Only few E. coli promoters interact with the ? 70 . Most promoters interact with

Question

Only few E. coli promoters interact with the ?70. Most promoters interact with variety of other specific ? factors.

True

False

3.5 points   

QUESTION 16

RNA polymerase ______________.

binds tightly to a region of DNA thousands of base pairs away from the DNA to be transcribed.

separates DNA strands throughout a long region of DNA (up to thousands of base pairs), then copies one of them.

can synthesize RNA chains de novo (without a primer).

has a subunit called ? (lambda), which acts as a proofreading ribonuclease.

synthesizes RNA chains in the 3' ? 5' direction.

3.5 points   

QUESTION 17

RNA polymerase forms phosphodiester bonds with the concomitant release of pyrophosphate (PPi).The subsequent conversion of pyrophosphate to _________ by pyrophosphatase drives the reaction in the direction of RNA synthesis.

deoxyribonucleotide (dNTP)

diphosphate (DePP)

ribonucleotide (rNTP)

water (H20)

inorganic phosphate (orthophosphate, Pi)

3.5 points   

QUESTION 18

A partial sequence of an mRNA is: 5'- AUG CAU AGC AAA GUC ACA AUC -3' The sequence of the corresponding DNA coding strand is 5'- Blank 1 Blank 2 Blank 3 Blank 4 Blank 5 Blank 6 Blank 7 -3' (Fill in the blanks in groups of 3-nucleotides.)

3.5 points   

QUESTION 19

A partial sequence of an mRNA is: 5'- AUG CAU AGC AAA GUC ACA AUC -3'. The sequence of the DNA non-coding strand corresponding to the mRNA sequence is 5'- Blank 1 Blank 2 Blank 3 Blank 4 Blank 5 Blank 6 Blank 7 -3' (Fill in the blanks in groups of 3-nucleotides.)

3.5 points   

QUESTION 20

Sigma factors ______________.

constitute part of the bacterial RNA polymerase holoenzyme.

facilitate promoter identification by RNA polymerases, are highly conserved proteins (that is, share considerable sequence homology in prokaryotes and eukaryotes) and are therefore known as general transcription factors

are general transcription factors that facilitate transcription of “general” constitutive genes by bacterial RNA polymerases, whereas in regulated genes similar functions are carried out by specialized factors such as the CAP (CRP) in the case of the lac operon.

constitute part of the bacterial RNA polymerase core enzyme.

3.5 points   

QUESTION 21

The promoters of E. coli can be grouped according to sequence similarity, but the sequences are rarely identical.

True

False

3.5 points   

QUESTION 22

The subunit makeup of the E. coli RNA polymerase core is

?2?2??&????;

?2??'?

?2??'??

?2?2?&????;

3.5 points   

QUESTION 23

The ?10 and ?35 sequences in bacterial promoters are separated by about two turns of the DNA double helix. How would transcription be affected if a deletion were introduced in the promoter region that moved the ?35 sequence to the ?29 position?

The deletion would move the ?35 sequence closer to the ?10 sequence by half a helical turn of the DNA. Since the actual sequences of the two promoter elements are not altered, we don't expect their being somewhat more proximal to one each other to be a major factor in the performance of the promoter.

The deletion would move the ?35 sequence closer to the ?10 sequence by full a helical turn of the DNA, putting the two elements on the same original face of the DNA duplex, only a bit closer. This would not dramatically affect the binding of sigma factor to the promoter nor make much of difference in the transcription efficiency.

The deletion would move the ?35 sequence closer to the ?10 sequence by full a helical turn of the DNA, putting the two elements on the same original face of the DNA duplex, but closer. This would dramatically increase the binding of sigma factor to the promoter by allowing it to more efficiently interact with the promoter, thereby increasing transcription efficiency.

The deletion would move the ?35 sequence closer to the ?10 sequence by half a helical turn of the DNA, putting the two elements on opposite faces of the DNA duplex. This would dramatically reduce binding of sigma factor to the promoter, thereby decreasing transcription efficiency.

3.5 points   

QUESTION 24

5'-end of coding strand

5'-end of template strand

3'-end of antisense strand

5'-end of RNA

3'-end of sense strand

3'-end of nonsense strand

Are you kidding me?

5

2

1

6

4

3

3.5 points   

QUESTION 25

In Fig 2, where do you expect to find the most important promoter elements?

