Proteins

• What are proteins?

  Polypeptide (polymers made up of amino acids) chains
• How many different amino acids are there and how do they differ?

  There are 20 different amino acids, and they all are the same apart from their R side groups.
• What is the simplest amino acid and what is it's R side group?

  Glycine - R side group is hydrogen
• What does the structure of an amino acid have?

  Amine group - NH2

  Carboxyl (acid) group - COOH

  Hydrogen group

  R side group
• R side group

  Different elements that determine the amino acids. Sometimes called side chains
• How are peptide bonds formed (and therefore broken)?

  Through the condensation reaction of a carboxyl group and an amine group. Releases water. Broken via hydrolysis
• What are essential amino acids?

  Amino acids that we, as humans, have to digest because our bodies cannot make them ourselves.
• Primary structure

  Sequence of amino acids. A change in this means a change in the shape and function of the protein.
• Secondary structure

  The sequence of amino acids that coil or fold up into either alpha helix or beta pleated sheet
• How do amino acid sequences coil up into their secondary structure?

  The hydrogen of the amine group forms weak hydrogen bonds with the oxygen of the carboxyl group. This is because the hydrogen is positively charged whilst the oxygen is negatively charged. This causes the protein to coil or fold.
• Alpha Helix

  A coiled secondary structure because of the hydrogen bonds keeping the structure together. There are 3.6 amino acids per turn of the helix shape.
• Beta pleated sheet

  A folded (fan-shaped) secondary structure
• Tertiary structures

  Secondary structures (a-helix or b-pleated sheet) coil/fold themselves into specific, 3D structures - final geometric shape
• The tertiary structure is the final geometric shape.
• What are the 3 bonds that occur on side chains in tertiary structures?

  Disulfide bridges (S-S bonds), ionic bonds and hydrogen bonds
• Disulfide bridges (S-S bonds)

  Strong bonds that are not easily broken. The sulfur atoms on the side chain (R group) of cysteine amino acids bond together.
• Ionic bonds

  Weaker than disulfide bridges, and are easily broken by pH changes. Electrostatic attraction between positive and negative charges on R groups.
• Hydrogen bonds

  They are weak and easily broken. They occur between slightly positively charged and slightly negatively charged R groups. Involves a hydrogen atom.
• Why do globular proteins form a spherical shape?

  Hydrophobic, non-polar R groups are oriented near the centre of the protein, away from the water whilst hydrophilic, polar R groups are oriented outside of the protein, close to the water.
• Quaternary structure

  Proteins are made of multiple polypeptide subunits (one subunit being one polypeptide chain). Gives a final 3D structure
• Prosthetic group

  When a polypeptide joins to an inorganic component e.g. iron haem group in haemoglobin.
• Globular proteins are:

  • spherical (shape)
  • functional
  • water soluble
  • irregular but wide range of R groups
  • compact (think energy storage)
• Fibrous proteins are:

  • long strands
  • water insoluble
  • fibres form a triple-helix of polypeptide chains held together by hydrogen bonds
  • structural
  • repetitive but limited range of R groups
  • found in skin, teeth and bones
• Haemoglobin is an example of a globular protein and it has 4 tertiary structures (polypeptide chains) and 4 haem prosthetic groups:

  • 2 tertiary structures are alpha helix subunits
  • the other 2 are beta pleated sheet subunits
• What does haemoglobin do?

  It carries oxygen around the body because it binds to the Fe2+ ion.
• Collagen is a long, strong structural or fibrous protein made up of 3 tertiary structures, twisted and held together by hydrogen bonds. These twisted structures are then held together to adjacent collagens by covalent bonds.
• What are enzymes?

  Globular tertiary structures that catalyse reactions.
• What is the active site?

  A small part of an enzyme that is specific and unique in shape. This attaches to a substrate that is complementary in shape in order to catalyse a reaction
• What is the enzyme-substrate complex?

  When the active site on an enzyme binds to a substrate that is complementary in shape
• What is the activation energy?

  The minimum amount of energy needed to activate the reaction. Enzymes lower the activation energy.
• What is the Lock and Key model?

  The enzyme is like a lock, with it's active site being a fixed shape. The active site attaches to a complementary substrate through random collisions between the enzyme and the substrate, forming an enzyme-substrate complex.
• What does the enzyme-substrate complex cause according to the Lock and Key model?

  It causes the substrate to slightly distort in its shape and, consequently, decreases the activation energy. The products are then released, and the active site is now empty and ready to be reused.
• What is the Induced Fit model?

  The enzyme is like a glove and the substrate its hand - the enzyme's active site slightly changes shape so that the active site moulds around the substrate to create an enzyme-substrate complex.
• What does the enzyme moulding around the substrate cause, according to the Induced Fit model?

  The moulding puts strain on the bonds and weakens them. This means the activation energy is lowered. The products are then removed, and the enzyme's active site reverts to it's original shape.
• Which model is more widely accepted nowadays?

  The Induced Fit model
• Why are enzymes sensitive to certain conditions?

  This is because of the bonds in the tertiary structure
• Different enzymes have different optimal pH (dependent on where the enzymes are produced e.g. in stomach, pancreas)
• Why are we 37 degrees celsius?

  • Increased body temperature requires more energy
  • Metabolic rates would be too fast
  • Enzymes may be denatured if you have a fever
• What is the equation in order to calculate the pH from a known concentration of H+ ions?


  pH = -log10(H+)
• What is the effect an increase in temperature has on enzyme action?

  Increasing temperature -> Increase in kinetic energy of molecules -> Molecules move around more rapidly + have more frequent successful collisions -> more enzyme-substrate complexes form -> rate of reaction increases