Biochem Soto 9/29, 10/1
Biochem Soto 9/29, 10/1 CHEM 351
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This 6 page Class Notes was uploaded by Kayli Antos on Friday October 2, 2015. The Class Notes belongs to CHEM 351 at Towson University taught by Ana Soto in Summer 2015. Since its upload, it has received 22 views. For similar materials see Biochemistry in Chemistry at Towson University.
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Date Created: 10/02/15
Biochem Soto Fall 2015 0 Protein Function 11 Reversible Binding gt gt VVV cu Myoglobin s function is dependent on its ability to bind oxygen and release it where and when it is needed The reversible binding process can be expressed with an association PL constant K K Pm The fraction of protein with ligand can be expressed as 6 g L up LKd When 6 05 1K L 1 K Kd When a molecule has a high binding affinity the K value is high PL PLP n inding Isotherms VV gt K can be determined from a plot of 6 vs L The plot of 6 vs L for myoglobin has a hyperbolic shape which is represented by xyyz For oxygen the partial pressure of oxygen can be substituted on the graph for concentration of free ligand 11 Oxygen Binding gt gt gt The oxygen interacts with the distal His His64 The binding of oxygen depends on the motions or breathing of the protein since the heme is located deep within the protein and only the exing of the protein enables oxygen to enter and leave Heme s specificity can be altered by ligands such as carbon monoxide It Hemoglobin gt Hemoglobin is a tetramer which means that it has four amino acid chains and subsequently four subunits Each subunit has a heme group and a structure similar to myoglobin Two of the subunits are a chains and two are B chains While hydrophobic interactions are most common hydrogen bonds and ion pairs also contribute to structure The a and B subunits have strong interactions at their interfaces 1 Hemoglobin Has Two Conformations gt gt gt gt There is the R state and the T state The R state is relaxed and has a higher affinity of oxygen The T state is tense and has a greater number of ion pairs which restrict the molecules ability to bind to an oxygen molecule We ll follow an all or nothing model of hemoglobin where all subunits are either R or T at once It Conformational Change gt When oxygen binds in the T state the conformation changes and some ion pairs are broken and others are formed When in the T state the iron of the heme group protrudes on the His group When the iron binds to the oxygen it gets smaller and can fit inside the planar ring This shifting affects the conformation of the whole protein Hemoglobin And Oxygen Binding gt gt It is necessary that hemoglobin be able to bind to oxygen in the lungs but release it in the tissues Erythrocytes red blood cells carry hemoglobin around the body Hemoglobin Cooperativity gt The graph of 6 vs pO2 for hemoglobin doesn t have the hyperbolic curve of myoglobin but rather has a sigmoid curve two to having different oxygen affinities for two different states The affinity of one subunit of hemoglobin affects the affinity of the others The first subunit will bind weakly to oxygen but the conformational changes that result increase the affinity of the other subunits making it easier to bind to oxygen Allosteric Binding gt gt gt gt An allosteric protein is one that can have a ligand bind at one site and affect the binding at another site These modulators can be activators or inhibitors When the modulator is the same as the normal ligand the interaction is homotropic Oxygen binding to hemoglobin is allosteric binding The Bohr Effect gt gt The Bohr Effect is the effect that pH and carbon dioxide have on the binding and release of oxygen by hemoglobin In tissues the pH is low and concentration of carbon dioxide is high so hemoglobin releases oxygen and binds protons and carbon dioxide In the lungs the pH is higher and the carbon dioxide is released allowing the hemoglobin to bind more oxygen The hemoglobin binds carbon dioxide because when it binds to the amino terminus of a subunit it stabilized the T state which allows the oxygen to be released In conclusion in the tissues there is a decrease in oxygen and pH and an increase in carbon dioxide and proton concentrations which leads to the T state being prominent In the lungs there are high levels of oxygen and a high pH There are also low levels of carbon dioxide and proton concentration These factors all lead to the R state being dominant Hemoglobin Also Transports Protons And Carbon Dioxide gt Oxygen binds to hemoglobin at the heme s iron 1 1 gt gt Protons will bind to select amino acids in the protein which allows them to form salt bridges which will stabilize the T state Carbon dioxide binds to the alpha amino of each chain as a carbamate group These can also form salt bridges 22 bisphosphoglycerate VVVV gt Also written as 23BPG or just BPG Is found in high concentrations in red blood cells Stabilized the T state and thus reduces hemoglobin s affinity for oxygen Adjusting the levels of 23BPG in the lungs has little effect but does have a large effect in the release of oxygen into the tissues 23BPG will bind to a positively lines cavity in the T state When the protein is in the R state the pocket narrows and 23BPG cannot bind Two Models To Describe Oxygen Binding gt gt MWC concerted model is the all or nothing model that we will use There is also the KNF sequential model that allows for many more conformations of hemoglobin o Enzymes 1 1 gt gt gt gt gt gt Even is a reaction is exergonic it still may move at a slow rate Catalysts can help increase the rate of such a reaction Without enzymatic action many of the chemical reactions necessary to sustain life will not occur fast enough Enzymes are very effective and are very specific to a substrate Enzymes work by accelerating kinetics