Biology of Amino Acids and Proteins

Biological Functions of Proteins

• Proteins have many important biological functions, including:
  • Enzymes: increase the rate of reaction by a factor of 1 billion
  • Carriers: hemoglobin, transferrin
  • Receptors: hormones, cytokines
  • Transport: membrane channels
  • Structure: collagen, elastin
  • Protective: immunoglobulins
  • Contractile: muscle, cytoskeleton
  • Regulatory: hormones, govern metabolic pathways

Amino Acids (aa) and Proteins

• There are over 300 amino acids found in nature, but only 20 are found in mammalian proteins and are coded for by DNA
• The nature of the side chain decides the role of an amino acid in a protein
• Amino acids can be classified according to the properties of their side chains
• Amino acids can function as an acid (donate H+) or as a base (accept H+)

Amino Acid Structure

• At physiological pH, an amino acid has a carboxyl group (-COO-) and an amino group (-NH3+)
• There are two forms of an amino acid: neutral and zwitterionic
• Zwitterion: a neutral molecule with equal numbers of + and - charges
• Isoelectric point: the pH at which there is no net charge on the zwitterion

α-Amino Acids

• Only 20 are common in nature
• All 20 are α-amino acids
• Alpha means the amine is adjacent to the carboxy group on the α-C
• Amino acids differ by their R groups
• 19 out of the 20 are stereoisomers

Classes of Amino Acids

• Amino acids are classified based on the polarity of their side chains:
  • Non-polar, hydrophobic
  • Polar, neutral
  • Negatively charged
  • Positively charged

Hydrophobic, Non-polar Amino Acids

• Non-polar amino acids don't bind or give off protons or participate in hydrogen or ion bonds
• They are "oily" or lipid-like material
• Hydrophobic amino acids do not "like" to reside in an aqueous (water) environment
• In aqueous solutions, hydrophobic amino acids tend to cluster together in the interior of the hydrophobic core of the protein or within the lipid portion of the membrane
• The hydrophobic interaction is important in stabilizing protein structure

Hydrophilic, Polar Amino Acids

• Uncharged side chains
• These amino acids have zero net charge at neutral pH
• Some side chains act as sites of attachment for compounds
• The -OH of serine and threonine can be linked to oligosaccharide in glycoprotein

Hydrophobic vs. Hydrophilic Amino Acids

• Within the membrane: nonpolar amino acids, hydrophobic, anchors protein into the membrane
• On outer surfaces of membrane in fluid: polar amino acids, hydrophilic, extend into extracellular fluid and into the cytosol

Charged Amino Acids

• Negatively charged amino acids: acidic R group
• Positively charged amino acids: basic R group

Positively Charged Amino Acids

• These amino acids have a positive charge at neutral pH
• These amino acids are proton acceptors at neutral pH
• Histidine has an important role in the catalytic mechanism of enzymes

Negatively Charged Amino Acids

• These amino acids have a negative charge at neutral pH
• These amino acids are proton donors at neutral pH
• Contain carboxyl-groups that are weaker acids than the α-carboxyl-group

Disulfide Bond Formation

• Two cysteines (each contains a sulfhydryl group -SH) in proximity will form a covalent bond
• The two –SH form a dimer “cystine” containing a covalent cross-link disulfide bond (disulfide bridge, or dicysteine bond)
• Significantly stabilizes tertiary structure (e.g. antibodies/immunoglobulins)
• Important component of the active site at many enzymes

Amino Acids - Summary

• 10 amino acids not synthesized by the body:
  • Met, Ile, Leu, Val, Phe, Trp, Thr, Arg, His, Lys
• Must be obtained from the diet

Structural Features of Amino Acids

• All 20 are α-amino acids
• For 19 of the 20, the α-amino group is primary; for proline, it is secondary (imino acid)
• Except glycine, the α-carbons for 19 of them are asymmetric (or chiral)

This quiz covers the structure and function of amino acids and proteins, including their features, reactions, peptide bonds, and types of protein structures. It also explores the biological functions of proteins, such as their role as enzymes.