Unit 1 Cell and Molecular Biology

1. Unit 1Cell and Molecular Biology Section 6 Catalysis

2. Chemical Reactions (Revision) • Synthesis (anabolic) • Condensation reactions • Removal of water to form a bond • Degradation (catabolic) • Hydrolysis reactions • Addition of water to break a bond

3. Enzymes • Proteases • Hydrolyse peptide bonds • break down proteins into amino acids • Nucleases • Hydrolyse phosphodiester bonds • Break down nucleic acids into nucleotides • ATPases • Hydrolyse ATP • Break ATP into ADP and Pi with the release of energy • Kinases • Catalyse the transfer of a phosphate group onto a molecule such as a carbohydrate or a protein

4. Specificity of enzymes

5. Induced-fit model • When substrate combines with the enzyme it causes a change in shape of the active site • The change in shape results in an optimal fit for the substrate-enzyme interaction • Once the product diffuses away, the enzyme returns to its original shape

6. Cyanide • Cyanide is found is a gas (sometimes liquid) • Used / found in • House fires • Apricot stones • Suicide pills • Gas chambers (both US and Nazi Germany) • Stock piled by US and Soviet Union in 50’s and 60’s • Mining • Photography • Electroplating

7. Binds to iron atom in the enzyme cytochrome C oxidase • This changes the shape of the enzyme • Knowing how this works has important applications for • Detection of poisoning • Treatment

8. Control of enzyme activity • Competitive Inhibitors • Decrease the rate of reaction • Inhibitor is similar in structure and electrical charge to substrate • It binds to the active site • An increase in the substrate can result in an increase of product formation (inhibitor is out competed) • Competitive inhibition can be reversible or irreversible (depending on mechanism of binding)

10. Non-competitive inhibitors • Decrease the rate of reaction • Inhibitors have no similarity to the substrate • Inhibitor binds to part of the enzyme (other than the active site) distorting the shape of the enzyme • Increase in substrate concentration does not increase product formation • Can also be reversible

11. Control of enzymes – Enzyme modulators • Allosteric enzymes • Allosteric enzymes have at least one other binding site than the active site (called an allosteric site) • Allosteric enzymes have 2 forms – active and inactive • When a substance binds to an allosteric site it changes the shape of the active site.

12. Positive modulation • The modulator changes the active site so the enzyme becomes active (substrate fits) • Positive modulators are activators • Negative modulation • The modulator changes the active site so the enzyme becomes inactive • Negative modulators are inhibitors

14. Control of enzymes – Covalent modifications • Addition, modification or removal of a variety of chemical groups • Changes the shape of the enzyme • Phosphorylation and dephosphorylation • Kinase enzymes add phosphate • Phosphatase enzymes remove phosphate • Some enzymes are activated by phosphorylation, others are inactivated (and vice versa for dephosphorylation)

15. Proteolytic cleavage • Conversion of an inactive enzyme to an active one • Example Trypsinogen – Trypsin • Trypsinogen is synthesised in the Pancreas • Activation occurs when trypsinogen has amino acids removed in the duodenum by another protease enzyme • This changes the trypsinogen into the active form trypsin • Trypsin then helps to activate more trypsinogen molecules

16. Control of metabolic pathways • End product inhibition • Chemical reactions are normally organised into metabolic pathways with enzymes controlling each chemical reaction • The end-product can act as a negative modulator, binding to the first enzyme preventing the metabolic pathway from proceeding because intermediary substrates are not produced • This is a process of negative feedback

17. Activity • Read and take notes from DART pg 61-68 • Scholar 6.3 and 6.4 • Check out http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter8/animations.html# • Find examples for each type of enzyme control