Notesale: Turn your study into money

Document Preview

Extracts from the notes are below, to see the PDF you'll receive please use the links above

---

CBG
...
, 2008)



Amino acid is first activated through the linkage of its carboxyl (-COO) group to an AMP moiety
...
This occurs after aminoacyl-AMP is
formed
...
A tRNA are held tightly when anticodon
forms complementary base pairing with codon on mRNA  “A” and “P” sites are close to each
other  2 tRNA molecules are forced to form base pairs with adjacent codons on the mRNA
molecule
o “A” = Aminoacyl-tRNA site
Site for tRNA that has amino acid covalently attached
o “P” = Peptidyl tRNA site
Site for tRNA that has peptidyl group attached
o “E” = Exit site
Site for tRNA without amino acid to leave

Translation Process


Machine: Ribosome (large and small subunit)



Initiation: Loading of tRNAi and initiation factors on small subunit  Mount of ribosome on mRNA
o “elF” = Eukaryotic initiation factor; additional
Adenosine at 3ʹ
end of tRNA

proteins
i

o tRNAi = Initiator tRNA;
o In Eukaryotes and archaea, tRNAi is charged with
methionine, whereas in bacteria and
endosymbionts, tRNAi is charged with
formylmethionine
o Methionine/formylmethionine is removed by

Ester bond

peptidase shortly after translation is completed
Methionine

Formyl group



Shine Dalgarno on prokaryotic mRNA;
o Is a sequence of 6 bases on polycistronic (multiple START codons) mRNA
o Allows anti-SDS at 3’ end of small subunit rRNA of ribosome to recognize the correct AUG
start codon
o Problems with polycistronic mRNA; AUG is ambiguous (found in 1/64 base sequence,
as AUG can be found in the middle of mRNA  reading out of phase codon
For example, |AUG|CCA|AUU|ACA|UG…C|AUG|CCA|



Reading frame starts in the first detection of AUG



In eukaryotes…

(Image source: Molecular Biology of the Cell 5th edition, page 380)

1

[ ] 3)
4

1
...
Small ribosomal subunit binds to 5’-end of an mRNA molecule
...
The small ribosome subunit moves along mRNA to search for the first AUG
...
(Why energy intensive? Anabolising amino acids into highly ordered
polypeptides decreases entropy!)
4
...
Initiation factors
dissociate to allow binding of large ribosomal subunit
...
EF1/EF-TU brings 2nd charged tRNA to “A” site and proofreads translation;
o Checks whether the tRNA-amino acid match is correct
o Correct matches have a narrowly-defined affinity for EF-TU  allows EF-TU to discriminate
and selects the correct ones into the ribosome
o Monitors interaction (hydrogen bond) between anticodon of aminoacyl-tRNA and codon on
mRNA at “A”
o As aminoacyl-tRNA bends when bound to GTP-form of EF-TU  codon pairing, BUT not
peptide bond formation  correct codon pairing gives GTP hydrolysis  EF-TU releases
tRNA and amino acid is donated for protein synthesis
6
...
EF2/EF-G hydrolyses GTP  LSU translocates relative to SSU  SSU translocates carrying its
tRNA a distance of 3 nucleotides through ribosome



Termination: STOP codons (UAA, UAG, UGA) bound by release factors

(Image source: Molecular Biology of the Cell 5th edition, page 381)

8
...
This allows them to enter “A” site]
9
...
Why? Some tRNAs can recognize more than 1 codon

5’ base of tRNA

3’ base of

anticodon

mRNA codon

A

U

C

G

G

C, U

U

A, G

I

A, C, U

o GU wobble; U = G is as strong as U = A (normal base-pairing)
...
This leads to production of other amino
acids e
...
selenocysteine, pyrrolysine (added post-transcriptionally by biosynthetic mechanisms) and Nformylmethionine (initial a
...
in bacteria, mitochondria, chloroplasts, removed post-transcriptionally)



Conclusion is there are 23 proteinogenic amino acids





(Image source: Molecular Biology of the Cell 5th edition, page 383)

In the case of selenocysteine
o Sulfur atom in cysteine is replaced by selenium
o Instead of a STOP codon, UGA is read as selenocysteine
...
As the protein folds, it loses energy



Protein folding can get trapped in local energy minima

Entropy

Energy

Molten
globule
states

Native state

Similarity
to native
state

Incorrect folded proteins  Protein chaperones


Examples: chaperonin, ‘heat-shock’ proteins

(Image source: Molecular Biology of the Cell 5th edition, page 390)



Misfolded protein is captured by hydrophobic interactions  ATP plus a protein cap increases diameter
of barrel rim



ATP is expensed to weaken the complex  refolding

Incorrect Unfoldable proteins  proteasomes


Unfoldable and unwanted proteins are ubiquinated and degraded in proteasomes
o Recognizes proteins with long ubiquitine tail and lysine residue
...

TGG (Trp),
TGA (Stop)

AT
pressure
reduced

2
...

TGA reappears,
unrecognized

3
...

tRNA (TGG) for Trp duplicates, and mutates
to recognize TGA
...
, Bray, D
...
, Raff, M
...
, Watson, J
...
& Grimstone, A
...
Garland Science
...




---