Exam1 - 03:5283’200? 14223 FAX 5124?18135 CH 359 Exam I...

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Unformatted text preview: 03:5283’200? 14223 FAX 5124?18135 CH 359 Exam I Name: eID: BIDEHEi-‘I IIII'u' UT AUSTIN l. (5 pts) Match the following Structures to the correct name. a. methionine b. cysteine e. serine d. threonine e. glutamate flaspartate g. phenylalanine h. proline i. histidine j.tymsine COD" ‘ | . ‘ N 1-1—1:—-cl-Ijgm- I. NEH-5‘ ([130) II—CIT—CH‘E \‘Hr' 2. 3’ ,, I i I J IllN ' 3. 1‘ Version 3 + ELEETHEINIE HESER 0023003 September 20. 2007 03:3283200? 14223 FAX 5124T1Ei135 BIDEHEi-‘I IIII'u' UT AUSTIN + ELEETHEINIE HESER 0033003 I]. (10 pts) Match the following: Use the BEST answer, one amino acid may fit more than one descriptions, but one description is either unique or better! 6. 7. 3. 9. 10. 11. 12. 13. 14. 15. Polar A) Aspartate First amino acid incorporated into most proteins during B) Mefltionine synthesis Non-polar C) Serine Largest aromatic D) Histidine Contains a hydroxyl group E) Glutamine Aromatic F) Arginine Has a pKa of about 7 G) Cysteine Acidic H) Isoleucine Makes disulfide bonds 1) Tyrosine Basic .1) Tryptophan ll]. (1 pt each) 16. 17. 13. 19. 20. 21. 22. 23. 24. Which of the following parts of the myosin molecule acts as the molecular lever? A) neck B) tail C) head The Bohr effect on hemoglobin is: A) the decrease in oxygen affinity in the presence of2.3-bisphophoglycerate B) the increase in oxygen affinity in the presence of excess heme C) the increase in oxygen affinity in the presence of carbon monoxide D) the decrease in oxygen affinity in the presence of dissolved C02 E) none of the above The motor activity of kinosin requires the free energy of hydrolysis of A) UTP B) GTP C) CTP D) ATP E) none of the above Restriction endonucleases are bacterial enzymes that cleave DNA at specific sequences. A) True El) False The power stroke in muscle contraction is directly associated with: A) the hydrolysis of ATP by the myosin ATP hydrolysis site B) dissociation of ADP from the myosin ATP hydrolysis site C) the binding of ATP to the myosin ATP hydrolysis site D) binding of myosin to actin E) none of the above The charged amino and carboxylate groups in biological molecules interact non-covalently by A) covalent bonds E) van der Waals forces C) ionic interactions D) all of the above E) none of the above Which of the following groups of elements are never incorporated into biomoleeules? A) Noble gases E) Transition metals C) Alkali metals At pH 1 1.5, the amino groups found in proteins would: A) carry a positive charge B) ltave no charge C) bear multiple ionic charges D) Alkaline earth metals E) Non-metals D) carry a negative charge E) none of the above Based on the following Tm values, what can be said about the these two strands of DNA? Tm values (degrees Celcius): Strand A = 80 Strand B = 100 A) Strand B has stronger stacking interactions (van der Waals). El) Strand A has a higher percentage of adenine bases. C) Strand B has a higher percentage cytosine bases. D) All ofthe above VersionB Page 2 UEIEBHECICI? 14223 FAX 25. 26. 27. 23. 29. 30. 31. 32. 33. 34. 35. 36. 37. 5124?18135 BIDEHEl-l [II'v' UT AUSTIN + ELEETHDNIE HESEH UGMQUEI The hydrogen atoms in a water molecule 'aeeept' a hydrogen bond and the unshared electron pairs 'donate' a hydrogen bond. A) True B) False The synthesis of glucose-fi-phosphate in the cell is carried out by the following reaction: glucose + ATP in} glucose-6- phosphatc -I- ADP. If the AG of1he synthesis of ATP is +305 kJ/mol and the AC: of the phosphorylation of glucose is +118 lei/moi, what is the AG of the overall reaction? A) +lfi.7 B) 46.7 C) «44.3 D) +443 E) none ofthe above Coupled reactions are important in biochemistry because: A) They allow the monomers of one biopolyrner to change into monomers of a different type ofbiopolyrner. B) They allow unfavorable thermodynamic reactions to occur in cells. C.) Coupled reactions mean that overall reaction has a positive AG. D) They only occur during photosynthesis. E) none of the above RNA interference (RNAi) A) makes use of an enzyme called Diccr. which binds to dsRNA and cleaves it into small pieces of RNA B) is now widely used as a method to study gene regulation C) is a natural regulatory mechanism that probably evolved to protect cells from invading viruses D) all of the above E) none of the above Cytoskeleton is static and never changes once formed in