Chem 280 Final Exam. Here is the summary of the total 150 points plus 6 points bonus. Carefully read the questions. Good luck!

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1 May 2 nd, 2012 Name: CLID: Score: Chem 280 Final Exam There are 32 multiple choices that are worth 3 points each. There are 5 problems and one bonus problem. Try to answer the questions, which you know first, and then try to solve the problems, which you are not sure about. Here is the summary of the total 150 points plus 6 points bonus. Carefully read the questions. Good luck! Multiple choice (32 total) 3 points each, total 96 points Problems #1 8 points #2 11 points #3 12 points #4 13 points #5 10 points #6 (bonus) 6 points Total 150 points + 6 points You could use your calculator if you need. No notes or books of any sort may be used during the exam. I have neither given nor received aid on the exam. Signature and date 1

2 I. Multiple Choice (3 points each): choose the best answer 1. means that amino acids are degraded to pyruvate or citric acid cycle intermediates, which can directly supply the pathway of gluconeogenesis and means that amino acids, are degraded to acetyl CoA or acetoacetate, which contribute to the formation of. a) glucogenic; ketogenic; fatty acids or ketone bodies b) glucogenic; ketogenic; nucelotides c) ketogenic; glucogenic; fatty acids or ketone bodies d) ketogenic; glucogenic; nucelotides 2. Proteins are essential nutrients for the human body. Digestion of dietary proteins typically begins in the stomach by and continued by in the small intestine. Before the absorption in the small intestine, most proteins are already reduced to single amino acid or peptides of several amino acids. Most of peptides longer than four amino acids are not absorbed. a) pepsin and trypsin; chymotrypsin b) chymotrypsin; pepsin and trypsin c) trypsin and chymotrypsin; pepsin d) pepsin; trypsin and chymotrypsin 3. Which of the following amino acid belongs to both glucogenic and ketogenic? a) Alanine b) Glycine c) Threonine d) Valine 4. Which of the following amino acid is glucogenic, but is not ketogenic? a) Glutamine b) Lysine c) Phenylalanine d) Threonine 5. The half-life of proteins can vary from a few minutes to several weeks. Ubiquitin is a small protein, which can be covalently attached to lysine in a target protein. A ubiquitin targeted protein will be degraded in the. In addition, protein degradation can occur in where contain. a) proteasomes; lysosomes; proteases and nucleases b) proteasomes; lysosomes; proteases but not nucleases c) lysosomes; proteasomes; proteases and nucleases d) lysosomes; proteasomes; proteases but not nucleases 2

3 6. DNA is typically a double stranded helix. The linkage between nucleotides is. What is the nucleotide sequence of the DNA strand that is complementary to 5 - ATTCCGGACT-3? a) 3 to 5 phosphodiester bonds; 5 -AGTCCGGAAT-3 b) 3 to 5 phosphodiester bonds; 5 -TAAGGCCTGA-3 c) 5 to 3 phosphodiester bonds; 5 -AGTCCGGAAT-3 d) 5 to 3 phosphodiester bonds; 5 -TAAGGCCTGA-3 7. The major end product of cytosine and uracil degradation in human is and the major end product of thymine degradation in human is a) acetyl CoA; uric acid b) acetyl CoA; succinyl CoA c) succinyl CoA; uric acid d) succinyl CoA; acetyl CoA 8. UV light will cause a dimer of, which can be repaired by. a) cytosine; deamination b) cytosine; photolyase c) thymine; deamination d) thymine; photolyase 9. The main function of the bile salts secreted from is to. a) gallbladder; cleave the ester bonds in triacylglycerols b) gallbladder; dissolve triacylglycerols in the intestine c) liver; cleave the ester bonds in triacylglycerols d) liver; dissolve triacylglycerols in the intestine 10. Which of the following metabolite is the source of carbon skeleton to synthesize proline? a) Glucose 6 phosphate b) α-ketoglutarate c) Phosphoenolpyruvate d) 3-phosphoglycerate 11. Degradation of triacylglycerols catalyzed by generates fatty acids and glycerol. Glycerol can be converted to glucose through. a) acyl transferase; glycolysis b) acyl transferase; gluconeogenesis c) phospholipases; glycolysis d) phospholipases; gluconeogenesis 3

