Protein Chemistry Part 1

Study Notes

Objectives for this lecture include: amino acid structure and importance, amino acid classification, and amino acid properties.
Amino acids are the building blocks of proteins.
There are more than 300 amino acids, but only 20 make up proteins.
These 20 are the building blocks of proteins.
A typical amino acid contains: an amino group (NH2), a carboxyl group (COOH), a hydrogen atom, and a side chain (R group).
Amino acid structures differ only in the R group.
Amino acids are α-amino acids.
The amino group is attached to the α-carbon, which is next to the COOH group
The L-amino acids are the ones that compose proteins. Some D-amino acids occur in nature, but not in proteins.

Each amino acid has four different groups attached to the α-carbon.
They are the amino group (NH2), the carboxyl group (COOH), hydrogen (H), and the side chain (R group).
The R group differentiates the 20 amino acids.

Chemical classification: based on the number of carbon atoms, acidic, basic, neutral, and amide group-containing amino acids, sulfur and hydroxy-containing amino acids, aromatic, heterocyclic, and aliphatic AAs, branched and nonbranched chain AAs.
Nutritional classification: based on whether the amino acid can or cannot be synthesized in the body.
Essential amino acids: cannot be synthesized in the body; must be obtained from the diet.
Semi-essential amino acids: can be synthesized but not always in sufficient amounts to meet needs, and may need supplementation in certain circumstances
Non-essential amino acids: can be synthesized in the body.
Examples of amino acids and their classification follow:

2 carbons: Glycine
3 carbons: Alanine, Serine, Cysteine
4 carbons: Methionine, Threonine
5 carbons: Arginine, Valine
6 carbons: Lysine, Leucine, Isoleucine
Other: Proline (imino acid), Aspartate (acidic), Glutamate (acidic), Arginine (basic), Histidine (basic)

Selenocysteine is a 21st amino acid with selenium in place of sulfur.
Classification based on polarity: hydrophilic (polar), basic, acidic, and uncharged polar side chains, and hydrophobic (nonpolar) side chains.
Classification based on nutritional requirements: essential, nonessential, and conditionally essential amino acids,
Classification based on metabolic fate (glucogenic, ketogenic, and mixed).
The presence of certain organic compounds and certain heavy metal ions can denature proteins.
Cooking causes proteins to be denatured, which in turn makes digestion easier,
Denaturation of a protein occurs when secondary, tertiary, and quaternary structures are lost, while the peptide bonds remain intact.
Denaturation usually is irreversible, but renaturation can occur with certain proteins such as hemoglobin.

Definition of proteins: nitrogenous macromolecules composed of many amino acids.
Biomedical importance of proteins:
- Proteins are main components of the cytoskeleton.
- Enzymes are proteinous biological catalysts.
- Immunoglobulins are proteins that serve as the first line of defense against pathogens.
- Hormones are proteinous molecules and they play a regulatory role in various cellular functions.
- Proteins are crucial for mechanical support, e.g., actin and myosin; and for movement.
Proteins are also present in cell membranes, cytoplasm, and nucleus as receptors. They bind specific substances and regulate cellular action.
Transport proteins carry specific substances across membranes or throughout the body.
Storage proteins store specific substances (iron, for example).
Proteins are involved in respiratory pigments (cytochromes, hemoglobin, myoglobin).
Proteins are catabolized for energy when other energy sources are depleted.
Proteins affect electrolyte and water balance through osmotic pressure.

Simple proteins: composed only of amino acids.
Conjugated proteins: contain a non-proteinous moiety (prosthetics group or conjugating group). Examples include lipoproteins (associated with lipids), glycoproteins (associated with carbohydrates), metalloproteins (associated with metal ions), and phosphoproteins (associated with phosphates).
Derived proteins: denatured or degraded products of simple or conjugated proteins.
Examples of simple proteins include: albumin, globulins, protamines, histones, sclero-proteins, and globin.
Specific protein structures(primary, secondary, tertiary, quaternary structure) are presented in detail in the later sections of the lecture notes