Biochemistry 1 (BCH 4053) Final Exam Review

Disclaimer: This guide should be utilized as a supplement to your studying and not entirely relied upon for your success. You are ultimately responsible for all of the material covered in class and book readings assigned. It is your responsibility to verify the accuracy of the information of this

sheet in the event of error.

1. An endergonic reaction with a ______ H and a ______ S can be changed into an exergonic reaction by decreasing the temperature.

a. positive, positiveb. negative, negativec. positive, negatived. negative, positivee. none of the above

2. How does the hydrophobic effect influence the structures of large molecules?a. Nonpolar molecules are not easily solubilized in water and aggregateb. Polar groups are oriented on the surface, interacting with the waterc. Nonpolar molecules can mask the polar characteristics of the hydrophilic moleculesd. a. and b.e. a. and c.

3. Translate following one letter amino acid code into three letter amino acid codea. LEARNINGSCIENCEISPHAT

3. The Henderson-Hasselbalch equation: a. a. allows the graphic determination of the molecular weight of a weak acid from its pH

alone.b. does not explain the behavior of di- or tri-basic weak acidsc. employs the same value for pKa for all weak acidsd. is equally useful with solutions of acetic acid and hydrochloric acide. relates the pH of a solution to the pKa and the concentrations of acid and conjugate

base

4. The pK1, pK2, and pKR for the amino acid Arg are 1.8, 9.0, and 12.5, respectively. At pH 7, Arg would be charged predominantly as follows:

a. -carboxylate 0, -amino 0, guanidino +1b. -carboxylate −1, -amino +1, guanidino +1c. -carboxylate +1, -amino 0, guanidino -1d. -carboxylate +1, -amino −1, guanidino −1e. -carboxylate −1, -amino 0, guanidino +1

5. Which amino acid does not have a primary α-amino group?a. Glycine

b. Histidinec. Prolined. Aspartic acide. none of the above

6. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) provides information ona. electrophoretic characteristics of a proteinb. net charge on a proteinc. total molecular weight of a multimeric proteind. molecular weight of a protein subunite. affinity of a protein for acrylamide

7. While proteins are usually composed of linear chains of amino acids, branched chains of amino acids and internally cross-linked chains can be found in certain proteins. Polypeptide chains are most commonly linked to each other through

a. hydrogen bonds.b. disulfide bonds.c. glycosidic bonds.d. peptide bonds.e. ester linkages.

8. Which of the following amino acids would be first to elute at pH 8.0 from an anion- exchange column?

a. Lysineb. Alaninec. Glutamic acidd. Asparagine

9. Which of the following pentapeptides will have the highest absorbance at 280nm?a. Tyr-His-His-His-Hisb. Phe-Phe-Phe-Ala-Hisc. His-His-Met-Met-Hisd. Trp-Glu-His-Trp-Cys e. Cys-His-Cys-His-Pro

10. Which of the following is commonly used to cleave disulfide bonds in polypeptides?a. beta-mercaptoethanolb. dansyl chloridec. iodoacetated. sodium dodecyl sulfatee. trypsin

11. Phosphoric acid is a polyprotic acid with pK values of 2.14, 6.86, and 12.38. Which ionic form predominates at pH 9.3?

a. H4PO4+

b. H3PO4

c. H2PO41-

d. HPO42-

e. PO43-

For questions 11-14, refer to the pKa table provided below.

Amino Acid pK1 pK2 pKR

Glycine 2.35 9.78Alanine 2.35 9.87Valine 2.29 9.74

Leucine 2.33 9.74Isoleucine 2.32 9.76

Phenylalanine 2.20 9.31Tryptophan 2.46 9.41

Tyrosine 2.20 9.21 10.46Histidine 1.80 9.33 6.04

Serine 2.19 9.21Threonine 2.09 9.10

Methionine 2.13 9.28Cysteine 1.92 10.70 8.37

Aspartic Acid 1.99 9.90 3.90Glutamic Acid 2.10 9.47 4.07

Asparagine 2.14 8.72Glutamine 2.17 9.13

Lysine 2.16 9.06 10.54Arginine 1.82 8.99 12.48Proline 1.95 10.64

12. Calculate the isoelectric point of the polypeptide: RDCSHa. 6.04b. 8.37c. 7.05d. 7.86e. 7.21

13. Calculate the isoelectric point of the polypeptide: AICEa. 3.04b. 2.00c. 4.07d. 6.17e. 7.02

14. Which of the following is a characteristic of the triple helix of collagen?

a. 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 reside

b. It is a left-handed triple helix. c. The molecule requires a proline residue every third amino acid residue.d. All of the above

