lec 3

• Amino acids are the basic unit of proteins
• Each amino acid consists of:

  • A carboxyl group (-COOH/-COO-)
  • An amino group (-NH2/-NH3+)
  • An α carbon (carbon adjacent to the carboxyl group)
  • An R group (side chain that gives each amino acid a unique property)
• There are twenty-two (22) proteinogenic amino acids, twenty (20) of which can be found in the genetic code
• Each amino acid has its own unique side chain
• Amino acids are classified based on the characteristics of their R group into:

  • Non-Polar amino acids
  • Polar Neutral amino acids
  • Acidic amino acids
  • Basic amino acids
• Essential amino acids are necessary for growth and normal body functions but cannot be synthesized by the body, so they must be obtained through the diet
• All protein-derived amino acids, except glycine, have at least one stereocenter (the α carbon) and are therefore chiral
• Amino acids may act as weak acids and bases within an aqueous environment
• The side chains of amino acids may also be ionized at varying pH
• At a certain pH, the net charge of an amino acid becomes zero, known as a zwitterion or its isoelectric pH (pI)
• Amino acids are linked together through peptide bonds, formed between the α-carboxyl group of the first amino acid and the α-amino group of the next amino acid in the chain
• Amino acids bonded by a peptide bond are referred to as amino acid residues
• Short chains of amino acids (up to 50 residues) are peptides, while longer chains (>50 residues) are polypeptides
• Proteins are biomolecules composed of one or more polypeptide chains with more complex, three-dimensional structures
• Proteins can be classified based on their levels of structure:

  • Primary (amino acid sequence)
  • Secondary (folding in specific areas)
  • Tertiary (3D folding of the entire polypeptide)
  • Quaternary (arrangement of multiple polypeptide chains)
• Proteins can also be classified based on their shape:

  • Fibrous proteins (mechanically strong, insoluble)
  • Globular proteins (folded into a spherical shape, soluble)
• Proteins can be classified based on their composition:

  • Simple proteins (only composed of amino acids)
  • Conjugated proteins (contain non-protein components called prosthetic groups)
• Proteins can denature, leading to a change in their native conformation and disruption of protein function
• Denaturation can be caused by physical or chemical agents
• Protein hydrolysis refers to the breakage of peptide bonds, producing free amino acids or smaller peptide chains
• Proteins serve various functions, including:

  • Structure (e.g., collagen, elastin)
  • Catalysis (enzymes)
  • Storage (e.g., casein, ovalbumin)
  • Transport (e.g., hemoglobin)
  • Regulation (e.g., insulin, glucagon)
  • Receptor (e.g., neuron receptors)
  • Movement (e.g., myosin, actin)
  • Protection (e.g., antibodies, fibrinogen)
• Protein function is highly dependent on its structure and amino acid composition
• Changes to the amino acid sequence can negatively impact protein function
• Proteins for catalysis must have amino acids that can interact and bind with their target molecule for the reaction to take place
• Proteins meant for transport can have polypeptide chains form a 'channel' for molecules to pass through
• Receptor proteins embedded in the cell membrane must have nonpolar amino acids to remain embedded and polar amino acids for interaction with the aqueous environment