Biochemistry:

ENZYMES AND ENZYME KINETICS

ENZYMES
 This explains enzyme specificity.
Enzyme as Biological Catalyst
 This explains the loss of activity
 Enzymes are proteins that increase
when enzyme denature.
the rate of reaction by lowering the
energy of activation.
 They catalyze nearly all the chemical
reactions taking place in the cells of
the body.
 Not altered or consumed during
reaction.
 Reusable.

Active Sites
 Enzyme molecules contain a special
pocket or cleft called the active sites.

Apoenzyme and Holoenzyme

 The enzyme without its non-protein
moiety is called as apoenzyme and
it is inactive.
 Holoenzyme is an active enzyme
Lock-and-Key Model with its non-protein component.
 In the lock-and-key model of
enzyme action:
o The active site has a rigid shape
o Only substrates with the
matching shape can fit
o The substrate is key that fits the Important Terms to Understand
lock of the active site Biochemical Nature and Activity of
 This is an older model, however, and Enzymes
does not work for all enzymes.  Cofactor
- A cofactor is a non-protein
chemical compound that is
bound (either tightly or loosely)
to an enzyme and is required for
catalysis.
Types of Cofactors
1. Coenzyme
- The non-protein component,
loosely bound to apoenzyme by
non-covalent bond.
 Examples: Vitamins or
Compound derived from
vitamins.

2. Prosthetic Group
- The non-protein component,
tightly bound to the apoenzyme
by covalent bonds is called a
Prosthetic group.

Enzyme Specificity
 Enzymes have varying degrees of
specificity for substrates.
 Enzymes may recognize and
catalyze.
o A Single Substrate
o A Group of Similar Substrates
o A Particular Type of Blood

Important Terms to Understand

Biochemical Nature and Activity of
Induced Fit Model
Enzymes
 In the induced-fit model of enzyme
Activation Energy or Energy of Activation:
action:
 All chemical reactions require some
o The active site is flexible,
amount of energy to get them
not rigid.
started.
o The shapes of the enzyme,
OR
 It is First push to start reaction. active site, and substrate
adjust to maximize the fit,
 This energy is called activation
which improves catalysis.
energy.
 This model is more consistent with a
wider range of enzyme.
Mechanism of Action of Enzymes
 Enzymes increase reaction rates by
decreasing the activation energy:
 Enzyme-Substrate Interaction:
- Formation of Enzyme Substrate
complex by:
 Lock-and-Key Model
 Induced Fit Model
  pH also affects the rate of enzyme-
substrate complexes.
- Most enzymes have an optimum
pH of around 7 (neutral)
 However, some prefer acidic or
basic conditions.
 Substrate Concentration

2. Cofactors and Coenzymes

 Inorganic substances (zinc, iron) and
vitamins (respectively) are sometimes
need for proper enzymatic activity.
Example:
 Iron must be present in the
quaternary structure -
hemoglobin in order for it to
pick up oxygen.

Effects of Enzyme Activity

Three Factors:
1. Environmental Conditions
 Extreme Temperature are the most
dangerous.
- High temperatures may denature
(unfold) the enzyme.
 Optimum Temperature. The
temperature at which enzymatic
reaction occur fast.
 CLASSIFICATION AND NOMENCLATURE
3. Enzyme Inhibitors OF ENZYMES
Reversibe Competitive Inhibition
 A competitive inhibitor:
- Has a structure like the
substrate.
- Competes with the substrate for
the active site.
- Has its effect reversed by
increasing substrate
concentration.

Noncompetitive Inhibition
 A noncompetitive inhibitor:
- Has a structure different than the
substrate.
- Distorts the shape of the enzyme,
which alters the shape of the active
site.
- Prevents the binding of the
substrate.
- Cannot have its effect reversed by
adding more substrate.
 ENZYME KINETICS

 Enzymes are protein catalysts that, like

all catalysts, speed up the rate of a
chemical reaction without being used
up in the process.

