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CHEM 431C - Biochemistry III > Chapter 27 - Transcription > Flashcards

Chapter 27 - Transcription Flashcards

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1
Q

Downstream

A

In the direction of the “current”. 5’ –> 3’. Position # is >0.

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2
Q

Upstream

A

Backwards. 3’ –> 5’. Position# is

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3
Q

Template strand

A

Also the anti-sense strand. Strand that is being used as the template for RNA synthesis.

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4
Q

Sense strand

A

Strand complementary to the template strand. Has the same sequence as the RNA being coded. This sequence makes “sense” to the ribosome.

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5
Q

Antisense strand

A

Strand that is being used as the template for RNA synthesis.

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6
Q

Describe prokaryotic promoter structure.

A

-10 Prifnow box (TATA on sense, untranscribed strand)
17bp spacer (because of σ width)
-35 element

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7
Q

How is promoter sequence related to gene expression?

A

Strong promoter –> recognized well, closer to consensus –> increased transcript amount –> increased gene expression

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8
Q

Prokaryotic transcription termination

A

(1) Sequence dependent (stem-loop)

(2) Protein-factor dependent

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9
Q

Sequence dependent termination

A

(1) GC-rich region causes RNA pol to pause.
(2) Pause allows the GC-region to pair into an RNA stem-loop/hairpin structure
(3) UUUU rich region has weak interactions with DNA (AU bonds), encouraging the DNA and RNA to break apart.

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10
Q

Protein factor dependent termination

A

(1) C-rich sequence signal on the RNA interacts with the ρ factor
(2) Using ATP, ρ moves toward 3’ end of RNA, which is being synthesized
(3) ρ (a RNA-DNA helicase) unwinds the DNA and RNA

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11
Q

Polycistronic

A

Has more than one protein coding region/codes for more than one protein

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12
Q

Eukaryotic RNA polymerase I

A

rRNA transcription

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13
Q

What is the most common method of transcription termination in prokaryotes?

A

Sequence-dependent termination

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14
Q

Eukaryotic RNA polymerase I

A
  • rRNA transcription
  • UBF-1 and SL-1 (TBP + 3TAFI) transcription factors
  • little regulation, always ON
  • terminated by steric hindrance
  • processed in nucleolus
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15
Q

TBP

A

TATA Binding Protein

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16
Q

TAF

A

TBP-associated factors

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17
Q

Eukaryotic RNA polymerase III

A
  • tRNA, 5sr RNA, snRNA
  • genes are separate (each with own promoter, many copies)
  • 700kDa, 17 subunits

(1) TFIIIA binds first to area downstream of transcription start site
(2) TFIIIIB and TFIIIIC binds to and upstream the TFIIIA, closer to transcription start site
(3) RNA pol III binds to the complex

18
Q

RNA pol IV

A

Synthesize siRNA and miRNAs

  • uncharacterized subunit composition
  • transcription THROUGH heterochromatin
19
Q

RNA pol V

A

Synthesize siRNA and miRNAs

  • uncharacterized subunit composition
  • transcription THROUGH heterochromatin
20
Q

RNA pol II

A

Transcribes protein encoding genes (mRNA)

(1) TFIID (TBP and TAFs)
(2) TFIIA stabilizes TFIID-DNA binding
(3) TFIIB recruits…
(4) TFIIF–RNA pol II which recruits…
(5) TFIIE (modulation of TFIIE, increased promoter melting) which recruits…
(6) TFIIH (helicase, promoter melting, promoter clearance)

21
Q

Cis acting element

A

Element/ regulatory region is on the same molecule as the gene being transcribed/regulated

22
Q

Cis-regulatory elements

A

Element/ regulatory region is on the same molecule as the gene being transcribed/regulated

23
Q

Element/ regulatory region is on the same molecule as the gene being transcribed/regulated

A

Cis-acting/regulatory elements

24
Q

Trans-acting elements

A

Regulatory element is NOT on the same molecule/strand as the gene being transcribed/regulated

25
Q

HDAC

A

Histone deacetylase, removes acetyl group from histone, making it less charged (and more positive), causing increased DNA-histone interaction

26
Q

HMT

A

Histone methyl transferase, transfers methyl group to amino group (NH3 —> N(CH3)3) making it positive charged, bind tightly to DNA

27
Q

Histone acetyl transferase

A

Adds acetyl group (AcCoA —> CoASH) to histone, encouraging loose interaction with DNA

28
Q

Chromatin remodelers

A

Move histones out of the way for access to DNA (uses ATP). Proteins that enable promoter regions to be able to accept the complex/bulky machinery necessary for transcription initiation.

