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activation energy : energy necessary for reactions to occur | https://openstax.org/books/biology/pages/6-key-terms |
active site : specific region of the enzyme to which the substrate binds | https://openstax.org/books/biology/pages/6-key-terms |
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 | https://openstax.org/books/biology/pages/6-key-terms |
anabolic : (also, anabolism) pathways that require an input of energy to synthesize complex molecules from simpler ones | https://openstax.org/books/biology/pages/6-key-terms |
ATP : adenosine triphosphate, the cellâs energy currency | https://openstax.org/books/biology/pages/6-key-terms |
bioenergetics : study of energy flowing through living systems | https://openstax.org/books/biology/pages/6-key-terms |
catabolic : (also, catabolism) pathways in which complex molecules are broken down into simpler ones | https://openstax.org/books/biology/pages/6-key-terms |
chemical energy : potential energy in chemical bonds that is released when those bonds are broken | https://openstax.org/books/biology/pages/6-key-terms |
coenzyme : small organic molecule, such as a vitamin or its derivative, which is required to enhance the activity of an enzyme | https://openstax.org/books/biology/pages/6-key-terms |
cofactor : inorganic ion, such as iron and magnesium ions, required for optimal regulation of enzyme activity | https://openstax.org/books/biology/pages/6-key-terms |
competitive inhibition : type of inhibition in which the inhibitor competes with the substrate molecule by binding to the active site of the enzyme | https://openstax.org/books/biology/pages/6-key-terms |
denature : process that changes the natural properties of a substance | https://openstax.org/books/biology/pages/6-key-terms |
endergonic : describes chemical reactions that require energy input | https://openstax.org/books/biology/pages/6-key-terms |
enthalpy : total energy of a system | https://openstax.org/books/biology/pages/6-key-terms |
entropy (S) : measure of randomness or disorder within a system | https://openstax.org/books/biology/pages/6-key-terms |
exergonic : describes chemical reactions that release free energy | https://openstax.org/books/biology/pages/6-key-terms |
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 | https://openstax.org/books/biology/pages/6-key-terms |
free energy : Gibbs free energy is the usable energy, or energy that is available to do work. | https://openstax.org/books/biology/pages/6-key-terms |
heat : energy energy transferred from one system to another that is not work (energy of the motion of molecules or particles) | https://openstax.org/books/biology/pages/6-key-terms |
heat energy : total bond energy of reactants or products in a chemical reaction | https://openstax.org/books/biology/pages/6-key-terms |
induced fit : dynamic fit between the enzyme and its substrate, in which both components modify their structures to allow for ideal binding | https://openstax.org/books/biology/pages/6-key-terms |
kinetic energy : type of energy associated with objects or particles in motion | https://openstax.org/books/biology/pages/6-key-terms |
metabolism : all the chemical reactions that take place inside cells, including anabolism and catabolism | https://openstax.org/books/biology/pages/6-key-terms |
phosphoanhydride bond : bond that connects phosphates in an ATP molecule | https://openstax.org/books/biology/pages/6-key-terms |
potential energy : type of energy that has the potential to do work; stored energy | https://openstax.org/books/biology/pages/6-key-terms |
substrate : molecule on which the enzyme acts | https://openstax.org/books/biology/pages/6-key-terms |
thermodynamics : study of energy and energy transfer involving physical matter | https://openstax.org/books/biology/pages/6-key-terms |
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/6-key-terms |
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. | https://openstax.org/books/biology/pages/7-chapter-summary |
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. | https://openstax.org/books/biology/pages/7-chapter-summary |
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. | https://openstax.org/books/biology/pages/7-chapter-summary |
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. | https://openstax.org/books/biology/pages/7-chapter-summary |
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. | https://openstax.org/books/biology/pages/7-chapter-summary |
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. | https://openstax.org/books/biology/pages/7-chapter-summary |
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. | https://openstax.org/books/biology/pages/7-chapter-summary |
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-chapter-summary |
acetyl CoA : combination of an acetyl group derived from pyruvic acid and coenzyme A, which is made from pantothenic acid (a B-group vitamin) | https://openstax.org/books/biology/pages/7-key-terms |
aerobic respiration : process in which organisms convert energy in the presence of oxygen | https://openstax.org/books/biology/pages/7-key-terms |
anaerobic : process that does not use oxygen | https://openstax.org/books/biology/pages/7-key-terms |
anaerobic cellular respiration : process in which organisms convert energy for their use in the absence of oxygen | https://openstax.org/books/biology/pages/7-key-terms |
ATP synthase : (also, F1F0 ATP synthase) membrane-embedded protein complex that adds a phosphate to ADP with energy from protons diffusing through it | https://openstax.org/books/biology/pages/7-key-terms |
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 | https://openstax.org/books/biology/pages/7-key-terms |
citric acid cycle : (also, Krebs cycle) series of enzyme-catalyzed chemical reactions of central importance in all living cells | https://openstax.org/books/biology/pages/7-key-terms |
dephosphorylation : removal of a phosphate group from a molecule | https://openstax.org/books/biology/pages/7-key-terms |
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 | https://openstax.org/books/biology/pages/7-key-terms |
GLUT protein : integral membrane protein that transports glucose | https://openstax.org/books/biology/pages/7-key-terms |
glycolysis : process of breaking glucose into two three-carbon molecules with the production of ATP and NADH | https://openstax.org/books/biology/pages/7-key-terms |
isomerase : enzyme that converts a molecule into its isomer | https://openstax.org/books/biology/pages/7-key-terms |
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 | https://openstax.org/books/biology/pages/7-key-terms |
oxidative phosphorylation : production of ATP using the process of chemiosmosis and oxygen | https://openstax.org/books/biology/pages/7-key-terms |
