1. Translation
Chapter 9

2. Terms to become familiar with…again
tRNA
Molecules that are the adapters that translate the three nucleotide codon in the mRNA corresponding to the aa
3 nucleotide anticodon
rRNA
Major components of ribosomes
Made up of several types of rRNA and proteins

3. Protein Structure Protein is a polymer composed of monomers call aa.
Also know as a polypeptide
All aa have two functional groups
AA linked together by covalent bonds called peptide bonds

5. The Peptide bond Removal of water for peptide bond to form
A polypeptide is formed by the removal of water between amino acids to form peptide bonds. Each aa indicates an amino acid. R1, R2, and R3 represent R groups (side chains) that differentiate the amino acids. (b) The peptide bond is a rigid planar unit with the R groups projecting out from the C–N backbone. Standard bond distances (in angstroms) are shown.

6. Level of Protein Structure
Primary Structure
Secondary Structure
Secondary Structure
α-helix
Β pleated sheet
Tertiary Structure
Quaternary Structure

7. Globular vs Fibrous Proteins
Enzymes have a pocket called the active site where the R groups of certain amino acids are strategically positioned to interact with a substrate and catalyze a specific chemical reaction.
AA sequences or protein folds associated with a particular function are called domains.
Proteins may contain one or more separate domains.
Enzymes and antibodies and hemoglobin are all globular proteins – compact structures
Skin, Hair and tendons are fibrous – linear shape

8. Review Question
The alpha-helix structure is stabilized by: A) covalent bonds between adjacent functional groups. B) hydrogen bonds along the peptide backbone. C) association with helicase stabilizing enzymes. D) noncovalent interactions with water.

9. The Genetic Code Non-overlapping 3 letters long Degenerate*
Degenerate meaning that each of the 64 triplets must have some meaning within the code and some of the aa must be specified by at least two or more different triplets
A code in which several code words have the same meaning.
Degenerate meaning that each of the 64 triplets must have some meaning within the code and some of the aa must be specified by at least two or more different triplets

10. The Genetic Code
Ochre : O-ka

11. The Genetic Code
Stop Codons UGA-opal UAA-ochre UAG-amber
Ochre : O-ka

12. Application Question
How many nucleotides would be expected for a gene coding for a protein with 300 amino acids?
300
900
603
903

13. tRNA: The Adapter DHU-arm named after the occurrence of dihydrouridine
DHU loop - The last arm of the tRNA is the DHU-arm named after the occurrence of dihydrouridine in all tRNAs

14. Codon Translation by tRNA
Aminoacyl-tRNA synthetases
Enzymes that attach aa to specific tRNAs
There are 20 of these enzymes…WHY?
Specificity comes from anticodon
The wrong aa will be incorporated into the peptide sequence if the wrong aa is attached to a tRNA

15. The Wobble: tRNA (not the song)
Wobble rule says nucleotides in the 3rd position can form normal hydrogen bonds with its normal complement or different nucleotides

16. The Genetic Code
Ochre : O-ka

17. Ribosomes
In all organisms, ribosomes consist of one small and one large subunit
Each subunit consists of 1 to 3 rRNA types and up to 50 proteins
Originally named based on sedimentation when spun in an ultracentrifuge
S – Svedburg units

19. Ribosome Features A site P site E site Aminoacyl tRNA binding site
Peptidyl-tRNA binding site bond
Exit Site

20. Application Question
A tRNA with the anticodon 3′-ACC-5′ would carry the amino acid: A) phenylalanine. B) tyrosine. C) serine. D) tryptophan.

22. Application Question
A tRNA with the anticodon 3′-ACC-5′ would carry the amino acid: A) phenylalanine. B) tyrosine. C) serine. D) tryptophan.

23. Translation: Initiation
Start codon is AUG – methionine
But the start AUG is a special tRNA called the initiator – tRNA Met i
In bacteria, a formyl group is added to the methionine at the start of translation (N-formylmethionine)
Formyl group is removed later
Translation machinery assembles in the 5’UTR
5’UTR essential in prokaryotes but NOT eukaryotes

24. Translation: Initiation Prokaryotes
Shine-Dalgarno Sequence
Recognizes by the 16S rRNA (part of 30S subunit)
Correctly positions the P site for the tRNA Met i binding
Three proteins – IF1, IF2 and IF3 (initiation factor)
Needed for correct initiation
IF3 – keeps the 30S subunit dissociated from the 50S subunit until the initiation complex is formed
30S, mRNA, and initiator tRNA
IF1 and IF2 ensure that only tRNA Met i enters the P site

25. Translation: Initiation Eukaryotes
Once mRNA arrives in the cytoplasm, it is covered with proteins forming secondary structure
Remove the secondary structure to expose AUG with eIF4A, B and G
eIF associated with 5’ cap and 40S subunit and initiator tRNA to form the initiation complex
Once it finds the start AUG, the 60S joins and forms the 80S ribosome
eIFs dissociate from the ribosome before elongation

26. Prokaryotes vs. Eukaryotes
In the human body, fMet is recognized as foreign material and stimulates the body to fight against potential infection.

27. Translation: Elongation

28. Translation: Termination