DNA and RNA: Building Blocks of Life

Exams 120:360 Biochemistry Spring 2018/Exam 3 Prof. Cervantes Student’s name (Last, First): , Multiple choice Quaternary structure refers to the non-covalent interaction(s) between polymeric units, such as two or more monomer protein units that noncovalently interact. Which of the following scenarios for nucleic acids most closely resembles quaternary structure? A) self-assembly of RNA-protein subunits in the tobacco mosaic virus B) interaction of DNA with proteins during replication C) RNA and protein association in ribosomes D) All of the above E) None of the above RNA molecules can form secondary structures (double stranded regions) if there are complementary bases in the right positions. Which of the following RNA strands would be most likely to form a specific secondary region? A) B) C) D) E) 5¢-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3¢ 5¢-UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU-3¢ 5¢-GGGAUUUUUUUUUUUUUUUUAAAAAAAAAAAAAAAAUCCC-3¢ 5¢-UGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUG-3¢ 5¢-GGAAAAGGAGAUGGGCAAGGGGAAAAGGAGAUGGGCAAGG-3¢ Which of the following characteristics is associated with the B form of DNA? A) B) C) D) E) the sugars are located in the interior of the double helix the distance between base pairs along the axis of the helix is 0.8 nm (8 Å) the major and minor grooves are readily apparent the planes of the bases make about a 20° angle with the helix axis None of the above In your research on DNA structure, you find a double stranded molecule that is located in GC-rich regions of chromosomes, has alternating purine-pyrimidine sequences, is left handed, has 13.6 base-pairs (bp) per turn, a diameter of 1.8 nm (18 Å), displays a deep minor groove, and an outer convex surface that is analogous to a major groove. You found DNA in the ___ conformation. A) B) C) D) E) A B P S Z A friend tells you that only four different kinds of bases are found in RNA. You disagree and your friend asks you to provide at least one reason for your answer. A reason you can pose is: A) B) C) D) E) RNA contains only the nucleotides C, G, T, and U. In some RNAs, uridine is methylated to thymidine. RNA contains only the nucelotides A, C, G, and U. RNA is unstable, and thus has variable nucleotide composition. All of the above Which of the following statements is true? A) B) C) D) E) Prokaryotic DNA is normally complexed with histone octamers forming nucleosomes. Bacterial ribosomes consist of 40S and 60S subunits. Eukaryotic ribosomes have a sedimentation coefficient of 80S. In eukaryotic cells, replication, transcription, and translation take place in the nucleus. All of the above 120:360 Biochemistry Exam 3 Page 2 of 8 Which type of topoisomerase can untwist the DNA double helix? A) B) C) D) E) O Type I only Type II only Both types I and II Topoisomerases cannot untwist the DNA double helix What are topoisomerases? What is the advantage for DNA from having thymine and not uracil? A) The replacement of uracil with thymine allows the replication machinery to differentiate between DNA and RNA. B) Cytosine can spontaneously deaminate to uracil, thus the extra methyl on thymine serves as a quality control check. C) There is no particular benefit from the T to U replacement in DNA compared to RNA. D) The extra methyl group on thymine as compared to uracil is key to the formation of the double-stranded DNA helix. E) An extra hydrogen bond can be formed with A by using T instead of U. O Why does double-stranded DNA (dsDNA) with a high A-T content have a lower transition temperature, Tm, than double-stranded DNA with a high C-G content? A) A-T-rich dsDNA requires more energy to separate into single strands than G-C rich dsDNA. B) Purine bases are more susceptible to hydrolysis at high temperature than are pyrimidine bases. C) Elevated temperature breaks the backbone bonds between C and G bases less easily than they break the backbone bonds between A and T bases. D) G-C-rich dsDNA requires more energy to separate into single strands than A-T rich dsDNA. E) A-T-rich dsDNA does not form propeller twists in dsDNA whereas