FINAL BIOCHEM
first stage of glycolysis
-6 carbon hexose is activated and cleaved to two 3 carbon fragments and two ATP consumed -converts one of the 3-carbon molecules into the other, having 2 GAP for the remaining steps of glycolysis
fates of pyruvate
1. conversion to acetyl CoA by PDH 2. conversion to lactate by lactate dehydrogenase 3. conversion to oxaloacetate by pyruvate carboxylase when there is a build up of acetyl CoA, this inhibits PDH and so the CoA goes to Beta Oxidation also pyruvate is no longer converted into acetyl CoA but goes to make oxaloacetate
Stearic Acid
18:0
Why does ATP have so much energy?
2 high-energy phosphate bonds (phosphoanhydride bonds)
Consider a mutant for of hemoglobin which has an interaction between the side chains of an aspartic acid residue and an arginine residue. B. Over what pH range would this ionic interaction between the two side chains remain?
3.86 < pH < 12.48
Triacylglycerols (triglycerides)
A glycerol molecule esterified to three fatty acid molecules; the most common form of fat storage in the body Overall nonpolar and hydrophobic Can be seen in oily droplets
chemiosmotic theory
A model to explain the synthesis of ATP. The theory proposes that the energy for ATP synthesis originates from the electrochemical gradient of protons across a membrane
Assuming physiological pH, how many hydrogen bonds can be donated by pyridoxal phosphate, also known as Vitamin B6? A. 1 B. 2 C. 3 D. 4 E. >4
A. 1
14. Calculate the isoelectric point, pI, for glutamic acid. A. 3.22 B. 5.37 C. 5.93 D. 6.96 E. None of the above; you need the pH of the solution to answer this question
A. 3.22
Oxidation of palmitic acid (C16) involves _____ rounds of -oxidation and yields _____ molecules of acetyl-CoA. A. 7; 8 B. 8; 8 C. 8; 16 D. 16; 7 E. 16; 8
A. 7; 8
Peripheral membrane proteins A. Are generally non-covalently bound to membrane lipids. B. Are usually denatured when released from membranes. C. Can only be released from membranes by treatment with detergent(s). D. May have functional units on both sides of the membrane. E. Penetrate across the entire lipid bilayer.
A. Are generally non-covalently bound to membrane lipids.
A suicide, or mechanism-based, inhibitor of an enzyme is one that A. Competes with the substrate for the active site B. Belongs to a class of reversible enzyme inhibitors C. Resembles the transition state of the catalyzed reaction D. Only works on thermodynamically irreversible steps
A. Competes with the substrate for the active site
Which of the following enzymes is primarily responsible for the regulation of glycogenolysis? A. Glycogen Phosphorylase B. Phosphoglucomutase C. Glucose-6-phosphatase D. Carboxylase E. Glucagon
A. Glycogen Phosphorylase
3. A suicide inhibitor of an enzyme is one that A. Is competitive with substrate B. Is reversible C. Decreases the KM of the enzyme for substrate D. Resembles the transition state of the catalyzed reaction
A. Is competitive with substrate
What happens to the density of naturally-occurring, monounsaturated free-fatty acid after hydrogenation? A. It increases B. It decreases C. It remains the same D. Cannot be answered without additional information
A. It increases
Hamsters love to run on exercise wheels. Prolonged running at a high rate of speed requires ATP. Under anaerobic conditions, could a hamster with a defective gene for the enzyme lactate dehydrogenase meet the extra ATP demand for prolonged, fast wheel-running by maintaining a high rate of glycolysis? A. No, not enough NAD+ can be regenerated for glycolysis to continue at a high rate. B. No, the defective gene will cause a rapid decline in pH in the muscles used for running. C. Yes, the defective gene has no effect on the glycolytic pathway. D. Yes, the citric acid cycle will supply the needed NAD+ if lactose dehydrogenase cannot.
A. No, not enough NAD+ can be regenerated for glycolysis to continue at a high rate.
Anaplerotic reactions A. Produce oxaloacetate and malate. B. Produce biotin needed by pyruvate carboxylase. C. Recycle pantothenate to make CoA. D. Make glucose from acetyl-CoA. E. All of the above
