BIOL120: Chapter 3 (Protein Structure and Function)

amino acids

functional groups

1. amino groups

2. carboxyl groups

3. carbonyl groups

4. hydroxyl groups

5. phosphate groups

6. sulfhydryl groups

ionization of amino acids

r-group side chains

three types:

• charged - acidic (-) and basic (+)

• uncharged polar

• nonpolar

structural formula for an amino acid

polymerization

the process of linking monomers togethers

condensation reaction (aka. dehydration synthesis)

monomer in, water out

decreases entropy

requires energy

hydrolysis

water in, monomer out

increases entropy

release energy

peptide bond

amino acids polymerize when a bond forms between a carboxyl group of one amino acid and an amino group of another, resulting in a C-N bond

backbone formation from peptide bonds

r-group orientation: side chains extend out and can interact with each other or water

directionality:

• free amino end: n-terminus

• free carboxyl end: c-terminus

• written with n-terminus on left

flexibility: single bonds on either side of the peptide bond can rotate

proteins

made of polypeptides (>50 linked amino acids), which are made of oligopeptides (<50 linked amino acids), which are made of amino acids (monomer subunits)

protein basic structures

secondary structure

hydrogen bonds (r-group interaction)

form between polar side chains and opposite partial charges

hydrophobic interactions (r-group interaction)

water forces hydrophobic side chains

van der waals interactions (r-group interaction)

weak electrical interactions between hydrophobic side chains

covalent disulfide bonds (r-group interaction)

forms bridges between two sulfhydryl groups

ionic bonds (r-group interaction)

form between groupos with full and opposing charges

normal folding

folding is often spontaneous because of the H bonds and van der waals interactions

• the folded molecule is more energeticaly stable

• a denatured (unfolded) protein is unable to function

molecular chaperones

help proteins fold correctly

prions

improperly folded forms of normal proteins

induce normal protein molecules to change their shape to the altered form