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bio 340 > RNA processing > Flashcards

RNA processing Flashcards

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Biology 101 flashcards
1
Q

what is the difference between primary prokaryotic and eukaryotic mRNA?

A

for prokaryotes, there’s messages for different proteins on the same coding sequence, they all work on the same metabolic pathway.
for eukaryotes, one coding sequence per mRNA. have 5’ cap and poly-A tail

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2
Q

what is polycistronic?

A

if one RNA can make more than one protein

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3
Q

what is noncoding sequence?

A

a part of mRNA that is not translated

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4
Q

what is 5’ capping?

A

interacts with CTD of polymerase II, does not interact with I or III bc they dont have a CTD

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5
Q

what is CTD?

A

extends out of RNA polymerase II, gets phospherylated by TFIIH, interacts with capping enzymes, t carries RNA-processing proteins on its tail that are transferred to the nascent RNA at the appropriate time

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6
Q

how does capping happen?

A

phosphate removed, guanyl transferase (transfer GTP), GMP added, methyl transferase (adds methyl to base), add methyl on ribose (sometimes)

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7
Q

what is a 5’ cap used for?

A

signify that the mRNA has been successful on the 5’ end

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8
Q

what is a cap binding complex?

A

proteins that help with processing and export (nucleus to cytosol), translation

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9
Q

what are introns?

A

need to remove, used to make complex proteins?

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10
Q

what are exons?

A

the pieces you want to keep

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11
Q

when does splicing occur?

A

splice during transcription, not done in invertebrates

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12
Q

how does we know how the splicing mechanism know where to cut and where to join?

A

compare cDNA (isolate mRNA from cells and use reverse transcriptase to turn it back into DNA) and genomic sequence (sequences on chromosome). compare them and find difference bc you found the introns then you eventually find exons bc they line up

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13
Q

whats at the 5’ and 3’ end of the consensus sequence?

A

GU at the beginning of the 5’ intron and AG at end of 3’ intron

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14
Q

higher eukaryotes have a ______ upstream of the 3’ end of the intron

A

pyridmidine-rich region

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15
Q

what is a branch point?

A

important for exon excising

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16
Q

what is trans-esterficiation?

A

2 exons merge, branch point A has a OH group and attacks phosphate group. OH attacks another phosphate and leaves introns (lariat)

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17
Q

what enzymes carry out splicing?

A

spliceosomes: composed of RNAs and proteins
5 snRNAs interact with proteins to form snRNP (proteins+snRNA, U1, U2, U4, U5, U6) they base pair with primary mRNA that are being spliced.

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18
Q

U1 does?

A

base pairs with introns

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19
Q

U2 does?

A

form base pairing with branch point

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20
Q

how does BBP and U2AF work?

A

BBP and U2AF recognize branch point, U2 replaces them

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21
Q

what the FUCK goes on with U1/U2/U4/U5/U6?

A

after BBP AND U2AF does their shit, the rest of them come in (u4/u6 come as a dimer) trans-esterfication occurs. after lariat forms, they are degraded

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22
Q

what is exon junction complex?

A

marked at exon junction called EJC

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23
Q

what is exon skipping?

A

where you skip an exon entirely

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24
Q

what is cryptic splicing?

A

exon looks like intron sequence so they are accidently cut

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25
Q

how is splicing error prevented?

A

splicing occurs as RNA is being synthesized, cant skip if it doesnt exists

26
Q

hows do exons by definition prevent errors in splicing?

A

intron sizes are all over the place while exons are about the same
SR proteins bind to exons so the cell knows that is the exon, they also recruit u1 and u2

27
Q

what is beta thalassemia?

A

disease caused by difficulties in RNA splicing. seen in Mediterranean areas, slow growth, bone issues, etc.

28
Q

how do some errors occur?

A

splice site is gone. and causes exon skipping
puts a new splice site, extends exon region
new splice site, has another “exon”

29
Q

how do you get protein variance from the same gene?

A

alternative splicing

30
Q

there is no 5’ capping, rna splicing, and 3’ polyadenylation in _____

A

bacteria

31
Q

how is the polyA tail put on?

A

mRNA gets cleaved 10-30 nt downstream of their AAUAAA/AUUAAA sequence and before their GU/U rich sequence. poly A tail is added and rich sequence is degraded

32
Q

what are the 2 cleavage factors?

A

CPSF and CstF, hitched a ride on CTD, cleaves 30 nt downstream

33
Q

what is PAP?

A

adds A’s to cleaved RNA

34
Q

what are polyA binding proteins?

A

assemble onto polyA tail and determine the final length of the tail

35
Q

in which organelle does transcription take place?

A

nucelus

36
Q

in which organelle does translation take place?

A

cytosol, mRNA must cross nucleus membrane

37
Q

what are SR proteins?

A

exon defining mechanisms

38
Q

what is hnRNP?

A

heterogeneous nuclear ribonuclear protein, helps with RNA processing and export packaging

39
Q

what is EJC?

A

exon junction complex, put at exon junction

40
Q

what is CBC?

A

cap binding complex

41
Q

what are nuclear export receptor ?

A

proteins that export things from the nucleus that holds onto them

42
Q

do all proteins associated with mRNA go through the nucleus membrane?

A

no, some are nucleus restricted so they stay inside

43
Q

what is CBC replaced with once the mRNA leaves the nucleus?

A

initiation proteins

44
Q

how does translation begin?

A

initiation protein interacts with polyA tail

45
Q

what happens to an improper complex?

A

gets degraded by enzymatic complex called exosomes in the nucleus

46
Q

what does RNA polymerase I translate?

A

rRNA and 5s rRNA

47
Q

what does RNA polymerase III translate?

A

tRNA

48
Q

does RNA polyermase I and II use the same shit?

A

no RNA polyermase I uses unique promoters and regulatory sequences called upstream element and core elements. uses their own general transcription factors

49
Q

does RNA polyermase I use amplification at the translation level

A

no

50
Q

how do we get 80% of rRNA if RNA polyermase I doesnt go through simplification?

A

theres 10 million copies of rRNAs, made from 200 copies of rRNA genes per haploid spread over 5 chromosomes

51
Q

is there chemical modification or cleavage for 5S rRNA?

A

no

52
Q

whats unique about RNA polyermase III’s promoter and regulatory sequence?

A

they are internal in the RNA and called A/B/C box

53
Q

what is snoRNA?

A

helps with modification and cleavage, transcribed by RNA polymerase II

54
Q

psuedouridine has a ______ ____

A

modified base

55
Q

2’O-methylated nucleotide has a ____ _____

A

modified sugar

56
Q

what is the nucleolus?

A

not defined by membrane, where rRNA is processed and assembled into ribosomes, disappears during metaphase

57
Q

when ribosomal problems are translated they were transported?

A

into the nucleolus and then assemble

58
Q

ribosome subunits are usually _____ until they are needed for translation

A

seperate

59
Q

the mitochondria has its own ___

A

circular DNA

60
Q

mitochondrial DNA i transcribed by ___ ____ ___

A

mitochrondiral RNA polymerase which is encoded in the nucleus DNA and then transported into the mitochondria

61
Q

mitochondrial DNA has ___ strands

A

2, one for each strand

62
Q

mitochondrial DNA is transcribed in ______ and yields?

A

entirety, mt mRNA, rRNA, and tRNA

bio 340 (13 decks)

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