G-C does. O Which of the following statement regarding replication forks is correct? O A) At a replication fork, two strands of dsDNA are separated, and a new DNA strand forms on each separate strand. B) A replication fork is the site of formation of new RNA. C) In bacteria, each origin of replication is associated with a single replication fork. D) A replication fork is the site on DNA at which RNA polymerase acts. E) Replication forks are formed by the DNA. DNA synthesis always takes place from the 5' to the 3' end. The template strands from dsDNA are aligned in opposite directions from each other. How does nature deal with this situation? A) A second type of DNA polymerase is used to synthesize DNA from the 3' to the 5' end. B) The 3'-to-5' template strand is synthesized in small chunks that are then ligated together. C) Okazaki fragments are synthesized on the 5'-to-3' template strand and then ligated together. D) The 5'-to-3' template strand wraps around in a trombone fashion so that the DNA polymerase can move along it in the 3'-to-5' direction, replicating the strand continuously. E) Mother Nature does not deal with these menial issues. O How do the DNA polymerases of eukaryotes differ from those of prokaryotes? A) Prokaryotic DNA polymerases usually do not have exonuclease activity, in contrast to DNA polymerases from eukaryotes. B) Prokaryotic DNA polymerases produce longer Okazaki fragments than eukaryotic DNA polymerases. C) Eukaryotic DNA polymerases synthesize DNA in the 5'-to-3' direction, whereas prokaryotic DNA polymerases can synthesize DNA in both directions. D) Eukaryotic DNA polymerases tend to be multimers while prokaryote DNA polymerases tend to be monomeric. E) DNA polymerases of eukaryotes do not differ from those of prokaryotes. How many origins of replication are there in eukaryotic chromosomes? A) B) C) D) E) None. The eukaryotic replication apparatus can manage without origins of replication. Only one, as in prokaryotes Two, one on each side of the centromere Many: from several hundreds (yeast) to many thousands (mammals) It is not known yet. 120:360 Biochemistry Exam 3 The universal features of DNA replication include A) B) C) D) E) release of PPi from a nucleoside triphosphate. synthesis from the 5' end to the 3' end. base pairing of A to T and G to C. use of a primer. All of the above Transcription of specific genes in eukaryotes requires A) A few types of sigma factors. B) A single sigma factor. C) Tissue (or cell)-specific transcription factors D) Time (developmentally)-specific transcription factors E) Both C) and D) How do enhancers differ from promoters? A) B) C) D) E) Enhancers do not bind RNA polymerase Enhancers include the upstream (UP) element Enhancers bind the sigma factor There is no difference: enhancer and promoter are synonymous My answer is not here Operons A) control the expression of constitutive genes. B) are subject to positive or to negative control. C) are not affected by mutations in the genes for repressors or inducers. D) occur in both prokaryotes and eukaryotes. E) only occur in eukaryotes. Which of the following refers to an exon? A) Its sequence is translated into protein B) Its RNA product is removed during mRNA processing C) Its sequence is not translated into protein D) It carries an amino acyl residue for translation E) It is not part of a mature, totally processed mRNA molecule There are several kinds of RNA polymerases in eukaryotic cells. Which assertion is incorrect? A) B) C) D) E) tRNA is synthesized by RNA pol III RNA pol II produces protein-coding mRNA Most of the rRNA in the cell is produced by RNA pol I All of the above None of the above Which of the following is a way in which RNA is processed after transcription? A) Introns are spliced out. B) The 3' end of mRNA has a poly-A tail appended. C) Individual bases are covalently modified. D) The 5' end of mRNA has a cap appended. E) All of the above Other than transmitting genetic messages, what other roles can RNA have in the cell? A) B) C) D) E) RNA trimming Gene silencing Peptidyl transferase activity All of the above None of the above Page 3 of 8 120:360 