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The Dissociation Constant (Ka)
The equilibrium constant for an ionization reaction
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Amino Acid
Alpha-amino substituted carboxylic acids; "the building blocks of proteins"
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Residue
An amino acid in the context of a protein
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R-group (side chain)
Variable portion of an amin acid, can represent any chemical structure
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Chiral Center
An atom with 4 different groups bound to it
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Stereoisomer
Chemical compounds that have the same chemical make-up and connectivity but different spacial arrangement (configuration!!!)
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Le Chatelier's Principle
When a stress in applied to a system at equilibrium the equilibrium will adjust to minimize the effect of the stress
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Amino Acid Composition
- alpha-carbon
- alpha-amino group (+ charge)
- alpha-carboxyl group (-charge)
- proton
- R-group
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Amino Acid R-Groups
- non-polar, aliphatic
- aromatic
- polar, uncharged
- positively charged
- negatively charged
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Nonpolar, aliphatic R-groups
Hydrophilic, made with hydrocarbon chains:
- Glycine Gly G
- Alanine Ala A
- Proline Pro P
- Valine Val V
- Leucine Leu L
- Isoleucine Ile I
- Methionine Met M
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Aromatic R-groups
Hydrophobic, contains 6-membered ring:
- Phenylalanine Phe F
- Tyrosine Tyr Y
- Tryptophan Trp W
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Polar, Uncharged R-Groups
No formal charges, but uses H-bonding:
- Serine Ser S
- Threonine Thr T
- Cysteine Cys C - Disulfide bridges!!
- Asparagine Asn N
- Glutamine Gln Q
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Positively Charged R-Groups
Basic, uses ionic interactions:
- Lysine Lys K
- Arginine Arg R
- Histidine His H
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Negatively Charged R-Groups
Acidic, uses ionic interactions, can protonate:
- Aspartate Asp D --> Aspartic Acid
- Glutamate Glu E --> Glutamic Acid
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Affinities For A Proton
- High affinity- Base- Small Ka- Large pKa
- Low affinity- Acid- Large Ka- Small pKa
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