15. By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to:a. Separate proteins exclusively on the basis of molecular weight.b. Preserve a proteins native structure and biological activity.c. Determine the amino acid composition of the proteins.d. Determine an enzymes specific activity.e. Determine a protein’s isoelectric point.

16. How does the term specific activity differ from the term activity?a. Specific activity is measured only under optimal conditions.b. Specific activity is the number of enzyme units (activity) per milligram of total protein.c. Specific activity is the total units of enzyme in solution.d. Specific activity refers to proteins, rather than enzymes.e. The terms are synonymous.

17. Amino acids commonly found in the middle of a turn are:a. Two Cysteine residuesb. Amino acids with ionized R-groupsc. Proline and Glycined. Alanine and Glycinee. Hydrophobic

18. Myoglobin and the subunits of hemoglobin have:a. very similar primary structures, but different tertiary structuresb. very similar tertiary structures, but different primary structuresc. no obvious structural relationshipd. very different primary and tertiary structurese. very similar primary and tertiary structures

19. Which of the following statements about protein-ligand binding is correct? (Pg.160)a. The Ka is equal to the concentration of ligand when all of the binding sites are occupiedb. The Ka is independent of such conditions as salt concentration and pHc. The larger the Ka, the weaker the affinityd. The larger the Ka, the faster is the bindinge. The larger the Ka, the smaller the Kd

20. During the T to R conformational shift, Fe(II) drags the F-helix via a bond to the side chain of (Pg. 164)

a. Leu F7

b. Leu F4c. His F8d. Leu FG3e. ValFG5

21. An allosteric interaction between a ligand and a protein is one in which: (Pg. 166)a. Binding of a molecule to a binding site affects binding of additional molecules to the

same site.b. Binding of a molecule to a binding site affects binding properties of another site on the

protein.c. Binding of the ligand to the protein is covalent.d. Multiple molecules of the same ligand can bind to the same binding site.e. Two different ligands can bind to the same binding site.

22. A prosthetic group of a protein is a nonprotein structure that isa. Permanently associated with the proteinb. A substrate of the proteinc. Transiently bound to the proteind. A ligand of the proteine. A part of the secondary structure of the protein

23. The Bohr effect refers to (Pg. 170)a. The decrease in affinity of Hb for O2 when the pH goes upb. The decrease in affinity of Hb for O2 when the pH goes downc. The increase in the affinity of Hb for O2 when the O2 concentration goes upd. The decrease in affinity of Hb for O2 when the BPG concentration goes upe. The decrease in affinity of Hb for O2 when the BPG concentration goes down

24. In sickle-cell anemia, which neutral amino acid residue in hemoglobin replaces the negatively charged glutamic acid residue? (Pg. 173)

a. Tyrosineb. Lysinec. Adenosined. Valinee. Glycine

25. The steady state assumption, as applied to enzyme kinetics, implies: (Pgs. 198-200)a. The enzyme is regulated.b. The ES complex is formed and broken down at equivalent rates.c. The Km is equivalent to the cellular substrate concentration.d. The maximum velocity occurs when the enzyme is saturated.

26. The concept of “induced-fit” refers to the fact that: (Pg. 196)

a. Enzyme-substrate binding induces an increase in the reaction entropy, thereby catalyzing the reaction.

b. Enzyme-substrate binding induces movement along the reaction coordinate to the transition state.

c. Enzyme specificity is induced by enzyme-substrate binding.d. Substrate binding may induce a conformational change in the enzyme, which then

brings catalytic groups into proper orientation.e. When a substrate binds to an enzyme, the enzyme induces a loss of water (desolvation)

from the substrate.

