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II. Enzymes • Proteins • Organic catalysts that speed up the rate of a reaction, but are not used up • Lower energy of activation • Are specific in action, i.e., act on a specific substrate
II. Enzymes, cont. • 1. Substrate (S) combines at active (catalytic) site of enzyme (E). • 2. Enzyme-substrate complex [ES] is formed. • 3. The substrate is transformed into a product (P). • 4. The products are released from enzyme. • 5. The enzyme is recovered.
E + S [ES] EP [ES] E + P EP S = Substrate P = Product E = Enzyme
II. Enzymes, cont. • Naming of enzymes according to reaction: • oxidoreductase Involved in oxidation and reduction reactions. • transferase Transfers functional groups. • hydrolase Hydrolysis. • lyase Removes atoms without hydrolysis. • isomerase Rearranges atoms in a molecule. • ligase Joins two molecules.
II. Enzymes, cont. • Location of enzymes: • intracellular Endoenzymes. Act inside the cell. • extracellular Exoenzymes. Act outside the cell. • Enzyme components: • apoprotein Protein portion. • cofactor Nonprotein portion. May be a metal ion or an organic molecule which is called a coenzyme. • holoprotein Apoprotein + cofactor.
II. Enzymes, cont. • Coenzymes • Bind to an enzyme transiently • Are “carrier” molecules. They carry atoms (or electrons) to the substrate or take atoms (or electrons) from the substrate. • Examples • NAD+ is an electron carrier. • NADP is an electron carrier. • ATP is a phosphate and energy carrier.
II. Enzymes - Factors affecting activity • 1.Temperature • Enzyme activity increases with increasing temperature. • Activity drops when heat denatures enzyme.
II. Enzymes - Factors affecting activity • 2. pH • Enzymes have an optimum pH. • Hydrogen ions alter protein structure.
II. Enzymes - Factors affecting activity • 3. Substrate Conc. • Rate of reaction increases until all active sites are filled. • At saturation, maximum rate is reached.
II. Enzymes - Factors affecting activity 4. Inhibitors • competitive - react at the substrate site. • noncompetitive -do not react at the substrate site. • e.g., allosteric inhibitors
II. Enzymes, cont. • Control of enzyme activity • genetic regulation The control of enzyme synthesis. • metabolic regulation The control of enzyme activity following enzyme synthesis. • Allosteric activators increase enzyme activity. • Allosteric inhibitors decrease enzyme activity, e.g., in feedback inhibition, the end product of a pathway turns off the first enzyme of the pathway.
III. Energy production • Carbohydrates, proteins, lipids are energy rich. • Each is a reduced molecule, i.e., has many hydrogen atoms (an electron, e- , & a proton, H+) • Upon being oxidized, the molecule loses electrons. • The energy associated with the electrons is ultimately conserved in ATP. • Are catabolic reactions
LARGE MOLECULES ANABOLISM CATABOLISM energy energy SMALL MOLECULES
Enzymes • Biological catalysts produced by cells • Nearly all are proteins • Enormous catalytic power • Reactions occur at lower temperatures and at higher rates • Ordinarily highly specific
Induced-Fit Model of Enzymes • Explains how enzyme works • Substrate: reacting substance • Active site: where chemical reaction takes place and where substrate fits
Cofactors • Something other than polypeptide chain required by enzyme • May be metal • Iron in hemoglobin • May be organic cofactor • Coenzyme • Apoenzyme: does not have cofactor
Inhibition of Enzymes • Lets cell control when an enzyme works • Inhibitor binds to allosteric site • Prevents substrate from binding
Enzyme Classification I Systematic Names and Recommended Names are based on the reaction type and the molecular structure of the substrates (But: they do not represent the holo-enzyme)
Enzyme Classification II • Oxidoreductases - catalyzing oxidation reduction reactions. • Transferases - catalyzing transfer of functional groups. • Hydrolases - catalyzing hydrolysis reactions. • Lyases - catalyzing group elimination reactions to form double bonds. • Isomerases - catalyzing isomerizations (bond rearrangements). • Ligases - catalyzing bond formation reactions couples with ATP hydrolysis.
1-Oxidoreductases 1.1 Acting on the CH-OH group of donors 1.1.1. With NAD or NADP as acceptor 1.1.2. With a cytochrome as acceptor 1.1.3.With oxygen as acceptor 1.1.4.With a disulfide as acceptor 1.1.5.With a quinone or similar compound as acceptor 1.1.99. With other acceptors 1.2 Acting on the aldehyde or oxo group of donors 1.3 Acting on the CH-CH group of donors 1.4 Acting on the CH-NH2group of donors …
2. Transferases 2.1 Transferring one-carbon groups 2.1.1. Methyltransferases 2.1.2. Hydroxymethyl-, Formyl- and Related Transferases 2.1.3. Carboxyl- and Carbamoyltransferases 2.1.4. Amidinotransferases 2.2 Transferring aldehyde or ketonic groups 2.3 Acyltransferases 2.4 Glycosyltransferase ...
3. Hydrolases 3.1 Acting on ester bonds 3.1.1 Carboxylic Ester Hydrolases 3.1.2 Thiolester Hydrolases 3.1.3 Phosphoric Monoester Hydrolases 3.1.4 Phosphoric Diester Hydrolases 3.1.5 Triphosphoric Monoester Hydrolases ... 3.2 Glycosylases 3.3 Acting on ether bonds 3.4 Acting on peptide bonds (peptidases)
4. Lyasen 4.1 Carbon-carbon lyases 4.1.1 Carboxy-lyases 4.1.2 Aldehyde-lyases 4.1.3 Oxo-acid-lyases 4.1.99 Other Carbon-carbon lyases 4.2 Carbon-oxygen lyases 4.3 Carbon-nitrogen lyases 4.4 Carbon-sulfur lyases 4.5 Carbon-halide lyases
5. Isomerases 5.1 Racemases and epimerases 5.1.1. Acting on Amino Acids and Derivatives 5.1.2. Acting on Hydroxy Acids and Derivatives 5.1.3. Acting on Carbohydrates and Derivatives 5.1.99. Acting on Other Compounds 5.2 cis-trans-Isomerases 5.3 Intramolecular isomerases 5.4 Intramolecular transferases (mutases) 5.5 Intramolecular lyases 5.99 Other isomerases
6. Ligases 6.1 Forming carbon—oxygen bonds 6.1.1. Ligases Forming Aminoacyl-tRNA and Related Compounds 6.2 Forming carbon—sulfur bonds 6.2.1. Ligases Forming Aminoacyl-tRNA and Related Compounds 6.3 Forming carbon—nitrogen bonds 6.4 Forming carbon—carbon bonds 6.5 Forming phosphoric ester bonds