Interaction of Amino Acids with Water
- 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/Non-essential 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.
Modified amino acids
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
Classification by Shape
- 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.
Classification by Composition
- 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.
Levels of protein structure
- 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.