Protein Synthesis and Controlled Protein Breakdown Chapter 24 Protein Synthesis and Controlled Protein Breakdown

Chapter Objectives Know the process of protein synthesis and the genetic code (don’t memorize the genetic code) Know how ribosomes work Initiation, elongation, termination Know the key steps in protein folding Understand how protein translation is controlled Know the process of protein degradation

The Genetic Code Nonsense mutation – stop codon Degenerate code – more than one codon per amino acid Conservation

Overview of Protein Synthesis Amino acids are activated by aminoacyl synthetases using ATP Amino acids are added to tRNA tRNA molecules with their attached amino acid are brought to ribosome The growing peptide chain is added to each new amino acid Energy cost = 1 ATP & 2 GTP

tRNA There are not 61 different tRNA molecules

tRNA Wobble Wobble allows for less tRNA molecules to be needed Notice orientation!!

Amino Acid Attachment to tRNA Must attach correct amino acid to tRNA Wrong amino acid will be incorporated into protein otherwise Specific aminoacyl-tRNA synthetase for each tRNA / amino acid pair Need 20! No consistent recognition Sometimes anticodon Sometimes other regions of tRNA Always side chain of amino acid Process driven by ATP hydrolysis

Specificity of Amino Acid Priming

Ribosomes Prokaryote ribosomes Subunits Total 23S and 5S pieces of RNA and 34 proteins 16 S piece of RNA and 21 proteins Total 50S (large subunit) 30S (small subunit)

http://www.mrc-lmb.cam.ac.uk/ribo/homepage/mov_and_overview.html

Translation Initiation 30S ribosome subunit binds to Shine-Dalgarno sequence placing AUG in P site Special met-tRNA recognizes IF2 (initiation protein factor 2) IF3 prevents binding of 50S subunit prematurely Shine-Dalgarno 50S subunit then associates IF2&3 are displaced GTP is hydrolyzed

Elongation

Termination This picture is from eukaryotes Think of 60S as 50S and 40S as 30S RF1 and 3 are RF1 and 2 in prokaryotes Still need to bring in IF3 to prevent interaction of 30S with 50S

Overview http://www.mrc-lmb.cam.ac.uk/ribo/homepage/mov_and_overview.html

Better overview http://www.mrc-lmb.cam.ac.uk/ribo/homepage/mov_and_overview.html

Drugs that inhibit Translation Chloramphenicol – peptidyl transferase Erythromycin – 50S inhibits translocation Kirromycin or fusidic acid – prevents EF-Tu release Sparsomycin –peptidyl transferase inhibitor Streptomycin – initiation misread Tetracyclin – inhibits tRNA from binding ribosome

Riboswitches

Selenocysteine Not a standard amino acid Made from cysteine and selenium (toxic) Uses UGA stop codon with special tRNA and EF Rare

Protein Folding Chaperones Protein Disulfide Isomerases (PDI) ATP dependant Heat Shock proteins Protein Disulfide Isomerases (PDI) Peptidyl proline isomerase (PPI)

GroEL GroES chaperone

Prion Proteins

Programmed Protein Death Proteasome Ubiquitin Poly Mono

Ubiquitin Pathway E1 is ubiquitin activating enzyme (ATP needed E2 accepts Ub E3 ligase activity Multiple E2/E3 combos