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BioChem > Lecture 7 > Flashcards

Lecture 7 Flashcards

1
Q

Coding strand

A

equivalent DNA strand to the RNA

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2
Q

Noncoding strand

A

Used as a template for transcription

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3
Q

RNA polymerase direction

A

5’ to 3’

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4
Q

mRNA

A

encode the amino acid sequences of all polypeptides found in the cell

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5
Q

tRNA

A

match specific amino acids to triplet codons in mRNA during protein synthesis. Processing occurs and trims the 5’ and 3’ end. CCA is added onto the 3’ end.

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6
Q

rRNA

A

RNA component of the ribosome, interact with tRNA during translation. Also get methylated

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7
Q

what does RNA polymerase use to elongate a strand

A

3’ OH to attack the alpha phosphorous atom on the incoming nucleotide and releases PPi

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8
Q

3 residues important in RNA polymerase attack

A

3 aspartic acids stabilize the 2 magnesium ions

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9
Q

Type of catalysis seen in RNA polymerase

A

general base catalysis

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10
Q

Footprint of transcription bubble, elongation phase, and initiation phase

A

transcription bubble: 17
Elongation phase: 35
Initiation phase: 100

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11
Q

Strand that is in the active site

A

Noncoding/template strand

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12
Q

Elongation rate

A

about 50-90 nucleotides per second.

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13
Q

5 core subunits of RNA polymerase and the 6th subunit

A

two alpha, Beta, Beta’, omega subunits with a sigma subunit.

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14
Q

Alpha subunit function

A

assembly and binding to UP elements

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15
Q

Beta subunit

A

main catalytic subunit

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16
Q

Beta’ subunit

A

responsible for DNA-binding

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17
Q

Omega subunit

A

protect the polymerase from denaturation

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18
Q

sigma subunit

A

directs enzyme to the promoter

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19
Q

Negative numbers in initiation

A

upstream of the start site. Correspond to the DNA’s 3’

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20
Q

Positive numbers in initiation

A

downstream of the start site, thus part of the new RNA polypeptide. Correspond to the DNA’s 5’

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21
Q

Position of two promoter regions

A

-10 (Pribnow/TATA box) and -35

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22
Q

UP elements are rich in what and bind to what

A

AT rich region and bind to the alpha subunits, thus allowing for higher expression rates

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23
Q

closed complex

A

polymerase first binds to the promoter

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24
Q

open complex

A

after polymerase binds to the promoter and the DNA is partially unwound near the -10 sequence

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25
Q

Ways to control initiation

A

promoter sequences, activators (Transcription factor), and repressors (transcription factor)

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26
Q

Activators

A

accessory proteins that bind near the promoter and facilitate the binding of the RNA polymerase

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27
Q

Repressor

A

bind to the sequence where the RNA polymerase wants to bind

28
Q

Way to stop RNA elongation

A

remove an RNA’s 3’ OH so that when incorporated it will not be able to attack the next nucleotide

29
Q

T or F: RNA polymerase can let go of DNA before it is finished making the complete RNA transcript

A

False. RNA polymerase is entirely processive.

30
Q

Types of termination

A

rho independent and rho dependent

31
Q

Rho independent termination

A

self-complenatry sequence of RNA forms a hairpin structure. Usually followed by AAA residues

32
Q

Rho dependent termination

A

rho (protein) is a helicase and hydrolyzing ATP in the 5’ to 3’ direction chasing behind RNA polymerase. CA rich region which likely causes the pause.

33
Q

RNA polymerase I

A

synthesizes the precursors of rRNAs

34
Q

RNA polymerase II

A

synthesizes mRNA precursors and it can recognize thousands of promoters of varying sequences

35
Q

RNA polymerase III

A

synthesizes precursors of rRNA, tRNA, and other small RNAs.

