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Introduction to Biochemistry (CHEM 501)

Exam I 10/01/08

1. The enzyme fumarase catalyzes the reversible hydration of fumaric acid to l-malate, but it will not catalyze the hydration of maleic acid, the cis isomer of fumaric acid. This is an example of:

A) biological activity. B) chiral activity. C) racemization. D) stereoisomerization. E) stereospecificity.

2. Enzymes are biological catalysts that enhance the rate of a reaction by:

A) decreasing the activation energy. B) decreasing the amount of free energy released. C) increasing the activation energy. D) increasing the amount of free energy released. E) increasing the energy of the transition state.

3. Energy requiring metabolic pathways that yield complex molecules from simpler precursors are:

A) amphibolic. B) anabolic. C) autotrophic. D) catabolic. E) heterotrophic.

4. Hydrophobic interactions make important energetic contributions to:

A) binding of a hormone to its receptor protein. B) enzyme-substrate interactions. C) membrane structure. D) three-dimensional folding of a polypeptide chain. E) all of the above are true.

5. Osmosis is movement of a:

A) charged solute molecule (ion) across a membrane. B) gas molecule across a membrane. C) nonpolar solute molecule across a membrane. D) polar solute molecule across a membrane. E) water molecule across a membrane.

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6. Three buffers are made by combining a 1 M solution of acetic acid with a 1 M solution of sodium acetate in the ratios shown below.

1 M acetic acid 1 M sodium acetate Buffer 1: 10 mL 90 mL Buffer 2: 50 mL 50 mL Buffer 3: 90 mL 10 mL

Which of these statements is true of the resulting buffers?

A) pH of buffer 1 < pH of buffer 2 < pH of buffer 3 B) pH of buffer 1 = pH of buffer 2 = pH of buffer 3 C) pH of buffer 1 > pH of buffer 2 > pH of buffer 3 D) The problem cannot be solved without knowing the value of pKa. E) None of the above.

7. A 1.0 M solution of a compound with 2 ionizable groups (pKa’s = 6.2 and 9.5; 100 mL total) has a pH of 6.8. If a biochemist adds 60 mL of 1.0 M HCl to this solution, the solution will change to pH:

A) 5.60 B) 8.90 C) 9.13 D) 9.32 E) The pH cannot be determined from this information.

8. Of the 20 standard amino acids, only ___________ is not optically active. The reason is that its side chain ___________.

A) alanine; is a simple methyl group B) glycine; is a hydrogen atom C) glycine; is unbranched D) lysine; contains only nitrogen E) proline; forms a covalent bond with the amino group

9. Which of the following statements about cystine is correct?

A) Cystine forms when the —CH2—SH R group is oxidized to form a —CH2—S—S—

CH2— disulfide bridge between two cysteines. B) Cystine is an example of a nonstandard amino acid, derived by linking two standard

amino acids. C) Cystine is formed by the oxidation of the carboxylic acid group on cysteine. D) Cystine is formed through a peptide linkage between two cysteines. E) Two cystines are released when a —CH2—S—S—CH2— disulfide bridge is reduced to

—CH2—SH.

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10. For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have:

A) a net negative charge. B) a net positive charge. C) no charged groups. D) no net charge. E) positive and negative charges in equal concentration.

11. The formation of a peptide bond between two amino acids is an example of a(n) ______________ reaction.

A) cleavage B) condensation C) group transfer D) isomerization E) oxidation reduction

12. The peptide alanylglutamylglycylalanylleucine has:

A) a disulfide bridge. B) five peptide bonds. C) four peptide bonds. D) no free carboxyl group. E) two free amino groups.

13. An octapeptide composed of four repeating glycylalanyl units has:

A) one free amino group on an alanyl residue. B) one free amino group on an alanyl residue and one free carboxyl group on a glycyl

residue. C) one free amino group on a glycyl residue and one free carboxyl group on an alanyl

residue. D) two free amino and two free carboxyl groups. E) two free carboxyl groups, both on glycyl residues.

14. Prosthetic groups in the class of proteins known as glycoproteins are composed of:

A) carbohydrates. B) flavin nucleotides. C) lipids. D) metals . E) phosphates.

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15. In a mixture of the five proteins listed below, which should elute second in size-exclusion (gel- filtration) chromatography?

A) cytochrome c Mr = 13,000 B) immunoglobulin G Mr = 145,000 C) ribonuclease A Mr = 13,700 D) RNA polymerase Mr = 450,000 E) serum albumin Mr = 68,500

16. By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to:

A) determine a protein’s isoelectric point. B) determine an enzyme’s specific activity. C) determine the amino acid composition of the protein. D) preserve a protein’s native structure and biological activity. E) separate proteins exclusively on the basis of molecular weight.

17. The first step in two-dimensional gel electrophoresis generates a series of protein bands by isoelectric focusing. In a second step, a strip of this gel is turned 90 degrees, placed on another gel containing SDS, and electric current is again applied. In this second step:

A) proteins with similar isoelectric points become further separated according to their

molecular weights. B) the individual bands become stained so that the isoelectric focus pattern can be

visualized. C) the individual bands become visualized by interacting with protein-specific antibodies in

the second gel. D) the individual bands undergo a second, more intense isoelectric focusing. E) the proteins in the bands separate more completely because the second electric current is

in the opposite polarity to the first current. 18. A protein retained on an affinity chromatography column is usually eluted off the column by

A) Gradually increasing the salt concentration of the elution buffer. B) Adding the protein’s free ligand. C) Changing the pH of the elution buffer. D) Allowing the retained protein to naturally come off the column after the non-specifically

bound proteins have first passed through the resin. E) None of the above.

