Module 5 – Heredity

Reproduction
How does reproduction ensure the continuity of a species?

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:
Reproduction

Reproduction is the process of producing offspring, either sexually or asexually

Sexual reproduction involves the combination of genetic material from two parents to produce genetically
different offspring

Asexual reproduction produces offspring which are genetically identical to the single parent

Sexual reproduction Asexual reproduction

Parents Requires 2 parents Requires 1 parent

Fertilisation (fusion of female and male

Fertilisation No fertilisation since there are no gametes
gametes to form a zygote) occurs

Cell type Sex cells act as reproductive units Somatic cells act as reproductive units

Genetic Genetic variation among offspring allows No genetic variation in offspring since all are
variation evolution to process identical

Speed Produces offspring less rapidly Produces offspring very rapidly

Sex organs Male and female reproductive organs required Reproductive organs are not required

Animals Internal and external reproduction ––

Plants Pollination and seed dispersal Apomixis, runners, rhizomes, suckers

Fungi Budding Fungal spores

Bacteria –– Binary fission

• animals: advantages of external and internal fertilisation

Reproduction in animals

Fertilisation is the union of male and female gametes to form a new cell, known as the zygote

• In animals, reproduction is solely sexual and requires the fertilisation of an egg with sperm

External fertilisation
• Takes place outside the body
• Most common in aquatic organisms where gametes can be released directly into open water (fish, frogs)
• Males and females have to produce very large amounts of gametes to ensure survival and successful fertilisation
• Predators, exposure and currents can all reduce the likelihood of successful fertilsation, so the large
amounts of gametes compensates for this
• But, this costs a lot of resources and energy
• In an aquatic environment, externalisation fertilisation is successful due to the aqueous environment which allows
for free movement of the gametes
• Cannot occur in terrestrial environments since gametes are unable to travel through air
Internal fertilisation
• Occurs inside the body of the female in animals
• Gametes are usually transferred internally from the male to the female through the use of sex organs
• Males produce large number of gametes while females produce fewer to conserve resources and energy
• Most common in terrestrial organisms, like mammals and reptiles
• In aquatic environments, internal fertilisation is not a necessary adaptation for most species but is still successful
• In a terrestrial environment, the internal body environment provides a water-rich environment to allow for the
movement and nurturing of the gametes and zygote
• Very few gametes are required as the internal environment is highly protective

Advantages and disadvantages of external and internal fertilisation

Advantages Disadvantages

Large number of gametes lost due to predation

Adequate level of success and exposure (must produce a very large amount
to compensate)

Success dependent on currents (gametes carried

Potential for a large number of offspring
Externa in the wrong direction may not fertilise)
l
Increased genetic variability, as gametes from
Very energetic and resource intensive
many different individuals can fertilise

Aquatic environment is well-suited to External fertilisation is poorly suited to terrestrial

supporting gametes environments

Very high level of success

Lower number of offspring compared to external
No need to produce large amounts of female fertilisation
gametes
Internal
Internal environment of female body is highly
Lower genetic variability of offspring population
protective

Success of fertilisation is independent of Risk of contracting a sexually transmitted disease

environmental conditions or parameters is much higher

Female sex organs

• Female sex organs are specialised to produce eggs and to nurture a developing embryo

Structure Function

Vulva Aids in reproduction functions through lubrication and provides an entry to the vagina

Passageway for the entrance of the penis during sexual intercourse, and for the birth of the
Vagina
child during childbirth

Cervix A very narrow passage which separates the vagina and the uterus

Uterus Site of implantation of the zygote, and development of the embryo/foetus

Oviduct Site of fertilisation of egg and sperm

Infundibulum Contains finger-like structures which sweep the eggs from the ovary into the oviduct

Ovary Produces eggs and various hormones related to reproduction

Ovarian
Fibrous ligament that connects the ovary to the lateral surface of the uterus
ligament
Male sex organs
• Male sex organs are specialised to produce sperm and to deposit these sperm into the female repoductive tract

Structure Function

Penis Deposits sperm into the female reproductive tract during sexual intercourse

Urethra Acts as a common passageway for urine and sperm out of the penis

Seminal
Produces components of semen which nourishes the sperm
vesicles

Prostate Produces components of semen which neutralises the acidic environment of the vagina

Vas deferens Carries sperm from the testicles to the urethra

Epididymis Site of maturation and storage of sperm

Testicles Produces sperm and various hormones related to reproduction

Scrotum Maintains the thermal environment of the testicles

Cowper’s gland Produces thick clear mucus prior to ejaculation that drains into the urethra

• plants: asexual and sexual reproduction

Reproduction in plants
• Often, plants employ a combination of sexual and asexual reproduction

Sexual reproduction in plants involves the union of pollen

(male gamete) and an ovule (female gamete)

Asexual reproduction in plants involves the propagation of genetically

identical clones without the need of sex cells
Sexual reproduction in plants
• Sexual reproduction in plants involves 2 steps, pollination and seed dispersal
• Angiosperms and gymnosperms are the 2 classes of plants which use sexual reproduction
• Gymnosperms (pines) use wind to pollinate distant males
• Angiosperms (flowering plants) use a wider variety of methods (wind, insects, birds, mammals) to
disperse pollen

Pollination

Pollination occurs when pollen from the male anther is deposited onto the female stigma and
fuses with ovule internally

• Flowers and pinecones act as the main sex organs for angiosperms and gymnosperms respectively
• The preferred scenario is when two different plants pollinate (cross-pollination)
• Increases genetic variability and increases the evolutionary fitness of the population
• This process requires the movement of pollen through a vector

Type Vector Flowers Pollen

• Big and brightly coloured • Located in the first flower such

• Strong aroma, like sweet, rotting that the insect must brush against
flesh-like or mimicking sex pheromones the pollen to reach the reward
Insects
• Produce energy-rich nectar (nectar)
• Have ultraviolet markings to guide • Nutritious to attract insects to
insects eat some of the nectar
Biotic
• Placed high on a sturdy stem • Located in the flower such that
• Out of the way of leaves and nearby the bird must brush against the
flowers, as to not entangle the bird pollen to reach the reward
Birds
• Brightly-coloured, nectar-producing, (nectar)
but odorless • Nutritious to attract bird to eat
• Shaped to accomodate a thin beak some of the nectar

• Low hanging anthers to expose the

pollen to the wind • Easily separable, light,
Wind • High-placed, feathery stigma to aid in aerodynamically favourable
catching pollen floating through the air pollen allows for wind travel
Abiotic • Dull, odourless flowers

• Able to float, or contained

Water • Dull, odourless flowers within a membrane with an air
bubble

• Plants that have both male and female parts are called hermaphrodites and can self-pollinate
 • Self-pollination can lead to lack of genetic variation, or inbreeding that results in deleterious traits
being shown in offspring
Seed dispersal

Seed dispersal is the movement of the developed seed some distance away from the plant

• It is disadvantageous to have the offspring take root very close to the parent since it will end up
competing with the parents for space and resources
• The seeds need to be dispersed some distance away from the parent to ensure success

Method Description

Seeds are often fine and aerodynamic, winged, or feathery to aid in travelling with
Wind
air currents.

Seeds have barbs or hooks to catch onto the fur of animals as they brush past. They
Animals may also give rise to fruits, which are eaten. The seeds are deposited some distance
away with the animal’s faeces.

Seeds are stored in pods, which only open when there is a fire. This removes
Fire
competition between the parents and the offspring.

Water Seeds are able to float in water, following the current into different areas.

Ballistic Seeds are contained in a pressurised pod. The pods explode when ripe, blasting the
s seeds away from the parent.

• After successful pollination and fertilisation, a seed will develop and may give rise to new offspring

Asexual reproduction in plants

• The offspring are genetically identical to the parent, and thus can be considered clones
• In plants, asexual reproduction can be achieved by:

Method Description Examples

The production of seeds without fertilisation, which are then dispersed using the Dandelion
Apomixis
methods described previously Hawthorns

Horizontally-running stems which grow along the soil (either above ground, or just
Strawberries
Runners below) and take root at its end, producing a new plant. The new plant can produce
Peppermint
more runner stems.

Horizontally-running, root-like stems which grow under the soil from the parent Asparagus
Rhizomes
and produce new plants at intervals Ginger

A new plant grows directly from a bud found at the base of the parent plant. These Red raspberry
Suckers
new plants can grow some distance away from the parent. Lilac

Meristem
• The tissue of the plant responsible for asexual reproductions is the meristem
• It is mitotically active, meaning that it contains cells that are constantly dividing and growing
 • fungi: budding, spores
Fungal reproduction
• Fungi constitute one of the main kingdoms of life, and is in the Eukarya domain

Multicellular fungi that grow as hyphae filaments and reproduce through and the production of
Moulds
reproductive spores

Mushroom
Multicellular fungi that grow fruiting bodies which distribute reproductive spores
s

Yeasts Unicellular fungi that reproduce through budding, a form of asexual reproduction

Budding in fungi

Budding is a form of asexual reproduction where the offspring develops from a small outgrowth of the parent

• The bud stays attached to the parent organism until the bud is mature, at which point it will detach itself
• As a form of asexual reproduction, offspring are genetically identical to the parent
• Occurs in yeast and other filamentous fungi
Process of budding

Fungal spores

Fungal spores are microscopic biological particles that allow fungi to be reproduced, similar to plant seeds

• Often are very hardy, having thick walls, a reserve energy source and low metabolic rate that allow them to
survive through environmental stress such as high temperature, high UV radiation and chemical damage
• Occurs in moulds, mushrooms, and Chicken on the Woods
• Spores can be involved in both sexual and asexual reproductive cycles
• The sexual life cycle can be divided into two phases
Gamete phase: cells are haploid, having half the number of chromosomes as the parent

• Fungi spend most of their time in the haploid phase as mycelium

• Mycelium can produce
• Haploid hyphae (moulds) which can fuse with other haploid hyphae
• More haploid spores, which can germinate and form more mycelium
• This is a form of asexual reproduction

• This process is called plasmogamy, and it produces a cell containing two

haploid nuclei (dikaryotic)
• The dikaryotic form is where fruiting bodies (as in mushrooms) will form

Zygote phase: cells are diploid after fertilisation, producing a cell with the full set of chromosomes

• bacteria: binary fission

Binary fission

Binary fission is the method by which bacteria asexually reproduce by splitting in half

• Bacteria cannot use sexual reproduction

• This requires the production of gametes, which prokaryotes are not capable of doing since gametes are a
type of cell and bacteria are unicellular
• Instead, bacteria solely use asexual reproduction, producing colonies of bacteria which are all genetically identical
• Occurs in three main steps
• Chromosome replication: the DNA is replicated
• Chromosome segregation: the chromosomes are moved to opposite ends of the cell
 • Cytokinesis: the organelles are replicated and are distributed between the two potential daughter cells
before the cell splits

