General Biology (Botany and Genetics)

Biology Module

Course Name: Biology 121

Course code: BIO 121

Lilongwe University of Agriculture and Natural Resources

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Lilongwe University of Agriculture and Natural Resources

Biology 121 Module

Course code: BIO 121

Module Authors:

Mattrina Mpeketula Soko

W.A.B Msuku

Thomson Sanudi

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Acknowledgement

The module authors gratefully acknowledge the support from ODL team at LUANAR
who were instrumental in the completing this Open Distance Learning material. We
are also thankful to Dr. Ndalapa Mhango for offering preliminary checking so that the
material meets ODL language format. This module was developed and produced by
LUANAR with the assistance of World Bank and their contributions are gratefully
acknowledged.

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Unit 1: Introduction to Botany

Introduction

As you may be aware by now that the field of biology is divided into several branches
based on the subject of study. In Biology module 1, you covered microbiology (study
of microorganisms) and zoology (study of animals). In this module you will be
introduced to other two branches of biology which are botany (the study of plants) and
genetics (the study of heredity).

Unit 1 learning objectives

By the end of this Unit, you should be able to:

a)

Unit 1 key terms

Bryophyta Gametophyte

Pteridophyta Alternation of generations

Angiosperms Archeoplastids

Gymnosperms Strobili

Tracheids Thalloid

Gametangia Resin

Sporogenous Needle

Autotrophs

Sporophyte

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Unit 1 content

1.0 Plant systematics

There are about 1.8 million species of organisms and several millions more remain
to be discovered. To study these species, a system for organizing, naming and
classifying them is essential. The field of biology that deals with the diversity of
living organisms and their evolutionary relationships is called systematics.
Taxonomy is the branch of science of dealing with the naming, describing and
classifying of organisms. On the other hand, classification refers to the branch of
science involving grouping of organisms based on their evolutionary similarities
and differences. Carolus Linnaeus devised the binomial nomenclature of naming
organisms which uses the genus and the species. The genus name always starts
with a capital letter followed by the species name which always starts with a small
letter. In printed form the scientific name is presented in italics and when it is hand
written the genus and the species names must always be underlined separately.

There are eight levels of classification which are hierarchical (from highest to
lowest). These levels are Domain, Kingdom, Phylum, Class, Order, Family, Genus,
and Species.

Domain refers to the broadest taxonomic category or group to which a living thing
belongs; each domain includes one or more kingdoms. As you may recall from
module 1, the three domain system consists of Archea (prokaryotic), Eubacteria
(prokaryotic) and Eukaryote (eukaryotic). There are five kingdoms to which all
organisms belong under these three domains. These kingdoms are Kingdom

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Monera, Kingdom Protista, Kingdom Fungi, Kingdom Plantae and Kingdom
Animalia.

1.1 Kingdom Plantae

The Kingdom plantae is also called as Kingdom Metaphyta. It includes all types
of eukaryotic, multicellular, photosynthetic and autotrophic plants with
differentiated tissues and organs. Most of the organisms in this kingdom are
autotrophs, which synthesize their own food with the help of solar energy through
photosynthesis. However, there are a few species, which are both autotrophs and
heterotrophs.

The history of life on earth and the success of many organisms literally depend on
the success of plants. The Kingdom Plantae contains about 300,000 different
species. Among the five kingdoms, Kingdom plantae is very important, as they are
the source of food for all other living creatures present on planet earth, which
depends on plants to survive.

Plants evolved from aquatic green algal ancestors known as charophytes or

stoneworts. Land plants are collectively classified as archaeplastids. Adaptations
to life on land that have evolved in plants include a waxy cuticle to prevent water
loss or desiccation; multicellular gametangia: (organs that protect developing
reproductive parts); stomata (tiny openings in the leaves and stems for gaseous
exchange); and for most plants, vascular tissues mostly the xylem and phloem for
transportation of nutrients and water throughout the plant. Plants undergo an
alternation of generations between multicellular gametophyte and sporophyte
generations.

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1.3 Characteristics and adaptations of plants

Besides the diversity of plants, plants share several characteristics. We will now
list the main characteristics that are shared among most plants. Most plants: -

a. are multicellular eukaryotic organisms with differentiated tissues and organs.

b. have cell walls made of cellulose.

c. have cells which frequently contain large vacuole and photosynthetic pigments
in plastids.

d. have photosynthetic pigments are chlorophylls a and b.

e. are nonmotile.

f. reproduce both asexually and sexually, with alternation of gametophyte (n) and
sporophyte (2n) generations.

1.4 Adaptation of plants

Here we will discuss the general adaptations of plants for life on land. Life as we
know today started in water and evolved to terrestrial environments. Terrestrial
plants had to attain the following adaptations.

 Plants have a waxy cuticle that covers the aerial portion and prevents
desiccation or drying out due to evaporation

 They have tiny openings called stomata on the leaves and stems which
facilitate gaseous exchange

 They have multicellular sex organs (gametangia) with an outer layer of sterile
cells that surrounds and protects the delicate gametes (eggs and sperm cells).
The fertilized egg develops into an embryo within the gametangium which

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 offers protection during development. This is not the case in algae where eggs
develop away from the ganetongium and in some algae, the gametes are
released before fertilization.

1.5 The plant life cycles and alternation of generations

Plants have two distinctive life cycles namely gametophyte generation and
sporophyte generation. These two phases alternate where by the plants spend the
first part of their life cycle in a multicellular haploid stage and second part of their
life cycle in a multicellular diploid stage.

Gametophyte generation: This is the haploid portion which gives rise to haploid
gametes by mitosis.

Sporophyte generation: This is the diploid portion of the life cycle which begins
when two gametes formed during the gametophyte generation fuse. The
sporophyte generation produces haploid spores by meiosis. These spores
represent the first stage in gametophyte generation.

This change during the life cycle from gametophyte generation to sporophyte
generation is called alternation of generations.

During alternation of generations, the haploid gametophytes produce male

gametangia known as Antheridia (singular antheridium) in which sperm cells form
and female gametangia known as archegonia (singular archegonium). Each
archegonium contains a single egg which is fertilized by a single sperm upon being
reached and forms a zygote.

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The formation of the diploid zygote marks the beginning of a sporophyte
generation. The formed zygote undergoes mitotic cellular division and develops
into a multicellular embryo which forms a young sporophyte plant which grows into
a mature sporophyte plant. The mature sporophyte has sporogenous cells which
are spore producing cells or spore mother cells which divide by meiosis to produce
haploid spores.

This can be summarized as follows:

Fertilisation of female sex cell by male sex cell

Zygote

Embryo

Mature sporophyte plant Mature gametophyte plant

Sporogenous cells Arhegonis (female sex cell)/

Meiosis Antheridia (male sex cell)

Spores

Gametophyte produces gametes (eggs/sperms) by mitosis, two haploid gametes

fuse to form a zygote, the zygote develops by mitosis into the sporophyte, special
cells of the sporophyte undergo meiosis to form spores and each spore has the
potential to undergo mitosis and develop into a gametophyte

The figure below shows the two distinct generations of the basic plant.

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 Figure 1.1: The basic plant life cycle

1.6 Classification of plants

Plants are divided into four main groups based on reproduction and vascular
tissues. The vascular tissues and reproduction cycle are mainly considered in plant
classification due to the significant roles that they play. For Instance vascular
tissues (the xylem and the phloem) play a vital role in transporting substances
(water, minerals and sugars) throughout the plant while seeds contain an embryo
that helps in storing food which is used during germination. The four major groups
of plants are Bryophytes, Seedless vascular plants, Gymnosprems and
Agniosperms which are seeded vascular plants.

The plant kingdom is made up of 10 phyla namely: Phylum Bryophyta, Phylum

Hepatophyta, Phylum Anthocerophyta, Phylum Pteridophyta, Phylum
Lycopodiophyta, Phylum Coniferophyta, Phylum cycadophyta, Phylum
Ginkgophyta, Phylum Gnetophyta, and Phylum Anthrophyta or Angiosperms.
However, the focus of this module is on the four main phyla: Bryophyta,
Pteridophyta, Angiosperms and Gymnosperms.

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1.6.1 Bryophyta

Bryophyta comes from the Greek words bryon meaning moss and phyton meaning
plant. It includes the lichens, mosses, algae and the fungi. Bryophytes are the
simplest and the most primitive of the land plants. They are believed to be the
earliest plant to colonize terrestrial habitat from aquatic environment They are
small nonvascular plants that lack a specialized vascular, or conducting system to
transport nutrients, water, and essential minerals (inorganic nutrients) throughout
the plant body. Their adaptation to a terrestrial mode of life is partial as water is
indispensable in one stage or another in their life cycle. Hence, they are also known
as the amphibians of the plant kingdom. They do not form true roots, stems, or
leaves. Instead of using the vascular tissues for transportation, these plants
depend mainly on osmosis and diffusion. Due to this utilization of osmosis and
diffusion for nutrient transportation, bryophytes do not grow as other higher plants.
Bryophytes have a restricted growth since some of their cells cannot obtain
sufficient necessary materials if they are to grow much larger. These plants occur
more commonly during rainy seasons and also in humid areas.

The Bryophytes are nonvascular plants with a dominant gametophyte generation.

They are further divided into three distinct phyla which differ in many ways and in
terms of evolutionary relatedness they may or may not be closely related. They
are grouped together because they lack vascular tissues and they have similar life
cycles. Bryophtes are grouped into three phyla names; Phylum Bryophyta

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(mosses), Phylum Hepatophyta (liverworts) and Phylum Anthocerophyta
(hornworts

The life cycle of bryophytes consists of two distinct phases. These phases are the
gametophytic phase and sporophytic phases which alternate with each other a
process called alternation of generations. For reproduction they reproduce and
disperse through haploid spores. Their life cycle consists of a marked alternation
of generations with dominant gametophyte generation.

1. Gametophytic phase: It is the main phase which is haploid, autotrophic,

gamete formative (male and female) and is responsible for sexual reproduction.
The gametophytes generally form dense green mats consisting of individual
plants

2. Sporophytic phase: It is diploid, heterotrophic, spore formative and

responsible for the asexual reproduction. Vegetative reproduction takes place
through fragmented tubers adventitious branches and gemmae. Sexual
reproduction takes place by sex organs antheridium (male) and archegonium
(female).

Fertilization takes place in the presence pf water. After fertilization, a zygote is

formed which undergoes divisions to form an embryo. The figure below shows
the life cycle of mosses as an example of bryophytes

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 Figure 1.2: The life cycle of moses.

1.6.2 Pteridophyta

These are seedless vascular plants. Evolutionarily, they are the first terrestrial
plants to possess vascular tissues – xylem and phloem. The pteridophytes are
normally found in swamps, marshes, stream banks, and tropical rain forests. Some
may grow in fields, crevices on cliffs or mountains.

