Biology Revision Notes - Unit 3 & 4

Is VCE Biology Unit 3 & 4
Chapter 1 - General Skills

Key Science Skills
● develop aims and questions, formulate hypotheses, and make predictions
● identify independent, dependent and controlled variables in controlled experiments
● identify and analyse experimental data qualitatively, handing where appropriate concepts of: accuracy, precision,
repeatability, reproducibility and validity of measurements; errors (random and systematic); and certainty in data,
including effects of sample size in obtaining reliable data
● analyse and evaluate data and investigation methods
● construct evidence-based arguments and draw conclusions
Controlled Experiment: an investigation into the effect of an independent variable on a

dependent variable, while keeping all factors constant
Independent Variable: the factor/s that is/are manipulated in an experiment
Dependent Variable: the factor/s measured in the experiment that are changed when the IV
is measured
Controlled Variable: a factor that is kept constant or accounted for throughout the
experiment
Research Question: a testable, achievable, and specific question that an investigation sets
out an answer
Aim: the objective of an investigation or experiment
Hypothesis: a testable prediction that describes how experimenters expect the dependent
variable to change as the independent variable changes
Reliable: describes an experiment, tool or measurement that produces similar results when
repeated or reproduced
Repeatable: an experiment/measurement in which the scientists, using the methods they
designed, can obtain the same results multiple times
Reproducible: an experiment/measurement in which a group of scientists, using methods
designed by others, can obtain the same results as another group’s experiment
Valid: a measurement or experiment that actually tests what it claims to be testing
Precise: two or more measurements that closely align with each other
Random Error: variation in results caused by uncontrollable conditions between replications,

resulting in a less precise spread of readings
Personal Error: mistakes or miscalculations due to human fault
Systematic Error: errors which cause the results to differ by a consistent amount each time,
typically due to faulty equipment or calibration, resulting in a less accurate result
Ethics in Biology
●
analyse and evaluate bioethical issues using relevant approaches to bioethics and ethical concepts, including the
influence of social, economic, legal and political factors relevant to the selected issue
Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Bioethics: the study of ethical issues pertaining to biology and medicine Consequences-
Based Approach: aims to maximise positive outcomes while minimising negative outcomes
Duty/Rules-Based Approach: promotes the responsibility of the agent above all else, and
places importance on the duty of each individual
Virtues-Based Approach: emphasises the individual goodness of the agent, and promotes
acting in accordance with the values of a ‘moral’ person such as honesty and compassion
Integrity: encourages a full commitment to knowledge and understanding as well as honest

reporting of all sources of information and results
Justice: encourages fair consideration of competing claims, and ensures that there is no
unfair burden on a particular group from an action
Beneficence: seeks to maximise benefits when taking a particular position or course of
action
Non-Maleficence: discourages causing harm, or when harm is unavoidable, ensuring that
the harm is not disproportionate to the benefits from any position or course of action
Respect: acknowledgement of the intrinsic value of living things, and considers the welfare,
beliefs, customs, and cultural heritage of both the individual and the collective
Unit 3 AOS 1
Chapter 2 - Nucleic Acids & Proteins
Protein Structure & Function
● amino acids as the monomers of a polypeptide chain and the resultant hierarchical levels of structure that give
rise to a functional protein
● proteins as a diverse group of molecules that collectively make an organism’s proteome, including enzymes as
catalysts in biochemical pathways
Polypeptide: a long chain of amino acids, also known as proteins, that are folded into a 3D
shape
Proteome: the entire set of proteins expressed by an organism at given time
- Enzymes: organic catalysts that speed up chemical reactions Eg. catalase: breaks
down hydrogen peroxide into water and oxygen
- Transport: typically embedded in membranes, controlling the entry and exit of
substances from a cell Eg. glucose channels
- Structural: support cell and tissue shape Eg. elastin: found in elastic connective
tissue such as skin
- Hormones: many peptide hormones are chemical messengers used to communicate
and induce changes in cells Eg. insulin: regulates blood sugar levels
- Receptors: receive signal from the environment Eg. hormone receptors
- Defence: involved in the immune system by recognising and destroying pathogens
Eg. antibodies / complement proteins
- Motor/Contractile: involved in the contraction and movement of muscles, the
movement of internal cell contents around the cytoplasm, and the movement of cilia
and flagella Eg. kinesin: moves along microtubules enabling mitosis and vesicular
transport

Amino Acids: serve as building blocks to proteins; each amino acid consists of a central
carbon atom that is bonded to a hydrogen atom, a carboxyl group (COOH), an amino
group (NH2), and an R-group; there are 20 types know in existence, each with a different
R-group.
- R-Group: is the differentiable region of an amino acid, meaning they can sometimes
into elements of sulphur as well as C, H, O and N; each has its own chemical
properties that can affect how different amino acids within a protein interact with
each other.
- when joined together, amino acids form a long chain known as a polypeptide chain,
or protein; different similar basic structures allows them to act as repeating subunits
called monomers; these a joined together to be called polymers
- a condensation reaction caused the formation of peptide bonds between adjacent
amino acids
- polypeptide chains have to fold carefully into the correct shape

