Biochemistry 406 Exam 3 DNA/RNA/Pro
A "coaxial stack" in an RNA structure means a. 2 RNA duplexes sharing a common axis and stacked one on the other b. 2 parallel RNA duplexes connected by a loop c. an interaction between 2 single-stranded RNA loops d. 2 perpendicular duplexes connected by a tether
a
Consider the following DNA sequence: 5'-CAACCGTTGATCGAC-3' Assuming that this is the sense strand and that the sequence is in the middle of a gene in frame, what would be the sequence of the corresponding peptide? Refer to the genetic code table on the first page of the exam. A) Gln-Pro-Leu-Ile-Asp B) Val-Asp-Gln-Arg-Leu C) Gln-Asn-Thr-Pro-Arg-Val-Leu D) Gln-Arg-Asp-Asp E) Val-Gly-Asn
a
Deamination of cytosine leads to the formation of _________________ a. uracil. b. thymine. c. 5-methyluracil. d. 5-methylcytosine.
a
How are amino acids activated for attachment to tRNA? a. adenylation b. formylation c. N-acetylation d. polyadenylation
a
Insertion or deletion of a single base in an open reading frame that initiates with AUG and terminates with UAA, UAG, or UGA would a. always cause a frameshift b. never cause a frameshift c. sometimes generate a premature termination codon in the open reading frame d. always generate a premature termination codon in the open reading frame
a
Mutations caused by ionizing radiation or chemical mutagens in non-dividing cells are NOT repaired by which ONE of the following repair mechanisms? A) Mismatch repair B) Base excision repair C) Nucleotide excision repair D) DNA photolyase E) Direct repair
a
Order the following steps in the transport of a secreted protein into the endoplasmic reticulum (ER). I. SRP binds to the SRP receptor at the ER membrane. II. SRP binds to the hydrophobic signal sequence at the N-terminal of the protein. III. Protein synthesis resumes and the nascent polypeptide is pushed through the Sec61 translocon. IV. SRP dissociates from the ribosome and the nascent polypeptide. V. SRP stops protein synthesis. A) II, V, I, IV, III B) II, I, V, IV, III C) I, V, II, III, IV D) V, I, II, III, IV E) I, V, IV, III, II
a
RNA polymerase II cannot "escape" the promoter area until the CTD is _________ . a. phosphorylated b. methylated c. proteolytically cleaved d. acetylated
a
Ricin is a toxic protein that breaks the glycosidic bond of a specific adenine residue in the large rRNA of the large subunit of the ribosome, but does not break the rRNA backbone. This prevents the ribosome from binding to elongation factors EF-Tu and EF-G (or their eukaryotic equivalents). What would be the effect of ricin on protein synthesis? A) Protein synthesis will be completely inhibited. B) The rate of protein synthesis will be slower, but accuracy will be increased. C) The rate of protein synthesis will not change, but accuracy will be decreased. D) The rate of protein synthesis will be faster, but accuracy will not change. E) There will be no effect of ricin on protein synthesis.
a
To a test tube containing CAACCA-fMet, puromycin, and the appropriate ionic buffer, what additional components must be added to catalyze the peptidyl transfer reaction? I. The small ribosomal subunit (30S) II. The large ribosomal subunit (50S) III. ATP IV. GTP A) II B) I, II C) II, IV D) I, III, IV E) I, II, III, IV
a
To be accurate, the aminoacyl-tRNA synthetase for serine should be able to distinguish serine from threonine and valine. Which of the following statements provides a possible mechanism of how threonine is prevented from being attached to the serine tRNA? A) Threonine won't fit into the acylation site of the enzyme and thus won't be adenylated. B) Threonine is phosphorylated, giving it a negative charge that is repelled by negative charges in the acylation site of the enzyme. C) The smaller serine fits into the enzyme's editing site and will be hydrolyzed if attached to the tRNA, but threonine won't fit into the editing site and won't be hydrolyzed. D) A positively charged metal ion in the enzyme acylation site coordinates serine through its hydroxyl group, but can't coordinate valine since it lacks a hydroxyl group. E) Adenylated threonine will be hydrolyzed by the enzyme's editing site, but adenylated serine won't be hydrolyzed.
a
Which ONE of the following statements about DNA and RNA hybridization is TRUE? A. DNA hybridization is mediated by hydrogen bonds. B. A DNA-RNA double helix adopts a structure similar to Z form DNA. C. A single stranded DNA or RNA molecule cannot base pair with itself. D. DNA hybridization is mediated by van der Waals forces. E. The melting temperature (Tm) of a double stranded DNA molecule is the temperature at which all of it has become single stranded.
