Mastery Questions

True or False: In eukaryotes, RNA polymerase I transcribes all of the rRNA components.

False, all three eukaryotic RNA polymerases contribute to synthesis of rRNA even though RNA polymerase I is the primary synthesizer

True or False: RNA polymerase transcribes all DNA sequences at an equal rate.

False, because some DNA sequences are harder to transcribe that others. Leads to pausing and backtracking

True or False: The only function of Uracil-DNA N-glycosylase is to remove dUMP residues in DNA that have been arisen by deamination of cytosine.

False, dUMP may be incorporated into DNA via deamination of cytosine or simple mismatch of A-U instead of A-T.

True or False: Peptide bond formation requires GTP hydrolysis

False, no GTP required to transfer peptide chain from peptidyl-tRNA to aminoacyl-tRNA in A site

True or False: In eukaryotes, genes encoding enzymes for metabolic pathways often exist as operons of several genes with a single regulatory region to provide coordinate regulation of all genes required for the pathway.

False, the enzymes are not operons themselves. The operon model is regarding the synthesis of the RNA molecules from the genes.

True or False: All processing of eukaryotic mRNAs take place in the nucleus after transcription has been completed.

False, translation takes place in cytosol.

True or False: Aminoacyl-tRNA synthetase does not contribute to the fidelity of transcription

False.

True or False: Site-specific recombination generally requires longer homologous sequences than does homologous recombination.

False.

True or False: The genetic code is universal for all organisms and organelles.

False.

In eukaryotes a set of ________ function in a comparable manner to the σ subunit of E. coli RNA polymerase.

Transcription factors

Splicing of mRNA occurs in spliceosomes and chemically is a series of _________ reactions.

Transesterification

The 5' cap added to eukaryotic mRNA serves to stabilize the mRNA and assists in the efficiency of ______.

Translation

Differences between eukaryote and prokaryote translation include the 40s ribosome recognizing the __________ rather than a Shine-Dalgarno sequence and the N-terminal amino acid is ___________.

7-methyguanine cap, methionine

Termination of translation occurs when a stop codon is translocated into the _________ site of the ribosome.

A

A partial diploid containing a wild type allele for lacI and a lacI mutant was unable to bind the inducer would: A. always show low levels of β-galactosidase gene expression B. show normal induction in the presence of an inducer C. express β-galactosidase at all times D. only show normal induction in the presence of an inducer in the absence of glucose E. show induction in the presence of an inducer in the presence of glucose

A, because lacI is the repressor gene. A repressor gene that cannot bind to an inducer will remain bound to the operator, inhibiting gene transcription

Antibiotics that inhibit translation are useful because: A. The translational machinery of eukaryotes is sufficiently different to that of bacteria B. Microorganisms can develop resistance to other antibodies C. Antibodies resistance genes are often carried on plasmids rather than the bacterial chromosome D. Different antibodies can inhibit different steps of translation E. They do not cross the cell membrane in higher animals

A.

Which of the following statements is FALSE? A. RNA polymerase II is responsible for the transcription of genes encoding protein-coding sequences only B. Many promoters recognized by RNA polymerase II contain regulatory elements several kbp upstream of the initiation site C. TFIIB has a role of converting a closed-promoter into an open-promoter complex D. The C-terminal domain of the largest subunit of RNA poly II undergoes extensive phosphorylation prior to transcription elongation E. A multi-protein complex is involved in communication between upstream control elements and proteins bound at the promoter

A. because RNA polymerase II isn't just responsible for mRNA synthesis. It also synthesizes some rRNAs

High levels of histone ________ correlate with high levels of transcriptional activity.

Acetylation

Transcriptionally active chromatin usually contains __________ histone, while ________ is normally inhibitory to transcription.

Acetylation, methylation

Conformation changes in the cAMP receptor protein upon binding to cAMP trigger _________ of the lac operon in the presence of lactose.

Activation

The physiological inducer of the lac operon is ____________.