29
Q

Insulators

A

Prevent TFs from influencing genes next door

30
Q

Polynucleotide phosphorylase

A

RNAn + NDP —-> RNAn+1 + P2

  • not template dependent
  • adding excess NDP will force the reaction
31
Q

Eukaryotic promoter escape

A
  • After several rounds of 10nt abortive initiation, TFIIH phosphorylates the serine on the C-terminus of RNA polII
  • TFIIB B-linker opens DNA –> open promoter complex
  • TFIIB B-reader threads DNA template to active center
  • When RNA chain promoter escape
  • TFIIF helps destabilize nonspecific RNA polII-DNA interactions
32
Q

Abortive initiation

A

RNA polymerase binds to a DNA promoter and enters into cycles of synthesis of short mRNA transcripts that are released before the transcription complex leaves the promotor.

  1. RNA polymerase binds to promoter DNA to form an RNA polymerase-promoter closed complex
  2. RNA polymerase then unwinds one turn of DNA surrounding the transcription start site to yield an RNA polymerase-promoter open complex
  3. RNA polymerase enters into abortive cycles of synthesis and releases short RNA products (up to 10 nucleotides in length)
  4. RNA polymerase escapes the promoter and enters into the elongation step of transcription
33
Q

Eukaryotic elongation

A

(1) Promoter release, core transcription factors are released, elongation begins with helicase clearing the way
(2) TFIIF–RNA polII moves along the DNA
(3) Elongation factors assist the enzyme in passing through pause sites (e.g. nucleosome remodeling factor, FACT elongation factor)

34
Q

Eukaryotic termination

A
  • RNApolII will usually transcribe well past to the end of the gene (unlike prokaryotic RNA pol)
    (1) Passes through one or more AATAAA signals past the 3’ end of the coding region
    (2) pre-mRNA (carrying the signal as AAUAAA) is then cleaved by a special endonuclease at 3’ end
    (3) A pol(A) tail is added by a special, nontemplate directed polymerase
    • mRNA stabilization
    • facilitation of transport from nucleus to cytoplasm
35
Q

Prokaryotic post-transcriptional processing

A

(1) Degradation
(2) cleavage
(3) Non transcriptive nucleotide addition
(4) Intron splicing

36
Q

Eukaryotic post-transcriptional processing

A

(1) Capping (5’ methyl capping, GTP added in reverse), position mRNA on ribosome, stabilization of message
(2) Splicing
(3) Alternative splicing
(4) RNA Editing

37
Q

Splicing

A

(1) U1 snRNP binds to E1 splice site, causing loop with branch site
(2) U2 snRNP binds to branch site, causing the strand to fully loop
(3) U4/6 and U5 bind
(4) With ATP, cleavage occurs at E1 site (U1/U4/U2 vs U6/U5 with the exons)
(5) With more ATP, cleavage occurs at E2 site and the exons are joined
(6) Ligated mRNA is released

38
Q

Alternative Splicing

A

Different combinations of exons from the same gene can be processed into different mature mRNAs and then undergo translation into different proteins in different tissues or at different developmental stages of the same organism. hnRNPL is the key player.

39
Q

RNA editing

A

changes nucleotide sequence of mRNA by changing one base to another

40
Q

Degradation

A

mRNA degradation (bacteria)

41
Q

Cleavage

A

pre-rRNA, pre-tRNA –> cleavage to rRNA, tRNA

30S rRNA transcript --> 16S, 23S, 5S
tRNA:
(1) endonuclease
(2) RNAseD removes nt one by one
(3) RNase P cuts 5' end
(4) RNaseD removes remaining two nt next to CCA sequence
(5) Modified bases

CHEM 431C - Biochemistry III (6 decks)

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