Bchem 393 Flashcards 2


Natasha Gidluck
Flashcards by Natasha Gidluck, updated more than 1 year ago
Natasha Gidluck
Created by Natasha Gidluck over 4 years ago

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Question Answer
Enzymes Ensure that all chemical reactions that happen in a cell happen at a rate that is relevant and necessary for the cell
Rate Enhancement Enzymes One of the main purposes of enzymes is to enhance the rate of the reaction. Example is carbonic anhydrase that converts CO2 to carbonic acid in the blood
Specificity Some enzymes are more specific than others Have low specificity, moderate specificity and high specificity
Gibbs Free Energy Energy that is able to do work At equilibrium, delta G is zero Delta G is independent from the transformation of substrate to product Tells us nothing about the rate of reaction Delta G tells us two things: 1) free energy required for the reaction 2) free energy difference between reactants and products
Spontaneous Reaction Delta G is negative
Non-spontaneous Reaction Delta G is positive
Reaction Rate (Enzymes) Enzymes alter the reaction rate, not the equilibrium Enzymes decrease the activation energy They do this by stabilizing the transition state
Active Site 1. Residues of active site come from different positions 2. Make up a small volume of the total protein 3. Form a unique microenvironment 4. Forms multiple weak interactions with substrates 5. Specificity depends on precise arrangement of active site
Cofactors Non-protein compounds that bind to proteins to help provide biological activity Coenzyme factors are derived from vitamins and are involved with catalyzing oxidation and reduction Metal cofactors are very common
Apoenzyme Enzyme without cofactor
Holoenzyme Enzyme with cofactor
Binding Energy Free energy that is released when many weak interactions form between the substrate and enzyme Maximal binding energy occurs during the transition state
Lock and Key Model The active site is complementary to the substrate
Induced Fit Model The active site is complementary to the transition state A dynamic event occurs upon binding the enzyme and substrate
Transition State Analogs Mimic the transition state but cannot be processed by the enzyme. Can be used as inhibitors
First Order Reactions Only one reactant in the reaction
Second Order Reactions Involves 2 reactants
Pseudo-First Order Reactions Appears to be first order as as although there are 2 reactants, the rate does not depend on one of them If [B] is much greater than [A], and A is present at low concentrations, then the reaction rate appears not to depend on [B]
Zero Order Reactions Does not depend on the concentration of the reactants
Velocity/Reaction Rate Does not depend on the concentration of the reactants
Km The Michaelis Constant describes the variation in enzyme activity as a function of substrate concentration It depends on the type of substrate, pH, ionic concentration and temperature The concentration of substrate at which half the active sites are filled
Vmax The number of substrate catalyzed per unit of time when an enzyme is in a fully saturated environment
Low Km Enzyme has a high affinity for its substrate
High Km Enzyme has a low affinity for its substrate
Turnover Number The number of substrate molecules that the enzyme can turn into product per unit time when fully saturated
K1 The rate of formation of the enzyme-substrate complex The rate limiting step
Kcat _____ Km A measure of catalytic efficiency
Sequential Reactions Characterized by the formation of ternary complex consisting of 2 substrates and the enzyme
Double-Displacement Reactions Characterized by the formation of a substituted enzyme intermediate A modified enzyme formed after the first product is released One or more products are released before all substrates bind
Reactions with Multiple Substrates Sequential and Double Displacement Reactions
Catalysis Strategies Covalent catalysis, General Acid Base Catalysis, Metal Ion Catalysis, Approximation and Orientation Catalysis
Covalent Catalysis The active site contains a reactive group that becomes temporarily covalently modified
