RNA processing

Question 1

what is the difference between primary prokaryotic and eukaryotic mRNA?

Answer 1

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

Question 2

what is polycistronic?

Answer 2

if one RNA can make more than one protein

Question 3

what is noncoding sequence?

Answer 3

a part of mRNA that is not translated

Question 4

what is 5’ capping?

Answer 4

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

Question 5

what is CTD?

Answer 5

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

Question 6

how does capping happen?

Answer 6

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

Question 7

what is a 5’ cap used for?

Answer 7

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

Question 8

what is a cap binding complex?

Answer 8

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

Question 9

what are introns?

Answer 9

need to remove, used to make complex proteins?

Question 10

what are exons?

Answer 10

the pieces you want to keep

Question 11

when does splicing occur?

Answer 11

splice during transcription, not done in invertebrates

Question 12

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

Answer 12

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

Question 13

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

Answer 13

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

Question 14

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

Answer 14

pyridmidine-rich region

Question 15

what is a branch point?

Answer 15

important for exon excising

Question 16

what is trans-esterficiation?

Answer 16

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

Question 17

what enzymes carry out splicing?

Answer 17

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.

Question 18

U1 does?

Answer 18

base pairs with introns

Question 19

U2 does?

Answer 19

form base pairing with branch point

Question 20

how does BBP and U2AF work?

Answer 20

BBP and U2AF recognize branch point, U2 replaces them

Question 21

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

Answer 21

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

Question 22

what is exon junction complex?

Answer 22

marked at exon junction called EJC

Question 23

what is exon skipping?

Answer 23

where you skip an exon entirely

Question 24

what is cryptic splicing?

Answer 24

exon looks like intron sequence so they are accidently cut

Question 25

how is splicing error prevented?

Answer 25

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

Question 26

hows do exons by definition prevent errors in splicing?

Answer 26

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

Question 27

what is beta thalassemia?

Answer 27

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

Question 28

how do some errors occur?

Answer 28

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

Question 29

how do you get protein variance from the same gene?

Answer 29

alternative splicing

Question 30

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

Answer 30

bacteria

Question 31

how is the polyA tail put on?

Answer 31

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

Question 32

what are the 2 cleavage factors?

Answer 32

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

Question 33

what is PAP?

Answer 33

adds A's to cleaved RNA

Question 34

what are polyA binding proteins?

Answer 34

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

Question 35

in which organelle does transcription take place?

Answer 35

nucelus

Question 36

in which organelle does translation take place?

Answer 36

cytosol, mRNA must cross nucleus membrane

Question 37

what are SR proteins?

Answer 37

exon defining mechanisms

Question 38

what is hnRNP?

Answer 38

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

Question 39

what is EJC?

Answer 39

exon junction complex, put at exon junction

Question 40

what is CBC?

Answer 40

cap binding complex

Question 41

what are nuclear export receptor ?

Answer 41

proteins that export things from the nucleus that holds onto them

Question 42

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

Answer 42

no, some are nucleus restricted so they stay inside

Question 43

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

Answer 43

initiation proteins

Question 44

how does translation begin?

Answer 44

initiation protein interacts with polyA tail

Question 45

what happens to an improper complex?

Answer 45

gets degraded by enzymatic complex called exosomes in the nucleus

Question 46

what does RNA polymerase I translate?

Answer 46

rRNA and 5s rRNA

Question 47

what does RNA polymerase III translate?

Answer 47

tRNA

Question 48

does RNA polyermase I and II use the same shit?

Answer 48

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

Question 49

does RNA polyermase I use amplification at the translation level

Answer 49

no

Question 50

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

Answer 50

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

Question 51

is there chemical modification or cleavage for 5S rRNA?

Answer 51

no

Question 52

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

Answer 52

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

Question 53

what is snoRNA?

Answer 53

helps with modification and cleavage, transcribed by RNA polymerase II

Question 54

psuedouridine has a ______ ____

Answer 54

modified base

Question 55

2'O-methylated nucleotide has a ____ _____

Answer 55

modified sugar

Question 56

what is the nucleolus?

Answer 56

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

Question 57

when ribosomal problems are translated they were transported?

Answer 57

into the nucleolus and then assemble

Question 58

ribosome subunits are usually _____ until they are needed for translation

Answer 58

seperate

Question 59

the mitochondria has its own ___

Answer 59

circular DNA

Question 60

mitochondrial DNA i transcribed by ___ ____ ___

Answer 60

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

Question 61

mitochondrial DNA has ___ strands

Answer 61

2, one for each strand

Question 62

mitochondrial DNA is transcribed in ______ and yields?

Answer 62

entirety, mt mRNA, rRNA, and tRNA