a
Which of the following is a function of the DNA polymerase I enzyme of E. coli? a. It removes RNA primers during replication b. it is required for complete replication of the leading strand c. It synthesizes the primers needed to initiate DNA synthesis d. It is the principal replication enzyme
a
Which of the following is true about spliceosomes that carry out the splicing of eukaryotic mRNA precursors? a. The first cleavage step of splicing results in the formation of an intron lariat intermediate b. ATP is required for the cleavage and ligation reactions c. The spliceosome acts in the cytoplasm d. The spliceosome consists of five proteins and about 50 RNAs
a
Which of the following proteins do NOT bind to the ribosome during protein synthesis? If ALL of the proteins bind the ribosome during protein synthesis, choose (E). A) Aminoacyl tRNA synthetases B) Initiation factors C) Elongation factors D) Release factors E) ALL of these proteins bind the ribosome during protein synthesis.
a
Which of the following proteins involved in transcription DOES NOT bind to DNA? a. mediator b. TBP c. sigma factor d. RNA polymerase
a
Which of the following proteins is MOST likely to have a hydrophobic sequence near its Nterminal? A) The mannose 6-phosphate receptor B) RNA polymerase II C) TATA-binding protein D) Aminoacyl tRNA synthetases E) SRP
a
Which of the following statements about eukaryotic mRNA splicing is FALSE? If all statements are TRUE, choose (E) A) ATP is required in the step in which two exons are ligated together. B) The intron is released as a lariat. C) Splicing is catalyzed by a ribonucleoprotein. D) Splicing begins before transcription has been completed. E) ALL of the above statements are TRUE.
a
Which of the following statements about eukaryotic transcription is TRUE? If all statements are FALSE, choose (E). A) Unprocessed transcripts from the same gene often have variable lengths. B) Translation of the mRNA begins before transcription has been completed. C) rRNA, mRNA and tRNA are all transcribed by the same RNA polymerase. D) The first step in transcription initiation is binding of RNA polymerase to the promoter. E) ALL of the above statements are FALSE.
a
Which of the following statements about telomeres or telomerase are TRUE? I. Telomeres are synthesized by a complex containing both RNA and protein. II. Telomerase is required for replication of the E. coli bacterial chromosome. III. Telomeres have a 5' single-stranded overhang. IV. Telomerase synthesizes DNA using a DNA template. A. I B. I, III C. II, III D. II, IV E. III, IV
a
Which of the following statements best describes the relationship between amino acids and tRNAs? A) The activation of an amino acid by formation of an aminoacyl-tRNA is coupled to the hydrolysis of ATP to AMP + 2 Pi. B) The conformation of an aminoacyl-tRNA facilitates the direct interaction between the amino acid and its appropriate codon in the mRNA-ribosome complex. C) Formation of the ester linkage between a tRNA and its corresponding amino acid is catalyzed by the tRNA itself. D) A tRNA binds to its appropriate amino acid through a covalent linkage of the amino acid's side chain to the base of the nucleotide immediately 5' of the anticodon. E) A tRNA is a six-nucleotide RNA molecule consisting of an anticodon followed by a CCA sequence that accepts amino acids.
a
Which of the following statements best describes the termination of protein synthesis? A) Release factors are proteins that bind to stop codons, leading to the transfer of the new polypeptide from tRNA to water. B) Release factors are specialized tRNAs that are not aminoacylated and that recognize stop codons in ribosome-bound mRNAs. C) Ribosome recycling factor (RRF) is a GTP-binding protein that escorts IF-3 to its binding site on the ribosomal small subunit. D) Termination of protein synthesis occurs when the rRNA of the small subunit recognizes the mRNA stop codon via base-pairing interactions. E) Termination of synthesis of cytoplasmic proteins requires SRP.
a
Which of these features of DNA is NOT mediated by a covalent interaction? A. Hybridization between the two strands B. Glycosidic linkage C. Phosphodiester backbone D. Anhydride bond E. None of the above. ALL the above (A-D) are covalent interactions.
a
What is the role of excinucleases in nucleotide-excision repair of DNA? a. They bind to DNA at the site of a nick and then degrade the DNA in a 5′ to 3′ direction. b. They cleave the damaged DNA strand at either side of a lesion. c. They cleave between a base and deoxyribose. d. They degrade the DNA between two nicks.