A. Produce oxaloacetate and malate.
Based on the buoyancy of lipoprotein particles, we can generally conclude that A. Proteins have greater densities than lipids B. Proteins have lower densities than lipids C. Proteins have roughly the same density as lipids D. There is no general trend
A. Proteins have greater densities than lipids
A patient is asked to fast for twelve hours prior to undergoing routine surgery. Which of the following would you expect to be least active? A. Pyruvate dehydrogenase B. Glucagon C. Glygenolysis (breakdown of glygogen) D. Pyruvate carboxylase
A. Pyruvate dehydrogenase
Which of the following is not a characteristic of signaling by a GPCR? A. Tyrosine phosphorylation B. Hydrolysis of GTP C. Activation of second messengers D. Activation of seven-transmembrane receptors E. Dissociation of one subunit from the others
A. Tyrosine phosphorylation
Hemoglobin contributes to buffering in the blood and the Bohr effect through roughly two dozen histidine residues. One important contributor is His 146, whose side chain is in close proximity to that of Asp 94 in the deoxy form of hemoglobin. Which of the following statements best describes the interactions that occur between the two side chains? A. Under acidic conditions, His 146 will form an ion pair with Asp 94, while the close proximity of Asp 94 increases the pKa value of His 146. B. Under acidic conditions, His 146 will form an ion pair with Asp 94, while the close proximity of Asp 94 decreases the pKa value of His 146. C. Under acidic conditions, His 146 will form a van der Waals interaction with Asp 94, while the close proximity of Asp 94 decreases the pKa value of His 146. D. Under acidic conditions, His 146 will form a van der Waals interaction with Asp 94, while the close proximity of Asp 94 increases the pKa value of His 146
A. Under acidic conditions, His 146 will form an ion pair with Asp 94, while the close proximity of Asp 94 increases the pKa value of His 146.
4. If a student were to become extremely anxious before an exam and begin to hyperventilate, what effects would it have on the student's pCO2 and blood pH? A. pCO2 would decrease and blood pH would increase B. pCO2 would increase and blood pH would increase C. pCO2 would decrease and blood pH would decrease D. pCO2 would increase and blood pH would decrease
A. pCO2 would decrease and blood pH would increase
Activates Phosphofructinokinase
AMP
inhibits phosphofructokinase
ATP and citrate
ETC complex V
ATP synthase
The following questions are regarding glycolysis and its regulation. A. Why is it advantageous for citrate, the product of the first reaction of the citric acid cycle, to inhibit phosphofructokinase, PFK? (4 Points)
An excess of citrate would signal that the cell's metabolic needs - in terms of energy and biosynthetic intermediates - have been met. As such, citrate would be ideal to slow down PFK, which catalyzes the first committed step of glycolysis.
ETC Complex III inhibitor
Antimycin A
Basic R-group
Arg
Consider a mutant for of hemoglobin which has an interaction between the side chains of an aspartic acid residue and an arginine residue. A. Why is the main interaction between these two side chains ionic, i.e. a salt bridge, at pH 7.4? (8 Points)
At this pH, the arginine residue will be protonated (in its positively-charged form) and the aspartic acid residue will be deprotonated (in its negatively charged form).
The pKa values of phosphoric acid, H3PO4, are 2.1, 6.8, and 12.3, respectively. At what pH would we expect phosphoric acid to have the lowest buffering capacity? A. 2.1 B. 4.6 C. 6.8 D. 7.4 E. 12.3
B. 4.6
Consider the interaction between the side chains of an Asp residue in a substrate-binding pocket of trypsin and a Lys residue of a substrate. Assuming that both side chains must be ionized, what would be the optimal pH range to maintain this interaction? A. 2 < pH < 5 B. 5 < pH < 8 C. 8 < pH < 11 D. 11 < pH < 14
B. 5 < pH < 8
Consider the binding of a protein, P, and its ligand, L: P + L → P·L Which of the following statements in relation to this binding process is true? A. A large KD value suggests that the protein and ligand bind tightly. B. A small KD value suggests that the protein and ligand bind tightly. C. If binding is strong, the association reaction lies to the left. D. If binding is weak, the dissociation reaction lies to the left.
B. A small KD value suggests that the protein and ligand bind tightly
2. ATP is both a substrate and a negative effector of the allosteric, glycolytic enzyme phosphofructokinase (PFK). Which of the following answers best explains this observation? A. ATP has equal affinity for the active site and the regulatory site of PFK B. ATP has a higher KM for the regulatory site than for the active site of PFK C. ATP has a higher KM for the active site than for the regulatory site of PFK D. ATP and ADP (the product of ATP hydrolysis) are both negative effectors of PFK
B. ATP has a higher KM for the regulatory site than for the active site of PFK
What is the main difference between active transport and facilitated transport? A. Active transport uses proteins but facilitated transport does not. B. Active transport uses ATP to accomplish transport but facilitated transport does not. C. Facilitated transport occurs across the plasma membrane but active transport does not. D. Facilitated transport moves solutes against concentration gradients but active transport moves them with concentration gradients.
