This document discusses plant physiology and enzymes. It defines plant physiology as the science concerned with the processes, functions, and responses of plants to the environment. It also discusses what enzymes are, how they work, and their characteristics. Enzymes are biological catalysts that speed up chemical reactions without being used up in the process. They work by lowering the activation energy of reactions and form enzyme-substrate complexes during catalysis.

1. Plant physiology
BIO 2101 PLANT PHYSIOLOGY
Kenneth Ssekatawa
B.Sc. Educ; M.Sc. Mol Bio & Biotech;
PhD

2. What is plant physiology??
• It is the science concerned with processes and functions,
responses of plants to the environment, and the growth and
development that result from the responses
• The complex physical and chemical processes necessary to
synthesize and transform substances into energy that is made
available for use by a plant organism.
 Conversion of solar energy to food /fuel
 conversion of food/fuel to energy to run cellular processes,
 conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some
carbohydrates,
 and the elimination of wastes.

3. Enzymes
Enzymes
Made of protein
Present in
all living cells
Converts substrates
into products
Biological
catalysts
Increase the rate of
chemical reactions
Remain unchanged
by chemical reaction

4. introduction
• Enzymes are catalysts that increase the rate of a chemical reaction
without being changed themselves in the process
• In the absence of an enzyme, the reaction may hardly proceed at
all, whereas in its presence the rate can be increased up to 107-fold
• Enzyme-catalyzed reactions usually take place under relatively mild
conditions (temperatures well below 100°C, atmospheric pressure
and neutral pH) as compared to the corresponding chemical
reactions
• Enzymes are also highly specific with respect to the substrates that
they act on and the products that they form
• In addition, enzyme activity can be regulated, varying in response
to the concentration of substrates or other molecules

5. Nomenclature
• Each enzyme is assigned two names.
– The first is its short, recommended name,
convenient for everyday use.
– The second is the more complete systematic
name, which is used when an enzyme must be
identified without ambiguity

6. Recommended name
• Most commonly used enzyme names have the
suffix “-ase” attached to the substrate of the
reaction (for example, glucosidase, urease,
sucrase), or to a description of the action
performed (for example, lactate dehydrogenase
and adenylyl cyclase).
• Some enzymes retain their original trivial names,
which give no hint of the associated enzymic
reaction, for example, trypsin and pepsin.

7. Systematic name
• The Commission on Enzymes of the International Union of Biochemistry
developed a system of nomenclature in which enzymes are divided into six major
classes.
• Enzymes are designated by code numbers consisting of four digits (E.C. number
or Enzyme Commission number)
 The first digit of the E.C. number indicates the major class,
 The second digit indicates the sub-class and
 The third digit indicates its sub-subclass
 The fourth digit denotes the systematic specific name of the enzymes,
 The first part of which indicates the name of the substrate and the second part
the nature of the reaction.
 For example - the code no. 1.1.1.1. stands for the enzyme alcohol dehydrogenase
where -1. Stands for oxidoreductase. 1.1. Stands for an enzyme that utilizes
substrate as – CHOH group. 1.1.1. Stands for those enzymes that utilize NAD as
an acceptor.

8. Tetrahydrofuran

10. Characteristics of enzymes
i. Enzymes remain unchanged qualitatively and quantitatively at the end of
the reaction they catalyze.
ii. Enzymes increase the rate of reactions but they do not initiate reaction.
iii.Enzymes do not alter the chemical equilibrium point of a chemical
reaction.
iv. Enzymes are required in very minute quantities with respect to the
substrate.
v. Enzymes are very efficient; an average enzyme undergoes about 1000
reactions per second.
vi. Enzymes are highly specific, that is an enzyme will generally catalyze
only a single reaction.
vii.Enzymes lower the activation energy of the reactions they catalyze.
viii.Enzymes form complexes with substrates.
ix. Enzyme activity is affected by pH, temperature, substrate, and enzyme
concentration.