b
Which of the following are not required for the transport of proteins in the secretory pathway from the endoplasmic reticulum (ER) to the Golgi? If ALL are required, choose (E). A) SNARE proteins B) A rise in the level of calcium in the cell C) Budding of vesicles from the ER D) Fusion of vesicles with the Golgi E) ALL of the above are required for transport of proteins from ER to Golgi.
b
Which of the following is the sequence of the mRNA encoded by the DNA sense strand 5'-ATGCCAGCAT-3'? A) 5'-AUGCUGGCAU-3' B) 5'-AUGCCAGCAU-3' C) 5'-UACGGUCGUA-3' D) 5'-ATGCTGGCAT-3' E) 5'-UACGACCGUA-3'
b
Which of the following is true about aminoacyl-tRNA synthetases? a. They add an amino acid to the 5′ end of a tRNA. b. They generate charged tRNAs. c. They cannot proofread. d. They only recognize the anticodon arm of tRNAs.
b
Which of the following is true about base-excision DNA repair? a. It uses DNA helicase. b. It uses DNA glycosylases. c. It cleaves the damaged DNA on either side of the lesion. d. It removes methyl groups from methylated DNA bases.
b
Which of the following is true regarding the difference between translation in prokaryotes and eukaryotes? a. Only prokaryotes have an initiation factor that binds the mRNA 5′ cap structure b. Translation and transcription are coupled only in prokaryotes c. A Shine-Dalgarno sequence is only needed for initiation of eukaryotic mRNAs d. Only eukaryotic mRNAs initiate with N-formylmethionine
b
Which of the following processes does NOT require the activity of a ligase? A) telomere synthesis B) mRNA splicing C) mismatch repair D) nucleotide excision repair E) base excision repair
b
Which of the following snRNPs (pronounced "snurps") does not participate in splicing eukaryotic mRNA precursors? a. U6 snRNP b. U3 snRNP c. U5 snRNP d. U1snRNP
b
Which of the following statements about the 5' cap of eukaryotic mRNA is FALSE? A) The cap helps to protect the mRNA from degradation by exonucleases. B) The 3' hydroxyl group of the 7-methylguanosine residue acts as a nucleophile to attack the 5' splice site of group I introns. C) The 5' end of the mRNA can be capped before transcription is completed. D) The cap is important for helping the ribosome find the initiator AUG codon. E) Synthesis of the cap requires energy that comes from the hydrolysis of high-energy phosphate bonds.
b
Which of the following statements is not true about the 5' end cap structure of mature eukaryotic mRNAs? a. It participates in the binding of the mRNA to the ribosome to initiate translation. b. The cap is a residue of 7-methyluridine. c. The cap is methylated. d. The cap protects the mRNA from degradation.
b
Which of these DOES NOT explain why many tRNA synthetases have an editing function? a. It's more advantageous to spend an extra ATP than survive with randomly mutated proteins. b. Editing confers a competitive advantage by increasing the speed of translation. c. Some amino acids are structurally similar and easily confused by even the cleverest tRNA synthetases. d. The accumulation of misincorporated amino acids in mature proteins can be harmful.
b
Which of these processes does not occur in the nucleus of eukaryotes? a. polyadenylation b. translation c. splicing of mRNA precursors d. capping the 5' end of mRNA precursors
b
You generate some mutations by using a chemical that specifically causes the deamination of cytosine. Which of the following changes would you expect at the protein level? Please consult the genetic code table on the first page of the exam. A) You might change a Val residue to an Ala. B) You might change a His residue to a Tyr. C) You might change a Tyr residue to a His. D) You might change a Ser residue to a stop codon. E) ALL of the above changes are possible.
b
You have discovered a new enzyme that specifically hydrolyzes phosphate groups from the sugar mannose when mannose is attached to proteins. Thus, it catalyzes the following reaction: mannose 6P ! mannose. What would happen if you added a lot of this enzyme to the Golgi? A) Nothing, because there is no mannose 6P attached to proteins in the Golgi. B) Lysosomal hydrolases will be secreted, leading to a disease similar to I-cell disease. C) Histones will be more positively charged and thus will bind tighter to DNA. D) This enzyme will be sent from the Golgi to peroxisomes. E) Someone who had type A blood will now have type O blood.
b
You make a mutation that specifically eliminates the 3'-5' exonuclease activity of DNA Pol I. What effect will this have on DNA synthesis? A) RNA primers will not be chewed up on the lagging strand. B) There will be a higher error rate. C) The processivity of the enzyme will be reduced. D) DNA synthesis will now occur in a 3' to 5' direction. E) The enzyme will no longer be able to add nucleotides to a 3' tail.
