Enzymes PDF

Enzymes Introduction to General, Organic, and Biochemistry, 11th Edition by Bettelheim, Brown, Campbell, Farrell, Torres Organic Chemistry, 11th Edition by Solomons et.al. Olivert M. Sitoy, M.Sc., R.Ch....

Enzymes Introduction to General, Organic, and Biochemistry, 11th Edition by Bettelheim, Brown, Campbell, Farrell, Torres Organic Chemistry, 11th Edition by Solomons et.al. Olivert M. Sitoy, M.Sc., R.Ch. Chemistry Department College of Arts and Sciences Xavier University – Ateneo de Cagayan  Enzymes Enzymes: A Biological Catalyst. Except some RNAs (catalyzes their own breakdown), enzymes are proteins. Can increase the rate of the reaction by a factor of 109 to 1020. Some catalyzes the reaction of one compound.  Enzymes Enzymes: A Biological Catalyst. Others are stereospecific (e.g. enzymes that catalyzes the reaction of only L-amino acids). Others catalyze reactions of specific type of compounds or bonds (e.g. trypsin breaks peptide bonds of Lys and Arg).  Classification of Enzymes Enzymes: A Biological Catalyst. Commonly named after their reaction they catalyze. E.g. Lactate dehydrogenase and Acid Phosphatase. Six major classification of Enzymes: Oxidoreductase: Oxidation-Reduction Reactions. Transferase: Group transfer reactions. Hydrolase: Hydrolysis reactions. Lyases: Addition of group to a double bonds, or removal of groups to create a double bonds. Isomerase: Isomerization reaction. Ligases: the joining to two molecules. (Commonly coupled with ATP hydrolysis)  Classification of Enzymes Enzymes: A Biological Catalyst. Oxidoreductase: Oxidation-Reduction Reactions. Lactate dehydrogenase: Catalyzes the oxidation of Lactate to Pyruvate (Note: Oxidation is typically the removal of hydrogen or addition of oxygen in Organic Chem)  Classification of Enzymes Enzymes: A Biological Catalyst. Transferase: Group transfer reactions. Aspartate Amino Transferase or Aspartate Transaminase: Catalyzes the transfer of amino group from Aspartate  Classification of Enzymes Enzymes: A Biological Catalyst. Hydrolase: Hydrolysis reactions.. Acetylcholinesterase: Cleavage of ester bonds in Acetylcholine by addition of water.  Classification of Enzymes Enzymes: A Biological Catalyst. Lyases: Addition of group to a double bonds, or removal of groups to create a double bonds. Aconitase: Addition of Water (–OH and –H) at the double bond of Aconitate ion.  Classification of Enzymes Enzymes: A Biological Catalyst. Isomerase: Isomerization reaction. Phosphohexose Isomerase: Isomerization of Glucose-6-phosphate to Fructose-6-phosphate.  Classification of Enzymes Enzymes: A Biological Catalyst. Ligases: the joining to two molecules. (Commonly coupled with ATP hydrolysis) Tyrosine-tRNA synthetase: Attachment of L-Tyrosine with tRNA through covalent bond formation with the expense of ATP. (Note: ATP = Adenosine Triphosphate; AMP = Adenosine Monophosphate; PPi = Inorganic Pyrophosphate)  Terms in Enzyme Chemistry Enzymes: A Biological Catalyst. Apoenzyme: Protein part of the enzyme. Cofactor: Non-protein portion of an enzyme that is essential for catalytic function (e.g., metallic ions like Zn2+ and Mg2+). Coenzyme: Non-protein organic molecule, commonly a B Vitamin, that acts a cofactor. Substrate: the compound(s) whose reaction an enzyme catalyzes. Active Site: the specific portion of the enzyme to which a substrate bind during reaction. Terms in Enzyme Chemistry Enzymes  Terms in Enzyme Chemistry Enzymes: A Biological Catalyst. Activation: Any process that initiates or increase the activity of an enzyme. Inhibition: Any process that makes an active enzyme less active or inactive. Competitive Inhibitor: Any substance that binds to the active site of an enzyme thereby preventing binding of substrate. Noncompetitive Inhibitor: Any substance that binds to a portion of the enzyme other than the active site and thereby inhibits the activity of the enzyme.  Enzyme Activity Enzyme Activity: a measure of how much a reaction rate is increased. Enzyme Concentration: Amount of enzyme present in the reaction. Substrate Concentration: Amount of substrate present in the reaction. Temperature: the extent of heating or cooling of the solution. pH: increase and decrease in acidity or basicity of the matrix.  Enzyme Activity Enzyme Activity: a measure of how much a reaction rate is increased. Effect of Enzyme Concentration on the rate of enzyme-catalyzed reaction at CONSTANT pH, Temperature and Substrate Concentration.  Enzyme Activity Enzyme Activity: a measure of how much a reaction rate is increased. Effect of Substrate Concentration on the rate of enzyme-catalyzed reaction at CONSTANT pH, Temperature and Enzyme Concentration.  Enzyme Activity Enzyme Activity: a measure of how much a reaction rate is increased. Effect of Temperature on the rate of enzyme-catalyzed reaction at CONSTANT pH, Substrate Concentration and Enzyme Concentration.  