4bot111 Notes - 2023

UNIVERSITY OF ZULULAND
FACULTY OF SCIENCE AND

AGRICULTURE
DEPARTMENT OF BOTANY
INTRODUCTION TO PLANT CYTOLOGY,

GENETICS AND PHYSIOLOGY
4BOT 111
COMPILER: PROF. N.R. NTULI
4BOT111 February – May 2023

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FACULTY OF SCIENCE AND AGRICULTURE

DEPARTMENT OF BOTANY
LEARNER
GUIDE
YEAR: 2023
Module Title Introduction to Plant Cytology, Genetics and Physiology
Module Code 4BOT111
Module Credit Value
Level of study 1
SAQA Credits 16
Notional Hours 160
NQF Level 5
Lecturer(s) Prof. NR Ntuli
Full Title of the Programme

BSc with Botany as a double major
the Module belongs to

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1 LEARNING COMPONENT
1.1 Purpose of the Module
The purpose of this module is to develop an understanding of the structure

of the cell and its metabolic processes as well as the principles of
hereditary.
1.2 Module outcomes

By the end of this unit the learner should be able to:
• Identify and solve problems related to: uptake of water by plants; various
parts of plant cell; and different stages of mitosis and meiosis.
• Construct disaccharides, lipids and peptides from given structures.
• Draw biochemical structures that are involved in respiration and
photosynthesis processes.
• Describe processes of transpiration, photosynthesis and respiration as
well as factors affecting them.
• Explain the hormonal action and effects in plant growth.
• Sketch and describe the fundamentals of Mendelian Genetics.
• Conduct experiments, analyze results and write reports thereafter in the
areas of transpiration, photosynthesis, respiration and Mendelian Genetics.
In addition, learners should be able to demonstrate the following critical cross

field outcomes:
• Identify and solve problems
• Work in a team
• Organize and manage themselves
• Collect, analyse and evaluate information
• Communicate effectively
• Use science and technology

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• Recognize problem solving contexts

• Reflect on and explore effective learning strategies
• Participate as a responsible citizen
• Be culturally and aesthetically sensitive
1.3 Chapter or Learning Unit breakdown
Theme Theory Practical Week

Essential elements, Macro and micro nutrients, Allocation of students into practical 1
carbohydrates, lipids, monosaccharides, glycosidic groups
proteins bonds disaccharides,
polysaccharides, fatty acids,
glycerol, amino acids, peptide
bonds,
The plant cell structure and Cell wall, cell membrane, Experiment 1: 2
functions, cell division nucleus, mitochondrion, How to use a compound
chloroplast, golgi apparatus, microscope and Estimation of
endoplasmic reticulum, ribosome, water potential in plant cell
vacuole. Mitosis, meiosis.
Photosynthesis Light phase, dark phase, C4 Experiment 1: 3
metabolism, differences between How to use a compound
C3 and C4 plants. microscope and Estimation of
water potential in plant cell
Respiration Glycolysis Experiment 2: 4
Transpiration and Stomatal index
Respiration Krebs cycle Experiment 2: 5
Transpiration and Stomatal index
Nucleic acids Structure of nucleic acids, 6
replication of DNA
Theory Test 1
Protein synthesis Transcription, protein synthesis in Practical Test 1 7
ribosomes
Movement of water through Water uptake by the roots; Experiment 3: 8
the plant Water potential: cohesion-tension Respiration
mechanism;

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Transpiration;
Regulation of transpiration;
Factors affecting transpiration rate
Movement of inorganic Uptake of inorganic nutrients; Experiment 3: 9
nutrients through the plant Transport of inorganic nutrients Respiration
Translocation: movement of Evidence of sugar transport in Experiment 4: 10
substances through the phloem; Mitosis, Meiosis and Genetics
phloem. Aphids in phloem research;
Conditions affecting the The mechanism of phloem
rate of photosynthesis and transport: pressure flow; Internal
respiration and external factors affecting the
rate of photosynthesis and
respiration
Regulating growth and Auxin; Cytokinins; Ethylene; Experiment 4: 11
development: plant Abscisic Acid; Gibberellins; Mitosis, Meiosis and Genetics
hormones The molecular basis of hormone
action
Genetics The principle of segregation; 12
Incomplete dominance;
Independent assortment;
Linkage
External factors and plant The tropism; Practical Test 2 13
growth Photoperiodism;
Hormonal control in flowering;
Dormancy in seeds and buds;
Cold and the flowering response;
Nastic movements;
Thigmomorphogenesis;
Solar tracking
1.5 Arrangements for self-study
Contact Study Notional Hours Self Study Notional Hours

Lectures 40 Research Based 40
Practical 30 Self Directed 8

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Tutorials 6 Observation 20
Field Trip Exam Preparation 8
Exams/Tests 4 Presentations 4
Total contact: 80 Total Self Study: 80
2 ASSESSMENT COMPONENT
2.1 Assessment Plan
Activity % Weighting
Assignments 4
Theory Tests 16
Practical reports 4
Practical Tests 16
Sub-Total = DP 40
Final Assessment 60
Total 100
• The duly performance (DP) will be calculated from the semester mark. A
minimum of forty percent (40%) in the semester mark will be the recommended
DP for the student to write the exam.
• Semester and final exam mark component of the whole module will be calculated
as follows: (semester mark – 40% and final examination weighting – 60%). A
subminimum of 40% in the final assessment (Exam) is needed for a pass.

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1 CYTOLOGY
1.1 INTRODUCTION
i. Life exists only in cells therefore organisms are made up of cells; the
activity of an organism depends on the activities of the cells, individual and
collectively; the cell is the basic unit through which energy is obtained,
converted, stored and utilized; the cell is the basic unit in which biological
information is stored, manipulated and expressed.
ii. The continuity of life has a cellular basis referring to genetic continuity
(genes and chromosomes).
iii. There is a relationship between structure and function thus biochemical
activities occurring within the cells are determined by structures organized
in an orderly manner.
The cytologists aim to:
➢ identify the kinds of cells that exist;

➢ understand their organization and structure in terms of their activities and
functions;
➢ understand the cell as a total entity (bacterium);
➢ understand the cell as an integral part of the tissues and systems of
multicellular plants.
Modern cell theory states that:
➢ All living things are composed of cells, where the smallest living organisms
are composed of single cells and the largest are made up of billions of
cells.
➢ Cells can be subdivided into two types, namely prokaryotic cells without a
membrane-bound nucleus and eukaryotic cells with a proper (membrane-
bound) nucleus.
➢ All cells originate by cell division from preexisting cells.
➢ Following cell division cells can differentiate into different cell types to form
different tissues and organs
➢ The structure and functioning of an organism is produced by the
organization and functioning of all its cells.
1.2 PROKARYOTIC AND EUKARYOTIC CELLS
The cells of all organisms fall into one of two major divisions according to the
number and arrangement of cellular membranes and the complexity of nuclear
region. The smaller and more primitive division, the prokaryotes (from pro =
before and karyon = nucleus), includes the only two major groups – bacteria
and cyanobacteria (or blue-green algae). Prokaryotic membranes are limited to

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the surface or plasma membrane and a relatively simple collection of inner

membranes in the cytoplasm. The nuclear region of prokaryotes, the nucleoid,
has no boundary membrane separating it from the surrounding cytoplasm.
The eukaryotes (from eu = true, and karyon = nucleus), includes all the
remaining organisms of the earth – animals, plants, fungi, and protozoa. A
plasma membrane covers the surface of the cells of these organisms as in the
prokaryotes. In addition, several distinct internal membrane systems of
eukaryotic cells extend into interior compartments with specialized functions.
Among these interior compartments is the nucleus, set off from the surrounding
cytoplasm by a double system of membranes.
Attention will be paid on the structures that occur within the eukaryotic cell.

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1.3 CELLULAR INFORMATION
1.3.1 THE NUCLEUS
Figure 1.1 The structure of the nucleus
Nucleus occurs only in eukaryotic cells. It is a large, complex structure with many
different functions. It contains nucleic acids such as DNA and RNA. Gross
analysis: 70-80% proteins, 3-10% lipids, 2-10% RNA and 10% DNA. It has four
main parts: the nuclear envelope (membrane), nucleoplasm, nucleoli and
chromosomes. DNA is the physical carrier of inheritance and with the exception
of plastid DNA (cpDNA and mDNA, found in the chloroplast and mitochondrion,

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respectively) all DNA is restricted to the nucleus. RNA is formed in the nucleus
and moves out into the cytoplasm where it functions in the assembly of proteins.
The nucleolus is responsible for nuclear protein synthesis and assembly of rRNA
and proteins. There are usually two nucleoli per nucleus. Ribosomes are the
sites for protein synthesis. Eukaryotic ribosomes are slightly larger than
prokaryotic ones. Structurally, the ribosome consists of a small and larger subunit
as shown in Figure 1.2.
Figure 1.2 Subunits of a ribosome
The nuclear envelope is a double-membrane structure. Numerous pores occur in

the envelope, allowing RNA and other chemicals to pass, but not the DNA.

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1.4 THE CELL BOUNDARY
1.4.1 CELL WALL
Figure 1.3 The Primary and Secondary structure of the cell wall
Primary walls: are physiologically active cells; made up of cellulose and other
polysaccharides (hemicellulose, etc.), lignin, pectic compounds and water.
Secondary walls: are non-physiological cells; made up of cellulose, lignin, water,
suberin, cutin, waxes and pectic compounds. It has intercellular cytoplasmic
connections called plasmodesmata.
Functions of primary walls
• Structural and mechanical support.

• maintain and determine cell shape.

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• resist internal turgor pressure of cell.

• control rate and direction of growth.
• ultimately responsible for plant architecture and form.
• regulate diffusion of material through the apoplast.
• carbohydrate storage - walls of seeds may be metabolized.
• protect against pathogens, dehydration, and other environmental factors.
• Source of biologically active signaling molecules.
• cell-cell interaction
1.4.2 MIDDLE LAMELLA
It is the pectic-rich layer that cements together the primary wall of adjacent cells.
Frequently, it is difficult to distinguish the middle lamella from primary wall,
especially in cells that develop thick secondary walls. In such cases, two
adjacent primary walls and the middle lamella, and perhaps the first layer of the
secondary wall of each cell, may be called a compound middle lamella.
1.4.3 PLASMA MEMBRANE (Cell Membrane, Plasmalemma)
Plasma membrane is a thin membrane surrounding the cytoplasm and function

as a semi-permeable barrier, allowing a very few molecules across it while
fencing the majority of organically produced chemicals inside the cell.
Figure 1.4 Plasma membrane structural components
Electron examinations of cell membranes have led to the development of the

lipid bilayer model also referred to as fluid-mosaic model. The most common
molecule in the model is the phospholipid, which has a polar (hydrophilic) head
and two non-polar (hydrophobic) tails. These phospholopids are aligned tail to tail
so the non-polar areas form a hydrophobic region between the hydrophilic heads

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on the inner and outer surfaces of the membrane. This layering is termed a
bilayer since an electron microscopic technique known as freeze-fracturing is
able to split the bilayer.
Cholesterol is another important component of cell membranes embedded in

hydrophobic areas of the inner (tail-tail) region. Most bacterial cell membranes do
not contain cholesterol. Cholesterol aids in the flexibility of a cell membrane.
Proteins are suspended in the inner layer, although the more hydrophilic areas of
these proteins “stick out” into the cells interior as well as outside the cell. These
proteins function as gateways that allow certain molecules to cross into and out
of the cell by moving through open areas of the protein channel. These integral
proteins are sometimes known as gateway proteins. The outer surface of the
membrane will tend to be rich in glycolipids, which have their hydrophobic tails
embedded in the hydrophobic region of the membrane and their heads exposed
outside the cell. These, along with carbohydrates attached to the integral
proteins, are thought to function in the recognition of self, a sort of cellular
identification system.

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1.5. ENERGY CAPTURE AND MOBILIZATION
1.5.1 INTRODUCTION
Plastids are heterogenous. There are three main groups of plastids: leucoplasts
(white); chloroplasts (green) and chromoplasts (yellow, orange). There are also
other plastids such as rhodoplasts (red); phaeoplasts (brown); cyanoplasts
(blue); proplastids (colourless). In young plant cells, reserve materials are stored
in amyloplasts, proteinoplasts and lipids or elaioplasts.
Figure 1.5 Plastids

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1.5.2 PROPLASTIDS
Amoeboid plastids; 0.4 – 0.9µm in diameter; unit-membrane envelope, stroma

with vesicles and lamellae (originate from envelopes). Inner membrane forming
sac-like compressed vesicles called thylakoids. Other structures in proplastids
include:
➢ Prolamellar body: aggregate of vesicles when leaves are kept in the dark.
If leaves are illuminated after a prolonged etiolation, the prolamellar
bodies become disorganized and a number of thylakoids are formed on its
surface.
➢ Osmiophilic globules: aggregate of fine fibrils termed the “stroma centre”.
➢ Ribosomes
➢ Nucleic acid fibrils (DNA). Areas of low density, network of fine fibrils, each
25-39Å in diameter.
➢ Microfilaments: 50-60Å in diameter, running lengthwise in the stroma near
the plastid envelope.
➢ Plastoglobuli: vary in size and number, lipid storage granules. Number,
size increases with age in chloroplasts.
➢ Phytoferritin: small particles - 55Å in diameter; iron source for
development of photosynthetic apparatus.
1.5.3. AMYLOPLASTS, PROTEINOPLASTS AND ELAIOPLASTS
In young plants proplastids store polysaccharides, lipids and proteins. Proplastids

change to an intermediate stage, the leucoplasts, which then differentiate to
amyloplasts (store polysaccharide – starch), elaioplasts (lipids) and
proteinoplasts (proteins).
1.5.4 CHLOROPLASTS
(a) MORPHOLOGY
Green coloured due to the presence of the pigment chlorophyll. It occurs in

almost all photosynthetic organisms except blue-green algae and photosynthetic
bacteria. There are 1-100 chloroplasts per cell, depending on a species; located
in cytoplasm. They are circular to ovoid in top view, 5µm across, discoidal or
ellipsoidal in side view, 2-3µm high; contains 30% lipids, 50% proteins and 5-
10% pigments.
Pigments with photosynthetic activity are found in small green discs called
grana. A granum is composed of the stacks of thylakoids (Figure 6).
(b) FUNCTIONS

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The main functions of the chloroplasts are photosynthesis; production of

enzymes for the Krebs cycle, and for the synthesis of fatty acids. They
incorporate amino acids in the presence of ATP and are capable of protein
synthesis. Synthesis of ATP occurs only in the presence of light through
photosynthetic phosphorylation (however, in mitochondria oxidative
phosphorylation also occurs in the dark).

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Figure 1.6 The structure of the chloroplasts

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1.5.5 CHROMOPLASTS
End-forms of plastid differentiation, from proplastids or chloroplasts (Figure 1.5).