• Helicase splits DNA into 2

separate strands
• Topoisomerase untangles
chromosome

• DNA polymerase reads a strand of

DNA and makes a copy
• Starts from the origin of replication
(oriR)

• Filamenting temperature-sensitive
mutant Z
• Assembles the cytoskeletal
scaffold at the future site of bacterial
cell division

• Results in two identical daughter

cells
• This is a type of asexual
reproduction (creating genetically
identical offspring)

• protists: binary fission, budding

Protist reproduction
• Protists are a diverse group of unicellular eukaryotes which do not fit into other classification for eukaryotes
• With a diverse group of organisms comes diverse methods of reproduction
• Many protists employ a combination of sexual and asexual reproduction methods

Budding in protists
• Similar to yeast, budding is when an outgrowth from a parent separates to become an identical offspring
• A small outgrowth from the cytoplasm will push the cell membrane our forming a bud, while mitosis produces an
identical daughter nucleus
• Daughter nucleus will then migrate into the bud which will mature and is cleaved to form identical offspring
• Occurs in Arcella

Binary fission in protists

• Binary fission is the most common method of asexual reproduction in protists
• Occurs in Paramecium
• Just like bacteria, binary fission involves:
• Chromosome replication (using mitosis, not just DNA
replication)
• Chromosome segregation
• Cytokinesis
 Multiple fission
• Many protists can perform more than one fission at once
Malaria life cycle
• Malaria is a disease caused by a genus of protists called Plasmodium spp.
• The life cycle of Plasmodium incorporates both sexual and asexual phases which occurs over two hosts
• Mosquitoes: the definitive host (host in which a parasite performs sexual reproduction in)
• Humans: the intermediate host (host in which a parasite performs asexual reproduction in)
• The female Anopheles mosquito acts as the main insect vector for the transmission of infective Plasmodium cells
to humans
Analyse the features of fertilisation, implantation and hormonal control of pregnancy and birth in mammals
Mammalian reproduction
• In all steps of mammalian reproduction, there is hormonal control to ensure the correct timing of these processes

Insemination

Insemination is the deposition of semen into the reproductive tract of a female, usually by sexual intercourse

• During intercourse, the penis of the male is thrust into the vagina of the female to deposit sperm as close to the
ovum as possible
• Sex drive (libido) is regulated by hormones in mammals

Fertilisation
• Once sperm has been deposited into the female reproductive tract, they
will swim up towards the ovum
• Once at the ovum, the sperm will attempt to burrow past the outer layer
(zona pellucida) of the egg
• Once a sperm nucleus enters ovum, zona pellucida becomes impenetrable
• Release of eggs by the female is controlled by hormonal changes over her
menstrual cycle
• The hormonal control of egg release regulates the timing of fertilisation and pregnancy
Menstrual cycle

Ovulation
Implantation

Implantation is the attachment of the fertilized egg or blastocyst to the wall of the uterus

• From days 1-4, the zygote develops a (a hollow ball of cells which determines the location of
the mouth and anus)
• From days 4-5, the zygote develops into a blastocyst (a group of specialised cells with the
features to make a placenta)

• Occurs once the blastocyst reaches the endometrium

• Doing this allows the zygote to bury into the wall of the endometrium
• This process is called implantation

• Placenta bridges the developing embryo’s cardiovascular system with the mother’s
• The capillaries of mother and baby come into close proximity but do not mix
• Protects the baby from the mother’s immune system whilst still allowing exchange

• Placenta itself also acts as a gland, secreting hormones like human chorionic gonadotropin
• This is important as the endometrium will be shed (along with the implanted embryo) in
menstruation so progesterone levels fall in the mother's bloodstream

Development

Development is the process in which a single-cell zygote becomes an embryo, a fetus, and then a baby

Childbirth

Childbirth is the labor and delivery of a child from the uterus

• If there are complications with vaginal delivery, or at the mother’s discretion, a Caesarean
section may be performed
• In a Caesarean section, the abdomen is cut open and an incision is made through the uterus to
deliver the child

• This allows the baby to pass from the uterus through the vagina for delivery

• The stretching and dilation of the cervix sends nervous signals to the brain causing the
release of oxytocin from the pituitary gland
• Oxytocin is a hormone which increases the strength and frequency of uterine contractions in
order to assist in the expulsion of the baby

• As the baby is pushed out of the uterus through uterine contractions, the cervix is further
stretched out, causing the release of more oxytocin
• This forms a positive feedback loop called the Ferguson reflex, creating an ever-increasing
cycle of uterine contractions until the complete expulsion of the baby
• Hormonal control plays a very important role in childbirth
Hormonal contraceptives

Hormonal contraception refers to birth control methods that act on the endocrine system

• Implantation, development and birth of a baby is controlled extensively through hormonal secretions
• Current female contraceptive pills come in 2 different formulations:
Combined formulations
• Contain a synthetic progestogen combined with an oestrogen (most commonly used pill)
• Progesterone and oestrogen feeds back onto the pituitary gland, telling it to produce less FSH and LH
• Normally, these hormones stimulate the ovaries to produce mature eggs (ovulation)
• This means that no eggs are released, preventing fertilisation
Progesterone only
• Progesterone-only pills contain a synthetic progestogen, but no oestrogen
• Feeds back onto the pituitary gland, telling it to produce less FSH and LH, and no egg is released

Continuity of species
• Of all the biological processes, organisms are especially equipped to preserve the continuity of their species
through reproduction
• Being able to reproduce in some way is considered one of the essential characteristics of living things
• Both sexual and asexual reproduction are valid methods of continuing the species
• Asexual reproduction produces genetically identical offspring, focusing on very large numbers of offspring
to quickly colonise areas (allows for maintenance and continuity of populations)
• Sexual reproduction produces genetically different offspring, focusing on a small number of variable
offspring (genetic variation helps to protect populations from selective pressure, ensuring continuity)

Evaluate the impact of scientific knowledge on the manipulation of plant and animal reproduction in
agriculture
Manipulation of reproduction
• Manipulating reproduction is the earliest known form of genetic engineering
• Nowadays, the tools used to manipulate reproduction in agriculture are complex and sophisticated
• This development in technologies has come about due to massive leaps in our scientific knowledge in genetics,
molecular biology, embryology and many other biological sub-specialities

Selective breeding

Selective breeding is the process by which humans use animal and plant breeding to selectively develop
particular phenotypic traits by choosing which males and females will reproduce and have offspring together

• Natural selection guides the changes in the gene pool over successive generations given no external influences
• Selective breeding is a form of artificial selection, where humans and their endeavours are the selective pressure
• This concept is called hybrid vigour, where a hybrid of the two parents with desirable traits demonstrate
the best of the two parents

Scientific knowledge Advantages Disadvantages Ethical issues

Employed observation Produces fitter and Can lead to loss of Violates animal rights,
and prediction to see that stronger animals species variety, so living since it is manipulating
breeding two favourable organisms express the animals for human gain
parents would produce Creation of high-quality same vulnerability to and treating animals as
offspring with hybrid products and therefore certain pathogens and property instead of beings
vigour higher profit diseases with their own rights

Experimentation with Helps eliminate diseases Genetic mutations can Characteristics that are
different combinations of by removing deleterious still occur since creation of damaging to animal
parents demonstrated the traits from the gene pool genes can’t be controlled, health may be reproduced
analytical processes of and previous traits may be and can bring discomfort
the scientific method No issues of safety completely lost to the organism
Artificial insemination

Artificial insemination involves the deliberate introduction of male sperm into female reproductive tract by a
method other than sexual intercourse

• Sperm is collected and kept from a male with desirable trains, and can also be frozen by cyropreservation
• Sperm is then deliberately inserted into the female reproductive tract when humans require offspring

Scientific knowledge Advantages Disadvantages Ethical issues

Employed observation, Prevents disease control Disturbs species during Repeated practice of the
prediction and by preventing skin to skin extraction and disrupts procedure may result in
experimentation contact their natural habitats discomfort for organism

Foresee combination of Allows for preservation of Requires use of May result in detrimental
parents that would a huge collection of anaesthetics to calm effects on organisms such
produce favourable genetic details since animals down during this as severe straining and
offspring in animals sperm can be frozen procedure bleeding

Artificial pollination

Artificial pollination occurs when humans manually facilitate the natural plant pollination process

• Pollen is collected and bagged to stop natural cross-pollination from occurring

• Pollen is then brushed deliberately onto the stigma when humans require seeds

Scientific knowledge Advantages Disadvantages Ethical issues

Employed observation, Is used for the creation of Very time consuming, not Reduces biodiversity
prediction and new species which may cost effective and results which makes the
experimentation have advantages in smaller fruits population vulnerable to
extinction, since a single
Foresee combination of Ensure that the flowers May alter the genetic disease may be able to
parents that would are pollinated with the composition of plant wipe out the entire
produce favourable recent extinction of bees, population and results in population because of
offspring in plants the natural pollinators less genetic variation their identical genes

In vitro fertilisation

In vitro fertilisation involves the fertilisation of an egg by a sperm outside of the body, usually a test tube

• Used to overcome a range of fertility issues, such as blocked fallopian tubes and reduced ovarian reserves
• The fertilised egg, or embryo, is allowed to grow in a protected environment for some days
• It is then transferred into the woman's uterus, increasing the chance that a pregnancy will occur

Scientific knowledge Advantages Disadvantages Ethical issues

Experimentation led to Helps many patients who IVF comes with a small Unclear distinction of
the birth of Louise Brown, would be otherwise chance of developing side when ‘human life’ and
the first IVF baby unable to conceive effects when a ‘person’ begins

Study of egg retrieval Embryos can be screened Risk of multiple Storage and destruction
increased oocyte yield per for inherited diseases by pregnancies if more than of surplus embryos and
retrieval and overall pre-implantation genetic one embryo is put back the number of days it has
pregnancy rates diagnosis into the uterus been alive
Cell Replication
How important is it for genetic material to be replicated exactly?

