Enzymology Flashcards
The molecules that enzymes act upon
Substrate
Enzymes convert substrates into
Products
______ depend upon enzymes to catalyze individual steps
Metabolic Pathways
Almost all enzymes are
Proteins
Enzymes follow the physical and chemical reactions of proteins. Notable exceptions include
Ribosomal RNAs and a handful of RNA molecules (Ribozymes)
Enzymes are
Heat-labile and Water-soluble
Enzymes can be precipitated by
Protein Precipitating Reagent
Enzymes contain how much percent of nitrogen?
16%
Enzymes that uses its first description in the earliest days of Biochemistry
Pepsin, Trypsin, Amylase
Enzymes that remove hydrogen atoms
Dehydrogenases
Enzymes that hydrolyze proteins
Proteases
Enzymes that catalyze the rearrangements in configuration
Isomerases
6 classes of enzymes according to IUBMB
Oxidoreductases, Transferases, Isomerases, Hydrolases, Lyases, Ligases
Classification of enzyme that transfers hydrogen or adds oxygen
Oxidoreductases
Oxidoreductases catalyze oxidation of one substrate while
Simultaneously reduces another substrate or Co-enzyme
Examples of oxidoreductases
Lactate dehydrogenase, Glucose-6-phosphate dehydrogenase, Succinate dehydrogenase
Classification of enzyme that transfers groups other than hydrogen
Transferases
Examples of transferases
Hexokinase, Aminotransferases
This type of enzymes can hydrolyze ester, ether, peptide, or glycosidic bonds by adding water and then breaking the bond
Hydrolases
Examples of Hydrolases
Amylase, Maltase, Lactase, Lipase, Sucrose, Proteases, Acetyl Choline Esterase, Trypsin
All digestive enzymes are
Hydrolases
Classification of enzymes that cleaves without adding water
Lyases
These enzymes can remove groups from substrates or break bonds by mechanisms other than hydrolases
Lyases
Examples of lyases
Aldolase, HMG CoA lyase, ATP citrate lyase
Compound with same number of atoms rearranged
Isomers
Intramolecular transfers
Isomerases
The enzymes can produce optical, geometric or positional isomers of substrates
Isomerases
Examples of isomerases
Racemases, Epimerases, cis-trans isomerases
Classification of ATP dependent condensation of molecules
Ligases
These enzymes link 2 substrates together, usually with the simultaneous hydrolysis of ATP
Ligases
Meaning of the latin word Ligare
To bind
Examples of ligases
Acetyl CoA Carboxylase, Glutamine synthetase, PRPP synthetase
These types of enzymes are ATP-dependent which belong to ligases
Synthetase
Examples of Synthetase
Carbamoyl phosphate synthetase, Arginine succinate synthetase, PRPP Synthetase, Glutamine synthetase
Enzyme that do not require ATP directly
Synthase
Enzymes that belong to other classes other than ligase
Synthase
Examples of synthase
Glycogen synthase, ALA synthase
The deficient enzyme in Phenylketonuria
Phenylalanine hydroxylase
Phenylalanine is converted into _______ without phenylalanine hydroxylases, this accumulates that results to metabolic derangement
Tyrosine
Lactose is not digested at a normal rate and accumulates in the gut where it is metabolized by bacteria
Lactase deficiency
Emphysema results from an inherited deficiency of _____ an enzyme that inhibits elastase action in the lungs
a1-antitrypsin
____ is a serine protease found in neutrophils that utilize the enzyme to destroy inhaled organisms in the air
Elastase
At times, elastase may escape from the _____ and then the protease beings to destroy the lung cells
Neutrophil
The circulating ______ blocks the action of elastases and protects the lung from damage
protein cx1-antitrypsin
Cigarette smoke contains ____that will destroy a key ____ residue in a1-antitrypsin and destroy a1-antitrypsin activity
oxidizing agents, methionine
Complex enzymes contain a non-protein part called the
Prosthetic group
The prosthetic group is also called the
Co-enzyme
The co-enzyme is
heat stable
The apoenzyme is
heat-labile
The protein part of the enzyme is called the
Apozyme
The apoenzyme and co-factor combined together is called the
Holo-enzyme
This is essential for the biological activity of the enzyme
Co-enzyme
Co-enzyme is a ______ organic substance
low molecular weight
Generally, co-enzymes combine loosely with the
Enzyme molecule
The enzyme and co-enzyme can easily be separated by
Dialysis
Inside the body, when the reaction is completed, the co-enzyme is ________ from the apo-enzyme and can bind to another enzyme molecule
Released
One molecule of the co-enzyme is able to convert a large number of
Substrate molecules
Most of the co-enzymes are derivatives of
Vitamin B complex group of substances
2 groups of co-enzymes
(1) 1st group - donates and accepts Hydrogen atoms/electrons, (2) 2nd group - transfers groups other than Hydrogen
Group of co-enzymes that take part in reactions catalyzed by oxidoreductases by donating or accepting H atoms/electrons
First group
In the first group of co-enzymes, the change occurring in the substrate is ______ by the co-enzymes
counter-balanced
Where counter balancing by co-enzyme occurs it can be considered as
Co-substrates or secondary substrates
Examples of 1st group co-enzymes
NADP-NADPH; FAD-FADH2, FMN-FMNH2
These group of co-enzymes take part in reactions transferring groups other than hydrogen
2nd group of co-enzymes
In 2nd group of co-enzymes, a particular group or radical is ______ from the substrate to another substrate
transferred
(2nd group of co-enzyme) what group is transferred in the co enzyme thiamine pyrophosphate (TPP)?
