Cell bio module 1

• Proteins are composed of amino acids
• Primary structure


  The linear array of amino acids
• Properties of amino acid side chains (R-groups)

  • Size
  • Shape
  • Charge
  • Hydrophobicity
  • Reactivity
• Hydrophilic


  Molecules that can form hydrogen bonds with water and are water-soluble
• Hydrophobic


  Molecules that cannot form hydrogen bonds with water and are water-insoluble
• Hydrophobic amino acids


  • Aromatic (phenylalanine, tyrosine, tryptophan)
  • Aliphatic (alanine, valine, isoleucine, leucine, methionine)
• Hydrophilic amino acids with charged side chains

  • Positively charged (lysine, arginine)
  • Negatively charged (aspartic acid, glutamic acid)
• Hydrophilic amino acids with uncharged polar side chains

  • Hydroxyl group (serine, threonine)
  • Amine group (asparagine, glutamine)
• Special amino acids


  • Cysteine (forms disulfide bridges)
  • Glycine (very small)
  • Proline (forms covalent bond with amino group)
  • Histidine (shifts between positive and neutral charge)
• Forming a peptide bond

  1. Condensation reaction (water is released)

  2. Covalent bond between carboxyl group of one amino acid and amino group of another
• Histidine


  Amino acid with an amino diethyl side chain that shifts between a positive charge and neutral charge, depending on the pH of the environment
• Knowing the properties of amino acids will be essential to understand the unique structure and function of different proteins
• Making a protein


  1. Amino acids covalently bound together through peptide bonds

  2. Peptide bond formed by a condensation reaction, releasing water
• Peptide bond


  Covalent bond formed between the carboxyl group of one amino acid and the amino group of another amino acid
• Protein chains


  • Typically depicted from N-terminus (amino end) to C-terminus (carboxyl end)
  • Protein synthesis occurs during translation, with new amino acids added to the carboxyl end
• Translation


  1. Occurs in the ribosome

  2. New amino acid residues are added to the carboxyl end of the growing polypeptide chain
• Polypeptide


  Linear array of amino acids that is not yet functional
• Functional 3D protein


  Has a series of loops, bends, and sheets that define structural and functional domains
• Levels of protein organization

  • Primary structure (linear array of amino acids)
  • Secondary structure (local interactions like hydrogen bonds and ionic bonds)
  • Tertiary structure (overall 3D shape)
  • Quaternary structure (multiple polypeptide chains)
• Primary structure


  Linear array or sequence of amino acids, determined by the sequence of nucleotides in the coding DNA
• The number of different polypeptide sequences is limited by the 20 distinct amino acids and the number of amino acids in the polypeptide
• Random coil


  Periodically ordered structure of a polypeptide, not a single stable structure but a collection of related structures
• Native structure


  The functional protein structure, stabilized by non-covalent interactions like ionic bonds, hydrogen bonds, Van der Waals forces, and the hydrophobic effect
• Ionic bond


  Attraction between a positively charged cation and a negatively charged anion
• Hydrogen bond


  Interaction between a partially charged hydrogen atom and an unpaired electron from another atom
• Hydrophobic effect


  Aggregation of nonpolar molecules in aqueous medium to reduce interactions with water
• Van der Waals interaction

  Weak non-specific attractive force resulting from a transient dipole when atoms are close together
• Van der Waals interactions in nature

  • Gecko's ability to walk on walls and ceilings due to millions of setae on their feet
• Protein folding


  1. Random process driven by interactions between amino acid residues

  2. Hydrophobic side chains aggregate in a core

  3. Hydrogen bonds and ionic bonds hold the structure together
• Understanding the chemical properties of amino acid side chains is important for understanding protein folding and function
• Identify and describe the four levels of protein organization

  1. Primary structure

  2. Secondary structure

  3. Tertiary structure

  4. Quaternary structure
• Primary structure


  Sequence of amino acids
• Secondary structure


  Local chemical interactions that fold a protein
• Secondary structures


  • Alpha helix
  • Beta sheet
  • Turns, loops, or connectors
• Alpha helix


  Spiral, rod-like structure
• Beta sheet


  Collection of associated beta strands
• Turns, loops, or connectors

  Bends in the polypeptide backbone that lie between the alpha helices and beta strands
• Formation of secondary structures

  1. Hydrogen bond formation between amino and carboxyl groups

  2. Periodicity of hydrogen bond formation defines the structure
• R groups are not involved in the formation of secondary structures but determine the properties of the structures
• Beta turn


  Conserved connector involving 3 or 4 amino acid residues, often found connecting beta sheet strands