(CHAPTER 13- Brooker Text)

Translation

Sept 25, 2008BIO 184

Dr. Tom Peavy

CODON = 3 nucleotides encode for 1 amino acid

DEGENERACY= more than one codon encodes for an amino acid (wobble base)

Code is UNIVERSAL (nearly)

Special codons= start codon (AUG) stop codons (UAA, UGA, UAG)

Figure 13.2

• Figure 13.2 provides an overview of gene expression

• During mRNA-tRNA recognition, the anticodon in tRNA binds to a complementary codon in mRNA

Recognition Between tRNA and mRNA

Figure 13.8

Proline anticodon

tRNAs are named according to the

amino acid they bear

Structure of tRNAFigure 13.10

cloverleaf folding pattern (stem-loop structures)

contain modified bases (>60 possible)

amino acyl tRNA synthetase= enzyme that conjugates appropriate amino acid to the 3’ end of tRNA (20 of them, one for each a.a.)

Wobble hypothesis= codon-anticodon recognition tolerates mismatches in the third position (but not first and second)

• Macromolecular complex of rRNA and proteins

• Prokaryotes = one type of ribosome (70S)

– Found in their cytoplasm

• Eukaryotes = two types of ribosomes– One type is found in the cytoplasm (80S)– The other is found in organelles (70S, like prok.)

• Mitochondria ; Chloroplasts

RIBOSOME STRUCTURE AND ASSEMBLY

Figure 13.13

Note: S or Svedberg units are not additive

A ribosome is composed of structures called the large and small subunits

Each subunit is formed from the assembly of Proteins + rRNA

Bacterial Ribosomes (and mitochondrial/chloroplast)

Figure 13.13

The 40S and 60S subunits are assembled in the nucleolus

Then exported to the cytoplasm

Formed in the cytoplasm during

translation

Eukaryotic Ribosomes

Ribosomes contain three discrete sites:

Peptidyl site (P site)

Aminoacyl site (A site)

Exit site (E site)

Release factors

Initiator tRNA

Three Stages: Initiation Elongation Termination

• The binding of mRNA to the 30S subunit is facilitated by a ribosomal-binding site or Shine-Dalgarno sequence– This is complementary to a sequence in the 16S rRNA

16S rRNAFigure 13.17

Hydrogen bonding

Component of the 30S subunit

Initiation Stage

• Initiation complex= mRNA + initiation factors + ribosomal subunits

Figure 13.16

70S initiation complex

This marks the end of the first

stage

The only charged tRNA that enters

through the P site

All others enter through the A site

Initiation completedafter assembly of

first tRNA(=formyl methionine)

Figure 13.18

• Charged tRNA binds to the A site (use of GTP and Elongation factor)

• Bond between polypeptide chain (P site) and incoming amino acid (A site) catalyzed by peptidyl transferase

• Polypeptide transferred to the A site

Elongation

• Ribosome translocates one codon to the right (GTP and elongation factor)• Uncharged tRNA released from the E site• Repeat Process until stop codon

Elongation Cont’d

– In most species there are three stop or nonsense codons• UAG• UAA • UGA

– These codons are not recognized by tRNAs, but by proteins called release factors

• Indeed, the 3-D structure of release factors mimics that of tRNAs

Termination Stage

Carboxyl group Amino group

Condensation reaction releasing a

water molecule

Polypeptide synthesis has a directionality that parallels the 5’ to 3’ orientation of mRNA

Aminoterminus

Carboxyterminus

• There are four levels of structures in proteins– 1. Primary (its amino acid sequence)– 2. Secondary (protein folds to form regular, repeating

known) – 3. Tertiary (short regions of secondary structure in a

protein fold into a three-dimensional) – 4. Quaternary (Proteins made up of two or more

polypeptides)

Levels of Structures in Proteins

Figure 13.6

A protein subunit