Biochem Lecture 2

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Biochem Lecture 2
2011-08-30 21:52:47
BC351 LN02

Lecture 2 Notes BC351
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  1. The Dissociation Constant (Ka)
    The equilibrium constant for an ionization reaction
  2. pKa
    -log Ka
  3. Amino Acid
    Alpha-amino substituted carboxylic acids; "the building blocks of proteins"
  4. Residue
    An amino acid in the context of a protein
  5. R-group (side chain)
    Variable portion of an amin acid, can represent any chemical structure
  6. Chiral Center
    An atom with 4 different groups bound to it
  7. Stereoisomer
    Chemical compounds that have the same chemical make-up and connectivity but different spacial arrangement (configuration!!!)
  8. Acids
    Proton donors
  9. Bases
    Proton acceptors
  10. 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
  11. Amino Acid Composition
    • alpha-carbon
    • alpha-amino group (+ charge)
    • alpha-carboxyl group (-charge)
    • proton
    • R-group
  12. Amino Acid R-Groups
    • non-polar, aliphatic
    • aromatic
    • polar, uncharged
    • positively charged
    • negatively charged
  13. 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
  14. Aromatic R-groups
    Hydrophobic, contains 6-membered ring:

    • Phenylalanine Phe F
    • Tyrosine Tyr Y
    • Tryptophan Trp W
  15. 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
  16. Positively Charged R-Groups
    Basic, uses ionic interactions:

    • Lysine Lys K
    • Arginine Arg R
    • Histidine His H
  17. Negatively Charged R-Groups
    Acidic, uses ionic interactions, can protonate:

    • Aspartate Asp D --> Aspartic Acid
    • Glutamate Glu E --> Glutamic Acid
  18. Affinities For A Proton
    • High affinity- Base- Small Ka- Large pKa
    • Low affinity- Acid- Large Ka- Small pKa
  19. Titration Midpoint
    • pH=pKa
    • [HA]=[A-]