The life cycle of pteridophytes has clearaly defined alternation of generations just
as in bryophytes. You may recall that in bryophytes the dominant phase in the life
cycle is the gametophytic plant body. However, in pteridophytes, the main plant
body is a sporophyte which is differentiated into true root, stem and leaves. These
organs possess well-differentiated vascular tissues. The leaves in pteridophyta are
small (microphylls) as in ferns. The sporophyte has a horizontal underground stem
(rhizome) that bears leaves known as fronds. Spore production occurs in the
fronds where sporangia developes. Most species bear the spores in clusters called
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sori (singular sorus). In the sporangia, sporagenous cells / spore mother cells
under-go meiosis to form haploid spores. The sporangia burst open and release
spores that may germinate and develop into gametophytes. A mature fern
gametophyte is a tiny heart shaped structure that grows against the ground called
a prothallus (plural prothalli). The prothallus lacks vascular tissues, it only has tiny
hair like absorptive rhizoids for anchorage. The prothallus produces both
archegonia and antheridia on its underside. A single egg is contained in each
archegonia while numerous sperm cells are produced in each antheridium.

The sporophytes bear sporangia that are held by leaf-like appendages called
sporophylls. In some cases sporophylls may form distinct compact structures
called strobili or cones.

The sporangia produce spores by meiosis in spore mother cells. The spores
germinate to give rise to very small but multicellular free-living, mostly
photosynthetic thalloid gametophytes called prothallus (free living haploid
gametophyte). These gametophytes require cool, damp, shady places to grow.
Because of this specific restricted requirement and the need for water for
fertilization, the spread of pteridophytes is limited and restricted to narrow
geographical regions. The gametophytes bear male and female sex organs called
antheridia and archegonia, respectively just as in bryophytes.

Water is required for transfer of antherozoids – the male gametes released from
the antheridia, to the mouth of archegonium. Fusion of a male gamete with the
egg present in the archegonium result in the formation of a diploid zygote that
grows into a multicellular embryo. This multicellular embryo is an immature
sporophyte which is attached to the gametophyte and depends on the
gametophyte. As the embryo matures, the prothallus withers and dies and the
prothallus becomes free living. Thus the pteridophyte life cycle alternates between

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the dominant sporophyte and which jas rhizome, roots, and fronds and the haploid
gametophyte (prothallus).The sporophyte generation is dominant over the
gametophyte generation not only because it is large than the gametophyte but
because it also persists over extended periods. A good example of the
pteridophytes are the ferns whose sporophytes are perennials while the
gametopytes die soon after reproducing.

In summary the pteridophytes

 Are seedless vascular plants, which contain vascular tissues but do not
produce seeds.

 Have their reproduction process carried out by spores

 Have a life cycle that alternates between the gametophyte and sporophyte
whereby the sporophyte dominates

 Some pteridophytes e.g. ferns and club mosses are heterosporous : produce
two types of spores which are microspores and mega spores unlike bryophytes
which are monosporous- producing only one type of spores

The figure below shows the life cycle of n example of a pteridophyte, the fern.

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 Figure 1.3: A typical life cycle of a pteridophyte

Figure 1.4: The basic life cycle of heterosporous plants

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Summary

1. Sporophyte plant produces sporangia in conelike strobilus containing

microsporangia and megasporangia. Microsprongia produce
microsporocytes / mother spore cells which undergo meiosis to form
microscopic haploid microspores.

2. Microspores develop into male gametophyte that produces sperm cells

within antheridia

3. Megasporangia undergoes meiosis to form haploid megaspores that

develop into female gametophyte to produce eggs in archegonia

4. Fertilization occurs followed by development of new sporophyte.

1.6.3 Gymnosperms

The gymnosperms are classified imto four phyla:coniferophyta, commonoy called

conifers; Ginkgophyta,Cycadophyta and Gnetophyta. The conifers are the most
familiar group of gymnosperms and they consist of pines, spruces, hemlocks and
firs. The conifers are woody plants that produce seed in cones.

Characteristics of conifers

 Conifers’ wood has tracheids which are long tapering cells with pits through
which water and dissolved minerals move from one cell to the other.

 They produce a viscous clear or translucent substance called resin; consisting

of several organic compounds which protects the plant from insect and fungi
attack.

 They have long, narrow, tough, and leathery leaves called needles.

 Most conifers are evergreen, apart from a very few that are deciduous shed
their needles at the end f he growing season.

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 Most conifers are monoecious, they have separate male and female
reproductive parts in different locations on the same plant.

Gymnosperms are non-flowering plants with undeveloped seeds, which are

present in an enclosed structure. In other terms they are plants in which the ovules
are not enclosed by any ovary wall and remain exposed before and after
fertilization. They produce naked seeds. The gymnosperms are heterosporous;
producing haploid microspores and megaspores. The two kinds of spores are
produced within sporangia that are borne on sporophylls which are arranged
spirally along an axis to form lax or compact strobili or cones. The strobili bearing
microsporophylls and microsporangia are called microsporangiate or male
strobili. The microspores develop into a male gametophytic generation which is
highly reduced and is confined to only a limited number of cells. This reduced
gametophyte is called a pollen grain. The development of pollen grains takes
place within the microsporangia. The cones bearing megasporophylls with ovules
or megasporangia are called macrosporangiate or female strobili. The male or
female cones or strobili may be borne on the same plant (trees). However in some
cases male cones and megasporophylls are borne on different plants (trees).

Unlike bryophytes and pteridophytes, in gymnosperms the male and the female
gametophytes do not have an independent free-living existence. They remain
within the sporangia retained on the sporophytes. The pollen grain is released from
the microsporangium. They are carried in air currents and come in contact with the
opening of the ovules borne on megasporophylls. The pollen tube that carries the
male gametes grows towards archegonia in the ovules and discharge their
contents near the mouth of the archegonia. Following fertilization, a diploid zygote
develops into an embryo and the ovules into seeds. These seeds are not covered.

1 Monocot begins with a single seed-leaf. The main veins of their leaves are
usually parallel and unbranched.

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2 Monocot plays an important role in providing us with our primary sources of
nutrition, which includes grains, fruits, etc.

1.6.4 Angiosperms

These are flowering plants, which develop the seeds within a protective structure.
They are the most diverse phylum of plants that form flowers for sexual
reproduction and they produce seeds enclosed in fruits. There are two main types
of angiosperms: monocots and eudicots/ dicot

Main characteristics of Angiosperms

 They develop their seeds within an ovary, which itself is embedded in a flower.
After the stage of fertilization, the flower falls and the ovary bulges to become
a fruit.

 Angiosperms in the class Dicotyledoneae grows into two seed-leaves

(cotyledons).

 An angiosperms leaf consists of a single, branched, main vein, which originates

from the base of the leaf blade. In few plats, it may also consist of four or more
main veins diverging from the same base.

Unit 1 activity

Unit 1 summary

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 Unit 1 test

Unit 2: Morphology and Anatomy of Flowering Plants

Introduction

Naturally, all flowering also known as seed plants develop from a seed. The seed is the
seat of partial development of the new sporophyte, the embryo and it thus plays a major
role in providing the continuity between successive generations of the plants. Given the
right environmental factors which include moisture, temperature, nutrients and light the
seed will germinate. This becomes possible after a more or less prolonged dormancy
caused by various internal factors such as rudimentary or physiologically immature
embryos, mechanically resistant or impermeable seed coats, or the presence of
germination inhibitors.

Germination is essentially a resumption of embryo growth after imbibition of water. During

imbibition, the water content of the seed rises, usually fast at first, then slower, and the
embryonic tissue becomes metabolically active. Enzymes already present are activated
and new proteins with specific enzymatic activities are synthesized for the digestion and
utilization of the different kinds of stored materials. Cell extension and cell divisions are
initiated and proceed according to the programmed pattern. This growth requires
continuous supply of water and nutrients. Before the embryo becomes a self-supporting
seedling it utilizes the food stored in the endosperm and/or the embryo itself.

Seedling growth leads to the development of three major vegetative organs, i.e. roots,
stem and leaf. Depending on the type of plants, time taken to grow into a full mature plant

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will vary. At maturity, these plants produce flowers (reproductive organs) which lead to
the development of fruits and seeds.

In this unit, we are going to study different morphological and anatomical structures of
these organs of the plants. You will also be introduced to the important roles, variations
and similarities of these organs.

Unit 2 learning outcomes

By the end of this unit, you should be able to:

1. State the primary functions and types of roots, stems, leaves and flowers.
2. Describe the external and internal parts of mature primary root, stems, leaves
and flowers.
3. Compare morphological and anatomical structures of monocotyledonous and
dicotyledonous stems and leaves.

Unit 2 key terms

Sporophyte Coalescence

Dormancy Inflorescence

Imbibition Gymnoecium

Enzymes Vegetative organs

Endosperm Reproductive organs

Androecium Morphology

Herbaceous Anatomy

Differentiation

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 Unit 2 Content

2.1 Roots

2.1.1 Functions of roots

In this section we will discuss the four major and primary functions of roots. You
may have noticed that some plants might use roots for other specialized functions.
Among major functions of the roots include anchorage, absorption, transportation,
and translocation. Specialized functions include storage, propagation, respiration,
balancing and support, growth, parasitism, and association with other living
organisms. We will begin our discussion by looking at the main function of the
roots.

Anchorage

This should be familiar to most of us that roots anchor trees firmly into the soil,
usually through an extensive branching network that constitutes about one third of
the total dry weight of the plant. The roots of most plants do not extend more than
3 to 5 meters down into the earth; those of many herbaceous species are confined
to the upper 0.6 to 0.9 meters. Some plants form very shallow root systems, but
these systems still effectively anchor the plants with a densely branching mass of
roots radiating out in all directions as far as 15 meters from the stem.

Absorption

You may also be familiar that roots absorb water and minerals in solution mostly
through feeder roots found in the soil.

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Transportation

After absorbing the water and mineral salts from the soil roots are also responsible
for transporting these materials through stems to the leaves by the use of vascular
bundles laid in a form of continuous pipes forming a body known as xylem. This
is a one way direction process from roots to leaves (Figure 1A).

Figure 2.1: Transportation of water, one way direction through xylem pipes (A),
and translocation of manufactured food, multidirectional process through phloem
pipes (B).

Translocation

Food manufactured in the leaves is supposed to be transported to plant parts

where it is required. As in the transportation of water, there are also specialized
pipes that are laid through the plant body stretching from roots to leaves. Such
pipes are known as phloem. Manufactured food is able to be moved from leaves
to roots and back from roots to upper parts of the plant where it is required.
Manufactured food can also be moved sideways through the root and stem bodies
to wherever it is required, hence the process is multidirectional (Figure 2B).

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2.1.2 Types of root systems

Based on the origin, position, function and morphological appearance of the root,
roots can be grouped into three major groups of taproot, adventitious or fibrous
and modified or specialized root systems. Let us now describe these root systems.

Tap root system

This is characterized by one large primary root (taproot) and smaller roots with
varying sizes called secondary roots which originate from the primary root. The
taproot originates from the embryonic root called radicle (Figure 2) and continues
to form the root systems of many dicotyledonous plants for example bean, mango,
orange, gmalina, and gymnosperms for example pines.

Figure 2.2: Development of taproot system from embryonic radicle (A, B, C, D)

Adventitious or fibrous root system

On the other hand you will notice that roots of monocotyledonous plants such as
maize, rice, wheat, grasses and bamboos and dicotyledonous plants that are
planted from stems for example cassava, sugarcane and sweet potatoes form
adventitious systems.

