cofactors

cofactors + classifications

• What does catalyctic diversity of an enzyme depend on?

  • Amino acids in active site

• 20% of enzymes need what for biocatalytic conversions, other than aa?

  • Cofactors

• LO1. Describe cofactors and their classifications

  • What is a cofactor?

    • Essential portion of the active site of cofactor-dependent enzymes, often participate in catalysis.

    • Catalysis meaning

      • Increasing rate of a chemical reaction with a catalyst

  • What requires a cofactor, to be converted into...?

    • Apoenzymes (inactive form) to be converted to holoenzymes (active form)

  • 2 types of cofactors

    • 1. Essential ions (inorganic compounds, mostly metal ions)

      • 2 types of essential ions

      • 1. Activator ions -

        • Loosely, reversibly bound

        • Participate in binding of substrates

      • 2. Metal ions of metalloenzymes

        • Tightly bound
          - Participate directly in catalytic reactions

    • 2. Coenzymes (organic compounds)

      • Act as group-transfer reagents. Specific for chemical groups that they accept + donate.

      • 2 types of coenzymes

      • 1. Cosubstrates -

        • Loosely bound

      • 2. Prosthetic groups -

        • Tightly bound

      • For some coenzymes, what is the chemical group they accept/donate? (2)

        • H or e-

        • Some - larger, covalently attached groups

      • Where are the mobile metabolic groups attached to on the co-enzyme?

        • Reactive centre of co-enzyme

    • In mammals, where are most of these coenzymes derived from?

      • Vitamins (dietary precursors)

    • Why are many minerals essential for organisms?

      • They are cofactors

  • Most abundant elements

    • CHNOPS

  • Examples of essential ions (5)

    • Na+

    • Mg2+

    • K+

    • Ca2+

    • Cl-

  • Examples of trace elements

    • 

inorganic cations

• LO2. Explain the chemical basis of requirement for metals in enzymes

• What do over a quarter of all known enzymes require for full catalytic activity?

  • Metallic cations

  • 2 groups of enzymes that require metallic cations

    • Metal-activated enzymes - either activated by what 2 ways?

      • Have an absolute requirement for added metal ions

      • Stimulated by metal ions

    • Metalloenzymes -

      • Have firmly bound metal ions at their active sites

      • Examples of metalloenzymes (common + less common) (2)

        • Common - zinc, iron

        • Less common - copper, cobalt

      • Roles of metalloenzymes (2)

        • Act as electrophilic catalysts, meaning?

          • d+, metal ions 'attract electrons', leading to bond polarization/destabilisation

        • Fe + Zn - reversible oxidation-reduction, by transferring e- from a reduced substrate -> an oxidised substrate

      • 2 examples of metalloenzyme compounds

        • Carbonic anhydrase

        • Iron-sulfur clusters

  • Example of monovalent cations

    • K+

  • Examples of divalent cations (2)

    • Ca2+, Mg2+

• What does Mg2+ help ATP with?

  • Releasing phosphate + pyrophosphate (diphosphate) group in order to phosphorylate molecules

  • Sheilds the -vely charged phosphate groups of ATP, making them more suspectible to nucleophilic attack (pic)

  • 

• LO3. Discuss example enzymes and reaction mechanisms

metalloenzymes - carbonic anhydrase

• Role as a catalyst (what does it convert?)

  • Assists rapid interconversion of CO2 + H2O -> carbonic acid, protons + bicarbonate ions by increasing rate of conversions up to 1 million x

• 2 roles this has in our body

  • Regulating pH

  • Fluid balance

• What happens if absence/malfunction of this?

  • Diseased states eg (3)

    • Loss of acid production in stomach

    • Kidney failure - (long term usage of carbonic anhydrase inhibitors)

    • Glaucoma - eye tissue (too much H2O causes vision problems)

• How to treat glaucoma?

  • Inhibitors of carbonic anhydrase, prevents full activation of it

• What is the cofactor of carbonic anhydrase?

  • Electrophilic Zn2+ atom bound to side chains of 3 histidine residues, and to 1 H2O

  • What does binding to Zn2+ do?

    • Causes H2O to ionise more readily

• What is in the active site of carbonic anhydrase?

  • Everything in blue lines

  • 

• Mechanism of carbonic anhydrase (3)

  • Zn2+ cation bound into active site -> ionises H2O -> H+ + OH-

  • Zn2+-OH- nucleophilic attack on C of CO2

  • Produces bicarbonate (HCO3-), released from enzyme

  • 

• Water's bond polarities and CO2's bond polarities (pic)

  • 

iron in heme and non-heme

• Roles of iron in heme and non-heme

  • Reversible oxidation and reduction by transfer of e-

  • 

• What 2 places do heme groups occur in?

  • catalse -

    • (catalyses conversion of H2O2)

  • cytochromes -

    • (associated with metalloenzymes in e.g. mitochondria and chloroplasts)

• Fe is part of non-heme groups as what form?

  • Iron-sulfur clusters. Most 2 common ones?

    • [2Fe-2S] and [4Fe-4S]

    • \

  • How is iron and sulfur structured together in iron-sulfer clusters?

    • Fe atoms complexed with an equal number of sulfide ions (S^2-), and with a thiolate group of Cys residues

• Oxidation-reduction of iron in non-heme

  • Transfer 1 e- at a time

  • Example

    • Photosynthesis mitochondria oxphos - heme and nonheme iron. PSI uses light energy to gnerate reduced ferredoxin (mobile form, moves e-)

    • (don't need detail)

• LO4. Understand basic classifications of vitamins and co-enzymes

• What are co-enzymes often derived from?

  • Vitamin precursors, need to undergo biochemical conversion, vitamins enzymatically transformed to their coenzyme

  • Animals lost most biosynthetic pathways (or gut microbiome that synthesise cofactors)

• What are the supply of reactive FGs available from?

  • Not amino acid residues

  • From coenzymes - cannot biosynthesise so need vitamins

• Coenzymes are part of the active site of enzymes as what 2 things?

  • Cosubstrates (loosley bound)

  • Prosthetic groups (tightly bound or covalently attached)

• Roles of cosubstrates (4)

  • Substrates in ES catalysed reactions

  • Altered and dissociates from AS

  • Regeneration of cosubstrate in subsequent reaction catalyzed by another enzyme

  • Recycled repeatedly (not like 'ordinary' substrate's product typically transformed further by some metabolic pathway)

  • Shuttle mobile metabolic groups (mobile carrier of chemical groups) among different enzyme-catalyzed reactions

• Roles of prosthetic groups (3)

  • Remains bound to enzyme

  • Either covalently attached to apoenzyme or tightly bound by many weak interactions to AS

  • Must return to original structure during each full catalytic cycle

• Vitamins and their associated nutritional-deficiency diseases (table)

  • 

  • 

• What are the 2 classes of vitamins?

  • 1. Water-soluble

    • Examples

      • B-vitamins

    • How is it required?

      • Daily, in small amounts

      • Readily excreted via urine

    • How are they stored?

      • In the cell, but unstable (so excreted by kidneys rapidly)

    • Example of a water-soluble vitamin that is not a precursor of a coenzyme, and what it does instead?

      • Vitamin C

      • A reducing agent during hydroxylation of collagen

  • 2. Fat-soluble (lipid vitamins)

    • Examples

      • Vit A, D, E, K

    • How are they stored?

      • By animals in adipose tissues

    • What is the name of the toxic conditions that excessive intake can induce?

      • Hypervitaminoses