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Enzymes
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Biochemistry
09/17/2011

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Term
Enzymes
Definition
provide cells with the ability to exert kinetic control over thermodynamic potentiality
Term
Enzyme Properties
Definition
1. Extremely Specific (Absolute Specificity- working upon only a single substrate, Group Specificity- working upon a related group or molecules containing a specific functional group, Linkage specificity- working on molecules that contain a specific type of chemical bond)
2. Stereospecific
3. RXNs catalyzed by enzymes produces only one product
4. A lot faster than man made catalysts
Term
6 major classes of Enzymes
Definition
1. Oxidoreductases
2. Transferases
3. Hyrdrolases
4. Lyases
5. Isomerases
6. Ligases
Term
Oxidoreductases
Definition
Catalyze oxidation reduction rxns. Subclasses: Dehydrogenases, reductases, oxygenases, oxidases, and peroxidases
Term
Transferases
Definition
catalyze group transfer rxns. transfer a functional group from donor molecule to an acceptor molecule. Ex: Kinases catalyze the transfer of a phosphoric group from a phosphate donor to a phosphate acceptor molecule; Aminotransferases transfer amino groups; Methyltransferases transfer methyl groups.
Term
Hydrolases
Definition
catalyze hydrolysis rxns. Ex: hydrolytix cleavage of ester, amide, etc. Subclasses: Exterases, Phosphatases, and Proteases
Term
Lyases
Definition
catalyze nonhydrolytic and nonoxidative elimination rxns to form double bonds or they catalyze the addition of a group across a double bond.
Term
Subclasses of Lyases that catalyze the removal of a group to form a double bond
Definition
decarboxylases, dehydrases, deaminases
Term
Synthases
Definition
Subclass of Lyases that add substrates across a double bond
Term
Isomerases
Definition
catalyze isomerization rxns: rearrangement of groups around a central atom. Subclasses: Mutases and Epimerases
Term
Ligases
Definition
Catalyze the joining of two small molecules into one larger molecule. Subclasses: Synthetases (use an outside energy source to drive formation of new double bond) and Carboxylases
Term
Cofactor
Definition
The prosthetic group of an enzyme is a metal
Term
Coenzyme/Cosubstrate
Definition
The prosthetic group necessary for enzymatic activity is a small organic molecule
Term
Coenzymes
Definition
Very tightly bound to the protein
Term
Cosubstrates
Definition
diffusible, moving around within the cell, associating with the enzyme when needed and diffusing away when not needed.
Term
Apoenzyme
Definition
Protein without its necessary prosthetic group
Term
Holoenzyme
Definition
active enzyme with its needed prosthetic group
Term
Substrate Binding Sites
Definition
noncontiguous subset of a.a. side chains within the protein that interacts with and binds the substrate
Term
Active Site
Definition
a noncontiguous subset of a.a. side chains within the three dimensional protein structure, necessary participants in the catalytic process
Term
ΔG (Free energy of activation)
Definition
the energy retired to reach the transition state
Term
An enzyme can lower the activation energy by ______
Definition
breaking the rxn into parts. (minimum of four steps)
1. Substrate binds to enzyme
2. Substrate is brought to the transition state
3. Product is formed bound to the enzyme
4. Product dissociate from the enzyme
Term
Emil Fischer
Definition
Lock and Key method: did not explain how if the substrate is exactly complementary to the substrate binding site where does the energy for the conversion of substrate to product come from? and also, how does the enzymes catalyze the reverse rxn? if it was exactly complementary to the substrate then the product wouldn't be, and therefore would not be able to bind to the enzyme
Term
Koshland
Definition
recognized that enzymes are conformationally dynamic molecules: Induced Fit Hypothesis- the empty substrate binding site has a three dimensional structure complementary to the structure of the transition state. Substrate binds to this site initially by one or two weak intermolecular interaction. these initial reactions contort the conformation of the binding site and brings the substrate closer to other groups on the enzyme with which it can interact, relieving the stress on the enzyme and begins to force the substrate into a conformation or configuration that begins to resemble the transition state
Term
Nucleophilic RXN
Definition
in which an electron rich group attacks an electron poor molecule
Term
Electrophilic
Definition
an electron poor group attacks an electron rich molecule
Term
Covalent Catalysis
Definition
Formation of a covalent intermediate between the enzyme and some or all of the substrate that splits the rxn up into several steps
Term
Acid-Base Catalysis
Definition
the rate acceleration is achieved by the transfer of a proton. Metal ion cofactors near or in the active site stabilize the intermediates formed during acid-base catalysis by forming salt bridges with negatively charged intermediates that transiently form within the active site
Term
the rate of enzyme catalyzed rxns with an increase in ____ up to a certain point but beyond that point the rate ________
Definition
temperature; decreases
Term
During the initial phase of the rxn, the ________ is measured
Definition
initial rate or initial velocity (Vo)
Term
the initial rate of an enzyme catalyzed rxn is dependent upon the _____
Definition
enzyme concentration
Term
Point of which an enzyme is saturated with substrate
Definition
with the continued increase of substrate concentration, the point at which adding more substrate results in very little if any increase in the initial rate. at this point the enzyme has attained its maximum velocity (Vmax)
Term
Michaelis-Menton equation
Definition
Vmax[S] / [S]+Km.
