Enzymes Flashcards
Enzymes Properties
- Almost all enzymes are proteins.
- They are heat labile.
- They are water-soluble.
- They can be precipitated
- They contain 16% weight as nitrogen
Almost all enzymes are proteins exception
ribozymes
few RNA molecules with enzymatic activity
ribozymes
enzymes are classified as
specialized proteins
They contain 16% weight as nitrogen because enzymes are made up of many
amino acids
Two general structural classes
Simple enzymes
Conjugated enzymes:
only of protein (amino acid chains)
Simple enzymes
nonprotein part + protein part
Conjugated enzymes
Parts of an enzyme molecule
Non-protein part
Protein part
Holoenzyme
Non-protein part
prosthetic group, cofactor or coenzyme
Protein part
apoenzyme
complete structure of apoenzyme and prosthetic group.
Holoenzyme:
enzymes that contain tightly bound metal ions are termed
metalloenzymes.
Prosthetic group examples
pyridoxal phosphate,
flavin mononucleotide (FMN),
flavin adenine dinucleotide (FAD),
thiamin pyrophosphate,
biotin,
tight, stable incorporation into a protein’s structure
Prosthetic group
bind in a transient, dissociable manner either to the enzyme or to a substrate such as ATP.
must be present/available in the medium surrounding the enzyme for catalysis to occur.
Cofactors
Enzymes that require a metal ion cofactor are termed
metal-activated enzymes
The most common cofactors also are
metal ions.
serve as substrate shuttles
Coenzymes
Coenzymes example
Dehydrogenases -Nicotinamide adenine dinucleotide
Specificity
- Absolute Specificity.
- Stereochemical Specificity.
- Group Specificity.
- Linkage Specificity
enzyme will catalyze (or speed up) a particular reaction for only one substrate.
- Absolute Specificity.
enzyme can distinguish between stereoisomers.
Stereochemical Specificity.
involves structurally similar compounds that have the same functional groups.
Group Specificity.
Group Specificity example
Carboxypeptidase
Stereochemical Specificity example
L-Amino-acid oxidase
Absolute Specificity example
Urease
glucose oxidase
Most general specificity Involves a particular type of bond, irrespective of the structural features in the vicinity of the bond.
Linkage Specificity
Linkage Specificity example
Phosphatases
takes the form of a cleft or pocket on the enzyme’s surface or, for some multimeric enzymes, at the interface between subunits.
The active site
The active site function
- provides a three-dimensional environment that both shields or protects substrates from solvent
- where a substrate binds with
- binds any cofactors and prosthetic groups that may be required for catalysis
substrate bind with the substrate-binding site
1st Substrate recognition site.
2nd Appropriate angle.
3rd Proximity.
4th Functional group.
5th Transition state complex.
6th Products.
Models for substrate binding
Lock-and-key model
Induced-fit model
Lock-and-key model proposed by
Fischer
active site already exists in proper conformation even in absence of substrate.
Lock-and-key model
Induced-fit model proposed by
Koshland in 1963
The substrate during its binding induces conformational changes in the active site to attain the final catalytic shape and form.
Induced-fit model
Six classifications of enzymes
- Oxidoreductase.
