Module 5 Heredity

Life continues through the processes of reproduction and heredity. Students expand their
knowledge of evolution by understanding the cellular processes involved in increasing
genetic diversity. They investigate reproduction and inheritance patterns in both plants and
animals as well as the role of DNA in polypeptide synthesis and the uses of technologies in
the study of inheritance patterns.
Students also learn about contemporary research and the work of geneticists across a variety
of industries, including medical applications and agriculture. They explore the effects on
society and the environment through the application of genetic research.

1. Reproduction
Inquiry question: How does reproduction ensure the continuity of a species?
1.1 Explain the mechanisms of reproduction that ensure the continuity of a species, by
analysing sexual and asexual methods of reproduction in a variety of organisms,
including but not limited to:
a) animals: advantages of external and internal fertilisation
Animals reproduce either externally or internally. The majority of animals that reproduce
externally live in aquatic environments but there are a number of aquatic animals that
reproduce internally.
i) advantages of external reproduction
There are a number of advantages in using external reproduction - It results in increased
genetic variation in the species due to the random mixing of gametes from different parents, it
produces a larger number of offspring ensuring that there is a significant increase in the
likelihood of a successful zygote formation and the gametes released can drift and therefore it
is easy to find mates. It is a simple reproductive strategy which does not require the
involvement of any hormones or mating rituals.
There are however some significant disadvantages - The success rate of fertilization is very
low. Unlike internal fertilization, a large number of gametes need to be produced by the male
and female to ensure reproductive success. A water body is required to initiate external
fertilization as the sperm’s design can only work in a fluid environment. It is considered by
most biologists to be a reproductive disadvantage for most of the animals because the vast
majority of the gametes die without being fertilized, or they die by unfavourable components
in the environment or by predation.
Some examples of external fertilization are given below:
Sea Urchins - they use chemotaxis to attract the sperms towards the eggs. Their spawning is
synchronized to prevent the eggs and sperms from diluting or drifting away.

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Frogs - The female releases the eggs into the water. The male also releases the sperms in the
water to fertilize them. The larval life of the frogs is in water, whereas the adult life is on
land.

Figure 1 – Stages in a frog life cycle

Salmon - They have an opening right in front of their anal fin through which the gametes are
released and then fertilized.

Figure 2 – Chinook salmon spawning.

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Most Coral - A large number of gametes are released in water during spawning of corals.
After fertilization, the coral larvae move up to the surface for maturation. Corals along the
length of the Great Barrier Reef all spawn on a single night in spring, during the first quarter
of the moon cycle and on the high tide.

Figure 3 – An example of synchronised coral spawning.

Starfish - They gather in groups and use chemical signals to indicate the other members of the
group that they are ready to spawn. This synchronized spawning increases the chances of
fertilization success.

Figure 4 – Spawning congregation of Crown of thorns starfish.

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External Fertilization in Humans - External fertilization also takes place in humans, but it is
not natural. A few females have blocked oviducts. The sperms cannot reach the eggs and the
female cannot conceive. In this situation, the doctors collect freshly released eggs and sperm
and keep them together for several hours for in-vitro fertilization. When the fertilization
occurs, the zygote is transferred to the uterus of the female after about a week, and the
development process occurs inside the female’s body.

Figure 5 – Stages in the IVF procedure.

ii) advantages of internal reproduction

Internal fertilization occurs most often in land-based animals, although some aquatic animals
also use this method. There are three ways that offspring are produced following internal
fertilization: oviparity, ovoviparity, and viviparity.

In oviparity, fertilized eggs are laid outside the female’s body and develop there in the
external environment, receiving nourishment from the yolk that is a part of the egg. This
occurs in most bony fish, many reptiles, some cartilaginous fish, most amphibians, two
mammals, and all birds. Reptiles and insects produce leathery eggs, while birds and turtles
produce eggs with high concentrations of calcium carbonate in the shell, making them hard.
These animals are referred to as oviparous.

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 Figure 6 – Baby tortoise emerging from its shell.

In ovoviparity, fertilized eggs are retained in the female, but the embryo obtains its
nourishment from the egg’s yolk; the young are fully developed when they are hatched. This
occurs in some bony fish, some sharks, some lizards, some constrictor snakes, some vipers,
and some invertebrate animals (such as the Madagascar hissing cockroach).

Figure 7 – Baby sand school shark embryo.

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In viviparity, the young develop within the female, receiving nourishment from the mother’s
blood through a placenta. The offspring develops in the female and is born alive. This occurs
in most mammals, some cartilaginous fish, and a few reptiles, making these animals
viviparous.

Figure 8 – Fossilised ichthyosaur giving birth.

Internal fertilization has the advantage of protecting the fertilized egg from dehydration on
land. The embryo is isolated within the female, which limits predation on the young. Internal
fertilization also enhances the fertilization of eggs by a specific male. Even though fewer
offspring are produced through this method, their survival rate is higher than that for external
fertilization.

b) plants: asexual and sexual reproduction

i) plant asexual reproduction
I -natural methods of asexual reproduction

Many plants are able to propagate themselves using asexual reproduction. This method does
not require the investment required to produce a flower, attract pollinators, or find a means of
seed dispersal. Asexual reproduction produces plants that are genetically identical to the
parent plant because no mixing of male and female gametes takes place. Traditionally, these
plants survive well under stable environmental conditions when compared with plants
produced from sexual reproduction because they carry genes identical to those of their
parents.

Plants have two main types of asexual reproduction: vegetative reproduction and apomixis.
Vegetative reproduction results in new plant individuals without the production of seeds or
spores. Many different types of roots exhibit vegetative reproduction. The corm is used by
gladiolus and garlic. Bulbs, such as a scaly bulb in lilies and a tunicate bulb in daffodils, are
other common examples of this type of reproduction. A potato is a stem tuber, while parsnip
propagates from a taproot. Ginger and iris produce rhizomes, while ivy uses an adventitious
root (a root arising from a plant part other than the main or primary root), and the strawberry
plant has a stolon, which is also called a runner.

Some plants can produce seeds without fertilization. Either the ovule or part of the ovary,
which is diploid in nature, gives rise to a new seed. This method of reproduction is known as
apomixis. Major cereals such as maize and wheat show apomixis. An advantage of asexual

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reproduction is that the resulting plant will reach maturity faster. Since the new plant is
arising from an adult plant or plant parts, it will also be sturdier than a seedling. Asexual
reproduction can take place by natural or artificial (assisted by humans) means.

Figure 9 - Different types of stems allow for asexual reproduction. (a) The corm of a garlic
plant looks similar to (b) a tulip bulb, but the corm is solid tissue, while the bulb consists of
layers of modified leaves that surround an underground stem. Both corms and bulbs can self-
propagate, giving rise to new plants. (c) Ginger forms masses of stems called rhizomes that
can give rise to multiple plants. (d) Potato plants form fleshy stem tubers. Each eye in the

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stem tuber can give rise to a new plant. (e) Strawberry plants form stolons: stems that grow at
the soil surface or just below ground and can give rise to new plants

Artificial Methods of Asexual Reproduction

These methods are frequently employed to give rise to new, and sometimes novel, plants.
They include grafting, cutting, layering, and micropropagation.

● Grafting

Grafting has long been used to produce novel varieties of roses, citrus species, and other
plants. In grafting, two plant species are used; part of the stem of the desirable plant is grafted
onto a rooted plant called the stock. The part that is grafted or attached is called the ‘scion’.
Both are cut at an oblique angle (any angle other than a right angle), placed in close contact
with each other and are then held together. Matching up these two surfaces as closely as
possible is extremely important because these will be holding the plant together. The vascular
systems of the two plants grow and fuse, forming a graft. After a period of time, the scion
starts producing shoots, and eventually starts bearing flowers and fruits. Grafting is widely
used in viticulture (grape growing) and the citrus industry. Scions capable of producing a
particular fruit variety are grafted onto root stock with specific resistance to disease.

Figure 10 – A ‘fruit salad’ citrus tree, consisting of grafted section of lemon, lime, orange and
grapefruit.

● Cutting

Plants such as coleus and money plant are propagated through stem cuttings, where a portion
of the stem containing nodes and internodes is placed in moist soil and allowed to root. In
some species, stems can start producing a root even when placed only in water. For example,
leaves of the African violet will root if kept in water undisturbed for several weeks.

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 Figure 11 – Sugar cane cuttings.

● Layering

Layering is a method in which a stem attached to the plant is bent and covered with soil.
Young stems that can be bent easily without any injury are preferred. Jasmine and
bougainvillea (paper flower) can be propagated this way.
In some plants, a modified form of layering known as air layering is employed. A portion of
the bark or outermost covering of the stem is removed and covered with moss, which is then
taped. Some gardeners also apply rooting hormone. After some time, roots will appear, and
this portion of the plant can be removed and transplanted into a separate pot.

