Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry > Transcription > Flashcards

Transcription Flashcards

1
Q

Tell me about rRNA

A
  • comprises 80% of cellular RNA
  • transcribed by RNAPI
  • are 5S, 5.8S, 18S, and 28S subunits of ribosome
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Template-product relationship b.w. DNA and mRNA

A

RNA product looks like the coding strand (not template)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

RNAP Prokaryotic Holoenzyme

A
  • 2 Alphas, 2 Betas, 1 omega subunits + sigma factor

- several different sigma subunits bind different promoter sequences

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Transcription Initiation in Prokaryotes

A
  • primary pt of regulation in prokaryotic transc.
  • sigma subunit binds -10 (Pribnow) and -35 regions
  • DNA gyrase resolves + supercoiling
  • TopoI resolves - supercoiling
  • no primer needed
  • when RNAP starts, sigma factor is left behind
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Rho Dependent vs. Rho Independent Termination

A
  • Rho protein binds specific RNA sequence as hexamer and contacts RNAP, causing dissociation
  • Independent: RNA hairpins generated by palindromic sequences followed by U rich sequences cause RNAP to fall off.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Operator in Prokaryotic Transcription Regulation

A
  • usually overlaps promoter

- negative regulatory element that binds repressor protein, which causes RNA to not bind promoter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Rifampicin

A
  • binds beta subunit of RNAP and inhibits initiation

- treats tuberculosis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Actinomycin

A
  • binds DNA template, phenoxazone ring intercalates b.w. Adjacent GC bps
  • blocks elongation
  • also interferes with eukaryotes, making it cancer treatment
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Eukaryotic Promoter Elements

A
  • 25 TATA box, the nucleation site
  • promoter proximal elements and enhancers are more upstream
    - PPEs are closer, binding sites for TFs of housekeeping genes. SP1 is a well categorized activator.
    - enhancers can be upstream, downstream, or even within a gene
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Tata Binding Protein

A

Part of TFIID

-binds TATA box, causes bend in DNA, allowing TFIIB to bind

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

TFIIB

A

Binds bent promoter DNA/TFIID

Allows RNAPII + TFIIF to assemble

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

TFIIE and TFIIH

A

Bind to DNAPII during initiation to help promoter melting

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

5’ Cap

A
  • 7-methylguanosine covalently linked to 5’ end of mRNA via 5’–>5’ triphosphate linkage
  • not encoded by DNA template
  • added to mRNA shortly after initiation
  • recognized by translation machinery to facilitate protein synthesis
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Poly-A Tail

A
  • happens during termination
  • specified by DNA seuqnce
  • endonucleolytic cleavage of nascent transcript
  • addition of 100-250 residue poly-a tail
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Steroid Hormone Receptors (structure and mechanisms of action)

A
  • have hormone binding and DNA binding domains
  • upon hormone binding, conformational change to allow for DNA binding and to create transcriptional activation domain that binds coactivator complex

2 cases:
Soluble in cytosol
Upon binding hormone, exposure of NLS
Enters nucleus, acts on DNA

Receptor is already in nucleus
Hormone binding either stimulates receptor-DNA binding or induces conformational change in receptor-DNA complex

BOTH REACT WITH COACTIVATOR COMPLEX TO STIMULATE RNA POL II

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Steroid Response Elements

A
  • enhancers for steroid responsive genes

- palindromic

17
Q

Mechanisms of Transcriptional Activation

A
  • some recruit or stabilize RNAPII/GTP to core promoter

- some clear a path by altering chromatin DNA template

18
Q

Coactivators

A

2 Classes of Chromatin Modifiers

  • catalyzes covalent modification of N-termini of histone tails
  • HATs (N termini of H3 and H4) and HDACs
  • some methlate, phosphorylate, ubiquitinate
  • ATP dependent nucleosome remodeling complexes
  • do not catalyze histone modification
19
Q

MMTV

A

Mouse mammary tumor virus
DNA virus that causes breast epithelial cell carcinoma
Genome includes sequence identical to estrogen enhancer
Integration of MMTV into human genome leads to cancer
Integrates adjacent to wnt-1-proto-oncogene, placing the regulator of cell proliferation under control of estrogens

20
Q

Tamoxifen

A

Antagonist of estrogen receptor

Fails to induce the conformational change in estrogen receptor that is required for subsequent coactivator binding

21
Q

TFIIH

A

Plays important role in coupling transcription with DNA damage repair
Altered TFIIH leads to XP, TTD, and CS

22
Q

Alpha-Amanitin

A
  • binds tightly and specifically to RNAPII
  • used to distinguish b.w. RNAPII from I and II
  • inhibits elongation
23
Q

When does splicing occur?

A

-either co or post-transcriptionally, but always before translation

24
Q

Mechanism of pre-mRNA splicing

A

Factors That Contribute to Splicing Fidelity

  • base sequence of intron begins with GU and ends with AG
  • consensus sequences are found at 5’ and 3’ ends of introns
  • branch sequence is found 20-50 nt away from 3’ end of intron
  • catalyzed by spliceosome, assembled denovo from SNURPs on precursor RNA that is ATP dependent
  • NO ATP is needed for actual transesterification

2 transesterification rxns

  • cleavage of PDE bond between exon 1 and intron 1
    - rxn uses 2’OH of branch pt A to form 2’-5’ PDE bond
  • 3’-OH of exon 1 cleaves PDE bond bw the intron and exon2
  • exon 1 is now joined to exon 2 and intron is released as lariat
25
Q

Splicing errors related to B-Thal

A
  • pt mutation in intron

- create longer or shorter forms of the B-globin

26
Q

SR Proteins

A

Bind RNA to define exons

27
Q

Factors that chill on CTD of RNAPII

A

Splicing factors, Cap adders, Poly-A tail proteins (endonuclease and poly-A bps)

28
Q

Proteins on mature mRNAs

A

Cap and tail proteins, SR proteins on exons

Ready by nuclear pore complex

29
Q

Exosome

A

Degrades RNA debris

Central channel is lined with 3’–>5’ exonucleases

30
Q

Lac Operon Control Elements

A

CAP binding site, upstream of promoter which binds to CAP-cAMP
(cAMP binds to CAP in low [Glucose])
THIS CAUSES BENDING IN DNA–>INCREASED AFFINITY FOR RNAPII–>TRANSCRIPTION

Operator: downstream of promoter, binds to repressor

When repressor binds lactose in low [Glucose], repressor can no longer bind operator.

Biochemistry (35 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions