers
weather : conditions of the atmosphere during a short period of time |
https://openstax.org/books/biology/pages/45-chapter-summary | Populations are individuals of a species that live in a particular habitat. Ecologists measure characteristics of populations: size, density, dispersion pattern, age structure, and sex ratio. Life tables are useful to calculate life expectancies of individual population members. Survivorship curves show the number of individuals surviving at each age interval plotted versus time.
All species have evolved a pattern of living, called a life history strategy, in which they partition energy for growth, maintenance, and reproduction. These patterns evolve through natural selection; they allow species to adapt to their environment to obtain the resources they need to successfully reproduce. There is an inverse relationship between fecundity and parental care. A species may reproduce early in life to ensure surviving to a reproductive age or reproduce later in life to become larger and healthier and better able to give parental care. A species may reproduce once (semelparity) or many times (iteroparity) in its life.
Populations with unlimited resources grow exponentially, with an accelerating growth rate. When resources become limiting, populations follow a logistic growth curve. The population of a species will level off at the carrying capacity of its environment.
Populations are regulated by a variety of density-dependent and density-independent factors. Species are divided into two categories based on a variety of features of their life history patterns:r-selected species, which have large numbers of offspring, andK-selected species, which have few offspring. Ther- andK-selection theory has fallen out of use; however, many of its key features are still used in newer, demographically-based models of population dynamics.
The worldâs human population is growing at an exponential rate. Humans have increased the worldâs carrying capacity through migration, agriculture, medical advances, and communication. The age structure of a population allows us to predict population growth. Unchecked human population growth could have dire long-term effects on our environment.
Communities include all the different species living in a given area. The variety of these species is called species richness. Many organisms have developed defenses against predation and herbivory, including mechanical defenses, warning coloration, and mimicry, as a result of evolution and the interaction with other members of the community. Two species cannot exist in the same habitat competing directly for the same resources. Species may form symbiotic relationships such as commensalism or mutualism. Community structure is described by its foundation and keystone species. Communities respond to environmental disturbances by succession (the predictable appearance of different types of plant species) until a stable community structure is established.
Behaviors are responses to stimuli. They can either be instinctual/innate behaviors, which are not influenced by the environment, or learned behaviors, which are influenced by environmental changes. Instinctual behaviors include mating systems and methods of communication. Learned behaviors include imprinting and habituation, conditioning, and, most powerfully, cognitive learning. Although the connection between behavior, genetics, and evolution is well established, the explanation of human behavior as entirely genetic is controversial. |
https://openstax.org/books/biology/pages/45-key-terms | age structure : proportion of population members at specific age ranges
aggressive display : visual display by a species member to discourage other members of the same species or different species
aposematic coloration : warning coloration used as a defensive mechanism against predation
Batesian mimicry : type of mimicry where a non-harmful species takes on the warning colorations of a harmful one
behavior : change in an organismâs activities in response to a stimulus
behavioral biology : study of the biology and evolution of behavior
biotic potential (rmax) : maximal potential growth rate of a species
birth rate (B) : number of births within a population at a specific point in time
camouflage : avoid detection by blending in with the background.
carrying capacity (K) : number of individuals of a species that can be supported by the limited resources of a habitat
classical conditioning : association of a specific stimulus and response through conditioning
climax community : final stage of succession, where a stable community is formed by a characteristic assortment of plant and animal species
cognitive learning : knowledge and skills acquired by the manipulation of information in the mind
commensalism : relationship between species wherein one species benefits from the close, prolonged interaction, while the other species neither benefits nor is harmed
competitive exclusion principle : no two species within a habitat can coexist when they compete for the same resources at the same place and time
conditioned behavior : behavior that becomes associated with a specific stimulus through conditioning
courtship display : visual display used to attract a mate
death rate (D) : number of deaths within a population at a specific point in time
demographic-based population model : modern model of population dynamics incorporating many features of ther- andK-selection theory
demography : statistical study of changes in populations over time
density-dependent regulation : regulation of population that is influenced by population density, such as crowding effects; usually involves biotic factors
density-independent regulation : regulation of populations by factors that operate independent of population density, such as forest fires and volcanic eruptions; usually involves abiotic factors
distraction display : visual display used to distract predators away from a nesting site
Emsleyan/Mertensian mimicry : type of mimicry where a harmful species resembles a less harmful one
energy budget : allocation of energy resources for body maintenance, reproduction, and parental care
environmental disturbance : change in the environment caused by natural disasters or human activities
ethology : biological study of animal behavior
exponential growth : accelerating growth pattern seen in species under conditions where resources are not limiting
fecundity : potential reproductive capacity of an individual
fixed action pattern : series of instinctual behaviors that, once initiated, always goes to completion regardless of changes in the environment
foraging : behaviors species use to find food
foundation species : species which often forms the major structural portion of the habitat
habituation : ability of a species to ignore repeated stimuli that have no consequence
host : organism a parasite lives on