Figure 12 – Methods of layering.

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 ● Micropropagation

Micropropagation (also called plant tissue culture) is a method of propagating a large number
of plants from a single plant in a short time under laboratory conditions. This method allows
propagation of rare, endangered species that may be difficult to grow under natural conditions
(Wollemi pines have been propagated this way), are economically important, or are in
demand as disease-free plants.

Figure 13- Wollemi pines grown by tissue culture methods.

To start plant tissue culture, a part of the plant such as a stem, leaf, embryo, anther, or seed
can be used. The plant material is thoroughly sterilized using a combination of chemical
treatments standardized for that species. Under sterile conditions, the plant material is placed
on a plant tissue culture medium that contains all the minerals, vitamins, and hormones
required by the plant. The plant part often gives rise to an undifferentiated mass known as
callus, from which individual plantlets begin to grow after a period of time. These can be
separated and are first grown under greenhouse conditions before they are moved to field
conditions.
ii) plant sexual reproduction
There are several different methods and processes involved in the sexual reproduction of
plants. Many of the structures associated with sexual reproduction in plants are valuable
commodities for humans (think fruits, berries, and vegetables). An equal number of them are
“baneful” (think seasonal allergies).

In angiosperms (flowering plants), pollination is defined as the placement or transfer of

pollen from the anther to the stigma of the same flower or another flower. In gymnosperms
(conifers and cycads), pollination involves pollen transfer from the male cone to the female
cone. Upon transfer, the pollen germinates to form the pollen tube and the sperm for
fertilizing the egg. Pollination has been well studied since the time of Gregor Mendel.
Mendel successfully carried out self- as well as cross-pollination in garden peas while
studying how characteristics were passed on from one generation to the next. Today’s crops
are a result of plant breeding, which employs artificial selection to produce the present-day
cultivars (a variety of the plant that has been developed to display specific characteristics). A
case in point is today’s corn, which is a result of years of breeding that started with its
ancestor, teosinte. The teosinte that the ancient Mayans originally began cultivating had tiny
seeds—vastly different from today’s relatively giant ears of corn. Interestingly, though these
two plants appear to be entirely different, the genetic difference between them is miniscule.

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 Figure 14 – Changes in the size of corn cobs due to selective breeding. ‘A’ is from about
800CE, ‘B’ is from 1300CE, ‘C’ is from 1800CE and ‘D’ is modern corn (cm scale shown)

Pollination takes two forms: self-pollination and cross-pollination. Self-pollination occurs

when the pollen from the anther is deposited on the stigma of the same flower, or another
flower on the same plant. Cross-pollination is the transfer of pollen from the anther of one
flower to the stigma of another flower on a different individual of the same species. Self-
pollination occurs in flowers where the stamen and carpel mature at the same time and are
positioned so that the pollen can land on the flower’s stigma. This method of pollination does
not require an investment from the plant to provide nectar and pollen as food for pollinators.

Figure 15 – Idealised flower structure.

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Living species are designed to ensure survival of their offspring; those that fail become
extinct. Genetic diversity is therefore required so that in changing environmental or stress
conditions, some of the progeny can survive. Self-pollination leads to the production of plants
with less genetic diversity, since genetic material from the same plant is used to form
gametes, and eventually, the zygote. In contrast, cross-pollination leads to greater genetic
diversity. Cross-pollination needs to rely on a ‘vector’ for the transport of the pollen from one
flower to another. This vector can be the wind or an animal. The advantage of self-pollination
is the removal of the need for the vector.
As cross-pollination allows for more genetic diversity, plants have developed many ways to
avoid self-pollination. In some species, the pollen and the ovary mature at different times.
These flowers make self-pollination nearly impossible. By the time pollen matures and has
been shed, the stigma of this flower is mature and can only be pollinated by pollen from
another flower. Some flowers have developed physical features that prevent self-pollination.
The primrose is one such flower. Primroses have evolved two flower types with differences
in anther and stigma length: the pin-eyed flower has anthers positioned at the pollen tube’s
halfway point, and the thrum-eyed flower’s stigma is likewise located at the halfway point.
Insects easily cross-pollinate while seeking the nectar at the bottom of the pollen tube.

Figure 16 – Pin and thrum primrose flowers.

This phenomenon is also known as heterostyly. Many plants, such as cucumber, have male
and female flowers located on different parts of the plant, thus making self-pollination
difficult. In yet other species, the male and female flowers are borne on different plants
(dioecious).

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 Figure 17 - Male and female flowers of a zucchini plant.

All of these are barriers to self-pollination; therefore, the plants depend on pollinators to
transfer pollen. The majority of pollinators are biotic agents such as insects (like bees, flies,
and butterflies), bats, birds, and other animals. Other plant species are pollinated by abiotic
agents, such as wind and water.

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 Figure 18 - Pollen being released from the male flowers on a pine tree.

Figure 19 – Method of pollination in a water environment.

c) Fungi: budding, spores
Fungi are more closely related to animals than plants. Fungi are not capable of
photosynthesis: they are heterotrophic because they use complex organic compounds as
sources of energy and carbon. Some fungal organisms multiply only asexually, whereas
others undergo both asexual reproduction and sexual reproduction with alternation of
generations. Most fungi produce a large number of spores, which are haploid cells that can
undergo mitosis to form multicellular, haploid individuals. Like bacteria, fungi play an
essential role in ecosystems because they are decomposers and participate in the cycling of

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nutrients by breaking down organic and inorganic materials to simple molecules (Haploid is
normally half the normal number of chromosomes in the nucleus).

Figure 20 – Sexual and asexual reproduction cycles in fungi.

In both sexual and asexual reproduction, fungi produce spores that disperse from the parent
organism by either floating on the wind or hitching a ride on an animal. Fungal spores are
smaller and lighter than plant seeds. The giant puffball mushroom bursts open and releases
trillions of spores. The huge number of spores released increases the likelihood of at least
some landing in an environment that will support growth.
Fungi reproduce asexually by fragmentation, budding, or producing spores. Fragments of
hyphae can grow new colonies. Mycelial fragmentation occurs when a fungal mycelium
separates into pieces with each component growing into a separate mycelium. Somatic cells
in yeast form buds. During budding (a type of cytokinesis), a bulge forms on the side of the
cell, the nucleus divides mitotically, and the bud ultimately detaches itself from the mother
cell.
The most common mode of asexual reproduction is through the formation of asexual spores,
which are produced by one parent only (through mitosis) and are genetically identical to that
parent. Spores allow fungi to expand their distribution and colonize new environments. They
may be released from the parent thallus, either outside or within a special reproductive sac
called a sporangium.
d) bacteria: binary fission
Bacteria are single celled microbes. The cell structure is simpler than that of other organisms
as there is no nucleus or membrane bound organelles. Instead their control centre containing
the genetic information is contained in a single loop of DNA. Some bacteria have an extra
circle of genetic material called a plasmid. The plasmid often contains genes that give the
bacterium some advantage over other bacteria. For example, it may contain a gene that makes
the bacterium resistant to a certain antibiotic.

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 Figure 21 – Bacterial structure showing plasmid.

Bacteria are found in every habitat on Earth: soil, rock, oceans and even arctic snow. Some
live in or on other organisms including plants and animals including humans. There are
approximately 10 times as many bacterial cells as human cells in the human body. A lot of
these bacterial cells are found lining the digestive system. Some bacteria live in the soil or on
dead plant matter where they play an important role in the cycling of nutrients. Some types
cause food spoilage and crop damage but others are incredibly useful in the production of
fermented foods such as yoghurt and soy sauce. Relatively few bacteria are parasites or
pathogens that cause disease in animals and plants.
Bacteria reproduce by binary fission. In this process the bacterium, which is a single cell,
divides into two identical daughter cells. Binary fission begins when the DNA of the
bacterium divides into two (replicates). The bacterial cell then elongates and splits into two
daughter cells each with identical DNA to the parent cell. Each daughter cell is a clone of the
parent cell. When conditions are favourable such as the right temperature and nutrients are
available, some bacteria like Escherichia coli can divide every 20 minutes. This means that in
just seven hours one bacterium can generate 2,097,152 bacteria. After one more hour the
number of bacteria will have risen to a colossal 16,777,216. That’s why we can quickly
become ill when pathogenic microbes invade our bodies.

