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Biol 213 Exam no2 Study Guide

by: Irvane Ngnie Kamga

Biol 213 Exam no2 Study Guide Biol 213

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This study guide covers the essential about chapters 8 through 10. It includes my notes from the lectures, integrated with the textbook material. Let me know if you have any questions.
Cell structure and Function
James Reid Schwebach (P)
Study Guide
Biology, Cell Biology, Enzymes, metabolism, Energy, glucose catabolism, Photosynthesis
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This 42 page Study Guide was uploaded by Irvane Ngnie Kamga on Tuesday March 15, 2016. The Study Guide belongs to Biol 213 at George Mason University taught by James Reid Schwebach (P) in Winter 2016. Since its upload, it has received 207 views. For similar materials see Cell structure and Function in Biology at George Mason University.


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Date Created: 03/15/16
Biol 213 Exam no2 Study Guide Chapter 8 8.1. What Physical Principles Underlie Biological Energy Transformations? A chemical reaction occurs when atoms collide with sufficient energy to combine or change their bonding partners. Ex: the hydrolysis of disaccharide sucrose into its monomers, glucose and fructose. In biochemical reactions, energy is neither created nor destroyed; rather, it is transformed. There are two basic types of energy:  Potential energy: energy of state or position –stored energy (in chemical bonds, as a concentration gradient, etc.)  Kinetic energy: energy of movement –energy that does work. N.B: Potential energy can be converted into kinetic energy and vice-versa. Form of Energy Example in Biology Chemical: stored in bonds Released during the hydrolysis of polymers Electrical: separation of charges Electrical gradients across cell membranes help drive the movement of ions through channels Heat: transfer due to temperature difference Can be released by chemical reactions Light: electromagnetic radiation stored as Captured by pigments in the eye photons Mechanical: energy of motion Used in muscle movements Table 1: Forms of Energy in Biology There are two types of metabolism:  Anabolism: simple molecules are linked to form + complex molecules; energy is required and captured in the chemical bonds that are formed.  Catabolism: complex molecules break down into simpler ones, releasing the energy stored in the chemical bonds. The energy released in catabolic reactions is often used to drive anabolic reactions. The laws of thermodynamics apply to all matter and all energy transformations in the universe.  First law of thermodynamics: in any energy conversion, energy is neither created nor destroyed.  Second law of thermodynamics: when energy is converted from one form to another, some of that energy is lost to disorder and becomes unavailable for doing work. No physical process or chemical reaction is 100% efficient. It takes energy to impose order on a system. In any system: which can be rewritten as: where H, G and S represent enthalpy, free energy and entropy respectively. The change in free energy of any chemical reaction is equal to the difference in free energy between the products and the reactants and is measured in calories or joules: N.B: If there is no free energy available, the reaction does not occur.  If ΔG < 0, free energy is released: the reaction is exergonic.  If ΔG ˃ 0, free energy is required: the reaction is endergonic.  ΔH is the total amount of energy added (ΔH ˃ 0) or released (ΔH < 0).  The magnitude and sign of ΔG can depend a lot on changes in entropy: a large positive ΔS (is synonym of an exergonic reaction) makes ΔG more negative. The second law of thermodynamics predicts that disorder tends to increase because of energy transformations.  Catabolic reactions decrease complexity (generate disorder): complex, ordered reactant smaller, more disordered products. They have a + ΔS and a – ΔG. They are exergonic reactions. As the bonds that were holding the complex molecule together break, energy is released. Ex: hydrolysis reactions.  Anabolic reactions increase complexity (generate order): They have a – ΔS and a + ΔG. They are endergonic reactions. Ex: condensation reactions. In principle, chemical reactions are reversible and can run in both directions. According to the law of mass action, the concentrations of A and B determine which direction will be favored. At chemical equilibrium, there is a balance between forward and reverse reactions: they take place at the same rate. It is characterized by ΔG = 0. ↔ Not every chemical reaction proceeds to completion.  Every reaction has a specific equilibrium point.  The further towards completion the equilibrium point lies, the more free energy is released.  ΔG ≈ 0 → readily reversible reaction.  ΔG also depends on the initial concentrations of reactants and products, pH, temperature, and pressure. 8.2. What is the Role of ATP in Biochemical Energetics? ATP → the currency of biological energy → captures and transfers free energy ATP can phosphorylate (donate a phosphate group to) many ≠ molecules, which gain some of the energy that was stored in the ATP. Figure 1: Molecule of ATP and its constituents. The hydrolysis of ATP releases a large amount of free energy: ΔG = -7.3 to -14kcal/mol.  