imprinting : identification of parents by newborns as the first organism they see after birth
innate behavior : instinctual behavior that is not altered by changes in the environment
intersexual selection : selection of a desirable mate of the opposite sex
interspecific competition : competition between species for resources in a shared habitat or environment
intrasexual selection : competition between members of the same sex for a mate
intraspecific competition : competition between members of the same species
island biogeography : study of life on island chains and how their geography interacts with the diversity of species found there
iteroparity : life history strategy characterized by multiple reproductive events during the lifetime of a species
J-shaped growth curve : shape of an exponential growth curve
K-selected species : species suited to stable environments that produce a few, relatively large offspring and provide parental care
keystone species : species whose presence is key to maintaining biodiversity in an ecosystem and to upholding an ecological communityâs structure
kin selection : sacrificing oneâs own life so that oneâs genes will be passed on to future generations by relatives
kinesis : undirected movement of an organism in response to a stimulus
learned behavior : behavior that responds to changes in the environment
life history : inherited pattern of resource allocation under the influence of natural selection and other evolutionary forces
life table : table showing the life expectancy of a population member based on its age
logistic growth : leveling off of exponential growth due to limiting resources
mark and recapture : technique used to determine population size in mobile organisms
migration : long-range seasonal movement of animal species
monogamy : mating system whereby one male and one female remain coupled for at least one mating season
mortality rate : proportion of population surviving to the beginning of an age interval that die during the age interval
Müllerian mimicry : type of mimicry where species share warning coloration and all are harmful to predators
mutualism : symbiotic relationship between two species where both species benefit
one-child policy : Chinaâs policy to limit population growth by limiting urban couples to have only one child or face the penalty of a fine
operant conditioning : learned behaviors in response to positive and/or negative reinforcement
parasite : organism that uses resources from another species, the host
pioneer species : first species to appear in primary and secondary succession
polyandry : mating system where one female mates with many males
polygyny : mating system where one male mates with many females
population density : number of population members divided by the area or volume being measured
population growth rate : number of organisms added in each reproductive generation
population size (N) : number of population members in a habitat at the same time
primary succession : succession on land that previously has had no life
quadrat : square made of various materials used to determine population size and density in slow moving or stationary organisms
r-selected species : species suited to changing environments that produce many offspring and provide little or no parental care
reflex action : action in response to direct physical stimulation of a nerve
relative species abundance : absolute population size of a particular species relative to the population sizes of other species within the community
S-shaped growth curve : shape of a logistic growth curve
secondary succession : succession in response to environmental disturbances that move a community away from its equilibrium
semelparity : life history strategy characterized by a single reproductive event followed by death
signal : method of communication between animals including those obtained by the senses of smell, hearing, sight, or touch
species dispersion pattern : (also, species distribution pattern) spatial location of individuals of a given species within a habitat at a particular point in time
species richness : number of different species in a community
survivorship curve : graph of the number of surviving population members versus the relative age of the member
symbiosis : close interaction between individuals of different species over an extended period of time that impacts the abundance and distribution of the associating populations
taxis : directed movement in response to a stimulus
zero population growth : steady population size where birth rates and death rates are equal |
https://openstax.org/books/biology/pages/46-chapter-summary | Ecosystems exist on land, at sea, in the air, and underground. Different ways of modeling ecosystems are necessary to understand how environmental disturbances will affect ecosystem structure and dynamics. Conceptual models are useful to show the general relationships between organisms and the flow of materials or energy between them. Analytical models are used to describe linear food chains, and simulation models work best with holistic food webs.
Organisms in an ecosystem acquire energy in a variety of ways, which is transferred between trophic levels as the energy flows from the bottom to the top of the food web, with energy being lost at each transfer. The efficiency of these transfers is important for understanding the different behaviors and eating habits of warm-blooded versus cold-blooded animals. Modeling of ecosystem energy is best done with ecological pyramids of energy, although other ecological pyramids provide other vital information about ecosystem structure.
Mineral nutrients are cycled through ecosystems and their environment. Of particular importance are water, carbon, nitrogen, phosphorus, and sulfur. All of these cycles have major impacts on ecosystem structure and function. As human activities have caused major disturbances to these cycles, their study and modeling is especially important. A variety of human activities, such as pollution, oil spills, and events) have damaged ecosystems, potentially causing global climate change. The health of Earth depends on understanding these cycles and how to protect the environment from irreversible damage. |
https://openstax.org/books/biology/pages/46-key-terms | acid rain : corrosive rain caused by rainwater falling to the ground through sulfur dioxide gas, turning it into weak sulfuric acid; can damage structures and ecosystems
analytical model : ecosystem model that is created with mathematical formulas to predict the effects of environmental disturbances on ecosystem structure and dynamics
apex consumer : organism at the top of the food chain
assimilation : biomass consumed and assimilated from the previous trophic level after accounting for the energy lost due to incomplete ingestion of food, energy used for respiration, and energy lost as waste
biogeochemical cycle : cycling of mineral nutrients through ecosystems and through the non-living world
