This preview has intentionally blurred parts. Sign up to view the full document

View Full Document

Unformatted Document Excerpt

100 BIBC FINAL EXAM WINTER 2008 BIBC 100 FINAL EXAM WINTER 2008 SECTION I CHOOSE ANY 4 OUT OF THE NEXT 5 QUESTIONS TO ANSWER. 5 points each. WRITE "OMIT" in LARGE LETTERS ON THE PAGE YOU DON'T WISH TO ANSWER. 41) Draw a diagram of a three-stranded, antiparallel sheet. Show the exact placement of main chain atoms. Be sure to indicate the pattern of hydrogen-bonding, and indicate where the R groups are situated relative to the main chain. Lehninger Fig. 4-7 R groups alternate above/below the plane of the sheet. 42) What are three similarities between the catalytic activity of chymotrypsin and protein kinases? What are two differences? (It is fine to list "Similarities: 1...... 2..... 3...... Differences: 1........2......") NOT ALL POSSIBLE ANSWERS ARE SHOWN BELOW Similarities: 1. both show a preference for certain substrates and not others, through interaction with specific regions of the enzyme (i.e. chymotrypsin specificity pocket, kinase binding on activation loop platform) 2. both use a nucleophilic attack from a hydroxyl group on to a substrate that will be cleaved by the attack (chymotrypsin Ser195, kinase attack from positioned substrate to phosphate of ATP) 3. both must become activated before their catalytic activity functions (chymotrypsin is cleaved into an active form, a protein kinase is activated through phosphorylation or other methods as described in the review article) 4. both use sets of residues to stabilize one another and assist catalysis (chymotrypsin Asp102 and His57, PKA Glu91 and Lys72) 5. both catalyze a reaction involving two different substrates, as opposed to catalyzing intramolecular rearrangements (I'd be surprised if anyone says this; chymotrypsin H20 and peptide, in two linked stages, kinase ATP and S/T/Y containing peptide) 6. both catalyze a reaction that uses a polypeptide chain as a substrate 7. both abstract a proton from a hydroxyl group with a catalytic base residue (I'd be surprised if anyone says this). Differences: 1. in chymotrypsin, the nucleophilic attacking group comes from Ser195, and later, water; in a protein kinase, the nucleophilic attacking group comes from the hydroxyl that is phosphorylated 2. substrates are different 3. chymotrypsin is transiently covalently bonded to a reaction intermediate, a protein kinase doesn't become covalently linked to a reaction intermediate 4. (similar to 3 above) the chymotrypsin mechanism proceeds in two main stages, while a protein kinase phosphorylates a residue in one reaction step 5. Once activated (by cleavage), the catalytic activity of chymotrypsin is permanently turned on. A protein kinases' catalytic activity may be turned on or off through methods described in the book and in the review article. 6. Chymotrypsin cleaves its peptide substrate, a protein kinase doesn't 43) The review article (Huse and Kuriyan, 2002) states "ATP is bound in a deep cleft between the two lobes and sits beneath a highly conserved loop connecting strands 1 and 2. This phosphate binding loop, or P loop, contains a conserved glycine-rich sequence motif (GXGXG) where is usually tyrosine or phenylalanine. The glycine residues allow the loop to approach the phosphates of ATP very closely and to coordinate them via backbone interactions." Which atoms in the loop coordinate the phosphates? Illustrate this through a diagram. There are only a few possibilities here. It wouldn't be the -carboxyl groups, because the oxygen in those groups has a slight negative charge and so do the phosphates. It won't be the hydrogen bonded to the -carbon, because the -carbon and that hydrogen share electrons equally, and thus that hydrogen never participates in hydrogen bonding. The phosphates would have to be coordinated via the hydrogens in the -amino groups, since those will have a slight positive charge. This is similar to how the backbone -amino group hydrogens coordinate the negatively charged transition state for chymotrypsin (the "oxyanion hole" arrangement). 