Biochemistry Exam 1

The three stages of the Calvin cycle are

(1) fix CO2 (fixation) (2) use NADPH and ATP (reduction) (3) regenerate the starting C5 molecule (regulation)

Urinary tract infections are caused by pathogenic strains of E. coli bacteria containing a cell surface lectin called FimH. This bacterial lectin binds to a glycan group on the human membrane protein uroplakin, which is expressed on urinary tract epithelial cells. a. Describe how a synthetic glycan array could be used to identify the glycan binding site of FimH on uroplakin. b. Assuming the specific glycan group was identified, how could this information be used to develop glycan mimetics to treat urinary tract infections?

(a) A synthetic glycan array could be constructed containing variations of common glycan groups most likely to be present on uroplakin. By comparing the binding capacity of fluorescently labeled pathogenic (expresses FimH) and nonpathogenic E. coli strains to the glycan array, it should be possible to identify one or more glycan groups on the array with selective binding to FimH-expressing pathogenic E. coli strains. If glycan structural analysis of uroplakin were available using HPLC or mass spectrometry, the predicted glycan structure should be consistent with results from the unbiased glycan array. (b) A glycan array could be constructed containing the FimH target glycan, as well as other glycans that serve as positive and negative controls. Positive controls would be glycans known to be binding sites for E. coli lectins not associated with pathogenicity. This would control for overall binding of bacteria to the array in case the drug candidate nonselectively blocked all binding. In contrast, negative controls would be structurally related glycans that are known to have only very low affinity for FimH, which should not be affected by the presence of drug candidates in the binding reaction.

Penicillin is an antibiotic that was discovered almost by accident when Alexander Fleming forgot to clean out old bacterial plates. Years earlier, Fleming had discovered that the enzyme lysozyme has antibacterial properties, but it was not amenable to commercial production as an antibiotic because lysozyme is chemically unstable. a. What did Fleming notice on the bacterial plate that gave him the idea to look for the presence of an antibiotic? Why did he call it "penicillin"? b. What is the biochemical target of penicillin in bacteria, and why is penicillin lethal to bacteria? c. Overuse of penicillin led to the emergence of penicillin-resistant bacteria. What is the most common mechanism of penicillin resistance in bacteria, and how did pharmaceutical companies solve this problem? d. Why is methicillin-resistant Staphylococcus aureus (MRSA) called the superbug? What is the molecular mechanism of antibiotic resistance in MRSA, and what might be a drug development strategy to overcome this resistance to treat MRSA infections?

(a) Fleming noticed that bacteria failed to grow in an area surrounding a large mold colony on the plate, and he hypothesized that the mold secreted an antibacterial compound. Fleming identified the compound and named it penicillin after the antibiotic-producing mold Penicillium notatum. (b) Penicillin targets the enzyme transpeptidase, which is required for bacterial cell wall synthesis. If bacteria cannot synthesize a functional cell wall at each cell division, the cell cannot divide and proliferate. (c) The most common mechanism of penicillin resistance in bacteria is expression and secretion of the enzyme β-lactamase, which cleaves the lactam ring of penicillin and destroys its transpeptidase-inhibiting activity. (d) MRSA is resistant to a wide range of antibiotics, including methicillin, which until recently was one of the most potent antibiotics available. Methicillin resistance in MRSA is due to expression of a functional transpeptidase enzyme that does not bind methicillin or penicillin. This methicillin-resistant transpeptidase was acquired by lateral gene transfer from another bacterial species.

. Defects in the pentose phosphate pathway enzyme glucose6-phosphate dehydrogenase represent the most common enzyme deficiency in humans. a. What explains the observation that individuals born with a deficiency in the enzyme glucose-6-phosphate dehydrogenase become clinically anemic if they have a diet rich in fava beans? b. Why is it thought that increased resistance to malaria is linked to glucose-6-phosphate dehydrogenase deficiencies?

(a) Glucose-6-phosphate dehydrogenase is required in the pentose phosphate pathway to generate reducing equivalents as NADPH, required to sustain a high level of reduced glutathione in red blood cells. Fava beans contain a toxic compound (vicine), reduced by glutathione. Individuals who cannot maintain NADPH levels are highly susceptible to favism, a diet-induced form of anemia. (b) Geographic overlap in Africa of glucose-6- phosphate dehydrogenase deficiencies and malarial resistance suggest a correlation. Also, growth of the malarial parasite Plasmodium is inhibited by an oxidizing environment in host cells. Glucose-6-phosphate dehydrogenase deficiencies result in an oxidative environment because of decreased levels of reduced glutathione, so individuals with this deficiency likely have red blood cells that are unsuitable for Plasmodium growth.

. Heparan sulfate and heparin are related glycosaminoglycans that differ primarily in the number of sulfate groups (heparin is more highly sulfated). Heparin has one of the highest negative charge densities ever found in a biomolecule and is used commercially to prevent blood clotting. The molecular structure of heparin is shown here. (p. 676) a. What accounts for the anticoagulant activity of commercially prepared heparin? b. Fatal accidental heparin overdoses have tragically occurred in hospitals because of poor labeling on heparin bottles and human error. How does infusion with protamine sulfate, a cationic protein, counteract the effects of a heparin overdose?

(a) Heparin binds with high affinity to antithrombin, which activates the inhibitory activity of antithrombin. This leads to inhibition of the blood-clotting cascade through antithrombin inactivation of thrombin and Factor Xa. (b) Protamine sulfate is positively charged and binds to the negatively charged heparin, which prevents heparin from binding to and activating antithrombin. This leads to inactivation of antithrombin and normal regulation of the blood-clotting cascade.

The glucagon signaling pathway in liver cells (shown in the following illustration) activates glycogen degradation through a series of amplification steps, including (1) stoichiometric binding of glucagon to the glucagon receptor, (2) Gsα stimulation of adenylate cyclase (AC), (3) cAMP activation of protein kinase A (PKA), (4) protein kinase A activation of phosphorylase kinase (PhK), (5) phosphorylase kinase activation of glycogen phosphorylase (Ph), and (6) glycogen degradation and release of glucose. Note that the enzyme cAMP phosphodiesterase (cAMP PDE) cleaves cAMP to terminate glucagon signaling. a. Which enzymes in the cascade are regulated by covalent modification? b. Calculate the theoretical number of molecules of glucose-1-phosphate generated per second from glycogen as a result of the interaction of one molecule of glucagon with its receptor on a liver cell membrane using the following assumptions: (i) Ten Gsα-GTP are formed for each molecule of glucagon bound to a receptor molecule. (ii) None of the downstream enzymes are rate limiting for the upstream glucagon signal. (iii) Adenylate cyclase, protein kinase A, phosphorylase kinase, and glycogen phosphorylase have a catalytic turnover rate of 1,000 per second. (iv) cAMP phosphodiesterase is equimolar to adenylate cyclase and has a catalytic turnover rate of 100 per second. (v) Two cAMP are required to activate one protein kinase A catalytic subunit (see Figure 8.26).

(a) Phosphorylase kinase and glycogen phosphorylase are both activated by the covalent addition of a phosphate. (b) This can be calculated from: 1 glucagon receptor activates 10 Gsα−GTP. 10 Gsα−GTP subunits activate 10 adenylate cyclase enzymes. 10 adenylate cyclase enzymes generate 10,000 cAMP per second, but 1,000 cAMP per second are degraded by cAMP phosphodiesterase. 9,000 cAMP activate 4,500 protein kinase A catalytic subunits per second. 4,500 protein kinase A catalytic subunits activate 4,500,000 phosphorylase kinase subunits per second. 4,500,000 phosphorylase kinase subunits per second activate 4,500,000,000 glycogen phosphorylase subunits per second. 4,500,000,000 glycogen phosphorylase subunits per second generate 4,500,000,000,000 glucose-1-phosphate per second. = 4.5 × 1012 glucose-1-phosphate formed per second

The intracellular signaling enzyme protein kinase A is activated by cyclic AMP (cAMP) binding, after upstream receptor activation through glucagon and epinephrine signaling. a. What is the downstream effect of protein kinase A activation on glycogen synthase and glycogen phosphorylase activities? b. Do these protein kinase A effects on glycogen synthase and glycogen phosphorylase increase or decrease the amount of stored glycogen in the body? c. Why does it make sense that glucagon and epinephrine have the same effect on glycogen metabolism, which is the exact opposite effect of insulin on glycogen metabolism?

(a) Protein kinase A activation results in the phosphorylation and inactivation of glycogen synthase, and in activation of glycogen phosphorylase through the phosphorylation and activation of phosphorylase kinase. (b) Protein kinase A activation results in decreases in stored glycogen because glycogen synthase is inactivated and glycogen phosphorylase is activated. (c) Glucagon signals a need for glucose in between meals, epinephrine signals a need for glucose when there is a need for quick energy. In contrast, insulin signals the fed state and a need to replenish glycogen stores.

Under which conditions will cyclic photophosphorylation will occur?

(i) PS - I only remains active. (ii) Photolysis of water does not take place. (iii) Requirement of ATP is more and (iv) Non-availability of NADP+. Cyclic Photophosphorylation: It is a process of photophosphorylation in which an electron expelled by the excited photo center( PS I) is returned to it after passing through a series of electron carriers. It occurs under conditions of low intensity, and when CO2​ fixation is inhibited. Absence of CO2​ fixation results in non- requirement of electrons as NADPH2​ is not being oxidized to NADP+. (aerobic conditions)

Chloroplasts are plant organelles that convert sunlight energy into chemical energy. Answer the following questions about this energy-converting process. a. What do photosystems I and II have in common with the mitochondrial electron transport chain? b. What two products of the photosynthetic electron transport system (in addition to H2O) are required by the Calvin cycle? c. What molecule is the C1 substrate in the Calvin cycle? d. Do plant cells have mitochondria? Explain your answer.

. (a) Both PSI and PSII and the mitochondrial ETS convert redox energy into proton-motive force. (b) ATP and NADPH. (c) CO2. (d) Plant cells have mitochondria in order to generate high levels of ATP at night to sustain metabolic activity. Per glucose, mitochondrial ETS produces many more ATP than glycolysis.

Pig feed can contain vegetables with a high content of raffinose-series oligosaccharides. a. Explain why farmers premix this feed with commercial-grade α-galactosidase before feeding the pigs, as a means to increase weight gain b. What causes flatulence in humans (and pigs) who consume vegetables such as broccoli, cabbage, and soybeans, but not when consuming potatoes, squash, and corn?

. (a) Pigs and other mammals lack the enzyme α-galactosidase and therefore cannot break the glycosidic bonds in raffinose oligosaccharides to metabolize this carbohydrate fully. By predigesting the raffinose oligosaccharides with α-galactosidase, the feed has more nutritional value (broken down to simple sugars) and the pigs gain more weight in less time. (b) The flatulence comes from intestinal bacteria that digest the raffinose oligosaccharides contained in broccoli, cabbage, and soybeans using their own α-galactosidase enzyme. Some of the products of anaerobic bacterial metabolism are hydrogen and methane gas. In contrast, potatoes, squash, and corn contain low amounts of raffinose but high amounts of starch, which is easily metabolized by animals using the enzyme α-amylase.

The Cori cycle provides a mechanism to replenish glycogen in muscle cells after anaerobic exercise by converting lactate, derived from muscle glycogen degradation, into glucose in liver cells, which is then exported back to the muscle cells. a. How many net ATP are generated in muscle cells per glucose-1-P generated by the glycogen phosphorylase reaction under these anaerobic conditions; that is, how many ATP are generated by reactions converting 1 glucose-1-P → 2 lactate? Explain. b. Once lactate is converted to glucose in liver cells by gluconeogenesis and then returned to the muscle to rebuild glycogen stores, how many ATP equivalents are required to incorporate each of these glucose molecules into glycogen; that is, 1 glucose + glycogen(n) → glycogen(n+1)? Explain. c. Considering the ATP yields and ATP investments involved in removing glucose from glycogen in muscle cells, converting lactate to glucose in liver cells, and then resynthesizing glycogen using this glucose, what is the net ATP investment of glycogen metabolism with regard to running the Cori cycle?

