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Enzyme = protein molecule that serves as a biological catalyst. allow life to go on. speed up and regulate metabolic reactions. Catalyst= a chemical that speeds up the rate of a reaction without itself being consumed in the process. Substrate = reactants in an enzyme catalyzed reaction. Each enzyme has a unique 3-D shape and recognizes and binds only the specific substrate of a reaction. Active site = small portion of enzyme molecule which actually binds the substrate.
The Nature of Enzyme Catalysis Enzyme provides a catalytic surface This surface stabilizes transition state Transformed transition state to product A B A B Catalytic surface Juang RH (2004) BCbasics
Bond Energy in Water Might Be Different Covalent bond Ionic bond Hydrogen bond Van der Waal force Bond length In vacuum Water solution 0.15 nm 90 90 0.25 nm 0.30 nm 80 4 3 1 0.35 nm 0.1 0.1 kcal/mole
Energy of Chemical Bonds in Cells Room Temperature ATP Hydrolysis Covalent bond Glucose Oxidation 0.1 1 10 100 Secondary bond kcal/mole Van der Waal force 0.1 kcal/mole Hydrophobic bond Hydrogen bond Ionic bond Covalent bond 1 kcal/mole 1 kcal/mole 3 kcal/mole 90 kcal/mole
Affinity between Two Molecules Like Dissolves Like Molecules having similar polarity will attract each other Polar Polar Nonpolar Nonpolar
Hydrogen Bond (H-Bond) The linearity is important for a perfect H-bond N H O Weaker H-bond O
Ionic Bond Is Not Stable in Water Solution Solvation - - - - - - - - - - - - - - - - - - - C - - H O O - - - - -? - - H N H But enzyme forms stable binding with its substrate in water
When the active site of an enzyme is unoccupied and its substrate is available the cycle begins An enzyme substrate complex forms with hydrogen and ionic bonds The substrate is converted to product The enzyme releases the product The enzyme is available for the next reaction Active sites
Active Site Is a Deep Buried Pocket Why energy required to reach transition state is lower in the active site? CoE (4) - (3) It is a magic pocke (1) Stabilizes transition (2) Expels water (1) (2) (3) Reactive groups (4) Coenzyme helps Juang RH (2004) BCbasics
Acts as a template for substrate orientation. Stabilizes the transition state Provides a favorable microenvironment May participate directly in reaction
Concerted Mechanism of Catalysis Active site pocket N Substrate peptide chain (270) Glu C COO - H 2 1 Carboxypeptidase A 3 4 C H O - O - His Zn Glu (196) (72) His (69) (248) Tyr N O - H C ACTIVE SITE COO - C-terminus R Check for C-terminal Site for specificity 5 Arg (145) Juang RH (2004) BCbasics
Lock and key
Binding of the first substrate (gold) induces a conformational shift (angular contours) that facilitates binding of the second substrate (blue), When catalysis is complete, the product is released, and the enzyme returns to its uninduced state.
Three factors: 1. Environmental Conditions 2. Cofactors and Coenzymes 3. Enzyme Inhibitors 15
The effects of temperature may be explained on the basis of kinetic theory - increased temperature increases the speed of molecular movement and thus the chances of molecular collisions, so within a narrow range (often 0-45 C), the rate of reaction is proportional to the temperature Temp vs rate Enzymes have denature at high temperatures, but will continue to work at lower temperature.
Each enzyme works best at a certain ph Altering the ph will denature the enzyme. This means that the structure of the enzyme is altered and the shape no longer works with its specific substrate
Inhibitors are chemicals that reduce the rate of enzymic reactions The are usually specific and they work at low concentrations They block the enzyme but they do not usually destroy it Many drugs and poisons are inhibitors of enzymes in the nervous system
There are some important differences between competitive inhibition and feedback inhibition. In competitive inhibition the inhibitor is similar in structure to the substrate and binds to the enzyme at the active site, preventing the substrate from binding. In feedback inhibition, the inhibitor binds to the enzyme at a site away from the active site and acts by altering the shape of the enzyme in such a way that it is incapable of catalyzing the reaction. Feedback inhibition is a natural part of the process by which an organism regulates the chemical reactions that take place in its cells. In that sense it is done on purpose. Competitive inhibition usually involves inhibitors, commonly called poisons, that do not belong in the cell.
Competitive: These compete with the substrate molecules for the active site The inhibitor s action is proportional to its concentration Resembles the substrate s structure closely E I Reversible reaction EI Enzyme inhibitor complex
2. Non-competitive:These are not influenced by the concentration of the substrate. It inhibits by binding irreversibly to the enzyme but not at the active site Examples Cyanide combines with the Iron in the enzymes cytochrome oxidase Heavy metals, Agor Hg, combine with SHgroups. These can be removed by using a chelating agent such as EDTA
Negative feedback: end point or end product inhibition Poisons snake bite, plant alkaloids and nerve gases Medicineantibiotics, sulphonamides, sedatives and stimulants ODWS
Cell processes (e.g. respiration or photosynthesis) consist of series of pathways controlled by enzymes e A e B e C e D e F A B C D E F Each step is controlled by a different enzyme (e A, e B, e C etc) This is possible because of enzyme specificity ODWS
Allosteric means other site Active site E Allosteric site ODWS
These enzymes have two receptor sites One site fits the substrate like other enzymes The other site fits an inhibitor molecule Substrate cannot fit into the active site Inhibitor molecule Inhibitor fits into allosteric site ODWS
Active site Substrate fits into the active site E The inhibitor molecule is absent Allosteric site empty Conformational change Substrate cannot fit into the active site E Inhibitor fits into allosteric site Inhibito r molecule is present
When the inhibitor is present it fits into its site and there is a conformational change in the enzyme molecule The enzyme s molecular shape changes The active siteof the substrate changes The substrate cannot bind with the substrate
The reaction slows down This is not competitive inhibition but it is reversible When the inhibitor concentration diminishes the enzyme s conformation changes back to its active form
Regulation of Enzyme Activity Inhibitor S o I or I I inhibitor x I Proteolysis x proteolysiso S Feedback regulation S o R x R regulator effector Signal transduction x (-) Regulatory subunit A or S Phosophorylation o x P A S o () phosphorylation P camp or calmodulin