but they do not change the thermodynamics of a reaction They accelerate a reaction reaching equilibrium but they cannot make a reaction occur that otherwise would not They help increase the yield because the rate of side reactions isn t increased too Enzymes Structure gt gt Most enzymes are proteins but there are some RNA molecules called ribozymes Enzymatic ability is dependent on the integrity of the native structure of the protein Some enzymes require a coenzyme or cofactor A cofactor is typically an inorganic ion like copper iron or potassium A coenzyme is a complex molecule like NADH A prosthetic group is a cofactor or coenzyme which is tightly bound to the enzyme Enzyme Classification VVV The names of many enzymes end in the suffix ase while other enzymes are named after their disovorer or source Sometimes an enzyme will even have more than one name or multiple enzymes will have the same name To help with this IUBMB has developed a naming system Each enzyme gets a number to describe its class subclass and catalyzed reaction Class 1 Oxidoreductases transfer electrons Class 2 Transferases are involved in group transfer reactions Class 3 Hydrolases are involved in hydrolysis reactions which is the transfer of functional groups to water Class 4 Lysases cleave single bonds by elimination or add groups to double bonds Class 5 Isomerases transfer groups within a molecule to form isomers Class 6 Ligases form bonds by condensation reactions with the use of ATP Active Sites gt gt gt gt Enzymes work by providing a location where a certain reaction can happen faster The reaction occurs in a pocket of the enzyme called its active site The molecules that the enzyme acts upon is called the substrate The amino acids that line this pocket have side chins that bind to the substrate Reaction Coordinate Diagram gt gt gt gt Catalysts only increase the reaction rate they do not affect the position or direction of equilibrium A reaction coordinate diagram shows the plot of free energy AG against the progress of the reaction The rate of the reaction is dependent on the activation energy Catalysts work by decreasing the activation energy necessary for a reaction Transition State gt gt The activation energy is necessary to reach the transition state The transition state is the point where the reaction has as much chance to proceed to products or revert to substrates The activation energy is the difference in energy states of the ground state and transition state Reaction Rates gt gt gt For the reaction of substrates S to products P with an enzyme E E S lt gt ES lt gt EP lt gt E P ES and EP are intermediates When a reaction has several steps the overall rate is determined by the step with the highest activation energy the rate limiting step The rate of a reaction is determined by the concentration of reactants and the rate constant K Chemical Kinetics 1 1 S lt gt P V APAP 0AT AT The only point in a reaction where the velocity can be measured with certainty is at the beginning The rate law of a reaction is V0 2 K S Many experiments with difference values of initial substrate can be run and the initial rate can be determined for each The slope of the plot of the AVO Vo 1s K or MS Enzyme Kinetics gt gt gt The rate of a reaction is dependent on the concentration of substrate The changing concentration throughout the reaction complicates this Instead we measure the initial rate As the concentration of substrate increases the initial rate increases as well This occurs almost linearly at first but at higher concentrations the rate begins to level off which leads to graph of V0 versus concentration of Vmax KMS 39 If an enzyme catalyzed reaction is written as E S lt gt ES 9 E P the rate determining step is shown as the step with the non reversible arrow When the enzyme is saturated represented as Vmax all enzymes exist as ES so a higher concentration of substrate will not increase the rate Vmax k2Etotal substrate to have a hyperbolic shape and is expressed as V0 2 The Michaelis Menten Equation gt V VVVVVVV At the start of the reaction there is a negligible amount of product so the reverse reaction can be ignored and the reaction can be presented as E S lt gt ES 9 E P the reversible arrow represents k1 and k1 and the second arrow represents k2 The rate limiting step is the second step because the substrate is chemically altered to become product which means that the rate law is Vo k2 ES When the enzymes are saturated the velocity is at its maximum so the rate law can be written as Vmax k2 Etotal If we assume a steady state the concentration of ES stays constant for a period of time the rate of ES formation and ES breakdown is equal and k1 ES k 1 ES k2 ES We don t know how much of the enzyme exists as an enzyme substrate complex and has a lone enzyme but we know that ET ES E So k1ET ESS k 1ES k2ES k1ETS k 1ES k1ETS k1ESS k1ES k2ES ETS ESS k1 k2k1 the blue term is Michaelis constant KM ETS ESS KM ES ETSS KM Since Vo k2ES Vok2 ETSS KM gt And finally Vo k2ETSS KM gt And since Vmax k2ET V0 V maxS KM S which is the equation for a rectangular hyperbola y ax b x n Michaelis Constant KM gt When V0 VmaX2 KM gt KM indicates the affinity of the enzyme for its corresponding substrate gt At low concentrations of S Vo VmaxS KM 31 Vmax And Kcat gt Kcat is the rate limiting substance and is equal to k2 in a twostep reaction but for more complicated reactions it can be a function of several constants gt It represents the number of substrate molecules converted to product for a given unit of time by a single enzyme when the enzyme is saturated gt The ratio of Kcat KM compares catalytic efficiencies gt When the concentration of substrate is much less than the Michaelis constant the MM equation is written as Vo KcatKMET S gt Vmax is also equal to KcatET
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