1. Proteomics 2010 蛋白質體學 Prelude- Amino acids 陳威戎 2010. 09. 14

2. COO - R group Amino group Carboxylic group L -Form Amino Acid Structure  H = Glycine CH 3 = Alanine H N 3 + H Juang RH (2004) BCbasics

3. Mirror Images of Amino Acid   Mirror image Same chemical properties Stereo isomers Juang RH (2004) BCbasics

4. LeuL -C-C-CONH 2 -C-CONH 2 -C-COOH-C-C-COOH -H -CH 3 -C-OH-C-SH -C-C-S-C PPro -C-C C N N + -C-C-C-C-NH 3 + -C- -C- -OH -C- N South line Circular line Central line Nan-Kan line Chung-San line Northwest line Aliphatic Amide Acidic Imino, Circular Basic SulfurHydroxy Aromatic -C-C-C-N-C-N N + = C -C-C-C C -C-C-C C C -C C C C HN C-COOH  -C-C OH GlnQAsnN AspDGluE PheF ArgR LysK HisH GlyG A AAlaVValI Ile Y Tyr SerS ThrTMetM CysC Amino Acid Subway Map TrpW Non-polar Polar Juang RH (2004) BCbasics

5. POLAR NON- POLAR TyrHis Gly AcidicNeutralBasic Asp Glu Gln Cys Asn Ser Thr Lys Arg Ala Val Ile Leu Met Phe Trp Pro Classification of Amino Acids by Polarity Polar or non-polar, it is the bases of the amino acid properties. Juang RH (2003) Biochemistry

6. - H 1.008 1 hydride + 1s - Hydrogen atom + - + Proton - Hydride, Hydrogen and Proton - Juang RH (2004) BCbasics

7. HighLow Proton ： abundant and small, affects the charge of a molecule H+H+ lone pair electrons H H H+H+ N H H N Amino H+H+ Ampholyte Ampholyte contains both positive and negative groups on its molecule Carboxylic C O O H C O O Proton Is Adsorbed or Desorbed pKapKa Juang RH (2004) BCbasics LowHigh pKapKa

8. COOH NH 2 H + COO - R - C - HR - C - H NH 2 H + R - C - HR - C - H COO - NH 2 R - C - HR - C - H Acidic environmentNeutral environmentAlkaline environment +1 0 pK 1 ~ 2 pK 2 ~ 9 Isoelectric point 5.5 Juang RH (2004) BCbasics

9. 12 9 6 3 0 [OH] → ★ ★ pK1pK1 pK2pK2 pH pI H-C-RH-C-R COO - NH 2 H + Isoelectric point = pK 1 + pK 2 2 Amino Acids Have Buffering Effect Juang RH (2004) BCbasics

10. Environment pH vs Protein Charge + Net Charge of a Protein Buffer pH Isoelectric point, pI - 3 4 5 6 7 8 9 10 0 - Juang RH (2004) BCbasics

11. pKa = 1.8~2.4 pKa = 3.9~4.3 pKa = 6.0 pKa = 8.3 pKa = 10 pKa = 8.8~11 pKa = 10~12.5 + H+H+ + H+H+ + H+H+ + H+H+ + H+H+ + H+H+ + H+H+ -COOH-COO - aa -COOH-COO - RR -Imidazole·H + -Imidazole His -SH-S - Cys -OH-O - Tyr -NH 3 + -NH 2 aa -NH 3 + -NH 2 RR Smaller pKa releases proton easier Residues on amino acids can release or accept protons pKa of Amino Acid Residues Only His has the residue with a neutral pKa (imidazole) pKa of  carboxylic or amino groups is lower than pKa of the R residues Juang RH (2004) BCbasics

12. Amino acids -COOH-NH 2 -R GlyG2.349.60 AlaA2.349.69 ValV2.329.62 LeuL2.369.68 IleI2.369.68 SerS2.219.15 ThrT2.6310.4 MetM2.289.21 PheF1.839.13 TrpW2.389.39 AsnN2.028.80 GlnQ2.179.13 ProP1.9910.6 AspD2.099.823.86 GluE2.199.674.25 HisH1.829.176.0 CysC1.7110.88.33 TyrY2.209.1110.07 LysK2.188.9510.53 ArgR2.179.0412.48 pK1pK1 pK1pK1 pK2pK2 pK2pK2 pK3pK3 [OH - ] pH pI pI ? pK 1 + pK 2 2 three pKa two pKa ? ? p K a of Amino Acids Juang RH (2004) BCbasics

13. HOOC-CH 2 -C-COOH NH3+NH3+ H HOOC-CH 2 -C-COO - NH3+NH3+ H - OOC-CH 2 -C-COO - NH3+NH3+ H NH 2 H +1 0 -2 pK 1 = 2.1 pK 2 = 3.9 pK 3 = 9.8 2.1 + 3.9 2 = 3.0 first second third Isoelectric point Isoelectric point is the average of the two pKa flanking the zero net-charged form pK1pK1 pK2pK2 pK3pK3 Aspartic acid +1 0 -2 Juang RH (2004) BCbasics [OH]