Log in to StudySoup
Get Full Access to UCONN - MCB 2000 - Study Guide - Midterm
Join StudySoup for FREE
Get Full Access to UCONN - MCB 2000 - Study Guide - Midterm

Already have an account? Login here
Reset your password

UCONN / Biology / BIOL 2000 / How do we increase the rate of a reaction?

How do we increase the rate of a reaction?

How do we increase the rate of a reaction?


School: University of Connecticut
Department: Biology
Course: Biochemistry
Term: Fall 2016
Cost: 50
Name: Biochem Exam 2
Description: These notes cover the notes for Exam 2
Uploaded: 11/10/2016
9 Pages 123 Views 0 Unlocks

How fast will reaction occur?

■ Why phosphorylate glucose?

■ Enzymes cannot make unfavorable reactions favorable, only increase velocity ■ How do we increase the rate of a reaction?

Bioenergetics  ■ Interactions and reactions lead to energy transformations ■ Critical for all living organisms Reaction Properties  ■ Will it occur at all? ■ Yes=spontaneous, products are energetically favored, depends on free energy  difference between reactants and products ■ EnzymDon't forget about the age old question of Why build telescopes on the ground when we can launch them into space?
Don't forget about the age old question of voppt
We also discuss several other topics like light from the left half of the world strikes what part of the retina?
If you want to learn more check out keenan kidwell
We also discuss several other topics like what coding scheme do mainframe computers use
Don't forget about the age old question of philosophy 1000
es cannot make unfavorable reactions favorable, only increase velocity ■ How do we increase the rate of a reaction? ■ Energy is always required to convert reactants into products (activation energy) ■ Example reaction: ATP+H2O<-->ADP+Pi+H+ ■ Favorable due to increase in entropy (two species-->3 species) ■ Removal of negative charges from ATP, decrease in interaction between neg  charges ■ Gibbs Free Energy=The amount of energy available to do work ■ Energy given off in ATP hydrolysis, for example, is able to do work ■ Coupled reactions: Pair an unfavorable reaction with a favorable one so that both can  occur ■ Favorable reaction may also use product from unfavorable reaction, driving  equilibrium for unfavorable to the right ■ First Law of Thermodynamics: Energy is neither created nor destroyed, only transferred ■ Organisms are open systems which lose and gain energy from environment ■ Change in energy=heat + work ■ Second Law of Thermodynamics: Systems favor disorder/randomness–entropy ■ Resonance forms lead to increased entropy ■ Reactions want to go to equilibrium and minimize potential energy ■ At equilibrium, forward and reverse reactions occur at the same rate ■ Organisms must shift away from equilibrium, because at equilibrium there is no  free energy to be harvested to do work ■ Favorable reactions release energy and are exergonic ■ Unfavorable reactions absorb energy and are endergonic ■ Example: ATP hydrolysis ■ Free energy of ATP>Free energy of products ■ Entropy of ATP<Entropy of products ■ Favorable reaction conditions, due to high energy bond between negatively  charged phosphate groups ■ Gibbs Free Energy=Energy available to do work■ Difference in chemical bond energy ■ Energy change necessary to reach equilibrium ■ Magnitude of Gibbs free energy tells you how much energy is available and how  far the system is from equilibrium (0 free energy) ■ A large Keq means that almost all reactants are converted to products ■ If you can measure Keq, you can calculate delta G naught ■ Knowing delta G for any reaction tells you how much energy is required or given off by  the reaction ■ Delta G naught prime used for biological systems, same as delta G naught, except  measured at pH 7 ■ Tells you ratio of products to substrate at equilibrium, and gives point of reference ■ Delta G naught prime for ATP hydrolysis is VERY negative due to negative  charge repulsion in phosphate groups ■ Reverse reaction (addition of phosphate to ADP) has same magnitude of delta G,  but opposite sign (positive and unfavorable) ■ Coupled reactions–allow unfavorable reactions to go forward ■ Example TCA Cycle: L-malate+NAD+-->OAA+NADH+H+ has G of 7kJ/mol ■ Acetyl CoA+OAA-->Citrate+CoA+H+ has G of -8kJ/mol ■ Second reaction provides energy for first to occur, also uses product of  first reaction, which drives the equilibrium of the first reaction to the  right–Le Chatelier's principle ■ As long as net of coupled reactions is negative, it will go forward ■ Example: Glucose+Pi-->Glucose-6-Phosphate (+ delta G) ■ ATP-->ADP+Pi (- delta G) ■ Reactions couple to make glucose phosphorylation favorable ■ Why phosphorylate glucose? ■ Trap glucose in cell by addition of negative charge, so it can be used for  energy How fast will reaction occur?  ■ Enzymes do not catalyze unfavorable reactions, only speed up favorable ones ■ Enzymes allow reactions to occur within seconds-->adaptive advantage ■ Function of enzymes determines effectiveness of drugs in different people ■ SNPs affect the efficiency of certain enzymes, drug effectiveness dependant on  how fast it is metabolized ■ Carbonic anhydrase increases rate of addition of water to carbon dioxide by a factor of 8  million ■ Properties of Enzymes■ Specificity ■ Catalysis ■ Regulation–cell only produces what it needs ■ Specificity–enzymes catalyze very specific reactions depending on structure and ability to  form noncovalent interactions ■ Example: Trypsin v. Thrombin→both catalyze peptide bonds, but  recognize different R groups ■ Trypsin cleaves next to Lys or Arg–positive charge binds with negative charge on  Trypsin, which stabilizes the trypsin-protein complex ■ Thrombin only cleaves next to Arg ■ Catalytic site comes together as a result of protein folding ■ The amino acids that make up the active site do not need to be next to each other  in the initial sequence ■ Mutations in catalytic site lead to decreased or eliminated catalysis ■ Enzymes are stereospecific ■ Example: enzyme that interacts with glucose can’t catalyse galactose, because  galactose is stereochemically different from glucose ■ Glucose is stabilized in enzyme by multiple H-bonds–can’t occur in galactose due  to different arrangement of -OH group ■ Induced fit change ■ Binding of substrate induces conformational change that forms active site ■ Example: binding of glucose to glucokinase ■ Lock and key fit involves less conformational change How do enzymes increase reaction rate?  ■ Reaction will reach same end point concentrations with or without enzyme ■ Reaction could take hours without enzyme to reach equilibrium, reaches  equilibrium in seconds with enzyme ■ Enzymes do not change Keq ■ Reactions plateau at equilibrium because… ■ Most/all substrate is used up ■ Enzyme is saturated with product ■ Forward reaction is occurring at same rate as reverse reaction ■ Activation energy=energy required to form transition state ■ Prevents molecule from falling apart ■ Activation energy does not factor into overall delta G ■ Enzymes lower the activation energy ■ Enzymes bind substrates, and stabilize them by noncovalent interactions■ Enzyme strains and distorts covalent bonds in substrate ■ Transition state occurs where bonds are most strained ■ In transition state, enzyme has maximum amount of noncovalent interactions with  substrate–stabilizes transition state and lowers activation energy ■ Enzyme also provides favorable microenvironment for catalysis ■ Active site is specifically designed to make noncovalent bonds with a specific  substrate’s transition state ■ 3 Phases of catalysis ■ 1) Binding of substrate E+S→ES ■ 2) conversion of substrate to product ES→EP ■ 3) Release of product EP→E+P ■ Enzymes return to original conformation and are not used up How can the reaction rate be measured?  ■ Rate of catalysis=moles of product formed/unit time ■ Determine initial velocity early in reaction–use to measure reaction rate ■ Michaelis-Menten equation–relationship between substrate concentration and velocity ■ k1=rate of formation of ES complex ■ k2=rate of dissociation of ES complex to E+S ■ k3=rate of conversion of ES complex to E+P ■ Michaelis-Menten assumptions: ■ ES complex rapidly forms and dissociates back to E+S ■ Breakdown of ES to E+P is the slowest rate ■ Michaelis Menten equation: Vi=Vmax[S]/Km+[S] ■ Km=(k2+k3)/k1 ←rate of ES dissociation v. rate of formation ■ Provides measure of ES complex strength ■ Vmax=k3[ET] ■ Maximum velocity at which the enzyme can catalyze a reaction ■ Depends on enzyme concentration ■ When [S]<Km, velocity is proportional to [S] ←addition of substrate will  increase reaction velocity linearly, first order kinetics ■ When [S]>>Km, velocity approaches Vmax, and substrate concentration does not  matter, zero order kinetics–enzyme is saturated ■ Km is a constant for a specific enzyme and a specific substrate ■ Estimate of