How Enzymes Work Pratt & Cornely Ch 6.
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Transcript of How Enzymes Work Pratt & Cornely Ch 6.
![Page 1: How Enzymes Work Pratt & Cornely Ch 6.](https://reader035.fdocuments.us/reader035/viewer/2022081503/5a4d1b657f8b9ab0599b00ee/html5/thumbnails/1.jpg)
How Enzymes Work
Pratt & Cornely Ch 6
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Enzymes
• Biocatalyst—active site• Proteins• Substrate• Reaction specificity• Stereospecificity• Coupled reactions• Regulation
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Rate Enhancement
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Orotidine Decarboxylase
• Key enzyme in production of nucleotides for DNA
• T1/2 = 14 ms• But what makes
it a great enzyme?
NH
O
ON
O
OHOH
HH
HH
OP-O
O-
OO2C
CO2
NH
O
ON
O
OHOH
HH
HH
OP-O
O-
O
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The Speed of the Uncatalyzed Rxn
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Mechanism and RDS
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EC Nomenclature
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Enzyme Classes
1. Oxidoreductase
• Recognize Redox reactions• Redox cofactors: NAD+/NADH, FAD/FADH2, Q/QH2 • Dehydrogenases, oxidases, peroxidases, reductase
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Enzyme Classes
2. Transferase
• 2 substrates• Coenzymes—PLP• Transferase, kinase
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Enzyme Classes
3. Hydrolase
• Water nucleophile• Phosphatase, nuclease, protease, peptidase
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Enzyme Classes
4. Lyase
• Hardest to recognize—not redox, hydrolysis• Elimination of a group to give double bond• Reversible• Hydratase, decarboxylase, (formerly synthases)
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Enzyme Classes
5. Isomerase
• Rearragement without loss/add• Racemase, isomerase, mutase (phosphate)
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Enzyme Classes
6. Ligase
• Joining together with ATP input• Irreversible• Synthetase
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Problem 10
• To which class do the enzymes that catalyze the following reactions belong?
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Problems 11-12
• Draw the structures of the products
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Problem 14
• Propose a name for each enzyme.
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Catalysis
• Thermodynamics• Kinetics• Rxn coordinate• Transition state• 5.7 kJ ~ 10x
change
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Mechanisms
• Two major mechanisms—any or all may be used in a given enzyme– Chemical Mechanisms• Acid-base catalysis• Covalent catalysis• Metal ion catalysis
– Binding Mechanisms• Proximity/orientation effect• Transition State Stabilization• Electrostatic catalysis
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1. Acid/Base Catalysis
• Sidechains affect most proton transfers
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General Acid-Base Catalysis• H+ and HO- are “specific acid/base” and
depend on pH• Amino acid sidechains are general acid-base,
and can conduct reactions inside active site pocket that aren‘t possible in solution
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What’s Wrong with This?
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Triose Phosphate Isomerase
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Mechanism
Be able to explain catalytic function of AA in each step of a mechanism
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2. Covalent Catalysis
• Can act as active site nucleophile• Can produce a more reactive electrophile• Example:
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Covalent Intermediate
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3. Metal Ion Catalysis
• Redox reactions• Stabilization of charges
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Metalloprotease
• Problem 47: Propose a mechanism for this protease:
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pH affects Enzyme Catalysis
Propose possible explanations of pH profile
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Binding Energy
• Binding based on intermolecular forces
• “Lock and Key”• Selectivity• Rate Enhancement– Effective
concentration– Entropy trap
Productive orientation of two molecules in the active site
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Effective Molarity
• May be higher than actual molarity possibility
• Entropic help
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Induced Fit
• “Lock and Key” too simplistic
• Enzymes are actually somewhat flexible
• Substrate specificity comes at catalytic price
• kcat = 103 per second, but worth cost
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Lowering Activation Energy
• Transition state stabilization is half the story
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Weak Binding of Substrate
• Substrate binding: too much of a good thing
• Thermodynamic pit
• KM ~ 10-4 M• Can be 10-6 M for
cofactors
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Case Study: Chymotrypsin
• Serine protease• Catalytic triad• Oxyanion hole
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Substrate Specificity
• Specificity pocket• Binding affinity• Promiscuity