biomagnification : increasing concentrations of persistent, toxic substances in organisms at each trophic level, from the primary producers to the apex consumers
biomass : total weight, at the time of measurement, of living or previously living organisms in a unit area within a trophic level
chemoautotroph : organism capable of synthesizing its own food using energy from inorganic molecules
conceptual model : (also, compartment models) ecosystem model that consists of flow charts that show the interactions of different compartments of the living and non-living components of the ecosystem
dead zone : area within an ecosystem in lakes and near the mouths of rivers where large areas of ecosystems are depleted of their normal flora and fauna; these zones can be caused by eutrophication, oil spills, dumping of toxic chemicals, and other human activities
detrital food web : type of food web in which the primary consumers consist of decomposers; these are often associated with grazing food webs within the same ecosystem
ecological pyramid : (also, Eltonian pyramid) graphical representation of different trophic levels in an ecosystem based of organism numbers, biomass, or energy content
ecosystem : community of living organisms and their interactions with their abiotic environment
ecosystem dynamics : study of the changes in ecosystem structure caused by changes in the environment or internal forces
equilibrium : steady state of an ecosystem where all organisms are in balance with their environment and each other
eutrophication : process whereby nutrient runoff causes the excess growth of microorganisms, depleting dissolved oxygen levels and killing ecosystem fauna
fallout : direct deposit of solid minerals on land or in the ocean from the atmosphere
food chain : linear representation of a chain of primary producers, primary consumers, and higher-level consumers used to describe ecosystem structure and dynamics
food web : graphic representation of a holistic, non-linear web of primary producers, primary consumers, and higher-level consumers used to describe ecosystem structure and dynamics
grazing food web : type of food web in which the primary producers are either plants on land or phytoplankton in the water; often associated with a detrital food web within the same ecosystem
gross primary productivity : rate at which photosynthetic primary producers incorporate energy from the sun
holistic ecosystem model : study that attempts to quantify the composition, interactions, and dynamics of entire ecosystems; often limited by economic and logistical difficulties, depending on the ecosystem
hydrosphere : area of the Earth where water movement and storage occurs
mesocosm : portion of a natural ecosystem to be used for experiments
microcosm : re-creation of natural ecosystems entirely in a laboratory environment to be used for experiments
net consumer productivity : energy content available to the organisms of the next trophic level
net primary productivity : energy that remains in the primary producers after accounting for the organismsâ respiration and heat loss
net production efficiency (NPE) : measure of the ability of a trophic level to convert the energy it receives from the previous trophic level into biomass
non-renewable resource : resource, such as fossil fuel, that is either regenerated very slowly or not at all
primary consumer : trophic level that obtains its energy from the primary producers of an ecosystem
primary producer : trophic level that obtains its energy from sunlight, inorganic chemicals, or dead and/or decaying organic material
residence time : measure of the average time an individual water molecule stays in a particular reservoir
resilience (ecological) : speed at which an ecosystem recovers equilibrium after being disturbed
resistance (ecological) : ability of an ecosystem to remain at equilibrium in spite of disturbances
secondary consumer : usually a carnivore that eat primary consumers
simulation model : ecosystem model that is created with computer programs to holistically model ecosystems and to predict the effects of environmental disturbances on ecosystem structure and dynamics
subduction : movement of one tectonic plate beneath another
tertiary consumer : carnivore that eat other carnivores
trophic level : position of a species or group of species in a food chain or a food web
trophic level transfer efficiency (TLTE) : energy transfer efficiency between two successive trophic levels |
https://openstax.org/books/biology/pages/47-chapter-summary | Biodiversity exists at multiple levels of organization and is measured in different ways depending on the goals of those taking the measurements. These measurements include numbers of species, genetic diversity, chemical diversity, and ecosystem diversity. The number of described species is estimated to be 1.5 million with about 17,000 new species being described each year. Estimates for the total number of species on Earth vary but are on the order of 10 million. Biodiversity is negatively correlated with latitude for most taxa, meaning that biodiversity is higher in the tropics. The mechanism for this pattern is not known with certainty, but several plausible hypotheses have been advanced.
Five mass extinctions with losses of more than 50 percent of extant species are observable in the fossil record. Biodiversity recovery times after mass extinctions vary, but have been up to 30 million years. Recent extinctions are recorded in written history and are the basis for one method of estimating contemporary extinction rates. The other method uses measures of habitat loss and species-area relationships. Estimates of contemporary extinction rates vary, but some rates are as high as 500 times the background rate, as determined from the fossil record, and are predicted to rise.
Humans use many compounds that were first discovered or derived from living organisms as medicines: secondary plant compounds, animal toxins, and antibiotics produced by bacteria and fungi. More medicines are expected to be discovered in nature. Loss of biodiversity will impact the number of pharmaceuticals available to humans.
Crop diversity is a requirement for food security, and it is being lost. The loss of wild relatives to crops also threatens breedersâ abilities to create new varieties. Ecosystems provide ecosystem services that support human agriculture: pollination, nutrient cycling, pest control, and soil development and maintenance. Loss of biodiversity threatens these ecosystem services and risks making food production more expensive or impossible. Wild food sources are mainly aquatic, but few are being managed for sustainability. Fisheriesâ ability to provide protein to human populations is threatened when extinction occurs.
Biodiversity may provide important psychological benefits to humans. Additionally, there are moral arguments for the maintenance of biodiversity.
