1 / 19

Amino Acids and Protein Structure: Essential Chemistry for Biology Studies

Explore the diverse world of amino acids, from their chemical structure to acid-base properties. Learn about protein structure levels and the role of amino acids. Dive into titration calculations and understand the titration of glutamic acid in detail.

kalvarez
Download Presentation

Amino Acids and Protein Structure: Essential Chemistry for Biology Studies

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. O C OH Amino Acids carboxylic acid H2N H C amine  H R R varies with amino acid R = H glycine

  2. -CH-CH3 CH3 -CH2-CH-CH3 CH3 -CH-CH2-CH3 CH3 Nonpolar R-groups -H glycine alanine -CH3 valine proline 2o amine leucine phenylalanine isoleucine methionine -CH2-CH2-S-CH3

  3. -CH2-C-NH2 -CH2-C-NH2 O O -CH-CH3 -CH2 OH Polar R-groups serine asparagine -CH2-OH threonine glutamine tyrosine tryptophan cysteine -CH2-SH

  4. O = -CH2-CH2-C OH O = -CH2-C OH Acidic R-groups glutamic acid aspartic acid

  5. -CH2-CH2-CH2-NH-C-NH2 = NH Basic R-groups lysine -CH2-CH2-CH2-CH2-NH2 arginine histadine

  6. C H H2N R O C OH Amino acids O- H3N+ H R glycine non-chiral all other -amino acids in proteins L-enantiomers zwitterion at neutral pH (pH = 7.0) very high b.p. (> 200oC) very soluble in water

  7. C H C H H3N+ H2N C H H2N R R R O O O C C C O- OH OH acid-base chemistry O- H3N+ low pH neutral pH high pH amine protonated amine and c.a. deprotonated amine and c.a. protonated c.a. deprotonated no net charge negative charge positive charge pH = pHI isoelectric point amino acids diprotic acids 2 pKa

  8. H3N+ C H R O C OH Titration of an amino acid alanine R = CH3 pKa1 = 2.34 pKa2 = 9.69 4.57 x 10-3 Ka1 = 10-2.34 = CH3 Ka1 = [H+][A-] [H+] [A-] [HA] 0.1 M [HA] initial 0 0 0.1 change +x +x -x equil. +x +x 4.57 x 10-3 = x2 0.1-x 0.1 - x • pH = 1.87 [H+] X = 2.14 x 10-2 =

  9. 9.0 8.0 7.0 6.0 pH 5.0 4.0 3.0 2.0 1.0 0 equivalents of OH- net charge +1 ×

  10. net charge 9.0 8.0 7.0 6.0 pH 5.0 4.0 3.0 2.0 × 1.0 0 equivalents of OH- +1 +1/2 0.05 M pKa1 = 2.34 0.05 M 0.05 M × pH = pKa + log [A-] [HA] 0.05 M 1/2 pH = pKa = 2.34

  11. pKa2 = 9.69 9.0 8.0 7.0 6.0 pH 5.0 4.0 3.0 × 2.0 × 1.0 0 equivalents of OH- net charge at equivalence point: +1 +1/2 0 pKa1 = 2.34 × isoelectric point pKa1 + pKa2 pH = 2 pH = (2.34 + 9.69)/2 1 1/2 pH = pHI = 6.02

  12. net charge 9.0 8.0 7.0 6.0 pH 5.0 4.0 3.0 2.0 × 1.0 0 equivalents of OH- at 2nd half-way point: +1 +1/2 0 -1/2 -1 × × pKa2 = 9.69 × pH = pKa2 = 9.69 1 1/2 3/2

  13. resonance structure amides dipeptide glycine alanine Ala-Gly +H2O

  14. H H H _ _ _ = = = O O O R R R _ _ _ Proteins “backbone” _ H N1- C1- C1- N2- C2- C2- N3- C3- C3- OH peptide bonds C-terminal residue N-terminal residue biological activity = structure 4 levels protein structure order of the amino acids Primary structure =

  15. H H H _ _ _ _ H N1- C1- C1- N2- C2- C2- N3- C3- C3- OH = = = O O O R R R _ _ _ Secondary structure hydrogen bonding backbone groups H-bond donors H-bond acceptors -helix Two main secondary structures: -sheet

  16. H C N = O C = O Alpha helix Every C=O bonded to N-H 4 residues away forms a helix core is backbone R-groups outside 3.6 amino acids per turn proline no H-bonding breaks helix

  17. Beta sheet Every C=O bonded to N-H far apart in 1o structure on different chains peptide chains extended side-by-side maximal H-bonding for anti-parallel chains small R-groups above and below the sheet if not -helix or -sheet random coil

  18. H3N+ C H O = CH2CH2C R OH O C OH glutamic acid R = - CH2CH2COOH (-COOH) pKa1 = 3.20 pKa2 = 4.25 (R-COOH) pKa3 = 9.67 (-NH3) It will take ___ equivalents to titrate glutamic acid 3 1st group 2nd group 3rd group

  19. O -2 +1 0 -1 C 12 OH H3N+ H C = O CH2CH2C 10 × OH 8 pKa1 = 3.20 × pH pKa2 = 4.25 pHI = 3.7 pKa3 = 9.67 × 4 × × = 3.7 3.2 + 4.25 2 2 = 7.0 4.25 + 9.67 2 1 2 3 equivalents OH-

More Related