Term
|
Definition
| provide cells with the ability to exert kinetic control over thermodynamic potentiality |
|
|
Term
|
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
|
Definition
| Catalyze oxidation reduction rxns. Subclasses: Dehydrogenases, reductases, oxygenases, oxidases, and peroxidases |
|
|
Term
|
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
|
Definition
| catalyze hydrolysis rxns. Ex: hydrolytix cleavage of ester, amide, etc. Subclasses: Exterases, Phosphatases, and Proteases |
|
|
Term
|
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
|
Definition
| Subclass of Lyases that add substrates across a double bond |
|
|
Term
|
Definition
| catalyze isomerization rxns: rearrangement of groups around a central atom. Subclasses: Mutases and Epimerases |
|
|
Term
|
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
|
Definition
| The prosthetic group of an enzyme is a metal |
|
|
Term
|
Definition
| The prosthetic group necessary for enzymatic activity is a small organic molecule |
|
|
Term
|
Definition
| Very tightly bound to the protein |
|
|
Term
|
Definition
| diffusible, moving around within the cell, associating with the enzyme when needed and diffusing away when not needed. |
|
|
Term
|
Definition
| Protein without its necessary prosthetic group |
|
|
Term
|
Definition
| active enzyme with its needed prosthetic group |
|
|
Term
|
Definition
| noncontiguous subset of a.a. side chains within the protein that interacts with and binds the substrate |
|
|
Term
|
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
|
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
|
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
|
Definition
| in which an electron rich group attacks an electron poor molecule |
|
|
Term
|
Definition
| an electron poor group attacks an electron rich molecule |
|
|
Term
|
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
|
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
|
|
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
|
|
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
|
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
|
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
|
Definition
| Chemical that interacts with an enzyme and decreases its activity, decreases that rate of product formation |
|
|
Term
|
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
|
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
|
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
|
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
|
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
|
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
|
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
|
Definition
| when the inhibitor binds to the free enzyme |
|
|
Term
|
Definition
| when the inhibitor binds to the enzyme-substrate complex |
|
|
Term
|
Definition
| Competitive and Mixed Type |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| Uncompetitive, Mixed Type, and noncompetitive |
|
|
Term
|
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
|
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
|
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
|
Definition
| stimulation of enzyme synthesis |
|
|
Term
|
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
|
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
|
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
|
|
Term
|
Definition
| Substrate binding to an allosteric enzyme |
|
|
Term
|
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
|
|
Term
|
Definition
| the protein exists in equilibrium between the T and R states. substrate can only bind to the R form |
|
|
Term
|
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
|
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
|
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
|
Definition
| the effect of hydrogen and bicarbonate ion on the R to T transition |
|
|
Term
|
Definition
| binds in the central cavity of the Hb molecule, decreasing the oxygen affinity of Hb |
|
|
Term
|
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
|
Definition
| catalyzes the back rxn and increases the rate of CO2 formation. |
|
|
Term
|
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. |
|
|