The core threats to biodiversity are human population growth and unsustainable resource use. To date, the most significant causes of extinctions are habitat loss, introduction of exotic species, and overharvesting. Climate change is predicted to be a significant cause of extinctions in the coming century. Habitat loss occurs through deforestation, damming of rivers, and other activities. Overharvesting is a threat particularly to aquatic species, while the taking of bush meat in the humid tropics threatens many species in Asia, Africa, and the Americas. Exotic species have been the cause of a number of extinctions and are especially damaging to islands and lakes. Exotic speciesâ introductions are increasing because of the increased mobility of human populations and growing global trade and transportation. Climate change is forcing range changes that may lead to extinction. It is also affecting adaptations to the timing of resource availability that negatively affects species in seasonal environments. The impacts of climate change are greatest in the arctic. Global warming will also raise sea levels, eliminating some islands and reducing the area of all others.
New technological methods such as DNA barcoding and information processing and accessibility are facilitating the cataloging of the planetâs biodiversity. There is also a legislative framework for biodiversity protection. International treaties such as CITES regulate the transportation of endangered species across international borders. Legislation within individual countries protecting species and agreements on global warming have had limited success; there is at present no international agreement on targets for greenhouse gas emissions. In the United States, the Endangered Species Act protects listed species but is hampered by procedural difficulties and a focus on individual species. The Migratory Bird Act is an agreement between Canada and the United States to protect migratory birds. The non-profit sector is also very active in conservation efforts in a variety of ways.
Conservation preserves are a major tool in biodiversity protection. Presently, 11percent of Earthâs land surface is protected in some way. The science of island biogeography has informed the optimal design of preserves; however, preserves have limitations imposed by political and economic forces. In addition, climate change will limit the effectiveness of preserves in the future. A downside of preserves is that they may lessen the pressure on human societies to function more sustainably outside the preserves.
Habitat restoration has the potential to restore ecosystems to previous biodiversity levels before species become extinct. Examples of restoration include reintroduction of keystone species and removal of dams on rivers. Zoos have attempted to take a more active role in conservation and can have a limited role in captive breeding programs. Zoos also may have a useful role in education. |
https://openstax.org/books/biology/pages/47-key-terms | adaptive radiation : rapid branching through speciation of a phylogenetic tree into many closely related species
biodiversity : variety of a biological system, typically conceived as the number of species, but also applying to genes, biochemistry, and ecosystems
biodiversity hotspot : concept originated by Norman Myers to describe a geographical region with a large number of endemic species and a large percentage of degraded habitat
bush meat : wild-caught animal used as food (typically mammals, birds, and reptiles); usually referring to hunting in the tropics of sub-Saharan Africa, Asia, and the Americas
chemical diversity : variety of metabolic compounds in an ecosystem
chytridiomycosis : disease of amphibians caused by the fungusBatrachochytrium dendrobatidis;thought to be a major cause of the global amphibian decline
DNA barcoding : molecular genetic method for identifying a unique genetic sequence to associate with a species
ecosystem diversity : variety of ecosystems
endemic species : species native to one place
exotic species : (also, invasive species) species that has been introduced to an ecosystem in which it did not evolve
extinction : disappearance of a species from Earth; local extinction is the disappearance of a species from a region
extinction rate : number of species becoming extinct over time, sometimes defined as extinctions per million speciesâyears to make numbers manageable (E/MSY)
genetic diversity : variety of genes in a species or other taxonomic group or ecosystem, the term can refer to allelic diversity or genome-wide diversity
heterogeneity : number of ecological niches
megafauna : large animals
secondary plant compound : compound produced as byproducts of plant metabolic processes that is usually toxic, but is sequestered by the plant to defend against herbivores
species-area relationship : relationship between area surveyed and number of species encountered; typically measured by incrementally increasing the area of a survey and determining the cumulative numbers of species
tragedy of the commons : economic principle that resources held in common will inevitably be overexploited
white-nose syndrome : disease of cave-hibernating bats in the eastern United States and Canada associated with the fungusGeomyces destructans |
https://openstax.org/books/microbiology/pages/1-summary | Microorganisms(ormicrobes) are living organisms that are generally too small to be seen without a microscope.
Throughout history, humans have used microbes to make fermented foods such as beer, bread, cheese, and wine.
Long before the invention of the microscope, some people theorized that infection and disease were spread by living things that were too small to be seen. They also correctly intuited certain principles regarding the spread of disease and immunity.
Antonie van Leeuwenhoek, using a microscope, was the first to actually describe observations of bacteria, in 1675.
During the Golden Age of Microbiology (1857â1914), microbiologists, including Louis Pasteur and Robert Koch, discovered many new connections between the fields of microbiology and medicine.
Carolus Linnaeus developed a taxonomic system for categorizing organisms into related groups.
Binomial nomenclatureassigns organisms Latinized scientific names with a genus and species designation.
Aphylogenetic treeis a way of showing how different organisms are thought to be related to one another from an evolutionary standpoint.
The first phylogenetic tree contained kingdoms for plants and animals; Ernst Haeckel proposed adding kingdom for protists.
Robert Whittakerâs tree contained five kingdoms: Animalia, Plantae, Protista, Fungi, and Monera.
Carl Woese used small subunit ribosomal RNA to create a phylogenetic tree that groups organisms into three domains based on their genetic similarity.
Bergeyâs manuals of determinative and systemic bacteriology are the standard references for identifying and classifying bacteria, respectively.
Bacteria can be identified through biochemical tests, DNA/RNA analysis, and serological testing methods.
Microorganisms are very diverse and are found in all three domains of life: Archaea, Bacteria, and Eukarya.
