Unit 3 Beta

Cellular Energetics: the one-page sheet

3.1 Enzyme Structure

Enzymes are biological catalysts, almost all of them proteins. Folding gives each enzyme an active site whose shape and pattern of charged, polar and nonpolar side chains match one substrate, or a few similar ones: that is specificity. The substrate binds by weak attractions to form the enzyme-substrate complex, and the active site shifts to grip it (induced fit). The products are released and the unchanged enzyme can act again. Anything that changes the active site's shape or charges, from heat to a single swapped amino acid, changes what the enzyme can bind.

An enzyme is a catalyst: it speeds up a reaction and comes out unchanged. Almost all enzymes are proteins; a few are RNA molecules.
The active site is a small part of a large protein, but the whole protein's folding creates it. A change far from the active site can still matter if it changes how the protein folds.
Specificity needs two matches: shape (the substrate fits) and chemistry (charges and polarity attract rather than repel). Data that change one but not the other let you tell them apart.
Induced fit: the active site is flexible. Binding the right substrate changes the enzyme's shape slightly; the old lock-and-key picture treated it as rigid.

The folded protein has a pocket or groove on its surface, the active site, lined by a particular set of side chains. A molecule binds well only if its shape and charges are complementary to that pattern. That molecule is the enzyme's substrate, and the match is called enzyme specificity. An enzyme-substrate complex forms, and the active site shifts slightly to grip the substrate more tightly: induced fit. Those bonds break or form, the substrate becomes product, and the product no longer fits as well, so it is released. Its active site is free to bind another substrate molecule, over and over: the enzyme is a catalyst. The substrate no longer fits or is no longer attracted, so little or no product is made.

catalyst: A substance that speeds up a chemical reaction and comes out of it unchanged, so it can act again. Enzymes are biological catalysts; most are proteins.
substrate: The molecule an enzyme acts on. It binds in the enzyme's active site and is changed into one or more products.
active site: The pocket or groove on an enzyme where the substrate binds and the reaction happens. Its shape and the charges and polarity of the side chains lining it come from how the protein folds.
enzyme specificity: An enzyme's ability to act on one substrate, or a small group of similar ones, because only those molecules match the shape and chemical character (charge, polarity) of its active site.
enzyme-substrate complex: The short-lived unit formed when a substrate is bound in an enzyme's active site, held by weak attractions such as hydrogen bonds and ionic attractions, before it is changed into products.
induced fit: The model in which an enzyme's active site changes shape slightly as the substrate binds, gripping it more tightly. It refines the older lock-and-key model, which pictured a rigid active site with a fixed shape.

3.2 Enzyme Catalysis

Every reaction has an activation energy: the energy reactants must absorb to reach the unstable transition state before becoming products. Enzymes lower the activation energy by holding the substrate in the active site in a strained, well-oriented position next to helpful side chains. More molecules can then react at the same temperature, so the reaction rate, measured as product made or substrate used per unit time, rises. The enzyme does not change the reactants, the products or the energy released, and it comes out unchanged, so it is used again and again.

Activation energy is the hill between reactants and products. A reaction can release energy overall and still be slow if its hill is high.
Enzymes speed reactions by lowering the activation energy. They do not add energy, change the products, or change how much energy the reaction releases.
Heat and enzymes both speed reactions, but differently: heat gives more molecules enough energy to clear the same hill, while an enzyme lowers the hill.
Reaction rate is product formed (or substrate used) per unit time. On a graph of product against time it is the slope; the steepest part, at the start, is the initial rate.

The molecules must first absorb energy and pass through an unstable, high-energy arrangement: the transition state. The energy needed to get there is the activation energy. Without a catalyst, many reactions that release energy still run extremely slowly. The transition state is easier to reach: the activation energy is lower. The reaction rate rises, often by millions of times. The same products form and the same amount of energy is released or absorbed; the reaction just happens faster. It binds another substrate: enzymes are not used up, so a little enzyme processes a lot of substrate.

