Biochemistry Exam Questions, Exams of Biochemistry

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CHM 521 Cumulative Final Exam Review

(previous exam questions)

EXAM 1 Material - A solution is made of 0.5 M K2HPO4 and 0.25 M KH2PO4 (pK = 6.82). The pH of the solution would be A) 1. B) 3. C) 6. D) 7. E) 9.34 - D) 7. Which of the following DNA sequences is (are) palindromic in double stranded form? A) AGCT B) AAGCTT C) AGGA D) A and B E) A, B, and C - D) A and B Which one of these characteristics is NOT true for the alpha helix? A) It is represented in ribbon diagrams as a cylinder. B) There is a requirement for glycine every third amino acid residue. C) A hydrogen bond forms between the carbonyl oxygen of the nth amino acid residue and the NH group of the (n+4)th amino acid residue. D) Proline is typically not found in the alpha helix E) All of the above are true of the alpha helix. - B) There is a requirement for glycine every third amino acid residue. A fast and common method for determining the concentration of protein in aqueous solution is: A) tandem mass spectrometry B) "salting in" with ammonium sulfate C) drying a portion and weighing the solid D) measuring light absorption at 280 nm E) Edman degradation - D) measuring light absorption at 280 nm

Amphiphilic molecules: A) have both oxidizing and reducing groups B) are micelles C) have chromophores in two different wavelength regions D) have both acidic and basic groups E) have both hydrophilic and hydrophobic groups - E) have both hydrophilic and hydrophobic groups Nucleotides contain phosphate groups bonded to the: A) C3' or C5' atoms B) C3 or C3' atoms C) C5 or N9 atoms D) C3 or N9 atoms E) none of the above - A) C3' or C5' atoms The disulfide bond between two cysteine molecules: A) is a peptide bond B) is an iconic bond that is stable at physiological pH C) is a covalent bond formed by oxidation D) is a hydrogen bond between the two sulfhydryl groups E) is a weak ion-induced dipole attraction - C) is a covalent bond formed by oxidation Highly active muscle generates lactic acid by respiration so fast that the blood passing through the muscle experiences a drop in pH from about 7.4 to 7.2. Under these conditions, hemoglobin releases about 10% more O2 than it does at pH 7.4. This is because of: A) allostery B) the Bohr effect C) heme protonation D) structural similarities with myoglobin E) presence of carbon monoxide at higher acidity - B) the Bohr effect Either dansyl chloride or Edman's reagent can be used to identify the ________________ of a protein. A) amino acid sequence B) N-terminal amino acid C) C-terminal amino acid D) quaternary structure E) none of the above - B) N-terminal amino acid The theory of evolution includes the following principles:

A) evolution is not directed toward a specific goal B) evolution is ongoing, and is constrained by its past, evolution requires some sloppiness for adaptation to changes C) A and B D) A, B, and C E) - E) A, B, and C The most important intramolecular interaction involved in stabilizing protein structure is: A) hydrogen bonds B) disulfide bonds C) hydrophobic interactions D) electrostatic interactions E) dipole-dipole interactions - C) hydrophobic interactions A(n) ___________ has a rigid, planar structure consisting of about 40% double bond character. A) amino acid B) water molecule C) purine base D) peptide bond E) pyrimidine base - D) peptide bond Nucleotides are linked together in nucleic acids by a _____________ bond. A) peptide B) phosphodiester C) glycosidic D) ester E) disulfide - B) phosphodiester Treatment of a protein with a reducing agent such as B-mercaptoethanol along with a detergent such as SDS disrupts all of the following interactions except: A) ionic interactions B) hydrogen bonds C) disulfide bonds D) peptide bonds E) hydrophobic interctions - D) peptide bonds In the tetrapeptide: Serine-Lysine-Arginine- Glutamate A) Serine is the N-terminal amino acid, Glutamate is the C-terminal amino acid B) Serine is the C-terminal amino acid, Glutamate is the N-terminal amino acid

C) Serine and Glutamate are both C-terminal amino acids D) Serine and Glutamate are both N-terminal amino acids E) Not enough information to tell - A) Serine is the N-terminal amino acid, Glutamate is the C-terminal amino acid The evolution of proteins over time involves the inevitable change of amino acids within the protein's primary structure. We have learned that amino acids crucial in the function of a protein will go through much more conservative (better) changes (if any) in order to maintain the function of that protein. Assuming the given amino acids below are important in the function of the protein, choose which amino acid substitution would result in a more conservative change in the protein. Wild-Type Amino Acid / More conservative substitution?

