Biochemistry Exam II Module Questions (12-22) PDF

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Biochemistry Exam II (Modules 12-22) MODULE 12 12.1: Amino Acid Deamination 1. Glucogenic amino acids are utilized as substrate for A. Anaerobic respiration B. Fatty acid synthesis C. Gluconeogenesis D. None of the above 2. The synthesis of glutamine from glutamate requires A. Pyridoxal phosphate B. ATP and NH3+ C. NADH and ATP D. ATP 3. In the transaminase reaction between glutamate/pyruvate, the amino acid produced is A. Aspartate B. Alanine C. Alpha ketoglutarate D. Serine 4. The metabolism of serine to pyruvate is an example of A. Oxidative deamination B. Transamination C. Anaerobic metabolism D. Substitution reaction

12.2: Glutamate and Oxidative Deamination 1. Glucogenic amino acids are utilized in the gluconeogenic pathway of the liver. A. True B. False 2. Glutamate is aminated to glutamine by the enzyme A. Glutamate dehydrogenase B. Glutaminase C. Glutamine synthetase D. Glutamine oxidase

3. N-acetyl-glutamate regulates the following pathway A. TCA Cycle B. ETS/ OX-Phos C. Glycolysis D. Urea Cycle 4. How is glutamate dehydrogenase allosterically controlled? A. Activated by ADP and GDP B. Inhibited by ADP and GTP C. Activated by ATP and GTP D. Activated by UTP and CTP 5. Which two amino acids are NOT substrate for aminotransferases? A. Alanine and aspartate B. Serine and threonine C. Oxaloacetate and malate D. Leucine and isoleucine

12.3: Transaminase Reactions 1. The cofactor found in the active site of ALL transaminase enzymes is A. Cobalamin phosphate B. Pyridoxal phosphate C. Ferrodoxin D. Biotin 2. Alanine is transported from the skeletal muscle to liver to be back converted to pyruvate. The pyruvate in the liver is then used for A. Glycolysis B. Homolactic Fermentation C. Gluconeogensis D. Fatty Acid synthesis 3. Glutamate is back converted to alpha ketoglutarate in liver mitochondria by A. Glutaminase B. Glutamate synthase C. Glutamate dehydrogenase D. All of the above 4. In the mechanism of all transaminases, the pyridoxal phosphate A. becomes reduced and the amino acid is oxidized B. receives the amine group through a Schiff’s base reaction C. becomes carboxylated D. All of the above

12.4: The Urea Cycle 1. The biological location of the Urea Cycle is A. Kidney tubule cells B. Pancreatic exocrine cells C. Skeletal muscle cells D. Hepatic cells of the liver 2. The cleavage of argininosuccinate to arginine involves this TCA intermediate A. Succinate B. Oxaloacetate C. Fumarate D. Alpha ketoglutarate 3. The source of the first NH3+ for the formation of carbamoyl phosphate in the mitochondria is aspartate. A. True B. False 4. The Urea Cycle intermediate that intersects with the AdoMet pathway is A. Ornithine B. Arginine C. Citrulline D. Urea

12.5: Amino Acid Pathways 1. Which statement about cysteine is NOT correct? A. Cysteine is a sulfur-containing amino acid B. Homocysteine is metabolized by the transulfuration pathway to cysteine C. Cysteine can be remethylated to form methionine D. Cysteine is a non-essential amino acid 2. The biochemical function of AdoMet is A. Methylation of tetrahdyrofolate B. Methylation of macromolecules C. Oxidation of enzymes D. Methlyation of nucleic acids only 3. Decarboxylated AdoMet becomes a donor of A. Methyl groups to macromolecules B. Adenosine for the salvage pathway C. Aminopropyl donor to form larger polyamines

D. All of the above 4. The remethylation of homocysteine to methionine requires which two cofactors? A. N5,N10-methylene & B6 B. FAD & B12 C. N5,N10-methyleneTHF & B12 D. B2 & B6

