Test 2 Study Guide
Test 2 Study Guide CHEM 351
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This 8 page Study Guide was uploaded by Kayli Antos on Friday October 30, 2015. The Study Guide belongs to CHEM 351 at Towson University taught by Ana Soto in Summer 2015. Since its upload, it has received 55 views. For similar materials see Biochemistry in Chemistry at Towson University.
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Date Created: 10/30/15
Biocbem Teri 2 0 Protein Function 0 Protein Binding O 69 Protein function is dependent on interactions with other molecules 69 Molecules can bind to ligands with high speci city 69 Proteins are exible and a change in conformation will affect the function 69 Binding to a ligand will often change the proteins conformation 69 In a protein with subunits a conformational change in one subunit will change th conformation of the others 02 Transport 69 Since oxygen is not easily dissolved in liquids proteins are used to carry it to tissues There are no amino acids that can be used for reversible binding to oxygen but some transition metals can be 69 Iron is often used When it s a part of a prosthetic group it s called a heme Heme The function of the nitrogens in the ring is to ensure that the iron stays at its 2 oxidation state instead of converting to its 3 oxidation state Fe3 binds only irreversibly to oxygen and will not be useful 69 When heme is free two of them can interact with one oxygen molecule causing the iron to change oxidation states To prevent this the heme is set deep into the protein so one oxygen molecule can only interact with one heme Myoglobin Myoglobin facilitates oxygen diffusion into muscle tissues white hemoglobin transports oxygen in the blood 69 Has one heme molecule Reversible Binding 69 WhenGO51K 69 A high K value means the molecule has a high binding affinity Binding Isotherms 69 K can be determined from a plot of 6 vs Myoglobins plot will be hyperbolic and represented by xy yz 69 To show the graph for oxygen partial pressure can be substituted for on the axis Hemoglobin 69 Has four subunits and four heme groups 69 Two subunits are oc chains and two are chains Hydrophobic interactions hydrogen bonds and ion pairs contribute to structure Hemoglobin Has Two Conformations 69 R state relaxed high affinity for oxygen 69 T state tense more restricted Hemoglobin Cooperativity Graph of 6 vs p02 has a sigmoid curve The first subunit to bind oxygen will bid weakly but then the other three have a higher affinity for oxygen 0 Allosteric Binding 69 69 When a ligand binds at a site different from the active site in order to effect the active site Ligands can function as activators or inhibitors When the modulator is the normal ligand it s a homotropic interaction Oxygen binds allosterically to hemoglobin 0 The Bohr Effect 69 The effect of pH and C02 on the binding and release of oxygen by hemoglobin 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 which causes the release of oxygen 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 which binds oxygen 0 Hemoglobin Also Transports Protons and Carbon Dioxide Protons may bind to certain amino acids When they do this salt bridges form which will stabilize the T state C02 can bind to the alpha amino of each chain to form a carbamate group This will also form a salt bridge 0 23Bisphosphoglycerate 23BPG Found in high concentrations in red blood cells Stabilizes the T state 0 Eanmes 0 EnZymes Structure 69 69 Most are proteins some are RNA molecules Some require a coenzyme or cofactor A coenzyme is a complex molecule A cofactor is typically an inorganic ion 0 EnZyme Classification 69 IUBMB naming system every enzyme has 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 O 69 Class 6 Ligases form bonds by condensation reactions with the use of ATP Transition State 69 The activation energy is the energy difference between the ground state and the transition state The transition state is the point Where the reaction has as much change to continue forward to products or revert back to substrates Michaelis Constant 69 When V0 2 Vim2 KM KM is the affinity of the enzyme for its substrate Vmax and Kcat 69 Km is the rate limiting substance and is equal to kg in a two step reaction It represents the number of substrate molecules converted to product for a given unit of time by a single enzyme when it s saturated To compare catalytic efficiencies Km KM This ratio should be a large number because Km should be big and KM should be small Double Reciprocal Plot 69 Lineweaver Burke plot X axis 1 S y axis 1 V0 X intercept 1 KM y intercept 1 Vmax Competitive Inhibitors Competes with substrate to bind to the active site Structurally similar to the substrate Increasing the substrate concentration decreased the amount of the enzyme