Model the processes involved in cell replication, including but not limited to:
• DNA replication using the Watson and Crick DNA model, including nucleotide composition, pairing
and bonding
DNA’s chemical structure
• Stands for deoxyribonucleic acid
• DNA is a large polymer made of many nucleotide subunits
• A nucleotide consists of:
• A sugar group
• A phosphate group
• A nitrogenous base
Base pairing
• There are 4 nitrogenous bases
• Adenine (A)
• Thymine (T)
• Cytosine (C)
• Guanine (G)
• Because of the chemical nature of the bases
• A only bonds with T
• C only bond with G
• Chemically, the bases are split into two groups
• Purines: Adenine and Guanine
• Pyrimidine: Cytosine and Thymine
• Purines bond with pyrimidines
Types of bonds
• Phosphodiester bond between
phosphate group and sugar
• Glycosidic bond between sugar and base
• Weak hydrogen bonds are between
corresponding bases
Double helix shape
• Ladder twists to form double helix
• Sugar-phosphate backbone of ladder is made of sugars and phosphate components
• DNA is directional since each of the two strands of the double helix runs from a 5’ end to a 3' end in an
antiparallel fashion
• Certain processes only occur from the 5’ to 3’ direction
• The numbering system comes from the carbon atoms in the deoxyribose sugar (5 since it is a pentagon)
• The phosphate group is always attached to the 5’ carbon
• The base is always attached to the 1’ carbon
• The hydroxyl group on the 3’ carbon allows for the strand to be elongated by DNA polymerase
• 5’ end of one strand interacts with the 3’ end of the other strand
• DNA’s directionality is preserved even when in garments

Forms of DNA

Chromatin Chromosome

Thin, long, uncoiled structure of DNA Wound, highly condensed structure of DNA in X shape

Occurs during interphase of cell cycle Occurs for cell division (metaphase and anaphase)

Purpose of usual packaging into nucleus Purpose of separation of genetic material

DNA replication in eukaryotes

DNA replication is the process of producing two identical daughter strands of DNA from one parent strand

• Occurs during both mitosis and meiosis to ensure daughter cells receive the correct amount of genetic material
• DNA in different cells replicate at different rates, as some cells need to divide more than others (skin vs brain
cells)
• The double stranded structure of DNA, with complementary bases, enables for replication to occur efficiently
• Each parent strand becomes a template for the two daughter strands
• The synthesis of a DNA polymer chain in DNA replication occurs in 3 steps

Initiation
• Topoisomerase unwinds the DNA strand
• DNA helicase acts like a zipper, breaking hydrogen bonds between bases and separating DNA strands
• This creates a replication fork
Elongation
• Primase adds a short RNA primer to
template strands
• DNA polymerase adds free-floating
nucleotides from the nucleus the
complementary base on strands
• Polymerase always moves along
the old strand from 3’ → 5’,
creating a new strand that has a 5’
→ 3’ direction
• Nucleotides are inserted onto the
daughter strands in antiparallel
• Leading strand has nucleotides being added towards the replication fork (continuous)
• Lagging strand has nucleotides being added away from the replication fork (discontinuous)
• Replication on the lagging strand occurs in short bursts, creating Okazaki fragments
• Exonuclease removes all RNA primers and replaces with appropriate bases
• DNA ligase joins the Okazaki fragments together to form one continuous strand
• DNA polymerase I proofreads and corrects any base pair errors
Termination
• Once the strands are fully synthesised, the replisome dissociates
• The two daughter strands re-twists into double helices
DNA replication in prokaryotes
• The bacterial chromosome is circular
• Similar process to DNA replication in eukaryotes
• Two opposing replication forks appear at the single replication origin
• They migrate away from each other and terminate on the opposite side

Semi-conservative replication
• DNA replication is said to be semi-conservative, as each daughter strand
“conserves” one old strand from the parent and pairs it with a newly synthesis strand
• Ensures that the process of DNA replication is accurate
• Produces two exact copies of the DNA strand due to DNA base pairing

DNA replication models

Advantages Disadvantages

Allows us to visualise the process since it is too small Doesn’t represent the correct size of the process

Simplifies the process Doesn’t show the true complexity of DNA replication

Colour codes allows us to distinguish between bases, Doesn’t allow us to comprehend the speed of the
phosphate group and sugar process

Flexibility of poppit beads allows us to twist into a

Complex shape of enzymes cannot be modelled
double helix shape

• mitosis and meiosis

Chromosomes

Chromosomes are thread-like structures in which DNA is tightly packaged within the nucleus

• Number of chromosomes in cells

• All somatic cells in the body are diploid (2N) cells because they contain two of each type of chromosome
• Gametes (or sex cells) such as sperm or ova are haploid (N( cells because they contain only one
chromosome of each type

Homologous chromosomes are a set of one maternal and one paternal chromosome that pair up with each other
inside a cell during meiosis

• Chromosome pairs are approximately the same length, centromere position, and staining pattern, for
genes with the same corresponding loci
• One is inherited from the mother, and the other from the father
• Humans have 46 chromosomes
 • 23 were inherited from the father (paternal)
• 23 were inherited from the mother (maternal)
Karyotype

Karyotypes the number and visual appearance of the

chromosomes in the cell nuclei of an organism

• Obtained by isolating, staining, and examining chromosomes

under the microscope
• Chromosomes are usually taken from white blood cells
• In humans, the 23rd chromosome is the sex chromosome and
determines the sex of the person
• Females have an X and X, while males have an X and Y

The cell cycle

The cell cycle is the repetitive sequence of cell division and enlargement

• Each complete cycle takes about 18-22 hours

• Mitosis and meiosis are part of the cell division process and takes about 1–2 hours
• Cells don’t partake in cell division without the right triggers
• The dysregulation of cell division is the driving force behind cancerous growths
• The cell cycle is a system of protein messengers which regulate the timing of cell division
• These proteins belong to a class of protein messenger called cyclins
Stages of the cell cycle

DNA structures
• In S phase, chromosomes replicate into two identical chromosome copies, called sister chromatids
• They are held together by a centromere
 Types of cells
• Cells that are actively undergoing cell cycle are able to divide using mitosis (mitotically active)
• Labile cells are constantly multiplying (skin cells)
• Stable cells multiply only when there is a need to (muscle and liver cells)
• Some cells are incapable of using mitosis to divide (permanent cells)
• Brain and heart cells
• G0 stage is sometimes used to describe this state
• Said to be terminally differentiated
• Can only re-enter the cell cycle under special circumstances

Mitosis

Mitosis is a type of nuclear division in eukaryotic cells that occurs when a parent cell divides to produce two
identical daughter cells, typical of ordinary tissue growth

• Cell division by mitosis leads to the formation of two daughter cells which are genetically identical to the parent
and each have a full set of chromosomes (2N)
• Occurs in somatic (body) cells and plays an important role in:
• Repair of damaged tissue and replacement of worn-out cells
• Growth of cells
• Asexual reproduction (growth of plants from cuttings, cloning of organisms)
• Genetic stability since it ensures the precise and equal distribution of chromosomes to each nucleus
• Only eukaryotes can use mitosis (prokaryotes use binary fission)

• DNA condenses to form chromosomes, each containing 2 copies of the DNA called sister
chromatids
Prophase
• Nuclear membrane breaks down
• Centrioles start to form spindle fibres and move to opposite poles

• Sister chromatids (double chromosomes) line up along the metaphase plate

Metaphase
• Spindle fibres from centrioles attach to the centromeres of the sister chromatids

Anaphase • Spindle fibres contract and separate the sister chromatids to cell poles

• Nuclear membrane reforms

Telophase • Cell elongates
• Cleavage forms
Meiosis

Meiosis is a type of reductive nuclear division that occurs when a diploid cell divides into four unique haploid
daughter cells, reducing the chromosome number, as in the production of gametes and plant spores

• Only occurs in gametes for reproduction so that two parents can pass genetic material to offspring
• Ensures that the chromosome number of each species is maintained, not doubled, during sexual reproduction
• DNA is replicated before division, then cell undergoes two successive divisions
• Meiosis I: diploid cell divides into two haploid cells
• Meiosis II: two cells divide again, results in four haploid daughter cells, each having half the number of
chromosomes the parent had
• Occurs in egg and sperm cells in animals, and pollen and ovules in seed-producing plants
• It is the process by which genetic variation is introduced into a species

Meiosis I Meiosis II (similar to mitosis)

• Cell grows • Cell grows

Interphase I • DNA replicates Interphase II • No DNA replication
• Centrioles divide • Centrioles divide

• DNA condenses to form

chromosomes • Nuclear membrane dissolves
• Nuclear membrane dissolves • Centrosomes start to form spindle
Prophase I • Centrioles start to form spindle Prophase II fibres and move to opposite poles
fibres and move to opposite poles • Cells are in haploid phase, which is
• Homologous chromosomes pair up the first time this occurs in meiosis
and crossing over occurs

• Homologous pairs line up along the • Sister chromatids line up along the
metaphase plate metaphase plate
Metaphase I • Spindle fibres from centrioles Metaphase II • Spindle fibres from centrioles
attach to the centromeres of the attach to the centromeres of the
homologous chromosomes sister chromatids

• Spindle fibres contract and

separate the homologous
Anaphase I
chromosomes to opposite cell poles
• Each daughter cell now has one
 chromosome with 2 sister chromatids • Spindle fibres contract and
separate the sister chromatids to cell
• Nuclear membrane reforms Anaphase II poles
Telophase I • Cell elongates • Each daughter cell now has one
• Cleavage forms chromosome with 1 sister chromatid

• Cells separate • Nuclear membrane reforms

Cytokinesis I • Cytoplasm and organelles are Telophase II • Cell elongates
equally distributed to daughter cells • Cleavage forms

• Cells separate
Cytokinesis II • Cytoplasm and organelles are
equally distributed to daughter cells

Mitosis vs. meiosis

Mitosis Meiosis
 Function Growth, repair and asexual reproduction Sexual reproduction

Type of reproduction Asexual Sexual

Cell types Somatic cells Gamete cells

DNA replication Yes Yes, only in meiosis I

Metaphase
Singular Pairs first, then singular
chromosome alignment

Number of divisions 1 2

Number of daughter
2 4
cells

Daughter cells Diploid, identical to parent Haploid, non-identical to parent

Checkpoints
• The cell cycle also has in-built checkpoints where the integrity of the cell and its DNA are assessed before it
continues dividing
1) G1/S (restriction) checkpoint
• The size of the cell and its environment are checked for suitability
• After this checkpoint, the cell will be committed to completing mitosis
2) G2/M checkpoint
• DNA is checked to ensure that no mutations or abnormalities are present and that DNA replication has
completed successfully
3) M (spindle) checkpoint
• Spindle fibre connection to the DNA is checked to ensure it is secure to chromosomes in metaphase
Abnormalities
• Should the cell encounter any abnormalities at the checkpoints, the cell can elect to:
1) Stop the cell progression and enter G0
• When a cell is permanently inactivated this way, it is deemed senescent
2) Repair DNA damage
• This involves removing the damaged portion and filling it in using DNA polymerase
3) Initiate the caspase pathway to start cell death by apoptosis
• Apoptosis is also referred to as programmed cell death, and is a normal kind of cell death
• Involves the fragmentation of the cell into small apoptotic bodies containing degraded cytoplasm

