Module 04: Enzymes (Stoker) Flashcards
(194 cards)
1
Q
They act as a catalyst for biochemical reactions. They can be denatured and activity is dramatically affected by alterations in pH, temperature and other protein denaturants
A
Globular Proteins (Enzymes)
2
Q
These are exceptions and ribonucleic acids with catalytic activity.
A
Ribozymes
3
Q
Enzymes are not consumed in the reactions; they are ______________.
A
Regenerated
4
Q
What is the effect of enzymes on equilibrium constant (Keq) along with retention factor (Rf) and Rb values?
A
It has no effect on Keq, increase both Rf and Rb reactions at same rate. It can increase rate a 10^3 to 10^6 fold
5
Q
What are the general characteristics of enzymes?
A
(1) Regulation (allosteric enzymes) activities of allosteric enzymes can be controlled or modulated by allosteric effectors
(2) Location: found in specific sites or organelles within the cell. Reason why enzymes are used as clinical markers for certain diseases.
6
Q
What are the two (2) types of enzymes?
A
(1) Simple Enzymes
(2) Conjugated Enzymes
7
Q
These are composed only of protein (amino acid chains).
A
Simple Enzyme
8
Q
These types of enzymes has a non-protein part in addition to a protein part.
A
Conjugated Enzyme
9
Q
This is the protein part of a conjugated enzyme (inactive).
A
Apoprotein
10
Q
This is a nonprotein part of a conjugated enzyme.
A
Cofactor
11
Q
These are constituted of an apoenzyme and co-factor. And is known to be the biochemically active conjugated enzyme
A
Holoenzyme (cofactor)
12
Q
This is important for the chemically inactive enzymes and are small organic molecules or Inorganic ions
A
Cofactors
13
Q
Cofactors are also known as ___________ or __________.
A
Coenzymes or substrates
14
Q
Coenzymes/cosubstrates are derived from “__________.”
A
dietary vitamins
15
Q
What are the typical metal ion cofactors?
A
Zn2+, Mg2+, Mn2+, and Fe2
16
Q
What are the typical non metallic ion cofactors?
A
Cl-
17
Q
Inorganic ion cofactors derived from “___________.”
A
dietary minerals
18
Q
The nomenclature of an enzyme is based on what factors?
A
(1) Type of reaction catalyzed
(2) Identity of the substrate
19
Q
This is the is the reactant in an enzyme-catalyzed reaction. This is the substance upon which the enzyme “acts.”
A
Substrate
20
Q
What are the three important factors of the naming process?
A
(1) Suffix -ase identifies it as an enzymes. Exception: The suffix -in is still found in the names of some digestive enzymes, E.g. trypsin, chymotrypsin, and pepsin
(2) Type of reaction catalyzed by an enzyme is often used as a prefix
(3) Identity of substrate is often used in addition to the type of reaction
21
Q
What are the six major classes (classification) of enzymes?
A
(1) Oxidoreductase
(2) Transferase
(3) Hydrolase
(4) Lyase
(5) Isomerase
(6) Ligase
22
Q
What type of reaction does Oxidoreductase catalyze?
A
Oxidation-reduction
23
Q
What type of reaction does Transferase catalyze?
A
Functional group transfer reactions
24
Q
What type of reaction does Hydrolase catalyze?
A
Hydrolysis reaction
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What type of reaction does Lyase catalyze?
Reactions involving the addition to a double bond or removal of groups forming a double bond
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What type of reaction does Isomerase catalyze?
Isomerization reactions
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What type of reaction does Ligase catalyze?
Reactions involving bond formation coupled with ATP hydrolysis
28
This is an enzyme catalyzes an redox reaction:
Oxidoreductase
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What does Oxidoreductase require?
coenzyme that is either oxidized or reduced, e.g. NAD+, FAD, FMN
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This pertains to the decrease in valence along with the gain of H or loss of O. This is undergone by oxidizing agent.
Reduction
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This pertains to the increase in valence along with the loss of H or the gain of O. This is undergone by reducing agent.
Oxidation
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This undergoes reduction, gain of e- or gain of H
Oxidizing Agent
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This undergoes oxidation, loses e-/donor of H
Reducing Agent
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This is an enzyme that catalyzes the transfer of a functional group from one molecule to another
transferase
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These catalyze transfer of an amino group to a substrate, catalyze transamination reaction
Transaminases
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This catalyze transfer of a phosphate group from adenosine triphosphate (ATP) to a substrate
Kinase
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This is a reaction of an amino acid and a-keto acid to form a new a-keto acid and a new amino acid
Transamination
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This is an enzyme that catalyzes a hydrolysis reaction
hydrolase
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What does hydrolase involve?