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 Figure 22 – Binary fission process in prokaryotes.

e) Protists: binary fission, budding

Protists (protists are eukaryotes, which means their cells have a nucleus and other membrane-
bound organelles. Most, but not all, protists are single-celled) reproduce by a variety of
mechanisms. Most undergo some form of asexual reproduction, such as binary fission, to
produce two daughter cells. In protists, binary fission can be divided being along a transverse
or longitudinal axis, depending on the axis of orientation. Some protists such as the true slime
moulds exhibit multiple fission and simultaneously divide into many daughter cells. Others
produce tiny buds that go on to divide and grow to the size of the parental protist

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 Figure 23 – Example of budding in a protist.
1.2 Analyse the features of fertilisation, implantation and hormonal control of pregnancy and
birth in mammals
a) Fertilisation in mammals
Fertilization is the fusion of haploid gametes, egg and sperm, to form the diploid zygote (a
fertilised cell with a complete chromosome set). Note though there can be subtle differences
in the fertilization process which occurs naturally within the body or through reproductive
technologies outside the body, the overall product in both cases is a diploid zygote. The
process of fertilization involves components of and signalling between, both sperm
(spermatozoa) and egg (oocyte).

Figure 24 – Fertilisation in humans.

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 Figure 25 – Fertilisation and implantation in humans.

For successful fertilisation to occur, sperm must be deposited in the vagina within 24-72
hours of ovulation since they have very limited lives. Once deposited within the vagina, the
sperm swim through the cervix and into the uterus, and then up into the fallopian tubes where
the ovum resides. The movement of sperm on this long journey is helped by muscular
contraction of the walls of the uterus and the fallopian tubes. Fertilisation of the ovum occurs
in the fallopian tube. Only one sperm will succeed in fertilising the ovum by penetrating its
cell membrane and depositing the male genetic material into the female cell, where the two
nuclei fuse.

Figure 26 – The process of a sperm entering an egg cell.

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The fertilised ovum (zygote) immediately becomes resistant to penetration by any other
sperm arriving later. After fertilisation occurs, the zygote remains in the fallopian tube for
about 72 hours, and during this time it develops rapidly into a ball of cells called a blastocyst.

b) Implantation in mammals

Between five to seven days after fertilisation, the blastocyst reaches the uterus and embeds
itself in the thickened endometrium (lining of the uterus). This process is called implantation,
and if the embryo survives, it is the beginning of a pregnancy.

If the blastocyst implants successfully in the uterus, the cells go on multiplying by cell
division and moving around into new locations to form two distinct structures:

a. Three or four blastocyst cells develop into the inner cell mass, which over the
next few weeks will form into the recognisable structures of a human embryo,
with a head, beating heart and tiny limbs. Some of these cells also develop into
the foetal membranes that form a fluid-filled protective ‘bag’ around the
embryo.
b. The remaining 100 or so blastocyst cells form a structure called the
trophoblast, which will provide the baby’s contribution to the placenta. The
first stage of development of the placenta is when the trophoblast cells (the
trophoblast cells form the outer layer of the blastocyst, providing the embryo
with nutrients and the foetal component of the placenta) burrow into the
endometrium.

c) Hormonal control of pregnancy and birth

Hormones play a vital role during pregnancy. Rising levels of the various hormones are
what is used in pregnancy testing. A wide range of hormones are involved, their roles
have been described below:

a. Human Chorionic Gonadotropin:

i. hCG's primary role is to keep the corpus luteum functioning, so that
the corpus luteum continues to produce estrogen and progesterone.
hCG begins to decrease when the placenta is developed enough to
become the major producer of these two hormones. However, it
continues to be present until several weeks after pregnancy has begun
and is mainly responsible for the early pregnancy symptoms ranging
from missed menstruation to nausea, vomiting and fatigue.
b. Progesterone
i. This hormone maintains the functionality of the placenta and prevents
sudden movement and contraction of the uterus.
c. Estrogen
i. Is an ovarian hormone that is controlled by the corpus luteum. Levels
of estrogen assist with the physical development of the foetus
according to its sex chromosomes.
ii. An important role of estrogen is to facilitate the maturation of
lungs, kidneys, adrenal gland, liver and bone density of the unborn

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 baby. Besides this it also aids the flow of blood to foetus. Estrogen also
protects the female baby from the masculine effects of androgen.
d. Other Hormones
i. Human chorionic somatomammotropin hormone (HCS) also known as
Human placental lactogen (HPL) hormone facilitates foetal
development and formation of lactation glands.
ii. Oxytocin facilitates the delivery process by helping in the
contraction of uterus and also stimulates the mammary glands to
produce milk.
iii. Calcitonin is useful in calcium metabolism and prevents the
bone calcium from entering the blood system.
iv. Prolactin and oxytocin help the woman to get rid of post
pregnancy problems.

1.3 Evaluate the impact of scientific knowledge on the manipulation of plant and animal
reproduction in agriculture
This material will be covered in Module 6.

2. Cell Replication
Inquiry question: How important is it for genetic material to be replicated exactly?
2.1 Model the processes involved in cell replication, including but not limited to:
a) mitosis and meiosis
There are two types of cell division: mitosis and meiosis. Most of the time when people refer
to “cell division,” they mean mitosis, the process of making new body cells. Meiosis is the
type of cell division that creates egg and sperm cells.
During mitosis, a cell duplicates all of its contents, including its chromosomes, and splits to
form two identical daughter cells. Because this process is so critical, the steps of mitosis are
carefully controlled by a number of genes. When mitosis is not regulated correctly, health
problems such as cancer can result.
The other type of cell division, meiosis, ensures that humans have the same number of
chromosomes in each generation. It is a two-step process that reduces the chromosome
number by half—from 46 to 23—to form sperm and egg cells. When the sperm and egg cells
unite during fertilisation, each contributes 23 chromosomes so the resulting embryo will have
the usual 46. Meiosis also allows genetic variation through a process of DNA shuffling while
the cells are dividing

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 Figure 27 – Comparison between the simplified stages of mitosis and meiosis.

In many ways, meiosis is a lot like mitosis. The cell goes through similar stages and uses
similar strategies to organize and separate chromosomes. In meiosis, however, the cell has a
more complex task. It still needs to separate sister chromatids (the two halves of a duplicated
chromosome), as in mitosis. But it must also separate homologous chromosomes, the similar
but nonidentical chromosome pairs an organism receives from its two parents. Since cell
division occurs twice during meiosis, one starting cell can produce four gametes (eggs or
sperm). Meiosis can be divided into two distinct steps called meiosis 1 and meiosis 2.

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 Figure 27 – Stages of meiosis 1 and 2.

Table 1 – Comparing the stages of mitosis and meiosis.

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 Table 2 – Comparison of the processes of mitosis and meiosis.

Cells move from meiosis I to meiosis II without copying their DNA. Meiosis II is a shorter
and simpler process than meiosis I.
The cells that enter meiosis II are the ones made in meiosis I. These cells are haploid—have
just one chromosome from each homologue pair—but their chromosomes still consist of two
sister chromatids. In meiosis II, the sister chromatids separate, making haploid cells with non-
duplicated chromosomes.
b) DNA replication using the Watson and Crick DNA model, including nucleotide
composition, pairing and bonding

Scientists in Watson and Crick's time knew that DNA was composed of subunits called
nucleotides. A nucleotide is made up of a sugar (deoxyribose), a phosphate group, and one of
four nitrogenous bases: adenine (A), thymine (T), guanine (G) or cytosine (C). C and T bases,
which have just one ring, are called pyrimidines, while A and G bases, which have two rings,
are called purines. Adenine can only join with thymine with two Hydrogen bonds. Cytosine
can only bond with guanine with three Hydrogen bonds. Hydrogen bonding is weak form of
bonding and can be broken by the chemical action of many substances and relatively low
levels of radiation. This leads to an accumulation of mutations in the DNA over time.
One other key piece of information related to the structure of DNA. This came from several
key observations:
- A, T, C, and G were not found in equal quantities (as some models at the time would have
predicted)
-The amounts of the bases varied among species, but not between individuals of the same
species
-The amount of A always equalled the amount of T, and the amount of C always equalled the
amount of G (A = T and G = C)
-These findings, called Chargaff's rules, turned out to be crucial to Watson and Crick's model
of the DNA double helix.

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 Figure 28 – Matching base pairs.
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as
monomeric units of the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA), both of which are essential biomolecules within all life-forms on Earth.
Nucleotides are composed of three subunit molecules: a nitrogenous base (also known as
nucleobase), a five-carbon sugar (ribose or deoxyribose), and a phosphate group consisting of
one to three phosphates. The four nitrogenous bases in DNA are guanine, adenine, cytosine
and thymine; in RNA, uracil is used in place of thymine.
The sequence or order of the nucleotides defines the primary structure of DNA and RNA.
The nucleotides of the polymer are linked by phosphodiester bonds connecting through the
oxygen on the 5' carbon of one to the oxygen on the 3' carbon of another. The Oxygen and
Nitrogen atoms in the backbone give DNA and RNA "polarity".

2.2 Assess the effect of the cell replication processes on the continuity of species
The purpose of mitosis is to maintain continuity among cell progeny, meaning that if a tissue
is made of thousands of cells (in a multicellular organism) that resulted from many mitosis
events, each cell has the same number of genes as the original cell. This is important because
tissues and organs have layers of cells that serve different functions, even though those cells
have the same genetic information. Because every cell has the same genetic information,
different cells from the same gene pool can become specialized to do different things.