Assess the effect of the cell replication processes on the continuity of species
Continuity of species
• Of all the biological processes, organisms are especially equipped to preserve the continuity of their species
through reproduction
• Being able to reproduce in some way is considered one of the essential characteristics of living things
• Both asexual and sexual reproduction are valid methods of continuing the species
• Asexual reproduction produces genetically identical offspring, focusing on very large numbers of offspring
to quickly colonise areas, allowing for maintenance and continuity of populations
• Sexual reproduction produces genetically different offspring, focusing on a small number of variable
offspring (this genetic variation helps to protect populations from selective pressure, ensuring continuity)

DNA replication
• DNA replication allows genetic material to be transmitted from:
• One cell to another through mitosis
• Allows for exact replication of genetic material of cells, maintaining stability
• This allows for a multicellular eukaryotic organism to grow, repair and maintain itself in a
controlled and coordinated way
 • Unicellular eukaryotic organisms also use mitosis as a form of asexual reproduction
• One generation to another through meiosis
• When a parent cell undergoes meiosis, it uses DNA replication to create genetic material which
can be distributed to the gametes
• Fertilisation with another gamete produced through meiosis forms genetically different offspring
• Genetic variation helps protect populations from selective pressures, ensuring continuity
• Errors in DNA replication can be due to mutations, or from replication errors
• Replication errors are when DNA polymerase places the wrong base as it is replication the DNA
• This interrupts the DNA replication process and can impede mitosis and meiosis
• This has implications for the continuity of the species
• DNA polymerase has 3’ → 5’ exonuclease activity which allows its to remove an incorrectly placed base
and replace it with the correct one

Cytokinesis
• Cytokinesis, where organelles and cytoplasm are equally split between daughter cells, occurs after nuclear
division
• Incorrect distribution of cytoplasm or cytokinesis at the wrong time can lead to death of the daughter cells,
wasting the time and energy investment in cell division processes • All cells share some characteristics
• Ribosomes
• Cell membraneand potentially ending the continuity of species
DNA and Polypeptide Synthesis
Why is polypeptide synthesis important?
Construct appropriate representations to model and compare the forms in which DNA exists in eukaryotes
and prokaryotes
Prokaryotic DNA
Nucleoid
• Prokaryotes do not have membrane-bound
organelles, so they can’t have a nucleus
• Instead prokaryotic DNA aggregate roughly in the
centre of the cell, forming a nucleoid
• Single large circular chromosome
Plasmids
• Also have plasmids, small rings of DNA that may
carry a few genes related to a specific function
• Many plasmids carry genes specifically related to
resistance against antibiotics
• Some highly resistant bacteria can carry hundreds of
plasmids, each related to a specific resistance
mechanisms against a class of antibiotics
• Plasmids can be transferred horizontally between neighbouring bacteria in a process called conjugation
• This means that as soon as a single bacterium mutates a resistance mechanisms in a plasmid, the
entire population is able to receive the plasmid and become resistant as well

Eukaryotic DNA
Nucleus
• In eukaryotes, DNA is carried in the
nucleus
• Nuclear membrane is porous and semi-
permeable, allowing it to control what
messages and signals go in and out
• Long strand is coiled around protein
octamers called histones
• DNA is usually in a ‘relaxed’ state
called a chromatin, but condenses into
multiple discrete linear chromosomes in
preparation for mitosis or meiosis for
precise movements
• Heterochromatin: chromatin is packed dense, so it is hard for machinery in the nucleus to read it
• Euchromatin: the chromatin is more relaxed so machinery in the nucleus can go in and read the DNA
;

Mitochondrial and chloroplast DNA

• The mitochondria and chloroplast both have their own
small circular DNA
• These are the double-membrane organelles in eukaryotes
• It is thought that these organelles are the remnants of the
endocytosed ancestral prokaryotes
• These chromosomes usually code for proteins that assist
in the organelle’s function
• This DNA is completely maternally inherited
• Some diseases occur due to mutations on these circular
chromosomes and can be traced back through mothers

Prokaryotic vs eukaryotic DNA

 Prokaryotic DNA Eukaryotic DNA

Nucleoids and plasmids Nuclear, mitochondrial and chloroplast DNA

Found in cytoplasm, not organelles Found in the nucleus, mitochondria and chloroplast

Circular Linear with 2 ends

Contains a small number of genes Contains a large number of genes

Organised into a singular chromosome with some

Organised into many chromosomes
plasmids

DNA replication occurs in cytoplasm DNA replication occurs in the nucleus

DNA replication is rapid DNA replication is slow

Model the process of polypeptide synthesis, including:

• transcription and translation and assessing the importance of mRNA and tRNA
RNA
• RNA is very similar to DNA, but has a few key differences

DNA RNA

Deoxyribose sugar Ribose sugar

A, T, C, G bases A, U, C, G bases

2 strands 1 strand

Only in the nucleus In the nucleus and cytoplasm

DNA mRNA, tRNA, rRNA

• RNA does not have the base thymine (T)

• In its place is a nitrogenous base called uracil (U)
• It acts much in the same way as thymine does, forming complementary hydrogen bonds to adenine (A)
mRNA
• mRNA (messenger RNA) is a single strand of RNA
which gets made in transcription
• It is a copy of a specific gene of DNA, but single
stranded and in RNA form
• It travels from the nucleus into the cytoplasm as a
messenger
• This is how the nucleus sends message to the rest of
the cell
• When mRNA is read by a ribosome, the correct amino
acids are placed in order specified by the mRNA molecule
rRNA
• rRNA (ribosomal RNA) is a noncoding type of RNA that
acts as the primary building block for ribosomes
• Ribosomes are a type of ribonucleoprotein
• This means that ribosomes are a biological complex of rRNA (ribosomal RNA) and protein
• The ribosome is formed through folding and complementary base pairing within the RNA strand into
hairpin loops
• Ribosomes consist of two separate subunits – one large and one small
 tRNA
• Transfer RNA connect mRNA codons to
the amino acids they encode
• Thus, they are involved in the translation
step of polypeptide synthesis
• One end of each tRNA has a sequence of
three nucleotides called an anticodon,
which can bind to specific mRNA codons
• The other end carries the amino acid
specified by the codons
• There are many different types of tRNAs,
and each type reads one or a few codons
and brings the right amino acid matching
those codons

Protein synthesis
• Protein synthesis is the process whereby biological cells generate new proteins
• All genes actually code for a polypeptide, the precursor for a protein
• When the gene is read and the polypeptide is created, we say that the gene has been expressed
Transcription

Transcription occurs when a particular segment of DNA is copied into mRNA by the enzyme RNA polymerase

• Just like DNA replication, synthesis of an mRNA molecule in transcription occurs in 3 steps:

Initiation
1) RNA polymerase binds to a promoter sequence just before the gene of interest
2) Several transcription factors bind to the promoter sequence and the RNA polymerase, forming an
active RNA polymerase-promoter complex
3) The RNA polymerase-promoter complex unwinds and unzips the DNA

Elongation
4) The RNA polymerase separates from the RNA polymerase-promoter complex and slides down the
template strand, attaching complementary ribonucleotides
• RNA polymerase builds strand in the 5' to 3' direction, adding each new nucleotide to the 3' end
• A → U, T → A, C → G, G → C

Termination
5) The RNA polymerase encounters a STOP codon and a terminator sequence
6) The RNA polymerase stops, and the newly synthesised mRNA strand detaches
• Now, the gene of interest has been copied onto an mRNA and has left the nucleus
• The original DNA molecule is reverting back into its original state
• In the cytoplasm, the mRNA is modified post-transcriptionally
• A 5’ cap and 3’ poly(A) tail (long string of adenine ribonucleotides) is added to the mRNA to protect it
from degrading in the cytoplasm
• The RNA is spliced to remove the non-coding regions of DNA
• The next stage of translation will now start

Translation

Translation occurs when the mRNA is decoded to build

a protein that contains a specific series of amino acids

• An mRNA encodes a polypeptide, or chain of amino acids

Genetic code
• RNA nucleotides read in groups of three, called
codons
• Each codon codes for one amino acid, or can
also be a start codon (AUG) or stop codon (UAA,
UGA, UAG)

1) The mRNA carrying information about the gene of interest encounters a ribosome. It attaches to the small
subunit first, then the large subunit attaches on top to enclose the mRNA
2) The ribosome scans along the mRNA in the 5’ to 3’ direction until it reads a start codon (AUG). The
ribosome can only read one codon at a time.
3) A tRNA carrying an amino acid, with a complementary anticodon, enters the ribosome at its aminoacyl (A)
site and attaches to the mRNA strand
4) The ribosome slides down 3 bases in the 3’ direction and reads the next codon. A second tRNA enters the
ribosome at its A site, and this pushes the first tRNA into the peptidyl (P) site
5) The ribosome slides down again, pushing the first tRNA exit (E) site, and the tRNA leaves the ribosome
6) This continues, with each amino acid linking into a chain with a peptidyl bond in the P site
7) When the ribosome hits a STOP codon and a terminator sequence, the mRNA has then been fully
translated and the gene of interest has been expressed
8) The ribosome subunits and the mRNA detach from each other when translation is finished. The mRNA
degrades in the cytoplasm to be recycled. The ribosomal subunits go searching for another mRNA strand
9) This marks the end of the translation stage
 • analysing the function and importance of polypeptide synthesis
The importance of expression
• When a gene is read through polypeptide synthesis, it has been expressed
• WIthout polypeptide synthesis, many cellular functions would be lost
• Enzymes will no longer exist
• Cell membranes would lose their ability to actively transport and much of their semi-permeability
• Cells cannot communicate to each other anymore
• ATP synthesis would stop, as every step is mediated by a protein or an enzyme
• Without ATP synthesis occurring and with no active transport (due to loss of polypeptide synthesis), no
biological processes would be able to occur, inevitably leading to cell death
• We can take advantage of the importance of polypeptide synthesis in developing medicine
• Many antibiotics block polypeptide synthesis in bacteria, killing them

• assessing how genes and environment affect phenotypic expression

Nature vs nurture

Genotype is a description of the genetic material you have in each of your cells

Phenotype is a description of your physical and biological features that are expressed

• There are two contributors to phenotypic variation:

• Genotype: an organism’s DNA is the main factor in determining phenotype
• Environmental factors: the environment significantly influences how the genotype is expressed
Phenotype = Genotype + Environment

Epigenetics

Epigenetics encompasses the changes in DNA that occur without changing the actual DNA base sequence

• Our chromosomes each have many genes

• We can consider our DNA like a long string of letters.
• Where genotype is the order of the letters, epigenetics is like the punctuation
• These epigenetic changes occurs as a result of the cell and nuclear environment, which is in turn affected by the
external environment of the organism
Histones

Changes Effect Transcriptional activity

Adding an acetyl group to a histone will

Histone relax the DNA wrapped around it, Makes the section of DNA
acetylation converting it from heterochromatic to transcriptionally active
euchromatin.