inhibitor complex When 8 is very high Vmax is unaffected When V0 2 KM1 ZVmax S and KM will increase On a double reciprocal plot the slope ocKMVmax and the x intercept 1 ocKM Uncompetitive Inhibitors Bind at a site other than the active site and only to ES complex Vmax and KM are decreased Increasing S has no effect On a double reciprocal plot the y intercept oc Vmax and the x intercept is oc KM Mixed Inhibitors Bind at a site different than the active site and bind to E or E8 Non competitive inhibitors bind to both with the same affinity but this is rare Affect both the Vmax and the KM On a double reciprocal plot the slope ocKMVmax and the y intercept oc Vmax and the x intercept oc ocKM Noncompetitive inhibitors only effect the slope and y intercept Review K13 v35 Competitive T Uncompetitive i i Mixed Ti i Noncompetitive i 0 Catalytic Power of EnZymes Enzymes can work covalently or non covalently Covalent Many types of chemical reactions take place between the functional groups of the enzyme and substrate The covalent interactions occur at the active site and lower the activation energy of the reaction be providing an alternative reaction pathway Non Covalent A lot of the energy needed to lower the activation energy comes from the formation of non covalent interactions between the substrate and enzyme like hydrophobic interactions or hydrogen bonding As each weak interaction forms some energy is released which stabilizes the interaction 0 Optimum Interactions 69 Enzymes are complementary to the transition state Weak interactions are formed between the substrate and the enzyme but interactions with the T8 are optimized Even when it interacts with the enzyme the TS is not stable 0 Binding Energy 69 The energy released from non covalent interactions forming is enough to offset the energy needed to reach the T8 0 Entropy Reduction 69 69 In solution molecules have freedom of movement which decreased the chances of a successful collision Enzymes use binding energy to properly orient the substrates to they can react 0 Other Contributions to Catalysis 69 When the substrate is bound to the enzyme there are different mechanisms that help the catalytic process General Acid Base Catalysis Proton transfer to or from the substrate help stabilize charged intermediates Covalent Catalysis Transient covalent bonds can form to provide an alternative reaction pathway with lower energy Metal lon Catalysis Ionic interactions can help properly orient the substrate or help to stabilize the TS Metals are also able to mediate redox reactions 0 AcidBase Catalysis Proton transfers by weak acids or bases besides water Amino acid chains at the enzymes active site function as donors or acceptors 0 Covalent Catalysis 69 For the reaction of A B 9 A B the covalent catalysis reaction is A B X 9 A X B9AXB Many amino acids or functional groups on cofactors can act as nucleophiles 0 Effect of pH on EnZyme Activity 69 The reliance on pH is due to amino acids requiring a certain ionization state to function The graph of activity vs pH will be a bell curve if there are at least 2 amino acids 0 Chymotrypsin Breaks peptide bonds adjacent to aromatic amino acids Phe Tyr Trp Two phases gt Acylation phase peptide bond is broken and a covalent bond forms between the enzyme and the substrate gt Deacylation phase covalent bond is broken and the enzyme is regenerated The deacylation occurs slower than the acylation and therefore is the rate determining step 0 Chymotrypsin Mechanism 69 When the substrate binds to the enzyme the side chain adjacent to the peptide bond that will be cleaved binds to a hydrophobic pocket There is a hydrogen bond network called the catalytic triad which consists of Ser195 Hi557 and Aspm The Ser can be deprotonated due to its proximity to the His which accepts the proton His is able to act as a base due to its proximity to Asp When Ser is deprotonated it becomes a strong nucleophile and prevents the formation of an unstable positive charge on Ser The alkoxide ion in Ser can then attack the peptide carbonyl and form a short live tetrahedral intermediate This bonding creates a negative charge on the carbonyl oxygen which is stabilized by hydrogen bonds in the oxyanion hole The negative charge on the carbonyl is unstable which causes the tetrahedral intermediate to collapse The double bond reforms to break the peptide bond The amino leaving group is protonated by His A water molecule gets deprotonated and becomes a strongly nucleophilic hydroxide ion This hydroxide ion attacks the carbonyl group generating a second tetrahedral intermediate which is again stabilized by hydrogen bonding in the oxyanion hole This second intermediate also collapses forming the carboxylate product 69 As this second product diffuses from the active site the enzyme is regenerated 0 