1. Glu / Asp versus Lys
2. Ile / Arg versus Val
3. W / G versus F
4. N / Q versus G
5. Hydrophobic with side chain of isopropyl/ A versus R - Substitution:
6. Asp
7. Val
8. F
9. Q
10. A What is the significance of Anfinsen's renaturation experiment? NOTE: I am not looking for a description of the experiment but rather the reason his findings were significant. - His findings showed that the primary sequence contains all that is needed for folding of a protein. Draw one possible restriction map for a 10kb linear piece of DNA given the following information about the sizes of DNA fragments produced from restriction enzymes. Enzyme / Size of fragment produced:
11. EcoR1 / 0.4, 4.3, 5.3 (2 cuts made)
12. Hind3 / 2.5, 7.5 (1 cut made)
13. EcoR1 + Hind3 / 0.4, 2.1, 2.2, 5.3 - EcoR1 Hind3 EcoR ------------------|---------|--------|----- 5.3 2.2 2.1 0. Two proteins have the following amino acid compositions:

• Protein 1: 5% G, 15% K, 25% L, 15% S, 20% I, 20% C
• Protein 2: 25% V, 25% T, 15% D, 25% F, 10% Q You do not have an antibody to either protein and both are or equal size. What type of chromatography would you use to isolate protein 1? Explain why. -

A segment of DNA containing 20 base pairs includes 7 guanine bases. How many adenine bases are in the segment? How many uracil bases are in the segment? - 13 adenine, NO uracil (since DNA, not RNA) You are studying a new peptide with the sequence QAFMKGYNRME. Predict the fragments you would expect to be produced if you digested the peptide with trypsin. Predict the fragments you would expecte to be produced if you digested the peptide with chymotrypsin. - Trypsin Fragments: QAFMK ; GYNR ; ME Chymotrypsin Fragments: QAF ; MKGY ; NRME EXAM 2 Material - Which of the following is true about membrane proteins? A) Integral membrane proteins span the membrane as a random coil. B) Lateral diffusion occurs unless other cellular components restrict their movement. C) They readily undergo transverse (flip-flop) diffusion every few seconds. D) They are never glycoproteins. E) They contain entirely nonpolar amino acids in their primary structure. - B) Lateral diffusion occurs unless other cellular components restrict their movement. Which of the following statements describes integral membrane proteins? A) They are easily removed by changes in pH or high salt. B) The proteins tend to be water-soluble. C) Amino acids that contact the fatty acid carbon chains of the membrane are hydrophobic. D) They interact with the membrane via a lipid anchor E) None of the above - C) Amino acids that contact the fatty acid carbon chains of the membrane are hydrophobic What type of transport does NOT require the assistance of a membrane protein? A) facilitated transport B) simple diffusion C) passive transport D) active transport E) none of the above - B) simple diffusion Which of the following is NOT true about enzymes? A) Enzymes catalyze the reaction in only the forward direction B) Enzymes are often very specific for their substrates C) Enzymes typically catalyze reactions at much higher rates than chemical catalysts D) Enzymes typically act under milder conditions of temperature and pH than chemical catalysts E) All of the statements given are true - A) Enzymes catalyze the reaction in only the forward direction.

How many stereoisomers are possible for an aldopentose such as ribose? A) 2 B) 4 C) 8 D) 16 E) 32 - C) 8 The protein that forms a transmembrane pore that allows preproteins to pass through the ER membrane is called the A) signal recognition particle B) signal peptidase C) docking protein D) translocon E) none of the above - D) translocon Which of the following amino acids would provide a side chain capable of increasing the hydrophobicity of a binding site? A) aspartic acid B) lysine C) isoleucine D) arginine E) serine - C) isoleucine What is the velocity of a first order reaction when the reactant concentration is 6 x 10^-2 and the rate constant is 8 x 10^3 sec^-1? A) 1.33 x 10^5 M^-1sec^- B) 1.33 x 10^5 Msec^- C) 7.5 x 10^-2 Msec^- D) 4.8 x 10^2 Msec^- E) not enough data are given here to make this calculation - D) 4.8 x 10^2 M*sec^- Which of the following is NOT a characteristic of the (Na+-K+)-ATPase? A) Aniporter B) It transports 3 Na+ ions out of the cell and 2 K+ ions into the cell. C) Transport is coupled to the hydrolysis of ATP D) Transport occurs against a concentration gradient E) None of the above - E) None of the above

