ENZYMES Flashcards
all reactions in our body are mediated by
ENZYMES
are protein that catalyzes and increases reactions without being changed in the overall process
ENZYMES
among the many biological reactions that are energetically possible, enzyme selectively channel ____
REACTANTS which are referred to as SUBSTRATES
direct all metabolic events
ENZYMES
concluded that fermentation was catalyzed by a vital force contained within the yeast cells called “ferments”, which were thought to function only within living organisms.
LOUIS PASTEUR
according to him, alcoholic fermentation is an act correlated with the life and organization of yeast cells not with the death or putrefaction of the cell
LOUIS PASTEUR
GLUCOSE molecular formula
C6H12O6
an enzyme found on yeast that is capable of converting carbohydrates (glucose) into two molecules of ethyl alcohol and two molecules of carbon dioxide
ZYMASE
first used the term enzyme, which literally means “in yeast”
1878, GERMAN PHYSIOLOGIST
WILHELM KUHNE
the word enzyme literally means
“IN YEAST”
- began to study the ability of yeast extracts that lacked any living yeast cells to ferment sugar.
- He also found that the sugar was fermented even when there were no living yeast cells in the mixture.
- He named the enzyme that brought about the fermentation of sucrose as zymase
1897
EDUARD BUCHNER
when did Eduard Buchner received a nobel prize in biochemical research & his discovery of cell free fermentation
1907
Essential for breakdown of nutrients that are used to supply energy and chemical building blocks.
ENZYMES
TRUE OR FALSE
most enzymes are proteins
TRUE
one of the most important role of an enzyme
CATALYSIS
most enzymes are proteins except
RIBOZYMES
are nucleic acids but act as enzymes
RIBOZYMES
structurally, most of the enzymes are
GLOBULAR
considered as the most efficient catalyst known
ENZYMES
enzymes can speed the rate of reaction by a factor up to
10, 20
more than a thousand folds
non enzymatic catalyst typically enhance the rate of the reaction by factors of
10, 10
the substance wherein the enzymes act upon
SUBSTRATE
has a specific geometric shape wherein specific substrate would fit in
ACTIVE SITE
The basic function of an enzyme
INCREASE THE RATE OF A REACTION
Most enzymes act specifically with how many reactant (called a substrate) to produce products
ONLY ONE
enzymes are regulated from a state of what activities
low to high and vice versa
the minimum energy needed to start a chemical reaction
ACTIVATION ENERGY
WITH OR WITHOUT ENZYME
higher activation energy is needed
WITHOUT ENZYME
WITH OR WITHOUT ENZYME
lower activation energy is need
WITH ENZYME
Enzyme that is capable of hydrolyzing or breaking down lactose to form glucose & galactose
LACTASE
Most genetic disorders are due to a deficiency in
ENZYME FUNCTION
a hereditary disease that is caused by the lack of a liver enzyme phenylalanine hydroxylase.
PHENYLKETONURIA
pku
Phenylektonuria is caused by the lack of what enzyme
PHENYLALANINE HYDROXYLASE
if nawala si phenylalanine hydroxylase, what set of enzyme would take effect
TRANSAMINASE
transaminase will lead to the accumulation of a substance known as
PHENYLPYRUVIC ACID
an amino acid that is most commonly found in protein-containing foods such as meat, cow’s milk, over the counter infant formulas (both regular and soy) and breast milk.
PHENYLALANINE
ratio of the case of pku
1:150,000
- common disease, 1:150,000
- an inborn error of metabolism
- can be found in the recessive genes that are found on the both sides of the parents
- probability of getting is 1 in 4 (high, 25% chance)
PHENYLKETONURIA
CAN CAUSE
* mental retardation
* convulsions
* behavior problems
* skin rash
* musty body odor
BABIES ARE TESTED USING
* formula fed
* breast fed
* reaction is needed to be checked within 24 hours after taking milk
* to confirm, retest in 7-10 days
IF POSITIVE, DIET RESTRICTIONS ARE:
NO
* meat
* dairy products
* dry beans
* nuts
* eggs
PHENYLKETONURIA
in testing pku, reaction is needed to be checked within how many hours after taking the milk
24 hours
to ensure the test for pku, how many days should the baby be retested to catch earlier false negatives
7 - 10 days
long term effect of pku
irreversible brain damage & mental retardation
treatment of pku
elimination of phenylalanine from the diet
RA about newborn screening
RA 9288
Enzymes may require a non-peptide (non-protein) component as a
COFACTOR
The peptide component is called
APOENZYME
cofactor is called
COENZYME
combined functional unit of apoenzyme + coenzyme is called
HOLOENZYME
Cofactors that are tightly bound to the polypeptide are called
PROSTHETIC GROUPS
an enzyme has what structure
complex 3D structure
- Important part of an enzyme.
