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Proteins + Translation

Proteins + Translation. Amino acids. Amino acids are the basic structural units of proteins. All proteins in all organisms are constructed from 20 primary amino acids. Amino acids. The side chains of the amino acids (R) vary in size, shape, charge, bonding, composition, and reactivity.

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Proteins + Translation

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  1. Proteins+Translation

  2. Amino acids Amino acids are the basic structural units of proteins. All proteins in all organisms are constructed from 20 primary amino acids.

  3. Amino acids The side chains of the amino acids (R) vary in size, shape, charge, bonding, composition, and reactivity. Amino acids are distinguished from one another by their side chains.

  4. 22 proteinogenic amino acids* = 20 primary amino acids** + pyrrolysine + selenocysteine *proteinogenic amino acids = amino acids that are found in proteins and are encoded by a genetic code. **primary amino acids = found in all proteins in all organisms

  5. Zillions of nonproteinogenic amino acids, e.g., b-naphthylalanine

  6. There are 20 primary amino acids.

  7. Amino acids With the exception of glycine (R = H), all amino acids can form mirror-image enantiomers around the  carbon: levorotatory (L) and dextrorotatory (D). In proteins synthesized via translation of mRNA, only L-amino acids are used.

  8. The smallest amino acid is Gly (molecular weight = 75). • The largest amino acid is Trp (molecular weight = 204). • Pro is an an imino acid. • Three amino acids (Phe,Tyr,Trp) have aromatic side chains. • Cys contains a sulfur atom. • Lys and Arg are positively charged at neutral pH. • Asp and Glu are negatively charged at neutral pH. • At pH = 6.0, ~50 percent of His are positively charged; at pH = 7.0, ~10 percent have a positive charge. • Gln and Asn are uncharged derivatives of glu and asp, respectively.

  9. Venn diagram showing the division of the 20 primary amino acids into overlapping categories according to size, polarity, charge, and hydrophobicity. Note that C appears in two distinct places, as reduced cysteine (CH) and as cystine (CS-S).

  10. Proteins: Four levels of structural organization: Primary structure Secondary structure Tertiary structure Quaternary structure

  11. Primary structure = the linear amino acid sequence

  12. Secondary structure = spatial arrangement of amino-acid residues that are adjacent in the primary structure

  13. a helix = A helical structure, whose chain coils tightly as a right-handed screw with all the side chains sticking outward in a helical array. The tight structure of the a helix is stabilized by same-strand hydrogen bonds between -NH groups and -CO groups spaced at four amino-acid residue intervals.

  14. The b-pleated sheet is made of loosely coiled b strands are stabilized by hydrogen bonds between -NH and -CO groups from adjacent strands.

  15. An antiparallel β sheet. Adjacent β strands run in opposite directions. Hydrogen bonds between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, stabilizing the structure.

  16. A parallel β sheet. Adjacent β strands run in the same direction. Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand.

  17. Silk fibroin

  18. Tertiary structure = three-dimensional structure of protein

  19. The tertiary structure is formed by the folding of secondary structures by covalent and non-covalent forces, such ashydrogen bonds,hydrophobic interactions,salt bridgesbetween positively and negatively charged residues, as well asdisulfide bondsbetween pairs of cysteines.

  20. Quaternary structure = spatial arrangement of subunits and their contacts.

  21. Holoproteins & Apoproteins Holoprotein Prosthetic group Apoprotein Holoprotein Prosthetic group

  22. Apohemoglobin = 2a + 2b

  23. Prosthetic group Heme

  24. Hemoglobin = Apohemoglobin + 4Heme

  25. Christian B. Anfinsen 1916-1995 Sela M, White FH, & Anfinsen CB. 1959. The reductive cleavage of disulfide bonds and its application to problems of protein structure. Biochim. Biophys. Acta. 31:417-426.

  26. The denaturation and renaturation of proteins

  27. Reducing agents: Ammonium thioglycolate (alkaline) pH 9.0-10 Glycerylmonothioglycolate (acid) pH 6.5-8.2

  28. Oxidant

  29. Intrinsically unstructured proteins, often referred to as “naturally unfolded proteins” or “disordered proteins,” are proteins characterized by a lack of stable tertiary structure when the protein exists as an isolated polypeptide under physiological conditions in vitro.

  30. Chouard T. 2011. Nature 471:151-153

  31. Translation RNA  Protein

  32. initiation: AUG mostly

  33. initiation

  34. glycylalanine  alanylglycine

  35. Genetic Codes

  36. Transcription Translation 魚 yú  fish

  37. translation = decoding Conversion of information from one language into another.

  38. George Gamow The Diamond Code (1956)

  39. 1 letter codons  4 possibilities 2 letter codons  16 possibilities 3 letter codons  64 possibilities translation = decoding Conversion of information from a language with a 4-letter alphabet (RNA) into one with a 20-letter alphabet (protein). What should the conversion minimal size (codon) be?

  40. Marshall Nirenberg (right) and Heinrich Matthaei

  41. Rules of Translation: The “Universal” Genetic Code

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