Exam 1
R is the highly active form of an allosteric enzyme and T is the less active form. What would happen to [T]/[R] if substrate concentration is decreased
Increase
Binding of glucose to hexokinase causes a conformational change in the enzyme. This is an example of the __________ model of enzyme catalysis.
Induced-fit NOT lock and key(not a thing)
Why is penicillin considered a suicide inhibitor?
It forms an irreversible covalent bond with its enzyme target.
Which of these modifications best describes the CD2 glycoprotein?
N-linked glycosylation that is covalent in nature
Would penicillin be expected to have an equal ability to kill both Gram-positive and Gram-negative bacteria? Why or why not?
No; the lipopolysaccharide layer surrounding Gram-negative bacteria can inhibit penicillin uptake by these bacteria.
Paraquat is an effective herbicide the kills plants by disrupting the photosynthetic electron transport system. Why then was the spraying of marijuana fields with paraquat discontinued in the 1980s?
None of the statements are correct CORRECT answer: People ingested marijuana anyway and there were concerns about health hazards due to paraquat-infused weed.
Individuals with which blood type are the exact opposite in terms of their ability to donate and receive blood products as compared to those with AB blood?
O
When NADPH/NADP+ ratios are high in chloroplasts, photophosphorylation via the cyclic e- pathway predominates. What best describes the consequences of the shift to this pathway.
O2 evolution decreases and NADPH formation decreases.
In the __________ of rubisco by __________, a mechanism is used to control the activity of the Calvin cycle in response to light
activation; increased pH
What accurately describes O-linked glycoproteins.
an oligosaccharide forms an O-glycosidic bond involving the anomeric carbon of the oligosaccharide and a Ser or Thr residue on the protein
Atrazine is an herbicide that disrupts the activity of photosystem II. It works in the same manner as the herbicide DCMU, which works by
binding to the site in PSII where PQB would normally bind, thus preventing PQA from transferring an electron to PQB.
The hormone insulin activates phosphofructokinase 2 (2PFK2). This leads to a(n) __________ in concentration of fructose 2,6 bisphosphate, which favors the __________ pathway.
increase: glycolysis
What differentiates the biochemical standard state from the standard state when discussing standard free energy changes?
pH of 7
When NADPH levels in the stroma are higher than stromal ATP levels, ferredoxin transfers its electron to which of the following?
plastoquinone PQB
What product of the pentose phosphate pathway is a major building block for nucleotides?
ribose-5-phosphate
A reaction is always spontaneous if
the change in free energy, ΔG, is negative.
The phosphorylation state of the light-harvesting complex II (LHC II) impacts the distribution of LHC II within the thylakoid membrane and, subsequently, the rates of cyclic photophosphorylation. When PQBH2 levels are high compared to levels of PQB, LHC II complexes are phosphorylated, causing them to redistribute to the
thylakoid lamellae, which leads to increased rates of cyclic photophosphorylation.
The O2 generated from photosynthesis is derived from
water molecules that directly reduce PSII
How are changes in enthalpy (H) and entropy (S), related to changes in free energy (G)?
ΔG=ΔH−TΔS
Digestion of fava beans generates free oxygen radicals and peroxide (H2O2). This can cause illness in people with reduced activity of what?
glucose-6-phosphate dehydrogenase
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?
-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. -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.
Competitive inhibitor:
-Does not affect the Vmax of the reaction -Binds to the active site of an enzyme -Higher concentrations of substrate can reduce the effect of the inhibitor -The y-axis intercept of the Lineweaver-Burk plot remains the same with or without this inhibitor
Mixed inhibitor:
-Does not bind to the active site of an enzyme, but can bind to the free enzyme or the enzyme-substrate complex
Uncompetitive inhibitor:
-Does not bind to the free enzyme -Increasing inhibitor concentration decreases both the Vmax and the Km
First Law of Thermodynamics
-Energy can not be created nor destroyed only transformed -Total amount of energy in the universe is a constant -Pressure and Volume do not change
Structure and Function of Enzymes
-Enzyme cofactors can increase the chemical functionality of enzymes which are otherwise limited by the R groups of amino acids -Enzymes increase the rates of biochemical reactions without changing the equilibrium constant -Stabilize transition state -Alternate path to product formation -Orient substrates appropriately for the reaction to occur
Autotrophs and Heterotrophs
-Heterotrophs are dependent on autotrophs to generate O2 from H20 in order to support aerobic respiration -The majority of autotrophs on Earth require aerobic respiration in order to survive -Heterotrophs depend on autotrophs for conversion of light energy to chemical energy
What best describe differences between the glycolytic and gluconeogenic pathways
-Insulin stimulates flux through the glycolytic pathway, whereas glucagon stimulates flux through the gluconeogenic pathway. -Gluconeogenesis generates glucose from non-carbohydrate sources, whereas glycolysis generates pyruvate from glucose. -Glycolytic enzymes are all found in the cytosol, whereas gluconeogenic enzymes are found in the cytosol and the mitochondrial matrix. Insulin inhibits flux through the gluconeogenic pathway, whereas glucagon inhibits flux through the glycolytic pathway.
The human gut microbiome is a collection of microbes that are necessary for proper function of the digestive system and that contribute to the overall health of the individual. Infants are colonized with these microbes at birth and their nutrition in the early days of life is important for supporting growth of these microbes. Milk sugars are important in development of the microbiome. What best explains how both lacto-N-tetraose and lacto-N-fucopentaose could contribute to proper development of an infant's microbiome?
-Lacto-N-fucopentaose binds to surface receptors on pathogenic bacteria and prevents them from entering epithelial cells in the intestine. -Lacto-N-tetraose is a food source for bacteria that aid in digestion of this and other oligosaccharides.
Accurately describe the difference between the oxidative phase and nonoxidative phase of the Pentose Phosphate Pathway
-The nonoxidative phase interconverts C3, C4, C5, C6, and C7 sugars with no change in total carbons, whereas in the oxidative phase the conversion of glucose-6P to ribulose-5P leads to a loss of a carbon as carbon dioxide. -The oxidative phase generates 2 NADPH for each glucose-6P that is converted to ribulose-5P, whereas the nonoxidative phase generates 5 glucose-6P for every 6 ribulose-5P that are metabolized in the oxidative phase. -The oxidative phase requires the enzyme glucose-6P dehydrogenase and the nonoxidative phase requires the enzyme transketolase.
Mutations in adenylate kinase have led to a hyperactive enzyme that ultimately ends up elevating ADP levels in a cell. Calculate the EC (energy charge) given the following atypical adenylate concentrations for the cell containing the mutant adenylate kinase: ATP = 0.5 mM, ADP = 12.2 mM, AMP = 80 μM Hint: Energy Charge equation
.52
Put the steps in photosynthesis in the correct order to generate 2 NADPH and 3 ATP following the absorption of 8 photons and return of 12 H+ from the thylakoid space to the stroma.
1- The sun comes up. 2- PSII absorbs 4 photons leading to photooxidation of 4 chlorophyll molecules and oxidation of 2 H2O to replace the 4 e- in chlorophyll and release 4 H+ into the thylakoid lumen. 3- Oxidation of pheophytin initiates a series of redox reactions culminating in the reduction of 4 plastocyanin and translocation of 8 H+ across the thylakoid membrane. 4- PSI absorbs 4 photons leading to the photooxidation of 4 plastocyanin and initiation of a series of redox reactions culminating in the reduction of 2 NADP+ to yield 2 NADPH. 5- A total of 12 H+ enter the chloroplast ATP synthase to generate 3 ATP when they return to the stroma and induce conformational changes in the head piece of the complex.
Given the following common reactions, which are entropically favored? 6CO2 + 6H2O ⇒ C6H12O6 + 6O2 ATP ⇒ ADP + Pi glucose6P ⇒ fructose6P 2 pyruvate ⇒ glucose
ATP ⇒ ADP + Pi
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
In 1932, Robert Emerson and William Arnold used isolated spinach chloroplasts to determine that it requires 2,400 chlorophyll molecules to generate one O2 molecule. Based on this number and your understanding of where and how O2 is formed in chloroplasts, if a spinach chloroplast absorbs 720 photons, then how many resonance energy transfer reactions occur in the light-harvesting complexes and how many O2 molecules are formed?
216,000 transfers and 90 O2 molecules 8 photons for 1 O2 molecule
Approximately how many ATP are synthesized per O2 molecule generated in photosynthesis light reactions?
3
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.
If a typical person hydrolyzes 100.0 mol of ATP per day, how much does this ATP weigh? (The molecular weight of ATP is 507 g/mol.)
50.7 kg 50700 g
In the production of one glyceraldehyde-3-phosphate as part of the net Calvin cycle, __________ are NOT required
6 ATP
Consider the two metabolic reactions below: Reaction 1: A + B → C ΔG˚ = 8.8 kJ/mol Reaction 2: C → D ΔG˚ = -15.5 kJ/mol If reaction 1 and 2 are coupled, what would the net reaction be? The net reaction would have ΔG˚ = ____kJ/mol.
A+B--> D -6.7
Maximal activity of pyruvate carboxylase depends on what substances?
Acetyl-CoA Biotin Bicarbonate [HCO3-] Pyruvate
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.
What is true regarding individuals with type AB blood?
AB individuals are universal plasma donors. AB individuals are universal recipients of red blood cells.