- The shape and the chemical environment inside this permits a chemical reaction to proceed more easily.
ACTIVE SITE
are the reactants that are activated by the enzyme.
SUBSTRATE
- May be inactive in its original synthesized structure;
- a protein that forms an active enzyme system by combination with a coenzyme and determines the specificity of this system for a substrate.
APOENZYME
inactive protein
APOENZYME
- nonprotein portion
- activates enzyme
- cofactor
- binds specifically to apoenzyme to complete the shape of the active site
COENZYME
- active protein
- capable of performing its job by catalysis
- product of apoenzyme + coenzyme
HOLOENZYME
- The inactive form of the apoenzyme
- May contain several extra amino acids in the protein which are removed, and allows the final specific tertiary structure to be formed before it is activated as an apoenzyme.
PROENZYME OR ZYMOGEN
proenzyme is also known as
ZYMOGEN
either one or more inorganic ions or metal ion activator
COFACTOR
complex organic or metalloorganic molecule
COENZYME
the site other than the active site
ALLOSTERIC SITE
- acts as transient carriers of specific functional groups
- Derived from vitamins, organic nutrients
COSUBSTRATE
- If a coenzyme or a cofactor is very tightly or even covalently bound to the enzyme protein
- Examples include derivatives of B vitamins: pyridoxal phosphate, FMN, FAD, thiamine pyrophosphate, biotin and METAL IONS of Co, Cu, Mg, Mn, and Zn.
PROSTHETIC GROUPS
FMN
Flavin mononucleotide
FAD
Flavin adenine dinucleotide
enzymes that contain tightly bound metal ions
METALLOENZYMES
common suffix for enzymes
-ase
hydrolyze proteins
PROTEASES
remove hydrogen atoms
DEHYDROGENASE
catalyze rearrangement in configuration
ISOMERASE
may be added to identify multiple forms of an enzyme
ALPHANUMERIC DESIGNATORS
NOMENCLATURE
MODIFIERS used to indicate
- substrate
- source
- regulation
- MOA (mechanism of action)
names that do not end with -ase
TRIVIAL NAMES
MAJOR CLASSES OF ENZYMES
6
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases
OTHILL
7th class of enzyme
TRANSLOCASES
- Catalyze a variety of oxidation-reduction reactions
- Common names include dehydrogenase, oxidase, reductase and catalase
OXIDOREDUCTASE
- Catalyze transfers of groups (acetyl, methyl, phosphate(kinases), etc.).
- The first three subclasses play major roles in the regulation of cellular processes.
- The polymerase is essential for the synthesis of DNA and RNA (polynucleotides)
TRANSFERASE
essential for the synthesis of DNA and RNA (polynucleotides)
POLYMERASE
- Catalyze hydrolysis reactions where a molecule is split into two or more smaller molecules by the addition of water
HYDROLASES
split protein molecules
PROTEASES
essential for HIV replication
HIV PROTEASE
plays a major role in apoptosis
CASPASE
splits nucleic acids (DNA & RNA)
NUCLEASES
Nucleases can be divided into
EXOnuclease
ENDOnuclease
progressively splits off single nucleotides from one end of DNA or RNA.
EXONUCLEASE
splits DNA or RNA at internal sites
ENDONUCLEASE
- catalyzes dephosphorylation (removal of phosphate groups).
- Example: calcineurin (aka protein phosphatase 3)
- Tacrolimus, Sirolimus, Everolimus and Cyclosporin A are the calcineurin inhibitors
PHOSPHATASE
- Catalyze the cleavage of C-C, C-O, C-S and C-N bonds by means other than hydrolysis or oxidation.
- Common names include decarboxylase and aldolase.
