Lecture 4 Enzymes Catalytic proteins. Enzymes. Enzymes 10/21/10. What enzymes do therefore is:

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1 Lecture 4 Catalytic proteins Are a type of protein that acts as a catalyst-speeding up chemical reactions A catalyst is defined as a chemical agent that changes the rate of a reaction without being consumed by the reaction are biological catalysts Chemical reactions involve the breaking and forming of bonds-requires energy Activation energy is the initial investment of energy needed to start a reaction In most chemical reactions this is provided in the form of heat humans need to maintain a temperature of 37⁰C provide the activation energy for reactions to proceed at normal temperatures in biological systems What enzymes do therefore is: Reactants Transi5on state Products (ready to react) act here Biochemists call reactants substrates Substrate Transi5on state Products (ready to react) act here are substrate- specific each substrate fits into the enzyme s ac5ve site 1

2 Eg. Sucrase How do they work? 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Glucose H O OH Fructose Enzyme (sucrase) Substrate (sucrose) 2 Substrate binds to enzyme. H 2 O Transi5on state Complex molecules have the potential to breakdown spontaneously (2 nd law of thermodynamics= the universe tends towards disorder) They continue to exist because the initial activation energy required to breakdown can t be reached to initiate a breakdown reaction 4 Products are released. 3 Substrate is converted to products. Hydrolysis of sucrose involves the breaking of the bond between glucose and fructose the breaking of a bond in the water molecule the forming of 2 new bonds An enzyme lowers the activation energy required for a reaction enabling the substrates to absorb enough energy even at a moderate temperature to reach transition state Enzyme shape are substrate specific The substrate fits like a key in a lock When the substrate and enzyme are joined the catalytic action of the enzyme converts the substrate to product The specificity of an enzyme for a substrate results from the shape of the enzyme due to a compatible fit between the active site and the substrate The substrate binds to the active site of the enzyme -This is the catalytic centre of the enzyme - The active site is typically a pocket or groove on the surface of the enzyme active site Is usually formed by only a few amino acids Is not rigid The side chains of the aa s in the enzyme interact with the chemical groups of the substrate- enzyme changes shape and fits even better around the substrate- INDUCED FIT Induced fit brings the chemical groups of the active site into new positions enhancing the ability of the enzyme to catalyse the reaction The rest of the protein structure provides the structural framework that determines the configuration of the active site 2

3 Induced fit Induced fit Induced fit 6 major types Types of 3

4 Types of ATPases - hydrolyse ATP. Many proteins with a wide range of roles have an energy-harnessing ATPase activity as part of their function, for example, motor proteins such as myosin and membrane transport proteins such as the sodium potassium pump. Kinases - catalyze the addition of phosphate groups to molecules. Protein kinases are an important group of kinases that attach phosphate groups to proteins. Nucleases - break down nucleic acids by hydrolyzing bonds between nucleotides. Phosphatases - catalyze the hydrolytic removal of a phosphate group Polymerases - catalyze polymerization reactions such as the synthesis of DNA and RNA. Proteases - break down proteins by hydrolyzing bonds between amino acids. Types of Simple enzymes composed wholly of protein Complex enzymes-called holoenzymes Composed of protein (apoenzyme)+ a simple small organic molecule (cofactor or prosthetic group) Metalloenzymes are composed of protein (apoenzyme) + metal 6 important features of enzymes 1. Side chains of amino acids make up the active site 2. Substrates bind via weak interactions: hydrogen bonds, hydrophobic interactions 3. Act at optimal ph, temperature and substrate concentration 4. May require other factors to work 5. Can be inhibited by drugs 6. Are activated or inhibited by chemical modification 1. Side chains of amino acids make up the active site Dependent on R group chemistry Dependent on final folding 3. Substrates bind via weak interactions: hydrogen bonds hydrophobic interactions 4

5 3. act at optimal ph and temperatures: 3. act at optimal substrate concentration Most enzymes are like this Enzyme ac5vity Enzyme ac5vity How well the enzyme is working = rate of activity 37 o C 7.4 temp Excep5ons: Thermophiles 70⁰C ph Excep5ons: ph 2 in stomach pepsin ph 8 in intes5ne - trypsin Concentration of substrate 3. act at optimal substrate concentration 3. act at optimal substrate concentration How well the enzyme is working = rate of activity Concentration of substrate Initial rate 5

6 Can define how well a substrate binds to an enzyme by the Km value Km value is the substrate concentration at which the enzyme is working at 50% activity 4. Many require non-protein helpers to aid catalysis - co-factors Eg: calcium, iron. Big Km = bad binding Low Km= good binding If the co-factor is organic it is a coenzyme - Most vitamins are coenzymes Eg: vitamin C Vitamin C is used by an enzyme to cross-link collagen. Vitamin C deficiency causes scurvy a disease of dysfunctional cross-linking of collagen 5. Inhibition of enzymes by drugs or molecules in the body Irreversible-destroys the enzyme Reversible Competitive-inhibitor resembles the substrate Noncompetitive-inhibitor binds to another site on the emzyme called an allosteric site 5. Many drugs inhibit enzymes Drugs can compete with the substrate and prevent the reaction happening Eg. Statins inhibit HMG-Co Reductase, a key enzyme in cholesterol synthesis statins therefore lower cholesterol and protect against heart disease. Lovostatin competes with the substrate for the active site HMG- CoA Mevalonic acid Cholesterol ENZYME: HMG- CoA reductase HMG- CoA or lovosta5n HMG-CoA reductase 6

7 6. Are activated or inhibited by a chemical modification Phosphorylation addition of phosphate grp Acetylation addition of an acetyl group Dephosphorylation-removal of a phosphate group Deacetylation-removal of an acetyl group 6. Cellular enzymes can be activated by phosphorylation Other enzymes add the phosphate group to the other enzyme, -these enzymes are called kinases Kinases are said to phosphorylate the protein Eg: Adrenalin activates Phosphorylase kinase which phosphorylates Glycogen Phosphorylase. -This enzyme in turn breaks down glycogen to release glucose P Adrenaline (hormone protein) =Phosphate group Signal cascade Receptor protein signals GP Glycogen Phosphorylase Phosphorylase Kinase Glycogen (protein kinase enzyme) GP P glucose Adrenaline results in the release of glucose which allows for rapid produc4on of energy In summary... are catalytic proteins Lower the initial activation energy required for a reaction to happen Are specific for their substrate shape The active site is usually made up of only a few amino acid side chains Induced fit There are 6 important features 7