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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

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  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 O H ║ → H2O + + NH2- C -COOH N “Peptide” bond: amide Large positiveDG: amino acids need to be “activated”

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

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

  6. a-carbonamino group (basic) carboxylic group (acidic)R group (gives the amino acid its identity) Generic a-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 • Name • R-group structure • R-group classification • Three-letter abbreviations • One-letter abbreviations

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

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

  13. +1 -1 +2 0 - - 0 - + + + 0 -0.5 +0.5 +1.5 0 + + 0 pI between pKR and pK2

  14. 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.)

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

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