Final 12 1. Of the 22 amino acids, which of the following pair is NOT used in catabolic reactions as bioenergetic fuel? A. Selenocysteine and pyrrolysine B. Leucine and valine C. Serine and threonine D. Methionine and tryptophan 2. Which of these is a necessary precursor enzyme for the incorporation of nitrogen into urea? A. phenylalanine hydroxylase B. oxidative decarboxylase C. glutamate dehydrogenase D. peptidyl transferase 3. In a reaction of the Urea Cycle, aspartate condenses with citrulline to form argininosuccinate. Which of the following is incorrect? A. This condensation reaction requires ATP B. Fumarate is also produced in this reaction C. This reaction takes place in the mitochondrial matrix D. One of the products of this reaction is arginine 4. Which two amino acids are deaminated by oxidative deamination only? A. Serine and threonine B. Glutamate and glutamine C. Aspartate and asparagine D. Tyrosine and serine 5. Glucogenic amino acids are utilized as substrate for A. Anaerobic respiration B. Fatty acid synthesis C. Gluconeogenesis D. None of the above

6. Alanine functions as a transport form of pyruvate between skeletal muscles, where it is formed from pyruvate, to the liver where it is converted back to pyruvate. A. True B. False 7. The synthesis of glutamine from glutamate requires A. ATP B. Pyridoxal phosphate C. ATP & NH3+ D. NADH & ATP

MODULE 13 13.1: Nucleotide Structure 1. Which of the following is the abbreviation for a nucleotide containing the nitrogenous base cytosine, a hydrogen at the 2’ carbon of its pentose sugar, and a di-phosphate group attached to the 5’ carbon of its pentose sugar? A. CDP B. CMP C. dCDP D. dCMP 2. Which of the following is the name of a nucleotide containing the nitrogenous base thymine, a hydrogen at the 2’ carbon of its pentose sugar, and a monophosphate group attached to the 5’ carbon of its pentose sugar? A. deoxythymidine B. thymidylate C. thymine D. thymidine 3. Which of the following is the name of a nucleoside containing the nitrogenous base uracil and a hydroxyl group at the 2’ carbon of its pentose sugar? A. uridylate B. uracil C. deoxyuridine D. uridine 4. Nucleotides and nucleosides differ by a single A. deoxyribose B. ribose C. hydroxyl group D. phosphate

13.2: De Novo Nucleotide Synthesis 1. Which of the following enzymes controls the committed step in purine biosynthesis? A. Carbamoyl phosphate synthetase B. Adenylosuccinate synthetase C. Thymidylate synthase D. Amidophosphoribosyl transferase 2. The starting substrates for pyrimidine biosynthesis are A. glutamine and 5’phosphribosyl-1-pyrophosphate B. carbamoylphosphate and aspartate C. asparatate and 5’phosphribosyl-1-pyrophosphate D. carbamoylphosphate and glutamine 3. The starting substrates for purine biosynthesis are A. carbamoylphosphate and aspartate B. asparatate and 5’phosphribosyl-1-pyrophosphate C. carbamoylphosphate and glutamine D. glutamine and 5’phosphribosyl-1-pyrophosphate 4. The end products of purine and pyrimidine de novo synthesis are A. B. C. D.

IMP and UMP GMP and IMP AMP and IMP TMP and GMP

5. Indicate the correct anti-tumoral compound and its mode of inhibition used in the chemotherapy of rapidly dividing cancer cells. A. fluorouracil….suicide inhibition of thymidylate synthase B. methotrexate….suicide inhibition of thymidylate synthase C. methotrexate….suicide inhibition of dihydrofolate reductase D. fluorouracil….competitive inhibition of dihydrofolate reductase

13.3: Nucleotide Salvage and Degradation Pathways 1. Why do cells prefer purine and pyrimidine salvage pathways over de novo synthesis? A. Because salvage pathways require more pentose phosphate pathway activity B. Because de novo synthesis puts demands on the need for increase pentose phosphate pathway activity

