exam 2 v3

e. both b. and c. are correct (sense/antisense and coding/template)

Transcription involves synthesis of an RNA chain representing one strand of a DNA duplex. The strand that has the "same" sequence as the RNA product is the ________ strand and the one with the complementary sequence (to RNA) is the ________ strand

e. a and c (it disengages from the beta clamp and it cycles to a new beta clamp that has been assembled at an RNA primer-DNA template junction closer to the replication fork.)

What happens when the DNA polymerase on the lagging strand template completes the synthesis of an Okazaki fragment?

b. An enzyme made up of RNA

What is a ribozyme?

d. poly A tails

Which of the following are not transcribed from DNA? a. introns b. miRNAs c. rRNA d. poly A tails e. snoRNAs

e. both b. and d. are not true

Which of the following does not constitute a difference between intron removal in nuclear pre-mRNAs and group II introns? a. Nuclear pre-RNA introns cannot autosplice and group II introns can. b. Nuclear pre-RNA introns can autosplice but group II introns cannot. c. Nuclear pre-RNAs require spliceosome to carry out the splicing but group II introns do not. d. Nuclear splicing proceeds through a lariat formation but group II intron splicing does not. e. both b. and d. are not true

b. miRNAs are essential components of spliceosome.

Which of the following is (are) false about RNA? a. snoRNAs aid in processing pre-rRNA transcripts in the nucleolus. b. miRNAs are essential components of spliceosome. c. If it can form an appropriate 3D structure it may act as a catalyst. d. snRNAs as parts of snurps are required for splicing of all nuclear pre-mRNAs e. none of the above.

e. both c and d (intrinsic transcription terminator and Poly A tail signal)

Which of the following is a type of cis-acting element primarily "acting" in RNA rather than DNA? a. promoter b. "up" element c. intrinsic transcription terminator d. Poly A tail signal e. both c. and d.

d. New phages are produced and released while killing the host.

Which of the following is characteristic of the lytic cycle? a. Many bacterial cells containing viral DNA are produced. b. Viral DNA is incorporated into the host genome. c. The viral genome replicates without destroying the host. d. New phages are produced and released while killing the host. e. The virus-host relationship usually lasts for generations.

e. both a. and c. are false

Which of the following is false about bacterial RNA polymerase catalyzed reactions (synthesis of RNA)? a. dNTPs act as substrates b. new nucleotides are always added at the 3' end c. these reactions occur at the catalytic site located in the sigma subunit d. they can occur in the absence of sigma e. both a. and c. are false

d. they are translated into r-proteins in the cytoplasm

Which of the following is false about nuclear genes for the 3 largest rRNAs in higher eukaryotes? a. they are transcribed in the nucleolus b. each "gene" is transcribed into a large precursor RNA that needs to be cut and trimmed to give rise to 3 mature rRNAs c. they are transcribed by RNA Pol I d. they are translated into r-proteins in the cytoplasm e. none of the above is false; all are true

e. none of the above

Which of the following is false about the E. coli general sigma factor ( σ70) a. it contacts promoter directly at -10 and -35 b. mutations in sigma may suppress mutations in promoters c. removal of N-terminus allows sigma (alone) to bind promoters d. It has several DNA binding domains e. none of the above

c. RNA polymerase I transcribes 5S rRNA

Which of the following is false? a. RNA polymerase I (generally) requires only two ancillary factors for efficient initiation of transcription b. RNA polymerase I requires TBP for initiation of transcription c. RNA polymerase I transcribes 5S rRNA d. RNA polymerase I promoters are bipartite consisting of core promoter and UCE e. None of the above

c. recognition of promoters

Which of the following is not an activity of bacterial core RNA polymerase? a. unwinding and rewinding of DNA b. catalyzing addition of ribonucleotides c. recognition of promoters d. holding a newly synthesized portion of RNA product e. holding separated DNA strands

b. All pre-mRNAs are modified, not just the ones that correspond to interrupted genes

Which of the following is/are true about gene expression in eukaryotic cells? a. Transcription, translation and even transcript degradation occur almost simultaneously b. All pre-mRNAs are modified, not just the ones that correspond to interrupted genes c. Modification of pre-mRNAs is "coordinated" by the CTD of the largest subunit of RNA Pol I d. only b. and c. are true e. none of the above

a. They are made up of both protein(s) and RNA.

Which of the following is/are true of snRNPs (snurps)? a. They are made up of both protein(s) and RNA. b. They bind to splice sites at each end of the exon. c. They are involved in splicing reactions of group II introns. d. all of the above. e. only a. and c

b. RNAP III promoters usually contain positions that lie downstream of the start point

Which of the following is/are true? a. RNAP III can initiate at its promoters in the absence of any additional factors b. RNAP III promoters usually contain positions that lie downstream of the start point c. RNAP III functions primarily within the nucleolus d. all of the above e. b. and c.only

e. None of the above.

