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Section 4 > Transcription/RNA processing > Flashcards

Transcription/RNA processing Flashcards

1
Q

What are 3 ways in which RNA differs from DNA?

A
  1. RNA does not contain thymine, but uracil instead.
  2. RNA is single-stranded
  3. RNA contains ribose (not deoxyribose)
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2
Q

Difference between RNA poly vs DNA poly? (2)

A
  1. RNA poly initiate RNA synthesis without a primer

2. more error prone then DNA

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3
Q

What are the 6 classes of RNA?

A
  1. mRNA
  2. rRNA
  3. tRNA
  4. snRNA
  5. snoRNAs
  6. other non-coding RNAs
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4
Q

What RNA functions to code for proteins?

A

mRNA

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5
Q

What RNA serves a number of functions in the nucleus, which includes pre-mRNA splicing?

A

snRNA

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6
Q

What RNA serves as components of the ribosome that are required for protein synthesis?

A

rRNA

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7
Q

What serves as adapters between mRNA and amino acids during protein synthesis?

A

tRNA

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8
Q

What serves to process and modify rRNAs?

A

snoRNAs

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9
Q

What types of functions do non-coding RNA’s have?

A

telomere synthesis
protein transport into the ER
transcriptional control

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10
Q

What is the poly for mRNA?

A

pol II

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11
Q

Poly for rRNA?

A

Pol I and poly III

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12
Q

Poly for tRNA?

A

Pol III

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13
Q

Poly for snRNA?

A

pol II and III

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14
Q

Poly for snoRNA?

A

pol II

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15
Q

Poly for other non coding RNAs?

A

pol III and II

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16
Q

What requires Pol II?

A

mRNA

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17
Q

What requires pol III?

A

tRNA

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18
Q

WHat requires Pol I and poly III?

A

rRNA

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19
Q

What requires pol II and pol III?

A

snRNA

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20
Q

Describe Pol I.

A

synthesizes rRNA; rRNA contains one copy of each of the four RrRNA molecules, 28S, 18S, 5.8S, and 5S.

Pol III makes some rRNA too

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21
Q

Describe Pol III.

A

responsible for rRNA but mainly tRNA. ( cells contain multiple copies of the gene for each tRNA, allowing sufficient quantities to be generated in a timely manner)

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22
Q

What transcribes the mRNA which is ultimately transcribed into proteins?

A

Pol II

23
Q

TATA box, CAAT box and GC region are all considered what?

A

consensus sequences

24
Q

What is TFIID?

A

factors that are required in order to initiate transcription at the promotor

25
Q

Steps of Pol II activation.

A
  1. TFIID has TBP on it, and this TBP binds to the TATA box.
  2. Binding causes a distortion and this causes TFIIE, F, and H to be recruited to the promotor.
  3. this forms the transcriptional initiation complex.
  4. TFIIH has DNA helicase activity, pulls apart, and Pol II begins to synthesize.
26
Q

Promotors have lots of what type of bases in them?

A

A/T bases since it is easier to pull them apart (only 2 H bonds)

27
Q

SP-1 binds to?

A

GC-rich regions

28
Q

NF1 binds to?

A

CAAT box

29
Q

What is an inhibitor of Pol II in humans?

A

death cap mushroom

30
Q

What are the 3 steps of processing pre-mRNA?

A
  1. capping
  2. introns cut out
  3. poly-a tail
31
Q

Explain how capping works?

A

5’ end of pre-mRNA modified

32
Q

Explain the process of cutting out introns?

A

splicing is catalyzed by splicesosomes:

  1. an adenine residue in the branch point of the intron attacks the 5’ splice site, cutting the sugar phos backbone
  2. cut 5’ end gets covalently bonded to adenine, and forms a loops
  3. newly generated 3’ end of the exon reacts with the 5’ end of the next exon
33
Q

What allows for more than one protein product to be generated from a single pre-mRNA transcript?

A

splicing

34
Q

Tropomyosin can be used for a specific topic in terms of splicing. What is it?

A

differential or alternate splicing: gives rise to a variety of different mRNA molecules

35
Q

Explain how polyadenylation works?

A
  1. 3’ end of the RNA has a polyadenylation signal
  2. signaled recognized by specific protein factors, and clevaged;
  3. a poly-A tail is added
36
Q

What are 2 things that are found in mRNA only?

A

5’ cap, and 3’ poly-A tail

37
Q

What is one of the best characterized conditions that can result from incorrect splicing?

A

B-thalassemia

38
Q

How does PKU result?

A

inability to convert phenylalanine to tyrosine; pts are found to have a single base change in the 5’ splice donor site which leads to incorrectly spliced mRNA and a truncated protein that lacks one exon

39
Q

What are 3 ways to regulate transcription in terms of gene availability?

A
  1. Chromatin Remodeling Complexes: use ATP hydrolysis to change structure to a less tightly bound histone core
  2. Histone Modification: HATS: increase; HDACS: decrease
  3. DNA methylation: cytosine –> methylcytosine: silences
40
Q

Where to DNA binding proteins bind to regulate transcription?

A

in the major groove because there are exposed poritons of bases

41
Q

What are 3 classes of gene regulatory proteins?

A
  1. helix-turn-helix
  2. Zinc finger proteins
  3. leucine zipper proteins
42
Q

Explain helix-turn-helix

A

2 a-helices

side chains of the AA in the C-term of the 2 a-helix help with DNA binding

43
Q

Explain zinc finger proteins.

A

zinc is coordinated in hisitidine and cysteine residues; zinc is required for protein folding and function

44
Q

What is an example of a receptor that is a zinc-finger DNA binding protein?

A

glucocorticoid receptor

45
Q

Explain leucine zipper proteins?

A

form dimers in which 2 a-helices form a coiled coil

-each a-helix contains a hydrophobic residue, typically a leucine, at every 7th position

46
Q

What are 2 examples of leucine zippers?

A

Fos and Jun

47
Q

Explain transcriptional regulation of the LDL receptor.

A
  1. low cellular cholesterol
  2. SP-1 binds GC-rich (requires CRSP as well)
  3. SREBP-1a is outside the nucleus and comes in and binds to SRE-1
  4. recruits a HAT, causing relaxation of chromatin, and LDL receptor gene transcription
48
Q

What is often found in teh promotor of the glucocorticoid response genes?

A

GRE

49
Q

What are 2 enzymes that are regulated by GRE?

A

PEP carboxykinase and liprotein lipase

50
Q

Where are receptors for thyroid hormones found?

A

inside the nuclues

51
Q

Explain regulation of thyroid hormone transcription.

A

No t3 bound: thyroid hormone receptor/RXR and HDAC

T3 bound: THR, RXR, and HAT

52
Q

EP300/CBP function as what?

A

HATS

53
Q

How does Tamoxifen work?

A

it is a competitive inhibitor of estrogen for receptor binding; inability to recruit factors to initiate transcription

Section 4 (7 decks)

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