Chromoplasts are of three types (differentiated according to the aggregation of
pigment carotene): Globular – carotene in lipid droplets (globuli)
Tubular: transformation from the thylakoid system into tubules (carotene
molecules)
Crystalline: contain microscopic crystals of carotenoids.
Root tip of young seedlings have proplastids filled with starch. Older roots have
crystals formed around this starch deposit. As the carotene crystals increase in
size and number the reserve material gradually disappears. The plastid envelope
does not break but all the other contents disintegrate to a watery fluid.
Chromoplasts contain 19-56% carotene, pigment portion 22% protein, 3.3%

RNA, 20% phospholipid and 37% ether-alcohol-soluble matter.
1.5.6 MITOCHONDRIA
(a) ORIGIN
There are three possibilities of origin:

i. de novo formation from previously unorganized cytoplasm. Most
difficult to prove and disprove. No convincing evidence to prove (a) the
starting point and (b) the sequence of mitochondria formation de novo.
ii. formation from other organelles. Some evidence exists for the certain
information of mitochondria from nuclear membranes at certain stages of
the life cycle, and perhaps also forms plastids.
iii. division of the pre-existing mitochondria. Seen in living cells. Electron
micrographs display mitochondrial profiles with narrow regions which
could be compatible with subsequent division. Division by a crystal in-
growth forming a complete plate and fragmentation. Indirect evidence
indicates that some unicellular algae have one mitochondrion which
divides at each cell division. The division hypothesis ascribes a high
degree of autonomy to mitochondria as self-reproducing particles.
Division of pre-existing mitochondria is the best documented at this stage.
(b) MORPHOLOGY AND DISTRIBUTION
In plant cells mitochondria appear as spheres, 1µm or less in diameter, or as

rods and filaments, several micrometers long and 1µm in width, sometimes
branched. Size and form vary greatly within a multicellular organism;
morphological features are fairly constant for any particular type of cell. Size and
shape depend on:

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➢ Functional stage of the cell

➢ Activity of the cell (demand of ATP)
➢ Osmotic pressure of the medium
➢ pH of the medium
➢ Genetic make up
➢ Age of the cell
Mitochondria are randomly distributed in cytoplasm, aggregate around nuclei of

actively metabolizing cells to supply energy. Distribution influenced by
cytoplasmic streaming; cell division – aggregation may occur around the polar
caps.
(c) STRUCTURE
Figure 1.7 The structure of mitochondrion
Mitochondrial envelope consists of two unit membranes. The inner one forms
cristae into the fluid matrix. Unit membranes and perimitochondrial space are
200Å wide (2x60Å+80Å). Pattern of membrane infoldings varies between species
and tissues. Higher plant mitochondria have tubular or saccular in-folds, hence
they are termed microvilli rather than cristae.
Matrix has soluble proteins and lipids. It also contains ribosomes, which account
for part of the RNA found in the mitochondria. Immature mitochondria of young
cells of Zea root tips also have a zone containing filaments, DNA fibrils. An
important feature of mitochondria is the large surface area they provide in the
cell. A cell having 1000 mitochondria (3.5µm long x 1.0µm diameter) has a total
area on the outer surface of the mitochondria 4 times the external surface of the
cell itself. Surface on the cristae double the total area.
(d) FUNCTIONS

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➢ Krebs Cycle: for complete oxidation of pyruvate.

➢ Electron Transport: cytochrome oxidase activity in mitochondria from
higher plant species. Enzyme succinic-cytochrome C reductase and
NADH-cytochrome C reductase have been found active in plant
mitochondria.
➢ Oxidation of Fatty Acids. Enzymes in plant mitochondria for amino acid
synthesis. Transaminases are located in mitochondria.
➢ Ionic composition. The mitochondria regulate the ionic composition of
the cytoplasm by accumulating ions (e.g. K, Ca, Mg, Mn & P) by active
transport mechanism.

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1.5.7 ENDOPLASMIC RETICULUM (ER)
Figure 1.8 The Endoplasmic Reticulum (ER) attached to the nucleus

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(a) STRUCTURE
Double unit membranes in cytoplasm which are separated by a space (watery

fluid and form canals and vesicles) of variable width. It is connected to nuclear
envelope, surrounds it and may be generated from it. Thus the nuclear envelope
and the ER are part of the same system. It is absent in cells of blue-green algae
and bacteria which lack a membrane-bound nucleus. The ER system is hollow
and internal spaces are continuous throughout the cell, connected to
plasmalemma and nuclear envelope and enchylema communicates with
perinuclear space. The surface area increases more or less proportionally with
the volume of the cell, e.g. 400µm2 ER in dividing cells against up to 1000µm2
ER in fully differentiated cells. The ER are either covered in their surface with
ribosomes, 20Å in diameter, and are called Rough Endoplasmic Reticulum, or
have smooth surface, the Smooth Endoplasmic Reticulum.
Factors that influence the structure:

➢ Type of cells, e.g. meristematic or mature cells.
➢ Oxygen concentration: lowering oxygen tension or anaerobic conditions
lead to proliferation and increase in ER.
➢ Chemical substances such as cyanide, ribonuclease, etc. induce
proliferation and increase in ER.
(b) FUNCTIONS
Based on its distribution and structure:

i. Movement of substances: Enchylema allows the movement of substances
throughout the cytoplasm and nuclear envelope.
ii. Distribution of enzymes: Large surface areas of ER allow for some pattern
in the distribution of enzymes.
iii. Protein synthesis: Occurring in rough-surfaces ER.
iv. Carbohydrate metabolism: Occurring in smooth-surfaces ER.
v. Secretion: The ER and Golgi bodies are concerned with transport of
substances to the surface and their secretion.
vi. Movement between cells: Within the enchylema of the ER tubules running
through the plasmodesmata.
vii. Wall synthesis: On the evidence of association with walls (ER lying close
to and parallel with walls).
viii. Synthesis of terpenes: The association in resin canal cells suggests that
ER and plastids are the synthetic units for the resin.
1.5.8 RIBOSOMES
(a) OCCURRENCE AND ORIGIN
Ribosomes are small particles, 20-40Å in diameter, that are responsible for
protein synthesis in cells. They occur in all cells; animal, plant and bacterial cells.

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They occur freely in the cytoplasm or attached to the ER. Ribosomes occurring in
clusters, spirals or circles are called polysomes, polyribosomes or
ergosomes. Ribosomes also occur in plastids, mitochondria and nuclei. There
are about half a million ribosomes in the cell, depending on the type of a cell.
Ribosomes originate in the nucleolus and migrate to the cytoplasm. Alternatively,
they could multiply themselves in the cytoplasm.
(b) STRUCTURE

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Figure 1.9 Structure of Prokaryotic and Eukaryotic Ribosomal Subunits
Ribosomes under electron microscope appear spherical or made of two parts.

Four different stable forms of sedimentation coefficients, expressed in Svedberg
(S) units, are found, namely, 100S, 70S, 50S and 30S. Plants have 80S
ribosomes (40S and 60S sub-units joined). Plastids, mitochondria and bacteria
have 70S ribosomes.
1.5.9 SPHEROSOMES
Spherical organelles, 0.5-1µm diameter, abundantly in nearly all plant cells. They
have single unit membrane and a fine granular appearance. They indicate that
the stroma consists of proteins as well as oil. They are formed by the
accumulation of oil at the end of ER strand, which then becomes cut off by a
constriction to form the growing vesicle. Thus resemble in origin the vacuoles of
some kinds of cells. Their presence indicates the lipid synthesis.

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1.5.10 LYSOSOMES
Figure 1.10 Lysosomes Structure and Functions
Lysosomes are enzyme-containing organelles, similar to spherosomes under the

electron microscope. It has about 0.4µm diameter, single unit membrane and a
dense granular stroma which sometimes contains a large vacuole. Weight is
intermediate between mitochondria and ribosomes.
In plants degradation of organelles or other structures by hydrolytic enzymes, is

part of normal process of differentiation; breakdown of the cross walls of xylem
vessels; degradation of cytoplasmic contents of laticifers; and senescence of
tissues. Lysosomes separate hydrolytic enzymes from cytoplasm thus preventing
autolysis of the cell. Enzymes have low pH optimum, contain large amounts of
acid phosphatase. Several hydrolytic enzymes, a ribonuclease,
deoxyribonuclease, protease, glucuronidase and galacturonidase also occur in
lysosomes and their rupture leads to the disintegration of proteins, nucleic acids,
carbohydrates, etc. Without the rupture of the lysosome membrane, these
enzymes will exhibit no activity.
Lysosomes are absent from bacteria where hydrolytic enzymes are often
secreted outside the cell. Lysosome originates from vesicles derived from Golgi
body or from plasmalemma. They can also be budded off directly from the ER.

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1.5.11 VACUOLE AND TONOPLAST
Together with plastids and a cell wall, the vacuole is one of the three
characteristic features that distinguish plant cells from animal cells. All plant cells
contain a vacuolar system: vacuole, ER, Golgi complex and nuclear envelope.
Vacuoles are membrane bounded regions within the cell that are filled with a
liquid called cell sap. Tonoplast is a single membrane bounding the vacuole.
Tonoplast also lacks ribosomes. The vacuole may originate directly from the
endoplasmic reticulum, but most of the tonoplast and vacuolar proteins are
derived directly from the Golgi complex.
Cell sap (contents of the vacuole) contains many kinds of substances dissolved
in the water or in a colloidal state. Cell sap is usually slightly acidic. In most
cases, vacuoles do not synthesize the molecules they accumulate but instead
receive them from other parts of the cytoplasm.
(a) FUNCTIONS
➢ Vacuoles are important storage compartments for primary metabolites,

such as sugars and organic acids and the reserve proteins in seeds.
➢ They remove toxic secondary metabolites, such as nicotine and tannin,
from the rest of the cytoplasm.
➢ They are often sites of pigment deposition, especially the anthocyanins
which are water-soluble pigments.
➢ They are involved in the breakdown of macromolecules and the recycling
of their components within the cell. Entire cell organelles, such as
mitochondria and plastids, may be deposited and degraded in the vacuole.
1.6 UPTAKE OF SUBSTANCES BY THE CELL
All molecules possess kinetic energy and are constantly in motion. Matter occurs
in any of three forms depending on the kinetic energy of the molecules (solids-
molecules vibrate, liquids-molecules slip passed one another, gas-molecules are
separated from each other).
The result of the constant movement of molecules in gasses and solutions is that
they tend to spread uniformly throughout available space (gas – whole of
container, liquids – whole of space occupied by liquid).
Diffusion can be defined as the net movement of a substance as a result of the

independent motion of its molecules from a region of higher concentration to a
region of lower concentration (concentration gradient).
A process occurring in both directions at equal rates is said to be in equilibrium.

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Matter may exist in mixed form. Individual molecules or ions of one substance,
the solute molecules are scattered among the molecules of another substance-
sugar or salt dissolved in water.
Water always moves from an area of higher water potential to an area of lower
water potential. Water potential is influenced by various factors:
1. increase in temperature results in an increases in KE of the molecules

increasing the water potential
2. the presence of dissolved substances decreases water potential
3. pressure increases water potential
Water moves freely through cellular membranes but the passages of most
dissolved substances are blocked. Such membranes are known as differentially
permeable membranes. The diffusion of water through a differentially permeable
membrane is known as osmosis (Figure 1.11).
Figure 1.11 Osmosis
The water potential of a cell, of which the content does not press against the cell
wall, is lower than that of pure water because of the presence of dissolved
substances in the cell sap (cell solution). If placed in pure water, there will be a
net movement of water into the cell. The increasing volume of the vacuole will
cause the cell content to be pressed against the cell wall. The resulting pressure
is known as turgor pressure and this will cause the water potential of the cell to
increase. Eventually a stage will be reached when the movement of water in both
directions (in and out) is equal (equilibrium).

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If the water potential of the cell is higher than that of the external solution the cell
will lose water. In plant cells in which water loss by osmosis has become severe,
the cytoplasm and plasma membrane pull away from the cell walls, and the cells
are then said to be plasmolyzed. This can be achieved by dissolving sucrose in
the external solution (Figure 1.12).
Figure 1.12 Plasmolysis
1.6.1 Transport of solutes across the membrane
Hydrophobic molecules (such as oxygen) and small, uncharged polar molecules

(such as water and carbon dioxide) can permeate cell membranes freely by
simple diffusion. Most substances required by cells are polar and require
transport proteins to transfer them across membranes. Three types of transport
proteins, forming part of the membrane, are present in a plant cells.
Carriers bind to the specific solute being transported and undergo a

conformational change in order to transport the solute across the membrane.
Channel proteins from water filled pores that extend across the membrane and,
when open, allow specific solutes (usually inorganic ions of appropriate size and
charge) to pass through.
Pumps are driven by either chemical energy (ATP) or light energy, and typically
are protons pumps (H+). This causes an electrical gradient across the
membrane and together with the concentration gradient it is known as the
electrochemical gradient. This facilitates the transport by carrier and channel
proteins of charged substances (K+, Ca2+ etc.) (Figure 1.13).

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Figure 1.13 Proton pump

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1.7. MITOSIS AND MEIOSIS
Interphase
Preparation phase for both mitosis and meiosis. Interphase can be divided into
three phases, namely:
Gap phase 1 (G1): cell doubles in size; organelles, enzymes, and other
molecules increase in size.
Synthesis phase (S): DNA replicated and associated proteins synthesized to
form two copies of cell’s genetic information.
Gap phase 2 (G2): structures required for cell division begin to assemble;
chromosomes begin to condense.
1.7.1 MITOSIS
Mitosis is a continuous process with four stages: prophase, metaphase,

anaphase and telophase. Interphase: replication of DNA and chromosomes.
Ensure equal distribution of chromosomes to daughter cells.
Prophase
Early prophase: Chromosome coiling begins. Late prophase: Coiling advances;
sister chromatids pair; nucleolus disperse throughout the nucleus. Breakdown of
nuclear envelope.
Metaphase
Presence of a complete spindle, composed of microtubules (250Å diameter);
continuous (pole to pole) and chromosomal microtubules (pole to centromere –
site of insertion is called the kinetochore); sister chromatids pairs become aligned
on the metaphase plate by their centromeres.
Anaphase
Division of centromeres. Chromatids separate – now called daughter
chromosomes, and move towards opposite poles.
Telophase
Nuclear envelope develops; nucleolus reforms; spindle microtubules disappear;
nucleus returns to interphase state. Chromosomes uncoil, telophase followed by
cytokinesis.
1.7.2 Duration of mitotic stages and chromosome numbers
Duration of mitotic stages (in minutes)
Species Inter Pro Meta Ana Telo

Onion (root tip) 20 71 6.5 2.4 3.2
Pea (root tip) 20 78 14.4 4.2 13.2

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Early Prophase
Late Prophase
Metaphase
Anaphase
Telophase
Figure 1.14 Stages of mitosis

31
1.7.3 MEIOSIS
Chromosome and DNA replication takes place during interphase, preceding

prophase of meiosis.
Important features of meiosis are: Meiosis reduces chromosome number from

diploid (2n) to haploid (n); Four haploids, each contain one set of chromosomes
with all the required genetic information.
Mechanism through which new gene combinations are formed:

➢ Homologous chromosomes (2n) are distributed in numerous combinations
(n).
➢ Genetic exchange during prophase
1.7.3.1 First Division (Meiosis I, reduction division)
Prophase I
Leptotene (Leptonema) marks the end of pre-meiotic interphase; chromosomes

are threadlike; a nucleolus is present.
Zygotene (Zygonema, Zynaptene) Chromatin threads have assumed the

typical chromosome appearance; Homologous pairs of chromosomes undergo
synapsis (i.e. line up side by side, chromomere to chromomere); Aligned lateral
elements are separated by a central region (1000Å diameter synaptinemal
complex dense, striated element – electron translucent gap – central dense
element – electron – translucent gap – dense, striated element).

