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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
– 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?