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92 Cards in this Set
- Front
- Back
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What is a cofactor?
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An inorganic element that may be required for enzyme activity
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What is a coenzyme?
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An organic or organometallic molecule required for the action of certain enzymes
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What is a prosthetic group?
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-a group other than the protein groups
-bound to a protein and essential to it's activity -tightly/covalently bound coenzyme or metal ion |
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What is a Holoenzyme?
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An enzyme plus a group (cofactor)
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What is an apoenzyme?
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aka an apoprotein
-An enzyme (protein) alone without a cofactor group |
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What can modifying groups do?
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They can activate or inactivate an enzyme?
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List some examples of enzyme modification?
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1. Phosphorylation
2. Glycosylation 3. Alkylation |
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What are some modifying grouops?
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1. phosphoryl-
2. glycosyl- |
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Why are biomolecules stable?
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Because bio-reactions are slow
-they need to be catalyzed |
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Keq and ^G indicate what? What do they not indicate?
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-they indicate equilibrium
-nothing about rate |
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What do enzymes indicate about a reaction?
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-rate only
-nothing to do with equilibrium |
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How do enzymes affect rate?
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By lowering the activation energy
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How is the substrate's size relative to enzyme?
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the substrate is typically much smaller than the enzyme
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What is an active site?
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the region of an enzyme surface that binds a substrate molecule and catalytically transforms it, (aka catalytic site)
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What is a substrate?
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The specific compound acted upon by an enzyme
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What is the rate limiting step in a multi-step rxn?
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The slowest rxn/step
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Equation for rate (velocity)? for one substrate and for 2?
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1. V = k[S]
2. V = k[S1][S2] |
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In k=CTe^(-^G++/RT) what does a small change in ^G++ translate to?
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it is a change in the activation energy and translates to a large change in k
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How much do enzymes typically increase rxn rates by?
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10^5-10^17 fold
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^Gb = what mathematically?
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the difference between the uncatalyzed and catalyzed ^G
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How do you account for the 10^5-10^17 increase in k?
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need ^Gb around 30-100kJ/mol, which is possible since weak interactions are typically 4-30 kj/mol each
-so approx. 10-20 of them are needed for the observed change in ^Gb |
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Binding energy is also related to what?
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Specificity
-the better a substrate fits into the active site of an enzyme the MORE WEAK INTERACTIONS it can form with the enzyme -an enzyme leads to the greatest rate increases for the substrate that it matches (binds to) most closely |
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List 4 ways that Binding energy contributes to catalysis?
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1. reducing entropy
2. desolvation 3. compensating for distortion 4. induced fit-change in enzyme conformation |
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Explain how reducing entropy relates to binding energy and contributes to catalysis?
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brings molecules together
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Explain how desolvation relates to binding energy and contr.s to catalysis?
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removes bound water from substrates
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Explain how compensating for distortion is related to binding energy and contributes to catalysis?
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-it holds a substrate in a distorted conformation so that it is more likely to react
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Explain "induced fit" and how it relates to binding energy and contibutes to catalysis?
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binding energy can distort the enzyme itself making it a better catalyst
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What are the 3 most common types of catalysts? Which one do most enzymes use?
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1. acid-base
2. covalent 3 metals -most enzymes employ more than one |
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Be aware that groups that accept protons generally look like what?
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have negative charges or unpaired electrons
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What does steady st. kinetics refer to?
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assumes that within a few seconds that most of the substrate turns into an enzyme substrate complex and this is what goes on to react.
-ES rises to stdy conc. and remains at that point |
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[S]
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substrate concentration
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Vo
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initial rxn velocity
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Vmax
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maximum achievable Vo
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Km
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the [S] at which Vo = 1/2 Vmax
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the michaelis constant
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Km
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Michaelis-Menten eqn?
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Vo = (Vmax[S])/(Km+[S])
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Where does Km = [S]
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where Vo = 1/2 Vmax
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Kcat
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rate constant for rate determining step
Kcat = Vmax / [Et] OR Vmax = Kcat * [Et] |
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What does the turnover number refer to?
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Kcat
-it is the number of substrate molecules converted to a product in a given unit of time, on a single enzyme molecule, when the enzyme is saturated with substrate |
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List 4 types of reversible enzyme inhibition?
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1. Competitive
2. Uncompetitive 3. Noncompetitive: rare 4. Mixed |
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Describe competitive inhibition?
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Inhibitor and Substrate tries to bind to same site
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How can competitive inhibition be overcome?
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By adding large amounts of substrate
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On plot of comp. inh. all lines meet where.
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on x axis
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Can other types of inhibition, besides competitive, be overcome?
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NO
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Describe Uncompetitive inhibition?
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Inh. binds to a site other that the active site of enzyme-substrate complex
-inh.s structure is different from substrates -inhibitor cannot bind until substrate does |
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Describe mixed inhibition?