Biochemistry Exam 3 Page 4 of 8 For codons that encode the same amino acid, there are often one or two nucleotides that are held in common. Why might this be advantageous? A) B) C) D) This makes harmful mutations less likely. This will allow codons to encode more amino acids in the future. This scheme reduces the number of nucleotides necessary to encode a protein. Deletion of one or two nucleotides from the transcribed mRNA would have no effect on the translated protein. E) None of the above O Fill in the blanks: The Shine-Dalgarno sequence is a _______ leader segment of prokaryotic mRNA It binds to a _________ sequence on the _______ part of the 30S ribosomal subunit and aligns the mRNA with the ribosome for proper translation, beginning with the _____ start codon. A) purine rich, pyrimidine rich, 16S rRNA, AUG B) pyrimidine rich, purine rich, 23S rRNA, UGA C) purine rich, pyrimidine rich, 5SRNA, UAG D) pyrimidine rich, purine rich, 16S rRNA, UAA E) None of the above O Consider a protein made up of 150 amino acid residues. How many GTP molecules will be required if, on average, 2 GTPs are consumed per peptide bond formed (one for elongation positioning and another for translocation)? A) B) C) D) E) O 150 total 149 total 300 plus 1 for initiation and 1 for termination = 302 298 plus 1 for initiation and 1 for termination = 300 Can I use a calculator? Which of the following statements is incorrect? A) B) C) D) Translation in eukaryotes uses only mRNA in which introns have been spliced out. With a few known exceptions, both eukaryotes and prokaryotes use fundamentally the same genetic code. In most prokaryotic genes no introns are found and generally speaking no RNA splicing occurs. In both prokaryotes and eukaryotes, protein synthesis occurs by a nucleophilic attack by the a-amino group of the A-site aminoacyl tRNA on the carbonyl of the growing peptide chain. E) None of the above O Which of the following types of protein are known to be translated using a CUG start codon? A) Immune system peptides displayed on the major histocompatibility complex (MHC) O B) Proteins in the cytoskeleton C) Transcription factors D) Antibodies E) Enzymes Find the mismatched aldose-ketose pair: O A) B) C) D) E) D-threose—D-mannose D-glucose—D-fructose Glyceraldehyde—Dihydroxyacetone D-ribulose—D-ribose D-xylose—D-xylulose From the following, which are characteristics of a reducing sugar? O A) B) C) D) E) The sugar is an aldose. The sugar is a ketose. The sugar is readily reduced. The sugar is only a hexose. None of the above The carbohydrate shown on the right is A) B) C) D) E) O a monosaccharide. a ketose. a hexose. All of the above None of the above 120:360 Biochemistry Exam 3 Page 5 of 8 Epimers are A) B) C) D) E) O stereoisomers that differ from each other in their configuration at two or more carbon atoms. stereoisomers that differ from each other in their configuration at a single carbon atom. the α and β forms of cyclic sugars. two related compounds, pyran and furan. None of the above. What make humans unable to digest plant materials with the effectiveness of fungi and some bacteria? A) The human genome do not code for cellulases. B) The enzymatic repertoire of humans does not include glycosidases capable to hydrolyze the b-(1−4) bonds between glucose residues in cellulose. C) The b-(1−4) bond between glucose molecules in cellulose is much more stable than the a-(1−4) and a-(1−4) bonds in starch (and glycogen). D) All of the above E) None of the above O The enantiomer of D-glucose is A) D-Fructose B) D-Glucose C) L-Glucose D) L-Idose E) D-Galactose O Consider the following information: phosphoenolpyruvate → pyruvate ADP + Pi → ATP ΔG°' = −61.9 kJ/mol ΔG°' = +30.5 kJ/mol How many molecules of ATP might theoretically have been produced when coupled to the conversion of one molecule phosphoenolpyruvate to pyruvate?Structural roles, such as cell walls in plants, fungi, Protista, and bacteria A) 1 B) 2 C) 3 D) 4 E) None of these O Which pair is mismatched regarding the use or production of ATP by glycolytic enzymes: A) B) C) D) E) Hexokinase—Used in reactions that consume ATP Aldolase—Used