32
Figure 1.15 Stages of Prophase 1

33
Pachytene (pachynema) Chromosomes shortened and thickened;

Chromosomes coiling and condensation continued; Sister chromosomes difficult
to distinguish, called bivalent (each synapsed set to homologoues, four
chromatids).
Diplotene (Diplonema) Repulsion among four chromatids. Complete repulsion

prevented by (i) centromeres (ii) chiasmata (singular chiasma) between non-
sister chromatids in a bivalent. (Chiasma: short lengths of synaptinemal complex
that have not been shed).
Diakinesis Chromosomes maximally condensed. Nucleolus and nuclear

envelope disappear.
Metaphase I
Spindle appears; bivalent chromosomes orient onto the equatorial plate;
Centromeres of bivalent chromosomes on long axis of spindle; Terminal
chiasmata between bivalents.
Anaphase I
Chiasmata released, migration towards poles; Chromatids held together by
centromeres.
Telophase I
Segregation completed.
NB: Two possibilities

Meiosis II follows immediately – no nuclear membrane, nucleolus, etc, or
Nuclear membrane formed, nucleolus reappears, chromosomes uncoil, cell
divides (haploid (n) chromosomes) and interphase before meiosis II.
1.7.3.2 Interphase
Brief – no replication of chromosomal DNA.
1.7.3.3 Second division (Meiosis II, equational division)
Meiosis II is indistinguishable from a mitotic division.
Prophase II
Nucleolus disappears, nuclear membrane disintegrates; Chromosomes haploid;
Chromatids different from mate, attached to centromere.
Metaphase II
Chromosomes migrate to equatorial plate with centromeres attached to spindle
fibres.
Anaphase II

34
Centromeres divide, separating chromosomes towards poles.
Telophase II
Chromosomes at poles, elongate; Nuclear membranes form; nucleoli reappear.
Cell division takes place (cytokinesis).
Figure 1.16 Stages of meiosis:

(a) Early Prophase I; (b) Late Prophase I; (c) Metaphase I; (d) Anaphase I; (e)
Telophase I; (f) Prophase II; (g) Metaphase II; (h) Anaphase II; (i) Telophase II;
(j) Haploid cells (gametes) after cytokinesis

35
2. PLANT BIOCHEMISTRY
2.1 PRINCIPAL CHEMICAL SUBSTANCES OF THE CELL
ESSENTIAL ELEMENTS
An element is regarded as essential to plants if plants cannot complete their life

cycles in the absence of such an element.
The following elements are essential to all plants:
Hydrogen (H) 1 Carbon (C) 4

Oxygen (O) 6 Nitrogen (N) 5
Phosphorus (P) 5 Potassium (K) 1
Calcium (Ca) 2 Magnesium (Mg) 2
Sulphur (S) 6 Iron (Fe) 2
Manganese (Mn) 2 Copper (Cu) 1
Zinc (Zn) 2 Chlorine (Cl) 7
Boron (B) 3 Molybdenum (Mo) 3
Some plants also require the following elements:
Sodium (Na) 1 Silicon (Si)
Organic substances contain carbon-hydrogen bonds and may also contain in

addition to this oxygen, nitrogen, sulphur and phosphorus. Carbon, hydrogen,
oxygen and nitrogen is responsible for about 90% of a plants dry weight. Carbon
combine with other carbon atoms to form chain-like molecules and this
comprises the backbone of organic compounds. Carbon has four electrons in its
outer shell and can therefore form 4 chemical bonds of the covalent type (Figure
2.1).
Figure 2.1. Covalent bonds between two carbon atoms

36
The sharing of one pair of electrons, between two carbon atoms, results in a
single bond, two pairs in a double bond and three pairs in a triple bond. Single
bonds between carbon atoms are referred to as saturated bonds while double or
triple bonds are called unsaturated.
Types of organic compounds and functional groups
Hydrocarbons (Figure 2.2)
Strait chain - pentane

Branched chain - methylbutane
Ring structure - cyclopentane
Figure 2.2 Types of organic compounds
Functional groups
Nearly all organic compounds composing the living cell are hydrocarbon
derivatives, possessing in addition to carbon and hydrogen the atoms oxygen
and nitrogen and to a lesser extent phosphorus, sulphur, and certain metals. In
most instances these additional atoms are chiefly responsible for the chemical
reactivity of the organic compound (Figure 2.3)

37
Figure 2.3 Functional groups
Alcohol or hydroxyl group
Carbonyl group
Aldehyde – carbonyl group on end of chain
Ketone – carbonyl group not on end of chain
Carboxylic acid group
Ester group
Amino group
Sulfhydryl group
Phosphate group
Carbohydrates
A carbohydrate as an organic compound that contains a carbonyl group

(aldehyde or ketone) in addition to two or more alcohol groups or that yields such
compounds upon hydrolysis.
Monosaccharides
Monosaccharides cannot undergo hydrolysis to form simpler sugars and are

classified according to the length of their chains (Figure 2.4)
Trioses (3-carbon compounds)

Tetroses (4-carbon compounds)

38
Pentoses (5-carbon compounds)

Hexoses (6-carbon compounds)
Figure 2.4 Monosaccharides
Disaccharides
If two monosaccharide molecules are united with the loss of a water molecule, a
disaccharide is formed. This process is known as dehydration synthesis (maltose
and fructose) (Figure 2.5)

39
Figure 2.5 Dehydration synthesis of sucrose and maltose
Polysaccharides
When many molecules of the same kind are linked together in a chain, the
product is called a polymer. Polysaccharides are composed of a large number of
monosaccharides chemically linked to each other (polymerization). The most
likely monomer is glucose and up to 10 000 glucose molecules can be linked to
form a polysaccharide. The most abundant polysaccharides in plants are starch
and cellulose. The building block of starch is – glucose (alpha-glucose) and of
cellulose – glucose (beta-glucose) (Figure 2.6). Other important polysaccharides
are inulin, hemicellulose, and pectic acid. The monomer of inulin is fructose.

40
A.
B.
C.
Figure 2.6 (A) Alpha-ring, straight chain, and beta-ring form of glucose. (B)
Straight-chain starch (amylose), branched-chain starch (amylopectin), and
the spiral structure of starch. (C) Cellulose.

41
Lipids
Fats
A fat consists of glycerol (a three carbon alcohol) with a fatty acid attracted to
each of its three carbon atoms. The fatty acid becomes attached to glycerol by a
dehydration between the hydroxyl group (-OH) of glycerol and the hydroxyl group
which is part of the carboxyl group (-COOH) on the end of the fatty acids (Figure
2.7).
Saturated fatty acids

Name Formula
Lauric CH3(CH2)10COOH
Myristic CH3(CH2)12COOH
Palmitic CH3(CH2)14COOH
Stearic CH3(CH2)16COOH
Unsaturated fatty acids

Name Formula
Oleic CH3-(CH2)7-CH=CH-(CH2)7-COOH
Linolenic?
Figure 2.7 Dehydration synthesis of a lipid molecule. Three water

molecules are lost during the synthesis of one lipid molecule

42
Phospholipids
These are fats in which molecules of fatty acid are attached to two carbon atoms
of glycerol, but phosphate is attached to the third carbon atom. This makes one
end of the molecule water soluble, while the rest is not (Figure 2.8).
Figure 2.8 Phospholipid molecule showing the hydrophilic head and the
hydrophobic tail
Waxes
Waxes are composed of a fatty acid combined with a long-chain alcohol.
Proteins
The fundamental constituents of proteins are amino acids. There are twenty
different amino acids found in proteins. All amino acids have two functional
groups, (amino group and carboxylic acid group) both attached to the – carbon
(Figure 2.9).

43
Figure 2.9 Structure of amino acids
The nature of R determines the characteristics of a particular amino acid.
Amino acids containing on amino group and one carboxyl group are neutral,
additional amino groups basic, and additional carboxyl groups acidic (Figure
2.10).
Nonpolar- R group does not participate in hydrogen bond formation

(hydrophobic).
Polar- R group participates in hydrogen bond formation (hydrophilic).
Acidic- Have two carboxylic acid groups.
Basic - Have two amino groups.

44
Figure 2.10 Different types of amino acids (different numbers of amino and
acid groups)

45
Peptides
Amino acids can react with each other by condensation: the amino group of one
amino acid molecule reacts with the carboxyl group of another with the
elimination of water (dehydration synthesis).
The bond that is formed is called a peptide bind, and the resulting compound is a
dipeptide. Three amino acid molecules will combine in this way to form a
tripeptide, and so on (Figure 2.11A). If many amino acids are joined in this way a
polypeptide is formed (Figure 2.11B).
A.
B.
Figure 2.11 (A) Formation of a peptide bond by a dehydration synthesis

between two amino acids, with a product of a dipeptide. (B) Polypeptide
Proteins
Proteins are polypeptides containing 50 or more amino acids. The primary
structure of a protein is the linear sequence of amino acids in its molecule.
Proteins differ from each other in the variety numbers and order of their
constituent amino acids.
The secondary structure of a protein refers to the tendency of the chain of amino
acids to assume a coiled or twisted structure rather than lying in a single plane
(Figure 2.12).

46
Figure 2.12 Primary and secondary protein structure
In addition to the coiling, there is a certain amount of folding of the long chain on
itself. This results from an attraction of certain amino acids to others in the chain.
This folding produces the tertiary structure (Figure 2.13).
Figure 2.13 Tertiary structure of a protein

47
Many complex proteins exist as aggregations of polypeptide chains held together

by various forms of bonding. Their precise arrangement is described as the
quaternary structure of proteins.
Nucleic acid
Nucleic acids are long, thread-like macromolecules built up of nucleotides, just as

proteins are long polymers or amino acids. A nucleotide consists of a pentose
sugar, a nitrogenous base, and phosphoric acid.
The sugars in nucleic acids are five carbon sugars (pentose), which exist in a
five-sided ring form. Two pentose sugars occur in nucleic acids namely
deoxyribose and ribose. Deoxyribose lacks an oxygen atom (indicated by the
prefix ‘deoxy’) which is present in ribose. (Figure 2.14)
Figure 2.14 Ribose and deoxyribose; and the nitrogenous bases of nucleic
acids

48
There are two major types of nucleic acids in cells, deoxynucleic acid (DNA) and
ribonucleic acid (RNA). DNA contains only deoxyribose and RNA only ribose.
There are two classes of nitrogen bases namely pyrimidines (one ring) and
purines (two rings) found in nucleic acids (Figure 30). Three pyrimidine-derived
bases (thymine (T); cytosine (C) and uracil (U) and two purine-derived bases
(adenine (A) and guanine (G)) are found in nucleic acids. DNA contains A, G, T
and C while RNA contains A, G, U and C (Figure 2.15).
Figure 2.15 Nucleotides the building blocks of DNA and RNA

49
A nucleic acid molecule is a string of nucleotides. The nucleotides are linked

together by covalent bonds between the phosphate group of one nucleotide and
the sugar of the next (Figure 2.16). DNA has a double stranded helical structure
with the nitrogen bases projecting towards each other forming base pairs as.
The bases are held together by hydrogen bonds (Figure 2.16).
Figure 2.16 The structure of one strand of DNA
Base pairing follows a very specific pattern and is only possible between bases:
adenine-thymine and guanine-cytosine (Figure 2.17). In RNA thymine is replaced
by uracil.

50
Figure 2.17 Base pairing in a double helical structure of DNA

51
PHOTOSYNTHESIS
Photosynthesis is the single most important biochemical process on earth. The

term photosynthesis (photo-light; synthesis-manufacture) refers to the process
whereby green plants use light energy for the synthesis of sugar from carbon
dioxide and water, with oxygen releases as by- product.
Light
6CO2 + 13H2O —› C6H12O6 +6H2O + 6O2
Chloroplast
With photosynthetic pigments
(Chlorophyll a and b, carotenoids and phycobilins)
Light
Light is a form of the electromagnetic radiation produced by the sun. Visible light
forms only a small fraction of the total electromagnetic radiation reaching the
earth (Figure 2.18).
Figure 2.18 Electromagnetic spectrum
Light from the end and blue regions of the spectrum is absorbed by plants while
most of the green light is reflected or transmitted.
If we describe light in terms of its detectable effects on matter light have both
wave and particle characteristics. Light travel in waves of different lengths, and
the amount of energy varies inversely with the wavelength of the light.
(Wavelength is the distance between the crest of one wave and the crest of the
next wave). Different wavelength can be separated by a prism (Figure 2.19).
According to the particle theory, light is composed of particles of energy called
protons.

52
Figure 2.19 Separation of different wavelengths of light
Pigments of photosynthesis
The first step in the conversion of light to chemical energy is the absorption of
protons by pigment compounds in photosynthetic cells. Chlorophyll a (Figure
2.20) is the principal pigment active in photosynthesis and occurs in all
photosynthetic eukaryotic cells and cyanobacteria. Other forms of chlorophyll are
active in bacteria.

53
Figure 2.20 Chlorophyll a and b
The other pigments involved in photosynthesis are all accessory pigments and
light energy absorbed by them is first passed on chlorophyll a before it is
transformed to chemical energy. These are: Chlorophyll b (found in vascular
plants, bryophytes, green algae, and euglenoid algae), carotenoid pigments (all
photosynthetic plants contain one or more carotenoids) (Figure 2.21), and
Phycobilins (found in cyanobacteria and red algae).

54
Figure 2.21 Beta-carotene
Absorption and action spectra
Absorption spectrum is a graph that shows the amount of light a pigment absorbs
at a particular wavelength (Figure 2.22).
Figure 2.22 Absorption spectra of pigments and action spectra of

photosynthesis
An action spectrum is a graph that shows the amount of photosynthesis that

takes place at a particular wavelength (Figure 2.22). From the graph it should be
clear that the photosynthetic pigments absorb light in the blue and red regions of
the spectrum, the wavelengths most effective in photosynthesis. Chlorophylls a
and b have a phytol tail and a porphyrin head. In the chloroplast the head
associates with proteins and the tail with lipids. Carotenoids are fat soluble and
embedded in the thylakoid membrane.