B. Active transport uses ATP to accomplish transport but facilitated transport does not.
An intestinal protease functions at maximal velocity when the pH is 8.0 and the temperature is 37°C. Which procedure would have the least effect on the rate of protein digestion? A. Adding more protease B. Adding more protein substrate C. Decreasing the pH to 6.0 D. Increasing the temperature to 45 °C
B. Adding more protein substrate
Proteins are effective buffers over a wide range of pH values because they usually contain A. A large number of amino acids B. Amino acid side chains with different pKa values C. Amino-terminal and carboxy-terminal residues that can donate or accept protons D. Peptide bonds that readily consume H+ and/or OH- ions E. A large number of hydrogen bonds in α-helices and beta-sheets
B. Amino acid side chains with different pKa values
Which of the following pharmaceutical products becomes more soluble in an aqueous solution as the pH decreases? A. Ibuprofen, pKa= 5.3 B. Amphetamine, pKa= 10.0 C. Levetiracetam, pKa= 16.1 D. Acetaminophen, pKa= 9.4
B. Amphetamine, pKa= 10.0
A good transition-state analog A. Binds covalently to the enzyme. B. Binds to the enzyme more tightly than the substrate. C. Has a higher apparent KM than the substrate. D. Is too unstable to isolate. E. Must be almost identical to the substrate.
B. Binds to the enzyme more tightly than the substrate.
Denaturing a protein by heat is called melting. Consider three proteins, one rich in valine residues, another rich in cysteine residues, and the last rich in serine residues. (You may assume that there are no other significant differences in the amino acid compositions of the proteins.) Assuming oxidizing conditions, which protein would you predict to have the highest melting temperature? A. Valine-rich protein B. Cysteine-rich protein C. Serine-rich protein D. Cannot be determined without additional information.
B. Cysteine-rich protein
Consider a group of enzymes that catalyze the hydrolysis of esters. Which of the statements below best describes how a biochemist might evaluate data when trying to select the enzymes most appropriate for her research? A. For experiments with low substrate concentrations it is best to use the enzyme with the lowest KM; but for experiments with high substrate concentrations it is best to use the enzyme with the lowest Vmax. B. For experiments with low substrate concentrations it is best to use the enzyme with the lowest KM; but for experiments with high substrate concentrations it is best to use the enzyme with the highest Vmax. C. For experiments with low substrate concentrations it is best to use the enzyme with the highest KM; but for experiments with high substrate concentrations it is best to use the enzyme with the lowest Vmax. D. For experiments with low substrate concentrations it is best to use the enzyme with the highest KM; but for experiments with high substrate concentrations it is best to use the enzyme with the highest Vmax.
B. For experiments with low substrate concentrations it is best to use the enzyme with the lowest KM; but for experiments with high substrate concentrations it is best to use the enzyme with the highest Vmax.
What would be the predominant intermolecular force between the side chains of glutamic acid and histidine at physiological pH? A. Salt bridge B. Hydrogen bond C. Hydrophobic interaction D. Peptide bond
B. Hydrogen bond
Which of the following statements is(are) true about oxidative phosphorylation? I. Electron transport provides energy to pump protons into the intermembrane space. II. An electrochemical gradient is formed across the inner mitochondrial membrane. III. Potassium and sodium ions form an ionic gradient across the inner mitochondrial membrane. IV. Complexes I, III, IV actively transport protons into the intermembrane space during electron transport. A. I, II, III, IV B. I, II, IV C. II, III, IV D. I, IV E. II, IV
B. I, II, IV
Based on the knowledge that in humans excess acetyl-CoA - i.e. that which is left over once all metabolic needs have been met - is converted to fatty acids, we can infer that the A. The citric acid cycle is anaplerotic B. No pathway exists that can convert acetyl-CoA to pyruvate C. ATP and NADH can be produced only under aerobic conditions D. The conversion catalyzed by pyruvate dehydrogenase is reversible
B. No pathway exists that can convert acetyl-CoA to pyruvate
What is the difference between a fat and fatty acid? A. Only one occurs in animals B. Only one contains esters C. Only one contains amides D. None of the above; they are synonymous
B. Only one contains esters
During a heart attack, oxygenated blood flowing to the heart muscle is interrupted by blockage of a coronary artery. How would you expect the metabolism in the heart to change? A. The rate of the citric acid cycle would increase in the mitochondria B. The rate of production of lactic acid would be stimulated C. The rate of ethanol production by the muscle tissue would increase D. The rate of oxidative phosphorylation would increase in the mitochondria
B. The rate of production of lactic acid would be stimulated
When subjected to the citric acid cycle, each molecule of acetyl-CoA yields two molecules of CO2. How many molecules of CO2 can be produced from a 16- carbon fatty acid molecule? A. 4 B. 8 C. 16 D. 32
C. 16
Which fatty acid would be expected to have the highest melting temperature? A. 16:0 B. 16:2 C. 18:0 D. 18:2
C. 18:0
An enzyme has a Vmax of 50 mMol of product formed per minute and a KM of 10 mM for the substrate. What percent of Vmax does the enzyme reach when [S] = 5 mM? A. 15% B. 25% C. 33% D. 41% E. 50%
C. 33%
12. The fluidity of the lipid side chains in the interior of a bilayer is generally increased by: A. A decrease in temperature. B. An increase in fatty acid chain length. C. An increase in the number of cis-double bonds in fatty acids. D. An increase in the number of cholesterol molecules. E. An increase in the number of trans-double bonds in fatty acids
