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1 CHEMISTRY 441A FINAL EXAM SET A Dec 14, 2017 S Manandhar N ame: ________________________________Student ID#: ____________________________ Instructions: 1. DO N OT begin the exam until instructed to do so. 2. SWITCH OFF your phones. 3. Make sure there is a total of 12 pages . 4. Write your N ame AND Exam number (A or B) on your Scantron. 5. When finished, place Exam sheet and Scantron and return all materials to the instructor. Summary of points: 1. Answer on Scantron Section A (Q# 1….60) (60 Points) 2. Answer on the Exam Sheet Section B, C, and D (Q# 61-90) (40 Points) 3. Answer on the Exam Sheet Section E (Q# 91-93) (6 Points) 4. TOTAL 100 + 6 points A B ______ C ______ 4 T O T A L Jerry Litteral 694205318008 1000 Shanna

2 SECTION A – Please, answer these questions on Scantron (1x60 = 60 points). 1. In the figure below, where is a hydrogen bond acceptor located? a) B b) C c) D d) A 2. )RU $73 ±VKRZQ EHORZ²³ FOHDYDJH RI WKH ERQG EHWZHHQ BBBBBBBBBB KDV WKH ODUJHVW ǻ* ƍ . a) adenine and ribose b) ȕ SKRVSKDWH DQG Ȗ SKRVSKDWH c) Į SKRVSKDWH DQG ȕ SKRVSKDWH d) ULERVH DQG Į SKRVSKDWH 3. All of the following are important for enzyme-substrate interactions EXCEPT a) hydrogen bonds. b) van der Waals interactions c) ionic interactions. d) covalent bonds. 4. When a protein folds in an aqueous solution, which of the following is correct? a) A mixture of polar and non-polar amino acids is found in the interior of the protein. b) Polar amino acids are found in the interior of the protein c) Water is always excluded from the active site in the interior of the protein. d) Non-polar amino acids are found in the interior of the protein. 5. Which of the following is correct about biological membranes? a) Phospholipid tails are directed toward the aqueous environment b) Biological membranes are made up of a lipid monolayer. c) Phospholipid head groups are directed toward the aqueous environment. d) Molecules freely pass through the membrane. 6. Which situation described below would result in the MOST rigid biological membrane? a) A high ratio of cholesterol b) A large number of bulky, glycosylated head groups c) A high ratio of unsaturated fatty acid tails in the phospholipids d) A small amount of cholesterol 7. Which of the following three-letter amino acid sequence match with this single-letter sequence FYAKGPE? a) Phe-Tyr-Asp-Lys-Gln-Phe-Glu b) Phe-Tyr-Asn-Lys-Gly-Pro-Glu c) Phe-Tyr-Ala-Lys-Gly-Pro-Glu d) Phe-Tyr-Ala-Lys-Glu-Phe-Gln IEent kind of bond Phosphoanhydrid o bonds I fi skIstr eEthe0x roar exy E x.EE S p Ix only some saw not enough for significance F Phenyl TX XP pre A 11 Jok Lys G Fin rated E 6 13

3 8. Transformation is a transfer of DNA a) Mediated through viral infection b) Mediated through bacterial mating c) Mediated through uptake of exogenous DNA from the medium d) All the above 9. Which of the following nucleotides are used in Sanger method of DNA sequencing? a) Deoxyribonucleotides b) Ribonucleotides c) Dideoxyribonucleotides d) Diribonucleotides 10. Which of the following is the correct order for DNA condensation in eukaryotes? a) Nucleosomes, chromatin, loops, condensed coils, chromosome b) Chromatin, nucleosomes, loops, condensed coils, chromosome c) Nucleosomes, condensed coils, loops, chromatin, chromosome d) Chromatin, nucleosomes, condensed coils, loops, chromosome 11. The figure below shows a nucleosome core particle. Which of the following is INCORRECT? a) H1 histone protein is not part of the histone protein core. b) The histone protein core consists of eight histone proteins. c) DNA wraps around the histone protein core twice. d) The interactions between the DNA and the histone protein core are sequence specific. 12. Which of the following is considered gene-rich chromatin? a) Euchromatin c) Heterochromatin b) Centromeres d) Telomeres 13. Which of the following is true for polycistronic genes? a) The coding sequences are randomly organized b) Each coding sequence has its own promoter c) The sequence can be an operon, coding for several proteins of a single biochemical process or pathway. d) The promoter is located downstream of the coding sequence. DNA for DNA only right statement RELAX ARNAX even a thing must start 0 vi loops make oil w nucleosomes II es ota 0 rissed condensed non coding bothtypes of heterochromatin one promoted multiple regions Poly multiple Istream One promoter multiple coding regions operon proteins in a single pathway

