Protein Chemistry Part 1 - Amino Acids

Protein Chemistry (Part 1)

• 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.

Amino Acid Structure

• 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.

Amino Acid Classification

• 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:

Examples of amino acids

• 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)

Other aspects

• 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.

Protein Chemistry (Part 2)

• 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.

Protein Classification based on chemical nature

• 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