Molecular Genetics Test 2

There are several repair systems in organisms to fix UV radiation "mutations". Which is the only mechanism used by humans?

NER

what is characteristic of the lytic cycle?

New phages are produced and released while killing the host.

what do mRNA's not contain?

Poly A tails

RNA polymerase and DNA polymerase differs in that

RNA polymerase can initiate RNA synthesis, but DNA polymerase requires a primer to initiate DNA synthesis.

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

RNA polymerase to read through transcription terminators

what statement best describes the termination of transcription in eukaryotes by RNA Pol II?

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.

What best describes the termination of transcription in prokaryotes?

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

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 __________ .

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

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 _________.

T A T A box/TFIID/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 _______.

TBP

The 5' end of each Okazaki fragment begins with:

a separate RNA primer.

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

sense/antisense or coding/template

What is not transcribed from DNA

poly A tails

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 ___________.

spliceosome/introns/exons

What is not an activity of bacterial core RNA polymerase?

recognition of promoters

Individuals with the disorder xeroderma pigmentosum are hypersensitive to sunlight because their cells have an impaired ability to

remove pyrimidine dimers by NER pathway

the best term to describe the extension of lagging strand template at vertebrate telomeres is

reverse transcription

What strategy is not used by phages to organize the expression of their genes into regulatory cascades

successive alternative ribosomes

In transcription-coupled repair (TCR), how is the presence of a lesion thought to be detected?

the lesion is signaled by a stalled RNA polymerase

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

the methylation state of As at oriC

DNA is composed of two strands, only one of which typically is used as a template for RNA synthesis. By what mechanism is the correct strand chosen?

the promoter acts to aim (position) the RNA polymerase.

Tobacco mosaic virus (TMV) has RNA rather than DNA as its genetic material. lets say that there is a very similar virus that has DNA as a genetic material and it is called TMV-related. In a hypothetical situation where DNA from a TMV-related viris was mixed with proteins from TMV the result could be a "hybrid" virus. If that hybrid virus were able to infect a cell and reproduce, what would the resulting offspring viruses be like?

the tobacco mosaic related DNA viruses (TMV-related)

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 _________.

trombone model

A eukaryotic cells lacking a telomerase activity would

undergo a reduction in chromosome length during each cell cycle.

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

- It disengages from the beta clamp. - It cycles to a new beta clamp that has been assembled at an RNA primer-DNA template junction closer to the replication fork.

What does not constitute a difference between intron removal in nuclear pre-mRNAs and group II introns?

- Nuclear pre-RNA introns can autosplice but group II introns cannot. - Nuclear splicing proceeds through a lariat formation but group II intron splicing does not.

What is true of mammalian telomeres `

- They all contain multiple copies of a short DNA sequence that is specific for each organism. - They may protect chromosomes from degradation. - They can be extended by an enzyme called telomerase that carries an RNA molecule that is complementary to the telomeric repeats. - They may protect the cell from chromosomal fusions.

What could have an effect on initiation of DNA replication in E. coli?

- binding of seqA at oriC - the methylation state at oriC - binding of DnaA-ATP to oriC

What is false about bacterial RNA polymerase catalyzed reactions (synthesis of RNA)

- dNTPs act as substrates - these reactions occur at the catalytic site located in the sigma subunit

Which of the following is a type of cis-acting element primarily "acting" in RNA rather than DNA

- intrinsic transcription terminator - Poly A tail signal

What is true about the E.coli general sigma factor

- it contacts promoter directly at -10 and -35 - mutations in sigma may suppress mutations in promoters - removal of N-terminus allows sigma (alone) to bind promoters - It has several DNA binding domains

Why do eukaryotic cells have multiple origins or replication of their chromosomes unlike bacteria that usually have only one per chromosome?

-cells of higher organisms can have up to 1000 times the amount of DNA as bacteria - eukaryotic cells replicate RNA at slower rates than prokaryotes.

How many differ DNA polymerases are involved at the eukaryotic nuclear replication forks?

3

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

3' to 5'; 3'

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:

3-2-4-1-5

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

5'-5' triphosphate bridge

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

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

Why must RNA splicing be absolutely precise?

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

What is a ribozyme?

An enzyme made up of RNA

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.

DnaA

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 ______ .

Enhancer

T or F: Chemicals that are genotoxic , at concentrations that are not cytotoxic, result in fewer colonies than on the control plates.

False

T or F: Mammalian telomeres can be extended by an enzyme called telomerase that carries a DNA molecule that is complementary to the telomeric repeats

False

T or F: Prokaryotes produce longer Okazaki fragments during DNA replication than eukaryotes.

False

T or F: RNA polymerase I transcribes 5S rRNA

False

T or F: Some bacterial chromosomes (genomes) that are single replicons may contain multiple origins to increase the efficiency of DNA replication.

False

T or F: at all origins of replication helicases are loaded by helicase loaders, directly onto single stranded DNA generated by the initiators

False

T or F: miRNAs are essential components of spliceosome.

False

T or F: the activation of origins of replication is very similar in all organisms and requires sequence-specific binding of initiator proteins, melting of AT rich region by initiators that is followed by recruitment of replication machinery.

False

T or F:nuclear genes in the 3 largest rRNAs in higher eukaryotes are translated into r-proteins in the cytoplasm

False

T or F: Telomerase does not require a primer

False: uses Reverse transcriptase as a primer

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?

G and T

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 ________.

Inr/T AF/TFIID

What must the mismatch repair system be able to distinguish in order to tell which nucleotide of a mismatched pair to replace?

It must be able to distinguish the newly made strand from the parental strand.

What is true of snRNPs?

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

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

Topoisomerase

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

Trick question: bases are never assigned a value of 0

T or F: All pre-mRNAs are modified, not just the ones that correspond to interrupted genes

True

T or F: An origin (e.g. oriC) is a cis -acting element that can support replication of any DNA sequence joint to it (in appropriate cell).

True

T or F: Eukaryotic RNA Pol. I and III terminate transcription right after specific terminator sequences are transcribed similarly to prokaryotic RNA Pol.

True

T or F: ORC in yeast can bind to ARS at any point of the cell cycle

True

T or F: 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

True

T or F: RNAP III promoters usually contain positions that lie downstream of the startpoint

True

T or F: in eukaryotes the pre-replicative complex can be formed only during G1 but it remains inactive until the onset of S phase

True

T or F: the ability to form pre-RCs or to activate them during different stages of the cell cycle is controlled by the level of activity of Cdk

True

A gene with 11 exons ________ introns

has 10

O6-methylG may be generated by________and this modified base has a tendency to pair with T. therefor, if it is not repaired prior to replication its presence in DNA would lead to___

alkylation/ transitions

a eukaryotic cell having a high level of telomerase activity would

be able to proliferate

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.

closed/open

Water can be DNA's "enemy" be participating in all of the following reactions except

deamination of T's converting them to C's

the function of eukaryotic telomerase is to

extend the lagging strand template at the end of each chromosome

The function of eukaryotic telomerase is to

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

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?

group I introns were involved

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

kinase/TFIIH

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

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

Assuming there are 9 TCGA sequences within a 600 bp long regulatory region of an eukaryotic gene. How many of these tetramers would you expect to find in a 600bp sequence anywhere else in the genome assuming that all 4 bases are present in equal proportions

maybe 2

What is not directly involved in mismatch repair in E.coli

methyltransferase

deoxyribose differs from ribose by having

one less oxygen