. (a) The net yield is 3 ATP, not 2, because isomerization of glucose-1-P to glucose-6-P generates the glycolytic metabolite without the investment of 1 ATP by hexokinase. (b) This reaction requires 2 ATP equivalents because glucose must first be phosphorylated by hexokinase to generate glucose-6-P, then isomerized to glucose-1-P and activated by UTP to form UDP-glucose. To regenerate UTP, a second ATP is required by nucleotide diphosphate kinase. (c) The net ATP investment is 5 ATP per glucose from glycogen in muscle cells: +3 ATP yield per glucose derived from glycogen to lactate in muscle cells −6 ATP to convert 2 lactate to 1 glucose in liver cells −2 ATP to add back each glucose into glycogen in muscle cells −5 ATP net cost

What are key concepts of enzyme regulation?

1. could be stimulatory or inhibitory activity 2. mediated by bioavailability of enzymes and control of catalytic efficiency 3. allosteric control

What are 2 examples of increased entropy in living systems?

1. degradation of large biomolecules into larger number of smaller molecules thru process of decay 2. flow of ions thru a channel in a cell membrane form a region of high ionic concentration to one of low concentration during action potential (i.e. nerve impulse)

What are the key concepts in carbon fixation?

1. enzyme rubisco carboxylate (RUBP) taking CO2 and taking carbon and adding it to C5 (ribulose biphosphate) ribulose-1,5-biphosphate carries carbon from CO2 and split in half (2-3 C compounds) 2. calvin benson cycle only active during day 3. light from sun activates calvin cycle enzyme increase rubisco activity in response to increase pH and Mg2+ in stroma thioredoxin-mediated reduction of disulfide bonds

Flux thru oxidative and nonoxidative phases of the pentose phosphate pathway is regulated to meet 3 metabolic states of the cell. What are the states?

1. if increased NADPH is required for biosynthetic pathways or to provide reducing power for detoxification, then fructose-6-phosphate and glyceraldehyde-3-phosphate are used to resynthesize glucose-6-phosphate, thereby maintaining flux thru oxidative phase of the pathway 2. if nucleotide pools need to be replenished because of high rates of DNA and RNA synthesis, then bulk of ribulose-5-phosphate is converted to ribose-5-phosphate, stimulating nucleotide biosynthesis 3. if ATP levels in cell are low, then enzyme glucose-6-phosphate dehydrogenase is inhibited, which shuts down PPP so that glucose-6-P can be metablozied directly by glycolytic pathway

What are the key concepts in photosystems I and II?

1. nuclear fusion reactions in sun release light energy to be absorbed by protein embedded chromophores in plants 2. light absorption by pigments excites electrons from ground state to a higher orbital called excited state 3 outcomes of photon wavelength absorption: resonance energy transfer (antenna), photooxidation (reaction center), fluorescence (waste) 3. Redox reactions in photosynthesis constitute Z scheme = 4 electrons from 2 H2O and 8 photons be absorbed by PSII and PSI 4. 12 H+ (4 from H20, 8 from cytochrome b6f) accumulate in thylakoid lumen for every O2 produced by oxidation of 2H2O and 2 NADPH produced in stroma

What are key concepts in phosphorylation and Calvin Cycle?

1. phosphorylation - process of converting light energy into chemical energy = ATP production 2.ATP synthase complex = takes 4 protons for each ATP to go thru complex 3. cyclic photophosphorylation - ATP required at a much higher rate than NADPH if NADPH levels are high - chloroplast is gonna switch to cyclic photophosphorylation to build up ATP levels

What are key concepts of photooxidation reactions?

1. photosynthesis is similar to electron transport system in mitochondria 2. oxidation of water to produce oxygen 3. ATP and NADPH convert CO2 to glyceraldehyde3P in carbon fixation pathways

How much H2O is needed to make an O2?

2

The first two reactions of gluconeogenesis are required to reverse reaction 10 (or the last reaction) of glycolysis. How many ATP equivalents are used by these first two reactions of gluconeogenesis? 2 6 3 1 4

2

The products of the oxidative portion of the pentose phosphate pathway are carbon dioxide and 2 NADH + 1 hexose phosphate. 2 NADPH + 1 hexose phosphate. 2 NADP+ + 1 pentose phosphate. 2 NADPH + 1 pentose phosphate.

2 NADPH + 1 pentose phosphate.

ATP contains what kind of bonds?

2 phosphoanhydride bonds which can be hydrolyzed to yield ADP and Pi, or AMP and PPi through coupled reactions

Approximately how many ATP are synthesized per O2 molecule generated in photosynthesis light reactions? 12 3 8 4

3

In C3 plants CO2 is first incorporated into __________, whereas in C4 and CAM plants the CO2 is first incorporated into __________.

3-phosphoglycerate oxaloacetate

What is the maximum number of covalent bonds a carbon atom can make?

4

Match the general type of carbohydrate in the first column (a-f)with the best specific example of that carbohydrate in the second column(1-6). Record your answer in the order from a through f. Type of carbohydrate a. disaccharide b. disaccharide heteropolymer c. monosaccharide d. oligosaccharide e. proteoglycan f. glycoprotein 1. fructose 2. raffinose 3. syndecan 4. lactose 5. chitin 6. lectin

4 - a 5 - b 1 - c 2 - d 3 - e 6 - f

How much net ATP is used when you run Cori Cycle?

4 ATP subtract 2 ATP from glycolysis 6ATP to make glucose (gluconeogensis)

Explain why 8 photons need to be absorbed just to move 4 electrons through the photosynthetic electron transport system

4 photons are absorbed by the PSII reaction center and result in electron flow from H2O to plastocyanin. 4 additional photons are required to excite the P700 reaction center in PSI to initiate redox reactions culminating in the reduction of NADP+ to NADPH. Therefore, a photon needs to be absorbed by each reaction center (PSII and PSI) for an electron to be transported through the photosynthetic electron transport system. (See pages 594-595)

How many molecules of CO2 are required for synthesis of each molecule of glucose?

6

Which of the following is correct concerning ATP production in chloroplasts? Choose one: A. Approximately one ATP is produced for every four H+. B. Four H+ are translocated into the lumen per O2 produced. C. Approximately one ATP is produced for every three H+. D. Eight H+ are translocated into the lumen per O2 produced.

A ATP production in chloroplasts appears to use one additional H+ (four total) compared to mitochondria (three total). A total of 12 H+ are translocated into the lumen per O2 produced.

You are preparing for a debate about climate change. Which of the following statements would support the idea that preservation of forests, or even expanding the world's forests, would help stabilize the greenhouse effect? Choose one or more: A.Expanding the amount of the Earth covered by forests and other photosynthesizing organisms would help restore the balance between the amount of CO2 expelled into the atmosphere and the amount consumed by Earth's photosynthesizing organisms. B.Decreasing global production of CO2 by burning fewer fossil fuels, for example, would help restore the balance between the amount of CO2 expelled into the atmosphere and the amount consumed by Earth's photosynthesizing organisms. C.Decreasing global production of N2 by burning fewer fossil fuels, for example, would help restore the balance between the amount of CO2 expelled into the atmosphere and the amount consumed by Earth's photosynthesizing organisms. D.Expanding the amount of the Earth covered by forests and other photosynthesizing organisms would help restore the balance between the amount of N2 expelled into the atmosphere and the amount consumed by Earth's photosynthesizing organisms.

A & B the Earth's atmosphere has been shaped over billions of years. The forces that have shaped it are both abiotic and due to the activities of living organisms. These forces are still at work, but humans over the past few hundred years have altered the amounts of gases in the atmosphere and impacted the mass of photosynthesizing organisms on land and in the oceans and lakes. To reverse the impacts of human activity on atmospheric CO2 levels, it is necessary to both reduce the amount of CO2 we generate and increase the amount of photosynthesizers on the planet.

Which of these modifications best describes the CD2 glycoprotein? N-linked glycosylation that is covalent in nature Correct; N-linked glycosylation that is covalent in nature is the best way to describe the type of glycosylation that the CD2 glycoprotein exhibits. The glycosylation occurs on a side-chain nitrogen atom, hence N-linked glycosylation. If a chemical analysis of this glycan were performed, which of the following results would be expected? A.high-level presence of N-acetylglucosamine B.high-level presence of N-acetylgalactosamine C.low-level presence of mannose D.low-level presence of sialic acid

A & D Correct; the CD2 glycoprotein contains a glycan that is enriched in both N-acetylglucosamine and mannose. Thus, a chemical analysis of the glycan would reveal high-level presence of N-acetylglucosamine and low-level presence of sialic acid.

The structure shown above is an N-linked glycan. What characteristic(s) of the structure confirm it as an N-linked glycan rather than an O-linked glycan? A.The structure contains a core group composed of N-acetylglucosamine and mannose in a specific arrangement characteristic of N-linked glycans. B.The oligosaccharide is linked to the glycoprotein by a glycosidic bond with an asparagine residue. C.The terminal residues are N-acetylneuraminic acid. D.The monosaccharide linked directly to the amino acid is N-acetylglucosamine.

A, B, D N-linked oligosaccharides are connected to glycoproteins through the formation of a glycosidic bond between the amide nitrogen atom in the side chain of asparagine and N-acetlyglucosamine. In addition, N-linked glycoproteins all contain a five-sugar core glycan group. This group is arranged in a specific order as shown in the illustration: Man (α-1,6) (Man α-1,3) Man (β-1,4) GlcNAc (β-1,4) GlcNAc β-1-Asn.

Based on the above reactions, why is the oxygenase activity of rubisco wasteful for plants? Choose one or more: A.The reaction uses O2, and the resulting salvage pathway consumes ATP that could instead be used for metabolically productive activities. B.High rates of photorespiration reduce the amount of carbon fixation, which stunts plant growth. C.A lot of ATP is expended in the glycolate pathway shuttling molecules between cellular compartments. D.Higher temperatures, such as those found in deserts and tropical rainforests, increase the oxygenase activity, which leads to greater production of the metabolically costly 2-phosphoglycolate.

A, B, D The oxygenation of ribulose-1,5-bisphosphate and the metabolism of 2-phosphoglycolate is called photorespiration because O2 is consumed and CO2 is formed. The oxygenase activity of rubisco consumes O2 and the glycolate salvage pathway releases CO2 and uses ATP to form 3-phosphoglycerate, which can enter the Calvin cycle. When O2 competes with CO2 for rubisco, less CO2 is fixed, so less metabolically useful products are formed. This means that the plant has fewer biochemical resources for growth, and is expending energy on forming 3-phosphoglycerate from 2-phosphoglycolate. The product 2-phosphoglycolate is costly to plants because it wastes CO2 and ATP. Plants that grow in hot climates are affected more by this problem because rubisco is less specific for CO2 than O2 at temperatures above 35 ºC.

Calculate the Delta G value (actual change in free energy) at 37 ºC for the aldolase reaction, which converts fructose-1,6-bisphosphate (F-1,6-BP) to glyceraldehyde-3-phosphate (GAP) and dihydroxyacetone-phosphate (DHAP), given the Delta Gº' value for this reaction of +23.8 kJ/mol and the concentrations of these metabolites at steady state; F-1,6-BP = 10 mM, GAP = 0.02 mM, DHAP = 0.02 mM. A. -20.1 kJ/mol B. +1.3 kJ/mol C. +67.7 kJ/mol D. -18.3 kJ/mol E. +49.9 kJ/mo

A. -20.1 kJ/mol Delta G = +23.8 kJ/mol +(8.315 x 10^-3 kJ/mol•K) • (310K) • [ln(2 x 10-5M) (2 x 10-5M)/ 1 x 10^-2M] Delta G = +23.8 kJ/mol +(8.315 x 10^-3 kJ/mol•K) • (310K) • (-17.73) Delta G = +23.8 kJ/mol +(-43.9 kJ/mol)) Delta G =-20.1 kJ/mol

Explain why 8 photons need to be absorbed by photosynthetic eukaryotic plants in order to transfer 4 electrons obtained from the oxidation of H2O through the photosynthetic Z scheme. A. Absorption of 4 photons by PSII leads to 4 e- being transferred from 2 H2O through the Z scheme to plastocyanin; 4 more photons need to be absorbed by PSI in order to generate 2 NADPH from 2 NADP+. B. Absorption of 4 photons by PSI leads to 4 e-being transferred from 2 H2O through the Z scheme to plastocyanin; 4 more photons need to be absorbed by PSII in order to generate 2 NADPH from 2 NADP+. C. Absorption of 8 photons by PSII leads to 8e- being transferred from 4 H2O through the Z scheme to plastocyanin, which is then used to generate 2 NADPH from 2 NADP+. D. Absorption of 4 photons by PSII leads to 4 e- being transferred from 2 H2O through the Z scheme to plastocyanin; 4 more photons need to be absorbed by PSI in order to generate 2 NADP+ from 2 NADPH. E. Absorption of 8 photons provides the energy needed to reduce 4 NADP+ and translocate 16 H+.