Some of the large amount of energy required to bring the phosphates groups (that repel one another because of their same negative charge) together in a covalent bond is stored in the two last P-O bonds of the molecule of ATP.  Free energy of this P-O bond ˃˃ free energy of the O-H bond that forms as a result of hydrolysis. Figure 2: Hydrolysis of ATP Bioluminescence is one of the many endergonic reactions driven by ATP hydrolysis. It converts ATP’s chemical energy into light energy: → ATP couples exergonic (its hydrolysis) and endergonic (its formation) reactions. ADP picks up energy from exergonic cellular reactions to become ATP, which is then used as a fuel to drive other endergonic reactions when it hydrolyses. Coupling of exergonic and endergonic reactions is very common in metabolism.  An active cell needs to produce millions of molecules of ATP/second to drive its biochemical machinery.  An ATP molecule is typically consumed within a second of its formation.  Each ATP molecule undergoes about 10,000 cycles of synthesis and hydrolysis every day. 8.3. What Are Enzymes? Most biological catalysts are proteins called enzymes (some are ribozymes –RNA molecules) that act as a framework or scaffold within which the chemical catalysis takes place. Most reactions need an input of energy to start. There is an energy barrier |b| reactants and products that must be overcome for a reaction to proceed. This is also known as the activation energy. The activation energy is the energy needed to change the reactants into unstable molecular forms with higher free energy than either the reactants or the products, called transition-state intermediates. The transition state favors the reaction: it makes it more likely to happen. The activation energy is not a part of the net free energy change, ΔG, of the reaction. The activation energy can come from heating the system, as the reactants gain kinetic energy. However, in living cells, catalysts speed up a reaction by lowering the energy barrier by bringing the reactants together. In an enzyme-catalyzed reaction, substrates (the reactants) bind to a particular site on the enzyme, the active site. Due to their unique 3D-shape and the exact structure of their active site, enzymes (and ribozymes) are highly specific. They recognize and bind to only one or a few closely related reactants, whose shape fits their active site. The interaction of an enzyme with its substrate(s), known as the enzyme-substrate complex (ES), is held together by hydrogen bonds, electrical attraction, or temporary covalent bonds. The ES complex favors the reaction. The enzyme may change slightly as it binds to its substrate, but it returns to its original form eventually (this is the definition of a catalyst ! it is not permanently altered). The lower the dissociation constant (K ),Dthe tighter the binding between the enzyme and the substrate, and the faster the catalysis. Enzymes only change the activation energy and the rate of reactions; they do not alter the overall change in free energy of the reaction (ΔG) or the final equilibrium point. 17 Enzymes can increase reaction rates by 1M to 10 times! 8.4. How Do Enzymes Work? In catalyzing a reaction, enzmes can use one or more mechanisms:  Enzymes can orient substrates properly so they can react when they collide.  Enzymes can induce strain in substrates, stretching their bonds, putting them in an unstable transition state.  Enzymes can temporarily add chemical groups to substrates, sometimes creating a charge unbalance. Most enzymes are much larger than their substrates which are relatively small in comparison. The high specificity of an enzyme depends upon a precise interlocking of molecular shapes and interactions of chemical groups at the active site. Hydrogen bonds, the attraction and repulsion of electrically charged groups, and hydrophobic interactions maintain the binding of substrates to active sites. Some enzymes slightly change shape when they bind to their substrate(s) to improve their catalytic ability, altering the shape of their active sites. This is known as induced fit. Some enymes require nonprotein chemical “partners” to function:  Prothestic groups: non-amino acid groups permanently bound to the enzyme. Ex: Heme, retinal, flavin.  Inorganic cofactors: ions permanently bound to the enzyme. Ex: iron, copper, zinc.  Coenzymes: small carbon-containing molecules; not permanently bound. Ex: coenzyme A, NAD, ATP. They stabilize the 3D-shape of the enzyme, assist with the binding of enzyme and substrate, and maintain active sites in an active configuration. Enzyme concentration is usually much lower than substrate concentration. The substrate concentration affects the rate of reaction. The reaction rate stabilizes to a maximum rate when the enzyme is saturated: all enzyme is bound to substrate. The maximum rate is used to calculate enzyme efficiency, the no of molecules of substrate converted to product per unit time (turnover number). 