C. An increase in the number of cis-double bonds in fatty acids.
21. Consider the reaction of Substrate → Product. An enzyme would lower the activation energy, Ea, of the A. Forward reaction only B. Reverse reaction only C. Both forward and reverse reactions D. Neither forward nor reverse reactions
C. Both forward and reverse reactions
Which of the following residues are never phosphorylated in a signal transduction cascade? A. S B. Y C. C D. T
C. C
Upon removing the primary tumor, histology demonstrates that the central portion of the tumor was hypoxic, an indicator of a more aggressive tumor. The decrease in available oxygen will most likely lead to which of the following metabolic outcomes in the tumor cells? A. Decreased conversion of pyruvate to lactate B. Increased turnover of the TCA cycle C. Decrease in the H+ ion potential across the inner mitochondrial membrane D. Increased activity of β-oxidation of free fatty acids
C. Decrease in the H+ ion potential across the inner mitochondrial membrane
Lipoprotein particles are necessary to transport cholesterol to and from the liver because cholesterol A. Is too big to penetrate cell membranes B. Is too easily oxidized by blood enzymes C. Does not dissolve in water D. Gives lipoprotein particles enough density to travel to the tissues
C. Does not dissolve in water
Consider Michaelis-Menten (v vs. [S]) or Lineweaver-Burk plots of enzyme activity. Which of the following cannot be inferred from either of these plots? A. Vmax B. KM C. Enzyme Concentration D. Reaction Rate
C. Enzyme Concentration
The electrons formed from the aerobic oxidation of glucose are I. ultimately transferred to O2 after several other transfer reactions II. transferred to the coenzymes NAD+ and FAD III. directly transferred to O2 during the citric acid cycle IV. transferred to succinate and oxaloacetate A. I only B. II only C. I, II D. II, III, IV E. I, II, III
C. I, II
Which of the following can generate glucose? I. kidney II. liver III. adipose tissue IV. muscle A. I, II, III, IV B. I, II, IV C. I, II D. II, IV E. II only
C. I, II
Which of the following would decrease activity of the citric acid cycle overall? I. high concentration of NADH II. high concentration of GDP III. high concentration of ATP IV. high concentration of citrate A. I, II, III, IV B. I, III C. I, III, IV D. I, IV
C. I, III, IV
Which of these is a general feature of the lipid bilayer in all biological membranes? A. Individual lipid molecules in one face of the bilayer readily diffuse (flip-flop) to the other monolayer. B. Polar, but uncharged, compounds readily diffuse across the bilayer. C. Individual lipid molecules are free to diffuse laterally in the surface of the bilayer. D. The bilayer is stabilized by covalent bonds between neighboring phospholipid molecules. E. The polar head groups face inward toward the inside of the bilayer.
C. Individual lipid molecules are free to diffuse laterally in the surface of the bilayer.
15. Metabolic pathways are usually regulated by A. The first step B. Endergonic steps C. Irreversible steps D. All of the above
C. Irreversible steps
1. Chymotrypsin is an example of an enzyme that catalyzes a A. Single substrate reaction B. Random bi-substrate reaction with a ternary complex C. Ordered bi-substrate reaction without a ternary complex D. Ordered bi-substrate reaction with a ternary complex
C. Ordered bi-substrate reaction without a ternary complex
A body builder has been consuming large quantities (i.e > 20 per day) of raw eggs with the hopes of building more muscle mass. However, he has noticed when he has not eaten in several hours he is becoming more lethargic than normal. You deduce the patient is suffering from a diet-induced biotin deficiency. Under these conditions, which molecule will the patient be unable to make? A. Pyruvate B. Malate C. Oxaloacetate D. Acetyl-CoA
C. Oxaloacetate
A patient comes into your clinic suffering from anorexia nervosa with decreased body weight, muscle mass, glycogen, and fat stores. Why would the acetyl-CoA generated by this patient not enter the TCA cycle in the liver? A. The liver does not express the enzyme necessary to utilize acetyl-CoA in this way B. The pyruvate dehydrogenase complex will not run in reverse C. Oxaloacetate is unavailable due to predominance of gluconeogenesis D. Acetyl-CoA is being used to generate glucose
C. Oxaloacetate is unavailable due to predominance of gluconeogenesis
5. What effect does hyperventilation have on the oxygen binding affinity of hemoglobin? A. P50 and oxygen affinity decrease. B. P50 and oxygen affinity increase. C. P50 decreases and oxygen affinity increases. D. P50 increases and oxygen affinity decreases. E. P50 and oxygen affinity remain the same.
C. P50 decreases and oxygen affinity increases.
The conversion of glucose-6-phosphate to glucose would be catalyzed by A. Glucokinase B. Hexokinase C. Phosphatase D. GTPase
C. Phosphatase
The type of membrane transport that uses one ion gradient as the energy source to drive transport of another ion is: A. Primary active transport B. Simple diffusion C. Secondary active transport D. Facilitated diffusion
C. Secondary active transport
Denaturing a protein by heat is called melting. Consider three proteins, one rich in valine residues, another rich in cysteine residues, and the last rich in serine residues. (You may assume that there are no other significant differences in the amino acid compositions of the proteins.) Assuming reducing conditions, which protein would you predict to have the highest melting temperature? A. Valine-rich protein B. Cysteine-rich protein C. Serine-rich protein D. Cannot be determined without additional information.