dissociation constant of E from S ■ Enzyme will have more than 1 Km if it has more than 1 substrate ■ Concentration of substrate that gives ½ Vmax ■ Low Km=tight binding–rate of formation of ES is much faster than rate of dissociation ■ Low Km<10-9M ■ Advantages: enzyme can operate at low [S], substrate is still soluble, fewer  osmotic effects ■ High Km=weak binding ■ High Km~10-6M, need to increase [S] for activity, but has higher reaction rate ■ Example: Glucokinase v. Hexokinase ←both catalyze glucose-6- phosphate ■ Glucokinase has higher Km, used primarily in liver for storage, higher [S] ■ Hexokinase has much lower Km, used in other tissues for energy release,  lower [S] ■ Glucokinase responds to high levels of glucose after eating, when  hexokinase is already saturated ■ Liver helps regulate glucose levels ■ What if the brain has glucokinase? ■ Would not be able to process low glucose concentration between meals ■ Brain needs glucose constantly–problematic for high Km glucokinase ■ Alcohol metabolism example–Aldehyde dehydrogenase works more slowly in  people who can’t metabolize alcohol as well, causes worse symptoms ■ Kcat is turnover number for a given enzyme and substrate ■ Kcat=Vmax/[ET] ←not measure of catalytic efficiency ■ Represents how fast enzyme can catalyze at saturation ■ Units of moles product formed/sec at saturation ■ Catalytic efficiency=Kcat/Km ←Important because most enzymes are not at  saturation, takes this into account ■ Reveals preference of enzyme for substrate and stability of ES interaction ■ Depends on number and type of noncovalent interactions between enzyme and  substrate ■ Cancer drugs reduce catalytic efficiency of certain enzymes ■ Lineweaver-Burk Plot: 1/[S] vs. 1/[V0] ■ Only applies to Michaelis-Menten enzymes ■ Useful for determining inhibitor presence and mode of inhibition ■ Enzyme inhibitors–reversible vs. irreversible ■ Reversible: bind via noncovalent interactions ■ Competitive, noncompetitive, uncompetitive ■ Irreversible: bind covalently to active site, or via strong noncovalent interactions ■ Competitive inhibitors: Bind to active site reversibly, prevents access of substrate to active site ■ Increase Km (more substrate needed to reach ½ Vmax), but competitively  inhibited enzymes will still eventually reach Vmax at a very high [S] ■ Inhibitor will dissociate, substrate can bind if [S] is high ■ Holds true even if competitive inhibitor binds tighter than substrate ■ Competitive inhibitors resemble substrate ■ Examples of competitive inhibitors; ■ Methotrexate binds enzyme in place of tetrahydrofolate–enzyme  cannot form purines and pyrimidines–cancer cells can’t proliferate ■ Ritonavir–inhibits HIV protease ■ Chronic myelogenous leukemia treatment: block access of ATP to  tyrosine kinase ■ Noncompetitive inhibition–inhibitor binds to site on enzyme other than active site ■ Changes structure of active site, removes ability to form optimal  noncovalent interactions ■ Lowers Vmax, but Km remains unchanged ■ Dependant on concentration of inhibitor–if [I] is low, reaction can proceed ■ Example: Doxycycline–noncompetitive inhibitor of bacterial collagenase ■ Noncompetitive inhibitors can bind either to E alone or to ES complex ■ Uncompetitive inhibition–Similar to noncompetitive, but bind only to ES  complex, not E alone ■ Decreases Km and Vmax ■ Irreversible Inhibitors–involve covalent bond formation or strong noncovalent ■ Usually bind in active site with serine (-OH) or cysteine (-SH) ■ Decrease in enzyme activity over time ■ Some are suicide inhibitors–permanently deactivate enzyme, can only get more by  transcription ■ Example: Penicillin binds to serine in active site of transpeptidase ■ Is also transition state analog–binds more tightly to enzyme ■ Not all transition state analogs are irreversible, not all suicide inhibitors are  transition state analogs ■ Example: Aspirin–anti-inflammatory ■ Prostaglandin synthetase activity increases and causes increased  inflammation ■ Have long hydrophobic channel, need long fatty acid chain to make  prostaglandin ■ Fatty acid needs to enter channel for synthesis■ Aspirin binds to serine at entrance to channel, prevents access of fatty acid ■ NOT suicide or transition state inhibitor–can be broken down by body ■ Example: DIPF–organophosphate extensively used in pesticides ■ Binds acetylcholinesterase with serine -OH group in active site ■ Prevents serine from interacting with substrate ■ Results