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spring-cell bio > Exam 4: lecture 12-transcription, mRNA, and splicing > Flashcards

Exam 4: lecture 12-transcription, mRNA, and splicing Flashcards

1
Q

function of promoter

A

recognition site for RNA to bind
tell rna to start (me, me, me)

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2
Q

What is the direction that RNA is read?

A

5’ by 3’

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3
Q

What is another name for template strand?

A

sense/ coding strand

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4
Q

what is another name for the non-template strand/

A

antisense

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5
Q

Does mRNA can be made wo a primer?

A

yes, de novo (from newness)
-added @ the 3’ end of growing chain
-they can be read one direction

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6
Q

How to know where transcription?

A

based on distance
-the beginning of the polymerase

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7
Q

the sequence of prokaryotes

A

-only has 1 RNA polymerase
TTGACAT ————————————–TATAAT
-35 region (15-17bp) -10 (the most common sequence

-> TATAAT box is 10 bp upstream of the polymerase (where transcription starts)
->15-17 bp(Y: any pyrimidine)

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8
Q

Why do certain sequences appear in all organisms?

A

they are conserved- not loss in evolution

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9
Q

where does transcription starts

A

<——upstream———–+1———–downstream———->

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10
Q

Eukaryotic promoters: RNA polymerase II

A

TATA box: -25
Py2CAPy5 (initiator) near +1

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11
Q

Eukaryotic promoters: RNA polymerase I

A

the majority of the rRNAs
-core promoter: -45—+1—–+20 (core promoter)
-upstream control element: -180+-107

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12
Q

Eukaryotic promoters: RNA polymerase III

A

-mostly tRNA

  1. tRNA gene
    +1—box A—-box B
  2. 5S-rRNA gene
    +1————–box A—–box B
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13
Q

What is an overview of transcription?

A

5’ —–===(promoter)===————===(terminator)====3”
3’—– ===(promoter)===————===(terminator)====5”
1) RNA polymerase binds & unwind DNA
—–( )———— (RNA polymerase binds to promoter)

2) Initiation of RNA synthesis (+NTPs)
5’—–(coding-antisense)
3’—–(template-sense) /<- RNA

3) elongation of RNA + further elongation
(elongates until termination signal)

4)Termination of RNA synthesis
5’—————————-3’
RNA transcript

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14
Q

what happens in Rho-independent termination regarding a hairpin loop?

A

+not dependent on enzymes
To terminate transcription, the RNA transcript goes towards each other that form a stem+ loop where the bases are complementary
-the loop leading to termination will be near the end of the transcription site- only when transcription is complete.

small loop: pauses
big loop: cause everything to dissociate

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15
Q

what happens in rho dependent termination

A

Rut, an enzyme that is being used as Rho utilization site
-found in mRNA near the end of transcription

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16
Q

Procaryotic mRNA vs Eukaryotic mRNA

A

Prokaryotic mRNA:
+5’ & 3’ untranslated regions

+usually polycistronic (a sequence that coordinately transcribed)
=> Operon: a cluster of genes that are transcribed together to give a single messenger RNA (mRNA) molecule, which therefore encodes multiple proteins
O: a: b: c

+is mature after being transcribed (ready to be translated immediately after)

+can be both transcribed & translated at the same time

Eukaryotic mRNA;
+5’ & 3’ untranslated regions
+ is not polycistronic
+is not mature after being transcribed (RNA has to move out of nucleus to be translated)
+can not be both transcribed and translated at the same time
=transcription: in the nucleus
=translation: cytoplasm

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17
Q

maturation of eukaryotic mRNA

A

1) addition of cap- help bind to ribosome
2) addition of poly(A) tail- stabilizing RNA (short lived)
3) intron excision:
-introns: interrupting sequences that needed to be removed because exons needed to be connected

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18
Q

What is the “standard” type of intron?

A

recognition sequence:
+5’: GU - 100% conserved
+3’: AG
(branch point(A)——-20-50bp———–(AG)3’ splice site

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19
Q

how are introns cut out

A

the mRNA goes thru the splicing enzyme complex
the strand goes thru small nuclear RNA
-3’ ontop/ 5’ inside the RNA

an OH connects the extrons tgt and is removed w the lariat structure

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20
Q

how many bases are in a codon?

A

1? no, bc 20 aa, 4 diff singlet codons would not cover it
2? no , bc 20aa, there are only 16 possible doublet combinations
3? YES, there would be 64 possibilities of triplets that covers all the possible aa
=> Occam’s razor: the simplest explanation is the best-unless proven otherwise

21
Q

what is the central dogma

A

DNA—-transcription—–> RNA—–translation—–> protein

22
Q

things to know about codons

A
  1. codes are degenerate “redundant”
  2. every gene start w AUG (met)
    3: stop codons (UAA,UAG,UGA)
  3. some codes only changes the 3rd position (Leu, Ser, Thr, Val, Ala)- allows leeway in 3rd position
  4. universal

+codon usage: some organism uses certain sets more regularly

23
Q

the molecular basis of sickle cell disease+ an example of what mutation?