Allolactose

Which of the following statements is FALSE? A. There does not need to be as many different tRNA types as there are codons B. The modified bases in the tRNAs are added during transcription C. The amino acid is attached at the 3' terminus of the tRNA D. The 3D structure of all tRNA molecules are such that they fit equally well into the ribosome E. tRNA exhibits unusual base paining including single bases pairing with two others

B, because modified bases are added through post-transcriptional modifications

Which of the following is FALSE when comparing DNA poly III and RNA polymerase? A. There are more copies of RNA polymerase in the cell B. DNA poly III is more processive C. RNA polymerase makes more errors D. RNA polymerase has a much slower kcat E. RNA polymerase does not need a primer

B.

O6-methylguanine has a high probability of base pairing with thymine to result in a post-replication mutation from a GC base pair to: A. TA B. AT C. CG D. GT E. TC

B. A-T Explanation: We start with G-C. G is methylated to mG. So, mG-C is the new mutation pair. This pair undergoes replication resulting in mG-T (because mG only has 2 hydrogen bonds available) and C-G. Upon the next round of replication, parent pair mG-T produces mG-T (because mG can only pair with T) and A-T because T pairs with A. So, parent strand mG-C will eventually lead to inclusion of A-T in DNA.

Which of the following is INCORRECT when considering the lac repressor? A. It is a tetramer of two dimers B. Binding to the operator site is cooperative C. Binding to each dimer is to different regions of the operator D. Binging of inducer forces the DNA-binding helices apart so they cannot contact the DNA-binding sites E. It is an allosteric protein

B. because binding a repressor to an operative does not activate transcription

Which of the following is NOT correct when considering the initiation of transcription in E. Coli? A. The sigma subunit of RNA polymerase makes strong contacts with the -10 region of promoters B. Only the -10 region of the promoter is required C. DNA melting near the transcription start site is essential for promoter recognition D. The phosphodiester bonds that are formed are not stable until about 10 nucleotides have been incorporated E. The RNA polymerase contacts about 50 bps of DNA

B. because both the -10 region and -35 region is required

After promoter clearance by RNA polymerase II: A. all associated factors remain bound to the polymerase for elongation B. a subset of factors remain at the promoter region C. no further elongation factors are acquired by the polymerase D. no further chromatin remodeling is required E. transcription continues until the polymerase reaches the poly(A) tail

B. because only the sigma factor dissociates from RNA polymerase II after the initial 10 nucleotides are incorporated

Which of the following statements about translation elongation in bacteria is TRUE? A. Charged amino acids are escorted to the A site of the ribosome by an initiation factor B. The growing polypeptide chain is moved from the A site to the P site before peptide bond formation C. GTP hydrolysis occurs after moving the aminoacyl-tRNA into the A site and before peptide bond formation D. The entire peptidyl-tRNA is translocated from the P site to the A site during peptide bond formation E. The uncharged tRNA leaves from the E site as the ribosome moves one codon in the 5' direction

C, because GTP is hydrolyzed with EF-Tu-GTP placing aa-tRNA in the A site

Which of the following BEST describes catabolite repression of the lac operon? A. The operon is transcriptionally inactive in the absence of lactose B. The operon is transcriptionally inactivated by a repressor protein which binds to glucose C. The operon is transcriptionally active when an activator protein binds to the promoter in the absence of glucose D. Glucose is the preferred energy source for E.Coli E. The operon is repressed by its protein products

C.

Strand-displacement in homologous recombination in E. Coli is facilitated by: A. the RecBCD complex B. ss-binding protein C. RecA D. RuvC E. the chi structure

C. RecA

The SOS response to DNA damage in bacteria is error-prone because: A. It uses DNA polymerase that lacks 3' exonuclease activity B. It is an inducible system C. The polymerases used lack 3'exonuclease activity D. More than one polymerase can be used to repair the damage E. It is stimulated by ultraviolet light that causes mutations

C. The polymerases used lack 3'exonuclease activity

Which of the following types of DNA damage cannot be repaired by base excision repair? A. Depurination B. Cytosine deamination C. Thymine dimer D. Single-strand break E. Base oxidation

C. Thymine dimer Explanation: Thymine dimer repaired via nucleoside excision repair

Degradation of bacterial mRNAs occurs: A. from the 3' end B. largely by the activity of non-specific nucleases C. from the 5' end D. relatively slowly E. from both 3' and 5' ends at the same time

C. from the 5' end

Translation is an RNA-directed process whereby amino acids are specified by ________ on the mRNA, which are complementary to __________ on aminoacyl tRNAs.

