Preface
Welcome to Biology, your new favourite subject! Especially with this updated and revised
syllabus, I promise you're going to love this course. Your year will consist of four modules,
covering Heredity, Genetic Change, Infectious Disease and Non-infectious Disease and Disorders. Basically, it's half molecular biology, half medical biology! Keep in mind the overall
aims in the form of the key inquiry questions of each section when studying so that you
approach each of them with the right mindset.
In terms of what you need to remember from the Year 11 syllabus, evolution is a must, and
understanding the basic concepts for cells and systems is also important so that you can
approach the Year 12 content with all the important terminology in mind.
It's important when studying throughout the year that you attempt to understand the key
concepts. In these notes, I have flagged what I think are the most fundamenta l ideas from
the syllabus, so as you come across them, make sure you understand them fully. Personally, I always liked to relate content to the real world. Think about where these biological
phenomena occur in nature, so that when you're in an exam you can look out the window
and easily trigger your memory! That's the great thing about Biology - it's all around us, and
you can constantly be learning about it!
Although at times the course can seem to be content heavy, with organisation, consistent
revision, and practice, you'll be totally fine. The course rests on a few key concepts. If you
understand these, chances are you'll be able to handle everything else. If you're less of a
daredevil, creating effective revision notes at the end of each week is the best way to keep
on top of the content. But be frugal - don't include unnecessary details; otherwise you'll be
overwhelming yourself with revision. Just identify the concept, give few detailed examples
where necessary, and think critically about what you might actually be asked in an exam.
Keep it simple!
I love studying Biology because I approach it in a creative way. Essentially, it's a whole lot
of different, intertwined systems, so I like to draw them out. So if you're like me, find the
biggest piece of paper you can, and fill it up I Draw out DNA structure, outline each step
in protein expression. See how they fit together, why it makes sense, and colour it in as a
memory aide. Sometimes these easy study exercises can make all the difference!
Lastly, don't forget about your practicals. Sometimes they can be confusing, and little details are easy to miss, so I would suggest drawing up a scaffold at the beginning of the year,
and filling it out for each practical. Include an aim, hypothesis, variables, materials, risk
assessment, method, results, discussion, and conclusion. That way, each of your experiments are consistent, and it's easy to flick back through for exams. Once again, to help you
remember your practicals, think about the big picture. What is each experiment trying to
explain about a fundamental aspect of Biology ? Your core content and practicals are meant
to complement each other, so treat it like that when you're studying.
Best of luck for Biology!
-
ll ■ ll ■ Ua at ■ I ■ II
Copyright © 2018 lnStudent Publishing Pty. Ltd.
Madeleine Wainwright
iii
Preface
Welcome to Biology, your new favourite subject! Especially with this updated and revised
syllabus, I promise you're going to love this course. Your year will consist of four modules,
covering Heredity, Genetic Change, Infectious Disease and Non-infectious Disease and Disorders. Basically, it's half molecular biology, half medical biology! Keep in mind the overall
aims in the form of the key inquiry questions of each section when studying so that you
approach each of them with the right mindset.
In terms of what you need to remember from the Year 11 syllabus, evolution is a must, and
understanding the basic concepts for cells and systems is also important so that you can
approach the Year 12 content with all the important terminology in mind.
It's important when studying throughout the year that you attempt to understand the key
concepts. In these notes, I have flagged what I think are the most fundamenta l ideas from
the syllabus, so as you come across them, make sure you understand them fully. Personally, I always liked to relate content to the real world. Think about where these biological
phenomena occur in nature, so that when you're in an exam you can look out the window
and easily trigger your memory! That's the great thing about Biology - it's all around us, and
you can constantly be learning about it!
Although at times the course can seem to be content heavy, with organisation, consistent
revision, and practice, you'll be totally fine. The course rests on a few key concepts. If you
understand these, chances are you'll be able to handle everything else. If you're less of a
daredevil, creating effective revision notes at the end of each week is the best way to keep
on top of the content. But be frugal - don't include unnecessary details; otherwise you'll be
overwhelming yourself with revision. Just identify the concept, give few detailed examples
where necessary, and think critically about what you might actually be asked in an exam.
Keep it simple!
I love studying Biology because I approach it in a creative way. Essentially, it's a whole lot
of different, intertwined systems, so I like to draw them out. So if you're like me, find the
biggest piece of paper you can, and fill it up I Draw out DNA structure, outline each step
in protein expression. See how they fit together, why it makes sense, and colour it in as a
memory aide. Sometimes these easy study exercises can make all the difference!
Lastly, don't forget about your practicals. Sometimes they can be confusing, and little details are easy to miss, so I would suggest drawing up a scaffold at the beginning of the year,
and filling it out for each practical. Include an aim, hypothesis, variables, materials, risk
assessment, method, results, discussion, and conclusion. That way, each of your experiments are consistent, and it's easy to flick back through for exams. Once again, to help you
remember your practicals, think about the big picture. What is each experiment trying to
explain about a fundamental aspect of Biology ? Your core content and practicals are meant
to complement each other, so treat it like that when you're studying.
Best of luck for Biology!
-
ll ■ ll ■ Ua at ■ I ■ II
Copyright © 2018 lnStudent Publishing Pty. Ltd.
Madeleine Wainwright
iii
Part I
Module 5: Heredity
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1
1. 1 Sexual and asexual reproduction methods
Topic 1
Reproduction
SYLLABUS:
Inquiry question : How does reproduction ensure the continuity of a species?
1.1 Sexual and asexual reproduction methods
( SYLLABUS:
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:
•
•
•
•
•
Animals : advantages of external and internal fertilisation
Plants: asexual and sexual reproduction
Fungi: budding, spores
Bacteria: binary fission
Protists: binary fission, budding
Reproduction is the process of creating offspring, either by sexual or asexual processes.
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Organism
Method of reproduction
Advantages
Disadvantages
Animals
Sexual re12roduction:
- Gametes are produced
by parent organisms
through meiosis.
- Each gamete contains
half the necessary number
of chromosomes.
- The male gamete (sperm)
fertilises the female gamete
(ovum or egg) by either
internal fertilisation
(mammals) or external
fertilisation (fish such as
salmon).
- Fusion of gametes results
in production of a zygote,
which contains a
combination of genetic
material from both parental
organisms.
Sexual re12roduction:
- Combination of
chromosomes from two
organisms increases
variation, which assists
with survival.
External fertilisation :
- Large number of
gametes produced
generally means more
offspring. It is also a
simpler behavioural
process which does not
require mating rituals.
Internal fertilisation:
- Increased likelihood
of fertilisation as egg
and sperm are in close
proximity, with
increased protection
from environment
leading to higher
survival rates of
offspring.
Sexual re12roduction:
- Requires mating of two
organisms which is
dependent on syncing fertility
cycles, and the production of
offspring is slower and less
prolific than asexual
reproduction .
External fertilisation:
- Species must produce large
numbers of gametes, which
requires extra energy. It also
requires a watery
environment (may be difficult
for amphibians).
Internal fertilisation :
- Fewer offspring are
produced, and it is more
difficult to bring males and
females into contact. There is
a higher risk of sexually
transmitted infections passing
between organisms.
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'
1. 1 Sexual and asexual reproduction methods
Plants
Fungi
ll ■ ll ■ Ua at ■ I ■ II
Sexual reeroduction: (e.g.
flowering plants)
- Flowers are the reproductive
organs of sexually reproducing
plants.
- As with animals, offspring
are produced by the fusion of
two haploid gametes.
- Male gametes (pollen) are
produced and transferred to
the female ovules. This
process is called pollination,
and can be assisted by wind or
insects.
- After pollination, fertilisation
occurs and the ovules grow
into seeds in a fruit, which
disperse once ripe. The seed
is then freed from the fruit.
Asexual reeroduction: (e.g.
vegetative reproduction)
- Structural modifications to
the stem or roots of the plant
results in the production of
new individuals, without the
need for production of seeds
or spores
Sexual reeroduction:
- Creates a genetic diversity
within a species, leading to
higher levels of disease
resis tance and a greater
ability to adapt to changing
conditions.
Asexual reeroduction:
- Offspring are clones of
parent plants, meaning
favourable traits are
effectively passed through
generations. This is
economically advantageous
for farmers to ensure
consistency in their crops.
- It is less energy intensive
than sexual reproduction,
meaning the population can
increase rapidly and exploit
suitable habitats quickly.
Sexual reeroduction:
- Plasmogamy: two
genetically different cells fuse
together.
- Karyogamy: the nuclei fuse.
- Meiosis: gametes are
generated which produce
spores that are distributed into
the environment.
Asexual reeroduction:
- Fragmentation : pieces of
hyphae can separate and
become new colonies.
- Budding: the nucleus
divides and a bulge forms in
the side of the cell, which is
then split off by cytokinesis,
and the bud detaches itself
from the mother cell.
- Spores: mitosis produces
genetically identical cells to the
parent, which are distributed
into the environment by wind
or vectors.
- Production of spores allows
for offspring to be widely
distributed in the
environment, increasing
colonisation. They can also
be produced easily in large
numbers.
- Combination of both sexual
and asexual methods means
that fungi may choose when
and how to propagate.
Asexual reproduction is fast
and not energy intensive, so
can occur even used when
the organism is under stress.
Sexual reproduction
increases genetic variability
in species.
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Sexual
reeroduction:
- Can prevent
favourable genes
from being passed
to offspring (if it's a
recessive gene),
which is not
possible for an
isolated organism.
Asexual
reeroduction:
- Pathogens may
spread easily from
parent to offspring.
This reduction in
genetic diversity
increases the
susceptibility of
species to new
diseases, and
evolution is reduced
due to the lack of
genetic variation.
-
- Asexual
reproduction may
result in offspring
which are only
suited to one
habitat.
3
1. 1 Sexual and asexual reproduction methods
Bacteria
Asexual reproduction : (binary fission )
- A single cell divides into two identical
daughter cells.
- Begins with DNA replication where the
genetic information of the bacteria is copied
and divided in two.
- The cell elongates and splits into two
(cytokinesis), producing daughter cells with
identical genomic information (i.e. clones of
the parent).
- Very rapid (e.g.
E.coli can
replicate as fast
as every 20
minutes in the
right conditions),
and only requires
a single organism
in order to
produce
offspring.
- Lack of genetic
diversity in the resulting
population lowers
chance of organism
survival. However, this
may be overcome by
high rates of mutation
during DNA replication,
and Horizontal Gene
Transfer (HGT) by
plasmids, which can be
passed from bacteria to
bacteria.
Protists
Sexual reproduction:
- For haploid protists, two haploid (1 n) cells
fuse to form a new cell, a zygote. Genetic
material is combined in a new, fused nucleus.
The zygote undergoes meiosis to form new
haploid cells.
- For diploid protists, adult cells undergo
meiosis to produce 4 gametes. Gametes fuse
during fertilisation to form a diploid zygote,
which will grow into a diploid adult.
Asexual reproduction :
- Binary fission (as above with bacteria) is the
predominant method of asexual reproduction
for protists.
- Budding occurs when a new organism
grows from the body of the parent organism
to form a new colony.
- The ability for
some protists to
reproduce
sexually provides
an evolutionary
advantage over
primitive,
asexually
reproducing
protists. Sexual
reproduction
allows for greater
variation within a
species, as
genes are mixed
recombinantly.
- Asexual reproduction
can often be quite
disadvantageous to
host organisms during
pathogenesis. Fast
reproduction at little
energy cost to the
protist makes them
more effective as
disease-causing
agents.
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Sexual reproduction
Advantages:
• Variation in the population
• Species better able to adapt to their environments
• Disease events less likely to affect entire
population
Disadvantages :
• Large time and energy investment
• Requires a mating partner
• Fewer offspring produced
11 ■11■ Ua at■I ■II
Asexual reproduction
Advantages:
• Rapid population of an environment
• No requirement for mates
• Able to be enacted under external pressures (i.e.
quick, and not energy intensive)
• No requirement for investment in care of offspring
Disadvantages:
• Lack of diversity
• May result in large-scale extinction events
• Reduced ability to adapt to external pressures
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1.2 Fertilisation and implantation
1.2
Fertilisation and implantation
SYLLABUS :
Analyse the features of fertilisation, implantation, and hormonal control of pregnancy and birth in mammals.
K EY P OINT:
Fertilisation: the fusion of gametes to initiate the development of a new organism.
Implantation : when a fertilised egg adheres to the wall of the uterus.
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Sexual reproduction begins with development of gametes. In females, this occurs in the ovaries, where
ovum (eggs) are produced and released into the fallopian tubes. There is a 12 - 24 hour window after release called ovulation, during which fertilisation, the fusion of an egg and a sperm cell, can be successful.
Once fertilisation has occurred, the zygote begins to divide and migrate from the fallopian tubes into the
uterus. Here, the now blastocyst embeds itself into the wall of the uterus, called the endometrium. This
is a nutrient-dense lining which will provide oxygen and nutrients to the growing embryo. This occurs about
7 days after fertilisation , establishing the pregnancy.
1.2.1
Hormonal contraception
Normal cycles of fertility are controlled by levels of hormones within the body. In order to prevent pregnancy
and birth, hormonal contraceptives vary the levels of important sex hormones in the body in order to prevent
ovulation (the release of an egg from the ovaries), fertilisation, and implantation .
There are two main types of hormonal contraceptives: combination methods (delivering both estrogen
and progestin) and progesterone-only methods. Oral contraceptive pills are a common form of hormonal
birth control which work by:
• Preventing the release of an ovum from the ovaries, inhibiting ovulation so that there is no egg to be
fertilised
• Thickening the cervical mucus to inhibit sperm mobility into the uterus, thus preventing fertilisation
• Changing the lining of the uterus so that implantation is difficult
Other forms of hormonal contraception include contraceptive patches, vaginal rings, intrauterine contraception (such as IUDs), and injectable contraception.
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5
1.3 Manipulating reproduction in agriculture
1.3
Manipulating reproduction in agriculture
SYLLABUS :
Evaluate the impact of scientific knowledge on the manipulation of plant and animal reproduction in
agriculture.
The increase in and proliferation of scientific knowledge has led to huge advancements in agriculture,
enabling processes to become more efficient and productive. By understanding the fundamental principles
of reproduction, we have been able to manipulate them in order to produce desired outcomes.
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• Selective breeding :
- This is based on the understanding that phenotypic traits are hereditary (i.e. able to be passed
from parent to offspring), so farmers selectively mate plants with desirable traits.
- This may influence cross-breeding or pure-breeding practices.
- Many current breeds used in agriculture have been produced through selective breeding practices (e.g. Jersey or Angus cows).
• Artificial insemination:
- Benefits:
• Timing (able to synchronise births)
• Passing of favourable traits (e.g. increased milk production or quality of meat)
• Ensuring successful pregnancy increases yields
- Method:
1. Detection of female cows in oestrus (animals 'in heat' i.e. sexually receptive)
2. Collection of semen (may be performed manually using an artificial vagina, or by stimulation)
3. Insemination usually preformed using an insemination gun which shoots semen into the
cervix of the desired animal
• Artificial pollination:
- Benefits:
• Cross-breeding of favourable traits
• Self-pollination (i.e. creation of genetically similar offspring)
• Ensuring successful pollination of all plants, resulting in high crop yields
- Method:
1. Pollen (sperm) removed from stamen of one plant
2. Pollen applied to the stigma of another plant
3. Pollen fertilises the ovum
• Genetic engineering:
- Knowledge of DNA structure and improvement of genetic techniques (e.g. gene cloning and
transgenics) has allowed agriculturalists to manipulate organisms on a fundamental level. This
has allowed the introduction of new desired traits into organisms, such as:
• Bt cotton - insect resistance
• Golden rice - increased nutritional value
• Strawberries - frost-resistance
- It is estimated that 170.3 million hectares of GM crops were grown globally in 2012.
For more information, see page 45 for the section on genetic technologies in Module 6.
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Cell Replication
Topic 2
Cell Replication
SYLLABUS :
Inquiry question: How important is it for genetic material to be replicated exactly?
2.1
Processes of cell replication
SYLLABUS:
Model the processes involved in cell replication, including mitosis and meiosis, and DNA replication
using the Watson and Crick DNA model, including nucleotide composition, pairing, and bonding.
2.1.1
Mitosis
K EY P OINT :
Mitosis: cell division resulting in two identical daughter cells, with the same number and kind of chromosomes as the parent cell.
lnterphase
• Cell prepares itself for division.
• DNA replication occurs to produce two copies of each
chromosome.
Prophase
• Duplicated chromosomes condense.
• The mitotic spindle forms at either end of the dividing
cell. These spindles are composed of strands of microtubules which lengthen and shorten to pull chromatids
apart.
Prometaphase
• Nuclear envelope breaks down.
Metaphase
• Pairs of condensed chromosomes (called sister chromosomes) line up along the equator of the cell.
Anaphase
• Sister chromatids are drawn to opposite poles of the dividing cell by the mitotic spindle.
• Microtubules bind to chromatids at the kinetochore and
begin to shorten, separating pairs from each other.
• There is now only one copy of each chromosome at
either end of the cell.
Telophase
• Two new nuclear envelopes begin to form around the
separated sister chromatids.
Cytokinesis
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• Two daughter cells are separated by the tightening of a
ring of proteins around the middle of the dividing parent
cell - the two nuclei are squeezed apart.
• Cytokinesis occurs simultaneously to anaphase and telophase - the pinching of the cellular membrane begins to happen as chromosomes are separated and new
nuclei are formed.
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7
2. 1 Processes of cell replication
2.1.2
Meiosis
K EY P OINT:
Meiosis: cell division resulting in four daughter cells (gametes), each with half the number of chromosomes of the parent cell.
Meiosis I
Meiosis II
lnterphase
• As with mitosis, DNA replication occurs to
produce two copies of each chromosome.
Prophase I
• Chromosomes condense and the nuclear envelope breaks down (prometaphase).
• Homologous chromosomes pair up, aligning
next to each other along their full length.
• Crossing over occurs between homologous
chromosomes. This is when segments of
DNA at the same locus swap to create new
gene combinations.
Metaphase I
• Homologous pairs (not individual chromosomes) line up along the equator of the separating cell.
Anaphase I
• Homologous pairs are separated, pulled to
opposite ends of the cell by the meiotic
spindle.
• Sister chromatids remain attached.
Telophase I
• Chromosomes arrive at opposite ends of the
cell.
• Two diploid daughter cells are formed by cytokinesis.
Prophase II
• Chromosomes condense and the nuclear envelope breaks down.
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Metaphase II
• Chromosomes line up along the equator of
the dividing cells.
Anaphase II
• Sister chromatids are separated by the
spindle microtubules and pulled towards opposite poles of the cell.
Telophase II
• Cytokinesis splits the dividing cell into two
new cells.
• Nuclear membranes form around each set of
chromosomes.
• Four haploid daughter cells are formed, each
containing half the number of chromosomes
of the parent ®
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2. 1 Processes of cell replication
2.1.3
DNA replication models
Model of DNA structure (Watson and Crick)
Deoxyribose nucleic acid, or DNA, is a double helical nucleic acid molecule which carries genetic information, encoded as sequences of nucleotide bases. DNA is double stranded, composed of stacked
and complementarily bonded nucleotides.
A single nucleotide is a phosphate, bound to a deoxyribose sugar group, bound to a nitrogenous base
(either Adenine -A, Thymine- T, Guanine - G, or Cytosine - C).
Nucleotides are phosphates bonded to sugar, forming a sugar-phosphate backbone. Inwardly facing nitrogenous bases are bonded C - G or A - T, by hydrogen bonding.
The process of DNA replication is as follows:
1. Initiation : ('unzipping') the enzyme helicase unwinds and separates complementary DNA strands
by breaking the hydrogen bonds between nitrogenous bases.
2. Elongation : small pieces of RNA called primers bind to the ends of the strands, signalling the
starting point of replication. DNA polymerase binds to separated DNA strands at primer sites, and
begins to add new base pairs which are complementary to the strand. For example, where the
polymerase recognises an A, it will bind a T.
E XTENSIO N :
Though this level of detail is unlikely to be examined, it's important to note that DNA is only replicated in the 5' to 3' direction. As DNA is antiparallel (one strand runs 5' to 3' and the other 3'
to 5'), replication will be continuous for one strand, the leading strand, and discontinuous for the
other strand, the lagging strand.
3. Termination: DNA polymerase reaches the end of the DNA molecule, and two identical daughter
strands have now been produced. Strands recoil into the double helix shape, creating two new and
beautiful DNA molecules ! Nuclease enzymes essentially 'proofread' the double helix structures.
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9
2.2 Continuity of species
2.2
Continuity of species
SYLLABUS:
Students assess the effect of the cell replication processes on the continuity of species.
2.2.1
DNA replication
• DNA is the fundamental hereditary unit, which directs all processes in a cell.
• Reproduction of cells is dependent upon DNA replication, as the creation of new cells requires more
DNA to be produced.
• By copying the genetic material of a cell, repllication ensures that information important for life is
transferred down through the generations.
• If DNA were not replicated before mitosis and meiosis, cell division would halve the amount of DNA,
and resulting cells would die due to inadequate amounts of genetic information.
• DNA replication is a high-fidelity process, ensuring that daughter DNA strands carry the same gene,
and encoding all the essential proteins for life.
2.2.2
Mitosis
• Mitosis is essential for development and growth of organisms. Mitosis increases the number of cells
in an organism, allowing for development of a multicellular body.
• Mitosis also allows for old cells to be replaced, ensuring that tissues continue to function effectively
and efficiently.
• For organisms like humans, mitosis allows us to develop to maturity when we can pass our genetic
information onto offspring through sexual reproduction.
• Some organisms reproduce by asexual reproduction, which is facilitated by mitosis. In these cases,
mitosis creates the next generation of organisms.
2.2.3
Meiosis
• Gametes are the end product of meiosis - haploid cells with half the number of requisite chromosomes to make a happy, fu ll cell capable of all the things cells can do!
• The combination of gametes during sexual reproduction creates new organisms, which have inherited
traits from both parents.
• Unlike mitosis, meiosis purposefully introduces variation. Processes of crossing over, independent
assortment and random segregation allow for combinations of different alleles, increasing variation
in offspring and the wider population (see pages 18-21 for more on this).
• Genetic diversity (introduced by meiosis and sexual reproduction) is very important for the continuity
of species, as mutation and variation are essential factors for survival and evolution.
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DNA and Polypeptide Synthesis
Topic 3
DNA and Polypeptide Synthesis
SYLLABUS:
Inquiry question: Why is polypeptide synthesis important?
3.1
3.1.1
Genetic material storage
Eukaryotes
SYLLABUS:
Construct appropriate representations to model and compare the forms in which DNA exists in eukaryotes and prokaryotes.
_j
The defining feature of eukaryotic cells is that they have a nucleus - this is where their DNA is stored.
Eukaryotic DNA is found wound tightly around small proteins called histones. This helps the DNA to
condense into a relatively small amount of space. Coiled DNA forms supercoils, which are then packed
together to form chromosomes.
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On average, eukaryotes have larger genomes than prokaryotes, with long non-coding and repetitive sequences. Eukaryotic DNA is also linear - it does not link up like prokaryotic DNA.
3.1.2
Prokaryotes
Prokaryotic cells have free-floating , circular chromosomes, found in the cytoplasm. The DNA is not bound
or packaged by proteins (unlike eukaryotic DNA which
is wound by histones).
Prokaryotes have smaller, more compact genomes,
with very little repetitive DNA. Prokaryotes also have
small, extra-chromosomal segments of DNA called
plasmids.
Plasmids are able to be transferred
between organisms to pass genetic material horizontally within generations.
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11
3.2 Polypeptide synthesis processes
3.2
Polypeptide synthesis processes
Transcription and translation are the processes
used to turn genetic information (i.e. DNA) into structural and functional molecules used in cells (i.e. proteins). Our cells contain a large amount of information, stored as DNA. This information needs to be expressed somehow. We can imagine DNA as a blueprint, which we read, and then from it we assemble the
building blocks of the cell: proteins.
The processes used to express genetic information aire called transcription and translation.
3.2.1
Transcription
K EY P OINT:
Transcription: the process of turning genetic information stored in the DNA into an intermediary molecule mRNA.
Q.
We have a lot of DNA in our cells, containing tens of thousands of genes, and even more non-coding DNA.
DNA is very important because it contains all of the information that makes up our cells, and so we need to
keep it safe. It is for these reasons - complexity and security - that we use an intermediary molecule called
mRNA to transmit information out of the nucleus for processing. mRNA is a messenger ribonucleic acid.
It is chemically quite similar to DNA, except that it is single stranded, contains a ribose sugar instead of
a deoxyribose sugar, and instead of a thymine (T) nitrngenous base, it has uracil (U) in its place. The cell
produces mRNA in a process called transcription. Similar to replication, the DNA is read by a polymerising
enzyme, which progressively adds complementary nucleotides (NTPs) to create a new molecule.
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Here are some simplified steps outlining the process of transcription:
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1. RNA polymerase binds to the promoter sequence upstream from a gene.
2. As RNA polymerase moves along the DNA strand, a small region of DNA is unwound.
3. RN A polymerase 'reads' the DNA template strand, matching complementary free-floating nucleotides (NTPs) to create a chain containing the same coding information.
4. A mRNA molecule is sequentially synthesised by RNA polymerase, as it continues to move along the
DNA strand.
5. Terminator sequences end the transcription of DNA, and the newly formed mRNA molecule is released.
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3.2 Polypeptide synthesis processes
After the mRNA molecule has been produced, there are a few modifications which occur, including addition
of molecules to the ends of the strand to protect it from degradation as it moves through the cell. The
mRNA molecule can also be edited at this stage in a process called splicing. This increases the variability
of information that can be expressed from a single gene.
In eukaryotes, the mRNA molecule will travel out of the nucleus through the nuclear pores, so that it can
be translated in the endoplasmic reticulum. For prokaryotes, which do not have a nucleus or membranebound organelles, transcription and translation both occur in the cytosol of the cell.
3.2.2 Translation
K EY P OINT:
Translation: the process of turning information encoded as mRNA into a polypeptide chain.
The genetic sequence of the mRNA molecule is 'read' by ribosomes. The code is translated in groups of
three nucleotides called a codon. However, some of our genetic code is redundant, meaning that there are
more codons than amino acids, so there is a little bit of overlap (i.e. both CCU and CCA encode for proline,
as you can see in the table below). This provides some leniency in case mutations are made to the ONA
during replication or mRNA during transcription.
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Second Base in Codon
u
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UGA Stop A
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CUC
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CGA Arg
CAA}
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The translation process is as follows:
1. mRNA docks to a ribosome.
2. The ribosome matches a complementary tRNA molecule to the mRNA by matching codon/anticodon sequences.
3. As subsequent tRNA molecules dock, a polypeptide bond is formed between the adjacent amino acid
molecules which they carry.
4. As the mRNA molecule continues to be read, the polypeptide chain is elongated by continued
addition of amino acids.
5. When a stop sequence is reached, the ribosome releases the mRNA and polypeptide molecule.
6. The polypeptide folds and undergoes post-translational modifications, resulting in a mature protein
ready for use in the cell.
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13
3.2 Polypeptide synthesis processes
G..-ow;"j pe.p+id.e.
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In summary:
transcription
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translation
DNA - - --- mRNA - - - Polypeptide
I remember the differences between the processes by thinking:
•
Transcription is literally just transcribing or 'copying.' You're using the same basic units (nucleotides) to create an intermediary molecule (RNA).
• Translation is actually changing the 'language.' We are turning information stored as nucleotide
sequences into amino acid sequences.
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3.2.3
Function and importance of polypeptide synthesis
(/)
00 •
Polypeptide synthesis is the method used to produce proteins in cells. As we will discuss in the next syllabus
dot point, proteins are super important for cell and organism structure and function. Effective polypeptide
synthesis is particularly important for multicellular organisms, which require a high degree of coordination ,
facilitated by protein interactions. Without protein synthesis, life probably wouldn't exist! And if protein
synthesis does not work properly, diseases such as cancer may occur.
Polypeptide synthesis is also important for increasing the complexity of organisms. If we compare the
number of genes in organisms to the number of proteins, we can see a large increase in the ratio of
proteins to genes as organisms become more complex.
Species
I Genes I
Proteins
Escherichia coli
4,288
~4,700
Saccharomyces cerevisiae
6,532
~12,000
Homo sapiens
20,067
~1,000,000
This is because at each stage in the polypeptide synthesis process - transcription and translation - there
are opportunities for variation. Segments of mRNA may be rearranged to produce different variants from
a single gene, and a variety of post-translational modifications mean that polypeptides may be edited to
perform different functions.
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3.3 Protein structure and function
3.2.4
How genes and the environment affect the phenotype
K EY P OINT:
Genotype: the genome or genetic make-up of an organism.
Phenotype: the outward appearance of an organism, including observable traits, biochemistry, and
physiology.
Whilst an organism's genetic make-up will remain static throughout its life, its observable traits may change
over time as a result of their environment. Our genotypes allow us to predict our phenotypes to a certain
extent, as we will discuss further in the next section. Genetic information inherited from parent organisms
serve as a list of instructions, sets of genes which are read out, telling the cell what to express to create
phenotypes.
However, external factors, such as the environment, lhave a say in how our genes are expressed. Certain
genes may be 'switched on' at different stages of development (such as homeobox genes during embryogenesis). or only expressed in response to certain events (such as extreme heat or cold). A great human
example is identical twins, who have the exact same genetic code, but who often develop different characteristics as they age.
We can consider genotype as containing a range of phenotypic possibilities due to different environmental
influences.
3.3
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Protein structure and function
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( SYLLABUS:
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Investigate the structure and function of proteins in living things.
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3.3.1
Structure
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Proteins are all composed of the same fundamental building blocks : amino acids. Amino acids are organic
compounds which have a central carbon, bound to an amine group, a carboxyl group, a hydrogen, and
a A-group. The way amino acids are differentiated is by the R-group, which varies in each type of amino
acid, and gives the molecule different properties. These side group properties define the structure and
function of the protein overall.
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Amino acid structure
Amino
Hy(Hr
Ca rbox I
- c
R-grou p
(va riant)
Amino acids become part of polypeptide chains through the formation of polypeptide bonds, which are
made between the amine and carboxyl groups in a condensation reaction. This is what occurs during
polypeptide synthesis in the ribosome, as described in the previous section.
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15
3.3 Protein structure and function
Amino Acid #1
Amino Acid #2
Di peptide
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3
,
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Polypeptide chains fold to become proteins. This folding process is influenced by interactions between
amino acid side groups. For example, amino acids with non-polar (hydrophobic) side chains will usually
be found on the inside of proteins, because they do not like to be bound with water. Inversely, amino acids
with polar (hydrophilic) side chains will usually be found on the outside of protein structures, because
they are attracted to water. Therefore, where there is a non-polar amino acid, the polypeptide chain will be
folded inwards in that area. Below is a summary of the four steps in the folding and formation of proteins.
Primary structure: the sequence of amino acids.
The primary structure of proteins refers to the arrangement of amino acids sequences in a polypeptide chain
(i.e. the placement of a methionine, next to a proline,
next to a valine etc.) determined by the mRNA code,
and formed during translation.
Secondary structure: the formation of alpha
helices and beta sheets. Hydrophobic interactions
and hydrogen bonding between amino acid side
groups influences the formation of two core structures: alpha helices and beta sheets.
Tertiary structure: formation of overall 30 shape. The
protein backbone will twist and bend to achieve maximum stability. This is facilitated by side group interactions; for example, disulphide bridges between
cysteines, salt bridges between positively and negatively charged side chains, or hydrophobic interactions.
The total of interactions within the polypeptide chain
will result in the formation of a 30 structure.
Quaternary structure: interaction of protein
subunits. Some proteins are composed of multiple polypeptide subunits. The interaction of
these influences quaternary structure. For example, haemoglobin is composed of four individual subunits, bound together to form the final
complex.
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Copyright © 2018 lnStudent Publishing Pty. Ltd.
3.3 Protein structure and function
3.3.2
Function
Proteins are seriously awesome, and they are so important to the function of living things. They perform
most of the work inside of cells, and are vital to tissue and organ structure, function, and regulation . Some
functions of proteins include:
Structure and support
Proteins form the basis of the
cellular cytoskeleton , as well as
composing important
macro-molecular structures such as
connective tissues, hair, and nails.
Transport and storage
Proteins in the cellular membrane
are responsible for trafficking
molecules into and out of the cell.
They may also carry small
molecules around to body.
Storage proteins reserve important
biological materials for use in the
body (for example, ferritin stores
iron).
Enzymes
cl
~
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Proteins may function as biological
catalysts, carrying out thousands of
chemical reactions inside of the
cell.
Enzymes are used in energy
production, DNA replication,
transcription, and translation ...
basically everything in the body enzymes are super!
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Protiens form an important part of
the immune response by
recognising and binding to foreign
particles.
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Hormones are proteins which
transmit signals around the body,
allowing the complex array of
biological processes which occur to
be coordinated effectively.
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17
Genetic Variation
Topic 4
Genetic Variation
SYLLABUS:
Inquiry question: How can the genetic similarities and differences within and between species be
compared?
4.1
Predicting variation
SYLLABUS:
Conduct practical investigations to predict variations in the genotype of offspring by modelling meiosis,
including the crossing over of homologous chromosomes, fertilisation, and mutations.
Variation is introduced to the population by a number of different factors. Let's look at an example to
demonstrate. We are going to trace the inheritance of two characteristics - hair and eye colour - assuming
they are controlled by a simple dominance pattern inheritance.
Brown eyes (B) is dominant over blue eyes (b). Brown hair (R) is dominant over red hair (r). Two individuals,
Alex and Jamie, decide to have a child. Alex is heterozygous for both brown eyes and brown hair (their
genotype is Bb, Rr). Jamie is homozygous for both blue eyes and red hair (their genotype is bb, rr).
Variation is introduced firstly during meiosis, as demonstrated in the diagram below. Crossing over of
homologous chromosomes creates new combinations of chromatids. Gamete formation sorts chromosomes independently of one another, meaning that a number of different chromosome combinations may
be formed. We can see for resulting gametes that there is a different combination of alleles in each. This
introduces variation.
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4.2 Combinations of genotypes
During ferti lisation, there is further opportunity for variation to be introduced. Alleles from Parent #1 are
combined with those from Parent #2 to restore a full set of chromosomes. This may result in the generation
of different offspring genotypes and phenotypes, as we can see in the diagram below.
Pos$i ble. o\tsprin.'.J
.9enolypa.. ,.,,J pl,~...olypc.3
bb - bl ...... e.yc.s
rr - re.I ho.i,-
Bb - b.-o..,11 ~..s
rr - .-a.I h.,.;,.
bb - bl...... ~c.S
Rr - b.....,~ ho.i,-
Bb - bro..,~ ~c.s
Rr - b.....,~ h.,.;,.
By tracing the inheritance to two characteristics very simply through meiosis and fertilisation, we can already
see a number of potential offspring variations. This variation is therefore amplified across the thousands
of genes present in the human genome, which all combine and recombine in different ways. In addition ,
some traits are not determined by simple dominance, but are the result of multiple alleles, further increasing the potential for variation. On top of this, mutation during meiosis (due to error in DNA replication) may
introduce new allele variants, which may be passed onto offspring.
We are able to predict possible offspring from parental genotypes to a certain extent, as we will see in the
following dot sections, through our understanding of forms of inheritance and how genes are passed during
meiosis and fertilisation.
4.2
Combinations of genotypes
SYLLABUS:
Model the formation of new combinations of genotypes produced during meiosis, including:
• Interpreting examples of autosomal, sex-linkage, co-dominance, incomplete dominance, and multiple alleles
• Constructing and interpreting information and data from pedigrees and Punnett squares
First, let's go through some key definitions:
Gene: a section of DNA encoding a particular
characteristics.
Allele: alternative forms of a gene.
Homozygous: identical alleles in a gene pair.
Heterozygous: different alleles in a gene pair.
Genotype: alleles present in an organism's
chromosomes.
Phenotype: outward appearance of an organism, determined by alleles expressed.
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DNA ,f,..... d ,....,• •• , ,f
.. ,,...4 c. -.ck.Ii.I.
4~~·
19
4.2 Combinations of genotypes
4.2.1
How do we determine phenotypes from genotypes?
During meiosis and sexual reproduction, half of a paternal and half of a maternal set of chromosomes
are combined. The interaction of alleles from each parent determines the genotype and phenotype of the
offspring. This re-combination of alleles allows for new traits to emerge in the population . The way that I
like to approach questions of inheritance is twofold:
• Where are the alleles located? This will determine whether an offspring inherits a trait, based upon
whether they inherit that chromosome.
• How do the alleles interact? Is it a matter of simple dominance, or something a little more complex
that will influence the phenotype of the offspring?
4.2.2
Where are alleles located?
There are two main categories of inheritance : autosomal and sex-linked.
K EY P OINT:
Autosomal inheritance: when traits (alleles) are passed on the autosomes (i.e. all chromosomes
except for X and Y chromosomes).
Sex-linkage inheritance: when traits (alleles) are passed on the sex chromosomes (X or Y). Traits
may either be X-linked (i.e. present only on the X chromosome) or Y-linked (i.e. present only on the Y
chromosome).
In autosomal inheritance, an offspring will inherit one set of chromosomes from each parent equally. In
humans, autosomal traits will have their genes located on the first 22 chromosomes - the non-sex chromosomes. Autosomal characteristics are passed on to both sexes with equal frequency.
Sex-linked traits are passed on the sex chromosomes of an organism . In humans, this means the X and
Y chromosomes. During sexual reproduction , female offspring inherit one maternal X chromosome and
one paternal X chromosome (XX). Male offspring inherit one maternal X chromosome and one paternal Y
chromosomes (XY). If different genes are present on either the X or the Y chromosome, one sex will be
more affected than the other due to this pattern of inheritance.
An example is haemophilia, an inherited X-linked disease. This means the gene for haemophilia is present
on the X chromosome. The equivalent, dominant allele (un-diseased) is also only present on the X chromosome. As females have two X chromosomes, they
may be carriers of the recessive gene encoding the disease, but they will be unaffected if they have a dominant
allele (e.g. the third child in the example on the right).
However, if a male inherits the X chromosome with the
defect, they will always have the disease, as there is no
equivalent gene on the Y chromosome to override it.
4.2.3
How do the alleles interact?
Mendelian genetics describes patterns of inheritance
where traits are influenced by the interaction of a single
pair of alleles. The interaction of these alleles, whether
they are dominant or recessive, will influence whether
what version of the gene is expressed.
Autosomal dominant inheritance is when a trait is determined by the expression of a dominant allele. This
means that the phenotype will always be expressed over
the other allele inherited. In order to express the dominant
phenotype, only one copy of an allele is necessary.
Examples of diseases passed by autosomal dominarnt inheritance include muscular dystrophy and Huntington's
disease.
11
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4.2 Combinations of genotypes
Autosomal recessive inheritance describes the pattern of inheritance where two recessive alleles are required to be inherited in order for a trait to be phenotypically expressed. Individuals may be carriers of recessive traits, meaning they don't exhibit them, but are able
to pass these traits onto offspring. Recessive traits may
skip generations, and generally are less prevalent in the
population than autosomal dominant characteristics.
Examples of diseases passed by autosomal recessive inheritance include sickle cell anaemia and cystic
fibrosis.
Sex-linked genes may also exhibit simple dominance or recessive patterns of inheritance. Genetics is, however, more complex than simply two alleles interacting. Some phenotypic traits are as a result of different
inheritance patterns, such as co-dominance, multiple alleles, and incomplete dominance.
K EY P OINT:
Co-dominance: when both alleles in a gene pair are fully expressed.
Some alleles in a gene pair may be co-dominant. This means that they are both fully expressed, resulting
in a third possible phenotype. For example, the ABO blood group system can involve alleles for blood type
A and blood type B both being dominant. When an offspring inherits an A allele from one parent and a B
allele from another parent, both are expressed phenotypically in the AB blood type.
K EY P OINT:
Incomplete dominance: when an allele for a certain trait is not completely expressed over its paired
allele. This results in the creation of a third phenotype which is a blended version of the phenotype of
both alleles.
Although both co-dominance and incomplete dominance are a result of co-expression of heterozygous alleles, incomplete dominance is different to
co-dominance because it is a result of alleles not
being fully expressed. Examples of incomplete
dominance include pink flowers (e.g. snapdragons,
carnations) which are a result of cross-breeding red
and white flowers, or rabbits with brown fur, a combination of alleles for red fur and white fur.
➔
KEY P OINT:
Multiple alleles: inheritance where three or more alleles exist for a single trait.
Although individually organisms may only inherit two alleles for any given gene, there may be multiple alleles
within the population. Multiple variations of these genes may display different patterns of dominance.
In order to illustrate, we can use the example of rabbit
Oenorypc
fur inheritance. The gene for fur colour, C, has four difcc
ferent alleles, C (black), cch (chinchilla), ch (Himalayan),
l'llfflocype
and c (albino). There is a pattern of dominance between
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-,1 ,...H,-MAl
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-YA-N-,11
these different alleles:
• C is dominant to all other alleles
• cch is dominant to ch and c, but recessive to C
• ch is dominant to c, but recessive to C and cch
• c is recessive to all other alleles
Inheritance patterns will be determined by the interactions of these different alleles.
cc
I
Al.BUI()
~~~ ~
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21
4.2 Combinations of genotypes
4.2.4
Constructing and interpreting pedigrees
K EY P OINT:
Pedigrees: charts displaying the phenotypic characteristics of organisms across generations.
Pedigrees are used to show how traits are passed within families, using standard symbols. Reading pedigrees may enable us to understand how traits are passed from parents to offspring, using our knowledge
of inheritance patterns explained previously.
When constructing pedigrees, it is very important to
create a clear chart. Individuals in each generation
should be on separate lines, level with one another,
and labelled (1, 2, 3 ...). Females are always represented by circles and males by squares. A key
must always be included, and should explain how
the chart is coloured (for example, affected individuals are shaded black, unaffected are white). Lines
are drawn as shown in the diagram on the right to
I[
indicate relations.
When interpreting pedigrees, we are trying to trace the passing of certain alleles from parents to offspring.
It is important to keep in mind that for each gene there may be a number of alleles, and that two may be
inherited by each individual. That means it's important to think about whether the parents are homozygous
or heterozygous for a trait. I find it easiest when solving pedigree problems to draw out potential punnet
squares (as we'll explore soon) and test different hypotheses. Memorising some common patterns may
also make interpretation simpler, for example :
• Dominant traits cannot skip generations; recessive traits can .
• Sex-linked traits generally affect one gender at a higher frequency.
AUTOSOMAL DOMINANT
~
Cannot be recessive as two affected parents
could not have an unaffected offspring
Cannot be dominant as two unaffected parents
could not have an affected offspring
Parents ID.Yl1 be heterozygous
Parents lll.lU1 be heterozygous
X-LINKED DOMINANT
ll ■~Ua at■I ■II
AUTOSOMAL RECESSIVE
X-LINKED RECESSIVE
Sex linkage~ be c;onfirmed
Sex linkage~ be ,onfirmed
I 00% incidence of affect ed daughters from an
affected fathe r ~ X-linked dominance
I 00% incidence of affected sons from an
affected mother ~
X-linked recessive
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4.3 Genetic data
4.2.5
Constructing and interpreting Punrnett squares
K EY P OINT:
Punnett squares: diagram used to predict the genetic outcome of sexual reproduction.
Punnett squares are super useful tools that allow us to theorise how alleles for genes may be passed
from parents to offspring. They may be used to calculate the probability of certain phenotypes based on
predicted genotypes.
1. Identify the genotypes of the parents. Remember: homozygous= two of the same allele, heterozygous = two different alleles.
2. Draw a square with four boxes.
3. Split up each parent's alleles to align one with each box. This is mimicking what would occur in
meiosis and gamete formation.
4. Fill in the Punnett square, keeping in mind whether alleles are dominant or recessive.
5. Interpret the information:
(a) What are the probabilities of offspring ge111otypes?
(b) What are the probabilities of offspring phenotypes?
(c) What are the ratios of different genotypes and phenotypes?
For example, in peas, the allele for purple flowers (P) is dominant over the allele for white flowers (p). A
heterozygous purple flower is cross-bred with a homozygous white flower. What are the potential offspring
of this cross?
Parental genotypes: paternal = Pp, maternal = pp
Paternal alleles (Pp)
Maternal alleles (pp)
4.3
p
p
p
Pp
pp
p
Pp
pp
Probabilities of offspring genotype:
• 50% Pp: heterozygous purple
• 50% pp: homozygous white
Probabilities of offspring phenotype:
• 50% purple
• 50%white
Genetic data
r
...
SYLLABUS:
Collect, record, and present data to represent frequencies of characteristics in a population in order to
identify trends, patterns, relationships, and limitatio111s in data, for example:
• Examining frequency data
• Analysing single nucleotide polymorphism (SNP)
4.3.1
Examining frequency data
Blood type inheritance is determined by a mixture of simple dominance and co-dominance. There are two
separate genes which influence your blood type:
• The gene for antigens present on blood cells (whether you are A, B, AB, or 0)
• The gene for rhesus factor (whether you are positive or negative)
Inheritance of these traits is determined separately.
A and B alleles are both co-dominant. This means that if you inherit an allele for A antigen (A) and an
allele for B antigen (B), you will express both antigens on the surface of your blood cells. The O allele (i)
is recessive. This means you need to inherit two O alleles in order to be an O blood type. Rhesus factor
(positive) is dominant. The allele for no rhesus factor (negative) is recessive.
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23
4.3 Genetic data
Grou.p
Red blood
cell typ<!.
An~ibodiu
in
pl o..sMa..
A Grou.p B G-rou.p AB
• - • -.
..\ _II --::::,
I
~
-i"~,
Anl, - B
Anti~ens in
re.d blood
c.e.lh
Grou. p 0
V
J<::t II
-(~
A,.,f; -A
T
A .,.li3&•S
-1...'i ,,'
.,.(
V
-r.- J_,,.
(None.)
Tr
I
...,
-f~
A,l;.A &A.t-B
8 Mli3~•S A&B Mli3&.s
(None.)
Inheritance patterns
I Phenotypes I Genotypes I
A
AA or Ai
B
BB or Bi
AB
AB
0
ii
• 0 - are universal donors (i.e. can give blood to anyone)
• AB + are universal acceptors (i.e. can receive blood from
any type)
Frequency data
Distribution of the blood groups within populations
is varied across the world. Blood group A has
high frequencies in the Scandinavia and Central
European regions. Australian Aboriginal population also display very high frequencies of A blood
groups. Blood group B has its highest frequency
in South Asia. It is believed that prior to arrival
of Europeans, the B blood group was entirely absent from native American and Australian Aboriginal populations. The table on the right displays
current statistics for blood group distribution in Australia.
4.3.2
Blood type
Frequency In Australian population
O+
40%
0-
9%
A+
31 %
A-
7%
B+
8%
8-
2%
AB+
2%
AB -
1%
Analysing single nucleotide polymorphism (SNP)
K EY P OINT:
Single nucleotide polymorphism: a change of a single nucleotide at a specific position on the genome.
This may be a substitution (e.g. changing A for G), insertion (adding a new nucleotide), or deletion
(removing a nucleotide).
SNPs account for more than 90% of all differences aciross the human population. They occur all throughout
our genomes, on average once every 300 nucleotides, however they are found most commonly within nonprotein coding DNA. Genome studies have identified around 85 million SNP variants across individuals.
This shows the potential for SNPs to drive human variation, and therefore evolution . Different SNPs have
been identified in populations, regions, and continents, as well as occurring at global frequencies. Analysis
of population genomes has shown that some mutations only in certain parts of the world.
II
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Inheritance Patterns in a Population
Topic 5
Inheritance Patterns in a Population
SYLLABUS:
Inquiry question : Can a population's genetic pattern be predicted with any accuracy?
5.1
DNA sequencing and profiling
S YLLA BUS:
Investigate the use of technologies to determine inheritance patterns in a population using, for example:
DNA sequencing and profiling.
DNA sequencing allows us to find single nucleotide information for entire human genomes. Each individual
will have a different genetic code (unless you are an identical twin), and these can be compared using
modern computation techniques to determine patterns of inheritance through generations. For a more
detailed explanation of how sequencing works, see page 52.
By compiling large amounts of sequencing data, we are able to model the changes in the frequencies of
genes and alleles in populations over space and time.
DNA profiling, also known as DNA fingerprinting, is a technique which allows scientists to determine an
individual's unique DNA characteristics. This technique is used widely in forensics, as it allows comparison
of DNA samples found at crime scenes to help identify individuals. It can also be useful to identify patterns of
inheritance between individuals. The technique is effective because human DNA contains large stretches
of junk DNA, which vary in length and contain different number of repeats. These are called variable
number tandem repeat sequences (VNTRs). The individual variability within these sequences allows us
to generate individual 'fingerprints' from our DNA.
1. Collection : DNA samples are collected from cells (blood, hair follicles, mouth swabs).
2. Digestion: DNA cut into small pieces using a restriction enzyme. Restriction enzymes cut along
DNA at specific nucleotide motifs - for example, EcoR1 cuts DNA every time there is a GAATTC
sequence in a DNA sample.
Eco RI
3'
GAAT
T C
~--------~
CT TAA G
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CT T A A
TT
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3. This creates a mixture of DNA fragments of differing sizes. The composition of this mixture will vary
from individual to individual, depending on their DNA sequence.
4. DNA fragments are separated using gel electrophoresis.
5. The gel is visualised to generate an image of the fragments separated into bands. Each band rep•
resents a segment of DNA of a certain size. Each individual sample will have a different band pattern
due to their individual gene sequence.
6. Patterns of bands are compared.
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Copyright© 2018 lnStudent Publishing Pty. Ltd.
25
5.2 Data analysis
As we can from the gel produced below, trends in inheritance can be visualised across a number of different
individuals. This example shows us how sequences from two parents (2nd and 3rd columns from the left)
are inherited by offspring.
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SYLLABUS:
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
• Population genetics studies used to determine the inheritance of disease or disorder
• Population genetics relating to human evolution
5.2.1
Conservation management
Conservation genetics is a field which combines knowledge and approaches from population and molecular
genetics with ecology and biodiversity sciences in order to identify and propose strategies to protect species
or variants at risk of extinction (preserving genetic diversity).
An example of a large-scale project which has used population genetics to guide future conservation management was The State of the World's Animal Genetic Resources for Food and Agriculture, published by
the United Nations FAO. The report, first published in 2007 and updated in 2015, used data on population
genetics across species to give an estimate of conservation status. This allows the international community
to understand the current state of species stability, and adapt appropriately in order to conserve diversity.
11
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5.2 Data analysis
5.2.2
Inheritance of diseases and disorders
There is an approximate 0.8% nucleotide base pair variance among human individuals. Whilst this represents a relatively small difference between people, improvements to computational technology and bioinformatics has allowed scientists to study these variations.
Firstly, some definitions to help us understand how scientists do this:
• Haplotype : a group of alleles inherited together from a single parent. These alleles are tightly-linked
in a cluster on certain chromosomes, meaning that they are very likely to be inherited together or
'conserved.'
• Haplogroup: a group of similar haplotypes which share a common ancestral single nucleotide polymorphism (SNP).
By sequencing large sets of populations, scientists lhave gathered information on how specific DNA sequences are passed down through generations, and have determined different haplotypes and haplogroups
that exist globally.
The International HapMap Project (www.genome.gov/ 10001688/international-hapmap-project/) is a collaborative project undertaken by researchers around the world which aims to develop a haplotype map of the
human genome in order to describe common patterns of genetic variation, such as the frequency and distribution of single-nucleotide polymorphisms (SNPs) in our global population. By using HapMap data, we
may be able to discover specific sequence variants which affect common diseases. This may help us to
understand how diseases or disorders are inherited across populations.
5.2.3
Human evolution
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Different cultural groups are often linked by the prevalence of certain haplotypes. By mapping haplotypes
globally, we can trace the movement and evolution of the human species from its ancestors.
A good example is tracing human mitochondrial DNA haplogroups. Each haplogroup is defined by differences in human mitochondrial DNA (mtDNA), which is inherited only from the mother ovum . This means
that sequencing mtDNA allows us to trace our maternal lines.
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By analysing mtDNA haplogroups, we have been able to trace evolution of the human race back to our
'Mitochondrial Eve,' the matrilineal most recent common ancestor (MRCA), who probably lived about
200,000 years ago in Africa.
An example of recent research in this area is an paper published in 2017 on which researchers from
Australia and a number of different countries around the world collaborated, entitled: 'Mitochondrial DNA
diversity of present-day Aboriginal Australians and implications for human evolution in Oceania,' N. Nagle
et. al. , Journal of Human Genetics (2017).
By analysing mtDNA, researchers have been able to identify lineages of Aboriginal Australians. A high
degree of genetic diversity was found across the continent, and various ancient haplogroups were identified
(estimated ages >40,000 years). The distribution of different haplogroups supports the hypothesis that
ancestors of Aboriginal Australians entered through at least two entry points. mtDNA data also supported
the hypothesis of long-term isolation of the Australian continent.
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Part II
Module 6: Genetic Change
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Mutation
Topic 1
Mutation
SYLLABUS:
Inquiry question: How does mutation introduce new alleles into a population?
1.1
Mutation operations
S YLLABUS :
Explain how a range of mutagens operate, including but not limited to:
• Electromagnetic radiation sources
• Chemical
• Naturally occurring mutagens
Mutations are permanent changes to the genetic information in a cell, and may be caused by mutagens.
By altering the genetic code, mutagens may change the phenotypic expression in an organism.
K EY P OINT:
Mutation: a permanent alteration to the nucleotide sequence of an organism's genome.
Mutagen : an agent which causes a genetic mutation.
Thinking back to our understanding of protein expression from the last module (see pages 15- 17 for a
reminder!), we know that DNA is transcribed to form mRNA, which is then translated into a polypeptide.
If there is a change to the original DNA, there may therefore be a change to the polypeptide, and this may
alter cell structure and function.
DNA
TAC CGTTTA GCG
+
mRNA
AUG GCA AAU COC
+
Polypeptide
Met Ala Asn Arg
+
Protein
I I
Functional enzyme
I I
I I
TACGGTTTAGCG
+
AUG C CA AAU CGC
+
Met Pro Asn Arg
I I
I I
+
Dysfunctional enzyme
Mutagens may be physical, chemical, or even biological. We are exposed to a variety of mutagens on a
daily basis; however, our DNA repair systems are usually able to detect changes to the DNA and fix the
errors. Mutagens become a problem when this repair system is compromised, and may lead to diseases
such as cancer.
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1. 1 Mutation operations
1.1.1
Electromagnetic radiation sources
Electromagnetic radiation, or electromagnetic waves, are emitted by electrically charged particles. These
waves are able to interact with and ionise atoms which they encounter in the body.
Radiation is highly penetrative because it is composed of high-energy waves. It is therefore able to enter
cells from external sources, and interfere with DNA molecules in the nucleus. Interference by electromagnetic radiation can cause bonds within the DNA structure to break. When this occurs, there may be
a change to the chemical composition of the DNA molecule. Parts may be deleted or rearranged, or the
shape of the molecule may change. This may lead to a mutation if the DNA repair system is unable to repair
the change, or repairs it incorrectly.
Examples of electromagnetic radiation includes gamma rays, X-rays, and ultraviolet (UV) light. The high
energy states of these radiation waves mean that they are able to disrupt the hydrogen bonds between
nitrogenous bases as well as bonding of the sugar-phosphate backbone.
Radiation may also damage DNA indirectly by ionising other molecules in the cell to produce free radicals.
These free radicals are highly reactive, because they have a set of unpaired electrons, which essentially
want to strip electrons from any molecules they encounter. These may also react with DNA to damage it.
A specific example is UV light, which we encounter every day in the form of radiation from the sun. Although
it is not always harmful, it can be damaging in high doses. Excitation of adjacent pyrimidines (T or C in the
genetic code) by UV induces the formation of covalent linkages - we call these pyrimidine dimers.
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On an average summer's day in Sydney, around 20,000 pyrimidine dimers are induced per hour per cell.
That's a lot of mutation for your DNA repair systems to fix, so you can imagine how repeated exposure for
long periods of time can lead to slip-ups, and therefore mutation. One missed dimer could result in incorrect
DNA replication or transcription of a gene. Pyrimidine dimer mutations are the main cause of melanoma
(skin cancer).
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1. 1 Mutation operations
1.1.2 Chemicals
There are many chemicals which interact with and have a mutagenic effect on DNA, both directly and
indirectly. Radioactive agents, such as uranium, release radiation in the form of alpha and beta particles
(as well as gamma waves, described previously) . These are able to penetrate the cell and interact with
DNA bonding to create disruptions.
Intercalating agents, such as ethidium bromide, have been used widely in the field of molecular biology
in order to visualise DNA during experiments. These chemicals insert or 'intercalate' themselves between
the nitrogenous bases of DNA, resulting in a colour change to the molecule While this makes them great
for identifying DNA in the lab, it can cause frameshift mutations during DNA replication, making them highly
carcinogenic in the human body. Below is an example of ethidium bromide reacting with DNA.
Lower
Nv..c.leotide.
dMdy
DNA
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Metals, such as arsenic, nickel , and cobalt, may also have mutagenic effects through a number of different
mechanisms.
• They have been shown to affect processes in DNA repair, such as the ability for proteins to recognise base-pair mismatching. This affects the cell's ability to correct errors, thus allowing mutations to
proliferate.
• It has also been demonstrated that some metals reduce fidelity during DNA replication. This means
that the cell does not correctly copy the genetic code when it is replicating, so errors are incorporated
into new DNA strands.
• Nickel has also been shown to inhibit the ability of histones to condense DNA, affecting chromosome
formation.
1.1.3 Naturally occurring mutagens
There are also a number of natural environmental factors which can create mutations in DNA.
Viruses replicate by inserting their DNA into host cells. This creates a disruption in normal cell function ,
and may lead to lasting mutational changes.
Bacterial infections can induce inflammation, which may reduce the efficiency of DNA repair systems,
increasing the rate of mutation. This is the reason that infection from Heliobacter pylori has been linked to
development of stomach cancer.
Transposons, or 'jumping genes,' are segments of DNA which can change their position in chromosomal
DNA. This can create mutations which alter gene expression in cells. They are responsible for phenomena
such as multi-coloured maize, colouring in peppered moths, and conferral of antibiotic resistance in bacteria.
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1.2 Processes and effects of mutations
1.2
Processes and effects of mutations
SYLLA BUS:
Compare the causes, processes, and effects of different types of mutation, including but not limited to:
• Point mutation
• Chromosomal mutation
1.2.1
Causes of mutation
Mutations to the genetic information of organisms may be a result of a number of different processes. As
outlined in the previous section, there exist many mutagens, both naturally occurring and as a product of
human activity and industry. These mutagens are not the only sources of mutation, however. The process
of DNA replication is complex, involving many inter-dependant chemical reactions and the coordination of a
wide variety of proteins. Errors in the replication of the genetic code are common. Usually, our DNA repair
systems are able to detect errors during replication. However, when the rate of mutation rises above the
statistical average, or when there is some inhibition of the system, the efficacy of repair may be diminished.
1.2.2 Types of mutations
There are two broad classifications of mutations :
-
• Point mutations: are those which only change or affect one (or a few) nucleotides within a gene
sequence. Point mutations may include any of the following :
- Substitution: when one nucleotide is switches out for a different one (e.g. an A within a
sequence is swapped for a C).
- Insertion : when nucleotides are added into a sequence.
- Deletion: when nucleotides are deleted from a sequence.
Insertion and deletion mutations are classified as frameshift mutations, because their effect is to
'shift' the sequence up or down so that codons are re-aligned. The effect of point mutations may be:
- Silent: the mutation has no effect on the codon (due to in-built redundancy of the genetic
code), and therefore has no effect on the amino acid the sequence encodes for. This results in
no change to the polypeptide or protein.
- Missense: the mutation affects one codon, introducing a different amino acid into the polypeptide sequence.
- Nonsense: the mutation prematurely introduces a stop codon, resulting in a shortened polypeptide chain, and thus a dysfunctional protein .
• Chromosomal mutations: are those which change or affect a long segment of DNA (i.e. a significant
portion of a chromosome). Types of chromosomal mutation include:
- Deletion: when a section of a chromosome is removed.
- Inversion : when a section of a chromosome is inverted (turned upside down) and re-inserted
into the chromosome.
- Translocation : when a section of one chromosome is moved to a different non-homologous
chromosome (e.g. a portion of chromosome 21 is moved to chromosome 22).
- Duplication: when a section of a chromosome is doubled.
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1.2 Processes and effects of mutations
POINT MUTATIONS
Normal Codon Sequence:
AGCAAGGCU
Ser - Lys -Ala
SUBSTITUTION
FRAMESHIFT
AUCAAGGCU
Mutation causing a downstream
shift in codon reading sequence
lie - Lys -Ala
I
\
INSERTION
DELETION
ACGCAAGGCU
A_CAAGGCU
Thr · Gin · Gly
Thr · Arg
CLASSIFICATION OF MUTATIONS
-
e.g. Substitution
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AGCAAGGCU
tS
Ser -Thr -Ala
'-&..I
tt
'-&..I
MISSENSE
NONSENSE
SILENT
AUCAAGGCU
AGCUAGGCU
AGUAAGGCU
lie - Lys -Ala
Ser- Stop
Mutation which edits codon Mutation which results
sequences to incorporate
in creation of astop
different amino acids
codon • prematurely
into the protein
term inating polypeptide
synthesis
Ser -Thr -Ala
Mutations which have
no effect on the
amino acid sequence
Point mutations are the cause of the most common type of genetic variation in human genomes: single
nucleotide polymorphisms (SNPs). SNPs are differences single nucleotides in genes, and they account for more than 90% of all differences in the population. Diseases such a sickle-cell anaemia, betathalassemia, and cystic fibrosis are all the result of SNPs.
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1.3 Somatic and germ-line mutations
STRUCTURAL
CHROMOSOMAL
MUTATIONS
DELETION
/~
INVERSION
TRANSLOCATION
I
OUPUCATION
i
MUTATIONSIN
CHROMOSOME NUMBER
~
ANEUPLOIDY
When the overall chromosome number
of the offspring isdifferent to the parent organisms
e.g. Down Syndrome
47 chromosomesinstead of uStJal 46
Trisomy21 •three copies of Chromosome 21
-
--------
POLYPLOIDY
When an organismcontains morethan two
sets of homologous chromosomes
e.g. Tri ploidy
Fetus has three copies of every homologous
chromosome instead of usual two copies
Chromosomal mutations involve the re-arrangement of large portions of DNA, and as such are very impactful upon organisms. Serious chromosomal mutations will usually lead to miscarriage early during pregnancy. Chromosomal mutation is usually a result of errors in meiosis:
• When crossing-over occurs incorrectly, it may lead to structural mutations.
• When sister chromatids are incorrectly separated during anaphase, this may lead to errors in chromosome number.
1.3 Somatic and germ-line mutations
SYLLABUS:
Distinguish between somatic mutations and germ-line mutations and their effect on an organism.
Somatic mutations are genetic alterations which a cell acquires, which may then be passed on to daughter
cells by cell division (mitosis in humans).
Somatic mutations are usually caused by environmental factors, such as the external mutagens we discussed earlier. These mutations affect any cells descended from the original cell in which the mutation
occurred. As the affected cell divides, a specific area of tissue with the mutation may develop, but the
mutation will not alter the genetic composition of other cells in the body. Somatic mutations are not passed
onto offspring. Many diseases, such as cancer, are the result of somatic mutations.
Germ-line mutations: are mutations in the germ cells (sperm or ovum) , which may be passed on to
offspring during fertilisation.
Germ cells, or gametes, are the basis of all other cells in the body. When fertilisation occurs, a paternal
gamete and a maternal gamete combine to form a zygote. This zygote undergoes mitosis to produce all
cells in the body. Therefore, any alteration to the genetic composition of the gamete will be passed onto all
cells of the offspring which inherit this information. Germ line mutations are caused by a variety of factors,
both internal and external. Diseases such as sickle-cell anaemia, cystic fibrosis, and colour blindness are
the result of germline mutations.
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1.4 Coding and non-coding DNA
1.4 Coding and non-coding DNA
SYLLABUS :
Assess the significance of 'coding' and 'non-coding' DNA segments in the process of mutation.
K EY P OINT:
Coding DNA: sequences of DNA which encode for protein (i.e. genes are coding DNA).
Non-coding DNA : sequences of DNA which do not encode for proteins.
The human genome is composed of over 3 billion base pairs, however not all of this information actually
encodes for protein in the cell. There are an estimated 19,000 - 20,000 protein-coding genes, comprising
only about 1.5% of the entire genome. These genes are expressed by the processes of transcription and
translation (see pages 12- 14).
The rest of the human genome is classified as 'non-coding' DNA, in that it does not encode sequences for
protein. Most non-coding DNA has been termed junk DNA - repeated sequences for which we have not
yet identified a purpose in the cell. Despite not serving a functional purpose, the highly variable nature of
these sequences across individuals does make them useful for DNA testing and forensic analysis. Some
portions of non-coding DNA have been identified as serving important functional purposes, such as:
• Genes for non-coding RNA (tRNAs and rRNAs) : RNA molecules produced from these non-protein
coding genes are used widely to regulate cell processes such as translation.
• lntrons are sequences which are spliced out of genes during post-transcriptional modifications (26%
of the genome) :
- These are important for gene expression and regulation.
- Some introns encode for functional regulatory RNAs.
- lntrons are involved in regulating alternative splicing, enabling the generation of many different
proteins from one gene.
• Regulatory DNA sequences (8% of the genome):
- Enhancers and silences: sequences of DNA in the genome which bind protein transcription
factors, therefore controlling when and where genes are expressed.
- Promotors: sequences of DNA situated upstream of genes, which transcriptional machinery
(e.g. RNA polymerase) recognise and bind to in order to transcribe the gene. Thus, proteins
are able to find the genes they need to express within the genome.
* For example, a TATA box is a sequence containing repeated T and A base pairs found in
promotor regions. This is recognised by the TATA-binding protein, which then assembles
proteins for transcription.
- Terminators: a section of DNA marking the end of a gene. These sequences trigger the release
of the completed mRNA construct.
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35
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1.5 Causes of genetic variation
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We know that mutation to a coding region of DNA may have serious effects on the proteins produced, and
therefore on the cell and organism. Recalling the types of mutations we discussed earlier, we can see that
even the smallest of single nucleotide changes can have an effect on the proteins expressed. Mutation
to non-coding sequences may also have effects on cell function. For example, if a mutation occurs in an
enhancer region of DNA, this may upregulate expression of a certain gene, causing over-expression, which
may be a strain on cell resources. Alternately, mutation to a promoter region, such that it no longer functions
to bind transcriptional machinery, may result in an important gene never being expressed in the cell.
1.5 Causes of genetic variation
SYLLABUS:
Investigate the causes of genetic variation relating to the processes of fertilisation, meiosis, and mutation.
-
Variation is essential to species survival. It is the driving force of evolution, allowing populations to adapt
to the environment, and ensuring survival in the face of selection pressures. But where does this variation
come from?
As outlined in the previous sections, mutagens or errors in ONA replication may lead to the development of
new mutations. Mutations lead to variation within a species, as they affect the composition of genes and
proteins. This could be positive, potentially leading to a more effective enzyme or desirable trait, or it could
be negative, causing the organism to die.
The processes of meiosis and fertilisation also allow for increased variation in the population. The human
genome is designed so that we have a sort of 'back-up' for most genes in the form of multiple alleles. During
sexual reproduction, our genes separate, rearrange, and are combined in new ways, so that what we inherit
is always slightly different to our parents. In a way, we can think of our biology as constantly testing new
combinations, seeing what works, hoping that the offspring produced will be stronger and better adapted.
1.5.1
Fertilisation variation
Fertilisation occurs during sexual reproduction
when two gametes, one ovum and one sperm, combine to form a zygote. The sperm inserts its genetic
material into the ovum, restoring a full set of 23
pairs of homologous chromosomes (46, or 2n chromosomes overall). After successful fertilisation, the
zygote begins to undergo mitosis, dividing to become an embryo.
Fertilisation increases variation because it requires two gametes from two different parent organisms to
combine in order to restore a full set of chromosomes. This process is random, allowing for any number
of potential combinations to occur with equal statistical probability (except potentially in the case of genetic
technologies, as we will discuss later in this module).
Additionally, because we inherit one set of genes from each parent, and therefore at least two alleles for
each trait, the dominant and recessive interaction of these alleles during expression will increase population
variability.
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1.5 Causes of genetic variation
For example, if your parents are both heterozygous brown-eyed, with blue-eyed recessive alleles, you and
your siblings may have different eye colours - a form of variation within a very small population . Now
amplify this over thousands of genes, and the possibility for a number of different alleles, not to mention
environmental factors affecting expression - we can start to see how variation is not just possible, but likely!
1.5.2
Meiosis variation
The process of meiosis is essential for the development of variability within offspring. The steps ensure that
inherited alleles are combined in multiple different ways, such that any daughter cell is different to the parent
cell, and there is an opportunity for new or recessive traits to be expressed. A more detailed explanation of
the steps of meiosis can be found on page 8. For the purposes of this syllabus dot point, we just need to
focus on what happens to alleles during meiosis. So how does variation occur?
1. We know that the first step of meiosis is DNA replication. The genetic material in the parent cell
doubles during interphase, so that we have 4n chromosomes (4 x 23 chromosomes = 92). The first
opportunity for variation during meiosis is therefore during DNA replication, when random mutations
may be introduced as a result of replication error.
2. The second opportunity for variation occurs during prophase I. Homologous chromosomes (those
encoding for the same traits) pair up, carefully aligning along their length. The close proximity allows
for a phenomenon called crossing over to occur. The homologues trade corresponding sections of
their genetic material, allowing for alleles to be switched from one chromatid to another. This creates
new combinations of alleles.
---+
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8
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C
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Let's use the diagram above to demonstrate this. Let Band b be the genes for eye colour, where B
is brown eyes and b is blue eyes. Let C and c be the genes for hair colour, where C is brown hair
and c is blonde hair. We can see that through the process of crossing over, the genes for hair-colour
were switched, so that we now have sister chromatids with brown eyes and blonde hair (Be) and blue
eyes and brown hair (bC), as well as the original brown hair/eyes (BC) and blonde hair blue eyes
(be). Because genes on the same chromatids are inherited together, those new combinations are
then passed onto the gametes. Imagine that happening with all of your chromosomes, and with all
of the thousands of genes they carry. You can see there is a huge opportunity for new combinations
and variation because of crossing over.
3. The third opportunity for variation occurs during anaphase I and II. The law of random segregation
states that alleles for each trait separate randomly from one another during gamete formation. This
means that alleles encoding the same trait are s eparated so that there is one in each gamete.
4. The fourth way that variation occurs is by Independent assortment. This law states that chromosomes are unrelatedly sorted into gametes. This effectively means that alleles situated on different
chromosomes, those encoding different traits, will sort independently of one another. Like random
segregation, this also occurs during anaphase I and 11, when the parent cell is dividing into diploid
(anaphase I) and then haploid (anaphase II) ce lls.
KEY P OINT:
Crossing over: when homologous chromosomes line up and exchange segments of DNA to produce
new gene combinations within sister chromatids.
Random segregation: alleles separate randomly from one another during gamete formation.
Independent assortment: alleles for different traits are unrelatedly sorted into gametes.
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1.6 Population genetics
Summary of genetic variation
Process
Variation
Meiosis
- The production of gametes (sperm and ovum)
- One parent cell becomes four daughter cells,
each with half the number of required
chromosomes (one chromatid of each
chromosome)
- Mutation during DNA
replication
- Crossing over
- Random segregation
- Independent assortment
Fertilisation
- Two gametes (one sperm and 0110 egg) come
together to form a zygote
- The full set of chromosomes is restored (23
pairs, 46 in total)
- Random selection of gametes
- Interaction of dominant and
recessive genes
1.6
Population genetics
S YLLABUS :
Evaluate the effect of mutation, gene flow, and genetic drift on the gene pool of populations.
Population genetics is the study of genetic differences within
and between populations. It largely involves the tracking of
genes, and their alleles across space and time. Understanding population genetics is important to evolutionary biology, as
it is a tool which enables us to comprehend how traits have become prevalent in populations, and therefore how populations
have changed and evolved into new species.
-
Theories in population genetics rely upon the fundamental
principles of the theory of evolution, which you will have
learned in the Year 11 course. Let's quickly revise Darwin and
Wallace's theory of evolution.
Mechani sm : Natural Selection
1. Variation occurs within a population as a result of mutation.
2. Environmental pressure is applied to the population (e.g.
physical, chemical, competition).
3. Phenotypes best suited to the changed environment (i.e.
the fittest individuals) survive.
4. Surviving organisms reproduce. This gradually changes
the frequency of population traits.
K EY P OINT:
Gene flow: transfer of genetic variation (different alleles) from one population to another.
Gene flow describes how the migration of individuals from one population to another will result in transfer-
ence of alleles into and out of populations. This will result in a change to the frequency of alleles, changing
the distribution of genetic diversity.
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1.6 Population genetics
K EY P OINT:
Genetic drift: when the relative frequency of alleles within a population changes, due to the disappearance of particular genes as a result of natural selecttion.
Don't be scared by the new term - genetic drift is just a fancy way of describing how traits become more
or less prevalent in a population overtime. Genetic drift may be as a result of a variety of factors, and may
occur slowly or quickly depending on the types of selection pressures applied to a population. Two causes
of genetic drift include bottlenecking and the founder e ffect.
K EY P OINT:
Bottlenecking : when there is an abrupt reduction in the number of individuals in a population (as the
result of a sudden and severe selection pressure) , causing a loss of diversity in the gene pool.
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Founder effect: when a new population is established by a small number of individuals separated from
a larger population, there will be a loss of genetic variation within the new group. This may lead to new
speciation events and evolutionary pathways.
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Copyright © 2018 lnStudent Publishing Pty. Ltd.
39
1.6 Population genetics
To demonstrate these concepts, let's apply them to an example.
On a magical, far-away island live a large population of highly-evolved ants. There are three different alleles
present in the population for exoskeleton colour: black, grey, and white.
Political differences within the ant population have
polarised their previously peaceful society. As a
result of irreparable ideological discrepancies, the
ALP (Ant Labor Party) and the LNP (Little Nippers
Party) decide to set out on their own to different
parts of the island, and start their own utopic communities.
• The ALP, comprised mostly of black ants and
a few grey ants, moves to the sunny northern
side of the island.
• The LNP, composed mostly of white ants and
a few grey ants, moves to the shady, forested
southern side of the island.
This difference in the new populations is a result of the founder effect.
Over time, these separate populations continue to
grow. The difference between the ALP and the LNP
populations becomes more distinct, as the difference in allele frequencies increases. This change
in number of black, grey, and white ants is called
genetic drift.
......
............
............
............
-
... ...
.............
...
GGo
IISASTUI • • •
One day, disaster strikes the island in the form of
a massive storm. Large numbers of the ants are
swept away. This heart-breaking event is called
bottlenecking.
In the wake of the disaster, both populations rebuild
their communities, not letting adversity beat them
down. However, as a result of the random bottleneck event, the gene composition of the populations has changed. A large number of black ants
were swept away from the ALP, so a grey exoskeleton has become the prevalent allele. Only white
ants in the LNP survived the storm , so the population has grown to exhibit only this allele. This is
another example of genetic drift.
Over many generations, the ants begin to forget
their political differences. A radical group of visionary ALP ants decide to offer an olive branch, and
move to the LNP in the hopes of improving trade
relations. This is an example of gene flow, as they
are introducing new alleles into the homogenous
population, increasing genetic diversity.
.......
........
.._...
.........
. .........
. ........
.........
........... ,
...............
..........
.............
._
............
...........
............
..........
......
And all the ants lived happily ever after!
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..I
Biotechnology
Topic 2
Biotechnology
SYLLABUS:
Inquiry question: How do genetic techniques affect Earth's biodiversity?
2.1
Applications of biotechnology
S YLLABUS :
Investigate the uses and applications of biotechnology (past, present, and future) including:
• Analysing the social implications and ethical uses of biotechnology, including plant and animal
examples
• Researching future directions of the use of biotechnology
• Evaluating the potential benefits for society of research using genetic technologies
• Evaluating the changes to the Earth's biodiversity due to genetic techniques
K EY P OINT:
Biotechnology: the exploitation of living systems and biological processes to develop tools for technological use. Applications may be used in areas such as industry (e.g. food, energy), medicine, environmental sciences, and computational design.
The field of biotechnology is very broad because there is such a wealth of biological phenomena which we
could harness for human benefit. Below is a short-list of a few wonderful technologies that scientists have
developed to address world issues.
2.1.1
Benefits of biotechnology
• Medical biotechnology:
- Pharmaceuticals:
• Vaccines: using an understanding of how the human immune system responds to invasion
by foreign materials such as viruses, we can develop molecules to strengthen this response
pre-emptively.
• Antibiotics: developments in the fields of microbiology and cell biology have allowed scientists to specifically identify important systems for bacterial cell growth and repair. We are
now able to synthetically design molecules (drugs) which specifically target certain proteins
in bacteria, inhibiting their function with increased efficiency and fewer patient side-effects.
- Stem cell treatments: development of therapeutic cloning (see page 49) has allowed scientists
to harness stem cells to create skin grafts and treat certain cancers and autoimmune diseases.
- Bioinspired materials: an example of this is cultural epithelial autographs (CEA) also known as
'spray-on-skin' which is a tissue engineering technology developed by Australian doctor Fiona
Wood that has been commercialised for use in treating burns.
- Diagnostics:
• Biosensors: analytical devices which can detect specific molecules with high sensitivity
have been developed using biologically inspired systems. They have been used to aid in
detecting glucose levels in diabetic patients, as well as in detecting the presence of certain
microbes or DNA sequences.
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2. 1 Applications of biotechnology
• Environmental biotechnology:
- Bioremediation : with our increased understanding of micro-organisms and their abilities and
roles in different ecosystems, scientists have developed techniques to clean up pollution. Bacteria able to metabolise pollutants may be augmented or introduced to a polluted site. Significantly, bacteria have recently been engineered with the capability to degrade polyethylene
terephthalate (PET) plastics.
- Agriculture: techniques of transgenesis have been used to produce genetically modified crops,
improving the plants' ability to survive and often increasing their nutritional value.
• Industrial biotechnology:
- Biodegradable plastics: creation of biopolymers derived from plant and bacterial systems
have helped to address issues of pollution, as well as improve living systems due to their increased biocompatibility.
- Improving efficiency of industrial proces.ses using enzymes: as we know from Year 11 ,
enzymes are biological catalysts that speed up reactions. Enzymes can be isolated , and sometimes modified, to speed up reactions in irndustrial chemical processes. This includes improving
important processes such as fermentation (for production of alcohols).
- Energy sources:
• Biofuels: technologies have been developed to extract fuel from biomass rather than petroleum, and to investigate the potential for organisms such as bacteria to produce fuels in
order to meet increasing demand.
• Photosynthesis: scientists have been investigating the potential of exploiting the natural
process of photosynthesis, which tums light energy into chemical energy, for the production
of energy (i.e. using photosynthetic bacteria like a biological solar cell).
2.1.2
Social and ethical implications
The development of biotechnologies has become and huge area of debate within society. This is because
in creating new technologies, particularly those with such potential for lasting impact, the interests of the
stakeholders (the community, scientists, and the government) need to be properly assessed.
This is a complex issue, and one which you probably won't have to form an extremely in-depth understanding of for the exam . You should , however, have at least a nuanced grasp of the overall interplay between
different groups' interests, and form some opinion on how we can continue to move positively into the future
of biotechnology. Below, I've outlined some of the key issues which you may want to think about when
considering responses to questions.
• Positive social and ethical uses:
- The fundamental aim of biotechnology is to improve people's quality of life by meeting the growing needs of society.
- Consider all the pressing issues that our world is facing as a result of our growing population
and its increasingly globalised nature. Many of these are addressed in the United Nations
Sustainable Development Goals, including :
• Ending poverty and hunger (Goal 1 and 2)
• Improving health and wellbeing (Goall 3)
• Providing access to clean water and sanitation (Goal 6)
• Producing affordable and clean energy (Group 7)
• Creating sustainable cities and communities (Group 11 )
- By using the biological tools around us to their fullest potential, we can come up with creative,
lasting solutions to these problems. Many of the biotechnologies outlined previously, if enacted
on a global scale, have the potential to contribute positively to these goals. If we do not address
these issues, they will likely have disastrous impacts for future generations.
- Genetic diversity: many biotechnologies involve editing genetic material within and across
species. This has the potential to create new arrangements of genes, increasing the diversity
of traits we see around us. This can have a positive impact upon the course of evolution, as we
continue to re-combine traits in order to best survive and thrive in our environments.
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2. 1 Applications of biotechnology
- Open-source directions: there has been a push within the scientific community, particularly
with the emergence of fields such as synthetic biology (see the section on future directions on
the next page!), to keep scientific information within the public sphere by creating open-access
databases. This has the potential to make science, and by implication biotechnology, a more
democratic process, in which a wider community of scientists are able to work on projects their
find important, regardless of location, background, and connections.
• Concerns regarding social and ethical uses:
- Ownership: information is an important commodity, and as we know from recent controversies
surrounding data mining and distributing information in the technology industry, personal and
private information is a valuable resource to large companies who will pay large amounts of
money for it! Biotechnologies and gene techniques such as gene sequencing allow us to understand more and more about ourselves as humans, on a fundamental level. While the value of
this information is not yet clear, there is potential for it to be exploited, for example, by insurance
companies or employers, who may use genetic information to discriminate.
- Intellectual property: we have developed a specific area of law called intellectual property
which allows for certain processes and products to be patented so that the people who invented
them are able to profit off their work. Whilst this is important in protecting the property rights
of individuals and companies, things can be more complicated when it comes to biotechnology.
Can you claim rights to a gene? Can some other person claim ownership of a sequence of DNA
in your body? In Australia, there was a landmark High Court ruling in D'arcy v Myriad Genetics
Inc & Anor (2015] in relation to the BRCA 1 breast cancer gene. It established that genetic
information is not patentable, as it is not 'made' or 'artificially created.' Whilst this is a positive
for Australians, there may be issues in the future, across different countries and jurisdictions.
This is particularly interesting in terms of synthetic genetics - in particular, the work of individuals such as J. Craig Venter who created the first synthetic microbial genome. Where are we
able to draw the line between a synthetic sequence of genes and a naturally arising one? How
much does a gene have to be edited to be classed as artificial?
- Commercial implementation:
• Monopolies: large and powerful companies have the potential to dominate the biotechnology market. When this happens they may create monopolies and drive up prices of
products to the detriment of those who need the technologies most. Companies may also
develop technologies which create dependency. For example, a company called Monsanto
have created 'terminator seed' crops which have been modified only to last one generation. This means that in order to access the improved, high yield products they offer,
farmers need to purchase new seeds from the company annually.
• Consumer rights and choices: witlh biotechnologies such as GM foods, it can often be
difficult to identify products which have been edited and those which haven't. This may
infringe on the consumer's rights to choose the food they would prefer to eat based on
their own moral proclivities (e.g. those who are vegetarian or vegan). This is why initiatives
such as clear and explanatory labelling of GMOs are important so that the consumer can
continue to be in control of their own diets.
- Regulation : in terms of globalisation , governments need to legislate biotechnology so that
they can safely control its development without stifling innovation. In addition to considering
local security, we should think about how we regulate biotechnology on a global scale. This
is because biotechnologies and their use will not only affect citizens in certain countries, but
the world as a whole. See the Cartagena Protocol on Biosafety adopted by the Convention on
Biological Diversity (UNEP) as an example of efforts towards this.
- Biohacking : due to the emergence of open-access information, availability of molecular biology
resources, and overall improved scientific literacy in the community, there has been a rise in
'do-it-yourself' biology, also known as biohacking. This democratisation of research has the
potential to advance social good, but also poses an interesting dilemma for regulation when
individuals are not operating in large and structured institutions such as universities.
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2. 1 Applications of biotechnology
• Future directions of biotechnology:
- In addition to continual improvements of the fields already mentioned, there has been a push
within research to extend biotechnology into the field of synthetic biology.
- Synthetic biology is an emerging area of research which aims to be increasingly interdisciplinary, combining engineering principle with biological tools. This diverse field includes disciplines from biotechnology, molecular biology, genetics, biophysics, computer engineering , and
evolutionary biology - all coming together with that aim to use our fundamental knowledge of
biological system to build new tools.
- The movement started out aiming to fully characterise the fundamental building blocks of biology, DNA, genes, proteins, and by understanding them as discrete units, test new combinations
in a logical and controlled fashion . Whilst this task has proven infinitely more complex than anticipated, the field represents exciting potential for future research.
- Progress in synthetic biology has been helped by the establishment of international research
competitions, such as iGEM (international genetically engineered machines) and BIOMOD.
These competitions capitalise upon the vast creative energy of researchers at the university
level (mostly undergraduates), and direct them towards developing technologies and techniques
to address world issues.
• Effect on biodiversity :
- Biotechnology itself is not inherently dangerous; it is merely a tool which we can use to change
the world around us, like any other technology. The difference, and therefore the main concern with its use, is that biotechnology has the potential to make irreversible changes to entire
species. Editing life at its most fundamental level may have incredibly positive, or incredibly detrimental, effects. It is very important to recognise that this potential is not found in the nature of
the technology, but rests on the shoulders of the people and the societies creating these tools.
- Biotechnology is not a new phenomenon - humans have been using tools to influence biology
and genetics for centuries, including practices such as selective breeding and artificial pollination. We have been deliberately editing our ecosystems for a very long time, and in doing
this we've created new species by influencing the emergence of traits which we have found
desirable. We have already had significant impacts upon the biodiversity which we see in the
world around us today. However, with the rise of genetic technologies, we have the potential to
implement changes at a more rapid rate.
- Some specific issues which need to be kept in mind as we develop biotechnologies are:
• Creation of monocultures: as we begin to observe the benefits of particular traits and
genes as a result of biotechnology, it is important that we do not rely so heavily on these
favourable genes so as to wipe competitive alleles from species gene pools. We should
continue to promote diverse agricultural practices (both of GMOs and 'natural' crops), as
variation is essential to species' survival.
• Horizontal gene transfer: refers to the acquisition of genetic information by transfer from
a member of a different species. As traits escape into ecosystems, they may pose competition to other naturally occurring alleles. This may ultimately also lead to a reduction in
biodiversity, and loss of variation.
- On the flip-side, we also have the ability to increase biodiversity. We may systematically test and
experiment with new genetic combinations, making the world around us a better, more efficient
place. Recombinant technologies (explored further in the next section) allow us to transplant
genes across species, and accelerate evolution in a potentially positive manner.
Ultimately, it is our duty as scientists and citizens to drive for positive change. The potential to enact good
using biotechnology is overwhelming, and considering the global issues we are currently facing (climate
change, food security, pollution, etc.) it may be considered more unethical not to act and not to use these
tools at our disposal than to ignore them. What we need to do is to ensure these tools are regulated and
used properly, so that biodiversity is not decreased, and we are using these tools in a sustainable manner
that helps our natural ecosystems.
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Genetic Technologies
Topic 3
Genetic Technologies
SYLLABUS:
Inquiry question: Does artificial manipulation of DNA have the potential to change populations forever?
3.1
Overview of current technologies
Below is a table summarising all of the techniques brought up throughout this section.
I Uses
Methods
Reproductive
technologies
Cloning
techniques
Artificial
insemination
- Livestock industry (animal
production)
- Fertility treatment (humans)
- Efficient, able to
synchronise pregnancies and
bypass issues of fertility
In vitro
fertilisation
(IVF)
- Fertility treatment (humans)
- Able to freeze embryos,
genetic screening
Artificial
pollination
- Pollinating crops
- Genetic experiments
- Controlled inheritance of
favourable traits
Wholeorganism
cloning
- Livestock industry
(production of genetically
identical offspiring)
- Definite inheritance of
desirable traits
Therapeutic
cloning
- Medicine (stem cell
technologies)
- Stem cells are able to
differentiate into any cell
Gene cloning
- Medicine and industry
(production of important
molecules on a large scale)
- Production of biologically
relevant proteins (e.g. insulin,
enzymes for industry)
Transgenesis
-Agriculture (development of
pest-resistant crops)
- Environmental
biotechnology
(bioremediation)
- Creation of organisms with
multiple functions,
transference of favourable
traits, reduce pesticide use,
exploit biological phenomena
Gene
sequencing
- Medicine (development of
personalised treatments)
- Genetic research
(improving understanding of
genomes, helping to identify
new genes)
- Identification of genetic
disorders and risk factors,
understanding of evolutionary
relationships, forensic biology
Gene therapy
- Medicine (reprogramming
of dysfunctional cells/tissues)
- Treatment of diseases such
as cystic fibrosis
ELISA
- Medicine (assay for
diagnosing disease)
- Forensic epidemiology,
identification of infections
CRISPR
- Molecular biology (gene
editing tool)
- Elegant and cost-effective
for gene therapy/transgenics
Recombinant
DNA
techniques
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I Advantages
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45
3.2 Processes and outcomes of reproductive technologies
This section of the syllabus touches upon a lot of different technologies - we can see that there has been a
lot of development into biological research tools! It will likely be necessary to have a cursory understanding
of each of these techniques, and then a more comprehensive grasp on just a few for potential 8 mark
questions. A key skill that you'll be tested on during your exams is critical judgement, so make sure you
can compare and contrast the types, uses, and advantages of each method.
3.2
Processes and outcomes of reproductive technologies
SYLLABUS:
Compare the processes and outcomes of reproductive technologies, including but not limited to:
• Artificial insemination
• Artificial pollination
Reproductive technologies have been used throughout history to improve selection of favourable characteristics. Humans have been able to directly affect the genetic composition of species' populations by
influencing how heritable traits are passed through generations.
These techniques have been used widely in agriculture to produce better livestock and crops, often to
increase yields and increase tolerance to environmental factors. Technological developments have also
allowed us to develop techniques for improving human fertility, and achieve pregnancy with desired partners.
3.2.1
Artificial insemination
K EV P OINT:
Artificial insemination: injection of semen through the cervix into the uterus without sexual intercourse
for the purpose of achieving fertilisation.
Artificial insemination involves the deliberate introduction of sperm into the uterus of an organism without
sexual intercourse. It has been used commonly in animal breeding , as well as in fertility treatments for
humans. Sperm is collected from male genitalia, processed (it may be washed or treated with antibiotics) ,
and then injected into the uterus of an organism, where fertilisation occurs.
The advantage of using this process for breeding is that humans are able to select desirable traits and
forcibly combine them to hopefully produce offspring with desired characteristics. It may be used to synchronise births in the livestock industry, or avoid injuries during mating. It also allows for favourable genetic
material to be sent around the world (this is commonplace for race-horse breeding). 75'% of dairy cattle inseminations, and 85% of pig inseminations within the agriculture industry are achieved through this artificial
insemination method.
A disadvantage of this process is that by selecting for the few traits we perceive as desirable, we may limit
genetic variation within a species. An increase in homogenous populations may cause issues for species
survival in the long term.
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3.2 Processes and outcomes of reproductive technologies
3.2.2
IVF
KEY POINT:
In vitro fertilisation : when an egg is fertilised by sperm outside the body, usually in a test tube (in vitro
meaning 'in glass').
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In vitro fertilisation is another fertility treatment used by humans when they have difficulty conceiving. Unlike
with artificial insemination, it involves removal of both the egg and the sperm gametes. Fertilisation occurs
outside of the body in a laboratory to ensure that viable embryos are produced. Once it has been confirmed
that an embryo has formed and begun to divide, these cells are implanted back into the uterus (or frozen
for future use).
As multiple eggs are removed from the ovaries, IVF may allow for multiple fertilisation events. This may
be advantageous as multiple embryos can be implanted into the uterus for a higher chance of successful
pregnancy. Additionally, any viable embryos produced may be frozen and stored for future use.
This process may be particularly advantageous as it allows for embryos to be genetically screened before
implantation. Thus, doctors may ensure that potential pregnancies do not have any genetic disorders that
may harm the foetus or the parent.
3.2.3
Artificial pollination
K EY P OINT :
Artificial pollination: when pollen (plant sperm) is purposefully taken from one plant and placed on the
stigma of another flower.
Ill
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47
3.3 Cloning
Artificial pollination is used in agriculture to influence the traits passed to subsequent generations of plants.
It is also known as mechanical pollination, as it involves manually transferring genetic material from one
plant to another.
This technique was famously used by Gregor Mendel in his pea-plant experiments to trace the inheritance
patterns of visible traits. In modern agriculture, it is used to ensure that all plants within a crop are pollinated and can produce fruit. This increases crop yields and profitability. It is also used to create new
species of plants with desired characteristics. The disadvantage of artificial pollination is that it may create
monocultures in which there is very little genetic variation. This may create species which are vulnerable
to sudden environmental changes. For example, the Irish Potato Famine (1845-1849) was the result of a
single strain of potato blight. Creation of monocultures also mean that natural varieties of plants are lost
due to competition, and biodiversity is reduced.
I Technology I Method
I Outcomes
Artificial
insemination
1. Extraction of sperm
2. Processing
3. Insertion into uterus
In vitro
fertilisation
1. Hormone treatment to stimulate egg
production
2. Removal of multiple eggs from ovaries
3. Fertilisation (eggs and sperm are
combined in the lab)
4. Incubation (hopefully leading to
production of embryos)
5. Embryos are implanted into the uterus,
or frozen
Artificial
pollination
1. Pollen (sperm) removed from the
stamen of one plant
2. Pollen applied to the stigma of another
plant
3. Pollen fertilises the ovum
(If the practice requires very controlled
passing of genetic material (for example
in Mendel's experiments), the anthers of
the plant receiving foreign pollen are
removed to avoid self-pollination .)
3.3
Positive:
- Favourable genes passed to offspring
- Increased efficacy of livestock industry
Negative:
- Limited genetic variation in population
Positive:
- Favourable genes passed to offspring
- Allows for genetic screening of
embryos to avoid disease
Negative:
- Expensive
Positive:
- Higher crop yields
- Selection of desirable traits
- Creation of new plant species
Negative:
- Creation of monocultures
- Loss of biodiversity
Cloning
SYLLABUS:
Investigate and assess the effectiveness of cloning, including whole organism cloning and gene cloning.
3.3.1
Whole organism cloning
KEV P OINT:
Whole organism cloning : also known as reproduction cloning, is the creation of a new molecular
organism that is genetically identical to its parent organism.
This occurs through somatic cell nuclear transfer - for example, Dolly the sheep in 1997).
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3.3 Cloning
1. An adult cell (somatic cell) is removed from the organism you want to clone (in Dolly's case, it was
removed from the mammary tissue in the udder). This contains their genetic material (i.e. what you
want in your offspring).
2. An unfertilised egg is removed from a donor organism. The DNA is removed from this egg - it is
denucleated. Basically, it becomes an empty vessel.
3. The denucleated egg and the stem cell are fused.
4. The resulting cell is cultured so that it begins to divide and become an embryo.
5. The embryo is implanted into a surrogate organism.
6. The surrogate gives birth to an organism which is genetically identical to the donor.
In terms of the effectiveness, the 'clone' produced is not strictly identical to its parent organism. Since we
are using somatic cells as the source of genetic mateirial, any mutations acquired in that cell will be passed
down (look up 'CC and Rainbow' for an example of this).
Furthermore, mitochondria present in the cytoplasm of the donor egg contains DNA which is passed on
to the cloned organism. Therefore, the clone has a different mitochondrial genome from its target parent
organism. Environmental factors also have an impact on how our genes are expressed (e.g. different phenotypes in identical twins). Hence, a genetic clone will not necessarily grow to be phenotypically identical to
its parent organism.
Cloning is also a very expensive and time-consuming process, so its effectiveness is limited.
3.3.2 Therapeutic cloning
K EY P OINT:
Therapeutic cloning: cloning techniques developed in order to produce therapies for disease. This involves the production of stem cells genetically identical to the donor which may be used to treat diseases
such as diabetes and Parkinson's.
Much like reproductive cloning, therapeutic cloning involves the use of somatic cell nuclear transfer
(SCNT). A nucleus containing genetic material is removed from a cell of the patient. This is inserted into
a denucleated egg cell. This new cell then begins to divide. After a few days, the cell has divided into an
embryo, and embryonic stem cells can be removed. These stem cells are cultured in a specific way so that
they remain in their undifferentiated state - this is the creation of embryonic stem cell 'lines.' These cells
will be genetically identical to the cells of the patient whose DNA was used.
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3.3 Cloning
This tends to have very good patient outcomes, as therapeutic cloning involves pluripotent stem cells that
can grow and differentiate into any type of cell in the body, meaning that we can treat many kinds of diseases
by replacing dysfunctional cells. There is no risk of immunological rejection because the cloned cells are
genetically identical to the patient, and can therefore be used without inducing an attack on transplanted
cells. However, it requires many attempts to create vi able eggs. Often , hundreds of attempts are required
because the eggs fused with the somatic nuclei are not stable and often do not propagate.
3.3.3 Gene cloning
K EY P OINT :
Gene cloning : also known as molecular cloning is the process of producing multiple copies of a specific
DNA sequence, ultimately to produce multiple copies of an identical molecule.
The aims of gene cloning are to assemble recombinant DNA containing a gene of interest, and then direct
this DNA into a host organism which will replicate the gene and produce the target protein in large amounts.
Gene cloning can be used to synthetically produce many different proteins from many different organisms,
as well as to combine different proteins recombinantly. Below is an example of the process whereby human
insulin is cloned and produced by bacteria.
1. A useful target gene is identified (for example, the gene for human insulin). As we
now have huge databases containing the information about gene sequences, we can
send this data to companies who synthesise
our desired DNA sequences for us.
2. Plasmids (circular pieces of DNA) are isolated from bacteria.
3. Both the bacterial plasmid and the DNA containing our target gene are treated using a restriction enzyme. Restriction enzymes 'cut'
DNA, breaking hydrogen bonds in the molecule. These enzymes create 'sticky ends,'
sequences of overhanging single stranded
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4. The complementary sticky ends of the target
gene and the plasmid come together through
base-pairing affinity. These are then annealed using DNA ligase.
5. This new recombinant plasmid is re-inserted into host bacteria by a process called transformation.
6. The host bacteria expresses lots and lots of copies of the target gene, producing large amount of
the target protein (insulin) . This protein can then be extracted from the cells, purified, and used by
humans.
This is relatively fast and cheap when performed correctly (it may only take a few weeks from initially
ordering your DNA sequences to obtaining purified protein). However, it is much harder to produce large
amounts of protein on an industrial scale. Also, bacteria are much easier to work with than mammalian
cells, hence this is currently used widely in scientific research.
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3.4 Applications of genetic technology
3.4
Applications of genetic technology
SYLLABUS:
Describe techniques and applications used in recombinant DNA technology, for example: the development of transgenic organisms in agricultural and medical applications.
3.4.1
Recombinant DNA technology
KEY P OINT:
Recombinant DNA technology: methods to join together DNA from two different species, in order to
produce new genetic combinations.
There has been a huge amount of research into recombinant DNA technologies over the past few decades.
It is now a commonplace practice used in many fields of biological research. The reason that these technologies have been so widely developed is because they allow us to get the best out of the world around
us, and to exploit all manner of biological phenomena for our own advantage. By combining various genes
in new ways across organisms, we are able to create better biological machines.
3.4.2 Transgenesis
KEY P OINT:
Transgenesis: introduction of exogenous genetic material (DNA from an external source/different organism) into a living organism. This is performed so that the organism exhibits a new trait, and transfers
this trait to its offspring.
Gene delivery
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All living organisms are made of the same fundamental building blocks: nucleic acids. This means that a
defined DNA sequence will encode the same protein in all organisms. This consistency within the biosphere
allows us to exploit the individual tools which organisms have by inserting them into other species.
• Plasmids: the most common form of transgenesis is gene editing in bacteria. This is faci litated by
the availability of naturally occurring plasmids (circular DNA) into which genes may be easily inserted.
• Retroviral vectors: the replicative life cycle of retroviruses may also be exploited to deliver foreign
genetic material to a cell. Retroviruses insert their own genetic material in the form of RNA into host
cells, which then reverse-transcribe them into their genomes. By editing retroviral RNA to encode for
a protein of interest, viruses may be used as a vector for transfection (see the image above).
• DNA microinjection : transgenic organisms may also be produced by DNA microinjection. The gene
of interest is injected into a reproductive cell by a fine glass needle (0.5 - 5 µm diameter). This cell
is then cultured in vitro until it develops into an embryo. The embryo is then implanted into a uterus
to grow into a fu ll organism.
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51
3.4 Applications of genetic technology
3.4.3
Gene sequencing
K EV P OINT:
Gene sequencing : techniques used to determine the sequence of nucleotides in a section of DNA.
Gene sequencing is widely used for a number of purposes. Its invention has accelerated the progression
of biological sciences, allowing for initiatives such as the Human Genome Project, and contributing to the
development of techniques such as molecular cloning , transgenics, and gene therapy. Parallel development
of computational tools and databases has allowed us to compare genomes across organisms. From this
we are better able to identify evolutionary relationships and determine patterns of inheritance.
In short, gene sequencing involves isolating DNA, and identifying the sequential order of the nucleotides
present in a section of genetic material. From this information, computational programs allow us to transcribe and translate genes in silico.
Sanger sequencing :
1. Clone many copies of the gene of interest.
2. Throw lots of things in a test tube. Basically, cut your gene up into lots of graduating pieces so that
there is a piece which terminates at every nucleotide place along the sequence.
3. Fluorescently tag the last nucleotide of each DNA
A
segment (e.g. A = green, T = red, C = blue, G =
!
yellow).
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arate out the pieces based on their molecular weight.
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Smaller pieces will run further than larger pieces,
A
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forming distinct 'bands.'
5. Irradiate gel to obtain the fluorescent profile of each
band. This will allow you to see the specific nucleotide at each place along the sequence. For example, the smallest piece (1 nucleotide long) w ill be
the furthest band on the gel. This band fluoresces
green, so we know that the nucleotide at the first
G C A T
place on the gene is A. The next band down (second
smallest) represents the second nucleotide in a sequence. It glows red, therefore it's T, and so on.
----
The input is cut up pieces of the gene of interest which can only sequence small sections of a genome.
The output is a fluorescent profile of the gene sequence.
Oxford Nanopore:
1. A nanopore membrane is assembled containing a number of small 'holes' through
which a current is passed.
2. As a strand of DNA passes through the hole,
the current changes based on what nucleotide is passing through (A, T, G, C).
3. A profile of the change in current over time
is generated, which gives us the nucleotide
sequence.
The input is large segments of DNA, potentially
whole genomes in their entirety.
The output is a graph of change in current over
time. We call this technique 'high-throughput' because the technology is capable of sequencing long
strands of DNA at a very efficient pace. Nanopore
is particularly promising because it is, in theory,
simple to use and portable.
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3.4 Applications of genetic technology
3.4.4
Gene therapy
K EY P OINT :
Gene therapy: the correction of genetic disorders by introducing normal, functional genes into cells.
Gene therapy is an important area of research for the medical field, because it has the potential to make
lasting changes to an individual's health, rather tha111 just treating symptoms. Gene therapy involves the
insertion of a corrected, functioning gene into a cell in which there is a defect.
By introducing this healthy genetic material,
it is hoped that the offspring of the cell of interest will inherit this healthy gene, and therefore repair the genetic disorder.
There are a number of techniques used to
insert new genetic material into cells, including gene guns, inorganic nanoparticles,
and viruses. In particular, scientists have
exploited the ability of viruses to evade the
immune system and insert themselves and
their genetic material into human cells. By
swapping out viral DNA for human genes,
and then allowing these non-infectious vectors to enter host cells, we are able to transfeet cells with the desired information.
Gene therapy can be administered in two
ways: in vivo (within the living), or ex vivo
(out of the living). In vivo treatment involves
the injection of the genetic material (usually
in a viral vector) directly into the organism
whose cells you want to edit. Ex vivo treatment involves removing the dysfunctional
cells from the body, transfecting them by any
of the methods outlined previously, and then
culturing (growing) them. These healthy, edited cells are then re-inserted into the body,
and allowed to grow into healthy tissue.
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Types of gene therapy include:
• Gene augmentation therapy : insertion of new, healthy genes, usually where the gene of interest is
essential to cell function.
• Gene inhibition therapy: insertion of a 'blocking' gene which will stop the expression of a dysfunctional gene not needed in the body.
• Somatic gene therapy: editing of adult somatic cells - this will only affect the cells which are descended from the ameliorated cell.
• Germline gene therapy: editing of gametes (ovum or sperm) - this will affect all cells in any offspring
generated as a result of fertilisation with the edited gamete.
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53
3.4 Applications of genetic technology
3.4.5
ELISA
KEY P OINT:
ELISA (£nzyme-.!:_inked !mmuno!orbent ~ssay): an analytical biochemistry tool used to detect the
presence of antigens in a liquid sample.
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ELISA is a diagnostic tool which exploits the natural binding affinity of antigens and antibodies. Antigens
are biological markers found on the outside of all cells, including infectious agents such as viruses and
bacteria. During an immune response, the body produces antibodies specific to invasive antigens.
By fixing either antigens or the antibodies to a surface, we can detect whether the corresponding molecule
is present in a sample. When a reporter molecule is washed over, and bound to the complex, its levels can
be measured, indicating the amount of antigens or antibodies in a sample.
ELISA can be designed to test if individuals have produced antibodies specific to an antigen, indicating
that they have been exposed to a disease (such as direct ELISA in the above diagram). It can also be
designed to test the presence of antigens in a sample, indicating that certain infective agents are present
(i.e. sandwich ELISA). In this way, ELISA is an effective tool for forensic epidemiology, enabling us to trace
the spread of infectious disease.
3.4.6
CRISPR
KEY P OINT:
CRISPR-Cas9: a gene editing system where point mutations are accurately introduced to genomes.
The CRISPR-Cas9 system is composed of 2 parts:
• A guide RNA, containing the nucleotide sequence complementary to the gene you want
to edit, bound to...