C. Serine-rich protein
Kinetics studies on an enzyme with mutations of some of the amino acid residues in its active site showed a decrease in the enzyme's catalytic activity but not its KM. The best interpretation of these results is that the A. KM for the substrate does not depend on any of the amino acids of the active site. B. kcat for the substrate does not depend on any of the amino acids of the active site. C. The amino acids which stabilize the transition state are different from those that stabilize the substrate. D. An enzyme with these characteristics cannot be described by the Michaelis-Menten model since it violates the assumptions.
C. The amino acids which stabilize the transition state are different from those that stabilize the substrate.
Why are triacylglycerols used in the human body for storage? A. They are highly hydrated, and therefore can store lots of energy B. They always have short fatty acid chains for easy access by metabolic enzymes. C. The carbon atoms of the fatty acid chains are highly reduced, and therefore yield more energy upon oxidation. D. Polysaccharides, which would actually be a better storage form would dissolve in the body
C. The carbon atoms of the fatty acid chains are highly reduced, and therefore yield more energy upon oxidation.
Which of the following decreases when a catalyst is added to a reaction? A. Forward rate constant, kf B. Reverse rate constant, kr C. Time to reach equilibrium D. Equilibrium constant, Keq E. Gibbs Free Energy, delta G°
C. Time to reach equilibrium
Which of the following enzymes does not regulate the glycolytic pathway? A. Pyruvate kinase B. Phosphofructokinase C. Triose isomerase D. Hexokinase
C. Triose isomerase
Considering the entire process of aerobic respiration, most of the oxygen consumed by breathing is converted to A. Acetyl-CoA B. Carbon dioxide C. Water D. ATP E. Glucose
C. Water
The amino group of an alpha-amino acid is _____ basic than that of an isolated amine because of the _____ effect of the neighboring carboxy group. A. more; resonance B. more; inductive C. less; inductive D. less; resonance
C. less; inductive
Citric Acid Cycle
Completes the breakdown of glucose by oxidizing a derivative of pyruvate to carbon dioxide. •It is also to provide key intermediates in the biosynthesis of a variety of substances. •Intermediates can be replenished by anaplerotic reactions •It is for this reason that the oxidation of acetyl-CoA to CO2 goes through such a complex set of reactions.
ETC complex IV inhibitors
Cyanid, Azide, Carbon monoxide
Side chain is usually used by proteins for lipid linkages
Cys
Based on the KM data, which substrate binds most tightly to the enzyme, phenylalanine dehydrogenase? A Phenylalanine 7.5 × 10-4 B Tyrosine 3.1 × 10-3 C Tryptophan 1.1 × 10-2 D Methionine 4.3 × 10-4
D Methionine 4.3 × 10-4
The enzyme hexokinase - or glucokinase in the liver - catalyzes the conversion of glucose to glucose-6-phosphate. Which of the following would be the best competitive inhibitor for the enzyme? A. D-ribose B. 2-deoxy-D-ribose C. L-glucose D. 6-deoxy-D-glucose E. D-fructose
D. 6-deoxy-D-glucose
The relative concentrations of ATP and ADP control the cellular rates of A. Glycolysis B. Pyruvate oxidation C. The citric acid cycle D. All of the above
D. All of the above
Which of the following are effects of insulin secretion? A. Muscle and adipose tissue are stimulated to take up glucose. B. Glycogen synthesis increases in the liver. C. Gluconeogenesis is inhibited in the liver and kidney. D. All of the above.
D. All of the above
To which of the following amino acids does the carbohydrate moiety get attached in glycoproteins? A. Ser, Thr, Tyr B. Asp, His, Ser C. Trp, Asn, Cys D. Asn, Ser, Thr E. Asp, Glu, Tyr
D. Asn, Ser, Thr
The three-dimensional structure of an enzyme in complex with a competitive inhibitor revealed that a cysteine residue in the active site of the enzyme is in close proximity to a cysteine on the substrate. Which of the following would be the predominant interaction between these two amino acids? A. Covalent bond B. Disulfide bond C. Hydrogen bond D. Dipole-Dipole interaction E. Hydrophobic interaction
D. Dipole-Dipole interaction
Muscle is considered a "selfish" tissue because muscle cells A. Only release glucose for use by other muscle cells B. Only convert pyruvate under aerobic conditions C. Do not store glycogen D. Do not express glucose 6-phosphatase
D. Do not express glucose 6-phosphatase
What type of inhibitor is Omeprazole? A. Competitive B. Noncompetitive C. Mechanism Based D. Group Specific
D. Group Specific
Which of the following statements about glycolysis is incorrect? A. It occurs without oxygen. B. It ends with the formation of pyruvate. C. It involves the reduction of NAD+ D. It catabolizes glucose to CO2 and H2O. E. All of the above are true about glycolysis
D. It catabolizes glucose to CO2 and H2O.
If the concentration of ATP is low, the availability of glucose and acetyl-CoA is high, and no other metabolic demands are made on the cell, what is the most likely fate of oxaloacetate? A. It is converted to phosphoenolpyruvate for gluconeogenesis. B. It is converted to glycogen via glycogenesis. C. It is converted to pyruvate. D. It is combined with acetyl-CoA and enters the TCA cycle.