in reactions that do not involve ATP Phosphofructokinase—Used in reactions that consume ATP Phosphoglycerate kinase—Used in reactions that produce ATP None of the above A) B) C) D) E) is so strongly exergonic that it does not require a catalyst. is an exergonic reaction not coupled to any other reaction. is an endergonic reaction that takes place because it is coupled to the exergonic hydrolysis of ATP. is an exergonic reaction that is coupled to the endergonic hydrolysis of ATP. None of the above O The phosphorylation of glucose to glucose 6-phosphate O 120:360 Biochemistry Exam 3 Page 6 of 8 Which of the following best describes the glycosidic bond in the disaccharide shown above? A) B) C) D) E) O a-(1−4) b-(1−4) a-(2−4) b-(2−4) None of the above The enzyme hexokinase A) phosphorylates a number of different sugars, including glucose, fructose, and mannose. O B) specifically phosphorylates glucose rather than other sugars. C) is the only kinase involved in glycolysis. D) does not participate in glycolysis. E) None of the above Which of the following enzymes interconverts an aldose and a ketose? A) B) C) D) E) O kinase isomerase mutase dehydrogenase phosphorylase In glycolysis, ATP is synthesized by A) substrate-level phosphorylation. B) oxidative phosphorylation. C) photophosphorylation. D) A) and B) E) A), B) and C) O Several of the enzymes of glycolysis fall into classes that are seen often in metabolism. Which of the following description is incorrect? A) Aldolases cleave aldols into two smaller molecules, one containing a keto group and one being an enol or enol precursor. B) Dehydrogenases catalyze redox reactions involving NADH + H+ or FADH2 in which the substrate's oxidation state changes and a hydrogen or hydrogens transfer from the substrate. C) Isomerases perform molecular rearrangement reactions in which the molecular formula of the substrate does not change, but the isomeric form of the molecule is altered. D) Kinases transfer phosphate groups from molecules containing high-energy phosphates to substrate molecules. E) None of the above O Which of the following exercise(s) allosteric control in the reaction of phosphofructokinase? A) B) C) D) E) O ATP fructose 2,6-bisphosphate ATP and fructose 2,6-bisphosphate ADP and glucose-1-phosphate None of the above 120:360 Biochemistry Exam 3 Page 7 of 8 Which group of small molecules best fit the boxes associated with the reaction shown? a b c I. ATP ADP H2O II. NADH + H+ NAD+ Pi III. NAD+ NADH + H+ H2O IV. NAD+ NADH + H+ Pi A) I B) II C) III D) IV E) None of these Why is the formation of fructose-1,6-bisphosphate a likely control step in the glycolytic pathway? A) Fructose-6-phosphate can be easily stored by the body. B) The irreversible formation of fructose-1,6-bisphosphate is the first committed step in glycolysis. C) It has the highest activation energy of any step in glycolysis. D) All of the above E) None of the above When humans consume ethanol, the first step in its metabolism is: A) B) C) D) E) conversion to lactate conversion to acetaldehyde conversion to acetone production of fatty acids conversion to ketone bodies Why is the reaction catalyzed by citrate synthase considered a condensation reaction? A) B) C) D) E) The number of species bound to a specific carbon in oxaloacetate reduces from four to three. The number of product molecules is greater than the number of reactants. A carbon-carbon single bond is converted to a double bond during the reaction. A C–C bond is formed during the synthesis of citrate. None of the above Which of the following reaction aspects is a component of the net reaction catalyzed by a synthetase? A) A group shifts from one carbon to an adjacent carbon on the substrate. B) A high-energy phosphate bond is utilized to synthesize a molecule. C) A reduction or oxidation occurs. D) All of the above E) None of the above NADH + H+ is an important coenzyme in catabolic processes, whereas NADPH + H+ appears in anabolic processes. How can the exchange of NADH + H+ and NADPH + H+ be effected? A) NADPH + H+ can be imported into the mitochondrion in conjunction with NADH + H+ export from