Flashcards
Bchem 393 Flashcards 2
Cards in this deck (96)
- 1EnzymesEnsure that all chemical reactions that happen in a cell happen at a rate that is relevant and necessary for the cell
- 2Rate Enhancement EnzymesOne 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
- 3SpecificitySome enzymes are more specific than others
Have low specificity, moderate specificity and high specificity - 4Gibbs Free EnergyEnergy 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 - 5Spontaneous ReactionDelta G is negative
- 6Non-spontaneous ReactionDelta G is positive
- 7Reaction Rate (Enzymes)Enzymes alter the reaction rate, not the equilibrium
Enzymes decrease the activation energy
They do this by stabilizing the transition state - 8Active Site1. 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 - 9CofactorsNon-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 - 10ApoenzymeEnzyme without cofactor
- 11HoloenzymeEnzyme with cofactor
- 12Binding EnergyFree energy that is released when many weak interactions form between the substrate and enzyme
Maximal binding energy occurs during the transition state - 13Lock and Key ModelThe active site is complementary to the substrate
- 14Induced Fit ModelThe active site is complementary to the transition state
A dynamic event occurs upon binding the enzyme and substrate - 15Transition State AnalogsMimic the transition state but cannot be processed by the enzyme. Can be used as inhibitors
- 16First Order ReactionsOnly one reactant in the reaction
- 17Second Order ReactionsInvolves 2 reactants
- 18Pseudo-First Order ReactionsAppears 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] - 19Zero Order ReactionsDoes not depend on the concentration of the reactants
- 20Velocity/Reaction RateDoes not depend on the concentration of the reactants
- 21KmThe 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 - 22VmaxThe number of substrate catalyzed per unit of time when an enzyme is in a fully saturated environment
- 23Low KmEnzyme has a high affinity for its substrate
- 24High KmEnzyme has a low affinity for its substrate
- 25Turnover NumberThe number of substrate molecules that the enzyme can turn into product per unit time when fully saturated
- 26K1The rate of formation of the enzyme-substrate complex
The rate limiting step - 27Kcat _____ KmA measure of catalytic efficiency
- 28Sequential ReactionsCharacterized by the formation of ternary complex consisting of 2 substrates and the enzyme
- 29Double-Displacement ReactionsCharacterized 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 - 30Reactions with Multiple SubstratesSequential and Double Displacement Reactions
- 31Catalysis StrategiesCovalent catalysis, General Acid Base Catalysis, Metal Ion Catalysis, Approximation and Orientation Catalysis
- 32Covalent CatalysisThe active site contains a reactive group that becomes temporarily covalently modified
- 33General Acid Base CatalysisA molecule other than water is used as a proton donor or acceptor
- 34Metal Ion Catalysis1. 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 - 35Approximation and Orientation Catalysis2 substrates are brought into close proximity and correct orientation
- 36Factors that Affect CatalysisTemperature, pH, inhibitors
- 37Tempertaure (Enzymes)Enzyme activity increases with temperature until the point of protein denaturation
- 38pH (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
- 39InhibitorsCan be reversible or irreversible. Small molecules that inhibit the function of the enzyme
- 40Reversible InhibitorsInclude Competitive, Uncompetitive and Non-competitive inhibitors
- 41Competitive InhibitorsCompete with the substrate for the active site. No product formed. Inhibitor resembles the substrate. No effect on Vmax, increases Km
- 42Uncompetitive InhibitorsBinds to the enzyme-substrate complex and prevents the enzyme from forming any product. Decreases Vmax and Km
- 43Non-Competitive InhibitorsInhibitor binds to the enzyme or the enzyme substrate complex. No product formed. Decreases Vmax and has no effect on Km
- 44Irreversible InhibitorsInhibitors 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
- 45Group Specific ReagentA type of irreversible inhibitor. Modify amino acid R-groups
- 46Affinity LabelA type of irreversible inhibitor. Are similar to substrate, modify active site residues
- 47Transition State AnalogA 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
- 48Suicide InhibitorA type of irreversible inhibitor. Inactivates the enzyme through covalent modification
- 49OxidoreductaseClass of Enzyme. Transfer electrons between molecules using oxidation reduction reactions
- 50TranferasesClass of Enzyme. Transfer functional groups between molcules
- 51HydrolasesClass of Enzyme. Cleave molecules by the addition of water
- 52LyasesClass of Enzyme. Add atoms or functional groups to double bonds to break them, or removes functional groups to form them
- 53IsomerasesClass of Enzyme. Move functional groups within a molecule
- 54LigasesClass of Enzyme. Join molecules together. Powered by ATP hydrolysis
- 55ChymotrypsinA 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
- 56Chymotrypsin Substrate PreferencePreferentially cleaves on the carboxyl side of bulky, hydrophobic amino acids due to a specificity pocket on the structure near the active site
- 57Affinity LabelsAre 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
- 58Group Specific ReagentsModify specific R groups of amino acids and are a type of enzyme inhibitor. Are less specific than affinity lables
- 59Catalytic Triad of ChymotrypsinHis57 (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) - 60Chromogenic SubstratesPeptides 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
- 61Chymotrypsin Hydrolysis StepsBurst State/Pre-Steady State
Steady State - 62HemoglobinIs an allosteric protein that has quaternary structure and has cooperative behaviour. Is a dimer of dimers with 2 alpha and 2 beta chains
- 63Allosteric ProteinA protein that has multiple binding sites to that cooperative binding is possible
- 64Globin FoldPresent in the monomer: myoglobin. Heme groups in myoglobin give O2 an opportunity to bind to an iron atom.