The process of meiosis preserves genetic continuity for future offspring by ensuring that two
sexually reproducing organisms produce offspring that have the same number of
chromosomes as the parents. This is important for several reasons. First, it ensures that each
offspring has all the genes that it needs in order to survive. Second, it ensures that the
offspring will be able to mate with other organisms of the same species. If the offspring have
the wrong number of chromosomes, they will not be able to mate with other members of the
same species, or type of animal. One important exception to this is the formation of ‘mules’
which are organisms that result from the mating of closely related animals. The offspring of
this mating almost always are unable to reproduce.

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3. DNA and Polypeptide Synthesis

Inquiry question: Why is polypeptide synthesis important?

3.1 construct appropriate representations to model and compare the forms in which DNA
exists in eukaryotes and prokaryote
The single characteristic that is both necessary and sufficient to define an organism as a
eukaryote is a nucleus surrounded by a nuclear envelope with nuclear pores. All extant
eukaryotes have cells with nuclei; most of a eukaryotic cell’s genetic material is contained
within the nucleus. In contrast, prokaryotic DNA is not contained within a nucleus, but rather
is attached to the plasma membrane and contained in the form of a nucleoid, an irregularly
shaped region that is not surrounded by a nuclear membrane.

Figure 29 – Comparison of eukaryote and prokaryote cells.

Eukaryotic DNA is packed into bundles of chromosomes, each consisting of a linear DNA
molecule coiled around basic (alkaline) proteins called histones, which wind the DNA into a
more compact form.

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 Figure 30 – The multiple packing system of DNA to form chromosomes.
Prokaryotic DNA is found in circular, non-chromosomal form. In addition, prokaryotes have
plasmids, which are smaller pieces of circular DNA that can replicate separately from
prokaryotic genomic DNA.
A major DNA difference between eukaryotes and prokaryotes is the presence of
mitochondrial DNA (mtDNA) and chloroplast DNA in plants and some protists in
eukaryotes. Because eukaryotes have mitochondria and prokaryotes do not, eukaryotic cells
contain mitochondrial DNA in addition to DNA contained in the nucleus and ribosomes. The
mtDNA is composed of significantly fewer base pairs than nuclear DNA and encodes only a
few dozen genes, depending on the organism.
3.2 model the process of polypeptide synthesis, including:
In humans, the nucleus of each cell contains 3 × 109 base pairs of DNA distributed over 23
pairs of chromosomes, and each cell has two copies of the genetic material except red blood
cells which do not have a nucleus). This is known collectively as the human genome. The
human genome contains around 30 000 genes, each of which codes for one polypeptide
(exons).
Large stretches of DNA in the human genome are transcribed but do not code for
polypeptides. These regions are called ‘introns’ and make up around 95% of the genome. The
nucleotide sequence of the human genome is now known to a reasonable degree of accuracy,
but we do not yet understand why so much of it is non-coding. Some of this non-coding DNA
controls gene expression but the purpose of much of it is not yet understood.

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 a) transcription and translation
The central dogma of molecular biology states that ‘DNA makes RNA makes proteins’. The
process by which DNA is copied to RNA is called transcription, and that by which RNA is
used to produce proteins is called translation.
Transcription is the process in which a gene's DNA sequence is copied (transcribed) to make
an RNA molecule (RNA polymerase is the main transcription enzyme) Transcription begins
when RNA polymerase binds to a ’promoter’ sequence near the beginning of a gene (directly
or through helper proteins). The RNA polymerase uses one of the DNA strands (the template
strand) as a template to make a new, complementary RNA molecule. Transcription ends in a
process called ‘termination’. Termination depends on sequences in the RNA, which signal
that the transcript is finished.
Translation involves “decoding” a messenger RNA (mRNA) and using its information to
build a polypeptide, or chain of amino acids. For most purposes, a polypeptide is basically
just a protein (with the technical difference being that some large proteins are made up of
several polypeptide chains).
In an mRNA, the instructions for building a polypeptide come in groups of three nucleotides
called codons.
Here are some key features of codons to keep in mind as we move forward:
● There are 61 different codons for amino acids
● Three “stop” codons mark the polypeptide as finished
● One codon, AUG, is a “start” signal to kick off translation (it also specifies the amino
acid methionine)
These relationships between mRNA codons and amino acids are known as the genetic code.
In translation, the codons of an mRNA are read in order (from the 5' end to the 3' end) by
molecules called transfer RNAs, or tRNAs. Each tRNA has an anticodon, a set of three
nucleotides that binds to a matching mRNA codon through base pairing. The other end of the
tRNA carries the amino acid that's specified by the codon.
b) assessing the importance of mRNA and tRNA in transcription and translation
In the simplest sense, expressing a ’gene’ means manufacturing its corresponding protein,
and this multilayered process has two major steps. In the first step, the information in DNA is
transferred to a messenger RNA (mRNA) molecule by way of a process called transcription.
During transcription, the DNA of a gene serves as a template for complementary base-
pairing, and an enzyme called RNA polymerase II catalyses the formation of a pre-mRNA
molecule, which is then processed to form mature mRNA. The resulting mRNA is a single-
stranded copy of the gene, which next must be translated into a protein molecule.

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 Figure 31 – The steps in translation and transcription.
During translation, which is the second major step in gene expression, the mRNA is "read"
according to the genetic code, which relates the DNA sequence to the amino acid sequence in
proteins. Each group of three bases in mRNA constitutes a codon, and each codon specifies a
particular amino acid (hence, it is a triplet code). The mRNA sequence is thus used as a
template to assemble, in order, the chain of amino acids that form a protein.

Figure 32 – Triplet codons and how they code for amino acids.

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The three roles of RNA in protein synthesis. Messenger RNA (mRNA) is translated into
protein by the joint action of transfer RNA (tRNA) and the ribosome, which is composed of
numerous proteins and two major ribosomal RNA (rRNA) molecules.
1. Messenger RNA (mRNA) carries the genetic information copied from DNA in the form of
a series of three-base code “words,” each of which specifies a particular amino acid.
2. Transfer RNA (tRNA) is the key to deciphering the code words in mRNA. Each type of
amino acid has its own type of tRNA, which binds it and carries it to the growing end of a
polypeptide chain if the next code word on mRNA calls for it. The correct tRNA with its
attached amino acid is selected at each step because each specific tRNA molecule contains a
three-base sequence that can base-pair with its complementary code word in the mRNA.
3. Ribosomal RNA (rRNA) associates with a set of proteins to form ribosomes. These
complex structures, which physically move along an mRNA molecule, catalyse the assembly
of amino acids into protein chains. They also bind tRNAs and various accessory molecules
necessary for protein synthesis. Ribosomes are composed of a large and small subunit, each
of which contains its own rRNA molecule or molecules.
Translation is the whole process by which the base sequence of an mRNA is used to order
and to join the amino acids in a protein. The three types of RNA participate in this essential
protein-synthesizing pathway in all cells; in fact, the development of the three distinct
functions of RNA was probably the molecular key to the origin of life.
c) analysing the function and importance of polypeptide synthesis
Protein synthesis is the process in which cells make proteins. It occurs in two stages:
transcription and translation. Transcription is the transfer of genetic instructions in DNA to
mRNA in the nucleus. It includes three steps: initiation, elongation, and termination. After
the mRNA is processed, it carries the instructions to a ribosome in the cytoplasm. Translation
occurs at the ribosome, which consists of rRNA and proteins. In translation, the instructions
in mRNA are read, and tRNA brings the correct sequence of amino acids to the ribosome.
Then, rRNA helps bonds form between the amino acids, producing a polypeptide chain. After
a polypeptide chain is synthesized, it may undergo additional processing to form the finished
protein.
Transcription is the first part of the central dogma of molecular biology: DNA → RNA.
It is the transfer of genetic instructions in DNA to mRNA. During transcription, a strand
of mRNA is made to complement a strand of DNA.

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 Figure 32 – First stage of polypeptide manufacture.
Transcription takes place in three steps: initiation, elongation, and termination.

1. Initiation is the beginning of transcription. It occurs when the enzyme RNA polymerase
binds to a region of a gene called the promoter. This signals the DNA to unwind so the
enzyme can read the bases in one of the DNA strands. The enzyme is ready to make a
strand of mRNA with a complementary sequence of bases.
2. Elongation is the addition of nucleotides to the mRNA strand.
3. Termination is the ending of transcription. The mRNA strand is complete, and it detaches
from DNA.