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In the monocotyledons the tap root commonly lives for a relatively short time and
the root system is formed by roots arising directly from the shoot (stem and leaves)
often in connection with axillary buds. Adventitious root system usually has many
uniform or homogenous roots and in appearance, they tend to look like a broom
or a mop. Such a fibrous broom structures is the origin of its name as fibrous root
system (Figure 3).

Figure 2.3: Adventitious or fibrous root system

Modified or specialized root systems

As mentioned earlier, most plants produce either adventitious or fibrous root

system, taproot system or more commonly combinations of the two types. Some
plants, however have roots with modifications that adapt them for performing
specific functions apart from the four basic functions. Some of the examples of the
modified root systems are given in Table 1 below.

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Table 1: Examples of modified roots

Modified/specialized root Examples

1. Freshy roots (Food and water Cassava, sweet potatoes, yams, and
storage roots) some members of pumpkin and
plantain familes.
2. Propagative roots – many plants Adventitious roots of ricepaper plants
produce adventitious buds (buds not (Tetrapanax papyrifera), Horseradish
appearing from the stem but other (Roroppa armoracia), roots of cherries,
organs of the plant ie roots growing apples, pears and other fruit trees often
along the surface and leaves which produce suckers.
will lead to production of a new plant.
3. Aerial roots
a. Includes respiratory or Black mangrove (Avicennia nitida),
pneumatophores used for gas yellow water weed (Ludwigia repens)
exchange in plants growing in
swampy environments.
b. prop roots are roots developing -maize and other grasses, fig trees
from stems to provide extra (Ficus sp)
support
4. Association with other living
organisms -roots of most forest trees and grasses
a. mycorrhizae: plant roots
associated with fungi for mutual
symbiotic purposes.

b. nodules in leguminous roots:

mutualistic symbiotic association -all roots of leguminous plants
between roots and bacteria

c. parasitic association: an
association where roots of crops -witchweed (Striga sp), Dodders,
or trees are associated with roots orchids.
of plant parasitic plants.

2.1.3 Root structure

You will appreciate that the root has different internal and external structures that
makes the root to perform the different functions. As the roots elongates, it displays
varying morphological and anatomical structural features. From the growing tip to
the mature part of the root, we observe six different structural regions (Figure 4).

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Such regions include root cap, apical meristem zone, elongation zone,
differentiation zone, root hair zone and mature root zone. These are discussed
below in relation to their type of cells and functions.

Root tip

The root tip is the growing point of the root. As the name suggests this is found at
the tip of the root. Within the root tip you will find the root cap, the apical meristem,
the elongation zone and the region of cell differentiation.

Root cap

The root cap is composed of parenchyma cells that produce and exude mucus-
like substance. This substance is smeared outside the root cap and acts as
lubricating oil as the root pushes through the soil particles. As you will notice, the
root cap protects the apical meristem. The root cap also assists the growing root
as it penetrates the soil.

Figure 2.4: Internal and external structure of a root

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Apical meristem zone

The apical meristem is a zone is made up of young and undifferentiated cells

(meristems). These cells are randomly arranged. The meristems are capable of
dividing mitotically increasing the numbers in a limited area hence pushing the root
tip forward (growing).

Elongation zone

In the elongation zone, cells start elongating and increase in size. As the cells
elongate they arrange themselves in chains

Differentiation zone

In this zone cells begin to differentiate into different tissue. The cells begin by
forming primary tissues for both structural and functional use. The first primary
tissues include dermal tissue (epidermis), ground tissue (cortex) and vascular
tissue (xylem, phloem and pericycle) (Figure 4). The outermost cells arrange
themselves into a skin like structure called dermal tissue (epidermis) while the
innermost cells organise themselves into translocating and transporting structures
called vascular tissues. The vascular tissue forms a solid vascular cylinder, or
pith is present then a hollow cylinder with a few parenchyma and sclerenchyma
cells embedded in them for support. The cells between the dermal and the vascular
tissue form ground tissues made of three major zones that is hypodermis or
exodermis, loose cortex and endodermis.

Root hair zone

In young roots the epidermis is specialized as an absorbing tissue and usually

bears root hairs which are tubular extensions of the epidermal cells. Root hairs
markedly extend the absorbing surface of the root. Root hairs have short life; they
disintegrate in the older epidermal cells as they reach mature stage.

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Mature root zone

In this region you will find fully grown up cells that make the mature body of the
root are well separated and differentiated in readiness for their different functions
they have to undertake in the root. They are seen to be grouped into three main
groups (Figure 5). The peripheral is made up of dermal tissue which acts as a
protective skin for the root. The central part of the body is taken up by a cylindrical
shaped vascular tissues that are meant to transport water and mineral salts and
translocate manufactured food. The area between the two is formed by cells
grouped as ground tissues. Their functions are many, among them include
storage, support and in aiding transportation and translocation.

Figure 2.5: Cross section of a mature root

Dermal tissue

Epidermis is the outermost one cell layer body which acts as a protective skin of
the root. At this stage, you will notice that most cells have lost their root hairs and
seen to be forming a very tightly held layer to prevent entry of water and other large
molecules from the soil. The layer is composed of epidermal cells of varying sizes.

29
Ground tissues

Ground tissue is a group of tissues that occupy the middle section of the body of
a mature root. The ground tissue is mostly composed of parenchyma cells but they
could also have collenchyma cells. The tissue is characterised with large
intercellular spaces (lacunae) formed by aerenchyma cells. Aerenchyma cells are
highly vacuolated and may contain plastids are devoid of chlorophyll. They
however as act storage for large amounts of starch.

The innermost layer of the ground tissue is differentiated into one cell layer called
endodermis. The outermost layer close to the dermal tissue (epidermis) is made
up of one or more cell layers called exodermis. The large layer between
exodermis and endodermis is composed of loosely packed cells which usually are
referred to as loose cortex.

Cells that form the endodermis have their cell walls coated with a waterproof
substance called suberin. This substance goes round the cells within the radial
and transversal wall forming a band-like region. However, the band does not
completely cover all cells. A few cells are left free allowing direct openings between
cortex and the vascular tissues. It is through these openings that water and soil
solutions find their way into the vascular tissues. The band is called casparian
strip. This band is important in the transportation of water and soil solutions
between cortex and vascular tissues, where water enters the vascular tissue pipes
through pressure and with the same pressure water and soil solutions are taken
up to the leaves.

30
Vascular tissue

Let us now finish our discussion of the root by looking at the vascular tissue. The
vascular tissue form a cylinder-like body of the innermost part of the mature root
(vascular cylinder). This cylinder has three main parts namely pericycle, xylem and
phloem. We will discuss the composition, positions and functions of each of these
parts below.

Pericycle

The pericycle is a one celled layer. The cells are either Parenchymatous or
sclerenchymatous. The pericycle acts as a source for lateral (secondary) roots,
vascular cambium and cork cambium (phellogen).

Xylem

The xylem forms a solid core with ridge like projections called archs. The number
of archs varies in different species. Among roots of the same plants and in relation
to this variation the roots are called Diarch with two projections, Triarch with three
projections, Tetrarch with four projections or Polyarch if the root has many
projections.

In general roots of dicotyledonous plants have 2, 3, or 4 archs (poles) and in

monocotyledonous plants they may have many archs.

Xylem pipes with varying sizes form a continuous pipe system from roots through
stems to the leaves. These pipes are responsible for the transportation of water
and mineral salts from roots to the leaves.

31
Phloem

Phloem pipes are grouped into bundles between the xylem archs. Like in the
xylem, these pipes also form a continuous system stretching from roots to leaves.
Their major function is to translocate or conduct manufactured food from leaves
throughout the plant body.

2.2 Stems

2.2.1 Functions of stems

We will begin by learning the main functions of plant stems. Stems have five main
functions which are a) carry, support and expose leaves to light and air b)
transportation of water and mineral salts c) translocation of manufactured food d)
storage of nutrients and e) perform metabolic functions such as photosynthesis
and respiration.

2.2.2 External structure

Hope you will agree that the close association of the stem with the leaves make
the aerial part of plant axis strictly more complex than the root. Shoot means stems
and leaves as one system which seems to express the association. In contrast to
the root, the shoot has nodes and internodes with one or more leaves per node.
Depending on the development of the internodes the shoot assumes different
aspects.

Visible or invisible internodes

Plants with well-developed internodes tend to have visible stems as in beans,

sunflower, maize, bamboos, gmelina, fruit trees and forest trees, while some plants
like onions and other bulbs and bananas have short invisible or hidden stems as
their internodes are not well developed.

32
One or more auxiliary buds per node

Another variation is the arrangement of leaves per node on the stem which will
lead to number of auxiliary buds hence number of the lateral shoots. Some plants
have one leaf per node hence one axillary bud; others have two leaves per node
leading to two axillary buds and yet others have three or more leaves per node
leading to three or more axillary buds.

The differences are also associated with type of growth and habitat of the shoot.
Air or underground stems for rhizome like in grasses, bulbs like in onions, corms
like in banana and tubers as in potatoes. Typical examples of land or water shoots
are rice plants and the water hyacinth. Some shoots are upright while others are
climbing or creeping. Vines creeping shoots, stolons are also creeping shoots as
in grasses while some varieties of beans are climbers (Figure 6).

Figure 2.6: Modified stems

33
2.2.3 Internal structure of primary stem

The stem like the root consists of three tissue systems namely dermal, ground and
vascular tissues. However the distribution of ground and vascular tissues vary
between stems of dicotyledonous and monocotyledonous plants. In stems of
dicotyledonous and gymnospermae plants, vascular tissues appear in separate
bundles and these bundles are arranged in a circular structure within the ground
tissue. The inner part of the ground tissue is called pith and the outer one cortex.
In stems of monocotyledonous plants, vascular tissues form vascular bundles
which are randomly distributed within the ground tissue where the pith and cortex
cannot easily be separated (Figure 7 a and b).

34
 b

Figure 2.7: a) Cross section of dicotyledonous b) cross section of a

monocotyledonous stem

Dermal tissue

The dermal tissue in stems continues to be a one celled layer as we have already
seen in roots and it is called epidermis. This skin is maintained up to maturity in all
cotyledonous plants and herbaceous dicotyledonous plants. Examples of the
herbaceous dicotyledonous plants include bean, peas, sunflower and other small
leguminous plants. However, in trees and other larger dicotyledonous plants,
another thicker skin called periderm replaces epidermis at maturity.

Ground tissue

Unlike in the root, the ground tissue has four major parts. The innermost part is
called pith and close to the dermal is called cortex with three different layers:
hypodermis, loose cortex and endodermis. In stems the endodermal layer does
not perform the function as in the root and its cells do not contain suberin. They
are mainly used to store starch hence referred to as starch cells.

35
Vascular tissue

Primary vascular system of stems of seed plants consist of strands variable in size
and degree of distinctness. Individual strands are referred to as vascular bundles.
Each bundle is composed of xylem and phloem pipes. Xylem and phloem show
variation in relative position in vascular bundles. The common arrangement is
called collateral where xylem pipes are grouped towards the inner part of the stem
and phloem takes the outer position (Figure 8)

Figure 2.8: Vascular bundle showing common arrangement of xylem and phloem
tissue

2.3 Leaves

In general sense there are quite a number of different types of leaves on a plant
based on origin, structure and function. Based on these characteristics we come
across four different types of leaves on a flowering plant i.e. cotyledons, cataphylls,
floral and foliage leaves. However, when we talk of leaves we mostly refer to
foliage leaves also known as true leaves.