Archaeaandbacteriaare classified as prokaryotes because they lack a cellular nucleus. Archaea differ from bacteria in evolutionary history, genetics, metabolic pathways, and cell wall and membrane composition.
Archaea inhabit nearly every environment on earth, but no archaea have been identified as human pathogens.
Eukaryotesstudied in microbiology include algae, protozoa, fungi, and helminths.
Algaeare plant-like organisms that can be either unicellular or multicellular, and derive energy via photosynthesis.
Protozoaare unicellular organisms with complex cell structures; most are motile.
Microscopicfungiincludemoldsandyeasts.
Helminthsare multicellular parasitic worms. They are included in the field of microbiology because their eggs and larvae are often microscopic.
Virusesare acellular microorganisms that require a host to reproduce.
The field of microbiology is extremely broad. Microbiologists typically specialize in one of many subfields, but all health professionals need a solid foundation in clinical microbiology. |
https://openstax.org/books/microbiology/pages/2-summary | Light waves interacting with materials may bereflected,absorbed, ortransmitted, depending on the properties of the material.
Light waves can interact with each other (interference) or be distorted by interactions with small objects or openings (diffraction).
Refractionoccurs when light waves change speed and direction as they pass from one medium to another. Differences in therefraction indicesof two materials determine the magnitude of directional changes when light passes from one to the other.
Alensis a medium with a curved surface that refracts and focuses light to produce an image.
Visible light is part of theelectromagnetic spectrum; light waves of different frequencies and wavelengths are distinguished as colors by the human eye.
A prism can separate the colors of white light (dispersion) because different frequencies of light have different refractive indices for a given material.
Fluorescent dyesandphosphorescentmaterials can effectively transform nonvisible electromagnetic radiation into visible light.
The power of a microscope can be described in terms of itsmagnificationandresolution.
Resolution can be increased by shortening wavelength, increasing thenumerical apertureof the lens, or using stains that enhance contrast.
Antonie van Leeuwenhoekis credited with the first observation of microbes, including protists and bacteria, with simple microscopes that he made.
Robert Hookewas the first to describe what we now call cells.
Simple microscopeshave a single lens, whilecompound microscopeshave multiple lenses.
Numerous types of microscopes use various technologies to generate micrographs. Most are useful for a particular type of specimen or application.
Light microscopyuses lenses to focus light on a specimen to produce an image. Commonly used light microscopes includebrightfield,darkfield,phase-contrast,differential interference contrast,fluorescence,confocal, andtwo-photonmicroscopes.
Electron microscopyfocuses electrons on the specimen using magnets, producing much greater magnification than light microscopy. Thetransmission electron microscope (TEM)andscanning electron microscope (SEM)are two common forms.
Scanning probe microscopyproduces images of even greater magnification by measuring feedback from sharp probes that interact with the specimen. Probe microscopes include thescanning tunneling microscope (STM)and theatomic force microscope (AFM).
Samples must be properly prepared for microscopy. This may involvestaining,fixation, and/or cuttingthin sections.
A variety of staining techniques can be used with light microscopy, includingGram staining, acid-fast staining,capsule staining,endospore staining,andflagella staining.
Samples for TEM require very thin sections, whereas samples for SEM require sputter-coating.
Preparation for fluorescence microscopy is similar to that for light microscopy, except that fluorochromes are used. |
https://openstax.org/books/microbiology/pages/3-summary | The theory ofspontaneous generationstates that life arose from nonliving matter. It was a long-held belief dating back to Aristotle and the ancient Greeks.
Experimentation by Francesco Redi in the 17th century presented the first significant evidence refuting spontaneous generation by showing that flies must have access to meat for maggots to develop on the meat. Prominent scientists designed experiments and argued both in support of (John Needham) and against (Lazzaro Spallanzani) spontaneous generation.
Louis Pasteur is credited with conclusively disproving the theory of spontaneous generation with his famous swan-neck flask experiment. He subsequently proposed that âlife only comes from life.â
Although cells were first observed in the 1660s by Robert Hooke,cell theorywas not well accepted for another 200 years. The work of scientists such as Schleiden, Schwann, Remak, and Virchow contributed to its acceptance.
Endosymbiotic theorystates that mitochondria and chloroplasts, organelles found in many types of organisms, have their origins in bacteria. Significant structural and genetic information support this theory.
Themiasma theory of diseasewas widely accepted until the 19th century, when it was replaced by thegerm theory of diseasethanks to the work of Semmelweis, Snow, Pasteur, Lister, and Koch, and others.
Prokaryotic cells differ from eukaryotic cells in that their genetic material is contained in anucleoidrather than a membrane-bound nucleus. In addition, prokaryotic cells generally lack membrane-bound organelles.
Prokaryotic cells of the same species typically share a similarcell morphologyandcellular arrangement.
Most prokaryotic cells have acell wallthat helps the organism maintain cellular morphology and protects it against changes in osmotic pressure.
Outside of the nucleoid, prokaryotic cells may contain extrachromosomal DNA inplasmids.
Prokaryoticribosomesthat are found in the cytoplasm have a size of 70S.
Some prokaryotic cells haveinclusionsthat store nutrients or chemicals for other uses.