36
Q

Number of subunits in RNA polymerase II

A

12 subunits

37
Q

Largest subunit on RNA poly II

A

RBP1 (similar to beta’ subunit) and has a long tail containing residues likely making up a beta turn and OH residues which allow for phosphorylation

38
Q

Proteins needed for initiation of RNA poly II

A

RNA Poly II, TATA-binding protein, TFIIA, TFIIB, TFIIE, TFIIF, TFIIH, and other elongation factors

39
Q

TBP

A

TATA-binding protein - recognizes the TATA box

40
Q

TFIIA

A

stabilizes the binding of TFIIB and TBP to the promoter

41
Q

TFIIB

A

binds to TBP and recruited the Pol II-TFIIF complex.

42
Q

TFIIE

A

Recruits TFIIH; has ATPase and helicase activites

43
Q

TFIIF

A

Binds tightly to Pol II; binds to TFIIB and prevents binding of Pol II to nonspecific DNA sequences. Guides it to the correct DNA sequences

44
Q

TFIIH and its functions

A

Unwinds DNA at promoter (TATA box); phosphorylates Pol II (within the C Terminal Domain); recruits nucleotide-excision repair proteins. Completes closed complex and creates open complex

45
Q

TATA box location in eukaryotes

A

-30

46
Q

Eukaryotic assembly

A

TBP binds to TATA box. TFIIB, TFIIF-RNA Poly II, TFIIE, and TFIIH

47
Q

What is released as RNA Pol II synthesizes after initiation

A

TFIIE and TFIIH

48
Q

What remains associated with RNA Pol II throughout elongation

A

TFIIF

49
Q

What is the 5’ cap

A

7-methylguanosine

50
Q

3’ tail

A

poly(A) tail of about 80-250 nucleotides

51
Q

Introns

A

what are spliced out (non coding part of a gene)

52
Q

Exons

A

What are kept in forming of the final transcript (coding part of a gene)

53
Q

Unique features of 5’ cap

A

5’ to 5’ triphosphate linkage. Methylated after it was added to mRNA. Comes from GTP

54
Q

Where and when is the cap methylated

A

N-7 and after it has been added to mRNA

55
Q

4 enzymes involved in the 5’ cap

A

Phosphohydrolase, Guanylyltransferase, Guanine -7-methyltransferase, and 2’-O-methyltransferase

56
Q

Phosphohydrolase

A

water attacks the gamma phosphorus position. Gamma will leave as an inorganic phosphate, leaving the 5’ end to be a diphosphate

57
Q

Guanylyltransferase

A

5’ cap comes from a GTP. An O- will be activated on the beta phosphorous atom of the ppNp. This acts as a nucleophile and will hit the alpha phosphorous atom and kick off the beta and gamma phosphorous atoms of GTP, creating a leaving pyrophosphate. This creates the 5’ to 5’ triphosphate linkage

58
Q

Guanine-7-methyltransferase

A

put the methyl group on the 7’ N of the guanine. Gets its methyl from SAM (adoMet - S+ region) which then goes to SAH (adoHcy)

59
Q

2’-O-methyltransferase

A

transfers a methyl to the 2’ O, sometimes on the first or first and second position. Methyl from SAM

60
Q

poly(A) site recognition sequence

A

AAUAAA

61
Q

poly(A) polymerase

A

adds 80-250 A residues to the trimmed transcript (which is trimmed by an endonuclease)

62
Q

Tail complex

A

endonuclease, poly A polymerase, and other proteins for sequence recognition, cleavage, and regulation of tail length.

63
Q

Four major groups of introns

A

Group I, Group II, Spliceosomal introns, and tRNA introns

64
Q

Group I introns

A

self-splicing. No consensus splice sites. Requires a gaunylate to start, which attacks the 3’ end of the first exon, freeing the 3’ OH to attack the 5’ end of the second exon

65
Q

Group II introns

A

self-splicing. There are consensus splice sites - GU…AG. Requires an adenosine residue (uses 2’ OH to attack) inside of the intron to attack, creating a lariat structure with 3 phopshodiester bonds.

66
Q

Spliceosomal introns

A

Consensus splice sites - GU …AG. Uses ribonuclear proteins (proteins with RNA) which bind to the 5’ GU and then looks for an A in the intron. ATP dependent and uses the proximity affect to create a lariat.

67
Q

Alternative splicing

A

way of having one gene encode multiple different proteins

BioChem (14 decks)

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