b
According to the wobble rules, what is the MINIMAL number of tRNAs that would be required for the amino acid serine (Ser)? Refer to the genetic code table on the first page of the exam. Note that there are 6 codons for Ser. A) 1 B) 2 C) 3 D) 4 E) 6
c
Based on the wobble rules, which of the following could NOT be the anticodon of a tRNA? Use the genetic code table on the first page of the exam. A) 5'-UAC-3' B) 5'-GCA-3' C) 5'-IUU-3' D) 5'-IGU-3' E) 5'-ICC-3'
c
Consider the following DNA sequence: 5'-CATTTCATGACAGACCAGTAT-3' Assuming that this is the antisense strand and that the sequence is in the middle of a gene in frame, what would be the sequence of the corresponding peptide in the N to C direction? Refer to the genetic code table on the first page of the exam. A) Tyr-Asp-Gln-Thr-Val-Leu-Tyr B) His-Phe-Met-Thr-Asp-Gln-Tyr C) Ile-Leu-Val-Cys-His-Glu-Met D) Val-Lys-Tyr-Cys-Leu-Val-Ile E) Met-Thr-Asp-Gln-Tyr
c
DNA-dependent RNA polymerases _______________ (remember that an exonuclease attacks the end of a nucleic acid, generating mononucleotides, whereas an endonuclease attacks internally, generating oligonucleotides) a. require all four deoxynucleotide triphosphates (dNTPs) b. does proofreading using its 3'-5' exonuclease activity c. synthesize RNA in the 5' to 3' direction d. require a primer to initiate synthesis
c
How many tRNA aminoacyl synthetases are found in every cell? a. between 10 and 20 b. 10 c. 20 d. 15
c
Promoters __________ a. can be found either upstream or downstream of genes b. tend to be G+C rich c. are the sites in DNA where RNA polymerase binds to initiate transcription d. are required for elongation of transcription
c
The covalent bond between the "f" and the "Met" in fMet-tRNA is a. an ester bond b. an ether bond c. a peptide bond d. a mixed anhydride bond
c
There are more tRNA species than amino acids because a. wobble allows some but not all tRNAs to interact with multiple codons b. every codon needs a different tRNA c. most amino acids are encoded by multiple codons d. some codons encode multiple amino acids
c
To be accurate, the aminoacyl-tRNA synthetase for threonine should be able to distinguish threonine from serine and valine. Which of the following statements provides a likely explanation how serine is prevented from being attached to the threonine tRNA? A) Serine won't fit into the acylation site of the enzyme and thus won't be attached to the tRNA. B) Serine is phosphorylated, giving it a negative charge that is repelled by negative charges in the acylation site of the enzyme. C) The smaller serine fits into the enzyme's editing site and will be hydrolyzed if attached to the tRNA, but threonine won't fit into the editing site and won't be hydrolyzed. D) A positively charged metal ion in the enzyme active site coordinates threonine through its hydroxyl group, but can't coordinate serine since it lacks a hydroxyl group. E) The enzyme can't distinguish serine from threonine, but it doesn't really matter at the protein level because they are structurally so similar.
c
Transcriptionally active chromatin tends to be (These concern the last 2 slides of Lecture 19, and will be covered on Monday before Lecture 20 begins.) a. highly condensed b. rich in histone H1 c. acetylated d. methylated
c
What are two ways in which lysine acetylation on histone tails affects transcription? Choose only ONE answer. A) By increasing the affinity of histones for DNA and by decreasing histone binding to the preinitiation complex (PIC). B) By reducing the affinity of histones for DNA and by stimulating mRNA splicing. C) By reducing the affinity of histones for DNA and by recruiting other factors that remodel nucleosomes and change the transcriptional accessibility of nearby genes. D) By reducing the affinity of histones for DNA and by increasing DNA methylation. E) By increasing the affinity of histones for DNA and by recruiting the mediator complex.
c
What is the role of the Shine-Dalgarno sequence? a. It acts as a signal for the termination of translation. b. It marks the polypeptide for translocation into the lumen of the endoplasmic reticulum. c. It guides the 30S ribosome to the initiating AUG of the mRNA. d. It targets proteins for degradation.