Km: the substrate concentration that results in an initial velocity, equal to one half of Vmax "Rough measure of affinity"
Term
Lineweaver-Burke/Double Reciprocal Plot
Definition
1/Vo= (Km/Vmax)(1/[S]) + (1/Vmax)
Vmax and Km are constants for a particular enzyme, but they are not the best constants for comparing different enzymes because they are dependent upon the enzyme concentration employed during their determination
Term
Turner Number/Kcat
Definition
the number of catalytic events per unit of time/the number of product molecules formed per enzyme active site per unit of time. Used to describe/compare enzymes
Kcat= Vmax/[Et]
[Et] is the total concentration of enzyme present in the experimental mixture.
Term
Specificity Constant
Definition
measure the rate of an enzyme catalyzed rxn at low substrate concentrations. Usually at or below Km. Measures the efficiency of an enzyme at cellular substrate concentrations.
Specificity Constant= Kcat/Km
Term
Inhibitor
Definition
Chemical that interacts with an enzyme and decreases its activity, decreases that rate of product formation
Term
Irreversible Inhibitor
Definition
Either binds exceedingly tightly to the enzyme or forms a covalent bond with one of the amino acid side chains necessary for catalysis. Ex: Diisopropylfluorophosphate- irreversibly inhibits enzymes that contain serene residues in the active site by forming a covalent bond with the hydroxyl group or serene side chain. (Inhibits hydrolase enzymes:trypsin, chymotrypsin, thrombin, etc.) and serene esterase's
Term
Inhibition of Acetyl Choline
Definition
What kills you the fastest. it is neurotransmitter in the synaptic space where it hydrolyzes acetylcholine into acetate and choline thereby stopping stimulation of the post synaptic neuron or muscle cell. When inhibited acetylcholine is not destroyed and muscle cell continues to contract
Term
Aspirin
Definition
Irreversible inhibits cyclooxygenase (key enzyme in the synthesis of the eicosanoids). When inhibited, the acetate group on the molecule is transferred to the hydroxyl group of the active site serene side chain.
Term
Reversible Inhibitors
Definition
bind to enzymes by weak noncovalent interactions: in equilibrium between a form bound to the enzyme and the free form
Term
3 main types of reversible inhibitors
Definition
Competitive, Uncompetitive, and Mixed Type (noncompetitive inhibitors are a special type of mixed type inhibitors)
Term
Ki
Definition
dissociation constant for the EI complex: measure of the affinity of the enzyme for the inhibitor. As Ki decreases, the affinity of the enzyme for the inhibitor increase
Term
Competitive Inhibitors
Definition
have three dimensional structure similar to the normal substrate and/or to the transition state. bind to the enzyme at the substrate binding site. They "compete" with the normal substrate for interacting with the enzyme.
Term
Uncompetitive, Mixed Type, and Noncompetitivie Inhibitors bind to ____
Definition
sites on the enzyme away from the substrate binding site
Term
Uncompetitive Inhibitors
Definition
either significantly slows or prevents the conformational changes in the enzyme required for induced fit and catalysis. Result in a decrease in the measured Vmax and an apparent decrease in the Km
Term
Mixed Type Inhibitors
Definition
Bind at a site away from the substrate site, but they can bind to either the free enzyme or to the enzyme-subnstrate complex. therefore they have two Kis.