Enzyme Activity Enzyme Activity: a measure of how much a reaction rate is increased. Effect of pH on the rate of enzyme- catalyzed reaction at CONSTANT Temperature, Substrate Concentration and Enzyme Concentration.  Mechanism of Enzyme Action Enzymes: A Biological Catalyst. Lock-and-Key model: The integrity of enzyme structure remains the same before, during, and after binding. Induced fit model: The structure of the enzyme modifies itself to accommodate the substrate.  Mechanism of Enzyme Action Enzymes: A Biological Catalyst. Conformational changes in Hexokinase  Mechanism of Enzyme Action Enzymes: A Biological Catalyst. Competitive Inhibition: An inhibitor competes with the substrate at the binding site causing decrease in enzyme activity.  Mechanism of Enzyme Action Enzymes: A Biological Catalyst. Competitive Inhibition: An inhibitor competes with the substrate at the binding site causing decrease in enzyme activity. Captopril (Black Sticks) acts as a competitive inhibitor of Human ACE. A fragment of Angiotensin I (Tyr-Ile-His- Pro) (Gray sticks).  Mechanism of Enzyme Action Enzymes: A Biological Catalyst. Noncompetitive Inhibition: An inhibitor binds at a site other than the binding site leading to conformational changes causing weaken or ineffective binding of the substrate at the active site. Thus, decrease in enzyme activity.  Mechanism of Enzyme Action Enzymes: A Biological Catalyst. Noncompetitive Inhibition: An inhibitor binds at a site other than the binding site leading to conformational changes causing weaken or ineffective binding of the substrate at the active site. Thus, decrease in enzyme activity. Methotrexate (black sticks) acts as noncompetitive inhibitor of Dihydrofolate reductase against NADPH (magenta sticks). NADPH is the original substrate of dihydrofolate reductase.  Mechanism of Enzyme Action Enzymes: A Biological Catalyst. Enzyme kinetics in the presence and absence of inhibitors  Mechanism of Enzyme Action Enzymes: A Biological Catalyst. Both the lock-and-key model and the induced-fit model emphasize the shape of the active site. However, the chemistry of the active site is the most important. Just five amino acids participate in the active sites in more than 65% of the enzymes studies to date. These five are His > Cys > Asp > Arg > Glu. Four of these are polar charged (acidic/basic) amino acids; the fifth has a thiol (-sulfhydryl) group.  Catalytic Power of Enzymes Enzymes: A Biological Catalyst.  Enzyme Regulation Feedback Control: an enzyme-regulation process where the product of a series of enzyme-catalyzed reactions inhibit their earlier reaction. Inhibition may either be competitive or noncompetitive.  Enzyme Regulation Proenzyme (Zymogen): inactive form of an enzyme. A polypeptide within the zymogen is hydrolyzed and removed to make an enzyme active. Example: Trypsin (Active form), Trypsinogen (Inactive form) Trypsinogen to Trypsin: hydrolysis of six amino acid fragment and removal from the N-terminal chain. Removal of the fragment changes not only the primary structure but also the tertiary structure, allowing the molecule to achieve its active form.  Enzyme Regulation Proenzyme (Zymogen): inactive form of an enzyme.  Enzyme Regulation Allosterism: Changes in other sites of enzyme causing changes in the active site. An enzyme regulated by this mechanism is called allosteric enzyme. Allosteric enzymes has multiple polypeptide chain. Negative Modulation: Inhibition of an allosteric enzyme. Positive Modulation: Stimulation of an allosteric enzyme. Regulator: a substance that binds an allosteric enzyme.  Enzyme Regulation Allosterism: Changes in other sites of enzyme causing changes in the active site.  Enzyme Regulation Allosterism: Changes in other sites of enzyme causing changes in the active site. Enzyme Regulation  Enzyme Regulation Protein Modification: Covalent bonding within the enzyme affecting its general effectivity. Example: phosphorylation/dephosphorylation PK = Pyruvate Kinase PKP = Pyruvate Kinase Phosphate  Enzyme Regulation Protein Modification: Covalent bonding within the enzyme affecting its general effectivity.  Enzyme Regulation Isoenzyme: Enzymes of multiple forms that catalyzes the same reaction. Example: Lactate dehydrogenase (LDH) catalyzes the oxidation of Different forms of LDH lactate to pyruvate. LDH is composed of M and H chains. H4 is predominant in heart muscle. M4 is predominant in liver and skeletal muscle. H3M, H2M2, and HM3 also exist. H4 is allosterically inhibited by pyruvate and is correlated with severity of heart attacks. Enzyme in Medicines  Transition State Analogs Transition State Analogs: A molecule whose shape mimics the transition state of a substrate.  Transition State Analogs Abzyme: An antibody that has catalytic activity because it was created using a transition state analog as an immunogen.