General Acid Base Catalysis A molecule other than water is used as a proton donor or acceptor
Metal Ion Catalysis 1. Stabilizes a negative charge on a reaction intermediate 2. Generates a nucleophile by increasing the acidity of the nearby molecules 3. Increases the binding energy by interacting with the substrate
Approximation and Orientation Catalysis 2 substrates are brought into close proximity and correct orientation
Factors that Affect Catalysis Temperature, pH, inhibitors
Tempertaure (Enzymes) Enzyme activity increases with temperature until the point of protein denaturation
pH (Enzymes) Optimal pH for enzymes vary, enzymes have amino acids that may require different ionization states, large amount of activity between the pKa of 2 amino acids, pH depend on the environment of the enzyme
Inhibitors Can be reversible or irreversible. Small molecules that inhibit the function of the enzyme
Reversible Inhibitors Include Competitive, Uncompetitive and Non-competitive inhibitors
Competitive Inhibitors Compete with the substrate for the active site. No product formed. Inhibitor resembles the substrate. No effect on Vmax, increases Km
Uncompetitive Inhibitors Binds to the enzyme-substrate complex and prevents the enzyme from forming any product. Decreases Vmax and Km
Non-Competitive Inhibitors Inhibitor binds to the enzyme or the enzyme substrate complex. No product formed. Decreases Vmax and has no effect on Km
Irreversible Inhibitors Inhibitors that dissociate very slowly from the enzyme. They are covalently or tightly non-covalently bound. Can be group specific reagent, affinity label, transition state analog, or suicide inhibitor
Group Specific Reagent A type of irreversible inhibitor. Modify amino acid R-groups
Affinity Label A type of irreversible inhibitor. Are similar to substrate, modify active site residues
Transition State Analog A type of irreversible inhibitor. Bind to the active site very tightly using non-covalent interactions. Able to do so because they are very similar in structure to the transition state analogs
Suicide Inhibitor A type of irreversible inhibitor. Inactivates the enzyme through covalent modification
Oxidoreductase Class of Enzyme. Transfer electrons between molecules using oxidation reduction reactions
Tranferases Class of Enzyme. Transfer functional groups between molcules
Hydrolases Class of Enzyme. Cleave molecules by the addition of water
Lyases Class of Enzyme. Add atoms or functional groups to double bonds to break them, or removes functional groups to form them
Isomerases Class of Enzyme. Move functional groups within a molecule
Ligases Class of Enzyme. Join molecules together. Powered by ATP hydrolysis
Chymotrypsin A hydrolase called a protease which catalyzes the breakdown of proteins into amino acids. Allows for these smaller components to be absorbed by the small intestine
Chymotrypsin Substrate Preference Preferentially cleaves on the carboxyl side of bulky, hydrophobic amino acids due to a specificity pocket on the structure near the active site
Affinity Labels Are structurally similar to the substrate and can covalently modify active site residues. Are a class of enzyme inhibitors. Used to find residues that are important for enzyme catalysis
Group Specific Reagents Modify specific R groups of amino acids and are a type of enzyme inhibitor. Are less specific than affinity lables
Catalytic Triad of Chymotrypsin His57 (accepts a proton from Ser195) Ser195 (hydroxyl group creates a powerful nucleophile) Asp102 (hydrogen bonds to His57 and orient it so that His57 acts as a general base and accepts a proton)
Chromogenic Substrates Peptides that react within enzymes to form a colour change. Can be used to see how many steps are in an enzymes normal reaction. Also rate of these steps
Chymotrypsin Hydrolysis Steps Burst State/Pre-Steady State Steady State
Hemoglobin Is an allosteric protein that has quaternary structure and has cooperative behaviour. Is a dimer of dimers with 2 alpha and 2 beta chains
Allosteric Protein A protein that has multiple binding sites to that cooperative binding is possible
Globin Fold Present in the monomer: myoglobin. Heme groups in myoglobin give O2 an opportunity to bind to an iron atom.