• A Cas9 endonuclease enzyme, which is able
to cut DNA
Using this system, we can direct our gene editing tool to a specific part of a genome with very
high accuracy, and with the same tool, cut and
edit the gene of interest. With CRISPR, we are
able to insert, delete, or substitute up to 20 base
pairs. This technology has the potential to improve
targeted gene therapy, reversing point mutations
which cause diseases such as cystic fibrosis. In addition, its efficiency and relatively low cost make it a
great tool for molecular biology research, improving
gene cloning and production of transgenic species.
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3.4 Applications of genetic technology
SYLLABUS:
Evaluate the benefits of using genetic technologies in agricultural, medical, and industrial applications.
I
Application
I
Techniques
I
Benefits
Agriculture
- Selective
breeding
- Artificial
pollination
- Transgenesis
- Creation of crop and livestock species which exhibit favourable
traits (i.e. higher yields, higher nutritional value, better temperament
in livestock)
- Creation of organisms which do not require use of insecticides or
herbicides, decreasing the impact on the environment
- Increased food security as a solution to global poverty and food
shortages
Medicine
- Therapeutic
cloning
- Gene cloning
- Gene
sequencing
- Gene therapy
- ELISA
- CRISPR
- Personalised medicine leading to pre-emptive diagnosis of
disorders for better treatment
- Treatment of genetic diseases leading to potential cures, rather
than merely addressing symptoms
- Improved diagnostic tools
- Cheaper, faster tools which can be used in remote locations,
increasing access to healthcare
- Improved creation of important biological molecules for treatment
of disease (e.g. insulin for diabetes)
Industry
- Gene cloning
- Transgenesis
- Increased speed of chemical reactions leading to more efficient
industrial processes
- Creation of organisms which produce industrially significant
products (e.g. biofuels, biomaterials, energy)
For more information on specific technologies and an evaluation of their importance for addressing global
issues, see the section on genetic technologies on pages 45-55.
3.4. 7
Evaluation of genetic technology
SYLLABUS:
Evaluate the effect of biodiversity using biotechnology in agriculture.
Positives:
Negatives:
• Insect and herbicide resistance (not re• Agricultural practices have always posed a
quired to use harsh chemicals which rethreat to biodiversity as the encourage the
duces the environmental impact of largegrowth of specific crops in large amounts, resscale agricultural practices)
ulting in widespread soil nutrient loss, monocul• Proliferation of knowledge-based agriculture
turing practices, and a reduction in ecosystem
• Increase stress-resistance and productivity
diversity
- Maximise use of restricted land
• Ability to out-compete un-modified crops
- Survive against increased environ- Could lead to the establishment of monomental pressures
culturing practices where immediate profit
- Ameliorate issues of biodiversity in
is prioritised over long-term sustainability
areas facing desertification or pollution
- Loss in genetic diversity and variation will
• Potential to deliberately and effectively inincrease susceptibility to serious selection
crease genetic diversity in crops through
pressures (e.g. superbugs)
transgenics
• Horizontal gene transfer into native ecosystems
- Competitive advantages may lead to a loss
in natural biodiversity
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55
3.4 Appli cations of genetic technology
Ultimately, it's all about balance. Biotechnology should be cleverly and strategically implemented to protect
natural ecosystems, whilst positively contributing to sustainable agricultural practices.
CA SE SPACE :
Golden Rice
Golden rice is a strain of rice which was developed through genetic engineering techniques. The variety
has been designed to produce beta-carotene, a precursor to vitamin A. The fortified rice is intended to
be grown in areas whose populations have a general shortage in dietary vitamin A.
Golden rice was created by inserting two genes for beta-carotene biosynthesis into the plant's genome:
• psy (phytoene synthase), derived from daffodil
• crtl (carotene desaturase) derived from a soil bacterium
These genes were inserted into the genome under the control of the endosperm promoter so that they
would only be expressed in the edible part of the plant.
Advantages
Disadvantages
- Public health benefits (e.g. aid with
vitamin A deficiency which is responsible
for 1- 2 million deaths annually)
- Introduction of new alleles into the gene
pool, increasing variation across rice
species
- Development of this technology paves
the way for future research into
nutritionally augmented foods
- The Golden Rice Project sets an
example of how biotechnologies can be
implemented for humanitarian use rather
than pure capital raising
- Potential loss of biodiversity in the
surrounding areas due to unsustainable
monoculturing practices
- Existing issues with agriculture are
exacerbated by corporate control of the
product
- Unforeseeable risks of introducing new
molecules into diet (though this has
largely been disproved in recent studies)
- Fears that widespread use of golden
rice will divert attention away from
continuing structural inequalities that are
the cause of vitamin A deficiency
SYLLABUS :
Interpret a range of secondary sources to assess the influence of social, economic, and cultural contexts
on a range of biotechnologies.
___
_J
Below is a outline which may be adapted to assess a variety of biotechnologies and genetic techniques.
These technologies tend to ignite quite emotional responses from communities and governments, so it
is important to clearly and logically address the issues associated with their use in an objective manner.
If we can troubleshoot our technologies and try to improve them on this basis, they will be vastly more
successful both scientifically and in terms of implementation in the community. Science should involve a
robust dialogue with the society which it is trying to help.
CA SE SPACE:
Genetically Modified Foods
Genetically modified foods are organisms (crops or livestock) whose genomes have been altered by
genetic engineering techniques. The aim of genetically modified foods is to introduce new traits (often
derived from different organisms) which confer a benefit such as resistance to insects or herbicides, or
increased nutritional value.
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3.4 Applications of genetic technology
Examples of genetically modified foods include:
• Bt cotton: cotton crops with the Bacillus thuringiensis bacterial toxin gene inserted into the genome, which confers resistance to insecticides due to expression of insecticidal protein
• Golden rice: insertion of genes so that the endosperm of the plant produces vitamin A precursor,
beta-carotene
• Virus resistant papaya: transgenic fruit tree with DNA of papaya ringspot virus incorporated into
its genome to confer resistance
There are currently 26 species of GM crops available for commercial sale in at least one country. Although GM livestock have been developed, including cattle, pigs, and goats, however none of these
organisms nor their products are currently available for commercial use.
Advantages
Disadvantages
Social impacts:
- Addresses matters of global inequality such
as poverty and food security, and aids in
fulfilling the UN Sustainable Development
Goals
- May increase the dialogue between
communities and scientists, and improve
scientific literacy
- Reduction in environmental footprint is
beneficial to the global community, as there is
less leeching of chemicals into ecosystems
- GM crops require less tillage, meaning there
are fewer greenhouse gas emissions, and the
production of drought-resistant crops enables
water conservation
Economic impacts:
- Stimulates agricultural economy
- May provide farmers in third world countries
with tools to grow crops easily and quickly
- Enables farmers with nutrient-poor soil or
poor access to water to continue growing
nutrient-rich foods, and increases the amount
of food produced per m 2
- May help to improve desertified ecosystems
Cultural impacts:
- Food has been an essential part of cultural
practices for centuries
- Agricultural practices, which are often
central to global cultures, can be preserved in
the face of changing climates
- May provide a tool for preserving important
foods and maintaining significant industries in
certain areas
Social impacts:
- May increase socioeconomic disparity if
implemented incorrectly, meaning the rich
get richer
- Lack of consistent regulation
internationally may restrict the ability for GM
foods to be imported effectively, which may
impact negatively on farmers whose only
choice given their environment and its
challenges is to use GM crops
Economic impacts:
- Potential for monopolisation by large
biotechnology companies
- Exploitation of patents on GM crop strains
to increase profits
- May cut small-scale and third world
farmers out of the market
- Development of 'terminator seed'
technologies may create dependence on
companies, and continual re-purchasing of
products may lead to uncertainty for farmers
in terms of price consistency
Cultural impacts:
- Traditional, region-specific farming
practices may be eradicated in favour of
large-scale agricultural methods (i.e. loss of
important parts of indigenous cultures)
- Lack of sufficient scientific communication
with regards to GM foods has led to
widespread mistrust amongst communities
(particularly the US) and a rise in
anti-science beliefs.
- Backlash from religious groups on ethical
grounds may lead to divisive debates
I
The above is just a brief outline, as there are many more factors that you might chose to consider in
formulating your own responses. For more discussion on this topic, see pages 41-42. I would also highly
recommend conducting your own research into the issues of gene techniques!
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57
Part Ill
Module 7: Infectious Disease
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Causes of Infectious Disease
Topic 1
Causes of Infectious Disease
S YLLABUS:
Inquiry question : How are diseases transmitted?
1.1
Pathogens
S YLLABUS:
Describe a variety of infectious diseases caused by pathogens, including micro-organisms, macroorganisms and non-cellular pathogens, and collect primary and secondary-sourced data and information
relating to disease transmission, including:
• Classifying different pathogens that cause disease in plants and animals
• Investigating the transmission of a disease during an epidemic
• Design and conduct a practical investigation relating to the microbial testing of water or food
samples
• Investigate modes of transmission of infectious diseases, including direct contact, indirect contact
and vector transmission
The following table explains the types of pathogens from smallest (prions) to largest (macro-parasite).
I
I Pathogen I Description
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Example
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Prion
Virus
- Proteinaceous infections particles
- Abnormally folded protein which propagates by transmitting the
misfolded protein state to other cellular proteins
- Non-cellular infective agent consisting of nucleic acid (DNA or RNA)
inside a protein coat (envelope)
- Replicates inside living cells
- HIV
- Measles
Bacteria
- Single-celled prokaryotic organism (no membrane-bound
organelles)
- Reproduce by binary fission
- Secrete toxins, invade cells, and form colonies (biofilms) which
disrupt cell function
- Salmonella
Protozoa
- Single-celled eukaryotic organism
- Hetereotrophic : absorb nutrients from hosts
- Secrete toxins, invade cells, and form colonies to disrupt cell and
tissue function
- Malaria
- Dysentery
Fungi
- Eukaryotic, heterotrophic organisms with cell wals
- Absorb nutrients from environment by secreting digestive enzymes
- Reproduce by spreading spores that can release harmful enzymes
- Thrush
- Ringworm
Macroparasite
-
- Ticks
-Tapeworms
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Visible with the naked eye
Ectoparasite: lives on an organism
Endoparasite: lives in an organism
Invade and destroy cells, create competition for nutrients
Copyright © 2018 lnStudent Publishing Pty. Ltd.
CD
- Mad cow
disease
- CreutzfeldtJakob
disease
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1. 1 Pathogens
1.1.1
Transmission during an epidemic
Disease
Cause
Transmission
Malaria
Plasmodium protozoa
Vector transmission via Anopheles mosquito:
1. Plasmodium sex cells reproduce in the Anopheles mosquito, forming
zygotes in cysts of its stomach wall.
2. Cysts burst and sporozoites travel to the salivary gland of the mosquito,
transferring to humans when bitten.
3. Sporozoites travel to the liver, enter red blood cells, and continually
multiply.
4. Infected cells burst, causing malarial fever.
5. Cycle continues when human host is bitten by mosquito, passing mature
cells back into the vector.
Malaria is prevalent in tropical environments where the climate suits mosquito
propagation, and temperatures at which plasmodium growth is successful.
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- The immune system attempts to clear the body of plasmodium by cell-mediated
response.
- Anaemia occurs as the red blood cells are damaged.
- This leads to an enlarged liver and spleen , sweating, fever, shivering, and
eventual death.
Epidemics
In order to pre-empt epidemics, organisation such as the World Health
Organisation attempt to forecast outbreaks by assessing a number of factors,
including:
- Identification of epidemic-prone areas based on past outbreaks, environmental
factors, and climate factors.
- Vulnerability assessment of population displacement, civil unrest, insecurity of
food supply, incidence of other diseases, drug resistance of parasite, and
infrastructure (e.g. agricultural projects, dams, flooding).
Ultimately this information is used to stop malaria transmission by proactively
breaking the malaria cycle.
Prevention
Mosquito nets, protective clothing , insect repellent
Control
ll ■~IQUa at■I ■II
Breaking the plasmodium life cycle by draining swamps and killing mosquitoes
Copyright © 2018 lnStudent Publishing Pty. Ltd.
1. 1 Pathogens
1.1.2 Testing for microbes
Aim
Hypothesis
Materials
Method
Variables
To investigate the presence of microbes in different water sources
That water extracted from a pond and from the sea will contain different microbes
Agar plates, parafilm, sterilised water, pond water, sea water, inoculating loop,
inculator, Bunsen burner
1. Light Bunsen burner to create a sterilised work area.
2. Label 8 agar plates (2 x nothing, 2 x sterilised water, 2 x pond water, and 2 x
sea water).
3. Seal two control agar plates labelled 'nothing' using parafilm and set aside.
4. Open agar plate labelled 'sterilised water' carefully at 45° angle.
5. Using an inoculating loop, swab agar plate with sterilised water and seal.
6. Repeat steps 4 - 5.
7. Repeat steps 4 - 6 using pond water, and then sea water.
8. Incubate plates for three days at 30°.
9. Remove plates from incubator and observe for colony growth.
10. Record observations of types of microbial growth, taking notes of colour, shape,
size, and frequen cy of colonies.
-
Independent variable: type of water (pond water or sea water)
Dependent variable: types of microbial growth
Controlled variables: temperature, incubation period, amount of water inoculum
Controls: agar plate inoculated with sterilised water, agar plate left uninoculated
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Risk
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- Precautions: wear personal protective equipment (PPE), including globes, coats,
and glasses. Take care when handling agar plates. Wash hands before and after
experiment.
- Response: seek medical assistance if feeling unwell.
Water spillage:
- Precautions: take care not to spill water, and wipe up all spillages immediately.
Do not perform experiment close to electrical outlets.
- Response: seek medical assistance if injury occurs.
Open flame:
- Precautions: wear PPE, tie back hair, use caution.
- Response: seek medical assistance if injury occurs.
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Different types of microbes are present in different types of water, and therefore can
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61
1.2 Koch and Pasteur
1.1.3
Modes of transmission
There are two key modes of transmission: horizontal and vertical.
Horizontal transmission
• Direct contact: this is the easiest way to catch an Infection. It happens when an individual physically
comes into contact with a person or animal with a disease. There are three types of direct contact
transmission:
- Person-to-person (touching, kissing, coughing , or sneezing on someone)
- Animal-to-person (handling, bites, or scratches)
- Mother-to-unborn-child (germs passing through the placenta during gestation , or transferring
from the vaginal canal during birth)
• Indirect contact: some pathogens are able to live outside of hosts for a period of time. They may
linger in the environment on inanimate objects such as doorknobs after being spread by infected
people. This Is why it's so Important to wash your hands after touching public surfaces and before
eating food!
• Vector transmission: some pathogens are passed by vectors, which are insects that carry diseases
from person-to-person. Examples of insect vectors Include mosquitoes (malaria) and ticks (Lyme
disease) .
• Contamination : pathogens may also be harboured in food and water where the abundance of nutrients allows them to grow.
Vertical transmission
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• Transplacental : to a foetus from the mother through the placenta.
• During vaginal birth: the microflora present in the mother's cervix and vagina is passed on to the
child as It passes through the birth canal. If the mother has an infection, such as a sexually transmitted
disease, this may pass on to the child.
• Breast feeding : when a mother is breast feeding, fluids and nutrients are passed to the baby through
the milk. If the mother has contracted an infectious disease, it may be passed to the child and
ingested.
1.2
Koch and Pasteur
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Investigate the work of Robert Koch and Louis Pasteur, to explain the causes and transmission of infectious diseases, including:
• Koch's postulates
• Pasteur's experiments on microbial contamination
Robert Koch was a German microbiologist working in the late 1800s. He is known as the founder of modern bacteriology, having correctly identified the microbial origins of many diseases, such as anthrax, cholera, and tuberculosis. Most notably, Koch developed a procedure for isolating and identifying diseasecausing microbes. This method directly linked microbial growth as a causative agent in disease progression.
Koch's Postulates
1. In all organisms suffering from disease, the micro-organisms must be present in abundance.
2. Micro-organisms must be isolated from the diseased organism, and grown in pure culture.
3. When a healthy organism is inoculated with the pure culture, it must develop the same symptoms as
the original sick organism.
4. Isolate and re-grow the micro-organism from newly infected organism. If it is identical to the microorganism cultured in step 2, it has been identified as the cause of the disease.
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1.3 Causes and effects of diseases in agriculture
Pasteur's Experiments
Louis Pasteur was a French microbiologist who worked during the 1800s. Through his experiments, Pasteur disproved the previously accepted theory of spontaneous generation by demonstrating that all microorganisms come from pre-existing microorganisms (germ theory of disease). In his work, he produced the
first vaccines for rabies and anthrax, making significant contributions to the field of immunology. He was
also involved in the discovery of microbial fermentation, and developed the now commonly used technique
of pasteurisation.
C ASE S PACE:
Swan-necked flask exoeriment
Pasteur's swan-necked flask experiment was used to disprove spontaneous generation. He took flasks
with bent necks ('swan-necked') through which particles in the air could not travel without getting stuck.
After filling the flasks, he sterilised the liquid by boiling them at high temperatures. One of the flasks
had its neck removed, and one did not. Pasteur showed that only the flask with an open, broken neck
was able to grow bacteria in the broth, whereas the other flask remained uncontaminated. Through this
he demonstrated that microbial growth was a result of particles in the air, and could not arise spontaneously in sterile environments. This finding contributed significantly to our understanding of disease, as
the scientific community began to accept that infectious diseases must be a result of micro-organisms,
originating from some external source.
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1.3 Causes and effects of diseases in agriculture
SYLLABUS :
Assess the causes and effects of diseases on agricultural production, including but not limited to:
• Plant diseases
• Animal diseases
1.3.1
Plant diseases
Causes
• There are a number of infectious agents which contribute to plant diseases, including bacterial,
fungal, viral, protozoic, and micro-parasitic agents. In addition, abiotic factors, such as drought,
frost, or nutrient deficiency may also have impacts upon plant health.
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63
1.3 Causes and effects of diseases in agriculture
• The Australian Government Department of Agriculture and Water Resources (AGDAWR) has identified a number of priority plant pests which greatly affect agriculture in Australia, including:
- Fruit flies (macro-parasite which infects fruits and vegetables)
- Wheat stem rust (fungal pest which infects wheat, barley, oats, and rye)
- Potato cyst nematode (microscopic round worm which eats potato, tomato, and eggplant roots)
- Sharka (plum pox virus which infects summer fruit, including cherries and plums)
Effects
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• Infectious diseases affect the ability for plants to carry out normal functions, and therefore have a
significant impact on the yield and quality of agricultural products.
• Due to the reduction in productivity, and costs associated with prevention, plant diseases cost Australia millions of dollars each year. In addition, agriculture is a significant Australian industry, and
reduction of its efficiency impacts our ability to trade both locally and internationally.
• Globally, it is estimated that plant pathogens cause 12.5% of crop losses.
• Plant disease can also have significant social impacts, particularly in developing countries, by contributing to diminished food security. For example, the Irish Potato Famine (1845-1849) was caused
by widespread potato infection, leading to the death of about one million people, as well as mass
emigration from Ireland.
• Plant diseases may adversely affect biodiversity in natural ecosystems, particular where they have
been transported from foreign countries. Biosecurity is the practice of protecting society (the economy, environment, and community) from the negative impacts of biological phenomena, such as
pests and disease. Australia has strict biosecurity laws and practices in order to maintain our status
as a relatively unaffected, isolated nation.
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As with plant disease, animal diseases may be caused by a number of different infectious agents
including bacteria, viruses, protozoa, and macro-parasites.
The AGDAWR lists a number of animal diseases which are of particular concern to Australian biosecurity, including:
- Avian influenza (bird flu - a severe viral disease affecting poultry for which there is no treatment)
- Foot-and-mouth disease (highly contagious viral infection affecting cloven-hoofed animals, often
leading to significant mortality levels in young animals)
- Bovine Spongiform Encephalopathy (BSE - a fatal neuro-degenerative disease caused by prions, otherwise known mad cow disease)
Effects
• Economic impacts:
- Australia's livestock industry has been fundamental to the growth of the Australian economy in
our recent history, contributing around $15 billion in export revenue and $18 billion to GDP in
2017. Animal diseases have the potential to significantly impact this.
- The CSIRO estimates that a major outbreak of foot-and-mouth disease may cost the Australian
economy around $50 billion.
• Food security : animal disease may severely impact agriculture, which has significant impacts upon
at-risk populations facing poverty or malnutrition.
• Health risks: animal diseases have the potential to infect humans hosts as well. This may affect
farmers and handlers, as well as those who consume the products.
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Copyright© 2018 lnStudent Publishing Pty. Ltd.
1.4 Transmission of pathogens
1.4 Transmission of pathogens
SYLLA BUS:
Compare the adaptations of different pathogens that facilitate their entry into and transmission between
hosts.
Pathogenic adaptations facilitating entry into hosts are as follows:
• Cell wall-degrading enzymes : break down the plant cell wall, releasing intracellular nutrients.
• Toxins: molecules produced by pathogens which promote infection. Toxins may damage host tissues
or disable the immune system (e.g. by inhibiting phagocytosis) . Examples include:
- Cholera secretes a toxic protein which binds to epithelial cells in the gut, helping the pathogen
to invade the host organism.
- Botulinum produces a deadly neurotoxin, which blocks the function of nerve cells, causing paralysis and eventually death.
• Effector proteins: proteins secreted into or around a host cell which suppress host defence processes. These are used by a number of pathogens, including bacteria and fungi. For example, type
three secretion systems (T3SS) is a protein nanomachine which bacteria have to inject proteins into
host cells, like a nanoscale needle.
• Adhesion to host cells : expression of adhesin molecules allows pathogens to stick in the extracellular environment, promoting their colonisation of tissues and organs of hosts.
• Extremophlles: pathogens with the ability to survive in hostile environments, such as very high
or low pH, temperature, oxygen , or salinity. This may enable some pathogens to survive inside or
outside of hosts for a long period of time to enact transmission.
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specific requirements (for a summary of the types of transmission, see page 62).
2.
Pathogenic adaptations facilitating transmission between hosts are as follows.
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• Reservoirs: sites (living and non-living) where pathogens may lay dormant for long periods of time.
For example, animals may act as reservoirs of human disease in zoonotic diseases (i.e. diseases
that can be passed from animals to humans).
• Use of vectors : increases transmission efficiency and provides a living organism in which pathogens
may continue to replicate in between human infections - for example, ticks and Lyme disease, or
mosquitoes and malaria.
• Protective coverings:
- Bacterial capsules: a viscous substance which covers the outside of some bacterial strains,
creating an extra protective layer over the cell wall. Capsules are usually composed of polysacharids, packed tightly together. Capsules may protect cells from being engulfed by macrophages and improve adherence to surfaces.
- Viral envelopes: composed of proteins or lipids, envelopes form a protective layer around the
outside of viruses, allowing for improved longevity outside of host cells and potentially may aid
in avoiding the host immune system.
• Rapid species evolution : high rates of mutation within the genomes of pathogens, coupled with
fast reproduction rates, allow pathogenic species (particularly viruses) to evolve at a rapid rate. This
means that they are better able to invade hosts.
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Responses to Pathogens
Topic 2
Responses to Pathogens
SYLLABUS:
Inquiry question : How does a plant or animal respond to infection?
2.1
Plant responses
( SYLLABUS :
Investigate the response of a named Australian plant to a named pathogen through practical and/or
secondary-sourced investigation, for example:
• Fungal pathogens
• Viral pathogens
Pathogen
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Myrtle rust is a fungal infection which attacks soft, new growth such as
leaves, shoot tips and young stems of plants. The infection begins as small
purple spots on leaves, from which bright yellow spores form inside of
bulbous pustules. The fungus spreads by releasing spores, which are easily
dispersible by wind, accounting for the high degree of transmission over a
relatively short period of time.
Prevalence
First detected in 201 O and since spread across eastern Australia
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Description
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Host response
Pre-formed defences:
- Mechanical barriers such as bark, thick cell walls composed of pectin and
lignin , and leaf cuticles
- At sites of infection, cell walls become reinforced by deposition of additional
structural proteins
- Secretory cells and glands transporting defensive substances
- For eucalypts, essential oils are produced and stored in sub-dermal
secretory cavities and can act as a chemical defence against fungal and
bacterial infections
- Production of antimicrobial peptides
Incurable defences:
- Innate defences activated by recognition of non-self cells
- Non-specific immune response
- Accumulation of harmful metabolites (such as reactive oxygen species of
salicylic acid) at the site of infection
- Upregulation of pathogenesis-related proteins, some with antifungal activity
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'
2.2 Lines of defence
2.2
Lines of defence
SYLLABUS:
Analyse responses to the presence of pathogens by assessing the physical and chemical changes that
occur in the host animal cells and tissues.
2.2.1
First line of defence
Humans have a number of pre-formed adaptations which inhibit pathogens from entering the body. These
adaptations attempt to deny pathogens entry so that infection does not occur. This includes:
• Skin: tightly packed cells forming a protective layer. Pores in the skin secrete anti-microbial fluids,
inhibiting surface microbial growth. The outermost layer of the skin (keratinocytes) is constantly
shed.
• Mucous membrane: cells lining the openings of the body (respiratory tract, urinary, and reproductive
systems) secrete a protective layer of mucous, which traps pathogens and other foreign particles.
• Cilia: hair-like projections which line the air passages (nose and throat). Movement of these structures pushes pathogens away from the lungs in a wave-like motion. Cilia beat in one direction at
about 12 beats per second, working with mucous membranes to move pathogens out of the body.
• Chemical barriers: substances such as stomach acid, alkali conditions in the small intestine, and
enzymes in the mouth all act to destroy pathogens. The variation of different pH conditions in the
digesti ve tract ensures that all pathogens are neutralised. Enzymes such as lysozymes dissolve cell
membranes to kill pathogens such as bacteria.
• Secretions: fluids are routinely secreted from the sweat glands, hair follicles, and open passages in
the body. These secretions contain antimicrobial chemicals which destroy bacteria and fungi, as well
as acting to flush out pathogens which may have settled on or in surfaces.
2.2.2
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Apart from pre-formed structures which block entry into the body, animals have also adapted responsive
defence systems which fight off foreign organisms in the body and stop the progression of disease from
pathogens. These are termed the 'second line of defence' as they are activated once a pathogen has
passed through external physical barriers, and may include:
• Lymph system : including the lymphatic vessels, the spleen , thymus, and lymph nodes. It produces
white blood cells (WBCs) responsible for enacting the immune response. Pathogens are drained to
the lymph nodes via lymph fluid, where they can be neutralised or killed by immune cells.
• lnflamation: the dilation of blood vessels and infiltration of inflammatory cells at the site of infection ,
causing heat, pain, redness, swelling, and acute loss of function. When tissues are damaged, they
release histamines, which increase the permeability of proximal blood vessels and allow WBCs to
travel more easily to the site. The purpose of inflammation is to eliminate the cause of injury (the
pathogen), clear out necrotic cells from the area of infection , and initiate tissue repair by stimulating
the flow of blood to the area. By heating the area, pathogens are subjected to higher temperatures,
which may deactivate them, stopping infection.