2.3.1 Types of leaves and their functions

Cotyledons

Cotyledons are the first embryonic leaves on the plant. The main function of
cotyledon is that they act as placenta and nurse the young plant.

36
Cataphylls

Structurally, you will notice cataphylls as bracts or scales on stems, roots and
flowers of plants. They are found on either stolons, rhizomes of grasses or bulbs.
Cataphylls offer protection to the shoot and they are also used for storage of food
and nutrients.

Floral leaves

Floral leaves are modified for reproduction processes. Structurally, flowers are
made up of four different types of leaves each modified for their own special
functions. Such leaves include calyx, corolla, stamen and pistil.

Foliage leaves

As we have already indicated, these are the true leaves. This group of leaves
represent the true leaves of the flowering plant. Structurally, the foliage leaf usually
shows a specialization as a photosynthetic organ of the plant.

Major basic functions of foliage leaves include photosynthesis, gaseous exchange

and translocation of manufactured food. However, they could also be modified to
carry out other functions including storage, protection, propagation and holding
onto other plants and objects.

2.3.2 External structure of foliage leaves

Foliage leaf normally shows its specialization as a photosynthetic organ by the

expanded platform of its lamina (Figure 9). The leaf shows six major external parts
including the tip/apex, base, blade/lamina, margins, main central vascular bundle
(midrib) and the stalk (petiole and/or sheath). Though having leaves with these
major parts, different plants show differences in size, shape, leaf arrangement and
morphological appearance of their tips/apices, margins and bases. Leaves of

37
monocotyledonous and gymnospermae usually tend to have long and flat or round
lamina while most leaves of dicotyledonous usually tend to be broad shaped.

Figure 2.9: Typical dicotyledonous and monocotyledonous leaves

2.3.3 External variations of a foliage leaf

Below, we will study the common variations that we can see among foliage leaves
of flowering plants. Apart from differences in shapes and size of the leaves (Figure
10), leaves show variation in tips, bases (Figure 11), margins and arrangement of
vascular bundles (venation) (Figure 12).

38
Figure 2.10 Common leaf shapes

39
 Figure 2.11 Common leaf apices and bases

Figure 2.12 common leaf margins and arrangement of vascular bundles

40
Leaves may also vary in their arrangement on the stem, pattern of attachment on
the stem and number of leaves attached at a node.

Leaf arrangement

This refers to the number of leaves on the node and how leaves position
themselves in relation to one another. There are four common leaf arrangements.
Alternate leaf arrangement where one leaf per node and these leaves are
positioned in alternating positions for example maize and beans. In Cyclic leaf
arrangement one leaf is attached per node but leaves are arranged in circular
form going up the stem. Opposite leaf arrangement has two leaves per node
positioned opposite to each other. The opposite arrangement could appear in two
forms. Some plants carry their leaves on one plane others on two planes where
two leaves on the lower node alternate with the two leaves immediately above
them for example Gmalina. Lastly, whorled leaf arrangement where there are
three or more leaves on one node and seem to make a whorl or ring around the
stem.

Petiole versus Sessile leaves and sheathing base

In most plants, leaves are seen to be attached to leaf stalks as they immerge from
a node. This stalk could be a strong round bodied structure (petiole) or flat flexible
structure (sheath). Such leaf appearance could be regarded as a normal situation.
However in some plats, leaves are seen to be directly emerging from the node. In
such situations it is either the stalk is too short that it can be recognized or there is
no stalk. In this kind of leaf attachment to the node, the leaf is referred to as a
sessile leaf. In other cases, leaf blade coming from the sheath will also be seen
coming straight from the stem with its sheath holding closely to the stem. Such
appearance is referred to as a sheathing base. See diagrams below.

41
 Figure 2.13: Leaf bases

Simple versus Compound leaves

A simple leaf has a single blade while the blade of a compound leaf is divided in
various ways into leaflets (Figure 15). Regardless of the number of leaflets, a
compound leaf still has a single axillary bud at its base. Pinnately compound leaves
have the leaflets in pairs along an extension of the petiole called rachis, while
palmately compound leaves have all the leaflets attached at the same point at the
end of the petiole. Sometimes, the leaflets of a pinnately compound leaf may be
subdivided into still smaller leaflets forming a bipinnately compound leaf and a
further subdivision forming a tripinnately compound leaf (Figure 16).

42
 Figure 2.14 Simple and compound leaves

Figure 2.15: Palmately compound leaf (C) and pinnately compound leaf (D)

2.3.4 Internal structure of a leaf

Internal structure of leaves vary depending on the prevailing environmental

conditions of the habitat plants have been adapted to. Plants can be grouped into
three groups based on their habitat and internal structural leaf arrangement. Such
groups include mesophytes, hydrophytes and xerophytes. Mesophytes are plants
that require environment that is neither too wet nor too dry. Hydrophytes plants
require a large supply of water and may grow partly or entirely submerged in water
while Xerophytes are adapted to a dry hot habitat.

43
Internal structure of a mesophytic leaf

Like roots and stems, the leaf also shows three major groups of tissues namely
dermal vascular and ground tissues (Figure 17).

Epidermis

The leaf is covered/protected by two skins, with both made up of similar type of
cells (epidermal cells) the skin that appears on the upper side of the leaf is referred
to as an upper epidermis and the one below is referred to as lower epidermis. For
its efficient functional purposes, epidermis is equipped with some structures
including cuticle, trichomes and stomata.

Figure 2.16: A composites cross section of a mesophytic leaf

Cuticle is a fatty waxy substance which repels water. It is mainly coated on the
surfaces of the epidermis for the same purpose of preventing direct entry of water
from the atmosphere. The other common structures found on the epidermis are
trichomes (hairs). The epidermal layer of roots has root hairs for the absorption of

44
water. The hairs either on stems or leaves are mainly for protection and
temperature regulation. The other popular structures found either on both or one
side are the natural openings called stomata. These act as openings for gaseous
exchange. Based on the position of the stomata, leaves may be referred to
Amphistomatic leaf if stomata appear on both sides. Epistomatic have stomata
on the upper side while hypostomatic have stomata on the lower side.

Ground tissue

The main part of the body of the leaf is covered by ground tissue and in leaves is
referred to as mesophyl. The mesophyll has the following characteristics:

a. mainly composed of parenchyma cells of varying sizes and shapes

b. cells contain many chloroplasts
c. large volume of intercellular spaces
d. It could be homogeneously be divided into palisade Mesophyll with
elongated cells appearing in columns or Spongy Mesophyll with regular
sloped cells.

Leaves may have one or more rows of palisade parenchyma cells. Leaves of
plants adapted to mesophytic habitats commonly have one row of palisade
parenchyma cells. On the other hand leaves adapted to xerophytic habitat tend to
have two or more rows of palisade parenchyma cells.

Vascular tissue

The Vascular System of the leaf is distributed throughout the blade and thus shows
a close spatial relation to mesophyll. Vascular strands form an interconnected
system in the median plane of the blade parallel with the surface of the leaf. The
Vascular bundles in the leaf are commonly called veins, and the patterns formed
by the veins, venation, as seen with the unaided eye. The venation appears in two
main patterns, the reticulate or netted which is mainly associated with leaves of

45
dicotyledonous plants, and the parallel which is mainly associated with leaves of
monocotyledonous plants.

2.4 Flowers

2.4.1 Functions, structure and variations.

You will recall that it was mentioned that flowers are a form of modified leaves.
They are modified for a purpose of carrying out reproductive processes.
Structurally, a standard flower depicts four groups of such modified leaves but this
is not common to all flowers. Other structural variations will be observed in size,
colour, number of parts and arrangement of these floral parts. Below we intend to
discuss functions, structure and common variations in flowers.

A flower as a group of specialized floral leaves are adapted for: -

a) Production and development of reproductive cells (pollen ♂ and ovules ♀)

b) Pollination:- the transfer of pollen
c) Fertilization:- the unification of two protoplasmic bodies usually from different
individual plants to form one body (protoplast - zygote).
d) The ultimate development of the seed and fruit.
e) Successful dispersal of the seeds (fruits)

2.4.2 Morphological structure.

Flowers are of many different forms. They also vary greatly in size, colour, number
of parts and arrangement of parts. Each flower is an assemblage of fertile and
sterile organs in preparation for the five activities above. See figure 18 below.

46
 Figure 2.17: Classification of floral parts

A typical flower is composed of four whorls of modified leaves. These are sepals,
petals, stamens, and a carpel or carpels. All attached to the receptacle, the
modified stem end that supports these structures (Figure 19).

Figure 2.18 a typical flower

The sepals enclose the other flower parts in the bud. Generally, they are green.
All the sepals taken collectively constitute the calyx; that is, the catalyx of a flower
is composed of more or less distinct parts, the sepals.

47
The petals are usually the conscpicuous, colored, attractive flower parts. Taken
together, the petals constitute the corolla.

The stamens form a whorl, lying inside of the corolla. Each stamen has a slender
stalk or filament, at the top of which is an anther, the pollen-bearing organ. The
whorl or grouping of stamens is called the androecium. Collectively the carpels
are spoken of as the gynoecium. Each individual structure in the gynoecium is
commonly referred to as a pistil. There are generally three distinct parts to each
pistil.

a) An expanded basal portion, the ovary, in which are borne the ovules,
b) The style a slender hollow stalk which lies between the ovary and the stigma
above.
c) The stigma: The pollen is deposited on the stigma for initiation of successful
fertilization.

Summary on the floral parts

The parts of the flower in outline are as follows:

Receptacle

Calyx, consisting of sepals

sterile parts collectively known as perianth
Corolla, consisting of petals

Androecium, consisting of stamens

fertile and essential parts
Gynoecium, consisting of carpels

Variations

(a) complete and incomplete / perfect vs imperfect

48
If a flower has a stamen, pistil, petals, and sepals, it is called a complete flower.
If one of these parts is missing, the flower is called incomplete. The stamen and
pistil are the essential parts of a flower and are involved in seed production. If a
flower contains both functional stamens and pistils, it is called a perfect flower,
even if it does not contain petals and/or sepals. If either stamens or pistils are
lacking, the flower is called imperfect. Female (Pistillate), and Male (Staminate)
flowers (figure 18).

Figure 2.19: Complete and incomplete flowers

(b) Whorled and spiral arrangements

In most flowers the sepals, petals, stamens, and carpels are in whorls or circles on
the axis of the flower. In contrast with this cyclic or whorled arrangement of flower
parts is the arrangement in which one or more sets of flower parts are in spirals.

49
 Figure 2.20: Whorled versus spiral arrangement

(c) Union of flower parts. coalescence.

In many flowers, the members of one or more whorls are to some degree united
with one another, or are attached to members of other whorls. The union with each
other of members of a given whorl is termed coalescence.