A. Absorption of 4 photons by PSII leads to 4 e- being transferred from 2 H2O through the Z scheme to plastocyanin; 4 more photons need to be absorbed by PSI in order to generate 2 NADPH from 2 NADP+.

A person who expresses both GTB enzyme and the GTA enzyme will have which blood type?

AB

What is the molecular currency of intracellular energy transfer and is able to store and transport chemical energy within cells?

ATP

In the five steps used by photosynthetic organisms to convert solar energy into chemical energy, which molecules store the solar energy before sugar synthesis? chlorophylls H2O and O2 NADH and FADH2 ATP and NADPH

ATP and NADPH

The Calvin-Benson Cycle requires which metabolites generated from light reactions?

ATP and NADPH

What are the two primary reasons why a suspension of chloroplasts is unable to synthesize glucose for an extended period of time when it is shifted from the light to the dark, even in the presence of the Calvin cycle substrates CO2 and H2O?

ATP and NADPH will be quickly depleted, and the Calvin cycle enzymes, most importantly rubisco, are inactivated in the dark

Associate each cellular condition or molecular state with its effect on the Calvin cycle.

Active Calvin Cycle NADP+ becomes limiting in the stroma.Ferredoxin continues to donate electrons to ferredoxin-thioredoxin reductase at night. Inhibited Calvin Cycle Chloroplast thioredoxin gene is unable to be expressed.Mutant version of ferredoxin-thioredoxin reductase irreversibly binds thioredoxin. Correct; if the chloroplast thioredoxin gene is turned off, then no thioredoxin will be available for this control system to work. The Calvin cycle enzymes under thioredoxin control will remain oxidized and thus inactive. This will inhibit Calvin cycle activity. Similarly, a mutant version of the enzyme that reduces thioredoxin but binds it irreversibly would likely prevent thioredoxin from reducing the Calvin cycle enzymes. This would also lead to their spontaneous oxidation and inhibition of Calvin cycle activity. On the other hand, if ferredoxin and ferredoxin-thioredoxin reductase continue to undergo a redox reaction at night, then thioredoxin will continue to be reduced, and that will lead to the Calvin cycle enzymes being reduced. This will maintain Calvin cycle activity at night. Finally, the natural system functions by having more than one reductase that can accept electrons from ferredoxin. The primary one transfers electrons to NADP+, but when that substrate is limiting, other reductases, including ferredoxin-thioredoxin reductase, are engaged.

Some types of wheat have been genetically manipulated to change the starch biosynthesis pathway. As a result, the modified wheat synthesizes more amylose than the unmodified wheat. Amylose is known as a resistant starch, meaning it resists digestion in the stomach and small intestine. Resistant starch is thought to be beneficial to the digestive system, in the same way that dietary fiber is beneficial. Why is amylose a resistant starch, whereas amylopectin is not?

Amylose contains only α-1,4 glycosidic bonds, whereas amylopectin contains both α-1,4 and α-1,6 glycosidic bonds. The absence of α-1,6 glycosidic bonds in amylose results in a linear structure with fewer accessible ends. Hydrolysis of amylose is therefore slower and more difficult in the gut.

Which of the following biochemical reactions are endergonic?

Anything with a positive kJ/mol These reactions required energy from their surroundings (ΔG>0) and are therefore endergonic.

Observe the amino acid that is shown. This is the amino acid that is chemically interacting with the glycan. Based on the molecular structure of the amino acid side chain, what is this amino acid?

Asparagine Correct; after removing the nine-sugar residue ligand from view within the CD2 glycoprotein molecular structure, an amide side chain is observed. Asparagine is the amino acid among these choices that has an amide side chain.

How do eukaryotic plants obtain energy at night to maintain sufficiently high levels of ATP

At night, plants rely on glycolysis and mitochondrial respiration to generate ATP for cellular process

What are examples of gluconeogenesis in everyday biochemistry?

Athletes after rigorous exercise build up large amounts of lactate in muscles as a result of anaerobic glycolysis warming down period of continual movement under aerobic conditions to increase circulation and remove lactate from muscle lactate transported to liver and converted to glucose by gluconeogenic pathway and shipped back to muscles to replenish glycogen (Cori Cycle)

A farmer in the Midwest discovered pigweed in her field that was resistant to atrazine. She sent some of the pigweed to a laboratory for analysis. The results showed that the atrazine-resistant pigweed had an amino acid substitution that blocked atrazine binding. Specifically, the serine residue at position 264 of the atrazine-binding protein had been replaced by a glycine. Based on what you know about the structures and properties of serine and glycine, and an examination of the structure of atrazine (shown below), what might be the molecular basis for atrazine resistance in the farmer's pigweed? Choose one: A. addition of charge repulsion due to like charges in glycine and atrazine B. loss of a hydrogen bond between serine and atrazine C. loss of an α helix due to the presence of glycine D. loss of an electrostatic bond between serine and atrazine

B Correct; serine is capable of forming hydrogen bonds through the hydroxyl group in its side chain. A mutation that changes serine to glycine results in the loss of that hydroxyl group and thus the loss of that hydrogen-bonding ability. Atrazine therefore loses its ability to function as a competitive inhibitor, rendering the pigweed atrazine-resistant.

Which of the following is NOT an outcome from excitation of an electron in a chlorophyll molecule? Choose one: A. Return of the chlorophyll molecule to the ground state with excitation of a nearby chlorophyll molecule via resonance energy transfer B. Photoreduction of the neighboring chlorophyll molecule C. Return of the chlorophyll molecule to the ground state via fluorescence D. Photooxidation of the chlorophyll molecule

B There are three main outcomes for a chlorophyll molecule that has been excited by an electron, but only two of these processes are useful for energy conversion. When a chlorophyll molecule returns to the ground state via fluorescence or a loss of heat, no useful work is accomplished. Resonance energy transfer is important for light energy harvesting, as it is a way for a chlorophyll molecule to absorb an electron and pass this energy to a nearby molecule. Chlorophyll can also undergo photooxidation, which leads to reduction of an acceptor molecule. These processes take place in protein complexes called reaction centers.

Which of the following statements best supports the idea that photon absorption by chlorophyll is an all-or-none phenomenon? Choose one: A. The polycyclic planar structure of chlorophyll, along with the presence of the central Mg2+ ion, enables an electron in chlorophyll to jump from the ground state to one of several higher levels, depending on the wavelength of the light it absorbs. B. Each delocalized electron above and below the porphyrin ring possesses an energy difference with its adjacent orbital that corresponds to the energy of a photon within the visible light range. C. The hydrophobic tail has a distribution of delocalized electrons around it that enables electrons to jump from the ground state to an adjacent orbital, depending on the energy of the absorbed photon. D. Chlorophylls a and b absorb photons of different energies because they possess porphyrin rings with different arrangements of the central nitrogen atoms and thus different patterns of delocalized electrons.

B electrons can move between orbitals only in discrete ways. That is, they must absorb the amount of energy equal to the energy difference between the orbital they are in and the next higher orbital. Since photons possess discrete amounts of energy, when one with an energy equal to the energy difference between two orbitals strikes a chlorophyll molecule, the energy of the delocalized electron increases and it jumps to the adjacent higher orbital.

Using the delta Gnotprime values for the reactions shown below, what is the delta Gnotprime value for the conversion of phosphoenolpyruvate to 3-phophoglycerate in the gluconeogenesis? a. +12.5 kJ/mol b. -6.3 kJ/mol c. +43.9 kJ/mol d. +25.1 kJ/mol e. -2.9 kJ/mol

B. -6.3 kJ/mol Phosphoenolpyruvate<--> 2-Phosphoglycerate DGº' = -1.7 kJ/mol 3-Phosphoglycerate <--> 2-Phosphoglycerate DGº' = +4.6 kJ/mol XXXXX 2-Phosphoglycerate <-->3-Phosphoglycerate DGº' = -4.6 kJ/mol ____________________________________________ Phosphoenolpyruvate<--> 2-Phosphoglycerate DGº'= -6.3 kJ/mo

Fructose-2,6-bisphosphate (F-2,6-BP) is an allosteric regulator that controls flux through the glycolytic and gluconeogenic pathways. Levels of F -2,6-BP increase in the cell in response to insulin and decrease in response to glucagon. Choose the number corresponding to the correct underlined answer. Insulin(1)/Glucagon (2) signaling in liver cells leads to the phosphorylation of PFK-2/FBPase-2, which activates PFK-2(3)/FBPase-2 (4) activity of the enzyme and dephosphorylation (5)/phosphorylation(6) of fructose-2,6-BP. The net result of increased(7) /decreased (8) levels of F-2,6-BP in liver cells is to stimulate flux through the gluconeogenic pathway by lowering the levels of this allosteric inhibitor of the enzyme FBPase-1(9)/phosphofructokinase-1 (10). Glucagon(11)/insulin (12) signaling stimulates protein phosphatase-1 in liver cells leading to the activation of the PFK-2 (13)/FBPase-2(14) domain. A. 1, 4,6, 8, 9, 12, 13 B. 2, 4, 5, 8, 9, 12, 13 C. 1, 4, 5,7, 9, 11, 14 D. 1, 3, 6,7, 10, 11, 14 E. 2,3,6, 8, 9, 12, 13

B. 2,4,5,8,9,12,13

Photons first enter the Z scheme via which molecule? a. plastoquinone b. chlorophyll P680 c. plastocyanin d. chlorophyll P700 e. NADPH

B. chlorophyll P680

Which statement below best describes the reason why the Cori Cycle has a net cost of 4 ATP for each glucose that is regenerated? A. Because it requires an investment of 6 ATP equivalents to generate glucose from lactate in the liver but the recovery of ATP in conversion of glucose to lactate in muscle is only 2 ATP. B. Because it requires an investment of 6 ATP equivalents to generate lactate from glucose in the liver but recovery of ATP in conversion of lactate to glucose in muscle is only 2 ATP C. It actually does not cost 4 ATP but rather generates 8 ATP in the total yield D. Because the investment of 2 GTP in gluconeogenesis counts as 4 ATP equivalents, therefore +4 ATP. E. Because there is an investment of 8 ATP in gluconeogenesis and a net yield of 4 ATP in glycolysis.

Because it requires an investment of 6 ATP equivalents to generate glucose from lactate in the liver but the recovery of ATP in conversion of glucose to lactate in muscle is only 2 ATP.

Who can use aerobic respiration? Autotrophs or heterotrophs?

Both

Define the greenhouse effect. Choose one: A. Radiation of heat from the Earth's surface is trapped by atmospheric gases, like O2, and warms the planet's surface above the temperature it would be without the presence of an atmosphere. B. Solar radiation is trapped by Earth's atmospheric gases, like CO2, and warms the planet's surface above the temperature it would be without the presence of an atmosphere. C. Radiation of heat from the Earth's surface is trapped by atmospheric gases, like CO2, and warms the planet's surface above the temperature it would be without the presence of an atmosphere .D. Solar radiation is trapped by Earth's atmospheric gases, like O2, and warms the planet's surface above the temperature it would be without the presence of an atmosphere.

C the Earth's atmosphere is like the glass of a greenhouse. The solar radiation travels through the atmosphere and warms the Earth's surface. The Earth emits radiation away from the surface as heat. But only some of it escapes the atmosphere, while a portion is trapped by greenhouse gases, like CO2, and thus further warms the surface of the Earth.

Process of rubsico taking CO2 out of the atmosphere and uses it to make sugar can sometimes take out O2. It is unproductive when it uses O2 in oxygenated reaction. The adaptation of plants to get around that in increased temperatures is:

C4 and CAM Pathways

What is more efficient than photorespiration?

C4 pathway

What's the difference between C4 and CAM pathways?

