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BMS-I > Transcription/RNA Processing/Gene Regulation > Flashcards

Transcription/RNA Processing/Gene Regulation Flashcards

1
Q

In what polarity does DNA transcription occur?

A

5’->3’

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2
Q

What strand of DNA does the RNA product come from?

A

Template strand.

Don’t get confused with coding strand. Call it the non-template strand when you see it.

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3
Q

When the sigma unit of prokaryotic RNA polymerase binds with the core enzyme, what does that generate?

A

Holoenzyme

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4
Q

In what direction does RNA polymerase read DNA?

A

3’->5’

Generates 5’ -> 3’

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5
Q

What is prokaryotic RNA pol composed of?

A

sigma unit
2 alpha units
2 beta units
1 omega unit.

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6
Q

What are the three stages of transcription?

A
  1. Initiation
    A. Holo-RNAP binds to promoter
    B. Sigma-dependent, promoter-dependent
    C. Principal site for regulation!!!
  2. Elongation
    A. RNAP leaves and starts reading 3’-5’
    B. Sigma dissociated from RNAP and promoter
  3. Termination
    A. DNA-RNA-RNAP complex disassembles depending on signals (2 terminators in bacterial transcription)
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7
Q

What are the structures of bacterial promoters?

A

Made of of consensus seq. 2 sigmas can binds

  1. -35 sequence [TTGACA]
    (19 BP later)
  2. Pribnow box [TATAAT]
    (7 BP)

Transcription starts

Promoter is always DS-DNA

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8
Q

What is the Rho-dependent termination sequence?

A

Hexamer protein. ATPase!!!

Binds with RNA, not DNA.

Will influence the dissociation of the complex.

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9
Q

What is the Rho-independent termination seq?

A

Stem-loop terminator.

Structure starts BP-ing with self and run of Us at 3’ end.

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10
Q

Clinical Correlation:

Where does Rifampin bind?

A

Bacterial RNA polymerase.

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11
Q

What is each of the eukaryotic RNA polymerases responsible for in Eukaryotic cells?

A

RNA Pol I -> rRNA

RNA Pol II -> mRNA

RNA Pol III -> tRNA

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12
Q

What kind of regulatory elements are present in Eukaryotic transcription? (Pol II)

A 
1. Core promoter: 
A. Transcription start site (INR) +1
B. TATA box (-25)
C. DPE (downstream promoter element) +30
D. General: binds site for Pol II and GTFs
  1. Proximal promoter
    A. 250 BP from start
    B. Can be b4,during, or downstream of gene
    C. Also binds activators.
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13
Q

What is TFIID?

A

Nucleates assembly of transcription preinitiation complex.

Composed of TBP and 14-tbp associated factors (TAFs)

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14
Q

What is composition of RNA Pol II? How is it different/similiar to prokaryotic RNA pol?

A

Eukaroytic = 12 subunits Rbp1-12 (6 in prokaryotic)

Rpb1 - B’
Rpb2 - B
Rpb3/11 - a2
Rpb6 - omega

There is no sigma counter part in RNAP II

If there was a counterpart, it would just be all these general transcription factors.

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15
Q

What is the 7-methylguanosine “cap”? Where is it located?

A

5’ end of mRNAs.

Prevents degradation

Need to prevent breakdown of mRNA being produced b/c it isnt being translated right away.

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16
Q

Why is the polyadenylation og primary transcript important? How is it added?

A

MRNA is cleaved after a cleavage signal

Poly-A tail added by poly(A) polymerase
ATP dependent!!!

17
Q

Why is TFIIH importaqnt in DNA repair?

A

Couples transcription with DNA repair.

18
Q

What is in poisonous mushrooms that makes them?

A

Alpha-amatin. Binds with RNA pol II and inhibits elongation.

19
Q

What are introns?

A

Intervening sequences

20
Q

What are the consensus seq for splicing mRNA precursors?

A

5’ (end of the upstream exon) -> “GU”

3’ (start of downstream exon) -> “AG”

21
Q

What kind of chemical reactions are involved in the mRNA splicing mechansim?

A

2 Transesterifications

22
Q

What is a snRNP? When do we see them appear in the spliceosome?

A

Small nuclear ribonucleo proteins

U1 - binds with 5’ GU seq

U2 - binds with 3’ A / AG seq

U4/5/6 complex comes in and starts removal of intron

23
Q

CLINICAL Correlation:

What happens in certains types of B-thalessemias?

A

SNP (single base mismatch) that makes the splice site change.

In B-thalessemia, this will make the exon site longer (b/c thinks it should be splicing sooner). Yields 18BP (6 codons extra) in functional exon area

24
Q

What is alternative splicing?

A

Production of miltiple, related proteins form single gene.

Happens when exons are skipped over during splicing.

Genes producing different mRNAs

25
Q

When are transcripted polycistronic? Monocistronic?

A

Poly - Prokaryotes

Mono - Eukaryotes

26
Q

What binds to the promoter in eukaryotic cells? Prokaryotics?

A

TFIID(TBP) - Eukaryotic promoter binding
(TBP, TFIIB, TFIIF- bind RNA Pol II)

Sigma factor (RNA pol holozyme subunit) binds to promoter.

27
Q

What are all steroid hormones derived from?

A

Cholesterol (c27)

Eventually get to :

Glucocorticoids (C21) - metabolism

Mineralocorticoids (C21) - Blood pressure

Androgens (C19 -male sex)

Estrogens (c18- female sex)

28
Q

What is an example of a hormone antagonist?

A

Tamoxifen - competitive inhibitor.

29
Q

What 4 domains are present on a steroid receptor?

A
  1. Activation Domain
  2. Dimerization domain
  3. DNA binding (contains Zn finger)
  4. Ligand binding
30
Q

What steroid receptor domain contains a zinc finger motif?

A

DNA-binding domain

31
Q

What is the difference between glucocorticoid response elements and estrogen response elements?

A

Both are 17 bp in length. Both are pallindromic. Both occur on dsDNA

Difference is 2 sets of BP in sequence.

Gluco: starts w/ AA(5’), ends w/ TT (3’)
Estrogen: startw/ GT (5’), ends w/ AC(3’)

32
Q

Binding of a ligand to a SRE recruits what?

A

Co-activators

33
Q

How do steroid hormones regulate intracellular transcription?

A
  1. Cortisol binds with receptor activating Zn finger DNA binding
  2. Steroid-receptor complex binds with specific regulatory seq.
  3. Hormone receptor complex with coactivators cause transcription modification
34
Q

What is actinomycin used for, how does it work?

A

Binds DNA, inhibiting transcription elongation in prokaryotes and eukaryotes

Effective cancer therapeutic

35
Q

What is the TATA binding protein?

A

TBP

Part of the TFIID complex.

36
Q

What is the RNA Pol II preinitiation complex compased of?

A

TFIIA/B/D (TBP)/F/

E/H (Downstream)

BMS-I (17 decks)

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