The reaction involves addition of a water molecule to a bond to cause bond breakage
40
What are the three integral hydrolysis reactions in the process of digestion?
(1) Carbohydrase
(2) Proteases
(3) Lipases
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These hydrolyze glyosidic bonds in oligo- and polysaccharides
Carbohydrase
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These effect the breaking of peptide linkages in proteins,
Proteases
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These effect the breaking of ester linkages in triacyclglycerols (TAGs) or fats.
Lipases
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This is an enzyme that catalyzes the addition of a group to a double bond or the removal of a group to form a double bond in a manner that does not involve hydrolysis or oxidation
lyase
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This effects the removal of the components of water forming a double bond
Dehydratase
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These effects the addition of the components of water to a double bonds
Hydratase
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These catalyze synthesis (joining of molecules) without use of ATP
Synthase
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This is an enzyme that catalyzes the isomerization (rearrangement of atoms) reactions.
Isomerase
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What does an isomerase involve?
Interconversion between D and L amino acid, between an aldose and a ketose or internal rearrangement.
50
This is an enzyme that catalyzes the joining of two molecules involving ATP hydrolysis as a source of energy
Ligase
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What does a ligase require?
ATP hydrolysis is required because such reactions are energetically unfavorable (Require the simultaneous input of energy obtained by a hydrolysis of ATP to ADP.)
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This is the relatively small part of an enzyme’s structure that is actually involved in catalysis:
Active Site
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What are some of the characteristics of the active site?
(1) Place where substrate binds to enzyme
(2) Formed by groups from different parts of protein, brought by folding and bending of the protein.
(3) Usually a “crevice like” location in the enzyme
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True or false: Some enzymes have more than one active site.
True
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What is the formula for the Enzyme Substrate Complex?
S + E --------------> <-----------------ES --------> P + E
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How do enzymes increase the rate?
Enzymes increase the rate by providing alternate route with lower energy of activation.
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This is the intermediate reaction species formed when substrate binds with the active site
Enzyme Substrate Complex
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What are the two models for Substrate Binding to Enzyme?
(1) Lock-and-Key Model
(2) Induced Fit Model
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In this model of substrate binding, enzyme has a pre-determined shape for the active site. In this, only substrate of specific shape can bind with active site
Lock-and-Key Model
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In this model of substrate binding, substrate contact with enzyme will change the shape of the active site. This allows small change in space to accommodate substrate
Induced Fit Model
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What are the Forces That Determine Substrate Binding (non covalent interactions?
(1) H-bonding
(2) Hydrophobic interactions
(3) Electrostatic interactions
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What kind of specificity does the Lock & key model explain?
absolute specificity
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What kind of specificity does the Induced fit model explain?
broad specificity
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This is the ability to discriminate between 2 competing substrate
Enzyme Specificity
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This acts on only one substrate. In this, an enzyme will catalyze a particular reaction for only one substrate
Absolute Specificity
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This is most restrictive of all specificities (not common)
Absolute Specificity
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In this, an enzyme acts only on a particular stereoisomer. Moreover, it can distinguish between stereoisomers. For example, an L-Amino-acid oxidase - catalyzes reactions of L-amino acids but not of D-amino acids.
Stereochemical Specificity
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In stereochemical specificity, this is inherent in an active site.
Chirality
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This acts on structurally similar compounds that have the same functional groups.
Group Specificity or broad
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This acts on 2 or more substrate containing a particular type of bond irrespective of the structural features in the vicinity of the bond
Linkage Specificity
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This is considered most general of enzyme specificities
Linkage Specificity
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What is the relationship between temperature and the rate of activation?
Higher temperature results in higher kinetic energy which causes an increase in number of reactant collisions, therefore there is higher activity.
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This is the temperature at which the rate of enzyme catalyzed reaction is maximum
Optimum temperature
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Optimum temperature for human enzymes is ______________.
37ºC (body temperature)
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Increased temperature (high fever) leads to: "_________"
decreased enzyme activity
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Drastic changes in pH can result in "_________________"
denaturation of proteins
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pH at which enzyme has maximum activity
Optimum ph
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At which pH range do enzymes have maximum activity
pH range of 7.0 - 7.5
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What is the optimum pH of pepsin?