C4 uses spatial separation to decrease rates of photorespiration C4 uses 2 different cell types (one that stores malate and one that does CB cycle) CAM uses temporal separation CAM uses time (uses CB cycle in absence of any O2 exchange = closes off plant from atmosphere during day) They both capture and sequester CO2 in the form of malate Difference is where and when CO2 is released for entry into Calvin Cycle

Rubisco takes _ out of atmosphere and uses it to make sugar.

CO2

What is required to synthesize 1 molecule of glucose from 6 CO2?

Calvin Benson Cycle 1. synthesis of 1 glucose molecule from 6 CO2 using 12 ATP and 12 NADPH 2. regeneration of 6 RUBP using 6 ATP

Catabolic pathways are always paired with anabolic pathways. Why? Catabolic pathways build up new molecules and anabolic break down molecules. Both require ATP to operate. Both require redox reactions to operate. Catabolic pathways break down molecules and anabolic build up new molecules.

Catabolic pathways break down molecules and anabolic build up new molecules.

Researchers identified a secreted glycoprotein enzyme in human serum and wanted to know if the glycan group is required for the normal function of the enzyme. To do this, they synthesized the glycoprotein in an in vitro system in such a way that they were able to purify the enzyme with and without the covalently attached glycan group. In vitro enzyme assays using a fluorogenic substrate showed that the enzyme has similar activity in the glycosylated and nonglycosylated forms, leading them to conclude that the glycan group is not required for normal biological function of this enzyme in cells. Give three reasons why this conclusion could be wrong.

Catalytic activity is not the only consideration for determining the in vivo function of an enzyme. First, the glycan groups may be required for targeting the enzyme to the proper secretion or folding pathway inside the cell, which would not be required in an in vitro protein synthesis system. Second, the glycan groups may be required for functional associations with the extracellular matrix, which were not tested in the in vitro enzyme assay. Third, the glycan groups may determine serum survival time for the enzyme, and again, this was not tested.

What is phosphorylation?

Chemical addition of a phosphoryl group (PO3-) to an organic molecule

Molecular O2 competes with CO2 for the active site of rubisco. When this happens, one of the reaction products is of little metabolic use to the plant. That product is then metabolized by the glycolate pathway, which uses enzymes located in three cellular compartments. Sort the glycolate pathway reactions into their proper cellular compartment.

Chloroplast Oxygenation of RuBP to form 2-phosphoglycolate Transfer of a phosphate group from ATP to glycerate to form 3-phosphoglycerate Peroxisome Conversion of serine to glycerate Transamination of glyoxylate to form glycine Oxidation of glycolate to glyoxylate and release of hydrogen peroxide Mitochondrion Deamination and decarboxylation of glycine to form serine

Which of the following activates FBPase-1?

Citrate The conversion between fructose-6-phosphate and fructose-1,6-bisphosphate is important for glycolysis and gluconeogenesis. Thus, the enzymes that catalyze these conversions are highly regulated in opposite manners. The glycolysis enzyme, PFK-1, is turned off when the gluconeogenesis enzyme, FBPase-1, is turned on and vice versa. The regulators are AMP, Fructose-2,6-BP, and citrate.

What does lyase do and name an example.

Cleaves C-C bonds without using a hydrolysis or oxidation reaction decarboxylase is an example

The DNA double helix is stabilized by the interactions between nucleotides because of __________ between nucleotides. a. hydrogen bonding b. ionic interactions c. sigma bonds d. pi-pi stacking

D

Which of the following is TRUE regarding hemes but FALSE regarding chlorophylls? Choose one: A. Contains five rings B. Porphyrin ring coordinates Mg2+ C. Contains a hydrophobic phytol tail D. Porphyrin ring coordinates Fe2+

D Chlorophylls are closely related to hemes and other protoporphyrins, but differ in three clear ways. Chlorophyll coordinates Mg+2, while heme coordinates Fe2+. Chlorophyll also contains a fifth ring and also has a hydrophobic tail.

The concentration of CO2 in the atmosphere is 300 to 400 parts per million (ppm). Some commercial growers artificially increase CO2 to 1,000 to 1,400 ppm in their greenhouses. Why do you think they increase the CO2 concentration and what effect does the higher CO2 concentration have on photosynthesis, if any? Choose one: A. This inhibits photorespiration by inhibiting the activity of mitochondrial glycine decarboxylase (through negative feedback) in the glycolate pathway. This results in a decrease in the oxygenation reaction of rubisco, thus increasing the efficiency of the Calvin cycle's conversion of CO2 into carbohydrates, which increases plant growth rates and enables higher yields. B. This enhances the carboxylation of phosphoenolpyruvate to oxaloacetate by stimulating the activity of phosphoenolpyruvate carboxylase in the first step of the Hatch-Slack pathway. This results in a decrease in the oxygenation reaction of rubisco, thus increasing the efficiency of the Calvin cycle's conversion of CO2 into carbohydrates, which increases plant growth rates and enables higher yields. C. This decreases the Kd of CO2 at the rubisco active site from 10 µM to 1 µM, thus increasing the efficiency of the Calvin cycle's conversion of CO2 into carbohydrates, which increases plant growth rates and enables higher yields. D. This enables CO2 to outcompete O2 for binding to the rubisco active site, which inhibits the oxygenation reaction of rubisco, thus increasing the efficiency of the Calvin cycle's conversion of CO2 into carbohydrates, which increases plant growth rates and enables higher yields.

D Correct; while rubisco's affinity for CO2 is substantially higher than for O2, the concentration of O2 in air is about 500 times that of CO2, enabling O2 to effectively compete with CO2 for binding to rubisco. Artificially increasing the CO2 concentration in the greenhouse air results in an increase in the ratio of productive carboxylation reactions by rubisco to costly oxygenation reactions.

Atrazine is an herbicide that disrupts the activity of photosystem II. It works in the same manner as the herbicide DCMU, which works by Choose one: A. binding near the site of pheophytin and preventing pheophytin from being reduced, thus preventing the photooxidation of P680. B. binding to ferredoxin-NADP+ reductase, siphoning electrons directly from ferredoxin-NADP+ reductase and donating them to O2. C. binding to the PQBH2 site on cytochrome b6f, and thus blocking the translocation of protons into the lumen. D. binding to the site in PSII where PQB would normally bind, thus preventing PQA from transferring an electron to PQB.

D PQB shuttles between PSII and cytochrome b6f depending on its oxidation state. When oxidized (as PQB), it binds to PSII. Upon accepting electrons from PQA, PQBH2 moves a short distance through the thylakoid membrane and binds to cytochrome b6f. There it donates its two electrons, and the oxidized form of plastoquinone B travels back through the membrane to bind again to PSII. DCMU and atrazine bind tightly to the PQB binding site in PSII, thus halting the transfer of electrons through PSII. This prevents the formation of the proton gradient and the reduction of P700. Thus, no ATP or NADPH is produced.

What are biochemical properties of enzyme active sites? Choose the TWO best answers. 1. Enzyme active sites contain metal ions as required components of enzyme reactions. 2. Enzyme active sites decrease the standard free energy of a reaction. 3. Enzyme active sites provide optimal orientation. 4. Enzyme active sites consist of only beta strand regions in proteins. 5. Enzyme active sites exclude excess solvent. 6. Enzyme active sites consist of only alpha helical regions in proteins. 7. Enzyme active sites provide an environment that increases the Keq of a reaction A. 4 and 7 B. 4 and 5 C. 1 and 3 D. 3 and 5 E. 2 and 4

D. 3 and 5

Two reduced plastoquinol molecules (PQBH2) are oxidized in the PQ cycle for every 2H2O that are oxidized by the oxygen evolving complex (OEC). How many protons are translocated into the thylakoid lumen by the PQ cycle? a. 12 protons b. 6 protons c. 10 protons d. 4 protons e. 8 protons

D. 4 protons

What type of antibody or antibodies is/are found in the plasma of a person with type A blood? A. A antibodies B. A + B antibodies C. O antibodies D. B antibodies E. No antibodies

D. B antibodies

In which case will a reaction be spontaneous only above a certain temperature according to the Gibbs free engery equation?

Delta H>0, Delta S>0 The Gibbs free energy change (ΔG) is a way to determine if a chemical reaction is spontaneous under a particular set of conditions. It takes into account the enthalpy (ΔH), the entropy (ΔS), and temperature, as seen in the equation ΔG = ΔH - TΔS. When ΔH is negative and ΔS is positive, a reaction is spontaneous at all temperatures. In the opposition situation, a reaction is never spontaneous at all temperatures. If ΔH is negative and ΔS is negative, the reaction is only spontaneous when T is less than ΔH/ΔS. If ΔH is positive and ΔS is positive, the reaction is only spontaneous when T is greater than ΔH/ΔS.

Light activation of PSI leads to the reduction of ferredoxin, which then reduces not only NADP+ (to form NADPH) but also thioredoxin, which uses the electrons to reduce disulfide bridges in several Calvin cycle enzymes, leading to their activation. What turns off these Calvin cycle enzymes when the Sun goes down?

Disulfide bridges are spontaneously oxidized in the absence of reduced thioredoxin.

A continual supply of reduced glutathione is required to protect red blood cells against the toxic effects of vicine, which is found at high levels in fava beans. Why would individuals with a defect in the enzyme glucose 6-phosphate dehydrogenase (G6PDH) be susceptible to vicine-induced hemolytic anemia? A. The enzyme G6PDH is responsible for reducing reactive oxygen species, so too many ROIs in cell. B. They are susceptible because they cannot release glucose from liver cells in response to glucagon. C. Individuals with a G6PDH deficiency detoxify vicine the kidneys instead of the liver. D. Vicine-induced hemolytic anemia is caused by cellulose in the fava bean cell wall. E. A G6PDH deficiency leads to insufficient NADPH to protect against vicine-induced anemia.

E. A G6PDH deficiency leads to insufficient NADPH to protect against vicine-induced anemia

Calculate the Energy Charge of a cell when the levels of ATP, ADP, and AMP are all equal to 1 mM; is this value for the Energy Charge within the physiological range? A. EC= 2; no, the cell's energy charge does not fall within physiological range. B. EC = 0.5; yes, the cell's energy charge does fall within physiological range. C. EC= 2; yes, the cell's energy charge does fall within physiological range. D. EC= 0.5; no, the cell's energy charge does not fall within physiological range. E . EC= 0.75; yes, the cell's energy charge does fall within physiological range.

EC= 0.5; no, the cell's energy charge does not fall within physiological range

What is the first law of thermodynamics?

Energy can be transferred and transformed, but it cannot be created or destroyed.

Select the TWO true statements from the list below regarding the structure and function of enzymes. Phosphorylation of serine residues, and conformational changes in enzyme subunits, always inhibit enzyme activity. Enzymes function only in their cellular environment. Enzymes decrease the equilibrium constant of biochemical reactions and increase the rates of reactions from years to minutes. Hydrogen bonding networks are all that is required for enzymes to catalyze biochemical reactions. Enzyme cofactors can increase the chemical functionality of enzymes, which are otherwise limited by the R groups of amino acids. The substrate can be predicted by simply knowing the structure of the unoccupied enzyme active site, similar to a key fitting a lock. Enzymes increase the rates of biochemical reactions without changing the equilibrium constant. All proteins are not enzymes but all enzymes are proteins.

Enzymes increase the rates of biochemical reactions without changing the equilibrium constant. Enzyme cofactors can increase the chemical functionality of enzymes, which are otherwise limited by the R groups of amino acids.

The Lineweaver-Burk plot shown below is for a(n) __________ inhibitor.

For competitive inhibitors, vmax remains the same, but Km increases. Both vmax and Km decrease for uncompetitive inhibitors. Mixed inhibitors decrease vmax, but can increase or decrease Km. Noncompetitive inhibitors decrease vmax, but have no effect on Km.

What does ligase do and name an example.

Forms covalent bonds between 2 carbon atoms using ATP cleavage Forms C-O, C-s, or C-N bonds using ATP cleavage Synthetase is an example

What are examples of the pentose phosphate pathway in everyday biochemistry?

G6PD deficiency - results in inability of RBCs to produce enough NAPDH to protect cells from reactive oxygen species

What hormone is activated when one has low blood glucose level?

