1. (CHAPTER 13- Brooker Text) Translation Sept 25, 2008 BIO 184 Dr. Tom Peavy

2.  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)

3. Figure 13.2 Figure 13.2 provides an overview of gene expression

4. 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

5. Structure of tRNA Figure 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)

6. 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

7. 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)

8. 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

9. Ribosomes contain three discrete sites: Peptidyl site (P site) Aminoacyl site (A site) Exit site (E site)

10. Release factors Initiator tRNA Three Stages: Initiation Elongation Termination

11. 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 rRNA Figure 13.17 Hydrogen bonding Component of the 30S subunit Initiation Stage Initiation complex= mRNA + initiation factors + ribosomal subunits

12. 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 completed after assembly of first tRNA (=formyl methionine)

13. 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

14. 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

15. –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

16. Carboxyl groupAmino group Condensation reaction releasing a water molecule  Polypeptide synthesis has a directionality that parallels the 5’ to 3’ orientation of mRNA Amino terminus Carboxy terminus

17. 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

18. Figure 13.6 A protein subunit