Protein translation stuff for final exam God help me

What is the genetic code?

The genetic code is a triplet, non-overlapping, continuous, and nearly universal code in which each 3-base codon specifies one amino acid.

What is a codon?

A group of 3 nucleotides on mRNA that specifies an amino acid.

What does “degenerate code” mean?

in most cases, each amino acid can be coded for by any of several triplet codons

Continuous vs non-punctuated code

The code is read continuously from a fixed start point and contains no punctuation.

Universality of the genetic code

Nearly all organisms use the same codon assignments.

What matches amino acids to tRNAs?

Aminoacyl-tRNA synthetases, which read the “second genetic code” in tRNA.

B2 Lecture 13 Su 13

aminoacyl-tRNAs

achieves codon recognition

reads codon through base pairing via its anticodon loop

Class I aminoacyl-tRNA synthetases

add the amino acid to the 2'-OH of the terminal adenylate residue of tRNA before shifting it to the 3'-OH

Class II aminoacyl-tRNA synthetases

Attach directly to 3′-OH.

Principle of codon–anticodon recognition

tRNAs “read” codons by forming base pairs with their anticodon loop.

Wobble hypothesis

The first two bases of the codon and the last two bases of the anticodon form canonical Watson-Crick base pairs

But pairing between the third base of the codon and the first base of the anticodon follows less stringent rules

Codon bias

Some codons are used more frequently because they match more abundant tRNAs.

Nonsense suppression

are mutations in tRNA genes that alter the anticodon so that the mutant tRNA could now read a particular “stop” codon and insert an amino acid

What is translation?

The process of converting mRNA sequence into an amino acid chain on ribosomes.

Ribosomes

are ribonucleoprotein particles, ~2/3 rRNA, found in cytosol, mitochondria, and chloroplasts.

ribosome 30S small subunit:

subunit is 930 kD with 21 proteins and a 16S rRNA

50S large subunit:

•is 1590 kD with 31 proteins and two rRNAs: 23S rRNA and 5S rRNA

E. Coli

has 7 operons encoding 16S, 23S, 5S rRNAs and several tRNAs, processed by RNases.

(begin as 30S RNA precursors)

translation phases

Initiation, elongation, termination.

The components required for peptide chain initiation

include (1) mRNA; (2) 30S and 50S ribosomal subunits; (3) a set of proteins known as initiation factors; (4) GTP; and f-Met-tRNA_i^fMet

Initiation factors

are soluble proteins required for assembly of these initiation complexes: 30S and 70S

Initiator tRNA in bacteria

f-Met-tRNAᶦᶠᴹᵉᵗ, which carries N-formyl-methionine and is used only for initiation.

Shine–Dalgarno sequence

A purine-rich sequence on mRNA that base-pairs with the 16S rRNA to correctly position the start codon. the ribosome binding site

30S and 70S initiation complexes

• 30S + IF-1, IF-3, IF-2-GTP + f-Met-tRNAᶦᶠᴹᵉᵗ → 30S initiation complex

• Addition of 50S → 70S initiation complex.

Ribosome binding site A

is the attachment site for an incoming aminoacyl-tRNA.

Ribosome binding site P

occupied by peptidyl-tRNA, the tRNA carrying the

growing polypeptide chain.

Ribosome binding site E

exit site is occupied by the “unloaded” or deaclyated,

tRNA, which has lost its peptidyl chain through the peptidyl

transferase reaction.

first elongation cycle step

aminoacyl-tRNAs are added to ribosome/mRNA

complex

second elongation cycle step

50S subunit catalyzes peptide bond formation

third elongation cycle step

Polypeptide chain grows by one amino acid at a time.

Role of EF-Tu

EF-Tu binds aminoacyl-tRNA + GTP and delivers it to the A site; GTP hydrolysis releases EF-Tu-GDP.

Role of EF-Ts

is a guanine nucleotide exchange factor (GEF) and it recycles EF-Tu by exchanging GTP for GDP

Termination

•The elongation cycle of polypeptide synthesis continues until 70S ribosome encounters a “stop” condon.

•At this point, polypeptidyl-tRNA occupies the P site and the arrival of a “stop” codon or nonsense codon in the A site signals the end of the polypeptide chain has been reached.

Stop codon recognition RF-1

UAA and UAG

Stop codon recognition RF-2

UAA and UGA

what are RF-1 and RF-2

RF-1 and RF-2 are members of the guanine

Nucleotide exchange factor (GEF) family of

Proteins which include EF-Ts.

Mechanism of peptide release

Presence of release factors with a nonsense codon at A site transforms the peptidyl transferase into a hydrolase, which cleaves the peptidyl chain from the tRNA carrier

Ribosome recycling

This leaves a ribosome/mRNA/Psite tRNA complex that must be

disassembled by a protein ribosome recyling factor (RRF) with the

help of EF-G.

The requirements for peptide chain elongation are:

1.An mRNA/70S ribosome/peptidyl-tRNA complex

(in the P site)

2. Aminoacyl-tRNAs

3. Proteins known as elongation factors

4. GTP

initiation factor proteins

IF-1, IF-3, IF-2-GTP