c
Which of the following are required during DNA replication? I. NTPs II. dNTPs III. Mg2+ ions IV. Ca2+ ions A. I, II B. II, III C. I, II, III D. II, IV E. I, III, IV
c
Which of the following is TRUE about base excision repair? I. Backbone distortions are recognized, not specific chemical groups or modifications. II. DNA polymerase removes the incorrect base III. The backbone is cleaved during the repair process. IV. DNA glycosylase removes a sugar-phosphate group. A) II, III, IV B) I, III C) III D) II, IV E) I, III, IV
c
Which of the following is not a form of RNA processing of eukaryotic RNA polymearse II primary transcripts? a. polyadenylation b. 5' end capping c. proteolytic cleavage d. splicing
c
Acetylation of the N-terminal tail of histone H4 prevents an interaction with a neighboring nucleosome and can lead to activation of transcription. What region of the nucleosome is likely responsible for this interaction with the N-terminal tail of H4? A) Methylated DNA B) Methylated histone C) The N-terminal tail of a neighboring H4 histone D) An acidic region in the core of the nucleosome E) A basic region in the core of the nucleosome
d
Consider the following DNA sequence: 5'-CATTTCATGACAGACCAGTAT-3' Which of the following mutations would be predicted to cause a premature stop codon in the section of the mRNA encoded by the sequence shown above? A) Deletion of the 5' C B) Deletion of the 3' T C) Deletion of the 5' CA D) Insertion of a C after the 3' T E) Deletion of the 5' CAT
d
DNA damage caused by sunlight can be repaired by __________________ 1. base-excision repair 2. DNA photolyase 3. mismatch repair 4. nucleotide-excision repair a. 3, 4 b. 2 c. 1, 3, 4 d. 2, 4
d
DNA ligase can be activated by which of the following? 1. the coupled hydrolysis of NAD+ to NMN+ + AMP 2. the coupled hydrolysis of ATP to AMP + PPi 3. the coupled hydrolysis of GTP to GMP + PPi a. 1 only b. 1, 3 c. 3 only d. 1, 2
d
Enhancers are DNA sequences that enhance transcription of genes a. in prokaryotes and lower eukaryotes b. only if located within a hundred base pairs of a gene's transcription start site c. only if located upstream from a gene's transcription start site d. regardless of their orientation in the DNA
d
Eukaryotic polysomes do not contain a. ribosomes b. mRNA c. polypeptides d. transcriptional termination factors
d
How do eukaryotes replicate their genomes in a reasonable time frame, even though their DNA genomes are considerably larger than those of bacteria? a. The rate of replication fork movement in eukaryotes is greater than in E. coli. b. Eukaryotic DNA polymerases synthesize DNA at a greater rate than do E. coli DNA polymerases. c. Eukaryotic DNA replication is bidirectional and prokaryotic DNA replication is unidirectional. d. Eukaryotic chromosomes have multiple origins of replication.
d
In all known life forms (prokaryotes, eukaryotes, and archaea) the peptidyl transferase activity that catalyzes peptide bond formation is found in a. the tRNAs. b. the small ribosomal subunit c. the EF-G protein. d. the large ribosomal RNA.
d
Reverse transcriptase is the major replicative polymerase of the HIV virus. During polymerization by reverse transcriptase, what functional group on the newly synthesized chain serves as the acceptor for additional bases? A. 3' phosphate B. 5' phosphate C. 2' hydroxyl D. 3' hydroxyl E. 5' hydroxyl
d
Signals that define the beginning and end of protein synthesis are contained in a. tRNA b. rRNA c. protein d. mRNA
d
The 3' end of the 16S bacterial ribosomal RNA (rRNA) has the sequence 5'-ACCUCCUUA-3'. You notice that this sequence is complementary to a sequence about 10 bases upstream of the start codon of most bacterial genes. What would be the direct effect of deleting the above sequence from the 3' end of the rRNA molecule? A) Transcription of most bacterial genes will increase. B) Transcription of most bacterial genes will decrease. C) Translation of most bacterial genes will increase. D) Translation of most bacterial genes will decrease. E) There will be no effect of deleting this sequence.
d
Which ONE of the following spaces is not topologically equivalent to the others? A) The inside of the endoplasmic reticulum B) The inside of the Golgi C) The inside of the lysosome. D) The nucleus. E) The outside of the cell.
d
Which ONE of the following statements about the synthesis of the lagging strand is FALSE? A. RNA primers are made by a DNA-dependent RNA polymerase called Primase. B. Okazaki fragments are synthesized by DNA Pol III. C. Okazaki fragments are synthesized in the 5' - 3' direction. D. Lagging strand synthesis does not require a sliding clamp. E. During lagging strand synthesis, DNA polymerase is moving in the opposite direction from the movement of the replication fork.
