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Advanced Molecular Biology Lab > Mid-term > Flashcards

Mid-term Flashcards

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1
Q

Transcription Definition

A

The process by which regions of DNA are copied into RNA molecules

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2
Q

What are Cis-Acting elements

A

features embedded in the DNA that regulate transcription

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3
Q

What are some examples of cis-acting elements

A

promoters, regulatory sequences, terminator

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4
Q

What are trans-acting elements

A

features that bind to the cis-acting element of a gene to control its expression

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5
Q

what are some examples of trans-acting elements

A

RNA polymerase, transcription factors, gene regulatory proteins.

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6
Q

What direction is the template strand read

A

3’ to 5’

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7
Q

What direction are transcripts made in

A

5’ to 3’

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8
Q

What is the non-coding strand

A

The template strand used for transcription

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9
Q

What is the coding strand

A

the non-template strand is the coding because it is almost identical to RNA

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10
Q

RNA polymerase definition

A

catalyzes phosphodiester bond between NTPS

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11
Q

What are some differences between prokaryotic transcription and eukaryotic transcription

A

prokaryotes have no membrane-bound organelles (aka no nucleus), circular genome, transcription and translation occur at the same time, there are no post transcriptional modifications like introns, extrons, 5’ cap, or poly-a tail

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12
Q

What is the holoenzyme

A

core enzyme + sigma factor

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13
Q

What is the core enzyme

A

No sigma factor

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14
Q

What is the sigma factor

A

a specificity factor that tells the polymerase which strand to use.

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15
Q

How did we figure out the purpose of sigma factor

A

core enzyme created double-stranded RNA by using both strands of DNA as a template. Holoenzyme only created one strand of RNA

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16
Q

Why is the sigma important for initiation of transcription

A

it recognizes the promoter at the -10 and -35 box, weakly binds to the double stranded DNA, then binds strongly to the single stranded DNA

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17
Q

How does sigma recognize the promoter

A

at the -35 and -10 box. there is always a conserved TT at the -35 box.

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18
Q

After sigma binds to the promoter, what happens?

A

The RNA polymerase moves to the right elongating the RNA and sigma dissociates. It can now rejoin with a different core, thereby creating another holoenzyme

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19
Q

How can sigma factors change in response to the different needs of the cell

A

There are multiple sigma factors and they each have different sequence specificities for promoters so they can bind to different promoters. The -10 and -35 box are still important for all sigma factors.

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20
Q

How does prokaryotic transcription terminate

A

Via Rho-independent or Rho-dependent termination

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21
Q

Explain Rho-independent termination

A

There is an inverted repeat in DNA followed by string of A residues that creates a hairpin structure. This structure helps pull apart the weak dA-rU interaction and RNA polymerase falls off

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22
Q

Explain Rho-dependent termination

A

RNA is thought to be threaded through Rho center and then when the polymerase stalls at the termination signal, Rho may break apart the DNA-RNA interaction

23
Q

What is Rho

A

a protein that reduces ability of RNA polymerase to transcribe

24
Q

Operon

A

a group of genes involved in the same response pathway that are regulated together

25
Q

How are operons regulated

A

by specialized proteins (repressors) binding to specific DNA elements (operators)

26
Q

Explain the lac operon with glucose only

A

LacI gene encodes the repressor monomer which binds to the operator blocking transcription

27
Q

Explain the lac operon with lactose only

A

allolactase binds to the repressor tetramer which blocks the repressor from binding to the operator. cAMP-CAP which rises when glucose levels fall, helps the RNA polymerase bind to the promoter.

28
Q

Explain the lac operon with glucose and lactose

A

only medium level of transcription of lac genes

29
Q

What is the trp operon

A

codes for protein that the bacterium needs to make the amino acid tryptophan

30
Q

Explain the trp operon with high tryptophan

A

trpR encodes the repressor. When tryptophan is bound to the repressor, it is able to interact with the operator and block it from transcribing but not 100%. There is an attenuator sequence that forms a stable hairpin causing ribosome to fall if transcription occurs.

31
Q

Explain the trp operon with low tryptophan

A

trpR encodes the repressor but no tryptophan can activate the repressor so transcription occurs and forms an unstable hairpin and ribosome stalls.

32
Q

Difference between operons and sigma factors

A

operons only control a handful of genes while alternative sigma factors change a lot more.

33
Q

anti-sigma factors

A

proteins that can bind to sigma factors and control their activity

34
Q

anti-anti sigma factors

A

promote sigma factors

35
Q

What helps regulation of sigma factors

A

anti-sigma factors, anti-anti sigma factors, transcription factors (assist sigma factor recognition of promoter elements)

36
Q

Difference between eukaryotic RNA polymerase II and prokaryotic polymerase II

A

eukaryotic polymerase cant recognize promoters without general transcription factors

37
Q

What binds to the TATA box

A

TBP (TFIID)

38
Q

What binds to BRE (B recognition element)

A

TFIIB

39
Q

What is the purpose of the Inr

A

Together with TATA and BRE promotes basal transcription of any gene

40
Q

what is the purpose of DCE

A

can replace TATA in TATA-less promoters

41
Q

What is the order of binding

A

TFIID binds to DNA via TBP at TATA box, TFIIA stabilizes binding of TFIIB and TBP, TFIIB binds to BRE and recruits RNA polymerase, TFIIF binds polymerase II and TFIIB, TFIIE recruits TFIIH, TFIIH unwinds promoter DNA and phosphorylates C-terminal domain of polymerase

42
Q

What are the two forms of RNA polymerase II

A

hypo-phosphorylated which can join the pre-initiation complex, hyper-phosphorylated which can mediate RNA synthesis initiation and elongation

43
Q

What transcription factors remain at the promoter

A

TBP and TFIIB

43
Q

What transcription factors remain at the promoter

A

TBP and TFIIB

44
Q

What transcription factors remain at the promoter

A

TBP and TFIIB

45
Q

What transcription factors that dissociate from the elongation complex

A

TFIIE and TFIIH

46
Q

What are activators

A

bind upstream of the promoter

47
Q

What are repressors

A

bind to silencers and inhibit transcription

48
Q

what are co-activators

A

aid activators by serving as a bridge

49
Q

How does acetylation of histones affect transcription

A

cause DNA to loosen up

50
Q

HATs

A

writer enzymes, they add acetylation

51
Q

HDACs

A

Eraser enzymes, that remove acetylation making DNA not active

52
Q

What is the purpose of polyadenylation

A

stability / protection from degradation, translation, gene expression regulation

Advanced Molecular Biology Lab (1 decks)

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