Codons, anticodons

Alignment of conserved sequences in promoters recognized by E. coli RNA polymerase revealed two ________ sequences upstream of the transcribed region, which are separated by similar lengths of DNA.

Consensus (similarly structured -10 and -35 regions)

In the secondary structure of rRNA, the regions of self-complementary are highly _________.

Conserved

____________ mutants of the lac operon express β-galactosidase at high levels in the absence of an inducer, while _________ mutants of the lac operon express only low levels of β-galactosidase even in the presence of inducer.

Constitutive, noninducible

Which of the following BEST describes the SOS response? A. DNA damage by UV light causes a lambda lysogen to be induced to the lytic life cycle B. It is an error prone DNA repair system C. Activation of RecA by sensing DNA damage and single-stranded DNA D. Coordinated activation of a set of unlinked genes whose protein products will collectively help the cell to respond to environmental damage E. Transcriptional depression by proteolytic cleave of the LexA repressor

D.

Which of the following BEST explains the "wobble" hypothesis proposed by Francis Crick? A. The genetic code is degenerate in that most amino acids have more than one codon B. The genetic code is ambiguous in that each codon can specify more than one amino acid C. The anticodon can pair wit any part of the corresponding codon D. The 5' base of the anticodon can make non Watson-Crick hydrogen bonds with several different bases at the 3' position of the codon E. Inosine can pair up with A, U, or C

D.

The dam methylase (MutHLS) has a role in which of the following DNA repair systems? A. Base-excision repair B. Nucelotide excision repair C. Non-homologous end-joining D. Mismatch repair E. Homologous recombination

D. Mismatch repair

Which of the following statements about E. coli RNA polymerase is INCORRECT? A. It has 5 different subunits B. The sigma subunit can be dissociated easily from the rest of the enzyme C. The sigma subunit is responsible for accurate determination of transcription start rates D. Without the sigma subunit, the enzyme has no RNA polymerase activity E. The sigma subunit has a role in regulation of transcription

D. is incorrect because E. Coli RNA polymerase can bind to other sites on the DNA The sigma factor directs the polymerase to the correct region that requires transcription

The affinity of the lac repressor for DNA ________ markedly when the inducer binds to the lac repressor.

Decreases

Which of the following BEST describes transcriptional regulation of the lac operon in E. Coli? A. On in the presence of lactose B. On in the presence of lactose and glucose C. Off in the presence of glucose D. On in the absence of lactose and presence of glucose E. On in the presence of lactose and absence of glucose

E

Which of the following statements about initiation of translation in bacteria is FALSE? A. fMet-tRNA is the only charged tRNA that can bind to the 30S subunit on its own B. The formyl group is transferred to Met-tRNA fMet from 10-formyl-tetrahydrofolate C. Three initiation factor proteins are required to bind the mRNA and initiator tRNA to the 30S ribosome D. Pairing between mRNA and rRNA places the initiation codon next to the P site in the ribosome E. The complete 70S initiation complex ready to receive a second charged tRNA is assembled without any GTP hydrolysis

E, because the removal of IF factors and the reassembly of 70S requires GTP hydrolysis

The greater complexity of humans compared to worms and flies is due to: A. a greater number of genes B. higher levels of alternative splicing C. a much greater number of transcriptional factors D. chromatin structure E. combinatorial regulation by a greater number of transcription factors

E.

Which of the following applies only to prokaryotic proteins? A. Secreted proteins have signal sequences in their N-terminal regions B. Some proteins are covalently modified after translation C. Hydrophilic proteins are able to either transverse or become embedded in hydrophilic membranes D. Some proteins are synthesized on polyribosomes E. Translation is coupled to transcription

E.

Which of the following types of post-transcriptional processing does NOT occur for bacterial tRNAs? A. Exonuclease cleavage B. Endonuclease cleavage C. Non-template directed addition of bases D. Methylation of bases E. Addition of a phosphate group to the 5' end

E.