hydroxy ethyl
(2nd group of co-enzyme) what group is transferred in the co enzyme pyridoxal phosphate (PLP)
amino group
(2nd group of co-enzyme) what group is transferred in the co enzyme biotin?
carbon dioxide
(2nd group of co-enzyme) what group is transferred in the co enzyme coenzyme-A (Co-A)
acyl groups
(2nd group of co-enzyme) what group is transferred in the co enzyme tetra hydrofolate (Fh4)
one carbon group
(2nd group of co-enzyme) what group is transferred in the co enzyme adenosine triphosphate (ATP)
phosphate
Considered as the energy currency in the body
ATP
in the ATP molecule, the ___ and ___ bonds are ‘high energy’ bonds
2nd; 3rd
During oxidation of food stuff, energy is released, a part of which is stored as ________ in the form ATP
chemical energy
These are enzymes which require certain metal ions for their activity
metallo-enzymes
What metal is contained in carbonic anhydrase, carboxy peptidase, alcohol dehydrogenase?
zinc
What metal is contained in hexokinase, phospho fructo kinase, enolase, glucose-6-phosphatase?
magnesium
What metal is contained in phospho gluco mutase, hexokinase, enolase, glycosyl transferases?
manganese
What metal is contained in tyrosinase, cytochrome oxidase, lysyl oxidase, superoxide dismutase?
copper
What metal is contained in cytochrome oxidase, catalase, peroxidase, xanthine oxidase?
iron
What metal is contained in lecithinase and lipase?
calcium
What metal is contained in xanthine oxidase?
molybdenum
Metal presence in enzymes can _____ activity
enhance
What do you call the enzymes that have enhanced activity when metal ions are added?
ion-activated enzymes
What are the mode of actions of enzymes?
lowering of activation energy, acid base catalysis, substrate strain, serine proteases, covalent catalysis, entropy effect
Enzymes lowers the
energy of activation
This is defined as the energy required to convert all molecules of a reacting substance from the ground state to the transition state
activation energy
Many acid-base catalysis reactions involve
histidine
why is histidine usually involved in acid-base catalysis?
because it’s pH is close to 7
Having a pH of almost 7 allow for
acting as both acid and base
this helps histidine in acting as either an acid or base
ribonuclease
Binding of a substrate to a performed site on the enzyme can induce ____ in the substrate
strain
in the presence of substrate strain, the energy level of the substrate is
raised
A combination of substrate strain and acid base catalysis is seen in the action of
lysozome
enzymes that cleave peptide bonds in proteins
serine proteases
examples of serine proteases
chymotrypsin, trypsin, clotting factors
in this mode of action, this involves the substrate forming a transient covalent bond with residues in the enzyme active site or with a cofactor.
covalent catalysis
An additional covalent intermediate to the reaction in covalent catalysis helps to _____ the energy of later transition states of the reaction
reduce
in this mode of action, enzymes enhance reaction rates by decreasing entropy
entropy effect
In entropy effect, this reduces disorder by ______ substrates for reaction
orienting
a product substrate orientation theory that is also the enzyme-substrate complex theory
michaelis-menten theory
in michaelis-menten theory, the enzyme and substrate combine to form the
enzyme-substrate (ES) complex
in michaelis-menten theory, the ES complex breaks down to enzyme and
product
This theory states that the 3D of the active site of the enzyme is complementary to the substrate. Thus, substrate and enzyme fit together, similar to a lock and key.