Hexokinase Mechanism Catalyzes the reaction of D Glucose to Glucose Phosphate Favors the reaction with glucose over water Reacts glucose and ATP to phosphorylate the glucose Has an induced t the conformation of the enzyme changes to have a higher af nity for the intermediate when glucose binds 0 Regulatory EnZymes 69 A sequence of enzymes will have a regulatory enzyme which modulates the rate of the reaction ls usually the rst enzyme in the sequence 69 Regulatory enzymes can be modulated by gt Noncovalently binding to allosteric modulators or effectors gt Reversible covalent modi cation gt Binding to other regulatory proteins gt Proteolytic cleavage ltgt Allosteric Enzymes Conformational changes connect the more and less active forms of the enzyme 69 Usually are larger and more complex than non allosteric enzymes 69 Usually have a sigmoid plot and do not follow MM kinetics 69 When the activator binds there s a transition from the T state to the R state 0 Phosphorylation Kinases phosphorylate and phosphatases dephosphorylate 69 Can greatly affect the conformation of the protein because they are negatively charged and bulky Occurs at Tyr Ser Thr and His 0 m 0 Monosaccharides 69 Straight carbon chains One aldehyde or ketone Other carbons have an OH group Many of these carbons are chiral centers 69 Marry Stereoisom ers gt The number of stereoisomers ZCMMCWBIS gt Stereoisomers that differ at only one chiral center are epimers chlic Structures gt Alcohols can be added to carbonyls or ketones to form hemiacetalsacetals or hemiketals ketals gt The resulting chiral center that forms can be at or gt These anomers can switch back and forth via mutarotation Hawortb Perspectives gt Groups on the right side of the chain point down in a ring and the left side points up gt When the anomeric hydroxyl group is on the same side of the ring as carbon 6 it s 5 conformation 0 Disaccharides O O 9 When the hydroxyl group of one sugar reacts with the anomeric carbon of another an o glycosidic bond is formed with one water molecule as a byproduct Glycosidic Band gt The non reducing end must be on the left to name the sugar gt To name it 11 The first monosaccharide its con guration and size 11 The atom numbers bound together connected by an arrow 11 The name of the second residue gt The short hand notation is the abbreviated names of the sugars and in parenthesis the anomeric carbon con guration and the carbons involved in bonding Polysaccharides Heteropolysaccharides and homopolysaccharides provide structure 69 Homopolysaccharides are also used to store monosaccharides Storage Homopolysaccharides Starch and glycogen store glucose Starch is made of amylose an unbranded chain and amylopectin which is a branched chain 69 Glycogen is heavily branched and more compact than starch Glucoses are linked by 194 linkages and branches start at 196 Branched polymers have a single reducing end and multiple nonreducing ends Structural Homopolysaccharides Cellulose consists of straight unbranched glucose chains It differs from storage polysaccharides by being made of glucoses The linkages are 6194 69 This causes it to fold differently than amylose which gives them different structures and physical properties 69 There are more hydrogen bonds this way Homopolysaccharide Folding 69 H bonding and hydrophobic electrostatic and van der Waals interactions are responsible for stabilizing the folding 69 Can rotate around the C 0 but there are sterics that limit this 69 Is most stable in a tightly coiled helix with 6 residues per turn 69 Cellulose is most stable when each chair is rotated 180 Heteropolysaccharides Bacterial walls are made up on heteropolymers of alternating N acetlyglucosamine and N acetlymuramic acid with 194 linkages 69 These chains are side by side and connected by shorter peptides Glycosaminoglycans Repeating disaccharides one is always N acetylglucosamine or N acetylgalactosamine 69 Some may contain esterif1ed sulfate groups 69 To limit repulsions and help stabilize the molecule it exists in an extended conformation 69 Not always 194 bonds The extended conformation can be very hydrated Glycoconjugates Polysaccharides and oligosaccharides can be information carriers when the have a protein or lipid component 69 Ptoteoglzcans gt found in ECM gt covalently bonded to a membrane bound or membrane secreted protein gt mostly carb with a little protein 69 Glzcogtoteins gt covalently bonded to protein gt found on outer surface of plasma membrane in ECM and in blood gt a signi cant part is protein 69 GIKCOIiQidS gt found on plasma membranes gt hydrophilic head mmade of oligosaccharides 69 Used for signaling 69 8 domain of many sulfate groups can be used to attract 2 positively charged molecules and allow them to interact
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