D. It is combined with acetyl-CoA and enters the TCA cycle.
N-hydroxy-L-arginine can bind to the active site of the enzyme, arginase, making its manganese reactive metal center unavailable for catalysis. How would an increased concentration of this compound be expected to affect the kinetic parameters of this enzyme relative to the natural substrate, arginine? A. Vmax will decrease B. KM for the substrate, arginine, will decrease C. Vmax will increase D. KM for the substrate, arginine, will increase
D. KM for the substrate, arginine, will increase
Histones are proteins that wrap around DNA backbones in eukaryotic cells. Recalling that the backbone of DNA consists of negatively-charged phosphate groups, in which of the following amino acids would you expect histones to be enriched? A. Glu B. Asn C. Ile D. Lys E. Tyr
D. Lys
Pyruvate is transported from the cytosol into mitochondria by A. Simple diffusion B. Facilitated diffusion C. Primary active transport D. Secondary active transport
D. Secondary active transport
Consider an enzyme and its mutated form in which some of the active site amino acids have been changed. Kinetic studies showed that the mutated enzyme had a lower turnover number than the wild-type enzyme but had the same KM for the substrate. What is the best interpretation of these results? A. The KM for the enzyme does not depend on any of the amino acid side chains found in the active site. B. KM and turnover number are inversely proportional. C. The transition state for this reaction is formed prior to the formation of the ES complex. D. The amino acid side chains involved in transition state stabilization are different than those involved in ES formation
D. The amino acid side chains involved in transition state stabilization are different than those involved in ES formation
When a chemical reaction reaches equilibrium A. The forward reaction stops B. The reverse reaction stops C. One of the reactants has been completely consumed D. The rates of the forward and reverse reactions are equal
D. The rates of the forward and reverse reactions are equal
Consider a mutant for of hemoglobin which has an interaction between the side chains of an aspartic acid residue and an arginine residue. C. Assuming all other conditions remain constant, would a mutation of arginine to glutamate destabilize or have no effect on this interaction? Why?
Destabilize because the glutamate side chain would be in its deprotonated, negatively-charged form. As such, there would be a repulsion between the like-charged side chains of aspartate and glutamate.
Consider a mutant for of hemoglobin which has an interaction between the side chains of an aspartic acid residue and an arginine residue. E. Assuming all other conditions remain constant, would a mutation of arginine to leucine destabilize or have no effect on this interaction? Why?
Destabilize since it would replace a charged residue with a hydrophobic one. As such, the salt bridge would be broken.
Which of the following amino acid sequences is likely to be found in the membrane-spanning domain of an integral membrane protein? A. -Leu-Ile-Glu-Asn-Cys-Trp- B. -Leu-Arg-Ala-Ser-Val-Phe- C. -Leu-Val-Pro-Asn-His-Met- D. -Leu-Arg-Ile-Asp-Val-Lys- E. -Leu-Val-Met-Phe-Ala-Ile-
E. -Leu-Val-Met-Phe-Ala-Ile-
What step of the electron transport chain and oxidative phosphorylation would be most affected if the inner mitochondrial membrane leaked protons? A. Complex I B. Complex II C. Complex III D. Complex IV E. Complex V (ATP Synthase)
E. Complex V (ATP Synthase)
Which pentapeptide, represented in one-letter symbols, would have a charge at physiological pH? A. C-L-E-A-R B. A-F-L-A-C C. H-A-P-P-Y D. C-R-E-S-T E. E-A-G-L-E
E. E-A-G-L-E
If a Lineweaver-Burk plot was made for an enzyme-catalyzed reaction, both with and without a noncompetitive inhibitor present, what difference would be seen? A. The x-intercept would be lower (more negative) for the inhibited reaction B. The x-intercept would be higher (less negative) for the inhibited reaction C. The slope would be less for the inhibited reaction D. The slope would be greater for the inhibited reaction E. None of the above
E. None of the above
Metabolic Pathways Couple
Endergonic Pathways to Exergonic Ones
Side chain contains amide functionality
Gln
Acidic R-group
Glu
The Glucose-Alanine Cycle
Glucose to alanine in the muscle (then blood to liver) Alanine to Glucose on Liver (Urea as byproduct)
Side chain can be reversibly phosphorylated
His
Consider a mutant for of hemoglobin which has an interaction between the side chains of an aspartic acid residue and an arginine residue. F. Assuming all other conditions remain constant, would a mutation of arginine to glutamine destabilize or have no effect on the overall structure of the protein? Why?
