BECOM Test 3

Which bases does RNA contain?

A, G, C, and U (uracil)

66. (1 point) Each of the following features are characteristics of introns except for which ONE? A. 100% conservation of a dinucleotide sequence at both their 5' and 3' ends B. Contain a poly purine sequence directly adjacent to their 3' end C. Always form a lariat through an A residue about 30 nt from the 5' end D. Bind to protein/RNA complexes called snRNP's to facilitate splicing E. Are not present in prokaryotes

B or C

38. (1 point) Resistance of HIV to nucleoside analogs commonly arises because of which ONE of the following? A. Human cells become impermeable to their uptake B. The virus produces a specific enzyme to degrade the analogs C. Error-prone replication of the viral genome leads to a reverse transcriptase with altered properties D. Reverse transcriptase is no longer needed by resistant viruses E. Viral components inhibit phosphorylation of the nucleoside

C

46. (1 point) Bidirectional replication is a phenomenon which is best described by which ONE of the following? A. Allows bacteria to grow in two directions at once B. Requires at least two replication origins C. Requires no more than two replisomes D. Cannot occur on linear chromosomes E. Is purely theoretical since it cannot be visualized

C

42. (1 point) All of the following components except for which ONE are necessary for replicating a prokaryotic chromosome? A. DNA polymerase III B. DNA primase C. RNA polymerase I D. DNA ligase E. Ribonucloside triphosphates

C

51. (1 point) When cytosine deamination occurs in DNA all of the following activities are needed to repair the lesion except for which ONE? A. DNA ligase B. AP endonuclease C. Uracil DNA glycosylase D. DNA primase E. DNA polymerase I

D

50. (1 point) Telomere shortening might be expected to occur in all of the following situations EXCEPT for which ONE? A. A down-regulation of telomerase activity B. Elimination of the telomerase RNA-encoding gene C. Highly differentiated mammalian cells D. Very old bacterial cells E. Enhanced 3' to 5' exonuclease activity in the cell

D or E

62. (1 point) Transcription in prokaryotes requires all of the following components except for which ONE? A. DNA B. tRNA C. Mg2+ ions D. rNTP's E. RNA polymerase

B

23. (2 points) Which of the following muscle enzymes will NOT be allosterically inhibited under conditions of high glucose levels in a normal individual? Consider the case of someone who has eaten a large carbohydrate-rich meal, and then gone to vegetate in front of the TV for the next two hours. This question may have more than one correct answer; indicate all correct answers on the answer sheet. A. Citrate synthase B. Fumarase C. Isocitrate dehydrogenase D. Phosphofructokinase-I E. Phosphoglycerokinase F. Pyruvate dehydrogenase

B, E

72. (1 point) Complementation in trans signifies which ONE of the following molecular scenarios? A. DNA in one strand is complementary to DNA in the other strand B. It is a technical term for referring to coupled transcription and translation C. The ability of DNA sequences on different chromosomes to hybridize to one another D. The protein product of a gene on one piece of DNA is able to compensate for a mutant, non-functional version of the protein encoded on another E. The transport of proteins from the cytoplasm to the nucleus, or vice-versa

D

Where is DNA located in eukaryotes?

mainly in the nuclei with small amounts in mitochondria

What are the aspects of DNA replication? Why is discontinuous synthesis required?

-occurs during S phase of cell cycle in eukaryotes, is catalyzed by a complex of proteins that includes the enzyme DNA polymerase -each strand of the parent DNA acts as a template for the synthesis of its complementary strand -DNA polymerase copies the template strand in the 3' to 5' direction and synthesizes the new strand in the 5' to 3' direction, deoxyribonucleoside triphosphates serve as the precursors -DNA polymerase cannot initiate the synthesis of a new strand. A short stretch of RNA serves as a primer. -other proteins and enzymes are required to unwind the parental strands and allow both strands to be copied simultaneously

73. (1 point) Finely tuned gene transcription levels in cells are typically controlled by which ONE of the following? A. Unique combinations of positively or negatively acting transcription factors B. A combination of messenger half-life and transport of mRNAs C. Presence of either F factor or TFIID D. The presence or absence of mutations in promoters or other regulatory regions E. The relative concentration of glucose versus lactose in the cells

A

70. (2 points) tRNA s have several unique features which distinguish them from other types of RNA. From what you have learned in this course, which of the following features are NOT UNIQUE to tRNA? This question may have more than one correct answer; be sure to indicate all correct answers on the answer sheet. A. Ability to form a 3D structure by virtue of intramolecular base pairing B. Modification of the 3' end by non-templated bases C. Presence of inosine residues D. Presence of a methylated G base (or bases) E. Presence of thymine base(s) F. Existence of covalent links to amino acids

A, B, D

34. (2 points) Nucleic acids are composed of which of the following component parts? A. Nitrogen-containing heterocyclic bases B. Diphosphate linkages C. Sugars with 6 carbon atoms comprising the ring structure D. 5' to 3' phosphodiester linkages E. Deoxyglucose sugars F. 2' hydroxyl or 2' deoxy substituents G. Peptide linkage between sugar and base

A, D, F

An RNA produced from a fragment of DNA has the sequence of AAUUGGCU. The sequence of the nontemplate stand in the DNA that gave rise to the sequence is what?

