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molekylær biologi > chapter 30 RNA synthesis and processing > Flashcards

chapter 30 RNA synthesis and processing Flashcards

1
Q

the catalytic site of RNA polymerase contain how many metal ions? their functions and placement?
Which aminoacids interact with them

A

2 -metal ions
one of them remain tightly bound to the enzyme
One comes in and leaves with pyrophosphate
three aspartat amino acids

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2
Q

where do RNA-polymerisation reactions take place? and how many base pairs are they?

A

transcription bubble

17 base pairs

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3
Q

what are sense + and antisense - strands?

A

sense is the coding strand

while antisense is the template strand

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4
Q

Most newly synthesized RNA-chains have ….. at their ….end

A

pppG or pppA at 5’end

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5
Q

What forces the separation of RNA-DNA hybrid after the transcription is complete

A

A structure in RNA-polymerase

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6
Q

what mechanism is used by RNA-polymerases to correct errors? the error is

A

back-tracking, in in 10^4 to 10^5

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7
Q

which subunit in RNA-polymerase holoenzyme helps recognise the promoter sequences

A

sigma subunit. RNA-polymerase bind DNA but very weakly and until the sigma unit finds the proper promoter sites

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8
Q

what are the two common promoters found in bacteria

A

TTGACA (-35)

TATAAT (-10)

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9
Q

The region containing the two common motifs in RNA-transcription initiation is called?

A

core promoter

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10
Q

strong promoter and weak promoter

A

don’t have many substitutions => frequent transcription

many subsitutation => attenuated transcription

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11
Q

When is sigma unit released

A

is released when 9-10 nucleotides are produced

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12
Q

How many sigma factors does e.coli have

A

7

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13
Q

closed and open promoter complexes
how many basepairs
how is DNA distorted

A

double helical DNA
Separated DNA-strands
17 basepairs
by being wrapped around RNA-polymerase

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14
Q

What signals termination in RNA-transcription in bacteria

at which end

A

A palindromic sequence of GC-rich area + AT-rich followed by a series of U-residues
The RNA-DNA hybrid is unstable because of the hairpin that disociate from the polymerase and cause the polymerase to dissociate from the DNA.
3’ end

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15
Q

riboswitches

A

messenger RNAs senstive to certain metabolites.

High concentration of the metabolite => more stability of hairpin => Terminator structure is formed

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16
Q

what is of the function of rho-protein in bacteria?

how does it function

A

terminate RNA-transcription. Detects termination signals that are not recognised by RNA-polymerase alone. It is a DNA-RNA helicase.
Pursues RNA polymerase until it catches it in the transcription bubble. Hydrolyses ATP in the presence of single stranded RNA

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17
Q

What is the common feature of protein-dependent and protein independent termination in RNA-transcription

A

Termination signals lie in the synthesised RNA rather than the DNA-template.

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18
Q

name some antibiotics that can inhibit transcription

A

Rifampicin and actinomycin D.

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19
Q

the function of rifampicin

A

inhibit RNA-transcription in bacteria
specifically, the initiation of RNA-synthesis
by blocking the channel into which RNA-DNA hybrid must pass

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20
Q

function of actinomycin D in both eukaryotes and prokaryotes

A

binds to double helical DNA and prevents it separation through an intercalation by the phenoxazone ring.

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21
Q

what enzymes trim and modify the precursors of tRNA and rRNA

A

nucleases

22
Q

the function of RNase P in e.coli

A

ribonuclease P generates the correct 5’ terminal of tRNAs

23
Q

Ribonuclease III (RNase III)

A

excises 5s, 16s and 23s from primary transcripts by cleaving double-helical hairpin regions at specific sites

24
Q

The RNA-polymerase CCA adding enzyme

A

Does not require A DNA-template

25
Q

Types of polymerases in eukaryotes table (30.2) page 997

A

3 types

26
Q

what does the polymeras II carboxyl terminal containn

And it is strongly inhibited by?

A

CTD and it contains repeats of YSPTSPS

alpha-amanitin

27
Q

where is TATA-box locatedd

A

between -30 and -100

28
Q

When and where is DPE normally found?

A

when there is no TATA box between +28 and +32

29
Q

where is the initiator element found

A

-3 and +5

30
Q

differences between CAAT and GC box (location) and -35 prokaryotes in terms of position on antisense or sense strands?

A

CAAT and GC (-40 and -150) can be effective when present on template strand but -35 region has to be on the coding strand

31
Q

The basal transcription apparatus

A

TFII complex +RNA polymerase

32
Q

The basal transcription apparatus

A

TFII complex +RNA polymerase

33
Q

The transcription process transitions from inititation to elongation in eukaryotes?

A

by TFIIH that phosphorylates CTD of RNA polymerase II

34
Q

The activity of promoters in eukaryotes is increased by ….

A

enhancers (cis-acting elements) and they are no promoters

35
Q

how is heat shock transcription factor different to sigma subunits in bacteria

A

HSTF bind directly to promoters rather than first binding response elements

36
Q

tRNA and rRNA have ….Caps

A

No

37
Q

How is poly (A) tail synthesized?

A

By cleavage conducted by endonucleases that recognise the sequence AAUAAA. Does not take place if 20 nucleotides are removed from its 3’side

38
Q

MicroRNAs come from RNA polymerase

A

II and in some cases III as well

39
Q

Which protein family does MicroRNA end up in?

A

Argonaute family. MicroRNAs guide the Argonaute to the genes to be regulated

40
Q

RNA-editiing

A

Changing the sequence without changing

41
Q

RNA-editiing

A

Changing the sequence without splicing

42
Q

The introns begin with and end with….

A

GU and AG

43
Q

Where is the polypyrimidin tract found and how long is it

A

at 3 ‘ end, 10 pyrimidines, followed by N and C

44
Q

The associatio of which complexes require ATP hydrolysis in RNA-splicing

A

U2 and when the pre assembled complex U4-U5-U6 joins the U2 and U1, mRNA and splicing factors to form spliceosomes

45
Q

which RNAs are released with intron lariates

A

U2, U5 and U6

46
Q

What are the processes of transcription and splicing of RNA coordinated by?

A

By CTD of polymerase II

47
Q

The function of RNA helicases in splicing

A

ATP powered to unwind RNA duplex intermediates that facilitate catalysis and induce the release of mRNPs from the mRNA.

48
Q

Group I introns

A

not found in vetebrates. Self splicing that requires guanosine cofactors (GMP, GDP and GTP)

49
Q

Group I introns

A

not found in vetebrates. Self splicing that requires guanosine cofactors (GMP, GDP and GTP)

50
Q

Group 1 and group 2 self-splicing are mediated by

A

1: guanosine cofactors
2: 2’-OH in an adenylate residue

51
Q

Differences between group II self-splicing introns and the spliceosome splicing of mRNA

A

Both use an 2’OH in an adenylate rather a guanosine factor + the intron is released as a lariat
and in some cases the introns are transcribed in pieces assembling later on

52
Q

the RNA-DNA helix? how many base pairs?

A

Between newly synthesized RNA and DNA-template

8 base pairs

molekylær biologi (14 decks)

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