• Phagocytosis: specialised WBCs, macrophages, and neutrophils are able to change their shape
to engulf pathogens or cellular debris. Once pathogens are enclosed within the immune cells, they
can be broken down by enzymes.
1. Phagocytic receptors on the surface of WBCs bind to microbes.
2. Bound materials are internalised, forming phagosomes.
3. The phagosome fuses with lysosomes in the cell, forming phagolysosomes.
4. Microbes inside phagolysosomes are killed/degraded by acidification (pH 3.5-4), antimicrobial
proteases and enzymes, reactive oxygen and nitrogen species (which bind to nucleic acids and
proteins and oxidise them, causing degradation), and antimicrobial proteins (e.g. defensins).
• Cell death to seal off pathogens: macrophages and lymphocytes may completely surround a
pathogen and undergo programmed cell death (apoptosis). This results in the formation of a cyst,
which blocks pathogen movement and any nutrient supply, causing it to also die.
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Immunity
Topic 3
Immunity
SYLLABUS:
Inquiry question : How does the human immune system respond to exposure to a pathogen?
3.1
Innate and adaptive immune systems
SYLLABUS:
Investigate and model the innate and adaptive immune systems in the human body.
3.1.1
Innate immune system
The innate immune system provides non-specific protection against pathogens by responding in a generic manner to all foreign invaders. The innate response is initiated immediately following exposure to a
pathogen, or within a few hours - this is a rapid respon se rate. This stage of the body's defence does
not have immunological memory to specific infections, but most aspects are consistently present to provide
continued protection to a broad array of pathogens.
There are two components of the innate immune response: the first line of defence, and the second line of
defence (as outlined previously).
3.1.2
Adaptive immune system
The adaptive immune system is highly specific, providing specialised protection against pathogens which
enter the body. The adaptive immune system needs time to develop upon primary exposure to a pathogen
(it is not as rapid as the innate immune response). However, it has Immunological memory, which means
response upon secondary exposure and thereafter is stronger and faster.
There are two main classes of cells in the adaptive immune system: B cells and T cells.
• B cells:
- Mature in the bone marrow, developing from hematopoietic stem cells
- Produce antibodies responsible for antibody-mediated immunity
- Once activated by pathogenic antigens, B cells undergo mitosis and differentiate into two types:
• Plasma cells (immediate protection) secrete antibodies of the same antigen specificity as
the selected parent B cell
• Memory B cells (persistent protection): circulate through the body initiating stronger, more
rapid responses upon secondary antigen detection
• T cells:
- Originate in the bone marrow and mature in the thymus
- Responsible for cell-mediated immunity
- There are a number of different types of T cells, each playing an important role in immunity:
• Helper T cells: assist other WBCs such as B cells in their immunological processes. Once
selected by antigens, helper T cells rapidly divide and secrete cytokines (signalling molecules) which help to coordinate the immune response.
• Cytotoxic ('killer') T cells: these are the destroyers! These T cells release cytotoxins,
such as perforin, and granzymes, that kill target cells by triggering apoptosis. Essentially
they send a signal to an infected cell , forcing it to kill itself and anything inside of it (like a
virus).
• Regulatory ('suppressor') T cells: control cell-mediated immunity by suppressing the
activity of other T cells once the immune reaction has achieved its purpose. Basically, they
stop the killer T cells from killing everything in a wild frenzy!
• Memory T cells: provide immunological memory by remaining in circulation after infection,
so that the body may mount a quicker, more effective response upon re-infection.
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3. 1 Innate and adaptive immune systems
Antigen-antibody interactions
Antigens are molecular markers present on the surface of all cells. Each type of cell exhibits a certain
antigen (all antigens have slightly different shapes) by which they are recognised. The body is able to recognise foreign pathogens as 'non-self' by their antigens. Antibodies bind specifically to antigens, allowing
for a number of immune responses.
Antibodies benefit the immune response in three ways:
1. Neutralisation: antibodies binding to pathogens or toxins to block their effect on host oells. Once
immobilised, toxins and pathogens may be degraded, either by macrophages or killer T cells.
2. Opsonisation: the binding of antibodies to antigens improves the efficiency of phagocytosis.
3. Complement system: by binding to pathogens present in the blood stream, antibodies activate lysis
and ingestion of infections.
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69
3. 1 Innate and adaptive immune systems
Clonal selection
Clonal selection is the process by which the adaptive immune system gains its specificity against pathogens. It occurs in both T and B cells. We can think of clonal selection kind of like rapid evolution of our
immune system.
1. Variation: our body has a pool of variable immune cells - millions of different T and B cells. These
naive cells will circulate in the body until they encounter an antigen.
2. Selection pressure: by binding to a specific immune cell receptor (due to the binding specificity
outlined above), the antigen selects that cell.
3. Reproduction : this selected cell rapidly divides, producing lots of copies of the cell which produces
antibodies best suited to the antigen. These cells differentiate into the different cells of the immune
response (i.e. plasma cells, memory cells).
This process is iterative, much like evolution. Within each generation of cell division, there will be small
changes to the conformation of antibodies on the cell surface, and this means that antigen affinity may be
continually improved.
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3.2 Innate and acquired immunity
3.2
Innate and acquired immunity
( SYLLABUS:
Explain how the immune system responds after a primary exposure to a pathogen, including innate and
acquired immunity.
The immune system enacts a coordinated response to pathogen exposure, mediated predominantly by
WBCs, B cells, and T cells.
1. When a pathogen first enters the body, it is detected as foreign due to the presence of non-self
antigens on its surface.
2. Inflammation allows increased blood flow to the site. Increased permeability of blood vessels allows
WBCs to migrate from the blood into the infected tissue.
3. Non-specific responses, including phagocytosis, occur. Macrophages engulf pathogens which
they encounter and release cytokines to call other immune cells to the site of infection.
4. The macrophages present the foreign antigens on their surface for recognition by B cells and T helper
cells which are recruited to the site by interleukins (a type of cytokine).
5. Band T cells specific to the pathogen are selected by the antigens (clonal selection).
6. B cells differentiate into plasma cells, and secrete pathogen-specific antibodies to immobilise the
foreign cells.
7. Cytotoxic killer T cells attack pathogenic cells by releasing cytotoxins (e.g. perforin).
8. Memory B and T cells are produced.
9. Pathogen is cleared from the site.
10. Suppressor T cells come in and dampen the immune response, suppressing killer T cells once the
infection has passed.
11 . Memory B and T cells remain circulating in the blood to provide long-term immunity.
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71
Prevention, Treatment, and Control
Topic 4
Prevention, Treatment, and Control
SYLLABUS:
Inquiry question : How can the spread of infectious disease be controlled?
4.1
Disease spread
SYLLABUS:
Investigate and analyse the wide range of interrelated factors involved in limiting local, regional, and
global spread of a named infectious disease.
There are three different levels we can target to control the spread of disease : local, regional, and global.
• Local:
- Immunisation to create herd immunity within local populations.
- Personal hygiene practices, including washing and drying hands regularly, covering coughs and
sneezes.and cleaning surfaces regularly.
- Safe health practices, including limiting spread of sexually transmitted infections by use of physical contraceptives, and staying at home when you are sick.
- Provision of public health information to improve public knowledge of diseases and prevention.
• Regional:
- Consideration of environmental conditions:
• Water supply: access to clean water significantly helps prevent disease
• Sanitation facilities: inadequate disposal facilities may lead to contamination of water
supplies, poor hygiene, and living conditions.
• Food: contamination or poor preservation may lead to a spread of food-borne infections.
It is important that food handlers and suppliers are properly trained to limit this.
• Climate: distribution and population size of disease vectors are affected heavily by climate
(e.g. mosquitoes which spread malaria breed in warm, humid climates).
• Flooding : may lead to sewage overflow and water contamination on a large scale.
Improving swift identification:
• Continued surveillance: systematic collection , analysis, interpretation, and dissemination
of health data.
• Rapid recognition of presence: disease awareness and reporting from the community,
reliant on public health programs and dissemination of information.
• Efficient diagnosis of microbial cause: this is a cornerstone of effective control and
prevention efforts, improved by dispe1rsion of technological advances.
- Appropriate and efficient responses, including isolation, treatment, identification of high-risk
groups, and the provision of supplies to prevent further transmission.
• Global:
- Communication between countries and with global health organisations is essential (e.g. World
Health Organisation member states are required to report within 24 hours any disease or event
which may constitute a public health emergency of international concern).
- Implementation of quarantine measures, which involves things like travel bans into or out of
countries significantly affected by disease outbreaks.
- Monitoring movement of potentially affected individuals.
Potential infectious diseases to investigate include influenza epidemics (e.g. avian flu, swine flu), malaria,
cholera, yellow fever, and SARS.
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4.2 Methods for preventing disease spread
4.2
Methods for preventing disease spread
SYLLABUS:
Investigate procedures that can be employed to prevent the spread of disease, including:
•
•
•
•
•
•
Hygiene practices
Quarantine
Vaccination, including passive and active immunity
Public health campaigns
Use of pesticides
Genetic engineering
Diseases are often caused by transmission of microscopic pathogens. These may be transmitted in food,
water, by vectors, in the air, and on the body without our knowledge. In order to prevent the spread of
disease, a number of different procedures may be implemented, ranging from personal to societal measures
which we can use to improve public health.
• Hygiene practices: washing hands, cleaning wounds, and undertaking responsible food preparation
all minimise the likelihood of micro-organisms entering the body.
• Quarantine: isolation of an individual for a set period of time in order to prevent the spread of disease.
This allows either for the infectious period to elapse, or for symptoms to develop. Quarantine may be
used for foods, plants, and animals. By physically detaining diseased individuals, it allows for other
individuals in the community to be protected.
• Vaccination : introducing attenuated pathogenic particles into the body can trigger a small-scale immune response. This allows for specific antibodies to be produced against certain diseases, allowing
for a stronger, more rapid response under second exposure. This reduces the likelihood of infection
from pathogens such as viruses.
- For example, the Human Papillomavirus (HPV) vaccination program in Australia began for females in 2007 and extended to males in 2013. By 2014, 73% of females and 60% of males
turning 15 were fully immunised. There has been a significant fall in HPV-related infection,
symptoms, and cervical abnormalities since dissemination of the program across the country.
• Public health campaigns: focus on management and prevention and aim to raise awareness and
spread understanding about causes and impacts of disease. This may lead to healthier choices in
the community, and thus prevent the spread of disease in the population.
- For example, the 'Ending HIV' initiative to stop the spread of HIV and AIDS was run by ACON
- a health promotion organisation funded by the NSW government. ACON aims to provide
education, information, and support to at-risk groups. This campaign centred around the slogan
"test often, treat early, stay safe" and was seen in advertisements {billboards, bus stops, posters)
and testimonials. ACON also sponsored HIV Testing Week, and established an online media
presence (www.endinghiv.org.au).
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• Pesticides: chemical or biological agents which control pests, including herbicides, insecticides, and
antimicrobials. Pesticides are used in agriculture to protect from crop damage, as well as to kill
vectors of disease, such as mosquitoes.
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73
4.3 Pharmaceutical treatments
• Genetic engineering: for example, engineering malaria-resistant mosquitoes using CRISPR. This
involved removing the host factor gene (FREP1 ) which encodes a protein that helps the malaria
parasite survive in the gut of the mosquito and develop for transmission. By deleting this gene from
mosquitoes, they become resistant to malaria, and the chain of transmission amongst humans is
broken. In order to pass the edited trait within the wild population , scientists may be able to use a
new technology called gene drive:
- A gene drive improves the odds that a specifically altered gene will be inherited in offsprint. To
achieve this, the CRISPR-Cas9 system is encoded into the mosquito genome (see page 54 for
more information on this technique).
- When passed on to offspring, the guide RNA directs Cas9 to cut the homologous wild-type
genome and remove the undesired allele present in the population. The cell then copies the
desired, altered gene into the chromosome at the same locus when it repairs the damage.
- The mosquito now has two identical copies on each chromosome, therefore all of the offspring
will inherit the alteration. The process is repeated each time sexual reproduction occurs, resulting in the spread of the altered trait throughout the population at increased frequency.
- There is a great explanatory video by the scientists who pioneered this technology here:
www.wyss.harvard.edu/media-post/crispr-cas9-gene-drives/
4.3
Pharmaceutical treatments
SYLLABUS :
Investigate and assess the effectiveness of pharmaceuticals as treatment strategies for the control of
infectious disease, for example: antivirals and antibiotics.
4.3.1
Antivirals
K EY P OINT:
Antivirals: a class of antimicrobial used to treat viral infections, but inhibiting the development of the
pathogen inside the host cell.
Unlike antibiotics, antivirals are not able to destroy viruses; they only inhibit development of the pathogen.
In order to inhibit development, antivirals may target a number of different stages in the virus life cycle.
Below is an example of the viral life cycle of HIV.
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vi r•I
4.3 Pharmaceutical treatments
Types of antivirals include:
• Before cell entry : blocking the virus' ability to infiltrate a cell. This may include:
- Drugs which interfere with the virus' ability to bind to cell surface receptors
- Drugs which specifically bind to virus-associated particles, inhibiting their mobility
• During viral synthesis : drugs which inhibit the ability for a virus to synthesise its requisite components inside the host cell. This may include:
- Inhibition of reverse transcription: the way that viruses replicate is by inserting their genomic material into the host genome by a process called reverse transcription. Drugs may be
developed to stop this process by deactivating the enzymes involved (e.g. aciclovir for HIV).
- Inhibition of transcription: after insertion of the viral genetic information into the genome
of the host cell, transcription must be performed to express the viral proteins. By blocking
trancription factors, this process can be stopped.
- Inhibition of protease activity: viruses include proteases, which are enzymes that cut viral
proteins into pieces so that they can assembled to their final configuration. By blocking protease
activity, drugs may inhibit the ability for viral proteins to assemble into their final form (e.g .
atazanavir for HIV).
• Release phase: blocking the ability for a virus to be released from the host cell, inhibiting its ability
to transmit to further cells. By blocking molecules found on the surface of viruses, drugs prevent the
release of viral particles (e.g. zanamivir for influenza).
It is very difficult to develop effective antiviral drugs because viruses use host cell machinery in order to
replicate. The key is to target molecules which interfere with the virus, but not with host cell processes.
Another barrier to effective antivirals is keeping up with the rapid evolution of viruses, and the wide variation
which exists between different viruses.
Furthermore, continued use of antivirals may result in antiviral resistance where the effectiveness of
drugs becomes reduced overtime. Research and development of antivirals is also very expensive, resulting
in high prices of treatment. For example, a twelve-week supply of hepatitis C drugs costs up to $113,400.
Such exorbitant costs may also be due to monopolies in the pharmaceutical market, and so companies are
able to drive up prices in order to increase profits.
4.3.2
Antibiotics
KEY P OINT:
Antibiotics: a class of antimicrobials used to treat bacterial infections. This may be achieved either by
killing the infective bacteria, or inhibiting its growth.
There are many ways by which drugs may stop the
growth of or kill bacteria. This involves inhibition
of a number of key processes in bacterial growth ,
including:
1. Interference with cell membrane permeability
2. Interference with nucleic acid synthesis
3. Interference with protein synthesis
4. Interference with cell wall synthesis
Antibiotic resistance is an increasing issue for disease control. As outlined in Module 3 of the Year 11
syllabus, there are a number of human factors that have contributed to this issue, including misuse and
overuse of antibiotics. This leads to the evolution of bacterial strains which do not respond to antibiotic
treatment, as they have developed mechanisms to either avoid or deactivate drugs.
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75
4.4 Environmental management and quarantine methods
Antibiotic-resistant strains of bacteria evolved using the fundamental principles of evolution by natural selection.
1. W ithin every population of bacteria, a few are antibiotic-resistant due to natural variation and mutation .
2. Whenever someone uses antibiotics, most of the bacteria are killed, but the few resistant ones survive.
3 . These are then able to reproduce, with antibiotic resistance becoming the dominant trait in the population, eventually leading to a new 'superbug' strain.
4. Additionally, we know that bacteria are able to pass genetic information to each other using plasmids
(circular pieces of DNA which bacteria can incorporate into their genomes).
This process speeds up the evolution of species, as those antibiotic-resistant individuals can pass their
genes for resistance onto others.
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Environmental management and quarantine methods
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SYLLABUS:
Investigate and evaluate environmental management and quarantine methods used to control an epidemic or pandemic.
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CA SE SPACE:
Australian ubllc health res onse to the swine flue e ldemic of 2009
Swine flue
The emergence of a novel influenza virus was first reported in early 2009 in Mexico. This was identified
as H1 N1 virus, commonly termed 'swine flu.' In April 2009, the WHO defined the epidemic as a "public
health emergency of international concern" after more than 882 reported cases in Mexico and several in
the United States, with 62 deaths.
By June 2009, the WHO declared the outbreak as a pandemic, with more than 30,000 reported cases
across 74 countries. By 2011, approximately 1.5 million people were infected in 214 countries, including
25,000 confirmed deaths.
Particular groups, including pregnant women, Indigenous peoples, and the morbidly obese, were identified as facing greater risk of serious illness from the infection.
Management and quarantine methods
In order to control the spread of the infection in Australia, significant public health action was required.
The Australian Health Management Plan for Pandemic Influenza (AHMPPI) outlined the following phases
for pandemic response:
• Delay (April 2009): the objective of this stage was to prevent or slow entry of the virus into
Australia. This was enacted by increasing boarder control measures and increasing vigilance.
Thermal imaging was used to screen arrivals to all international Australian airports, in addition to
arrivals cards. Customs officers also surveyed aeroplane cabins for anyone exhibiting flu symptoms prior to disembarkation.
11 ■71§11. at■I ■II
Copyright© 2018 lnStudent Publishing Pty. Ltd.
4.5 Interpreting prevalence data
• Contain (May 2009): after identification of numerous cases within Australia, contain phase was
activated. These measures aimed to prevent community transmission. All states were authorised
with the option to close schools if they identified that students were at risk. Students returning
from overseas travel in widely affected countries were told not to return to school for a week after
re-entering Australia. A Commonwealth hotline for swine influenza was set up, so that suspected
cases could be reported quickly. Public health posters with hygiene practice recommendations
(particularly for health professionals) were also published, advising on the use of protective equipment, hand washing, and sterilisation.
• Protect (June 2009): in recognition that efforts to contain swine flue had not been entirely effective, this phase identified high-risk groups, and aimed to protect those most at risk of developing
severe illness from infection. A large-scale public vaccination was rolled out across Australia in
September 2009.
Evaluation
• Preparedness:
- Previous outbreaks of other influenza strains in the Asia-Pacific region in 2003 and 2004
meant that Australia had instituted comprehensive pre-pandemic planning before the appearance of the H1 N1 virus.
- This involved designing mechanisms for forward planning and forecasting, communication,
surveillance, reducing transmission, andl optimising health services.
- Responses to pandemics based on these plans were trialled in large-scale pandemic exercises (2006 and 2008).
• Public health leadership:
- A significant number of personnel were involved in the pandemic control, with teams tracking
patients, tracing contacts, running laboratory tests, collecting and analysing data, as well as
creating supply chains for medications and vaccines.
- Coordination of these efforts was attributed to the successful leadership of the Minister for
Health and Ageing and the Commonwealth Chief Medical Officer.
• Media management:
- Frequent comparisons were made between the outbreak and the 1918 flu pandemic, which
was a significantly more serious epidemic infecting 500 million people worldwide.
- This hype of public fear meant that emergency departments were overwhelmed, and resources such as antiviral drugs were drained. This practice jeopardised access to resources
for higher risk patients.
4.5
Interpreting prevalence data
SYLLABUS :
Interpret data relating to the incidence and prevalence of infectious disease in populations, for example:
• Mobility of individuals and the portion that are immune or immunised
• Malaria or dengue fever in south-east Asia
KEY P OINT :
Incidence: the frequency of new cases of a disease over a specified period of time.
Prevalence: the proportion of a particular population affected by a disease.
Mortality rates: the number of deaths within a particular population as a result of a certain disease,
over a specified period of time.
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77
4.5 Interpreting prevalence data
CASE SPACE:
Dengue fever in south-east Asia
Description - Mosquito-borne tropical disease caused by dengue virus
- Spread by the Aedes type of mosquito
- Infection results in fever, headache, joint pain, and rashes
- May lead to development of dengue hemorrhagic fever (DHF - bleeding, low
levels of blood platelets, blood plasma leakage), or develop into dengue shock
syndrome (dangerously low blood pressure)
Incidence
- 390 million infections globally per year (96 million manifest clinically)
- Current global estimates are that 3.9 billion people in 128 countries are at risk of
infection
- 75% of global population exposed to DF live in the Asia-Pacific region
Prevalence
- Found in tropical and sub-tropical climates
- Most countries in south-east Asia experience a higher burden of DF or DHF with
frequent cyclical epidemics (3-5 year cycles)
- Higher ratio of males than females hospitalised
- Typically affects children (2 - 15 years old) at a higher rate than adults
- Epicentres of outbreaks are located in major cities, mostly affecting urban and
semi-urban areas
- Currently associated with rainy season and El Nino phenomenon
- Expected rate of DF will increase over time due to viral evolution, climate change,
globalisation, travel and trade factors, and settlement and socioeconomic factors
Mortality
rates
- 22 million deaths globally per year
Sources
- World Health Organisation DengueNet database: www.who.int/denguecontrol/en/
- Rajesh Bhatia, Aditya P Dash, Temmy Sunyoto, 'Changing epidemiology of
dengue in South-East Asia', South-East Asia Journal of Public Health (2013)
- Natasha Murray, Mikkel Quam, and Annelies Wilder-Smith, 'Epidemiology of
dengue: past, present and future prospects', Clinical Epidemiology (2013}
- Eng-Eong Ooi and Duane J. Gubler, 'Dengue in Southeast Asia: epidemiological
characteristics and strategic challengers in disease prevention', Cadernos de
Saude Publica (2009)
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11 ■71Qlla at■I ■II
Copyright © 2018 lnStudent Publishing Pty. Ltd.
4.5 Interpreting prevalence data
SYLLABUS:
Evaluate historical, culturally diverse, and current strategies to predict and control the spread of disease.
The ability to predict and control the spread of disease has historically been linked to our ability to collect
data on patterns of disease through surveillance, and analyse this data to ascertain trends and patterns.
The development of the field of epidemiology has therefore been crucial in improvement of public health
systems worldwide, allowing professionals to identify causes, risk factors, and in turn propose mechanisms
for control of diseases.
460 BCE370 BCE
Hippocrates, an ancient Greek physician, sparks the idea of collecting and
analysing data to predict and control disease. He believed that disease was a
result of local conditions, and collected data about the natural environment to
determine when and where illnesses would occur.
1348 CE
Venetian Republic attempts to control the spread of the bubonic plague by
appointing public health officials to monitor incoming ships, and exclude those
with infected individuals aboard.
1377 CE
The city of Marseille uses quarantine to control the spread of disease by
detaining individuals who had travelled from plague-infected areas for 40
days.
1662 CE
John Graunt publishes 'Natural and Political Observations Made upon the
Bills of Mortality', which quantifies the patterns of disease within the London
population in order to study the cause of disease.
1741 CE
First example of legislative surveillance of disease - Rhode Island passes a
law requiring businesses to report instances of contagious diseases among
patrons.
1776 CE
Johann Peter Frank formulates a comprehensive health policy for Germany,
detailing injury prevention, maternal and child health, and public water and
sewage treatment. This had impacts in other European countries such as
Hungary, Italy, and Russia.
1834 CE
Edwin Chadwick identifies the link between poverty and disease using
surveillance data in England. This lead to reform in the Poor Law system to
improve disease control and spread in the population.
1849 CE
Dr. John Snow investigates the causes of cholera in the 19th century. By
mapping cases on a dot-map, Snow illustrated a cluster of affected individuals
around a public water pump, identifying it as the source of the outbreak.
1965 CE
Director General of the World Health Organisation establishes the
epidemiological surveillance unit to predict and track the spread of
communicable diseases globally.
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79
4.5 Interpreting prevalence data
Current strategies for prediction
• Event-based surveillance: based on reporting by healthcare professionals, as well as news reports,
social media, and internet searches.
- Global Public Health Intelligence Network (GPH IN) systematically scans a multitude of informal
sources (web sites, electronic discussion forums, new reports, online newspapers) for unusual
disease events and rumours for outbreaks. Data is investigated, then verified through official
sources. GPHIN issued the first alert of unusual respiratory illness for the SARS outbreak in
2002, triggering an international response from the WHO.
- Event-based surveillance is particularly effective in countries where there is weak or minimal
public health infrastructure, and is able to provide real-time data on local disease activity.
• Web-based surveillance :
- For example, Google Flu Trends monitors real-time influenza activity based on the finding that
there is a correlation between the number of people searching the web using influenza-related
keywords and the number of people actually experiencing influenza symptoms.
- It has been shown that this tool is able to predict region outbreaks 1 - 2 weeks earlier than
disease control centres.
• Modelling of disease emergence and spread :
- A model uses prescribed rules to describe how an infectious disease may spread within a
population. This requires collection of data on factors such as:
• Human factors: population density, travel and trade, and how these each affect disease
transmission
• Ecological factors: climate change, agricultural practices, and how these each affect disease transmission
- Using models, scientists may conduct computer simulations of outbreak events.
- This information may be used to inform pre-emptive public health policies and to design rapid
response plans to epidemics or pandemics.
SYLLABUS:
Investigate the contemporary application of Aboriginal protocols in the development of particular medicines and biological materials in Australia and how recognition and protection of Indigenous cultural and
intellectual property is important, for example:
• Bush medicine
• Smoke bush in Western Australia
Bush medicine
Bush medicine is a term describing the skills and practices used to maintain health , based on Indigenous
beliefs and experiences. This refers not only use of native flora and fauna traditionally prepared, but includes
preventative and diagnostic techniques, and treatment of mental illnesses. Bush medicine denotes a holistic
view of health, emphasising the interplay between physical, emotional, social, and spiritual aspects of
wellbeing. Indigenous Australians are a diverse people, composed of many culturally distinct groups, each
with their own individual practices. Thus, there is no single set of Aboriginal medicines and remedies.
The National Aboriginal Health Strategy has defined bush medicine "not just physical wellbeing of the
individual, but the social, emotional, and cultural wellbeing of the whole community. This is the whole-of-life
view and it also includes the cyclical concept of life-death-life." Bush medicine includes the use of plant
materials, such as bark, leaves, seeds, and some animal products, in order to create herbal medicines.
