MCAT Biochemistry Review - Ch 1: Amino Acids, Peptides, and Proteins

Amino Acids

Amino acids
Amino group
Carboxyl group
Alpha-carbon
Side chain/R group
Gamma carbon
Proteinogenic amino acids

AA’s with alpha-carbon

All but glycine, with hydrogen atom as R group

Chiral amino acids

All but cysteine have S absolute configuration (cystein has R configuration due to CH2SH group)

Nonpolar, nonaromatic side chains

Glycine
Alanine
Valine
Leucine
Isoleucine
Methionine
Proline

Aromatic side chains

Tryptophan
Phenylalanine
Tyrosine

Polar side chains

Serine
Threonine
Asparagine
Glutamine
Cysteine

Negatively charged (acidic) side chains

Aspartic acid (aspartate)
Glutamic acid (glutamate)

Positively charged (basic) side chains

Lysine
Arginine
Histidine

Hydrophobic side chains

Alanine
Isoleucine
Leucine
Valine
Phenylalanine

Hydrophilic side chains

Histidine
Arginine
Lysine
Glutamate
Aspartate
Asparagine
Glutamine

Acid-base chemistry of amino acids

Amphoteric species
pK_a
Protonated/deprotonated
Zwitterions
Titration
Isoelectric point (pI)

Peptide bond formation and hydrolysis

Peptides
Residues
Dipeptides/tripeptides
Oligopeptides/polypeptides
Peptide bonds
Condensation/dehydration reaction
N-terminus/C-terminus
Trypsin
Chymotrypsin
(Both add hydrogen to amide nitrogen, OH group to carbonyl)

Primary and Secondary Protein Structure

Proteins
Primary structure
Sequencing
Secondary structure
Alpha helices (keratin)
Beta pleated sheets (fibroin)
Proline

Tertiary and Quaternary Protein Structure

Fibrous (collagen) vs. globular (myoglobin) proteins
Tertiary structure
Disulfide bonds (cysteine (oxidation, loss of two proteins + two electrons)—> cystine molecule)
Molten globules
Denaturation
Collapsing (hydrophobic interactions + hydrogen bonds)
Solvation layer
Hydrophobic + Water: negative change in entropy
Hydrophilic + Water: positive change in entropy
Quaternary structure
Subunits
E.g., hemoglobin (heme), immunoglobulin G (IgG)
Cooperativity/allosteric effects
Roles of quaternary structure
1) more stable
2) reduce DNA needed to encode protein coplex
3) bring catalytic sites closer together

Conjugated Proteins

Conjugated proteins
Prosthetic groups
Lipoproteins
Glycoproteins
Nucleoproteins
Heme

Denaturation

Denaturation
Temperature, solutes, and detergents