Chymotrypsin preferentially cleaves a peptide bond adjoining a bulky, non-polar side chain because chymotrypsin's "specificity pocket" A) contains a sulhydryl group that forms a disulfide bond with the substrate B) is lined with small hydrophobic side chains, leaving considerable room in the pocket and making it nonpolar C) contains a negative charge D) is mostly filled with large side chains E) is positively charged - B) is lined with small hydrophobic side chains, leaving considerable room in the pocket and making it nonpolar If you add an enzyme to a solution containing only the product (P) of the reaction R <--> P, would you expect any R to form? A) Yes, because the enzyme reduces the standard free energy change for the reaction B) No, because the enzyme lowers the transition state energy barrier C) No, because product inhibits the enzyme D) No, because enzymes only catalyze the forward reaction E) Yes, because the reaction proceeds backwards until reaching equilibrium - E) Yes, because the reaction proceeds backwards until the reaching equilibrium The rate of an enzyme-catalyzed reaction is determined by A) the overall free energy change of the reaction B) the equilibrium constant of the reaction C) the activation energy D) the number of subunits a single enzyme has E) all of the above - C) activation energy Which of the following amino acids do NOT comprise the catalytic triad of chymotrypsin? A) histidine B) glutamic acid C) serine D) aspartic acid - B) glutamic acid All of the following are components of membranes EXCEPT A) cholesterol B) triglycerides C) glycerophospholipids D) sphingolipids E) cerebrosides - B) triglycerides

Hexokinase and glucokinase both catalyze the phosphorylation of glucose to form glucose-6- phosphate. The values of Km for the enzymes are 10 uM and 0.02 M, respectively. If blood glucose is 5 mM under fasting conditions and 20 mM after a high carbohydrate meal A) hexokinase will function at less than one-half Vmax after a high carbohydrate meal B) glucokinase will function near its Vmax under fasting conditions C) hexokinase will function near its Vmax under fasting conditions D) glucokinase will function at less than one-half Vmax after a high carbohydrate meal - C) hexokinase will function near its Vmax under fasting conditions Glycophorin A is a 131-residue integral membrane protein that includes on bilayer spanning segment. Identify (underline) the bilayer-spanning segment in the glycophorin A amino acid sequence (one letter code is given below). (Hint - the spanning portion requires ~18-20 amino acids!) LSTTEVAMHTTTSSSVSKSYISSQTNDTHKRDTYAATPRAHEVSEISVRTVYPPEEETGERVQLA HHFSEPEIFLIIFGVMAGVIGVILLISYGIRRLIKKSPSDVKPLPSPDTDVPLSSVEIENPETSDQ - ...SEPE [IFLIIFGVMAGVIGVILLI] SYGIRR... Be able to calculate chemical potential difference. - (see exam 2 short answer) Be able to calculate the electrochemical potential. - (see exam 2 short answer) Be able to calculate Vmax and Km using a Lineweaver-Burke Plot. -

1. Memorize equations Be able to describe the catalytic mechanisms for enzyme substrate reactions. - (see exam 2 short answer) You have isolated two different inhibitors for the enzyme Examase. You have studied the kinetics of Examse in the absence and presence of each of these inhibitors and have plotted the kinetic data on Lineweaver-Burk plots. The two plots are shown below (see short answer question). Describe the type or inhibitor each molecule is based on the kinetic data you have analyzed and give a reason why for each. -
2. Uncompetitive inhibition because both Km and Vmax are decreased with more inhibitor.
3. Competitive because Vmax (see short answer) Regulation of enzymes. List two mechanisms of enzyme regulation and give an example of an enzyme regulated by each type of enzyme regulation. -
4. Allosteric Regulation - example: ATCase (aspartate/carboxylase)
5. Protein phosphorylation - example: glycogen phosphorylase EXAM 3 Material - The beta cells of the pancreas secrete _______ in response to ________ glucose levels.

A) insulin, low B) insulin, high C) glucagon, low D) glucagon, high E) None of the above - B) insulin, high Which of the following is (are) associated with cAMP binding to protein kinase A? A) cAMP binds to the regulatory subunits B) regulatory subunits dissociate from catalytic subunits C) catalytic subunits phosphorylate multiple targets D) All of the above E) None of the above - D) All of the above Consider the following metabolic reaction: Succinyl-CoA + Acetoacetate --> Acetoacetyl-CoA + Succinate (change in standard fee energy = -1.25 kJ/mol) This reaction is: A) Favorable under standard conditions B) Not favorable under standard conditions C) Always exergonic and can never proceed in the opposite direction D) Spontaneous as written when [succinate] and [acetoactyl-CoA] are high E) None of the above - A) Favorable under standard conidtions If you are running away from a bear, A) your muscle cells will be running glycolysis, and your liver cells will be running gluconeogenesis B) your muscle cells will be running gluconeogenesis, and your liver cells will be running glycolysis C) both your muscle cells and liver cells will be running glycolysis D) both your muscle cells and liver cells will be running gluconeogenesis - A) your muscle cells will be running glycolysis, and your liver cells will be running gluconeogenesis Increased levels of epinephrine in the blood will: A) Activate cAMP production in liver and muscle cells B) Stimulate glycogen synthesis C) Inhibit glycolysis in the muscle cell D) Stimulate gluconeogenesis in the muscle cell E) Inhibit the formation of cAMP - A) Activate cAMP production in liver and muscle cells The Keq is 0.503 at 25 C for the following reaction. What is the standard free energy for this reaction? D-Glucose-6-posphate --> D-Fructose-6-phosphate

