Transcript Slide 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 Chapter 3 • Reading – Won’t cover details of Edman degradationmediated 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 Condensation of two amino acids to form a peptide bond -COOH + NH2- → O ║ C H N + “Peptide” bond: amide Large positive DG: amino acids need to be “activated” H2O Amino terminus N-terminus Peptide bond Carboxyl terminus C-terminus Proteins/polypeptides are polymers of amino acids N-terminus C-terminus Generic a-amino acid a-carbon amino group (basic) carboxylic group (acidic) R group (gives the amino acid its identity) (Most) amino acids have a stereocenter “L” isomer: L for life 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 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) Things to know about amino acids 1. 2. 3. 4. 5. Name R-group structure R-group classification Three-letter abbreviations One-letter abbreviations Two cysteine residues oxidize to form a disulfide bond -Covalent bond: stronger than a hydrogen bond -Reversible: readily reduced back to free sulfhydryls Free amino acid: “acid” & “base” 0 1 +1 0.5 -1 +1 -0.5 -1 -1 pI: “isoelectric point” pH at which the species has no net charge No net mvmt within electric gradient Uncharged side chain: pI = ½ (pK(NH3+) + pK(COOH)) +1 +2 0 + - + + +1.5 + -1 0 + +0.5 - 0 0 -0.5 0 pI between pKR and pK2 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.) Free amino acid vs. polymers Pentapeptide (five a carbons!) What’s the charge at pH=7?