Amino Acids and Peptides Overview

Amino Acid Nomenclature

• Three-letter abbreviations are used to name standard amino acids
  • Abbreviation is the first three letters of the amino acid name
  • Exceptions: Isoleucine (Ile), Tryptophan (Trp), Asparagine (Asn), and Glutamine (Gln)
• One-letter symbols are used for comparing amino acid sequences of proteins
  • Usually the first letter of the name
  • When more than one amino acid has the same letter, the most abundant amino acid gets the first letter

Cysteine: A Chemically Unique Amino Acid

• Standard amino acid that contains a sulfhydryl group (-SH group)
  • Sulfhydryl group imparts cysteine a unique chemical property
• Cysteine dimerizes to form a cystine molecule in the presence of mild oxidizing agents
  • Cystine contains two cysteine residues linked via a covalent disulfide bond

Peptides

• Amino acids can bond together to produce a peptide chain under proper conditions
  • Peptide: Unbranched chain of amino acids
  • Dipeptide: Compound containing two amino acids
  • Oligopeptide: Peptide with 10 to 20 amino acid residues
  • Polypeptide: Long unbranched chain of amino acids
• Reaction occurs between the amino group of one amino acid and the carboxyl group of another amino acid

General Structural Characteristics of Proteins

• Protein: Naturally-occurring, unbranched polymer in which the monomer units are amino acids
• Peptide: At least 40 amino acid residues are present
  • The terms polypeptide and protein are often used interchangeably
  • Some proteins have >10,000 amino acid residues
  • Common proteins contain 400–500 amino acid residues
  • Small proteins contain 40–100 amino acid residues
• More than one polypeptide chain may be present in a protein
  • Monomeric: Protein which contains one polypeptide chain
  • Multimeric: Protein which contains two or more polypeptide chains

Protein Classification Based on Chemical Composition

• Simple protein: Protein in which only amino acid residues are present
  • More than one protein subunit may be present
• Conjugated protein: Protein that has one or more non-amino-acid entities (prosthetic groups) present in its structure
  • One or more polypeptide chains may be present
  • Non-amino-acid components may be organic or inorganic

Primary Structure of Proteins

• Specific protein's primary structure is the same within the organism
  • Structures of some proteins are similar among different species of animals
    • Example: Insulin from pigs, cows, sheep, and humans are similar but not identical
• Amino acids are linked to one another by peptide linkages

Secondary Structure of Proteins

• Arrangement in space adopted by the backbone portion of a protein
• Types: Alpha-helix (α helix) and beta-pleated sheet (β pleated sheet)
• Alpha-helix structure: A single protein chain adopts a shape that resembles a coiled spring (helix)
  • Coil configuration maintained by hydrogen bonds
  • Twist of the helix forms a right-handed, or clockwise, spiral

Protein Classification Based on Function

• Catalytic proteins are known for their role as catalysts
  • Almost every chemical reaction in the body is driven by an enzyme
• Defense proteins are central to functioning of the body’s immune system
  • Known as immunoglobulins or antibodies
• Transport proteins bind to small biomolecules, transport them to other locations in the body, and release them as needed
• Messenger proteins transmit signals to coordinate biochemical processes between different cells, tissues, and organs
  • Examples: Insulin, glucagon, and human growth hormone
• Contractile proteins are necessary for all forms of movement
  • Examples: Actin and myosin
  • Human reproduction depends on the movement of sperm, which is possible because of contractile proteins
• Structural proteins confer stiffness and rigidity
  • Collagen is a component of cartilage
  • α-keratin gives mechanical strength and protective covering to hair, nails, feathers, and hooves
• Transmembrane proteins control the movement of small molecules and ions through the cell membrane
  • Have channels to help molecules enter and exit the cell
  • Selective, allow passage of only one type of molecule or ion

This quiz covers the nomenclature and chemical properties of amino acids, focusing on standard amino acids and their abbreviations. It also discusses the unique characteristics of cysteine and the formation of peptide chains from amino acids. Test your knowledge on these essential biomolecules!