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BCHM 218 > Module 4 > Flashcards

Module 4 Flashcards

1
Q

transcription start site differnce btw prokaryotes and eukaryotes

A

p- 5’UTR=10-30 nt
e- 5’UTR= 100nt

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2
Q

rna poly differnce btw pro/eur

A

p- one rna poly
- sigma factor allows for
- specificity of promtor
- RNA holoenzyme- 5 subunits + sigmafactor
- dna entry, exit and ddntp entry channel

dna unwind bubble is 17nt long and the rna-dna is 8-10nt

e- 3 rna poly
poly1 -rRNA most abundant 80%

poly 2- mRNA
- can be blocked by alpha-aminitin
RPB1 is largest subunit
30s is small subunit
50s is large subunit
-TATA

poly 3- tRNA
- TATA

even if they dont have TATA box they still will have TATA binding protein complex

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3
Q

Proofreading of bacterial RNA polymerase

A

kinectic proofreading
- creates a stall in RNA poly and uses pyrophosphoratlysis involve PPi

nucleophilic proofreading
- if not stalled it will fray and then backtraking and rna and dna will fray into the rNTP channel of RNA poly
- rna poly intrinsic nuclease will remove fray by H20

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4
Q

Prokaryottic promotor

A

transcriptional start site= downstream of promototr
-35 to -10 where sigma factor binds
-60 to -40 interact with alpja subunit of RNA poly and it AT rich

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5
Q

eukaryotic promotor

A

binding sites can be upstream or downstream
transwcription factors bind promoter region (+1)

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5
Q

what binds to the minor groove

A

tata binding protein

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6
Q

σ70 close and open complex

A

closed- n-terminus of sigma factor blocks dna entry

open- sigma factor unblocks site and bubble opens

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7
Q

what is the prokaryotic sigma factor that is for house keeping genes

A

σ70

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7
Q

what is abortive inititian

A

prokaryotes must have built 8-10 nt before it is stable
- or the RNA can dissociate from the DNA

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7
Q

using transcription factors for nuclear reprogramming

A
  1. induced pluripotency
  2. irect reprogramming
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8
Q

what is induced pluripotency

A

when a differnted stem cell is pushed back up the moutain to become a stem cell again
- so that it can rediffrentiate

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9
Q

what is direct reprogramming

A

changing the transcription factors to change a differnted cell to another differnented cell

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9
Q

intitation of transcription in prokaryotes

A

shine dalgarno sequence
- purine rich
- the 302 subunit has a 16s subunit that reconizes a shine dalgarno sequence

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10
Q

what is EMSA (electrophorectic mobility shift assay)

A

asseccing DNA binding to protein
- higher weight will go to top
- on native non-denaturing gel

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10
Q

initatiation of transcription in eukaryotes

A

kozak sequence
is 2-3 purine rich before the aug and G after the aug
interact with anticodon arm of Met-tRNAiMet

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11
Q

DNA footprinting steps

A
  1. amplify dna from one end radiolabeled (PCR)
  2. cleave DNA in the presence or absense of a dna binding protein
    - one break per strand
  3. separate strand by gel electrophorisis and then the spots that come empty mean that a dna binding protein was their
    - products close to primer will fall first
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12
Q

DNA foot printing vs EMSA

A

dna footprinting tells where the dna is bound emsa tell if the dna binds

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13
Q

processing of pre-mRNA

A
  • 5’ cap
    -3’ tail
  • splicing
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13
Q

5’ capping methylated

A

that it prevents exoribonuclease activity from attacking the mRNA

  • allow for circulation of mRNA- by elf4f

-enhance stability

  • mediate binding of mRNA to the ribosome
  • happens during transcription afte 20-30nt added
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13
Q

3’ poly a tail

A

prevent exoribonuxlease activity
- allow for circulation of mRNA- by elf4f
-added when their is a polyadenalation signal and gt rich signal

  • recruite endonuclease to cut btw the two signals then PAP and PABP add A residues
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13
Q

splicing

A

allow for variation between genes but not chnage exons around just inclusion and exclusion

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14
Q

prokaryotes processing of mRNA

A

transcription and translation happen simultationously

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15
Q

what is not spliced out during splicing of premrna

A

5’utr and 3’utr

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16
Q

processing mRNA on quatifying gene expression

A

on RT and qPCR and RNA-seq
- can allow for more precess process since the exons are together can allow for more specific primers

on qpcr primer
- primer to span exon-exon so that it can exclude genomic dna and only inculde cdna