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4 14. Iodine and Na + are transported in the same direction and have an overall – ǻ G . This occurs in a) passive symporter b) primary active transporter c) secondary active symporter d) secondary active antiporter 15. Sigmoidal curve of hemoglobin saturation is due to a) Multiple subunit compositions b) Cooperativity c) Low affinity to O 2 d) All of the above 16. Which of the following is INCORRECT regarding eukaryotic genes? a) 7KH ±ƍ 875 DQG ²ƍ 875 DUH QRW WUDQVODWHG EXW SOD\ LPSRUWDQW UHJXODWRU\ UROHV b) 0DWXUH 51$V KDYH D ±ƍ FDS DQG D ²ƍ poly(A) tail c) Exon sequences are removed from the primary transcript prior to translation. d) Alternative splicing allows for one gene to produce several different protein products 17. Which component of a common plasmid cloning vector is necessary for blue-white screening? a) lacZ gen c) Antibiotic-resistance gen b) Multiple cloning sites (MCS) d) Origin of replication 18. Which of the following is correct about restriction enzymes? a) All restriction enzymes produce the same type of cleaved ends b) Type II and Type III restriction enzymes cut outside of their recognition sequences. c) Type II restriction enzymes recognize palindrome sequences. d) Restriction enzymes degrade foreign DNA by cleaving methylated DNA 19. The figure below shows the temperature cycling used for a typical PCR reaction. Which of the following is occurring at step B? a) Denaturation of target DNA b) Annealing of primers to target DNA c) Extension of primers d) Denaturation of primers 20. Which of the following is NOT true for Sanger DNA sequencing compared to Maxam-Gilbert DNA sequencing? a) Sanger DNA sequencing is a high efficiency method of DNA sequencing. b) Sanger DNA sequencing relies on chemical degradation of DNA. c) Sanger sequencing is also called chain termination sequencing. d) Sanger DNA sequencing uses ddNTP Eno ATP anti same dirxn heme units E O 0 Intestine sina.EE stick Titan Imethated Item Temp Iem relies on this

5 21. Which of the following is correct concerning a peptide backbone? a) The peptide bond allows for free rotation due to its single bond character b) A Ramachandran plot shows the allowable ࢥ DQG ȥ DQJOHV IRU D SHSWLGH c) The torsional angle between the C Į and the R group is called ࢥ (phi). d) The torsional angle between the amide nitrogen and the C Į LV FDOOHG ȥ ³SVL´ 22. A __________ mutation will not lead to a change in the protein product of a gene. a) Frameshift b) silent c) nonsense d) missense 23. Disulfide bonds stabilize __________ level of protein structure and above. a) Quaternary b) tertiary c) primary d) secondary 24. In the figure shown below, which of the following is labeled “B”? a) $QWLSDUDOOHO ȕ VWUDQG b) ȕ WXU n c) Loop d) 3DUDOOHO ȕ VWUDQGV 25. In the figure shown below, C is which of the following classes? a) 3UHGRPLQDQWO\ Į KHOL ces b) Įµ ȕ c) Į ¶ ȕ d) 3UHGRPLQDQWO\ ȕ VKHHWV 26. An antigen binds to an antibody at which of the following locations. a) Only at the light chain b) Only at the heavy chain c) At the constant domain d) At the variable domain 27. For Anfinsen’s studies of RNaseA folding, which of the following is not correct? a) ȕ -mercaptoethanol was used to reduce disulfide bonds. b) 5HPRYDO RI ȕ -mercaptoethanol, followed by removal of urea, resulted in active RNaseA. c) Removal of ȕ -mercaptoethanol and urea at the same time resulted in active RNaseA. d) Urea was used to disrupt polar interactions within the protein. 28. Which of the following protein-folding diseases is a loss-of-function disease? a) Huntington’s disease b) Alzheimer’s disease b) Cystic fibrosis c) Creutzfeldt-Jakob disease 2x bond EFI 1 de n or insertion Eagle nut changer Effans Hands loop A helices β sheet NB d B domains are in these I S es in Inactive s ty again toxicity damage Godin misfolding loss OR CFTR function