Some prokaryotic cells are able to formendosporesthroughsporulationto survive in a dormant state when conditions are unfavorable. Endospores cangerminate, transforming back intovegetative cellswhen conditions improve.
In prokaryotic cells, thecell envelopeincludes aplasma membraneand usually a cell wall.
Bacterial membranes are composed of phospholipids with integral or peripheral proteins. The fatty acid components of these phospholipids are ester-linked and are often used to identify specific types of bacteria. The proteins serve a variety of functions, including transport, cell-to-cell communication, and sensing environmental conditions. Archaeal membranes are distinct in that they are composed of fatty acids that are ether-linked to phospholipids.
Some molecules can move across the bacterial membrane by simple diffusion, but most large molecules must be actively transported through membrane structures using cellular energy.
Prokaryotic cell walls may be composed ofpeptidoglycan(bacteria) orpseudopeptidoglycan(archaea).
Gram-positive bacterial cells are characterized by a thickpeptidoglycanlayer, whereas gram-negative bacterial cells are characterized by a thin peptidoglycan layer surrounded by an outer membrane.
Some prokaryotic cells produceglycocalyxcoatings, such ascapsulesandslime layers, that aid in attachment to surfaces and/or evasion of the host immune system.
Some prokaryotic cells havefimbriaeorpili, filamentous appendages that aid in attachment to surfaces. Pili are also used in the transfer of genetic material between cells.
Some prokaryotic cells use one or moreflagellato move through water.Peritrichousbacteria, which have numerous flagella, userunsandtumblesto move purposefully in the direction of a chemical attractant.
Eukaryotic cells are defined by the presence of anucleuscontaining the DNA genome and bound by anuclear membrane(ornuclear envelope) composed of two lipid bilayers that regulate transport of materials into and out of the nucleus through nuclear pores.
Eukaryotic cell morphologies vary greatly and may be maintained by various structures, including the cytoskeleton, the cell membrane, and/or the cell wall
Thenucleolus, located in the nucleus of eukaryotic cells, is the site of ribosomal synthesis and the first stages of ribosome assembly.
Eukaryotic cells contain80S ribosomesin the rough endoplasmic reticulum (membrane bound-ribosomes) and cytoplasm (free ribosomes). They contain 70s ribosomes in mitochondria and chloroplasts.
Eukaryotic cells have evolved anendomembranesystem, containing membrane-bound organelles involved in transport. These include vesicles, the endoplasmic reticulum, and the Golgi apparatus.
Thesmooth endoplasmic reticulumplays a role in lipid biosynthesis, carbohydrate metabolism, and detoxification of toxic compounds. Therough endoplasmic reticulumcontains membrane-bound 80S ribosomes that synthesize proteins destined for the cell membrane
TheGolgi apparatusprocesses proteins and lipids, typically through the addition of sugar molecules, producing glycoproteins or glycolipids, components of the plasma membrane that are used in cell-to-cell communication.
Lysosomescontain digestive enzymes that break down small particles ingested byendocytosis, large particles or cells ingested byphagocytosis, and damaged intracellular components.
Thecytoskeleton, composed ofmicrofilaments,intermediate filaments, andmicrotubules, provides structural support in eukaryotic cells and serves as a network for transport of intracellular materials.
Centrosomesare microtubule-organizing centers important in the formation of the mitotic spindle in mitosis.
Mitochondriaare the site of cellular respiration. They have two membranes: an outer membrane and an inner membrane with cristae. The mitochondrial matrix, within the inner membrane, contains the mitochondrial DNA, 70S ribosomes, and metabolic enzymes.
The plasma membrane of eukaryotic cells is structurally similar to that found in prokaryotic cells, and membrane components move according to the fluid mosaic model. However, eukaryotic membranes contain sterols, which alter membrane fluidity, as well as glycoproteins and glycolipids, which help the cell recognize other cells and infectious particles.
In addition to active transport and passive transport, eukaryotic cell membranes can take material into the cell viaendocytosis, or expel matter from the cell viaexocytosis.
Cells of fungi, algae, plants, and some protists have acell wall,whereas cells of animals and some protozoans have a stickyextracellular matrixthat provides structural support and mediates cellular signaling.
Eukaryotic flagella are structurally distinct from prokaryotic flagella but serve a similar purpose (locomotion).Ciliaare structurally similar to eukaryotic flagella, but shorter; they may be used for locomotion, feeding, or movement of extracellular particles. |
https://openstax.org/books/microbiology/pages/4-summary | Prokaryotes are unicellular microorganisms whose cells have no nucleus.
Prokaryotes can be found everywhere on our planet, even in the most extreme environments.
Prokaryotes are very flexible metabolically, so they are able to adjust their feeding to the available natural resources.
Prokaryotes live incommunitiesthat interact among themselves and with large organisms that they use as hosts (including humans).
The totality of forms of prokaryotes (particularly bacteria) living on the human body is called the human microbiome, which varies between regions of the body and individuals, and changes over time.
The totality of forms of prokaryotes (particularly bacteria) living in a certain region of the human body (e.g., mouth, throat, gut, eye, vagina) is called themicrobiotaof this region.
Prokaryotes are classified into domains Archaea and Bacteria.
In recent years, the traditional approaches to classification of prokaryotes have been supplemented by approaches based on molecular genetics.