8.5. How Are Enzyme Activities Regulated? The thousands of chemical reactions occurring in living cells are organized in interconnected metabolic pathways. Each reaction is catalyzed by a specific enzyme. The regulation of enzymes and thus of reaction rates helps maintain internal homeostasis. Inhibitors regulate enzymes. Naturally occurring inhibitors regulate metabolism, whereas artificial inhibitors can be used to treat diseases, to kill pests, or to study how enzymes work. Irreversible inhibition: inhibitor covalently binds to certain side chains at the active site of an enzyme and permanently inactivates the enzyme. Reversible inhibition: inhibitor binds noncovalently to a site on the enzyme (not necessarily the active site) and prevents the reaction from proceeding.  A competitive inhibitor competes with the natural substrate for the active site; when it is bound to the enzyme, it prevents substrate binding. If the concentration of substrate is or if the concentration of inhibitor is the substrate is more likely to bind the active site, and the enzyme is functional again.  An uncompetitive inhibitor binds to the ES complex (close but not directly to the active site) and prevents the release of products.  A noncompetitive inhibitor binds at a site other than the active site and changes the enzyme structure so that normal substrate binding cannot occur. Allosteric regulation: an effector molecule binds to a site other than the active site of an enzyme, inducing the enzyme to change its shape and resulting in a change of the affinity of the active site for the substrate. Enzymes have two forms –active (can bind the substrate) and inactive (cannot bind the substrate) –that can be interconverted, depending on the binding of effector molecules at sites other than the active site. Binding of an inhibitor stabilizes the inactive form, and binding of an activator stabilizes the active form. Allosteric activator product formation. Allosteric inhibitor no product formation. Most enzymes that are allosterically regulated are proteins with quartenary structure. The active site is on the catalytic subunit. Activators and inhibitors bind to other polypeptides called regulatory subunits. Some allosteric enzymes have multiple subunits containing active sites, and the binding of substrate to one of the active sites causes allosteric effects: the adjacent subunit has a slight change in its structure that makes its active site + likely to bind to the substrate. The reaction rate as the sites become sequentially activated. For a nonallosteric enzyme with a single active site, the plot of the reaction rate versus the concentration of substrate is hyperbolic. The reaction rate first increases sharply with increasing substrate concentration, and eventually stabilizes to a constant maximum rate as the enzyme becomes saturated. For an allosteric enzyme with multiple active sites, the plot is sigmoid (S-shaped). It is only after the substrate binds to the first active site of the enzyme (which then leads to subsequential activation of other sites) that the reaction truly speeds up. Within a certain range, the reaction rate is extremely sensistive to relatively small changes in substrate concentration. Moreover, allosteric enzymes are very sensitive to low concentrations of inhibitors. Thus, they are important in regulating metabolic pathways. Metabolic Pathways  The first reaction is the commitment step. Once it has occurred, the process is in motion, and the other reactions happen in sequence.  Feedback inhibition: the end product acts as a noncompetitive inhibitor and allosterically inhibits the enzyme catalyzing the commitment step, thus shutting down its own production. Many enzymes are regulated through reversible phosphorylation. An enzyme can be activated by a protein kinase, which adds a phosphate group to 1 or + specific amino acids, and deactivated by a protein phosphatase. Every enzyme is most active at an optimal pH and within a very narrow range of temperatures. - pH influences the ionization of functional groups and thus affects enzyme structure and function. - Heat causes denaturation, thus affecting enzyme structure and function. Organisms can use isozymes to adjust to temperature changes. Enzymes in humans have higher optimal temperature than enzymes in most bacteria. Chapter 9 9.1. How Does Glucose Oxidation Release Chemical Energy? In cells, energy from fuel molecules is used to make ATP, which in turn drives endergonic reactions. Glucose is the most common fuel in cells. Five principles govern metabolic pathways:  A complex transformation occurs in a series of separate reactions that constitute a metabolic pathway.  Each reaction is catalyzed by a specific enzyme.  Many metabolic pathways are similar in all organisms.  In eukaryotes, many metabolic pathways are compartmentalized, certain reactions occuring inside specific organelles.  Key enzymes in each pathway can be activated or inhibited to alter the rate of the pathway. Cells get energy from glucose by chemical oxidation in a series of metabolic pathways. The combustion/burning of glucose proceeds according to the equation: This is a redox reaction in which glucose loses electrons (becomes oxidized) and oxygen gains them (becomes reduced). It is a highly exergonic reaction (ΔG = -686kcal/mol) and drives the endergonic formation of many ATP molecules. Three catabolic processes harvest the energy from glucose:  Glycolysis is the starting point of glucose catabolism. 