activation energy: The energy reactants must absorb before a reaction can start: the climb from the reactants' energy up to the transition state. Enzymes speed reactions by lowering it.
transition state: The unstable, highest-energy arrangement that reactants pass through on the way to becoming products, when old bonds are partly broken and new ones partly formed. An enzyme's active site holds the substrate in a way that makes this state easier to reach.
enzymes are reusable: Enzymes are not used up by the reactions they catalyze. After the products are released the enzyme has its original structure and can bind another substrate, so a small amount of enzyme can process a large amount of substrate.
reaction rate: How fast a reaction goes, measured as the amount of product formed, or of substrate used up, per unit of time (for example µmol per minute or mL of gas per second). Often called enzyme activity when an enzyme catalyzes the reaction.
energy diagram: A graph of the energy of the reacting molecules (vertical axis) as the reaction proceeds (horizontal axis). The height of the hill above the reactants is the activation energy; the difference between reactants and products is the energy released or absorbed.

3.3 Environmental Impacts on Enzyme Function

An enzyme's rate depends on its surroundings. Warming speeds collisions until heat denatures the enzyme past its optimal temperature; pH away from the optimum changes side-chain charges and, at extremes, denatures it. More substrate raises the rate until the active sites are saturated, after which the enzyme amount limits the rate. Inhibitors lower the rate: competitive ones occupy the active site and can be outcompeted by substrate, noncompetitive ones bind an allosteric site and lower the maximum, and irreversible ones bind for good. Many enzymes need a cofactor to work.

Each enzyme has an optimal temperature and optimal pH that match where it works: about 37 °C for most human enzymes, pH 2 for stomach pepsin, pH 8 for intestinal trypsin.
Cold slows an enzyme without unfolding it: warm it up and the rate returns. Heat past the optimum unfolds it; mild damage may reverse (renaturation), severe damage usually does not.
On a rate-against-substrate graph, the rising part is limited by substrate and the plateau by enzyme. To raise the plateau, add enzyme.
Competitive: same maximum, reached at higher substrate. Noncompetitive: lower maximum. Irreversible inhibitors bind for good. Many enzymes also need a cofactor, such as a metal ion.

They meet more often and more of those collisions have enough energy to react, so the rate rises. The active site loses its shape (denaturation), so the rate falls steeply. Side-chain charges change, so attractions inside the protein and with the substrate change, and the rate falls; extreme pH denatures the enzyme. The rate rises, then levels off at a maximum once nearly all active sites are busy (saturation). Now the amount of enzyme is the limiting factor. Fewer active sites hold substrate; adding much more substrate outcompetes the inhibitor, so the same maximum rate is eventually reached. Those enzyme molecules work poorly whatever the substrate level, so extra substrate cannot restore the rate and the maximum is lower.

optimal temperature: The temperature or pH at which an enzyme works fastest. Away from it the rate falls: below the optimal temperature because molecules move more slowly, above it because the enzyme starts to denature; on either side of the optimal pH because side-chain charges change.
molecular collisions: Meetings between moving molecules, such as a substrate and an enzyme's active site. Higher temperature and higher concentrations make collisions more frequent, so the reaction rate rises until something else limits it.
substrate concentration: As substrate concentration rises, the reaction rate rises and then levels off at a maximum rate (Vmax) when nearly every active site is occupied at any moment. Past that saturation point, adding substrate no longer speeds the reaction.
enzyme concentration: The amount of enzyme per volume. With plenty of substrate, the rate is proportional to enzyme concentration: twice the enzyme, twice the active sites, about twice the rate.
limiting factor: The one condition in short supply that holds a rate down at a given moment. Increasing it raises the rate; increasing anything else does not. On an enzyme rate curve, substrate limits the rising part and enzyme amount limits the plateau.
enzyme inhibitor: A molecule that binds an enzyme and lowers its reaction rate. Inhibitors may compete for the active site (competitive) or bind elsewhere and change the enzyme's shape (noncompetitive); most bind reversibly, some permanently.
competitive inhibitor: An inhibitor that resembles the substrate and binds the active site, blocking the substrate. Because the two compete, enough extra substrate outcompetes it: the maximum rate is still reached, but at a higher substrate concentration.
allosteric regulation: Control of an enzyme by a molecule that binds an allosteric site (a place on the enzyme other than the active site) and changes the enzyme's shape. An allosteric inhibitor shifts the active site to a less active shape; a molecule that speeds the enzyme up shifts it to a more active one.
noncompetitive inhibitor: An inhibitor that binds an enzyme away from the active site (an allosteric site) and changes the enzyme's shape so the active site works poorly. Extra substrate cannot undo it, so the maximum rate is lowered.
irreversible inhibitor: An inhibitor that binds an enzyme permanently, usually by a covalent bond, so the enzyme molecule never works again. Activity returns only when the cell makes new enzyme. Examples include many nerve-gas poisons and the antibiotic penicillin.
cofactor: A non-protein helper an enzyme needs to work, often bound in the active site. Inorganic cofactors are metal ions such as zinc, iron or magnesium; organic cofactors, called coenzymes, are often made from vitamins.
renaturation: A denatured protein folding back into its working shape when normal conditions return. It happens for some proteins after mild heating or a pH change; severe or long denaturation is usually permanent.

