Module 3 - Enzymes and Kinetics PDF

Section 1-properties of enzymes Enzymes: catalyst for chemical reactions - Are typically globular proteins with multiple domains and complex structure, act as **catalysts** for chemical reactions. Increase rates by 103-108 times - They catalyze reactions by binding to a substrate (rea...

Section 1-properties of enzymes Enzymes: catalyst for chemical reactions - Are typically globular proteins with multiple domains and complex structure, act as **catalysts** for chemical reactions. Increase rates by 103-108 times - They catalyze reactions by binding to a substrate (reactant) and lower the energy (activation energy) of the chemical reaction. - The activation energy is lowered through enzyme stabilization known as (**transition state;** chemical species that has the highest free energy and the lowest concentration of those on the pathway from a substrate to a product), high energy molecules that usually has a structure in between the substrate and product. - Most enzymes are from proteins, but there are others made from RNA (RNA enzymes are ribozymes) Essential Enzyme Properties - Active site (where substrate binds) makes them ideal for biochemical pathways - Have specificity, they can only catalyze one type of reaction on a specific substrate - Six classes of enzymes - **Oxidoreductase**: enzyme that transfer electrons between molecules. Catalyze oxidation and reduction reactions - **Lyase**: adds atoms or functional groups to a double bond/removes them to form double bonds - **Transferase**: transfer functional groups *between* molecules. Ie; Aminotransferases are prominent in amino acid synthesis and degradation/shuffle amine groups between donor and acceptor molecules. - **Isomerase**: move functional groups *within* molecules - **Hydrolase**: cleave molecules by the (+) of H2O. ie; trypsin (a proteolytic enzyme that breaks peptide bonds) - **Ligase**: join 2 molecules in reaction powered by ATP hydrolysis. Ie; DNA ligase Enzyme complexes - Some enzynes require additional components for activity. When these enzymes exist alone, they are inactive called **apoenzymes.** - When binding to appropriate **cofactor**, the enzyme becomes active. - **Holoenzyme** refers to complex containing initial apoenzyme and bound cofactor - **Cofactors** is a non-protein molecule, performing chemical reactions that amino acids can't, thus aiding the catalytic activity of the enzymes - Include metal ions: (inorganic metal ions Zn 2+ and Fe2+) and coenzymes (non-protein organic molecules that can loosely or tightly bind to enzymes/ ATP, NADH, NADPH, coenzyme A) when tightly bound they are referred to as prosthetic groups The Chemistry of An Active site - Active site is where chemical reaction occurs. Complementary to substrate or the transition state - Made of a binding site for the substrate and a catalytic site, where chemical reaction occurs - Binding sites bind and orient the substrate, and catalytic sites reduce the chemical activation energy making reaction more favourable - Structure of enzymes is crucial in supporting/positioning the active site. Critical in supporting the transition state/lowering activation energy of reaction - Inhibitors mimic enzyme shape or charge of the transition state chemistry. - **Enzymes are specific for the substrates and can only catalyze one type of reaction. Determined by the shape and chemistry of the active site.** Interaction in the Active Site - Amino acids that make up active site can have R groups participate in general acid-base chemistry/or form temporary covalent bonds creating enzyme-substrate complex. - Multiple different interaction can take place in a single active site. It can go through a series of **intermediate conformational changes** that are necessary to facilitate the chemical reaction producing product. Enzyme Models of the Active Site - **Lock and Key Model**: how substrate and enzyme active site fit tightly together like a key fitting into a lock. Upon interaction, the enzyme-substrate complex forms, and reaction occurs. The resulting product has a different shape and is released from the active site of the enzyme. This hypothesis explains the specificity of the binding of substrate but not the flexibility of enzymes. It does not account for transition state stabilization or catalyzation of reaction. - **This theory works well to explain antibodies bind to their specific antigen but does not work well for enzymes as they go through a conformational change to catalyze chemical reactions** - **Induced Fit Model:** states that enzymes are flexible, so active site is continually reshaped by interaction with substrate and enzyme. Active site can modify the overall shape of the enzymes, and sometimes substrate. - This then stabilizes the substrate into the transition state, allowing reaction to move forward. Enzyme Reactions and Reversibility - Many enzymes can work in both directions. They can readily catalyse both forward and reverse reaction. In mammalian cells, this means that the enzymes will try to reach equilibrium/have significant amounts of both the reactant and product, (although normally one is favoured) - Other reactions require 2+ separate enzymes, one for forward and reverse reaction Isozymes - Isozymes can catalyze more than one enzyme for particular reaction. They are encoded by different genes but catalyze the same chemical reaction - May be expressed in different parts of the cell in different organs of the body. - Have different modes of regulation, reaction rates, or substrate specificity. These redundancies are not accidental, but often are key to how the cell and body regulate metabolism. - Expressed a different levels at different location Enzymes in Clinical Diagnosis - Many proteins/enzymes are elevated and lowered in response to disease. This is measured in the blood to help determine/diagnose many diseases often determines from the blood plasma or serum sample. Section 2- Chemical reactions and enzymes as catalysts Gibbs free energy - Direction and extent of reaction occurs depends upon three factors; enthalpy, entropy and temperature