HL proteins

• The R group of amino acids is a side chain specific to each amino acid that confers particular chemical properties to that amino acid
• In a neutral aqueous solution, both the amino group and the carboxyl groups ionize
• The carboxyl group acts like an acid and donates a hydrogen ion, resulting in a net negative charge; the amino group acts like a base and accepts a hydrogen ion, resulting in a net positive charge
• For a protein to be functional, it has to fold into a very specific shape, with the R group determining its function
• The immense diversity in protein form and function is based on the chemical diversity in the R-groups of amino acids
• The primary structure of proteins is the linear sequence of amino acids in a polypeptide
• The backbone of a polypeptide chain is a repeating sequence of atoms linked by covalent peptide bonds
• The primary structure of a protein containing only non-polar R-groups can result in beta-pleated sheet and alpha helix shapes
• Hydrogen bonds are formed between non-adjacent amino and carboxyl groups in beta-pleated sheets and alpha helices
• Proteins with a purely alpha helix or beta-pleated sheet shape do not form a unique and complex globular shape
• Tertiary structure is the folding of a whole polypeptide chain into a three-dimensional structure, stabilized by interactions between the R-groups
• Ionic bonds form between ionized R-groups with opposite charges
• Hydrophobic interactions occur when non-polar amino acids fold into the interior of the polypeptide to avoid water molecules
• Disulfide covalent bonds form between pairs of cysteine amino acids within a polypeptide
• Polar amino acids form hydrogen bonds with each other, typically found on or near the exterior of the polypeptide due to their hydrophilic properties
• Tertiary structure of proteins depends on:

  • Hydrogen bonds
  • Ionic bonds
  • Disulfide covalent bonds
  • Hydrophobic interactions
• Amino acids in proteins can be categorized into non-polar (hydrophobic) and polar or charged (hydrophilic)
• Globular proteins need to be soluble in water as they function in the cytoplasm or aqueous solutions outside the cell
• Proteins with hydrophilic amino acids on their surface in contact with water and hydrophobic amino acids clustered in the center stabilize the tertiary structure by maximizing hydrophobic interactions and hydrogen bonding
• Some proteins in contact with non-polar substances have hydrophobic amino acids on parts of their surface
• Transmembrane proteins have a hydrophobic belt with hydrophilic regions inside and outside, stabilizing their tertiary structure and positioning them correctly in the membrane
• Channel proteins in membranes have a tunnel lined with hydrophilic amino acids for specific hydrophilic ions or molecules to pass through
• Proteins have at least one polypeptide, with some consisting of two or more linked polypeptides and others having non-polypeptide components
• In non-conjugated proteins, polypeptides are linked by interactions like those in tertiary structure to form the quaternary structure
• In conjugated proteins, non-polypeptide subunits increase chemical and functional diversity, like in hemoglobin where each polypeptide chain is associated with a haem group for oxygen transport
• The form of a protein determines its function, with fibrous proteins consisting of elongated polypeptides and globular proteins having a rounded shape
• Fibrous proteins lack the folding of typical tertiary structure and are stabilized by hydrogen bonds between the chains
• The primary structure of fibrous proteins is a repeating sequence of three amino acids, with proline or hydroxyproline preventing alpha helix formation
• Cryo-EM allows imaging of single protein molecules and their interactions without the need for protein crystallization
• Cryo-EM involves applying a protein sample to a grid, plunging it into liquid ethane to freeze, trapping protein molecules in ice for imaging with electrons
• Cryo-EM generates high-resolution 3D images of proteins, allowing reconstruction of structural information and study of large intact complexes like ribosomes and viruses