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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 |
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