Glucagon needs more glucose- activates gluconeogenic pathway needs to reduce levels of F26BP - activates FBPase domain

Explain why 3 net ATP are generated in glycolysis using glucose-1-P derived from glycogen degradation, whereas dietary glucose only produces 2 net ATP by glycolysis.

Glucose-1-P is converted to glucose-6-P, which then bypasses the first investment phase of glycolysis (hexokinase). Because only 1 ATP is invested, the net ATP is 3 (4 total ATP are generated in glycolysis).

In the reaction of glutathione reductase, which molecule is oxidized and which is reduced?

Glutathione is reduced while NADPH is oxydized Correct; in this redox reaction, glutathione gains electrons and so is reduced, whereas NADPH donates electrons, or gets oxidized, to NADP+.

Choose the best statement below that accurately describes O-linked glycan to a protein. A. Glycan forms an O-glycosidic bond between a non-reducing sugar and an amino terminal Asn. B. Glycan forms an O-glycosidic bond with an Asn residue of the protein C. Glycan forms an N-glycosidic bond between the protein and -OH group on oligosaccharide D. Glycan forms an O-glycosidic bond with the α-carbon on a residue of the protein E. Glycan forms an O-glycosidic bond involving the anomeric carbon of the oligosaccharide and a Ser or Thr residue on the protein.

Glycans for an O-glycosidic bond involving the anomeric carbon of the oligosaccharide and a Ser or Thr residue on the protein

What happens to the glyceraldehyde - 3P produced by the Calvin Cycle in the chloroplast stroma and why is this important to plant survival?

Glyceraldehyde-3P is used in the stroma to synthesize hexose sugars to produce starch. Alternatively, glyceraldehyde-3P is exported to the cytosol where it is used to synthesize sucrose for export to plant tissues or catabolized by glycolysis to generate pyruvate for aerobic respiration in the mitochondria. This is important for plant survival because it ensures a source of energy at night, when photosynthesis cannot occur.

Which FOUR statements below best describe differences between the glycolytic and gluconeogenic pathways. Glycolytic enzymes are all found in the cytosol, whereas gluconeogenic enzymes are found in the cytosol and the mitochondrial matrix. Insulin stimulates flux through the glycolytic pathway, whereas glucagon stimulates flux through the gluconeogenic pathway. Insulin inhibits flux through the gluconeogenic pathway, whereas glucagon inhibits flux through the glycolytic pathway. Flux through glycolysis is activated by low energy charge in the cell, whereas flux through the gluconeogenic pathway is inhibited by high energy charge in the cell. Citrate inhibits glycolysis but activates gluconeogenesis, whereas F-1,6-BP activates glycolysis and inhibits gluconeogenesis. Gluconeogenesis is only found in liver and kidney cells, whereas glycolysis is only found in liver and pancreatic cells. Gluconeogenesis generates glucose from non-carbohydrate sources, whereas glycolysis generates pyruvate from glucose. Three of the enzymes in glycolysis are reciprocally regulated by allosteric effectors that convert them into gluconeogenic enzymes, i.e., PFK-1 becomes PFK-2 and FBPase-1 becomes FBPase-2. This is not true of any enzymes in the gluconeogenic pathway.

Glycolytic enzymes are all found in the cytosol, whereas gluconeogenic enzymes are found in the cytosol and the mitochondrial matrix. Insulin stimulates flux through the glycolytic pathway, whereas glucagon stimulates flux through the gluconeogenic pathway. Insulin inhibits flux through the gluconeogenic pathway, whereas glucagon inhibits flux through the glycolytic pathway. Gluconeogenesis generates glucose from non-carbohydrate sources, whereas glycolysis generates pyruvate from glucose.

Which of the following is an example of a heterotroph?

Heterotrophs are unable to convert solar energy into chemical energy directly. Yeast is not capable of photosynthesis and is a heterotroph. Plants, single-cell algae, and photosynthetic bacteria like cyanobacteria are autotrophs capable of converting solar energy into chemical energy

Observe the multiple subunits of glycogenin and compare them to one another at both the overall structural level and that of the amino acid sequence. Which of the following is the best description of this protein?

Homodimer glycogenin is a protein that is comprised of two identical polypeptide chains. Therefore, glycogenin is a homodimer.

Under what conditions do wasteful side reaction of O2 with rubisco become significant?

Increased levels of soluble O2 than CO2

Under what condition(s) do the wasteful side reaction of O2 with rubisco become significant?

Increased temperature and intense light

What hormone is activated when one has high blood glucose level?

Insulin activates glycolytic pathway needs to increase F26BP - activates PFK-2 domain

Describe two ways in which oligosaccharides in human milk provide probiotic benefits to newborn babies . Use specific examples of characterized oligosaccharides

Lacto-N-tetraose offers a growth advantage to bifidobacterial, which contain the glycosidases required to metabolize this oligosaccharide. The bifidobacteria are thought to be beneficial bacteria because they bind to intestinal cells and protein the gut from toxins and other damaging agents. Lacto-N-fucopentaose I inhibits pathogenic bacteria from invading intestinal epithelial cells by providing many competing glycan binding sites.

The Biosphere 2 project, in Tucson, Arizona, was an experiment involving a large sealed terrarium with humans and photosynthetic plants living in balance. Why did the project have to be interrupted after only a few months?

Levels of Co2 rose to dangerous levels

What is LHC?

Light Harvesting Complex large protein complex involved in resonance energy transfer (transfers energy to reaction centers) chlorophyll molecules not transferring electrons = transferring energy from different parts of thylakoid membrane which is in chloroplasts into reaction center once energy is transferred = photooxidation event >> redox series

What is the metabolic logic that explains why liver cells contain the enzyme glucose-6-phosphatase but muscle cells lack this enzyme?

Liver cells use glycogen as a source of exporting glucose. Following isomerization of glucose-1-P to glucose-6-P, the phosphate must be removed for export. Muscle cells use the glucose-6-P derived from glycogen as a source of metabolic energy for muscle contraction and need it to remain phosphorylated so that it is not exported.

Lipoamide is a covalently attached coenzyme that plays a key role in several decarboxylase reactions, including glycine decarboxylase, and is attached to a lysine residue in the enzyme.Review the molecule again. Manipulate it in order to identify the specific lysine residue that serves as the attachment site for lipoamide in the enzyme glycine decarboxylase. You may want to view the hint if you need help.

Lysine 63 Lipoamide is a coenzyme, and the example of pea glycine carboxylase illustrates that these cofactors like lipoamide can covalently attach to the enzyme. Coenzymes provide additional chemical flexibility for facilitating the catalytic reaction, which the protein component of the enzyme may be unequipped to do. Coenzymes are usually derived from vitamins and were first discovered as biomolecules required for health.

C4 plants inhibit photorespiration and increase CO2 fixation efficiency by separating the capture of CO2 and the Calvin cycle into two adjacent cell types. Sort the following reactions based on whether they occur in mesophyll cells or bundle sheath cells.

Mesophyll Cells:Reduction of oxaloacetate to malatePyruvate + ATP → PEPHCO3- + PEP → oxaloacetate Bundle Sheath Cells:Malate + NADP+ → Pyruvate + NADPH + CO2Calvin cycleGlyceraldehyde-3-P → Starch and Sucrose Correct; atmospheric CO2 is captured as oxaloacetate via its reaction with phosphoenolpyruvate. Oxaloacetate is converted to malate, which is shuttled from mesophyll cells into bundle sheath cells through channels that connect the two layers of cells. In the bundle sheath cell chloroplasts, malate is decarboxylated to form pyruvate and CO2, which enters the Calvin cycle. To complete the cycle, pyruvate leaves the bundle sheath cells through channels leading to the mesophyll cells, where it is converted to phosphoenolpyruvate that can be used again in the fixation of CO2.

What is the advantage of using methicillin compared to using penicillin as an antibiotic? A. Methicillin does not bind to transpeptidase B. Penicillin is inactivated by mutant transpeptidase enzymes. C. Methicillin is resistant to beta - lactamase activity. D. Penicillin causes mutation in DNA. E. Methicillin is more soluble in water.

Methicillin is resistant to beta -lactamase activity.

What are the key enzymes in gluconeogenesis?

Mnemonic: Pathway Produces Fresh Glucose -- Pyruvate carboxylase -- PEP carboxykinase -- Fructose 1,6, bisphosphatase-1 -- Glucose 6 phosphatase

What does transferase do and name an example.

Moves functional groups transaminase and kinase are examples

Why does it make sense that muscle and liver glycogen phosphorylase are differentially regulated by glucose and AMP?

Muscle phosphorylase is activated by AMP, a signal for a low energy state. Glucose inhibits liver phosphorylase by feedback inhibition, signaling that glucose is not being exported rapidly and reducing glycogen degradation. Muscle phosphorylase is not inhibited by glucose because muscle cells use glucose for energy production. Degradation of glycogen in the liver is independent of the energy needs of the liver cell.

What molecule activates the pentose phosphate pathway? ribulose-5-phosphate NADP+ NADH ADP

NADP+

what functions as a strong reductant in both biosynthetic pathways and in detoxification reactions?

NADPH

What are 7 small biomolecules?

NH4+ Co2 NADH FADH2 O2 ATP H20

A person who expresses neither GTB or GTA enzyme will have which blood type?

O

Electrons from plastocyanin are passed on to O2. P680+. cytochrome b6f. P700+.

P700+.

What are the domains of PFK-2/FBPase-2?

PFK-2 domain kinase domain when active, makes more F26BP activates glycolytic pathway FBPase phosphate domain when active, reduces F26BP stimulates gluconeogenisis

What controls levels of F26BP?

PFK-2/FBPase-2 dual function enzyme

Which statement below best describes the glycoconjugate structure of bacterial cell walls? A. Proteoglycans that contain long glycosaminoglycan chains covalently attached to protein . B. Variant glycosyltransferases that primarily function in the extracellular matrix . C. Peptidoglycans with multiple strands of hexosamine polysaccharide chains linked together. D. Transpeptidases that generate the interstrand crosslinking of polysaccharide chains . E. Glycosaminoglycans consisting of glycan sugars attached to hyaluronic acid through linker protein

Peptidoglycans with multiple strands of hexosamine polysaccharide chains linked together.

Which enzyme, shown as 4 in the figure below, processes oxaloacetate that has been shuttled from the matrix via malate transport to enter gluconeogenesis?

Phosphoenolpyruvate carboxykinase NADH is needed in the cytosol for gluconeogenesis to proceed. This is done by transporting malate. Oxaloacetate is converted to malate via mitochondrial malate dehydrogenase, which produces NAD+ in the matrix. Once transported to the cytosol, malate is converted back to oxaloacetate by cytosolic malate dehydrogenase, which produces NADH.

Which state of glycogen phosphorylase gives the enzyme its highest activity?

Phosphorylated glycogen phosphorylase Correct; the enzyme glycogen phosphorylase becomes active when it is phosphorylated.

What is the energy source for sustaining the electrochemical proton gradient in chloroplasts; what is the biochemical function of this gradient? A. Metabolite oxidation; reduction of NADP+ B. Metabolite oxidation; production of ATP via chloroplast ATP synthase complex C. Metabolite oxidation; production of ATP via mitochondrial ATP synthase complex D. Photon absorption; production of ATP via chloroplast ATP synthase complex E. Photon absorption; reduction of NADP+

Photon absorption; production of ATP via chloroplast ATP synthase complex

In terms of photorespiration and ATP requirements, what explains the observation that crabgrass, which uses the C4 pathway of carbon fixation, has a growth advantage over turfgrass when temperatures are high and the O2-to-CO2 ratios are elevated because of increased O2 solubility?

Photorespiration is a "wasteful" reaction because 2-phosphoglycerate must be salvaged by the glycolate pathway at the expense of ATP hydrolysis. Therefore, the C4 plant has an advantage in summer because it minimizes loss of carbon to photorespiration when CO2-to-O2 ratios are low (elevated soluble O2). However, the C4 pathway requires an investment of ATP to regenerate metabolites in a reaction that is not required by C3 plants. Therefore, at low temperatures, when the CO2- to-O2 ratio is still relatively high, this extra ATP investment by C4 plants comes at an energy cost, thereby giving C3 plants a growth advantage.