the cell. A) True 13) False What is the term used to define binding behavior of proteins in which the binding of one ligand alters the affinity of binding for another ligand at a difierent site? A) denaturation 13) none are correct C) complementary D) stereOSpecificity E) cooperativity It is oxidation when an animal breaks down a monosaccharide to obtain metabolic energy. A) True B) False The neck structure in kinesin is flexible while the neck structure in myosin is stiff. A) True B) False A is a compound consisting of a nitrogenous base linked to a five—carbon sugar (ribose or deoxyribose). A) nucleoside E) purine/pyrimidine C) nucleotide D) none of the above The primary method of determining ifs plasmid has been taken up by bacteria during transformation is to use an antibiotic resistance gene. A) True E) False A triple helix is the right-handed helical structure formed by three left-handed helical polypeptide chains in A) keratin B) myosin C) collagen D) kinesin E) none of the above To form the coiled coil in intermediate filaments, the ----- sides of the two alpha helices come in contact with each other. A) Nonpolar B) Polar Micro'filamcnts may rapidly assemble actin monomrs at one end and disassemble at the other and resulting in changes in the shape or movement of a cell. A) True B) False Version 3 Page 3 033'283’200? 14223 FAX 512|1T18135 ElIEIEHEl-‘I [II'v' UT AUSTIN + ELEETHEINIE HESER Uflfifflflfl 38. Polymerization of monomers into polymers... Which correctly completes the statement? A) is the breakdown of large molecules into their components. B) is the linkage of smaller molecules to few larger ones. C) is necessary to synthesize biologically active macromolecules such as proteins. D) occurs in the synthesis of proteins and polysaccharides. but not nucleic acids. E) E and C are correct F) A and D are correct G) none ofthe above 39. An angstrom is smaller than a nanometer. A) True B) False 40. Pure water has A) very high tendency to ionize into l—l+ and OH‘ C) slight tendency to ionize into H+ and DH' B) no tendency to ionize into H’“ and OH" D) none of the above 41. An amphipathic molecule is one which A) often has along hydrocarbon tail. D) all of the above 13) will form micelles in water E) none of the above C) has a polar head bonded to a nonpolar tall 42. Water is a polar molecule because: A) the electrons in the 0—H bond spend more time close to the oxygen. B) it has asymmetrically arranged polar bonds. C) the hydrogens have a partial positive charge and the oxygen has a partial negative charge. D) in the 0-H bonds in water, the oxygen is the more electronegative. E) all of the above are correct. F) none of the above are correct IV. 2 pts each Answer the following questions about the polymerase chain reaction and DNA sequencing. 43. In PCR, at which cycle of the amplification (generally 30 cycles are done) do the double-stranded DNA fragments of defined length appear? A)4 m5 o)1o)2 ms 44. In a DNA cycle sequencing reaction, The newly synthesized DNA product can also be used as a template. A) False B) True 45. Which ofthe following reagents is NOT needed for FOR? A) All are needed 13) DNA polymerase C) decxynucleotides D) oligonucleotide primer E) di-deoxynucleotides 46. Ofthe six proteinsI actin, myosin. tubulin, kinesin. keratin, and collagen. which are considered to he motor proteins? Esed on 5—2. A) actin and tubulin D) myosin and kinesln El) keratin and collagen E) none of the above are correct C) actin. myosin, tubulin, and kinesin 47. Which of the following deoxyoligonuclcotides will hybridize with a DNA containing the sequence (5') TCAGGTTAACG(3')? A) (5')CTCATTGAGGC(3') D) (5‘)AGTCCAATTGC(3') B) (5‘)CGTTAACCTGA(3') E) (5')GCAATTGGACT(3') C) (5‘)GAGTCAACTGC(3') F) none of the above Version 3 Page 4 DSIEBHEDQT 14230 FAX 43. 49. 50. 51. 52. 53. 54. BIDEHEl-l IIII'Ii' UT AUSTIN + ELEETHDNIE HESEH 008E003 5124T18135 What is the pH of a 2 x 10'5' M solution of H01? A) 8.7 a) 5.7 C) 9.7 o) 10.7 E) none ofthe above Place the events of a round of kincsin movement in order. Assume one round has ended. 