Removing the acetyl group on a histone

Histone
will tighten the histone, converting Deactivates the section of DNA
deacetylation
euchromatin to heterochromatin

Aan either deactivate or activate DNA,

Histone
adding a methyl group to a histone depending on the amino acid that is
methylation
modified

Significance
• Even if an organism has multiple copies of a gene with very strong promoters, the gene won’t be
expressed at all if its packaged as heterochromatin (either through histone deacetylation or DNA
methylation)
• The genotype is not producing the phenotype we expect, as the genotype’s expression is being modified
by the environment
Temperature
• Siamese cat hairs can either have no pigment (dominant allele: D) or black
pigmentation (recessive allele: d)
• However, we see no completely dark Siamese cats
• The dark pigmentation only occurs at the extremities of the body, such as the
paws, tail, ears and face
• The recessive allele, which produces dark pigment, only activates in colder
temperatures
• The extremities, like the paws and tail, are colder in temperature
• The face is colder due to the movement of air through the nose and mouth
• This explains the patterning of dark pigment
• The environment is significantly affecting the way that the dark pigment is
expressed physically

Humans
• Our height and weight have genetic foundations, but are influenced by the environment
• Factors such as nutrition, toxins, diseases and exercise can alter growth
• Your genes may code for good muscle growth, but this is not guaranteed without the right diet and exercise
• Identical twins have the same genetic material, but visually they differ slightly
• Because the genotype is the same, all differences we see are due to the environment

Investigate the structure and function of proteins in living things

Proteins

Proteins are large molecules composed of one or more long chains of amino
acids, and are important for structural components of body tissues, enzymes
and antibodies

• The amino acid is the subunit of oligopeptides, polypeptides and proteins

• It is a special kind of chemical with a very specific chemical structure
• There are 21 different amino acids
• Distinguishing factors are the differences in their R group

Protein structure

Protein folding is the physical process by which a protein chain acquires its native 3D structure

• When connected together by a series of peptide bonds, amino acids form a polypeptide
• Polypeptide will fold into a specific conformation depending on interactions between its amino acid side chains to
make a protein
• Small deviations in the way the protein folds can completely take away its function or structure
• Four levels of protein structure contribute to its final shape
 Primary Secondary Tertiary Quaternary

Dimension 2D 3D 3D 3D

Small scale
The overall 3D shape Interactions with
interactions of the
Linear description of that the entire protein multiple other
atoms of the backbone
Description the sequence of amino folds into, guided by polypeptide chains to
(ignoring side chains) ,
acids in a protein interactions between form larger protein
commonly alpha helix
amino acid side chains structure
and beta sheets

Multiple polypeptide
Small sections of Encompasses entire
Size Various length chains, DNA and other
polypeptide chain polypeptide chain
cofactors

Example

Functions of proteins
• Proteins are the most diverse group of macromolecules in the body
• They can have a structural function, a physiological function, or both
• This diversity in function can be attributed to the vast variation in protein structure (primary, secondary, tertiary are
quaternary)
• There are structural proteins and functional proteins (gas transport, hormones, membrane components, enzymes,
antibodies and movement)
Structural proteins
• Structural proteins build cells and bodies
• Acts either as a framework for cells to form tissues and organs, or as the material that builds bodily structures

Collagen Acts as a foundation for the formation of tissue; forms loose connective tissue

Keratin A hard and durable material that makes up nails, hair, skin, horns, hooves and claws

A structural material that allows many tissues to resume their original shape after
Elastin
deformation, such as the skin

Gas transportation proteins

• Some proteins participate in the transport of gases
• This is especially important for gases which can’t readily dissolve in water, such as oxygen
• For these molecules, these proteins act as an emulsifying agent
• Has both hydrophobic and hydrophilic parts
• Enables hydrophobic substances to be soluble in hydrophilic solvents, and hydrophobic substances
to be solubilised in hydrophilic solvents like water

Haemoglobin The main gas transport protein found in blood (holds 4 oxygen)

A gas transport protein found in muscles that provides muscles with oxygen when blood
Myoglobin
oxygen is low (holds 1 oxygen)

A gas transport protein found in nerves and the brain that provides nervous structure with
Neuroglobin
oxygen to protect them from hypoxia when blood oxygen is low

Hormonal proteins
• Hormones are chemical messengers which initiate an action within a cell

Insulin Causes cells to take glucose from the blood to their cytoplasm.

Human growth
Stimulates cells to grow, reproduce and regenerate
hormone

Regulates social and sexual interaction by facilitating “feel-good” emotions, induces uterine
Oxytocin contractions in labour, the ejection of milk from the breasts and maternal behaviour towards
children

Membrane component proteins

• Cell membrane has many embedded proteins, such as transmembrane integral proteins and peripheral proteins

Consists of an integral membrane protein with a carbohydrate attached to it and is used for
Glycoprotein
cell-to-cell communication

Protein channel Allows for the facilitated diffusion of substances through the cell membrane

Protein pumps Allows for active transport of substances through the cell membrane

Enzyme proteins
• Enzymes are biological catalysts, implicated in facilitation almost every biochemical process in the body

Na/K–ATPase Hydrolyses ATP in order to move 2 Na+ ions out of the cell and 3 K+ ions into the cell

Amylase Breaks down starch into glucose

DNA polymerase Synthesises daughter DNA strands from a parent strand

Antibody proteins
• Antibodies (also called immunoglobulins, or Ig) are produced by B lymphocytes
• They find invading pathogens and toxins to disable them, signalling phagocytes to
endocytose them or kill them
• A strong antibody response is key to defending your body from diseases
• Antibodies are generally represented with a Y shape
• They specifically bind to antigens to protect the body from disease.

The first antibody to be released in response to disease and is very good at clumping
IgM
invaders together and immobilising them

IgG Main antibody produced in a strong immune response that is produced in very large amounts

IgA Found in bodily secretions such as breast milk to help defend the baby from infections

Movement proteins
• Some highly specialised proteins allow organisms to move

The contractile proteins in muscle that causes muscle to shorten on contraction and allows
Actin and myosin
for movement

The motor proteins in the bacterial flagellum that powers a propeller-like projection in some
Fli proteins
bacteria to allow movement

Kinesins Moves vesicles around in the cell’s cytoplasm

Protein synthesis summary

• The overall process of protein synthesis can be summarised in the following model
Genetic Variation
How can the genetic similarities and differences within and between species be compared?

Conduct practical investigations to predict variations in the genotype of offspring by modelling meiosis,
including the crossing over of homologous chromosomes, fertilisation and mutations
Crossing over

Crossing over is the exchange of chromosome segments between non

sister chromatids in meiosis

• Occurs in prophase I of meiosis when homologous chromosomes pair up

• The arms intertwine, forming a chiasma, and exchanging genetic material
• Resultant chromosomes have some material from the maternal and
paternal chromosome
• Can occur hundreds of times along the chromosome
• Creates new combinations of genes in the gametes that are not found in either parent

Mendel’s Law of Segregation

Mendel’s Law of Segregation states that in anaphase I of meiosis, the pairs of homologous chromosomes split
from each other

• The resulting daughter cells will have one chromosome from each homologous pair
• By splitting the chromosomes, this ensures that the daughter cells (and thus offspring) will definitely be different
from the parent, and different from other offspring
• It is concerned with how 1 trait is inherited
• Mendelian ratio for monohybrid cross is 3:1

Mendel’s Law of Independent Assortment

Mendel’s Law of Independent Assortment states that in metaphase I of meiosis, each pair of homologous
chromosomes assort independently of one another when lining up along the metaphase plate

• It’s not always the case that paternal and maternal chromosomes are on different sides of the metaphase plate
• The more chromosome pairs the organisms has, the greater the number of possibilities
• For x pairs of chromosome, Mendel’s Law of Independent Assortment alone produces 2x possible unique
gamete
• It is concerned with how 2 or more traits are inherited
• Mendelian ratio for dihybrid cross is 9:3:3:1

Fertilisation
• Females and males produce millions of genetically unique gametes, each with N chromosomes
• During fertilisation, there is a union of gametes, to give a diploid offspring with 2N chromosomes
• The selection of gametes in fertilisation is random and there are over 64 trillion possible outcomes for any one
offspring, which contributes to genetic variation
• The offspring will definitely be genetically different from the parents and genetically different to other individuals
• Each fertilisation event is independent of one another

Mutation
• A mutation is a change in the sequence of nitrogenous bases in an organism’s genome which can lead to a change
in the protein that is coded for in that segment of DNA
• It creates diversity within populations by introducing new alleles that were not previously present
• When a mutation is present in a DNA repair gene, the gene may be expressed in an altered form or not expressed
at all
• For example, it has been found that people who have the disease Xeroderma pigmentosum (XP) are unable to
repair DNA and so they are more vulnerable to DNA damage from ultraviolet rays and, as a result, to skin cancer
Model the formation of new combinations of genotypes produced during meiosis, including but not limited to
interpreting examples of the following alleles:
Alleles and genes

A gene is a section of DNA which codes for a specific trait by producing

a protein

Alleles are alternative forms of a gene which found at the same place
on a chromosome

• Any chosen gene will be made of a sequence of bases, and the different
alleles will be different sequences
• Alleles belonging to the same gene must be written with the same letter (dominant capital, recessive lowercase)

Mendel’s Law of Dominance states that when both the dominant and recessive allele are present in a gene pair,
the dominant is expressed and the recessive is not

Terminology Description Genotype Phenotype Expression

Homozygous dominant The genotype only has the dominant allele AA A Dominant

The genotype has both the dominant and

Heterozygous Aa A Dominant
recessive alleles

Homozygous recessive The genotype only has the recessive allele aa a Recessive

Punnett squares
• Genotype is the combination of alleles that an individual possesses for a specific gene
• Phenotype is the organism’s observable characteristics resulting from interaction of genotype with environment

Advantages Limitations

Predicts genotype and phenotype of the next Cannot accurately predict the distribution and
generation given that we know the genotype of the prevalence of offspring genotype of a particular trait in
parents a populations

It determines the probability of an offspring having a Doesn’t account for the fact that some traits are coded
particular genotype and phenotype for by multiple genes

• autosomal
Mendel’s experiments
• Mendel experimented with the garden pea (Pisum sativum)
• Peas were available from seed merchants in a wide array of distinct shapes and colors that could be
easily identified and analysed
• Peas can either self pollinate or be cross pollinated
• Mendel chose 7 characteristics so study
• He performed detailed experiments with good scientific
technique
• Research material well suited to the study of the
problem at hand
• Designed his experiments carefully
• Collected large amounts of data
• Used mathematical analysis to show that the results
were consistent with his explanatory hypothesis
• Predictions of the hypothesis were then tested in a
new round of experimentation
Mendelian cross
• The pure-bred parent stocks were self-fertilised then cross-fertilised with each other
• Then all offspring were self-fertilised
• A Mendelian cross involves one autosomal gene and 2 alleles (one dominant and one recessive), resulting in a
Mendelian ratio of 3:1 for a monohybrid cross