C. Because salvage pathways require less energetic input than de novo synthesis D. Because de novo synthesis requires too many amino acids as substrate 2. Which of the following molecules directly inhibits xanthine oxidase and thus helps to correct high levels of urate? A. allopurinol B. amethopterin C. alloxanthine D. fluorodeoxyuridylate 3. Gout is one of the leading causes of arthritis in the United States. It is caused by the formation of ______ ________ crystals in the joint tissue. A. phosphoric acid B. uric acid C. acetic acid D. amino acid 4. The degradation of pyrimidine bases ultimately forms which two compounds? A. uridylate and thymidylate B. uric acid and water C. xanthine and hypoxanthine D. urea and water 5. A deficiency of which of the following enzymes results in Lesch-Nyhan syndrome? A. thymidine phosphorylase B. adenine phosphoribosyltransferase C. hypoxanthine-guanine phosphoribosyltransferase D. uridine kinase 6. Allopurinol, used to treat gout inhibits, affects A. the salvage pathway of AMP to IMP B. the salvage pathway of purines, inhibiting the enzyme HGPRT C. the de novo synthesis pathway of purines D. the activity of xanthine oxidase to inhibit the production of uric acid

Final 13 1. N10-formyl tetrahydrofolate (N10-formyl THF) is used in which of the following reactions?

A. B. C. D.

Building of AMP Building of UMP Building of TMP All of the above

2. Guanine and guanosine differ by one A. phosphate B. deoxyribose C. ribose D. hydroxyl 3. Which of the following is the abbreviation for a nucleotide containing the nitrogenous base adenine, a hydroxyl group at the 2’ carbon of its pentose sugar, and a tri-phosphate group attached to the 5’ carbon of its pentose sugar? A. dATP B. ATP C. ADP D. dADP 4. A deficiency of the the enzyme hypoxanthine-guanine phosphoribosyltransferase is the cause of Lesch-Nyhan syndrome. Which biochemical reaction(s) does this enzyme catalyze? A. the conversion of guanine to GMP B. the conversion of hypoxanthine to IMP C. All of the above D. None of the above 5. Which of the following molecules is used in both pyrimidine and purine de novo synthesis? A. formyl-tetrahydrofolate B. 5-phosphoribosyl-1-pyrophosphate C. carbamoyl phosphate D. glycine 6. An excess of GTP will stimulate the formation of which of the following molecules? A. AMP B. UMP C. TMP D. CMP 7. Which of the following enzymes is(are) involved in the early events of pyrimidine biosynthesis? A. carbamoyl phosphate synthetase B. amidophosphoribosyltransferase C. aspartate transcarbamoylase

D. A and C

MODULE 14 14.1: Nucleic Acid Structure 1. Replication of DNA is A. conservative B. semi-conservative C. non-conservative D. liberal 2. Chromatin consists mainly of A. histones B. RNA C. DNA and histones D. DNA 3. Indicate the FALSE statement. A. Nucleic acid bases are covalently linked to ribose sugars by glycosidic bonds B. Deoxyribose lacks a 2'-hydroxyl C. In B-DNA the two strands run in the same direction and are held together by G-C and A-T base pairs D. Deoxynucleotides in DNA have negative charge

14.2: DNA Replication 1. What is the function of telomerase? A. Fill in the lagging strand at the telomere B. Replicate and stabilize the telomeric ends of DNA C. Make an RNA primer for the telomere D. Hold the telomere in place while DNA replication takes place 2. Which of the following statements is FALSE? A. Both strands of DNA are replicated B. Replication is bidirectional C. Only genes are replicated D. The timing of replication in eukaryotic cells is tightly controlled 3. The discontinuous synthesis of one strand of DNA during replication results in A. DNA primers B. reverse transcription

C. Okazaki fragments D. Mutations 4. Telomerase A. helps replicate the ends of chromosomes B. shortens the ends of chromosomes during replication C. creates Okazaki fragments D. all of the above 5. DNA polymerases extend the primer by joining deoxynucleotides with A. the 5' phosphate of the primer B. the complementary strand C. the promoter site D. the 3' OH of the primer

