MODULE 6: Chapter 7.2 Flashcards
What is the formal definition of a catalyst?
A catalyst increases the rate of a chemical reaction without changing the chemical equilibrium and is not consumed by the reaction.
How do enzymes increase the rate of a reaction inside cells?
- Stabilizing the transition state to lower the activation barrier.
- Providing an alternative path for product formation.
- Orienting substrates appropriately for the reaction.
What can lead to increased reaction rates besides enzymes?
Raising effective substrate concentrations or elevating the reaction temperature or pressure.
How do enzymes optimize molecular structure and function?
Through natural selection to achieve increased rates of reactions under physiologic conditions.
What is the role of enzyme active sites?
They provide a physical and chemical environment that promotes product formation.
What are the three specific physical and chemical properties of enzyme active sites?
- Sequestered microenvironment.
- Binding interactions that facilitate formation of the transition state.
- Presence of catalytic functional groups.
What does the enzyme active site do to the substrate?
It provides an optimal orientation relative to reactive chemical groups and increases the reactivity of some functional groups.
How do enzyme active sites exclude excess solvent?
By either an induced-fit mechanism or by sequestering the active site away from the surface.
What is the induced-fit mechanism in enzyme activity?
Conformational changes in the protein create significant shape and chemical complementarity between the substrate and enzyme, ejecting excess water.
What happens when glucose binds to hexokinase?
Numerous water molecules are displaced from the substrate binding site.
What is the significance of the aldolase reaction?
It converts two phosphorylated three-carbon compounds into one bisphosphorylated six-carbon compound.
What is the reaction coordinate diagram used for in enzyme-catalyzed reactions?
To compare the activation energy of enzyme-catalyzed reactions to uncatalyzed reactions.
What is the transition state stabilization model?
It proposes that the active site shares more complementarity with the transition state than with the substrate or product.
Fill in the blank: Enzymes stabilize the _______ within the active site.
[transition state]
True or False: The free energy change (ΔG) for a reaction changes in the presence of an enzyme.
False.
What types of interactions contribute to substrate binding in enzyme-catalyzed reactions?
Hydrogen bonds, ionic interactions, and van der Waals interactions.
What is the significance of the hydrophobic effect in enzyme activity?
It increases the entropy of water molecules released upon substrate binding.
What happens after the enzyme-bound substrate is converted to the enzyme-bound product?
The product is released from the enzyme.
What is the relationship between enzyme active sites and excess water?
Active sites are designed to exclude excess water that can interfere with reactions.
How do hydrophobic substrate channels function in enzymes?
They prevent water molecules from entering the active site while allowing access to hydrophobic substrates.
What is an example of a metabolic enzyme discussed in the content?
Aldolase.
What is the role of the amino acid functional groups within the aldolase active site?
They position the substrates to favor aldol condensation.
How does the enzyme ensure that product release does not interfere with reaction rates?
Binding should not be too tight to allow product release and new substrate binding.
What is the role of the ES complex in lowering activation energy?
Formation of the ES complex initiates bond formations that lower activation energy required to reach the transition state
What is the transition state in enzyme reactions?
The transition state is the midpoint of the ES ⇌ EP reaction and is stabilized by the enzyme active site
True or False: The enzyme active site has a higher affinity for the product than for the transition state.
False
What are transition state analogs?
Stable molecules that mimic the proposed transition state and bind tightly to enzyme active sites
What is the estimated affinity of an enzyme for a transition state analog?
10−13 M, exceeding the affinity for substrate or product by approximately a factor of 108
What are the three most common catalytic reaction mechanisms in enzyme active sites?
- Acid–base catalysis
- Covalent catalysis
- Metal-ion catalysis
What is acid-base catalysis?
Involves proton transfer through mechanisms that add or remove a proton
What are the two types of acid-base catalysis?
- Specific acid–base catalysis
- General acid–base catalysis
What amino acid is often involved in enzyme-mediated acid-base catalysis?
Histidine
What is covalent catalysis?
Formation of a transient covalent bond between substrate and enzyme to create an unstable intermediate
Provide an example of covalent catalysis.
Formation of 1,3-bisphosphoglycerate from glyceraldehyde-3-phosphate by glyceraldehyde-3-phosphate dehydrogenase
What is metal-ion catalysis?
Enzymes require metal ions as cofactors in catalytic reactions
What are metal-activated enzymes?
Enzymes with loosely bound metal ions
What are metalloenzymes?
