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

function of promoter

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

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What is the direction that RNA is read?

5’ by 3’

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What is another name for template strand?

sense/ coding strand

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what is another name for the non-template strand/

antisense

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Does mRNA can be made wo a primer?

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

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How to know where transcription?

based on distance
-the beginning of the polymerase

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the sequence of prokaryotes

-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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Why do certain sequences appear in all organisms?

they are conserved- not loss in evolution

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where does transcription starts

<——upstream———–+1———–downstream———->

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Eukaryotic promoters: RNA polymerase II

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

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Eukaryotic promoters: RNA polymerase I

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

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Eukaryotic promoters: RNA polymerase III

-mostly tRNA

tRNA gene
+1—box A—-box B
5S-rRNA gene
+1————–box A—–box B

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What is an overview of transcription?

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

+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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what happens in rho dependent termination

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

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Procaryotic mRNA vs Eukaryotic mRNA

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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maturation of eukaryotic mRNA

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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What is the “standard” type of intron?

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

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how are introns cut out

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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how many bases are in a codon?

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

what is the central dogma

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

things to know about codons

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

+codon usage: some organism uses certain sets more regularly

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

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

Mutation: Base insertion

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

mutation: Base substitution

replace 1 letter with another => change the aa

mutation: base deletion

a letter is taken out

mutation: nonsense

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

mutation: missense

altering from one aa to another

mutation: frame shift

base deletion/ base insertion

mutation: null

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

mutation: silent

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

In order to get translation, what is needed?

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

Bases in the anticodon

Alanine ---O(ester bond)---ACC [conserved] UH2: altered bases (dihydrouracil) M2G: dimethyl guandine MG: methyl guadine mI: methyl Inosine Y: pseutouracil

structure of tRNA

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

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

tRNA(ala0 3'--HO--ACC =========== +Alanine ========= ester bond+ ACC

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

-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

what is the wobble postion in tRNA anticodon loop?

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)

wobble hypothesis

-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)

What is the structure of prokaryotic rRNA

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

Eukaryote rRNA

40S+ 60S=80S

Ribosome structure in specific (prokaryotic)

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

what is the Shine-Dalgarno sequence

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

Initiation of translation in prokaryotes

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

Function of IF 2

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

function of IF3

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

function IF1

hold small+large subunits from each other

initiation of translation of eukaryotes

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)

the process of polypeptide chain elongation in prokaryotes

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

termination of translation

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