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 Figure 33 – The steps in transcription.
In eukaryotes, the new mRNA is not yet ready for translation. At this stage, it is called pre-
mRNA, and it must go through more processing before it leaves the nucleus as mature
mRNA. The processing may include splicing, editing, and polyadenylation. These processes
modify the mRNA in various ways. Such modifications allow a single gene to be used to
make more than one protein.
Splicing removes introns from mRNA, as shown in the diagram below. Introns are regions
that do not code for the protein. The remaining mRNA consists only of regions called exons
that do code for the protein. The ribonucleoproteins in the diagram are small proteins in the
nucleus that contain RNA and are needed for the splicing process.
Editing changes some of the nucleotides in mRNA. For example, a human protein called
APOB, which helps transport lipids in the blood, has two different forms because of editing.
One form is smaller than the other because editing adds an earlier stop signal in mRNA.
Polyadenylation adds a “tail” to the mRNA. The tail consists of a string of As (adenine
bases). It signals the end of mRNA. It is also involved in exporting mRNA from the nucleus,
and it protects mRNA from enzymes that might break it down.

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 Figure 34 – Examples of introns and exons.

Translation is the second part of the central dogma of molecular biology: RNA → Protein.
It is the process in which the genetic code in mRNA is read to make a protein. Translation is
illustrated in the diagram below. After mRNA leaves the nucleus, it moves to a ribosome,
which consists of rRNA and proteins. The ribosome reads the sequence of codons in mRNA,
and molecules of tRNA bring amino acids to the ribosome in the correct sequence.
To understand the role of tRNA, you need to know more about its structure. Each tRNA
molecule has an anticodon for the amino acid it carries. An anticodon is complementary to
the codon for an amino acid. For example, the amino acid lysine has the codon AAG, so the
anticodon is UUC. Therefore, lysine would be carried by a tRNA molecule with the
anticodon UUC. Wherever the codon AAG appears in mRNA, a UUC anticodon of tRNA
temporarily binds. While bound to mRNA, tRNA gives up its amino acid. With the help of
rRNA, bonds form between the amino acids as they are brought one by one to the ribosome,
creating a polypeptide chain. The chain of amino acids keeps growing until a stop codon is
reached.

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 Figure 35 – The example of how transcription and translation operate.
After a polypeptide chain is synthesized, it may undergo additional processes. For example, it
may assume a folded shape due to interactions between its amino acids. It may also bind with
other polypeptides or with different types of molecules, such as lipids or carbohydrates.
Many proteins travel to the Golgi apparatus within the cytoplasm to be modified for the
specific job they will do.

d) assessing how genes and environment affect phenotypic expression

The expression of genes in an organism can be influenced by the environment, including the
external world in which the organism is located or develops, as well as the organism's
internal world, which includes such factors as its hormones and metabolism. One major
internal environmental influence that affects gene expression is gender, as is the case with
sex-influenced and sex-limited traits. Similarly, drugs, chemicals, temperature, and light are
among the external environmental factors that can determine which genes are turned on and
off, thereby influencing the way an organism develops and functions.

Sex-influenced traits are those that are expressed differently in the two sexes. Such traits are
autosomal, which means that the genes responsible for their expression are not carried on the
sex chromosomes. An example of a sex-influenced trait is male-pattern baldness. The
baldness allele, which causes hair loss, is influenced by the hormones testosterone and
dihydrotestosterone, but only when levels of the two hormones are high. In general, males
have much higher levels of these hormones than females, so the baldness allele has a stronger
effect in males than in females. However, high levels of stress can lead to expression of the
gene in women. In stressful situations, women's adrenal glands can produce testosterone and
convert it into dihydrotestosterone, which can result in hair loss.

Sex-limited traits are also autosomal. Unlike sex-influenced traits, whose expression differs
according to sex, sex-limited traits are expressed in individuals of only one sex. An example
of a sex-limited trait is lactation, or milk production. Although the genes for producing milk
are carried by both males and females, only lactating females express these genes.

The presence of drugs or chemicals in an organism's environment can also influence gene
expression in the organism. An example of how chemical environments affect gene
expression is the case of supplemental oxygen administration causing blindness in premature
infants. In the 1940s, supplemental oxygen administration became a popular practice when
doctors noticed that increasing oxygen levels converted the breathing pattern of premature
infants to a "normal" rhythm. Unfortunately, there is a causal relationship between oxygen
administration and retinopathy of prematurity (ROP), although this relationship was unknown
at the time; thus, by 1953, ROP had blinded approximately 10,000 infants worldwide.
Finally, in 1954, a randomized clinical trial identified supplemental oxygen as the factor
causing blindness. Complicating the issue is the fact that too little oxygen results in a higher
rate of brain damage and mortality in premature infants. Unfortunately, even today, the
optimal amount of oxygenation necessary to treat premature infants while completely
avoiding these complications is still not clear.

Another example of the way in which chemicals can alter gene expression involves
thalidomide, a sedative, antiemetic (stops people throwing up), and nonbarbiturate (this
means that the drug will not be addictive) drug that was first manufactured and marketed

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during the mid-1950s. While thalidomide has no discernible effect on gene expression and
development in healthy adults, it has a profoundly detrimental effect on developing foetuses.
When the drug was first created, however, its impact on foetuses was not known. Moreover,
because of its apparent lack of toxicity in adult human volunteers, thalidomide was marketed
as the safest available sedative of its time and rapidly became popular in Europe, Australia,
Asia, and South America for countering the effects of morning sickness. Not until 1961 did
Australian researcher William McBride and German researcher Widukind Lenz
independently report that thalidomide was a teratogen, meaning that its use was associated
with birth defects (the drug interrupts the sequence of genes being activated that leads to
progressive limb devekopment). Sadly, the drug was withdrawn too late to prevent severe
developmental deformities in approximately 8,000 to 12,000 infants, many of whom were
born with stunted limb development. Interestingly, despite the fact that thalidomide is
dangerous during embryonic development, the drug continues to be used in certain instances
yet today. For example, it has therapeutic potential in treating leprosy, and in recent years, it
has also been used to treat cancers and enhance the effectiveness of cancer vaccines.

Figure 36 – Examples of deformation caused by thalidomide.

In addition to drugs and chemicals, temperature and light are external environmental factors
that may influence gene expression in certain organisms. For example, Himalayan rabbits
carry the C gene, which is required for the development of pigments in the fur, skin, and
eyes, and whose expression is regulated by temperature. Specifically, the C gene is inactive
above 35°C, and it is maximally active from 15°C to 25°C. This temperature regulation of
gene expression produces rabbits with a distinctive coat colouring. In the warm, central parts
of the rabbit's body, the gene is inactive, and no pigments are produced, causing the fur
colour to be white. Meanwhile, in the rabbit's extremities (i.e., the ears, tip of the nose, and
feet), where the temperature is much lower than 35°C, the C gene actively produces pigment,
making these parts of the animal black. Similar gene expression is seen in coat colours in
some cats (Siamese).

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 Figure 37 – Example of temperature induced coat colour variation in rabbits.

3.3 Investigate the structure and function of proteins in living things

Proteins are large, complex molecules that play many critical roles in the body. They do most
of the work in cells and are required for the structure, function, and regulation of the body’s
tissues and organs.
Amino acids are the building blocks of all proteins, no matter their function. Proteins are
typically a long chain of up to 20 different amino acids. The human body can use
combinations of these same 20 amino acids to make any protein or polypeptide it needs. Most
amino acids follow a structural template in which a carbon is bonded to the following forms:

● A hydrogen atom (H)

● A carboxyl group (-COOH)
● An amino group (-NH2)
● A "variable" group

Across the different types of amino acids, the "variable" group is most responsible for
variation as all of them have hydrogen, carboxyl group and amino group bonds.
Amino acids are joined through peptide bonds. When a number of amino acids are linked
together by these bonds, a polypeptide chain is formed. One or more polypeptide chains
twisted into a 3-D shape forms a protein.
The structure of a protein may be globular or fibrous depending on its particular role (every
protein is specialized). Globular proteins are generally compact, partly soluble, and spherical
in shape (eg. Haemoglobin and insulin). Fibrous proteins are typically elongated and
insoluble (eg. Keratin and collagen). Globular and fibrous proteins may exhibit one or more
types of protein structures.
There are four structural levels of protein: primary, secondary, tertiary, and quaternary. These
levels determine the shape and function of a protein and are distinguished from one another
by the degree of complexity in a polypeptide chain. The primary level is the most basic and
rudimentary while the quaternary level describes sophisticated bonding.

36
 Figure 38 – The four different levels of structure in proteins.
A single protein molecule may contain one or more of the protein structure levels and the
structure and intricacy of a protein determine its function. Collagen, for example, has a super-
coiled helical shape that is long, stringy, strong, and rope-like—collagen is great for
providing support. Haemoglobin, on the other hand, is a globular protein that is folded and
compact. Its spherical shape (in a red blood cell) is useful for manoeuvring through blood
vessels.
Proteins can be described according to their large range of functions in the body, listed in
alphabetical order:
Examples of protein functions

Function Description Example

Antibody Antibodies bind to specific foreign particles, such as Immunoglobulin G (IgG)

viruses and bacteria, to help protect the body. These
would generally be found in the bloodstream and the
lymph nodes.