2.0
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What is the optimum pH of trypsin?
8.0
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In this, Enzymes are not consumed in the reactions they catalyze
Enzyme Concentration
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What happens at constant substrate concentration?
At a constant substrate concentration, enzyme activity increases with increase in enzyme concentration. In this, the greater the enzyme concentration, the greater the reaction rate.
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What happens to the substrate concentration at constant enzyme concentration?
At a constant enzyme concentration, the enzyme activity increases with increased substrate concentration
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This is the concentration at which it reaches its maximum rate and all of the active sites are full
Substrate saturation
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This is the number of substrate molecules converted to product per second per enzyme molecule under conditions of optimum temperature and pH
Turnover Number
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This is the rate equation that relates the velocity of the reaction to substrate concentration
Michaelis-Menten Equation
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What does the Michaelis-Menten Equation yield?
When initial velocity, Vo is plotted against [S], a hyperbolic curve (MM plot) results, where Vmax represents the maximum reaction velocity.
83
This represents the maximum reaction velocity.
Vmax
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What is the state of enzyme saturation at Vmax?
At the Vmax, all available enzyme is "saturated" with bound substrate, meaning only the ES (enzyme-substrate) complex is present.
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What happens at 1/2 Vmax?
At 1/2Vmax, the substrate concentration is equal to Km, the enzyme is half saturated
85
What is the state of part A in the graph of the Michaelis-Menten Equation?
[S] < KM (Michaelis constant) only a portion of the total number of active sites are saturated by the substrate
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What is the state of part B in the graph of the Michaelis-Menten Equation?
[S] = Vmax/2 half of the total number of active sites are saturated
86
What is the state of part C in the graph of the Michaelis-Menten Equation?
[S] > KM all enzymes’ active sites have bound substrate. Increasing the substrate concentration will no longer affect the rate because the enzyme is saturated.
87
If Vo is set equal to 1/2 Vmax, then ______________
Km = [S]. Km is equal to Substrate concentration at ½ Vmax.
87
What does it mean when Km is equal to Substrate concentration at ½ Vmax
This means that at one half of the maximal velocity, the substrate concentration needed to half saturate the enzyme to be equal to the Km
88
What is the relationship between the affinity of the enzyme for the substrate and the Km (Michaelis constant)?
It is an inverse measure of the affinity of the enzyme for the substrate (low Km = high affinity; low S concentration to attain Vmax)
89
What is the reciprocal for the Michaelis-Menten equation?
Lineweaver Burk Plot
89
The Lineweaver Burk Plot is a ____________________.
Double reciprocal plot
90
Why is the format of the equation a straight line?
x = 1/[S] and the y-intercept, b = 1/Vmax. When this relation is plotted, the result is a straight line graph
91
This is an enzyme that has an additional site called regulatory site or allosteric site for the binding of a regulatory molecule.
allosteric enzyme
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This is a simple enzyme that has only an active site for the binding of its substrate.
non-allosteric enzyme
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This is a site other than the active site. Site where small molecules (effectors) bind and cause conformational changes in the enzyme. It may cause the enzyme to be more active or less active.
Allosteric or Regulatory Site
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The plot of allosteric enzymes contain multiple subunits; thus they do not follow the Michaelis- Menten kinetics, which results to them being ________________.
sigmoidal
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Allosteric enzymes display this kind of binding
Displays cooperative effect – binding of S to one subunit facilitates the binding of the other substrates.
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This is any molecule that acts directly on an enzyme to lower its catalytic rate or stop it. These can be cellular metabolites, or foreign substances such as drugs or toxins that have either a therapeutic or toxic (can be lethal) effect.
Inhibitor
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How do inhibitors inhibit?
It acts directly on an enzyme to lower its catalytic rate or stop it.
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What are the two types of inhibition?
(1) Irreversible Inhibition
(2) Reversible Inhibition
a) Competitive
b) Uncompetitive
c) Mixed/Noncompetitive
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How does an irreversible enzyme inhibitor work?
The inhibitor bonds strongly and increasing substrate concentration does not reverse the inhibition process . Enzyme is permanently inactivated.
99
This inactivates enzymes by forming a strong covalent bond with the enzyme’s active site.
Irreversible Enzyme Inhibitor
100
This is used as an organophosphorus insecticide.
diisopropylfluorophosphate
101
What does the diisopropylfluorophosphate (DIFP) inhibit?
acetyl choline esterase
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This is a Non-steroidal anti-inflammatory drugs (NSAID) that inhibits an enzyme by acetylating a serine residue at the enzyme’s active site.