the mitochondrion. B) NADH + H+ is consumed in the conversion of oxaloacetate to malate, and malate can produce pyruvate and NADPH + H+. C) The citric acid cycle can be modified to produce NADPH + H+ rather than NADH + H+. D) NADH + H+ can be converted to nicotine, which then can be metabolized to NADPH + H+. E) None of the above o Three of the following reactions act as control points in the citric acid cycle, i.e., they are the most favorable reactions. Which one is not a control point? A) B) C) D) E) e Oxaloacetate + Acetyl-CoA + H2O → CoA-SH + Citrate Isocitrate + NAD+ → a-Ketoglutarate + CO2 + NADH + H+ a-Ketoglutarate + CoA-SH + NAD+ → Succinyl-CoA + CO2 + NADH + H+ Citrate → Isocitrate None of the above 120:360 Biochemistry Exam 3 Page 8 of 8 Which of the following statements explains why acetyl-CoA is considered the central molecule of metabolism? A) Acetyl-CoA feeds directly into the citric acid cycle. B) Acetyl-CoA contains a thioester bond that makes it one of the high energy compounds in metabolic pathways. C) Acetyl-CoA can be formed from many compounds, such as fats, carbohydrates, and many amino acids. D) Acetyl-CoA can form fats and ketone bodies. E) All of the above O Why is the citric acid cycle considered as part of aerobic metabolism, even though O2 does not appear in any reaction? A) The reducing units produced by the citric acid cycle couple to aerobic ATP production mediated by the electron transport chain. B) The citric acid cycle can function in the presence of O2. C) Oxidation can occur in the absence of molecular oxygen. D) None of the components of the citric acid cycle are reduced as the cycle progresses. E) CO2 is produced in the cycle proper and during the production of acetyl-S-CoA. o Bonus questions Why are all the reactions of electron transport, when written as redox half reactions, written with the electrons on the reactant side? A) B) C) D) E) Because these are half reactions, they always run in the direction with electrons as reactants. The reactions of the electron transport chain all run in this direction. The reactions do not run in the reverse direction, i.e. with the electrons as products. The chemical convention for redox half reactions is to write them as reductions. None of the above What unusual property do cytochromes have in common with hemoglobin or myoglobin? A) B) C) D) E) They all bind strongly to RNA as well as small ligands. All of them contain heme groups. All of them participate in electron transfers in biological reactions. They all are found in plants, animals, and bacteria. All of the above Which of the following statements explains why acetyl-CoA is considered the central molecule of metabolism? A) Acetyl-CoA feeds directly into the citric acid cycle. B) Acetyl-CoA contains a thioester bond that makes it one of the high energy compounds in metabolic pathways. C) Acetyl-CoA can be formed from many compounds, such as fats, carbohydrates, and many amino acids. D) Acetyl-CoA can form fats and ketone bodies. E) All of the above Why is the citric acid cycle considered to be part of aerobic metabolism, even though molecular oxygen does not appear in any reaction? A) The reducing units produced by the citric acid cycle couple to aerobic ATP production mediated by the electron transport chain. B) The citric acid cycle can function in the presence of O2. C) Oxidation can occur in the absence of molecular oxygen. D) None of the components of the citric acid cycle are reduced as the cycle progresses. E) CO2 is produced in the cycle proper and during the production of acetyl-S-CoA. What is the underlying reason for the difference in the yield of ATP from the complete oxidation of one mole of glucose in brain cells compared to that in kidney cells? A) B) C) D) The level of dissolved O2 is greater in kidney cells than it is in brain cells. Glucose transport to brain cells is less efficient than it is to kidney cells. The ATP synthase complex is less efficient in brain cells compared to kidney cells. The brain cells use the glycerol-phosphate shuttle whereas the kidney cells use the malate-aspartate shuttle. E) None of the above