# General Genetics/Translation
## The ribosome

Each ribosome is a complex consisting of protein and catalytic ribosomal RNA (rRNA). They consist of large and small subunits. The small subunit is what binds mRNA, while the large subunit has three tRNA binding sites (peptidyl, aminoacyl, and exit).
Transfer RNA (tRNA) molecules have an anticodon at one pole and an acceptor stem at the other pole. There are about 20 aminoacyl tRNA synthetase enzymes which recognize the anticodon and acceptor stem. Each tRNA synthetase can attach a specific amino acid to any uncharged (un-aminoacylated) tRNAs that are specific enough for the enzyme. First, tRNA synthetase binds the amino acid and a molecule of ATP to produce pyrophosphate and the amino acid attached to AMP. The tRNA binds into the active site, and the amino acid is attached to the ribose of the last ribonucleotide of the RNA chain, producing a charged (aminoacylated) tRNA.

### Prokaryotic Translation
#### Prokaryotic Translation Initiation Factors

Initiation Factor (IF)-1 is bound to the small subunit, impeding the large subunit from binding. IF-2 is bound to fMet-tRNA, which is always the first tRNA to bind. It binds GTP. IF-3 prevents the large subunit from binding and is required for binding of the small subunit binding to the initiator site on mRNA.

#### Initiation in Prokaryotes

The rRNA within the small unit is homologous to the prokaryotic recognition sequence in mRNA called the Shine-Dalgarno sequence.

#### Prokaryotic Translation Elongation Factors

EF-Tu binds to charged tRNAs and GTP. Ts is an elongation factor that removes GDP from EF-Tu and attaches GTP to EF-Tu. EF-G hydrolyzes GTP to displace tRNAs from A and P to P and E sites.

#### Prokaryotic Translation Release Factors

RF3 is ubiquitous. RF1 and RF2 are codon-specific, with RF1 recognizing UAA and UAG and RF2 recognizing UAA and UGA. Ribosome recycling factor (RRF)

#### Termination in Prokaryotes

RF1/RF2 bind to the stop codon in the A site. Catalytic RNA in RF1/RF2 cleave the ester linkage between the polypeptide chain and the tRNA in the P site. RF3 hydrolyzes GTP to release the RF1/RF2. RRF binds to the A site, and EF-G again causes translocation of the ribosome. All remaining factors dissociate.

### Eukaryotic Translation

The RNA Looping Model postulates that the poly-A tail along with poly-A binding protein (PABP) forms an initiation factor complex with the methyl cap that is recognized by the small ribosomal subunit.

## Redundancy in the genetic code
### Purpose

Most of the redundancy is in the first two letters. A substitution in the third letter is often "silent," meaning that it does not affect the amino acid that it codes for. Furthermore, amino acids with similar properties (e.g. basic, acidic, polar, nonpolar) often have similar codons. Therefore, substitutions will often replace one amino acid with one of similar function, decreasing the significance of the mutation.

### The wobble hypothesis

The wobble hypothesis postulates that the requirement for base pairing at the third position of the codon is less stringent than at the first positions. Ergo, identical charged tRNAs are often able to bind with multiple codons, provided that the first two nucleotides of the codon match the tRNA's anticodon.

## Proteins

Any polypeptide that passes through the cell membrane will have an alpha-helical secondary structure so that the polar R groups can be turned inward.