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17
Q

genetic code degenerate

A

61 amino acids codons with 20 aa
3 stop codons

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18
Q

robust genectic code allows

A

to absorb mutation= snps

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19
Q

Rules of the genetic code

A

non overlapping - tested by subsitution and it chnaged only one amino acid
- if not would effect 3 aa

read in triplets and no pauses- tested by insertion and deletion
linear

linear and c terminal- cterminal end was eaten first
3h and 14c were not linear

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20
Q

code mutations

A
  1. translation mutations
    - pur -> pur or pyr->pyr
  2. silent mutations
    - change nt and but no aa change
  3. missense mutations
    - chnage in aa which chnages the aa can be deterious or non deterious
  4. nonsense mutations
    -codes for termination, causes non-funtionl/degragation of protein within first round of translation
  5. non stop mutations
    - remove termination
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20
Q

Nonsense mediated mRNA decay (NMD)

A
  1. detection of exon junction complex can tell it stoped premature
  2. decaping
  3. prone to exoribonuclease
  4. if pass this phase it can still be detected in final exon and trigger NMD at the 3’UTR
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21
Q

non stop mrnas detection

A

rna poly will read the poly a tail createing many lys= this triggers 3’-5’ exoribomnuclease to degrade the protein and the transcript

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22
Q

trna - features

A

small non-coding rna
cca amino acid arm and anticodon

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22
Q

what direction is the anticodon

A

5’-3’

23
Q

their is ___ aminoacyl-tRNA synthetase for each amino acid

A

one

  • 20
24
Q

tRNA language
1. charged
2. uncharged
3. prokaryote met
4. prokaryote intitaition met
5. eukaryote met
6. eukaryote initiation met

A
  1. leu-tRNA^leu
  2. tRNA^leu
  3. tRNA^met
  4. tRNA^fmet
  5. tRNA^met
  6. tRNAi^met
25
Q

fidility of charging is govered by

A

amino acyl-tRNA synthetase not the ribosome

26
Q

what governs the fidility of codon anticodon parirting

A

the ribosome decoding center

27
Q

subunits of prokaryotic ribosome and eukaryotiv ribosome

A

30s and 50s
making up the 70 s ribosome

40s and 60s
making up the 80s ribosome

28
Q

wooble hypothesis rules

A
  1. codon 5’-3’ first wo bases must watson and crick
  2. anticodon 5’-3’ if C or A has one codon
  3. anticodon 5’-3’ if G or U has two codons
  4. I can be found on anticodon and it can wooble with C, A, U three codons
28
Q

The ribosome

A

peptidyl transferase center and decoding center - 60% is rRNA and 40% is r protein

A site- aminoacyl tRNA entry on 3’ of mRNA

P site- growing peptide - transfer p sit to a site

E site- exit site for uncharged tRNA

28
Q

prokaryotic intition

A

IF-1 blocks A site and ensure alignment of tRNA^fmet

IF3 stablize 30 s

IF2 is a chaperon which moves tRNA^fMet to the psite

29
Q

what is the role of transformylase

A

to add formyl group to methonine preventing met from preforming in eleongation in a two step process(block N terminus)

30
Q

what is polyscitronic mRNA

A
  • it is in prokaryotes and a shine dalgarno seqeucne can be used mutiple times depending on the reading frame
  • one transcript, multiple proteins
31
Q

what is considered a poycistronic mRNA

A

prokaryotoes with overlapping genes
- shine-dalgarno sequnce can have overlapping start and stop to shift the reading frame

32
Q

Fact: prokaryotes can also have non-overlapping so multiple SDS

A
32
Q

eukaryotes have non-overlapping genes what does this mean

A

one mRNA will only have one protein

33
Q

prokaryotic initition complex

A

tRNA^fmet with large and small ribosomal subunit and the intion factors dissociate uses GTP

33
Q

eukaryotic intition factors

A

circulzation of mRNA by the 3’ poly a tail and the 5’ capping that will interact with elf4f

  • multiple translation events on the same mrna
  • polysome
33
Q

what is a polysome

A

1 mrna multiple transcribing ribosomes

33
Q

steps of elongation

A
  1. aminoacycl trna sythetase charges trna and EF-Tu brings into A site
  2. correct pairing causes ribosome A site (A1493-2/3 adensosine) to flip out and pair
  3. cause conformational change of 30s subunit opening the 16s subunit
  4. EF-Tu-GTP is hydrolyxed into EF-Tu-GDP + pi to provide enrgy for accomodation of tRNA
  5. if this was incorrect it will dissocaite

pt 2

  1. aa nucleophilic attact on fMEt (catalyzed by peptidyl transferase)
  2. tRNA to E site and growing chain onto A site then Asite opens up - translocation
33
Q

what is EF-Tu

A

brings the charged trna to the a site for eleongation

34
Q

what are aminoglycosides

A

they cause the flip out of the ribosome and reduce transitional fidelity

  • kill bacteria through incorrect translation fidelity
  • does not effect eukaryotes
35
Q

termination
class 1
and class 2

A

class1: RF-1 and RF-2
reconzie stop and goes into A site mimic tRNA
class2: RF-3
removes RF1 and 2 by hydrolying to remove RF-3