55
Photosynthesis II and I
The photosynthetic pigments are located in the thylakoid membranes and are
organized into two different types of photosystems. The photosystems consist of
about 300 pigment molecules, various enzymes, and electron-acceptor
molecules. In each photosystem these are arranged into two closely linked
components: an antenna protein complex and a reaction centre protein-pigment
complex. A pair of chlorophyll a molecules are situated at the core of each
reaction centre. The absorption maxima of the chlorophyll molecules at the
reaction centres of photosystem II and I 680 nm and 700 nm respectively. The
difference in absorption maxima is caused by the proteins holding the chlorophyll
molecules in position. All other pigment molecules are arranged in such a way
that the energy they absorb is channeled to the reaction centre.
The electron carriers associated with photosystem II (P680) are Q, cytochrome b3,
plastoquinone cytochrome f, and plastocyanin.
The electron carriers associated with photosystem I (P700) are ferredoxin,

flavoprotein and NADP (Figure 2.23)

56
Figure 2.23 Photosystem II and I

57
Synthesis of NADPH and ATP
When a P680 molecule is excited by energy received from the antenna molecules,
its energized electron is transferred to an acceptor molecule designated Q. This
high energy electron is passed down a chain of electron carriers to plastocyanin.
When a P700 molecule is excited by energy received from the surrounding
antenna molecules, its energized electron is transferred to ferredoxin. This high
energy electron is passed on to a flavoprotein and then to NADP + which is
reduced to NADPH.
The electron lost form P680 is replaced by electrons extracted from water. This
light-dependent oxidative splitting of water molecules is called photolysis. The
electron lost from P700 is replaced by an electron from reduced plastocyanin.
Thus, in the light there is a continuous flow of electrons from water to
photosystem II to Photosystem I to NADP+. Whenever a substance in this chain
receives an electron it is reduced. When the electron is passed to the next
electron carrier it is oxidized. This flow of electrons can be seen as a chain of
REDOX reactions.
During the protolysis of water, protons (a hydrogen atom does not have a
neutron but only one electron and one proton-a hydrogen atom without an
electron is a proton are released on the inside of the thylakoid membrane. The
transfer of electron from Q to plastocyanin results in the transfer of protons from
the outside of the thylakoid to its inside. The reduction of NADP+ to NADPH
results in a further lowering of the proton concentration on the outside of the
thylakoid (stroma). All this result in the creation of a proton concentration
gradient from the inside of the thylakoid to the outside. This gradient causes the
H+ to move from the thylakoid space back into the stroma through the enzyme
ATP synthetase located in the thylakoid membrane. For every three H+ flowing
through the ATP synthetase one ATP is synthesized (Figure 2.24)

58
Figure 2.24 Chemiosmotic coupling mechanism of photophosphorylation
The products of the light reaction of photosynthesis are NADPH and ATP. Both
are produced in the stroma.
Dark reaction-assimilation of CO2
The ATP and NADPH produced in the stroma during the light reaction drives the
reduction of CO2 to carbohydrate. There are two major carbon assimilation
pathways namely the C3 pathway or Calvin cycle and the C4 pathway.
C3 pathway (Calvin cycle) (C3 plants)
The initial reaction is the joining of CO2 to the five-carbon sugar ribulose 1,5-
bisphosphate (RuBP) to form a short-lived six-carbon molecule that breaks down
into two molecules of the three-carbon sugar 3-phosphoglycerate. The enzyme
that catalyzes the addition of carbon dioxide to RuBP is RuBP carboxylase
(Rubisco). In the following reactions 3-phosphoglycerate is converted to 1, 3

59
bisphosphoglycerate. The energy and phosphate needed for this reaction comes
from ATP (product of the light reaction) which is converted to ADP. In the next
reaction the 1, 3-bisphosphate is reduced to glyceraldehyde 3-phosphate by
NADPH (Figure 2.25). The diagram shows six turns of cycle (6 CO2 molecules
assimilated). The glyceraldehydes 3-phosphate is a key compound.
Glyceraldehyde 3-phosphate molecules can be used for the regeneration of
RuBP and the synthesis of other products.
Figure 2.25 C3 pathway of carbon assimilation
C4 pathway (C4 plants)
In C4 plants the C3 pathway is coupled to the C4 pathway. The enzymes

catalyzing the C4 pathway are located in the mesophyll cells and those catalyzing
the C3 pathway in the bundle sheath cells. In the C4 pathway CO2 reacts with
phophoenolypyruvate (PEP). This reaction is catalyzed by phosphoenolpyruvate
carboxylase (PEP carboxylase). The oxaloacetate, a four carbon compound
formed in the process is reduced to malate. The malate diffuses from the
mesophyll cells to the bundle sheath cells where it is decarboxylated to yield
CO2. The CO2 then enters the C3 pathway. The PEP resulting from the
decarboxylation diffuses back to the mesophyll cells and is now available for
another cycle. (Figure 2.26)

60
Figure 2.26 C4 pathway and its interaction with the C3 pathway
RESPIRATION
Respiration is the process by which the chemical energy of carbohydrates is

transferred to ATP, the universal energy carrier molecule. When ATP is
converted to ADP this energy is made available to other energy-requiring
processes. The process of respiration, starting with glucose and ending with

61
carbon dioxide and water is commonly viewed as taking place in three major
phases called glycolysis, the Krebs cycle, and electron transport.
Glycolysis
In the first portion of glycolysis two molecules of high- energy ATP are used to
add two phosphate groups to the 6-carbon sugar, resulting in the displacement of
two protons (Figure 2.27). This double phosphorylated sugar, that is, as 6-carbon
sugar with a phosphate group on each end, is then split to produce two 3-carbon
sugar phosphates. In the next portion each of these 3-sugar phosphates is again
phosphorylated, this time using phosphate available in the cytoplasm, instead of
phosphate from ATP. These 3-C sugar bisphosphates are then oxidized, that is,
they lose two electrons and a proton to NAD+, reducing it to NADH. In the last
portion of the glycolysis the two phosphates on each of the 3-sugar
bisphosphates are used in the synthesis of two molecules of ATP from ADP.
The oxidation and loss of phosphates produces pyruvic acid, the 3-C end-product
of glycolysis. The summary equation for glycolysis may be written in the following
way (where Pi stands for inorganic phosphate, PO43-):
Glucose + 2ATP +4ADP+ 2NAD+ + 2Pi

→ 2 pyruvic acid + 2ADP + 4ATP +2NADH

62
Figure 2.27 Steps in glycolysis
Krebs cycle
Pyruvic acid produced in glycolysis moves into the inner compartment of the
mitochondria where it undergoes a complex enzyme catalyzed reaction referred
to as an oxidative decarboxylation. Loss of a carbon from the 3-C pyruvic acid

63
leaves a 2-C unit called an acetyl group. This group becomes attached to a large
molecule called coenzyme A to form acetyl coenzyme A (acetyl CoA) (Figure
2.28). In the first step of the Krebs cycle the 2-C acetyl group from CoA combines
with a 4-C organic acid called oxaloacetic acid to form a 6-C oxaloactic acid by a
series of reactions involving the loss of two carbon atoms as CO2. Thus, the
reaction series is truly a cycle since it begins with oxaloacetic acid, a 2-C
fragment is added, and then two carbons are removed as CO2, producing
oxaloacetic acid again. Four of the steps of the Krebs cycle are Redox reactions
in which intermediates are oxidized and coenzymes reduced (3 NAD+ and 1 FAD
per cycle).

64
Figure 2.28 The Krebs cycle and its link with glycolysis

65
Electron-transport pathway
The electrons that reduce the coenzymes during glycolysis and the Krebs cycle
are high energy electrons (compare NADPH in photosynthesis with NAD). In a
series of oxidation reduction reactions, along the electron transport chain the
energy content of the electrons is gradually lowered as they are transferred to
oxygen to form water. The energy released by the electrons is used for the
synthesis of ATP (3 ATP is synthesized for every NADH and 2 ATP for every
FADH2) (Figure 2.29).
Figure 2.29 A summary of respiration showing the electron transport chain
Synthesis of ATP
The electron carriers (electron transport chain) are arranged in the membrane so
that protons are picked up on one side of the membrane and released on the
other. This results in a proton gradient and an electrical gradient generated
across the membrane. The flow of protons back into the matrix, along this
gradient, through the enzyme complex ATP synthase, drives the synthesis of
ATP from ADP and Pi (compare with photosynthesis) (Figure 2.30).

66
Figure 2.30 ATP synthesis
ATP yield from the complete oxidation of a glucose molecule
Glycolysis (in ground substance of the cytoplasm) ATP

Phosphorylation of glucose -1
Phosphorylation of fructose-6-p -1
Dephosphorylation of 2x (1, 3-bisphosphoglycerate) +2
Dephosphorylation of 2x (phosphoenolpyruvate) +2
2 NADH formed
Pyruvate to acetyl CoA 2x (in mitochondria)
2 NADH formed
Citric acid cycle 2x (in mitochondria)
6 NADH
2 FADH2
Oxidative phosphorylation (in mitochondria)
2 NADH from glycolysis +6

2 NADH from oxidative decarboxylation of pyruvate +6
6 NADH from citric acid cycle +18
2 FADH2 from citric acid cycle +4
Total +36

67
SYNTHESIS OF NUCLEIC ACIDS AND PROTEINS
The main form for incorporation of nitrogen into organic form is by means of
amination of –ketoglutaric acid, a Krebs cycle intermediate, to form glutamic acid.
Other amino acids formed by the transfer of the amino group from glutamic acid
to other organic acids (pyruvic acid, fumaric acid etc.).
Amino acids can be joined to each other by means of peptide bonds to form
proteins. The role of DNA is to instruct the cell to make specific proteins. The
sequence of bases in DNA (genetic code) determines the sequence of amino
acids of a protein.
Because of the pairing pattern the two strands of DNA are complementary. If the
double helix uncoils the single strands can act as templates for the synthesis of
new complementary strands. In the self-replication of DNA a strand of DNA with
base composition ATCGGACG will determine a complementary strand of bases
that reads TAGCCTGC (T-thymine, A-adenine, G-guanine, C-cytosine), since T
always pairs with A, A with T, G with C, and C with G. The synthesis of new
strands is catalyzed by enzymes known as DNA polymerases (Figure 2.31).

68
Figure 2.31 DNA-self replication and mRNA synthesis
Molecules of RNA are synthesized by a process known as transcription, which is

similar to DNA replication. In eukaryotic cells, there are different enzymes, called
RNA polymerases, for the transcription of messenger RNA (mRNA), transfer
RNA (tRNA), and ribosomal RNA (rRNA). Each single stranded RNA molecule is
formed along one strand of the DNA helix by the same base-pairing copying
principle that applies to the formation of a new strand of DNA. The presence of
adenine in the parent DNA strand leads to the insertion of uracil, instead of
thymine, in the RNA strand
Proteins are made from twenty different types of amino acid. An average protein
contains several hundred amino acids, condensed together in a specific
sequence. DNA consists of only four different bases. Thus there are only four
‘letters’ to the base code ‘alphabet’. A combination of three bases is required to
code for a particular amino acid. The triplet codes for all amino acids have been
determined. Only two amino acids are coded for by a single triplet code: AUG-
methionine and UGG-tryptophane. A few others have two codons. Most amino
acids are coded for by several triplet codes, up to a maximum of six.
DNA directs the formation of proteins through the activities of three different RNA
intermediates.
mRNA is synthesized on the DNA template in the nucleus and is composed of a

single strand ranging from 1000 to 10000 bases. In order for mRNA synthesis to
occur, the hydrogen bonds of the DNA double helix must separate into two
complementary single strands. The single-stranded DNA determines the
synthesis of an mRNA strand that is exactly complementary to itself. A DNA base
sequence of ATCGGACG will determine a complementary base sequence that
reads UAGCCUGC (note that U (Uracil) has replaced T (thymine), in RNA). After

69
mRNA is synthesized in the nucleus, it moves from the nucleus across the
nuclear membrane to the cytoplasm, where protein synthesis occurs.
Ribosomes are composed of two unequal subunits, and these contain rRNA and
numerous proteins. The mRNA attaches itself to the smaller of the two subunits.
There is a specific tRNA molecule for every one of the twenty different amino
acid (for most there is more than one-triplet code above). On the one side it
attaches to an amino acid while the other side attached to mRNA as directed by
the triplet codes. In this way the amino acids are lined up in the sequence of a
particular DNA.
All metabolic activities in the cell are controlled by enzymes which are all
proteins. All activities of the cell are therefore controlled by DNA.

70
Figure 2.32 An overview of transcription and translation

71
3. MOVEMENT OF WATER THROUGH THE PLANT
3.1 WATER UPTAKE BY ROOTS (ABSORPTION)
Absorption takes place through the epidermis of the younger roots. Root hairs
provide an increased surface area for absorption. Soil-plant-atmosphere
pathway: soil – root hairs – exodermis (if present) – cortex – endodermis –
pericycle – vascular cylinder – xylem (of the root) – stem – leaves – atmosphere.
Water may follow one or more of the three possible pathways across the root
(Figure 3.1):
➢ Apoplastic: water movement via the cells’ walls.
➢ Symplastic: water movement from protoplast to protoplast via
plasmodesmata.
➢ Transcellular: water movement from cell to cell, passing from vacuole to
vacuole.
In roots without an exodermis, water can move apoplastically as far as the
endodermis (because of the presence of Casparian strips).
Figure 3.1 Water uptake by the roots

72
(a) Root Pressure and Guttation
The driving force for the movement of water across the root is the difference in
water potential between the soil solution at the surface of the root and the fluid
contents of the xylem – the xylem sap. When transpiration is very slow or absent,
the gradient of water potential is brought about by the secretion of ions into the
xylem. Because the vascular tissue of the root is surrounded by the endodermis,
ions do not leak back out of the xylem. The water potential of the xylem becomes
more negative, and water moves into the xylem by osmosis through the
surrounding cells. A positive pressure, called root pressure, is created, and it
forces both water and dissolved ions up the xylem. Dew-like droplets of water at
the tip of grass and other leaves in the early morning demonstrate the effects of
root pressure. These droplets come from within the leaf by a process known as
guttation (Figure 3.2). They exude through openings in special structures called
hydathodes (stomata that lack the capacity to close and open), which occur at
the tips and margins of leaves. Root pressure is:
➢ Least effective during the day.
➢ Never becomes high enough to force water to the top of a tall tree.
➢ Many plants (e.g. pine), do not develop root pressure.
Figure 3.2 Guttation through hydathodes

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Thus, root pressure can perhaps be regarded as a by-product of the mechanism

of pumping ions into the xylem and as a subsidiary means of moving water into
the shoot under special conditions.
(b) Passive Water Absorption
During periods of high transpiration rates, ions accumulated in the xylem of the
root are swept away in the transpiration stream and the amount of osmotic
movement across the endodermis decreases. The root become passive
absorbing surface through which water is pulled by bulk flow generated in the
transpiring shoots. Most absorption of water by the roots of transpiring plants
occurs in this passive manner. Roots come into contact with additional water by
growth.
3.2 WATER POTENTIAL: THE COHESION-TENSION MECHANISM
Experiments using radioactive isotopes and staining confirm that water travel by
way of vessel elements (tracheids) in the xylem. When water evaporates from
the cell wall surfaces bordering the intercellular spaces in the interior of a leaf
during transpiration, it is replaced by water from within the cell. This water
diffuses across the plasma membrane, which is freely permeable to water but
not to the solutes of the cell. As a result, the concentration of solutes within the
cell increases and the water potential of the cell decreases. A gradient
(imbalance) of water potential then becomes established between this cell and
adjacent, more saturated cells. These cells, in turn, gain water from other cells
until eventually this chain of events reaches the vein and exerts a “pull’, or
tension, on the water of the xylem. Because of the cohesiveness (strong
bonding) of water molecules, this tension is transmitted all the way down the
stem to the roots, so that the water is withdrawn from the roots, pulled up the
xylem, and distributed to the cells that are loosing water vapour to the
atmosphere. This water loss makes the water potential of the roots more
negative and increases the capacity to extract water from the soil. Hence, the
lowered water potential in the leaves, brought by transpiration and/or by the use
of water in the leaves, results in a gradient of water potential from the leaves to
the soil solution at the surface of the roots. This gradient of water potential
provides the driving force for the movement of water along the soil-plant-
atmosphere continuum. This is known as the cohesion-tension theory because
it depends on the cohesiveness of water, the property of water that permits it to
withstand tension.
However, the theory might also be known as the cohesion-adhesion theory

because the adhesion of the water molecules to the walls of tracheids and
vessels of the xylem and to the cell walls of the leaf and root cells is as important
as the rise of water are cohesion and tension (Figure 3.3). The cell walls along
which the water moves have evolved as a very effective water-attracting surface,
taking maximal advantage of water’s adhesiveness and thus providing a situation