1 molecule of glucose is converted to 2 molecules of pyruvate, a 3-Carbon product; anaerobic process.  Cellular respiration: each molecule of pyruvate is converted into 3 molecules of CO 2 (complete oxidation); aerobic process.  Fermentation: pyruvate is converted into lactic acid or ethanol (incomplete oxidation); anaerobic process. Glycolysis + cellular respiration (2 present) ˃˃ glycolysis + fermentation (O 2bsent) 32 – 36 ATP/glucose vs 2 ATP/glucose Oxidation and reduction always occur together. The compound that loses electrons is the reducing agent, and the one that gains electrons is the oxidizing agent. Confusing, right?! Think of it this way: in order to become oxidized, a reactant has to give away electrons; thus it reduces another reactant: it’s the reducing agent. On the other hand: in order to become reduced, a reactant has to gain electrons, taking them away from another reactant, oxidizing it: it’s the oxidizing agent. Ex: in the glucose metabolism mentioned above, glucose is the reducing agent, and oxygen is the oxidizing agent. + - Transfer of electrons is often associated with the transfer of hydrogen ions. H = H + e The more reduced a molecule is (the more hydrogen atoms it has), the higher its stored free energy. In a redox reaction, some energy is transferred from the reducing agent to the reduced product. Most reduced state Most oxidized state (Highest free energy) (Lowest free energy) Coenzyme NAD is a key electron carrier in redox reactions. Its reduced form, NADH, is an important energy intermediary in cells (and is a larger package of free energy than ATP). + After being reduced from NAD , NADH is then oxidized by O : 2 ΔG = -52.4kcal/mol. Eukaryotic and prokaryotic cells harvest energy using ≠ combinations of metabolic pathways.  When O is2present, glycolysis is followed by the 3 pathways of cellular respiration: pyruvate oxidation, the citric acid cycle (Krebs cycle), and electron transport/ATP synthesis. Pyruvate is converted to CO , a2d O is 2he final electron acceptor.  When O is2unavailable, glycolysis is followed by fermentation. Some prokaryotes, however, are able to harvest energy by anaerobic respiration. 9.2. What Are the Aerobic Pathways of Glucose Catabolism? For both eukaryotes and prokaryotes, glycolysis takes place in the cytoplasm, more specifically in the cytosol. It involves 10 enzyme-catalyzed reactions. The products are 2 molecules of pyruvate, 2 ATP, and 2 NADH. Steps 1-5 are energy-investing reactions that require the hydrolysis of 2 ATP. Steps 6-10 are energy-harvesting reactions that yield 4 ATP and 2 NADH. The energy released by the breaking of the C-C and C-H bonds as glucose is oxidized is stored in ATP and NADH. 1. Step 6 is a very exergonic redox reaction. The free energy released is trapped via the reduction of NAD to NADH. 2. Step 7 is an exergonic substrate-level phosphorylation. The energy is used to transfer a phosphate from the substrate to ADP to form ATP. In eukaryotes, after glycolysis, pyruvate is transported into the mitochondrial matrix where pyruvate oxidation occurs. This step oxidizes pyruvate to a 2-C acetate molecule and CO . 2 Acetate then binds to coenzyme A to form acetyl CoA, the starting point of the citric acid cycle. + It is an exergonic multi-step reaction, and 1 NAD is reduced to NADH. Citric Acid Cycle  Takes place in the mitochondrial matrix as well.  It has 8 steps.  Acetyl CoA is the starting point.  Combined with the 4-C acceptor molecule oxaloacetate, it gives rise to citrate, the 1 st 6-C molecule of the cycle.  The 2-C acetyl group is completely oxidized to 2 CO mo2ecules.  The last 4-C molecule is the regenerated Oxaloacetate. +  The free energy released is captured by NAD , FAD, and GDP.  End products: 2 CO , 3 H , 3 NADH, 1 FADH , and 1 ATP (obtained from GTP). 2 2 The citric acid cycle harvests a great deal of chemical energy from the oxidation of acetyl CoA. It has four exergonic redox reactions. Let’s take a look at the last one (step 8): + The energy released is trapped by NAD , forming NADH. Both pyruvate oxidation and the citric acid cycle occur twice in a single chain of reactions (remember glycolysis yields 2 molecules of pyruvate!). Overall, the oxidation of glucose yields: 6 CO , 20 NADH, 4 ATP, and 2 FADH . 2 Pyruvate oxidation and the citric acid cycle are regulated by the concentrations of starting materials. For the cycle to continue, the starting materials –acetyl CoA and oxidized electron + carriers (NAD and FAD) –must be replenished. The reduced electron carriers must be reoxidized. When O is2present, it is the oxidizing agent and is reduced to H O. 2 9.3. How Does Oxidative Phosphorylation Form ATP? Oxidative phosphorylation: the overall process of ATP synthesis resulting from the reoxidation of electron carriers in the presence of oxygen. 1. Electron transport: the electrons from NADH and FADH pass throug2 the respiratory chain, a series of membrane-associated electron carriers. Electron flow active transport of protons (H ) out of the mitochondrial matrix across the inner mitochondrial membrane into the intermembrane space, which results in a proton concentration gradient. 