Proteobacteriais a phylum of gram-negative bacteria discovered by Carl Woese in the 1980s based on nucleotide sequence homology.
Proteobacteria are further classified into the classes alpha-, beta-, gamma-, delta- and epsilonproteobacteria, each class having separate orders, families, genera, and species.
Alphaproteobacteriainclude several obligate and facultative intracellular pathogens, including the rickettsias. Some Alphaproteobacteria can convert atmospheric nitrogen to nitrites, making nitrogen usable for other forms of life.
Betaproteobacteriaare a diverse group of bacteria that include human pathogens of the genusNeisseriaand the speciesBordetella pertussis.
Gammaproteobacteriaare the largest and the most diverse group of Proteobacteria. Many are human pathogens that are aerobes or facultative anaerobes. Some Gammaproteobacteria areentericbacteria that may be coliform or noncoliform.Escherichia coli, a member of Gammaproteobacteria, is perhaps the most studied bacterium.
Deltaproteobacteriamake up a small group able to reduce sulfate or elemental sulfur. Some are scavengers and form myxospores, with multicellular fruiting bodies.
Epsilonproteobacteriamake up the smallest group of Proteobacteria. The generaCampylobacterandHelicobacterare human pathogens.
Gram-negative nonproteobacteria include the taxaspirochetes; theChlamydia,Cytophaga,Fusobacterium,Bacteroidesgroup; Planctomycetes; and many representatives ofphototrophic bacteria.
Spirochetes are motile, spiral bacteria with a long, narrow body; they are difficult or impossible to culture.
Several genera of spirochetes contain human pathogens that cause such diseases as syphilis and Lyme disease.
Cytophaga,Fusobacterium, andBacteroidesare classified together as a phylum called theCFB group. They are rod-shaped anaerobic organoheterotrophs and avid fermenters.Cytophagaare aquatic bacteria with the gliding motility.Fusobacteriainhabit the human mouth and may cause severe infectious diseases.Bacteroidesare present in vast numbers in the human gut, most of them being mutualistic but some are pathogenic.
Planctomycetes are aquatic bacteria that reproduce by budding; they may form large colonies, and develop a holdfast.
Phototrophic bacteria are not a taxon but, rather, a group categorized by their ability to use the energy of sunlight. They include Proteobacteria and nonproteobacteria, as well as sulfur and nonsulfur bacteria colored purple or green.
Sulfur bacteria perform anoxygenic photosynthesis, using sulfur compounds as donors of electrons, whereas nonsulfur bacteria use organic compounds (succinate, malate) as donors of electrons.
Some phototrophic bacteria are able to fix nitrogen, providing the usable forms of nitrogen to other organisms.
Cyanobacteriaare oxygen-producing bacteria thought to have played a critical role in the forming of the earthâs atmosphere.
Gram-positive bacteria are a very large and diverse group of microorganisms. Understanding their taxonomy and knowing their unique features is important for diagnostics and treatment of infectious diseases.
Gram-positive bacteria are classified intohigh G+C gram-positiveandlow G+C gram-positivebacteria, based on the prevalence of guanine and cytosine nucleotides in their genome
Actinobacteria is the taxonomic name of the class of high G+C gram-positive bacteria. This class includes the generaActinomyces, Arthrobacter, Corynebacterium, Frankia, Gardnerella, Micrococcus, Mycobacterium, Nocardia,Cutibacterium, Rhodococcus,andStreptomyces. Some representatives of these genera are used in industry; others are human or animal pathogens.
Examples of high G+C gram-positive bacteria that are human pathogens includeMycobacteriumtuberculosis, which causes tuberculosis;M. leprae, which causes leprosy (Hansenâs disease); andCorynebacteriumdiphtheriae, which causes diphtheria.
Clostridiaspp. are low G+C gram-positive bacteria that are generally obligate anaerobes and can form endospores. Pathogens in this genus includeC.perfringens(gas gangrene),C. tetani(tetanus), andC. botulinum(botulism).
Lactobacillales include the generaEnterococcus,Lactobacillus,Leuconostoc, andStreptococcus. Streptococcusis responsible for many human diseases, including pharyngitis (strep throat), scarlet fever, rheumatic fever, glomerulonephritis, pneumonia, and other respiratory infections.
Bacilli is a taxonomic class of low G+C gram-positive bacteria that include rod-shaped and coccus-shaped species, including the generaBacillusandStaphylococcus.B. anthraciscauses anthrax,B. cereusmay cause opportunistic infections of the gastrointestinal tract, andS.aureusstrains can cause a wide range of infections and diseases, many of which are highly resistant to antibiotics.
Mycoplasmaspp. are very small,pleomorphiclow G+C gram-positive bacteria that lack cell walls.M. pneumoniaecauses atypical pneumonia.
Deeply branching bacteriaare phylogenetically the most ancient forms of life, being the closest to the last universal common ancestor.
Deeply branching bacteria include many species that thrive in extreme environments that are thought to resemble conditions on earth billions of years ago
Deeply branching bacteria are important for our understanding of evolution; some of them are used in industry
Archaeaare unicellular, prokaryotic microorganisms that differ from bacteria in their genetics, biochemistry, and ecology.
Some archaea are extremophiles, living in environments with extremely high or low temperatures, or extreme salinity.
