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Enzymes are biological catalysts
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e
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Each enzyme has 2 names: a short one and a systematic one
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🡺 Systematic: it is more complete, when the enzyme must be unambiguously
identified
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NOTE: Some enzymes retain their original ordinary names that do NOT give
clues to the associated enzymatic reaction, such as trypsin and pepsin
(proteases of the digestive system)
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Ared + Box 🡪 Aox + Bred

Example: Lactate Dehydrogenase

They catalyze the transfer of C-, N- or P-containing groups
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A-B + H2O 🡪 A-H + B-OH
Example: Urease
They catalyze the breaking of C-C, C-S and some C-N bonds
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They catalyze the rearrangement of optical or geometric isomers
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A + B + ATP 🡪 A-B + ADP + Pi

Example: Pyruvate carboxylase
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Phosphorylase 🡪 uses Pi to cleave a bond and generate a phosphorylated
product
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Dehydrogenase 🡪 NAD+ or FAD is an electron acceptor in a redox reaction
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Some RNAs (Ribozymes) can catalyze rxns that affect
reactions

phosphodiester and peptide bonds
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It is a special gap or cleft in enzyme molecules, formed by the folding of the
protein and contains side chains of a
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The substrate binds to the enzyme non-covalently forming an
Enzyme-Substrate (ES) complex, which becomes an enzyme-product (EP)
complex that then dissociates into enzyme and product (E + P)
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Turnover number (kcat): number of substrate molecules converted to product
per enzyme molecule per second
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The kcat is a rate
constant for the conversion of ES to E+P
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The set of
enzymes produced in a cell determines which reactions occur in that cell
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a
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The active center of the enzyme
generally consists of the substrate binding site and the catalytic center
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The
first digit indicates one of the 6 major enzyme classes (oxidoreductases,
transferases,

hydrolases,

lyases

(synthases),

isomerases,

ligases

(synthases)); the next two digits include subclasses and sub-subclasses of
substrates; the fourth digit indicates the serial number of the specific
enzyme
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Active enzyme with its non-protein component
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e
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It lacks activity
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Non-protein part
that is metal ion (Fe+2 or Zn+2)
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They are
commonly derived from vitamins
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They dissociate from the enzyme in an
altered form
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Enzyme activity can be increased or decreased depending on the rate at
which the cell needs the product
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This serves to isolate
the substrate or reaction product from other competing reactions, providing a
favorable environment for the reaction and also organizes the thousands of
enzymes in the cell into useful pathways
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e
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different energetically favorable, as opposed to non-catalyzed
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The activation energy (Ea) is the barrier that every chemical reaction has, it
separates reactants and products
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Enzymatic reactions involve functional groups in one-sided chains of a
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A ⇄ T* ⇄ B

Effect of enzyme on activation
energy
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As can be seen,

Ea

is high in

a reaction without enzyme, which generally leads to a slow chemical
reaction
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The rate of reaction is
determined by the number of these energized molecules
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The enzyme allows a reaction to proceed rapidly under the conditions in
which the cell is found by providing an alternate reaction pathway with a
lower activation energy
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The active site is a complex molecular machinery that, with a variety of
chemical mechanisms, facilitates the conversion of substrate to product
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By stabilizing T*, the enzyme
increases the concentration of the reactive intermediate that can be
converted to product and, as a consequence, accelerates the reaction
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The active site can provide catalytic groups that increase the probability of
forming the transition state
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a
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In other enzymes, catalysis may involve the
formation

of

a

covalent

enzyme-substrate
3

complex
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Substrate (S)

1

2
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Transition state (T*)

2
4

4
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The rate or velocity of a reaction (v) is the
number of substrate molecules that a r e
c o n v e r t e d to product per unit time
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of

enzyme that

catalyzes the

conversion of 1 mole of substrate into 1 mole

Michael-Menten kinetics
Hyperbolic curve

of product per second (1 kat = 1 mol/s)
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It is usually
expressed in µmoles of product formed per
minute (1 IU = 1 µmol/min)
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The leveling of the reaction rate at high substrate concentration reflects
the saturation with substrate of all available binding sites on the enzyme
molecules present
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Allosteric enzymes, on the other hand, do not follow such kinetics and
present a sigmoidal curve
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The optimum temperature for most human enzymes is 35 to 40ºC, since they
begin to denature at 40ºC and above
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The concentration of protons ([H+]) can affect the rate of reaction, since
the catalytic process generally requires that the enzyme and substrate
have specific chemical groups (ionized or not) in order to interact
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The sensitivity
of enzymes to pH is due to the effect of pH on the ionic charge of the a
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The pH at which maximum enzyme activity is obtained is different for
different enzymes and often reflects the [H+] at which the enzyme
functions in the body
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k1