2. Chemiosmosis: the coupling of protein diffusion back into the matrix through ATP synthase and ATP synthesis by ATP synthase. Why does the electron transport chain have so many steps? It is an extrememly exergonic process. The released energy could not be harvested by the cell all at once. The respiratory chain is located in the inner mitochondrial membrane (extensive folding). Four large protein complexes contain the electron carriers and the associated enymes. Free energy is released as electrons travel successively down the chain –as NADH and FADH are 2 oxidized. Oxygen is the final electron acceptor and is reduced to water: N.B: cytochrome c is the one protein of the respiratory chain that is not embedded in the inner mitochondrial membrane; it lies in the intermembrane space. During electron transport, protons are actively transported from the mitochondrial matrix to the intermembrane space. This results not only in a concentration gradient but also in a charge difference across the inner mitochondrial membrane, making the intermembrane space more acidic and positive than the matrix. NADH pumps 3 H into the intermembrane space, FADH pumps 2. 2 For every H pumped, 1 ATP molecule will be formed. Together, the proton concentration gradient and the electrical charge difference constitute a source of potential energy called the proton-motive force. This force drives the protons back across the membrane to the matrix through a channel protein, ATP synthase, which couples this diffusion to the synthesis of ATP. This process is known as chemiosmosis. The energy of the proton-movement back into the mitochondrial matrix is harnessed by ATP synthase to make ATP. ATP synthesis is reversible, and ATP synthase can also act as an ATPase, hydrolyzing ATP into ADP and P :i Two facts explain why ATP synthesis is favored however:  ATP leaves the mitochondrial matrix for use elsewhere in the cell as soon as it is made, keeping the ATP concentration in the matrix low. +  The H gradient, which drives the reaction towards the left, is maintained by electron and proton transport. The first chemical evidence of chemiosmosis came from studies on chloroplast thylakoid membranes. The studies demonstrated that an H gradient across a membrane that contains ATP synthase is necessary and sufficient to stimulate ATP synthesis. The structure and function of ATP synthase is the same in all living organisms. It is a molecular motor with 2 parts:  F0unit: the transmembrane H channel  F unit: points inside the mitochondria and projects into the mitochondrial matrix; 1 contains the active sites for ATP synthesis; rotates/spins. These molecular motors can make up to 100 ATP molecules per second! Although O is an excellent electron acceptor, incomplete electron transfer can result in toxic 2 intermediates. Ex: Superoxide damage has been implicated in several human conditions, involving renal failure, stroke, and aging. 9.4. How Is Energy Harvested From Glucose In The Absence of Oxygen? Many bacteria and archaea have evolved pathways that enable them to achieve anaerobic respiration in the absence of O by2using other electron acceptors (e.g. CO , NO ,2Fe 3- 3+ and others). For most prokaryotes however, in the absence of O , glycolysis is followed by fermentation, 2 which also occurs in the cytosol. + All types of fermentation operate to regenerate NAD to keep glycosis going. Lactic acid fermentation  Pyruvate is the electron acceptor (without intermediates) and lactate is the product.  Occurs in microorganisms and some muscle cells. During active exercise, muscle cells carry out lactic acid fermentation because O c2nnot be delivered fast enough for aerobic respiration. As lactate , pH , and causes muscle pain. Alcoholic fermentation  Pyruvate is converted to acetaldehyde, and CO is2released. Acetaldehyde is then reduced to ethanol.  Occurs in yeasts and some plant cells.  Used to produce alcoholic beverages. Reminder that glycolysis is summarized by the equation: Glucose is only partially oxidized in fermentation: fermentation by-products have a lot of energy remaining. This coupling is far less efficient, energy-wise, than glycolysis + cellular respiration. In some eukaryotes, ATP must be used to transport NADH into the mitochondrial matrix. Glycolysis coupled to cellular respiration has a net yield of 30 ATPs for those organisms. NADH shuttle systems transfer the electrons captured by glycolysis onto substrates that can move across the mitochondrial membranes. The increase in atmospheric O le2els (due to photosynthesis) and the development of aerobic metabolic pathways led to the evolution of multicellular organisms. 9.5. How Are Metabolic Pathways Interrelated and Regulated? Metabolic pathways do not operate in isolation. On the contrary, they are interconnected and share intermediate molecules. As mentioned before, anabolism and catabolism are linked. Catabolic interconversions  Polysaccharides are hydrolyzed to glucose, which then enters glycolysis (followed by cellular respiration in the presence of O2) where its energy is captured in ATP.  Lipids are hydrolyzed to glycerol and fatty acids. - Glycerol is converted to DHAP, an intermediate in glycolysis - Fatty acids are converted to acetyl CoA, which enters the citric acid cycle.  