Which of the following statements about mammalian telomeres is incorrect? a. They all contain multiple copies of a short DNA sequence that is specific for each organism. b. They may protect chromosomes from degradation. c. They can be extended by an enzyme called telomerase that carries an RNA molecule that is complementary to the telomeric repeats. d. They may protect the cell from chromosomal fusions. e. None of the above.

c. It does not requires a primer.

Which of the following statements about telomerase is incorrect? a. It is a DNA Polymerase that generates single stranded DNA. b. It is a reverse transcriptase. c. It does not requires a primer. d. It dos not require a template at the end of the chromosome because it carries its own template in the form of RNA. e. None of the above.

c. RNA polymerase transcribes through the polyadenylation signal, causing proteins to associate with the transcript and cut it free from the polymerase, which continues to synthesize more "nonfunctional" RNA.

Which of the following statements best describes the termination of transcription in eukaryotes by RNA Pol II? a. RNA polymerase transcribes through a stop codon, causing the polymerase to stop advancing through the gene and release the mRNA. b. RNA polymerase transcribes through the terminator sequence, causing the polymerase to fall off the DNA and release the transcript. c. RNA polymerase transcribes through the polyadenylation signal, causing proteins to associate with the transcript and cut it free from the polymerase, which continues to synthesize more "nonfunctional" RNA. d. Once transcription has initiated, RNA polymerase transcribes until it reaches the end of the chromosome. e. It may be a, b or c. depending on a gene.

b. RNA polymerase transcribes through the terminator sequence, causing the polymerase to fall off the DNA and release the transcript.

Which of the following statements best describes the termination of transcription in prokaryotes? a. RNA polymerase transcribes through a stop codon, causing the polymerase to stop advancing through the gene and release the mRNA. b. RNA polymerase transcribes through the terminator sequence, causing the polymerase to fall off the DNA and release the transcript. c. RNA polymerase transcribes through an intron, and the snRNPs cause the polymerase to let go of the transcript. d. Once transcription has initiated, RNA polymerase transcribes until it reaches the end of the chromosome. e. RNA polymerase transcribes through the polyadenylation signal, causing proteins to associate with the transcript and cut it free from the polymerase.

e. The ends of eukaryotic and prokaryotic chromosomes comprise telomeres.

Which of the following statements is false when comparing prokaryotes with eukaryotes? a. The prokaryotic chromosome is usually circular, whereas eukaryotic nuclear chromosomes are linear. b. Prokaryotic chromosomes usually have a single origin of replication, whereas eukaryotic chromosomes have many. c. The rate of elongation during DNA replication is higher in prokaryotes than in eukaryotes. d. Prokaryotes produce longer Okazaki fragments during DNA replication than eukaryotes. e. The ends of eukaryotic and prokaryotic chromosomes comprise telomeres.

d. successive alternative ribosomes

Which of the following strategies is not used by phages to organize the expression of their genes into regulatory cascades? a. successive alternative sigma factors b. phage specific RNA polymerase(s) c. antitermination proteins d. successive alternative ribosomes e. All of the above may be used by different phages

c. Topoisomerase

Which protein/enzyme is used to decatenate E. coli chromosomes after replication?

c. A single base error at a splice junction will change the reading frame and result in mRNA mistranslation.

Why must RNA splicing be absolutely precise?

c. DNA Polymerase I / 5' to 3' exonuclease activity

#3 indicates __________ that is a single polypeptide protein with several enzymatic activities. One of these activities is a ___________________ that could be used in nick translation to label double stranded DNA molecules.

d. undergo a reduction in chromosome length during each cell cycle.

A eukaryotic cell lacking a telomerase activity would

c. has 10

A gene with 11 exons ________ introns

a. group I introns were involved

A scientist studying a "new" organism isolated splicing intermediates, representing excised intron(s), and determined their structure. These molecules were linear and all had a G at the 5' end. From what you know about splicing what is the most likely explanation of these results?

c. many nucleotides may be present within 5' and 3'UTRs.

A specific prokaryotic transcription unit that is 5,000 nucleotides long uses only 1,200 nucleotides to make a protein consisting of 400 amino acids. This is best explained by the fact that

c. Poly A tail

All mRNAs contain all of the following except: a. 3' - UTR b. coding sequence c. Poly A tail d. 5'-UTR e. c. and d.

c. RNA polymerases to initiate transcription using a new (different) set of promoters

Alternative sigma factors are used as a means to regulate gene expression in bacteria. A replacement of one sigma factor for another on bacterial RNA polymerase will enable __________ .

d. Enhancer

An eukaryotic DNA sequence containing regulatory elements (binding sites for transcription factors) that can influence transcription activation from a distant location that may even be downstream from the regulated gene is called ______ .

c. trombone model

As replication proceeds, the lagging strand of DNA is looped back on itself so that it has the same orientation as the leading strand template; the looped DNA repeatedly grows and shortens during lagging strand replication. This model is often referred to as the _________.