It would have little to no effect on the overall structure of the protein. Though the salt bridge would be disrupted, the amino group of the glutamine side chain would be a hydrogen bond donor to the aspartate hydrogen-bond acceptor.
The following questions are regarding glycolysis and its regulation. Glucose is frequently administered intravenously to patients as a food source. Since the first step of glycolysis is the phosphorylation of glucose, would it be advantageous to administer glucose-6-phospate instead? Why or why not?
It would not be advantageous to administer glucose-6-phosphate because it would not be able to diffuse across the cell's membrane. (Recall that the reason phosphorylation is the first step of glycolysis is to keep glucose-6- phosphate in the cell.)
Branched, hydrocarbon side chain
Leu
Activates Glucose-6-phosphate
Low glucose levels Glucose-6-phosphate
Side chain contains sulfur
Met
ETC Complex I
NADH dehydrogenase proton pump
The following questions are about the electron-transport chain (ETC) and oxidative phosphorylation. A. Does FADH2 or NADH yield more ATP? Why?
NADH enters the ETC through Complex I which transfers electrons to Complex III and pumps protons into the intermembrane space of the mitochondrion thereby creating a gradient. FADH2, in contrast, enters the ETC through Complex II which also transfers electrons to Complex III, but does NOT pump protons into the intermembrane space. As such, oxidation of NADH creates a more significant proton gradient than that of FADH2.Since the proton gradient ultimately drives ATP synthesis, oxidation of NADH yields more ATP than that of FADH2
The following questions are regarding glycolysis and its regulation. More generally, to what category of inhibition does allosteric control belong? Please be as specific as possible.
Noncompetitive inhibition
ATP synthase inhibitors
Oligomycin
Hydrophobic, aromatic R-group
Phe
Rarely, if ever, found in alpha helices
Pro
ETC Complex I inhibitor
Rotenone
Polar, non-charged side chain
Ser
The following questions are about the electron-transport chain (ETC) and oxidative phosphorylation. B. What happens to the pH of the mitochondrial matrix and the intermembrane space as electrons progress through the ETC? Why?
Since protons are pumped from the mitochondrial matrix to the intermembrane space as electrons progress through the ETC, the pH of the matrix increases and that of the intermembrane space decreases. (Remember that pH is inversely related to H+ ion concentration.)
Citric Acid Cycle Regulation
The overall rate of the citric acid cycle is controlled by the rate of conversion of pyruvate to acetyl-CoA and by the flux through Citrate synthase Isocitrate dehydrogenase a-ketoglutarate dehydrogenase. ATP and NADH are inhibitory. NAD+ and ADP are stimulatory.
oxidative phosphorylation
The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.
Consider a mutant for of hemoglobin which has an interaction between the side chains of an aspartic acid residue and an arginine residue. D. Assuming all other conditions remain constant, would a mutation of arginine to lysine destabilize or have no effect on this interaction? Why?
There would be minimal to no effect since the lysine side chain would be in its protonated, positively-charged form. Since the lysine side chain is roughly the same length as that of arginine there salt bridge should not be disrupted.
Why does thiamine deficiency lead to metabolic acidosis?
Thiamine is an essential co-factor for the enzyme pyruvate dehydrogenase that allows oxidation of pyruvate to acetyl CoA
Hexokinase
This enzyme can phosphorylate the -OH group at the 6-position of other hexoses Requires a Mg2+ ion to stabilize negative charges on ATP Allosteric enzyme that is inhibited by G-6-P
Side chain contains ring N atom
Trp
Pyruvate dehydrogenase is inhibited by its products
acetyl-CoA and NADH
second stage of glycolysis
aledehyde is oxidized to a carboxylic acid, then phosphorylated GAP-->NADH (highly exergonic step)
ETC Complex II inhibitor
carboxin
ETC Complex IV
cytochrome c oxidase
ETC Complex III
cytochrome oxidoreductase
Activated carrier molecules contain
high-energy covalent bonds AND reduces the amount of energy lost as heat
•Cellular respiration
is the process by which cells extract energy in the forms of ATP from biochemical molecules
substrate level phosphorylation in glycolysis
means that something is phosphorlyated aka ATP is produced by direct transfer of a phosphate to ADP -only a small amount ATP is released this way
The citric acid cycle takes place in the
mitochondrial matrix
key enzyme in control of glycolysis
phosphofructokinase
carbons sources for glucoenogenesis
pyruvate and oxaloacetate
ETC Complex II
succinate dehydrogenase Not a proton pump
The Cori Cycle
the cycle of lactate to glucose between the muscle and liver
The following questions are regarding glycolysis and its regulation. B. Why is it useful for hydronium ions to inhibit PFK?