Proteins are hydrolyzed to amino acids, which feed into glycolysis or the citric acid cycle. Anabolic interconversions  Gluconeogenesis: glycolytic and citric acid cycle intermediates are reduced to form glucose.  Acetyl CoA can be used to form fatty acids.  Some intermediates in the citric acid cycle are reactants in pathways that synthetize important components of nucleic acids, such as purines and pyrimidines. With so many possible pathways, how do cells “decide” which path to take? The levels of biochemical molecules in what is called the metabolic pool are quite constant. Organisms allosterically regulate key enzymes to maintain a balance |b| anabolism and catabolism. Ex: during jogging, energy is needed by legmusclesto perpetuate movement andby heartmuscles to circulate blood. Glucose is catabolized to provide this energy, and in the liver, more glucose is formed by the anabolism of amino acids and pyruvate. The pathways are regulated so that levels of molecules such as blood glucose remain constant. Negative feedback: a high concentration of a metabolic product inhibits the action of the first enzyme involved in its catalyzed-formation. Positive feedback: excess product of one pathway can activate an enzyme in another pathway, diverting raw materials away from the synthesis of the first product. ATP and NADH act as inhibitors at various control points in glycolysis and cellular respiration. Key regulated enzymes include phosphofructokinase (glycolysis), citrate synthase, isocitrate dehydrogenase (citric acid cycle), and fatty acid synthase. Brown fat cells make UCP1, a protein that makes the mitochondrial inner membrane permeable to protons. It thus prevents ATP synthesis by ATP synthase because the H + concentration gradient is not established. CHAPTER 10 10.1. What Is Photosynthesis? Photosynthesis – “energy from sunlight” Energy from sunlight is captured and used to convert CO to more complex carbon 2 compounds. A typical terrestrial plant uses light from the sun, water from the soil, and carbon dioxide from the atmosphere for photosynthesis. CO ente2s and O and H 2 exit t2e leaves through pores on the surface called stomata. 18 Using the stable isotope O, Ruben and Kamen demonstrated by their experiments that the oxygen released by photosynthesis comes from water rather than carbon dioxide. The isotopic ratio of O2produced was similar to that of H O 2ot to that of CO , in2both experiments. The revised balanced equation for photosynthesis is: Thus, photosynthesis is a redox reaction in which H O i2 oxidized to O , and2CO is red2ced to a complex carbohydrate. In oxygenic photosynthesis, water is the donor of protons and electrons. In anoxygenic photosynthesis, other molecules such as H S d2nate the protons and electrons. Photosynthesis, which occurs in the chloroplast, consists of two pathways:  Light reactions: convert light energy to chemical energy in the form of ATP and NADPH; take place in the thylakoids.  Light-independent reactions: do not directly require light energy and use ATP and NADPH from the light reactions, as well as CO , to 2roduce carbohydrates; take place in the stroma. 10.2. How Does Photosynthesis Convert Light Energy into Chemical Energy? Light –form of energy; electromagnetic radiation stored as photons. Light propagates as waves, and its energy is inversely proportional to its wavelength. where h is Plank’s constant, c is the speed of light, and λ is the wavelength. In photosynthetic organisms, receptive molecules absorb photons (of specific wavelength) in order to harvest their energy for biological processes. When a photon meets a molecule, it can: 1. Bounce off the molecule –be scattered or reflected. 2. Pass through the molecule –be transmitted. 3. Get absorbed by the molecule, adding energy to it. The molecule is raised from a ground state to an excited state, more unstable and reactive. Molecules that absorb specific wavelengths in the visible domain and transmit all others (wavelengths) are called pigments. Chlorophyll absorbs blue and red light and scatters green. Absorption spectrum: plot of the light absorbed by a purified pigment with respect to wavelength. Action spectrum: plot of the rate of photosynthesis carried out by an organism with respect to the wavelengths of light to which it is exposed. The rate of photosynthesis can be measured by the amount of O r2leased. The major pigment used to drive the light reactions in oxygenic photosynthesis is chlorophyll a. It has a complex ring structure with a magnesium ion at the center, and a long hydrocarbon “tail” that anchors the molecule within a large multi-protein complex called a photosystem, which spans the thylakoid membrane. The molecular structure of a chlorophyll a. Chlorophyll a and various accessory pigments (such as chlorophyll b and c, carotenoids, and phycobilins) are arranged into light-harvesting complexes (aka antenna systems) that surround a single reaction center within the photosystem. They capture light energy in the form of photons and transfer it to the reaction center, where the conversion of light energy into chemical energy occurs. Those accessory pigments absorb light in