1. Amino Acids Colorless, crystalline, water soluble substances Distinguishing features are a -COOH group and a -NH 3 group attached to the same carbon R group gives individuality R group varies from a simple H to a complex phenyl ring Classification reflects structural feature or property of R groups

2. Non-PolarPolar but UnchargedPolar charged (+) glycine alanine valine leucine isoleucine methionine proline phenylalanine tryptophan serine threonine asparagine glutamine tyrosine cysteine lysine arginine histidine Polar charged (-) aspartic acid glutamic acid Classification

3. Charges on Amino Acids  COOH C- H R Zwitterion (Rhymes with “bitter ion”) pKa = 2 pKa = 9.5 N : HH R C-  COO N H + H H H See Tutorial “Ionization” on Web

4. GLYCINE HC - NH 3 COO - HCH 3 Alanine CH 2 OH Serine Stereochemistry COO - CH3NH3N H R L-amino acid * Amine group left Chiral center Take Home: All amino acids that occur in proteins are of the L configuration Carboxyl group up When R=H, no chiral center

5. Chirality or “handedness” 4 Different Substituents LLD COO H3NH3N HC + R H C R NH 3 + LD Mirror Image

6. Reproduced Mirror Image Not Reproduced Chiral Center No Chiral Center

7. CHARGE ON AMINO ACIDS DEPENDS ON pH OF SOLUTION COOH C CH 3 H3NH3NH + COO C CH 3 H3NH3NH + COO C CH 3 H2NH2NH + 10 Conjugate pH 1-2pH 3-8pH 9-12

8. GlycineGlyG2.349.6 AlanineAlaA2.349.69 ValineValV2.329.62 LeucineLeuL2.369.6 IsoleucineIleI2.369.6 SerineSerS2.219.15 ThreonineThrT2.63 10.43 MethionineMetM2.289.21 PhenylalaninePheF1.839.13 TryptophanTrpW2.839.39 AsparagineAsnN2.028.8 GlutamineGlnQ2.179.13 ProlineProP1.99 10.6 CysteineCysC1.71 10.788.33 HistidineHisH1.829.176.0 Aspartic acidAspD2.099.823.86 Glutamic acidGluE2.199.674.25 TyrosineTyrY2.29.11 10.07 LysineLysL2.188.95 10.79 ArginineArgR2.179.04 12.48 2.20 9.52 Amino Acid AbbreviationspK 1 pK 2 pK 3

9. Know these values Biochemical Strategies p. 32

10. Titration Curve for an Amino Acid pK 1 =2 pK 2 =9.5 pH 0 1.0 1.5 2.0 0.5 2.0 9.5 -COOH Equivalents OH- Glycine -COOH -COO - H 3 N- + H 2 N- H 3 N- + To draw a titration curve, (1) determine number of dissociable groups, (2) place pK values in center of range (3) draw curve. COOH H -N-C-H H H H +

11. pH pK 3 = 9.5 pK 2 = 4.0 pK 1 = 2.0 01.02.03.0 2 4 8 Equivalents of OH - See Strategies p. 33 -H COOH C CH 2 COOH H 3 N- + -H COO - C CH 2 COOH H 3 N- + -H COO - C CH 2 COOH H 3 N- + -H COO - C CH 2 COO - H 3 N- + -H COO - C CH 2 COO - H 3 N- + -H COO - C CH 2 COO - H 2 N- -H COOH C CH 2 COOH H 3 N- + L-Glutamate

12. Isoelectric Points 1. pH at neutral charge (note the word “pH” in the definition) (pI) of Amino Acids 2.pI = pK 1 + pK 2 2 pK 1 pK 2 Simple Amino Acid pIpI pK 1 + pK 2 2

13. pI for an Amino Acid with a Charged R Group COOH C CH 2 COOH H3NH3NH + 1 pK = 2 2 pK = 4 3 pK = 9.5 2 4 6 8 pH pK 1 pK 2 pK 3 ? ? 0-2 +1 Rule: Always use the 2 pKs that border the “0” charged species

14. COO C-H H 3 N- + CH 2 H3NH3N + pH 7 = +1 H pH 1= +2 2 4 6 8 10 12 +2+10 pI = about 10 pK 1 = 2 pK 2 = 9.5 pK 3 = 10.5 pI = pK 2 + pK 3 2 = 9.5 + 10.5 2 = 10 Lysine is a basic amino acid Isoelectric Point of Lysine

15. See Strategies, p 35

16. Non-polar Polar non- charged Charged acidic Charged basic

17. CH 2 N N H H Imidazole + Phenyl L-Histidine L-Phenylalanine CH 2 CH 3 H3CH3C Isopropyl L-Valine Thioether L-Methionine S CH 3 CH 2 NH H 2 N=C NH 2 + Guanidino L-Arginine CH 2 OH L-Serine CH 2 SH L-Cysteine CH2 COO - L-Glutamate H Glycine CH 3 L-Alanine C COO - H3NH3N H +

18. N H L-Proline Secondary amine L-Tryptophan Indole ring N H CH 2 H3NH3N + L-Lysine L-Threonine H-C-OH CH 3 * C COO - H3NH3N H + See Tutorial on Amino Acid Structures on Web See Tutorial on Amino Acid Structures on Web

19. A= Alanine C =Cysteine D =Aspartic acid E =Glutamic acid F =Phenylalanine G =Glycine H =Histidine I =Isoleucine K=Lysine L =Leucine M =Methionine P =Proline Q =Glutamine N = Asparagine R = Arginine S =Serine T = Threonine V =Valine W = Tryptophan Y = Tyrosine