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

10. Polarity can be hard to quantify

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

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

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

14. Some pK a facts The lower the pK a, the stronger the acid (smaller pK a --> larger K a --> larger [H + ]) Acetic acid has pK a 4.8 –K a = 10^-4.8 = 1.5 x 10 -5

15. Henderson-Hasselbach equation relates pK a, pH, and [A-]/[HA]

16. Applications of the Henderson- Hasselbach Equation When pH = pK a, [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

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

18. Amino acids join together by forming peptide bonds

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

20. Two backbone torsion angles : phi (  and psi (  )

21. Possible  and  angles are given in a Ramachandran plot

22. Cysteines can form disulfide bonds

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

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

25. Protein synthesis occurs at ribosomes

27. The Genetic code

28. After translation, some proteins undergo further covalent modification Proteolytic processing Phosphorylation: addition of a phosphate group (PO 4 3- ) to a Ser or Tyr residue. Glycosylation: addition of sugar groups to Asn (N- glycosylation) or Ser (O-glycosylation). Alteration of chain termini –Removal of N-Met –Acetylation and amidation

29. Preproinsulin is cleaved after translation to give insulin

30. Phosphorylation can modulate protein function

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