K2

E + S ⇄ EN ⇄ E + P
WhereE

k-1

is the

enzymeP is the product

S the substrate

ESthe enzyme-substrate

complex k1, k-1 and k2 (or kcat) are rate constants

This describes how the rate of the reaction varies with respect to the substrate
concentration:
𝑉𝑜 =

𝑉max
𝑚

𝑘+ [𝑆]

WhereVo = initial reaction rate

Vmax =
Km =

maximum velocity = kcat [E]Total

Michaelis constant = (k-1 + k2) / k1

[S] = substrate concentration
There are certain assumptions in deriving the Michaelis-Menten velocity
equation
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The percentage of
total substrate bound by the enzyme is, at any given time, small
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•

The reaction rate is measured from the time the enzyme binds with
the substrate (at the initiation of the reaction), at which time the
product concentration is low, so the reverse reaction rate (product to
substrate) is ignored
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a low km indicates high affinity of the enzyme to the
substrate, since
that can operate with low concentrations of the same
a high

km

indicates a low affinity of the enzyme to the

substrate, since a high substrate concentration is necessary to
saturate half of the enzyme
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-When [S] is much less than km, the reaction rate is approximately
proportional to [S]
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- When [S] is much larger than km, the velocity is constant and equal to Vmax
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It is said to be of zero order
with respect to [S]
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This graph can be used to
calculate

km

and

Vmax,

as well as to determine the mechanism of action of

enzyme inhibitors
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This plot does not compress the data at high
substrate concentrations
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They can be reversible or irreversible
•

Irreversible inhibitors: they bind to enzymes through covalent bonds
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•

Reversible inhibitors: they bind to enzymes by non-covalent bonds and,
therefore, dilution of the enzyme-inhibitor complex results in the dissociation
of the reversibly bound inhibitor and recovery of enzyme activity
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The chemical structure of
the substance must be similar to that of the substrate
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At a
sufficiently high [S], Vmax does not change
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e
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-

Vmax remains

unchanged

-

Km increases

because -1/km

approaches zero from a negative
value
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Red line = competitive inhibitor Black
line = no inhibitor

Statin drugs are a good example of competitive inhibitors
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The catalyst for the reaction is HMG CoA reductase; the statins
atorvastatin and pravastatin are structural analogs of that enzyme, thus, they
compete effectively to inhibit the enzyme, at the same time inhibiting de novo
cholesterol synthesis and consequently reducing plasma cholesterol levels
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This type of inhibition occurs

when the inhibitor and substrate bind at different sites on the enzyme
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This type of inhibition cannot be overcome by increasing [S], therefore,
the apparent

Vmax

of the reaction is reduced
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In the presence of a non-competitive inhibitor, km remains the same
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NOTE: The slope increases if [S]
increases
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This is why noncompetitive inhibition is more complex and alters both km and Vmax
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The lower the Ki (the stronger the binding), the more efficient the
inhibition of the reaction
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Drugs including captropril, enalapril and lisinopril act at the
extracellular level, inhibiting the reactions that occur there, as occurs
in the inhibition of the ACE enzyme, blocking it from the plasma which
cleaves angiotensin I to form the potent vasoconstrictor angiotensin
II, causing vasodilation thus reducing blood pressure
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Enzyme regulation is essential for an organism to coordinate numerous metabolic
processes
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Thus, when the

substrate concentration ([S]) increases, the reaction rate increases, and when that
happens, [S] returns to normal
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Regulated by molecules called effectors that bind non-covalently at a site
other than the active site
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•
•

Negative effectors: inhibit enzyme activity
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5), modify the enzyme's activity (k0
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The maximum velocity
increases with a positive effector and decreases with a negative effector
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An allosteric substrate functions as a
positive effector
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substrate, i
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, their binding sites exhibit cooperativity
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The effector will be heterotropic when the substrate is different from the
effector
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Feedback inhibition provides cells with
appropriate amounts of a product it needs by regulating the flow of
substrate molecules through the pathway that synthesizes that product
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Protein kinases, which use ATP as a phosphate group donor,
catalyze phosphorylation reactions
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It depends on the specific enzyme, since phosphorylation may
increase or decrease its activity
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Allosteric and covalent modifications in enzyme activity occur within seconds to
minutes
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Induction or repression of
enzyme synthesis leads to alteration in the total population of active sites
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Alterations in enzyme levels resulting from the induction or repression of protein
synthesis are slow and can take hours to days
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5

Immediate

Covalent modification

Another enzyme

Enzyme
Hormone or
synthesis/degradation metabolite

Change in Vmax
and/or km
Change in the
amount of
enzyme

Immediate to
minutes
Hours to days



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