Biochemistry 1-2

Biochemistry 1-2

1. Proteins

   • biopolymers of alpha-L-amino acid bound by peptide bonds
   • Amino acids that form proteins
   • Structure
     • Primary
       • sequence of amino acids
     • Secondary
       • Amino acids linked by H-bonds
         • alpha-helix (3.6 amino acid residues forming H-bonds with eachother)
         • Beta-sheet (H-bonds between NH and CO groups of neighbouring parallel/anti-parallel chains)
     • Tertiary
       • Attractions between alpha-helices and pleated sheets
     • Quaternary
       • More than one amino acid chain
   • Functions
     • Catalytic
     • Transport
     • Regulatory
       • Receptors & transcription factors (binds to specific DNA sequences)
     • Hormonal
       • Some hormones are proteins
     • Immune responses
       • Antibodies are proteins
     • Nutrition
     • Structural
     • Energy source
     • Genome regulation
   • Domain
     • Folds independently of rest of protein chain
     • Regulatory domain
       • binds activating proteins
     • DNA binding domain
       • binds target genes
     • Ligand binding domain
       • binds hormones

2. Enzymes

   • Apo-enzyme
     • The enzyme itself
   • Co-enzyme
     • Prosthetic group attached to enzyme
   • Active site
     • Recognition site
     • Catalytic site
   • Classes
     • Oxidoreductases
       • Catalyse oxidation/reduction reactions
     • Transferases
       • Transfer atoms from one molecule to another
     • Hydrolases
       • Catalyse hydrolysis reaction
     • Lisases
       • Attach functional groups to pi-bonds
     • Isomerases
       • Catalyse isomerisation reactions
     • Ligases
       • Catalyse biosynthesis reactions
   • Activation and Inhibition
     • Speed of an enzyme reaction is described by Michelis-Menthen equation
     • Allosteric activation
       • Allosteric modulator interacts with allosteric site causing conformational change in shape of active site & activation
     • Allosteric inhibition
       • Interacts with allosteric site causing confirmational change of active site & inhibition (substrate can no longer fit)
       • Usually irreversible
     • Isosteric inhibition
       • Inhibitor competes with substrate for interaction with active site
       • Usually reversible
   • Other
     • Specifity
       • Absolute substrate
         • Enzyme converts only one substrate
       • Absolute group
         • Enzyme recognises groups of atoms (from several substrates)
     • Iso-enzymes
       • Same function, different structure
     • Multi-enzyme systems
       • Catalyse sequential conversion of the same substrate

3. Prosthetic groups

   • Nucleoproteins
     • nucleic acid prosthetic group
   • Glycoproteins
     • Carbohydrate prosthetic group
   • Lipoproteins
     • Lipid prosthetic group
   • Chromoproteins
     • Coloured compounds like heme
   • Phosphoproteins
     • H3PO4 prosthetic group
   • Metalloproteins
     • Metal cation prosthetic group

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