Last Lecture: IntroductionChemistry Review

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Last Lecture Introduction/Chemistry
Review Today Chemistry and Amino Acids
Web CT http//www.ualberta.ca/ELEARNING
http//www.biochem.ualberta.ca/MacMillanLab Cour
se Notes
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Henderson-Hasselbach
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Titration Curves of Acids and Bases
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Water
-polar solvent, can interact with both positive
and negative ions, other polar groups
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Hydrophilic and Hydrophobic Groups
Hydrophobic
Hydrophilic
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Hydrophobic Effect
Entropy and Structure of Bulk Water
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Interactions Within/Between Molecules
Covalent 60-100 kcal/mol
Hydrogen Bonding 1-5 kcal/mol
Van der Waals 0.2 - 1.5 kcal/mol
Ionic Interaction 1-10 kcal/mol
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Problems to consider Ignoring entropy, how much
is the formation of a 5 kcal hydrogen bond
worth (in terms of equilibrium) ie A B
C? What proportion (per cent) of a carboxylic
acid (pKa 4) is ionized at pH 3, pH 4.5, pH
6? Draw a chemical mechanism for the
deprotonation of a carboxylic acid by an amine.
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a-amino acids
20 natural aa
L configuration
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Isomers - different but same chemical formula
Stereoisomers - different arrangement in space
Chirality - handedness
enantiomers - mirror images
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Properties of Chiral Molecules
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Chirality in Bio-Active Molecules

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Amino Acids
Glycine (Gly, G)
Alanine (Ala, A)
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Amino Acids - Polar, Neutral
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Amino Acids - Hydrophobic
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Amino Acids - Hydrophobic
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Amino Acids - Polar, Neutral
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Amino Acids - Basic
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Amino Acids - Acidic
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pKas of Amino Acid Side Chains
4.0
Asp
_
Glu
4.5
His
6.5

HN
NH
N
NH
Cys
8.0
_
Lys
10.5

Tyr
10.3
_
OH
O
Arg
12.5

9.3

2.1
_
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Chemical Reactivity (a) Aliphatic -
unreactive Imidazole - His Phenol -
Tyr -OH - Ser, Thr -COOH - Asp,
Glu -NH3 -Lys -SH
-Cys (b) Oxidation of -SH of Cys
-Asn,Gln
-Arg
disulfide
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Reducing Agents
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Peptide Bond Formation
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Peptide Bond
rotation 16 kcal/mol
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Rotation about the peptide bond
trans
cis
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Peptides and Polypeptides