LYASES
- Catalyze atomic rearrangements within a molecule.
- Examples include rotamase, protein disulfide isomerase (PDI), epimerase and racemase
ISOMERASES
- Catalyze the reaction which joins two molecules
- Examples include peptide synthase, aminoacyl-tRNA synthetase, DNA ligase and RNA ligase
LIGASES
means that there is no net change in the concentrations of the reactants and products
REACTION EQUILIBRIA
Rate enhancements that enzymes bring about are in the range of ____ orders of magnitude (MO)
5 - 17
- Formation of transient (temporary) covalent bond with a substrate
- Transient transferring of chemical group from the substrate to the enzyme
- Usually happens in the active site
REARRANGEMENT OF COVALENT BONDS
Much of the energy required to lower activation energies is derived from ____ interactions between the enzyme and substrate mediated by the same forces that stabilize protein structure.
WEAK, NONCOVALENT
- the energy derived from enzyme-substrate interaction
- energy released that stabilizes the interaction
- major source of free energy used by enzymes to lower the activation energies of reactions
- contributes to specificity as well as to catalysis
BINDING ENERGY
- first postulated in 1894 by Emil Fischer;
- The lock is the enzyme and the key is the substrate;
- Only the correctly sized key (substrate) fits into the keyhole (active site) of the lock (enzyme).
LOCK AND KEY THEORY
Lock & key theory is first postulated by
EMIL FISCHER
- Enzymes were structurally complementary to their substrates - perfect fit
- May be misleading when applied to enzyme catalysis
- “An enzyme completely complementary to its substrate would be a very poor enzyme.”
LOCK & KEY HYPOTHESIS
An enzyme must be complementary to the
REACTION TRANSITION STATE
optimal interactions (weak interactions) between the enzyme and substrate occur only in the
TRANSITION STATE
- Postulated by Daniel Koshland
- It states that, when substrates approach and bind to an enzyme they induce a conformational change
- This change is analogous to placing a hand (substrate) into a glove (enzyme).
INDUCED FIT THEORY
Induced fit theory is postulated by
DANIEL KOSHLAND
In induced fit theory:
enzymes are
REUSABLE
In induced fit theory:
active site changes
SHAPE
This explains the enzymes that can react with a range of substrates of similar types.
INDUCED FIT THEORY
MECHANISMS TO FACILITATE CATALYSIS
- For molecules to react, they must come within bond-forming distance of one another
- The higher the concentration, the more frequently they will encounter one another and the greater will be their rate of interaction aka entropy reduction
CATALYSIS BY PROXIMITY
MECHANISMS TO FACILITATE CATALYSIS
- Refers to proton transfers mediated by other classes of molecules
- General or Specific
- The active sites of some enzymes contain amino acid functional groups that can participate in catalysis as proton donors or acceptors
ACID-BASE CATALYSIS
MECHANISMS TO FACILITATE CATALYSIS
Reaction between bound molecules doesn’t require an improbable collision of 2 molecules – they’re already in “contact” (increases the local concentration of reactants).
PROXIMITY
MECHANISMS TO FACILITATE CATALYSIS
Reactants are not only near each other on enzyme, they’re oriented in optimal position to react, so the improbability of colliding in correct orientation is taken care of.
ORIENTATION
MECHANISMS TO FACILITATE CATALYSIS
- Involves the formation of a transient covalent bond between the enzyme and one or more substrates
- Common among enzymes that catalyze group transfer reactions
COVALENT CATALYSIS
MECHANISMS TO FACILITATE CATALYSIS
- Ionic interactions between an enzyme-bound metal and a substrate can help orient the substrate for reaction or stabilize charged reaction states
- Metals can also mediate oxidation-reduction reaction by reversible changes in the metal ion oxidation state
METAL ION CATALYSIS
MECHANISMS TO FACILITATE CATALYSIS
- When substrate binds to enzyme, water is usually excluded from active site
- causes local dielectric constant to be lower, which enhances electrostatic interactions in the active site, and also
- results in protection of reactive groups from water, so water doesn’t react to form unwanted by-products.