1. New leading head binds tublin 2. ADP released 3. Trailing head hydrolyzes ATP 4. Trailing head swings forward 5. ATP binds leading head A) none are in the correct order B) l.4,3,2,5 C) 2,5,l,3,4 D) 3,2,1,4,5 E) 5,4,1,2,3 Advantages of quanternary structure include A) allows proteins to use structural changes to communicate B) increase in the size of a functional protein C) minimization of transcription or translation errors D) all of the above are correct E) none of the above are correct Which amino acid substitution would you expect to disrupt protein function the most? A) Glu replaced by Asp D) Tyr replaced by Phe E) Scr replaced by Thr E) Gln replaced by His C) Lys replaced by Arg Of the six proteins, actin, myosin, tubulin, kinesin, keratin, and collagen, which are not motor proteins but can undergo structural changes? A) actin, myosin, tubulin, and kinesin E) actin and tubulin C) keratin and collagen D) myosin and kinesin E) none of the above are correct (4-3) Biochemists sometimes link a recombinant protein to a protein known as green fluorescent protein (GFP), which was first purified from bioluminescent jellyfish. The fluorophore in GFP (shown below) is a derivative of three consecutive amino acids that undergo cyclization of the polypeptide chain and an oxidation. Identify the three residues involved in this reaction. n“ t} t?” CH l-Idt.‘ a U l) l \\ |l_ —NI-|—t‘.1I—r:— —r:i-|.—r.,— A) tyr,his,tbr B) phe, pro, thr C) phe, gly, ser D) phe, pro, ser E) tyr,gly, set Of the six proteins, actin, myosin, tubulin, kinesin, keratin, and collagen, which contain nucleotide-binding sites? Based on 5-2. A) myosin and kinesin El) actin. myosin, tubulin, and kinesin C) keratin and collagen D) actin and tubulin E) none of the above are con‘ect You have isolated a decapeptide with anti-viral and anti-tumor activity from a rare species of salamander you are trying to save fiom extinction. Several pharmaceutical companies will support your research efforts if you can get the sequence of the peptide. You digest with trypsin and get 3 peptide fragments and obtain the sequences of the peptides using Edman degradation. peptide A: phe-mct-lys peptide B: asp—cys-gly-arg peptide C: ser-ala—glu 55. From this data alone you can determine the correct sequence of the peptide. A) True B) False Version 3 Page 5 032232200? 14230 Fhii 5124718135 BIDEHEl-l IIII'u' UT AUSTIN + ELEETHEINIE HESEH 0072003 56. From this data you can assign the C-terrninal fragment. A) True 13) False 57. From this data you can assign the N—terminal fragment. A) True 13) False Use the information in the following questions to make 0.5 L of 0.1 M, pH 7.7 phosphate buffer. Jr NOTE: Read all 4’ of the next questions before answering. pr 5 53. [Note: this problem may require extra time, do not attempt until the rest of the exam is complete] To make 0.5 L of 0.1 M phosphate buffer, pH 7.7 you discover you only have solid NaH2P04 (MW 120 g/mol). Which is the most correct "recipe" to make this buffer? A) 12 g NaHzPOrEZ ml. 1 M NaOH, 473 mL water D) 6 g NaHzPOa22 ml. 1 M HC], 473 mL water 13) 6 g Nal'lzPDa,-44 1111., 2 M NaOH, 456 mL water E) 6 g NaHsli’Oa_ 22 mL 2 M NaOI—l, 473 mL water C) 12 g NaHzPOa, 44 mL I M NaOH, 456 mL water 59. What is the correct ratio of components to make pH 7.7 phosphate buffer? A) 8/1 E) 3/1 C) 2.5/1 D) 10/1 E) 2/1 F) 4/] (3) 5/1 60. What amount of 0.1 M NaHzPO4 and 0.1 M NazflPCh would be required to make 0.5 L of 0.1 M phosphate buffer pH 7.7? A) 240 mL 0.1 M NaI-IzPOn and 260 mL 0.1 M Nazi-IP01 C) 444 mL 0.1 M NBH2POn and 56 mL 0.] M NRZI'IP04 E) 561111.. 0.1 M Hal-121504 and 444 mL 0.] M NazHPOa D) 122 mL 0.1 M Hal-121304 and 373 mL 0.1 M Neal-IP04 61. You wish to prepare 1 L of 0.1 M phosphate buffer at pH 7.7. Which is the relevant equation/pKa A) Hal’Cl-r" cm:- HPer + H“, pKa=6.8 C) HPOfi o»: For-3 + H“, pKa =12.4 B) I-lsPCla sin-la H2FDa']+ Hl', pKa= 2.2 D) none of the above 62. Which of the following is the correct equation for the Henderson-Hasselbalch equation A) pH= -log [H‘“] B) pl-l= -pl<.a -I- [A‘]/[HA] C) pl-I allpitta + log [A']/[HA] D) pl(a= -pl-I~log [HA]/[A'] (3 preach) 63. (Based on 5-33) Your sister prepares your Mother's famous lime gelatin dessert to impress your fatnin visiting for the game this weekend. However. she decides to add some fresh papaya to make it more adVentureste. When she takes it out of the refrigerator, she is horrified to discover it is not congealed, but liquid. She comes to you and asks you what went wrong. Using your biochemical skills. you explain to your sister what happened. Note that gelatin is composed primarily of collagen from domestic animal bone/skin. A) Th refrigerator temperature was too high to allow the molecules of collagen in gelatin to congeal. B) The papaya contains a protease that hydrolyzed the collagen to smaller fragments that do not congeal. C) The papaya contains so much water that it caused a dilution of the gelatin so that it could not congeal. D) The papaya caused the pH of the gelatin to be too low and inhibited the collagen from congealing. E) none ol’the above are plausible explanations and your sister tells you to make the dessert Version 3 Page 6 (ZIEIIEBIEICIICI? 