27. The benefit of measuring the initial rate of a reaction, V0, is that at the beginning of a reaction: (Pgs. 198-199)

a. [ES] can be measured accurately.b. Changes in [S] are negligible, so [S] can be treated as a constant.c. Changes in Km are negligible, so Km can be treated as a constant.d. V0 = Vmax

e. Varying [S] has no effect on V0.

28. Which of the following statements about a plot of V0 vs. [S] for an enzyme that follows Michaelis-Menten kinetics is false? (Pgs. 199-201)

a. As [S] increases, the initial velocity of reaction V0 also increases.b. At very high [S] the velocity curve becomes a horizontal line that intersects the y-axis at

Km.c. Km is the [S] at which V0 = ½ Vmax.d. The shape of the curve is a hyperbola.

29. In a plot of 1/V against 1/[S] for an enzyme-catalyzed reaction, the presence of a competitive inhibitor will alter the: (Pg. 209)

a. Curvature of the plot.b. Intercept on the 1/[S] axis.c. Intercept on the 1/V axis.d. pK of the plot.e. Vmax

30. One of the enzymes involved in glycolysis, aldolase, requires Zn2+ for catalysis. Under conditions of zinc deficiency, when the enzyme may lack zinc, it would be referred to as the:

a. Prosthetic groupb. Holoenzymec. Coenzymed. Apoenzymee. Substrate

31. Which of the following constitute the catalytic triad? (Pg. 215)a. Gly, Pro, 4-Hyp

b. His93, Asp64, Ser195

c. His57, Asn102, Ser195

d. His57, Asp102, Ser195

e. His93, Asp64, Cys195

32. Which of following is an anomeric pair? (244-245)a. -D-glucose and -D-glucoseb. D-glucose and D-fructosec. D-glucose and L-fructosed. D-glucose and L-glucosee. -D-glucose and -L-glucose

33. Which of the following is not a reducing sugar? (250-251)a. Fructoseb. Glucosec. Glyceraldehyded. Ribosee. Sucrose

34. Which of the following statements about starch and glycogen is false? (253-254)a. Both are homopolymers of glucoseb. Both serve primarily as structural elements in cell wallsc. Both starch and glycogen are stored intracellularly as insoluble granulesd. Glycogen is more extensively branched than starch

35. Which one of the following is true of the pentoses found in nucleic acids? (280)a. C-5 and C-1 of the pentose are joined to phosphate groupsb. C-5 of the pentose is joined to a nitrogenous base, and C-1 to a phosphate groupc. The pentoses are always in the -furanose formd. The straight-chain and ring forms undergo constant interconversion

36. The nucleic acid bases: (284)a. Absorb ultraviolet light maximally at 280 nmb. Are all about the same sizec. Are relatively hydrophilicd. Are roughly planare. Can all stably base-pair with one another

37. Inside our cells, free nucleotides are almost always associated with ______.

a. Proteinsb. Cholesterolc. Mg2+ counterionsd. fatty acidse. Cl- counterions

38. Which of the following DNA sequences is considered palindromic?a. GAACTTb. AAGCTTc. GAACAAd. AAGCAAe. AAGTTC

39. DNA polymerase from Thermus aquaticus is used in PCR because

a. It is a soluble proteinb. It is stable at high temperaturesc. Its genes from are readily distinguished from those of ‘normal’ organismsd. The enzyme is readily deactivated by heat, effectively halting the reactione. It is not infectious

40. Double stranded DNA molecules can be cleaved at specific recognition sites bya. RNA polymeraseb. DNA ligasec. reverse transcriptased. Type II restriction endonucleasese. DNA polymerase

41. Certain restriction enzymes produce cohesive (sticky) ends. This means that they: (322-323)a. Cut both DNA strands at the same base pairb. Cut in regions of high GC content, leaving ends that can form more hydrogen bonds

than ends of high AT contentc. Make a staggered double-strand cut, leaving ends with a few nucleotides of single-

stranded DNA protrudingd. Make ends that can anneal to cohesive ends generated by any other restriction enzymee. Stick tightly to the ends of the DNA they have cut