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4.5 Interpreting prevalence data
Examples include:
• Tea tree oil (Melaleuca alternifolia):
- Bundjalung Aboriginal peoples from the NSW coast
- Crushed tea-tree leaves applied as a paste to wounds
- Brewing into a tea for throat aliments
- Strong antiseptic
- Used in western medicine to treat fungal infections and acne
• Eucalyptus oil (Eucalyptus sp.):
- Infusions used to treat muscle aches, fevers, and chills
- Western uses commercially in mouthwash and cough lollies
• Kakadu plum (Terminalia ferdinandiana):
- Extremely rick source of vitamin C (50x more than oranges)
- Found in Northern Territory and Western Australian woodlands
- Major food source for tribes in the area
• Desert mushrooms ( Pycnoporus sp.) :
- Bright orange mushroom variety
- Used to treat sore mouths and lips, or babies with oral thrush, by sucking on the fruiting body of
the plant
• Emu bush (Eremophila sp.):
- Used by tribes in the Northern Territory to treat sores and cuts
- Current research has identified the leaves of the plant as possessing strong antibiotic properties,
equal to established pharmaceuticals
• Witchetty grub (Endoxyla leucomochla):
- Made into a paste, these insects were used to treat burns and soothe skin
- Recorded use by Central Australian tribes
• Kangaroos apple (Solanum laciniatum) :
- Juice from the fruit was applied to swollen joints to relieve pain
- Research has found that the fruit contains a steroid which promotes the production of cortisone,
accounting for its healing properties
Smoke bush in Western Australia
Conospermum, or smokebush, is a plant native to the south-west region of Western Australia. Smokebush
has been used traditionally by the Aboriginal people of the region as a medicine. In the 1960s, the US National Cancer Institute was granted a licence by the Western Australian Government to collect plant samples
in order to screen them for the presence of cancer-fighting molecules. Specimens of the smokebush plant
were tested, but found to be ineffective in treating cancer. However, in a quest to find potential treatments
for the growing AIDS epidemic in the 1980s, the smokebush was again screened, and miraculously found to
be one of only four plants out of 7,000 which contained an active molecule, conocurovone, able to combat
the HIV virus in low concentrations. The US Department of Health and Human services filed patents (US
in 1993 and Australia in 1994) for exclusive rights to use the compound in AIDS treatment.
Rights to develop the patent in Australia were licensed exclusively to a Victorian Pharmaceutical company,
AMRAD. In order to gain access to rights over the plant for research, $1.65 million was paid to the WA
Government. Additionally, estimations were made that if conocurovone was successfully commercialised,
the WA government would likely recoup royalties of up to $100 million per year. Whilst this may at its
face seem like a win for the WA Government, the smokebush story is another in a long line of incidents
in Australian history where the significant contributions of our Indigenous peoples has been forgotten or
disregarded, and their expertise and importance to Australian culture has been exploited for financial gain.
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81
4.5 Interpreting prevalence data
Inter-generational nurturing of the plant, and its continued use in Indigenous medicine resulted in the knowledge that the smokebush is a healing plant, indicating the potency which led to its selection as a plant to
be screened. However, no royalties, compensation, or even acknowledgement was ever presented to the
Aboriginal Australians of Western Australia. This demonstrates a significant flaw in our patent law system
and its inability to protect traditional knowledge of Indigenous peoples. For a system of law which has been
designed to protect an individual's right to their intellectual inventions, their property, this must be viewed
an egregious breach.
This also represents a threat to Aboriginal communities and their traditional cultural practices. There is a
possibility that the rights to use an entire species of flora may be sold to large multi-national drug companies. This would prevent groups, including Aboriginal peoples, from using such plants subject to exclusive
agreement (presumably involving a paid licence). Essentially, the patenting of traditional medicinal plants
may prevent Indigenous Australians from continuing to autonomously use their own cultural knowledge.
There is a known wealth of information which Aboriginal and Torres Strait Islander Australians possess,
stemming from a continued connection to the land for over 65,000 years, and a region -specific knowledge
of not only resources, but also of horticulture and how best to prepare medicines using different parts of
plants. It is important that when undergoing bioprospecting practices, companies consider the contribution
of Indigenous peoples to discovery, and the rights which may accumulate as a result of cultural practices.
It is also extremely important that we understand the culture-specific rules associated with Indigenous
knowledge. Ownership manifests itself in very different ways across Indigenous and Western societies. As
Aboriginal Australians have used oral histories to pass their cultural information through the generations,
there may be complex rules governing the dissemination of information. Some information is sacred, only
able to be used by those within a group possessing certain authority, and not permitted to be made public.
Customary laws and community values should be respected during any commercialisation process, so that
Indigenous knowledge may be protected as intended. This is particularly important in light of the limited
control our Indigenous peoples now have over their homelands.
Positive developments
There currently exist a number of patents which have been successfully designed with Indigenous coowners, where business and entrepreneurship have been balanced with cultural necessities. The following
is an example of how research may be responsibly enacted to include Indigenous peoples, and respectfully
lead to the mutual success of stakeholders in culturallly significant information.
CA SE SPACE:
The mudjala plant patent
The myardoo majala tree has been known to the Nyinkina Mangala community as possessing healing
powers and pain relief. It also features in their creation story of the Fitzroy River. Elders of the community
approached researchers at Griffith University in order to create a research partnership. This resulted
in identification and isolation of the active compounds in the plant which contributed to its medicinal
properties.
The Jarlmadangah community and Griffith University became joint patent holders of the biotechnology.
It is hoped that in the future, the IP technology will be successfully commercialised. The Jarlmadangah
Buru community continues to actively participate in harvesting and monitoring trials which will ensure
that many Aboriginal communities benefit from any large-scale commercialisation opportunity.
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Part IV
Module 8: Non-infectious Disease and
Disorders
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83
Homeostasis
Topic 1
Homeostasis
SYLLABUS :
Inquiry question: How is an organism's internal environment maintained in response to a changing
external environment?
1.1
Feedback loops
S YLLABUS:
Construct and interpret negative feedback loops that show homeostasis by using a range of sources,
including but not limited to temperature and glucose.
K EY P OINT:
Homeostasis: the process by which an organism maintains a stable internal environment, despite
fluctuating external environmental conditions.
It is essential for organisms to maintain a consistent internal environment for a number of reasons. Firstly,
as you will have learnt in Module 1 of the Year 11 course, enzymes are very important biological catalysts,
which require specific conditions to function at their best. By maintaining constant conditions (temperature,
pH, levels of water, etc.) in the body, our enzymes are able to carry out their functions efficiently. Secondly,
cells survive best in an isotonic solution, which needs to be maintained so that cells do not shrink or expand,
and can efficiently carry out their individual functions.
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Homeostasis occurs in two stages; firstly, the body detects changes from the stable state (the body at
optimal conditions), and secondly, the body counteracts the changes. In order to demonstrate the process
of homeostasis, we can construct negative feedback loops, which show how the body detects, processes,
and counteracts changes in the external environment.
Temperature
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Copyright© 2018 lnStudent Publishing Pty. Ltd.
1.2 Homeostatic mechanisms
Water levels
1.2
Homeostatic mechanisms
SYLLABUS:
Investigate the various mechanisms used by organisms to maintain their internal environment within
tolerance limits, including:
• Trends and patterns in behavioural, structural, and physiological adaptations in endotherms that
assist in maintaining homeostasis
• Internal coordination systems that allow homeostasis to be maintained, including hormones and
neural pathways
• Mechanisms in plants that allow water balance to be maintained
1.2.1
Behavioural, structural, and physiological adaptations
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Endotherms: organisms which are able to maintain a constant internal body temperature, independent
of the environment.
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Adaptations
Behavioural
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Movement: shaded areas or wet environments help regulate heat exposure
Deliberate use of muscles: muscle contractions produce metabolic heat
Sunbaking : increasing surface area available for heat absorption
Licking : enabling more heat to be evaporated through saliva
Drinking water: to replenish fluids to maintain cells in a consistent, isotonic state
Structural
- Insu lation (e.g. feathers, hair, fur) trap a layer of air next to the skin which
reduces transfer of heat to the environment
- Surface area to volume ratio as more compact bodies reduce the surface area
available for heat exchange, allowing for animals to retail heat more effectively
Physiological
- Vasoconstriction (narrowing blood vessels) and vasodilation (widening blood
vessels) allows animals to regulate the surface area to volume ratio of their
circulatory systems to retain or expel heat when required
- Metabolic rates can be increased to increase the production of heat energy
internally, or decreased to cool body temperature
- Muscle contraction (shivering) or making small movements in the skeletal
muscles to produce heat energy
- Sweating as perspiration allows sweat to evaporate from the surface of the skin,
which has an evaporative cooling effect
- Panting allows evaporation from internal body surfaces, such as nasal passages,
mouth , and lungs which also has an evaporative cooling effect
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iii"
I Trends and patterns
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85
1.2 Homeostatic mechanisms
1.2.2 Internal coordination systems
Hormones
Hormones are signalling molecules used by the body to regulate physiology and behaviour. They are
produced in the glands, and transported around the body using the circulatory or lymph systems. Hormones
affects cells by binding to specific receptors on their surfaces, enacting changes in a process called signal
transduction.
STEP2
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Step 1 : Reception
The hormone binds to a receptor displayed on the
outside of the cell.
Step 2: Transduction
The binding event on the cell surface triggers a signalling cascade within the cytoplasm.
Step 3: Response
Cell signalling initiates a response, usually in the
form of gene transcription within the nucleus.
Through these steps, we can see how hormones are able to enact physiological changes by regulating
the expression of certain proteins in the cell to dictate cell structure and function. Hormones may affect
the metabolism of target cells, tissues, and organs, by either increasing or decreasing levels of activity.
Hormones are also responsible for regulating digestion, respiration, sleep, growth and development, reproduction, and mood.
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Neural pathways occur as part of the nervous system:
• Central Nervous System (CNS): brain and spi nal cord
Control centre that coordinates responses within the body
- Receives information from the PNS, interprets the information, and then initiates an appropriate
response by sending messages to the PNS to enact effector responses
• Peripheral Nervous System (PNS): nerves branching from the CNS throughout the body
- Facilitates communication in the body
- Passes messages to and from the CNS rapidly, allowing the body to respond to changes (both
internal and external)
-
The nervous system is composed of neural cells (neurons), which pass information in the form of chemical
signals around the body. The movement of nerve impulses is facilitated by the transmission of an action
potential along the nerve axon, which triggers the release of neurotransmitters, and therefore creates signal
transduction between cells.
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1.2 Homeostatic mechanisms
Neurons interface with cells, allowing them to communicate through release of neurotransmitters (as we
can see in the diagram above). These chemicals trigger signalling cascades within cells, enacting specific
physiological responses.
Neural pathways are excited by the triggering of sensory receptors (thermoreceptors detect changes in temperature, mechanoreceptors detect changes in pressure or distortion, and chemoreceptors detect changes
in levels of certain chemicals). When these receptors are triggered, they pass the signal onto neurons,
which then pass the signal onto effectors. Effectors work to counteract the detected change, therefore
maintaining homeostasis within the organism.
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1.2.3
Balancing water levels in plants
Plants may be adapted in a number of ways which allow them to balance water levels. Mechanisms for water
retention are observed widely in Australian flora, as they are often subject to harsh, drought-like conditions.
Firstly, we need to recall the process of water transport in plants (Transpiration-Cohesion-Tension theory)
from Module 2 of the Year 11 course :
KEY POINT:
Theory of Transpiration-Cohesion-Tension theory: the mechanism by which water flows through the
xylem of plants is due to the combined effects of:
• Transpiration (evaporation of water through the stomata of plants)
• Cohesion (that water molecules are attracted each other, so w ill move in a cohesive stream)
• Tension (water molecules are attracted to the surfaces which they touch)
By regulating the levels at which transpiration occurs, plants are able to retain or release water as required.
This may be achieved by:
• Smaller leaves : reduces surface area to volume ratio (reducing surface available for transpiration
reduces water loss)
• Closing stomates : inhibits ability for water to leave plant through the leaves
• Movement: angling leaves away from the sun at different times of the day may reduce rates of transpiration (cooler temperatures result in less evaporation)
• Dropping leaves during summer and droughts: conserves water to essential parts of plant
• Large cavities for water storage in stems/trunks
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Causes and Effects
Topic 2
Causes and Effects
SYLLABUS:
Inquiry question : Do non-infectious diseases cause more deaths than infectious diseases?
2.1
Overview of causes and effects
SYLLABUS:
Investigate the causes and effects of non-infectious diseases in humans, including but not limited to:
•
•
•
•
Genetic diseases
Diseases caused by environmental exposure
Nutritional diseases
Cancer
Non-infectious disease
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Causes
Examples
Genetic diseases
- Gene or chromosomal abnormalities
caused by point or chromosomal
mutations
- Such mutations may result from errors
during gamete formation, or exposure to
mutagens
- Genetic diseases may be inherited from
parents, or as a result of acquired
changes to pre-existing genes
- Down syndrome
(chromosomal abnormality)
- Cystic fibrosis (single gene
disorder)
Environmental diseases
- Interaction with the environment and
exposure to physical factors such as
radiation
- Exposure to harmful or toxic chemicals
such as toxic metals or noxious gases
- Minamata (ingestion of
large amounts of mercury)
- Mesothelioma (cancer as a
result of asbestos exposure)
Nutritional diseases
- Issues with diet (e.g. excessive of
insufficient consumption of food)
- Problems with digestion
- Consumption of incorrect amounts of
specific foods (e.g. essential vitamins or
minerals)
- Scurvy
- Type 2 diabetes
Cancer
- Many cancers are caused by many
different factors, including infectious
agents, genetic disorders, exposure to
mutagenic factors in the environment
(e.g. radiation), and lifestyle habits (e.g.
smoking, alcoholism)
- Cervical cancer (from HPV
exposure)
- Breast cancer (from
inheritance of BRCA 1 gene)
- Melanoma (from repeated
sun exposure)
- Lung cancer (from
smoking)
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Copyright© 2018 lnStudent Publishing Pty. Ltd.
2.2 Case studies of incidence, prevalence, and mortality rates
2.1.1
Cancer
Cancer is a disease in which abnormal cells grow in an uncontrolled manner. It is the result of changes
to the fundamental molecular functions of a cell, due to mutation. In normal cells, growth and division are
tightly regulated, so that cells are able to perform their functions correctly. In cancerous cells, aspects of
cellular regulation have been altered, so that cells are able to:
•
•
•
•
•
Replicate indefinitely
Evade growth suppressors in the body
Resist cell death
Induce increased blood flow to the tumour site (angiogenesis)
Invade other tissues and metastasise
Changes to cellular function in different tissues and organs may result in a number of negative symptoms,
including reduction in system function . In addition , cancerous cells have the potential to metastasise invade or spread around the body, which can further contribute to disease progression. When cancerous
cells begin to grow and divide uncontrollably they create tumours. This is called tumorigenesis.
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Cancers are caused by a number of different factors. Mutations to cells may be as a result of genetic,
environmental, or lifestyle factors. Often, specific agents are the cause of specific cancer types, due to the
cells which they directly affect.
2.2
Case studies of incidence, prevalence, and mortality rates
SYLLABUS:
Collect and represent data to show the incidence, prevalence, and mortality rates of non-infectious
diseases, for example:
• Nutritional diseases
• Diseases caused by environmental exposure
CA SE SPACE:
Nutritional disease: Type 2 diabetes
Description
- Condition in which the body becomes resistant to insulin and is gradually
unable to produce it
- This leads to a build-up of glucose in the blood, which can cause damage to
systems in the body
- Causes include genetic factors, sedentary lifestyles, and unhealthy diets
Incidence
- Number of people with diabetes has quadrupled over the past 30 years
- Predicted increase in adults with diabetes between 2010 and 2030 (20% in
developed countries and 69% in developing countries)
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89
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2.2 Case studies of incidence, prevalence, and mortality rates
Prevalence
- 1 in 11 adults aged 20-79 years old had diabetes in 2015 (415 million
people); 90% of these cases were type 2 diabetes
- This is expected to rise to 642 million by 2040
- Asia is the epicentre of the epidemic with China and India being the top two
countries for type 2 diabetes prevalence
Mortality rates
- Currently causes 5 million deaths per year (the equivalent of one death
every six seconds) mostly as a result of cardiovascular disease
- Type 2 diabetes is expected to become the seventh most prevalent cause of
death globally by 2030
Sources
- Yan Zheng, Sylvia H. Ley & Frank b. Hu, 'Global aetiology and
epidemiology of type 2 diabetes mellitus and its complications,' Nature
Reviews Endocrinology (2018)
- Epidemiology of type 2 diabetes - Diapedia, www.diapedia.org/ type-2diabetes-meIlitus/31 042871 23/epidemiology-of-type-2-diabetes,
(2016)
CASE SPACE:
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Environmental disease: Melanoma
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Description
- The most lethal type of skin cancer, developing from mutation of
melanocytes
- Caused by exposure to ultraviolet radiation , usually from the sun, as a result
of lifestyle factors such as levels of outdoor activity, or genetic factors such as
melanin levels
Incidence
- Worldwide, there were 351 ,880 new cases of melanoma in 2015
- In Australia, there were an estimated 14,320 new cases diagnosed in 2018
(10.4% of all new cancers diagnosed that year)
Prevalence
- Worldwide, melanoma is the nineteenth most common cancer with the
highest rates reported in Australia (37 per 100,000)
- In Australia, an estimated 51 ,697 people living with melanoma at the end of
2012
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Mortality rates
Sources
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- Worldwide, there were 59,782 deaths in 2015
- In Australia, there were an estimated 1,905 deaths in 2018 (3.9% of all
deaths from cancer in 2018)
- Karimkhani C. et al. 'The global burden of melanoma: results from the
Global Burden of Disease Study 2015,' The British Journal of Dermatology,
(2017)
- Melanoma of the skin statistics, melanoma.canceraustralia.gov.au/statistics,
(2018)
- Z. Ali, N. Yousaf, and J , Larkin, 'Melanoma epidemiology, biology and
prognosis', EJC Supplement, (2013)
Copyright© 2018 lnStudent Publishing Pty. Ltd.
Epidemiology
Topic 3
Epidemiology
SYLLABUS:
Inquiry question: Why are epidemiological studies used?
3.1
Patterns of disease and epidemiological studies
SYLLABUS:
Analyse patterns of non-infectious diseases in populations, including their incidence and prevalence,
including but not limited to:
• Nutritional diseases
• Diseases caused by environmental exposure
KEY P OINT:
Epidemiology: the study of incidence, distribution, and possible control of diseases. It describes the
patterns and causes of diseases within populations.
Valid epidemiology studies:
• Have large sample sizes
• Select populations with unequal exposure to possible causes (essentially, the study must include an
independent variable, to allow valid conclusions to be drawn)
• Collect data on other factors which may affect disease, such as age, sex, ethnicity, lifestyle, occupation, etc.
There are a number of different diseases which affect health globally. Factors contributing to development
of these diseases varies depending on the different environmental and lifestyle factors present in different
countries and cultures.
When researching patterns of disease globally, I recommend visiting the following sites to find information:
• World Health Organisation:
- Fact-Sheets: www.who.int/news-room/fact-sheets
- Global Health Statistics: www.who.int/gho/publications/world health statistics/en/
• United Nations: www.un.org/en/sections/issues-depth/health/index.html
• Our World in Data: ourworldindata.org/health-meta
• Statista: www.statista.com/topics/4274/global-health/
Data may be analysed according to a number of different factors, allowing different conclusions to be drawn .
Comparisons may be made across countries or divided by gender, giving a holistic view of how disease
affects our global population.
Below is an example of how you could collate information drawn from the sources above to create effective
study notes. The important thing to remember is that this dot point is about patterns, so try to include information about why diseases affect populations in the way that they do, and why incidence and prevalence
may vary from country to country. There are more examples on in-depth data presentation in the previous
section as well.
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3. 1 Patterns of disease and epidemiological studies
CA SE S PACE :
Obesity
Nutritional disease
Classification
Cause
- High calorie diets
Sedentary lifestyle
I-
n 2016, 650 million adults were obese (13% of adults over 18)
- 41 million children over 5 were overweight or obese
- 340 million children and adolescents 5-19 were overweight or obese
Global ~
patterns
-
- Obesity has tripled worldwide since 1975
- At least 2.8 million die per year as a result of being overweight or obesity
- Prevalence of obesity is highest in the Americas (26%) and lowest in
south-east Asia (3%)
- In the Americas, Europe, and Eastern Mediterranean, roughly 25% of all
women are obese (in all regions, women are more likely to be obese than
men)
Contributory
factors
- 'Nutritional transition' is a term used to define a set of changing risk factors
that a country may face as they develop
- Changes in diet: as countries become more developed, populations usually
begin to purchase more processed food, rather than grow or buy fresh
ingredients, leading to diets with more fat and lower complex carbohydrates
- Changes to lifestyle: as food production technologies develop, populations
undergo changes to their work and leisure activities, usually resulting in more
sedentary lifestyles
- The effects of these factors can be seen in India and China among urban
residents and high-income rural residents
...___
_____ I
.__
CA SE SPACE:
Cancer
Classification
Cause
Global patterns
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Environmental/lifestyle
- Physical, chemical, and biological carcinogens, as well as genetic
factors, resulting in transformation of normal cells into abnormal tumour
cells
-
Second leading cause of death globally (8.8 million deaths in 2015)
70% of cancer deaths occur in low and middle income countries
Tobacco use is responsible for approximately 22% of cancer deaths
Most fatal cancers globally: lung, liver, colorectal, stomach, breast
Copyright© 2018 lnStudent Publishing Pty. Ltd.
3.2 Treatment, management, and reasearch
3.2
Treatment, management, and reasearch
SYLLABUS:
Investigate the treatment/management, and possible future directions for further research, of a noninfectious disease using an example from one of the non-infectious diseases categories listed above.
3.2.1
Nutritional disease: type 2 diabetes
Type 2 diabetes is a condition whereby the body becomes resistant to the effects of insulin, and gradually
becomes unable to produce insulin effectively. The result of this is that individuals are unable to regulate
their blood glucose levels effectively. Type 2 diabetes may lead to other medical complications, such as
vision problems, cardiovascular disease, and nerve and kidney damage. A number of genetic and familyrelated risk factors are known to contribute to the devellopment of the disease, as well as lifestyle behaviours,
such as diet, exercise, and weight.
• Prevention:
- Maintaining a normal weight
- Eating a healthy and varied diet
- Exercising regularly
• Treatment and management:
- Lifestyle changes:
• Eating well: helps to manage levels of blood glucose. Diets should include high-fibre,
low-fat foods (fruits, vegetables, grains) and avoid refined sugars and carbohydrates. Low
glycaemic index foods are also recommended as they help to maintain more stable blood
sugar levels.
• Exercising: lowers blood pressure and helps insulin to work effectively, reducing the risk of
heart disease. Physical activity also helps to lower blood sugar levels, as glucose is being
used by cells to enact aerobic respiration.
- Monitoring: testing blood glucose levels regularly allows patients to effectively manage their
treatment, ensuring that these levels stay within a healthy range.
- Treatment:
• The first step in diabetes treatment is usually a medication called metformin which decreases the amount of glucose produced in the liver, as well as increasing insulin sensitivity
in many tissues, including the liver, skeletal muscle, and adipose tissue. Overall, this helps
to decrease blood sugar levels.
• As type 2 diabetes progresses, and the pancreas continues to become less effective at
producing insulin, patients may also be required to take insulin injections. Insulin signals to
cells to take up glucose, and therefore helps to lower blood glucose levels in diabetics.
• For obese patients suffering from diabetes, bariatric surgery may also help in reducing its
effects. This involves reducing the size of the stomach, either by removing a portion of
the stomach, or restricting it using a gastric band. This may potentially reset metabolism,
essentially curing diabetes.
• Future directions for research:
- An increased understanding of the factors contributing to development of type 2 diabetes would
help scientists and public health workers to design better prevention measures and create effective treatment and management strategies.
- Future research may be conducted into understanding genetic risks and analysing genomes
to identify genes which may place an individual at risk of developing the disease. This would
allow the tailoring of pre-emptive, personalised medicine, which would be particularly effective
as prevention is the best form of treatment.
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3.3 Evaluating epidemiology
- Type 2 diabetes is commonly treated by taking insulin shots. Synthetic production of insulin is
an important area of research, particularly in terms of how to make this process faster, more
efficient, and less expensive, in order to increase world-wide access. This could involve genetic engineering, cloning , or large-scale synthetic protein production . An example of current
research in this area is the 2017 Sydney University iGEM team, who aimed to provide an opensource solution to the issue of insulin access globally: 2017.igem.org/Team :Sydney Australia
- Another treatment option for diabetes is whole-organ pancreas transplantation, a surgical procedure in which an entirely new, functional pancreas is placed into a patient in order to cure
the disease. This option may be developed by research into creation of artificial pancreases
to substitute function. This may be faci litated by the development of 3D printing techniques, or
growth of pancreatic cells in vitro.
- Instead of inserting entirely new organs into patients, islet cell transplants may be an option for
diabetics. As islet cells are dysfunctional in diabetic patients, unable to properly produce insulin ,
transplanting these specific cells into patients may represent a less complex and less invasive
option. Research would need to be done into how to grow healthy cells outside the body, and
how to insert these into the pancreas in order to restore function.
3.3
Evaluating epidemiology
SYLLABUS :
Evaluate the method used in an example of an epidemiological study.
There are three main types of epidemiological studies :
• Descriptive: a study of the patterns of distribution within and across populations.
• Analytical : a study examining known associations, or testing specific hypotheses.
• Experimental: a study which measures the effectiveness of interventions, such as clinical or community trials of new treatments.
An example of an analytical study was the groundbreaking work by Richard Doll and Austin Bradfrord Hill
'Smoking and Carcinoma of the Lung' (British Medical Journal, 1950). This study was the first rigorous
identification of the link between smoking tobacco and the development of lung cancer.
CA SE SPACE:
'Smokin_g_and Carcinoma of the Lun9.'..
lnltlal hypothesis: that the significant increase in deaths attributed to cancer of the lung in England
and Wales between 1922- 1947 (from 612 to 9,287 per annum, a roughly fifteenfold increase) was as
a result of either: (1) atmospheric pollution from car exhaust fumes, surface dust of tarred roads, gasworks, industrial plants and coal fires, or (2) the smoking of tobacco, both of which had become more
prevalent in the 50 years prior to the study.
Methodology:
20 London hospitals in the north-west area were asked to participate in the study.
Whenever a patient was admitted to said hospitals presenting with carcinoma of the lung, a researcher
would visit the hospital and interview the patient. Four designated researchers conducted all interviews
of all patients over the period of the study using a set questionnaire.
For each lung-carcinoma patient interviewed, an individual of the same sex and in the same 5 year age
group affected by a cancer other than carcinoma was interviewed, using the same questionnaire, in the
same hospital at or about the same time.
A total of 2,475 patients participated in the study. The study was conducted for a period of one year.