d. G and T

Assume that the following single strand of DNA was synthesized using standard dATP, dGTP, dCTP, and dTTP precursors; however, the innermost phosphate (alpha phosphate) of all the dATPs was labeled with 32P. 3'—CTAGTAT—5' Assume also that the strand was degraded to completion by the enzyme spleen diesterase. Spleen diesterase cleaves DNA at the covalent bond that connects the 5' carbon of the sugar to the phosphate. Which of the resulting nucleotide(s) might now carry the 32P?

d. 3-2-4-1-5

Bacterial RNA polymerase passes through several steps prior to elongation. These steps include 1. release or change of association with sigma, 2. formation of an open binary complex. 3. formation of a closed binary complex. 4. abortive initiation. 5. promoter clearance. The correct sequence of events is:

d. kinase/TFIIH

Before RNA polymerase II can leave the promoter its CTD needs to be phosphorylated by the ________ activity of ________.

a. closed/open

Concerning the promoters recognized by general sigma factor (σ70) in E. coli, mutations in the -35 region tend to affect the formation of the ______ complexes and the mutations in the -10 region affect the formation of the ______ complexes.

e. spliceosome/introns/exons

During splicing of nuclear pre-mRNAs the splicing apparatus called _________ has to be assembled in a specific sequence in order to precisely remove all of the _________ and splice together the ___________.

d. 5'-5' triphosphate bridge

How would one describe the bond that holds the inverted methylguanosine cap on the 5' end of a mature mRNA?

d. RNA polymerase to read through transcription terminators

If antitermination is utilized to regulate gene expression, this mechanism enables _____

e. positions closest to letters (d) and (e)

If arrow outside the bubble represents the 5' end of the strand it is nearest, where is(are) the most likely place(s) to see the Okazaki fragments?

e. none of the above because bases are never assigned a value of 0 (zero)

If the position of a nucleotide (base) in (or near) a transcription unit is assigned the value of 0 (zero), this base is _________.

a. DnaA

In order to create the replication forks (initiate DNA replication) in E.coli, oriC needs to be "activated". The first step in this process involves binding of _______ proteins to oriC and melting of short stretches of DNA before other proteins can join the complex. ________ protein is required only at oriC.

d. 5' end.

In the figure above the correct designation for the structure or position labeled C is:

e. both b. and c. (composed of DNA and RNA and called okazaki fragments)

In the figure above the structures represented by the letter E (black and white) are:

d. Inr/T AF/TFIID

Many of the RNA polymerase II promoters are TATA-less but they are still recognized by the same specific GTF in a sequence specific manner. These promoters must contain ______ plus DPE or DCE that are all recognized by a _______ subunit of ________.

d. T A T A box/TFIID/TBP

Many of the RNA polymerase II promoters contain ______ , an element generally present at a "fixed" distance upstream from startpoint. When present, this element is bound by ________ via its subunit called _________.

b. TBP

One of the RNA polymerase I ancillary factors, SL1, consists of four proteins. One of its component proteins is also required for the initiation by RNA polymerase II and RNA polymerase III as a part of a "positioning" factor. This protein common to all three "positioning" factors is called _______.

c. the methylation state of As at oriC

One of the factors that may affect initiation of DNA replication in E.coli

b. 3' to 5'; 3'

RNA polymerase moves along the template strand of DNA in the ____ direction, and adds nucleotides to the ____ end of the growing transcript.

a. only A. is true

Statement A. An origin (e.g. oriC) is a cis -acting element that can support replication of any DNA sequence joint to it (in appropriate cell). Statement B. Some bacterial chromosomes (genomes) that are single replicons may contain multiple origins to increase the efficiency of DNA replication.

c. both A. and B. are true

Statement A. Prokaryotic intrinsic transcription terminators consist of two features that are both required for termination to occur: a hairpin that is followed by a run of Us Statement B. Eukaryotic RNA Pol. I and III terminate transcription right after specific terminator sequences are transcribed similarly to prokaryotic RNA Pol.

d. both A. and B. are false

Statement A. Some of the nuclear eukaryotic RNA polymerases do not require any accessory factors for recognition of their promoters and the initiation of transcription. Statement B. Recognition and stable binding to promoters by prokaryotic RNA polymerases requires only core subunits.

d. a separate RNA primer.

The 5' end of each Okazaki fragment begins with:

c. extend the lagging strand template at the end of each chromosome.

The function of eukaryotic telomerase is to

d. helicase/A TP

The hexameric protein complex indicated by #5 is a __________ . It uses ___________ as an energy source.

d. 6

The location of topoisomerase is indicated by # ___

b. A purine start point, -10 hexamer composed only of As and Ts and -35 hexamer separated from -10 region by 17-19 nucleotides

The optimal promoter for the RNA polymerase holoenzyme with the general sigma factor in E. coli consists of the following features:

b. 2

The sliding clamp (beta clamp) would be found associated with structure # ___________ and greatly increase its processivity.