Exam (elaborations)
Enzymology catalyst
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Exam of 23 pages for the course MBE at MBE (Enzymology catalyst)
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Enzymology catalystCatalyst - correct answer-1. Chemical or biological substance or structure that lowers
activation energy
2. Accelerates the rate of a chemical rxn
Enzymes - correct answer-Biological catalysts that are capable of performing multiple rxns
(are recycled). They can be proteins or RNA, are faster than chemical catalysts, and act
under mild conditions (bodily temperature/pressure). They are highly specific and tightly
regulated.
Enzyme functions - correct answer-- cell shape and motility
- surface receptors
- metabolism
- cell cycling
- protein synthesis
- transcription
- hormone release
- muscle contraction
Enzyme properties - correct answer-1. Vital for chemical rxns in the cell through breaking,
forming, and rearranging bonds on a substrate
2. Modify substrate (now a product) to perform a different task
3. Able to:
- transform energy and matter in the cell
- perform cell-cell and intracellular communication
- allow for cellular homeostasis to persist
Enzyme specificity - correct answer-The active site dictates specificity:
- specific for one type of chemical group
- substrates interact in stereospecific manner (must fit)
- substrates bind relatively well
-substrates must react
Substrate affinity - correct answer-Must bind relative well, but not have a perfect fit. Binding
is through H-bonds, electrostatics, and hydrophobic interactions.
If substrate fits perfectly, the enzyme will not convert and release the substrate, which
inactivates the enzyme.
Substrate reactivity - correct answer-Bonds that will be broken and formed must have proper
reactivity with the enzyme.
Inhibitors - correct answer-Substances that fit and bind an enzyme, but do not have the
proper reactivity.
,Active site - correct answer-Complements the structure of the substrate - most commonly
the transition state of the substrate.
Contains amino acid residues that function in substrate binding, chemical catalysis, and
product release.
Catalytic domain - correct answer-Protein domain that contains the active site and allows for
proper folding of entire structure.
Stabilizes the active site to form a key microenvironment. Serves as site of regulation, can
hold an allosteric site, maintains the distinguishing features of enzymes.
Membrane binding domain - correct answer-Allows enzyme to localize on the membrane
where the substrate is found.
Domain - correct answer-Conserved portion of a protein that is capable of independent
function, folding, and stability.
Motif - correct answer-Conserved portion of a protein that does not have independent
function or folding.
Microenvironment - correct answer-Everything in and around the active site that allows
catalysis of the substrate to occur.
Contains a large number of hydrophobic residues to allow for interaction with the substrate.
Structural biology of enzymes - correct answer-Use of x-ray crystallography to solve the
structure of enzymes.
Can use with or without substrate provides functional and biological info.
Can be used to identify amino acids involved in chemical catalysis.
Catalytic competence - correct answer-When the active site is in the correct orientation for
catalysis to occur.
Enzyme regulation - correct answer-Usually tightly regulated through several means.
Unregulated enzymes can become constitutively active or inactive, and can disrupt cell
homeostasis, leading to disease states.
Allosteric regulation - correct answer-Allosteric activator/inhibitor binds at a site away from
the active site, which alters the conformation of the enzyme to either allow or block substrate
binding.
Activators change the active site to fit the substrate.
Inhibitors change the active site to block out the substrate.
Cooperativity regulation - correct answer-Seen in enzymes with multiple active sites. Active
form of an enzyme is stabilized by the binding of one substrate molecule, increasing its
affinity for more substrate molecules to bind.
First binding changes the conformation in such a way that the enzyme can accommodate
more substrate.
, Regulation of downstream signalling by RTKs - correct answer-When a ligand binds RTK
surface receptors, RTK dimerizes and is able to phosphorylate molecules that trigger
downstream signalling.
When PTP is reduced, it is able to block RTK phosphorylation and therefore downstream
signalling. When PTP is oxidized, it is unable to do so and signalling can occur. PTP is
oxidized through the production of hydrogen peroxide produced by NADPH oxidase, which is
activated by RTK.
Proximity effects - correct answer-Rate increase due to two reactants being brought out of a
dilute environment and being placed close together. Made possible by the catalytic domain.
Include:
- increase in effective concentration (same effect as formation of ES complex)
- binding energy
- desolvation
Increase in effective catalytic group concentration - correct answer-Result is an increase in
the effective concentration of catalytic groups in an enzyme.
Effects:
- increases chances of a rxn since molecules are close together in an ES complex
- ES complex is an intramolecular entity that reduces entropy loss
Binding energy - correct answer-Enzymes provide a docking site and microenvironment for
proper substrate orientation for reaction.
The binding energy from this interaction can be used for rate enhancement.
Formation of the ES complex releases free energy, used to increase rate of rxn. Same effect
as adding more catalyst. The ES complex has a unimolecular orientation that loses entropic
penalties.
Desolvation - correct answer-Removal of the substrate from water or other solvents, or
dehydration of substrate. Eliminates the energy barrier imposed by ordered solvent
molecules that would slow a rxn. This results in an accelerated rxn.
Transition state theory - correct answer-Reactants pass through high-energy transition states
before forming products.
Reactants and products are usually stable in their ground states.
Activation energy - correct answer-Represents the different in energy between the reactants
and transition state(s). The higher the activation energy, the slower the rxn will proceed.
Enzymes accelerate rxn rates by reducing activation energy. They do not affect the Gibbs
energy of the reaction, and have no effect on the equilibrium.
Transition state stabilization - correct answer-Enzymes reduce activation energy by
stabilizing the transition state structure. Often neutralize negative or positive charges in the
TS.
The catalytic residues of an enzyme are not crucial for this.
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