biochemistry

• Proteins are highly organised biopolymers formed by a-L-amino acid residues.
• Proteins are bound together by peptide bonds.
• Proteins form proteins.
• Biopolymers are a large biologically active molecule.
• D can be used when the light turns right.
• The L in L-amino acids stands for left, which comes from the direction of light turns when shone on acids.
• L-amino acids are used as analogues of optical isomerism (isomers).
• Greek letters are used to number carbon atoms in an acid (which is where a comes from).
• Positively charged- 2 amino groups.
• Negative charged- 2 COOH groups.
• Amino acids are separated into 5 groups as the carbon is attached to different R groups.
• Non-polar aliphatic a-radical

  Electroneutral compounds as the proton donated by COO- is given to +H3N. This means that they are unreactive and hydrophobic.

  Examples of these are:

  • Glycine
  • Alanine
  • Proline
  • Valine
  • Leucine
  • Isoleucine
  • Methionine

  
• Aromatic a-radical

  Contains an aromatic chain

  Examples of these are:

  • Phenyl-alanine
  • Tyrosine
  • Tryptophan

  
• Polar uncharged alpha radicals

  Amino acids with polar side chains- can be in a hydrogen bonding interactions

  Examples of these are:

  • Cysteine
  • Threonine
  • Serine
  • Asparagine
  • Glutamine

  
• Positively charged alpha radical

  Amino acids with at least one NH3+ group on its side chain (basic side chain)

  Examples of these are:

  • Lysine
  • Arginine
  • Histidine

  
• Negatively charged alpha radical

  Amino acids with an acidic side chain

  Examples of these are:

  • Aspartic acid
  • Glutamic acid

  
• Structure of proteins

   

  Primary structure of the proteins- Amino acid residues upon binding to each other. This forms polypeptide chains, which is the primary structure. It is a sequence of a chain of amino acids

  An example of this is lysozyme- which helps wounds in the mouth to heal quicker

   
• Secondary structure

  • Alpha helix-each spiral of the helix is 3.6 amino acid residues long. Hydrogen bonds forms between each other which links sequence of amino acids together

  Residue is a term for a monomeric unit of a polymer

  
• • Beta sheetsformed by hydrogen bonds between the NH group of one amino acid and the CO groups of neighbouring parallel/antiparallel chains
• Tertiary structure

  This is formed by certain attractions between alpha helices and beta pleated sheets.

  There can be disulfide covalent bonds, hydrogen bonding, van der waals etc
• Quaternary structure

  Haemoglobin has a quaternary structure as it has 4 16kDa subunits that form a single protein. Several protein molecules are bound together to create a single unit
• Protein structural domain

  It is an independently folder region within the 3D structure of a protein. Different parts of the protein are responsible for a range of different chemical interactions. Protein structural domains can do specific jobs and comes together to build a protein with various functions.
• Enzymes are specific proteins that catalyse biochemical reactions.
• There are different parts of an enzyme: Apo-enzyme, Co-enzyme, and Active site.
• Apo-enzyme is the protein part of the enzyme that has its own primary, secondary, tertiary and quaternary structure.
• Only 10% of enzymes have only the apo-enzyme part and not the co-enzyme.
• Co-enzyme is the non-protein (prosthetic) part of the enzyme and is the small part.
• Co-enzyme can be associated with the apo-enzyme through covalent and non-covalent bonds.
• Co-enzyme plays a vital role in catalysis.
• Active site is the part of the enzyme that recognises the substrate (recognition site) and performs catalytic reaction (catalytic site).
• Active site contains both the recognition sites and the catalytic site.
• The recognition site recognises the bond and the catalytic site applies force to the bond.
• Mechanism of enzymatic reaction

  
• All known enzymes are divided into 6 classes: Oxidoreductases, which catalyse oxidation/reduction reactions, attaching and removing electrons; Transferases, which transfer groups of atoms from one molecule to another, for example, kinase attaches phosphoric acid to a protein to stimulate proteins activity; Hydrolases, which catalyse reactions associated with hydrolysis, using water to break compounds; Liases, which attach functional groups to pi- bonds; Isomerases, which catalyse reactions of isomerisation, for example, the catalysis of glucose and fructose as they have the same molecular for
• Classes are divided into subclasses and subclasses are further divided into sub-subclasses.
• Each enzyme has its own EC number, which is a 4 digit number.
• Michaelis-Menthen test: A test used to determine the concentration of a solution.

  
• The speed of the enzyme reaction is described by the equation of the Michaelis-Menthen where:

  
• Direct activation and inhibition of enzyme reactions

  Allosteric site

  Is the amino acid sequence recognising and binding to the allosteric modulator or inhibitor.

  It turns the enzyme on and off the regulate energy uses

   

  Allosteric activation

  • The allosteric modulator interacts with the allosteric site of the enzyme causing conformational change and activation
  • This allows the substrate to fit into the active site as they have a complementary structure

  
• Allosteric inhibition

  • The allosteric inhibitor interacts with the allosteric site of the enzyme causing conformational change and inhibition
  • The substrate can no longer bind to the active site of the enzyme