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Biochemistry > L19-20 Transcription > Flashcards

L19-20 Transcription Flashcards

1
Q

The best description of gene expression is the decoding of:

a) genetic information into RNA
b) RNA into genetic information
c) proteins into genetic information
d) genetic information into proteins

A

d) genetic information into proteins
a) genetic information into RNA is also true, but it is not the best description as it does not mention the subsequent decoding of those RNAs to build proteins.

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2
Q

Gene expression is a…

A

Multi-step process

Transcription & translation

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3
Q

Why study gene expression in E. coli (3)…

A
  1. It’s a key human pathogen
  2. The target of antibiotics (rifampicin, streptolydigin, lipiarmycin)
  3. Important host for recombinant protein production (research / industry/ medical applications)
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4
Q

The sense strand of DNA is…

A

The strand which matches the codons of the mRNA

The terms template and coding strand are used inconsistently (i.e. sometimes the sense strand is referred to as coding, sometimes as non coding)and are v. confusing :-(

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5
Q

The transcribed region in E. coli lies between:

a) promoter and consensus sequence
b) -35nt and +142nt
c) terminator and promoter
d) core and terminator

A

c) terminator and promoter

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6
Q

The more similar a promoter sequence is to the consensus sequence the…

A

Stronger the promoter (better binding)

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7
Q

The stronger the promoter (and better the binding)…

A

more mRNA and therefore more protein is produced

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8
Q

RNA polymerase is a (single / multi) subunit protein…

A

Multi

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9
Q

Core RNA polymerase is comprised of subunits (4)…

A

2x ⍺
1x β
1x βʹ
1x ⍵

(⍵ = omega)

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10
Q

The core RNA polymerase combined with sigma factors is known as the…

A

Holoenzyme

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11
Q

The holoenzyme ( can / cannot ) bind to a promoter

A

Can!

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12
Q

The core RNA polymerase enzyme (can / cannot) bind to a promotor

A

Cannot!

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13
Q

RNA polymerase is dependent on which ion?

a) NaCl
b) Cl-
c) Mg2+
d) Zn2+
e) Sigma factor

A

c) Mg2+

Magnesium ion

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14
Q

The main sigma factor is…

A

σ 70

Sigma 70

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15
Q

The process of transcription can be summarised in 3 main steps…

A
  1. Initiation
  2. Elongation
  3. Termination
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16
Q

When does the transcription bubble appear?

A

After initiation

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17
Q

The transition from a closed to open complex is marked by the appearance of the…

A

Transcription bubble

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18
Q

RNA polymerase builds the RNA chain from ( 3’ -> 5’ / 5’ -> 3’ )…

A

5’ -> 3’

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19
Q

After elongation begins, the sigma factor:

a) is released immediately
b) remains bound to RNA polymerase
c) is released at about 9-10 nts
d) is released at about 19-22 nts

A

c) is released at about 9-10 nts

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20
Q

Because the sigma factor is released early in elongation, the process can be said to be catalysed by the…

A

RNA polymerase core complex

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21
Q

Like DNA polymerase, RNA polymerase also required which ion?

A

Magnesium

Mg2+

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22
Q

RNA polymerase elongates at a (faster / slower / similar) rate to DNA polymerase

A

Slower, 20-50 nt/s (versus 1000 for DNA polymerase)

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23
Q

Which of the statements are true?

Which polymerases have proofreading functions?

a) Neither DNA polymerase nor RNA polymerase
b) Only RNA polymerase
c) Only DNA polymerase
d) Both DNA and RNA polymerase

A

c) Only DNA polymerase

24
Q

RNA polymerase does not have a proofreading function, but it can…

A

Backtrack

25
Q

The error rate of RNA polymerase (1 in 10,000) is much higher than that of DNA polymerase.

Give two reasons why this is acceptable when producing mRNA in E.coli

A
  • mRNA is for short term use

* E.coli genes are short in length (<10,000nts)

26
Q

Termination occurs at a…

A

Termination sequence!

27
Q

Termination can be either (2)…

A
  • Factor independent

* Rho (ρ)dependent

28
Q

Factor independent termination sequences result in a…

A

Hairpin/stem-loop structure which causes transcript to dissociate

29
Q

Factor independent termination sequences feature 4-10 consecutive…

A

ATs

30
Q

Factor independent termination sequences feature G & C rich palindromic sequences where?

A

Preceding the consecutive ATs

31
Q

Weak RNA/DNA hybrid is formed between bases A and…

A

U

32
Q

When the transcript dissociates from the DNA, RNA polymerase…

A

Falls off

33
Q

Rho is built from…

a) 6 identical subunits
b) a single subunit
c) 3 identical subunits
d) 3 alpha and 3 beta subunits (6 total)

A

a) 6 identical subunits

34
Q

Rho is a helicase powered by…

A

ATP hydrolysis

35
Q

Rho loads onto the…

A

RUT (Rho Utilisation site)

36
Q

RUT regions are…

a) A rich
b) C rich
c) A poor
d) U rich

A

b) C rich

37
Q

Rho unwinds any…

A

DNA-RNA or RNA-RNA duplexes

38
Q

The start site (TG/AT) is located at

a) +1
b) 0
c) -1
d) -35
e) -10

A

a) +1

39
Q

The consensus sequences must be separated by around…

A

16-19 bps

40
Q

In E. coli, consensus sequence ‘TTGACA’ is found at…

A

-35 (in promoter region)

41
Q

In E. coli, consensus sequence ‘TATAAT’ is found at…

A

-10 (in promoter region)

42
Q

Hairpin structure in mRNA results from the…

A

Self-complementary sequences in the termination sequence

43
Q

At any given time, only a subset of…

A

Genes is being expressed to produces protein

44
Q

Cells react to changes…

A

In the environment

45
Q

Gene expression can be regulated at all steps, but the key target is…

A

Transcription

46
Q

In transcription, initiation is a key target for regulation as it is the…

A

Rate limiting step

47
Q

Strategies for regulation at initiation can be divided into (2)…

A
  1. Repression

2. Activation

48
Q

In regulation by repression…

A

A repressor blocks RNA polymerase from transcribing the gene

49
Q

In regulation by activation…

A

A weak promoter, therefore RNA polymerase requires the addition of a positive regulatory factor known as an activator in order to proceed

50
Q

In the lac operon, lactose acts as an…

A

Inducer (removes repressor)

51
Q

In the lac operon, CAP acts as a…

A

Positive regulatory factor/ activator

52
Q

In the presence of lactose and glucose, there is little transcription of the lac gene because…

A

There is no CAP and the promoter alone is weak

53
Q

When glucose levels drop, cAMP levels…

A

Increase

54
Q

cAMP binds to CAP to form the…

A

cAMP-CAP complex

55
Q

Contact between the CAMP-CAP complex and RNA helps binding to the promoter, thus increasing transcription by…

A

50x

56
Q

CAP (Catabolite activator protein) is alternatively known as…

A

CRP (cAMP Receptor protein)

Biochemistry (21 decks)

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