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in which cohesiveness is readily expressed. The tensile strength of water

prevents the pulling apart of water molecules under the tension required to move
water up the xylem of tall trees. The calculated values for the tensile strength of
water are very high: between 130 and 150 megapascals, or possibly as high as
1500 megapascals.
Figure 3.3 Water Transport in Plants (Cohesion and Adhesion Mechanism)

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The cohesion-tension mechanism can be tested by:

➢ Measuring the tension of water within the xylem (pressure chamber).
➢ Measuring the velocity of sap flow in various parts of the tree (small
heating element; a sensitive thermocouple).
➢ Measurement of minute (small) changes in the diameter of the trunk.
NB. The energy for evaporation of water molecules and thus for movement of
water and inorganic nutrients through the plant body is supplied by the sun and
effected by the cohesive and adhesive properties of water.
3.3 TRANSPIRATION
Transpiration is the loss of water from the plant, in the form of vapour, though the
stomata of leaves and sometimes young stems. Plants “imbibe” (absorb) much
greater amounts of water than animals and nearly 99% of the absorbed water is
released by plant into the air as water vapour. Plants loose a lot of water
because they spread their leaves to trap sunlight and also open their stomata to
allow CO2 entrance for the process of photosynthesis. Carbon dioxide must be
absorbed in a form of solution, therefore water is exposed to the air when it
comes into contact with CO2 and hence transpiration occurs.
3.4 REGULATION OF TRANSPIRATION
Excessive transpiration (exceeding water uptake) retards growth and kills plants
by dehydration. Plants have not developed a structure favourable to the entrance
of the CO2 essential for photosynthesis but unfavourable to the loss of water
vapour by transpiration. A number of special adaptations minimize water loss
while optimizing CO2 gain.
(a) Cuticle and Stomata
Cuticle is a transparent, protective layer of leaves and young stems, composed

of wax embedded in cutin (cuticular wax). Leaves are covered by a cuticle that
makes their surfaces impervious to both water and CO 2. A small fraction is
transpired through this protective outer coating and another small fraction
through the lenticels in the bark. Stomata are small openings surrounded by two
guard cells, which can change their shape to bring about the opening and closing
of the pore. Stomata are abundant in the leaves but are also found in young
stems. The number of stomata may be quite large; for example, there are
approx. 12 000 stomata/cm2 of leaf surface in tobacco (Nicotiana tabacum)
leaves.
The stomata lead into the air spaces that surround the thin-walled mesophyll
cells within the leaf. The air in these spaces is saturated with water vapour that
has evaporated from the surfaces of the mesophyll cells. Although the stomatal

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openings account for only about 1-2% of the total leaf surface, more than 90% of
the water is lost through the stomata. Stomatal transpiration involves two steps:
➢ Evaporation of water from cell wall surfaces bordering the intercellular

spaces or air spaces of the leaf.
➢ Diffusion of the water vapour from the intercellular spaces into the
atmosphere by way of the stomata (along a water potential gradient).
Stomatal closure prevents water vapour loss from the leaf and also the entry of
CO2 to the leaf. A certain amount of CO2 is produced by the plant during
respiration but this CO2 is very low to sustain photosynthesis in the presence of
light.
(b) The Mechanism of Stomatal Movement
Stomatal movement results from changes in turgor pressure within the guard
cells where opening occurs when solutes are actively accumulated in the guard
cells. The accumulation of solutes (and decrease in water potential) causes
osmotic movement of water into the guard cells and an increase in turgor
pressure in excess of that in the surrounding epidermal cells. Stomatal closing is
brought about by the reverse process. Thus turgor is maintained or lost due to
the passive osmotic movement of water into or out of the cells along a gradient of
water potential.
The potassium ion (K+) is the major solute responsible for the gradients in water
potential. This ion has been found in the guard cells of open stomata of more
than 50 species, including Crassulean Acid Metabolism (CAM) plants, whose
stomata are open at night. Techniques for estimating potassium levels within a
single guard cells show that the K+ concentration rises when the stomata open
and drops when the stomata close. The surrounding cells provide the required
reservoirs of K+. The gradient of K+ between the guard cells and the surrounding
cells changes significantly and is accompanied by the osmotic flow of water and
the resultant turgor changes. Transported with K+ ions are the negatively charged
ions (chloride and malate, an ion with two –COO – groups) needed to counter the
positive charge. Evidence now indicates that guard cell chloroplasts fix CO2
photosynthetically and that sugar from guard cell photosynthesis can contribute
to the solute build-up required for stomatal opening.
The cellulose microfibrils of the guard cell walls and the attachment at the ends
of the guard cells, are important constrains in regulation of opening and closing.
Radial micellation allows the guard cell to lengthen while preventing them to
expand laterally. The common wall remains almost constant in length during
opening and closing of the stomata. Increase in turgor pressure causes the outer
(dorsal) walls of the guard cells to move outward relative to their common walls.
Radial micellation transmits this movement to the wall bordering the pore (the

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ventral wall), and the pore opens. Figure 3.4 depicts the process of stomatal
movement.
(c) Factors Affecting Stomatal Movements
Environmental factors affect stomatal opening and closing:
(i) Water loss
When the turgor of a leaf drops below a critical point (varies with different
species) the stomatal opening becomes smaller. The effect of water loss
overrides other factors affecting the stomata, but stomatal changes can occur
independently of overall water gain or loss by the plant, e.g. in species in which
the stomata open regularly in the morning and close in the evening, even though
there may be no changes in the amount of water available to the plant.
Figure 3.4 Mechanism of Stomatal movement
(ii) Abscisic acid (ABA)
The ABA level increases during water stress, causing stomatal closure. Solute
(K+) loss from the guard cells begins when ABA of the mesophyll origin arrives at

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the stomata, signaling the stomata that the mesophyll cells are experiencing
water stress.
(iii) CO2 Concentration
An increase in CO2 varies greatly from species to species and with the degree of
water stress a given plant has undergone or is undergoing. In corn (Zea mays),
the stomata mat respond to changes in CO2 in a matter of seconds. The site for
sensing the level of CO2 is located within the guard cells. In most species, the
stomata open in the light and close in the dark, thus explaining the utilization of
CO2 during photosynthesis, bringing reduction in CO2 level in leaf.
(iv) Light
Light have more direct effect on stomata. Blue and red light stimulate stomatal
opening independently of CO2. The guard cells of onion (Allium cepa) swell in the
presence of K+ when illuminated by blue light. The blue-absorbing pigment (a
flavin or a flavoprotein located in the tonoplast or possible the plasma
membrane) promotes K+ uptake by the guard cells. The blue light response is
involved in the stomatal opening in the early morning and in stomatal responses
to sunflecks (small patch of colour or light). The red-light-stimulated stomatal
opening is mediated by the guard cell chloroplasts. The chloroplasts supply the
ATP that fuels proton pumping at the guard cell plasma membrane, the site of
active K+ uptake.
(v) Temperature
Temperature changes within normal ranges (10° - 25°C) have little effect on
stomatal behaviour but temperatures above 35°C can lead to stomatal closure.
Temperature changes work primarily by affecting the leaf CO 2 concentration. An
increase in temperature results in the increase in respiration and a concomitant
increase in the concentration of intercellular CO2 which may be the cause of
stomatal closure in response to heat. Many plants in hot climates close their
stomata regularly at midday, apparently because of the effect of temperature on
CO2 accumulation and in response to excessive transpiration.
(vi) Structural adaptation
A wide variety of succulents (cacti, the pineapple (Ananas comosus), and

Crassulaceae) open their stomata at night, when conditions are least favourable
to transpiration. The Crassulean Acid Metabolism (CAM) characteristic of such
plants has a pathway for carbon flow not substantially different from that of C 4
plants. At night when their stomata are open, CAM plants take in CO 2 and
convert it to organic acids. During the day when their stomata are closed, the
CO2 is released from these organic acids for use in photosynthesis.

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3.5 FACTORS AFFECTING THE RATE OF TRANSPIRATION
a) Stomatal opening and closing: the major factor affecting the rate of
transpiration.
b) Temperature. The rate of water evaporation doubles for every 10°C rise
in temperature. Evaporation cools the leaf surface; its temperature does
not rise as rapidly as that of the surrounding air. Stomata close when
temperature exceeds 30-35°C.
c) Humidity. Water is lost much slowly into air already laden with water
vapour (water potential difference). Compare plants growing in shady
forests with plants of grasslands or other exposed areas – light and water
loss.
d) Air currents. It blows away water vapour that has accumulated near the
leaf surface and so accelerates the rate of water evaporation. Sometimes
if the air is very humid, wind may decrease transpiration by cooling the
leaf, but dry breeze will greatly increase evaporation. Leaves of plants that
grow in exposed, windy areas are often hairy; the hairs protect the leaf
surface from wind action and so slow the rate of transpiration by stabilizing
the boundary layer of air over the leaf surface.
4. MOVEMENT OF INORGANIC NUTRIENTS THROUGH THE PLANT
4.1 UPTAKE OF INORGANIC NUTRIENTS
The uptake or absorption of inorganic ions takes place through the epidermis of
young roots, following the symplastic route until they reach the parenchyma cells
of the vascular cylinder by diffusion, aided by cytoplasmic streaming. Mycorrhizal
fungi associated with the root systems of plants are especially important in the
absorption and transfer of phosphorus, zinc, manganese and copper. These
nutrients are relatively immobile in the soil, and depletion zone of them quickly
develop around the root and root hairs. The hyphal network of mycorrhizae
extends several centimeters out from colonized roots, thus exploiting a large
volume of soil more effectively.
Inorganic ions may also be absorbed in small amounts through the leaves, thus
direct application of micronutrients to the foliage has become a standard
agricultural practice for some crop plants. The mineral composition of the root
cells is higher than that of the medium in which the plant grows. Therefore,
minerals are absorbed by active transport, and this process is energy-requiring.
If roots are deprived of oxygen (reduced respiration) and light (depleted
carbohydrate reserves), mineral uptake is decreased, and will finally release
back into the soil solution. Ion transport from the soil to the xylem requires two
active, carrier-mediated membrane events:
a) Uptake at the plasma membrane of the epidermal cells and,
b) Secretion into the vessels at the plasma membrane of the parenchyma
cells bordering the vessels.

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4.2 TRANSPORT OF INORGANIC NUTRIENTS
Once secreted into the xylem vessels or tracheids, the inorganic ions are rapidly
transported upward and throughout the plant in the transpiration stream. Some
ions move laterally from the xylem into the surrounding tissues of the roots and
stems, while others are transported into the leaves. Within the leaf, the ions are
transported along with water in the leaf apoplast, that is, in the cell walls. Some
ions may remain in the transpiration stream and reach the main regions of water
loss – the stomata. Ions may then move symplastically to other parts of the leaf,
including the phloem. Substantial amounts of inorganic ions that are imported
into the leaves through the xylem are exchanged with the phloem and exported
from the leaf together with sucrose in the assimilate or translocation stream.
Recycling may occur in the plant as nutrients reaching the roots in the
descending assimilate stream of the phloem are transferred to the ascending
transpiration stream of the xylem. Only phloem-mobile ions (e.g. K+, Cl- and
HPO42-) can be readily exported from the leaves but not Ca2+ (phloem-immobile).
5. TRANSLOCATION: THE MOVEMENT OF SUBSTANCES THROUGH THE

PHLOEM
The xylem and phloem forms a continuous vascular system that penetrates every
part of the plant. Water and inorganic solutes ascend the plant in the
transpiration stream of the xylem. Sugars manufactured through photosynthesis
move in the assimilate stream of the phloem to the sites where they are utilized,
such as growing shoots and root tips, and to sites of storage, such as fruits,
seeds, and the storage parenchyma of stems and roots.
Assimilate movement follow a source-to-sink pattern. Storage tissues may also

serve as important sources. All plant parts unable to meet their own nutritional
needs may act as sinks (importers of assimilates). In young seedlings,
cotyledons are major source whereas growing roots are major sink. In older
plants, upper mature leaves distribute photosynthetic products to shoot tips;
lower leaves distribute them to roots; whereas those in the middle distribute
photosynthates to both upper and lower directions. This pattern of assimilate
distribution is altered during the change from vegetative to reproductive growth.
In such cases, developing fruits become competitive sinks that lead to decline of
vegetative growth.
5.1 THE MECHANISM OF PHLOEM TRANSPORT: PRESSURE FLOW (PF)
The pressure-flow hypothesis asserts that assimilates are transported from

sources to sinks along a gradient of turgor pressure developed osmotically. The
sucrose from the leaves is transported through the sieve tube (Figure 5.1). This
active process (phloem loading) decreases the water potential in the sieve tube
and causes water entering the leaf in the transpiration stream to move into the

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sieve tube by osmosis. The sucrose in the sieve tubes is then carried passively
by the water to the sink where it is removed (used-up, unloaded). The sucrose
removal results in an increased water potential in the sieve tubes at the sink and
subsequent movement of water out of the sieve tube. The sucrose may be either
utilized in growth or respiration or stored at the sink, but most of the water returns
to the xylem and is re-circulated in the transpiration.
Figure 5.1 Sucrose transport in the leaves
Note that the pressure-flow hypothesis casts the sieve tubes in a passive role in
the movement of sugar solution through them. Active transport is also involved in
the pressure-flow mechanism. However, active transport is not directly involved
with the long-distance transport through the sieve tubes but rather with loading
and possibly unloading of sugars and other substances into and out of the sieve
tubes at sources and sinks. Considerable evidence indicates that the driving
force for sucrose accumulation (phloem loading) at the source is provided by a
proton pump that is energized by ATP and mediated by ATPase at the plasma
membrane, and involves a sucrose proton cotransport (symport) system.
Metabolic energy is required for loading and unloading. Phloem loading is a
selective process. Sucrose is the most common sugar transported; amino acids
and ions are selectively loaded into the phloem.

