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 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
Condensation of two amino acids to form a peptide bond
-COOH + NH2- → C║O
N
HH2O+
“Peptide” bond: amideLarge positive G: amino acids need to be “activated”
Amino terminusN-terminus
Carboxyl terminusC-terminus
Peptide bond
Proteins/polypeptides are polymers of amino acids
N-terminus
C-terminus
-carbonamino group (basic) carboxylic group (acidic)R group (gives the amino acid its identity)
Generic -amino acid
(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. Name
2. R-group structure
3. R-group classification
4. Three-letter abbreviations
5. 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”
pI: “isoelectric point”
pH at which the species has no net charge
No net mvmt within electric gradient
+1 +1
-1-1
Uncharged side chain:
pI = ½ (pK(NH3+) + pK(COOH))
10.5
0-0.5
-1
+
+
+
+
+---
0
0
0
0+2 +1 0 -1
+1.5 +0.5 -0.5
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 carbons!)What’s the charge at pH=7?