fisher’s template theory
the fisher’s template theory cannot explain
the flexibility shown by enzymes
this theory states that conformational changes are occurring at the active site of enzymes concomitant with the combination of enzyme with the substrate
koshland’s induced fit theory
this is the region of an enzyme where substrate molecules bind and undergo a chemical reaction
active site
the active site consists of amino acids residues that form ___ with the substrate (binding site) and residues (catalytic site) that catalyze a reaction of that substrate
temporary bonds
catalytic triad of amino acids in the catalytic site
his (57), asp (102), ser (195)
important amino acid at the catalytic site of chymotrypsin
his (57), asp (102), ser (195)
important amino acid at the catalytic site of trypsin
ser, his
important amino acid at the catalytic site of thrombin
ser, his
important amino acid at the catalytic site of phosphoglucomutase
ser
important amino acid at the catalytic site of alkaline phosphatase
ser
important amino acid at the catalytic site of acetyl cholinesterase
ser
important amino acid at the catalytic site of carbonic anhydrase
cysteine
important amino acid at the catalytic site of hexokinase
his
important amino acid at the catalytic site of carboxy peptidase
his, arginine, tyr
from the standpoint of energy, the enzymatic reactions are divided into 3 types:
exothermic/exergonic, isothermic, endothermic/endergonic
important amino acid at the catalytic site of aldolase
lysine
here energy is released from the reaction, and therefore reaction essentially goes to completion
evergonic/exothermic
examples of exergonic
urease enzyme
at equilibrium of exergonic reactions the substrate will be at ___ and the product will be at ___
0.5%; 99.5%
reactions for this type are generally invisible
exergonic
type of reaction where energy exchange is negligible and the reaction is easily reversible
isothermic
type of reaction where energy is consumed and external energy is to be supplied for these reactions
endergonic
in the body, this is usually accomplished by coupling the endergonic reaction with an exergonic reaction
endergonic
factors influencing enzyme activity
enzyme concentration, effect of substrate concentration, effect of concentration of products, effect of temperature, effect of hydrogen ion concentration (pH), presence of activators, presence of inhibitors, feedback inhibition and repression, stabilization and compartmentalization
rate of a reaction or velocity is directly proportional to the enzyme concentration , when sufficient substrate is present
enzyme concentration
as substrate concentration is increased, the velocity is also correspondingly increased in the initial phases, but the curve flattens afterwards
effect of substrate concentration
this represents the maximum reaction rate attainable in presence of excess substrate
Vmax
this is the concentration of substrate which permits the enzyme to achieve half Vmax
Km (Michaelis constant)
this is also the signature of the enzyme
Km
this value is a constant for an enzyme
Km value
It is the characteristic feature of a particular enzyme for a specific substrate
Km value
Type of factor where in a reversible reaction, S ↔ P, when equilibrium is reached, as per the law of mass action, the
reaction rate is slowed down. So, when product concentration is increased, the reaction is
slowed, stopped or even reversed.
Effect of Concentration of Products
In effect of concentration of products, in inborn errors of metabolism, one enzyme of a metabolic pathway is
blocked
Type of factor where the velocity of enzyme reaction increases when
temperature of the medium is increased; reaches
a maximum and then falls (Bell shaped curve).
Effect of Temperature
The temperature at which maximum amount of
the substrate is converted to the product per unit
time is called the
optimum temperature
Most human enzymes have the optimum
temperature around
37°C
Factor where each enzyme has an optimum pH, on both sides of which the velocity will be drastically reduced.
Effect of Hydrogen ion concentration (pH)
Optimum pH may vary depending on the
temperature, concentration of substrate, presence
of ions etc. Usually, enzymes have the optimum
pH _______. Some important exceptions
are ______
between 6 and 8, pepsin (with optimum pH 1-2); alkaline
phosphatase (optimum pH 9-10) and acid
phosphatase (4-5)
Factor where in presence of certain inorganic ions, some enzymes show higher activity. Thus, chloride ions
activate salivary amylase and calcium activate lipases.
