Amino Acids & Protein Structure

Amino acids are the building blocks of proteins. Each amino acid contains an amino group (−NH₂), a carboxyl group (−COOH), a hydrogen atom, and a distinctive R group (side chain) — all bonded to a central α-carbon.

The 20 standard amino acids encoded by DNA can be classified by the chemical properties of their R groups:

Nonpolar (Hydrophobic) Amino Acids

These amino acids have hydrocarbon or aromatic R groups that avoid water. They are typically found in the interior of globular proteins and in transmembrane domains.

• Glycine (Gly, G) — The smallest amino acid with just a hydrogen as its R group. Its small size gives it exceptional conformational flexibility, which is why it is found at tight turns in protein structure and is the most abundant amino acid in collagen.
• Alanine (Ala, A) — A simple methyl group side chain. Important in the glucose-alanine cycle between muscle and liver.
• Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I) — The branched-chain amino acids (BCAAs). These are essential amino acids degraded primarily in muscle tissue rather than liver. Their accumulation is the hallmark of Maple Syrup Urine Disease, caused by deficiency of branched-chain α-keto acid dehydrogenase.
• Proline (Pro, P) — Unique because its side chain cyclizes back to the amino group, forming a rigid ring. This introduces kinks in polypeptide chains and is particularly important in the triple helix of collagen.
• Phenylalanine (Phe, F) — Contains a benzyl group. Accumulation of phenylalanine due to deficiency of phenylalanine hydroxylase causes Phenylketonuria (PKU), one of the most commonly tested metabolic disorders.
• Tryptophan (Trp, W) — Contains an indole ring; precursor to serotonin, melatonin, and niacin (vitamin B3).
• Methionine (Met, M) — Contains a thioether group and serves as the universal start codon amino acid (AUG). It is also the precursor to S-adenosylmethionine (SAM), the principal methyl group donor in biological reactions.

Polar (Uncharged) Amino Acids

These can form hydrogen bonds with water and are often found on protein surfaces.

• Serine (Ser, S) and Threonine (Thr, T) — Hydroxyl groups that can be phosphorylated by kinases, acting as molecular on/off switches in cell signaling.
• Asparagine (Asn, N) and Glutamine (Gln, Q) — Amide derivatives of aspartate and glutamate; glutamine is the most abundant amino acid in blood and is critical for nitrogen transport.
• Tyrosine (Tyr, Y) — A hydroxylated phenylalanine. Precursor to catecholamines (dopamine, norepinephrine, epinephrine), thyroid hormones, and melanin. Also a target for phosphorylation in receptor tyrosine kinases.
• Cysteine (Cys, C) — Contains a thiol (−SH) group that can form disulfide bonds (−S−S−) with other cysteine residues, critical for stabilizing extracellular proteins like immunoglobulins.

Charged Amino Acids

At physiological pH (7.4), some amino acids carry a net charge:

• Positively charged (basic): Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H). Histidine is special because its pKa (~6.0) is near physiological pH, allowing it to act as a proton shuttle — this is why it is found in the active site of many enzymes and in hemoglobin's buffering system.
• Negatively charged (acidic): Aspartate (Asp, D) and Glutamate (Glu, E). Glutamate is also the primary excitatory neurotransmitter in the central nervous system.

Amino acids are linked together by peptide bonds — a type of covalent amide bond formed between the α-carboxyl group of one amino acid and the α-amino group of the next, with the release of a water molecule (condensation reaction).

Key Properties of the Peptide Bond

• Partial double-bond character — Due to resonance, the C−N bond in the peptide linkage has ~40% double-bond character, making it rigid and planar. This restricts rotation around the peptide bond.
• Trans configuration — Almost all peptide bonds adopt the trans configuration (the α-carbons on opposite sides of the bond), which minimizes steric clashes between R groups. The exception is bonds preceding proline, which can adopt cis configuration (~10% of the time).
• No charge at physiological pH — The peptide bond itself is uncharged, but the free amino and carboxyl termini of the polypeptide chain carry charges.

The primary structure of a protein is simply the linear sequence of amino acids from the N-terminus to the C-terminus. This sequence is directly encoded by the mRNA and determines all higher levels of protein structure.

Proteins fold into complex three-dimensional shapes that determine their function. There are four levels of protein structure:

Secondary Structure

Local folding patterns stabilized by hydrogen bonds between backbone atoms (not R groups):

• α-Helix — A right-handed coil where each backbone C=O forms a hydrogen bond with the N−H four residues ahead. Common in transmembrane proteins and structural proteins like keratin. Proline residues break α-helices because proline's ring prevents the necessary backbone geometry.
• β-Sheet — Extended strands that run alongside each other, connected by hydrogen bonds. Can be parallel (strands run in the same direction) or antiparallel (opposite directions). Antiparallel sheets have stronger hydrogen bonds. Found in silk fibroin and many globular proteins.
• β-Turns and Loops — Short segments that connect α-helices and β-sheets, often found on the protein surface. Glycine and proline are commonly found in turns.

Tertiary Structure

The overall 3D arrangement of a single polypeptide chain, stabilized by interactions between R groups:

• Hydrophobic interactions — Nonpolar R groups cluster in the protein interior, away from water. This is the primary driving force of protein folding.
• Hydrogen bonds — Between polar R groups.
• Ionic bonds (salt bridges) — Between oppositely charged R groups.
• Disulfide bonds — Covalent bonds between cysteine residues, especially important in extracellular proteins (e.g., antibodies, insulin).
• Van der Waals forces — Weak but numerous interactions between closely packed atoms.

Quaternary Structure

The arrangement of multiple polypeptide subunits into a functional complex. Not all proteins have quaternary structure — only those with more than one subunit.

• Hemoglobin — A tetramer of two α and two β subunits (α₂β₂), exhibiting cooperative oxygen binding.
• Collagen — A triple helix of three polypeptide chains (tropocollagen), providing tensile strength to connective tissues.