Enzymes are good catalysts Why??? Enzymes have reaction specificity for a particular substrate (Many enzymes also have stereo specificity) 2. Reactions with enzymes are typically 103 to 1020 times faster than without enzymes. 3. Enzymes are biologically relevant because they function in mild conditions (aqueous solution, pH~7, etc.) 4. Enzymes are good at coupling different reactions.

Hydrolyzes peptide bonds on carboxyl side of aromatic and aliphatic residues

What do we want to know about enzymes?? What reaction do they catalyze? How does the enzyme work. (mechanism) Is the enzyme regulated or controlled? What happens if the enzyme stops functioning? As in chapter 4, what are the structural features of the enzyme. (e.g., complex or simple, 1o, 2o, 3o, 4o etc.) 6. Does the enzyme require a cofactor for activity? Apoenzyme + Cofactor Holoenzyme (Protein only) Inactive (Active) Note: not all enzymes are proteins, some are RNA based

Cofactors and the vitamin in supplements B12__> cobalamin-a porphryin--Cobalamin (Vitamin B12) is a water-soluble, cobalt-containing vitamin with an important role in biochemical processes referred to as single carbon transfers.

The six major classes of enzymes Oxidoreductases Transferases Hydrolyases Lyases Isomerases Ligases Distribution of all known enzymes by EC classification number. 1: oxidoreductases, 2: transferases, 3: hydrolases, 4: lyases, 5: isomerases, 6: ligases. Distribution of known enzymes

1. Oxidoreductases catalyze oxidation-reduction reactions reduced Electron are stored oxidized C is more reduced (1 H and 1 O bonded) C is more oxidized (2 bonds to oxygen) Recall: Carbon is more reduced when more H’s are bonded, while carbon is more oxidized with more O’s bonded. Compare CH4 vs CO2 When something is oxidized, something else must be reduced Electrons MUST be transferred. (NAD+ is reduce to NADH) NAD+ - nicotinamide adenine dinucleotide

Transferases catalyze group transfer reactions -These enzymes usually require a coenzyme be present. -coenzyme: complex organic molecule (often a vitamn) needed for catalysis ammonium group transfer

3. Hydrolyases catalyze hydrolysis. -A special class of transferase- water is the key acceptor of the group transferred. Water is added to break a one of the -P-O-P- bonds. Phosphoanhydride bond

4. Lyases catalyze lysis of a substrate. A double bond is generated. -The reverse reaction is called an addition reaction the enzymes are synthases. CO2 was removed (a double bond was formed)

5. Isomerase catalyze structural changes within a single molecule -Simply an isomerization reaction Ammonium group switched places The D-alanine produced by alanine racemase is used for peptidoglycan biosynthesis. Peptidoglycan is found in the cell walls of all bacteria, including many which are harmful to humans. The enzyme is absent in eukaryotes but found everywhere in prokaryotes, making alanine racemase a great target for antimicrobial drug development

6. Ligases catalyze ligation or joining of two substrates -These reactions are usually coupled with a second reaction. (chemical potential energy, or stored energy, from the second reaction is used to drive the first reaction.) Stored chemical energy Two substrates were ligated The second reaction: ATP ADP + Pi

DGo’-The Standard Free Energy at pH = 7 A measure of where equilibrium lies for a reaction If DGo’ < 0, [products] > [reactants] If DGo’ > 0, [reactants] >[products] If DGo’ = 0, [products] = [reactants] Many biochemical reactions are near equilibrium. Some biochemical reactions are irreversible or “spontaneous” and is largely dependent on conc. - THE ENZYME DOES NOT ALTER FREE ENERGY

The energy of activation DG╪ IS a measure of Enzymatic “Speed” The energy of activation Enzymes help to lower the barrier as the reaction progresses

Active sites may include distant amino acid residues The transition state is energetically more favorable once the enzyme-substrate complex is formed. Figure 6.4 Active site is small Active sites are unique environments Substrate binds via non- covalent interactions

Figure 6.6- Induced-fit model of enzyme-substrate binding The enzymes structure changes as the substrate binds Specificity of binding depends on arrangement and type of atoms in active site Glucose binding to the enzyme hexokinase The Induced Fit

Assignment Read Chapter 6 Read Chapter 7 Topics not covered: Details of ΔG equations on pages 97 and 98