Presence of Activators
Another type of activation is the ______ of an inactive pro-enzyme or zymogen to the active
enzyme.
conversion
BY splitting a single peptide bond, and removal of a small polypeptide from trypsinogen, the _______ is formed
active trypsin
types of inhibition
competitive, non-competitive, uncompetitive inhibition, allosteric regulation
Here inhibitor molecules are competing with the normal substrate molecules for binding to the active site of the enzyme
competitive inhibition
In competitive inhibition, the inhibitor is a ______ of the substrate
structural analog
type of inhibition which is usually reversible
competitive inhibition
In competitive inhibition, the excess substrate _____ the inhibition
abolishes
In competitive inhibition, _____ is increased in presence of competitive inhibitor but Vmax is not changed
Km
E + S -><- E-S ——-> E + P
Competitive inhibition
Example of medication that exhibits competitive inhibition
metotrexate
type of inhibition that is usually irreversible
non-competitive inhibition
poisons such as ____, ____, & _____ act as irreversible non-competitive inhibitors
lead, cyanide, mercury
In non-competitive inhibition, substrates can bind but the reaction is
blocked
The Vmax is reduced but the ___ is not
Km value
type of inhibition that does not have any affinity for free enzyme
uncompetitive inhibition
this may be reversible or irreversible
in uncompetitive inhibition, inhibitors bind to the ____ but not the free enzyme
enzyme-substrate complex
in uncompetitive inhibition, both Vmax and Km are
decreased
Example of uncompetitive inhibition
finasteride in benign prostatic hyperplasia
______ has one catalytic site where the substrate binds and another separate allosteric site where the modifier binds
allosteric enzyme
in allosteric regulation, the binding of the regulatory molecule enhances the activity of the enzyme, this is known as
allosteric activation
in allosteric activation, the regulatory molecule is known as the
positive modifier
in allosteric regulation, the binding of the regulatory molecule inhibits the activity of the enzyme, this is known as
allosteric inhibition
in allosteric inihibition, the regulatory molecule is known as the
negative modifier
what does the body use allosteric enzymes for?
regulating metabolic pathways
the regulatory enzyme in a particular pathway is called the
key enzyme/rate limiting enzyme
The allosteric inhibitor is most effective when substrate concentration is
low
in allosteric regulation, when more substrate molecules are available, there is less necessity for
stringent regulation
in heme biosynthesis what is the end product?
heme
heme will allosterically inhibit the
ALA synthase
this is the key enzyme in heme synthesis
ALA synthase
another factor influencing enzyme activity, where for its mechanism, the accumulated end products binds with the enzyme and inhibits the enzyme activity
feedback inhibition
another factor influencing enzyme activity, where for its mechanism, the accumulated end products works as a repressor and inhibits the enzyme synthesis at a genetic level
feedback repression
in feedback inhibition, end products binds with the ____
active site of the enzyme
in feedback repression, end products binds with the _____ that encode the enzyme and prevent its synthesis
DNA of the gene
in this factor influencing enzyme activity, the enzyme molecules undergo usual wear and tear and finally get degraded. such degradation if prevented can lead to increased overall enzyme activity
stabilization of enzyme
degradation of tryptophan pyrrolase is retarded by
tryptophan
what stabilizes phospho fructo kinase
growth hormone
SH groups
papain, urease, succinate dehydrogenase
what stabilizes enzymes with SH groups?
glutathione
this is used to inhibit the enzyme thymidylate synthase
5-fluorouracil (5-FU)
this factor influencing enzyme activity is exhibited by certain enzyme pathways being located in mitochondria whereas others of the same pathway cytoplasmic
compartmentalization
this enzyme converts deoxyuridine monophosphate (dUMP) to deoxy-thymidine monophosphate (dTMP) which provides the thymine for DNA synthesis
thymidylate synthetase
this drug irreversibly inhibits the enzyme cyclooxygenase and interferes with the generation of prostaglandins and thromboxanes
aspirin
this is the secondary mediator of pain signaling
thromboxane
this drug is a suicide inhibitor of xanthine oxidase and is used in the treatment of gout
allopurinol
xanthine oxidase will recognize allopurinol as a substrate and oxidize it to create _____, which binds so tightly to the active site that it is not released and then inhibits further reactions by the enzyme
oxypurinol
this is a drug that is used to treat alcoholism irreversibly inhibits the enzyme aldehyde dehydrogenase leading to an accumulation of acetaldehyde whenever alcohol is ingested
disulfiram
acetaldehyde leads to ____ and may deter the patient from drinking alcohol
hangover symptoms