44) Explain through text and diagrams, or any other method, how the MHC Class I + peptide and T-cell receptor interface is formed (Explain how the protein structure allows a given T-cell receptor to recognize an MHC Class I receptor and bound peptide). T cell receptor/MHC/peptide (specificity loops colored, these are similar to the specificity loops in IgG) (peptide thick yellow) Ig domain structure of T-cell receptor Gave credit for many things, including discussions of how the MHC Class I binds peptide, but full credit only for a full understanding of this interface. 45) Why is it energetically unfavorable for a K+ ion to pass through a membrane? How does the K+ channel from Streptomyces lividans (the channel discussed in lecture and in the book) overcome this problem and allow K+ ions, but not the smaller Na+ ions, to pass through the bacterial membrane? (a diagram would be a useful part of this answer) Ions and their associated hydration shells are extremely hydrophilic, and do not pass through the hydrophobic interior of a membrane. If just the ion is going to pass through, and not take along its associated shell of water molecules, these water molecules must be stripped off of the ion as it passes through the transporter protein. A channel protein can replace interactions with water molecules by weak interactions with protein atoms, so that the process of giving up the hydration shell is not so energetically unfavorable. See Fig. 11-28, Fig. 11-48, Fig. 11-49. An important part of the answer must be that the pore diameter in the K+ channel is such that K+ ions can be stabilized (water can be replaced by interactions with carbonyl oxygens), but Na+ ions would be too far away from the carbonyl oxygens and therefore the water (solvation shell) couldn't be replaced by these interactions. SECTION II ANSWER ALL OF THE QUESTIONS IN THIS SECTION. Two points each. NO PARTIAL CREDIT! 46) Which amino acids have branched hydrophobic side chains (non-aromatic)? (can use the full name, one letter or three letter codes) Valine, Leucine, Isoleucine (Val, Leu, Ile or V, L, I) 47) Which amino acids have charged side chains? Indicate the charge for each amino acid in your answer. negative: Aspartate, Glutamate (Asp, Glu or D, E) positive: Lysine, Arginine, Histidine (Lys, Arg, His or K, R, H) 48) Which amino acids have aromatic side chains? Draw the side chain for one of these amino acids (indicate which a.a. side chain you are drawing). Phenylalanine, Tyrosine, Tryptophan (Phe, Tyr, Trp or F, Y, W) see Fig 3-5 49) Which amino acids have amide groups in their side chains? Draw the amide group contained in these amino acids. Aspargine, Glutamine (Asn, Gln or N, Q) Q see Fig 3-5 only the terminal group for N, 50) Which amino acids' side chain is only weakly acidic? Draw the structure of this side chain. Histidine (His or H) Fig 3-5, Fig 6-9 51) What is the name of the prosthetic group contained in myoglobin? What unusual atom (for organic molecules) does this prosthetic group contain? heme, iron (or Fe or Fe2+) 52) Give one example of an unusual (not one of the standard 20) amino acid contained in some proteins? (hint: collagen) hydroxyproline or 4-hydroxyproline, hydroxylysine, and others. See section 3.1. 53) If you were to replace Ser195 in chymotrypsin with some other amino acid, which substitution might you predict would have little to no effect on chymotrypsin catalytic activity? Threonine, Thr or T 54) What molecule acts as a fluidity buffer in eukaryotic cell membranes, preventing them from altering their state dramatically if temperature increases or decreases? cholesterol 55) Draw the general structure of a glycerophospholipid. Label the major component parts of this type of molecule. see Fig 10-9 56) Draw the head-group structure of one of the common uncharged glycerophospholipids. see Fig 10-9 57) An _________allosteric____________________ modulator, generally a small metabolite, regulates certain enzymes through reversible, noncovalent binding. 