Whorl No Coalescence Coalescence

Sepals aposepalous synsepalous, synsepaly

Petals apopetalous sympetalous, sympetaly

Stamens apoandrous synandrous, synandry

Carpels apocarpous syncarpous, syncarpy

50
(d) Elevation of flower parts

In this variation, we consider the relationship between the position of the ovary and
the rest of the other parts. In some flowers, the receptacle is convex or conical and
the different flower parts are arranged one above the other. They occur in the
following order (beginning with the lowest): sepals, petals, stamens, and carpels.
A flower of this type is said to be Hypogynous. (Superior Ovary) (Figure 20).

Figure 2.21 superior ovary positioned above other floral parts

If the sepals, petals and stamens appear to come from the top of the ovary, the
flower is said to be Epigynous (Inferior Ovary) (figure 21). Intermediate between
the hypogynous and epigynous types are those flowers in which the sepals, petals
and stamens have their origin, not above or below the pistil, but around the ovary.
This type of flower is said to be perigynous (Figure 22).

51
 Figure 2.22: inferior ovary epigynous as depicted by pumkin flowers

Figure 2.23: intermediate ovary perigynous

(e) The composite flower

As the name implies the composite flower is a group of many small flowers
arranged to give the appearance of a single typical flower. Good examples are
depicted by sunflower, pineapples, mangoes and maize (Figure 21).

52
 Figure 2.24 Composite flowers

(f) The Grass Flower

Flowers of monocotyledonous plants have their flower parts (whorls), in threes or

multiples of three as opposed to flowers of dicotyledonous plants which tend to be
in fours or fives or multiples of four and/or five i.e. sepals, petals, stamens, and
gynoecium.

The grass flower is regarded as an extremely reduced form of a basic

monocotyledonous flower type. In the gramineae family (Grasses), the perianth
(Sepals + Petals), is reduced to two segments which appear as scales called
lodicules. Stamens appear in threes with very large lobes of anthers (Two on each
filament). Gynaecium is reduced to a single chamber ovary (One seed ovary) with
two feathery styles and with a wide feathery stigma. Such flower is referred to
floret (Figure 24). The flower is adapted to wind pollination.

53
 Figure 2.25 Individual grass flower called floret

Individual flower in grasses appear as composite flowers in form of inflorescence

(Figure 25). Each ellipse represents a complete spikelet. Grass flowers generally
grow in a head or spike.

In all instances the individual small flowers or florets are associated in groups
known as spikelets. Each spikelet is separated from its neighbours by two small
modified leaves or bracts, known as glumes (Figure 26). They are found at the
base of the spikelet. A separation of the glumes reveals the individual florets which
vary in numbers ranging from three to eight depending on type grasses. The
spikelet is attached to a slender stalk called the rachilla. Each floret is in turn is
protected by two additional bracts, the lemna and the palea (Figures 24 and 26).

The lemna may have attached to it a long slender whip-like structure called awn.
The essential parts consist of the androecium composed of three stamens and
the gynoecium of two fused carpels. When the flowers are mature the palea and
lemna separate slightly, exposing two featherly stigmas and allowing the anthers

54
to hang free from the spikelet on greatly lengthened filaments. At the base of the
floral parts there may be distinguished two small protuberances called lodicules.
These are thought to be the greatly modified perianth parts and are supposed to
function in the separation of the lemna and palea at pollination time. Lodicules act
as sponges, when filled with water they expand hence pushing lemna and palea
apart.

Figure 2.26: Common types of grass inflorescence

Figure 2.27 Spikelet and floret

Unit 2 Practical activities

Refer to Unit 2 of the practical module.

55
Unit 2 Summary

In this unit, we have discussed the morphology, anatomy and functions of

the basic organs that make a flowering plant ie roots, stems, leaves and
flowers.

Roots are basically there to provide anchorage of the plants in the soil.
However, they also have other functions including absorption and
transportation of water and mineral salts from the soil, storage of
manufactured food, translocation of manufactured food to other required
places, and other specialised functions. Roots are basically devided in three
structural and functional groups called tissues. Such tissues include dermal,
ground and vascular.

Stems are subdivided into nodes and internodes. Leaves and any other
appendages of the plants grow from the nodes of the stems. Apart from this
function, stems are also known to transport water from roots to leaves. They
also translocate manufactured food between leaves and roots and within its
own body. Other functions include storage, support and other specialised
ones as discussed in the text. Like in roots, they also show three structural
and functional groups of tissues are present in the stem. However the
arrangement of these tissues especially the ground and vascular is different
in stems as in roots.

We have learnt that based on origin, structure, function and position, plants
may produce four different types of leaves i.e cotyledons, cataphylls, floral
and foliage leaves. Much emphasis of our discussion has been mainly on
the foliage leaves. These leaves are basically present on the plants for

56
photosynthetic activities. Apart from this function they also perform other
specialised functions. As a photosynthetic apparatus, leaves tend to be
broad-shaped as solar panels. The leaf body is covered with two skins, one
on the upper side and another on the lower side. The space between the
two skins is mostly covered by ground tissues. But here and there, we see
vascular tissues in form of veins appearing.

Flowers in plants appear as modified stems and leaves for reproductive

purposes. Each standard flower is made up of four basic parts i.e. sepals,
petals, stamens and pistils. However, we see a lot of variations in flowers
with regards to the numbers, arrangement, sizes, colour and shapes of
these four parts.

Unit 2 Test

1. Name the three basic tissues present in all three vegetative organs
of a plant.
2. With aid of well labelled diagrams, show how the above tissues are
arranged in:
a) Roots
b) Monocotyledonous stems
c) Dicotyledonous stems
d) Leaves
3. Draw and label a root tip
4. State five main functions of a normal root
5. Name and state a function of any five specialised roots
6. Define the following terms:
a) Meristem
b) Sessile leaf
c) Cataphylls
d) Senescence

57
 e) Floret
f) Perfect flower
g) Trichome
h) Whorled arrangement of leaves
i) Epidermis
j) Phloem
7. Differentiate between:
a) Taproot and adventitious root systems
b) Arrangement of vascular tissues in dicotyledonous and
monocotyledonous stems
c) Unisexual and bisexual flowers
d) Amphistomatic and hypostomatic leaves
e) Annual and perennial plants
f) Hypogenous and epigynous flowers
8. Write short notes on the following:
a) Veination in plant leaves
b) Patterns of leaf arrangements on the stem
c) Life cycle of flowering plants
d) Endodermal tissue of the root

Unit 2 answers

Reading Assignment

58
Unit 3: Introduction to genetics

Introduction

You may be surprised as you read human history that people were unaware of the
scientific details of how offspring were conceived and how heredity worked. Clearly
they noticed the hereditary relationship between parents and children but not
hereditary mechanisms.

In this unit we will try to understand the genetic basis of hereditary mechanism.
However, before we discuss these we will start by recapping what you learnt in
Biology I module, unit 2; structure and function of the cell. We will also look at the
theories that tried to explain the origin of life and how variations occur between
parents and offspring. Finally we will discuss how allele and genotype frequencies
vary from generation to generation within a family and populations.

Unit 3: learning objectives

By the end of this unit, you should be able to:-

a. recap the structure and function of a cell

b. discuss the theories of the origin of life
c. evaluate Mendelian monohybrid ratios, dihybrid ratios and test cross
d. identify conditions that may lead to a modification of Mendelian monohybrid
and dihybrid ratios
e. analyse allele and genotype frequencies in a population

59
Unit 3 key terms

Ensure that you understand the key terms or phrases used in this unit as listed
below:-

chromatin monohybrid

nucleolus spontaneous F1 generation

generation F2 generation
inheritance of acquired law of segregation
characteristics
law of independent
blending theory assortment
particulate theory test cross
cross-fertilisation heterozygosity
self-pollination zygosity
hybridisation
dominance

Unit 3 Content

3.1 Structure and function of the cell (recap)

By now you should know that although living things have different forms, they are
all cellular meaning that they are composed of at least one cell as a basic unit of
life and that each cell comes from a pre-existing cell. Robert Hooke was the first
to describe cells after observing cork slices using a microscope and coined the
term Cell.

You will also appreciate that our knowledge of cells has grown dependent on
advances done in the field of microscopy.
60
In unit 2 of Biology I, we discussed that cell at its basic structure has cell
membrane, nucleus, organelles and the cytoplasm. The cell membrane is a thin
bi lipid layer which separates the cell contents from its immediate environment.
Plant cells also have in addition the cell wall which gives shape to the cell. The
nucleus is specialised for storage of DNA and controls cell functioning including
reproduction. The cytoplasm is a liquid substance between the nucleus and the
cell membrane in which the organelles are located. Organelles on the other hand
are small bodies with specific structures and functions within the cell. The
organelles include the endoplasmic reticulum (both smooth and rough),
ribosomes, polysomes, golgi apparatus, vacuoles and storage vesicles,
mitochondria, chloroplasts and plastids, cytoskeleton, microtubules and
microfilaments. Some cells may contain cilia and flagella. In addition plants have
chloroplasts and plastids for harvesting light energy for photosynthesis.

Our interest in this section is to revise structure and function of the nucleus. The
nucleus has two major functions: it stores the cell's hereditary material and it
coordinates the cell's activities. Do not forget that only eukaryotic cells have a
nucleus enclosed in a nuclear membrane

The nucleus is membrane bound enclosing a semifluid matrix called nucleoplasm.

The nucleoplasm contain most of the cells genetic materials organized as long
multiple linear DNA molecules in complex with a large variety of proteins such as
histones to form chromosomes. Chromatin is the less condensed form of the
nucleus. The DNA is the genetic code of the cell.

The nucleus also contains one or more nucleoli. Nucleoli are nucleus organelles
that synthesize protein-producing macromolecular assemblies called ribosomes
and a variety of other smaller components. Through the microscope, the nucleolus
looks like a large dark spot within the nucleus. A nucleus may contain up to four
nucleoli, but within each species the number of nucleoli is fixed. After a cell divides,

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a nucleolus is formed when chromosomes are brought together into nucleolar
organizing regions. During cell division, the nucleolus disappears.

A section of a chromosome which controls a particular trait is a gene. A locus

(plural: loci) is the position of a gene (Figure 3.1). The genes within these
chromosomes are the cells nuclear genome and structured in such a way to
promote cell function. The gene controls cellular activities by production of
proteins. Other places where you find DNA molecules are mitochondrion and
chloroplasts. DNA in these organelles are involved in the control of the specific
processes of those organelle.

Figure 3.1: The central dogma of molecular biology

At this point I am sure you are not surprised why the nuclear envelope is a double-
layered membrane with space between the layers called the perinuclear space and
appears to connect with the rough endoplasmic reticulum. The envelope is
perforated with tiny holes called nuclear pores. These pores regulate the passage
of molecules between the nucleus and cytoplasm, permitting some to pass through
the membrane, but not others. The inner surface has a protein lining called the
nuclear lamina, which binds to chromatin and other nuclear components. During
mitosis or cell division, the nuclear envelope disintegrates but reforms as the two
cells complete their formation and the chromatin begins to unravel and disperse.

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3.2 Theories of the origin of life

Together with the advancement in knowledge about the cell did the motivation to
answer the question about the origin of life (the cell) advanced. Scientists have
tried to explain the origin of life on earth which have evolved to produce a number
of theories.