AATTGGCT The nontemplate strand in the DNA is the same as the coding strand and will have the same sequence of the RNA that is produced, except that T is in place of U. Both the nontemplate strand and RNA produced will be a complementary sequence to the template strand. All sequences are written in 5' to 3' direction, unless otherwise specified, an RNA sequence of AAUUGGCU would correspond to a DNA sequence, on the nontemplate strand, of AATTGGCT. The template strand would be the complement of the nontemplate strand, or AGCCAATT (written 5' to 3'). Note that this sequence is also the complement of the RNA that has been produced. The base U is not found in DNA.

49. (1 point) The Ames test attempts to identify potential mutagens in which ONE of the following ways? A. By converting Salmonella into E. coli B. By selecting for a "back mutation" to convert an inactive gene to an active one C. By using chemically exposed bacteria to infect human cells D. By killing Salmonella bacteria E. By creating mutations in the histidine codon

B

52. (1 point) Mismatch repair is characterized by each of the following observations EXCEPT for which ONE? A. Recognition of a mismatch site by a specialized "mut" protein B. The presence of 5-methyl cytidine in the sequence GATC C. The existence of a mismatch within 1 kb of a GATC sequence D. Endonuclease cleavage at the 5' side of GATC E. A high incidence of cancer when one of the "mut" proteins is lacking

B

55. (1 point) The key mechanistic failure in Xeroderma Pigmentosum patients involves which ONE of the following? A. Mutation in the photolyase gene B. Inability to excise a section of UV damaged DNA C. Mutation on one of the mismatch repair components D. Inability to synthesize DNA across the damaged region E. Loss of proofreading capacity

B

48. (2 points) Which of the following processes would NOT increase the chances of causing mutations in DNA? This question may have more than one correct answer; be sure to indicate all correct answers on the answer sheet. A. Exposure to UV light B. Incorrect charging of tRNA C. Loss of 3' to 5' exonuclease activity in DNA polymerase D. Translational frameshifting by ribosomes E. Deamination of cytosine bases F. Eating large quantities of wild mushrooms

B, D, F

67. (2 points) Most eukaryotic genes produce mRNAs that are processed. Which of the following are correct statements regarding this process? This question may have more than one correct answer; indicate all correct answers on the answer sheet. A. All processing occurs before the mRNA is fully synthesized B. Capping of the 5' end occurs as soon as the 5' end emerges from the polymerase C. The capping machinery uses methylated GTP to create the cap D. Polyadenylation occurs after the repeated sequence AUUUA is produced at the 3' end E. All processing is completed before transport of the mature mRNA to the cytoplasm F. Alternative splicing only occurs when mutations in or around the intron sequences have been sustained

B, E

40. (1 point) Repeating dinucleotide sequences are very common in eukaryotic genomes, e.g. .......ACACACACACACACACACACAC........ Based on what you know, which ONE of the following statements is likely to be correct? A. When occurring within genes they will give rise to a monotonous run of a single amino acid B. depending on the reading frame they will give rise to repetitive runs of 1, 2 or 3 amino acids C. Irrespective of reading frame they will produce a run of the same two alternating amino acids D. Ribosomes will rapidly dissociate from mRNAs containing such sequences E. If located within introns they will precipitate alternative splicing events

C

45. (1 point) Okazaki fragments show all of the following characteristics except for which ONE? A. Are mixed DNA/RNA polymers B. Are typically 1000 nucleotides long in prokaryotes C. Are joined together by DNA primase D. Are formed as part of the lagging strand E. Allow a replisome to move in one direction on double stranded DNA

C

53. (1 point) 5-methyl cytidine is present in high quantities in mammalian DNA, so it is likely to be a hot-spot for mutation because of which ONE of the following? A. It is unable to base pair with G, hence creating a distortion in DNA B. It is hydrolyzed to give 5-methyl uracil, which is removed by uracil DNA glycosylase to leave an unrepaired gap in DNA C. It is deaminated to thymine, which results in a G:T mismatch D. It should not be there in the first place E. It causes DNA polymerase to utilize incorrect bases when encountering it on the template strand

