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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | ENZYME | NOTED BY FAKHRY (IG @SFAKHRYM)
v Basic Principle
o Among the many biologic reactions that are energetically possible, enzymes selectively channel reactants (called substrates) into
useful pathways
v Nomenclature
o Recommended name
• Most commonly names have the suffix "-ase" attached to the substrate of the reaction (e
...
, glycosidase and urease); or to
a description of the action performed (e
...
, lactate dehydrogenase and adenylyl cyclase)
• Some enzymes retain their original trivial names, which give no hint of the associated enzymatic reaction (e
...
, trypsin and
pepsin)
o Systematic name
• In this system, enzymes are divided into six major classes, each with numerous subgroups

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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | ENZYME | NOTED BY FAKHRY (IG @SFAKHRYM)

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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | ENZYME | NOTED BY FAKHRY (IG @SFAKHRYM)
o

Potentially confusing enzyme nomenclature
• Synthetase, requires ATP
• Synthase, No ATP required
• Phosphatase, use water to remove phosphoryl group
• Phosphorylase, use Pi to break a bond and generate a phosphorylated product
• Dehydrogenase, NAD+/FAD is an electron acceptor in a redox reaction)
• Oxidase, O2 is the acceptor, and oxygen atoms are not incorporated into substrate
• Oxygenase, one or both oxygen atoms are incorporated

v Properties
o Enzymes are protein catalysts that increase the velocity of chemical reaction and are not consumed during the reaction; the
reactions of the cell would not occur rapidly enough to sustain life if enzyme were not present
• Note: Some RNAs can act like enzymes, usually catalyzing the cleavage and synthesis of phosphodiester bonds
...
Binding is thought to cause a conformational
change in the enzyme (fit model) that allows catalysis
§ ES is converted to an enzyme-product (EP) complex that subsequently dissociates to enzyme and product
o Catalytic efficiency
• Enzyme-catalyzed reactions are highly efficient, proceeding from 103-108 times faster than uncatalyzed reactions
• The number of molecules of substrate converted to product per enzyme molecule per second is called the turnover
number, or Kcat (typically is 102-104s-1
o Specificity
• Enzymes are highly specific for their substrate and products
§ Many enzymes recognize only a single compound as a substrate
§ Some enzymes, such as those involved in digestion, are less specific
o Holoenzymes, apoenzymes, cofactors, and coenzymes
• Some enzymes require molecules other than proteins for enzymic activity
• Holoenzyme refers to the active enzyme with its nonprotein component
§ If the nonprotein moiety is a metal ions, such as Zn2+ or Fe2+, it is called cofactor
§ If it is a small organic molecule, it is termed a coenzyme

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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | ENZYME | NOTED BY FAKHRY (IG @SFAKHRYM)
Coenzymes that only transiently associate with the enzyme are called cosubstrates; cosubstrates dissociate
from the enzyme in an altered state (NAD+ is an example)
• If the coenzyme permanently associated with the enzyme and returned to its original form, it is called a
prosthetic group (FAD is an example)
• Coenzyme commonly derived from vitamins
• Apoenzyme, enzyme without its nonprotein moiety, it is inactive
Regulation
• Enzyme activity can be regulated;
• The rate of product formation responds to cellular need
Location within the cell
• Many enzymes are localized in specific organelles within the cell
•

o

o

v How Enzyme Work
• Two perspectives: First, treats catalysis in terms of energy changes that occur during reaction (enzyme provide an alternate,
energetically favorable reaction pathway different from the uncatalyzed reaction); second, how active site chemically facilitates
catalysis
o Energy changes occurring during the reaction
• Free energy:
§ Virtually all chemical reactions have an energy barrier separating the reactants and the products
§ It is the energy difference between that of the reactants and a high-energy intermediate that occurs during the
formation of product
§ Rate of reaction
§ The rate is determined by the number of such energized molecules
§ In general, the lower the free energy of activation, the more molecules have sufficient energy to pass through the
transition state, and, therefore, the faster the rate of the reaction
§ Alternate reaction pathway
§ An enzyme allows a reaction to proceed an alternate reaction pathway with a lower free energy of activation
§ Enzyme does not change the equilibrium of the reaction, however, it accelerates the rate by which equilibrium is
reached

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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | ENZYME | NOTED BY FAKHRY (IG @SFAKHRYM)
o

Chemistry of the active site
§ It is a complex molecular machine employing a diversity of chemical mechanisms to facilitate the conversion of substrate
to product
§ Factors are responsible:
§ Transition-state stabilization
• By stabilizing the transition state, the enzyme greatly increases the concentration of the reactive
intermediate that can be converted to product and, thus, accelerated the reaction
§ Other mechanisms
• Catalytic groups that enhance the probability that the transition state is formed
• These groups can participate in general acid-base catalysis in which amino acid residues provide or
accept protons
• In other enzymes, catalysis may involve the transient formation of a covalent ES complex
• Note: the mechanism action of chymotrypsin, an enzyme of protein digestion in the intestine,
include general base, general acid, and covalent catalysis]
§ Visualization of the transition state
• This can be visualized as being similar to removing a sweater from an uncooperative infant

v Factors Affecting Reaction Velocity
o Substrate Concentration
§ Maximal Velocity (v)
§ V: number of substrate molecules converted to product per unit time
§ It is usually expressed as μmol/min
§ The rate of an enzyme-catalyzed reaction increases with substrate concentration until a maximal velocity (Vmax) is
reached
§ The leveling off of the reaction rate at high substrate concentrations reflects the saturation with substrate of all
available binding sites on the enzyme molecules present
§ Hyperbolic shape of the enzyme kinetics curve
§ Most enzyme shoe Michaelis-Menten kinetics, in which the plot of initial reaction velocity (v0) against substrate
concentration ([S]), is hyperbolic
§ In contrast, allosteric enzyme do not follow Michaelis-Menton kinetics and show a sigmoidal curve