3.2.1 Spontaneous generation

This is the first theory to be recorded that tried to address the origin of life. The
belief in spontaneous generation where life is believed to have evolved from non-
living matter dates back to the time of Aristotle and ancient Greek philosophy. The
theory was advanced together with a belief in heterogenesis where one form of life
can be derived from a different form.

The first experimental evidence against spontaneous generation came in 1688

when Francesco Redi showed that no maggots appeared in meat when flies were
prevented from laying eggs. In 1768, Lazzaro Spallanzani demonstrated that
microbes were present in the air and could be killed by boiling. In 161, Louis
Pasteur performed a series of experiments that demonstrated that organisms such
as bacteria and fungi do not spontaneously appear in sterile, nutrient rich media
but could only appear by invasion from without.

As you can see, the belief of spontaneous generation was disapproved and
begged for an alternative theory. Besides the theory also failed to explain the
occurrence of variations among parents and offspring.

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3.2.2 Inheritance of acquired characteristics

This theory was developed to partially address the existence of variations among
parents and offspring. The theory was developed by Lamarck who argued that
physiological changes acquired over the life of an organism (such as the
enlargement of a muscle through repeated use) may be transmitted to offspring. It
is also commonly referred to as the Theory of Adaptation which is related to the
Evolutionary Theory of French naturalist Jean-Baptiste Lamarck known as
Lamarckism.

This theory was disapproved by a simple interesting experiment conducted by

Weismann who removed the tails of 68 white mice, repeatedly over 5 generations
and observed that no mice were born in consequence without a tail or even with a
shorter tail. Unfortunately, the theory was consequently disproved and that
necessitated another theory.

3.2.3 Blending theory

Weismann then developed the blending theory which aimed at explaining the
existence of variations between parents and offspring. The theory states that
offspring express phenotypic characters intermediate between those of the
parents. However, the theory could not explain how traits that seemingly
disappeared for several generations often reasserted themselves down the line
unaltered. The theory could not explain for example the existence of some
characteristics such as albinism from parents with normal skin and hair colour.

3.2.4 Mendelian inheritance theory

Gregor Mendel (1822-1884) was an Austrian monk who discovered the basic rules
of inheritance. From 1858 to 1866, he bred garden peas, Pisum sativum, in his
monastery garden and analysed the offspring of these crossings.

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Gregor Mendel proposed Inheritance theory/ Particulate theory which states that
similarities and differences between parents and off springs are as a result of
passage of discrete hereditary factors/genes. The work of Mendel was
rediscovered after many years after his work was rejected theory when they could
not find a robust theory to address the shortfalls in the previous theories.
Mendel succeeded to come up with principles that lead to the development of this
theory that has not been challenged to date because of the following factors:-

a) knowledge of statistics which he used to predict and verify outcome of his

experiments
b) choice of subjects for experiments, he used garden peas which can be
cross pollinated or self-pollinated
c) choice of traits, he looked at one trait at a time
d) many varieties were available that bred true for clear cut quantitative traits
analysis such as seed texture, seed colour, flower colour, growth habit
e) the way of presenting results, he used numbers to represent whatever he
discovered
f) his background, he was interested in breeding experiments

3.3 Mendelian monohybrid, dihybrid ratios and test cross

Prior to his work with pea plants plant breeders had conducted experiments
aimed at obtaining flowers with new varieties of colours. You probably are
aware that when two distinct individuals with different characteristics are
crossed to each (hybridization) their offspring are referred to as hybrids. Mendel
chose the garden pea to investigate the natural laws that govern plant hybrids.
In some experiments, Mendel carried out self-fertilisation which means that the
pollen and egg were derived from the same plant. Cross pollination is when
pollen from one plant is placed on a stigma of a different plant.

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Before starting his experiments he concentrated on obtaining several varieties
of peas that were considered to be distinct. These plants were different with
regards to many morphological characteristics. The general characteristics of
an organism are called characters. The term trait and variant are typically used
to describe the specific properties of a character. A variety that produces the
same trait after several generations of self-fertilization is called true breeding
line.

After obtaining true breeding lines for seven traits (Figure 3.2), Mendel studies
these characters by crossing the variants to each other. A cross in which an
experimenter is observing only one character is called monohybrid cross also
called single factor cross. When the two parents are different variants for a
given character, this type of cross produces single character hybrids also called
monohybrids.

Figure 3.5: Seven Characteristics of peas Mendel studied

Mendel’s experimental procedure began with true breeding plants that differed
with regards to a single character. These are termed the parental generation of
P generation. When the true breeding parents were crossed to each other, this
is called p cross and the offspring constitute the F1 generation for first filial
generation. Mendel observed that all F1 generation showed the phenotype of
one parent. This prompted Mendel to follow the transmission of this character

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for another generation. To do this, the F1 generation were allowed to self-
fertilize to produce a second generation called F2 generation for second filial
generation.

P = Parentals (True breeding,

Homozygous and Homogametic)

F1 generation (Heterozygous,
Heterogametic)

F2 generation (Gives 3:1 Mendelian

monohybrid ratio)

Figure 3.3: Mendelian monohybrid cross

From the data that he obtained from this experiment, Mendel made a
quantitative analysis of data from which he was able to propose the following
important ideas.

a) Mendel data argued strongly against a blending mechanism of heredity.

b) Variant for one character is dominant over another variant. The term
recessive is used to describe a variant that is masked by the presence of a
dominant trait that is masked by the presence of a dominant trait but
reappears in subsequent generations.
c) Dominant trait was always observed in F1 generation for heterozygous
plants.
d) Genetic determinants of traits are passed along as unit factors from
generation to generation. His data were consistent with a particulate theory

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 of inheritance in which the genes that govern traits are inherited as discrete
units that remain unchanged as they are passed from parents to offspring.
e) Mendel compared the numbers of dominant and recessive traits in the F2
generation, he noticed as recurring pattern. Within experimental variations,
he always observed approximately a 3:1 ratio between the dominant traits
and the recessive trait.

Mendel was the first scientist to apply this type of quantitative analysis in a
biological experiment. This quantitative approach allowed him to propose a law
of segregation of genes.

Law of Segregation of genes (the "First Law")

The Law of Segregation states that every individual organism contains two
alleles for each trait, and that these alleles segregate (separate) during meiosis
such that each gamete contains only one of the alleles. An offspring thus
receives a pair of alleles for a trait by inheriting homologous chromosomes from
the parent organisms: one allele for each trait from each parent.

Molecular proof of this principle was subsequently found through observation

of meiosis by two scientists independently, the German botanist Oscar Hertwig
in 1876, and the Belgian zoologist Edouard Van Beneden in 1883. Paternal
and maternal chromosomes get separated in meiosis and the alleles with the
traits of a character are segregated into two different gametes. Each parent
contributes a single gamete, and thus a single, randomly successful allele copy
to their offspring and fertilization.

Law of Independent Assortment (the "Second Law")

After understanding heredity mechanisms of monohybrid traits Mendel

proceeded to investigate the pattern of inheritance for two different characters.
He carried out two factor crosses also known as dihybrid crosses in which he

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followed the inheritance of two different characters within the same groups of
individuals.

Let us consider an experiment in which one of the characters was seed shape
found in round or wrinkled variants, the second character was seed colour
which existed as yellow and green variants.

Mendel took peas with round (R) and green (Y) seeds and crossed them with
wrinkled (R) and yellow (y) seeds in a cross as shown below.

P1: RRYY x rryy

Gametes (heterogametic): RY ry
F1: RrYy (round and green seeds)

He then selfed F1 to obtain F2 and or this we use a Punnett square as shown

in Figure 3.4 below.

Figure 3.4: Punnet square for Mendelian dihybrid cross

This gave Mendelian dihybrid ratio, 9:3:3:1 of round green seeds: round yellow
seeds: wrinkled green seeds: wrinkled yellow seeds. From these results, he
came up with the law of independent assortment which states that alleles for

69
separate traits are passed independently of one another from parents to
offspring.

You can simplify this when you consider that the law states that the biological
selection of an allele for one trait has nothing to do with the selection of an
allele for any other trait. Mendel found support for this law in his dihybrid cross
experiments. In his monohybrid crosses he idealized a 3:1 ratio between
dominant and recessive phenotypes while in dihybrid crosses he found a
9:3:3:1 ratio. This shows that each of the two alleles is inherited independently
from the other, with a 3:1 phenotypic ratio for each.

Test cross

In genetics, a test cross, first introduced by Gregor Mendel, involves the

breeding of an individual with a phenotypically recessive individual, in order to
determine the zygosity of the former by analysing proportions of offspring
phenotypes. Zygosity can either be heterozygous or homozygous. Those that
are heterozygous have one dominant and one recessive allele. Individuals that
are homozygous dominant have two dominant alleles, and those that are
homozygous recessive have two recessive alleles

Figure 3.5: Genetic test cross

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Test crosses involve breeding the individual in question with another individual
that expresses a recessive version of the same trait. Analysing the proportions
of dominant and recessive offspring determines if the individual in question is
homozygous dominant or heterozygous. If all offspring from the test cross
display the dominant phenotype, the individual in question is homozygous
dominant; if half the offspring display dominant phenotypes and half display
recessive phenotypes, then the individual is heterozygous (Figure 3.5). Since
the homozygous recessive individual can only pass on recessive alleles, the
alleles the individual in question passes on determine the phenotypes of the
offspring.

Modification of Mendelian monohybrid and dihybrid ratios

Mendel explained inheritance in terms of discrete factors ‘genes’ that are

passed along from generation to generation according to the rules of
probability. Mendel's laws are valid for all sexually reproducing organisms.
However, Mendel's laws stop short of explaining some patterns of genetic
inheritance. Cases where Mendel's laws can strictly account for the patterns of
inheritance are relatively rare. Often, the inheritance patterns are more
complex.

Until the end of this section we will discuss some of the cases which may lead
to modification of Mendelian monohybrid and dihybrid ratios which include
codominance, multiple alleles, lethal alleles, duplicate genes, epistasis, non-
epistasis, complementary genes, polygenic, linkage, sex linkage, autosomal
linkage and mutations,
Dominance is a relationship between alleles of one gene in which the effect on
phenotype of one allele masks the contribution of a second allele at the same
locus. The first allele is dominant and the second allele is recessive.
Dominance is a key concept in Mendelian inheritance and classical genetics.

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Often the dominant allele codes for a functional protein whereas the recessive
allele does not. Inheritance of such alleles reads to the classical Monohybrid
ratio of 3:1 or Mendelian dihybrid 9:3:3:1 ratio.

Incomplete dominance
Incomplete dominance is a form of intermediate inheritance in which one allele
for a specific trait is not completely expressed over its paired allele. This results
in a third phenotype in which the expressed physical trait is a combination of
the phenotypes of both alleles.

e.g. P1 Flower colour: RR (red) x WW (white)

Gametes (Homogametic) R W
F1: RW (pink)
F2: RR RW RW WW

Genotype ratio = 1:2:1 (RR:RW:WW) and

Phenotype ratio of 1:2:1 (red: pink: white)

Codominance

Co dominance occurs when the contributions of both alleles are visible in the
phenotype. Co dominance where allelic products co-exist in the phenotype is
different from incomplete dominance where the quantitative interaction of allele
products produce an intermediate phenotype. In co dominance for example, a
red homozygous flower and a white homozygous flower will produce offspring
that have red and white spots. When plants of the F1 generation are self-
pollinated, the phenotype and genotypic ratio of the F2 generation will be 1:2:1.