- 65Heme GroupsHave 6 coordination sites, 4 of which are occupied by nitrogen. Myoglobin and hemoglobin bind oxygen in heme groups
- 66Cooperative BehaviourIn hemoglobin. Requires a quaternary structure and greatly increases the productivity/specific activity of the enzyme
- 67Tense Form of HemoglobinIs the deoxyhemoglobin that has a low affinity for O2
- 68Relaxed From of HemoglobinIs the oxyhemoglobin that has a high affinity for O2
- 69Concerted ModelDemonstrates Cooperative Behaviour. When one substrate is bound, the enzyme turns into the relaxed state in all binding sites
- 70Sequential ModelDemonstrates Cooperative Behaviour. When one substrate is bound, the enzyme turns into the relaxed state in only that specific binding site
- 71Allosteric Regulator2,3-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
- 72Fetal HemoglobinMust 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
- 73Bohr EffectH+ and Co2 regulate oxygen binding to hemoglobin because of their effect on pH
- 74DigestionThe 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
- 75MetabolismThe process of getting energy from molecules that have been broken down through digestion
- 76Digestion in MouthHomogenation into an aqueous slurry
Enzymes in saliva include amylase and lipase - 77AmylaseBreaks up starches
- 78LipaseCleaves the lipids
Is important in babies to digest the fat in breastmilk - 79Digestion in StomachDenatures 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
- 80Digestion in PancreasReleases NaHCO3 to neutralize the pH and digestive enzymes to digest proteins, lipids and carbohydrates
- 81Digestion in Gall BladderReleases bile salts (derived from cholesterol in the liver) required to digest lipids, which are not soluble. Triacylglycerols form an emulsion
- 82ZymogensThe inactive forms of digestive proteases that prevent preemptive cleaving of proteins (including themselves)
- 83Digestion of ProteinsZymogens 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
- 84Digestion of CarbohydratesAlpha-amylase cleaves alpha-1,4 bonds. Maltase, a-glucosidase and a-dextrinase complete the hydrolysis of starch
- 85Transport of Carbohydrates in DigestionSGLT (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 - 86Digestion of LipidsLipases 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
- 87Micelles and ChylomicronsChylomicrons package triacylglycerols with other proteins, cholesterol and fat-soluble vitamins
Both micelles and chylomicrons help shield hydrophobic lipid groups for transport - 88Metabolic PathwaysInterconnecting reactions catalyzed by an enzyme using common molecules
- 89MetabolismA series of linked chemical reactions that transform one molecule to another as required by the organism
- 90MetabolitesMetabolic molecules
- 91MetabolomicsThe mechanism of metabolism
- 92CatabolismA metabolic process where fuel molecules are turned into CO2, H2O and useful energy
A degradative pathway - 93AnabolismA metabolic process where simple molecules and energy form complex molecules
A biosynthetic pathway - 94ATP Energy CurrencyThe 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 - 95Activated CarriersAre a high energy forms that can carry electrons or 2-carbon molecules. Are kinetically stable
- 96Regulation of MetabolismAmounts of Enzymes
Catalytic Activities of Enzymes
Accessibility of Substrates