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Fall08 Exam1 - 1 Which of the following is NOT a type of...

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Unformatted text preview: 1. Which of the following is NOT a type of catalysis used by enzymes? General acid-base catalysis Specific acid-base catalysis éhosphorylation catalysis Metal ion catalysis Covalent catalysis 2. Many proteins are phosphorylated on non-terminal amino acid residues that contain a hydroxyl (OH-) group. Which of the following amino acids does NOT get phosphorylated? Serine Threonine ll-listidine yrosine All of the above get phosphorylated 3. The labels for the axes of the Flamachandran plot are which combination below? dandB tpandtp pandq; yand§ Tandx LA/Which of the following proteins has quaternary structure? Hemoglobin Troponin c Amy’ropect‘rrr Syndecan, aflgtgotjl ca core protein Myoglobin 5. I want to determine the three dimensional structure of a large protein, but I cannot make a crystal yet. Which laboratory method should I use? X-ray Diffraction High-Performance Liquid Chromatography Dialysis Nuclear Magnetic Resonance Spectroscopy Sanger method 6. Which molecule/s has/have a greater affinity for the heme iron group in hemoglobin than oxygen? NO 002 CO H+ ~ None of the above have greater affinity than oxygen 7. Which amino acid would contribute to the pl of a protein if it is located 22 amino acids from the amino terminus? «Vat Phe Lee -He Lys 8. Which of the following statements ileALSEfiegarding buffers? ’ Buffering results from a reversible reaction, both directions of which are in equilibrium with equal concentration of a proton donor and its conjugate proton acceptor. Two especially important biological buffers are the phosphate and bicarbonate systems. In the bicarbonate buffer system Wepends the concentrations of H2003 and CO? _. The buffering power of the system is directly related to the number of ionizable groups on the buffer molecules. A small increase in H+ concentration will not significantly change the pH of a buffered solution. 9. Which of the following molecules Is a protein Without'ienzymatlclactIVIty? Myosin A zymogen that catalyzes condensation of amino acids when it becomes activated A cytosolic___ lectin A small mm on the plasma membrane A kinase expressed' In t e nuclear matrix 10. DNA was heated until both strands completely unwound and separated, then cooled slowly. Which of the following statements is TRUE about this situation? The DNA strands could reassociate normally and spontaneously to form a helix again The DNA strands may spontaneously form secondary, but not tertiary cr quaternary structures The DNA strands could form weak interactions spontaneously again, but cannot make the covalent interactions necessary to form the original DNA structure The heat would cause the bases to be in the puckered conformation, preventing reassociation of chains. e. None of the statements above is true. 11. In the peripheral tissues, hemoglobin' s affinity for 02 decreases. Why IS this? in the tissues, the high concentration at ‘1‘1’ and the high concentration of 002 bind to hemoglobin and decrease hemoglobins’ affinity for 02. it tn the issues, the high concentration of H+ and the low concentration of 002 bind to JP hemoglobin and decreases hemoglobin's affinity for 02. In the issues, the low concentration of H+ and the high concentration of 002 bind to hemoglobin and decreases hemoglobin’s affinity for 02. In the issues, the low concentration of H+ and the low concentration of C02 bind to hemoglobin and decreases hemoglobin's affinity for 02. e. None of the Above 12:;Pyruyate’Kin'as‘e requires potassium (K) andflrnagnesium (Mgz‘) to function properly. it catalyzes the transformation 6f Phosphoenapyuruvatgto Pyruvate. In this case, Mg +and K+ serve as . for Pyruvate Kinase, and Phosphoenolpyruvate is the COenzymes, Substrate Cofactors, Substrate boactivators, Substrate Apoenzymes, Holoenzyme Substrates, Apoenzyme 13. Many pharmaceutical companies are trying to design drugs that inhibit enzymes permanently. What sort of inhibitors might these companies be looking for? ’ Mixed inhibitors Uncompetitive inhibitors Noncompetitive inhibitors Suicide inactivators Allosteric inhibitors 14. What are lectins? Proteins that bind carbohydrates with high specificity A class of proteins that act as chaperones in bacteria The rigid component of bacterial cell walls A part of chitin ‘ Aldoses with one reducing end 15. Carbohydrates o 'are attached to the polypeptide though: a glycosidic in to e —o ‘of a Ser or a Thr residue , a N—glycosyl link to the -OH of a Ser or a Thr residue i a N-glycosyl link to the amide nitrogen of an Asn residu ya glycosidic link to the amide nitrogen of an Asn residue a and c ‘ 16. What feature of DNA backbones below is most important