C

54. (1 point) The enzyme telomerase synthesizes DNA strands at the end of chromosomes through which ONE of the following mechanisms? A. By converting DNA polymerase into a continuously cycling mode B. By adding each of the 4 nucleotides in turn to produce a repetitive sequence C. By extending the leading strand via instructions from its own internal template D. By violating the usual rule and synthesizing DNA 3' to 5' E. By adding long poly A tails to the leading strand

C

35. (1 point) A typical purine base may be identified by which TWO of the following characteristics? A. 4 carbons and 2 nitrogens in the ring structure B. At least one oxygen atom linked to the ring structure C. 5 carbons and 4 nitrogens in the ring structure D. A nitrogen atom in the 9 position E. 6 carbons and 3 nitrogens in the ring structure F. A carbon atom in the 1 position

C, D

44. (2 points) Which of the following enzymatic activities are NOT contained within DNA polymerase I? This question may have more than one correct answer; be sure to indicate all correct answers on the answer sheet. A. Making internucleotide linkages in the 5' to 3' direction B. Destroying internucleotide linkages in the 5' to 3' direction C. Having an exonuclease activity specific for RNA but not DNA D. Making internucleotide linkages in the 3' to 5' direction E. Destroying internucleotide linkages in the 3' to 5' direction

C, D

68. (2 points) Promoters are ubiquitous elements for all eukaryotic genes. Which TWO of the following statements regarding eukaryotic promoters are INCORRECT? A. Many, but not all, promoters contain a TATAA consensus at ca. -30 bp B. The TATAA sequence is on the sense strand, thereby defining the other strand as the template for transcription C. Many genes need only a TATAA sequence for efficient transcription D. Upstream regulatory elements within 200 bp of the TATAA sequence bind to TFII initiation factors (such as TFIIA and B) and help to recruit TFIID E. Enhancers are typically not considered part of the promoter, though they can affect transcription rates F. Many of the factors that bind at a TATAA promoter are themselves complexes of several individual proteins

C, D

69. (2 points) In comparing protein synthesis in eukaryotes and prokaryotes there are many similarities. Which TWO of the following are clearly different between these two groups of organisms? A. Number of GTP molecules consumed per peptide bond completed during elongation B. Presence of polyribosomes on individual mRNA molecules C. Requirement of a chemically modified form of methionine at initiation D. Requirement for a capped mRNA in order to get efficient translation E. Requirement for two species of methionine-specific RNA F. Large numbers of ancillary proteins in both the small and large ribosomal subunits

C, D

How is DNA packaged in eukaryotic nuclei? What enzymatic activities are required to free DNA from the packaging for access by other proteins?

Chromatin of eukaryotic cells consists of DNA complexed with histones in nucleosomes -histones are relatively small, basic proteins with a high content of arginine and lysine (prokaryotes do not have histones) -8 histone molecules form an octamer around which approx 140 base pairs of DNA are wound to form a nucleosome core -the DNA that joins one nucleosome core to the next is complexed w histone H1 The "beads on a string" nucleosomal structure of chromatin is further compacted to form solenoid structures (helical, tubular coils) -euchromatin: less densely packed, accessible to transcription factors -heterochromatin: concentrated near periphery of nucleus, not accessible to transcription factors

37. (1 point) The reason there are 64 possible codons is which ONE of the following? A. There are 64 aminoacyl tRNA synthetases B. Each base is able to participate in wobbling C. All possible reading frames can be used in this way D. There are 4 possible bases at each of three codon positions E. The more codons, the faster protein synthesis can be accomplished

D

47. (1 point) DNA replication requires primers in order to proceed because of which ONE of the following? A. DNA primase cannot work de novo B. DNA polymerases need a template from which to copy DNA C. Replication origins cannot be melted in their absence D. DNA polymerases require free 3' ends in order to both make DNA and check it E. DNA primase only works at replication origins

D

64. (1 point) In order for prokaryotic transcription to be initiated all of the following have to occur except for which ONE? A. The promoter needs to be recognized by holoenzyme B. DNA downstream of the promoter has to be "melted" C. Sigma factor has to accompany the polymerase to the promoter D. The DNA strand that acts as template is the one that reads 5' to 3' E. Two molecules of rNTP are condensed to form the first phosphodiester bond

D

43. (2 points) Which of the following characteristics of proof-reading are essential to maintain fidelity in DNA replication? This question may have more than one correct answer; be sure to indicate all correct answers on the answer sheet. A. Degrading DNA in the 5' to 3' direction B. Using wobble pairing to increase efficiency C. Using methylation differences to determine parent vs daughter strand D. Always having a free 3'-OH end on the strand being synthesized E. Having both a nuclease and a polymerase activity on the same molecule F. Ensuring the correct amino acid is bound to its cognate tRNA