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6. CONDITIONS AFFECTING THE RATE OF PHOTOSYNTHESIS AND

RESPIRATION
6.1 PHOTOSYNTHESIS
Photosynthesis is the process where by plants use the radiant energy to convert
CO2 and water to complex organic compounds that can be used by both plants
and animals as energy source. The rate of photosynthesis is very important in
food and fibre production and will be affected by internal and external factors.
6.1.1 INTERNAL FACTORS
The internal factors (conditions in the plant itself) affecting photosynthesis rate
include (a) the structure of a leaf and its chlorophyll contents; (b) accumulation
within the chlorophyll-bearing cells of the products of the photosynthesis; and (c)
protoplasmic influences, including enzymes.
(a) Leaf Structure
The leaf structural features such as size, position, and behavior of stomata, and
the amount of intercellular spaces, influence the amount of CO2 that reaches the
chloroplasts. The intensity and quality of light that reaches the chloroplasts are
influenced by thickness of the cuticle and epidermis, the presence of epidermal
hairs, the arrangement of mesophyll cells, the position of the chloroplasts in the
cells, etc.
(b) Products of Photosynthesis
Increase in the concentration of the products of photosynthesis in the mesophyll

cells results in the decrease in photosynthesis rate. Starch accumulation in the
chloroplasts during the day retards the photosynthesis rate.
(c) Protoplasm
If the cells have water deficit and the protoplasm is dehydrated, photosynthesis
slows down. Disturbance of certain enzyme activities influences the
photosynthesis rate.
6.1.2 EXTERNAL FACTORS
External conditions that affect photosynthesis rate are (a) temperature; (b) light
intensity, quality and duration; (c) carbon dioxide content of the air; (d) water
supply; and (e) mineral elements in the soil.

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(a) Temperature
Photosynthesis occurs at temperatures below 0°C (cold climate), or at

temperatures as high as 75°C (algae in hot springs). Photosynthesis is best
between temperatures of 10°C and 35°C. At this temperature range, adequate
light intensity and a normal CO2 supply, results in an increased photosynthesis
rate with an optimum at about 25°C, followed by a continuous fall in the rate as
the temperature is raised. At these higher temperatures, the time of exposure is
of importance. At a given constant high temperature (40°C) the rate of
photosynthesis decreases with time. Under conditions of low light intensity, an
increase in temperature beyond a certain minimum will not produce an increase
in photosynthesis. If the temperature is raised too high, plant suffer because
photosynthesis rate is not changed but respiration rate is increased by the higher
temperature.
(b) Light
Three light elements are considered: intensity, quality (wavelength) and

duration. With proper temperature and sufficient CO2, carbohydrates produced
by a given area of leaf surface increase with increasing light intensity up to a
certain point (optimum light intensity), after which their production decreases.
Important, is the intensity to which the chloroplasts are exposed. The light
intensity diminishes from the leaf surface to the chloroplasts, owing to surface
hairs, thick cuticle, thick epidermis, and other structural features. Intense light
retards the rate of photosynthesis. Desert plants therefore have structural
adaptations that help them to diminish intensity of light that reaches the
chloroplasts. Leaves on the surface of the plants receive light of greater intensity
than shaded ones. Therefore, some leaves receive light of optimum intensity,
whereas others may receive light either above or below the optimum.
Light quality striking green plants may vary widely. Important for seedling-survival
and growth on forest floors. Canopy of leaves of the forest absorb red and blue
light. Lower leaves of taller plants, screened from direct sunlight by upper leaves,
receive light rich in green wavelengths. Plants (marine algae) growing in deep
water are subject to light rich in the shorter (blue-green) wavelengths. Such
plants have developed accessory pigment systems adapted to absorb blue-green
light. The ability of the plant to adapt to the quality of light it receives is important
for its survival.
(c) Carbon dioxide
CO2 utilized by plants is absorbed by the leaves from the atmosphere (78% is N 2,
21% is O2, the balance is 0.03% CO2, argon, and the traces of hydrogen, neon,
helium, and other gases. CO2 in the air surrounding the leaves reaches the
chloroplast by inward diffusion paths through the stomata to the intercellular
spaces, through walls of palisade and spongy parenchyma cells, to cytoplasm.

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The walls of the palisade and spongy parenchyma cells contain water. CO2 is
passed through the cell walls in aqueous solution. In the process of
photosynthesis, the cells remove CO2 from solution in cell sap through the
diffusion of gas inward from the wet cell walls. This loss of CO 2 from the cell wall
allows the water in the walls to dissolve more CO2 from the air in the intercellular
spaces. The CO2 content of the intercellular spaces is lowered below that of the
outside atmosphere through diffusion. Thus a diffusion gradient is for CO2 is set
up between the outside atmosphere and the chloroplasts. At the same time,
oxygen liberated in photosynthesis is used in respiration, or it diffuses outward in
aqueous solution through the cell walls to intercellular spaces.
Several natural processes are continually releasing carbon dioxide to the

atmosphere:
a) All living cells (plants and animals – respiration).
b) Decay of dead bodies of plants and animals, and the excretion of animals
(bacteria and fungi).
c) When wood, coal, oil, gas, or other carbon compounds burns.
d) From mineral springs and volcanoes.
e) The oceans are important reservoirs of carbon dioxide.
Increase of CO2 up to a concentration of 0.5% may give an increase in

photosynthesis rate for a limited period. It appears that this high level of CO2 is
injurious to plants after 10-15 days of exposure.
(d) Water
Although the water content of an actively photosynthesizing cell is high and large
amounts of water lost from the cell by transpiration, only about 1% or less of the
water absorbed by the plant is actually used in photosynthesis. The rate of this
process may be changed by small differences in water content of the chlorophyll-
bearing cells. In some instances, the rate of photosynthesis is increased by mild
dehydration (15% water loss) and retarded by vigorous drying (45% water loss).
Since stomata close when the plant is deprived of water, conditions of drought
tend to reduce the rate of photosynthesis. Thus, though water is one of the raw
materials in the process, it rarely is, directly a limiting factor in photosynthesis.
(e) Minerals
The chemical formula of chlorophyll a is C55H72O5N4Mg and of chlorophyll b is

C55H70O6N4Mg. The synthesis of chlorophyll depends upon a supply of nitrogen
and magnesium (from salts in the soil). Chlorophyll is not formed unless iron is
available, although this element is not a component of the chlorophyll molecule.
Leaves of plants deficient in nitrogen, magnesium, or iron are pale and yellow, a
condition termed chlorosis, resulting in lowering of the rate of photosynthesis.

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6.2 RESPIRATION
Respiration is the process where by plants breaks down organic molecules,

principally glucose, and access energy from them which is converted to ATP – a
more versatile form of energy. Any condition either inside or outside the cell that
affects the rate of respiration will influence cellular activities. In addition to the
degree of hydration of the cell, factors such as temperature, oxygen supply, food
availability, CO2 concentration, the presence of certain chemicals, and the age of
the cell, influence cell respiration.
(a) Cell Hydration
Many seeds remain viable for long periods of time when stored in relatively dry
air – (water content <10% of the seed weight). Water content of active
protoplasm is 90% or more. Under low moisture conditions, respiration and some
other cellular activities slow to a very low rate. Energy is needed only to maintain
a certain little-understood steady state in the quiescent (dormant) protoplasm.
Growth has ceased, mineral salts are not being absorbed, and cell division and
reactions involving synthesis of new materials have stopped. If imbibition
(hydration) occurs, the seeds swell, respiration increases and the temperature
increases.
(b) Temperature
Temperature effect most biological reactions especially those that are controlled
by enzymes. In the temperature range from near freezing (0°C) to about 30°C, an
increase of 10°C approximately doubles respiration rate. Above 30°C the harmful
effects of high temperature on the cell may become marked – cellular enzymes
progressively become inactivated and respiration decreases. Nevertheless, over
the long time of evolution, certain organisms have evolved characteristics that
have enabled them to survive in otherwise hostile environments. Certain species
of algae and bacteria are adapted to respire and grow in hot springs and streams
(60°C).
(c) Food
Respiration involves the utilization of food where food is necessary if a cell is to

continue to respire and stay alive. Photosynthesizing leaf cells are able to
produce their own food in light. Under normal conditions, they must also form
enough food to supply the needs of all the non-photosynthetic cells in the plant. If
a plant is kept in the dark, continued food usage without food synthesis will
rapidly deplete the available food. Stored food reserves (starch and sugars), may
be drawn upon by all living cells. If the plant is prevented from carrying out
photosynthesis and if food is not supplied, the plant will eventually starve to
death.

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(d) Oxygen
Although most plants cells can continue for a time to oxidize foods even in the
absence of gaseous oxygen (anaerobic respiration), molecular oxygen is
normally necessary for the health of higher plant cells. Rarely does the
concentration of oxygen in the atmosphere deviate enough from the normal 21%
to appreciably affect the rate of respiration. However, underground stems, seeds
and roots may be in an oxygen-poor environment, since the microorganisms in
the soil as well as the plant parts themselves may use the oxygen in the soil
atmosphere faster than it is replaced from the air. Under these conditions,
respiration in the roots may be decreased. Similar conditions of low oxygen level
and high carbon dioxide concentration may occur in the internal cells in bulky
plant organs such as large fleshy fruit.
7. REGULATING GROWTH AND DEVELOPMENT: PLANT HORMONES
Plant hormones are organic substances that play a major role in regulating
growth. Some hormones are produced in one tissue and transported to another
tissue, where they produce specific physiological responses; while others act
within the same tissue where they are produced. Hormones are active in very
small quantities. The word hormone comes from Greek, meaning “to set in
motion”. Some hormones have inhibitory influences. Therefore, it is more useful
to regard them as chemical regulators. The same hormone can elicit different
responses in different tissues or at different times of development in the same
tissue. Five groups or classes of hormones are generally recognized: auxin,
cytokinins, ethylene, abscisic acid and gibberellins.
7.1 AUXIN
Auxin comes from Greek, meaning “to increase”. Indole-3-acetic Acid (IAA) is the
only natural occurring auxin and is synthesized primarily from tryptophan. Auxin
is synthesized in the coleoptile tips of grasses, shoot tips, leaf primordia and in
young leaves and is also found in flowers, fruits and seeds. Auxin is transported
to the root tips.
Auxin Transport: Movement of auxin in both shoots and roots is slow (1 cm/hr).
Its transport is polar or unidirectional, towards the base (basipetal) in the stems
and leaves and towards the tip (acropetal) in roots – through phloem
parenchyma cells and parenchyma cells surrounding the vascular tissues. In
plant parts capable of secondary growth, auxin transport also occurs through
cells in the region of the vascular cambium. Move by diffusion within cells but the
mechanism of auxin transport is active, requiring metabolic energy for its
accomplishment.

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(a) Auxin and Cell Differentiation
The gradient of auxin caused by basipetal transport influences the differentiation

of vascular tissue in the elongating shoot. When a stem of cucumber (Cucumis
sativus) or some other herbaceous dicotyledon is severely wounded and portions
of vascular bundles removed, new vascular tissues will form from pith cells and
will connect the wounded bundles. However, if the leaves and buds above the
wound are removed, the formation of new cells is delayed. With the addition of
IAA to the stem just above the wound, new vascular tissue begins to form. Auxin
similarly plays an important role in the joining of vascular traces from developing
leaves the bundles in the stem. In calluses (mass of undifferentiated cells that
form when plant is wounded or when isolated cells are grown in tissue culture),
auxin promotes cell division and cell differentiation especially of the xylem tissue.
(b) Auxin and the Vascular Cambium
In woody plants, auxin promotes activity of the vascular cambium. With

expansion of buds and resumption of their growth in the spring, auxin moves
downward in the stems and stimulates the cambial cells to divide, forming
secondary vascular tissue.
(c) Auxin and Root Growth
Auxin promotes initiation of adventitious roots in cuttings. The practice of treating

cuttings with auxin is commercially important, especially for the vegetative
production of woody plants. High auxin concentrations to already-growing roots
usually inhibit their growth.
(d) Auxin and Fruit Growth
Auxin promotes the growth of many fruits. By treating the pistillate flower parts
(carpels) of certain species with auxin, it is possible to produce parthenocarpic
fruit (fruit produced without fertilization, e.g. seedless tomatoes, cucumber and
eggplants). In many or most of these seedless fruits, immature ovules still exist in
the fruit. Developing seeds are a source of auxin. If auxin is applied to the
deseeded receptacle of the strawberry (Fragaria ananassa), growth proceeds
normally.
(e) Auxin and the control of abscission
Abscission (the dropping of leaves or other plant parts) has been correlated with
a lowered production of auxin in leaf, among other factors. Under many
circumstances abscission can be prevented by the application of auxin. The
control of abscission of leaves, flowers and fruits is extremely important in
agriculture. Auxin (and ethylene) has been used commercially for treatment of a

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number of plant species. For instance, auxin prevents leaf and berry drop from
evergreen holly (Ilex aquifolium) and therefore minimizes looses during shipment.
Auxin also prevents preharvest drop of citrus fruits. On the other hand, large
amounts of auxin promote fruit drop. Thus auxin has been used for the thinning
of fruit in the production of olives, apples and other tree fruits.
(f) Auxin and control of Weeds
Synthetic auxins such as 2.4-D have been used extremely for the control of
weeds on agricultural lands. In economic terms, this is the major practical use for
plant growth regulators. The mechanism by which herbicides kill only certain
weeds is largely unknown.
7.2 CYTOKININS
Cytokinins is a group of growth regulators that are involve primarily in the

cytokinesis (cell division) and this group was named after kinetin, one of its
growth regulator. Zeatin is the most common cytokinin in plants and it was
isolated from kernels of corn (Zea mays). Cytokinins have now been isolated
from many different species of seed plants, where they are found primarily in
actively dividing tissues, including seeds, fruits, leaves and root tips. They have
also been found in plant bleeding sap (pruning cuts, cracks, other wounds).
Cytokinins have also been identifies in two seedless vascular plants, a horsetail
(Equisetum ervense) and the fern (Dryopteris crassirhizoma). Cytokinins are
central for tissue culture methods and are extremely important for biotechnology.
Treatment of lateral buds with cytokinin often causes the buds to grow, even in
the presence of auxin, thus modifying apical dominance.
(a) Cytokinins and Cell Division
Undifferentiated plant cells can enlarge and divide or they can elongate. The cell
that divides repeatedly remains essentially undifferentiated meristematic,
whereas elongating cell will ultimately differentiate. In studies of tobacco stem
tissue, the addition of IAA to the tissue culture produces rapid cell expansion, so
that giant cells are formed. Kinetin alone has little or no effect, but IAA plus
kinetin results in rapid cell division, so that large number of relatively small
undifferentiated cells are formed. Cells therefore remain meristematic in the
presence of both kinetin and IAA.
(b) Cytokinins and Organ Formation in Tissue Cultures
In the presence of high auxin concentration, leaf yellowing (loss of chlorophyll)

and abscission occurs in plants. Yellowing can be delayed by cytokinins. For
example, when cocklebur (Xanthium strumarium) excised leaves are floated on
water, yellowing occurs in about 10 days. However, with the presence of 10mg/l
kinetin in water, much of the green colour and fresh appearance of the leaf is

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maintained. If an excised leaf is spotted with kinetin-containing solutions, the

spots remain green while the rest of the leaf yellows. It is widely accepted that
cytokinins are synthesized in root tips and transported in the xylem to all other
parts of the plant.
7.3 ETHYLENE
The gas ethylene (C2H4) is synthesized from methionine. It is the only

hydrocarbon with a pronounced effect on plants. Ethylene acts in concentrations
as low as 0.06ppm in air. It is biosynthesized and exerts major influence on many
aspects of growth and development in plants, in response to stress, also
including fruit maturation, fruit and leaf abscission and senescence. Being a gas,
ethylene moves by diffusion from its site of biosynthesis.
(a) Ethylene and Fruit Ripening
Ripening in fleshy fruit involves a number of changes:
1. The chlorophyll is degraded and other pigments may form changing the
fruit colour.
2. The fleshy part of the fruit softens as a result of the enzymatic digestion of
pectin.
3. Starches and organic acids or oils (in avocado (Persea americana)) are
metabolized into sugars.
4. During the ripening of many fruits (tomatoes, avocados, apples and pears)
there is a large increase of cellular respiration evidenced by an increased
uptake of oxygen.
This phase is known as the climacteric, and such fruits are called climacteric
fruits. Fruits that show a steady decline or gradual ripening, such as citrus,
grapes and strawberries, are called non-climacteric fruits. As little as 1ppm of
ethylene in the air will speed up the onset of the climacteric. The effect of
ethylene in fruit ripening has agricultural importance. A major use is in promoting
the ripening of tomatoes that are picked green and stored in the absence of
ethylene until just before marketing. It is also used to hasten ripening of walnuts
and grapes.
(b) Ethylene and Abscission
Ethylene promotes the abscission of leaves, flowers and fruits in a variety of

plant species. In leaves, ethylene presumably triggers enzymes that cause cell
wall dissolution associated with abscission. Ethylene is commercially used to
promote fruit loosening in cherries, blackberries, grapes and blueberries, thus
making mechanical harvesting possible. It is also used as a fruit thinning agent in
commercial orchards of prunes and peaches.