Only archaea are known to produce methane. Methane-producing archaea are calledmethanogens.
Halophilic archaea prefer a concentration of salt close to saturation and perform photosynthesis using bacteriorhodopsin.
Some archaea, based on fossil evidence, are among the oldest organisms on earth.
Archaea do not live in great numbers in human microbiomes and are not known to cause disease. |
https://openstax.org/books/microbiology/pages/5-summary | Protistsare a diverse,polyphyleticgroup of eukaryotic organisms.
Protists may be unicellular or multicellular. They vary in how they get their nutrition, morphology, method of locomotion, and mode of reproduction.
Important structures of protists includecontractile vacuoles, cilia, flagella,pellicles, and pseudopodia; some lack organelles such as mitochondria.
Taxonomy of protists is changing rapidly as relationships are reassessed using newer techniques.
The protists include important pathogens and parasites.
Helminth parasites are included within the study of microbiology because they are often identified by looking for microscopic eggs and larvae.
The two major groups of helminth parasites are the roundworms (Nematoda) and the flatworms (Platyhelminthes).
Nematodes are common intestinal parasites often transmitted through undercooked foods, although they are also found in other environments.
Platyhelminths includetapewormsandflukes, which are often transmitted through undercooked meat.
The fungi include diverse saprotrophic eukaryotic organisms with chitin cell walls
Fungi can be unicellular or multicellular; some (like yeast) and fungal spores are microscopic, whereas some are large and conspicuous
Reproductive types are important in distinguishing fungal groups
Medically important species exist in the four fungal groups Zygomycota, Ascomycota, Basidiomycota, and Microsporidia
Members of Zygomycota, Ascomycota, and Basidiomycota produce deadly toxins
Important differences in fungal cells, such as ergosterols in fungal membranes, can be targets for antifungal medications, but similarities between human and fungal cells make it difficult to find targets for medications and these medications often have toxic adverse effects
Algae are a diverse group of photosynthetic eukaryotic protists
Algae may be unicellular or multicellular
Large, multicellular algae are called seaweeds but are not plants and lack plant-like tissues and organs
Although algae have little pathogenicity, they may be associated with toxicalgal bloomsthat can and aquatic wildlife and contaminate seafood with toxins that cause paralysis
Algae are important for producingagar, which is used as a solidifying agent in microbiological media, andcarrageenan, which is used as a solidifying agent
Lichensare a symbiotic association between a fungus and an algae or a cyanobacterium
The symbiotic association found in lichens is currently considered to be a controlledparasitism, in which the fungus benefits and the algae or cyanobacterium is harmed
Lichens are slow growing and can live for centuries in a variety of habitats
Lichens are environmentally important, helping to create soil, providing food, and acting as indicators of air pollution |
https://openstax.org/books/microbiology/pages/6-summary | Viruses are generally ultramicroscopic, typically from 20 nm to 900 nm in length. Some large viruses have been found.
Virionsare acellular and consist of a nucleic acid, DNA or RNA, but not both, surrounded by a proteincapsid. There may also be a phospholipid membrane surrounding the capsid.
Viruses are obligate intracellular parasites.
Viruses are known to infect various types of cells found in plants, animals, fungi, protists, bacteria, and archaea. Viruses typically have limitedhost rangesand infect specific cell types.
Viruses may havehelical,polyhedral,orcomplexshapes.
Classification of viruses is based on morphology, type of nucleic acid, host range, cell specificity, and enzymes carried within the virion.
Like other diseases, viral diseases are classified using ICD codes.
Many viruses target specific hosts or tissues. Some may have more than one host.
Many viruses follow several stages to infect host cells. These stages includeattachment, penetration, uncoating, biosynthesis, maturation,andrelease.
Bacteriophages have alyticorlysogeniccycle. The lytic cycle leads to the death of the host, whereas the lysogenic cycle leads to integration of phage into the host genome.
Bacteriophages inject DNA into the host cell, whereas animal viruses enter by endocytosis or membrane fusion.
Animal viruses can undergolatency, similar to lysogeny for a bacteriophage.
The majority of plant viruses are positive-strand ssRNA and can undergo latency, chronic, or lytic infection, as observed for animal viruses.
The growth curve of bacteriophage populations is aone-step multiplication curveand not a sigmoidal curve, as compared to the bacterial growth curve.
Bacteriophages transfer genetic information between hosts using eithergeneralizedorspecialized transduction.
Viral cultivation requires the presence of some form of host cell (whole organism, embryo, or cell culture).
Viruses can be isolated from samples by filtration.
Viral filtrate is a rich source of released virions.
Bacteriophages are detected by presence of clearplaqueson bacterial lawn.
Animal and plant viruses are detected bycytopathic effects, molecular techniques (PCR, RT-PCR), enzyme immunoassays, and serological assays (hemagglutination assay, hemagglutination inhibition assay).
Other acellular agents such asviroids,virusoids, andprionsalso cause diseases. Viroids consist of small, naked ssRNAs that cause diseases in plants. Virusoids are ssRNAs that require other helper viruses to establish an infection. Prions are proteinaceous infectious particles that causetransmissible spongiform encephalopathies.
Prions are extremely resistant to chemicals, heat, and radiation.
There are no treatments for prion infection. |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.