D, E

39. (2 points) In comparing DNA and RNA which features are UNIQUE to one or the other molecule? This question may have more than one correct answer; indicate all correct answers on the answer sheet. A. Contain phosphodiester linkages B. Are synthesized in the 5' to 3' direction C. Can participate in G-C base pairs D. Usually contain both single stranded and double stranded regions E. Are created from nucleoside triphosphates F. Can participate in G-U base pairs G. May undergo post-synthetic modification of bases H. Frequently have a 3' poly A tail I. Are considered informational macromolecules J. Are typically repaired in vivo

D, F, H, J

A bacterial mutant grows normally at 32C but at 42C accumulates short segments of newly synthesized DNA. Which one of the following enzymes is most likely to be defective at the nonpermissive temp (the higher temp) in this mutant? -DNA primase -DNA polymerase -an exonuclease -an unwinding enzyme (helicase) -DNA ligase

DNA ligase -the short segments of the newly synthesized DNA that accumulate are Okazaki fragments. They are usually joined together by DNA ligase, which most likely exhibits reduced activity at 42C in this mutant. If the ligase is not functioning, Okazaki fragments would not be joined during replication, so the cells would contain short fragments of the DNA. Endonucleases and exonucleases cleave DNA strands in the middle and at the ends, respectively. They do not join fragments together, nor does DNA polymerase. Unwinding enzymes "unzip" the parental strands, and if these were defective, DNA synthesis most likely would not occur at the nonpermissive temp, and short DNA fragments would not accumulate.

36. (1 point) Typical anti-HIV drugs like AZT are toxic to humans because of which ONE of the following reasons? A. Inhibition of the poly A polymerase enzyme B. Incorporation into mRNA C. Completely inhibits the polymerizing ability of DNA polymerase D. Incorporation into full-length viral DNA and thus enhance mutation frequency E. Incorporation into cellular DNA causing termination of replication

E

41. (1 point) The stop codons in mRNA are UAA, UAG and UGA. Considering only the 3rd position of the codon, how many other codons are subject to sustaining a nonsense mutation that would lead to the production of one of these? Choose the ONE best answer. A. 1 B. 2 C. 3 D. 4 E. 5 F. 6

E

63. (1 point) Several different proteins can be synthesized from a typical prokaryotic mRNA because of which ONE of the following? A. Any of the 3 reading frames can be used B. There is redundancy in the choice of codon/tRNA interactions C. The gene contains several operator sequences from which to initiate translation D. Alternative splicing events are commonly found E. Many mRNAs are organized in a series of consecutive translational cistrons

E

71. (1 point) Lac repressor displays each of the following characteristics except for which ONE? A. Binds to a specific dyad symmetric DNA sequence B. Typically functions in a tetrameric complex at the lac operon C. Blocks passage of RNA polymerase D. Requires allolactose to inhibit its ability to bind to DNA E. Regains its ability to bind to DNA in the absence of glucose

E

74. (1 point) Frequently seen features among DNA binding proteins include all of the following EXCEPT for which ONE? A. The existence of a specific " helix that lies across the major groove of DNA B. The ability to form dimers between identical or non-identical partners C. The ability to form multiple hydrogen bonds between amino acid side chains and the edges of base pairs in the double strand D. The ability to interact with small molecule effectors to alter DNA binding ability E. The ability to recognize RNA molecules with the same sequence

E

65. (2 points) mRNAs in prokaryotes and eukaryotes have differences in all of the following features except for which TWO? A. Structure at the 5' end of the mRNA B. Structure at the 3' end of the mRNA C. Temporary existence of lariat structures D. Require transport to the site of translation E. Are translated 5' to 3' F. Are transcribed in the nucleus G. Require initiation factors to be assembled with ribosomes for translation

E, G

What are the problems with telomere replication?

Telomeres are repetitive sequences at the ends of chromosomes -they are synthesized by the ribonucleoprotein telomerase -the RNA in telomerase is complementary to the telomere repeat sequence and acts as a template for addition of DNA These repeats ensure that incomplete chromosome replication does not affect vital genes As cells differentiate, telomerase function is lost, telomeres shorten -after hundreds of cell divisions, the chromosome ends become damaged, leading cells to stop dividing and to enter Go of the cell cycle, ultimately undergo apoptosis

What does each nucleotide contain?

a heterocylic nitrogenous base, a sugar, and a phosphate

Which bases does DNA contain?

adenine (A), guanine (G), cytosine (C), and thymine (T)