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(c) Ethylene and expression of flower types
Ethylene appears to play a major role in determining the type of flowers in some
monoecious plants. In cucurbits (Cucurbitaceae family; cucumber, squash), high
levels of gibberellins are associated with the formation of staminate flowers and
treatment with ethylene changes the expression of pistillate flowers.
7.4 ABSCISIC ACID
Abscisic acid (ABA) is synthesized from mevalonic acid. It is biosynthesized in

most tissues in response to water stress and may also be synthesized in leaves.
ABA is exported from leaves in the phloem. If a small sport of ABA is placed on a
leaf, the treated area yellows rapidly even though the rest of the leaf stays green,
an effect that is opposite to cytokinins.
(a) Abscisic Acid and Seed Development
ABA levels increase during early seed development in many plant species,
where it stimulates the production of seed storage proteins and is also
responsible for preventing premature germination. The breaking of dormancy in
many seeds is correlated with declining ABA levels in the seed. In corn, there are
single-gene mutants that lack the ability to make ABA. As a result, mutant
embryos lack the ability to become dormant and germinate directly on the cob.
Such mutants are called viviparous mutants.
(b) Abscisic Acid and Water Relations
ABA stimulates the closing of stomata in most plant species. Since its synthesis
is stimulated by water deficiency (water stress), ABA is most likely involved in the
stomatal regulation of transpiration. In support of this idea, mutant plants
incapable of synthesizing ABA show wilting phenotype; that is, they are only
capable of growing normally in very humid environment.
7.5 GIBBERELLINS
More than 78 gibberellins now have been isolated and identifies chemically and
they vary slightly in structure. The best studied group is GA3 (Gibberellic acid), a
fungal (Gibberella fujikuroi) product that is most widely available. GA1 is probably
the most important gibberellin in plants. Gibberellic Acids (GAs) are synthesized
from mevalonic acids. It is biosynthesized in young tissues of the shoot and
developing seeds. It is uncertain whether synthesis also occurs in roots. GAs are
probably transported in xylem and phloem. The gibberellins effects stem and leaf
elongation in intact plants by stimulating both cell division and cell elongation.

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(a) Gibberellins and Dwarf Mutants
When gibberellins are applied to dwarf mutants (Figure 7.1), such plants become
indistinguishable from normal tall plants. This indicates that mutants are unable
to synthesize gibberellin and that tissue growth requires gibberellin.
Figure 7.1 Phenotypic rescue of stumpy with GA3 application to the shoot
apex
(b) Gibberellins and Seeds
The seeds of many plants require a period of dormancy before they will
germinate. In certain species, including lettuce, tobacco and wild oats,
gibberellins will substitute the dormancy-breaking cold or light requirements and
promote the growth of the embryo and the emergence of the seedling.
Specifically, the gibberellins enhance cell elongation, making it possible for the
root to penetrate the growth-restricting seed coat or fruit wall. In barley and other
grass seeds the aleurone (a specialized layer of endosperm cells that lies just
inside the seed coat) are rich in protein. When the seeds begin to germinate the
embryo releases gibberellins, which diffuse to which to the aleurone cells and
stimulate them to synthesize hydrolytic enzymes. One of these enzymes is α-
amylase which hydrolyzed starch. The enzymes digest the stored food reserves
of the starchy endosperm. These food reserves, in the form of sugars, amino
acids and nucleic acids, are absorbed by the scutellum and are then transported
to the growing regions of the embryo (Figure 7.2).

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Figure 7.2 Action of Gibberellin in barley seeds.
(c) Gibberellins and Flowering
Some plants, such as cabbages (Brassica oleracea var. capitata) and carrots
(Daucus carota), form rosettes before flowering. Flowering can be induced by
exposing to long days, to cold or to both. Following the appropriate exposure, the
stem elongates (a phenomenon called bolting) and the plant flowers. Bolting is
an increase in both cell number and in cell elongation. Application of gibberellin
to such plants causes bolting and flowering without cold or long-day exposure.
(d) Gibberellins and Fruit Development
Gibberellins, like auxin, can cause the development of parthenocarpic fruits

(apples, currants, cucumber and eggplants). Gibberellins have been effective in
the promotion of fruit development where auxin has not (e.g. mandarin, oranges,
almonds and peaches). In the production of table grapes, gibberellins cause
larger fruits and much looser clusters.

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7.6 THE MOLECULAR BASIS OF HORMONE ACTION
The development of organs (morphogenesis) can be described in terms of

coordinated series of cell divisions and subsequent cell enlargement.
Differentiation is the result of the selective expression of a particular set of genes
within the genome of each individual cell. The coordination of these cellular
processes during development requires that individual cells communicate with
each other, where plant hormones act as chemical messengers between cells.
All five groups of hormones can act either to stimulate or to repress (inhibit)
specific genes within the nucleus, and hormone responses are the result of such
differential gene expression.
(a) Hormonal Control of Gene Expression
All genes present in the zygote are also present in each living cell of the adult
plant, though the process of totipotency. Totipotency is the potential of a plant
cell to develop into an entire plant. In cells only selected genes are expressed
and transcribed into mRNA and subsequently translated into proteins. The
specific proteins that are produced determine the identity of the cell. It is the
proteins (enzymes) that catalyze most of the cell’s chemical reactions and that
produce most of the structural elements within and around the cell. Thus a
cortical cell in the root and mesophyll cell in a leaf differ from each other
structurally and functionally because of differences in gene expression during the
course of their development.
A eukaryotic gene is composed of a coding sequence, which specifies the amino

acid sequence of the gene’s protein product, and regulatory sequences, region of
DNA bordering the coding sequence that play a regulatory role in gene
transcription. Proteins called regulatory transcription factors can bind directly to
specific DNA sequences within a regulatory sequence, activating (switching on)
or repressing (switching off) that particular gene. Plant molecular biologists are
currently studying a number of plant genes that are either activated or repressed
by factors such as light, environmental stress and hormones
(b) Hormonal regulation of cell expansion
The rate at which plant cells grow depend on several factors, including their
position in the plant, the cell type, and a variety of environmental influences. The
rate at which the individual cell expands is controlled by:
➢ the amount of turgor pressure inside the cell pushing against the cell wall,
and
➢ the extensibility of cell wall.
Extensibility is the measure of how much the wall will stretch permanently when a
force is applied to it. All five groups of hormones are capable of influencing the
rate of cell expansion. Hormones affect the extensibility of the cell wall but have

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little direct influence on the turgor pressure. Auxin and gibberellins stimulate plant
growth by increasing the extensibility of cell walls, whereas ABA and ethylene
inhibit plant growth by causing a decrease in extensibility.
Acid growth hypothesis:

➢ Hormones, particularly auxin, activate a proton-pumping enzyme in the
plasma membrane.
➢ Protons are pumped from the cytoplasm to the cell wall.
➢ The resulting drop in pH is thought to cause a loosening of the cell wall
structure through the breakage and reformation of non-cellulosic
polysaccharides, which normally cross-link the cellulose microfibrils.
An alternative hypothesis:
➢ It is based on recent discoveries that auxin activates the expression of
specific genes within a few minutes of application.
➢ The product of these genes is thought to influence the delivery of new wall
materials in such a way as to affect cell wall extensibility.
In addition to affecting the rate of cell expansion, plant hormones can also
influence the direction of expansion. Once a cell has divided, the shape assumed
by the daughter cells as they enlarge will determine the ultimate form of the
developing tissue or organ. For example, many of the cells in the developing leaf
tend to expand primarily in a lateral direction. This lateral expansion, in addition
to the pattern of cell division, results in formation of a plate-like organ.
The cells in growing stem tissues tend to expand longitudinally, resulting in the
unidirectional growth characteristic of an elongating stem. These differences in
the direction of cell expansion are determined by the orientation of the cellulose
microfibrils as they are deposited in the developing cell wall. The arrangement of
microtubules is influenced by hormones. Gibberellins promote a transverse
arrangement of microtubules, resulting in greater longitudinal growth. In stems,
ethylene treatment causes reorientation of microtubules to the longitudinal
direction, which promotes a more lateral (radial) expansion in the cells. This
response to ethylene results in stem that is shorter and thicker.
(c) Hormone receptors and response pathways
In order for plant hormones to operate as signals between cells, the targeted
cells must have mechanism for identifying the specific hormone, measuring the
amount that is present, transferring this information via biochemical pathways,
and converting the information into a complex set of developmental changes.
Plant hormones may be recognized by the cell through their interaction with
specific cell proteins called receptors. Each receptor protein would contain a
hormone-binding site that is specific for a particular hormone. Binding of the
hormone to the receptors would activate a particular response pathway in the

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cell. Figure 7.3 illustrates a variety of pathways in which a hormone-receptor

complex may activate response pathway.
Figure 7.3 Hormone response pathways
Binding of the hormone to its receptor results in a change in conformation

(shape) of the receptor protein. This conformational change alters the receptor
protein, allowing the receptor to interact with other components of the cell. The
activated receptors may interact directly with regulatory sequences of DNA to
stimulate the transcription of specific hormone-activated genes. Through their
interaction with other membrane proteins, some of these receptors may activate
ion pumps, such as the proton pump; others may act to open ion channels in the
membrane.
The calcium ion Ca+ is of a particular interest in hormone action. Ca + levels in the
cytoplasm are very low. Binding of Ca+ to the calcium-binding sites of certain
proteins alters the activity of these proteins, much as hormones activate receptor
proteins. Protein kinases are a class of enzymes that may be activated by Ca + or
other second messengers. The protein kinases may modify “target” proteins by
transferring phosphate group onto certain amino acids of the target protein,

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altering its activity. Substances, such as calcium, that mediates hormonal

responses, are often referred to as second messengers (Figure 7.4).
Figure 7.4 Second messengers in hormone response pathway
Second messengers perform two important functions:

➢ they are involved in the transfer of information from the hormone-receptor
complex to its target proteins, and
➢ they amplify the signal produced by the hormone.
Receptor activation of a single calcium channel may result in the release of

hundreds of calcium ions into the cytoplasm. Each calcium ion can in turn
activate a protein kinase molecule and each protein kinase molecule can
phosphorylate many molecules of target protein.

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8. EXTERNAL FACTORS AND PLANT GROWTH
8.1 The Tropism
Tropism is the growth response involving bending (curving) of a plant part

towards or away from an external stimulus. A response towards the stimulus is
positive and response away from the stimulus is negative. Phototropism is the
curving of growing shoot tips towards light, which is caused by the elongation of
the cells on the shaded side of the tip, under the influence of auxin. There are
three hypotheses on the role of light in phototropic response:
➢ light decreases the auxin sensitivity of the cells on the lighted side;
➢ light destroys auxin; or
➢ light drives auxin to the shaded side of the growing tip.
Experiments emphasize that auxin migrates from light side to the shaded side
(3rd option is valid). Gravitropism is a growth response to gravity. If a seedling
is placed on its side, its root will grow downward (positive gravitropism) and its
shoot will grow upward (negative gravitropism) (Figure 8.1).
Figure 8.1 Gravitropic response in the shoot of a young tomato plant

(Lycopersicon esculantum) that was placed on its side and kept in a
stationery position.
The original explanation of this mechanism involved the redistribution of auxin

from the upper to the lower side. Roots are more sensitive in their response to
auxin than stems, and at high auxin concentrations root growth is inhibited. The
lower part of the shoot is stimulated by the auxin and grows faster than the upper
side. The result is a curving upward of the stem. For the roots, the relatively high
level of auxin on the lower side inhibits growth, thus the root curves downward.

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The perception of gravitropism is correlated with the sedimentation of

amyloplasts (starch-containing plastids) within specific cells of the shoot and root.
In roots these cells are localized in the central column of the root cap. When a
root is placed in a horizontal position, the amyloplasts, which are sedimented
near the transverse walls of the vertically growing roots, slide downward and
come to rest near what were previously vertically oriented walls (Figure 8.2).
After several hours, the root curves downward, being influenced by gravity
sensors (statoliths), and the amyloplasts return to their previous position along
the transverse walls.
Figure 8.2 The response to gravity of amyloplasts in the columella cells of a

root cap
Thigmotropism is a growth response to contact with a solid object.

Thigmotropism is the most common in tendrils (modified leaves or stems).
Tendrils wrap around any object with which they come into contact and so enable
the plant to cling and climb. A tendril can rapidly wrap around a support one or
more times in less than an hour. Cells touching the support shorten slightly and
those on the other side elongate.
8.2 Photoperiodism
Photoperiodism is a biological response to change in the proportions of light

and dark in a 24-hour daily cycle. Plants that flower only under certain day-length
conditions are said to be photoperiodic.
There are 3 general types of photoperiodic plants, namely, short-day, long-day

and day-neutral plants. Short-day plants flower in early spring or fall (autumn).
They must have a light period shorter than a critical length. The common
cocklebur (Xanthium strumarium) is induced to flower by 16 hours or less of light.
Other short-day plants are some chrysanthemums, poinsettias, strawberries and
primrose.