14.3: DNA Repair 1. Which of the follow enzyme(s) is required for excision repair of DNA damage? A. DNA polymerase B. DNA polymerase and DNA ligase C. endonuclease D. DNA polymerase, DNA ligase, and exonuclease 2. Which of the following DNA repair mechanisms require the formation of Holliday junctions? A. Excision repair B. Nucleotide-excision repair C. Replication D. Recombination 3. What base can spontaneously deaminate requiring repair? A. Guanine B. Cytosine C. Adenine D. Thymine 4. Thymine dimers are caused by A. mutagens B. deamination C. reactive oxygen species D. ultra-violet radiation

Final 14

1. Which is false? A. In eukaryotes, histones are bound to RNA B. During replication one original strand of DNA remains in one of the daughter cells C. DNA is double helical D. Strands of DNA are held together by GC and AT base pairs 2. Which of the following is false? A. Only genes are replicated B. Both strands of DNA are replicated. C. Replication is bidirectional D. The timing of replication in eukaryotic cells is tightly controlled 3. Okazaki fragments result because A. DNA synthesis is discontinuous B. RNA synthesis is discontinuous C. DNA polymerase is conservative D. proof reading has occurred 4. DNA polymerases extend the primer by joining deoxynucleotide triphosphates nucleotides with: A. the complementary strand B. the 5'OH of the primer C. the promoter site D. the 3'OH of the primer 5. Which of the following best describes the role of helicase in the replication of DNA? A. Add nucleotides to the growing DNA strand B. Prevent the supercoiling of DNA C. Unwinds double stranded DNA D. Removes mismatched nucleotide bases 6. Which of the following is true concerning thymine? A. The presence of thymine in DNA instead of uracil ensures genetic fidelity B. Dimerization between adjacent thymine residues can not be repaired in e. coli C. Thymine bases are present in both RNA and DNA D. None of the above are true concerning thymine 7. Which of the following best describes a nucleosome? A. DNA wrapped around a core of 4 histone proteins B. RNA wrapped around a core of 8 histone proteins C. DNA wrapped around a core of 8 histone proteins D. RNA wrapped around a core of 4 histone proteins

MODULE 15 15.1: Introduction 1. Which is the smallest RNA molecule on the list below? A. Piwi-interacting RNA B. Small nucleolar RNA C. Small interfering RNA D. Small nuclear RNA 2. What is the direction of the synthesis of RNA? A. In the 5’ to 3’ direction B. In the 3’ to 5’ direction C. It depends on which strand is being transcribed D. Either direction, depending on the RNA polymerase 3. In the initiation of transcription, what is the function of the promoter region? A. It activates the gene to be copied B. It is the site for the binding of transcriptional activating factors to the DNA C. It is the site for the binding of RNA polymerase to bind to the DNA upstream of transcription initiation D. It the site for the binding of DNA polymerase 4. Which strand of the DNA is copied to transcribe to the mRNA? A. The coding strand B. Either strand C. The templating strand D. The one oriented in the 3’ to 5’ direction 5. Why do eukaryotic cells have a nucleus? A. To separate transcription from translation B. To protect the DNA C. To keep ribosomes out of the nucleus D. So that no other RNA’s can interfere in transcription 6. Why are there three different isoforms of RNA polymerase in eukaryotic cells? A. To copy the large number of genes in eukaryotes B. Due to the different promoters, this increases the number of different promoters C. Increases the number of possible initiator sequences D. Increases how many genes can be transcribed at the same time

15.2: Transcription

1. The consensus sequence found for the Pribnow box, also known as the -10 site, is A. GAGAAG B. TGTGTG C. GGGGAA D. TATAAT 2. What is the difference between core and holoenzyme? A. The binding of sigma factor to core enzyme B. The binding of rho factor C. The binding of upstream transcription factors D. The binding of sigma factor to holoenzyme 3. Which is true of bacterial transcription? A. One of the promoter sites is the Pribnow box. B. One of the promoter sites is the TATA box. C. One of the promoter sites is the CAAT box. D. One of the promoter sites is the GC box. 4. Which is true during the elongation phase of transcription? A. The sigma subunit remains bound to RNA polymerase. B. The coding strand of the DNA is transcribed. C. Transcription occurs in the 5' to 3' direction of the RNA. D. RNA polymerase alternately binds and releases DNA. 5. Transcription begins: A. upstream from the promoter region B. upstream from the Shine-Delgarno sequence C. downstream from the promoter region D. when repressor protein binds