Why is photorespiration considered wasteful, and how do Saguaro and Sugarcane plants reduce this waste under conditions of high temperatures?

Photorespiration is considered wasteful because the product of the oxygenase reaction, 2-phosphoglycolate, provides no obvious metabolic benefit to the cell and must be converted to 3-phosphoglycolate through the glycolate pathway, which requires the investment of 1ATP. Saguaro cacti limit this waste by capturing CO2 at night when evaporation rates are low. Sugarcane plants reduce this waste by separating gas exchange and CO2 fixation into two different cell types.

Name three processes affecting enzyme bioavailability and three mechanisms controlling catalytic efficiency.

Processes affecting enzyme bioavailability are: RNA synthesis (gene transcription), RNA processing, protein synthesis (amount of enzyme produced), protein degradation, and protein targeting (organelle sub localization or membrane insertion). Mechanisms controlling catalytic efficiency: Binding of regulatory molecules, covalent modification, and proteolytic processing.

When phosphorylated, changes conformation of enzyme

R conformation - active, relaxed T conformation - tight/taught, inactive

Why is photorespiration a bigger problem for plants at high temperatures, and which enzyme is responsible for this wasteful process? A. Ratio of soluble O2: CO2 is decreased; PEP Carboxylase B. Ratio of soluble O2: CO2 is decreased; Rubisco C. Ratio of soluble O2: CO2 is increased; Rubisco D. Ratio of soluble O2: CO2 is increased; PEP Carboxylase E. Ratio of soluble O2: CO2 is 1.0; PEP Carboxylase

Ratio of soluble O2: CO2 is increased; Rubisco

Which is a way that light controls the Calvin cycle activity? Reduced ferredoxin from the light reactions keeps thioredoxin reduced, which keeps Calvin cycle enzymes in an active form. Calvin cycle or dark reaction enzyme activators are present at higher levels in the dark. Calvin cycle enzymes are inhibited by the lower H+, which is pumped out of the stroma by light reactions. High levels of ATP and NADPH from the light reactions inhibit the Calvin cycle enzymes.

Reduced ferredoxin from the light reactions keeps thioredoxin reduced, which keeps Calvin cycle enzymes in an active form.

The Light Harvesting Complex (LHC) molecules are arranged to facilitate A. Photooxidation reactions between LHC I and II B. Excitation of a photon by electrons in chlorophyll C. Resonance energy transfer to the reaction center D. Transfer of electrons to the reaction center E. Absorption of photons initially at plastocyanin

Resonance energy transfer to the reaction center

A middle-Eastern family presents for evaluation because their infant son died in the nursery with severe hemolysis and jaundice. The couple had two prior female infants who are alive and well, and the wife relates that she lost a brother in infancy with severe hemolysis induced after a viral infection. Red blood cells from the patient have very low concentrations of reduced glutathione. Defective synthesis of which of the following pairs of compounds would likely be found in this patient? Glucose-6-phosphate and NADH Fructose-6-phosphate and ATP Glucose and NADH Deoxyribose and NADP+ Lactate and NADPH Ribose and NADPH

Ribose and NADPH

Choose the ONE true statement referring to the following coupled: Rxn1 A↔B DG°' = -2 kJ/mol Rxn2 B↔C DG°' = +7 kJ/mol Rxn3 C↔D DG°' = -8 kJ/mol Net Rxn A↔D DG°' = -3 kJ/mol The net reaction of A→D is unfavorable because the DG°' value is less than 0. Rxn2 (B↔C) is unfavorable in the forward direction on its own, but if coupled to Rxn3 (C↔D), the overall conversion of B to D will occur. Rxn1 is a favorable reaction and will proceed in cells even if cellular concentrations of reactants and products change. For Rxn2, if the DG°' value changes to +9 kJ/mol, the rate of the overall reaction A↔D will decrease.

Rxn2 (B↔C) is unfavorable in the forward direction on its own, but if coupled to Rxn3 (C↔D), the overall conversion of B to D will occur.

In the light, what is the pH in the thylakoid lumen and stroma?

TL = 5 Stroma = 8

Glucose-6-phosphate (G6P) is a central metabolite in carbohydrate metabolism. Describe the regulatory mechanism that controls the relative flux of G6P through the Pentose Phosphate Pathway or the Glycolytic Pathway.

The NADP+:NADPH concentration ratio in the cytosol allosterically regulates the activity of G6P. When the concentration of NADP+ is high, G6P dehydrogenase (G6PD) is allosterically activated, increasing flux through the pentose phosphate pathway and leading to the production of NADPH. High NADPH concentrations compete with NADP+ binding to G6PD, thereby reducing the activity of the enzyme

What must be the chemical property of the electron acceptor molecule that is reduced by electron transfer when chlorophyll photooxidized? Choose the one best answer. A. The acceptor molecule must have a lower reduction potential than chlorophyll (more positive). B. The acceptor molecule must have a higher reduction potential than chlorophyll (less positive). C. The acceptor molecule must have a higher reduction potential than chlorophyll (more positive). D. The ring structures of the acceptor molecule and chlorophyll cannot both contain nitrogen. E. The metal ion in the acceptor molecule and chlorophyll both contain manganese

The acceptor molecule must have a higher reduction potential than chlorophyll (more positive)

Penicillin kills bacteria by inhibiting the biosynthesis of the cell wall. How does penicillin cause the inhibition?

The beta lactam ring of penicillin forms a covalent intermediate with transpeptidase

Choose the statement that describes what the actual change in free energy (DG) tells you about an enzymatic reaction, which cannot be determined by the standard free energy (DGº') change. A. The spontaneity of the reaction in the presence of an inhibitor. B. The temperature of the reaction at 1 atmosphere pressure. C. The direction of the reaction under steady state conditions D. The direction of the reaction at 1M substrate concentration at pH7 E. The actual change in free energy = 0, so it does not tell you anything.

The direction of the reaction under steady state conditions

What is Gibbs free energy?

The energy associated with a chemical reaction that can be used to do work difference between entropy and enthalpy of a system at a given temperature

What is the third law of thermodynamics?

The entropy of a system approaches a constant value as its temperature approaches absolute zero. DeltaG=-RTlnKeq

An individual with chronic hypoglycemia was suspected of having a defect in one of the enzymes unique to gluconeogenesis. To identify the defective enzyme, tissue samples from a normal liver were compared to samples from the patient's liver biopsy, using a biochemical assay that measures glucose production from glycerol or malate. It was found that incubation with glycerol produced normal amounts of glucose in both the control and biopsied liver samples; however, incubation with malate did not lead to glucose production in the liver biopsy, even though it did lead to glucose production in the control liver sample. On the basis of these observations, which of the four unique gluconeogenic enzymes is most likely defective in this individual? Hint: See Figure 9.48 to review glycerol entry into the gluconeogenic pathway and Figure 10.39 to review the transport of citrate cycle metabolites in and out of mitochondria.

The finding that glycerol addition to the biopsied liver sample leads to glucose production suggests that fructose-1,6- bisphosphatase and glucose-6-phosphatase are normal. The defect could be in phosphoenolpyruvate carboxykinase or pyruvate carboxylase. Because malate, converted to oxaloacetate by malate dehydrogenase, does not lead to glucose production suggests that the defective gluconeogenic enzyme is phosphoenolpyruvate carboxykinase. A defect in pyruvate carboxylase would still allow glucose production after malate addition.

What is biochemical basis for ABO human blood types? Explain why AB type individuals can accept packed red blood cells from any donor but cannot accept plasma from O type individuals

The human ABO blood types are determined by expression of one, both, or neither of the two related enzymes GTA and GTB. Therefore, expression of GTA yields A-type blood, expression of GTB only yields B-type blood, expression of GTA and GTB yields AB-type blood, and expression of neither yields O-type blood. AB type individuals can accept packed red blood cells from all blood types be cause AB plasma does not contain A or B type antibodies. AB type individuals cannot accept O-type plasma because it contains both anti-A and anti-B antibodies, which will recognize the A and B antigens and trigger an immune response

There are nine lysine residues within pea gylcine carboxylase. Why would a specific lysine attachment site for lipoamide be conserved among orthologous decarboxylase proteins?

The lipoamide needs to be precisely located near the enzyme active site. Some coenzymes are covalently linked to amino acid functional groups in enzymes and serve as integral components in the catalytic reaction. One example of this is the attachment of lipoic acid to a specific lysine residue in enzymes that catalyze redox and acyl transfer reactions. In pea glycine decarboxylase, lipoamine covalently attaches at lysine 63, which locates the coenzyme near the enzyme active site, allowing it to participate in the catalytic reaction.

Observe the ribbon structure of pepsin. Determine the relative proportions of secondary and quaternary structure(s). What best describes these structures?

The major secondary structures are beta sheets, and there is no quaternary structure. Correct; pepsin is comprised of a single polypeptide chain and therefore does not have quaternary structure. The major secondary structures within this polypeptide chain are beta sheets, of which there are many. There are only five examples of very short alpha helices.

Considering that gluconeogenesis requires a net input of 4 ATP equivalents compared to glycolysis , why would a cell utilize this pathway, ie., what is the metabolic advantage of this pathway?

The metabolic advantage of the gluconeogenic pathway is to provide glucose from the liver when it is needed in the blood, e.g., in between meals or after intense physical activity when blood lactate levels accumulate

Why are 8 photons required for the net reaction of the photosynthetic electron transport system (2 H2O + 8 photons + 2 NADP+ + 3 ADP + 3 Pi → O2 + 2 NADPH + 3 ATP)?

The oxidation of 2 H2O generates 4 e−; however, 4 photons are required at each of the PSII and PSI reaction centers to move the e− through the photosynthetic electron transport system.

The cytochrome b6f complex of the photosynthetic electron transport system is responsible for translocating 8 H+ into the thylakoid space from the stroma in response to light. However, a total of 12 H+ accumulate inside the thylakoid space as a result of photon absorption by PSII and PSI. What is the origin of the other 4 H+?

The oxidation of 2 H2O to form O2 + 4 H+ + e−

What redox reaction ultimately replaces the transferred electron so that the chlorophyll molecule becomes reduced and can therefore undergo another round of photooxidation?

The oxidation of H2O generates the e− that reduces chlorophyll.

Heparin has one of the highest negative charge densities ever found in a biomolecule and is used commercially to prevent blood clotting. Heparin binds to and activates antithrombin, thereby inhibiting the blood clotting cascade. An accidental heparin overdose can be fatal. How does infusion with protamine sulfate, a cationic protein, counteract the effects of a heparin overdose? A. The positively charged protamine sulfate binds to the negatively charged heparin and inactivates it. B. Protamine binds to and inhibits antithrombin and thereby indirectly counteracts heparin overdose. C. Protamine stimulates antithrombin degradation by the proteasome and thereby counteracts heparin D. The negatively charged heparin molecule is degraded by protamine sulfate through ionic interactions. E. Protamine sulfate binds to glutathione and prevents it from be oxidized, which is required for clotting

The positively charged protamin sulfate binds to the negatively charged heparin and inactivates it

What is the second law of thermodynamics?

The principle stating that every energy transfer or transformation increases the entropy (dispersion of energy) of the universe. in absence of energy input - all natural processes in the universe tend toward disorder

What is a proton gradient?

The product of the electron transport chain. A higher concentration of protons outside the inner membrane of the mitochondria than inside the membrane is the driving force behind ATP synthesis.

T is the less active form of an allosteric enzyme and R is the more active form of enzyme. What happens to the value for the ratio of [ inactive enzyme]/[active enzyme] when the substrate concentration decreases relative to high substrate levels? A. The ratio is decreased B. The ratio is increased C. Unchanged ratio D. Ratio = 10 E. Ratio = 0.1

The ratio is increased

What is the carbon shuffle?