for the overall formation of a B-Fomi DNA molecule? ~ They are hydrophilic They are planar They are hydrophobic They form Hydrogen bonds with bases They lack internal rotation on phosphate and carbon bonds 17. hich of the following molecules is NOT found commonly on-glt these: sphin'golipidsr-t ycero. hos holi i ii ids? onosaccharides Glycerol . Fatty-acid- Choline . Sphingosine 18. Which of the following is true fihingolipidsfi They often contain carboh rate moieties They can serve as sources of intracellular messengers in cell membranes of neurons They account for the variability of blood types in humans A and C A, Band C 19. Phosphoric acid esters of nucleosides are also known as which of the following? Ribonucleic acids. Purines Glycosides Nucleotides Purines 20. Which of the following carbohydrates has linear portions composed of repeating disaccharides? Peptidoglycan Amylose Chitin Agrecan None of the above 21. Which of the following is NOT a membrane lipid? Cholesterol Glycerophospholipid Sphingolipid Triaclyglycerol All of the above are membrane lipids 22. Which of the following is arpyr Ridinelbase with only one carbonyl group? Guanine Thymine Adenine Cytosine 'Uridine 23. Which of the following statements about nucleic acids is FALSE? There is a free hydroxyl group on the 3' end of a newly synthesized RNA molecule The higher the A-T content of base pairs in DNA, the higher the melting point Hairpin structures may contain unpaired bases Hoogsteen pairings sometimes do not have the same number of H-bonds as so-called Watson-Crick pairings. Deamination is considered permanent change, however the DNA is often repaired . ri-fi ‘I y...— 24. Which of the following is NOT a function associated with nucleotides? ’ ‘Coenzymes in oxidation-reduction reactions A source of chemical free energy for enzymatic reactions Signaling through a cyclic form inside the cell that increases in concentration Regulation of cellular metabolism and metabolic pathways Enzymes that Join carbohydrate groups to polypeptides 25. Which of the following would be the best thing to use to make sticky ends for using bacteria to make a large amount of a goat protein? (Restriction endonucleases and an expression vector Phospholipases and an expression vector DNA ligases and a bacterial proteome Restriction endonucleaes and two specific hybrids constructed in yeast A shuttle vector and a cDNA library 26. DNA Sequence analysis requires that we make which of the following? A complementary copy of the DNA we are trying to sequence A complementary copy of the probe DNA A hybrid duplex between, the original DNA and the sequences generated with dideoxynucleotides A non-denaturing gel to separate the generated DNA sequences A set of DNA sequences with no bases added to the 5’ end of the primers 27. What Constant' Is derived from Vmax for an allosteric enzyme? Km W Kd K 0.5 Kcat Alpha 28. Which type of reversible enzyme inhibitor can only bind the Enzyme—Substrate complex? Competitive Mixed Mechanism-based Uncompetitive Ping-Pong Eggecently discovered an enzyme that condenses exotic monosaccharides (called Blueoses) dimers and I ran some kinetic trials on it. It could make the disaccharide product at 4. 5 mM/min, or at least that' Is the fastest initial rate | couldestlmatefmmthe'hypem This rate would be possible at about 2 mM Blueose and at 25°C. Given this information, which of the following other pieces of information can be obtained? The Gas Constant: 8. 315. AG=’° -2464, 5 In (4. 5/2) Km would be the Blueose concentration corresponding to 2 .25 mM/min Keq must be less than 1.0 Given the low product concentration, there must be a Competitive Inhibitor” In the system =.-2 91 log (2.25/2) 30. D—ribose is a sugar that has 3 chiral carbon atoms. How many stereoisomers can it have? 2 3 2 2 t3 9 31. p—glucose and Q—galactose differ only in rotation around 04 carbon atom. They are best described as which of the following? Aldoses Reducing sugars Enantiomers Anomers Epimers 32. What is the purpose of the yeast two—hybrid system? To identify a region of unknown DNA in yeast for sequencing purposes To find the sites of homologous recombination in yeast To quantitate the level of transcription of the target gene in yeast To identify protein-protein interactions in yeast None of the above 33. Which of the following statements is true of DNA microarrays? DNA polymerase is used to convert cDNA to mRNA _Each spot represents many copies of one complete gene They are similar to Southem Blots, except that the gel is run in two dimensions RNA polymerase converts mFiNA into cDNA None of the above are true concerning DNA microarrays 34. Which statement is FALSE? The place on actin where myosin binds could be called a Domain Motifs are groups of secondary structures and there can be more than one secondary structure in a motif Mixed Inhibitors can bind to either the enzyme or the enzyme-substrate complex The equilibrium constant is really a statement about how much product exists compared to substrate(s) concentration It BPG (2,3-bisphosphoglycerate) concentrations increase as normal at high altitudes, the Bohr effect is inhibited. 