Nucleotide excision repair: A. Involves a multisubunit enzyme B. Preferentially repairs genes that are being actively transcribed C. Involves making nicks on either side of a DNA legion D. Uses helicase, polymerase and ligase to repair the DNA E. All of the above

E. All of the above

Which of the following enzyme activities is NOT used in base excision repair? A. Glycosylase B. Apyriminidic endonuclease C. Deoxyribose-5-phosphatase D. DNA polymerase E. Helicase

E. Helicase

Which of the following mechanisms is NOT involved in the generation of antibody diversity? A. Recombination with excision of DNA between a V gene sequence and a J sequence B. Splicing out of RNA sequences between a J region and a C region C. Somatic hypermutation D. Non-homologous end joining and DNA repair E. Transposition

E. Transposition

Alternative splicing can: A. be tissue-specific B. produce proteins with different functions from the same gene C. contribute to temporal control of gene expression D. produce mRNAs that are nonfunctional E. all of the above

E. all of the above

True or False: Bacteria cannot use homologous recombination for DNA repair as they only have a single copy of their genome.

False. Bacteria may use daughter-strand gap repair to continue replication if there is a damage site in the parent-strand.

True or False: Photoreactivation using DNA photolyase is responsible for direct repair of thymine dimers in all organisms.

False. Explanation: Photolyase is the enzyme responsible for fixing DNA damage due to UV radiation. ONLY IN BACTERIA (E. Coli)

Base excision repair starts with cleavage of the _________ between the damaged base and the deoxyribose.

Glycosidic bond

The direct DNA repair enzymes DNA photolyase and O6-alkyguanine alkytransferase are unusual in that they are ________ after one catalytic cycle.

Inactivated

An ____________ is a sequence within an mRNA that is bound by stop and start codons that can be continuously translated.

Open reading frame

All the tRNA genes are transcribed by ________ in eukaryotes.

RNA polymerase III

The lambda repressor is inactivated by proteolytic cleavage stimulated by the _________ protein.

RecA

The lambda phage genome is inserted into the E. Coli genome in the lysogenic pathway by the use of _________ recombination.

Site-specific

The anticodon ends of tRNAs contact the _______ subunit and the acceptor ends contact the _________ subunit of the ribosome.

Small, large

Most _______ of transcription in prokaryotes is based on a weakened interaction due to ______ base pairing between the template and transcript as well as a stable stem loop structure in the nascent transcript which eliminates base pairing between the template and transcript upstream of the AU interaction.

Termination, AU

________ and bulky adducts on DNA can be repaired using the nucleotide excision repair process.

Thymine dimers

True or False: A partial diploid containing a wild type allele for lacO and a lacO mutant that was unable to bind to the lac repressor would always express β-galactosidase.

True

True or False: Catabolite of glucose repression of the lac operon is a regulatory system, which depends on the levels of cAMP in the cell

True

True or False: Eukaryotic transcription normally takes place on a chromatin template at nuclease-accessible sites.

True

True or False: Rho-dependent termination of transcription makes use of a hexameric protein, which has RNA-DNA helicase activity.

True

True or False: The Helix-turn-helix is a common protein motif that is able to interact with DNA in the major grooves by both electrostatic and specific interactions between amino acids of the helix and the bases of the DNA.

True

True or False: The bacterial SD-sequence aligns the mRNA with the 16S rRNA to start translation at the correct position.

True

True or False: The lambda repressor can as a transcriptional activator as well as a repressor.

True

True or false: Homologous recombination occurs by nicking followed by strand invasion, ligation, then branch migration.

True

True or False: In bacteria, mRNA, tRNA, and rRNA are all transcribed by the same RNA polymerase.

True.

True or False: In bacteria, post-transcriptional processing of pre-rRNA species can yield mature tRNAs.

True.

True or False: Termination of translation requires GTP hydrolysis and direct interaction of a release factor with a termination codon.

True.

True or False: Transcription-coupled repair usually repairs the template strand.

True.

The different sensitivities to the toxin ________ revealed that eukaryotes have three distinct RNA polymerases for synthesis of mRNA, rRNA, and small RNAs including tRNA and the 5S species of rRNA.

α-amanitin