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3.3 Evaluating epidemiology
Smoking habits were assessed by asking whether patients:
•
•
•
•
a) whether they had smoked at any period of their lives
b) the ages at which they started and stopped
c) the amount which they were in the habit of smoking before the onset of illness
d) the main changes in their smoking history and maximum they had ever been in the habit of
smoking
• e) the varying proportions smoked in pipes and cigarettes
• f) whether or not they inhaled
A smoker was defined as a person who had smoked as much as one cigarette a day for as long as one
year.
Comparisons were made between smokers and non-smokers, as well as between groups with varied
amounts of smoking (expressed as cigarettes per day).
Evaluation: the study had a large sample size (2,475 patients), with a clearly identified control group with
controlled variables (same age and sex) between the populations. Studies were collected across a large
number of hospitals. There was consistent use of the same interviewers over the study, using the exact
same questionnaire each time. The questionnaire used attempted to thoroughly investigate the history
of patients, and collected data not only on smoking habits but on other lifestyle factors. The study was
conducted for long period of time. The clear and consistent approach to these surveys meant that the study
may be reasonably relied upon to have extracted and represented accurate data. However, reliability may
have been improved by taking data from hospitals outside of the immediate London area (for example from
rural hospitals) , so that environmental variables could be more sufficiently taken into account. In addition, a
study monitoring individuals across a larger period of their lives, rather than only after they had developed
a disease, may have provided a more statistically sound conclusion.
S YLLABUS:
Evaluate, using examples, the benefits of engaging in an epidemiological study.
Epidemiology is an interdisciplinary field which combines the expertise of epidemiologists, laboratory
technicians, statisticians, doctors, and public health professionals. This means that studies are often comprehensive and wide-reaching in their implications and applications.
The use of a thorough, rigorous methodology to trace the origins of disease ensures that findings remain
objective, and may at times uncover unexpected findings. For example, when Doll and Hill first began
studying causes of lung cancer, they believed that it was mostly due to either car fumes or new material
tarmac. However, they discovered that tobacco smoking was the only significant common factor between
patients with carcinoma.
Epidemiology is concerned with disease surveillance, investigating outbreaks, and conducting observational studies which help to identify risk factors in disease. By identifying the causes of disease, epidemiology provides public health professionals information so that they can strategise and plan programs and
campaigns to help prevent disease. For example, the Australian Cancer Council is currently undertaking the
ABC study (Australian Breakthrough Cancer Study) , with an outlook towards designing better preventative
measures.
By determining the levels of disease impact at national, regional, and global levels, organisations such as
the World Health Organisation are able to effectively develop strategies and tools to address global health
and inequality. This displays how epidemiology makes an important link between research and public
health policy, and the overall benefits of a community-based approach to disease treatment and health .
Additionally, identification of the causes of disease allows scientists to better understand where to direct
research efforts.
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Prevention
Topic 4
Prevention
SYLLABUS:
Inquiry question : How can non-infectious diseases be prevented?
4.1
Efficacy of disease prevention
r
SYLLABUS:
Use secondary sources to evaluate the effectiveness of current disease prevention methods and develop
strategies for the prevention of non-infectious disease, including but not limited to:
• Education programs and campaigns
• Genetic engineering
4.1.1
Education programs and campaigns
CASE SPACE:
Educational campaign: Slip! Slop! Slap!
Disease: Skin cancer
Methods:
• Television advertisements and community service announcements, including a catchy jingle
• Aimed to raise awareness of skin cancer and the risks posed by ultraviolet light exposure from the
sun
• A cartoon seagull, Sid, appeared in the campaign, encouraging people to "slip on a shirt, slop on
sunscreen, and slap on a hat!"
• The original campaign, launched in the 1980s, was later modified by the SunSmart campaign in
2007, promoting 'Slip! Slop! Slap! Seek! Slide!' in which people were encouraged to also seek
shade and slide on sunglasses
• Since the success of the program in the 1980s, SunSmart have incorporated further strategies to
their campaign, including:
- Implementation of legislative changes
- Development of educational resources for schools and workplaces
- Sponsorship of sporting events
Effectiveness:
• One of the most successful health campaigns in Australia's history
• Believed to have played a key role in the shift of Australian attitudes towards sun safety
• Incidence of two most common skin cancers (squamous cell carcinoma and basal-cell carcinoma)
has decreased since introduction of the campaign
• Incidence of most lethal skin cancer (melanoma) has, however, increased
• Program has been shown to be particularly effective amongst younger people
• For people aged 20 - 24, the rate of melanoma has fallen from 25 per 100,000 to 14 per 100,000
between 1996 and 2010
• Estimated to have prevented more than 43,000 skin cancers in Victoria (where the campaign was
started) between 1988 and 2011
• The SunSmart programs are considered to be extremely cost effective, saving the Victorian government $2.20 for every dollar spent in the Victorian public health program
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4. 1 Efficacy of disease prevention
Slip
Slop
Slap
Seek
Slide
C ASE SPACE:
Educational program: beyondblue - secondary schools program
Disease: Mental illnesses (including depression and anxiety)
Methods:
• Development of a comprehensive curriculum for high-school students to equip them with skills to
deal with adverse events (development of 'life skills') to help prevent mental health problems
• Program encourages development of a sense of self worth, sense of control, sense of belonging,
sense of purpose, sense of future, and sense of humour
• Aimed to reduce levels of depression in young people, as well as increase awareness and understanding of depression in adolescents
• The program is based on cognitive behavioural therapies
• Designed to be delivered over 3 years, with 10 weekly sessions 30 - 45 minutes in length per year
• Consistent delivery, in which principles are built upon, allowing students to develop these skills
progressively and concretely
• Program delivery based on principles of best-practice
• Uses interactive teaching tools such as small group exercises, discussions, role plays, deeplearning tasks, and quizzes
Effectiveness:
• Draws on current research conducted nationally and internationally (cognitive behaviour therapies
and resilience-based framework)
• Pre-emptive approach to tackling mental health issues that aims to strengthen protective factors,
thus reducing the risk of developing mental illness
• Targeted towards early high-school students (Years 8 - 10) to address issues before the onset of
stressful periods later in life
• Displays sound logic in its approach as a result of collaboration between multiple interstate initiatives (Secondary Schools Research Initiative by University of Queensland, Centre for Adolescent
Health (Victoria), and South Australian Department of Education and Children's Services)
• Reported high levels of school engagement with the program between 2003 and 2007
• Difficult to assess the lasting impacts of the program due to difficulties in diagnosis of mental
illnesses, and the influence of multiple factors contributing to its incidence
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4. 1 Efficacy of disease prevention
4.1.2
Genetic engineering
Many non-infectious diseases are the result of mutations to our genetic material. If we are able to trace
the causes of disease to specific changes in our DNA sequences, this opens up the possibility of curing
diseases using genetic engineering. Genetic engineering techniques allow us to make changes to the
genetic code, thus allowing us to edit sequences causing non-infectious disease. A number of genetic
engineering techniques may allow for the prevention of non-infectious disease, including :
• Gene therapy: the correction of genetic disorders by introducing a normal, functioning gene into
cells. This is achieved by inserting corrected geine sequences into a cell where a defect has occurred.
Techniques used to inject new genetic material include the insertion of viral vectors, use of a gene
gun, and inorganic nanoparticles. For more detail, see page 53. This can be used to treat:
- Severe combined immune deficiency
- Haemophilia
- Parkinson's disease
• CRISPR: a gene editing system by which point mutations may be accurately introduced into genomes. CRISPR may be used to improve gene therapies by making point mutations (up to 20bp) to
dysfunctional cells. Such changes will alter the genomes of all edited cells, as well as any cells which
grow from them, resulting in a lasting somatic cell edit.
• Embryo screening or editing : increased access and decreased costs of whole genome sequencing opens up the possibility of screening embryos for genetic disorders. This may be particularly
beneficial for couples who carry known genes for disease. Screening allows selection of embryos
only without genetic defects for implantation. Editing technologies, especially at the early embryo
stage, open up the possibility that whole organism changes may be made to the offspring.
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Technologies and Disorders
Topic 5
Technologies and Disorders
SYLLABUS:
Inquiry question : How can technologies be used to assist people who experience disorders?
5.1
Causes of disorders
SYLLABUS:
Explain a range of causes of disorders by investigating the structures and functions of the relevant
organs, for example:
• Hearing loss
• Visual disorders
• Loss of kidney function
5.1.1
Hearing loss
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The ear is composed of three sections:
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• The outer ear (pinna and ear canal)
• The middle ear (ossicles and ear drum)
• The inner ear (the cochlea, and auditory nerve and the brain)
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the bones of the middle ear, the ossicles, to move in a chain-like fashion. This movement 'knocks' on a
membrane window of the cochlea. The cochlea is filled with fluid, which moves in response to this knock.
Hair cells lining the cochlea are bent in response to the fluid vibrations, which creates an electrical impulse
to be sent along the auditory nerve and to the brain.
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• Conductive hearing loss: occurs when there is damage to the outer or middle ear, resulting in
ineffective sound transfer. In these cases, the cochlear may still be functional , but does not receive
sufficient signal to create an auditory impulse. Conductive deafness may result from ear infections,
otosclerosis (abnormal bone growth in the middle ear), or perforation of the eardrum.
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99
5. 1 Causes of disorders
• Sensorineural hearing loss: occurs when there is damage to the inner ear. Sound may arrive at
the cochlear, but it is not properly passed on to the auditory nerve, or the auditory nerve itself may be
damaged. Damage may be congenital (hearing1loss present at birth), as a result of genetic factors or
disease, or acquired due to a wide range of factors such as age, noise exposure, physical trauma, or
diseases such as meningitis.
Hearing loss may be a combination of both conductive and sensorineural hearing loss.
5.1.2
Visual disorders
Light enters the eye firstly through the cornea, a clear, curved 'window' on the front of the eye. The cornea
refracts light through the pupil, an opening at the front of the eye, the width of which is controlled by the
movement of the iris. Pupils are able to dilate and contract, the shape of the iris changing how much
light enters the eye. Light then passes through the lens, a curved, flexible structure which focuses light by
shortening or lengthening its width. The globe of the eyeball is filled with vitreous gel, a dense transparent
substance that gives the eye its spherical shape whilst still allowing light to be transmitted to the back of
the eye. Light rays come to a focal point, where the image is focused, at the retina in the back of the eye.
The retina acts like a kind of camera and is composed of two types of cells: rods and cones. These cells
are excited by different wavelengths of light. As light hits the retina, light energy is converted into electrical
impulses by the rods and cones, which send the messages onto the optical nerve, and through to the brain
for processing.
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As a complex organ, there are a number of disorders which may contribute to malfunction of the eye.
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• Refractive errors: occur when the eye does not focus light properly, due to incorrect shaping of the
cornea.
• Myopia : or near sightedness, occurs when the cornea is too curved or the eyeball is too long,
resulting in light refracted at an angle which places the focal plane in front of the retina. In this case,
objects far away are blurry.
• Hyperopia : or far-sightedness, occurs when the cornea is too flat or the eyeball is too short, resulting
in light being focused beyond the retina. In this case, objects close-up are blurry.
• Astigmatism : is a disorder where vision is blurred at all distances, as a result of a misshapen cornea
where curvature is not uniform in all directions.
• Other prevalent disorders include :
- Glaucoma: blindness due to a build-up of pressure in the eye, causing optic nerve damage
- Cataracts: clouded areas in the lens, causing blurry or tinted vision
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5. 1 Causes of disorders
5.1.3
Loss of kidney function
Kidneys are the body's cleaners, processing blood to filter out waste products, and balance salt and water
levels. Waste products are collected as urine, which moves from the kidneys to the bladder through the
ureters, and then out of the body through the urethra.
Blood enters the kidney from the renal artery, and leaves via the renal vein. The main areas of the kidney
are the cortex (outermost layer of the kidney), medulla (petal-like inner structures) , and pelvis (drainage
area at centre of kidney, connected to the ureter).
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Filtering is performed by microscopic structures called nephrons, situated across the cortex and the
medulla. Every kidney has about a million nephro111s, each performing the job of filtration. Capillaries
are wound around the nephron structures, providing an interface across which exchange of nutrients may
occur. When blood first enters the kidneys, the capillaries are squeezed into a very tightly wound structure called a glomerulus. This structure is so compact that all fluid in the blood (everything except red
blood cells) is squeezed out, into the Bowmans cap sule. In the proximal convoluted tubule, essential
molecules such as water, glucose, salts and nutrients are transferred back into the capillary. The rest of
the nephron structure performs a balancing function, regulating the return of salts back into the blood
in response to bodily requirements. Hormones may also act on the nephron, increasing permeability to
certain substances to promote their reabsorption into the blood. All wastes, excess substances and fluids
are then drained into the collecting duct, which leads to the renal pelvis to eventually be drained out of
the kidney and the body.
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Henle
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5.2 Technological developments
Loss of kidney function may result in build-up of wastes, electrolytes, and dangerous levels of fluid in the
blood. However, symptoms of kidney disease often have a very late onset. It is possible to lose up to 90%
of kidney function before any noticeable symptoms occur. Kidney failure may be as a result of a number of
factors, including:
•
•
•
•
•
Diabetes
High blood pressure
Inflammation of important filtration structures
Obstruction of the kidney (i.e. kidney stones or tumours)
Infections
5.2 Technological developments
SYLLABUS :
Investigate technologies that are used to assist with the effects of a disorder, including but not limited to:
• Hearing loss: cochlear implants, bond conduction implants, hearing aids
• Visual disorders: spectacles, laser surgery
• Loss of kidney function: dialysis
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Hearing loss
Cochlear implants
Cochlear implants are electronic devices which replace the function of damaged inner ears (the cochlea).
It enables sound, received through an external transmitter, to be transferred to the auditory nerve, allowing
individuals who have damaged the hair cells of the inner ear to hear. A sound processor captures sound,
and turns it into digital code. This digitally-coded sound is transmitted to the implant, which converts it to
electrical impulses. These impulses are then sent along the electrode, which is placed in the inner ear. The
electrode then stimulates the hearing nerve, which sends impulses to be brain to be interpreted as sound.
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Bone conduction implants
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This technology is used as an alternative to hearing aids, where individuals have conductive or mixed
hearing loss. Sound waves are detected by a processor placed behind the ear. Sounds are converted
digitally to vibrations, which are transmitted by the implanted section of the device, through the bone, and
to the inner ear. Sound vibrations then cause movement in the fluid of the inner ear, stimulating movement
of the hair cells, and therefore generating electrical impulses. These are then sent along the hearing nerve,
as with normal hearing.
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Hearing aids
These devices are worn either in or behind the
ear, and are used to amplify sound for patients
with hearing loss. By magnifying the sound vibrations which enter the ear, hearing sensitivity
can be increased. There are two types of hearing aids available, analogue (which convert sound
waves into electrical signals, amplify them , then
feed them back to the ear) or digital {which convert sound waves to numerical codes before ampli-
fication). Digital aids are more flexible to individual
patient needs and environments.
Copyright © 2018 lnStudent Publishing Pty. Ltd.
5.2 Technological developments
5.2.2
Visual disorders
Spectacles
Glasses correct vision by changing the angle at which light hits the cornea, adjusting for misshapen corneas
which cause the focal point to deviate from the norm. This allows the eye to focus light in the right spot in
the eye, on the retina. Glasses are available with a prescription, which means that they are made for each
individual person depending on their needs. For short-sightedness, where the focal point falls in front of
the retina, concave lenses allow light to focus on the retina. For far-sightedness, where the focal point falls
behind the retina, convex lenses allow light to focus properly on the retina.
Laser surgery
This is used to re-shape the cornea in order to correct vision problems. The surgeon will create a thin flap
in the top of the cornea, which is folded back so that the underlying stroma can be accessed. An excimer
laser uses short-wave ultraviolet light to remove tiny amounts of tissue. This reshapes the cornea so that
it focuses light more accurately (near-sightedness = flatten cornea, far-sightedness = increase curve of
cornea).
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5.2.3
Loss of kidney function
Dialysis
Dialysis refers to the removal of metabolic wastes, salt, and extra water from the blood by allowing dissolved
solutes to pass across a semipermeable membrane. Dialysis is used when kidneys have lost their ability
to filter waste products from the blood. It is essential that these products are removed so that the body can
continue to fun ction effectively.
• Haemodialysis : waste filtered from the blood outside of the body in a dialyser machine. An A-V
fistula is made in the patient's arm, from which blood is drawn , and then passed through a series of
semi-permeable membranes. This allows for toxins to be drawn out of the blood into dialyser fluid,
and clean blood returned to the body
• Peritoneal dialysis : cleansing fluid is flown into the peritoneal cavity in the abdomen by a catheter
(tube). Wastes are filtered into the cavity from the blood. The fluid with the waste products is then
drawn from the abdomen and discarded. Peritoneal dialysis can be performed by yourself at home
or whilst travelling, allowing for more flexibility in lifestyle and independence.
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5.3 Evaluation of haemodialysis
5.3
Evaluation of haemodialysis
S YLLA BUS:
Evaluate the effectiveness of a technology that is used to manage and assist with the effects of a dis-
l
order.
J
A number of technologies have been briefly outlined in the previous section, each with its own merits and
effectiveness. Below is a table providing an example of how these medical technologies can be assessed
and evaluated. Remember to be critical, and rationally weigh up considerations when evaluating technologies. Good students will think about the practical implementation , as well as the scientific aspects of the
tools.
CASE SPACE:
Disorder: Kidney failure
Technology
Haemodialysis
Description
Haemodialysis is a type of dialysis in which waste is filtered outside of the
body, using a dialyser machine (or 'artificial kidney'). An A-V fistula is made
across the patient's veins, from which blood is drawn. Blood is circulated
through a dialyser, through a series of semipermeable membranes, allowing
for toxins to be filtered from the blood by passive transport. Dialysers have:
- A compartment for blood
- A compartment for dialysate fluid (which is specifically balanced in order to
allow excess wastes to pass into it by passive transport along the
concentration gradient)
- A semipermeable membrane separating the two liquids
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Effectiveness
Positive effects:
- Allows for removal of metabolic wastes (urea) when kidneys no longer
function (a build-up of urea, known as uremia, may lead to seizures or a
coma, and ultimately death)
- Provides a long-term solution (people are able to be treated using dialysis
for many years), and gives patients time when waiting for kidney transplants
- Most hospitals are able to offer dialysis, so access in metropolitan areas is
quite good
Negative effects:
- Works only by passive, not active transport, so not all wastes can be
filtered, as they will only move into the dialysate until equilibrium is reached
across the membrane
- Requires repeated, large blocks of time (3 - 4 hour sessions in hospital a
few times a week) , particularly in cases of advanced kidney failure, so can
have a large impact upon patient quality of life, both in terms of time
consumption and the requirement to travel to hospital regularly
- Limits patient mobility, and may be expensive
- Dialysis requires that diet and fluid consumption are regulated, and often
restricted
- Dialysis does not cure kidney disease ; it merely mitigates its effects, so if
patients have severe kidney failure, they may need dialysis for the rest of their
lives, or until they have a kidney transplant
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5 .3 Evaluation of haemodialysis
Summary
Despite the downfalls of haemodialysis, it is evident that this technology is
life-saving, and essential for many patients with kidney failure. Ultimately, the
technology preserves some quality of life, and extends life expectancy in the
case of chronic kidney failure. Although the technology is not a cure for
kidney failure, it may be used in tandem with kidney transplants, giving
patients more time as they wait for donor organs to become available.
Individual patients' conditions may determine whether haemodialysis or
peritoneal dialysis is used. The widespread availability of both these
technologies in Australia means that there are multiple avenues for treatment
of patients with kidney failure.
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105
Part V
Exam and Revision Tips
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Biology Study Tips
Acing Biology exams is a combination of a number of different skills, like memory, critical thinking, evaluation , and data interpretation name just a few. No student is perfectly suited to the subject, but anyone
can do well if they put in the work! How successful you are will depend on the work you put in throughout
the year, both in study and exam techniques. These are the key tips that I used during the HSC, and even
continue to use for university biology. I promise that if you give them a go, you'll begin to see better results!
Summarise
Biology can be content heavy at times, but it's definitely manageable if you keep on top of the work. To
avoid falling behind, summarise everything you've learned each week. Set aside an hour at the end of the
week to sit down and just clearly outline any new content. If you miss a class, ask your teacher and friends
for help so that you don't miss out on any dot points. There's a possibility that any of the dot points could
be tested, even the totally ran dom research ones, so spending a little time while its fresh goes a long way
in the long run.
The good news is that you've already started out strong by purchasing these notes! Most of your exams will
be internal though, so it's important to keep up to date with class content and listen to what your teachers
specifically want.
Draw pictures and diagrams
A lot of the syllabus is about processes. How is DNA expressed? What are the steps of the immune
response? The best way to understand these, and commit them to memory, is to draw them out. By understanding how everything fits together, and why steps logically occur, it makes it way easier to memorise.
Sketch as many pictures as you can, organs, cells, proteins, etc. Taking time out to just copy pictures can
be relaxing and educational I
The same goes for big chunks of content. Try to break it down into a table or a diagram, down to the bare
essentials to memorise. I made posters for my HSC subjects, and it was a great way to visualise all the
content on one page.
Use colour
Colour is a very effective study tool. By continuing to use it consistently throughout the year, content will
begin to become linked on a number of levels, plus it makes your notes fun! For example, when I did
the HSC, I assigned each module a different colour. This made it easier to recall information in an exam
situation . If the question asked anything about DNA , it was associated with blue, and immediately I was
thinking about all the blue syllabus dot points and pieces of information for that. Memory aides like this are
always super useful under exam conditions.
Identify content overlap
There are a couple of sections of the syllabus that have a lot of overlap with others, and you should use
that to your advantage. Identify these areas, and make sure you understand the concepts really well,
because there's a high chance they'll be assessed. Where you need to know specific details about things
like disease, pick one disease for every dot point. For example, in non-infectious disease and disorders,
pick something like lung cancer. Know the causes, epidemiological data, and public health campaigns
associated with it. Make life easy for yourself and knock out four dot points in one fell swoop.
Be critical
Many of the dot points for this new syllabus require you to 'evaluate.' This means that you need to be
critical, weigh up both pros and cons, and come to an informed decision or standpoint. Each time you come
upon one of these dot points, make sure your notes include some deeper analysis. This will be especially
important for concepts in the biotechnology and Indigenous bush medicine parts of the syllabus. These
will likely form the basis of more essay-style questions, so think about how you would create a logical,
persuasive argument in each case.
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Practise, practise, practise
The best way to maximise marks in any science subject is through practice. Understanding content will
only get you part of the way; often in Biology, markers are looking for specific phrasing and will ask you
questions in unusual ways to separate out the good students from the best students. In order to prepare
for every possible scenario, I recommend doing as many worksheets and past papers as you can get your
hands on. When doing past papers, work on the questions that you feel the least confident with. Don't
waste time doing easy multiple choice - try to extend yourself and practice longer response questions, and
get used to writing out clear, structured answers under a time limit.
Use online resources
There are so many resources out there for HSC students. If you don't understand something the way your
teacher has phrased it, try to seek out advice from other students online. There are lots of students out
there who are willing to help and learn , especially on atarnotes.com. Particularly when it comes to specific
research examples, past paper discussions, and getting feedback on answers, going online is an invaluable
resource for all students.
Biology Exam Tips
Definitions
A really important part of answering Biology questions effectively, which students often forget, is defining all
the key terms in a question. The good news is this is a really easy way to get marks, because all you have
to do is memorise a few important phrases from your notes. In any 2 - 8 mark question where a term has
been brought up but not identified, you will get marks for explaining it.
For example, if a question asks 'What is the structure and function of DNA?' you can very easily get a mark
for simply defining what DNA is: DNA, or deoxyribose nucleic acid, is the molecule which carries genetic
information in most organisms.
Core concepts
There are a number of very important core concepts which underpin a lot of the content across the syllabus,
particularly concepts such as mutation , DNA structure, and adaptation. You will probably be examined on
these in some way, so make sure going into the exam that you understand them, and have a rough idea of
how they link across the syllabus. Make sure you have definitions, examples, and diagrams prepared for
these. This will save you time in the exam.
Detail and length of answers
During the exam, it's easy to get flustered and forget to include details which may help you to push your
marks from a Band 5 to a Band 6. Remember to always be looking at the mark allocations and reading the
questions carefully, as this will give you an indication of how much detail you need to include in an answer.
On average, you should be writing 1 - 2 sentences per mark. Use the number of lines given as a guide to
the length of your answer. If you are writing way past the space provided, you're probably writing too much .
Where possible, include examples and diagrams, especially for longer response questions. This helps your
marker to understand your point, and often will help the structure and clarity of your answers.
Structure of answers
When answering extended response questions, it is essential that you plan your answers before writing .
Highlight key words, and think about how you should order your response to best address the ideas in the
question . You should be including a brief introduction which re-phrases the question and outlines what you
will be talking about in your answer.
Definitely use paragraphs in your long responses, but don't limit yourself! Tables can be a super useful tool
for comparing ideas, particularly where you are talking about advantages and disadvantages. These show
your marker that you clearly understand the content, and are able to present it in a concise and effective
manner.
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Subheadings are another useful techniques, especially for 6 - 8 mark questions. It makes it super easy for
markers see that you've included all the information, especially in the HSC where markers are also under
time pressure and may not read your responses more than once. Make it easy for them, and they'll love
you. It will also help you to clarify your argument, and stay on track with your points of discussion. Try to
decide upon paragraph subheadings whilst planning your response at the beginning .
Flow charts and diagrams are always useful, and if you have time to draw them, they will definitely help you
to maximise marks. Keep them simple and clear, they don't have to be works of art!
Strategy
Exam nerves can cause students to get a little frantic, especially when we are placed under time pressure.
Having a solid strategy for how to approach the exam before you go in can help to manage this. It will
help to make things a little calmer, especially because you aren't sitting there trying to calculate how long
to spend on a particular question down to the second during writing time, instead of actually writing your
answers.
Think about how much time you have before you go into the exam room , and try to break it down (for
example, allocate 30 minutes to the multiple-choice section). Use this as a rough guide on exam day to
keep you on track.
I always recommend going through the paper in order. Start with your multiple choice, and do them as
quickly as you can so that you maximise time for longer questions. It's a nice warm up, and will jog your
memory a bit as they tend to touch on a number of different parts of the syllabus.
If you find yourself struggling with a particular question as you go through, stick with it for a little while. Try
to think what dot point it might be testing, and jot down any important definitions. If you are really unsure,
but a big star next to it and move on. Try to answer all questions to the best of your ability before going
back through and answering the tricky ones. This way, you are maximising your time for questions which
you find hardest.
If you have time left at the end, proof read. Add any detail or diagrams you think might help, and make sure
all if your answers actually address the question.
Best of luck for your Biology assessments !
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