Module 04: Enzymes (Stoker) Flashcards
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
Globular Proteins (Enzymes)
These are exceptions and ribonucleic acids with catalytic activity.
Ribozymes
Enzymes are not consumed in the reactions; they are ______________.
Regenerated
What is the effect of enzymes on equilibrium constant (Keq) along with retention factor (Rf) and Rb values?
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
What are the general characteristics of enzymes?
(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.
What are the two (2) types of enzymes?
(1) Simple Enzymes
(2) Conjugated Enzymes
These are composed only of protein (amino acid chains).
Simple Enzyme
These types of enzymes has a non-protein part in addition to a protein part.
Conjugated Enzyme
This is the protein part of a conjugated enzyme (inactive).
Apoprotein
This is a nonprotein part of a conjugated enzyme.
Cofactor
These are constituted of an apoenzyme and co-factor. And is known to be the biochemically active conjugated enzyme
Holoenzyme (cofactor)
This is important for the chemically inactive enzymes and are small organic molecules or Inorganic ions
Cofactors
Cofactors are also known as ___________ or __________.
Coenzymes or substrates
Coenzymes/cosubstrates are derived from “__________.”
dietary vitamins
What are the typical metal ion cofactors?
Zn2+, Mg2+, Mn2+, and Fe2
What are the typical non metallic ion cofactors?
Cl-
Inorganic ion cofactors derived from “___________.”
dietary minerals
The nomenclature of an enzyme is based on what factors?
(1) Type of reaction catalyzed
(2) Identity of the substrate
This is the is the reactant in an enzyme-catalyzed reaction. This is the substance upon which the enzyme “acts.”
Substrate
What are the three important factors of the naming process?
(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
What are the six major classes (classification) of enzymes?
(1) Oxidoreductase
(2) Transferase
(3) Hydrolase
(4) Lyase
(5) Isomerase
(6) Ligase
What type of reaction does Oxidoreductase catalyze?
Oxidation-reduction
What type of reaction does Transferase catalyze?
Functional group transfer reactions
What type of reaction does Hydrolase catalyze?
Hydrolysis reaction
What type of reaction does Lyase catalyze?
Reactions involving the addition to a double bond or removal of groups forming a double bond
What type of reaction does Isomerase catalyze?
Isomerization reactions
What type of reaction does Ligase catalyze?
Reactions involving bond formation coupled with ATP hydrolysis
This is an enzyme catalyzes an redox reaction:
Oxidoreductase
What does Oxidoreductase require?
coenzyme that is either oxidized or reduced, e.g. NAD+, FAD, FMN
This pertains to the decrease in valence along with the gain of H or loss of O. This is undergone by oxidizing agent.
Reduction
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
This undergoes reduction, gain of e- or gain of H
Oxidizing Agent
This undergoes oxidation, loses e-/donor of H
Reducing Agent
This is an enzyme that catalyzes the transfer of a functional group from one molecule to another
transferase
These catalyze transfer of an amino group to a substrate, catalyze transamination reaction
Transaminases
This catalyze transfer of a phosphate group from adenosine triphosphate (ATP) to a substrate
Kinase
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
This is an enzyme that catalyzes a hydrolysis reaction
hydrolase
What does hydrolase involve?
The reaction involves addition of a water molecule to a bond to cause bond breakage
What are the three integral hydrolysis reactions in the process of digestion?
(1) Carbohydrase
(2) Proteases
(3) Lipases
These hydrolyze glyosidic bonds in oligo- and polysaccharides
Carbohydrase
These effect the breaking of peptide linkages in proteins,
Proteases
These effect the breaking of ester linkages in triacyclglycerols (TAGs) or fats.
Lipases
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
This effects the removal of the components of water forming a double bond
Dehydratase
These effects the addition of the components of water to a double bonds
Hydratase
These catalyze synthesis (joining of molecules) without use of ATP
Synthase
This is an enzyme that catalyzes the isomerization (rearrangement of atoms) reactions.
Isomerase
What does an isomerase involve?
Interconversion between D and L amino acid, between an aldose and a ketose or internal rearrangement.
This is an enzyme that catalyzes the joining of two molecules involving ATP hydrolysis as a source of energy
Ligase
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.)
This is the relatively small part of an enzyme’s structure that is actually involved in catalysis:
Active Site
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
True or false: Some enzymes have more than one active site.
True
What is the formula for the Enzyme Substrate Complex?
S + E ————–> <—————–ES ——–> P + E
How do enzymes increase the rate?
Enzymes increase the rate by providing alternate route with lower energy of activation.
This is the intermediate reaction species formed when substrate binds with the active site
Enzyme Substrate Complex
What are the two models for Substrate Binding to Enzyme?
(1) Lock-and-Key Model
(2) Induced Fit Model
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
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
What are the Forces That Determine Substrate Binding (non covalent interactions?