58) The technique used to change one amino acid in a protein, or swap a stretch of amino acids from one protein to another in order to dissect protein function, is known as: site-directed mutagenesis 59) What is one name for the type of receptor that responds to odorant molecules (binds to them)? GPCR, Serpentine receptor, 7-transmembrane receptor 60) What is the name of the small signaling molecule that binds to the regulatory subunits of PKA? What is the name of the compound (not the enzyme) that is used to generate this signaling molecule? cAMP, ATP SECTION III ANSWER ALL OF THE QUESTIONS IN THIS SECTION. ONE POINT EACH. 1) In a highly basic solution, pH = 13, the dominant form of alanine is: A) B) C) D) E) NH2-- CH(CH3)--COOH NH3+-- CH(CH3)--COONH2-- CH2+(CH3)--COONH3+-- CH(CH3)--COOH. NH2--CH(CH3)--COO- 2) By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to: A) B) C) D) E) determine a protein's isoelectric point. separate proteins exclusively on the basis of molecular weight. determine the amino acid composition of the protein. preserve a protein's native structure and biological activity. break disulfide linkages between protein subunits. 3) Which of the following pairs of bonds within a peptide backbone show free rotation around both bonds? A) C=O and N--C B) N--C and C--C C) C--C and N--C D) N--C and N--C E) C=O and N--C 4) The structural classification of proteins (based on motifs) is based primarily on their: A) B) C) D) E) function. secondary structure content and arrangement. subunit content and arrangement. amino acid sequence. evolutionary relationships. 5) Myoglobin and the subunits of hemoglobin have: A) B) C) D) E) very similar primary structures, but different tertiary structures. very different primary and tertiary structures. very similar tertiary structures, but different primary structures. very similar primary and tertiary structures. no obvious structural similarity. 6) Which of the following is a correct statement concerning 2,3-bisphosphoglycerate (BPG)? A) B) C) D) E) It binds next to the heme groups of hemoglobin. It is positively charged. It must be added to hemoglobin by biochemists after the hemoglobin is purified. It binds with lower affinity to fetal hemoglobin than to adult hemoglobin. It increases the affinity of hemoglobin for oxygen. 7) Which part of the IgG molecule is involved in binding to an antigen? A) B) C) D) Light chain Fc Constant domain Disulfide linkage E) Papain cleavage site 8) The primary sequence (primary structure) of a protein A) B) C) D) E) can be used to predict exactly, by computer, its secondary and tertiary structure. is often rearranged enzymatically after translation. is sufficient to determine its specific secondary and tertiary structure. can never, by itself, contain as clues to the protein's function. is the linkage of peptide bonds between side chains. 9) In the protein represented by the structure shown above: A) B) C) D) E) the subunit comprised largely of -sheet binds ATP. the smallest subunit interacts with GTP. the largest subunit is known as the heavy chain. the largest subunit undergoes a conformational change upon binding GTP. phosphorylation of the large subunit results in dissociation of the subunits. 10) 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 acyl chain length. C) an increase in the number of double bonds in fatty acids. D) an increase in the percentage of phosphatidyl ethanolamine E) the binding of water to the fatty acyl side chains. 11) Serpentine receptors: A) B) C) D) E) are examples of G (GTP-binding) regulatory proteins. are mainly involved in the regulation of ion transport. are present in prokaryotic cells but not in eukaryotic cells. are present in the nucleus and affect gene expression. have multiple membrane-spanning helical domains. 12) Which of the following is not involved in signal transduction by the -adrenergic (epinephrine) receptor pathway? A) B) C) D) E) Adenylyl cyclase activation GTP hydrolysis GTP-binding protein Protein kinase All of the above are involved. 13) Peripheral membrane proteins: A) B) C) D) E) are generally noncovalently bound to membrane lipids. are usually denatured when released from membranes. can be released from membranes only by treatment with detergent(s). may have functional units on both sides of the membrane. penetrate deeply into the lipid bilayer. 14) Mechanisms of signaling pathways include all of the following except: flippase-catalyzed movement of phospholipids from the outer to the inner leaflet. migration of signal proteins into the nucleus. phosphorylation of target proteins at Ser, Thr, or Tyr residues. the ability to be switched off instantly by hydrolysis of a single phosphate-ester bond. E) the assembly of multiprotein complexes. A) B) C) D) 15) The role of an enzyme in an enzyme-catalyzed reaction is to: A) bind a transition state intermediate, such that it cannot be converted back to substrate. B) ensure that all of the substrate is converted to product. C) ensure that the product is more stable than the substrate. D) increase the rate at which substrate is converted into product. E) make the free-energy change for the reaction more favorable. 