phosphorylation : addition of a high-energy phosphate to a compound, usually a metabolic intermediate, a protein, or ADP | https://openstax.org/books/biology/pages/7-key-terms |
prosthetic group : (also, prosthetic cofactor) molecule bound to a protein that facilitates the function of the protein | https://openstax.org/books/biology/pages/7-key-terms |
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 | https://openstax.org/books/biology/pages/7-key-terms |
redox reaction : chemical reaction that consists of the coupling of an oxidation reaction and a reduction reaction | https://openstax.org/books/biology/pages/7-key-terms |
substrate-level phosphorylation : production of ATP from ADP using the excess energy from a chemical reaction and a phosphate group from a reactant | https://openstax.org/books/biology/pages/7-key-terms |
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 | https://openstax.org/books/biology/pages/7-key-terms |
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/7-key-terms |
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. | https://openstax.org/books/biology/pages/8-chapter-summary |
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. | https://openstax.org/books/biology/pages/8-chapter-summary |
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. | https://openstax.org/books/biology/pages/8-chapter-summary |
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-chapter-summary |
absorption spectrum : range of wavelengths of electromagnetic radiation absorbed by a given substance | https://openstax.org/books/biology/pages/8-key-terms |
antenna protein : pigment molecule that directly absorbs light and transfers the energy absorbed to other pigment molecules | https://openstax.org/books/biology/pages/8-key-terms |
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 | https://openstax.org/books/biology/pages/8-key-terms |
carbon fixation : process of converting inorganic CO2gas into organic compounds | https://openstax.org/books/biology/pages/8-key-terms |
carotenoid : photosynthetic pigment that functions to dispose of excess energy | https://openstax.org/books/biology/pages/8-key-terms |
chemoautotroph : organism that can build organic molecules using energy derived from inorganic chemicals instead of sunlight | https://openstax.org/books/biology/pages/8-key-terms |
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 | https://openstax.org/books/biology/pages/8-key-terms |
chlorophyllb : accessory pigment that absorbs blue and red-orange light and consequently has a yellowish-green tint | https://openstax.org/books/biology/pages/8-key-terms |
chloroplast : organelle in which photosynthesis takes place | https://openstax.org/books/biology/pages/8-key-terms |
cytochrome complex : group of reversibly oxidizable and reducible proteins that forms part of the electron transport chain between photosystem II and photosystem I | https://openstax.org/books/biology/pages/8-key-terms |
electromagnetic spectrum : range of all possible frequencies of radiation | https://openstax.org/books/biology/pages/8-key-terms |
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 | https://openstax.org/books/biology/pages/8-key-terms |
granum : stack of thylakoids located inside a chloroplast | https://openstax.org/books/biology/pages/8-key-terms |
heterotroph : organism that consumes organic substances or other organisms for food | https://openstax.org/books/biology/pages/8-key-terms |
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 | https://openstax.org/books/biology/pages/8-key-terms |
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) | https://openstax.org/books/biology/pages/8-key-terms |
light-independent reaction : second stage of photosynthesis, though which carbon dioxide is used to build carbohydrate molecules using energy from ATP and NADPH | https://openstax.org/books/biology/pages/8-key-terms |
mesophyll : middle layer of chlorophyll-rich cells in a leaf | https://openstax.org/books/biology/pages/8-key-terms |
P680 : reaction center of photosystem II | https://openstax.org/books/biology/pages/8-key-terms |
P700 : reaction center of photosystem I | https://openstax.org/books/biology/pages/8-key-terms |
photoact : ejection of an electron from a reaction center using the energy of an absorbed photon | https://openstax.org/books/biology/pages/8-key-terms |
photoautotroph : organism capable of producing its own organic compounds from sunlight | https://openstax.org/books/biology/pages/8-key-terms |
photon : distinct quantity or âpacketâ of light energy | https://openstax.org/books/biology/pages/8-key-terms |
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 | https://openstax.org/books/biology/pages/8-key-terms |
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) | https://openstax.org/books/biology/pages/8-key-terms |
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 | https://openstax.org/books/biology/pages/8-key-terms |
pigment : molecule that is capable of absorbing certain wavelengths of light and reflecting others (which accounts for its color) | https://openstax.org/books/biology/pages/8-key-terms |
primary electron acceptor : pigment or other organic molecule in the reaction center that accepts an energized electron from the reaction center | https://openstax.org/books/biology/pages/8-key-terms |
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 | https://openstax.org/books/biology/pages/8-key-terms |
reduction : gain of electron(s) by an atom or molecule | https://openstax.org/books/biology/pages/8-key-terms |
spectrophotometer : instrument that can measure transmitted light and compute the absorption | https://openstax.org/books/biology/pages/8-key-terms |
stoma : opening that regulates gas exchange and water evaporation between leaves and the environment, typically situated on the underside of leaves | https://openstax.org/books/biology/pages/8-key-terms |
stroma : fluid-filled space surrounding the grana inside a chloroplast where the light-independent reactions of photosynthesis take place | https://openstax.org/books/biology/pages/8-key-terms |
thylakoid : disc-shaped, membrane-bound structure inside a chloroplast where the light-dependent reactions of photosynthesis take place; stacks of thylakoids are called grana | https://openstax.org/books/biology/pages/8-key-terms |
thylakoid lumen : aqueous space bound by a thylakoid membrane where protons accumulate during light-driven electron transport | https://openstax.org/books/biology/pages/8-key-terms |
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/8-key-terms |
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. | https://openstax.org/books/biology/pages/9-chapter-summary |
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. | https://openstax.org/books/biology/pages/9-chapter-summary |
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). | https://openstax.org/books/biology/pages/9-chapter-summary |
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