4 12. Which is NOT a path entered by acetyl CoA? a) Citric acid cycle b) Fatty acid synthesis c) Formation of ketone bodies d) Amino acid biosynthesis 13. The general excision repair mechanism for the DNA repair has the following order: a) Endonuclease exonuclease DNA polymerase DNA ligase b) Endonuclease DNA polymerase exonuclease DNA ligase c) Exonuclease endonuclease DNA ligase DNA polymerase d) Exonuclease DNA ligase endonuclease DNA polymerase 14. The human (Homo sapiens) genome is stored on 23 chromosome pairs and in the small mitochondrial DNA. Twenty-two of the 23 chromosomes belong to autosomal chromosome pairs, while the remaining pair is sex determinative. The haploid human genome has about base pairs and contains about protein-coding genes, which are far fewer than had been expected before sequencing. a) 2.95 x 10 6 ; 25,000 b) 2.95 x 10 6 ; 250,000 c) 2.95 x 10 9 ; 25,000 d) 2.95 x 10 9 ; 250, Which of the statements about DNA polymerase and RNA polymerase is most likely correct? a) DNA polymerase requires a primer to initiate DNA synthesis from 3 5 while RNA polymerase do not require a primer for start of RNA synthesis from 3 5. b) DNA polymerase requires a primer to initiate DNA synthesis from 5 3 while RNA polymerase do not require a primer for start of RNA synthesis from 5 3. c) RNA polymerase requires a primer to initiate RNA synthesis from 3 5 while DNA polymerase do not require a primer for start of DNA synthesis from 3 5. d) RNA polymerase requires a primer to initiate RNA synthesis from 5 3 while DNA polymerase do not require a primer for start of DNA synthesis from Neurotransmitters are endogenous chemicals that transmit signals from a neuron to a target cell across a synapse. Neurotransmitters are synthesized from plentiful and simple precursors, such as amino acids, which are readily available from the diet and which require only a small number of biosynthetic steps to convert. Which of the following amino acids can function as neurotransmitters? a) alanine, glutamine, and asparagine b) alanine, glutamate and aspartate c) glycine, glutamine, and asparagine d) glycine, glutamate and aspartate 4

5 17. A patient is found to have a high concentration of cholesterol in the blood and deposits of cholesterol under the skin. What is the likely cause of this condition? a) A deficiency in insulin production by the pancreas. b) Insufficient lipoprotein concentration in the blood c) Overproduction of lipases d) Lack of lipoprotein receptors 18. The major end product of guanine degradation in human is, which enter carbohydrate metabolism. a) uric acid; can b) uric acid; cannot c) urea; can d) urea; cannot 19. Which of the following statements about difference of transcription between eukaryotic and prokaryotic cells is NOT correct? a) Newly synthesized heterogenous nuclear RNAs (hnrna) are modified by 5 -m 7 -GTP cap and 3 -polya tail in eukaryotic cells, but not in prokaryotic cells. b) Genes in eukaryotic cells may contain exons and introns, but no introns in prokaryotic cells. c) RNAs in eukaryotic cells have splicing process, but no RNA splicing is found in prokaryotic cells. d) One mrna can code for one or more polypeptides in eukaryotic cells, but one mrna can code only for one polypeptide in prokaryotic cells. 20. Which of the following statements on DNA double helix is most likely NOT true? a) James Watson and Francis Crick discovered DNA double helix in 1953, and they obtained Nobel Prize in b) A-T base pairs are stabilized by two hydrogen bonds whereas G-C base pairs are stabilized by three hydrogen bonds. c) In the "double helix" model of Watson and Crick the polynucleotide chains interact to form a left-handed double helix with the two chains running in opposite directions. d) The information that DNA carried is within the unique base sequence of the DNA. 21. You are given a mrna sequence: 5 -AUGGCUAAUGAAUGCUAA-3. What will be the DNA sequence of the template strand for this mrna sequence? a) 5 -TACCGATTACTTACGATT-3 b) 3 -TACCGATTACTTACGATT-5 c) 5 -ATGGCTAATGAATGCTAA-3 d) 3 -ATGGCTAATGAATGCTAA-5 5

6 22. Nucleosomes form the fundamental repeating units of eukaryotic chromatin, which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it (in mammalian cells approximately 1 meter of linear DNA have to be packed into a nucleus of roughly 5 µm diameter). One nucleosome is the basic unit of DNA packaging in eukaryotes, consisting of an about DNA segment wound in sequence around eight histone protein cores. a) 50 bp; negatively charged b) 150 bp; negatively charged c) 50 bp; positively charged d) 150 bp; positively charged 23. Which of the following features control start and stop sites of translation respectively? a) OriC and TUS b) Start codon and stop codon c) Promoter and terminator d) Exon and intron 24. Photosynthesis is a process that photosynthetic organisms (plants, algae and photosynthetic bacteria) require light to convert to? a) CO 2 and H 2 O; carbohydrate and O 2 b) CO 2 and NH 3 ; carbohydrate and O 2 c) CO 2 and H 2 O; lipid and O 2 d) CO 2 and NH 3 ; lipid and O The virus causes Acquired Immunodeficiency Syndrome (AIDS). It was first exposed in 1981 in central Africa. More than 25 million HIV patients were dead by 2006 and 45 million people are estimated to be infected by HIV. What is the correct order of viral proteins in HIV life cycle from the first to last step? a) DNA polymerase integrase reverse transcriptase gp120 b) gp120 DNA polymerase reverse transcriptase integrase c) gp120 reverse transcriptase integrase DNA polymerase d) gp120 reverse transcriptase DNA polymerase integrase 26. Atmospheric nitrogen must be processed, or "fixed" (see page on nitrogen fixation), to be used by plants. Some fixation occurs in lightning strikes, but most fixation is done by free-living or symbiotic bacteria. The correct sequence of enzymes used to for nitrogen atoms to incorporate into amino acids is: a) nitrogenase glutamate dehydrogenase glutamine synthetase b) nitrogenase glutamine synthetase glutamate dehydrogenase c) glutamine synthetase nitrogenase glutamate dehydrogenase d) glutamate dehydrogenase nitrogenase glutamine synthetase 6

