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Protein Metabolism

Protein Metabolism. The genetic code Protein synthesis (translation) Protein targeting & degradation. What are needed for protein synthesis? >70 ribosomal proteins >20 enzymes to activate amino acid precursors >12 proteins/enzymes for the initiation, elongation & termination

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Protein Metabolism

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  1. Protein Metabolism • The genetic code • Protein synthesis (translation) • Protein targeting & degradation

  2. What are needed for protein synthesis? >70 ribosomal proteins >20 enzymes to activate amino acid precursors >12 proteins/enzymes for the initiation, elongation & termination of polypeptides ~100 enzymes for the final processing of proteins >40 tRNAs & rRNAs The most complex biosynthetic process!

  3. Three major advances for the understanding of protein synthesis 1) Paul Zamecnik et al., 1950s (p.1021) newly synthesized, radiolabeled proteins are accumulated at small ribonucleoprotein particle (i.e., ribosome) in liver.

  4. Three major advances for the understanding of protein synthesis (cont’d) 2) Mahlon Hoagland & Zamecnik activated amino acids are attached to a heat-stable soluble RNA (i.e., tRNA), forming aminoacyl-tRNAs. Aminoacyl-tRNA synthetases are involved.

  5. 3) Francis Crick’s adaptor hypothesis a small nucleic acid (perhaps RNA) could serve the role of an adaptor, one part binding a specific a.a. and aother part recognizing the nt sequence encoding that a.a. in the mRNA.

  6. The triplet, nonoverlapping code Insertion or deletion mutations alter the sequence of triplets. Adding/subtracting 3 nt leaves the remaining triplet intact, providing evidence that a codon has 3 nt.

  7. codon: a triplet of nucleotides that codes for a specific amino acid. reading frame: established by the first codon, then begins a new one every 3 nucleotide residues.

  8. The Genetic Code Was Cracked Using Artificial mRNA Templates Marshall Nirenberg, 1961 enzymatic methods to synthesize poly(U) > phenylalanine poly(C) > proline poly(A) > lysine … Nirenberg & Philip Leder, 1964 trinucleotides induce specific binding of aminoacyl-tRNA to ribosome. H. Gobind Khorana, 1960s chemical methods to synthesize polynucleotides with repeating sequences of 3 & 4 bases > polypeptides

  9. “Dictionary” of amino acid code words as they occur in mRNAs. termination codon (red) initiation codon (green)

  10. Each reading frame gives a different sequence of codons, but only one is likely to encode a given protein. Open reading frame (ORF): a reading frame without a termination codon among 50 or more codons.

  11. Codon is degenerate: an amino acid may be specified by more than one codon.

  12. Alignment of the two RNAs is antiparallel

  13. Codon pairing relationships when the tRNA anticodon contains inosinate

  14. Protein Metabolism • The genetic code • Protein synthesis (translation) • Protein targeting & degradation

  15. Wobble Allows Some tRNAs to Recognize More than One Coden

  16. Reading frame and amino acid sequence

  17. “Dictionary” of amino acid code words as they occur in mRNAs. termination codon (red) initiation codon (green)

  18. EF-Tu EF-G GDP (red) C-terminus (green) mimics tRNA tRNA (green)

  19. Overlapping Genes in Different Reading Frames Are Found in Some Viral DNAs fX174

  20. Overlapping Genes in Different Reading Frames Are Found in Some Viral DNAs: Genes within genes

  21. Protein Synthesis involves five stages

  22. The Ribosome Is a Complex Supramolecular Machine Masayasu Nomura et al., 1960s (p.1037) both ribosomal subunits can be broken down into their RNA and protein components, then reconstituted in vitro.

  23. Structure of the bacterial ribosome at near-molecular resolution

  24. Ribosomal subunits are identified by their S (Svedberg unit) values, sedimentation coefficients that refer to their rate of sedimentation in a centrifuge.

  25. The sequences of the rRNAs of many organisms have been determined. Each has a specific three-dimensional conformation featuring extensive intrachain base pairing. Models for the secondary structure of E. coli 16S and 5S rRNAs

  26. Transfer RNAs Have Characteristic Structure Features Robert H. Holley et al., 1965 (p.1038) yeast tRNAAla cloverleaf conformation 苜蓿葉形

  27. General cloverleaf secondary structure of all tRNAs

  28. Three-dimensional structure of yeast tRNAPhe deduced from X-ray diffraction analysis

  29. Protein Synthesis • Stage1:Aminoacyl-tRNA synthetases attach the correct amino acids to their tRNAs • Stage 2: A specific amino acid initiates protein synthesis • Stage 3: Peptide bonds are formed in the elongation stage

  30. Amino acid + tRNA + ATP Mg2+ Aminoacyl-tRNA synthetase aminoacyl-tRNA + AMP + PPi

  31. Proofreading by aminoacyl-tRNA synthetase e.g., Ile-tRNAIle synthetase favors activation of Ile over Val by a factor of 200, i.e., it distinguishes between Val and Ile.

  32. Interaction between an aminoacyl-tRNA synthetase and a tRNA: a “second genetic code” Recognition sites by: unique enzyme (orange) several enzymes (green) all enzymes (blue)

  33. Gln-tRNA synthetase Asp-tRNA synthetase (dimeric) tRNA (green) bound ATP (red)

  34. The tRNAAla elements recognized by the Ala-tRNA synthetase are usually simple. Just a single G=U base pair (red)! Synthetic simple form also works!

  35. Protein Synthesis • Stage1: Aminoacyl-tRNA synthetases attach the correct amino acids to their tRNAs • Stage 2:A specific amino acid initiates protein synthesis • Stage 3: Peptide bonds are formed in the elongation stage

  36. Howard Dintzis, 1961 polypeptides grow by addition of new amino acid to the carboxyl end

  37. synthetase Met + tRNAfMet + ATP Met-tRNAfMet + AMP + PPi N10-Formyltetrahydrofolate + met-tRNAfMet tetrahydrofolate + fMet-tRNAfMet transformylase tRNA The distinction between initiating AUG and internal one is straightforward...

  38. Three steps of initiation: Aminoacyl site Peptidyl site Initiation Factor (IF) the initiation complex forms in the expense of the hydolysis of GTP to form GDP and Pi.

  39. The initiating AUG is guided by the Shine-Dalgarno sequence in the mRNA

  40. Protein complexes in the formation of a eukaryotic intiation complex eIF

  41. Protein Synthesis • Stage1: Aminoacyl-tRNA synthetases attach the correct amino acids to their tRNAs • Stage 2: A specific amino acid initiates protein synthesis • Stage 3:Peptide bonds are formed in the elongation stage

  42. Peptide Bonds Are Formed in the Elongation Stage • Elongation requires: • the initiation complex • aminoacyl-tRNAs • elongation factor (EF-Tu, -Ts,-G) • GTP Proofreading on the ribosome: EF-Tu.GTP/EF-Tu.GDP complexes (~milliseconds) provide opportunities for the codon-anticodon interactions. Elongation step 1: Binding of the second aminoacyl-tRNA

  43. Elongation step 2: Formation of the first peptide bond Peptide transferase

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