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Biochem > Transcription lecture 1 > Flashcards

Transcription lecture 1 Flashcards

1
Q

what does RNA polymerase do ?

A

synthesises RNA in the 5’ to 3’ direction

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2
Q

does an RNA polymerase require a primer ?

A

no

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3
Q

what is a gene

A

a DNA sequence that is transcribed

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4
Q

what is the top strand called

A

the coding strand (sense strand)

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5
Q

what is the bottom strand called

A

template strand (antisense strand)

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6
Q

which strand is used as a template for RNA synthesis ?

A

the template strand

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7
Q

The template strand is copied from its ..

A

3’ end to its 5’ end

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8
Q

what is the RNA product identical in sequence to ?

A

the coding strand except that U replaces T

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9
Q

the gene is said to be transcribed from the 5’ end to the 3’end true or false

A

true

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10
Q

does the RNA product remain base-paired to the template DNA strand

A

no,

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11
Q

give two differences between DNA replication and transcription

A

RNA polymerase, unlike DNA polymerase, doesn’t require a primer to start polymerisation.
The RNA product does not remain base paired to the DNA template strand.

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12
Q

The DNA-RNA complex that forms during transcription is about 100 nucleotides long

A

false, it’s only about 10 nucleotides long

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13
Q

how many types of RNA polymerases are in prokaryotes ?

A

one

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14
Q

moving along a gene in the 5’ to 3’ direction is described as moving upstream

A

false, downstream

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15
Q

what are the regions of DNA that serve as sites of transcription initiation ?

A

they are called promoters

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16
Q

what is special about promoter regions in bacteria ?

A

several genes are often co-transcribed from a single promoter; such a transcription unit is called an operon. Polycistronic transcripts are formed. In eukaryotic cells, each gene usually has its own promoter.

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17
Q

where are promoters found

A

upstream of the transcription start site

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18
Q

many RNA polymerases transcribe the genes at the same time

A

true

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19
Q

what is the advantage of an operon ?

A

only one promoter controls the initiation of transcription of several genes that encode proteins that are similar in function.

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20
Q

what is the disadvantage of an operon ?

A

mutation in the single promoter may affect transcription of several genes, as supposed to one

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21
Q

what does trp mRNA contain

A

several start sites for protein synthesis

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22
Q

what type of reaction does RNA polymerase catalyse ?

A

a nucleotidyl-group-transfer reaction, resulting in formation of a new phosphodiester linkage and the release of pyrophosphate

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23
Q

what does DNA polymerase 3 and RNA polymerase have in common ?

A

they both catalyse polymerisation in the 5’ to 3’ direction. Highly processive

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24
Q

what is the overall reaction of RNA synthesis ?

A

RNAn - OH + NTP arrow RNAn+1 - OH + PPi

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25
Q

why is the Gibbs free energy for RNA synthesis highly favourable

A

because of the high concentration of NTP’s relative to RNA

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26
Q

how is the RNA polymerase reaction and the DNA polymerase reaction thermodynamically assisted ?

A

by the subsequent hydrolysis of pyrophosphate by pyrophosphatase inside the cell

27
Q

how many phosphoanhydride linkages are expende for every nucleotide added to the growing chain ?

A

two

28
Q

what are the substrates for RNA polymerase ?

A

ribonucleoside triphosphates (UTP, GTP , ATP and CTP) as substrates rather than deoxyribonucleoside triphosphates

29
Q

which is slower transcription or DNA replication ?

A

transcription

30
Q

what is the error rate in of RNA synthesis

A

10^-6 ,

31
Q

why is the error rate of RNA synthesis that that of DNA synthesis ?

A

RNA polymerase does not possess an exonuclease proofreading activity

32
Q

what is RNA polymerase ?

A

its an oligomeric protein

33
Q

how many different types of subunits make up the core E. coli RNA polymerase ?

A

4

34
Q

what is the stoichiometry of the core enzyme of E.coli RNA polymerase ?

A

a2 B B’ w

35
Q

which subunits of the RNA polyermase make up the active site ?

A

B and B’

36
Q

what does B’ do ?

A

contributes to DNA binding

37
Q

what does B do ?

A

contains part of the polymerase active site

38
Q

alpha subunit role of RNA polymerase ?

A

scaffolding role. transcription factors interact with RNA polymerase by binding to the alpha subunits

39
Q

w subunit role ?

A

unknown

40
Q

sigma subunit role

A

several different types of this subunit. , main type is o-^70. the sigma subunit recognises the promotor, and is required for the formation of a transcription complex.

—- the sigma factor is made up of four different subunits

41
Q

what does the 3D structure of RNA polyermase resemble

A

resembles a crab claw

42
Q

what does the 3D structure of DNA polymerase resemble ?

A

a hand

43
Q

what is a promotor ?

A

a nucleotide sequence that instructs transcription complexes: initiate a transcript here

44
Q

what is means when thee promotor is described as bipartite ?

A

there are two separate regions in sequence similarity

45
Q

what is the -10 region known as

A

the TATA box.

46
Q

what is the -35 region found ?

A

35 base pairs upstream of the start site ?

47
Q

what is the -35 region referred to as ?

A

-35 region

48
Q

what is the average distance between the two parts of the promotor ?

A

17 bp

49
Q

what defines the promotor for the E.coli holoenzyme containing sigma^70.

A

-10 region and the -35 region

50
Q

when does a transcription complex form ?

A

when one or more proteins bid to the promotor sequence and to RNA polymerase. These DNA-binding proteins direct RNA polymerase to the promotor site .

51
Q

what is the consensus sequence for the -35 region ?

A

TTGACA

52
Q

what is the consensus sequence for the -10 region ?

A

TATAAT

53
Q

what does sigma 2 of the sigma 70 subunit bind to

A

to the -10 region , melts within the active site

54
Q

what does sigma 4 of the sigma 70 subunit bind to ?

A

-35 region, involved in the recognition of the promotor site

55
Q

would ribosomal RNA genes have strong promoters ?

A

yes, the promotor would also include an UP-element which is part of all promotors. UP-element further increases the efficiency of transcription of the gene

56
Q

when the RNA polymerase bind to the DNA.. a …. complex is formed

A

closed, when the DNA is in the active site and is unwound forming a transcription bubble, it is referred to as an open complex..to achieve this, the RNA polymerase undergoes isomerisation

57
Q

what is the rate limiting step in transcription

A

initiation because it requires unwinding of the DNA helix and synthesis of a short stretch of RNA that serves as a primer for subsequent chain elongation.

58
Q

which enzyme unwinds DNA and synthesises a primer during transcription

A

the RNA holoenzyme itself. During DNA replication, a helicase and a primase carry out these steps.

59
Q

what can sigma 70 be referred to as

A

an initiation factor

60
Q

what happens when the RNA polymerase holoenzyme undergoes a transition from the initiation mode to elongation mode

A

a conformational change in the holoenzyme that causes the release of the sigma subunit

61
Q

what binds to the RNA polymerase to promote its conversion to elongå†ion mode?

A

accessory proteins, such as NusA

62
Q

what are the two mechanisms for transcription termination ?

A

Rho-dependent

Rho-indepdent

63
Q

what is Rho

A

a six ringed protein with a potent ATPase activity
binds the RNA at termination recognition sites called Rut sites which are on the DNA
binds to single stranded RNA
doesn’t bind to RNA being translated
Rho facilitates disassembly of the transcription complex, template, and mRNA by destabilising the RNA-DNA hybrid

64
Q

how are operons regulated ?

A

positively or negatively

Biochem (7 decks)

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