Near 5 (and 6)

Near 1 (and 2)

Near 3

Near 4

3.5 points   

QUESTION 26

Transcription termination in E. coli  

depends conserved sequences on the DNA to which a Rho factor binds preventing further forward movement of the polymerase (Rho-dependent mechanism) or requires the polyemerase to encounter another promoter to which a Sigma factor is bound Rho-independent mechanism).

either requires a a Rho factor to actively pull the mRNA off the DNA (Rho-dependent mechanism) or depends on sigma factor accomplishing essentially the same thing (sigma-dependent mechanism)  .

either requires the Rho factor (Rho-dependent mechanism) or depends on the RNA polymerase working in reverse (Rho-independent mechanism).

either requires the Rho factor to actively pull the mRNA off the DNA (Rho-dependent mechanism) or depends on a stem loop structure followed by an AU-rich region in the mRNA causing its dissociation from the DNA (Rho-independent mechanism).

3.5 points   

QUESTION 27

Which of the following best characterizes the average rates and error frequencies of DNA synthesis and RNA synthesis in vivo?

The rate of transcription increases when the error frequency of DNA replication increases.

The rate of transcription decreases when the error frequency of DNA replication increases.

Transcription is slower and more error-prone than DNA replication.

Transcription is faster and less error-prone than DNA replication.

Transcription is slower and less error-prone than DNA replication.

Transcription is faster and more error-prone than DNA replication.

3.5 points   

QUESTION 28

Which of the following most accurately describes the relative diversity (i.e., number of different transcripts) of RNA species inside cells?

rRNA < tRNA < mRNA

tRNA < rRNA < mRNA

mRNA < rRNA < tRNA

mRNA < tRNA < rRNA

tRNA < mRNA < rRNA

3.5 points   

QUESTION 29

Which of the following sequences would interact with RNA polymerase holoenzyme that contain a ?70 subunit most efficiently?

        –35                 –10          +1
5' …GAGCCC …… CACTTT… Start Site... 3'

         –35                 –10          +1
5' …TTGACT …… TATAAA… Start Site... 3'

        –20              –10        +1
5' …TAAGAA … CACAAT… Start Site....3'

     –20            –10          +1
5' …TTGACA … TATAAT… Start Site... 3'

    –35                  –10           +1
5' …ACAAGA …… CACGTT… Start Site... 3'

3.5 points   

QUESTION 30

Which of the following statements may provide an explanation as to why does RNA synthesis need not be as carefully monitored for errors as does DNA synthesis?

An error will affect only one molecule of mRNA out of many synthesized from a gene thus the effect is diluted. Furthermore RNA transcripts are labile (degrade relatively fast), so the effects is only short lived. In addition, the errors do not become a permanent part of the genetic information that is passed on to the cell progeny.

DNA seldom adopts stable tertiary structure folds, whereas RNA does so more readily.

At any given instant, only a fraction of the genome (total DNA) is being transcribed. Consequently, high fidelity is not essential. In contrast, during the S phase of the cell cycle, the whole genome is being replicated requiring a more concerted effort to keep incorporation errors to a minimum.

RNA and DNA polymerases do not share significant levels of homology between them. In particular, their active sites are related by convergent evolution. Therefore it is not surprising that one process has higher fidelity as compared to the other.

Since cytosines can spontaneously mutate into uracils and since RNA is full of uracils, the fidelity of RNA polymerase is not as important.

3.5 points   

QUESTION 31

Write the sequence of the messenger RNA molecule synthesized from a DNA template strand having the sequence:

5'- CGTTACGTAC -3'

5’- Blank 1Blank 2Blank 3Blank 4Blank 5Blank 6Blank 7Blank 8Blank 9Blank 10 -3'.

binds tightly to a region of DNA thousands of base pairs away from the DNA to be transcribed.

separates DNA strands throughout a long region of DNA (up to thousands of base pairs), then copies one of them.

can synthesize RNA chains de novo (without a primer).

has a subunit called ? (lambda), which acts as a proofreading ribonuclease.

synthesizes RNA chains in the 3' ? 5' direction.

Explanation / Answer

Q15. FALSE

Sigma factor is an essential protein required for the initiation of RNA synthesis (transcription initiation factor). Sigma factor allows the gene promoters with RNA polymerase. The 70 is primary sigma fator (or house keeping sigma factor) is the most commonly occuring sigma factor in E.coli, most promoters bind with the 70.

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