14:30 Fnii 51247'18135 EiIEIEHEl-‘I [II'v' UT AUSTIN + ELEETHEINIE HESEH QQBHICICIEI (based on 445) The developing fetus has a different kind of hemoglobin than most normal adults. Fetal hemoglobin (hemoglobin F) consists oftwo Ct chains and two it chains, whereas adult hemoglobin (hemoglobin A) consists of two o. chains and two it chains. Fetal hemoglobin is synthesized beginning at the third month of gestation and continues up through birth. After birth, hemoglobin F synthesis declines and synthesis of hemoglobin A increases (synthesis of the 7 chain declines and synthesis of the [3 chain increases). By the time the baby is six months old. 98% of its hemoglobin is hemoglobin A. 64. The y chain differs slightly in structure from the [El chain and has fewer Lys and His residues in its central cavity than the B chain. What do the structural differences do to the ability to interact with 3-bis-phosphoglycerate (3BPG) and oxygen binding? A) decreases BBPG interactions, decreasing ability to bind oxygen B) increases BBPG interactions, decreasing ability to bind oxygen C) no effect on BBPG D) increases SEPG interactions, increasing ability to bind oxygen E) decreases BBPG interactions, increasing ability to bind oxygen 65. Which hemoglobin has the higher the higher affinity for oxygen: A) neither, they have the same affinity B) fetal C) adult 66. (based on 4-41) Hemoglobin is 50% saturated with oxygen when 1303 = 26torr.1,E hemoglobin exhibited hyperbolic binding (as myoglobin does) with 50% saturation at 26 torr, the fractional saturation when pill: in 30 torr w0uld be 0.54 and at 100 torr would b: 0.79. What does this tell you about hemoglobin's sigmoidal oxygen-binding curve? races Lungs as 0.6 ' on . I fill I‘ l as ,‘II I ,ltll. .,.|,I .. _.. .I_.. .. . . .L.. _ ......_I_. 20 i so an EU IOD pct, [turn A) IF the hemoglobin binding curVe were hyperbolic, the change in oxygen binding would be 40% B) none of the above. C) The sigmoidai curve allows the over all change in oxygen binding to b ~25%. D) If the hemoglobin binding curve were hyperbolic, it would allow more oxygen to be released to the tissues. E) The sigrneidal curve allows more oxygen to be bound in the lungs and then released in tissues. (5-30) The effect of the drug minoxidil (Regaine) was measured in cultured human skin fibroblasts and the data are shown in the table below. Fibroblasts were incubated with radioactive [3H]~proline or [3H]-lysine to allow collagen to incorporate the radioactively labeled amino acids into the polypeptide chains. Following treatment with minoxidil (controls were untreated), the cells were harvested and the subjected to enzyme treatment, which hydrolyzed all cellular protein. The amount of [3H]-proline or [3H]hlysinc incorporation into collagen was then measured in terms of radioactive 31-120 released. Fro'lyl hydroxylnuc Lqu hydrarylnno Coltufl: actlvity (clam. activity (Elma, conditions inflow punch) *Hzotmg pmtcln) we use arena 67. What would you predict the long term effects eftopical minoxidil use might be based solely on the biochemical data? A) no effect 5) increased collagen stability in skin C‘.) decreased collagen stability in skin Wt: {oupew> Version3 Page 7 (JEEEBHECIL’JT 14:31 FAX 5124?18135 BIEIEHEl-‘I EII'u' UT AUSTIN + ELEETHEINIE HESEH 0033’003 63. What is the effect of minoxidil on cultured fibroblasts? A) It is an inhibitor of hydroxlylation of lysines in collagen B) It is an activator of the hydrolysis of collagen. Answer Key C) It is an inhibitor of hydroxlylation of prolines in collagen D) it is an inhibitor of the hydrolysis of collagen. E) It is an activator of hydroxlylation of lysines in collagen F) It is an activator of hydroxflarion of prolincs in collagen. G) none of the above are correct oh: Ov- P W H 61. A D 62. C 63. B E 64. E E. 65. B H 66. E J 67. C \DMHGMPP’PH tr] Version3 Page 8 53' ...
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Exam1 - 03:5283’200? 14223 FAX 5124?18135 CH 359 Exam I...

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