3.4 Cellular Energy

Energy is never created or destroyed (first law), and each conversion releases some as unusable heat, raising disorder (second law). So living things need a constant energy input to stay ordered; without it they die. Cells organize their reactions into enzyme-run metabolic pathways. Exergonic reactions, such as breaking down food, release energy that is used to make ATP. ATP hydrolysis is then coupled to endergonic processes, usually by phosphorylating a reactant or protein, so the combined process releases energy and can go. Electrons moving in redox reactions carry much of this energy, and feedback inhibition shuts a pathway down when its product is plentiful.

Exergonic reactions release energy (ΔG negative); endergonic reactions need energy (ΔG positive). An endergonic reaction goes only if it is coupled to an exergonic one so the total ΔG is negative.
ATP is an energy carrier, not a long-term store. Fats and starch store energy; ATP moves it from where it is released to where it is used, minutes later.
In a redox reaction, one molecule loses electrons (oxidized) and another gains them (reduced). Breaking food down moves electrons from fuel molecules toward oxygen, releasing energy.
Metabolic pathways are chains of enzymes. Catabolic pathways break molecules down and release energy; anabolic pathways build them and use it.

A cell cannot make its own energy; it must take in energy, as food or sunlight, and convert it. Building and keeping the cell's order uses energy up, so living things need a constant energy input. Part of the released energy is captured by adding a phosphate to ADP, making ATP. Its energy can drive an endergonic process if the two are coupled, usually by transferring ATP's phosphate to a reactant or a protein (phosphorylation). The coupled process releases energy overall, so it goes: building molecules, pumping ions, moving muscle. It binds an allosteric site on the first enzyme and slows the whole pathway (feedback inhibition), so raw materials and energy are not wasted.

first law of thermodynamics: Energy cannot be created or destroyed, only changed from one form to another (conservation of energy). Cells do not make energy; they convert energy from food or sunlight into other forms.
second law of thermodynamics: Every energy conversion turns some energy into heat that can no longer do work, so the disorder (entropy) of the universe increases. No conversion in a cell is 100% efficient.
energy input and order: Living things are highly ordered, and staying ordered works against the second law. They need a constant input of energy to build and repair molecules and keep gradients across membranes; without it, order is lost and the organism dies.
metabolism: All the chemical reactions in a cell or organism, organized into metabolic pathways: chains of steps, each catalyzed by its own enzyme, where the product of one step is the reactant of the next. Catabolic pathways break molecules down and release energy; anabolic pathways build molecules and use energy.
exergonic reaction: An exergonic reaction releases energy: its products hold less free energy than its reactants (ΔG is negative), and it can occur without an energy input. An endergonic reaction absorbs energy (ΔG is positive) and occurs only if energy is supplied, usually by coupling it to an exergonic reaction.
ATP hydrolysis: Breaking the bond to ATP's last phosphate with water: ATP + H₂O → ADP + inorganic phosphate (Pi), releasing about 30 kJ per mole under standard conditions. Cells remake ATP from ADP and Pi using energy from food, so the same molecules cycle over and over (the ATP cycle).
energy coupling: Using the energy released by an exergonic reaction to drive an endergonic one, so that the combined process releases energy overall. In cells the exergonic partner is usually ATP hydrolysis.
phosphorylation: Adding a phosphate group to a molecule, often taken from ATP. Phosphorylation can make a reactant less stable and more reactive, or change a protein's shape and so switch it on or off. Removing the phosphate is dephosphorylation.
redox reaction: A reaction in which electrons move from one molecule to another. The molecule that loses electrons is oxidized (oxidation); the one that gains them is reduced (reduction). In cells, electrons often move together with hydrogen atoms, and electrons moving toward oxygen release energy.
feedback inhibition: Control of a metabolic pathway by its own end product: when the end product builds up, it binds an allosteric site on an enzyme early in the pathway, usually the first, and slows the whole pathway, saving raw materials and energy.

