1. Notes Schedule updated: tomorrow Exp.2 pre-lab Lab report –Citations: Think about intellectual contribution Lab notebook definitely needs cited Henderson-Hasselbalch –I owe you some additional practice problems To be added to website soon

2. Chapter 3 Reading –Won’t cover details of Edman degradation- mediated protein sequencing (part of 3.4) –Won’t cover Chapter 3.5 (yet) Suggested HW –2, 3, 4, 5, 7, 8, 9, 10, 12, 13, 14, 18

3. Condensation of two amino acids to form a peptide bond -COOH +NH 2 - → C ║ O N H H2OH2O + “Peptide” bond: amide Large positive  G: amino acids need to be “activated”

4. Amino terminus N-terminus Carboxyl terminus C-terminus Peptide bond

5. Proteins/polypeptides are polymers of amino acids N-terminus C-terminus

6.  -carbon amino group (basic) carboxylic group (acidic) R group (gives the amino acid its identity) Generic  -amino acid

7. (Most) amino acids have a stereocenter “L” isomer: L for life

8. 20 ‘common’ amino acids Make up vast majority of amino acids in natural proteins Coded for in the genetic code Other amino acids: –Posttranslational modifications –Intermediates in metabolic pathways

9. Two main groups of side chains (plus subgroups) Nonpolar (hydrophobic) –Aliphatic (non-aromatic, mostly straight chains) –Aromatic (conjugated ring structures) Polar (hydrophilic) –Uncharged Hydrogen bonds –Positively charged “basic” –Negatively charged “acidic” At physiologic pH (~7)

10. Things to know about amino acids 1.Name 2.R-group structure 3.R-group classification 4.Three-letter abbreviations 5.One-letter abbreviations

13. Two cysteine residues oxidize to form a disulfide bond -Covalent bond: stronger than a hydrogen bond -Reversible: readily reduced back to free sulfhydryls

17. Free amino acid: “acid” & “base” pI: “isoelectric point” pH at which the species has no net charge No net mvmt within electric gradient +1 Uncharged side chain: pI = ½ (pK (NH3+) + pK (COOH) ) 1 0.5 0 -0.5

18. + + + + + - - - 0 0 0 0 +2 +1 0 +1.5 +0.5 -0.5 pI between pK R and pK 2

19. Free amino acid vs. polymers Terminology –Dipeptide (two amino acids) Tri-, tetra-, penta-peptide (etc) –Oligopeptide (several a.a. ~3-30?) –Polypeptide (multiple a.a.) –Protein (multiple a.a.)

20. Free amino acid vs. polymers Pentapeptide (five  carbons!) What’s the charge at pH=7?