35. Which of the following types of protein chromatography is most like polyacrylamide gel Affinity Gel filtration Anion exchange Thin Layer lsoelectric Focusing ____________'_. , .iirvfl . V MCDB 310 Fall 2008 Exam 1 Written Section v NAME l ' SCORE ”745 .____’._.— Please answer the following questions only in the space provided (not in the margins, which will not be graded). Answers are often one word or a short phrase. 1 point per blank 36. molecules have both polar and nonpolar regions. 37. is the constant that denotes the Biochemical Standard Free Energy Change of a chemical reaction. 38. Mannose binding protein is a lectin. Which type of chromatography would you use to separate this protein from a mixture of liver proteins? is one of the amino acids that are grouped as having a 9. posit ively charged R-group at pH 7.0. 40. Peptide bonds are formed from 2 functional groups, the of one molecule and 3 the of the other molecule. 41. . is one specific type of rotational symmetry. 42. Although oxygen binds to either State of hemoglobin, it has a significantly higher affinity for the State. 43. is the structural Form of DNA that is favored in environments that are relatively devoid of water. 44. A protein may have specific amino acids replaced individually using a cloning method called in which the original codon is altered. ’45: are phospholipids that contain phosphocholine or phosfi'hoethanolamine as'the polar head group. , are lipid-soluble vitamins that act as antioxidants, due largely to their ring structure that stabilizes free electrons from radicals. OUT OF 12 \ 47. , are the group of enzymes that are used to break phosphodiester bonds at specific short base sequences during construction of a plasmid. o ) 48. is one of the three classes of Glycoconjugates. ) 49. is an enzyme that can remove a portion of a glycerophos holipid, often producing a molecule that acts as an intracellular signal. 3 50. is the class of lipids that act as energy storage molecules. /51. What specific constants are used for the following? Turnover Number Dissociation Constant, as a measure of affinity Rate Constant 52. (4 points) After countless hours of preparation (or maybe just a couple hours of cramming) you have come across a number of basic techniques used in biological studies. Please state what a DNA microarray is used for (i.e. what is its purpose?) and briefly (a couple sentences) state how it works. What do the fluorescent spots represent? Use only the space provided! AIRPQSE: METHOD: 53. (4 pts) Draw a disaccharide of glucose that contains an alpha’ 1—* 5 ulvcosidic linkage OUT OF 15 54. (3 points) Please draw the chemical structure of Thymlne: V 55. (3 points This is art of an x-ra from a DNA sequenCing gel. What is the. sequence of bases of the ori inal section of DNA? se accepted conventions when giving the sequence and label the ends properly. A C G T 56. (4 points) You are working for Roche Pharmaceuticals and did an experiment that ‘ compares the activity of an enzyme before and after the addition of compound that may be an inhibitor from another department in the company. After constructing a Lineweaver-Burk plot with your data, you. notice that the Vmaxrdid notchange, but the Km was‘éig'h'rfica'ntly higher. What can y_ou conclude from the data? ls the inhibitor working, and if so, how does it Work to alter enzyme activity? MCLUSION: ANALYSIS: “"’ , OUT OF 10 mm 57. (4 pts) You purified a mixture containing significant amounts of three proteins. One has a high concentration of basic amino acids, one has a high concentration of acidic amino acids, V and the third is nearly all non-polar amino acids. How will you distinguish them using sOme electrophoresis method? Name one electrophoresis method and identify the position these proteins would occupy on the result of'th‘e” mEth'od. ETHOD: . P ITIONS 0N RESULTS: A.acidic proteins: B.neutral (nonpolar) proteins: 7 C.basic proteins: 58. (4 points) Palmitic acid and Oleic acid are two naturally occurring fatty acids and they are sometimes found in membrane lipids. W0" M“ Palmitic Acid Oleic Acid ' What is the correct nomenclature for these two structures? Palmitic Acid Oleic Acid 3 POINT BONUS: Dr. B. only used the internet for one thing this term: to show a 3-D chemical model that he rotated in space. What concept or specific 811er was he demonstrating using that model (no credit forjust the name f the molecule in the model)? \ OUT OF 11 ”—— ...
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