under anaerobic conditions pyruvate is converted to lactic acid which, under physiological conditions, donates hydronium ions to the cytosol. Inhibition by hydronium ions, therefore, prevents excessive formation of lactic acid, which can lead to metabolic acidosis.
catabolism
•: larger molecules are broken down into smaller ones in a process that usually releases energy •Catabolic processes are often oxidative
PFK allosteric regulation
•ATP, Citrate, and H+ •Inhibition by ATP and citrate signals that metabolic needs of the cell have been met •Inhibition by H+ is meant to prevent excessive formation of lactic acid
endergonic, or energy-absorbing, processes tend to be
•Anabolic •Reductive
•Exergonic, or energy-releasing, processes tend to be
•Catabolic •Oxidative
BILE SALTS
•Detergents synthesized from cholesterol by the liver and stored in the gall bladder •Used to solubilize dietary lipids in the small intestines by emulsifying them
beta oxidation of fatty acids
•Each cycle shortens the fatty acid by 2C. •Acetyl-CoA, NADH, and FADH2 are the final products. • •Occurs in mitochondria of nearly every cell • •Activation occurs through coupling to Coenzyme A to form acyl-CoA
•G-6-P serves to signal that the cell no longer requires glucose for
•Energy •Storage in the form of glycogen •For synthesis of other substances
•Glycolysis is controlled by regulation of the enzymes that catalyze the three irreversible steps
•Hexokinase (Step 1: Glucose ® Glucose-6-phosphate) •Phosphofructokinase (Step 3: Fructose-6-phosphate ® Fructose-1,6-bisphosphate) •Pyruvate kinase (Step 10: Phosphoenolpyruvate ® Pyruvate)
Diabetes and Ketoacidosis
•In all types of diabetes, insufficient amounts of glucose are available in the muscle, liver, and adipose tissue. •Liver cells synthesize glucose by gluconeogenesis, which elevates levels of acetyl CoA. •Excess acetyl CoA undergoes ketogenesis, and ketone bodies accumulate in the blood. •Since most of the ketone bodies are acidic, their excess formation can lead to acidosis of the blood.
Ketogenesis
•In ketogenesis, two molecules of acetyl CoA combine to form acetoacetyl CoA and HS—CoA. •This condensation is in the opposite direction of the last step of β-oxidation.
Energy Yield of Respiration
•In theory, respiration should yield •38 ATP per glucose molecule for bacteria •36 ATP per glucose molecule for eukaryotes •Actual energy yield, however, is •30 ATP per glucose molecule for eukaryotes •Yield is lowered due to "leaky" inner membrane and use of the proton gradient for purposes other than ATP synthesis •Also, yield per molecule of FADH2 is lowered because Complex II does not act as a proton pump.
Ketone Bodies
•Ketones formed by the body to meet energy needs when there is •A shortage of carbohydrates •An excess of acetyl Co-A in the liver •The accumulation of ketone bodies may lead to a condition called ketoacidosis
•Pyruvate is produced from
•Lactate •Alanine (and other amino acids)
Phosphofructokinase (PFK)
•Most important glycolytic enzyme because it catalyzes the first committed step, i.e. the first irreversible reaction unique to the glycolytic pathway •In general, the enzyme that catalyzes the first committed step in a metabolic sequence is the most important control element in the pathway.
•Oxaloacetate is produced from
•Pyruvate •Malate
•Metabolic processes are compartmentalized allowing
•Separate pools of metabolites in a cell •Simultaneous operation of opposing metabolic paths •High local concentrations of metabolites •Coordinated regulation of enzymes
Glucose Use in Humans
•The brain, skeletal muscle and red blood cells (RBCs) are the three tissues that primarily use glucose as their energy source. •The brain uses about 75% of an adult's daily glucose use •RBCs do not have mitochondria so they cannot harvest energy from other pathways • •In absence of carbohydrate intake, i.e. during times of starvation, blood and glycogen can provide an adult with about one day's supply of glucose.
Gluconeogenesis
•The synthesis of glucose from non-carbohydrate sources •About 90% of time occurs in liver; remaining 10% of the time, or so, takes place in the kidneys •Process mostly takes place in cytoplasm
Chylomicron
•They are the lowest density of all the lipoprotein particles. •They transport dietary fatty acids through the bloodstream to the liver, muscle, and adipose tissues. •In the target tissues, triglycerides are broken down to monoglycerides and two free fatty acids.
Pyruvate kinase
•Two main classes •L form: predominates in liver •M form: predominates in muscle and brain •Allosterically inhibited by ATP and alanine •Allosterically activated by Fructose-1,6-bisphosphate
Anabolism
•larger molecules are made from small ones in a process the usually requires energy •Anabolic processes are often reductive
•The glycolytic pathway provides carbon skeletons for synthesis of
•non-essential amino acids •glycerol found in triglycerides
In the small intestine, triacylglycerides (TAGs) are partially hydrolyzed by pancreatic lipases
•producing monoacylglycerols and fatty acids.