1. Protein Functions: catalyze reactions (enzymes) receptors (eg. pain receptors) transport (ions across membranes, oxygen in blood) molecular motors recognition (eg. antibodies) signals (eg. insulin) structural support

2. Protein structure chains of amino acids 4 levels of structure range of functional groups carb. acids amides amines hydroxyl thiol aromatic rings interact with other proteins: assemblies flexibility, movement (doors, hinges, levers, etc.)

3. Amino acids: 20 building blocks characterized by R group in nature, S (L) configuration

4. Notice: glycine is not chiral! Conformationally free Hydrophobic side-chains

6. Proline: side chain is bonded to main chain amine conformationally restricted - effect on structure

7. Aromatic planar

8. Hydroxyl

9. Thiol

10. Cysteine thiols can form disulfide linkages important for 3, 4 structure

11. Positively charged Lys: pKa ~ 10.8 Arg: pKa ~ 12.5 His: pKa ~ 6.0 Depends on environment!

12. Question: Why is Lys more acidic than Arg? Lys: pKa ~ 10.8 Arg: pKa ~ 12.5

13. Lys: pKa ~ 10.8 Arg: pKa ~ 12.5 + is stabilized in Arg “happier” with + Arg less like to give up proton Arg less acidic

14. Acids Amides pKa of acid ~ 4.1 amides not acidic or basic!

15. AA chain formed via peptide bonds - polypeptide Carbox acid + amine forms amide lose water

17. 50-2000 amino acids: protein <50 amino acids: peptide (eg. insulin, spider venom) primary structure: a.a. sequence

18. AA sequence is specific to each protein/peptide Sequence coded by DNA (gene): 3 base ‘codon’ encodes one amino acid, plus start/stop codons. eg: GAC = aspartate

19. Peptide bonds are planar: 6 atoms in a plane C , C, O, N, H, C 

20. Source of planarity: N is sp2 barrier to rotation about C-N bond free rotation between C-C , N-C  flexibility/rigidity

21. Notice: R group on opposite sides

22. Peptide bonds are trans: If cis, R groups clash

23. Free rotation, but only some angles possible due to steric clashes - limits possible folding patterns phi psi

24. Secondary structure: helices

25. R groups point out right handed/clockwise (alpha) found in proteins (energetically favorable) 3.6 residues per turn H-bonds between main chain O and N 4 aa’s down (next slide)

27. Ribbon form for depicting helices

28. Secondary structure: Beta sheet fully extended: parallel, anti-parallel H-bond between main-chain N and O R groups perpendicular

29. Ribbon depiction of Beta-sheets

30. hairpin turn

31. Tertiary structure (myoglobin) (oxygen carrier in muscle heme prosthetic group (contains iron)

32. Tertiary structure Beta-sheet rich many proteins have both helices and sheets Notice loops (no regular structure, but often still ordered (not random). Often act as doors or flaps

33. A: space-fill picture of myoglobin; blue = charged yellow - hydrophobic B : cross-section: hydrophilic outside hydrophobic inside When unfolded, most proteins are insoluble in water

34. Some proteins form distinct domains CD4 cell-surface protein: HIV virus attaches to this

35. Quaternary structure:  2  2 hemoglobin

36. F6P aldolase (use Jmol – 1L6W) Notice: Quaternary structure (homodecamer) ‘tails’ tie subunits together Beta barrel (conserved tert. structure motif)

39. Primary structure determines higher structure, function Classic study with ribonuclease (cuts RNA)

40. Enzyme loses function when denatured, reduced regains activity when dialized all the info necessary is contained in sequence (originally in DNA sequence!

41. Primary structure (sequence) is easy to determine: sequence DNA So shouldn’t we be able to predict structure from sequence? Yes, in theory - but haven’t figured out yet! Secondary structure prediction is somewhat accurate

42. We can predict structure, function by sequence alignment myoglobin: carries oxygen in muscle hemoglobin: carries oxygen in blood structure and function are related: sequences are similar

43. Protein structure is visualized by x-ray crystallography (Chapter 4) Static picture - but proteins are dynamic! Small peptides can be visualized by NMR - but complex!

44. Proteins are often post-translationally modified (in eukaryotes) expands repertoire of 20 aa’s eg. phosphorylation often turns proteins ‘on and off’