Autosomal genes

Autosomal genes are genes located on an autosome, which is any chromosome that is not a sex chromosome

• Alleles are inherited as a pair, with one allele from each parent
• All organisms express the alleles consistently, regardless of sex

Monohybrid cross

A monohybrid cross is a mating between two organisms with different variations of one genetic trait of interest

• Used to see if one single trait is autosomal

• An autosomal trait will produce a consistent F2 3:1 Mendelian ratio

• The recessive trait will be expressed every second generation
• Start with parental cross between two homozygous individuals, then a cross between two heterozygous offspring

P → F1 (AA x aa) P → F1 (AA x aa)

P1/P2 A A Genotype Phenotype P3/P4 A a Genotype Phenotype

50% heterozygous
a Aa Aa A AA Aa
100% 50% Aa 25% homozygous
100% Aa homozygous 25% AA dominant
dominant 25% aa 25% homozygous
a Aa Aa a Aa aa
recessive

• sex-linkage
Non Mendelian crosses
• There are many cases where crosses deviate from this Mendelian ratio

Sex-linked genes

Sex-linked genes genes are located on a sex chromosome (X or Y chromosome)

• As males and females differ in their sex chromomes, this changes the phenotypical ratios
• In Mendelian crosses, gender didn’t matter, but it does in crosses with sex-linked genes

X chromosome Y chromosome

Carried by both males and females Only carried by males

Carries genes associated with sexual male

Carries both sexual and non-sexual genes
characteristics

Large Small since doesn’t carry many genes

Often the site of sex-linked diseases Very rarely the site of sex-linked diseases
• Sex-linked diseases are found on the X chromosome, and are usually recessive
• Women have the “protection” of another X chromosome, but men do not
• The male Y chromosome acts as a recessive allele
• Men are much more likely to have sex-linked diseases compared to women, such as colour-blindness
• When drawing punnett squares, use
• Normal script to show gender (XX or XY)
• Superscript to show allele only on X (H or h)

Phenotype Females Males

Homozygous recessive XhXh Affected XhY Affected

Heterozygous XhX Carrier None since only one X chromosome

Homozygous dominant XX Unaffected XY Unaffected

• There are 2 scenarios for a monohybrid cross for a recessive sex-linked disease
Situation 1
• Mother is unaffected and father is affected
P → F1 (XX x XhY)

P1/P2 X X Genotype Phenotype

Xh XhX XhX
50% XhX 50% carrier females
50% XY 50% unaffected males
Y XY XY

F1 → F2 (XhX x XY)

P3/P4 Xh X Genotype Phenotype

X XhX XX 25% XhX 25% carrier females

25% XX 25% unaffected females
25% XhY 25% affected males
Y XhY XY 25% XY 25% unaffected males

• After 2 generations of offspring, the ratio of unaffected to affected is 3:1

Situation 2
• Mother is affected and father is unaffected
P → F1 (XhXh x XY)

P1/P2 Xh Xh Genotype Phenotype

X XhX XhX
50% XhX 50% carrier females
50% XhY 50% affected males
Y XY
h
XY
h

F1 → F2 (XhX x XY)

P3/P4 Xh X Genotype Phenotype

Xh XhXh XhX 25% XhXh 25% affected females

25% XhX 25% carrier females
25% XhY 25% affected males
Y XhY XY 25% XY 25% unaffected males

• After 2 generations of offspring, the ratio of unaffected to affected is 1:1

 • codominance
Codominance

In codominance, there is more than one dominant allele and a heterozygous

individual expresses both traits simultaneously without blending

• An example is cattle which can have a red coat allele (CR) or a white coat allele (CW)
• Cattle homozygous for red coats (CRCR) will have red coats, same for white
• Cattle that are heterozygous (CRCW) will express both the red and white coat
alleles, producing a roan coat
• Another example is ABO blood types

In blood types, A and B are equally dominant. O is recessive. Letter I is used for genotype.
P → F1 (IAIA x IBIB)

P1/P2 IA IA Genotype Phenotype

IB IAIB IAIB
100% IAIB 100% blood type AB (codominance)
IB
I I
A B
I I
A B

F1 → F2 (IAIB x IAIB)

P3/P4 IA IB Genotype Phenotype

IA IAIA IAIB 50% IAIB 50% blood type AB (codominance)

25% IAIA 25% blood type A
IB IAIB IBIB 25% IBIB 25% blood type B

• incomplete dominance
Incomplete dominance

In incomplete dominance, alleles aren’t dominant over each other, but instead represent
“dosage” to result in the blending of traits to create a third allele

• Ratio of phenotypes is 1:2:1 in the F2 generation

• In flowers, the red (R) colour is incompletely dominant over white (W) flowers, and the
heterozygous condition (RW) results in plants with pink flowers

A red parent rose (RR) and a white parent rose (WW) produce pink offspring roses (RW). The white allele (W)
represents no pigment and the red allele (R) represents a “dose” of red pigment
• Having one R is like having a small splash of red, giving pink
• Having two R’s is like having a bucketful of red, giving red

P → F1 (RR x WW)

P1/P2 R R Genotype Phenotype

W RW RW
100% RW 100% pink (incomplete dominance)
W RW RW

F1 → F2 (RW x RW)

P3/P4 R W Genotype Phenotype

R RR RW 50% RW 50% pink (incomplete dominance)

25% RR 25% red
W RW WW 25% WW 25% white
 • multiple alleles
Multiple alleles

Multiple alleles occurs when there are more than two alleles for a single trait

• ABO blood group genes are a prime example since they can take on one of three alleles: IA, IB and i

Blood type A Blood type B Blood type AB Blood type O

Homozygous Homozygous
IAIA IBIB
type A type B
Heterozygous Homozygous
IAIB ii
type AB type O
Heterozygous Heterozygous
IAi IBi
type A type B

Dihybrid crosses
• Two locus crosses (dihybrid) are used to see how two traits are inherited together
• Mendelian ratio for a dihybrid cross is 9:3:3:1
• Consider two genes with alleles (B, b) and (T, t) where both parents have genotype BbTt
Gamete cross
• First, we do a gamete cross for each individual that shows the possible genotypes of gametes

Females (BbTt) Male (BbTt)

Gx B b Egg genotypes: Gx B b Sperm genotypes:

25% BT 25% BT
T BT bT 25% Bt T BT bT 25% Bt
25% bT 25% bT
t Bt bt 25% bt t Bt bt 25% bt

Dihybrid cross
• Next, we consider the possible genotypes of offspring during fertilisation by the male and female
• We do this by putting all possible gametes into a 4x4 Punnett square.
Eggs x Sperm

DX BT Bt bT bt Genotype Phenotype

BT BBTT BBTt BbTT BbTt BBTT 1

BBtt 1
BBTt 2
Bt BBTt BBtt BbTt Bbtt B, T 9
BbTT 2
B, t 3
BbTt 4
b, T 3
bT BbTT BbTt bbTT bbTt Bbtt 2
b, t 1
bbTt 2
bbTT 1
bt BbTt Bbtt bbTt bbtt bbtt 1

Test crosses
• Test crosses are used to test an individual's genotype by crossing it with an individual of a known genotype
• First, observe the phenotype of individual (dominant and recessive phenotypes must be known)
• If an individual is phenotypically recessive, then its genotype is homozygous recessive
• If an individual is phenotypically dominant, it can either be homozygous dominant or recessive
• The phenotypically dominant individual is then bred with a homozygous recessive individual
• If all offspring display the dominant phenotype, the individual is homozygous dominant
• If half of the offspring display dominant phenotypes and the other half display recessive phenotypes, then
the individual is heterozygous
Recombinations and linkage
• Law of segregation states that homologous chromosomes, and thus alleles, are separated in metaphase I
• When we performed our gamete cross, this was to find out what allele combinations could be made due
to the Law of segregation
• If two genes are found on the same chromosome they can be separated by crossing over, followed by
segregation

Linked genes are genes on a single chromosome that are in close proximity, are more likely to be inherited
together, and are very rarely separated

• First example: linked because there is a low

chance of the two genes being separated by
crossing over since they are close together
• Second example: not linked because they are on
different chromosomes and can easily be
separated by Law of Segregation
• Third example: not linked because the genes are
far apart and can be separated by crossing over
• If 2 genes are very close together on a chromosome, the probability of crossing over between them is very low
• There will be fewer recombinant gametes (gametes with a mix of paternal and maternal genetic material)

Dihybrid cross with linked genes

• If two genes are linked, this will change the outcome of a dihybrid cross
• A gamete cross is no longer required since we assume no crossing over takes place
• The 2 linked genes can be treated as just 1 gene in a 2x2 Punnett square
Gamete cross
• Consider the following dihybrid cross given that
• BT and bt are linked in the female
• Bt and bT are linked in the male

Female (BbTt) Male (BbTt)

Egg genotypes: Sperm genotypes:

49% BT 49% Bt
49% bt 49% bT
1% Bt (recombinant) 1% BT (recombinant)
1% bT (recombinant) 1% bt (recombinant)

Dihybrid cross
• Recombinant chromosomes for linked genes have a very small chance of occurring so they are not
considered

P1/P2 BT bt Genotype Phenotype

Bt BBTt Bbtt 25% BBTt

50% B, T
25% Bbtt
25% B, t
25% BbTT
bT BbTT bbTt 25% b, T
25% bbTt

• In the end, there is still a 3:1 ratio for each gene

Linkage maps
• Although Punnett squares don’t predict it, recombinant chromosomes are still possible for linked genes
• The chance that crossing over will happen is very low, but it’s not 0
• We can take advantage of this fact to build linkage maps
• The more often crossing over happens between two genes, the further apart they must be
• There is a directly proportional relationship between genetic distance and recombination frequency
• The equation to calculate the relative distance between two genes is given by the following:

• 1 centiMorgan (cM) is the genetic length needed to create 1% recombinant offspring

• It only calculates relative distance, not absolute distance because it is only to compare 2 genes
• The actual length of 1 cM is approximately 15,000 bases long

Example Question 1
In cross-breeding experiments, you observed phenotypes of flies. You count 1600 offspring in the F2 generation.
Expected number shows a number derived from a Punnett square. The genes for colour and wing shape are
linked.

Phenotype Genotype Expected number Actual number

Brown winged BbNn 0 85

Black winged Bbnn 800 728

Brown wingless bbNn 800 712

Black wingless bbnn 0 75

What is the genetic distance between the colour and wing genes?
85 + 75
𝑑𝐵→𝑁 = 1600
× 100%
= 10 𝑐𝑀
The relative distance between (B, b) and (N, n) is 10 cM.