DESOLVATION
MECHANISMS TO FACILITATE CATALYSIS
Involvement of charged enzyme functional groups in stabilizing otherwise unstable intermediates in the chemical mechanism can also correctly be called
ELECTROSTATIC CATALYSIS
MECHANISMS TO FACILITATE CATALYSIS
- Strain is created by binding to substrates in a conformation slightly unfavorable for the bond to undergo cleavage
- The strain stretches or distorts the targeted bond, weakening it and making it more vulnerable to cleavage
CATALYSIS BY STRAIN
MECHANISMS TO FACILITATE CATALYSIS
the most important rate enhancing mechanism available to enzymes
CATALYSIS BY STRAIN
MECHANISMS TO FACILITATE CATALYSIS
a more modern concept: it is not the substrate that is distorted but rather that the transition state makes better contacts with the enzyme than the substrate does, so the full binding energy is not achieved until the transition state is reached.
TRANSITION STATE STABILIZATION
MECHANISMS TO FACILITATE CATALYSIS
assumes that the active site of an enzyme is not complementary to that of the transition state in the absence of the substrate. Such enzymes will have a lower value of kcat/Km, because some of the binding energy must be used to support the conformational change in the enzyme. Induced fit increases Km without increasing kcat.
INDUCED FIT
The field of biochemistry concerned with the quantitative measurement of the rates of enzyme-catalyzed reactions and the systematic study of factors that affect these rates.
ENZYME KINETICS
Describes how reaction velocity varies with substrate concentration
MICHAELIS MENTEN EQUATION
k1, k-1, and k2
RATE CONSTANTS
Michaelis constant
(k-1 + k2) / k1
ASSUMPTIONS
[S] >[E], so [ES] at any time is small
RELATIVE CONCENTRATIONS OF E & S
ASSUMPTIONS
- [ES] does not change in time
- E + S = ES = E + P, the rate of formation of ES is equal to that of the breakdown of ES
STEADY STATE ASSUMPTION
ASSUMPTIONS
- Used in the analysis of enzyme reactions
- Rate of reaction is measured as soon as E and S are mixed
- [P] is very small, the rate of back reaction from P to S can be ignored
INITIAL VELOCITY
CHARACTERISTICS OF Km
reflects high affinity of the E for S because a low concentration of S is needed to half-saturate the enzyme – that is, reach a velocity that is 1⁄2 Vmax
small Km
CHARACTERISTICS OF Km
Reflects low affinity of E for S because a high concentration of S is needed to half-saturate the enzyme
Large Km
The rate of reaction is ____ to the enzyme concentration at all substrate concentrations
DIRECTLY PROPORTIONAL
ORDER OF REACTION
[S] < Km, the velocity of reaction is roughly proportional to the enzyme concentration
FIRST ORDER
ORDER OF REACTION
[S] > Km, the velocity is constant and equal to Vmax; the rate of reaction is then independent of substrate concentration
ZERO ORDER
- Also called a double-reciprocal plot
- If 1/v0 is plotted VS 1/[S], a straight line is obtained
- The intercept on the x-axis is equal to -1/Km
- The intercept on the y-axis is equal to 1/Vmax
- Can be used to calculate Km and Vmax as well as to determine the mechanism of enzyme inhibitors
LINEWEAVER-BURK PLOT
lineweaver-burk plot is also called
DOUBLE-RECIPROCAL PLOT
substance that can diminish the velocity of an enzyme catalyzed reaction
INHIBITOR
- tend to compete with the substrate to the active site
- Inhibitors tend to resemble the structures of a substrate, and thus are termed as substrate analogs
COMPETITIVE INHIBITION
competitive inhibitors are also termed as
SUBSTRATE ANALOGS
- Malonate ( ̄O−CO−CH2−COO ̄) competes with Succinate ( ̄OOC−CH2−CH2−COO ̄) for the active site of succinate dehydrogenase (SDH)
- SDH catalyze the removal of one H atom from each of the 2 methylene C’s of succinate
COMPETITIVE INHIBITION
CONSEQUENCES OF COMPETITIVE INHIBITION
At high levels of substrate all of the inhibitor is displaced by substrate.
Vmax is unchanged
CONSEQUENCES OF COMPETITIVE INHIBITION
Higher substrate concentrations are required to reach the maximal velocity.
Km is increased
NONCOMPETITIVE INHIBITION
At high levels of substrate the inhibitor is still bound.