other (than red and blue like chlorophyll a) wavelengths of the visible domain, and thus broaden the range of wavelengths that can be used for photosynthesis, as can be seen in the absorption and action spectra above. ≠ photosynthetic organisms have ≠ combinations of accessory pigments. When a pigment molecule absorbs a photon, it enters an excited state. Because this situation is -12 unstable, the molecule quickly (within picoseconds, 10 s) returns to its ground state, releasing most of the absorbed energy. Within a light-harvesting complex, energy from a photon is transferred from one pigment molecule to an adjacent one, until it reaches a chlorophyll a molecule in the reaction center. To return to its ground state, the chlorophyll a (Chl*) molecule gives up its excited electron to a chemical acceptor. This redox reaction is the first consequence of light absorption by chlorophyll. The electron acceptor reduced by Chl* is the 1 in a chain of electron carriers in the thylakoid membrane. Electrons are passed from one carrier to another in an energetically “downhill” series of reductions and oxidations. The final electron acceptor is NADP , which gets reduced to NADPH: Noncyclic electron transport uses two photosystems:  Photosystem I has the P 700chlorophyll and absorbs light energy best at 700nm.  Photosystem II has the P 680chlorophyll and absorbs light energy best at 680nm. The noncyclic electron transport begins with Photosystem II and has a rotated Z shape. Both ATP and NADPH are produced by noncyclic electron transport. Photosystem II: After the excited chlorophyll (Chl*) gives up its energetic electron, the molecule lacks an electron and is very unstable. It had a strong tendency to grab an electron from another molecule to replace the one it lost –it is a strong oxidizing agent. Water is the electron donor: The energetic electrons are passed through a series of membrane-bound carriers to a final acceptor at a lower energy level. A proton gradient, as well as a charge difference across the thylakoid membrane, is generated and used to drive ATP synthesis by ATP synthase. Photosystem I: + An excited electron from Chl* reduces an acceptor. The oxidized Chl then grabs another electron from the last carrier in photosystem II. The energetic electrons are passed through + several carriers and end up reducing NADP to NADPH. Cyclic electron transport uses photosystem I and electron transport to produce ATP only. It is cyclic because an excited electron is passed from Chl* to a chain of electron carriers and eventually recycles back to the same chlorophyll. The energy from the electron flow is captured in the form of ATP. ATP is produced by photophosphorylation, a chemiosmotic mechanism: electron transport is coupled to the transport of protons (H ) from the stroma to the lumen (thylakoid interior), resulting in a proton gradient and an electrical charge difference across the thylakoid membrane. Water oxidation leads to more H in the lumen and NADP reduction leads to less H in the + stroma. Both reactions contribute to the proton gradient. + The high concentration of H in the lumen (very acidic w.r.t the stroma) drives the movement of H back into the stroma through protein channels in the thylakoid membrane, called ATP synthases. Similarly to what happens in the mitochondrion, ATP synthase couples the diffusion of protons back into the stroma with the production of ATP. N.B: chloroplast ATP synthase is about 60% identical to human mitochondrial ATP synthase. 10.3. How Is Chemical Energy Used to Synthesize Carbohydrates? CO f2xation: biological process through which inorganic carbon (CO ) is 2onverted to organic compounds. CO fix2tion occurs in the stroma and uses the chemical energy stored in NADPH and ATP. In the 1950s, Benson and his colleagues conducted an experiment to trace the pathway of CO 2 during photosynthesis and identify the compounds formed from it. They used the 14C radioisotope for that purpose. The experiment showed that the first product of CO fi2ation is a 3-carbon sugar phosphate called 3-phosphoglycerate (3PG): The pathway of CO fi2ation is cyclic, and is called the Calvin cycle. At the end of every “turn” of the cycle, a carbohydrate is produced and the initial CO acceptor (RuBP) is 2 regenerated. CO first binds to 5-C RuBP. The intermediate 6-C compound quickly breaks down into 2 2 molecules of 3PG. The enzyme rubisco (ribulose biphosphate carboxylase/oxygenase) which catalyzes the intermediate 6-C compound is the most abundant protein in the world! The Calvin cycle is made up of three distinct processes:  The fixation of CO 2o 3PG, catalyzed by rubisco.  The reduction of 3PG to G3P, glyceraldehyde-3-phosphate aka triose phosphate, involving a phosphorylation and a redox reaction.  The regeneration of RuBP, the initial CO a2ceptor. In a typical leaf, ≈ 5/6 of the G3P is recycled into RuBP. What happens to the remaining G3P?  Some is exported out of the chloroplast into the cytosol, where it is converted to hexoses (glucose and fructose). These molecules may be used in glycolysis and cellular respiration or converted to the disaccharide sucrose. In the latter case, sucrose is transported to other parts of the plants where it is hydrolyzed; its constituent monosaccharides can be used as sources of energy or serve as building blocks for other molecules.  