3.5 Photosynthesis

Photosynthesis stores light energy in sugar. In the thylakoid membranes, pigments in photosystems II and I absorb light and energize electrons. Photosystem II replaces its electrons by splitting water, releasing O₂. The electrons flow down an electron transport chain that pumps H⁺ into the thylakoid space, then end up in NADPH. The H⁺ gradient drives ATP synthase to make ATP. In the stroma, the Calvin cycle uses that ATP and NADPH to fix CO₂ into sugar. This process began in cyanobacteria, the ancestors of chloroplasts, and filled the atmosphere with oxygen.

Overall: 6 CO₂ + 6 H₂O + light energy → C₆H₁₂O₆ + 6 O₂. The O₂ comes from water; the carbon in sugar comes from CO₂.
Two stages, two places: the light reactions in the thylakoid membranes make ATP, NADPH and O₂; the Calvin cycle in the stroma uses ATP and NADPH to fix CO₂. Each needs the other's products.
Pigments absorb some wavelengths: chlorophylls absorb blue and red and reflect green. An action spectrum that is high where accessory pigments absorb shows they pass energy on.
Photosynthesis that releases O₂ first arose in cyanobacteria. Chloroplasts descend from cyanobacteria taken in by an ancestral eukaryote, and their oxygen built up the atmosphere.

An electron in a special chlorophyll a is raised to high energy and handed to an acceptor molecule. It takes replacement electrons from water, splitting it: 2 H₂O → 4 H⁺ + 4 e⁻ + O₂. The O₂ is released and the H⁺ stay in the thylakoid space. The cytochrome complex uses that energy to pump H⁺ from the stroma into the thylakoid space, building a proton gradient. They are passed to NADP⁺, which is reduced to NADPH in the stroma. Their flow turns ATP synthase, which joins ADP and Pi into ATP in the stroma (chemiosmosis). CO₂ is reduced to sugar, and ADP, Pi and NADP⁺ go back to the light reactions to be recharged.