35
Q

lac operen rule

A

the lac operon is on when lactose is opresent and glucose is absent

  • negative regulation
36
Q

it is polyscietrnic mRNA

A

has a repressor (lac I) and operator (lac o)
- both have promotors

laz z - b galactoside to metabolize lactose

lac y- gaactside permease for lettting lactose into cell

lac a- modifies toxic galactosides

37
Q

Lac repressor

A

seprate promoto and transcribed independently and consitituly

  • binding of 2-3 operator sites tieing dna in a loop- on the major groove
  • binds inverted repeats - since it is a heterodimer
38
Q

what is the role of allolactose

A

is their when th lac operon is off but leaky and is broken down by lac z

  • is a allosteric effector of the repressor and chnages its affintity to bind dna
  • turns on the lac operon
39
Q

The role of effectors in negative regulation

A

activation- bind to repressor to remove it from dna (on)

inhibition- bind to repressor to add the repressor (off)

39
Q

The role of effectors in positive regulation

A

activation- bind to activator increase transcription ()

inhibition- bind to activator decrease transcription ()

40
Q

positive regulation of the lac operon- catabolic repression

A

metabolism of lactose is blocked in the presence of glucose

41
Q

what is the role of an activator

A

-they increase transcription dial up or down

42
Q

differnce between negative and positive reghulation of the lac operon

A

negative regulation is dealing with on and off with the repressor

postitive is high or low and deals with the activator

43
Q

CRP is a activator that works in the resence of cAMP which is a effector

A

when glucose is low cAMP is high (increase production, decrease export)
- increasing cAMP allows binding of CRP with increase lac operon expression

44
Q

CRP structure

A

homodimer with cAMP as an effector

45
Q

merodiploid cell

A

partially dipliod, haploid genome (lac operon) into a plasmid with an exisiting lacoperon

46
Q

lac I properties

A
  • repressor
  • can be rescued with a working repressor lac operon
  • if broken lac operon is always on
47
Q

lac o - operator

A
  • cant be rescued if broken the lac operon is always on
48
Q

activator

A

in positive regulaton
-bind to dna and effect rna poly to turn on lac operon

-cAMP is its effector

49
Q

effector

A

bind to repressor or activator to chnage its affinity for rna polymerase

49
Q

repressor

A

in negative regulation
- bind to dna and effect rna poly to turn off lac operon

-allolactose is its effector

49
Q

housekeeping genes

A

always being expressed since they are essential like the lac repressor

50
Q

co-activator/co-repressor

A

they act as a bridge between activator and the rna poly

  • co-activator with induce bindingn

-co repressor prevent binding

51
Q

post transcriptional gene silencing (PTGS)

A

by mirna and sirna

  • they will degrade mRNA after its been transcriped
52
Q

how does mirna work

A

mirna is made with many self complementary parks and then exonucleases to cute the tail then exported out of the nucleus
- then they are recuirted by RISC and AGO and then a strand is descarded
- bind to mrna and is degraded since low complemaerity by AGO

53
Q

how does sirna work

A

in the cytoplasm is is from virus, recruited by RISC and AGO and then a strnad is removed

  • mrna is is cleaved when is bound
54
Q

what is RISC

A

rna-induced silencing complec that cleaves dna that is complementart to the the match the rn its bound to

55
Q

mirna and sirna bind? in pro and euk

A

p- the coding region
e- the 3’utr

56
Q

reporter plasmid

A
  • included a portion if mirna to see if its expressed
  • the gene mrna will decrase glowing if more mirna is bound

more mirna= decrease in translation and increase in degragation of mrna

57
Q

role of non-coding rna in mangment of mirna

A

such as incrna - they can compete for binding with mrna and then so that expression of mrna can happen

  • remove saturation of mirna by having the 3’utr binding site
58
Q

how to increase and decrease tanslation with mirna

A

increase Trans= decrase mirna

decrase trans= increase non-coding rna

BCHM 218 (2 decks)

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