in too much acetylcholine in synapse–impairs muscle function and  breathing Allosteric Enzymes  ■ DO NOT FOLLOW MICHAELIS-MENTEN KINETICS!! ■ Relationship between [S] and V is sigmoidal rather than hyperbolic ■ Extremely important for regulating metabolism ■ Undergo conformational change, can bind non-substrate molecules to allosteric sites ■ Enzymes can have more than 1 allosteric site and more than 1 allosteric regulator ■ Binding of allosteric regulators influence R/T conformation ■ Have cooperativity and quaternary structure which contribute to sigmoidal kinetics ■ Example: PFK-1–uses ATP and fructose-6-phosphate as substrate to produce fructose 1,6  bisphosphate ■ Addition of fructose 2,6-bisphosphate (allosteric modifier) shifts curve to left,  makes curve more hyperbolic ■ Decreases amount of substrate needed to reach 50% max velocity ■ Example of positive allosteric modifier, allows PFK-1 to be active at lower [S] ■ Decreases K0.5, enzyme does not have to wait for substrate to build up ■ Shows that allosteric enzymes work on sliding scale of concentration depending  on regulators bound ■ Allosteric behavior is a form of enzyme regulation! ■ PFK-1 is major control point in glycolysis ■ Negative modifiers shift curve to the right, increase K0.5, makes curve more sigmoidal ■ Allosteric enzymes never fully inhibited, only slowed down, but never turned off ■ Example: ATCase ←+ modified by ATP, catalyzes chain that produces CTP,  which is a - modifier ■ Keeps balance between purine (ATP) and pyrimidine (CTP) in cell ■ Positive modifiers stabilize R state, increase enzyme activity ■ Negative modifiers stabilize T state, decrease enzyme activity ■ Negative modification of the beginning of a chain of reactions slows entire chain ■ Allosteric enzymes are sensitive to product accumulation ■ Concerted v. Sequential models for T→R transition ■ Concerted: all subunits are either T or R■ Substrate binding to 1 subunit changes conformation of all subunits ■ Disrupts T←→R equilibrium in favor of R–explains cooperativity ■ Explains sharp increase in enzyme activity ■ Sequential: Binding of substrate initiates conversion, but change happens  gradually ■ Allows for negative cooperativity–binding of substrate reduces affinity for  other substrates to bind Enzyme Regulation–Adaptation  ■ Hormones control metabolism, alter enzymatic activity ■ Enzyme will only produce as much product as the cell needs ■ Enzyme activity varies with physiological states ■ How are enzymes regulated? ■ Substrate concentration←Major mechanism ■ Enzyme concentration ■ Increase synthesis through gene activation–slow ■ Will not satisfy immediate needs of cell ■ Good for long term adaptation ■ Degradation–can happen very rapidly ■ However, if you need protein again, you need to start from scratch ■ Cyclins are most rapidly degraded proteins ■ Govern phases of cell cycle ■ Allosteric control–very rapid ■ +/- allosteric modifiers ■ Feedback inhibitors (CTP w/ATCase) ■ Reversible Covalent modification ■ Introduce phosphate to protein, affect electrostatic interactions due to -  charge ■ Change enzyme conformation and alter activity ■ Phosphate is added to hydroxyl group (Ser, Tyr, Thr) ■ Over 500 kinases catalyze these reactions, use ATP as substrate ■ Phosphatases reverse this reaction ■ Phosphorylation can either increase or decrease activity depending on  protein and pathway ■ Sequence surrounding Ser/Tyr/Thr recognized by different kinases,  allowing for specificity ■ Phosphorylation/dephosphorylation is initiated by external signal, like  hormone, cytokine, neurotransmitter, light, etc.)■ Signal is relayed to cell, eventually reaches kinase/phosphatase ■ Other covalent modification ■ Acetylation–add acetyl group to amino group of Lys or Arg–removes +  charge and decreases electrostatic interaction ■ Important in gene expression–causes histone proteins to relax hold  on DNA ■ ADP ribosylation–adds large, bulky, charged group–affects activity  significantly ■ Zymogen activators ■ Zymogen=larger precursor molecule, which is cleaved to form  active form of protein ■ Structure preserved after cleavage by disulfide bonds ■ Zymogen advantage–digestive enzymes cannot be active all the  time, otherwise they will digest stomach lining–only activated in  presence of food ■ Also seen in blood clotting proteins

Page Expired
It looks like your free minutes have expired! Lucky for you we have all the content you need, just sign up here