Enzyme Enzymes carry out almost all of the thousands of Phenylalanine hydroxylase
chemical reactions that take place in cells. They also
assist with the formation of new molecules by reading
the genetic information stored in DNA.

Messenger Messenger proteins, such as some types of hormones, Growth hormone

transmit signals to coordinate biological processes
between different cells, tissues, and organs.

37
 Structural These proteins provide structure and support for cells. Actin
component On a larger scale, they also allow the body to move.

Transport/storage These proteins bind and carry atoms and small Ferritin
molecules within cells and throughout the body.

4. Genetic Variation
Inquiry question: How can the genetic similarities and differences within and between
species be compared?

4.1 Conduct practical investigations to predict variations in the genotype of offspring by

modelling meiosis, including the crossing over of homologous chromosomes, fertilisation and
mutations

a) Variations due to Fertilization, Crossing Over of Chromosomes and Mutations:

During the formation of a zygote, the single celled zygote (diploid) receives 50% of the
information for a trait from each parent. Thus, the genotype of the zygote is a “mixture” of
that of the parents and thus, the zygote, when it develops into a complete organism shows
non-identical characteristics to the parents.
Crossing over during meiosis cell division also accounts for genetic variation, because due to
the swapping of genetic material during crossing over, the chromatids held together by the
centromere are no longer identical. Homologous chromosomes, one inherited from each
parent pair along their lengths, gene by gene. Breaks occur along the chromosomes, and they
re-join, trading some of their genes. The chromosomes now have genes in a unique
combination in each gamete.

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 Figure 39 – Steps in crossing over during meiosis.
Mutations (alterations in genes due to a number of external factors including chemicals and
environmental radiation) have a great amount of contribution in genotypic variation because:

● Mutations can introduce new characteristics which means a new genotype

● Mutations can alter certain traits by silencing a particular gene thus producing
genotypic variation
● Mutations can also produce different products from similarly sequenced mRNA
transcripts (point mutations)
Example of genotypic variation due to mutation:
Sickle Cell Anaemia (covered again in Module 8):

● Sickle-Cell Anaemia is an autosomal recessive disorder that affects 1 in 500 African

Americans.
● The single replacement of the sixth amino acid in the beta-globin, glutamic acid, with
valine results in deformed red blood cells.
● These sickle-shaped cells cannot carry nearly as much oxygen as normal red blood
cells and they get caught more easily in the capillaries, cutting off blood supply to
vital organs.

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 Figure 40 – The example of sickle-cell anaemia.

4.2 Model the formation of new combinations of genotypes produced during meiosis,
including but not limited to:
NOTE: using punnet squares for monohybrid and dihybrid crosses is the standard technique
used in Biology.
a) interpreting examples of autosomal, sex-linkage, co-dominance, incomplete dominance
and multiple alleles
i) autosomal
Combination of genes found in autosomes (chromosomes except for the sex chromosome).
For genes on an autosome, the alleles and their associated traits are autosomal dominant or
autosomal recessive.
Example: A cross was conducted between peas that may be round, associated with allele R,
or wrinkled, associated with allele r. In this case, three combinations of alleles (genotypes)
are possible: RR, Rr, and rr. The RR individuals have round peas and the rr individuals have
wrinkled peas. In Rr individuals the R allele masks the presence of the r allele, so these
individuals also have round peas. Thus, allele R is dominant to allele r, and allele r is
recessive to allele R.
https://www.bbc.co.uk/bitesize/guides/z2rm3k7/revision/1
https://www.bbc.co.uk/bitesize/guides/zy7vw6f/revision/1
ii) sex-linkage
There are a number of alleles that are carried on the sex chromosome. These genes are
considered sex-linked because their expression and inheritance patterns differ between males
and females.

Example: A case study on Haemophilia:

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Haemophilia is an X linked disorder, meaning that the cause of haemophilia is a mutation in
the genes of X chromosome. In females, the X chromosome remains in double copy (XX), so
for haemophilia to occur, both the X chromosomes need to have a mutant gene. In males,
presence of a single mutant X chromosome (since male sex chromosomes have a
combination of XY) is enough to cause haemophilia.

Analysis by Punnett square:

Let,
XH = normal functioning X gene
Xh = haemophilic X gene

From the above Punnett square, it can be seen that in a cross between a normal male and
carrier female, only 25% of the F1 generation are found to haemophilic and are males.

Figure 42 – Pedigree of European royal families showing the appearance of haemophilia.

iii) Co-dominance
A type of gene interaction in which both the alleles are fully expressed resulting in a
combined phenotype of both alleles.

Example and representation using Punnett square:

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In chickens, a cross was conducted between a black Andalusian rooster and a white
Andalusian hen.

Figure 43 – Black Andalusian rooster and white Andalusian hen.

Let,
BB = genotype for black feathers in the rooster
bb = genotype for white feathers in the hen
After the cross it was observed that all the offspring having Bb genotype are neither black nor
white rather were black with white spots.

Co-dominance

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The best example in humans is blood type, which is an inherited trait that determines which
kind of protein markers are found on the surface of the red blood cells we produce. Therefore,
the blood type of your parents directly impacts what your blood type is.
When we inherit genes for a particular trait, we inherit one allele from our mother and one
from our father. Therefore, you have two alleles for blood type. The possible alleles that you
could inherit are A, B, or O.
(Additionally, if you know your blood type, you may also know that your blood type can be
positive (+) or negative (-). These terms refer to the presence of another protein called the Rh
factor. Positive blood types produce Rh protein and negative blood types do not. Thus, there
are actually eight different blood types: A+, A-, B+, B-, AB+, AB-, O+ and O-)
Before we can understand blood type inheritance, we must remember that some alleles are
dominant and some are recessive. Dominant alleles will mask recessive alleles. In the case of
blood type, A and B are both dominant over O. Therefore, if you inherit one A or B allele and
an O allele, your blood type will be the dominant type (A or B). This also means that the only
way for someone to have type O blood is if they have two O alleles. Type A and B are
codominant, meaning that neither is dominant over the other. Thus, a person who inherits an
A allele and a B allele will have type AB blood and your red blood cells will have both A and
B markers.

Figure 44 – Table showing the genotype and phenotype of human blood types.

iv) incomplete dominance

In this process of gene interaction, none of the alleles are dominant/fully expressed resulting
in the creation of a different phenotype from the parents. Examples are snapdragons and four
o’clock flowers.

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 Figure 45 – Snapdragons showing the co-dominance of colour alleles.
Example and representation using Punnett square:
Let,
Cr = genotype for red flower (dominant)
Cw = genotype for white flower (dominant)
Both of the genes are dominant in their own locus. When they combine, the flowers having
both the genes are neither red nor white rather, they exhibit a pink colour.
Punnett Square representation:

In a cross between a red and a white flower, the resultant F1 generation are all pink flower.
Two members of the F1 generation are taken and crossed again to give F2 which will give the
following results.

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 v) multiple alleles
Three or more alternative forms of an allele that can create a variant number of phenotypes
when exist in different numbers.
As an example, let's consider a gene that specifies coat colour in rabbits, called the C gene.
The C gene comes in four common alleles: C, cch, ch, and c:
A CC rabbit has black or brown fur
A cchcch, rabbit has chinchilla coloration (greyish fur)
A chch rabbit has Himalayan (colour-point) patterning, with a white body and dark ears, face,
feet, and tail
A cc rabbit is albino, with a pure white coat.

Figure 46 – Coat colours seen in rabbits.

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Taking the example of Drosophila melanogaster (fruit fly)
In Drosophila, two pairs of characters are involved in a dihybrid cross. A mutant fly having
the recessive characters of pink eyes (r) and curled wings (s) is crossed with a wild fly having
dominant characters of red eyes (R) and straight wings (S).

● In this cross, all the progeny of F1 hybrid shows red eyes and straight wings having
genotype RrSs.
● Now a female from these F1 hybrids is crossed with a double recessive male of the P
generation (parent generation) which is known as a test cross. This F1 hybrid female
will produce four types of gametes.
● When F1 female gametes mated with single type of male gametes, the F2 generation
consists of 49% flies with red eyes and straight wings, 49% with pink eyes and curled
wings, 1% with red eyes and curled wings and 1% with pink eyes and straight wings.

