BioChemistry Lecture

• Peptides are chains of covalently linked amino acids
• Peptide is an unbranched chain of amino acids, each joined to the next by a peptide bond
• Classification of peptides:

  • Dipeptide: compound containing two amino acids
  • Tripeptide: three amino acids joined together
  • Oligopeptide: peptides with 10 to 20 amino acid residues
  • Polypeptide: peptide containing many amino acid residues with a molecular weight less than about 5000
• Peptide Bonds:

  • Bonds that link amino acids together in a peptide chain
  • Covalent bond between the carboxyl group of one amino acid and the amino group of another amino acid
• Nature of Peptide Bonds:

  • Reaction: carboxylic acid and an amine react to produce an amide
  • Products: molecule of water and a molecule containing the two amino acids linked by an amide bond
• Parts of a Peptide Chain:

  • C-terminal end: the end with the free COO- group
  • N-terminal end: end with the free H3N+ group
  • Amino acid residue: individual amino acids within a peptide chain
• Biologically Important Small Peptides:

  • Peptide Hormone: Vasopressin
  • Peptide Hormone: Oxytocin
  • Peptide Neurotransmitter: Enkephalins
  • Peptide Antioxidant: Glutathione
• Selected Roles of small peptides:

  • Hormonal action
  • Neurotransmission
  • Antioxidant activity
• Proteins:

  • Naturally occurring unbranched polymers with amino acid monomer units
  • Elemental composition includes carbon, oxygen, sulfur, hydrogen, and nitrogen
  • Levels of Protein Organization:
  • Primary Structure: linear sequence of amino acids
  • Secondary Structure: spatial arrangement by twisting of the polypeptide chain, includes α helix and β pleated sheet
• Beta-Sheet:

  • Two fully extended protein chain segments in the same or different molecules are held together by hydrogen bonds
  • When viewed edge-on, form a zigzag or pleated pattern in which the R groups of adjacent residues project in opposite directions
  • Two types: Parallel (weaker H-bonds) and Antiparallel (stronger H-bonds, more common)
• • Hydrophobic Interactions: result when nonpolar R groups are close to each other
• Tertiary Structure:

  • The overall three-dimensional shape of a protein resulting from interactions between widely separated amino acid side chains (R groups) within a peptide chain
  • Interactions responsible for tertiary structures:
  • Covalent-Disulfide Bonds: result from -SH groups of two cysteine residues reacting to form a covalent disulfide bond
  • Electrostatic Interactions (salt bridges): involve interaction between acidic and basic side chains
  • Hydrogen Bonds: can occur between amino acids with polar R groups, relatively weak and disrupted by changes in pH and temperature
• Quaternary Structure:

  • The highest level of protein organization
  • Organization among various peptide chains in a multimeric protein
  • Found only in multimeric proteins with two or more independent peptide chains
  • Subunits held together mainly by hydrophobic interactions between amino acid R groups
  • Example: Hemoglobin is a tetramer with two identical α chains and two identical β chains, each enfolding a heme group
• Breakdown of Proteins:

  • Hydrolysis of Proteins: Heating a protein in a strong acid or base solution hydrolyzes peptide bonds, producing free amino acids
  • Protein Denaturation: Disorganization of a protein's 3D shape due to disruption of structural interactions, leading to loss of biochemical activity and possible coagulation
• Classification of Proteins:

  • According to Shape:
  • Fibrous Proteins: elongated shape, tend to aggregate
  • Globular Proteins: folded into spherical shapes, hydrophobic side chains inside and hydrophilic outside
  • According to Composition:
  • Simple: composed of only amino acid residues
  • Conjugated: amino acids with additional components like prosthetic groups
  • Derived: underwent change, examples include processes and peptones in protein breakdown
• Functional Versatility of Proteins:

  • Ability to bind small molecules specifically and strongly
  • Ability to bind other proteins to form fiber-like structures
  • Ability to bind to and integrate into cell membranes
• • Storage: bind and store small molecules for future use, e.g., ferritin, myoglobin
  • Regulatory: embedded in cell membranes, e.g., transcription factors
  • Nutrient: support nourishment, growth, and repair, e.g., casein, ovalbumin
• Protein Functions:

  • Catalytic: biochemical catalysts/enzymes like ALT, AST
  • Defense: bind to foreign substances to combat invasion, e.g., immunoglobulins/antibodies
  • Transport: bind and transport small biomolecules, e.g., hemoglobin, transferrin
  • Messenger: transmit signals between cells, e.g., insulin, glucagon
  • Contractile: involve contraction and extension, e.g., actin, myosin
  • Structural: confer stiffness and rigidity, e.g., collagen, keratin
  • Transmembrane: control movement of molecules through cell membrane, e.g., integral membrane proteins