Translation Chapter 9

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

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

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.

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

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

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.

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

The Genetic Code Ochre : O-ka

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

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

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

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

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

The Genetic Code Ochre : O-ka

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

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

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

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

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

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

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

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

Translation: Elongation

Translation: Termination

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