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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
Ways to control initiation
promoter sequences, activators (Transcription factor), and repressors (transcription factor)
26
Activators
accessory proteins that bind near the promoter and facilitate the binding of the RNA polymerase
27
Repressor
bind to the sequence where the RNA polymerase wants to bind
28
Way to stop RNA elongation
remove an RNA's 3' OH so that when incorporated it will not be able to attack the next nucleotide
29
T or F: RNA polymerase can let go of DNA before it is finished making the complete RNA transcript
False. RNA polymerase is entirely processive.
30
Types of termination
rho independent and rho dependent
31
Rho independent termination
self-complenatry sequence of RNA forms a hairpin structure. Usually followed by AAA residues
32
Rho dependent termination
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
RNA polymerase I
synthesizes the precursors of rRNAs
34
RNA polymerase II
synthesizes mRNA precursors and it can recognize thousands of promoters of varying sequences
35
RNA polymerase III
synthesizes precursors of rRNA, tRNA, and other small RNAs.
36
Number of subunits in RNA polymerase II
12 subunits
37
Largest subunit on RNA poly II
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
Proteins needed for initiation of RNA poly II
RNA Poly II, TATA-binding protein, TFIIA, TFIIB, TFIIE, TFIIF, TFIIH, and other elongation factors
39
TBP
TATA-binding protein - recognizes the TATA box
40
TFIIA
stabilizes the binding of TFIIB and TBP to the promoter
41
TFIIB
binds to TBP and recruited the Pol II-TFIIF complex.
42
TFIIE
Recruits TFIIH; has ATPase and helicase activites
43
TFIIF
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
TFIIH and its functions
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
TATA box location in eukaryotes
-30
46
Eukaryotic assembly
TBP binds to TATA box. TFIIB, TFIIF-RNA Poly II, TFIIE, and TFIIH
47
What is released as RNA Pol II synthesizes after initiation
TFIIE and TFIIH
48
What remains associated with RNA Pol II throughout elongation
TFIIF
49
What is the 5' cap
7-methylguanosine
50
3' tail
poly(A) tail of about 80-250 nucleotides
51
Introns
what are spliced out (non coding part of a gene)
52
Exons
What are kept in forming of the final transcript (coding part of a gene)
53
Unique features of 5' cap
5' to 5' triphosphate linkage. Methylated after it was added to mRNA. Comes from GTP
54
Where and when is the cap methylated
N-7 and after it has been added to mRNA
55
4 enzymes involved in the 5' cap
Phosphohydrolase, Guanylyltransferase, Guanine -7-methyltransferase, and 2'-O-methyltransferase
56
Phosphohydrolase
water attacks the gamma phosphorus position. Gamma will leave as an inorganic phosphate, leaving the 5' end to be a diphosphate
57
Guanylyltransferase
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
Guanine-7-methyltransferase
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
2'-O-methyltransferase
transfers a methyl to the 2' O, sometimes on the first or first and second position. Methyl from SAM
60
poly(A) site recognition sequence
AAUAAA
61
poly(A) polymerase
adds 80-250 A residues to the trimmed transcript (which is trimmed by an endonuclease)
62
Tail complex
endonuclease, poly A polymerase, and other proteins for sequence recognition, cleavage, and regulation of tail length.
63
Four major groups of introns
Group I, Group II, Spliceosomal introns, and tRNA introns
64
Group I introns
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
Group II introns
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
Spliceosomal introns
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
Alternative splicing
way of having one gene encode multiple different proteins

BioChem (14 decks)

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