The MN blood group in humans is under the control of a pair of co-dominant

alleles, LM and LN based based upon two genes (glycophorin A and glycophorin
B) on chromosome 4.

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If an individual with M blood type (LMLM) is married to an individual with N blood
type (LNLN) the F1 will have MN blood type (LMLN) as shown below.

P1: MN blood group: LMLM (M) x LNLN(N)

Gametes (homogametic): M N
F1: LMLN (MN)

Multiple alleles
Multiple alleles is a type of non-Mendelian inheritance pattern that involves
more than just the typical two alleles that usually code for a certain
characteristic in a species. With multiple alleles, there are more than two
phenotypes available depending on the dominant or recessive alleles that are
available in the trait and the dominance pattern. However, only two forms of the
alleles exist in a diploid individual. Why?

We will look at the most well-known ABO blood type system to help us
understand how multiple alleles work. There are four principal types A, B, AB
and O. There are two antigens and two antibodies that are mostly responsible
for the ABO types. A and B are co-dominant and both are dominant over O.
Below are the phenotypes you would expect for each genotype.

Genotype IAIB = Phenotype AB

Genotype IAIA and IAIO = Phenotype A
Genotype IBIO = Phenotype B
Genotype IOIO = Phenotype O

Lethal alleles
Lethal alleles are alleles that cause 100% mortality in the organism that carry
them. They are usually a result of mutations in genes that are essential to

73
growth or development. Lethal alleles may be recessive, dominant or
conditional depending on the gene or genes involved. Lethal alleles can cause
death of an organism prenatally or any time after birth, though they commonly
manifest early in development.

Lethal alleles were first discovered by Lucien Cuénot in 1905 while studying
the inheritance of coat colour in mice. The agouti gene in mice is largely
responsible for determining coat colour. The wild-type allele produces a blend
of yellow and black pigmentation in each hair of the mouse. This yellow and
black blend may be is referred to as 'agouti' in colour. One of the mutant alleles
of the agouti gene results in mice with a much lighter, yellowish colour. When
these yellow mice were crossed with homozygous wild-type mice, a 1:1 ratio of
yellow and dark grey offspring were obtained. This indicated that the yellow
mutation is dominant, and all the parental yellow mice were heterozygotes for
the mutant allele.

Let us consider what was happening in these crosses.

e.g. Wild type genotype (agouti) = AyAy

Ayay = Yellowish colour,
if we take P1: Ayay x AyAy
Gametes: Ay/ay Ay
F1: AyAy and Ayay (in what ratio?)

selfing agouti P2: Ay ay x Ay ay (self the F1)

Gametes: Ay /ay
F2: AyAy, Ayay, Ayay, ayay
( ratio of 2:1 of agouti:black rats)

Duplicate genes

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This occurs if alleles duplicated. Duplication of alleles can result from any
process that result DNA replication or repair. Let us consider this by looking at
a hypothetical example where by a gene controlling height is duplicated.

P1: AABB (tall) x aabb(short)

Gametes: AB ab
F1: AaBb (tall)

All the F1 generation will be tall. Now if we self F1 in a case where

there are duplicate genes.

Parents 2: AaBb x AaBb

Gametes: AB/Ab/aB/ab

Using a punnet square we obtain the following

AB Ab aB ab

AB AABB AABb AaBB AaBb

Ab AABb Aabb AaBb Aabb

aB AaBB AaBb aaBB aaBb

ab AaBb Aabb aaBb aabb

All offspring will be tall except one. The ratio will be 15:1 of tall: short
instead of the monohybrid 3:1 or dihybrid 9:3:3:1 ratio

Epistasis genes
Epistasis is the phenomenon of the effect of one gene being dependent on the
presence of one or more 'modifier genes'. This is a situation where there is a
gene at locus A which masks expression of another gene at locus B. Locus A
suppresses the expression of the gene at locus B and it depends on whether

75
there is a dominant or a recessive gene on locus A. Thus, epistatic mutations
have different effects in combination than individually.

I hope you will understand this easily by looking at an example of position of

flowers. Let gene A be responsible for lateral flower position and B is terminal.
If A and B are epistatic where A maskes the expression of B then.

Genotype AABB will give lateral flower position regardless of the presence of
a dominant gene for terminal flower. If aa, a recessive gene for lateral flower is
present then a terminal flower phenotype will be observed. Terminal flower will
only be expressed where aa is recessive. If loci A is heterozygous, that is there
is Aa at this locus, lateral flower position will be the phenotype.

Complementary genes
This is a situation in which two independent pairs of non-allelic genes neither
of which is functional without the other. These are genes that produce an
observable effect in an organism only in conjunction with another gene. If seed
texture is controlled by two alleles A and B and that they two alleles are
complementary to each other it means if AABB is the multilocus genotype the
seed will be smooth. The following genotypes will give wrinkled seed because
the other locus is recessive and hence does not complete the other allele.

i.e. AA + BB = smooth seed

AA + bb = wrinkled seed
aa + BB = wrinkled seed
aa + bb = wrinkled seed

Polygenic inheritance
These are multiple genes determining the degree of a characteristic. One of a
group of genes in which the number of the genes present collectively
determines the extent of a characteristic. The term “polygenic inheritance” is

76
used to refer to the inheritance of quantitative traits, traits which are influenced
by multiple genes. In addition to involving multiple genes, polygenic inheritance
is also influenced by the environment in someone's development.

Because many traits are spread out across a continuum, rather than being
divided into black and white differences, polygenic inheritance helps to explain
the way in which these traits are inherited and focused. A related concept is
pleiotropy, an instance where one gene influences multiple traits.

A typical example would be human height which is controlled by a number of

gene and depending on the number of genes contributing to the character. The
individual has a range of possible heights not just discrete values.

Linkage
Genetic linkage is the tendency of alleles that are close together on a
chromosome to be inherited together during the meiosis phase of sexual
reproduction. Genes whose loci are nearer to each other are less likely to be
separated onto different chromatids during chromosomal crossover, and are
therefore said to be genetically linked. In other words, the nearer two genes are
on a chromosome, the lower is the chance of a swap occurring between them,
and the more likely they are to be inherited together.

Genes that are on the same chromosome are called linked genes. These genes
are associated in their inheritance, they are inherited together and in the same
position. The linkages are found either in sex cells/sex chromosomes or
autosomal cells/autosome chromosomes.

Sex linkage
Morgan observed that inheritance of a characteristic depends on whether the
characteristic is on a male or a female organism. He made these observations
when he was studying inheritance pattern of eye colour in fruit flies.

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When he crossed wildtype female fruit flies and red eyed males he observed
that all females offspring were red eyed but the males had wild type eyes. The
pattern was different when he crossed red eyed females and wild type eyed
males. In this crossed he observed that all the offspring had red eyes.

These crosses can be represented as shown below.

Parents: Female (wildtype) x Male (red eyes)

XcXc XCY
Gametes: XC XC, Y
F1: XC Xc , XcY, XC, XC, XcY
(all females had red eyes while males had wild type)

When the characteristics are reversed the following phenotypes are observed.

P1: Female (red eyes) x Male (wild type)

XC XC XcY
F1: XC XC, XCXC, XCY, XCY
(all of them had red eyes)

There are several examples of sex linked characteristics in human beings

however for this purpose it should suffice to mention the following characteristic
which most of you are familiar with.

1) colour blindiness associated with X

2) haemophilia, mainly suffered by females
3) baldnes

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Autosomal linkage
On the other hand there are two types of autosomal linkages; complete and
partial autosomal linkages. Genes that are linked completely do not assort
themselves independently as a result they are inherited in a block.

Partial linkages come as a result of crossing over at meiosis to make new

combinations with other genes called recombinants. The frequency of
recombinants is used to estimate the distance between genes.

You will recall that we noted that genes that are far apart have a higher
probability of crossing over than genes that are close together. Morgan
proposed a standard percentage combinations that 1% of recombinants
represent 1 map unit. This you can understand easily when you consider that
when you have a 1% frequency of recombinants then the two genes are one
map unit apart. The map unit was named after him as centimorgan hence 1%
means the two genes are 1 cM (centimorgan) apart.

Let us look at an example from a typical cross of coloured smooth seeds and
coloured wrickled seeds from which the following combinations were found

Coloured smooth seeds 48.25%

Coloured wrickled seeds 48.25%
Colourless wrickled seeds 1.75%
Colourless smooth seeds 1.75%

Total percentage of recombinants for this experiment is 1.75% + 1.75% = 3.5%.

We can therefore conclude from this data that the gene for colour and texture
are 3.5cM apart

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Mutations
We will start by defining mutations as sudden changes to chromosomal DNA
that results into some heritable characteristics. Factors that cause mutations
also known as mutagens or mutagenic factors have potential of denaturing
proteins and DNA. Mutagenic factors can be categorised as radiation which
includes X rays, Alpha rays, gamma rays and beta rays. Ultra violet (UV) light
is also a radiation that is a mutagen. Another category of mutagenic factors are
oxidation. Oxidation factors are Hydrogen peroxide H2O2 and Mustard gas.

There are two types of mutation – gene and chromosome mutation affecting
the gene and the chromosome respectively

Types of gene mutations

1) Substitution- nucleotide is replaced by another. The nucleotides work in
triples and they code for a particular amino acid. When one nucleotide is
changed the amino acid changes and it affects its function.
2) Insertion/addition- nucleotide(s) are added to a DNA strand
3) Inversion- nucleotides are cut off and pasted to the same strand in an
inverted way
4) Deletion- the nucleotide(s) is cut and disappear

These mutations have been illustrated in figure 3.6 below.

Figure 3.6:. Types of gene mutations

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Types of chromosome mutations
1) Substitution- a small part of the chromosome is cut and lost but is replaced
by another part
2) Translocation/ addition- this involves transfer of a chromosome part to
another chromosome
3) Inversion- part of a chromosome is cut and joins the same chromosome
after flipping over.
4) Deletion- when part of a chromosome disappears
5) Duplication – a section of a chromosome is repeated
6) Mutations involving change in chromosome number- non- disjunction at
anaphase of mitosis or meiosis, this may result in one cell having less or
more than 2n
e.g. Male XY female XX . Non disjuction in male may result in XO = tuner
female, XXY = super male or XXX = super female

Figure 3.7: types of chromosomal mutations

3.4 Population genetics

Until now we have focused our attention on genes within individuals and their
related family members. The field of population genetics is concerned with
understanding changes in genetic variations within a group of individuals over
time. Population genetics seeks to know the extent of genetic variations within
populations.

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Different alleles within a population can be identified by phenotypic effects (for
example colour, size, shape), variations in molecular structure (such as protein
or DNA).