d
Which of the following best accounts for the large number of different cell types in multicellular organisms? A) Different types of cells have different genes. B) Different types of cells have different subcellular compartments. C) Rates of DNA damage are different in different cell types. D) Different genes are expressed in different cell types. E) Different types of cells use different genetic codes.
d
Which of the following does NOT consist of both RNA and protein? A) The signal recognition particle (SRP) B) The ribosome C) The spliceosome D) The Sec61 preprotein translocase E) Telomerase
d
Which of the following enzymes builds a polynucleotide chain in a reaction that does NOT use a nucleic acid template? A) telomerase B) primase C) RNA pol I D) poly-A polymerase E) DNA pol I
d
Which of the following is TRUE about nucleotide excision repair? I. Distortions to the DNA double helix are recognized rather than specific chemical groups or modifications. II. Defects in nucleotide excision repair often cause skin cancer in humans III. The DNA backbone is cleaved twice during the repair process. IV. DNA glycosylase enzymes remove damaged nucleotides. A) I, II B) I, III C) II, IV D) I, II, III E) I, II, III, IV
d
Which of the following is false? Class I and Class II tRNA aminoacyl synthetases a. have similar but not identical catalytic mechanisms b. recognize opposite "faces" of tRNA c. aminoacylate different ribose hydroxyls d. charge tRNAs with some of the same amino acids
d
Which of the following is not a feature of tRNA molecules? (You can do this by elimination, or go back to Lecture 19 on transcription... even career molecular biologists and biochemists often have trouble remembering which eukaryotic RNA polymerases transcribe which RNAs!) a. They are linked to amino acids at their 3' end b. They contain many unusual bases. c. About half the nucleotides in tRNA are base-paired. d. They are synthesized by RNA polymerase II. e. Each is a single chain between 73 and 93 ribonucleotides.
d
Which of the following mutations in a eukaryotic protein coding gene is LEAST likely to impair the function of the protein? A) An insertion of one base in an exon B) A deletion of one base in an exon C) An insertion of two bases in an exon D) An insertion of three bases in an exon E) A base substitution in the most 3' base of an intron
d
Which of the following mutations in the DNA of a eukaryotic protein-coding gene are likely to impair the function of the protein encoded by this gene? I. An insertion of one base in the middle of an exon II. An insertion of one base in the middle of an intron III. A point mutation that changes the first base of an intron from G to A. IV. A mutation of a TGG codon to TGA. A) I, II B) II, III C) I, II, IV D) I, III, IV E) I, II, III, IV
d
Which of the following reactions requires an RNA primer? I. DNA synthesis on the leading strand II. DNA synthesis on the lagging strand III. DNA ligation A. I B. II C. II & III D. I & II E. I, II, & III
d
Which one of these explains why many prokaryotes have "operons" that are transcribed as a single RNA but encode several different (often functionally related) proteins? a. prokaryotic mRNAs circularize using initiation factor IF3 b. prokaryotic mRNAs begin with a 5' triphosphate c. fMet-tRNA enables prokaryotic ribosomes to initiate with the tRNA in the A site d. prokaryotic ribosomes can initiate at internal AUGs using internal Shine-Dalgarno sequences
d
You discover a new form of life in Mono Lake. You find that its DNA is always singlestranded and consists of only 3 different kinds of bases, but it uses 100 different amino acids in its proteins. What is the minimal number of bases per codon in this organism to encode for its complete set of amino acids? A "codon" refers to the set of bases coding for a single amino acid. A) 2 B) 3 C) 4 D) 5 E) 34
d
How can one tRNA recognize multiple codons? A) If the 3' base of the anticodon is a cytosine, it can bind to codons with a 5' guanine or uracil B) If the 5' base of the anticodon is a uracil, it can bind to codons with a 3' adenine or thymine C) If the 5' base of the anticodon is an inosine, it can bind to codons with a 3' uracil, cytosine, or guanine D) If the 3' base of the anticodon is an inosine, it can bind to codons with a 5' uracil, cytosine, or adenine E) If the 5' base of the anticodon is a guanine, it can bind to uracil or cytosine.