The series of regeneration reactions that produce ribulose-1,5-bisphosphate

The term greenhouse effect refers to the idea that A. the capacity of the earth's plant matter to store CO2 is increasing. B. the temperature of the earth is increasing because of heat trapped by gases such as CO2. C. tropical rainforests are gradually being eliminated by development of fires. D. the global production of plant matter is increasing to the point where it insulates the earth E. the number of greenhouses being used to grow cannabis as a commercial crop is increasing

The temperature of the earth is increasing because of heat trapped by gases such as CO2

Which statement below most accurately describes the biochemical basis for the emergence of MRSA infections? Staph aureus express high levels of beta-lactamase The transpeptidase enzyme in Staph aureus does not bind methicillin Penicillin and methicillin are structurally similar, which causes antibiotic resistance. Staph aureus exports methicillin faster than it can inhibit the transpeptidase

The transpeptidase enzyme in Staph aureus does not bind methicillin

Some Calvin Cycle enzymes contain disulfide bonds that must be reduced through a mechanism involving thioredoxin in order for the enzyme to be active in sunlight. What is the name of the key regulatory protein that inactivates these same Calvin Cycle enzymes by oxidation when the sun goes down? Choose the ONE best answer. Thioredoxin requires sunlight for proper folding into its functional three dimensional structure, so in the absence of light, it is unfolded and cannot reduce these enzymes. There is no regulatory protein that oxidizes these Calvin Cycle enzymes; oxidation is spontaneous. Sunlight is a reducing energy and moonlight is an oxidizing energy, so when the moon comes out at night, the Calvin Cycle enzymes are oxidized spontaneously. Thioredoxin has multiple light-sensing properties and when the sun goes down it turns into a strong oxidant. The protein is called ferredoxin-thioredoxin reductase.

There is no regulatory protein that oxidizes these Calvin Cycle enzymes; oxidation is spontaneous.

Which statement regarding CAM plants is true? They use one cell type to absorb and store CO2 before utilizing it in the Calvin cycle in another cell type.XXXX They are more efficient than C4 plants. They absorb CO2 at night and release it to the Calvin cycle during the day. They store CO2 in 3-phosphoglycerate before releasing it to the Calvin cycle.

They absorb CO2 at night and release it to the Calvin cycle during the day. A plant that uses an adaptation for photosynthesis in arid conditions in which carbon dioxide entering open stomata during the night is converted to organic acids, which release CO2 for the Calvin cycle during the day, when stomata are closed.

Why are C4 plants better adapted to hot climates than C3 plants? A. They can produce sugar molecules at night using the Calvin-Benson cycle and during the day. B. They are able to increase rates cyclic photophosphorylation and produce more ATP in warm climates. C. They can capture CO2 and store it during times that O2 levels are high and minimize photorespiration. D. They can release the CO2 that was stored in the form of malate back into the atmosphere. E. They can synthesize more amylopectin than amylose and thereby have more sugar available.

They can capture CO2 and store it during times that O2 levels are high and minimize photorespiration.

How do individuals with decreased levels of the pentose phosphate enzyme G6PD respond to oxidative stress?

They do not have the ability to regenerate reduced glutathione as rapidly as individuals with normal levels of the enzyme

Why is referring to the Calvin cycle reactions as the dark reactions a misnomer?

They require an active photosynthetic system in the light, so are not the "dark reactions" in everyday biochemistry.

5. Consuming large amounts of alcohol when blood glucose levels are low can lead to hypoglycemia due to low rates of gluconeogenesis. Considering that ethanol is oxidized to acetaldehyde by the enzyme alcohol dehydrogenase, how do you explain the inhibitory effect of alcohol consumption on gluconeogenesis and the subsequent hypoglycemia?

This high level of NADH produced by alcohol dehydrogenase drives the lactate dehydrogenase reaction in the direction of lactate production, leading to depletion of pyruvate. Moreover, NAD+ becomes limiting for glyceraldehyde-3-phosphate dehydrogenase, inhibiting glycolysis, further depleting pyruvate and thus inhibiting gluconeogenesis. The excess NADH meanwhile stimulates malate dehydrogenase to produce malate, depleting the gluconeogenic substrate oxaloacetate.

4. Given that glucose-6-phosphate is a substrate for both glycolysis and the pentose phosphate pathway, determine which pathway will have the highest metabolic flux of glucose-6-P under the following conditions.

To Glycolysis o Low cellular ATP o Elevated Levels of ADP and AMP To Pentose Phosphate Pathway o High NADP+ to NADPH ration in the cell o High levels of ROS in a cell Correct; the energy demand for ATP overrides glucose-6-P entry into the pentose phosphate pathway. Otherwise, glucose can enter the pentose phosphate pathway if needed.

Which of the following best defines the first law of thermodynamics? All spontaneous processes in the universe tend toward dispersal of energy. Total amount of energy in the universe is a constant. There is no entropy at zero Kelvin. Entropy is a measure of disorder.

Total amount of energy in the universe is a constant.

The amino acid sequence of a protein determines its structure. Which of the following statements is true? Two proteins with similar amino acid sequences will always have the same function in a cell. It is impossible to determine how proteins will fold based on the amino acid sequence alone. Two proteins with similar amino acid sequence should have similar structures. Two proteins with different amino acid sequences will have identical structures.

Two proteins with similar amino acid sequence should have similar structures.

Paper is made from cellulose fibers. Explain why paper loses its shape and planar strength when it is soaked in water but not when it is soaked in oil.

Water disrupts the intrafiber hydrogen bonds that hold the cellulose fibers together, whereas oil has no effect on hydrogen bonds

What is cyclic photophosphorylation?

When e- is transferred from photosystem I back to the cytochrome b6-f complex to pump more protons and make more ATP. uses PSI as energy converting machine to take solar energy and convert to redox energy

Which of the following mutations would likely be the most devastating to the glucosyltransferase activity of glycogenin, especially when it comes to linking the reducing end of the initial glucose molecule to the protein?

Y to A Correct; the genetic mutation that causes the Y to A change is most likely to destroy the glucosyltransferase activity of glycogenin. This is because the glycogenin protein has a glucosyltransferase activity—an enzyme that adds glucose units to a glycan group—that links the reducing end of the initial glucose molecule to a tyrosine residue on the protein. Tyrosine contains a hydroxyl functional group while alanine does not.

R is the highly active form of an allosteric enzyme and T is the less active form of enzyme. What would happen to [T]/[R] if substrate concentration is decreased?

[T]/[R] would increase An allosteric enzyme has multiple subunits, each with an active site. In positive cooperativity, the binding of substrate to the R state stabilizes it and enhances binding of other substrate molecules. Thus, increasing the substrate concentration will decrease the ratio of [T] to [R]. The opposite occurs when substrate is decreased: less substrate is bound, so less R state enzyme is stabilized. Therefore, the T state concentration increases, increasing the ratio of [T] to [R].

What is an active site?

a region on an enzyme that binds to a protein or other substance during a reaction.

A high proton concentration is also an acidic/basic solution?

acidic

In the gluconeogenic reaction catalyzed by pyruvate carboxylase, CO2 is _?

activated by ATP energy

What are examples of proteoglycans?

aggrecan syndecan glypican

What does carbon fixation accomplish for the cell?

aka Calvin Cycle enzymes use energy available from ATP and NADPH to reduce Co2 to form glyceraldehyde3P (carb used to synthesize glucose) photosynthetic cells use carbs made by carbon fixation reactions as chemical energy for mitochondrial respiration (in eukaryotic cells)

The product Beano contains __________, which helps humans digest raffinose-series oligosaccharides. lactase beta-galactosidase alpha-galactosidase amylase

alpha-galactosidase

What are the 6 primary metabolite groups?

amino acids, nucleotides, fatty acids, glucose, pyrvuate, Acetyl-CoA

Which statement below accurately describes O-linked glycoproteins? an oligosaccharide forms an O-glycosidic bond between a residue on the protein and an -OH group on the oligosaccharide an oligosaccharide forms an O-glycosidic bond with an Asn residue of the protein an oligosaccharide forms an O-glycosidic bond with the α-carbon on a residue of the protein an oligosaccharide forms an O-glycosidic bond involving the anomeric carbon of the oligosaccharide and a Ser or Thr residue on the protein

an oligosaccharide forms an O-glycosidic bond involving the anomeric carbon of the oligosaccharide and a Ser or Thr residue on the protein

What is a heterotroph?

an organism that cannot make its own food and eat other organisms to get proteins and energy aka "consumer" (eg. humans)

Maximal activity of pyruvate carboxylase depends on which of the following substances? Choose the FOUR that apply. Coenzyme A Biotin Acetyl-Coenzyme A [Acetyl-CoA] Thiamine pyrophosphate NADH Pyruvate ADP GTP Bicarbonate [HCO3-] Oxaloacetate

biotin acetyl-CoA Pyruvate Bicarbonate

What are examples of glycolipids?

blood antigens membrane anchors

What type of antibody or antibodies is/are found in the plasma of a person with type O blood? neither anti-A or anti-B anti-A both anti-A and anti-B anti-B

both anti-A and anti-B

C4 plants are thought to be more efficient than C3 plants because they make larger sugar molecules from CO2. can concentrate the CO2 in chloroplasts and therefore minimize side reactions with O2. can live in dry climates. can produce sugar molecules at night in addition to during the day.

can concentrate the CO2 in chloroplasts and therefore minimize side reactions with O2.

What are the 4 major macromolecules?

carbohydrates, lipids, proteins, nucleic acids

Cellulose and cell wall synthesis is dependent on what to be able to build the plant?

carbon fixation

What is the role of catalyst in increasing rate of reaction without changing standard change in free energy?

catalysts change rate, don't change delta G

What would the predicted enzymatic product be when cellulose is exposed to cellulase? cellotetraose glucose hemicellulose pectin

cellotetraose

The primary difference between ATP synthesis during the photosynthetic light reactions and ATP synthesis in the mitochondrial electron transport chain is the

cellular location of the proton motive force.

What is the most abundant carbohydrate?

cellulose

What is aerobic respiration?

chemical reaction using oxygen that transfers energy to cells aka breathing waste products = CO2 and H2O

Electrons from plastocyanin are passed onto _.

chlorophyll p700+

A living cell must convert energy under conditions of:

constant pressure and volume

What does photosynthetic electron transport system accomplish for the cell?

converts light energy into redox energy used to generate ATP by chemiosmosis and reduce NADP+ to for NADPH

What kind of attachment of sugars do glycoconjugates of proteins have?

covalent

Glycogen phosphorylase is an enzyme that catalyzes the rate - limiting step in glycogen degradation. The catalytic activity of this enzyme is stimulated by phosphorylation. What is the best description of this type of enzyme regulation? A. Protein targeting B. Covalent modification C. Allosteric regulation D. Enzyme Inhibition E. RNA synthesis

covalent modification

Which is a way light controls calvin cycle activity?

decrease ferredoxin from light reactions keeps thioredoxin reduced, which maintains Calvin cycle enzymes in active form

What would be an advantage of having a G6PD deficiency?

decreased number of malarial infections

Insulin activates the phosphofructokinase-2 (PFK-2) activity in the dual function enzyme PFK-2/FBPase-2 by _ . This leads to a(n) _ in concentration of F26BP, which stimulates flux through the _ pathway.

dephosphorylation (glucagon activates phosphorylation) increase glycolysis

The mitochondrial electron transport system and the photosynthetic electron transport system are different in many ways. In what way are they similar? A. Electrons are transferred from one electron carrier to the other by redox reactions in both systems B . The inner mitochondrial membrane and the thylakoid membrane are both permeable to protons C . Chemical energy captured in mitochondrial electron transport system and in photosynthetic electron transport system both utilize NADPH as the reductant. D . Mitochondrial electron transport and photosynthetic electron transport both transfers electrons from soluble proteins (not membrane bound) that transfer 2 electrons at a time. E . The PQ cycle is used to translocate protons across the proton impermeable membrane in both systems with a common reaction mechanism involving antioxidants.

electrons are transferred from one electron carrier to the other by redox reactions in both systems

What is the difference between entropy and enthalpy?

entropy - disorder; measure of system's thermal energy that is unavailable for doing useful work (always increasing) enthalpy - heat content of a system, measure energy change

What is covalent modification?

enzymes can be regulated by transfer of molecule or atom from a donor to an amino acid side chain that serves as an acceptor of the transferred molecule raises active site/catalytic efficiency

If Gibbs free energy change value for a reaction is <0, reaction is: a. exothermic b. exergonic c. endothermic d. endergonic

exergonic

Which reaction in metabolism is favorable? Exergonic or endergonic?