6 29. Disulfide bonds in proteins are a) only involved in the tertiary structure b) only involved in the quaternary structure c) important for proteins found in oxidizing environments d) irreversible. 30. Which of the following fibrous proteins contains 4-hydroxyproline as part of its repeating pattern? a) Fibroin light chain c) Keratin b) Fibroin heavy chain d) Collagen 31. To specifically isolate a negatively charged protein, _____________ chromatography would be most useful. a) anion-exchange c) cation-exchange b) affinity d) gel filtration 32. Which of the following amino acids would not be cleaved by chymotrypsin? a) K b) W c) Y d) F 33. Polyclonal antibodies differ from monoclonal antibodies in that polyclonal antibodies are a __________ mixture of immunoglobulin proteins that recognize __________ on an antigenic protein. a) homogeneous; a single epitope b) heterogeneous; a single epitope c) heterogeneous; one or more epitopes d) homogeneous; one or more epitopes 34. Which of the following procedures is NOT used for polyclonal antibody generation? a) Isolation of blood serum from immunized anima b) Affinity chromatography to isolate desired antibodies. c) Fusion of B cells with immortalized tumor cells to form hybridoma d) Immunization of animal with an antigen. 35. In the figure below depicting a Western blot experiment, which step is depicted in C? a) Incubation and binding of the primary antibody b) Transfer of proteins to membrane c) Protein location identified by presence of enzyme product d) Incubation and binding of the secondary antibody 3 4 stray 0 plants oranges 499 size 0 x x x GIEEIIF.EE hetero I Ti

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7 36. Which of the following statements are true regarding hemoglobin? a) When hemoglobin shifts from the T-state conformation to the R-state conformation, many covalent interactions are broken and reformed. b) The T state of hemoglobin has a higher affinity for oxygen than the R state c) When hemoglobin shifts from the T-state conformation to the R-state conformation, many noncovalent interactions are broken and reformed. d) The R state of hemoglobin has a higher affinity for oxygen than the T state. 37. The lock-and-key model of enzyme catalysis a) involves structural adjustments of the enzyme-substrate complex upon binding b) involves a rigid fit between the substrate and the enzyme c) accounts for how enzymes are regulated. d) explains how substrates can bind sites deep within an enzyme. 38. 7KH ¨* ‡ for a catalyzed reaction is indicated by which letter in the figure below? a) D b) C c) A d) B 39. Which of the following is best described as a prosthetic group? a) Heme c) NAD + b) Thiamine pyrophosphate d) Zn 2+ 40. In nature, glucose is a) typically found in its linear form in solution b) a ketose monosaccharide c) typically found as the L isomer d) known as gluocopyranose when in its cyclic form. 41. Which of the following is NOT an outcome of glycolysis? a) Generation of 1 Pyruvate b) Generation of 2 NADH c) Generation of 2 net ATP molecule d) Generation of 2 H 2 O 42. Which of the following is correct about the link between Ras and cancer? a) Mutated Ras is an oncogene b) The role of Ras in cancer is due to a recessive mutation. c) Mutant Ras has enhanced GTPase activity d) Ras is considered a tumor suppressor gene . F tense Revelaxed bind To 0 Ears take 2 pyruvate oncogene oncology cancer