e
In most organisms, replication proceeds in a ________ manner from the ________. a. discontinuous; chromosome ends b. discontinuous; leading strand c. unidirectional; chromosome ends d. bidirectional; chromosome ends e. bidirectional; replication origin
e
Let's say you come across a cytosine in the DNA that has been modified by methylation on its 5 position. Which of the following is TRUE? I. This is rare - very few methylated cytosines are not repaired by the DNA repair system. II. Formation of the methyl group was most likely caused by oxidative damage. III. In the 5'-3' direction, the cytosine is likely immediately adjacent to a guanine. IV. This modification could alter the binding of transcriptional activators. A) IV B) II, III, IV C) I, II, IV D) I, II, III, IV E) III, IV
e
Which of the following indicates a high rate of translation of a particular mRNA? A) Introns B) Signal sequence C) 7-methyl guanosine cap D) Enhancers E) Polysomes
e
Which of the following is NOT a mechanism cells use to reduce the occurrence of mutations? If all are used by cells to reduce the occurrence of mutations, choose (E). A) Proofreading activity by DNA polymerase. B) Direct repair of chemically modified bases. C) Excision of damaged DNA and resynthesis using the complementary strand as a template. D) Use of thymine in DNA instead of uracil E) ALL of the above mechanisms are used by cells to reduce the occurrence of mutations.
e
Which of the following molecules checks to make sure that the correct amino acid is attached to a tRNA? A) The small subunit of the ribosome B) The large subunit of the ribosome C) EF-Tu D) IF-2 E) None of the above
e
Which of the following mutations in the coding sequence of a gene would change the reading frame of that gene? A) A 3-base pair insertion combined with a 2-base pair deletion and a 2-base pair insertion. B) A 1-base pair insertion combined with a 5-base pair insertion. C) A 12-base pair deletion. D) ALL of the above mutations would change the reading frame. E) NONE of the above mutations would change the reading frame.
e
Which of the following processes is mediated by at least one reaction involving nucleophilic attack by a 3'-OH group? I. Transcription II. Splicing of introns III. Synthesis of telomeres IV. Attachment of amino acids to tRNA A) I, III B) II, III C) I, III, IV D) I, II, IV E) I, II, III, IV
e
Which of the following statements about DNA methylation is FALSE? If all the statements are TRUE, choose (E). A) DNA methylation can lead to mutations due to base mispairing. B) DNA methylation is important in bacteria for proper mismatch repair. C) DNA methylation can lead to changes in chromatin structure. D) DNA methylation can cause a decrease in transcription. E) ALL of the above statements are TRUE.
e
Which of the following statements about transcription in eukaryotes is FALSE? If all of the statements are TRUE, choose (E). A) RNA polymerase II (RNAP II) and General Transcription Factors (GTFs) together fom the pre-initiation complex (PIC) and assemble at the promoter. B) Once the pre-initiation complex (PIC) is formed, it sits on the DNA but is not able to initiate transcription until there is an activating signal. C) A helicase activity is required to unwind the DNA strands and allow for transcription. D) For efficient transcription from all RNAP II promoters, the mediator complex must act to connect transcriptional activators bound to enhancers to the core machinery bound at a promoter. E) ALL of the above statements are TRUE.
e
Which of the following synthesizes DNA in a 3' to 5' direction? A. DNA Pol I on the leading strand B. DNA Pol I on the lagging strand C. DNA Pol III on the leading strand D. DNA Pol III on the lagging strand E. None of the above
e
You set up a protein synthesis reaction in a test tube containing everything you need for protein synthesis: ribosomes, initation & elongation factors, aa-tRNAs, etc. The mRNA consists entirely of U and G nucleotides in random order. Assume that initation does not require aa-tRNA[fMet]. Which amino acids are polymerized into the resulting polypeptide? Consult the genetic code table on the first page of the exam. A) Phe, Leu B) Phe, Ser, Leu, Pro C) Cys, Val D) Pro, Thr, His, Gln, Asn, Lys E) Phe, Leu, Val, Gly, Cys, Trp
e
DNA Polymerase I has two exonuclease activities I. 5' to 3' exonuclease activity is a separate domain that digest RNA primers (or DNA) to mononucleotide ahead of the polymerase II. 3' to 5' exonuclease is near the polymerase active site and can remove a mismatch nucleotide at the growing 3' end (remove mispaired base) True or False
T
Alternative splicing enables cells to make a variety of tissue-specific protein isoforms from a single ________________ . a. protein precursor b. gene c. uncapped mRNA precursor d. fully spliced mRNA
b
Consider the following DNA sequence: 5'-CAACCGTTGATCGAC-3' Which of the following mutations would be predicted to cause a premature stop codon in the section of the mRNA encoded by the sequence shown above? A) Insertion of a T just after the 5' C B) Deletion of the 5' C C) Deletion of the 5' CA D) Deletion of the 5'CAA E) None of the above
b
DNA helicases separate the parental DNA strands at the replication fork by a. using ATP to walk along duplex DNA. b. using ATP to walk along single stranded DNA. c. using GTP to walk along duplex DNA. d. using centrifugal force of a rotary ATPase-like motor
b
DNA polymerase I (pol I) synthesizes new DNA with very high fidelity because of its a. high processivity b. 3′ → 5′ exonuclease activity. c. 5′ → 3′ exonuclease activity.