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Long-day plants flower chiefly in summer. Will flower only if the light periods are
longer than a critical length. Examples are spinach, some potatoes, wheat
varieties, lettuce and henbane (Hyoscyamus niger). Day-neutral plants flower
without respect to day length. Examples are cucumber, sunflower, rice, corn and
garden pea.
The photoperiodic response can be remarkably precise and also affected by

environmental conditions. At 22.5°C, the long-day plant henbane will flower when
exposed to photoperiods of 10hrs & 20min, but not with a photoperiod of 10hrs.
However, the same species will require 8.5 hrs of light at 28.5°C to flower. The
response varies with different species. Some plants require only a single
exposure to the critical day-night cycle, whereas others (spinach) require several
weeks of exposure.
8.3 Hormonal Control in Flowering
Leaves form a hormone, florigen, that moves via the phloem to the stem apex
and initiates flowering. Florigen moves from one plant tissue to the other only if
they are connected by the living tissue. Florigen consists of two classes of
hormones: gibberellin and anthesin. If the upper portion of the plant is
defoliated and the lower parts are exposed to a short-day induction period, short-
day plants flower but long-day plants do not. This means that long-day plants
produce anthesin but not gibberellin during non-inducing photoperiods, since
gibberellin at this time can cause flowering. However, short-day plants produce
gibberellin but fail to make anthesin when they are grown under non-inducing
conditions, therefore they flower.
8.4 Dormancy
Dormancy is a special condition of growth arrest. During unfavourable seasons,

plants limit their growth or cease to grow altogether. This ability enables the plant
to survive periods of water scarcity or low temperature. After dormancy growth
resumes when any limiting factor (temperature, water) becomes available again.
A dormant bud or embryo, however, can be “activated” only by certain, often
precise environmental cues. This adaptation if of great survival importance to
plants. The dormant seed or bud does not respond to apparently favourable
conditions because of endogenous inhibitors, which must first be removed or
neutralized. Commercial seeds are artificially selected for their readiness to
germinate promptly when they are exposed to favourable conditions.
(a) Dormancy in seeds
The seeds of almost all plants growing in areas with seasonal temperature
variations require a period of cold prior to their germination. This requirement is
normally satisfied by winter temperatures. Stratification means the exposure of
the moist seeds to low temperatures, for many days (5°C for 100 days), in order

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to break seed dormancy and induce germination. Many seeds require drying
before they germinate, to prevent their germination within the moist fruit of the
parent plant.
Some seeds will not germinate until they have been abraded (soil action) or
mechanically abraded (scarification) to wear away the seed coat, permitting
water or oxygen to enter the seed or removing inhibitors. Hard seed coats that
interfere with water absorption and embryo enlargement are common among
legumes. Germination may also be induced by soaking seeds in alcohol or some
other fat solvent (to dissolve waxy substances that impede entry of water) or
concentrated acids.
(b) Dormancy in buds
Dormant buds may undergo meristematic activity during various phases of

dormancy, although they do not exhibit observable growth. The dormant bud is
an embryonic shoot consisting of an apical meristem, nodes and internodes (not
yet extended), and small rudimentary leaves or leaf primordia with buds or bud
primordia in their axils, all enclosed by bud scales. The bud scales help prevent
desiccation, restricts the movement of oxygen into the bud axes and leaves
within buds.
In many respects the role of the bud scales parallel those of the seed coat. The
plant tissue begins to undergo numerous physical and physiological changes to
prepare the plant for winter, a process known as acclimation. Decreasing day
length is the primary factor involved in the induction of dormancy in buds.
Acclimation to cold leads to cold hardiness – the ability of the plant to survive
the extreme cold and drying effects of winter weather. To break dormancy, the
buds of plants require cold (apple, chestnut, peach, bulbs of tulips), dry storage
(potatoes), photoperiodic response (trees) or hormone treatment (gibberellins in
peach). Dormancy may be a state of balance between growth inhibitors and
growth stimuli. Addition of any growth stimulator (or removal of inhibitors, such as
ABA) may alter the balance so that growth begins.
8.5 Cold and the Flowering Response
Cold may affect the flowering response. If winter rye (Secale cereale) is planted
in autumn, it germinates during the winter and flowers the following summer,
seven weeks after growth resumes. If it is planted in the spring, it does not flower
for 14 weeks. The flowering of the winter rye and other cereals can be influenced
by controlling the temperature of the germinated seeds.
If the seeds of the winter strain are kept near freezing (1°C) temperatures during
germination, the winter rye, even when planted in late spring, will flower the same
summer it is planted (vernalization). Even after vernalization, the plant must be
subjected to a suitable photoperiod, usually long days. The vernalized winter rye

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behaves like a typical long-day plant, flowering response to the long days of
summer. In some plants the cold treatment affects the photoperiodic response.
Spinach, a long-day plant, does not usually flower until the days are 14 hours in
length. If the spinach seeds are cold treated, however, they flower when the days
are only eight hours long. Similarly, cold treatment of the clover (Trifolium
subterraneum) can move its dependency on the day length for flowering.
Gibberellin treatment can substitute for the cold requirement.
8.6 Nastic Movements
Nastic movements are plant movements that occur in response to a stimulus but
whose direction of movement is independent of the position of the origin of the
stimulus (sleep movement). Known technically as nyctinastic movements, they
constitute the up and down movements of leaves in response to daily rhythms of
light and darkness. The leaves are oriented vertically in darkness and
horizontally in the light (leguminous plants). Nyctinastic leaf movement results
from changes in the size of parenchyma cells in the joint-like thickenings
(pulvinus) at the base of each leaf.
The pulvinus is a flexible cylinder with the vascular system concentrated in the
centre. Palvini consist of a core of vascular tissue surrounded by a bulky cortex
of thin-walled parenchyma cells. Turgor changes in the contracting and
expanding cells are brought about by the shuttling of phosphorus ions between
the two sides of the pulvinus, under the control of the biological clock and
phytochrome. Thigmonastic (seismonastic) movements are nastic movements
resulting from mechanical stimulation. The leaflets and sometimes entire leaves
of Mimosa pudica droop suddenly in response to touch, shaking, electrical or
thermal stimulation. As with sleep movements (also exhibited by M. pudica) this
response is a result of a sudden change in turgor pressure in specific cells of the
pulvinus at the base of each leaflet and leaf.
8.7 Thigmomorphogenesis
In addition to the specialized responses touch and other mechanical stimuli,

plants also respond to mechanical stimuli by altering their growth patterns, a
phenomenon known as thigmomorphogenesis. The regular rubbing or bending
of stems inhibits their elongation and stimulates their radial expansion, resulting
in shorter, stockier plants. Plants in a natural environment are normally subject to
similar stimuli, in the form of wind, rain drops, rubbing by passing animals and
machines. Such growth responses are caused by changes in gene expression.
8.8 Solar Tracking
The leaves and flowers of many plants have the ability to move diurnally,
orienting themselves either perpendicular or parallel to the sun’s rays, known as
solar tracking or heliotropism. The leaf movement of heliotropic plants (cotton,

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soybeans, cowpeas, lupine and sunflowers), is not the result of the asymmetric
growth. Movements involve pulvini at the bases of leaves or leaflets. Some
petioles appear to have pulvinal characteristics along most or all of their length.
There are two types of heliotropism: diaheliotropism and paraheliotropism. In

diaheliotropism the movement of the leaves is such that the broad surfaces of the
blades remain perpendicular to the sun’s direct rays, through the day. In
paraheliotropism, plants actively avoid direct sunlight during periods of drought
by orienting their leaves parallel to sun’s rays. This orientation minimizes
absorption of solar radiation rather than maximizing it, decreasing leaf
temperature and transpirational water loss and enhancing survival during drought
periods.
9. GENETICS
Mendel carried out studies (from 1856 to 1863) in pea and concentrated on
discrete, qualitative characteristics, such as differences in flower colour and seed
shape. He made a large number of experimental crosses and analyzed the
numerical relationships among the progenies (offspring); he first obtained true-
breeding lines for each of the traits in which he was interested.
Crosses between individuals that differ in one trait are called monohybrid
crosses and those that involved two traits are called dihybrid crosses. When
Mendel crossed plants with contrasting characteristics, he observed that in every
case, one of the alternative characteristics could not be seen in the first
generation (F1). For example, the seeds of all the progeny of the cross between
yellow-seeded plant and green-seeded plant were as yellow as the yellow-
seeded parent. Mendel called the characteristics for yellow seeds, as well as
other characteristics that were seen in the F1 generation, dominant and the
characteristics that did not appear in the first generation recessive. When plants
of the F1 generation are allowed to self-pollinate, the recessive characteristic
reappeared in the F2 generation in ratios of approximately 3 dominant to 1
recessive. Thus, the characteristics were still present in the F1 generation, but
masked.
These results can be easily understood in terms of meiosis. The characteristics

of diploid organisms are determined by interactions between alleles. An allele is
one of the two or more alternative forms of the same gene. Alleles occupy the
same site, or locus, on homologous chromosomes. Hence, each diploid cell has
two alleles for each gene, one on each of the homologous chromosomes.
Consider a cross between a red-flowered plant and white-flowered plant. The

allele for red flower colour, which is dominant, is indicated by a capital letter R.
The contrasting allele for a white flower, which is recessive, is indicated by a
lowercase r. The genotype for a red and a white flower will be RR and rr,
respectively. Individuals which have two identical alleles at a particular locus, are

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said to be homozygous. The F1 generation receives a R allele from the red-

flowered parent and a r from the white-flowered parent, and the genotype will be
Rr. Such an individual is said to be heterozygous for the gene for flower colour.
The R and r gametes derived from two parents will recombine to form one RR,
one rr and two Rr individuals. In terms of their appearance, or phenotype, the
heterozygous Rr and homozygous RR will be red-flowered. The products of the
allele from the red-flowered parent are sufficient to mask those of the allele from
the white-flowered parent. This then is the basis for the 3:1 phenotypic ratios that
Mendel observed.
The testcross experiment is done to prove whether the genotype of a plant with
red flowers is RR or Rr. This experiment is performed by crossing the progeny
with a homozygous recessive parent; if the phenotypic ratio is 1:1 then the
genotype of the progeny would have been heterozygous (Rr).
9.1 The Principle of segregation
The principle of segregation is also called Mendel’s First Law. According to

this principle, hereditary traits are determined by discrete factors (now called
genes) that appear in pairs, one of each pair being inherited from each parent.
During meiosis, the pairs of factors are separated, or segregated. Hence, each
gamete that is produced by an offspring at maturity contains only one member of
each pair that the offspring possesses. This concept of discrete factors explained
how a characteristic could persist from generation to generation without blending
with other characteristics, as well as how it could seemingly disappear and then
reappear in a later generation.
9.2 Incomplete dominance
In cases of incomplete dominance, the phenotype of the heterozygote is

intermediate between the phenotype of the parent homozygotes, since the action
of one allele does not completely mask the action of the other. In snapdragons a
cross between a red-flowered plant and white-flowered plant produced a plant
that has pink flowers. When the F1 generations are intercrossed, the
characteristics segregate again, the result in the F2 generation being one red-
flowered (homozygous) plant to two pink-flowered (heterozygous) plants to one
white-flowered (homozygous) plant (Figure 9.1). Thus, cases of incomplete
dominance also conform to Mendel’s principle of segregation.

104
Figure 9.1 Monohybrid cross showing incomplete dominance
9.3 Independent assortment
In inheritance patterns involving more than one gene, certain differences in the
patterns depend on whether the genes are located relatively close together on
the same chromosome or on the different chromosomes. Mendel studied hybrids
that involved two pairs of contrasting characteristics and are called dihybrid
crosses. He crossed strains of garden peas in which one parent had seeds that
were round and yellow and other parent had seeds that were wrinkled and green.
The alleles for round seeds and yellow seeds are both dominant, the wrinkled
and green alleles are recessive. All the plants of the F 1 generation had seeds
that were round and yellow. When plants from F1 generation were allowed to
self-pollinate, a new combination, with a phenotypic ratio of 9 round yellow to 3
round green to 3 winkled yellow to 1 wrinkled green, was observed.
Mendel formulated his second law, the principle of independent assortment.

This law states that the inheritance of a pair of factors for one trait is independent
of the simultaneous inheritance of factors for other traits; in other words, such
factors assort independently, as though no other factors were present. This
independent assortment results directly from the random manner in which the
centromeres of the bivalents line up on either side of the equatorial plane at
metaphase I.

105
9.4 Trihybrid cross
Trihybrid cross is the extension of the principle of independent assortment. This

cross involves three traits which assort themselves independently. Like in other
crosses, the F1 generation of a trihybrid cross is also composed of dominant
traits of the cross. An F2 generation has 64 possible combinations with the ratio
of 27:9:9:9:3:3:3:1. The 27 portions have all the dominant traits; each of 9
portions has two dominant traits; each of 3 portions has one dominant trait; while
one portion has recessive traits only.
Consider a cross where a grape cultivar with homozygous alleles of red colour,
tasty and soft skin is crossed with green, sour and hard skin grape cultivar. The
resulting F1 generation had red, tasty and hard rind.

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UNIVERSITY OF ZULULAND

FACULTY OF SCIENCE AND

INTRODUCTION TO PLANT CYTOLOGY,

COMPILER: PROF. N.R. NTULI

4BOT111 February – May 2023

FACULTY OF SCIENCE AND AGRICULTURE

Module Title Introduction to Plant Cytology, Genetics and Physiology

Module Code 4BOT111

Module Credit Value

Notional Hours 160

Lecturer(s) Prof. NR Ntuli

Full Title of the Programme

4BOT111 February – May 2023

1.1 Purpose of the Module

The purpose of this module is to develop an understanding of the structure

1.2 Module outcomes

In addition, learners should be able to demonstrate the following critical cross

4BOT111 February – May 2023

• Recognize problem solving contexts

1.3 Chapter or Learning Unit breakdown

Theme Theory Practical Week

4BOT111 February – May 2023

1.5 Arrangements for self-study

Contact Study Notional Hours Self Study Notional Hours

4BOT111 February – May 2023

2.1 Assessment Plan

4BOT111 February – May 2023

The cytologists aim to:

➢ identify the kinds of cells that exist;

Modern cell theory states that:

1.2 PROKARYOTIC AND EUKARYOTIC CELLS

4BOT111 February – May 2023

the surface or plasma membrane and a relatively simple collection of inner

4BOT111 February – May 2023

1.3 CELLULAR INFORMATION

1.3.1 THE NUCLEUS

Figure 1.1 The structure of the nucleus

4BOT111 February – May 2023

Figure 1.2 Subunits of a ribosome

The nuclear envelope is a double-membrane structure. Numerous pores occur in

4BOT111 February – May 2023

1.4 THE CELL BOUNDARY

1.4.1 CELL WALL

Functions of primary walls

• Structural and mechanical support.

4BOT111 February – May 2023

• resist internal turgor pressure of cell.

1.4.2 MIDDLE LAMELLA

1.4.3 PLASMA MEMBRANE (Cell Membrane, Plasmalemma)

Plasma membrane is a thin membrane surrounding the cytoplasm and function

Figure 1.4 Plasma membrane structural components

Electron examinations of cell membranes have led to the development of the

4BOT111 February – May 2023

Cholesterol is another important component of cell membranes embedded in

4BOT111 February – May 2023

1.5. ENERGY CAPTURE AND MOBILIZATION

Figure 1.5 Plastids

4BOT111 February – May 2023

Amoeboid plastids; 0.4 – 0.9µm in diameter; unit-membrane envelope, stroma