CH 4 Purdue University BCHM 307 Biochemistry

Amino and carboxyl

Two functional groups of an amino acid that are ionizable

Nonpolar, polar charged, polar uncharged

Three categories for amino acid R groups

Nonpolar

Hydrophobic amino acid R groups

Polar

Hydrophilic amino acid R groups

Glycine

Smallest amino acid

Functional moieties

Amino acid R group that is isomerized to another molecule, but behaves the same

Protein

What can be determined by UV light absorption of tryptophan

Proline

Only amino acid whose side chain loops back onto its own backbone. Induces non-rotational kinds in a polypeptide sequence

Polar

Polar/nonpolar amino acids are found on active sites of enzymes as catalysts

Disulfide bonds

Bonds between sulfur groups that link methionine and cystine residues

Serine and threonine

Two amino acids that have hydroxyl groups that assist in hydrogen bonding and are prominent nucleophiles

Tyrosine

Amino acid derivative of phenylalanine that has a polar uncharged R group. Common in neurotransmitters

Asparagine and glutamine

Two amino acids that contain polar uncharged R groups

Histidine

Amino acid with a polar uncharged R group. Has a five membered ring system that can be charged at certain pH values

Lysine and arginine

Two amino acids with positively charge polar R groups and long side chains with a positively charged amino group

Aspartate and glutamate

Two amino acids with negatively charged polar R groups that have carboxylate groups

Condensation reaction

Chemical reaction that links amino acids via peptide bonds to create amino acid residues

Polypeptide

Chain of amino acids that has not reached it fully functional form to become a protein

Protonated

Protonated/deprotonated/neutral at pH < 3.5

Neutral

Protonated/deprotonated/neutral at pH > 3.5 and < 9.0

Deprotonated

Protonated/deprotonated/neutral at pH < 3.5

Primary

Protein structure: Sequence of amino acids

Secondary

Protein structure: Localized conformation of polypeptide backbone

Tertiary

Protein structure: Three dimensional structure of an entire polypeptide, including all its side chains

Quaternary

Protein structure: Spatial arrangement of polypeptide chains in a protein with multiple chains/subunits

Alpha helix

Secondary structure that forms from hydrogen bonding between carbonyl O and amino H in the same molecule

Beta sheet

Secondary structure that forms from hydrogen bonding between carbonyl O and amino H in molecules that are adjacent

Parallel

Beta sheet formation that has amino groups all pointing in the same direction

Antiparallel

Beta sheet formation that has amino groups pointing in different directions

Hydrophobic effect

What primarily drives the formation of tertiary structures