autotroph: An organism that makes its own organic molecules from carbon dioxide, usually using energy from sunlight (plants, algae, cyanobacteria). A heterotroph gets organic molecules by eating other organisms or their products.
cyanobacteria: Photosynthetic bacteria that split water and release oxygen. Ancient cyanobacteria were the first organisms to do this kind of photosynthesis, and chloroplasts descend from cyanobacteria taken in by an early eukaryotic cell.
light energy: Energy carried by light, which travels in packets called photons. Each wavelength of light carries a different amount of energy per photon; visible light runs from about 400 nm (violet) to 700 nm (red).
pigment: A molecule that absorbs some wavelengths of light and reflects others. Chlorophyll a is the main photosynthetic pigment; chlorophyll b and carotenoids are accessory pigments that absorb other wavelengths and pass the energy to chlorophyll a. Leaves look green because chlorophylls reflect green light.
absorption spectrum: A graph of how strongly a pigment absorbs each wavelength of light. An action spectrum instead shows how fast photosynthesis runs at each wavelength; comparing the two shows which pigments drive photosynthesis.
photosystem: A cluster of proteins and pigments in the thylakoid membrane. Its light-harvesting complex gathers light energy and passes it to the reaction center, where a special chlorophyll a loses an excited electron. Photosystem II (P680) acts first and splits water; photosystem I (P700) acts second and passes electrons toward NADP+.
light reactions: The first stage of photosynthesis, in the thylakoid membranes: light energy splits water, releases O₂, drives electrons along an electron transport chain, and makes ATP and NADPH for the Calvin cycle.
water splitting: Splitting water at photosystem II: 2 H₂O → 4 H⁺ + 4 e⁻ + O₂. It replaces the electrons photosystem II loses to light, releases the oxygen made in photosynthesis, and adds H⁺ to the thylakoid space. It is driven by the oxidized reaction center, not directly by light, though it is often called photolysis.
electron carrier: A molecule that picks up electrons (and usually hydrogen) in one reaction and delivers them to another. In photosynthesis the carrier is NADP⁺, which is reduced to NADPH by the light reactions and oxidized back to NADP⁺ by the Calvin cycle.
electron transport chain: A series of proteins and other molecules in a membrane that pass electrons from one to the next in redox reactions. Each transfer releases a little energy, which some of the proteins use to pump H⁺ across the membrane.
proton gradient: A difference in H⁺ (proton) concentration, and in charge, across a membrane. It stores potential energy, like water behind a dam: the proton-motive force. In chloroplasts H⁺ builds up inside the thylakoids; in mitochondria, in the intermembrane space.
ATP synthase: A membrane protein that lets H⁺ flow down its gradient through a channel and uses that flow to turn part of the protein, which joins ADP and phosphate into ATP. It is found in thylakoid membranes, inner mitochondrial membranes and bacterial membranes.
chemiosmosis: Making ATP with energy stored in an H⁺ gradient: an electron transport chain pumps H⁺ across a membrane, and the H⁺ flowing back through ATP synthase drives ATP synthesis.
photophosphorylation: Making ATP from ADP and phosphate using light energy, through the light reactions' electron transport chain, H⁺ gradient and ATP synthase in the thylakoid membrane.
carbon fixation: Building carbon dioxide from the air into an organic molecule. In the Calvin cycle, CO₂ is attached to a five-carbon sugar and then, using ATP and NADPH, made into three-carbon sugar.
rubisco: Names used in describing the Calvin cycle (enrichment, not required for the exam): rubisco is the enzyme that attaches CO₂ to RuBP, a five-carbon sugar; G3P is the three-carbon sugar the cycle makes, used to build glucose and other molecules.
Calvin cycle: The second stage of photosynthesis, in the stroma: a cycle of enzyme-catalyzed reactions that fixes CO₂ and uses ATP and NADPH from the light reactions to make sugar, regenerating its starting molecule and returning ADP, Pi and NADP⁺. Sometimes called the light-independent reactions, though it stops in the dark when ATP and NADPH run out.
photosynthesis equation: 6 CO₂ + 6 H₂O + light energy → C₆H₁₂O₆ + 6 O₂. The carbon and oxygen in the sugar come from CO₂; the O₂ released comes from the water.
photosynthetic rate: How fast photosynthesis runs, measured as O₂ released, CO₂ taken up or sugar made per unit time (or by how fast leaf disks float). It rises with light intensity, CO₂ concentration and temperature until another factor becomes limiting.
oxygenic photosynthesis: Photosynthesis that splits water and releases O₂, first done by ancient cyanobacteria. The oxygen they released over hundreds of millions of years built up in the oceans and air, making the oxygen in the atmosphere that most life now depends on.

3.6 Cellular Respiration

Cellular respiration releases the energy in glucose in stages. Glycolysis in the cytosol makes pyruvate, 2 ATP and 2 NADH. In the mitochondrial matrix, pyruvate oxidation and the Krebs cycle release the carbons as CO₂ and load electrons onto NADH and FADH₂. In the inner membrane, the electron transport chain passes those electrons to oxygen, forming water, and pumps H⁺ into the intermembrane space; ATP synthase uses the gradient to make most of the 30-32 ATP. Without oxygen, fermentation regenerates NAD⁺ so glycolysis continues, for only 2 ATP. Energy not captured as ATP is released as heat, which uncoupling proteins increase.

Overall: C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O + energy. The CO₂ comes from the carbons of glucose (pyruvate oxidation and Krebs cycle); the water forms when O₂ accepts electrons at the end of the chain.
Most ATP is made by chemiosmosis, exactly as in chloroplasts, but here the energy comes from electrons moving to oxygen, and H⁺ is pumped into the intermembrane space.
Fermentation makes no extra ATP. Its only job is to regenerate NAD⁺ so glycolysis can continue without oxygen.
Energy not captured as ATP is released as heat. Uncoupling proteins in brown fat let H⁺ leak back without making ATP, turning the gradient's energy into heat.