A) -1,700 J/mol B) -2,870 J/mol C) +143 J/mol D) +1.70 kJ/mol E) none of the above - D) +1.70 kJ/mol In skeletal muscle, the main purpose of fermentation of pyruvate to lactate is: A) Remove toxic pyruvate from the cell B) Regenerate NAD+ used during glycolysis C) Provide a precursor for amino acid synthesis D) Activate pyruvate for the citric acid cycle E) Prevent you from becoming intoxicated through ethanol fermentation - B) Regenerate NAD+ used during glycolysis Which of the following metabolic convesions is considered to be the major control point of glycolysis? A) Fructose-1,6-biphosphate --> dihydroxyacetone phosphate +glyceraldehyde-3-phosphate B) Glucose --> glucose-6-phosphate C) 2-phophoglycerate --> phophoenolpyruvate D) Fructose-6-phosphate --> fructose-1,6-bisphosphate E) Pyruvate --> lactate - D) Fructose-6-phosphate --> fructose-1,6-bisphosphate The metabolic fate(s) of glucose-6-phosphate include: A) glycogen and glucose B) Ribose-5-phosphate and acetyl-CoA C) Both of the above D) None of the above - C) Both of the above During Glycolysis, the steps between glucose and the formation of the triose phosphates: A) Consume two ATP and two NADH molecules B) Consume two ATP molecules C) Produce two ADP and two NAD+ molecules D) Produce two ATP and two NADH molecules E) Consume tow NADH molecules - B) Consume two ATP molecules In eukaryotes, the enzymes that catalyze the reactions of glycolysis are located in: A) The cell nucleus B) The endoplasmic reticulum C) The mitochondria D) The lysosomes E) The cytosol -

E) The cytosol The hormone secreted by the pancreas under low blood sugar conditions is A) insulin B) glucagon C) epinephrine D) neuropeptide Y E) jurisisawesomeine - B) Glucagon Which of the following statements about glycogen and glucose metabolism in skeletal muscle is correct? A) Glycogen is hydrolyzed to free glucose that can enter the glycolytic pathway B) Glucose residues from glycogen yield a net of 3 ATP when converted to lactate in skeletal muscle C) No nucleotide is required to convert glucose to glycogen D) Phosphorylase is the only enzyme required to totally degrade glycogen to glucose-6-phosphate E) ATP is directly required for the conversion of glycogen to glucose-1-phosphate - B) Glucose residues from glycogen yield a net of 3 ATP when converted to lactate in skeletal muscle The enzyme catalyzing the reaction fructose-6-phosphate --> fructose-1,6-bisphosphate A) is allosterically activated by AMP B) is allosterically inhibited by ATP C) is activated by fructose-2,6-bisphosphate D) A, B, and C E) A and C - D) A, B, and C The carbons of galactose enter glycolysis at the level of A) Glucose-6-phosphate B) Fructose-6-phosphate C) Dihydroxyacetone phosphate D) 3-phosphoglycerate - A) Glucose-6-phosphate What is the overall purpose of the pentose phosphate pathway? What enzyme catalyzes the rate- limiting step of this pathway? How is this enzyme regulated to ensure the pentose phosphate pathway proceeds when necessary? - Overall, it is to create R5P and NADH, precursors for nucleotide biosynthesis and other important reactions. Enzyme is G6PDH, first reaction in stage 1. The concentration of NADP+ regulates the action of the enzyme. Know Hormonla controls of metabolism -

Know how to calculate delta G Standard and delta G. - We learned in class that PFK is the major flux-controlling enzyme of glycolysis. One major regulator of PFK is fructose-2,6-bisphosphate. Describe/diagram the control of PFK in the liver through the regulation of fructose-2,6-bisphosphate. Be sure to include mechanisms of production and degradation of fructose-2,6-bisphosphate and the hormonal control of fructose-2,6-bisphosphate levels. -

1. Memorize diagram.
2. If glucagon is released in response to decreased glucose levels, then glucagon activates cAMP, cAMP activates PKA, PKA activates FBPase to regenerate glucose, thereby inhibiting PFK. If FBPase is activated, then F-2,6-B will be degraded. Occurs in gluconeogenesis. Be able to diagram the discussed pathway steps fro glycolysis and gluconeogenesis. Primarily, draw the three irreversible steps of glycolysis, including reactants, products, enzymes, and other molecules required for the reactions. Also, for each of these reactions, give the reverse reactions required for gluconeogenesis (including enzymes and other molecules required). -