Amino Acids

• Non-polar amino acids: NEUTRAL - hydrocarbon side group (hydrophobic)
• Polar amino acids: NEUTRAL - side groups form H-bonds (hydrophilic)
• Acidic amino acids: NEGATIVE CHARGE - contain carboxylate groups
• Basic amino acids: POSITIVE CHARGE - form ionic bonds with acidic amino acids

ESSENTIAL AMINO ACIDS - cannot be made by the body; must be supplied by food

(Isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Histidine is semi-essential because the body does not always require dietary sources of it.)

NON-ESSENTIAL AMINO ACIDS - made by the body from the essential amino acids or normal breakdown of proteins.

(arginine, alanine, asparagine, aspartic acid, cysteine, glutamine, glutamate, glycine, proline, serine and tyrosine.)

COMPLETE PROTEINS - proteins that contain all NINE of the essential amino acids.

(Typically proteins from animal foods such as meats, poultry, fish, dairy and eggs are complete.)

INCOMPLETE PROTEINS - sources usually include nuts and vegetables.

High-carbohydrate meals can increase the brain's TRYPTOPHAN levels and therefore the SEROTONIN that promotes contentment and normal sleep.

A high-protein meal increases TYROSINE levels causing neurons to produce NOREPINEPHRINE and DOPAMINE (neurotransmitters that promote alertness and activity).

• Tyrosine is required for your body to make active THRYOID hormones. Low levels of tyrosine in the blood is associated with an underactive thyroid gland.
• Extreme thyroid deficiency causes severe mental retardation known as CRETINISM. 

• Lysine is an essential amino acid and so must be replenished often as it cannot be stored or made in the body. 
• Within 6 to 8 weeks of lysine deficiency, the amino acid imbalance causes a deficiency in the B Vitamin NIACIN and symptoms begin to develop such as bloodshot eyes, fatigue, dizziness, nausea, loss of appetite, anaemia and kidney stones.

• Amino acids exist in either L (levo) or D (dextro) form. The L and D refer to the absolute confirmation of optically active compounds.
• With the exception of GLYCINE, all other amino acids are mirror images that cannot be superimposed.
• Most of the amino acids found in nature are of the L-type.
• Therefore eukaryotic proteins are always composed of L-amino acids.
• Howevere, D-amino acids are found in bacterial cell walls and in some peptide antibiotics.

Derivatives act as chemical messengers - neurotransmitters.

• Glutamate derivative - y-amino butyric acid (GABA)
• Tryptophan derivative - serotonin, melatonin

Hormonal action - thyoxine (tyrosine derivative)

Almost all peptide bonds are in the TRANS position

• Steric clashes (exlusion) between side groups in CIS position attached to the α-carbon
• Rotation about the α-carbon, degrees of freedom allows protein folding - angle restriction (phy and psi)
• The shape will depend on the type of side chain interaction, R group, and environmental factors, energy efficiency - limits the number of structures possible.

Twisting and folding of amino acid chain into:

• helices with H-bonds (includes α-helix)
• extended regions that H-bond together (b structures)
• loops and turns that link the helices and extended regions together
• random coil

• GLOBULAR PROTEINS - roughly spherical, usually water-soluble. e.g. myoglobin, lysozyme, insulin, enzymes, antibodies.

• FIBROUS PROTEINS - elongated, fibre-like shape, usually water-insoluble. e.g. collagen, keratins, actin.

• INTEGRAL MEMBRANE PROTEINS - have water-soluble ends and loops, interspersed with water-insoluble membrane - spanning sequences. e.g. rhodopsin, glycophorin, ATP synthase.

• SIMPLE PROTEINS - made up only of amino acids. e.g. albumin, collagen, keratins, histones.

• CONJUGATED PROTEINS - made up of amino acids plus other compounds called prosthetic groups. e.g. lipoproteins, glycoproteins, haemoproteins, flavoproteins.

• PRIMARY - sequence of amino acids

• SECONDARY - twisting and folding of chain, (alpha-helix & beta-pleated sheet structures)

• TERTIARY - arrangement of the secondary structures with respect to each other in space. Can consist of motifs and domains.

• QUARTERNARY - packing arrangement of polypeptide subunits in oligomeric proteins.