- Transferases
- Hydrolases:
- Lyases
- Isomerases
- Ligases
oxidoreductase requires a ________ that is ________ as the substrate is ________
coenzyme (a carrier) ; oxidized or reduced ; reduced or oxidized
Oxidoreductase Examples:
alcohol dehydrogenase,
lactate dehydrogenase,
xanthine oxidase,
glutathione reductase,
glucose-6-phosphate dehydrogenase
Alcohol + (NAD+) → Aldehyde + NADH + (H+)
Oxidoreductase; Alcohol dehydrogenase
(IUB)
International Union of Biochemistry
transfer of a functional group (except hydrogen) from one substrate to another
Transferases:
Alcohol dehydrogenase; IUB name
Alcohol-NAD-oxidoreductase;
transfer of an amino group from one molecule to another
transaminases
transfer of a phosphate group from adenosine triphosphate (ATP) to give adenosine diphosphate (ADP) and a phosphorylated molecule
kinases
Transferases Examples:
aspartate and alanine transaminase (AST/ALT),
hexokinase,
phosphoglucomutase,
hexose-1-phosphate uridyltransferase,
ornithine carbamoyl transferase,
Hexose + ATP → Hexose-6-phosphate + ADP
Transferases; Hexokinase
Hexokinase systematic name is
ATP-Hexose–6-phosphatetransferase
bring about hydrolysis
Hydrolases
hydrolyze ester, ether, peptide or glycosidic bonds by adding water and then breaking the bond
Hydrolases:
breaking of glycosidic bonds in oligo- and polysaccharides
carbohydrases:
breaking of peptide linkages in proteins,.
proteases:
effect the breaking of ester linkages in triacylglycerols
lipases
Hydrolases Examples:
glucose-6-phosphatase,
pepsin,
trypsin,
esterases,
glycoside hydrolases
Acetyl choline + H2O → Choline + acetate
Hydrolases; or Acetyl choline hydrolase
All ________ enzymes are hydrolases.
digestive
removal of small molecule from a large substrate
Lyases
remove groups from substrates or break bonds by mechanisms other than hydrolysis
Lyases
effects the removal of the components of water from a double bond
dehydratase:
effects the addition of the components of water to a double bond.
dehydratase:
effects the addition of the components of water to a double bond.
hydratase:
One of the product of dehydratase
Water
Lyases Examples:
fumarase,
arginosuccinase,
histidine decarboxylase.
Lyases reverse reaction
Synthase
Fructose-1,6-bisphosphate → Glyceraldehyde-3-phosphate + dihydroxy acetone phosphate
Lyases; Aldolase
isomerization of substrate
Isomerases
produce optical, geometric or positional isomers of substrates. Catalyzes the isomerization of a substrate in a reaction, converting it into a molecule isomeric with itself.
Isomerases
Isomerases Examples:
UDP-glucose,
epimerase,
retinal isomerase,
racemases,
triosephosphate isomerase.
Glyceraldehyde-3-phosphate → Di-hydroxy-acetone-phosphate
Isomerases; Triose phosphate isomerase
joining together two substrates
Ligases
link two substrates together, usually with the simultaneous hydrolysis of ATP
Ligases
Ligases examples
alanyl-t. RNA synthetase, glutamine synthetase, DNA ligases
Acetyl CoA + CO2 + ATP → Malonyl CoA + ADP + Pi
Ligases; Acetyl CoA carboxylase
Factors affecting enzymatic activity
Temperature
pH
Substrate concentration
Enzyme concentration
Concentration of the end-products
Inhibition
temperature at which an enzyme exhibits maximum activity
Optimum temperature
higher than the optimum temperature → more the atoms vibrate →
breaking of hydrogen bonds and
other forces
The enzymatic activity is maximum at a particular pH which is called its
optimum pH.
Each human enzyme has a characteristic optimum pH, which usually falls within the physiological pH
range of _______ (EXCEPT digestive enzymes).
7.0–7.5
the rate equation for one substrate-enzyme catalyzed reaction.
Michaelis-Menten equation
Non-substrate molecules → decrease in enzymatic activity
Inhibition
active site or catalytic site of an enzyme is occupied by a substance other than the substrate → activity is inhibited
Competitive inhibition (Reversible)
the inhibitor can be removed from its site of binding without affecting the activity of the enzyme. Attaches but not to the active site
Reversible-Non-competitive Inhibition
the inhibitor can be removed only at the loss of enzymatic activity.
Irreversible Non-competitive Inhibition:
enzyme is used for estimation of “true glucose” in blood and body fluids.
“Glucose oxidase”
used for estimation of serum uric acid.
“uricase”
used for estimation of urea in blood and body fluids.
“urease”