(1) H-bonding
(2) Hydrophobic interactions
(3) Electrostatic interactions
What kind of specificity does the Lock & key model explain?
absolute specificity
What kind of specificity does the Induced fit model explain?
broad specificity
This is the ability to discriminate between 2 competing substrate
Enzyme Specificity
This acts on only one substrate. In this, an enzyme will catalyze a particular reaction for only one substrate
Absolute Specificity
This is most restrictive of all specificities (not common)
Absolute Specificity
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
In stereochemical specificity, this is inherent in an active site.
Chirality
This acts on structurally similar compounds that have the same functional groups.
Group Specificity or broad
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
This is considered most general of enzyme specificities
Linkage Specificity
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.
This is the temperature at which the rate of enzyme catalyzed reaction is maximum
Optimum temperature
Optimum temperature for human enzymes is ______________.
37ºC (body temperature)
Increased temperature (high fever) leads to: “_________”
decreased enzyme activity
Drastic changes in pH can result in “_________________”
denaturation of proteins
pH at which enzyme has maximum activity
Optimum ph
At which pH range do enzymes have maximum activity
pH range of 7.0 - 7.5
What is the optimum pH of pepsin?
2.0
What is the optimum pH of trypsin?
8.0
In this, Enzymes are not consumed in the reactions they catalyze
Enzyme Concentration
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.
What happens to the substrate concentration at constant enzyme concentration?
At a constant enzyme concentration, the enzyme activity increases with increased substrate concentration
This is the concentration at which it reaches its maximum rate and all of the active sites are full
Substrate saturation
This is the number of substrate molecules converted to product per second per enzyme molecule under conditions of optimum temperature and pH
Turnover Number
This is the rate equation that relates the velocity of the reaction to substrate concentration
Michaelis-Menten Equation
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.
This represents the maximum reaction velocity.
Vmax
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.
What happens at 1/2 Vmax?
At 1/2Vmax, the substrate concentration is equal to Km, the enzyme is half saturated
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
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
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.
If Vo is set equal to 1/2 Vmax, then ______________
Km = [S]. Km is equal to Substrate concentration at ½ Vmax.
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
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)
What is the reciprocal for the Michaelis-Menten equation?
Lineweaver Burk Plot
The Lineweaver Burk Plot is a ____________________.
Double reciprocal plot
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
This is an enzyme that has an additional site called regulatory site or allosteric site for the binding of a regulatory molecule.
allosteric enzyme
This is a simple enzyme that has only an active site for the binding of its substrate.
non-allosteric enzyme
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
The plot of allosteric enzymes contain multiple subunits; thus they do not follow the Michaelis- Menten kinetics, which results to them being ________________.
sigmoidal
Allosteric enzymes display this kind of binding
Displays cooperative effect – binding of S to one subunit facilitates the binding of the other substrates.
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
How do inhibitors inhibit?
It acts directly on an enzyme to lower its catalytic rate or stop it.
What are the two types of inhibition?
(1) Irreversible Inhibition
(2) Reversible Inhibition
a) Competitive
b) Uncompetitive
c) Mixed/Noncompetitive
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.
This inactivates enzymes by forming a strong covalent bond with the enzyme’s active site.
Irreversible Enzyme Inhibitor
This is used as an organophosphorus insecticide.
diisopropylfluorophosphate
What does the diisopropylfluorophosphate (DIFP) inhibit?
acetyl choline esterase
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
What enzyme does aspirin inhibit?
cyclooxygenase
What kind of synthesis does aspirin inhibit?
prostaglandin and thromboxane synthesis
This is an irreversible inhibitor that inhibits transpeptidase?
penicillin
This is the enzyme involved in bacterial cell wall synthesis
transpeptidase
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
What is the inhibitor in Reversible Competitive Inhibition?
structural analog of the normal substrate
In what kind of interactions does the enzyme inhibitor form?
weak interactions (hydrogen bonds, etc.).
How is Competitive inhibition reduced?
Competitive inhibition can be reduced by simply increasing the concentration of the substrate
What is the kinetic effect of competitive inhibition?
Vmax is unchanged and Km is increased (affinity decreased)
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.
This is the inhibitor of succinate dehydrogenase.
Malonate
This is the normal substrate found in the Krebs Cycle.
Succinate
These are competitive inhibitors of 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase
Statins
How do statins inhibit 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase?
limiting enzyme in cholesterol biosynthesis
What are the competitive inhibitors of cyclooxygenase?
Ibuprofen, acetaminophen, naproxen
This is an antidote for ethylene glycol or methyl alcohol poisoning. Competes for binding to alcohol dehydrogenase.
Ethanol
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
What happens during reversible noncompetitive inhibition?
Causes a change in the structure of the enzyme and prevents enzyme activity.
Can reversible noncompetitive inhibition be reduced?
No, increasing the concentration of substrate does not completely overcome inhibition.