b
Okazaki fragments __________________ a. do not require a primer b. are found on the lagging strand c. are ligated together by DNA polymerase I d. require a DNA primer
b
Synthesis of telomeres requires the enzyme ______ , a specialized ______ , which copies a _____ template to make ______. a. ribotelase, ribonucleoprotein, DNA, RNA b. telomerase, ribonucleoprotein, RNA, DNA c. telomerase, deoxynucleoprotein, RNA, DNA d. ribotelase, deoxynucleoprotein, DNA, RNA
b
The poly(A) tail on eukaryotic mRNAs a. is located 20-30 nucleotides on the 5′ (upstream) side of the polyadenylation addition sequence (AAUAAA) b. does not require a template for synthesis c. begins at the site where RNA polymerase II falls off d. is synthesized by RNA polymerase II
b
What chemical group would you expect to find at the 5´ terminal position of a typical RNA primer? a. 5' N... b. 5' pppN... c. 5' ppN...
b
What does it mean when the genetic code is described as "degenerate"? a. It means that two or more anticodons can base pair with the same codon. b. It means that more than one codon can specify the same amino acid. c. It means that the translation machinery is prone to making errors. d. It means that there are fewer codons than amino acids.
b
What is the function of an N-terminal signal peptide on a protein? A) It is the site of acetylation. B) It binds to the signal recognition particle (SRP) and directs the protein to the endoplasmic reticulum. C) It targets the protein for degradation by the proteasome. D) It functions as a translation start signal. E) Both the answers (A) and (D) are TRUE.
b
Which of the following statements best describes the chemistry of peptide bond formation? A) The amino group of a free amino acid at the A site performs a nucleophilic attack on the peptidyl tRNA at the P site, leading to the transfer of this amino acid to the end of the nascent polypeptide chain at the P site. B) The amino group of the C-terminal amino acid of the polypeptide attached to the tRNA at the P site performs a nucleophilic attack on the carboxyl group of the aminoacyl tRNA at the A site, leading to the transfer of the amino acid from the A site tRNA to the end of the nascent polypeptide. C) The amino group of the amino acid attached to the tRNA at the A site performs a nucleophilic attack on the carboxyl group of the amino acid directly attached to the tRNA at the P site, leading to the transfer of the entire nascent polypeptide chain from the P site tRNA to the aminoacyl-tRNA at the A site. D) The 3' hydroxyl group of the tRNA at the A site performs a nucleophilic attack on the adenylated amino acid attached to the tRNA at the P site, leading to the transfer of the entire nascent polypeptide chain from the P site tRNA to the tRNA at the A site.
c
Which of the following statements best describes the function of enhancers in gene regulation? A) They are DNA sequences that directly bind RNA polymerase and regulate transcriptional initiation. B) They are DNA sequences that directly bind eukaryotic general transcription factors to regulate formation of the pre-initiation complex. C) They are DNA sequences that directly bind transcription factors and regulate transcriptional initiation. D) They are DNA sequences that directly bind transcription factors and regulate transcriptional elongation. E) They are mRNA sequences that directly bind initiation factors and regulate translational initiation.
c
Which of the following statements best explains why cancer rates increase as we age? A) The older we get, the more cells we have. Thus, there is a greater chance that a cell becomes cancerous. B) Metabolism is decreased as we age. Thus, there are more free radicals that damage DNA. C) As we age, we accumulate more mutations and thus have an increased likelihood of mutations in important genes that control cell division. D) Rates of cell division increase as we age. E) We don't hear as well, and thus we are less able to hear about new products that we can take to reduce the risk of cancer.
c
Which of the following statements is TRUE about transcription by RNA polymerase II? (Consult the textbook or another source if any terms are unfamiliar.) a. Elongation factors are needed for formation of a closed transcription complex b. RNA polymerase II is inhibited by rifampicin c. The phosphorylation of the carboxyl-terminal domain (CTD) of RNA polymerase is required for entry into the elongation phase of transcription d. RNA polymerase II alone is sufficient to initiate RNA synthesis
c
Which of these serves as the nucleophile for attack on the LaTeX: \alpha α ,LaTeX: \beta β phosphoanhydride bond of the incoming dNTP or rNTP of a DNA or RNA polymerase? a. 2' OH b. 5' OH c. 3' OH
c