6. Which of the following represents post-transcriptional modification of mRNA? A. 5' methylated capping B. polyadenylation of the 5’ end C. aminoacylation D. phosphorylation of serine or theonine

15.3: Translation 1. Why is the triplet code degenerate? A. Because there is only one start codon B. Because there are three stop codons

C. Because there are 64 codons for 20 amino acids D. Because only 61 of the possible 64 codons code for amino acids 2. What is the anti codon? A. The complementary sequence to the codon of mRNA that codes for an amino acid B. The sequence of bases at the 3’ end of tRNA to attach an amino acid C. The initiator sequence for translation to begin D. The tRNA site that binds to the ribosomes 3. What is the Shine-Delgarno sequence? A. It is the RNA initiator of translation region found on the mRNA B. It is the ribosomal binding site on the mRNA C. It is the enhancer region D. It is the sequence for tRNA binding to the ribosome 4. What is present at the 3’ end of eukaryotic mRNA? A. The methyl cap B. The stop codons C. The poly A tail D. The poly G tail 5. Why does the presence of lactose induce the lac operon to be transcribed and translated? A. Lactose activates the transcription of the gene by binding to the promoter B. Lactose binds to the repressor and allows the RNA pol to bind and transcribe the DNA C. Lactose activates mRNA binding to ribosomes D. Lactose binds to the Shine-Delgarno sequence

6. In prokaryotic cells the initiator AUG codes for A. cysteine B. alanine C. methionine D. tryptophan

Final 15 1. Which statement about codons is true? A. There is one termination codon. B. There are three initiation codons. C. The initiation codon is AUG.

D. There are four termination codons. 2. Which of the following represents post-transcriptional modification of mRNA? A. 5' capping B. aminoacylation C. phosphorylation of serine or theonine D. polyamidation 3. Bacterial transcription begins A. downstream from the Pribnow box B. at the Shine-Delgarno sequence C. upstream from the promoter region D. when TFIID binds 4. Which statement about eukaryotic mRNA is FALSE? A. it as a 3' poly A tail B. it usually has introns spliced out C. it contains exons D. it has a 3' methylated cap 5. Which of the following statements about bacterial transcription is true? A. Introns are spliced out of mRNA. B. There are two promoter sites: the Pribnow box and the GC box. C. One of the promoter sites is the CAAT box. D. One of the promoter sites is the Pribnow box. 6. A feature which distinguishes DNA polymerases from RNA polymerases is that A. the latter has proofreading capacity B. the former enzyme is not processive during replicative synthesis C. the latter requires both a template and a primer D. the former requires both a template and a primer 7. Which of the following statements about tRNA is FALSE? A. tRNA binds sigma factor B. tRNA contains 3 loop-like regions C. tRNA contains an anticodon D. tRNA contains "unusual" bases

MODULE 16 16.1: Nucleic Acid Technology: Introduction 1. Which of the following are used as labels for nucleic acid probes? A. Fluorescent molecules B. Radioactive atoms

C. Nanoparticles D. All of the above 2. In nucleic acid hybridization procedure, which step allows single stranded nucleic acids to bind to one another? A. heating step B. cooling or annealing step C. mixing step D. labeling step 3. Flush cut restriction endonucleases are not as useful as staggered cut restriction endonucleases when it comes to assembling DNA fragments into new constructs. A. True B. False 4. The staggered cut restriction endonuclease generates "sticky ends" as a result of: A. generating single stranded regions from asymmetric cleavage of DNA B. generating single stranded regions from symmetric cleavage of DNA C. generating double stranded regions from symmetric cleavage of DNA D. generating double stranded regions from asymmetric cleavage...