What is the kinetic effect of the noncompetitive inhibition?
Vmax is decreased and Km is unchanged but s can still bind with the enzyme
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:
what are examples of noncompetitive inhibitors?
Heavy metals mercury and silver
This is a non-competitive inhibitor of cytochrome oxidase of the ETC/ Respiratory Chain. It binds to its allosteric site.
Cyanide
What does arsenate inhibit?
glyceraldehyde phosphate dehydrogenase
In this, the inhibitor binds at a site other than the active site and, binds only to the ES complex.
Uncompetitive Inhibition
What is the kinetic effect of Uncompetitive Inhibition?
Both Km and Vmax are decreased.
This is a rarer phenomenon in uncompetitive inhibition
Uncompetitive inhibition of single-substrate enzyme-catalyzed reactions is a rare phenomenon,
What does hydrazine inhibit?
aryl sulphatase
What does phenylalanine inhibit?
intestinal alkaline phosphatase
What are the general mechanisms involved in regulation? (APCOFEEN)
Allosteric regulation
Proteolytic enzymes and zymogens
covalent modification of enzymes
Feedback control regulation
Enzyme concentration
What kind of structures do allosteric enzymes have?
All allosteric enzymes have quaternary structure (Composed of two or more protein chains/ subunits)
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
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
These regulators increase are enzyme activity
Activators
These regulators decrease are enzyme activity
Inhibitor
This is the binding of an allosteric modulator that changes activity of the active site.
Allosteric Modification
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
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
In this form of inhibition, the product of the reaction inhibits its own formation by inhibiting an early enzyme in the pathway.
Feedback Inhibition
Feedback Inhibition is also known as “_________”
End product Inhibition
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
They hydrolyze peptide bonds in proteins and are generated in an inactive form then converted to their active form.
proteolytic enzymes
What are examples of proteolytic enzymes?
digestive and clotting enzymes
These are called inactive forms.
zymogens
The zymogens are activated by _______
proteolytic cleavage
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
This is the most common form of covalent modification and is often derived from an ATP molecule
Phosphate group
This pertains to the addition of a phosphate group
phosphorylation
What catalyzes phosphorylation?
Kinase
This pertains to the removal of a phosphate group
dephosphorylation
What catalyzes phosphorylation?
phosphatase enzyme
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.
This is the is the major regulatory enzyme in glycogen breakdown (glycogenolysis).
Glycogen phosphorylase
Glycogen phosphorylase is activated by what
activated by phosphorylation
This is the major regulatory enzyme in the synthesis of glycogen from glucose. This is inhibited Phosphorylation.
Glycogen synthase
What activates Glycogen synthase?
activated by dephosphorylation
In the regulation of glycogen synthesis and degradation to maintain glucose levels, this is where the glycogen synthesis is activated
Well fed state
In the regulation of glycogen synthesis and degradation to maintain glucose levels, this is where the glycogen degradation is accelerated
Fasting
In the skeletal system, degradation is activated during
exercise
In the skeletal system, glycogen accumulation is activated during
rest
How are glycogen synthase and phosphorylase regulated?
allosterically and hormonally regulated
This regulatory enzyme in glycogen synthesis is activated by dephosphorylation
Glycogen synthetase
This regulatory enzyme in glycogen breakdown is activated by phosphorylation
Glycogen phosphorylase
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
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
This is used to treat high blood pressure as well as other heart conditions.
angiotensin converting enzyme inhibitors
This is an octapeptide hormone involved in BP regulation, it increases BP by narrowing blood vessels.
Angiotensin
What are examples of angiotensin?
lisinopril, enalapril and captopril.
This is a substance that kills bacteria or inhibits their growth
antibiotic
What are the two families of antibiotics?
(1) sulfa drugs
(2) Penicillin
These are derivatives of sulfanilamide which exhibit antibiotic activities
Sulfa drugs
Why are humans not affected of sulfa drugs?
Sulfa drugs don’t affect humans because we absorb folic acid from our diet
Where is sulfanilamide structurally?
PABA (p-aminobenzoic acid)
Why is sulfanilamide a competitive inhibitor?
Sulfanilamide is a competitive inhibitor of enzymes responsible for converting PABA to folic acid in bacteria
What is the coenzyme of PABA (p-aminobenzoic acid?
Folic acid
This retards bacterial growth and that eventually kills them
Folic acid deficiency
Who accidentally discovered penicillin?
Accidently discovered by Alexander Fleming in 1928
What structures do penicillin have?
All have structures containing a four-membered Beta-lactam ring fused with a five-membered thiazolidine ring
What does penicillin inhibit?
Selectively inhibits transpeptidase by covalent modification of serine residue
This catalyzes the formation of peptide cross links between polysaccharides strands in bacterial cell walls,
Transpeptidase
How does penicillin inhibit transpeptidase?
It weakens it and so it easily undergo lysis