8 43. Which enzyme’s activity is controlled by the levels of glucose-6-P and fructose-6-P in the cell? a) Hexokinase b) Phosphofructokinase-1 c) Phosphoglucoisomerase d) Aldolase 44. Which enzyme is readily reversible, and can, therefore, be used in both glycolysis and gluconeogenesis? a) Phosphofructokinase-1 b) Phosphoglycerate mutase c) Hexokinase d) Pyruvate kinase 45. All the following are parts of a cell signaling pathway EXCEPT a) ligand-induced activation of a receptor protein b) no amplification of signal after ligand binding c) activation of second messengers. d) a measurable cellular response 46. Under anaerobic conditions, pyruvate is metabolized to either ethanol or lactate to provide which important coenzyme? a) NAD b) FAD c) NADH d) FADH 2 47. Coenzyme A is derived from which of the following vitamins? a) Riboflavin c) Pantothenic acid b) Niacin d) Thiamine 48. Beriberi results from a deficiency in which of the following vitamins? a) Niacin c) Pantothenic acid b) Riboflavin d) Thiamine 49. Which of the following is responsible for the production of GTP in the citrate cycle? a) Malate dehydrogenase b) Succinyl-CoA synthetase c) Succinate dehydrogenase d) Isocitrate dehydrogenase 50. ATCase is an enzyme that is regulated by a) covalent modification b) allosteric effectors such as substrate and the end product c) proteolytic trimming d) phosphorylation 51. Which of the following enzymes is not regulated by ATP concentrations? a) Isocitrate dehydrogenase b) Į -ketoglutarate dehydrogenase c) Fumarase d) Citrate synthase GGP FGP but high energy usage F energy than Hextinas F 1,6 BisP PHAP 6 3 7 not reversible steps 1,310 ste eversible OX y docustream cascade not MEET 0 0000 qq.ae Succinyl lot EAf binds to Fte all irreversible steps

9 52. Oxaloacetate is transported both into and out of the mitochondrial matrix via which of the following molecules? a) Malate c) Citrate b) Į -ketoglutarate d) Succinyl-CoA 53. Which of the following is a net result from the electron transport system? a) ATP hydrolysis c) Reduction of NAD b) Reduction of FAD d) Reduction of molecular oxygen 54. Cytochrome c is responsible for transporting single electrons to complex IV from which enzyme? a) Complex III c) Glycerol-3-P dehydrogenase b) Complex I d) Complex II 55. Which enzyme is crucial for transfer of electrons from cytosolic NADH into the mitochondrial matrix in muscle cells? a) Glyceraldehyde-3-P dehydrogenase b) Malate dehydrogenase c) Glycerol-3-P dehydrogenase d) Aspartate aminotransferase 56. 2,4-dinitrophenol is NOT a) a chemical decoupler of the proton gradient. b) a safe diet aid. c) hydrophobic and able to diffuse across the inner mitochondrial membrane. d) a stimulator of oxygen production in mitochondrial suspensions that have been treated with oligomycin. 57. Inherited mitochondrial diseases a) can pass to the next generation only through mitochondrial gene mutations in females b) originate in neuronal cells c) have equal severity in all affected individuals d) do not worsen in severity with age. 58. Which of the following enzymes is not regulated by ATP concentrations? a) Į -ketoglutarate dehydrogenase b) Fumarase c) Citrate synthase d) Isocitrate dehydrogenase 59. Which enzyme of the electron transport system is also a part of the citrate cycle? a) NADH-ubiquinone oxidoreductase b) Ubiquinone-cytochrome c oxidoreductase c) Succinate dehydrogenase d) Cytochrome c oxidase 60. Which amino acid is NOT a target for kinases? a) Asp b) Thr c) Ser d) Tyr stereo t irreversible imagine a TTCAT.SE cohticpathwiy0 Atnflisn age.se en'EtsE Irreversible IrreverIFeversible I Gives e reductase 0