In the 5 steps used by photosynthetic organisms to convert solar energy into chemical energy, which molecules store the solar energy before sugar synthesis?
ATP and NADPH
Consider the pathway A → B → C → D → E. Reactions A → B, B → C, and D → E have a ΔG near equilibrium, while C → D has a ΔG << 0. What is true about this pathway if it were operating within a cell? Again consider the pathway above. Under what conditions would adding more A to the system not lead to an increase in the flux of the pathway from A to E?
Adding more A to the system will increase the amount of B and C in the system. An allosteric inhibitor of the enzyme that catalyzes C → D is also present in the system. The enzyme that catalyzes C → D has already reached 100% of Vmax.
What reaction is occurring at step 4 of the rubisco reaction
Aldol Cleavage
What enzyme from glycolysis does NOT have an equivalent enzyme involved in stage 2 of the Calvin cycle?
Aldolase
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.
Evaluate which of the following statements is/are true about enzymes and the transition from reactants to products.
An enzyme lowers the activation energy of a reaction, which means the transition state is not as energetically unfavorable as it would be without the presence of an enzyme. An enzyme does not change the energy of the reactants or product, nor does it change the equilibrium constant of a reaction.
An example of decreasing entropy
Anabolic pathway
What is true regarding apoenzymes and holoenzymes?
Apoenzymes do not have a non-amino, acid-based cofactor bound, whereas holoenzymes do.
What is correct concerning ATP production in chloroplasts?
Approximately one ATP is produced for every four H+.
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
Which of the following statements is correct? A. An endergonic reaction drives an exergonic reaction in living systems. B. The overall free energy of a coupled reaction is the difference of the free energies for the individual reactions. C. An exergonic reaction drives an endergonic reaction in living systems. D. ATP is rarely used in coupled reactions.
C
There are several ways in which the Calvin cycle is regulated by light. Sort the following conditions within a chloroplast at night
CA1P is upregulated. Stromal pH is 7.
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
What activates FBPase-1?
Citrate
Which of the following is an example of a heterotroph? A. Single-cell algae B. Cyanobacteria C. Plants D. Yeast
D
What statement best supports the idea that photon absorption by chlorophyll is an all-or-none phenomenon?
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.
How does the O2-evolving complex (OEC) link the oxidation of H2O with the restoration of P680?
For every P680 chlorophyll molecule that is photooxidized, one electron from the OEC is used to reduce P680+. The four electrons formed from the oxidation of H2O to O2 in the PSII are held by a Mn4 cluster in the OEC.
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.
why is the oxygenase activity of rubisco wasteful for plants?
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. The reaction uses O2, and the resulting salvage pathway consumes ATP that could instead be used for metabolically productive activities. High rates of photorespiration reduce the amount of carbon fixation, which stunts plant growth.
Why is cyclic photophosphorylation an efficient alternative pathway for plant chloroplasts?
It restores the 3:2 ratio of ATP to NADPH needed in the stroma for the Calvin cycle to operate.
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.
How can an unfavorable reaction (Delta G > 0 ) still occur in a metabolic pathway?
Link to a favorable reaction
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 malate -Pyruvate + ATP → PEP -HCO3- + PEP → oxaloacetate Bundle Sheath Cells: -Malate + NADP+ → Pyruvate + NADPH + CO2 -Calvin cycle -Glyceraldehyde-3-P → Starch and Sucrose
There are several ways in which the Calvin cycle is regulated by light. Sort the following conditions within a chloroplast during the day
Mg2+ moves from the lumen into the stroma. Reduced thioredoxin is available. Stromal pH is 8.
Which enzyme's activity is controlled by the levels of glucose-6-P and fructose-6-P in the cell?
Phosphoglucoisomerase
What is NOT an outcome from excitation of an electron in a chlorophyll molecule?
Photoreduction of the neighboring chlorophyll molecule
Where do electrons come from to re-reduce the oxidized P700+ state in PSI?
Plasotocyanin
What is TRUE regarding hemes but FALSE regarding chlorophylls?
Porphyrin ring coordinates Fe2+
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.
A rat colony has been bred to have an enzyme deficiency. After being deprived of food for 24 hours, the animals exhibit low blood glucose concentration [hypoglycemia] and are comatose. Giving them intravenous glucose arouses them by raising their blood glucose concentration to normal. Giving them intravenous lactate or alanine does not improve their blood glucose concentration. However giving them an intravenous infusion including amino acids that can make oxaloacetate or α-ketoglutarate in the liver also arouses them. What liver enzyme deficiencies is the most likely in these animals?
Pyruvate Carboxylase
Biotin is a cofactor for which enzyme of gluconeogenesis?
