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The amino acids, peptide bonds, and the primary structure of proteins

The amino acids, peptide bonds, and the primary structure of proteins. Chem 333 week #1 9/10/01 - 9/14/01. Protein structure is often discussed in terms of a hierarchy. Amino acids are the building blocks of proteins. Three major parts: carboxyl group, amino group, and side chain.

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The amino acids, peptide bonds, and the primary structure of proteins

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  1. The amino acids, peptide bonds, and the primary structure of proteins Chem 333 week #1 9/10/01 - 9/14/01

  2. Protein structure is often discussed in terms of a hierarchy

  3. Amino acids are the building blocks of proteins • Three major parts: carboxyl group, amino group, and side chain. • Central C atom called alpha carbon. • Amino acids can differ in their side chains (R). • The alpha carbon is a chiral center.

  4. Two enatiomers possible for most amino acids L-form found almost exclusively in naturally occurring proteins

  5. The nonpolar amino acids

  6. The charged amino acids

  7. The polar amino acids

  8. Glycine is pretty unique • Smallest side chain • No chiral center • Neither very polar or nonpolar

  9. Polarity can be hard to quantify

  10. Review: acid-base chemistry • Acid : Proton (hydrogen ion, H+) donor • Base: Proton (hydrogen ion, H+) acceptor Acid Hydronium ion Base

  11. The reaction when an acid is dissolved in water can written as an equilibrium: acid conjugate base base conjugate acid

  12. The acid-base equilibrium is characterized by a constant Ka pKa = -log Ka

  13. Some pKa facts • The lower the pKa, the stronger the acid (smaller pKa--> larger Ka --> larger [H+]) • Acetic acid has pKa 4.8 • Ka = 10^-4.8 = 1.5 x 10-5

  14. Henderson-Hasselbach equation relates pKa, pH, and [A-]/[HA]

  15. Applications of the Henderson-Hasselbach Equation • When pH = pKa, [A-] = [HA] • Concentrations of protonated and unprotonated forms are equal • If you know the pH and pKa, you can determine whether an amino acid is charged or uncharged

  16. pKa’s can vary depending on environment • Effect of solvent environment. • Effect of specific local interactions.

  17. Amino acids join together by forming peptide bonds

  18. Proteins are chains of these peptide units (polypeptides)

  19. Two backbone torsion angles : phi (f) and psi (y)

  20. Possible f and y angles are given in a Ramachandran plot

  21. Cysteines can form disulfide bonds

  22. Proteins are synthesized in vivo based on information encoded in genes DNA--->RNA-->Protein

  23. RNA is synthesized from a DNA template Chromosomal DNA Nascent RNA molecules

  24. Protein synthesis occurs at ribosomes

  25. The Genetic code

  26. After translation, some proteins undergo further covalent modification • Proteolytic processing • Phosphorylation: addition of a phosphate group (PO43-) to a Ser or Tyr residue. • Glycosylation: addition of sugar groups to Asn (N-glycosylation) orSer (O-glycosylation). • Alteration of chain termini • Removal of N-Met • Acetylation and amidation

  27. Preproinsulin is cleaved after translation to give insulin

  28. Phosphorylation can modulate protein function

  29. Proteins can be glycosylated at either Asn (N-linked) or Ser/Thr (O-linked)

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