biochemistry sixth edition chapter 30 protein synthesis part i copyright © 2007 by w. h. freeman...
TRANSCRIPT
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BiochemistrySixth Edition
Chapter 30Protein Synthesis
Part I
Copyright © 2007 by W. H. Freeman and Company
Berg • Tymoczko • Stryer
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Translation: one language to another more complex than replication & txn
1. Many steps and many proteins2. Must be fast (20 amino acid/sec)3. Must be accurate
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speed vs. accuracy
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Fidelity of translation: correct recognition of codons on mRNA
An amino acid itself cannot recognize codon: A transfer is required: tRNA
tRNA: adapter molecule that binds to a specific codon and brings an amino acid for incorporation into
polypeptide chain
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alanyl-tRNA:First nucleic acid to be sequenced
76 ribonucleotides
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Anticodon on alanyl-tRNAis complementary to one of the codons for alanine
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General structure of tRNA:
* Cloverleaf* Half of residues are base-paired* Many common structural features why?
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General structure of tRNA:
1. 73-93 ribonucleotides2. Enzyme-modified bases
* prevent base pairs
* create hydrophobicity* allow protein interxn
* allow codon recognition
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General structure of tRNA:
3. Half of nucleotidesform ds helices5 places without ds:
*acceptor stem*TψC loop*extra arm*DHU loop*anticodon loop
Different butstructurally similar
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General structure of tRNA:
4. 5’ pG5. Activated amino acid
attached to 3’ A-OH6. Anticodon (near
center of seq.)
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3D structure of yeast phenyl-alanyl-tRNA
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3D structure of yeast phenyl-alanyl-tRNA
Important properties:1. L-shaped2. 4 helices 2 ds3. H-bond interactions for nonhelical regions4. 3-terminus: flexible ss5. Anticodon loop: exposed at other end
A good adaptor
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Linkage of amino acid to tRNA is crucial:
1. Amino acid-tRNA establishes genetic code2. Activate amino acid for later peptide bond
formation (peptide bond formation: unfavorable)
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Activated intermediates:Amino acid esterscarboxyl 2’ or 3’OHof A (tRNA)
Aminoacyl-tRNA orcharged tRNA
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Activation reaction of an amino acid
Catalyzed by specific aminoacyl-tRNA synthetases (or activating enzymes)
Amino acid + ATP amionacyl-AMP + PPi
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Or amionacyl-AMP
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The second step of the reaction
amionacyl-AMP + tRNAaminoacyl-tRNA + AMP
Sum of reaction
Amino acid + ATP + tRNA + H2Oaminoacyl-tRNA + AMP + 2Pi
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* Equivalent of 2 ATP is consumed in activation
* Activation and transfer steps for a particular amino acid are catalyzed by the same amino- acyl-tRNA synthetase (intermediate does not dissociate from enzyme, stably bound to active site)
* Acyl adenylate intermediate (also in fatty acid activation
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How does aminoacyl-tRNA synthetase incoporate the correct amino acid?
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1. Specific structure of theamino acid binding site
zinc ion + Asp
other synthetase havedifferent active sitestructures
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2. Proofreading by amino-acyl-tRNA synthetase
what happens when:threonyl-tRNA synthetase+ Ser-tRNAThr
serine + tRNA
editing: hydrolysis of wrong amino acid
(carried out by editing site; size exclusion)
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editing: hydrolysis of wrong amino acid(carried out by editing site; size exclusion)
Most synthetases contain both editing site& activation site
Activation (or acylation) site rejects largeramino acids
Editing site cleaves activated amino acids thatare smaller than the correct one
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Editing mechanism:
The flexible CCA arm can swing out of the activation site and into the editing site
Editing without dissociating (fidelity )
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Editing mechanism:
High accuracy can stillbe achieved without editing
Proofreading: initial a.a.binding interaction is not good enough
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How do synthetases choose their tRNA partners?
synthetases are the only molecules that “know”the genetic code! precise recognition of tRNAs recognition is different for each synthetase- tRNA
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How do synthetases choose their tRNA partners?
1. Anticodon?
Some synthetases recognize their tRNA partnersprimarily based on the anticodon loop.
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Threonyl-tRNA synthetase& tRNAThr
5’-CGU-3’ H bonds with G and U
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How do synthetases choose their tRNA partners?
2. microhelix in tRNA
A 24 nt microhelix canbe aminoacylated by alanyl-tRNA synthetase(without anticodon)
Mutated tRNACys
can be recognized bysynthetase (alanine)
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Aminoacyl-tRNA synthetases: diverse (independent evolution?)
Structural and sequence comparisons They are related
Synthetases fall into two classes!
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Differences between the two classes:
1. Different binding surfaces2. CAA arm conformations3. OH group acylation4. ATP-binding conformations5. Monomeric vs. dimeric
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Ribosome: ribonucleoprotein particle with large and small subunits
L1-L3423S & 5S rRNA
S1-S2116S rRNA
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Ribosome:RNA is 2/3 of total mass
30S primary transcript 5S, 16S, 23S
Extensive foldingInternal base pairs(conserved base-pairs,not conserved seq.ex. G-C vs. A-U)
16S rRNA 2o structure* Defined structure* Short duplex
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“ Chicken and egg” question:If ribosomes synthesize proteins, where doribosomal protiens come from?
Protein: catalysisRNA: structural
OR
RNA: catalysisProtein: structural and regulation
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Proteins are synthesized in the N to C direction
How is mRNA read?
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The direction of translation is 5’ 3’
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The direction of txnis also 5’ to 3’ Same direction
So there is a couplingbetween txn and tsl Efficiency
Polyribosome or polysome
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Translation initiation The first codon is more than 25nt from 5’
Ribonuclease digestion: initiator region on mRNA
12
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3 ~ 9 bp
Two kinds of interactions determine tsl initiation
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Translation is initiated by
formylmethionyl-tRNAf
tRNAf vs. tRNAm
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Ribosomes have 3 tRNA-binding sites
ExitPeptidylAminoacyl
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Tunnel for protein escape
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Mechanism of protein synthesis
1. 30S + mRNA
2. tRNAf Met
3. 50S
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Peptidyl transferase center on 23S rRNA
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Center: promote reaction & stabilize intermediate
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The peptide chain remains in the P site on the 50S (tunnel)
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The amino acid in the aminoacyl-tRNA does not play a role in selecting a codon
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Codon-anticodon interaction:
* Watson-crick base pairing* Anti-parallel* One anticodon for one codon?
Some tRNA recognize morethan one codon:Alanyl-tRNA: GCU, GCC, GCA
Degeneracy of genetic code:XYU & XYCXYA & XYG
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Wobble: steric freedom
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Appears in several anticodon
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Anticodon of yeast alanyl-tRNA: IGCCodons: GCU, GCC, GCA
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Codon-anticodon interactions:
1. The first two bases of codon:standard pairing codons differ in the first 2 bases are recognized by different tRNAs
(ex. UUA and CUA of leucine)
2. First base of anticodon determines how many codons to be read degeneracy of genetic code: from wobble interxn
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Why wobble only in the third base of codon?
30S/16S rRNA:A1492, A1493, G530 forms H bond with first 2 paired anticodon-codon (check WC bp)
Ribosome plays an active role in decoding codon-anticodon interactions