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Inhibitor binds to a site other than the Active Site of the Enzyme alone or of the Enzyme-substrate complex
-inhibitor can bind whether substrate binds or not -inhibitors structure is different from substrates |
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Is competitive inh. possible to overcome?
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yes
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Is uncompetitive inh. possible to overcome?
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no
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Is mixed/noncompetitive inh. possible to overcome?
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no
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In competitive inh. the inhibitor binds to what?
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the active site
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In uncompetitive inh. the inh. binds to what?
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other site
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In mixed/noncompetitive inh. the inh. binds to what?
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other site
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In competitive inh. describe the structure of the inh.
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similar to substrate
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In uncomp. inh. describe the struc. of the inh.
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different from the substrate
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in mixed. noncomp. inh. describe the structure of the inh.
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different from the substrate
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In competitive inh. the inh. binds to what?
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the enzyme alone
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In uncomp. inh. the inh. binds to what?
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the ES complex
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In mixed/noncomp. inh. the inh. binds to what?
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the enzyme alone or the ES
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In competitive inh. the apparent Km does what?
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increases
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In uncompetitive inh. the apparent Km does what?
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decreases
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In mixed/non-competitive inh. the apparent Km does what?
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changes/unchanged (increases)
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In competitive inh. the apparent Vmax does what?
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Remains unchanged
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In uncomp. inh. the apparent Vmax does what?
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decreases
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In mixed/noncomp. inh. the apparent Vmax does what?
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decreases
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Describe irreversible inhibitors?
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-bind to or destroy an essential function of an enzyme
-they kill it |
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What are suicide inactivators?
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a special class of irreversible inhibitors
-binds to enzyme as a normal substrate, but it is then converted to a reactive compound that compounds irreversibly with the enzyme, very specific, with few side effects -kills the enzyme and itself -very promising drug candidates -ex. penicillin |
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Enzymes have pH optima, explain?
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Enzymes typically want physiologic pH of about 7 BUT some, like pepsin, found in stomach acid work best at low pH...useless if moved to digestive tract
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List 4 types of regulatory enzymes?
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1. Allosteric
2. Regulated by covalent modification 3. Regulated by other regulatory enzymes 4. Activated by peptide cleavage |
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Describe allosteric regulatory enzymes?
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-can be either inhibitory or stimulatory
-can be either homotropic or heterotropic -large -changes sigmoidal curve...raises or lowers it |
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If an allosteric modulator/effector is inhibitory what does that mean?
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it decreases the activity
-negative modulation -lowers sigmoidal curve |
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If an allosteric modulator/effector is stimulatory what does it indicate?
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-increase activity
-positive modulator -will raise sigmoidal curvea |
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Feedback inh. is an example of what?
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allosteric modulation
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Key example of reversible covalent modification?
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Phosphorylation
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What is phosphorylation, describe the two different actions?
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- inv. with enzymes regulated by reversible covalent modification
1. protein kinases: adds phosphoryl groups 2. Protein phosphatases: removes phos. groups |
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What is a Zymogen?
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-Involved with enzymes modified by peptide cleavage
-irreversible -it is an inactive precursor of an enzyme |
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What is a proenzyme?
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Related to enzymes modified by peptide cleavage
-cleave zymogens |
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Give examples of zymogens to active proteins?
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1. Inactive chymotrypsinogen is cleaved to become active chymotrypsin
2. inactive trypsinogen is cleave to become active trypsin |
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What reaction does chymotrypsin catalyze?
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hydrolytic cleavage of a peptide bond
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How does the reaction with chymotrypsin work?
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acid-base and covalent catalysis
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How does hexokinase work?
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induced fit
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How does enolase work?
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metal ion
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How does lysozome work
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covalent and generalized acid base
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What reaction does hexokinase catalyze?
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interconversion of glucose and + ATP, and Glucose-6-phosphate + ADP
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What reaction does enolase catalyze?
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reversible dehydration of 2-phosphoenolpyruvate
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What reaction does lysozome catalyze?
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uses two successive nucleophilic displacement reactions
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Chymotrypsin acts on polypeptides at points adjacent to Phe, Trp, and Tyr. Based on this structure and the function of the enzyme, how do you explain this specificity?
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the hydrophobic pocket of chymotrypsin is an ideal binding site for an aromatic amino acid
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How do you figure out the # residues?
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Mr/MW
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Mr chymotrypsin?
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about 25,000
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Mr hexokinase?
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about 108,000
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Mr enolase?
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about 93,000
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Mr lysozome?
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about 14,000
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Why does water not have the same effect on hexokinase as glucose? Which one of the four factors contributing to binding energy is this an example of?
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induced fit, h20 cannot form as many bonds, glucose can and it forms a structural change (glucose is the normal substrate of hexokinase)
-this is why it does not readily add PO4 to H20 |
