How Cells Read the Genome:
from RNA to protein (BOOK)
Chapter 6 pp 333-349, 351 (+ Fig. 6-87)
From RNA to protein
DNA can act as a direct template for the synthesis of RNA by complementary base-pairing. The
conversion of the information in RNA into protein represent a translation of the information into
another language that uses different symbols. This translation cannot be accounted for by a direct
one-to-one correspondence between a nucleotide in RNA and an amino acid in a protein because
there are only 4 nucleotides and 20 amino acids.
The sequence of nucleotides in the mRNA molecule is read in consecutive groups of three called
codons and each codon specifies either one amino acid or a stop to the translation process. An RNA
sequence can be translated in any of the three different reading frames, depending on where the
decoding begins.
tRNA molecules
The translation of mRNA into protein depends on adaptor molecules that can recognise and bind
both to the codon and at the other side to the amino acid. These adapters consist of a set of transfer
RNAs (tRNAs).
One region on the tRNA forms the anticodon which can pair with the complementary codon in an
mRNA molecule, this is the site where the amino acid that matches the codon in attached to the
tRNA.
Recognition and attachment of the correct amino acid depends on enzymes called aminoacyl-tRNA
synthetases. The synthetase-catalysed reaction that attaches the amino acid to the 3’ end of the
tRNA is one of the many reactions coupled to the energy-releasing hydrolysis of ATP.
, Editing by tRNA synthetases
Several mechanisms working together ensure that an aminoacyl-tRNA synthetase links the correct
amino acid to each tRNA. The correct amino acid has the highest affinity for the active-site pocket of
its synthetase and is therefore favoured over the other 19. A second discrimination step occurs after
the amino acid has been covalently linked to AMP: when tRNA binds, the synthetase tries to force
the adenylated amino acid into a second editing pocket in the enzym. The pocket excludes the
correct amino acid, while allowing closely related amino acids, in the pocket the amino acid is
removed from the AMP by hydrolysis. This hydrolytic editing is analogous to the exonucleolytic
proofreading by DNA polymerases.
Adding amino acids
The fundamental reaction of protein synthesis is the formation of a peptide bond between the
carboxyl group at the end of a growing polypeptide chain and a free amino group on an incoming
amino acid.
Ribosomes
Protein synthesis is performed in the ribosome,
which is made from more than 50 different proteins
and several RNA molecules. Eukaryotic and bacterial
ribosomes have similar structures and functions,
being composed of one large and one small subunit.
The small subunit manages the matching of the
tRNAs to the codons and the large subunit catalyses
the formation of the peptide bonds that link amino
acids together. When not active, the two subunits
are separated.
A ribosome contains four binding sites for RNA
molecules, one is for the mRNA and three (A site, P
site and E site) are for the rRNAs. A tRNA molecule
is held tightly at the A and P sites only if its
anticodon forms base pair with a complementary
codon.
Once protein synthesis has been initiated, amino
acids are added by four major steps:
1. tRNA binding
2. Peptide bond formation
3. Large subunit translocation
4. Small subunit translocation
Two elongation factors enter and leave the ribosome during each cycle, each hydrolysing GTP to
GDP. These factors are called EF-Tu and EF-G in bacteria and EF1 and EF2 in eukaryotes.
To increase the accuracy of the binding reaction between a codon and anticodon, the ribosome and
EF-Tu work together in a couple ways.
from RNA to protein (BOOK)
Chapter 6 pp 333-349, 351 (+ Fig. 6-87)
From RNA to protein
DNA can act as a direct template for the synthesis of RNA by complementary base-pairing. The
conversion of the information in RNA into protein represent a translation of the information into
another language that uses different symbols. This translation cannot be accounted for by a direct
one-to-one correspondence between a nucleotide in RNA and an amino acid in a protein because
there are only 4 nucleotides and 20 amino acids.
The sequence of nucleotides in the mRNA molecule is read in consecutive groups of three called
codons and each codon specifies either one amino acid or a stop to the translation process. An RNA
sequence can be translated in any of the three different reading frames, depending on where the
decoding begins.
tRNA molecules
The translation of mRNA into protein depends on adaptor molecules that can recognise and bind
both to the codon and at the other side to the amino acid. These adapters consist of a set of transfer
RNAs (tRNAs).
One region on the tRNA forms the anticodon which can pair with the complementary codon in an
mRNA molecule, this is the site where the amino acid that matches the codon in attached to the
tRNA.
Recognition and attachment of the correct amino acid depends on enzymes called aminoacyl-tRNA
synthetases. The synthetase-catalysed reaction that attaches the amino acid to the 3’ end of the
tRNA is one of the many reactions coupled to the energy-releasing hydrolysis of ATP.
, Editing by tRNA synthetases
Several mechanisms working together ensure that an aminoacyl-tRNA synthetase links the correct
amino acid to each tRNA. The correct amino acid has the highest affinity for the active-site pocket of
its synthetase and is therefore favoured over the other 19. A second discrimination step occurs after
the amino acid has been covalently linked to AMP: when tRNA binds, the synthetase tries to force
the adenylated amino acid into a second editing pocket in the enzym. The pocket excludes the
correct amino acid, while allowing closely related amino acids, in the pocket the amino acid is
removed from the AMP by hydrolysis. This hydrolytic editing is analogous to the exonucleolytic
proofreading by DNA polymerases.
Adding amino acids
The fundamental reaction of protein synthesis is the formation of a peptide bond between the
carboxyl group at the end of a growing polypeptide chain and a free amino group on an incoming
amino acid.
Ribosomes
Protein synthesis is performed in the ribosome,
which is made from more than 50 different proteins
and several RNA molecules. Eukaryotic and bacterial
ribosomes have similar structures and functions,
being composed of one large and one small subunit.
The small subunit manages the matching of the
tRNAs to the codons and the large subunit catalyses
the formation of the peptide bonds that link amino
acids together. When not active, the two subunits
are separated.
A ribosome contains four binding sites for RNA
molecules, one is for the mRNA and three (A site, P
site and E site) are for the rRNAs. A tRNA molecule
is held tightly at the A and P sites only if its
anticodon forms base pair with a complementary
codon.
Once protein synthesis has been initiated, amino
acids are added by four major steps:
1. tRNA binding
2. Peptide bond formation
3. Large subunit translocation
4. Small subunit translocation
Two elongation factors enter and leave the ribosome during each cycle, each hydrolysing GTP to
GDP. These factors are called EF-Tu and EF-G in bacteria and EF1 and EF2 in eukaryotes.
To increase the accuracy of the binding reaction between a codon and anticodon, the ribosome and
EF-Tu work together in a couple ways.