19. In the α helix the hydrogen bonds:

A) are roughly parallel to the axis of the helix. B) are roughly perpendicular to the axis of the helix. C) occur mainly between electronegative atoms of the R groups. D) occur only between some of the amino acids of the helix. E) occur only near the amino and carboxyl termini of the helix.

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20. In the diagram below, the plane drawn behind the peptide bond indicates the:

A) absence of rotation around the C—N bond because of its partial double-bond character. B) plane of rotation around the Cα—N bond. C) region of steric hindrance determined by the large C=O group. D) region of the peptide bond that contributes to a Ramachandran plot. E) theoretical space between –180 and +180 degrees that can be occupied by the φ and ψ

angles in the peptide bond. 21. An α helix would be destabilized most by:

A) an electric dipole spanning several peptide bonds throughout the α helix. B) interactions between neighboring Asp and Arg residues. C) interactions between two adjacent hydrophobic Val residues. D) the presence of an Arg residue near the carboxyl terminus of the α helix. E) the presence of two Lys residues near the amino terminus of the α helix.

22. Amino acid residues commonly found in the middle of β turn are:

A) Ala and Gly. B) hydrophobic. C) Pro and Gly. D) those with ionized R-groups. E) two Cys.

23. Which of the following statements is false?

A) Collagen is a protein in which the polypeptides are mainly in the α-helix conformation. B) Disulfide linkages are important for keratin structure. C) Gly residues are particularly abundant in collagen. D) Silk fibroin is a protein in which the polypeptide is almost entirely in the β conformation. E) α-keratin is a protein in which the polypeptides are mainly in the α-helix conformation.

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24. Proteins often have regions that show specific, coherent patterns of folding or function. These regions are called:

A) domains. B) oligomers. C) peptides. D) sites. E) subunits.

25. The α-keratin chains indicated by the diagram below have undergone one chemical step. To alter the shape of the α-keratin chains—as in hair waving—what subsequent steps are required?

A) Chemical oxidation and then shape remodeling B) Chemical reduction and then chemical oxidation C) Chemical reduction and then shape remodeling D) Shape remodeling and then chemical oxidation E) Shape remodeling and then chemical reduction

26. Which of the following statements about oligomeric proteins is false? A) A subunit may be similar to other proteins. B) All subunits must be identical. C) Many have regulatory roles. D) Some oligomeric proteins can further associate into large fibers. E) Some subunits may have nonprotein prosthetic groups.

27. In the binding of oxygen to myoglobin, the relationship between the concentration of oxygen and the fraction of binding sites occupied can best be described as:

A) hyperbolic. B) linear with a negative slope. C) linear with a positive slope. D) random. E) sigmoidal.

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28. Which of the following statements about protein-ligand binding is correct? A) The larger the Ka (association constant), the weaker the affinity. B) The Ka is independent of such conditions as salt concentration and pH. C) The Ka is equal to the concentration of ligand when all of the binding sites are occupied. D) The larger the Ka, the faster is the binding. E) The larger the Ka, the smaller the Kd (dissociation constant).

29. An allosteric interaction between a ligand and a protein is one in which: 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.

30. In hemoglobin, the transition from T state to R state (low to high affinity) is triggered by: A) Fe2+ binding. B) heme binding. C) oxygen binding. D) subunit association. E) subunit dissociation.

31. Which of the following is not correct concerning 2,3-bisphosphoglycerate (BPG)?

A) It binds at a distance from the heme groups of hemoglobin. B) It binds with lower affinity to fetal hemoglobin than to adult hemoglobin. C) It increases the affinity of hemoglobin for oxygen. D) It is an allosteric modulator. E) It is normally found associated with the hemoglobin extracted from red blood cells.

32. The amino acid substitution of Val for Glu in Hemoglobin S results in aggregation of the protein because of ___________ interactions between molecules.

A) covalent B) disulfide C) hydrogen bonding D) hydrophobic E) ionic

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33. An individual molecular structure within an antigen to which an individual antibody binds is as a(n):

A) antigen. B) epitope. C) Fab region. D) Fc region E) MHC site.

34. The proteins of the Major Histocompatibility Complex (MHC) bind and display:

A) antigen fragments. B) B cell fragments. C) immunoglobin fragments. D) macrophage fragments. E) T cell fragments.

35. A monoclonal antibody differs from a polyclonal antibody in that monoclonal antibodies: A) are labeled with chemicals that can be visualized. B) are produced by cells from the same organism that produced the antigen. C) are synthesized by a population of identical, or “cloned,” cells. D) are synthesized only in living organisms. E) have only a single polypeptide chain that can recognize an antigen.

Key

1 E 11 B 21 E 31 C 2 A 12 C 22 C 32 D 3 B 13 C 23 A 33 B 4 E 14 A 24 A 34 A 5 E 15 B 25 D 35 C 6 C 16 E 26 B 7 A 17 A 27 A 8 B 18 B 28 E 9 A 19 A 29 B 10 B 20 A 30 C