16) Enzyme X exhibits maximum activity at pH = 6.9. X shows a fairly sharp decrease in its activity when the pH goes much lower than 6.4. One likely interpretation of this pH activity is that: A) B) C) D) E) a Glu residue on the enzyme is involved in the reaction. a His residue on the enzyme is involved in the reaction. the enzyme has a metallic cofactor. the enzyme is found in gastric secretions. the reaction relies on free protons. 17) A good transition-state analog: A) B) C) D) E) binds covalently to the enzyme. binds to the enzyme more tightly than the substrate binds to the enzyme. binds very weakly to the enzyme. is too unstable to isolate. must be almost identical to the substrate. 18) Membrane proteins: A) B) C) D) E) are sometimes covalently attached to lipid moieties. are sometimes covalently attached to carbohydrate moieties. are composed of the same 20 amino acids found in soluble proteins. diffuse laterally in the membrane unless they are anchored have all of the properties listed above. 19) Which of these statements is generally true of integral membrane proteins? A) A hydropathy plot reveals one or more regions with a high hydropathy index. B) The domains that protrude on the cytoplasmic face of the plasma membrane nearly always have covalently attached oligosaccharides. C) They are unusually susceptible to degradation by trypsin. D) They can be removed from the membrane with high salt or mild denaturing agents. E) They undergo constant rotational motion that moves a given domain from the outer face of a membrane to the inner face and then back to the outer. 20) Taking this test is more fun than A) B) C) D) E) listening to Dr. Towb drone on and on and on...... drinking cod liver oil. hitting myself with a hammer. watching the presidential candidates debate. being bitten by a genetically-enhanced "super spider". 21) Which of these is a general feature of the lipid bilayer in all biological membranes? A) Individual lipid molecules are free to diffuse laterally in the surface of the bilayer. B) Individual lipid molecules in one face (monolayer) of the bilayer readily diffuse (flip-flop) to the other monolayer. C) Polar, but uncharged, compounds readily diffuse across 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. 22) The shortest helix segment in a protein that will span a membrane bilayer has about _____ amino acid residues. A) B) C) D) E) 5 20 50 100 200 23) The fluidity of a lipid bilayer will be increased by: A) decreasing the number of unsaturated fatty acids. B) decreasing the temperature. C) increasing the length of the alkyl chains. D) increasing the temperature. E) substituting 18:0 (stearic acid) in place of 18:2 (linoleic acid). 24) Enzymes are potent catalysts because they: A) B) C) D) E) are consumed in the reactions they catalyze. are very specific and can prevent the conversion of products back to substrates. drive reactions to completion while other catalysts drive reactions to equilibrium. increase the equilibrium constants for the reactions they catalyze. lower the activation energy for the reactions they catalyze. 25) Which of these statements about the composition of biological membranes is false? A) In a given eukaryotic cell type (e.g., a hepatocyte), all intracellular membranes have essentially the same complement of lipids and proteins. B) The carbohydrate found in membranes is virtually all part of either glycolipids or glycoproteins. C) The plasma membranes of the cells of vertebrate animals contain more cholesterol than the mitochondrial membranes. D) The ratio of lipid to protein varies widely among cell types in a single organism. E) Triacylglycerols are not commonly found in membranes. 26) A hydropathy plot is used to: A) B) C) D) E) determine the water-solubility of a protein. deduce the quaternary structure of a membrane protein. determine the water content of a native protein. extrapolate for the true molecular weight of a membrane protein. predict whether a given protein sequence contains membrane-spanning segments. 