7 27. Most of the carbon translocated throughout plants is in the form of. a) glucose b) ribulose 1,5-bisphosphate c) starch d) sucrose 28. Photorespiration in plants consumes and is catalyzed by a) ribulose 1,5-bisphophate and O 2 ; photosystem complexes b) ribulose 1,5-bisphophate and CO 2 ; photosystem complexes c) ribulose 1,5-bisphophate and O 2 ; rubisco d) ribulose 1,5-bisphophate and CO 2 ; rubisco 29. More than 100 proteins have been identified in the blood serum. Serum albumins are the most abundant group of proteins. One of their major functions is to transport of. a) cholesterol b) fatty acids c) hormones d) triglycerides 30. Which of the following is not one of the ketone bodies? a) Acetoacetate b) Acetone c) β-hydroxybutyrate d) β-methylglutarate 31. A virus that infects roaches is purified and the nucleic acid fraction is hydrolyzed and analyzed. The base composition is found to be 22% A : 28% C : 28%G : 22% U. Based on this information, what is the form of the viral genome? a) Single-stranded DNA b) Double-stranded DNA c) Single-stranded RNA d) Double-stranded RNA 32. Photosynthesis could be divided into two types of reactions: light reactions and dark reactions. In light reactions, electron transport is coupled with generation of proton gradient. The correct sequence of electron transport process in the light reactions is. a) H 2 O Photosystem II Cytochrome bf Photosystem I NADP + b) H 2 O Photosystem I Photosystem II Cytochrome bf NADP + c) NADPH Photosystem II Cytochrome bf Photosystem I H 2 O d) NADPH Photosystem I Photosystem II Cytochrome bf H 2 O 7

8 II. Problems 1. The urea cycle is a cycle of biochemical reactions occurring in many animals that produces urea ((NH 2 ) 2 CO). This cycle was the first metabolic cycle discovered (Hans Krebs and Kurt Henseleit, 1932), five years before the discovery of the TCA cycle. (a) Draw the urea cycle and specify its importance. (6 points) (b) Specify where the urea cycle takes place in mammals. (2 points) 8

9 2. Fatty acids are an important source of energy and adenosine triphosphate (ATP) for many cellular organisms. Excess fatty acids, glucose, and other nutrients can be stored efficiently as fat. (a) Write the activation reaction of palmitate. (2 points) (b) Write the four reactions in the first cycle/round of β-oxidation of palmitic acyl CoA. (4 points) (c) When palmitic acyl CoA is completely oxidized by β-oxidation, acetyl CoA, FADH 2 and NADH will be formed? If acetyl CoA, FADH 2 and NADH are converted to ATP, how many total ATP molecules are produced after a complete β-oxidation of a palmitic acyl CoA? Justify your answer. (3 points) (d) Based on your knowledge, explain why triglycerides yield more than twice as much energy for the same mass as do carbohydrates or proteins. (2 points) 9

10 3. (a) Show carbon and nitrogen sources in purines biosynthesis. (2 points) (b) Draw a simple diagram to show biosynthesis of AMP and GMP. (3 points) (c) Show carbon and nitrogen sources in pyrimidine biosynthesis. (2 points) (d) List all the pathways through which a carbon atom from glucose can enter into CMP. (3 points) (e) Propose a mechanism of how cells maintain the correct balance of deoxyribonucleotides. (2 points) 10

11 4. The maintenance of genetic information from generation to generation requires that DNA replication be both rapid and accurate. (a) Explain the importance of DNA replication. (2 points) (b) What are the proteins and enzymes involved in DNA replication of prokaryotic cell? Briefly explain the biochemical function(s) for each protein and each enzyme in DNA replication process. (8 points) (c) DNA replication is a semiconservative, bidirectional and semidiscontiunous process. Explain semiconservative, bidirectional and semidiscontiunous. (3 points) 11

12 5. Fatty acid synthesis is the creation of fatty acids from acetyl-coa and malonyl-coa precursors through action of enzymes called fatty acid synthase. (a) Show all the steps of how an eight carbon fatty acid becomes a ten carbon fatty acid during fatty acid biosynthesis. (4 points) (b) Why do acetyl CoA and malonyl CoA need to be converted to acetyl ACP and malonyl ACP respectively in fatty acid biosynthesis? (2 points) (c) Briefly discuss how to synthesize triacylglycerols and phospholipids. What are functions of triacylglycerols and phospholipids? (4 points) 12

13 6. A bonus question (Total 6 points). IT IS GOOD TO KNOW YOU! I BELIEVE YOU HAVE TRIED YOUR BEST IN THIS COURSE! HAVE A GOOD SUMMER! BEST WISHES! (a) Which error would cause more damage to a cell: A DNA replication or a DNA transcription error? Justify your answer. (3 points) (b) Caffeine, a methylated xanthine found in chocolate, coffee, and tea. Use your knowledge, suggest what will be the end product of caffeine. Specify one enzyme for converting caffeine to its end product. (3 points) 13