Aspirin
103
What enzyme does aspirin inhibit?
cyclooxygenase
104
What kind of synthesis does aspirin inhibit?
prostaglandin and thromboxane synthesis
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This is an irreversible inhibitor that inhibits transpeptidase?
penicillin
106
This is the enzyme involved in bacterial cell wall synthesis
transpeptidase
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This inhibition competes with the substrate for the same active site, resembles normal substrate in shape and charge (thus making it bind to the active site without changing the inhibitor - no reaction).
Reversible Competitive Inhibition
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What is the inhibitor in Reversible Competitive Inhibition?
structural analog of the normal substrate
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In what kind of interactions does the enzyme inhibitor form?
weak interactions (hydrogen bonds, etc.).
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How is Competitive inhibition reduced?
Competitive inhibition can be reduced by simply increasing the concentration of the substrate
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What is the kinetic effect of competitive inhibition?
Vmax is unchanged and Km is increased (affinity decreased)
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How does a competitive inhibition transpire?
Inhibitor has close structural similarities to the normal substrate and therefore competes with the substrate for the active site. Inhibitor binds only with the free enzyme.
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This is the inhibitor of succinate dehydrogenase.
Malonate
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This is the normal substrate found in the Krebs Cycle.
Succinate
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These are competitive inhibitors of 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase
Statins
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How do statins inhibit 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase?
limiting enzyme in cholesterol biosynthesis
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What are the competitive inhibitors of cyclooxygenase?
Ibuprofen, acetaminophen, naproxen
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This is an antidote for ethylene glycol or methyl alcohol poisoning. Competes for binding to alcohol dehydrogenase.
Ethanol
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This type of inhibition does not compete with the normal substrate for the active site but decreases enzyme activity by binding to a site other than the active site.
noncompetitive enzyme inhibitor
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What happens during reversible noncompetitive inhibition?
Causes a change in the structure of the enzyme and prevents enzyme activity.
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Can reversible noncompetitive inhibition be reduced?
No, increasing the concentration of substrate does not completely overcome inhibition.
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What is the kinetic effect of the noncompetitive inhibition?
Vmax is decreased and Km is unchanged but s can still bind with the enzyme
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What does the non competitive inhibition transpire?
Inhibitor binds at a site other than the active site (E or ES) (and free enzyme( and causes changes in the overall 3-D shape of the enzyme that leads to a decrease in activity:
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what are examples of noncompetitive inhibitors?
Heavy metals mercury and silver
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This is a non-competitive inhibitor of cytochrome oxidase of the ETC/ Respiratory Chain. It binds to its allosteric site.
Cyanide
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What does arsenate inhibit?
glyceraldehyde phosphate dehydrogenase
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In this, the inhibitor binds at a site other than the active site and, binds only to the ES complex.
Uncompetitive Inhibition
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What is the kinetic effect of Uncompetitive Inhibition?
Both Km and Vmax are decreased.
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This is a rarer phenomenon in uncompetitive inhibition
Uncompetitive inhibition of single-substrate enzyme-catalyzed reactions is a rare phenomenon,
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What does hydrazine inhibit?
aryl sulphatase
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What does phenylalanine inhibit?
intestinal alkaline phosphatase
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What are the general mechanisms involved in regulation? (APCOFEEN)
Allosteric regulation
Proteolytic enzymes and zymogens
covalent modification of enzymes
Feedback control regulation
Enzyme concentration
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What kind of structures do allosteric enzymes have?
All allosteric enzymes have quaternary structure (Composed of two or more protein chains/ subunits)
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What are the two binding sites of allosteric enzymes
Substrate (active site) and regulator binding site (allosteric site), wherein the active and regulatory binding sites are located independently and the shapes of the sites (electronic geometry) are different
135
what happens to the binding in regulatory sites?
Binding of molecules at the regulatory site causes changes in the overall three dimensional structure of the enzyme:
Change in three dimensional structure of the enzyme leads to change in enzyme activity
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These regulators increase are enzyme activity
Activators
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These regulators decrease are enzyme activity
Inhibitor
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This is the binding of an allosteric modulator that changes activity of the active site.
Allosteric Modification
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A process in which activation or inhibition of the first reaction in a reaction sequence is controlled by a product of the reaction sequence.