A

normal hemoglobin DNA : CTT
mRNA : GAA
normal hemoglobin : Glu (hydrophilic)

mutant hemoglobin DNA: CAT
mRNA :GUA
sickle cell hemoglobin: : Val (hydrophobic)
=subtitution mutation: replace 1 letter by another

causes:
hard radiation
chemicals
UV
viruses

24
Q

Mutation: Base insertion

A

+ another letter
=> reading frame will be out of position

25
Q

mutation: Base substitution

A

replace 1 letter with another
=> change the aa

26
Q

mutation: base deletion

A

a letter is taken out

27
Q

mutation: nonsense

A

UAC (Tyr)—> UAG (stop)
putting a stop codon

28
Q

mutation: missense

A

altering from one aa to another

29
Q

mutation: frame shift

A

base deletion/ base insertion

30
Q

mutation: null

A

replacing w something chemically similar
dna change–> mRNA change–> AA (not losing much function)

31
Q

mutation: silent

A

have a mutation but do not have any effect
-a change in DNA, but no change in mRNA

32
Q

In order to get translation, what is needed?

A

a. an mRNA transcript
b. a ribosome (rRNA)
c. charged tRNA (w aa attached)

33
Q

Bases in the anticodon

A

Alanine —O(ester bond)—ACC [conserved]

UH2: altered bases (dihydrouracil)
M2G: dimethyl guandine
MG: methyl guadine
mI: methyl Inosine
Y: pseutouracil

34
Q

structure of tRNA

A

all tRNA have similar but not identical structure =cloverleaf
*~75 nt
*acceptor arm: CCA-3’
*TYC arm
*variable length extra arm (3~20nt)
*anticodon arm
*D arm
*canonical position
*identity elements

35
Q

What occurs when tRNA(ala)-> Alanyl-tRNA(ala)

A

tRNA(ala0
3’–HO–ACC
===========
+Alanine
=========
ester bond+ ACC

36
Q

What is the process of aa activation by aminoacyl-tRNA synthetase?

A

-aa & pyrophosphate bind to aminoacyl-tRNA synthetase (PPP–> P: 2 r taken out)
-tRNA bind to whats left of of the one P
= aminoacyl tRNA (“activated aa”) is an AA+tRNA

37
Q

what is the wobble postion in tRNA anticodon loop?

A

refers to the 3rd nucleotide in a codon
its much looser in this position so that its easier reduce the number of tRNA needed

-61 codons codes for aa (1 tRNA for each)

38
Q

wobble hypothesis

A

-proposed by francis crick in 1966
-occurs at 3’ end of codon/5’ end of anticodon
-result of the arrangement of H-bonds of base pairs @ 3rd pos.
-degeneracy of the code is such that wobble always results in translation of the same aa
-complete set of codons can be read by fewer than 61 tRNAs

5’ anticodon. 3’codon
G U/C
C G
A U
U A/G
I A,U,C

I(post-transcription modified purine)

39
Q

What is the structure of prokaryotic rRNA

A

small subunit (30s)
-16S RNA
-21 proteins (S1(small)-S21): scaffold proteins that help support+ hold up 16sRNA to give it structure

large subunit (50s)
-5S and 23S RNA
-36 proteins [L1(large)-L36)
=70S

40
Q

Eukaryote rRNA

A

40S+ 60S=80S

41
Q

Ribosome structure in specific (prokaryotic)

A

23S: contains the peptidyl transferase activity (where ribosomal activity is; attach 1 aa to the next=makes a peptid bond)

16S: directly involved in both initiation & termination of translation

5S: mostly structural

=overall , structure is highly conserved

42
Q

what is the Shine-Dalgarno sequence

A

this is where the binding of bacterial mRNA to ribosome takes place in the 5’ UTR

-allows mRNA to bind to the ribosome proten

5’ ———- SD——-N5-10-AUG-//—3’n

43
Q

Initiation of translation in prokaryotes

A
  1. IFs bind to 30s ribosomal subunit
  2. Initiator tRNA (w/ fMet formyl methenamine) and mRNA binds to the 30s subunit
  3. 50S subunit binds thru GTP hydrolysis = 70S initiation complex
44
Q

Function of IF 2

A

chaperones in initator tRNA (ensure tRNA get to its desired location)

45
Q

function of IF3

A

chaperones the 30S subunit to help bind to S-D site

46
Q

function IF1

A

hold small+large subunits from each other

47
Q

initiation of translation of eukaryotes

A
  1. small subunit binds to the 5’ Cap
  2. scan for AUG
  3. find the AUG based on the kozak sequence nearby

Kozak sequence: mRNA 5’-ACCAUGG_

ribosomal scanning: move down the length of RNA until bind at the end of the initiation site (KZ)

48
Q

the process of polypeptide chain elongation in prokaryotes

A
  1. binding of aminoacyl tRNA
  2. peptide bond formation
    3.translocation

A site: AA site, new tRNA come in as new aa needed to be added
P site: polypeptide site, newly made sit as new aa come in (nascent: growing, unfinished)
E site: exit site

EF-Tu: chaperone protein for initiation
ET-Ts: carrier protein, carry Gtp transfer GTP to EF-TU (transfer energy)
EF-G: move the ribosome down 1 triplet

49
Q

termination of translation

A

release factor (stop codon) binds to A site
-> causes the whole things to dissociate

spring-cell bio (15 decks)

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