Chapter 4 Amino Acids

1. Chapter 4 Amino Acids Read entire chapter Learn to draw the 20 standard amino acids. Learn both the 3 letter and the 1 letter codes. (pages 66 & 67)

2. Proteins • Abundant biomolecules • Occur in all cells and all parts of cells • Occur in great variety (small to really large) • Polymers of amino acids • Joined by a specific type of covalent bond • Almost all proteins are built from the same set of 20 amino acids • Covalently linked in characteristic linear sequence • Exhibit diversity in biological functions

3. Side chain is different in each amino acid General Structure of an a-Amino Acid All amino acids have this general structure except proline which is cyclic

4. Phenylalanine R = -CH2-Ph

5. Amino acids can act as acids and bases Forms of amino acids Does not occur in significant amounts in aqueous solution Predominates at neutral pH

6. * Can act as acid or base* Subtances with dual nature are called ampholytes or amphoteric Dipolar Ion

7. Amino acid R • carbon is bound to four different groups • carbon atom is a chiral center

8. Page 66

9. Page 67

10. AA name 3-letter 1-letter You need to know the one- and three-letter abbreviations for each AA. You also need to know which group each one is in.

13. Nonpolar side chains with different degrees of hydrophobicity

14. Unchanged, polar side chains Hydrogen bond donors and acceptors

15. Changed, polar side chains Acidic and basic groups

16. Reversible formation of a disulfide bond by the oxidation of two molecules of cysteine Disulfide bonds stabilize the structure of many proteins

17. The condensation of 2 a-amino acids to form a dipeptide Peptide bond is shown in RED

18. Condensation and hydrolysis From Lehninger Principles of Biochemistry

19. The Pentapeptide Ser-Gly-Tyr-Ala-Leu or Serylglycyltyrosylalanylleucine Learn to draw peptides and calculate net charge at a given pH N or C or From Lehninger Principles of Biochemistry

20. Nonstandard amino acids These are found in proteins.

21. These are derived from the standard AAs but are not found in proteins.

22. Stereoisomerism in a-amino acids The object and its mirror image are not superimposable From Lehninger Principles of Biochemistry

23. Project out of the plane of the paper behind it From Lehninger Principles of Biochemistry

24. Assumed to project out of the plane of the paper behind it From Lehninger Principles of Biochemistry

25. Steric relationship of the stereoisomers of alanine to the absolute configuration of L- and D- glyceraldehyde L-amino acids have a amino group on left a R group below a C l and d designations were used historically for levo and dextro rototary Not all L-amino acids are levorotatory

26. Looking down the H-C bond, toward the a-carbon, clockwise you get "CORN".

27. The amino acid residues in proteins are exclusively L stereoisomers • Formation of stable repeating substructures in proteins require the amino acids to be only one stereo isomer • Cells can specifically synthesize L isomers of amino acid because the active site of the enzymes are asymmetric causing the reactions catalyzed to be stereospecific

28. Amino acids have characteristic titration curves At this pH predominant species is species 2 (dipolar ion) 1 2 3 At midpoint in the first stage of titration [species 1] = [species 2] pKa of Carboxyl group = 2.34 pKa of amino group = 9.6 At low pH predominant species is species 1 Know the pKa roughly for various groups From Lehninger Principles of Biochemistry

30. Titration of Glycine Isoelectric point: pH at which net charge is zero From Garrett & Grisham

31. From Lehninger Principles of Biochemistry

32. Titration of Glutamic Acid From Garrett & Grisham

33. Titration of Lysine From Garrett & Grisham