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cmb2001 > lecture 1 > Flashcards

lecture 1 Flashcards

1
Q

what is gene expression?

A

the process by which information in genes (DNA) is decoded into protein

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2
Q

how do cells react to changes in their environment?

A

changing the number, identity and level of genes they express

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3
Q

what does gene expression drive?

A

cellular identity

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4
Q

what is transcription?

A

transfer of genetic information from double stranded DNA to single stranded RNA (mRNA)

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5
Q

how does transcription in prokaryotes (bacteria) occur?

A
  1. holoenzyme makes contact with sequences upstream
  2. RNA polymerase makes initial contact with promoter sequence to form closed complex
  3. DNA prized open over transcription start site to become ssDNA
  4. template strand used to make RNA copy
  5. sigma factor is released
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6
Q

what does the promoter region contain?

A

signals that tell RNA polymerase to bind and start transcription

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7
Q

what does the holoenzyme consist of?

A

RNA polymerase + sigma factor

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8
Q

what are promoters?

A

cis acting DNA regulatory element through which transcription is initiated and controlled

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9
Q

what are the core/basal promoter elements (eukaryotic promoters)?

A

CpG islands

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10
Q

what do 60-70% of protein coding genes lack in mammals?

A

obvious TATA and initiator element

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11
Q

what are promoters associated with?

A

regions with high frequency of CG rich sequences

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12
Q

what is methylation of CpG islands associated with?

A

silencing of the promoter (transcription turned off)

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13
Q

what is the definition of UAS?

A

upstream activating sequence

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14
Q

what is the function of the UAS?

A

activator binding sites - enhances or promotes transcription

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15
Q

what is the definition of URS?

A

upstream repressor sequence

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16
Q

what is the function of the URS?

A

repressor/silencing binding sites - inhibits initiation of transcription

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17
Q

what are the tools for identifying promoter elements?

A
  1. sequence comparison (identification of TATA box)
  2. reporter analysis
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18
Q

what is the function of reporter genes?

A

encode proteins whose levels can be easily measured

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19
Q

what are examples of reporter genes?

A

GFP, luciferase, LacZ

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20
Q

what does the amount of reporter protein measure?

A

gene expression

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21
Q

what is the amount of reported G protein proportional to?

A

activity of the promoter

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22
Q

what can reporter genes be used to identify?

A

when a gene is expressed, where its expressed, what signals it responds to, what factors and sequences control its expression

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23
Q

what are the 3 major eukaryotic RNA polymerases?

A

RNA pol I (nucleolus), RNA pol II (nucleus), RNA pol III (nucleus)

24
Q

what is the structure of bacterial RNA pol?

A

beta subunit, beta’ subunit, 2x alpha subunits, omega (w) subunit

25
Q

what is the structure of yeast RNA pol II (eukaryotic)

A

12 subunits

26
Q

what are GTFs?

A

general transcription factors

27
Q

what does bacterial RNA polymerase require to recognise promoter DNA?

A

sigma factor (brings RNA to promoter to allow transcription)

28
Q

what does the job of the sigma factor in eukaryotes?

A

TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH

29
Q

what are the functions of these GTFs?

A

RNA pol specific, multicomponent factors (minus TFIIB), form complex on TATA box, recruits RNA pol II to promoter, direct initiation at start site

30
Q

how is the pre initiation complex (PIC) assembled?

A
  1. interaction of TFIID with TATA box
  2. TFIIA and TFIIB (signal that allows the recruitment of polymerase) are added/joined
  3. RNA polymerase can now join with TFIIF to form the complex
  4. assembly of TFIIE and TFIIH
31
Q

how is transcription initiated by RNA pol II?

A

helices activity of TFIIH separates the template strand at the start site - requires ATP hydrolysis

32
Q

what occurs in promoter clearance?

A

pol II begins transcribing and is phosphorylated on the C terminal domain (CTD)

33
Q

what is the CTD?

A

series of repeats located at the C terminal end of the largest subunit of pol II

34
Q

what does transcription initiation require?

A

that the series of repeats becomes hyperphosphorylated

35
Q

what happens to TFIID and TFIIA after initiation?

A

may stay behind/ remain bound

36
Q

what happens to TFIIB, TFIIE and TFIIH?

A

they are released

37
Q

what happens to TFIIF?

A

moves down template with pol II

38
Q

what are the properties of TFIID? LEARN

A

binds to TATA box, recruits TFIIB

39
Q

what are the properties of TFIIA?

A

stabilises TFIID binding, anti repression function

40
Q

what are the properties of TFIIB?

A

recruits RNA pol II TFIIF, important for start site selection

41
Q

what are the properties of TFIIF?

A

stimulates elongation, destabilises no specific RNA pol IIDNA interactions

42
Q

what are the properties of TFIIE?

A

recruits TFIIH and modulates TFIIH activity

43
Q

what are the properties of TFIIH? LEARN

A

promoter melting and clearance, CTD kinase activity, DNA repair coupling

44
Q

what is the structure of TFIIH?

A
  • 9-10 subunits
    -core region and CAK module
    -contains ATPase called XPB (promoter melting)
    -binds last, opens up DNA over transcription start site
45
Q

what does the CAK module contain?

A

kinase that phosphorylates the CTD of RNAP II

46
Q

what is the structure of TFIID?

A

-TATA binding protein (TBP) and TBP associated factors (TAFs)
-triblobular structure

47
Q

what are the properties of TBP?

A

-can direct the assembly of PIC on TATA containing promoter (TAFs not needed)
-cant on TATA less promoter

48
Q

what do TAFs do?

A

-promote interaction of TFIID with basal promoter
-interact directly with activators

49
Q

what is the core basal promoter?

A

-consists of the region around the transcription start-site
-associated with elements such as the TATA Box and the Initiator (Inr) element

50
Q

what is the enhancer?

A

DNA regions close or far from the start-site
-binding sites for activator proteins
-often composed of multiple UAS elements

51
Q

what is the silencer?

A

-DNA regions close or far from start site
-binding site for repressor proteins

52
Q

what are general transcription factors (GTFs)?

A

-set of factors that recruit RNA pol II to promoter and direct initiation at start site

53
Q

what is basal transcription machinery?

A

-another name for GTFs and RNA pol II

54
Q

what is the pre initiation complex (PIC)?

A

assembly of basal machinery at core promoter

55
Q

what is the activator?

A

factor that binds to gene specific regulatory sequences and stimulates transcription initiation

56
Q

how is basal transcription activated?

A

-level of transcription from a core promoter
-increased levels of transcription mediated by activator protein

57
Q

what is the carboxyl-terminal domain (CTD)?

A

-CTD of largest subunit go RNA pol II binds to mediator complex and becomes phosphorylated during initiation of transcription

cmb2001 (10 decks)

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