Example Question 2
Another series of cross-breeding experiments showed that the recombination frequency between wing size and
antenna length is 5%. Draw all possible linkage maps for the genes for colour, wing size and antenna length.
Let (B, b) be wing size
(N, n) be colour
(A, a) be antannaue size
dB→N = 10 cM
dB→A = 5 cM
Map 1 Map 2

We need to find dA→N in order to identify which map is correct.

 • constructing and interpreting information and data from pedigrees and Punnett squares
Pedigrees

A pedigree is a flowchart that shows the relationships within a family over several generations

• Given a good pedigree, we can deduce the genotype of any individual in a family to a certain degree
• Pedigrees are used to:
• Determine if a particular trait is genetically inherited
• Identify and trace genetic disorders over several generations
• Determine the probability of future offspring inheriting these genetic disorders
• Each generation in a pedigree is labelled with a Roman numeral

• For questions about pedigrees, use the following tips:

• Start by identifying if black or white is the recessive trait using these pointers

White is recessive Black is recessive

• Work from the top up, starting from the family with the most recessive members
• Ensure to consider all possible genotypes because there may be more than one

Patterns and trends

Inheritance Generations Affected parents Affected child Gender Example

Two affected parents Equally present

Autosomal Occurs in every Has at least one Huntington’s
can have unaffected in both males
dominant generation affected parent disease
child and females

Two affected parents Equally present

Autosomal Skips Has both carrier Sickle cell
only have affected in both males
recessive generations parents anaemia
children and females

Affected males pass

X-linked Skips Has at least one More females
onto all daughters and Rett syndrome
dominant generations affected parent affected
no sons

Affected mothers have Affected sons can

X-linked May skip affected sons. have unaffected More males
Haemophilia
recessive generations Affected daughters father and carrier affected
have affected fathers. mother

Occurs in every Fathers always pass Affected sons have Only males Y chromosome
Y-linked
generation trait onto sons affected fathers affected infertility
Pedigree analysis

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:
• examining frequency data
Allele frequencies

Allele frequency is the relative rate of occurrence of an allele at a particular locus in a population, expressed as a
fraction or percentage

• It is a measure of the genetic diversity of a gene pool

Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species, and serves as
a way for populations to adapt to changing environments

The gene pool is the set of all or genetic information in any population, usually of a particular species

• When looking at a gene in a population, genes can be monomorphic or polymorphic

Monomorphic
• A monomorphic population only has one allele for the gene (fixed allele) represented by a single letter
• All individuals only have this allele
• Allele frequency for this gene is 100%
Polymorphic
• A polymorphic population has two or more alleles for the gene
• An example is dominant and recessive alleles
• For a gene with two alleles, the two allele frequencies are represented by p and q
• Allele frequencies are represented as decimal percentages.
• All allele frequencies for a single gene must add to 100%

Polygenic inheritance data

Polygenic inheritance occurs when a specific trait is coded for

by many genes

• Genes interact with each other to display a single trait

• No two genes are dominant over one another
• Phenotypes observed in the trait usually occur in a continuum,
where extremities are quite rare and intermediates are common
• Traits are shown as a range, rather than a few outcomes
• Examples are height and skin colour
• Often identified by its distribution in a population, where
frequency occurs in a bell curve
 Frequencies of human height
Sample group
• Before collecting data, an appropriate sample group should be chosen
• Group must be carefully selected to best reflect the frequency of heights in the entire human population

Validity Accuracy Reliability

Diverse range of people should be

Repeat experiment and average
chosen from different genders, age Large sample size (>30)
results
groups, races and demographics

All individuals should have shoes

Preferably a longer ruler or tape
off and be standing against a wall Collate data from an entire class
measure with millimeter markings
with their backs straight

Limitations of allele frequency data

• Phenotypes only provide indirect evidence of the genotype and so are an inaccurate guide to gene frequency
• Dominant alleles may appear more in the phenotype but less in the genotype, and vice versa depending
on the humber of heterozygous individuals
• Recessive alleles may be potentially ignored as they can be carried without appearing in the phenotype
• Traits may be affected by more than one gene, which is not accounted for
• Environment may also have an affect on the expression of traits, also resulting in misleading data
• Collecting data is depended on observational data and obtaining accurate family records

Trends
• A trend is the general tendency of a set of data to change
• Data points may vary slightly, but overall data moves in one direction
• Simple trends include linear and exponential relationships
• For more complex trends with more than one set of data, consider
• Differences in height between data sets
• Slope of lines

Patterns
• Detected when there are similar trends over time
• Pattern is when data repeats in a predictable way
• An example if Gregor mendel and the identification of dominant and recessive alleles

Hardy–Weinberg principle
• Based on the idea that the frequency of alleles in a population remains constant from one generation to another if
none of the evolution influences are acting
• Assumes that a population is in a hypothetical state of equilibrium given:
• No natural selection (alleles are equally beneficial)
• No sexual selection (mating is completely random)
• No mutations (no random modification to gene pool enough)
• No effect from genetic drift (population is large)
• No gene flow (no immigration or emigration)
Estimating genotype frequency
• A modified Punnett square can be used to estimate genotype frequency in the next generation

P1/P2 pA qa • Includes allele frequencies (p and q) for the alleles A and

a
pA p2 AA pq Aa • If one allele frequency is known, genotype of the next
generation can be calculated
•𝑝 + 𝑞 = 1
qa pq Aa q2 aa 2 2
•𝑝 + 2𝑝𝑞 + 𝑞 = 1
 Microevolution

Microevolution is the change in allele frequencies in a gene pool of a population over

generations

• The hypothetical allele frequencies calculated above can be compared to actual allele frequencies
• The difference between these two values indicate microevolution
• Hardy-Weinberg equation can be useful to describe the degree of microevolution that is taking
place over successive generations

• analysing single nucleotide polymorphism (SNP)

Single nucleotide polymorphism (SNP)

Polymorphism refers to individuals with different phenotypes which arise as a result of a mutation, which occurs
in more than 1% of the population

A single nucleotide polymorphism is a substitution of a single nucleotide that occurs at a specific position in the
genome, where each variation is present at a level of more than 1% in the population

• Usually occurs during DNA replication where a single nucleotide is incorrectly

inserted
• It is the most common form of genetic variation, so analysis gives us information of
the genetic variability of a population
• SNPs may be associated with phenotypic change, such as change in appearance,
enzyme function, disease susceptibility or response to drugs
• SNPs may occur within a gene or in a regulatory area near a gene
• May directly affect the gene’s function and the resulting trait
• SNPs are important genetic markers that are currently used to distinguish individuals and to identify things such
as disease susceptibility in individuals

A genetic marker is an identified sequence of DNA at a known site on a chromosome, such as a SNP or STR

SNPs vs mutations

SNPs Mutations

Substitution of a single nucleotides that occurs at a Change that occurs in the DNA sequence and may be a
specific position in the genome change to many nucleotides

Frequency within a population is greater than 1% Frequency within a population is less than 1%

SNPs and polymorphisms in general are types of mutations

Genome-wide association studies

• Individuals within a population show great variation in the genetic markers they have on their DNA
• Gives scientists a relatively easy way to tell individuals apart
• For example, there are approximately 10 million known SNPs in the human genome
• However, a SNP does not necessarily have to be responsible for causing a trait in order to be correlated with it
• If a SNP is close enough to the trait-causing alleles, they may be inherited together
Process
• Scientists look for SNPs that occur in higher frequencies in people with a particular disease, compared
with people who do not have the disease
• In GWAS, computer technology is used to rapidly scan genetic markers across the genomes of many
people to find genetic variations associated with a particular disease
• The SNPs that occur in a higher frequency are said to be associated with that disease
• Some genetic markers are associated with specific traits, but do not necessarily cause them
 • GWAS are based on the presence of a group of SNP markers (haplotype) associated with a trait, rather
than trying to link an individual SNP with a trait (osteoporosis, asthma, diabetes, Alzheimer’s)

Advantages Limitations

Can be used as indicators of disease Data is less accurate if SNPs are further away

Can establish family lineage and determine the genetic Crossing over during meiosis can affect the SNPs that
relatedness of individuals are inherited

Advances in technology allow hundreds or thousands Data is reliable as long as the regions selected are
of SNPs to be analysed at the same time fairly evenly distributed throughout the genome

Faster and cheaper than sequencing whole genomes Cannot assess rare genetic variants

By studying SNPs in groups of 25–50 people, scientists

Unable to fully explain the genetic risk of diseases and
are able to detect polymorphisms occurring in 1- 3% of
has difficulty in identifying true causal associations
the population with approximately 95% confidence

Mapping genes to traits in dogs

Process
• Analysing genes that influenced length, growth pattern and texture of dog coats
• Researchers performed a genome-wide scan of SNPs in 1000 individual dogs representing 80 breeds
• They found that variations in just three genes acting in different combinations account for all different dog hair
types
Significance
• Scientists found the genes involved in dog coats and figured how they work together, rather than just genes
themselves
• This same notion was applied to human health studies
• It is predicted that this approach will help pinpoint multiple genes involved in complex human
conditions such as cancer, heart disease, diabetes and obesity
• Genes can also be associated with embryonic development, cell growth, tissue repair and tumour growth
• Understanding functions of various genes in dogs can help scientists better understand the
mechanisms of many diseases that affect both dogs and humans since the genomes are very similar
Inheritance Patterns in a Population
Can population genetic patterns be predicted with any accuracy?

