Characteristics of the 20 amino acids

characteristics of glycine (Gly, G)

Smallest amino acid; only non-chiral one; adds flexibility to protein chains

• only amino acid where two protons bounded to the central carbon

characteristics Alanine (Ala, A)

Methyl R group; non-bulky; often found in alpha-helices

Valine (Val, V)

Branched-chain; contributes to hydrophobic cores

Leucine (Leu, L)

Similar to valine but bulkier; important for hydrophobic packing

Isoleucine (Ile, I)

Isomer of leucine; also branched and bulky; important for structural integrity

Methionine (Met, M)

Contains thioether (S) group; often the first amino acid in protein synthesis

• Unable to do disulfide bonds cuz Methionine's side chain contains a thioether group: –CH₂–CH₂–S–CH₃

  • This sulfur is bonded to a methyl group, making it non-reactive.

• It does not have a free –SH (thiol) group, which is necessary for forming disulfide bonds.

Proline (Pro, P)

Cyclic R group; rigid; breaks α-helices; adds kinks and turns

• Only amino acid where the side chain makes a covalent bond with a nitrogen to form a cyclic amino acid, important for protein structure 

• Proline severely limits the folding a protein has 

characteristics of Aromatic Amino Acids

These have ring structures that can absorb UV light, are generally hydrophobic or amphipathic.

All aromatic ones have significant delocalization 

• Phenylalanine absorbs the most light 

Phenylalanine (Phe, F)

Nonpolar benzyl side chain; participates in stacking interactions

Tyrosine (Tyr, Y)

Contains phenol group; polar due to -OH; can be phosphorylated

• Has polar functional group (OH) not as hydrophobic is able to make hydrogen bonds 

Tryptophan (Trp, W)

Largest side chain; indole ring; absorbs UV (~280 nm); amphipathic

• Two rings very rigid, lots of double bonds, absorb lots of uv rays 

• Is biggest and heaviest amino acid is able to fluoresce, is slightly polar 

characteristics of Polar, Uncharged Amino Acids

These side chains are hydrophilic and often participate in hydrogen bonding.

Serine (Ser, S)

Small; contains -OH group; often phosphorylated; active site in enzymes

Threonine (Thr, T)

Similar to serine but bulkier; also -OH group; can be phosphorylated

• not as polar as serine

Asparagine (Asn, N)

Amide derivative of aspartate; important in N-linked glycosylation

Glutamine (Gln, Q)

Amide of glutamate; involved in nitrogen metabolism and transport

Cysteine (Cys, C)

Contains -SH group; forms disulfide bonds (oxidized form is cystine)

• Can lose protons, able to lose a full hydrogen atom 

• Only cysteine can make disuldife in an oxidizing environment due to the SH (thiol) group. at the end 

Why an oxidizing environment?

• Oxidation removes hydrogen atoms from the thiol groups, allowing the two sulfur atoms to bond.

• Extracellular spaces (outside the cell) are oxidizing — so disulfide bonds are more common in secreted or membrane proteins.

• Intracellular spaces are reducing — so disulfide bonds are rare inside the cytosol unless maintained by special enzymes.

what do disulfide bonds help with

help with stabilizing protein structure

characteristics of Acidic (Negatively Charged) Amino Acids

These have carboxylate groups in their R chains and are negatively charged at physiological pH.

Aspartate (Asp, D)

Short chain; carboxyl group; participates in salt bridges and enzyme active sites

Glutamate (Glu, E)

Like Asp but with one extra -CH₂; plays roles in neurotransmission and energy metabolism

characteristics of Basic (Positively Charged) Amino Acids

These amino acids are positively charged at physiological pH and often found in DNA-binding regions or protein active sites.

Lysine (Lys, K)

Long aliphatic chain ending in NH₃⁺; often acetylated on histones

Arginine (Arg, R)

Contains guanidinium group; can make multiple H-bonds; very basic

Histidine (His, H)

Contains imidazole ring; pKa ~6.0, so can be protonated or neutral at physiological pH; key role in enzyme catalysis (acts as acid or base)

• At pH 7, about 10% of histidine is protonated