42. In the laboratory, recombinant plasmids are commonly introduced into bacterial cells by: (325)a. Electrophoresis – a gentle low-voltage gradient draws the DNA into the cellb. Infection with a bacteriophage that carries the plasmidc. Microinjection

d. Mixing plasmids with an extract of broken cellse. Transformation – heat shock of the cells incubated with plasmid DNA in the presence of

CaCl2

43. Which of the following statements is true of lipids? a. Testosterone is an important sphingolipid found in myelin b. They play only passive roles as energy-storage molecules c. They are more soluble in water than in chloroform d. Most are simply polymers of isoprene

44. Which of the following statements concerning fatty acids is correct? a. Phosphatidic acid is a common fatty acidb. Fatty acids all contain one or more double bondsc. A fatty acid is the precursor of prostaglandinsd. Fatty acids are a constituent of sterolse. Fatty acids are strongly hydrophilic

45. Membrane proteins:a. Are sometimes covalently attached to lipid moietiesb. Are sometimes covalently attached to carbohydrate moietiesc. Diffuse laterally in the membrane unless they are anchoredd. Have all of the properties listed above

46. Facilitated diffusion through a biological membrane is:a. Driven by a difference of solute concentrationb. Endergonicc. Generally irreversibled. Not specific with respect to the substratee. Driven by ATP

47. A ligand-gated ion channel (such as the nicotinic acetylcholine receptor) is:a. Always requires a second ligand to close the channel once it is openedb. A charged lipid in the membrane bilayer that allows ions to pass throughc. A molecule that binds to the membrane thereby allowing ions to pass throughd. A membrane protein that permits a ligand to pass through the membrane only when

opened by the appropriate ione. A membrane protein that permits an ion to pass through the membrane only when

opened by the appropriate ligand

48. Which of the following is not involved in the specificity of signal transduction?a. Transmembrane transport of signal molecules by receptor moleculesb. Interactions between receptor and signal moleculesc. Location of receptor moleculesd. Structure of receptor molecules

e. Structure of signal molecules

49. The force that drives an ion through a membrane channel depends upon the:a. Charge on the membraneb. Difference in electrical potential across the membranec. Size of the channeld. Size of the ione. Size of the membrane

50. Which of the following correctly states an essential step in the function of heterotrimeric G protein function?

a. Binding of GTP to the receptor protein must induce a change in conformation of the receptor

b. A cascade of events must occur that ultimately activate protein kinase Cc. Binding of cAMP to the α subunit of the G protein must initiate translocation of the

subunitd. Binding of a hormone to a receptor must signal the exchange of GDP for GTPe. All of the above are correct

51. Which of the following statements concerning signal transduction by the insulin receptor is not correct?

a. The substrates of the receptor protein kinase activity are mainly proteins that regulate transcription

b. Binding of insulin to the receptor activates a protein kinasec. Activation of the receptor protein kinase activity results in the activation of additional

protein kinasesd. Binding of insulin to the receptor results in a change in its quaternary structuree. The receptor protein kinase activity is specific for tyrosine residues on the substrate

proteins

52. Draw the fischer projection, Haworth, chair conformation of D-galactose:

53. Design a 6-nucleotide forward and reverse primer for the following genes of interest:a. 5’-GTACTAGTAGACCGTATGCCTCAGTA-3’b. 5’-GCTGTAAGAGGATTTACTACCGTCCA-3’

55. Which of the following primers would have the highest Tm value:

a. 5’-GCTAATAA-3’b. 5’-ATATATATA-3’c. 5’-GTACGTACG-3’d. 5’-GCGTGCGCA-3’

56. The following pictures represent which type of inhibition:

57. Find the oxidation state of all atoms in formaldehyde:

58. Find the oxidation state of nitrogen in NO2-:

59. Free rotation of peptide bond in a protein is restricted primarily because of b. Partial double bond characterc. Hydrogen bonding to amide backbone groupd. Partial bond character of N-C alpha bonde. Restrictions caused by local folding patternsf. Steric hindrance of neighboring amino acid chains

60. In hemoglobin, the transition from T to R state is triggered by a. Subunit associationb. Subunit dissociationc. O2 bindingd. Heme binding