Vmax is decreased
NONCOMPETITIVE INHIBITION
Noncompetitive inhibitors do not interfere the binding of substrate to enzyme
Km is not changed
FACTORS AFFECTING ENZYME REACTIONS
The rate of enzyme catalyzed reaction ____ with substrate concentration until a maximal velocity (Vmax) is reached
INCREASES
FACTORS AFFECTING ENZYME REACTIONS
The rate of enzyme-catalysed reactions increases as the temperature rises to the ____
OPTIMUM TEMPERATURE
FACTORS AFFECTING ENZYME REACTIONS
Above a certain temperature, activity begins to decline because the enzyme begins to ____
DENATURE
Enzymes are usually damaged above about what temperature
45C
example of enzyme that work best at a pH of about 2.0
GASTRIC PROTEASE
molecules that regulate allosteric enzymes that bind noncovalently at a site other than the active site
EFFECTORS
EFFECTORS
inhibit enzyme activity
NEGATIVE EFFECTORS
EFFECTORS
increases enzyme activity
POSITIVE EFFECTORS
- Substrate itself serves as an effector
- Most often a positive effector
- The presence of a substrate molecules at one site on the enzyme enhances the catalytic properties of the other substrate-binding sites ⎯ (their sites exhibit cooperativity)
HOMOTROPIC EFFECTORS
The effector may be different from the substrate
HETEROTROPIC EFFECTORS
A form that may be more or **less active **than the unphosphorylated enzyme
PHOSPHORYLATED FORM
(degrades glycogen)
Glycogen phosphorylase
(synthesize glycogen)
Glycogen synthase
Alter the total population of active sites rather than influencing the efficiency of existing enzyme molecules
INDUCTION & REPRESSION OF ENZYME SYNTHESIS
Enzymes that are needed at only one stage of development or under selected physiologic conditions are subject to
REGULATION OF SYNTHESIS
Enzymes that are in constant use are NOT regulated by
ALTERING THE RATE OF ENZYME SYNTHESIS
a common form of enzyme regulation in which the product inhibits the enzyme
FEEDBACK INHIBITION
enzymes are most active at what temperature
OPTIMUM TEMPERATURE
usually 37C in humans
enzymes show little activity at what temperature
LOW TEMPERATURES
enzymes lose activity at what temperature as denaturation occurs
HIGH TEMPERATURES
what is disrupted in the structure of enzymes at high or low pH
TERTIARY STRUCTURE
- HMG Coenzyme A reductase inhibitors
- lower serum lipid concentration
STATINS
- inhibitors of viral reverse transcriptase
- block replication of HIV
EMTRICITABINE and TENOFOVIR DISOPROXIL FUMARATE
antihypertensive agents
ACE inhibitors
inhibitors of alanyl alanine carboxypeptidase-transpeptidase, thus blocking cell wall synthesis
Lactam Antibiotics (Penicillin and Amoxicillin)
may indicate tissue damage accompanied by increased release of intracellular enzymes, thus useful as a diagnostic tool
ELEVATED ENZYME ACTIVITY
aminotransferase is also called
GLUTAMATE
- Enzymes that catalyze the same reaction but differ in their physical properties because of genetically determined differences in amino acid sequence
- Different organs frequently contain characteristic proportions of different isoenzymes
ISOENZYMES
isoenzymes are also called
ISOZYMES
present in more than 5% in myocardial muscles
CK2 (MB)
Creatine kinase is also called
CREATININE PHOSPHOKINASE (CPK)
each isoenzyme is a ____ composed of 2 polypeptides
DIMER
- Appears approximately 4 to 8 hours following onset of chest pain, and reaches a peak in activity at approximately 24 hours
CK, CREATININE KINASE
- Elevated following an infarction peaking 3 to 6 days after the onset of symptoms
- Of diagnostic value in patients admitted more than 48 hours after the infarction
LACTATE DEHYDROGENASE
ENZYME INDUCER
Phenobarbital
Rifampicin
Carbamazepine
Phenytoin
Griseofulvin
Smoking
Chronic addiction
REMEMBER: PRC
ENZYME INHIBITOR
Cimetidine
Ketoconazole
Fluconazole
Miconazole
