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BIO130—sec 1 MR > week 5 > Flashcards

week 5 Flashcards

1
Q

molecular definition of a gene

A

the entire nucleic acid sequence that is necessary for the synthesis of a protein (and its variants) or RNA.
-segments of DNA that are transcribed into RNA

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2
Q

what are the two types of genes

A
  1. when transcribed the resulting RNA encodes a protein (e.g. mRNA)
  2. when transcribed the resulting RNA functions as RNA and may not be translated into protein (e.g. rRNA or tRNA)
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3
Q

why is transcription highly regulated?

A

transcription is energy intensive (cell doesn’t want to do it if it doesn’t have to)

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4
Q

What is RNAP’s function?

A

catalyzes the sequential addition of ribonucleotides 5’-3’

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5
Q

How are RNA nucleotides linked?

A

phosphodiester bonds

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6
Q

what is the template of an RNA transcript?

A

ssDNA

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7
Q

compare RNAP and DNAPol

A

RNAP can make new strand w/o primer but makes more mistakes than DNAPol

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8
Q

Does RNAP has proofreading capacity?

A

yes (backspace), but doesn’t have the same ability as DNAPol and doesn’t have repair mechanisms

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9
Q

What does the Sigma Factor do?

A

binds to RNAP and finds promoter sequence (start site)

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10
Q

What happens after sigma factor finds promoter sequence?

A

-localized unwinding of DNA and a few short RNAs are synthesized initially (abortive attempts)
-RNAP clamps down (goes through conformational change after about 10 attempts)
Sigma factor is released

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11
Q

RNAP is highly processive. What does this mean?

A

it can add nucleotides quickly without falling off

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12
Q

why can RNAP find promoter sequence and how does it know which strand?

A

reading 5’-3’ the sequences are different and are reasonably specific and asymmetric. Sequence determines for sigmas factor which strand to bind to. There are different sigma factors that recognize different promoter sequences.

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13
Q

RNA secondary structure

A

as new RNA transcript leaves the RNAP (especially in short RNA/DNA duplex area), it can begin to bp with itself forming loops and hair pins (happens often because it’s single stranded)

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14
Q

are terminator sequences transcribed?

A

yes

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15
Q

what do terminator sequences do

A

way for RNAP to recognize when its job is done and when its mRNA should be released—don’t want to replicate entire RNA sequence

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16
Q

terminator sequences are rich w which nucleotides?

A

c & g (not sure this is correct)

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17
Q

how do the hairpin sequences (termination signals) help to dissociate the RNA transcript from the polymerase?

A

They disrupt H-bonding of new mRNA transcript with DNA template

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18
Q

what does “gene expression” mean

A

it just means transcription of a gene if it’s an mRNA and translated into protein

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19
Q

how is euk gene expression more complicated than pro

A

euks have more DNA to fit into nucleus and a more complex gene structure (introns and exons), chromatin structures to deal with, more processing

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20
Q

how many RNA polymerases do euks need

A

3 RNAPs because they are more complicated

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21
Q

do RNAPs have quaternary structure

A

yes all 3 euk RNAPs is a multi-subunit protein

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22
Q

compare the genes transcribed of RNAP I and RNAP II

A

RNAP I: most rRNA genes, RNAP II: all protein-coding genes, miRNA genes, plus genes for other noncoding RNAs

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23
Q

compare the number of subunits of bacterial RNAP and euk RNA Pol II

A

bacterial RNAP has 5, euk RNA Pol II has 12

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24
Q

what is unique about the structure of RNA Pol I

A

it has a carboxyl terminal domain (CTD)

25
Q

what is unique about the structure of RNA Pol I

A

it has a carboxyl terminal domain (CTD)

26
Q

what is the difference b/w a nucleoside and a nucleotide

A

nucleoside is just pentose sugar and nitrogenous base, nucleotide has phosphate grp attached

27
Q

what are transcription factors?

A

proteins that help eukaryotic RNA polymerases position at the promoter, make sure what is being transcribed is correct, not held to RNAP for long

28
Q

what has a similar function to transcription in bacterial transcription?

A

the sigma subunit of RNA polymerases

29
Q

eukaryotic RNA polymerases need to deal with ________________

A

chromosomal structures

30
Q

where is the TATA box found

A

~30 bp upstream from transcription start site

31
Q

what number is the transcription start site given

A

+1

32
Q

How many types of promoter sequences do euks often need

A

2 or 3

33
Q

what is the first step in the initiation of transcription (consider drawing a flowchart for this)

A

binding of TBP subunit of TFIID near TATA box sequence, this mobilizes the binding of TFIIB complex adjacent to TATA box

34
Q

what does TBP stand for?

A

TATA box binding protein

35
Q

TFIID quite significantly bends DNA, what does this do

A

acts as a signpost for other transcription fators

36
Q

TFIID quite significantly bends DNA, what does this do

A

acts as a signpost for other transcription factors

37
Q

what does TFIIF do?

A

helps to stabilize interaction with TFIIB and TFIID

38
Q

what does TFIIE do

A

attracts and regulates TFIIH

39
Q

what does TFIIH

A

helicase activity (uses ATP to pry apart DNA strands) and phosphorylation of CTD of RNAP II (Activates it)

40
Q

when can transcription be initiated

A

CTD is phosphorylated, most TFs are released, elongation mode of RNAP

41
Q

what is the structure of the CTD

A

tandem repeats of 7 amino acids

42
Q

how many repests does the CTD of RNAP II in yeast have?

A

26

43
Q

how many repeats does the CTD of RNAP II in humans have?

A

52

44
Q

what is the sequence of aa that is repeated in the CTD

A

Tyr-Ser-Pro-Thr-Ser-Pro-Ser

45
Q

what does phosphorylation of RNAP II do

A

activates RNAP II, includes conformational change in RNAP so it can go into elongation mode

46
Q

What is phosphorylates?

A

adding phosphate groups on Ser located on the CTD

47
Q

how many proteins are involved in initiating euk transcription

A

> 100 subunits of many proteins

48
Q

3 main steps of mRNA processing

A

addition of 5’ cap, removal of introns (splicing), processing and polyadenylation of 3’ tail

49
Q

different proteins are used to recruit splicing factors, when the CTD is phosphorylated it is used to recruit capping factors, splicing factors, and polyadenylation factors

A

yes

50
Q

phosphorylation of the CTD of RNAP II results in the binding od:

A

RNA processing proteins, additional phosphorylation of CTD including Ser 2

51
Q

5’ capping does what for RNA

A

protects it from exonucleases (false starts won’t have 5’ cap and will be digested)

52
Q

when does 5’ capping happen

A

before mRNA is fully transcribed

53
Q

what are the two steps to the removal of introns

A
  1. Branch-point A attacks the 5’ splice site of the intron sequence
  2. 3’ of one exon reacts with 5’ of the next exon to release the intron
54
Q

what is the structure of intron splicing called

A

lariat

55
Q

what are snRNPS

A

snRNAs bound to protein (found in spliceosomes)

56
Q

why are nRNPS needed

A

pre-mRNAs not able to self-splice

57
Q

how is mRNA spliced

A

spliceosomes assemble on mRNA to remove introns, move from CTD of RNAP to new mRNA
- when splicing is complete exon junction complex is added

58
Q

examples of abnormal splicing

A

exon skipping, single nucleodide changes destroy normal splice sites, single nucleotide changes create new splice sites (cause new exons to be incorporated)

59
Q

why is abnormal splicing bad

A

~15% of genetically inherited diseases arise from mutations/errors at splice sites or spliceosomal proteins

BIO130—sec 1 MR (5 decks)

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