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Genes > Prokaryotic Transcription > Flashcards

Prokaryotic Transcription Flashcards

1
Q

Which direction does transcription take place?

A

5’ to 3’

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2
Q

What is the coding strand?

A

DNA strand that has same sequence as mRNA

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3
Q

Define promoter

A

Region of DNA where RNAp binds to initiate transcription

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4
Q

Define terminator

A

Sequence of DNA that causes RNAp to terminate transcription

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5
Q

Define transcription unit

A

Sequence between site of initiation and termination by RNAp

May include more than one gene

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6
Q

What is the start point?

A

+1
Position on DNA where the first base is incorporated into RNA

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7
Q

What happens during transcription?

A

Separates DNA strands
Transient transcription bubble
Template strand
DNA duplex reforms behind bubble = displacing RNA

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8
Q

How is the bubble maintained?

A

Bubble is maintained within bacterial RNA polymerase

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9
Q

Define nascent RNA

A

RNA chain that is still being synthesized
Its 3’ end is still paired with DNA where RNAp is elongating

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10
Q

What happens in initiation of transcription?

A

RNAp binds promoter on DNA = forms CLOSED complex
RNAp initiates transcription after opening DNA duplex to form transcription bubble = OPEN complex

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11
Q

What happens in elongation of transcription?

A

Transcription bubble moves along DNA and RNA chain is extended 5’ to 3’ direction

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12
Q

What happens in termination of transcription?

A

Transcription stop
DNA duplex reforms
RNAp dissociates at a terminator

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13
Q

Why does abortive initiation occur?

A

Suboptimal promoter sequences, such as weak or non-consensus sequences

Low availability and activity of initiation factors, such as sigma factors in bacteria or general transcription factors in eukaryotes

Regions with high GC content or secondary structures may hinder the progression of RNA polymerase and promote abortive initiation

Availability of nucleotides

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14
Q

How does abortive initiation stop?

A
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15
Q

What is a holoenzyme?

A

A fully active form of an enzyme

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16
Q

What subunits are part of the RNAp holoenzyme?

A

Core enzyme with 5 subunits = 2 alpha, beta, beta’ and omega
And a sigma factor

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17
Q

What do the beta and beta’ subunits do?

A

Catalytic centre
Make up most of enzyme mass

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18
Q

What is the role of alpha subunit?

A

Scaffold for assembly
Interacts with promoter and regulatory factors through its CTD

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19
Q

What is the role of sigma factor?

A

Promoter specificity
Melting/unwinding

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20
Q

What does RNAp closed complex mean?

A

When RNAp binds the promoter = DNA remains double stranded

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21
Q

What is the ternary complex?

A

Initiation of transcription complex
RNAp, RNA and nascent RNA

22
Q

When is the elongation complex formed?

A

When initiation succeeds and nascent RNA chains ~ 10 bases
Sigma factor is released
Elongation ternary complex is formed

23
Q

What happens when the sigma factor dissociates?

A

Core enzyme contracts to -35 then after a few more bases = compacts into general elongation complex

24
Q

Why does sigma factor change its structure?

A

To expose its DNA-binding regions when it associates with core enzyme

25
Q

What is the UP element?

A

Sequence in bacteria next to promoter = enhances transcription
Upstream of -35 element

26
Q

What is the structure of sigma factor?

A

Sigma 2 & 4 = DNA-binding domain
N terminus blocks binding region when not associated with core enzyme
DNA displaces N-terminus when complex forms

27
Q

What is the promoter sequence?

A

Idealized sequence, where each position represents the base most found when sequences are compared

28
Q

What does the promoter sequence consist of?

A

Purine at start point
Hexamer TATAAT at -10
Hexamer TTGACA at -35

29
Q

Do E.coli have different sigma factors?

A

Yes, 7 sigma factors = each causing RNAp to initiate a set of promoters defined by specific -35 and -10 sequences

30
Q

What are the differences between the sigma factors?

A

Induced by particular environmental conditions
Recognize promoters with different consensus sequences
Different uses and genes encoding them

31
Q

What is sigma factor 70 used for?

A

General transcription

32
Q

When is a cascade of sigma factors created?

A

When one sigma factor is required to transcribe the gene coding for the next sigma factor

33
Q

How is termination induced?

A

Termination requires recognition of terminator sequence in DNA
AND the formation of a hairpin structure in the RNA product

34
Q

What does antitermination cause?

A

Readthrough = enzyme to continue transcription past the terminator seqeunce

35
Q

What is intrinsic termination?

A

Core enzyme can terminate at certain sites
In absence of other factors

36
Q

What does intrinsic termination require?

A

G-C rich hairpin in RNA product
U-rich region where termination occurs

37
Q

Why does the hairpin need G-C rich region?

A

G-C is stronger = need a stable stem otherwise termination would be compromised

38
Q

What is needed in Rho-dependent terimination?

A

Rho factor = terminator protein
rut site on nascent RNA

39
Q

What is the rut site?

A

rho utilization site

Where Rho factor bind to RNA and translocates along RNA until it hits RNAp

40
Q

How do transcription and translation occur in bacteria?

A

Simultaneously = they are coupled
mRNA is transcribed, translated, and degraded simultaneously in bacteria

41
Q

What is bacterial mRNA properties?

A

Unstable
Half-life of a few minutes

As opposed to in eukaryotes = RNA relatively stable and continued to translate for several hours

42
Q

What regions do bacterial mRNA include?

A

Untranslated and translated regions

43
Q

What do 5’UTR and 3’UTR stand for?

A

5’ = untranslated sequence upstream from coding region of mRNA
3’ = untranslated sequence downstream from coding region

44
Q

What is a monocistronic mRNA?

A

mRNA that encodes one protein

45
Q

What is the intercistronic distance?

A

When start and stop codons overlap
This can occur because of different reading frames in prokaryotes

46
Q

Does the intercistronic distance vary?

A

Yes, varies from -1 to +40 bases

47
Q

What does it mean for bacterial mRNA to be polycistronic?

A

Having several coding regions that represent different cistrons

48
Q

What is electrophoresis-mobility shift assay used for?

A

Te detect protein-DNA interactions

49
Q

What is immunoprecipitation used for?

A

To isolate and concentrate a particular protein from a mixture of many different proteins

50
Q

What is DNA footprinting used for?

A

To locate a protein binding site on a particular DNA molecule

Genes (6 decks)

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