A net 2 ATP are made by substrate-level phosphorylation, and electrons are loaded onto 2 NAD⁺, making 2 NADH. Each pyruvate loses a carbon as CO₂ and gives electrons to NAD⁺; the rest enters the Krebs cycle as acetyl CoA. Its carbons leave as CO₂, a little ATP is made, and most of the energy is loaded onto NADH and FADH₂. As electrons move toward oxygen, the chain pumps H⁺ from the matrix into the intermembrane space, building a proton gradient. ATP synthase makes most of the ATP: about 26-28 of the 30-32 ATP per glucose (oxidative phosphorylation). Cells that ferment pass NADH's electrons to pyruvate (making lactate, or ethanol and CO₂), regenerating NAD⁺ so glycolysis can keep making its 2 ATP.

NAD+: NAD⁺ and FAD are electron carriers in cellular respiration. Each picks up electrons and hydrogen from food molecules, becoming NADH or FADH₂, and delivers them to the electron transport chain, which turns them back into NAD⁺ and FAD.
glycolysis: The first stage of breaking down glucose, in the cytosol: one glucose (6 carbons) is split into two pyruvate (3 carbons each), with a net gain of 2 ATP and 2 NADH. It needs no oxygen and runs in nearly every living cell.
pyruvate: The three-carbon molecule made by glycolysis. With oxygen it enters the mitochondrion and is oxidized; without oxygen it is turned into lactate or ethanol by fermentation.
substrate-level phosphorylation: Making ATP by an enzyme moving a phosphate group directly from a phosphorylated molecule onto ADP. It makes the ATP of glycolysis and the Krebs cycle, a small share of the total.
pyruvate oxidation: The step linking glycolysis to the Krebs cycle, in the mitochondrial matrix: each pyruvate loses one carbon as CO₂ and gives electrons to NAD⁺, and what is left (acetyl CoA) enters the Krebs cycle.
Krebs cycle: A cycle of reactions in the mitochondrial matrix (also called the citric acid cycle) that oxidizes acetyl CoA completely to CO₂. Per glucose it releases 4 CO₂ and makes 2 ATP, 6 NADH and 2 FADH₂.
oxidative phosphorylation: Making ATP with energy from electrons passed to oxygen: the electron transport chain in the inner mitochondrial membrane pumps H⁺ into the intermembrane space, and H⁺ flowing back through ATP synthase makes ATP. It makes most of the ATP from each glucose.
final electron acceptor: The molecule that takes electrons at the end of an electron transport chain. In aerobic respiration it is oxygen, which combines with the electrons and H⁺ to form water. Without it the chain backs up and stops.
aerobic: Aerobic respiration uses oxygen as the final electron acceptor and makes about 30-32 ATP per glucose. Anaerobic respiration, in some prokaryotes, uses another acceptor such as sulfate. Fermentation, by contrast, uses no electron transport chain at all.
fermentation: A way to keep glycolysis running without oxygen: pyruvate (or a molecule made from it) accepts the electrons from NADH, regenerating NAD⁺. Lactic acid fermentation makes lactate (muscles, some bacteria); alcohol fermentation makes ethanol and CO₂ (yeast). It yields only the 2 ATP of glycolysis per glucose.
ATP yield: The ATP made per glucose: a net 2 from glycolysis and 2 from the Krebs cycle, plus about 26-28 from oxidative phosphorylation, for about 30-32 in all with oxygen; only 2 by fermentation. Older books give 36-38; the real number varies.
respiration equation: C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O, releasing energy, part of which is captured as ATP. Glucose is oxidized to CO₂; oxygen is reduced to water.
fats and proteins as fuel: Cells also break down fats and proteins for energy. Fats are split into glycerol and fatty acids, which are cut into pieces that enter as acetyl CoA; amino acids lose their nitrogen and their carbon skeletons enter glycolysis or the Krebs cycle.
metabolic heat: The heat released by cellular respiration, because only part of the energy in food is captured as ATP and every use of ATP releases more. Endotherms such as birds and mammals use this heat to keep their bodies warm.
uncoupling protein: An uncoupling protein (such as thermogenin in brown fat) is a channel that lets H⁺ flow back into the matrix without passing through ATP synthase. Electron transport and oxygen use continue, but the gradient's energy is released as heat instead of making ATP. Chemical uncouplers do the same.