exergonic endergonic is unfavorable

A way to determine if a chemical reaction is favorable or unfavorable under given pressure and temperature using a function called:

free energy

Which hormone slows down glycolysis while stimulating gluconeogenesis through the phosphorylation of phosphofructokinase 2 (PFK2) and fructose-2,6-bisphosphatase? ATP protein kinase insulin glucagon

glucagon

What is the final molecule made from the oxidation of H2O by solar energy?

glucose

What are examples of monosaccharides?

glucose galactose mannose

what are examples of polysaccharides?

glucose homopolymers: cellulose, starch glycogen disaccharide heteropolymers: chitin, keratan sulfate

What are the key enzymes to the pentose phosphate pathway?

glucose-6-phosphate dehydrogenase transketolase transaldolase

What is the commitment step in the PPP and what is it inhibited by?

glucose-6-phosphate dehydrogenase converts glucose-6-phosphate to 6-phosphogluconolactone inhibited by NADPH

What are examples of glycoproteins?

glycotransferases, mucin proteins

Red blood cells are placed into a solution of unknown solute concentration. After an hour they have all burst open. The best explanation is that the solution had no solutes. had a very high concentration of solutes. had a very high concentration of solvent was at equilibrium.

had no solutes

What are examples of PETS and Calvin Cycle in everyday biochemistry?

herbicide paraquat prevents reduction of NADP+ by accepting electrons from intermediate reductants in photosystem I

Raffinose-series oligosaccharides are hard for humans to digest because: A. humans do not have the enzyme alpha-1,4-glycosidase necessary to hydrolyze the glycosidic bonds. B. they function as soluble decoys that inhibit pathogenic bacteria from invading the epithelial cells. C. humans have a large number of competing glycan binding sites on their intestinal cells. D. the cell wall is hydrogen bonded to form an impermeable cellulose that prevents amylase from working. E. humans do not have the enzyme alpha-1,6-glycosidase necessary to hydrolyze the glycosidic bonds.

humans do not have the enzyme alpha-1,6-glycosidase necessary to hydrolyze the glycosidic bonds.

How can a proton gradient give rise to ATP synthesis?

if you take a proton and permeable membrane, you take a proton pump, activated by light; take ATP synthase (from another organism) = build vesicle = build up proton gradient

Where does the Calvin-Benson cycle occur?

in chloroplast stroma of a cell

How does light regulate Calvin-Benson cycle enzymes?

in the mitochondria in eukaryotic plants, they use aerobic respiration a do in the dark - allows them to make ATP

Low concentrations of protons = increase/decrease pH

increase

What does citrate inhibit and activate?

inhibits glycolytic pathway activates gluconeogenic pathway

What is the Hatch-Slack Pathway?

involves carboxylation of phosphoenolypyruvate (PEP) by enzyme PEP carboxylase to form oxaloacetate (4C intermediate that serves as transient CO2 carrier molecule) fixes low levels of photorespiration

What is the advantage of the increased branching in glycogen compared with amylopectin and amylose?

it generates more non reducing ends for efficient removal/addition of glucose residues

What does gluconeogenesis accomplish for the organism?

liver and kidneys use gluconeogenesis to generate glucose from noncarbohydrate sources for export to other tissues that depend on glucose for energy - primarily brain and erythrocytes plants use the pathway to convert glyceraldehyde-3-p into glucose which is used to make sucrose and starch

Molecules of NADH are not moved across the mitochondrial membrane. Instead, __________ is the molecule transported to move reducing equivalents of NADH out of the mitochondrial matrix.

malate Correct; malate is transported out of the mitochondria where, in the cytosol, it is converted to oxaloacetate, producing NAD+.

What is Energy Charge (EC)?

measure of ATP, ADP, & AMP in cell and reflects amount of ATP for metabolic reactions **ideal = ATP levels high when EC high ADP, Pi, AMP levels high then EC low

What is an application of gluconeogenesis in everyday biochemistry?

measuring glucose devices based on assay using enzyme glucose oxidase which produces gluconate and hydrogen peroxide from glucose

What are examples of oligosaccharides?

milk oligosaccharides, raffinose

How are plants able to stay alive in the absence of light? A. Mitochondria use carbohydrates as an energy source for cellular respiration B. Without light the "dark reaction" will take place and provide ATP C. The plant will continue photosynthesis with stored energy D. Plants will decrease metabolic flux through glycolysis E. Plants are not living and do not need ATP to survive

mitchochondria use carbohydrates as an energy source for cellular respiration

In humans, to maintain flux through the glyceraldehyde-3-phosphate dehydrogenase reaction in the gluconeogenic pathway, NADH equivalents must be moved from the _.

mitochondrial matrix to the cytosol. Correct; NADH must be moved from the matrix to the cytosol since the mitochondria are still producing NADH. Glycolysis, a primary source of NADH in the cytosol, does not function when gluconeogenesis is active.

What is a dimer molecule?

molecule consisting of 2 identical molecules linked together

In increased temperatures, O2 is more soluble/less soluble than CO2.

more soluble rubsico uses O2 instead of CO2 which negates ability to do CF in high temperatures

What type of antibody or antibodies is/are found in the plasma of a person with type AB blood? anti-A neither anti-A or anti-B both anti-A and anti-B anti-B

neither anti-A or anti-B

When dietary sources of glucose are insufficient and glucose stores have been depleted, where do cells synthesize glucose from?

noncarbohydrate compounds by a series of cytosolic reactions in an anabolic pathway = gluconeogenesis

What are cofactors?

nonprotein enzyme helpers inorganic ions metal elements Fe, Mg, Mn, Cu, Zn, Ni, K, Se, Molybdate

At night, what is the pH in stroma and lumen?

normal (7) Mg levels low in stroma

Why is fructose-2,6-biphosphate unusual?

not part of glycolytic or gluconeogenic pathway very active allosteric regulator when its high - favors glycolysis, when its low - favors gluconeogensis

What is an autotroph?

organism that is able to form nutritional organic substances from simple inorganic substances such as CO2 aka "producer"

What does the pentose phosphate pathway accomplish for the cell?

oxidative phase generates NADPH which is required for many biosynthetic pathways and for detoxification of reactive oxygen species. nonoxidative phase interconverts C3-C7 monosaccharides to produce ribose-5-phosphate for nucleotide synthesis. it also regenerates glucose-6-P to maintain NADPH production by oxidative phase

What are the 2 phases of the pentose phosphate pathway and explain each.

oxidative phase: generates NADPH for biosynthetic pathways also converts glucose-6-phosphate to ribulose-5-phosphate nonoxidative phase: interconverts C3-C7 sugar phosphates using carbon shuffle reactions like the Calvin cycle also generates ribose-5-phosphate for nucleotide synthesis also converts ribulose-5-phosphate to glyceraldehyde-3-phosphate and fructose-6-phosphate

What is oxidative phosphorylation?

pathway where cells use enzymes to oxidize nutrients, thereby releasing chemical energy of molecular oxygen, which is used to produce ATP

What are the 3 primary pathways for anabolic carbohydrate metabolism in nonphotosynthethic organismms?

pentose phosphate pathways gluconeogenesis glycogen degradation and synthesis

What chemical process is able to take place in the presence of solar energy?

photosynthesis

What is the Calvin Cycle aka Carbon Fixation?

plants ability to take atmospheric CO2 and convert to sugar works only during light needs ATP and NADPH from photosynthetic reactions to build carbon structures that it needs

What are examples of autotrophs?

plants, algae, and bacteria

Shared intermediates are used so effectively in coupled reactions because they

products become reactants without diffusing away

What are key enzymes in PETS and Calvin Cycle?

proteins of PETS Chloroplast ATP ribulose-1,5-biphosphate carboxylase/oxygenase (Rubisco)

The catalytic acitivity and/or conformational stability of this protein is likely dependent upon _ of peripheral amino acid side chains. These side chains are expected to have a _ value.

protonation low pKa *pepsin is secreted into the very acidic nature of the stomach. The catalytic acitivty and/or conformational stability of this protein is likely dependent upon protonation of peripheral amino acid side chains.

Why is ribose 5-phosphate important?

provides ribose sugar backbone that anchors nucleotide base to DNA and RNA polymers

What's an oligosaccharide that has an alpha-1,6 bond that we don't have enzymes to digest?

raffinose

Flux is defined as

rate at which metabolites are interconverted

What is the Cori Cycle?

recycles lactate produced in anaerobic muscle cells during exercise by exporting it to the liver where it is converted to pyruvate and used to synthesize glucose by gluconeogenesis

What are coenzymes?

small organic compounds often derived from vitamins B1, B2, B7, B6, B12 NADH, FADH2, Coenzyme A

What are examples of disaccharides?

sucrose maltose lactose

What is solar energy?

sunlight converted to chemical energy

What is glycolysis?

the breakdown of glucose by enzymes, releasing energy and pyruvic acid. breaks down into two 3-C compounds

A reaction is always spontaneous if

the change in free energy, ΔG, is negative.

Cytoplasmic levels of NADH must be maintained in order for gluconeogenesis to occur. What generates NADH for this pathway? the glycolysis pathway the TCA cycle the movement of NADH equivalents from inside the mitochondria via malate transport the mitochondrial electron transport chain

the movement of NADH equivalents from inside the mitochondria via malate transpor

The chloroplast contains a highly folded membrane called the

thylakoid

During photophosphorylation, the protons are pumped into the __________, and the ATP is made in the __________. thylakoid lumen; cytoplasm stroma; thylakoid lumen thylakoid lumen; stroma cytoplasm; stroma

thylakoid lumen; stroma

Why is glutathione important?

to fight oxidative stress

What is the role of most chlorophyll molecules in a photosynthetic membrane? a. to directly convert NADP+ to NADPH b. to participate in fluorescence reactions c. to serve as a light-harvesting antennea d. to photooxidize electron carrier proteins e. to reduce O2 to generate H20

to serve as light-harvesting antennae

Which enzyme does penicillin target in bacteria? alpha-galactosidase beta-lactamase peptidase transpeptidase

transpeptidase

Which of the following correctly describes the biochemistry of the amino acids at the termini of pepsin?

two nonpolar amino acids at the N-terminus and one polar amino acid at the C-terminus Correct; regarding the biochemistry of the amino acids at the termini of pepsin, there are two nonpolar amino acids at the N-terminus and a polar amino acid at the C-terminus.

The O2 generated from photosynthesis is derived from

water molecules that directly reduce PSII

A hydrogen bond can best be described as a strong ionic interaction. strong covalent interaction. weak covalent interaction. weak noncovalent interaction.

weak noncovalent interaction.

Under what conditions does cyclic photophosphorylation take place? in an acidic stroma with high levels of ATP with low levels of ATP with high levels of NADH with an inactivated photosystem I

with low levels of ATP

What is the difference between actual change in free energy ( D G) and standard change in free energy ( D Gº ) with regard to the spontaneity of a given reaction in a living cell?

ΔG° can be used to predict the spontaneity of a reaction under standard conditions, which are 1 atm, 298K, and all reactants and products are initially set at [1M]. Under these conditions, the reaction will be spontaneous if ΔG°<0 as defined by ΔG°=-RT lnKeq. Under cellular conditions, the actual change in free energy (ΔG) is the sum of the ΔG° and a function of the mass action ratio, which includes concentrations of products and reactants under steady state conditions (RT lnQ)

Different racial and ethnic groups have different distributions of blood types within their populations, but type O is universally the predominant form. In all populations, type O is found in approximately 44% of individuals, while the remaining 56% is split unequally among type A (42%), type B (10%), and type AB (4%). The availability of blood products to meet the needs of the whole population is a serious issue. The low donor pool in many countries, along with the frequent use of type O blood to avoid compatibility issues, results in an overdependance on type O blood, while many donations of other bood types go unused. If an incompatible blood source is used for transfusion, it can be lethal to the patient due to hemolysis, which can lead to agglutination. Many researchers are focused on techniques that could convert all donated blood into a universal blood source, increasing the ability to use all donated blood and decreasing the risk of adverse effects from incompatible transfusions. One method of generating a universal blood supply is to use enzymes to modify the glycan structure of the blood group antigens. Which of the following enzymes could be used to convert type B blood to type O?

α-galactosidase an α-galactosidase would hydrolyze the terminal α-galactose residues from glycoproteins or glycoconjugates. Cleavage of the terminal α-galactose residue from the B antigen would produce the O antigen.