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Understanding Protein Synthesis and Controlled Breakdown: Key Processes and Mechanisms

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This chapter explores the intricate processes of protein synthesis and controlled protein degradation. It covers the fundamental aspects of the genetic code and the roles of ribosomes in initiation, elongation, and termination of protein translation. Key mechanisms such as amino acid activation, tRNA attachment, and protein folding are discussed, along with factors that influence protein translation controls. The chapter also examines protein degradation through the ubiquitin-proteasome pathway, highlighting the significance of chaperones and the role of mutations in the genetic coding process.

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Understanding Protein Synthesis and Controlled Breakdown: Key Processes and Mechanisms

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  1. Chapter 24 Protein Synthesis and Controlled Protein Breakdown

  2. 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

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

  4. Overview of Protein Synthesis • Amino acids are activated by aminoacylsynthetases 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

  5. tRNA There are not 61 different tRNA molecules

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

  7. Amino Acid Attachment to tRNA • Must attach correct amino acid to tRNA • Wrong amino acid will be incorporated into protein otherwise • Specific aminoacyl-tRNAsynthetase 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

  8. Specificity of Amino Acid Priming

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

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

  11. 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

  12. Elongation

  13. 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

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

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

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

  17. Riboswitches

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

  19. Protein Folding • Chaperones • ATP dependant • Heat Shock proteins • Protein Disulfide Isomerases (PDI) • Peptidylprolineisomerase (PPI)

  20. GroELGroES chaperone

  21. Prion Proteins

  22. Programmed Protein Death • Proteasome • Ubiquitin • Poly • Mono

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

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