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10 SECTION B - TRUE & FALSE - Read the sentences carefully and choose whether they are TRUE OR FALSE. Mark T for TRUE and F for FALSE (1x10 = 10 points). 61. MCS is located on Lac-Z gene of a cloning plasmid. 62. Splicing allows for one gene to produce several different protein products. 63. Sanger DNA sequencing uses ddNTPs. 64. FADH 2 oxidation contributes H + to the proton gradient. 65. Phosphate translocase only acts as a symporter in transporting H 2 PO 4 and OH – . 66. Citrate synthase catalyzes an endergonic free energy reaction in the citrate cycle? 67. All monosaccharides are reducing, but only a few of disaccharides are reducing sugars. 68. cAMP and cGMP are synthesized by different enzymes, but degraded by the same enzyme phosphodiesterase (PDE). 69. Simvastatin is an inhibitor that inhibits HMG-CoA reductase, an enzyme involved in regulation of cholesterol biosynthesis. 70. 2,3-bisphosphoglycerate has high affinity to fetal than mother hemoglobin and thus help in O 2 delivery from mother blood. SECTION C – MATCHING - Match the best suited description given below to the correct term in the box. Make sure only one match and there are more terms than the descriptions ( 1x10 = 10 points ) 71. Biological cell membranes are mostly composed of specific types of lipids. 72. Increased UV light absorption at wavelength 260nm by DNA stands upon denaturation. 73. This bond that is sensitive to DNase. 74. The greater affinity for oxygen is explained by the lack of fetal hemoglobin's interaction with this chemical compound. 75. These amino acids promote the formation of D -helices in the protein. 76. The protein structural motif that binds to NAD+/NADP+. 77. A technique of separation of protein based on m/z ratio. 78. Protein kinase A consists of two regulatory and two catalytic subunits that dissociate upon binding to the 2 nd messenger. 79. The enzyme speeds up the chemical reaction by decreasing this energy. 80. The regulatory enzyme in the ‘pay off’ phase of glycolysis. SECTION D – FILL IN THE BLANKS – complete the following sentences with appropriate terms (2x10 = 20 points). A. Fatty acids B. Renaturation C. Hyperchromicity D. Phosphorylation E. Phosphodiester bond F. Peptide bond G. 2,3-bisphosphoglycerate H. Amino acids MALEK I. Bulky amino acids WYP J. Positively charged AAs K. cAMP L. TIM barrel fold M. SDS-PAGE N. Rossmann fold O. Phospholipids P. Energy of activation Q. Mass spectrometry R. cGMP S. Free energy T. Pyruvate kinase U. Phosphoglycerate kinase T T di deoxy nucleotide I 5 3,4 9 d t T T Fj 253 BPG highaffinity in adults b Phospholipids Hyperchrenicity Phosphodiester MALEK HI.ES EEts cA Activator energy Pyruvate kinase irreversible step

11 81. Weak polar interactions that stabilizes protein structures in a tertiary structure of proteins. a. ___________________ b. ___________________ 82. TIM Barrel fold has alternating _____________ and _____________secondary structures. 83. Monoclonal antibodies differ from polyclonal antibodies in that polyclonal antibodies are a __________ mixture of immunoglobulin proteins that recognize __________ on an antigenic protein. 84. Phosphorylation of proteins is catalyzed by ___________________________, whereas dephosphorylation is catalyzed by ___________________________________. 85. Following two enzymes catalyze reactions in TCA cycle to generate NADH. a. ---------------------- b. ---------------------- 86. The following two intermediates of TCA cycle are used up in amino acids biosynthesis. a. ________________ b. ________________ 87. The following two chemical compounds inhibit cytochrome C oxidase in ETC. c. ____________. d. ____________. 88. ____________________ measures the winding DNA strands around each other and ____________________ measures crossing of the DNA strands. 89. ________________ has more non-reducing ends that allows _______________enzyme to quickly liberate glucose in the form of glucose-1-phosphate during starvation . 90. Many kinds of hormones can bind to GPCR, but the following two hormones share the same type of GPCR to stimulate the production of cAMP as a second messenger. a. ___________________ b. ___________________ Ht bonds Ionic bonds β a heterogenous 1 epitope kinases Phosphatases IE E a icescO HaSgeleYectrophores f glycogen phosphorylase Calcitonin Glucagon

12 SECTION E – MULTIPLE CHOICE QUESTIONS – (Extra credits – 6 points) 91. :KHQ WKH IUHH HQHUJ\ FKDQJH IRU D PROHFXOH WR FURVV D FHOO PHPEUDQH LV SRVLWLYH ±´¨*²³ which type of transport mechanism is required? a) Active transport carrier b) Passive transport channel c) Passive transport carrier d) Diffusion 92. The following are critical for enzyme structure and function, EXCEPT a) covalent modification affecting the bioavailability of an enzyme b) enzymes commonly binding substrates with high affinity c) that the catalytic efficiency of an enzyme can be controlled by regulatory molecules d) binding of a substrate inducing changes in protein structure. 93. To specifically isolate a negatively charged protein, _____________ chromatography would be most useful. a) affinity b) cation-exchange c) gel filtration d) anion-exchange END OF THE EXAM I SG 0 Allosteric Tegulators O

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