11. Properties of Enzymes
 Enzymes are proteinaceous in nature.
 Catalytic Property - Enzymes are capable of catalyzing
biochemical reactions. The catalytic power.
 Colloidal Nature - High molecular weight and low diffusion rate
 Reversibility
 Specificity -.
 Heat Sensitivity (Thermostability) –
 pH Sensitivity

12. What do enzymes actually do?
E + S <---> [ES] <---> E + P
enzymes catalyze reactions by lowering the energy of activation (Ea)

13. Concept of enzymes
Active site
These residues are called
catalytic group,–
i. The active site takes up a
relatively small part of the
total volume of an enzyme
ii. The active site is a three-
dimensional structure
iii. Substrates are bound to the
enzymes by multiple weak
bonds
iv. Active sites are cleft or
crevices
v. The specificity of binding
depends on the precisely
defined arrangement of atoms
in an active site.

14. Active Site
• The active site contains
amino acid side chains that
create a three-dimensional
surface complementary to
the substrate .
• The active site binds the
substrate, forming an
enzyme–substrate (ES)
complex.
• ES is converted to an
enzyme–product (EP)
complex that subsequently
dissociates to enzyme and
product

15. Enzyme-Substrate Complex Details
• The part of the enzyme combining with the
substrate is the active site
• Active sites characteristics include:
– Pockets or clefts in the surface of the enzyme
• R groups at active site are called catalytic groups
– Shape of active site is complimentary to the shape of
the substrate
– The enzyme attracts and holds the enzyme using
weak noncovalent interactions
– Conformation of the active site determines the
specificity of the enzyme

16. Lock and Key Enzyme Model
• In the lock-and-key model, the enzyme is assumed
to be the lock and the substrate the key
– The enzyme and substrate are made to fit exactly
– This model fails to take into account proteins
conformational changes to accommodate a substrate
molecule

17. Induced Fit Enzyme Model
• The induced-fit model of enzyme action
assumes that the enzyme active site is more a
flexible pocket whose conformation changes to
accommodate the substrate molecule

18. Catalytic efficiency
• Most enzyme-catalyzed reactions are highly
efficient, proceeding from 103 to 108 times faster
than uncatalyzed reactions.
• Typically, each enzyme molecule is capable of
transforming 100 to 1,000 substrate molecules
into product each second.
• The number of molecules of substrate converted
to product per enzyme molecule per second is
called the turnover number, or kcat.

19. Parts of an enzyme
• A cofactor is a nonprotein substance that is essential for some
enzymes to fxn efficiently
• Holoenzyme refers to the active enzyme with its non-protein
component.
• The enzyme without its cofactor is termed an apoenzyme and is
inactive.
• If the nonprotein moiety is a metal ion such as Zn2+ or Fe2+, it is
called a cofactor/ activator/inorganic ions
• If it is a small organic molecule, it is termed a coenzyme.
• If the coenzyme/cofactor is permanently associated with the
enzyme, it is called a prosthetic group.
• Coenzymes frequently are derived from vitamins.

20. Function of Cofactors/coenzymes
i. In some enzymes, cofactors are required for completion
of the active site.
ii. Cofactor acts as a donor of electrons in the enzymatic
reactions.
iii.Cofactors may serve as temporary recipients of either
one of the reaction products/electrons/ protons.