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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | ENZYME | NOTED BY FAKHRY (IG @SFAKHRYM)
o

o

Temperature
§ Increase of velocity with temperature
§ It is the result of the increased number of molecules having sufficient energy to pass over the energy barrier and
form the products of the reaction
§ Decrease of velocity with higher temperature
§ Further elevation of the temperature causes a decrease in reaction velocity as a result of temperature-induced
denaturation of the enzyme
§ NOTE: The optimum temperature for most human enzyme is between 35° C and 40°
...

§ Effect of pH on enzyme denaturation
§ Extreme of pH can lead to denaturation of the enzyme, because the structure of the catalytically active protein
molecule depends on the ionic character of the amino acid side chains
§ Variable pH optimum
§ The pH at which maximal enzyme activity is achieved is different for different enzymes and often reflects the [H+]
at which the enzyme functions in the body

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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | ENZYME | NOTED BY FAKHRY (IG @SFAKHRYM)
v Inhibition of Enzyme Activity
o Inhibitor: Any substance that can decrease the velocity of an enzyme-catalyzed reaction
o Can be reversible or irreversible
§ Irreversible inhibitors bind to enzyme through covalent bonds
§ Reversible inhibitors bind to enzyme through noncovalent bonds and, thus, dilution of the enzyme-inhibitor complex
results in dissociation of the reversibly bound inhibitor and recovery of enzyme activity
§ Two types: Competitive and noncompetitive
• Competitive Inhibition (when the inhibitor binds reversibly to the same site that the substrate would normally occupy and,
therefore, competes with the substrate for that site
§ Effect on Vmax: the effect is reversed by increasing [S] (At a sufficiently high substrate concentration, the reaction velocity
reaches the Vmax observed in the absence of inhibitor)
§ Effect on Km: the presence of a competitive inhibitor, more substrate is needed to achieve 1/2Vmax
§ Effect on the Lineweaver-Burk plot
§ Statin drugs as example of competitive inhibitors
§ It competes effectively to inhibit HMG-CoA reductase
Noncompetitive
inhibitions (They are recognized by its characteristic effect on Vmax; they occur when the inhibitor and substrate
•
bind at different sites on the enzyme)
§ Effect on Vmax
§ They cannot be overcome by increasing the concentration of substrate; therefore, they decreases the apparent
Vmax of the reaction
§ Effect on Km
§ They do not interfere with the binding of substrate to enzyme; therefore, the enzyme shoes the same Km in the
presence or absence of the noncompetitive inhibitor
§ Effect on Lineweaver-Burk Plot
• Enzyme inhibitors as drugs

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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | ENZYME | NOTED BY FAKHRY (IG @SFAKHRYM)
v Regulation of enzyme activity
• Regulation of allosteric enzymes
§ These enzymes are regulated by molecules called effectors (positive-increase and negative-decrease) that bind
noncovalently at a site other than active site
• Positive and negative effectors can affect the affinity of the enzyme for its substrate (K0
...

§ These enzymes are almost always composed of multiple subunits, and the regulatory (allosteric) site that binds the effector
is distinct from the substrate-binding site and may be located on subunit that is not itself catalytic
§ Homotropic effectors
§ It is homotropic when the substrate itself serves as an effector
§ Most often, an allosteric substrate functions as a positive effector
§ See the curve figure 5
...
63)
§ Heterotrophic effectors
§ It is heterotrophic when the effector may be different from the substrate
• Regulation by covalent modification
§ Phosphorylation and dephosphorylation
§ Phosphorylation reactions are catalyzed by a family of enzymes called protein kinases (use ATP as the phosphate
donor)
§ Response of enzyme to phosphorylation
§ Depending on the specific enzyme, the phosphorylated enzyme may be more or less active than unphosphorylated
enzyme
§ Induction and repression of enzyme synthesis
§ Cells can also regulate the amount of enzyme present by altering the rate of enzyme degradation or, more typically,
the rate of enzyme synthesis
§ The increase (induction) or decrease (repression) of enzyme synthesis leads to an alteration in the total population
of active sites
§ Alteration in enzyme levels as a result of induction or repression of protein synthesis are slow compared with
allosterically or covalently regulated

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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | ENZYME | NOTED BY FAKHRY (IG @SFAKHRYM)
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Enzymes in Clinical Diagnosis

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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | ENZYME | NOTED BY FAKHRY (IG @SFAKHRYM)

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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | ENZYME | NOTED BY FAKHRY (IG @SFAKHRYM)

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