Feedback Control
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Regulators of a particular allosteric enzyme may be:
(1) Products of entirely different pathways of reaction within the cell
(2) hormones compounds produced outside the cell
141
In this form of inhibition, the product of the reaction inhibits its own formation by inhibiting an early enzyme in the pathway.
Feedback Inhibition
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Feedback Inhibition is also known as "_________"
End product Inhibition
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This is another mechanism of regulating enzyme activity wherein the productions of enzymes are in inactive forms and are turned on at the specific time or place.
Proteolytic Enzymes and Zymogens
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They hydrolyze peptide bonds in proteins and are generated in an inactive form then converted to their active form.
proteolytic enzymes
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What are examples of proteolytic enzymes?
digestive and clotting enzymes
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These are called inactive forms.
zymogens
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The zymogens are activated by _______
proteolytic cleavage
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This is a process in which enzyme activity is altered by covalently modifying the structure of the enzyme. This involves adding or removing a group from an enzyme
Covalent Modification
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This is the most common form of covalent modification and is often derived from an ATP molecule
Phosphate group
150
This pertains to the addition of a phosphate group
phosphorylation
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What catalyzes phosphorylation?
Kinase
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This pertains to the removal of a phosphate group
dephosphorylation
152
What catalyzes phosphorylation?
phosphatase enzyme
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What happens in phosphorylation?
Phosphate group is added to (or removed) from the R group of a serine, tyrosine, or threonine amino acid residue in the enzyme regulated.
154
This is the is the major regulatory enzyme in glycogen breakdown (glycogenolysis).
Glycogen phosphorylase
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Glycogen phosphorylase is activated by what
activated by phosphorylation
156
This is the major regulatory enzyme in the synthesis of glycogen from glucose. This is inhibited Phosphorylation.
Glycogen synthase
157
What activates Glycogen synthase?
activated by dephosphorylation
158
In the regulation of glycogen synthesis and degradation to maintain glucose levels, this is where the glycogen synthesis is activated
Well fed state
159
In the regulation of glycogen synthesis and degradation to maintain glucose levels, this is where the glycogen degradation is accelerated
Fasting
160
In the skeletal system, degradation is activated during
exercise
161
In the skeletal system, glycogen accumulation is activated during
rest
162
How are glycogen synthase and phosphorylase regulated?
allosterically and hormonally regulated
163
This regulatory enzyme in glycogen synthesis is activated by dephosphorylation
Glycogen synthetase
164
This regulatory enzyme in glycogen breakdown is activated by phosphorylation
Glycogen phosphorylase
165
What happens in induction or repression of enzyme synthesis during a well fed state?
When the level of insulin increases, the synthesis of key enzymes involved in glucose degradation are activated
166
What happens in induction or repression of enzyme synthesis during a starvation state?
When the level of glucagon increases, the synthesis of key enzymes involved in glucose synthesis are activated
167
This is used to treat high blood pressure as well as other heart conditions.
angiotensin converting enzyme inhibitors
168
This is an octapeptide hormone involved in BP regulation, it increases BP by narrowing blood vessels.
Angiotensin
169
What are examples of angiotensin?
lisinopril, enalapril and captopril.
170
This is a substance that kills bacteria or inhibits their growth
antibiotic
171
What are the two families of antibiotics?
(1) sulfa drugs
(2) Penicillin
172
These are derivatives of sulfanilamide which exhibit antibiotic activities
Sulfa drugs
173
Why are humans not affected of sulfa drugs?
Sulfa drugs don’t affect humans because we absorb folic acid from our diet
173
Where is sulfanilamide structurally?
PABA (p-aminobenzoic acid)
173
Why is sulfanilamide a competitive inhibitor?
Sulfanilamide is a competitive inhibitor of enzymes responsible for converting PABA to folic acid in bacteria
173
What is the coenzyme of PABA (p-aminobenzoic acid?
Folic acid
173
This retards bacterial growth and that eventually kills them
Folic acid deficiency
174
Who accidentally discovered penicillin?
Accidently discovered by Alexander Fleming in 1928
175
What structures do penicillin have?
All have structures containing a four-membered Beta-lactam ring fused with a five-membered thiazolidine ring
176
What does penicillin inhibit?
Selectively inhibits transpeptidase by covalent modification of serine residue
177
This catalyzes the formation of peptide cross links between polysaccharides strands in bacterial cell walls,
Transpeptidase
178
How does penicillin inhibit transpeptidase?
It weakens it and so it easily undergo lysis
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