2. AP Biology Proteins

3. AP Biology 2008-2009 Proteins Multipurpose molecules

4. AP Biology Proteins  Most structurally & functionally diverse group (100,000 different proteins?)  Function: involved in almost everything  enzymes (pepsin, DNA polymerase)  structure (keratin, collagen, silk) hair, skin, nails, feathers, horns  carriers & transport (hemoglobin, aquaporins, membrane proteins

5. AP Biology Functions continued  cell communication  signals (insulin, adrenalin & other hormones)  Receptors in membranes  defense (antibodies – immunoglobulins)  movement (actin & myosin in muscle, tubulin in microtubules)  storage (bean seed proteins, milk- casein, eggs-albumin)

6. AP Biology Proteins  Structure – they contain C, H, O, N and sometimes P &/or S  monomer = amino acids  20 different amino acids  polymer = polypeptide  protein can be one or more polypeptide chains  large & complex molecules (Ex. Hemoglobin is C 3032 H 4811 O 872 N 780 S 8 Fe 4 )  complex 3-D shape hemoglobin growth hormones H2OH2O

7. AP Biology Amino acids  Structure  central carbon  amino group (base)  carboxyl group (acid)  R group (side chain)  variable group  different for each amino acid  confers unique chemical properties to each amino acid —N——N— H H C—OH || O R | —C— | H Oh, I get it! amino = NH 2 acid = COOH

8. AP Biology Kinds of R groups Nonpolar Why are these nonpolar & hydrophobic?  nonpolar & hydrophobic

9. AP Biology Polar  polar - hydrophilic - some are charged Why are these polar & hydrophilic?

10. AP Biology Review of R groups  Non-polar ex. R is -CH 3 or –(CH 2 ) n CH 3  Polar (uncharged) ex. R includes –OH, -SH  Polar, + charge (Basic) ex. R is –NH 2 which becomes –NH 3 +  Polar, - charge (acidic) ex. R is –COOH which becomes –COO-

11. AP Biology R- groups or side chains Determine the properties of the amino acids  -NH 2 accepts H+ and is therefore BASIC  -COOH donates H+ and is therefore ACIDIC  Non-polar groups are hydrophobic Where in a protein would they be found? On the inside (away from the water)

12. AP Biology Building proteins  Peptide bonds  covalent bond between NH 2 (amine) of one amino acid & COOH (carboxyl) of another  C–N bond peptide bond dehydration synthesis H2OH2O

13. AP Biology Building proteins  Polypeptide chains have direction  N-terminus = NH 2 end  C-terminus = COOH end  repeated sequence (N-C-C) is the polypeptide backbone  can only grow in one direction

14. AP Biology Protein structure & function hemoglobin  Function depends on structure  3-D structure (fibrous, globular)  twisted, folded, coiled into unique shape collagen pepsin

15. AP Biology Levels of structure  Primary  Secondary  Tertiary  Quartenary – not all proteins

16. AP Biology Primary (1°) structure  Order of amino acids in chain  determined by gene (DNA)  slight change in amino acid sequence (caused by DNA mutation) can affect protein’s structure & its function  even just one amino acid change can make all the difference! lysozyme: enzyme in tears & mucus that kills bacteria

17. AP Biology Sickle cell anemia I’m hydrophilic! But I’m hydrophobic! Just 1 out of 146 amino acids!

18. AP Biology Primary structure  Is held together by peptide bonds (which are covalent)  Primary structure can only be broken by hydrolysis (digestion)  Determines all other levels of structure

19. AP Biology  There are 20 different amino acids  How many possible sequences could a protein have that is 100 amino acids long? 20 100  DNA determines the correct sequence Question

20. AP Biology Secondary (2°) structure  “Local folding” interactions between nearby amino acids  Held by H bonds  weak bonds between H (from NH 2 and O (from COOH) Two kinds of secondary structure  Alpha helix   -pleated sheet

21. AP Biology

22. Alpha Helix Wool has alpha helices

23. AP Biology Beta pleated sheet Silk has beta pleated sheets

24. AP Biology Tertiary (3°) structure  “Whole molecule bending and folding”  interactions between R groups of distant amino acids  Gives protein its 3D shape  Held by 4 kinds of interactions or bonds

25. AP Biology 1. H bonds – between H and O usually 2. Ionic bonds – between positive and negative groups( -COO- and -NH 3 +) Also called salt bridges 3. Disulfide bonds – Strong (covalent) bonds between sulfhydral groups (-S---S-) 4. Hydrophobic interactions cytoplasm is water-based. Non-polar amino acids cluster away from water VanderWaals’ Interactions

26. AP Biology Quaternary (4°) structure  More than one polypeptide chain bonded together  only then does polypeptide become functional protein  Not all proteins have this collagen = skin & tendons hemoglobin

27. AP Biology Fibrous or Globular

28. AP Biology  http://www.youtube.com/watch?v=lijQ3 a8yUYQ http://www.youtube.com/watch?v=lijQ3 a8yUYQ

29. AP Biology Bonds involved in protein structure

30. AP Biology Which bonds do you see?

31. AP Biology Protein structure (review) amino acid sequence peptide bonds 1° determined by DNA H bonds R groups hydrophobic interactions disulfide bridges (H & ionic bonds) 3° multiple polypeptides 4° 2°

32. AP Biology Example of a protein  Do you see an alpha helix?  Bending and folding?

33. AP Biology Shape Protein shape allows the protein to function  Ex. An enzyme must fit its substrate A hormone must fit its receptor Even minor changes in shape can affect its work

34. AP Biology Protein denaturation  Unfolding a protein  conditions that disrupt H bonds, ionic bonds, disulfide bridges  temperature  pH  Salinity  Heavy metals  alter 2° & 3° structure (3-D shape)  destroys functionality In Biology, size doesn’t matter, SHAPE matters!

35. AP Biology Change in Temperature  Heat disrupts the H + bonds and other weak links

36. AP Biology  Why do we cook meat?  To denature the proteins to make it easier to chew.

37. AP Biology Change in pH  Adding acids increases the amount of H+ in the solution  The H+ are attracted to negative parts of protein and disrupt the original attractions Ex. sour milk

38. AP Biology Heavy metals  Arsenic, lead, mercury, etc. are poisonous because  They disrupt the salt bridges by attaching to the –COO-  This changes the shape of proteins and they don’t work! Arsenic poisoning

39. AP Biology Stirring – mechanical  Weak bonds (attractions) can be changed by stirring or whipping Whipped cream from heavy cream Meringue from egg white

40. AP Biology Alcohol denatures bacterial proteins It interferes with the H bonds

41. AP Biology Oxidation-reduction  Perms cause oxidation and reduction of disulfide bonds

42. AP Biology  What would happen if you moved a protein from water and put it in an organic (non-polar) solvent?  The non-polar amino acids would move to the outside of the protein, changing its shape

43. AP Biology Chaperonin proteins  Guide protein folding  provide shelter for folding polypeptides  keep the new protein segregated from cytoplasmic influences