Investigate the use of technologies to determine inheritance patterns in a population using, for example:
Inheritance and genetics

Inheritance is the process by which an offspring acquires characteristics of its parent organism

Genetics is concerned with the study of genes, the distinct sequence of nucleotides forming a chromosome

• Difference between these two words can be seen in the case of diseases
• Hereditary diseases are also caused by genetic mutations, and can be passed down a line of generations
• Genetic diseases occur as a result of a mutation in an individual’s genome, but may not be hereditary

Genetic testing

Genetic testing is the study of a person’s DNA in order to identify genetic differences or susceptibility to
particular diseases or abnormalities

Molecular genetic Study of single genes or short lengths of DNA to identify variations or mutations that lead
testing to a genetic disorder

Study of chromosomal structure, location and function in cells, including the number,
Cytogenetic testing
appearance, physical location of genes and chromosomal behaviour in processes

Biochemical
Study of enzymes or proteins in the body that may be unusual in some way
genetic testing

• DNA sequencing and profiling

DNA sequencing

DNA sequencing involves obtaining the exact base sequence through a variety of lab techniques

• The Human Genome Project in 2003 was the first attempt to sequence the human genome
• It is the biggest collaborative biological project to date and took 13 years and $5 billion to complete
• Sequencing technologies have progressed since then, with a full genome taking only a few hours and
about $1000 to complete
Pyrosequencing

Pyrosequencing is a next generation sequencing protocol where DNA polymerase uses

fluorescent nucleotides which emit light when they are incorporated onto the DNA of interest

• Relies on specially made nucleotides with attached fluorescent tags

• Each different base has a different fluorescent tag which will emit different wavelengths of light when
incorporated onto the template strand
1) The template strand (DNA of interest) is attached to the bottom of a well with DNA polymerase
2) Sequentially, modified nucleotides (A, T, C, G) are poured into the well then washed out
3) DNA polymerase attaches to the nucleotide and the fluorescent tag is cleaved off, emitting light
4) A camera captures the light, and corresponds the flashes of light with the base
5) The sequence is determined
 Sanger sequencing

Sanger sequencing is a first generation sequencing protocol where special terminating

nucleotides are used to produce different DNA fragments of different sizes

• Sanger sequencing relies on the use of terminating dideoxynucleotides

• These nucleotides can be incorporated into DNA, and they terminate the chain
• Produces a fragment of DNA for every base in the fragment, each differing in length by 1 base
• Although the fragments only differ in length by one base, they can be separated from each other
using gel electrophoresis
• This allows us to read the sequence of DNA
• Although first-generation sequencing protocols can’t read very long fragments and are slower
• However they are highly optimised due to how long we’ve been using them
• Also end up being cheaper per bas
1) The template strand is amplified (copied many times), then placed into 4 separate containers
2) Each container has the terminating nucleotides of one base added to it, with the 3 other bases having
normal nucleotides)
3) DNA polymerase is allowed to produce complementary DNA
4) A camera is used to detect the fluorescent tag placed on the terminating nucleotide
5) The sequence is determined

Applications of sequencing
• Genome sequencing can help trace the inheritance of identified genes through populations
• By sequencing the members of a population, scientists can determine how these genes change over
multiple generations
• Sequencing has already been applied extensive to study evolutionary relationships within and between
species
• These applications are examples of comparative genomics, where multiple genomes are analysed
together for similarities and differences
Accuracy of sequencing
• Shorter sequences have a much higher accuracy rate
• Pyrosequencing and Sanger sequencing can read 500 to 1000 base pairs, and have a 99.9% accuracy
• On the other hand, single-molecule real-time sequencing (Pacific Biosciences) can read 30,000 base
pairs, but have only an 87% accuracy
Ethics of sequencing
• Once a person’s DNA has been analysed, there is the dilemma of the owner of this information and who
can access it
• A person may be incorrectly identified by DNA profiling even if the procedure is carried out accurately
DNA profiling

DNA profiling or DNA fingerprinting is the use of genetic markers to identify individuals and their relationship
with others

• Usually, DNA profiling analyses for polymorphisms (differences) in intron segments

• Introns are not expressed in proteins, and so mutations in these regions do not affect evolutionary fitness
• This leads to the accumulation of mutations and quick divergence of these regions of DNA
• Ideally, a genetic marker is
• Polymorphic and variable within a population
• Not under any selective pressure
• Easy and affordable to work with
• The most common genetic marker used in DNA profiling is short tandem repeats (STRs), also called
microsatellites

Short tandem repeats are small repeating segments of DNA that occur in specific non-coding
regions of the chromosomes

• Common STR motifs include AGAGAG, GCTGCT, and TTTTTT

• If two individuals share the same length of STRs in multiple regions, they are much more likely to be closely
related
• DNA fingerprints are made by a 3 step process:

Polymerase chain reaction (PCR)

Polymerase chain reaction is used to amplify a DNA strand to about 2 billion copies

• The reaction is prepared by mixing heat-stable DNA polymerase, deoxynucleotides and the DNA of
interest together
1) Denaturation: reaction is heated to 95˚C to separate dsDNA (double strand) into ssDNA (single
strand)
2) Annealing: reaction is cooled to 60˚C to allow a DNA primer to attach to the template strands
3) Elongation: reaction is heated to 77 ̊C to allow DNA polymerase to synthesise complementary DNA

Gel electrophoresis

Gel electrophoresis is a technique that separates DNA fragments based on size

1) The DNA fragments are placed at the negative end of an electrically conductive gel
2) An electric current is passed through the gel
3) The DNA fragments will move towards the positive anode at varying speeds, depending on its weight
• DNA is negatively charged and is attracted to the positive electrode
• Heavier DNA fragments will move slower
 • The DNA fragments are labelled with a radioactive marker prior to electrophoresis
• This allows a picture to be taken of the pattern produced

Applications of DNA profiling

• Paternity tests
• Gene flow through populations for management and conservation of
endangered species
• Creating highly accurate pedigrees
• Track the inheritance of particular genes, such as for genetic diseases
• Providing forensic evidence in court

Investigate the use of data analysis from a large-scale collaborative project to identify trends, patterns and
relationships, for example:
• the use of population genetics data in conservation management
Conserving species
• For a population of organisms to remain viable through a changing environment, it must have genetic variation
• This protects the population from selective pressure
• Genetic variation of a population also prevents inbreeding, where mutations and disadvantageous alleles
are conserved and concentrated between generation due to lack of genetically variable mates
• Population geneticists can measure genetic variation by analysing allele frequency and genetic markers
• This produces data which can be used to ensure species conservation
Causes of low genetic variability in endangered species
• If a species is endangered, it means that the
abundance of that population is low
• In efforts to conserve the species, the small number of
individuals will be made to inbreed
• The resultant larger population are all descendants of
the smaller population, meaning that the genetic
variability is lower
• This phenomenon is known as genetic bottlenecking
Using population genetics to conserve species
• Population genetics and sequencing allows scientists
to classify species or identity unknown organisms
• Measuring the genetic variation in a population helps
scientists make predictions about future generations of the species
• Sequencing, combined with phylogenetic analysis, allows scientists to identify invasive species and where
they came from
 • population genetics studies used to determine the inheritance of a disease or disorder
Population genetics

Population genetics is the study of genetic variation within a population

• Includes changes in the frequency of genes and alleles within and among populations over time
• Alleles of all the genes in a particular population are known as the gene pool
• Factors that affect variation within the gene pool:
• Size of population
• Mutation
• Natural selection
• Genetic drift
• Diversity of the environment
• Genetic differences between species can be used to determine the evolutionary history of populations
• Those with the most similar gene pools are most closely related

Genomics

Genomics is the study of the structure, function, evolution, mapping, and editing of genomes

• A genome is all of the genetic material of an organism, consisting of DNA on the genes, noncoding DNA,
mitochondrial DNA and chloroplast DNA

Polymerase chain reaction (PCR) is a method used to amplify, or make several copies of, a
PCR
specific DNA segment

DNA sequencing The process of obtaining the exact nucleotide base sequence of a DNA molecule

The use of genetic markers to identify individuals their relationships with others and to
DNA profiling
determine an individual's DNA characteristics

A collection of microscopic DNA spots attached to a solid surface used to measure the
DNA microarrays expression levels of large numbers of genes simultaneously or to genotype multiple regions
of a genome

Determining disease inheritance

• We use pedigrees when we have plentiful data available detailing medical history and conditions (the disease in
question must also be a fairly simple one)
• When diseases are more complex (polygenic traits), or when there is not enough data available, population
genetics can provide us with more useful information
• Techniques in population genetics, such as allele frequency calculation and genetic equilibrium, allow us to track
where a genetic disease came from and how it is spreading
• For example by calculating the allele frequencies of the disease in question in every generation, we can
see whether the disease is spreading or receding
• Studying monozygotic twins can give us information about disease that we think may be genetically inherited
• If a condition occurs in both identical twins less than 100% of the time, it is not just genetic (there is an
environment component to it)
• Psychological research is an example of where this is applied
• Psychological diseases are often a very complex interaction between genetics and environment
• This information can only be teased out through extensive twin studies
• For example, if an identical twin has schizophrenia, there is a 50% chance that the other will as well
• In contrast, the same relationship only produces a 10% change in fraternal twins
Case study – Breast and ovarian cancer
• Case study of an inherited trait in a population
• Breast screens involving a mammogram are used to identify abnormalities in
breast tissue
• Mutation of the BRCA1 and BRCA2 genes put women at a much higher risk of
developing one particular ‘basal-like’ breast cancer
• BRCA1 and BRCA2 are tumour suppressor genes found on chromosome 17 and
chromosome 13
• Responsible for coding for proteins that repair genes involved in
regulating the process of cell division
• Mutations of these genes means that the genes that control cell division
are not repaired, which ultimately results in uncontrolled cell division
associated with cancer
• Mutations are inherited and carried by 1 in 600 women
• Presence of these mutated genes increase risk of developing this cancer by 85%

• population genetics relating to human evolution

Case study – Movement of our ancestors out of Africa

Aim
To use data from secondary source investigations to determine the route taken by our ancestors when they
migrated out of Africa

Background
• mtDNA is ideal for tracing human evolution because it is inherited only through the maternal line and is not
subject to remobinations, as nuclear DNA is
• There are 1016 molecules of mtDNA within every human, each usually identical to the others
• Mean rate of mtDNA divergence within humans is 2–4% per million years
• Worldwide survey of mtDNA drawn from 147 people from 5 geographic locations where conducted
• Sub-Saharan Africa (n = 20)
• Asian from China, Vietnam, Laos, the Philippines, Indonesia and Tonga (n = 34)
• Australian Aborigines (n = 21)
• Caucasians from Europe, North Africa and the Middle East (n = 46)
• Aboriginal New Guineans (n = 26)
Data
The table below shows the mDNA divergence within and between the five human populations

Sequence diversion (%)

Population
African Asian Australian Caucasian New Guinean

African 0.47

Asian 0.45 0.35

Australian 0.40 0.31 0.25

Caucasian 0.40 0.31 0.27 0.23

New Guinean 0.42 0.34 0.29 0.29 0.25

Case study – Population genetics data and conservation of the koala (Phascolarctos cinereus)
Background
• Tissue samples were obtained from 662 wild koalas
• Collaboration between Port Macquarie Koala Hospital, Australia Zoo Wildlife Hospital and Australian Museum
Tissue Collection
• Mitochondrial DNA control region (mtDNA CR) of each tissue sample was analysed by next-generation
methods, such as pyrosequencing
• Used to identify different haplotypes (a group of genes within an organism that was inherited together from a
single parent) in the koala tissue
• In koalas, the genes are inherited down the mother’s lineage as mtDNA
• Two or more koalas that have the same haplotype will be closely related to each other
Haplotypes
• Haplotypes can be used to compare individuals of different populations in order
to determine which populations are closely related, and to map their recent
evolutionary history
• Haplotype network is a 2D summary of genetic diversity within a group
• Each circle represents a unique haplotype
• Size of circle is proportional to the number of individuals that belong to
that haplotype
• Lines connect each haplotype to its most similar relative
• Number of bars on the lines represent the mutational steps between
haplotypes, indicating genetic divergence
Aims
• To investigate the degree of diversity in koala populations
• To interpret genetic data and diagrams and infer trends and patterns
Data