Some is used to synthetize glucose (which then becomes starch as glucose molecules accumulate) in the chloroplast. The stored starch can then be used at night so that the photosynthetic tissues can continue to export sucrose to the rest of the plant, even when photosynthesis is not taking place. The products of the Calvin cycle are crucially important to Earth’s entire biosphere. The C-C and C-H covalent bonds generated by the cycle provide almost all of the energy for life.  Photosynthetic organisms (autotrophs) release most of this energy by glycolysis and cellular respiration, and use it to support their growth, development, and reproduction.  Heterotrophs cannot photosynthesize and depend on autotrophs for both energy and raw materials. Light stimulates the Calvin cycle:  Light-induced pH changes (because of the movement of H from the stroma to the lumen) in the stroma favors the activation of rubisco.  Light-induced electron transport reduces disulfide bridges in 4 of the Calvin cycle enzymes, altering their 3D-shape and thereby activating them. 10.4. How Have Plants Adapted Photosynthesis to Environmental Conditions? Rubisco is both an oxygenase and a carboxylase: it can add O to RuBP instead of CO , 2 2 lowering the overall amount of CO that 2s fixed. Rubisco’s affinity for CO is 10 x 2tronger than its affinity for O2, hence carboxylation is usually favored. However, if there is a much greater O conc2ntration in the leaf than CO concentr2tion, photorespiration occurs: O is2combined with RuBP: Phosphoglycolate is a 2-C compound that does not enter the Calvin cycle, but another metabolic pathway converts it to 3PG (it is hydrolyzed into glycolate, which is then converted into glycine, which is converted into serine, which is converted into glycerate, which becomes 3PG by phosphorylation): This pathway reclaims 75% of the carbons from Phosphoglycolate for the Calvin cycle; photorespiration –which consumes O and re2eases CO and occurs2only in the light –reduces CO f2xation by 25%. In the leaf, the relative concentrations of CO and O vary, determining whether carboxylation 2 2 or photorespiration occurs. Photorespiration is more likely at high temperatures. On hot, dry days, stomata (pores on the leaf surface) close preventing water loss and gas exchange |b| the plant and the atmosphere. Because of photosynthesis, CO conc2ntration and O c2ncentration , resulting in photorespiration being favored. Plants differ in how they fix CO . 2  C 3lants (e.g. roses, wheat and rice): 3PG is the first product of CO fixatio2. These plants are abundant in rubisco (in mesophyll cells). On hot days, their leaves close their stomata, preventing entry of CO and 2xit of O and H 2; photo2espiration occurs.  C 4lants (e.g. corn, sugarcane, and tropical grasses): oxaloacetate (4-C compound) is the first product of CO fi2ation. These plants have a mechanism for increasing CO 2 near rubisco and isolating the enzyme from O . CO i2 fixe2 in mesophyll cells by PEP carboxylase to a 3-C compound, phosphoenolpyruvate (PEP) to form oxaloacetate. N.B: Unlike rubisco, PEP carboxylase does not have oxygenase activity and fixes CO even at 2 very low levels. In C plants, oxaloacetate is converted to malate, which diffuses into bundle sheath cells that 4 have modified chloroplasts designed to concentrate CO around r2bisco. Malate is decarboxylated to pyruvate and CO . Whi2e pyruvate regains mesophyll cells to regenerate PEP –a reaction that requires ATP –CO enters2the Calvin cycle. C 4lants must use some energy to pump CO from mesop2yll cells to bundle sheath cells where the Calvin cycle takes place. For C 4lants, CO fix2tion and the Calvin cycle are separated in space: the former takes place in mesophyll cells and the latter takes place in bundle sheath cells. In cool, cloudy conditions, C pla3ts have an advantage in that they don’t expend energy concentrating CO nea2 rubisco, but in warmer, dryer climates, C plants hav4 the advantage since they undergo much less photorespiration. In CAM (Crassulacean Acid Metabolism) plants, the 1 product of CO fixation by2PEP carboxylase is oxaloacetate. They undergo much less photorespiration than C plants. 3O 2 fixation and the Calvin cycle are separated in time.  At night, when it is cooler and water loss is minimized, the stomata open. CO fixatio2 occurs and malate is stored in the mesophyll vacuoles.  During the day, when the stomata close to reduce water loss, malate moves to chloroplasts where it is decarboxylated. The resulting CO enter2 the Calvin cycle as the light-reactions provide ATP and NADPH. 10.5. How Does Photosynthesis Interact with Other Pathways? Green plants are autotrophs: they can synthetize all the molecules they need from simple starting materials and use the carbohydrates formed in photosynthesis to produce energy by glycolysis and cellular respiration for processes such as active transport and anabolism. Only 5% at most of sunlight energy is converted into plant growth, meaning that up to 95% of energy is lost! However, this 5% is a considerable amount of free energy.


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