27) The bend or elbow in the graph shown above arises because A) the substrate has been depleted. B) acetic acid has built up and downregulated the enzyme. C) most all of the enzyme has been converted to a acyl-linked form. D) p-Nitrophenylacetate is binding to the enzyme active site. E) p-Nitrophenol is being produced. 28) Experimental evidence diagrammed in the graph shown above question 27 suggests that A) chymotrypsin has a serine residue in its active site. B) chymotrypsin does not hydrolyze peptide bonds through direct addition of water. C) chymotrypsin hydrolyzes ester linkages better than peptide bonds. D) chymotrypsin binds small substrates better than large ones. E) chymotrypsin has a distinctly different reaction mechanism from that of trypsin. 29) Myosin in sarcomeres is different from actin in that myosin A) binds nucleotides. B) has no -helical structure. C) is composed of one polypeptide chain. D) has a globular head and a fibrous tail. E) forms filamentous structures and actin does not. 30) When oxygen binds to a heme-containing protein, the two open coordination bonds of Fe2+ are occupied by: one O atom and one amino acid atom. one O2 molecule and one amino acid atom. one O2 molecule and one heme atom. two O atoms. E) two O2 molecules. 31) The fundamental cause of sickle-cell disease is a change in the structure of: A) B) C) D) E) blood. capillaries. hemoglobin. red cells. the heart. A) B) C) D) 32) During muscle contraction, hydrolysis of ATP results in a change in the: A) B) C) D) E) conformation of actin. conformation of myosin. structure of the myofibrils. structure of the sarcoplasmic reticulum. structure of the Z disk. 33) At the isoelectric pH of a tetrapeptide: A) B) C) D) E) the amino and carboxyl termini are not charged. only the amino and carboxyl termini contribute charge. two internal amino acids of the tetrapeptide cannot have ionizable R groups. there are four ionic charges. the total net charge is zero. 34) In an helix: A) B) C) D) E) the hydrogen bonds are at right angles to the axis of the helix. the hydrogen bonds occur between main chain atoms in the helix. runs of Glu residues tend to stabilize the structure . every turn of the helix contains five residues. Pro residues are often found centrally located. 35) Cyclins A) bind to and regulate PKA. B) contain an SH2 and SH3 domain. C) activate kinases that lack an C. D) activate kinases that have a PSTAIRE motif. E) cycle in and out of the nucleus. 36) The toxic compound DIFP, ______________ and this gives us clues about the nature of the enzyme's active site. i. reacts with serines on chymotrypsin ii. reacts with denatured chymotrypsin iii. reacts with Ser195 in chymotrypsin iv. reacts with other enzymes in the body v. is slowed from reacting with chymotrypsin when a peptide substrate is present A) iii and v B) i, iii, iv C) ii and iv D) ii, iii, iv E) i, iii, v 37) You would like to determine the structure of a 35 kDa soluble protein found in a small number of neurons. You might A) dissect the protein from cow brains. B) use NMR to study the protein structure in intact cells. C) try to express the protein in bacteria. D) perform 2D gel electrophoresis on those neurons. E) treat the neural tissue with a radioactive tracer. 38) G-proteins undergo conformational changes in three regions named "switches" when A) they bind to effector proteins. B) they hydrolyze GTP to GDP. C) they exchange bound GDP for GTP. D) A and C. E) B and C. 39) Which of the following statements about allosteric control of enzymatic activity is false? A) Allosteric effectors give rise to sigmoidal V0 vs. [S] kinetic plots. B) Allosteric proteins are generally composed of several subunits. C) An effector may either inhibit or activate an enzyme. D) Binding of the effector changes the conformation of the enzyme molecule. E) Heterotropic allosteric effectors compete with substrate for binding sites. 40) If I have to answer another multiple choice question, I will A) scream. B) shave my head and move into a Tibetan monastery. C) join Britney in the psych ward. D) quit college and go on the Jerry Springer show. E) sigh deeply and bravely press on. ... View Full Document

End of Preview

Sign up now to access the rest of the document