Enzyme reaction rates are determined by

several factors.
 The Concentration of Substrate
Molecules
- The more of them available, the
quicker the enzyme molecules
collide and bind with them).
- The concentration of substrate is
designated [S] and is expressed in
unit of molarity.
 The Temperature
- As the temperature rises, the
molecular motion – and hence
collisions between enzyme and
substrate – speed up. But as
enzymes are proteins, there is an
upper limit beyond which the
enzymes become denatured and
ineffective.
 The Presence of Inhibitors
- Competitive Inhibitors are
Over The HILLS molecules that bind to the same site
1. Transferase – Transfer functional as the substrate – preventing the
group from one molecule to another. substrate from binding as they do so
2. Ligase – Ligates or joining two – but are not changed by the
molecule together. Forms bond by enzyme.
condensation reaction by ATP - Noncompetitive Inhibitors are
cleavage. molecules that bind to some other
3. Oxidoreductases – Move electrons site on the enzyme reducing its
between molecules. catalytic power.
4. Isomerase – Convert molecules from  pH
one isomerge to another. - The conformation of a protein is
5. Hydrolases – Break down bonds influenced by pH and as enzyme is
using water (H20) crucially dependent on its
6. Lyase – Break down bonds without conformation, its activity is likewise
using water and oxidation. affected.

Michaelis–Menten kinetics
 Plotting Vi as a function of [S], we
find that
 At low values of [S], the initial
velocity, Vi, rises almost linearly with
increasing [S].
 But as [S] increases, the gains in Vi
level off (forming a rectangular
hyperbola).
 But as [S] increases, the gains in Vi
level off (forming a rectangular
hyperbola).
 The asymptote represents the
maximum velocity of the reaction,
designated Vmax.
 The substrate concentration that
Lineweaver-Burk plot
produces a Vi that is one-half of
 Plotting the reciprocals of the same
Vmax is designated the Michaelis-
data points yields a “double-
Menten constant, Km (named after
reciprocal” or Lineweaver-Burk plot.
the scientists who developed the
This provides a more precise way to
study of Enzyme Kinetics).
determine Vmax and Km.
 Km is (roughly) an inverse measure
 Vmax is determined by the point
of the affinity or strength of binding
where the line crosses the 1/Vi = 0
between the enzyme and its
(so the [S] is infinite). Note that the
substrate. The lower the Km, the
magnitude represented by the data
greater the affinity (so the lower the
points in this plot decreases from
concentration of substrate needed to
lower left to upper right. Km equals
achive a given rate).
Vmax times the sloper of line. This is
easily determined from the intercept
on the X axis.

Vi

Vi = Initial Velocity (moles/time)

[S] = Substrate Concentration (molar)
Vmax = Maximum Velocity
Km = Substrate Concentration when Vi is
one-half Vmax (Michael-Menten Constant)
 CARBOHYDRATES

 Are the most abundant biomolecules

on Earth
 Are polyhydroxy aldehydes and
ketones, or substances that yield such
compounds on hydrolysis.
 Empirical formula is (Ch2H)n’ but some
also contain nitrogen, phosphorus, or
sulfur
 Carbohydrates occur in four main size
classes: monosaccharides,
disaccharides, oligosaccharides,
and polysaccharides. The most
abundant monosaccharide in nature is
D-glucose, which is also known as
dextrose.

Common Monosaccharides
 Coomon aldoses and ketoses of
three-, five-, and six-carbon lengths
are shown. The simplest
monosaccharides are two three-
carbon trioses: D-glyceraldehyde, an
aldotriose; and dihydroxyacetone, a
ketotriose.
 The most common monosaccharides
in nature are the aldohexose D-
glucose, and the ketohexose D-
fructose. The aldopentoses D-ribose
and 2-deoxy-D-ribose are components
of nucleotides and nucleic acids.