The Genetic Code links nucleic acid and protein information

Features of the Genetic Code

1. Three nucleotides code an amino acid

2. The code is nonoverlapping

3. The code has no punctuation

4. The code is degenerate

Transfer RNAs are adapter molecules that connect specific amino acids to specific codons in RNA

Transfer RNAs have a common design

1. There is at least one tRNA for each aa

2. Each tRNA is a single chain of 73-93 nts

3. All tRNA molecules are L shaped

4. tRNAs contain many unusual bases derivedby modification. Methylation prevents formation of certain base pairs, favoringalternative interactions. Methylation increases hydrophobicity and interactions with proteins

5. All tRNAs have a clover leaf design with about half the nts in base paired double helices and the other half represented as5 specific functional motifs:

a. 3’ CCA terminal region of the acceptor stemb. The TC loop contains a ribothymine- psedouracil-cytosine sequencec. The “extra arm” containing a variablenumber of residuesd. The DHU loop contains several dihydrouracil residuese. The anticodon loop - complementary bonds to mRNA codons

6. The 5’ end of tRNAs are phosphorylated and is usually pG

7. Activated amino acids are attached to the adenosine residue at the end of the 3’ CCA component of the acceptor stem

8. The anticodon is present in a loop near the center of the sequence

“Wobble” allows some transfer RNAs to recognize more than one codon

Yeast alanyl-tRNA has the anticodon IGC whichbinds to three codons: GCU, GCC and GCA

The first two nucleotides are the same whereas the third varies – it “wobbles”

The first two bases of the codon bind precisely so that codons that differ in either of the first two bases require a different tRNA

Part of the degeneracy of the code arises from wobble in pairing of the third base of the codon with the first base of the anticodon

Amino acids are activated by adenylation

Amino acids used for protein synthesis must beattached to specific tRNA molecules; this is the “translation” step of protein synthesis

The amino acid attached to a specific tRNA will then be incorporated into the polypeptide according to the anticodon on that tRNA

Energy must be provided to make peptide bond formation thermodynamically favorable

This is accomplished by the formation of aminoacyl-tRNA

Aminoacyl-tRNA synthetases attach amino acids to the 2’ or 3’ hydroxyl group of the ribose unit at the 3’ end of tRNA

The first step of the aminoacyl-tRNA synthetase reaction is the formation of aminoacyl-adenylate from an amino acid and ATP

amino acid + ATP aminoacyl-AMP + PPi

The second step is to transfer the aminoacyl group of aminoacyl-AMP to a specific tRNA to form aminoacyl-tRNA

aminoacyl-AMP + tRNA aminoacyl tRNA + AMP

G0’ of this reaction is close to 0, therefore pyrophosphate must be hydrolyzed to drive the reaction

Thus the overall reaction is:

amino acid + ATP + tRNA aminoacyl-tRNA + AMP + 2Pi

Aminoacyl-tRNA synthetases have highly discriminating amino acid activation sites

Because aminoacyl-tRNA synthetases performthe actual translation process they must bebe highly specific for their appropriate amino acid and cognate tRNA molecule

Thus there must be a different aminoacyl-tRNA synthetase for each different tRNA molecule

Different aminoacyl-tRNA synthetases recognizespecific tRNAs via interactions with their anticodon loops and acceptor stems, especially modified bases and ribose units

Ribosomes are ribonucleoprotein particles composed of two subunits

Ribosomes constitute about 25% of the mass of an E. coli cell

Ribosomes dissociate into a large subunit (50S) and a small subunit (30S)

The large subunit contains 34 different proteins plus two RNA molecules (23S and a 5S)

Ribosomal RNAs are central to ribosome function

rRNAs fold into complex structures with many short duplex regions

Key catalytic sites in ribosomes are composed largely of rRNA; contributions from proteins are minor

Messenger RNA is translated in the 5’ to 3’ direction

The direction of translation is 5’ 3’

Thus mRNA can be translated as it is transcribed

In prokaryotes transcription and translation areclosely coupled in space and time