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Enzyme Basics
Biochemistry, Medicine, Phase 1
| Term | Definition |
|---|---|
| Enzymes | biological catalysts; speed up the rate of a reaction, without altering the final equilibrium between reactants and products; extremely efficient; reduces the amount of free energy necessary to overcome the activation energy |
| Catalase | catalyses the breakdown of its substrate H202 into water at a rate of 10^14 faster than the uncatalysed breakdown at 30C |
| Combustion | or oxidation; enzymes are responsible for the oxidation/? of foods; allows you to breakdown the steps of the reaction whilst reducing the amount of energy needed; glucose to form water and carbon dioxide but a lot of the energy is captured |
| Enzyme catalysis | enzymes contain an active site; the substrate binds to the enzyme at the active site producing an enzyme-substrate complex; catalysis results in ES complex > enzyme-product complex; the enzyme is then disregarded at the final product is revealed |
| "Stickase" | metaphor that illustrates that enzymes should be complementary to the substrates transition phase rather than the substrate itself to bring about the activation of the reaction > product |
| Substrate specificity | enzymes will usually catalyse only one type of reaction and will act only on a few related molecules ("Group..."); a few are so specific that they will act only on a certain enzyme even to the point will it will only act on one stereoisomer |
| Determines substrate specificity | the presence of a groove or cleft of defined shape called the active site into which only the substrate of the correct shape and charge can fit |
| Consequences of enzyme specificity (1) | a group of enzymes present together in one compartment of a cell can give rise to a complex and co-ordinate metabolic pathway in which the initial substrate is converted through a sequence of specific enzyme catalysed reactions to the product |
| Consequences of enzyme specificity (2) | the systematic classification scheme; enzymes divided into 6 main classes according to the type of reaction the catalyse; six classes are divided into subgroups according to their substrate or source; each enzyme IDed by individual 4 digit number |
| I.U.B. Commission on Enzymes | established the systematic classification on enzymes |
| Catalase 4 digit classification code | E.C. 1.11.1.6. |
| Six classes of enzymes | oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases |
| Oxidoreductases | add O2 or remove 2H |
| Lactase dehydrogenase | e.g. of an oxidoreductas; catalyses the transfer of hydrogen atoms and electrons |
| Transferases | transfer of function groups from donors to acceptors; a way of producing non-essential amino acids and moving around carbon skeletons and nitrogen |
| Alanine amino transferase | e.g. of a transferase |
| Hydrolases | hydrolytic reactions |
| Trypsin | e.g. of a hydrolyase; pH dependent; creates charged dipeptides at a specific point |
| Lyases | add a group to -C=C bonds; catalyse the cleavage of C-C, C-O or C-N bonds |
| ATP-citrate | e.g. of a lyase |
| Isomerases | isomerisation reactions; catalyse the transfer of functional groups within the same molecule |
| Phosphoglucose isomerase | e.g. of an isomerase; prepares the way for glycolysis by altering the sugar e.g. glucose 6-phosphate to fructose 6-phosphate |
| Ligases | form C-C or C-N-bonds with ATP cleavage to catalyse the formation of new covalent bonds; the loss of a phosphate group (going one way) |
| DNA ligase | e.g. of a ligase; DNA synthesis and repair plus in molecular biology |
| Alcohol dehydrogenase | NAD (substrate), oxidoreductase (reaction type + ase); E.C. 1.1.1.1 |
| Enzyme structure | proteins; composed of one or more polypeptide chains folded into a complex 3-dimensional shape |
| Enzyme structure stability | dependent on many weak bonds e.g. hydrogen bonds, electrostatic salt links and hydrophobic interactions; makes enzymes sensitive to changes in their environment |
| Inactive, denatured enzyme state | weak bonds that enzyme structure depends on are easily broken e.g. by heat ing the protein, giving rise to a disorganised or tangled structure in which the enzyme no longer has any catalytic activity |
| Active site of enzymes | contains functional groups that stabilise the transition state of the reaction; 3 dimensional |
| First model for enzymes | not perfect; Lock and Key hypothesis; enzyme has two substrates that it tries to bring together to interact |
| Induced Fit Model | Unfilled binding site suggests that the enzyme alters the shape of a substate to make it more suitable for a reaction; catalysis |
| Chymotripsin | involved in the catalysis of peptide bonds on the carboxyl side of tyrosine, tryptophan and phenylalanine and or large hydrophobic residues such as methionine |
| Chymotrypsin mechanism - Phase 1 | enzyme creates nucleophile from serine side-chain; nucleophile attacks substrate; covalent intermediate is formed with second product (PN) bonded to serine, and first product (PC) is released |
| Chymotrypsin mechanism - Phase 2 | enzyme creates a nucleophile from a water molecule; nucleophile attacks covalent intermediate, breaking covalent bond to serine (second product, PN, is released) |
| Nucleophile | a chemical species that donates an electron pair to an electrophile to form a chemical bond in relation to a reaction |
| Effect of temperature of enzyme reactions | between 20C, 30C and 40C for enzymes found in the body, you will usually speed up the reaction; up to 50C and beyond, denaturing of the protein will occur, similarly going to far below 20C will also reduce reaction velocity |
| Effect of pH on enzyme reactions | enzymes in the body have evolved to perform best in the pH of where they are found in the body |
| Pepsin | enzyme in the stomach; most effective around pH of 2 |
| Trypsin | enzyme in the digestive system (intestines); most effective around pH of 6 |
| Alkaline phosphate | enzyme in the bloodstream; most effective around pH of 8 |
| Inorganic elements | some act as co-factors for enzymes (non-protein chemical compound that is required for the protein's biological activity); can be bound into the enzyme or can be provided by something else |
| Mains in-organic co-factors | small; Cu2+, Fe2+/3+, K+, Mg2+, Ni2+, Se, Zn2+ |
| Cu2+ | aids cytochrome oxidase (redox systems); often form active part of centre |
| Fe2+/3+ | aids cytochrome oxidase, catalase, peroxidase (redox systems); often form active part of centre |
| K+ | aids pyruvate kinase (enzymes that aid phosphates to other enzymes) |
| Mg2+ | aids hexokinase, C-6-phosphate, pyruvate kinase (enzymes that aid phosphates to other enzymes) |
| Ni2+ | aids urease |
| Se | aids glutathione peroxidase (redox systems); often form active part of centre |
| Zn2+ | aids carbonic anhydrase, alchohol dehydrogenase |
| Co-enzymes | also known as co-substrates; part of the reaction; e.g. NAD+ (aids alcohol dehydrogenase), FAD (succinate dehydrogenase), ATP (e.g. glucokinase) |
| Isoenzymes (1) | enzymes with different protein structures which catalyse the same reaction; coded for by different genes; different isoenzymes; |
| Isoenzymes (2) | different isoenzymes found in different cellular compartments (cytoplasm or mitochondria) because they have different biochemical roles |
| Hexokinase/glycokinase, lactate dehydrogenase | examples of isoenzymes |
Created by:
emmaallde
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