Term
Noncompetitive Inhibitors
Definition
bind either to the free enzyme or to the enzyme-substrate complex at a site away from the substrate site. Unlike in the mixed type inhibitor, Kia = Kib
Term
Kia
Definition
when the inhibitor binds to the free enzyme
Term
Kib
Definition
when the inhibitor binds to the enzyme-substrate complex
Term
Increase Km
Definition
Competitive and Mixed Type
Term
Decrease Km
Definition
uncompetitive
Term
No Change in Km
Definition
Noncompetitive
Term
No Change in Vmax
Definition
Competitive
Term
Decrease in Vmax
Definition
Uncompetitive, Mixed Type, and noncompetitive
Term
Substrate Availability
Definition
availability of substrates, cofactors, coenzymes, and/or cosubstrates will determine the rate of cellular enzymatic rxns. if the concentrations of these are low then the rate of the rxn will be slow
Term
Equilibrium Considerations
Definition
ratio of product to substrate concentration affects the rate of enzyme catalyzed rxns since many of the rxns in the cell are reversible rxns. In Vivo: the rxns will be in equilibrium and an equilibrium constant can be calculated. Removing product or increasing substrate concentration increases the rate of the rxn
Term
Product Inhibition
Definition
The enzyme being inhibited by their product. as the concentration of product increases it acts as a competitive inhibitor toward the enzyme. Ex: Feedback Inhibition
Term
Enzyme Synthesis
Definition
genetic controls over the synthesis and cellular concentrations of certain key enzymes. when a particular substrate becomes available the cell synthesizes the enzymes necessary for its utilization
Term
Induction
Definition
stimulation of enzyme synthesis
Term
Repression
Definition
inhibition of enzyme synthesis
Term
Irreversible Covalent Modification
Definition
Aymogens/Proenzymes enzymes that are synthesized in their inactive states.
Activation Peptides- small peptide(s) that is(are) removed by enzymes that activates zymogens.
Ex: Hemostasis Cascade
Term
Proteases
Definition
catalyze the removal of activation peptides
Term
Reversible Covalent Modification
Definition
some group is added to or removed from specific sites on the enzyme, resulting in either an increase or decrease in the activity of the enzyme. Phosphoryl group is the most commonly added to or removed from an enzyme to modulate its activity. RAPID FORM OF ENZYME CONTROL
Term
Allosteric Control
Definition
requires an allosteric enzyme (always multimeric proteins). There is a substrate binding/active site in which the substrate binds and catalysis occurs, and a allosteric site in which Allosteric Effectors or Allosteric Modulators bind.
If the subunits of the multimeric protein are different then there is a Catalytic subunit that carries the substrate/active site and the other (Regulatory) subunit contains the allosteric site
Term
Tense Conformation/ T-State
Definition
when the enzyme is in its low affinity state.
Term
Relaxed Conformation/ R-State
Definition
High affinity state
Term
Cooperative Event
Definition
Substrate binding to an allosteric enzyme
Term
Effector Molecules
Definition
bind to allosteric enzymes and cause a change in enzyme activity, can be the product of the allosteric enzyme, the product of a different enzyme, or some "signal molecule"
Term
Negative Allosteric Effectors (Negative Allosteric Modulators0
Definition
bind to their allosteric sites, shift the enzyme conformation more toward the T state and thereby decrease the activity of the enzyme
Term
Positive Allosteric Effectors (Positive Allosteric Modulators)
Definition
Shift the enzyme more towards the R conformation and therefore increasing the enzymatic activity.
Term
Most Rapid method for controlling enzyme activity
Definition
Allosteric Control
Term
Concerted Theory
Definition
the protein exists in equilibrium between the T and R states. substrate can only bind to the R form
Term
Sequential Theory
Definition
in the absence of substrate all the enzyme molecules are in the T state. when substrate binds, one of the subunits of the protein shifts to the R form. as more substrate binds to the enzyme more of the subunits switch to the R conformation. allosteric modulators bind only to the T state
Term
Hemoglobin
Definition
When Hb is deoxygenated it is in the T state. as partial pressure of oxygen is increased it reaches a point at which the first oxygen molecule binds to Hb causing the subunit to switch from T to R. after 2 or 3 molecules of oxygen have bound, the entire Hb molecules is in the R conformation.
Term
Max Perutz
Definition
determins X-ray structure of deoxygenate Hb and oxygenated Hb. When Hb switches from T to R then Alpha-1Beta-1 subunit pair shifts 15 degrees relative to the Alpha-2Beta-2 subunit pair, closing the central cavity of the molecule
Term
3 negative allosteric effecters of Hb
Definition
Hydrogen Ion, Bicarbonate Ion, and 2,3-Bisphosphoglycerate
Term
Bohr Effect
Definition
the effect of hydrogen and bicarbonate ion on the R to T transition
Term
2,3-Bisphosphoglycerate
Definition
binds in the central cavity of the Hb molecule, decreasing the oxygen affinity of Hb
Term
Hbs Function in Lungs
Definition
Partial Pressure of oxygen is high and carbon dioxide is low in the lungs, forces the first oxygen to bind to Hb, beginning the T to R transition. Since C02 is low in the lungs, equilibrium is shiftered towards CO2 production
Term
Carbonic Anhydrase
Definition
catalyzes the back rxn and increases the rate of CO2 formation.
Term
In tissues
Definition
PP of Oxygen is low and PP of CO2 is high, the low PP oxygen starts the shift from R to T as oxygen begins to dissociate from the Hb molecule. High concentration of CO2 in tissue and low CO2 connotation in the RBC drives diffusion of CO2 into RBC.