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Protein structure (linkage)? Functions?
- condensation polymers, polyamide of amino acids (aka peptide bonds)
- Structure, contraction (myofilament), transport (hemoglobin), energy storage, hormones (GH, insulin), enzymes, protections (IgE)
General amino acid structure. α, ϐ, etc? L vs R?
- α, ϐ, etc refer to C that amine is located on. Proteins use α amino acids
- L/R refer to location of NH2 group
- L amino acids are "natural"
# of amino acids? Essential?
Categories of amino acids w/ types of R groups and pI
- Nonpolar (neutral): hydrocarbon, benzene ring; pI 6
- Polar (neutral): SH, OH, amide; pI 6
- Acidic: additional COOH; pI 3
- Basic: additional NH2; pI 10
isoelectric point - The pH at which the zwitterion is formed
- Net charge = 0
Neutral, acidic, and basic amino acids at pH 1, 3, 6, 10, 12
- Neutral: 1 (+1), 3 (+1), 6 (0), 10 (-1), 12 (-1)
- Acidic: 1 (+1), 3 (0), 6 (-1), 10 (-2), 12 (-2)
- Basic: 1 (+2), 3 (+2), 6 (+1), 10 (0), 12 (-1)
How would each type of amino acid react in electrophoresis, gel pH 6?
- Neutral AA (no charge) - stays stationary
- Acidic AA (negative) - moves toward cathode
- Basic AA (posative) - moves toward anode
- N-terminus: NH2 end of amino acid
- C-terminus: COOH end of amino acid
Various lengths of amino acids and names
- 1-8 C: dipeptide, tripeptide,..., octapeptide
- 9-19 C: oligopeptide
- 20-49 C: polypeptide
- 50+ C: protein
How are amino acid sequences written? How to determine amount of possibilities?
- sequenced in order, left to right (N-terminus on left)
- Total amount of possabilities = n! where n = # of amino acids
- n! = n·(n-1)·(n-2)·(n-3)·,...,·1)
Primary protein structure
- Number, type, and sequence of AA
- Determined by applying HCl to protein which breaks all bonds allowing determination of number and type of AA.
- Other chemicals react with different AAs to produce varied lengths and breakages, a combination of this information will lead to the correct sequence
Secondary Protein Structure
- H bonding in the back bone
- Alpha helix - every 3-5C H-bonding between carbonyl and amine of another AA
- Beta pleated sheet - A sort of "bent" alpha helix
- vanderwalls, H bonding, disulfide bridge, electrostatic interactions (between R groups)
- Gives overall 3D form with hydrophobic R facing in and hydrophilic R facing out
Van der walls, H bonding, electrostatic interactions (between multiple tertiary structures)