21. Types of enzymes
a. Abzyme: An abzyme is a monoclonal antibody with catalytic activity and is
commonly called a catalytic antibody. Abzymes have only weak, modest
catalytic activity and have not proved to be of any practical use. Besides this, it
has academic importance to understand the mechanism and catalytic behavior of
enzymes.
b.Ribozymes: This enzyme is made up of ribonucleic acid (RNA) instead of protein
and extracted from protozoa – Tetrahynema thermophila in 1981.., for example –
peptidyl transferase.
c.Zymogens: zymogens or pro-enzymes or pre-enzymes.
d. Isozymes/isoenzymes: Some enzymes occur imore than one form in the same
species, tissue, or even in the same cell which catalyze the same biochemical
reaction but have different molecular structure and kinetic properties (two or more
enzymes with identical function but different structure), for example – lactate
dehydrogenase,

22. Types of enzymes
E. Allosteric enzymes:
• Allosteric enzymes contain two or more receptor sites, which
are geometrically different and non-overlapping.
• One is an active site and the other is an allosteric site or
regulatory site.
 Positive modulators (allosteric activator)
 Negative modulators (allosteric inhibitors

23. Factors affecting reaction velocity
• Temperature
– The reaction velocity increases with temperature
until a peak velocity is reached. This increase 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 results in a
decrease in reaction velocity as a result of
temperature-induced denaturation of the enzyme.
– The optimum temperature for most human
enzymes is between 35 and 40°C. Human enzymes
start to denature at temperatures above 40°C.

25. Factors affecting reaction velocity
• pH
– Effect of pH on enzyme denaturation: Extremes 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.
– The pH optimum varies for different enzymes: 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. For
example, pepsin, a digestive enzyme in the stomach, is
maximally active at pH 2, whereas other enzymes,
designed to work at neutral pH, are denatured by such
an acidic environment.

27. • In 1913, Leonor Michaelis
and Maud Menten
• Hyperbolic relationship
between reaction velocity,
v, and substrate
concentration [S].
• Michaelis–Menten kinetics
• This type of plot is known
as a saturation plot
Enzyme Kinetics
• Enzyme kinetics is the quantitative study of enzyme catalysis
which depends on the substrate concentration.
• At the maximum speed of reaction (Vmax)

28. • According to this
model, enzyme
catalysis takes place in
two stages.
• E + S ↔ ES → EP → E
+ P
• Thus, as the substrate
concentration is
increased, a point will
be reached at which all
the enzyme molecules
are in the form of the
ES complex, and the
enzyme is saturated
with substrate.
Enzyme Kinetics

29. • Pre–steady-state period.
• Steady state period.
• Normally enzyme kinetic values
are measured under steady-
state conditions, and such
conditions usually prevail in the
cell.
• Michaelis–Menten equation:
• v = Vmax [S] ∕ Km + [S]
• Where v is the initial rate of the
reaction, Vmax is the maximum
substrate-saturated rate of the
reaction and the Km is the
substrate concentration that
provides half of the maximal
substrate saturated rate of the
reaction (1/2 Vmax).
Enzyme kinetics
• Michaelis constant Km,
represents the affinity of the
enzyme for the substrate.
• Km is inversely proportional to
the affinity

30. Lineweaver-Burk plot
• The x-intercept is
equal to -1/KM
• The y-intercept is
equal to 1/Vmax
• The slope is equal
to KM/Vmax
• The values of KM
and Vmax are,
therefore, readily
determined by
extrapolation of the
line drawn from a
relatively few points
• Kcat = Vmax.[E]

31. Substrate concentration
[S]/ (mM) Velocity (v) (mM/m)
0 0
10 12.5
20 21.4
30 30.1
50 37.5
100 51.3
150 56.3
200 58.3
Example
An experiment was conducted using different substrate
concentrations [S] at a constant enzyme concentration [E] and
37°C. The results obtained are shown in the table below
• Using the results plot the Hyperbolic curve
• Determine Vmax, Km, and Kcat
• Lineweaver-Burk plot determine Vmax, km and
Kcat

32. Enzyme Inhibitors
1. Irreversible inhibitors-Bind to the enzyme covalently
 Toxins
 Antibiotics and other drugs
 Protease inhibitors
2. Reversible inhibitors-Bind to the enzyme noncovalently
 Competitive inhibition
 Non-competitive inhibition
 Uncompetitive inhibitions
 Mixed inhibition

33. Reversible, Competitive Inhibitors