Figure 47 – Common mutations in Drosophila melanogaster

● This result in F2 generation shows that the two types are non-cross overs which
combine to form 98% and two types of new combinations or re-combinations of the
remaining 2% are produced due to crossing over.
● This experiment shows that both the genes for each allelic pair are situated in the
same chromosome. They are connected together in 98% gametes having no
chromosomal interchange but in the remaining 2% of gametes there is interchange
between their non-sister chromatids of the homologous chromosomes. This
interchange of segments of chromatids occurs due to crossing over.

b) constructing and interpreting information and data from pedigrees and Punnett squares
See above.

46
4.2 collect, record and present data to represent frequencies of characteristics in a population,
in order to identify trends, patterns, relationships and limitations in data, for example:
a) examining frequency data
Usually a sample size of greater than 100 samples is sufficient to make reliable projections
about a genotype's frequency in a larger population. The larger the population size, the more
accurate the predictions.

The first step in turning data into information is to create a distribution. The most primitive
way to present a distribution is to simply list, in one column, each value that occurs in the
population and, in the next column, the number of times it occurs. It is customary to list the
values from lowest to highest. This simple listing is called a frequency distribution. A more
elegant way to turn data into information is to draw a graph of the distribution. Customarily,
the values that occur are put along the horizontal axis and the frequency of the value is on the
vertical axis.
To describe a population, you need to describe the picture or graph of its distribution. The
two things that need to be described about the distribution are its location and its shape.
Location is measured by an average, most often the arithmetic mean. The most important
measure of shape is a measure of dispersion, roughly width, most often the variance or its
square root the standard deviation.

Figure 48 – Distribution of heights of men and women globally.

b) analysing single nucleotide polymorphism (SNP)
A single-nucleotide polymorphism (SNP, pronounced ‘snip’) is a DNA sequence variation
occurring when a single nucleotide adenine (A), thymine (T), cytosine (C), or guanine (G) in
the genome (or other shared sequence) differs between members of a species or paired
chromosomes in an individual. For example, two sequenced DNA fragments from different
individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this
case we say that there are two alleles: C and T. Almost all common SNPs have only two
alleles.

47
Within a population, SNPs can be assigned a minor allele frequency — the lowest allele
frequency at a location on a chromosome (sometimes called the ‘locus’) that is observed in a
particular population. This is simply the lesser of the two allele frequencies for single-
nucleotide polymorphisms. There are variations between human populations, so a SNP allele
that is common in one geographical or ethnic group may be much rarer in another.
Single nucleotides may be changed (substitution), removed (deletions) or added (insertion) to
a polynucleotide sequence. Single nucleotide polymorphisms may fall within coding
sequences of genes, non-coding regions of genes, or in the intergenic regions between genes.
SNPs within a coding sequence will not necessarily change the amino acid sequence of the
protein that is produced, due to degeneracy of the genetic code.
A SNP in which both forms lead to the same polypeptide sequence is termed synonymous
(sometimes called a silent mutation). If a different polypeptide sequence is produced they are
nonsynonymous. A nonsynonymous change may either be missense or nonsense, where a
missense change results in a different amino acid, while a nonsense change results in a
premature stop codon. SNPs that are not in protein-coding regions may still have
consequences for gene splicing, transcription factor binding, or the sequence of non-coding
ribonucleic acid (RNA).

Figure 49 – diminishing frequency distribution.

5. Inheritance Patterns in a Population

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Inquiry question: Can population genetic patterns be predicted with any accuracy?
5.1 Investigate the use of technologies to determine inheritance patterns in a population
using, for example:
a) DNA sequencing and profiling
Technologies like DNA sequencing and profiling are helpful in determining the inheritance
patterns in the population. DNA sequencing is used in molecular biology to study genomes
and the proteins they encode. DNA profiling is a chemical test that shows the unique genetic
makeup of a person or other living things.

Figure 50 – The difference between DNA profiling and DNA sequencing.

i) DNA sequencing is the process of determining the sequence of nucleotides (As, Ts, Cs, and
Gs) in a piece of DNA. Sequencing an entire genome (all of an organism’s DNA) remains a
complex task. It requires breaking the DNA of the genome into many smaller pieces,
sequencing the pieces, and assembling the sequences into a single long "consensus."
However, thanks to new methods that have been developed over the past two decades,
genome sequencing is now much faster and less expensive than it was during the Human
Genome Project.
In Sanger sequencing, the target DNA is copied many times, making fragments of different
lengths. Fluorescent “chain terminator” nucleotides mark the ends of the fragments and allow
the sequence to be determined. Regions of DNA up to about 900base pairs in length are
routinely sequenced using Sanger sequencing or the chain termination method. Sanger
sequencing was developed by the British biochemist Fred Sanger and his colleagues in 1977.

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In the Human Genome Project, Sanger sequencing was used to determine the sequences of
many relatively small fragments of human DNA. (These fragments weren't necessarily 900bp
or less, but researchers were able to "walk" along each fragment using multiple rounds of
Sanger sequencing.) The fragments were aligned based on overlapping portions to assemble
the sequences of larger regions of DNA and, eventually, entire chromosomes.
Although genomes are now typically sequenced using other methods that are faster and less
expensive, Sanger sequencing is still in wide use for the sequencing of individual pieces of
DNA, such as fragments used in DNA cloning or generated through polymerase chain
reaction (PCR).
Next-generation sequencing techniques are new, large-scale approaches that increase the
speed and reduce the cost of DNA sequencing.
There are a variety of next-generation sequencing techniques that use different technologies.
However, most share a common set of features that distinguish them from Sanger
sequencing:
● Highly parallel: many sequencing reactions take place at the same time
● Micro scale: reactions are tiny and many can be done at once on a chip
● Fast: because reactions are done in parallel, results are ready much faster
● Low-cost: sequencing a genome is cheaper than with Sanger sequencing
● Shorter length: reads typically range from 50-70 nucleotides in length
Conceptually, next-generation sequencing is kind of like running a very large number of tiny
Sanger sequencing reactions in parallel. Thanks to this parallelization and small scale, large
quantities of DNA can be sequenced much more quickly and cheaply with next-generation
methods than with Sanger sequencing. For example, in 2001, the cost of sequencing a human
genome was almost $US100 million. In 2015, it was just$US1245.
The ability to routinely sequence genomes opens new possibilities for biology research and
biomedical applications. For example, low-cost sequencing is a step towards personalized
medicine, that is, medical treatment tailored to an individual's needs, based on the gene
variants in his or her genome.
ii) DNA profiling is a technique by which individuals can be identified and compared via
their respective DNA profiles. Within the non-coding regions of an individual’s genome there
exists satellite DNA – long stretches of DNA made up of repeating elements called short
tandem repeats (STRs). As individuals will likely have different numbers of repeats at a
given satellite DNA locus, they will generate unique DNA profiles

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 Figure 51 – Examples of how STRs vary from person to person.
DNA profiling is commonly used in criminal investigations (forensics) and to settle paternity
disputes. The procedure involved is common for both:

● A DNA sample is collected (e.g. from blood, semen, saliva, etc.) and then amplified
using PCR
● Satellite DNA (with STR sequences) are cut with specific restriction enzymes to
generate fragments
● Fragment length will differ between individuals due to the variable length of their
short tandem repeats
● The fragments are separated using gel electrophoresis and the resulting profiles are
compared
Forensic Investigations:
Suspects should be a complete match with the DNA sample taken from the crime scene if a
conviction is to occur. The number of loci used to generate a unique profile depends on the
size of the population being compared, eg. America (population: ~ 320 million) uses 13 loci
for comparison; Australia (population: ~ 25 million) uses only 9 loci.

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 Figure 52 – AN example of forensic DNA profiling. Who is guilty?

Paternity Testing:
Children inherit half their chromosomes from each parent and thus should possess a
combination of parental fragments. In other words, all fragments produced in the child should
also be produced by either the mother or father.

Figure 53 – Example of paternity DNA profiling. Who is the father?