Heme Groups Have 6 coordination sites, 4 of which are occupied by nitrogen. Myoglobin and hemoglobin bind oxygen in heme groups
Cooperative Behaviour In hemoglobin. Requires a quaternary structure and greatly increases the productivity/specific activity of the enzyme
Tense Form of Hemoglobin Is the deoxyhemoglobin that has a low affinity for O2
Relaxed From of Hemoglobin Is the oxyhemoglobin that has a high affinity for O2
Concerted Model Demonstrates Cooperative Behaviour. When one substrate is bound, the enzyme turns into the relaxed state in all binding sites
Sequential Model Demonstrates Cooperative Behaviour. When one substrate is bound, the enzyme turns into the relaxed state in only that specific binding site
Allosteric Regulator 2,3-BPG binds to a pocket only found on the T-state of hemoglobin and stabilizes it. So 2,3-BPG is a negative allosteric regulator and promotes the release of oxygen at the tissues
Fetal Hemoglobin Must bind to oxygen when it is released from maternal hemoglobin and has a serine instead of a histidine which makes 2,3-BPG binding more difficult
Bohr Effect H+ and Co2 regulate oxygen binding to hemoglobin because of their effect on pH
Digestion The process of breaking down large molecules into smaller units as a way to prepare for their use in metabolism. The hydrolysis of fats, polysaccharides and proteins
Metabolism The process of getting energy from molecules that have been broken down through digestion
Digestion in Mouth Homogenation into an aqueous slurry Enzymes in saliva include amylase and lipase
Amylase Breaks up starches
Lipase Cleaves the lipids Is important in babies to digest the fat in breastmilk
Digestion in Stomach Denatures proteins with the lob pH so they are better substrates for pepsin. Low pH can change the protonation of amino acids, affect H bonding and ionic interactions. The low pH is sustained with and ATP dependent proton pump
Digestion in Pancreas Releases NaHCO3 to neutralize the pH and digestive enzymes to digest proteins, lipids and carbohydrates
Digestion in Gall Bladder Releases bile salts (derived from cholesterol in the liver) required to digest lipids, which are not soluble. Triacylglycerols form an emulsion
Zymogens The inactive forms of digestive proteases that prevent preemptive cleaving of proteins (including themselves)
Digestion of Proteins Zymogens are stored in granules near the cell membrane and are packed in high concentrations. Peptidases that cleave oligopeptides are attached to the outside surface of intestinal cells
Digestion of Carbohydrates Alpha-amylase cleaves alpha-1,4 bonds. Maltase, a-glucosidase and a-dextrinase complete the hydrolysis of starch
Transport of Carbohydrates in Digestion SGLT (sodium glucose linked transport) passes glucose and galactose into the intestinal cell GLUT5 transport fructose into the intestinal cell GLUT2 passes all 3 into the bloodstream
Digestion of Lipids Lipases attach to lipid droplets and cleave off 2 fatty acid tails. These fatty acids and monoacylglycerols form micells and chylomicrons that can be absorbed across the plasma membrane
Micelles and Chylomicrons Chylomicrons package triacylglycerols with other proteins, cholesterol and fat-soluble vitamins Both micelles and chylomicrons help shield hydrophobic lipid groups for transport
Metabolic Pathways Interconnecting reactions catalyzed by an enzyme using common molecules
Metabolism A series of linked chemical reactions that transform one molecule to another as required by the organism
Metabolites Metabolic molecules
Metabolomics The mechanism of metabolism
Catabolism A metabolic process where fuel molecules are turned into CO2, H2O and useful energy A degradative pathway
Anabolism A metabolic process where simple molecules and energy form complex molecules A biosynthetic pathway
ATP Energy Currency The hydrolysis of ATP to form ADP and inorganic phosphate or pyrophosphate provides energy because of its energy rich phosphoanhydride bonds Not used for long term storage An activated carrier of phosphoryl groups
Activated Carriers Are a high energy forms that can carry electrons or 2-carbon molecules. Are kinetically stable
Regulation of Metabolism Amounts of Enzymes Catalytic Activities of Enzymes Accessibility of Substrates
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