Pyruvate carboxylase
If an excess of a compound that reacts with primary amines were introduced to a cell, how would the activity of newly synthesized pyruvate carboxylase be affected
Pyruvate carboxylase activity would decrease
The spontaneous direction of a metabolic reaction is dictated by the ratio of substrate and products under equilibrium conditions (K) and under cellular conditions (Q). Compare the two reactions A→B and C→D. For A→B, ΔG˚ = -13 kJ/mol. For C→D, ΔG˚ = 3.5 kJ/mol. The cellular concentrations are as follows: [A] = 0.050 mM, [B] = 4.0 mM, [C] = 0.060 mM, and [D] = 0.010 mM. What correctly describes the relationship between Q and K for both reactions? Are these reactions spontaneous as written under cellular conditions?
Q < K for both reactions. Both are spontaneous at those concentrations of substrate and product.
Define the greenhouse effect.
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.
Consider two reactions. Reaction 1 (P → Q) has ΔG = 2.3 kJ/mol. Reaction 2 (Q → R) has ΔG = 12.3 kJ/mol. Which reaction is more likely to require coupling to ATP or the equivalent in order to be spontaneous under cellular conditions?
Reaction 2 (Q → R). This reaction is non-spontaneous and operates far from equilibrium in the cell. It will not be able to proceed as written in the cell without coupling to a process with a large negative free energy change (such as ATP hydrolysis).
Why can we not refer to the Calvin Cycle as dark reactions?
They require active photosynthetic system in the light They need NADPH and ATP
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?
Ribose and NADPH
Galactose is a component in many types of carbohydrates. Rank these galactose-containing carbohydrates in order of polymer length. Lacto-N-tetraose Keratan sulfate Lactose Verbascose Raffinose
Shortest to Longest: Lactose, Raffinose, Lacto-N-tetraose, Verbascose, Keratan sulfate
During which stages of the Calvin cycle are NADPH and ATP consumed?
Stages 2 and 3
What is least likely to affect the metabolic flux of a metabolic pathway?
Steady-State Substrate concentrations
What statement about the Calvin cycle is accurate?
The Calvin cycle does not operate at night. If it did, then the simultaneous degradation of starch and biosynthesis of carbohydrates would decrease pools of ATP and NADPH in the stroma.
For cells without the hyperactive adenylate kinase mutation, how would you expect the EC to change?
The EC would increase
Why does light energy transfer readily occur from chlorophyll in the light-harvesting complex I (LHC I) to chlorophyll in the reaction center (RC), even though isolated LHC I chlorophyll is indistinguishable from isolated RC chlorophyll?
The chlorophyll molecules in the RC and the LHC I exist in two different chemical environments, which results in a higher reduction potential in the RC chlorophyll.
What explains why humans and other nonruminating animals cannot digest raffinose series monosaccharides?
The galactose residues in these oligosaccharides are joined by an α-1,6 glycosidic bond.
Beano is a dietary supplement that allows humans to digest oligosaccharides such as stachyose by supplying the enzyme necessary to hydrolyze the α-1,6 glycosidic bond in these carbohydrates. However, other dietary carbohydrates such as amylopectin contain α-1,6 glycosidic bonds and these polysaccharides are easily digested by humans. How is this possible?
The residues connected by the α-1,6 glycosidic bond are different in stachyose and amylopectin.
describe the biochemical basis for the emergence of MRSA infections
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?
There is no regulatory protein that oxidizes these Calvin Cycle enzymes; oxidation is spontaneous.
How would individuals with decreased levels of the pentose phosphate enzyme glucose-6-phosphate dehydrogenase respond to oxidative stress?
They would not have the ability to regenerate reduced glutathione as rapidly.
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?
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.
What enzyme provides the building blocks for aldolase to be used in the carbon shuffling reactions of the Calvin cycle?
Triose phosphate isomerase
What best explains why vancomycin can also be used to kill penicillin-resistant bacteria?
Vancomycin would inhibit transpeptidase activity by blocking access to substrates.
Could a bacterium be resistant to both penicillin and methicillin?
Yes; it is possible for a bacterium to express both ß-lactamase and the variant transpeptidase.
The enzyme in the photosynthetic Z scheme that catalyzes the PQ cycle, which is analogous to Complex III and the Q cycle in the mitochondrial electron transport chain, is
cytochrome b6f
What is the difference between actual change in free energy (DG) and standard change in free energy (DGº) with regard to the spontaneity of a given reaction in a living cell?
ΔG° (pronounced delta G nought prime) is the free energy change of a reaction under standard conditions. Standard conditions = 1 atm, 298K, 1M concentrations of reactants/ products.
In which case will a reaction be spontaneous only above a certain temperature according to the Gibbs free energy equation?
ΔH > 0; ΔS > 0
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