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5.2 investigate the use of data analysis from a large-scale collaborative project to identify
trends, patterns and relationships, for example:
a) the use of population genetics data in conservation management
Habitat loss, overexploitation of natural resources, invasion by alien species, and global
climate change are among the most important factors that threaten biodiversity and can work
together to increase species extinction risk in the future.
Information used to decide if a species is at risk of extinction, and what threatened category it
falls into is generally based on ecological and demographic data such as the number of
known individuals, actual or projected declines in population size, and the extent of
occurrence (EOO) or area of occupancy (AOO).
The EOO is an estimate of the total area currently occupied by a taxon and the risks within
this area. The AOO is a measurement of current occupation of suitable habitats within the
EOO and measures the risks to a taxon occurring within small patches or in few patches
within the EOO. Demographic information is fundamental in conservation biology, but in
several species, it is difficult to directly estimate.
There is a consensus among conservation biologists as to the importance of genetic factors in
determining the fates of populations or species, but these factors are not generally used to
define the conservation status of a species. The “genetic health” of a population or species is
dependent on its genetic diversity and inbreeding level. Rare and endangered species tend to
have reduced genetic diversity within populations and low gene flow rates among them,
because in general the populations are small and highly disjointed. Furthermore, habitat loss
and fragmentation processes can lead to the disruption of pollination and dispersion, resulting
in low reproductive success and making populations more isolated and prone to inbreeding
depression, i.e., a reduction in the capacity for survival and reproduction of the offspring of
inbreeders.
The genetic diversity and degree of inbreeding in a population are directly dependent on the
effective population size (NE), a fundamental parameter for the conservation of threatened
species. The NE of an actual population can be defined as ‘the size of an ideal population that
suffers the same magnitude of genetic drift as the actual population’; this genetic drift is
generally measured as a loss of genetic difference, increase of identity by descent, or change
in allele frequency over time. The difficulty and impracticality of directly counting
individuals in most species, coupled with the importance of genetic parameters in threatened
species, led to the use of NE in place of census population size in species conservation.
Furthermore, several population genetic tools are currently available for estimating the
change over time of NE and detecting population genetic structure and migration rates among
populations. Information about these genetic parameters could be used to gain knowledge
about how global habitat loss, fragmentation and novel environments will affect a species and
thus help to optimize its conservation. These genetic studies are even more important in
poorly known species, as they could help to infer a species’ conservation status and aid in
making decisions about its conservation.

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Case Study: Two endemic palm species of the Itremo Massif in central Madagascar, Dypsis
ambositrae and D. decipiens, are known to be threatened with extinction and conservation
management for these species is a priority for the newly created protected area in the region.
The genetic diversity of these two species was studied. DNA fragments generated using three
combinations were analysed for 20 and 50 individuals of the two species, respectively, from
across their ranges.
Genetic diversity was relatively low for both species. The two sites where the highly
restricted D. ambositrae grows were found to be genetically distinct (although overall genetic
diversity was low). Despite having a much wider distribution and relatively large population,
D. decipiens did not show clear geographical nor genetic groupings and had similarly low
genetic diversity to D. ambositrae.
With so few individuals remaining in the wild and two genetically distinct subpopulations, it
is recommended that both sites of D. ambositrae are conserved and that seed are collected
from both for both storage and potential future reintroduction. It may be less important to
focus resources on conserving or collecting storage material from all sites where D. decipiens
is found, as the genetic diversity represented by each subpopulation is limited and increasing
sampling may not protect significantly higher levels of genetic diversity.

Figure 54 – (A) Dypsis decipiens (IUCN Endangered) and (B) Dypsis ambostirae (IUCN
Critically Endangered).

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b) population genetics studies used to determine the inheritance of a disease or disorder

Generally, isolated populations → inbreeding occurs more frequently → unfavourable

recessive genes are inherited → unfavourable genetic traits become more common.
Observation of interactions between genes can give idea about what alleles might be
dominant and whether disease causing alleles will show dominancy or not. Based on such
ideas, it is possible to predict the likelihood of whether a disease can be inherited or not.
A number of techniques in population genetics are used to measure allelic frequencies in a
population, thus giving us an image of what number of alleles are being lost during evolution
and what amount are being transferred through gene flow. Analysing these data can give us a
rough image of the probabilities of inheriting disorders within a population. For example,
genetic studies of Amish, a group of isolated people mainly in Pennsylvania show Health
among the Amish is characterized by higher incidences of particular genetic disorders,
especially among the Old Order Amish. These disorders include dwarfism, Angelman
syndrome (delayed development, problems with speech and balance, intellectual disability,
and sometimes, seizures), and various metabolic disorders, such as Tay-Sachs disease (caused
by the absence of an enzyme that helps break down fatty substances. These fatty substances,
called gangliosides, build up to toxic levels in the child's brain and affect the function of the
nerve cells. As the disease progresses, the child loses muscle control. Eventually, this leads to
blindness, paralysis and death.), as well as an unusual distribution of blood types.
In many cases, the effects of natural selection on a given allele are directional. The allele
either confers a selective advantage, and spreads throughout the gene pool, or it confers a
selective disadvantage, and disappears from it. In other cases, however, selection acts to
preserve multiple alleles within the gene pool and a balanced equilibrium is observed. This
situation, labelled balanced polymorphism, can arise because of a selective advantage for
individuals heterozygous for a given allele. For example, the disease sickle cell anaemia is
caused by a mutation in one of the genes responsible for the production of haemoglobin.
Individuals with two copies of the mutant gene for sickle haemoglobin (HbS/HbS) develop
the disease. Individuals that are heterozygous - one copy of the sickle gene and one copy of
the normal gene (HbS/HbA) - are carriers of the condition. It is believed that these
heterozygous individuals are more resistant to malaria than individuals homozygous for the
normal gene (HbA/HbA), and that this selective advantage maintains the presence of the HbS
gene in the population. As a result of balanced polymorphism, the gene pools of most
populations contain a number of deleterious alleles that reduces the overall fitness of the
population (known as the genetic load).
d) the Hardy-Weinberg Principle
The Hardy-Weinberg principle is a mathematical series of steps that allow the prediction of
the occurrence of a particular allele in a given population.
● The principle predicts that the frequencies of alleles in a given population will not
change from one generation to the next
● This prediction can only be true if certain conditions are met – a very large
population, no migration, no mutation or natural selection, all parts of the population
have the opportunity to interbreed
● The principle allows for the prediction of certain alleles and genotypes within the
population
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 ● The principle can be used to test whether selection or some other factor is influencing
the allele frequency
The mathematical side of the principle can be used to:
i) Predict allele frequency
You can figure out the frequency of one allele if you know the frequency of the other, using:
p + q = 1 where p is the frequency of the dominant allele
q is the frequency of the recessive allele
eg, a plant produces either red flowers (R) or white flowers (r). If the frequency of the red
flower (R) is 0.4 then the frequency of the white flower (r) can be calculated
p + q = 1 or
q=1–p
q = 1 – 0.4
q = 0.6
ii) Predict genotype frequency
You can figure out the frequency of one genotype if you know the frequency of the
others, using:
p2 + 2pq + q2 = 1 where p2 = the frequency of the homozygous dominant
genotype
2pq = the frequency of the heterozygous genotype
q2 = the frequency of the homozygous recessive
genotype
eg, if there are two alleles for flower colour (R and r), then there are three possible
genotypes – RR, Rr and rr. If the frequency of RR (p2) is 0.34, and rr (2pq) is 0.27, the
frequency of genotype rr (q2) is 1 – 0.34 – 0.27 = 0.39

iii) Predict the percentage of a population that has a certain genotype

The frequency of cystic fibrosis (genotype ff) in the country is approximately one birth in
2000. From this it is possible to estimate the proportion of people in the country that are
cystic fibrosis carriers (Ff). To do this you need to find the frequency of the heterozygous
genotype Ff, ie. 2pq, using both equations.
First calculate q:
Frequency of cystic fibrosis (homozygous recessive, (ff) is 1 in 2000
ff = q2 = 1/2000 = 0.0005
So q = 0.0005
= 0.022

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 Next, calculate p:
Using p + q = 1
p = 1 – 0.022
p = 0.978
Then calculate 2pq:
2pq = 2 x 0.978 x 0.022
= 0.043
The frequency of genotype Ff is 0.043, so the percentage of the population that are
carriers is 4.3%.
iv) Show if external factors are affecting the allele frequency
If the frequency of cystic fibrosis is measured 50 years later, it might be found to be 1 in
3000 births
From this information you can estimate the frequency of the recessive allele (f) in the
population.
To calculate q:
Frequency of cystic fibrosis allele (f) is 1 in 3000
ff = q2 = 1/3000 = 0.00033
So, q = 0.00033
= 0.018
The frequency of the recessive allele is now 0.18 compared to 0.22 50 years earlier. As
the frequency of the allele has changed between generations the Hardy-Weinberg
principle doesn’t apply so there must some factors affecting the allele frequency such as
immigration, migration, mutation or natural selection in play.

d) population genetics relating to human evolution

Questions about human evolution are addressed through analysis of the fossil and
archaeological records, combined with analyses of diversity in living human populations.
Higher genetic diversity in Africa has been said to indicate an origin in Africa, but in fact, the
characteristic pattern of this diversity indicates only a larger number of ancestors, not greater
time-depth, within Africa. The oldest fossils showing modern human characteristics have
been found in Africa and date to about 130,000 years ago. The oldest related modern human
fossils outside of Africa appear in the Middle East, dating from about 90,000 years ago.
An alternative view is that humans have been evolving within a single evolutionary
population, which, though structured, has been prevented from divergence into a new species
within the last million years by gene flow. Larger genetic distances between populations in
sub-Saharan Africa and those in Europe or Asia generate ideas that people have migrated out
of Africa and thus, the genetic variations in populations have split globally.

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Figure 55 – Evolutionary tree of humans.

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