Population genetics is an extension of our understanding of Mendel’s laws of

inheritance and molecular genetics. Conceptually, all of the alleles of every
gene in a population make up the gene pool. Population genetics study the
genetic variation within the gene pool and how such variation changes from
one generation to the next.

We will define a population as a group of individuals of the same species that

occupy the same region and can be interbreed with one another. A large
population usually is composed of smaller groups called local populations or
demes.

Population genetics is concerned with allele and genotype frequencies. In

population genetics we want to understand the prevalence of polymorphic
genes within populations. The goal is to identify the causative factors that
govern changes in genetic variation. Allele frequencies can be used to make
inferences about mating patterns, selection, migration etc.

Two fundamental calculations are central to population genetics:-

𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑐𝑜𝑝𝑖𝑒𝑠 𝑜𝑓 𝑎𝑛 𝑎𝑙𝑙𝑒𝑙𝑒 𝑖𝑛 𝑎 𝑝𝑜𝑝𝑢𝑙𝑎𝑡𝑖𝑜𝑛

𝐴𝑙𝑙𝑒𝑙𝑒 𝑓𝑟𝑒𝑞𝑢𝑒𝑛𝑐𝑦 =
𝑇𝑜𝑡𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑎𝑙𝑙𝑒𝑙𝑒𝑠 𝑓𝑜𝑟 𝑡ℎ𝑎𝑡 𝑔𝑒𝑛𝑒 𝑖𝑛 𝑎 𝑝𝑜𝑝𝑢𝑙𝑎𝑡𝑖𝑜𝑛

𝐺𝑒𝑛𝑜𝑡𝑦𝑝𝑒 𝑓𝑟𝑒𝑞𝑢𝑒𝑛𝑐𝑦
𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 𝑤𝑖𝑡ℎ 𝑎 𝑝𝑎𝑟𝑡𝑖𝑐𝑢𝑙𝑎𝑟 𝑔𝑒𝑛𝑜𝑡𝑦𝑝𝑒 𝑖𝑛 𝑎 𝑝𝑜𝑝𝑢𝑙𝑎𝑡𝑖𝑜𝑛
=
𝑇𝑜𝑡𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠𝑠 𝑖𝑛 𝑎 𝑝𝑜𝑝𝑢𝑙𝑎𝑡𝑖𝑜𝑛

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Hardy and Weinberg proposed that allele frequencies in a population remain
constant—that is, they are in equilibrium—from generation to generation unless
specific disturbing influences are introduced. These disturbing factors include
non-random mating, mutations, selection, limited population size and
migration.

The Hardy-Weinberg equation is a mathematical equation that can be used to

calculate the genetic variation of a population at equilibrium. To explore the
Hardy-Weinberg equation, we can examine a simple genetic locus at which
there are two alleles, A and a. The Hardy-Weinberg equation is expressed as:

p2 + 2pq + q2 = 1

where p is the frequency of the "A" allele and

q is the frequency of the "a" allele in the population.

The formula is sometimes written as (p2) + (2pq) + (q2)= 1, representing the

trivial fact that frequencies must add up to one. The final three possible
genotypic frequencies in the offspring become: f(AA) = p2, f(Aa) =pq and f(aa)
= q2. These frequencies are called Hardy–Weinberg frequencies (or Hardy–
Weinberg proportions).

In the equation, p2 represents the frequency of the homozygous genotype AA,

q2 represents the frequency of the homozygous genotype aa, and 2pq
represents the frequency of the heterozygous genotype Aa. In the simplest
case of a single locus with two alleles: the dominant allele is denoted A and the
recessive a and their frequencies are denoted by p and q; freq(A) = p; freq(a)
= q; p + q = 1.

If the p and q allele frequencies are known, then the frequencies of the three
genotypes may be calculated using the Hardy-Weinberg equation. In

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population genetics studies, the Hardy-Weinberg equation can be used to
measure whether the observed genotype frequencies in a population differ from
the frequencies predicted by the equation. If the population is in equilibrium,
then we will have freq(AA) = p2 for the AA homozygotes in the population,
freq(aa) = q2 for the aa homozygotes, and freq(Aa) = 2pq for the
heterozygotes.

Let us consider data that was collected in Britain on MN blood system. The
study found out that the frequency of M to be 0.54 while the frequency of N was
0.46. From this data we can calculate the frequency of MM, MN and NN blood
types.

You will notice that the frequency of M is given as p = 0.54 and the frequency
of N is given as q = 0.46. Assuming that the population is in Hardy-Weinberg
equilibrium then expected genotypic frequencies will therefore be

MM MN NN

p2 2pq q2

0.294 0.496 0.209

Now let us assume that 1000 individuals were sampled in the following
generation and there were 298 individuals with genotype M, 489 with MN
genotype and 213 were NN. We can measure if this population is in Hardy
Weinberg equilibrium using Chi square test.

We start by calculating the expected genotypes under Hardy Weinberg

equilibrium. Then we can proceed to test if the data is in agreement with Hardy
Weinberg equilibrium.

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 Genotypes MM MN NN

Expected 294 496 209

Observed 298 489 213

The table below summaries the steps that we follow to test whether the
frequencies are in agreement with Hardy-Weinberg equilibrium. We start by
subtracting the expected from the observed and to remove the negatives the
value is squared. Then in the next column you divide this value by the expected.

In the column the values are added to give a χ2 number which you look up in
the χ2 table. Refer to the practical module for more practise and examples.

Observed (O) Expected (E) (O-E)2 (O − E)²

E

298 294 16 0.054

489 496 49 0.099

213 209 16 0.077

χ2 = 0.230

3.5 Principles of genetic evolution

We will define evolution as a change in heritable characteristics of biological

populations over successive generations. Evolutionary processes give rise to
biodiversity at every level of biological organisation.

It is believed that all life on Earth shares a common ancestor known as the last
universal common ancestor (LUCA) which lived approximately 3.5–3.8 billion
years ago. Repeated formation of new species (speciation), change within
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species (anagenesis), and loss of species (extinction) throughout the
evolutionary history of life on Earth are demonstrated by shared sets of
morphological and biochemical traits. These shared traits are more similar
among species that share a more recent common ancestor, and can be used
to reconstruct a biological "tree of life" based on evolutionary relationships
(phylogenetics) using both existing species and fossils.

In the mid-19th century, Charles Darwin formulated the scientific theory of

evolution by natural selection, published in his book On the Origin of Species
(1859). Evolution by natural selection is a process demonstrated by the
observation that more offspring are produced than can possibly survive, along
with three facts about populations: phenotypic variation, differential fitness and
heritability of fitness. Thus, in successive generations members of a population
are replaced by progeny of parents better adapted to survive and reproduce in
the biophysical environment in which natural selection takes place. Natural
selection, including sexual selection, is the only known cause of adaptation but
not the only known cause of evolution. Other, non-adaptive evolutionary
processes include mutation, genetic drift and gene migration.

Over a long period of time, precise mechanisms of reproductive heritability and

origin of new traits have remained a mystery. However, in the 1920s and 1930s
a modern evolutionary synthesis connected natural selection, mutation theory
and Mendelian inheritance. Modern evolutionary synthesis explains how
evolution acts on patterns of change within individuals. Some of the
mechanisms include heredity, variations, mutation, recombination, gene flow,
natural selection, genetic drift, genetic hitchhiking, adaptation, coevolution,
cooperation, speciation, extinction.

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Evidence of genetic evolution

Scientist have demonstrated that organisms have evolved from a common

ancestor. This evidence constructs the theoretical framework on which
evolutionary theory rests, demonstrates that evolution does occur and is able
to show the natural processes that led to the emergency of earth's biodiversity.
This evidence supports the modern evolutionary synthesis.

1. Comparative physiology and biology where strongest evidence comes from

comparative sequence analysis which examines relationship between DNA
or protein sequences of different species and used in generating
phylogenetic trees.
2. Comparative anatomy in which groups of organism reveal basic similarities
of certain structural features. This has been demonstrated by atavism which
is the reappearance of lost characters typical of ancestors and seen in
recent ancestors, similarity in embryogenesis, homologous structures and
divergent adaptive evolution, nested hierarchies in classification, vestigial
structures
3. Paleontology which is the evidence obtained from the study of past life
based on fossil records and their relation to different geologic time periods.
However, because of limitations inherent in the record, there are not fine
scales of intermediate forms between related groups of species.
4. Biogeography in which there is evidence that organisms are adapted to their
environment. Data about the presence or absence of species on various
continents and islands (biogeography) can provide evidence of common
descent and shed light on patterns of speciation. Further evidence can be
found in continental distribution, island biogeography, endemism, adaptive
radiations and rings species.

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 5. Artificial selection demonstrates the diversity that can exist among
organisms that share a relatively recent common ancestor. Experimental
evolution uses controlled experiments to test hypotheses and theories of
evolution.
6. Speciation is the evolutionary process by which new biological species
arise.
7. Computer science allows mathematical modelling that iteration of self-
changing complex systems to be studied, allowing a mathematical
understanding of the nature of the processes behind evolution; providing
evidence for the hidden causes of known evolutionary events. The evolution
of specific cellular mechanisms like spliceosomes that can turn the cell's
genome into a vast workshop of billions of interchangeable parts that can
create tools that create tools that create tools that create us can be studied
for the first time in an exact way.

Unit 1 activity

Unit 1 Summary

Unit test

1. The ability to taste a bitter chemical, phenylthiocarbamide (PTC), is due to

a dominant gene. Use T and t to symbolize the two alleles of this gene. a.
What is the genotype of a non-taster? What are the possible genotypes of
a taster? b. Could a person with two tasters as parents be a non-taster?
How?

2. In the fruit fly Drosophila melanogaster, vestigial wings and hairy body are
produced by two recessive genes located on different chromosomes. The

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 normal alleles, long wings and hairless body, are dominant. Give the
genotype and phenotype of F1 progeny obtained from a cross between a
vestigial-winged, hairy male and a normal, homozygous female. If the F1
from this cross are permitted to mate randomly among themselves, what
phenotypic ratio would be expected in the F2 generation?

3. In humans, sickle-cell anemia is caused by a recessive lethal allele Hbs;

individuals who are HbaHbs have sickle-cell trait, but are healthy. a. What
is the probability of two heterozygous individuals giving birth to a child with
sickle-cell trait? b. What is the probability of two heterozygous individuals
giving birth to a child with sickle-cell anemia? c. If a normal HbaHba
individual receives a blood transfusion from a HbaHbs individual
(heterozygous for sickle cell) what are the chances that the HbaHba man
and his HbaHba wife will have HbaHbs children?

4. A study on blood types in a population found the following genotypic

distribution among the people sampled: 1101 were MM, 1496 were MN and
503 were NN. Calculate the allele frequencies of M and N, the expected
numbers of the three genotypic classes (assuming random mating). Using
X2, determine whether or not this population is in Hardy-Weinberg
equilibrium.

5. The compound phenylthiocarbamide (PTC) tastes very bitter to most

persons. The inability to taste PTC is controlled by a single recessive gene.
In the American white population, about 70% can taste PTC while 30%
cannot (are non-tasters). Estimate the frequencies of the Taster (T) and
nontaster (t) alleles in this population as well as the frequencies of the
diploid genotypes.

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Unit answers

Reading assignment/List

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