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BMS I > DNA to RNA synthesis > Flashcards

DNA to RNA synthesis Flashcards

1
Q

Which way are strands read/synthesized

A

read 3’ to 5’, sun 5’ to 3’-ASK SOMEONE

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2
Q

RNA polymerase structure

A

5 subunits with sigma cofactor at top, reads with sequence specificity, not gene specificity-holoenzyme

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3
Q

template strand vs coding strand

A

coding strand is nontemplate

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4
Q

initiation

A

holoenzyme bindsto promoter
RNAP begins RNA synthesis
Sigma/promoter dependent
Principal start site for trx

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5
Q

Elongation

A

Lengthens transcript by addition of nucleotides to 3􏰂 end of
RNA located in active site of RNA pol II.
Sigma dissociates from RNAP and promoter.

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6
Q

Termination

A

RNA synthesis stops
Release of RNA Transcript
Dissociation of RNAP from the DNA template
Depends of DNA-encoded, RNA signals

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7
Q

Structure of bac promoter

A

tss, 7bp, pribnow box, 19bp, ~35 sequence

pribnow and 35 sequence are recognized by holoenzyme

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8
Q

rho dependent termnation

A

rho follows behind polymerase and when it catches termination occurs-uses ATP

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9
Q

Rho independent term

A

Creates stem loop that pinches off polymerase, this mechanism is encoded in DNA

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10
Q

RNA poly subunits

A

two beta are the pincers for the claws, alpha and omega are structural

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11
Q

Rifampicin

A

binds to bacterial polymerase and inhibits (tuberculosis)

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12
Q

Euk vs Prok polymerases

A

Pro only has one polymerase-has many different sigma factors though

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13
Q

DNA sequence elements

A

Promoter (where RNA polymerase binds)-TATA box-DS seq-just after the TSS
Proximal Promoer (CpG islands) (where regulatory/housekeepings proteins bind)-cell metabolism-roughly 120 bps upstream TSS
Enhancer-way upstream- DS sea-regulatory proteins
Pol II
Can have more promoters downstream

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14
Q

Pol II Core Promoter Elements

A

BRE-TFIIB Recognition Element
TATA Box-Binds TBP
INR-Initiator
DPE-downstream promoter element binding site

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15
Q

TFIID

A

TBP +14 other factors-nucleates assembly of trx pre initiation complex
Different factors of TFIID bind to other locations (TATA, INR, DPE)
Most responsible for recognition site where RNA Pol II should bind

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16
Q

RNA Pol II vs Prok RNA poly

A

Bigger and more complicated-no sigma factor in Euk

17
Q

TFIIH

A

Helicase activity

18
Q

How does pol II know where to go

A

Bunch of promoters are recognized by proteins

19
Q

GTFs

A

analgous to sigma factor

euk promoter with different sequence elements that recognize where to place Pol 2

20
Q

5’ cap

A

7-methylguanosine
Added as soon as part leaves pol 2
5’ to 5’ triphosphate linkage
ONLY IN EUKS-proks have coupled trx/trans so no need to protect

21
Q

Poly A tail

A

Only in EUKS
Not encoded in DNA
Uses ATP

22
Q

Similarities between Rep and Trx

A
  1. DNA template-dependent
  2. Chemical mechanism 3’OH attacks alpha phosphate of NTP
  3. 5’ to 3’ synthesis
  4. Energy requirement from NTP or dNTP substrates
23
Q

Dif between Rep and Trx

A
  1. no primer requirement
  2. trx utilizes small segments of DNA (genes)
  3. only one of two strands serve as template in try
  4. trx is conservative, replication is semi conservative
  5. NTP and UTP is trx, dNTP and DTTP in replication
24
Q

Dif between euk and pro try

A
  1. 1 poly vs 3
  2. sigma factor binds to promoter as subunit or RNA Poly, TFIID (TBP) binds to promoter and TBP, TFIIB, TFIIF bind RNA poly 2
  3. core and reg are close vs far
  4. Polycistronic vs monocistronic transcripts
  5. COupled vs uncouped trx/trans
  6. No histones vs histones
25
Q

RNA poly

A

TBP binds to promoter, then TFIIB, TFIIF bind, whole thing is called TFIID

26
Q

Mono vs polycistronic

A

1 gene in mRNA vs multiple genes in mRNA

27
Q

alpha-amanitin

A

bind to RNA pol II and inhibits trx, mushroom toxin

28
Q

FEN1

A

5’ end removal

Okazaki-rna primer off

BMS I (30 decks)

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