Week 2 Amino Acids

Nonpolar, Aliphatic Amino Acids

• Amino acids with hydrocarbon side chains, include:

• Glycine, alanine, proline

• Valine, leucine, isoleucine

Aromatic Amino Acids

• Amino acids with hydrocarbon ring side chains:

• Phenylalanine, tyrosine, tryptophan

Polar, Uncharged Amino Acids

• Have branches side chains with N or O

• Their polarity allows them to hydrogen bond and participate in chemical reactions

• Includes aspargine, glutamine, serine, threonine

Sulfur Containing Amino Acids

• Includes cysteine and methionine

• Important in protein structure because S-S bonds can be formed between cysteine residues to stabilize the conformation of a protein

Charged Amino Acids

• Carry a charge on their side chain

• The backbone of the amino acid is a zwitterion (uncharged), the molecule is not

• Positive:

  • arginine, lysine, histidine

• Negative:

  • aspartate, glutamate

Types of Amino Acids

• Essential - must be obtained from diet

• Non-essential - produced by the body

• Conditionally essential - essential (must be eaten) when the body’s demand exceeds its production capacity

When does arginine become conditionally essential?

Arginine is conditionally essential, it is made from lysine and becomes essential if there is no lysine in the diet

Peptide chains and proteins get their unique properties from:

• Amino acid sequence (primary structure)

• Side chain interactions between residues

Residues

amino acids in a chain that remain after H2O is removed during the formation of peptide bonds

Amino acid structure

• alpha carbon

• amino group

• carboxylic acid group

• hydrogen

• R group

Zwitterion

• Molecule with a net neutral charge that has positively (amino) and negatively (carboxylic acid) charged regions or groups

• Backbone of all amino acids

When do amino acid backbones “stop” being zwitterions?

If pH deviates too far to either direction. Low or high pH will alter the protonation (addition of H+) of one or both of the groups leading to a net charge in the backbone.

Effect of pH on Amino Acids

As pH changes, the protonation of side chains changes, influencing the reactions the amino acids can participate in.

Peptide bond

• A bond formed between the carboxylic acid group of one amino acid and the amino group of another

• Catalyzed by ribosomes during translation

• N-terminus: the start of a peptide chain

• C-terminus: the end of a peptide chain

Side Chain Interactions Include:

• Disulfide bonds

• Electrostatic interactions

• Hydrogen bonds

• Hydrophobic interactions like Phe ring stacks

Disulfide bonds

• Occurs when the SH (sulfhydryl) groups of two cysteine are spontaneously oxidized to create a strong covalent bond where they shared electrons between them.

• Important for folding and stability of proteins

Electrostatic (Ionic) Interactions

Charged groups of some amino acids can interact with each other and form ionic bonds

Hydrophobic Interactions

• Nonpolar groups cluster together to avoid aqueous environments typically in the interior of a protein

• Due to the closeness between the hydrophobic residues, the positive nuclei of one atom can attract the electrons of another atom to form weak interactions

Hydrogen Bonds

Intermolecular dipole-dipole interactions can form between H, N, O resulting in a hydrogen bond

Post Translational Modifications

• Occur at specific amino acids and are catalyzed by dedicated enzymes

• They can alter the structure or function of a protein allowing other molecules to interact with them and alter the location of the protein in the cell

Acetylation

Addition of acetyl to reduce positive charges of histone proteins and weaken their interaction with negatively charged DNA