Enzymes with tightly bound metal ions
What is the role of Zn2+ in carbonic anhydrase?
Catalyzes the reversible reaction of bicarbonate formation from carbon dioxide
What are the three general categories of enzyme-mediated reactions?
- Coenzyme-dependent redox reactions
- Metabolite transformation reactions
- Reversible covalent modification reactions
What do coenzyme-dependent redox reactions involve?
Energy conversion processes in cells
What are the two main types of compounds involved in redox reactions?
- Electron donors
- Electron acceptors
What coenzymes are used in redox reactions at C─O bonds?
- NAD⁺/NADH
- NADP⁺/NADPH
What coenzymes are used in redox reactions at C─C bonds?
- FAD/FADH2
- FMN/FMNH2
What are the three common types of metabolite transformation reactions?
- Isomerization reactions
- Condensation reactions
- Hydrolysis or dehydration reactions
What is an isomerization reaction?
A reaction that does not change the molecular formula of the product compared to that of the substrate
What occurs during a condensation reaction?
Two substrates combine to form a larger molecule with the loss of a smaller molecule
What is the effect of water in hydrolysis reactions?
Water is added to cleave the substrate
What is isomerization?
A reaction that does not change the molecular formula of the product compared to that of the substrate.
Involves the conversion of one isomer to another, such as dihydroxyacetone phosphate to glyceraldehyde-3-phosphate.
What does the enzyme triose phosphate isomerase catalyze?
The isomerization of dihydroxyacetone phosphate to glyceraldehyde-3-phosphate.
This reaction involves metabolites with the same molecular formula, C3H7O6P.
What is a condensation reaction?
A reaction that combines two chemically similar substrates to form a larger molecule, with the loss of a smaller molecule, usually water.
Example: The condensation of dimethylallyl diphosphate and isopentenyl diphosphate to form geranyl diphosphate.
What role does the enzyme aldolase play in metabolic pathways?
Catalyzes the condensation reaction leading to the formation of fructose-1,6-bisphosphate.
This reaction is part of the gluconeogenic pathway.
What is the significance of water (H2O) in enzymatic reactions?
It is a critical component of many enzymatic reactions, participating as a substrate or product.
Water is involved in acid-base catalysis mechanisms and hydrolytic cleavage reactions.
What type of reaction does chymotrypsin catalyze?
A hydrolytic cleavage reaction that breaks a peptide bond in proteins.
This reaction uses water as a substrate.
What is a dehydration reaction?
A reaction that cleaves a substrate into two products by the removal of water.
Example: Conversion of 2-phosphoglycerate to phosphoenolpyruvate by the enzyme enolase.
What is the function of kinases in cellular processes?
Add a phosphoryl group to signaling molecules, altering their activity or recognition.
Often phosphorylate proteins at Ser, Thr, or Tyr residues using ATP.
What do phosphatase enzymes do?
Remove a phosphoryl group from a biomolecule.
This process often involves hydrolysis and releases inorganic phosphate (Pi).
What does DNA methyltransferase do?
Transfers a methyl group to the C-5 position of cytosine in DNA, generating 5-methylcytosine.
This modification is associated with gene inactivation.
What is 5-methylcytosine associated with?
Decreased rates of transcriptional initiation.
Its presence in regulatory regions recruits transcriptional silencing proteins.
What is the role of the enzyme active site in lowering activation energy?
Provides selective binding of substrates and optimal configuration for reactive groups.
This lowers the ΔG‡ through stabilizing the transition state or providing alternative pathways.
What is a metalloenzyme?
An enzyme containing a tightly bound metal-ion cofactor.
What is NADP⁺/NADPH?
A coenzyme that mediates redox reactions that take place at carbon–oxygen bonds.
What is the definition of hydrolysis?
A reaction that cleaves a substrate into two products by the addition of water.
What is the function of endoproteases?
Enzymes that cleave peptide bonds within proteins.
What is S-adenosyl-L-methionine used for?
Functions as the methyl donor in a variety of biochemical reactions.
What is flavin adenine dinucleotide (FAD/FADH2)?
A coenzyme that mediates redox reactions at carbon–carbon bonds.
Fill in the blank: The presence of _______ in the regulatory region of genes is associated with decreased rates of transcriptional initiation.
5-methylcytosine
True or False: Antibodies generally catalyze reactions.
False.
What is polyethylene glycol (PEG) used for in biochemistry?
Serves as a water-soluble polymer to identify hydrophobic channels in enzyme active sites and facilitate precipitation of bacteriophage particles.