Primary Structure: the sequence (order) of amino acids in a polypeptide chain
- changes to the original sequences can result in misfolding and an unfunctional
protein
Secondary Structure: amino acids arrangement into alpha-helices, beta-pleated sheets
and random coils because of the folds and coils by formation of hydrogen bonds between
an amino acids different sections of the polypeptide chain
Tertiary Structure: the overall functional 3D shape of a protein; a protein must have a
minimum of tertiary structure to be functional;
Quaternary Structure: the bonding of multiple (two or more) polypeptide chain together; not
all proteins have this structure
Nucleic Acids
● nucleic acids as information molecules that encode instructions for the synthesis of proteins: the structure of DNA,
the three main forms of RNA (mRNA, rRNA and tRNA) and a comparison of their respective nucleotides
- polymers of nucleotide monomers, which not only store genetic information, but also
form molecules that aid in the production of proteins
Nucleotide: includes a phosphate group, a five-carbon (pentose) sugar and a nitrogen-
containing base
- each carbon is assigned a number in a clockwise direction, with the first carbon
labelled 1’ (one prime) and the last carbon 5’
- 1’ attaches to the nitrogenous base
- 3’ attaches to the phosphate of the following nucleotide
- 5’ attaches to the phosphate group of the nucleotide
- the bonds joining nucleotides are strong covalent bonds known as phosphodiester
bonds, which form via condensation reactions and exist between the sugar group
of one nucleotide and the phosphate group of another
- the linkage is often referred to as the sugar-phosphate backbone of nucleic acids
Deoxyribonucleic Acid: consists of two strands of nucleotides bonded together via

complementary base pairing, forming a double-helix which runs in an antiparallel fashion
- a deoxyribose sugar ( denoting the absent of oxygen)

- found inside the nucleus of human eukaryotic cells
- the complete set of DNA is referred to as the genome
- adenine (A) will always pair with thymine (T) with two hydrogen bonds
- guanine (G) will always pair with cytosine (C) with three hydrogen bonds
Ribonucleic Acid: a single strand of nucleotides that comes in a variety of different forms
and is found in many different parts of the cell; primarily involves in the synthesis of proteins
- Messenger RNA: carries genetic information from the nucleus to the ribosomes for
protein synthesis
- Transfer RNA: delivers specific amino acids to the ribosome after recognising
specific nucleotide sequences on mRNA
- Ribosomal RNA: serves as the main structural component of ribosomes within cells
- contains ribose sugar; no thymine, uracil instead; temporary molecules
Structure of Genes
● the structure of genes: exons, introns and promoter and operator regions
Promoter: the region is an upstream (5’ end) binding site for RNA polymerase (the enzyme
responsible for transcription; RNA polymerase binds to the promoter region of a gene,
allowing for transcription of that particular gene; denotes the starting position and direction
of transcription
Introns: regions of non-coding DNA that do not contribute to the final protein as they are
removed during RNA processing (only in eukaryotic cells)
Exons: regions of coding DNA that are transcribed and translated into the final protein (in
both eukaryotes and prokaryotes
Termination Sequence: represents a sequence of DNA that signals for the end of
transcription
Operator: the region that serves as a binding site for repressor proteins, that can inhibit
gene expression, typically only found in prokaryotic genes, as eukaryotes have different
regions for regulating gene expression
Protein Synthesis & Gene Expression

● the genetic code as a universal triplet code that is degenerate and the steps in gene expression, including
transcription, RNA processing in eukaryotic cells and translation by ribosomes
- a complex series of events which results in the formation of functional gene
products such as proteins or non-coding strands of RNA
-
Protein Synthesis: relies on the existence of the genetic code, which is a series of rules that
determine how genetic information is transcribed and translated into functional proteins
- a group of three adjacent DNA nucleotides in known as a triplet, when
transcribed into an mRNA molecule, the three nucleotides become a codon
- instruct the start (AUG) and stop (UAA, UAG, UGA - to signal termination of
translation) of protein synthesis, and the order of amino acids in a protein
- use a codon table to determine the amino acids
Universal: nearly all living organisms use the same codons to code for specific amino acids
Unambiguous: each codon is only capable of coding for one specific amino acid Eg. UUA
only codes for leucine

Degenerate: each amino acid may be coded for by multiple different codons Eg. UUA and
UUG code for leucine
Non-Overlapping: each triplet or codon is read independently, without overlapping from
adjacent triplets or codons
1. Transcription: copying DNA into pre-mRNA

- occurs within the nucleus of eukaryotic cells, but in the cytoplasm of prokaryotic
cells
- Initiation: specific proteins called transcription factors bind to the promoter region t
initiate transcription, RNA polymerase binds to the promoter region and signals
bonds to break so that the DNA helix is unwound and unzipped
- Elongation: RNA polymerase moves along the template strand of NDa, to read
nucleotide sequences and uses free-floating complementary RNA nucleotides to
produce a new single-stranded RNA molecule known as pre-mRNA; the strand not
read is called the coding strand that is identical to the pre-mRNA strand
- Termination: the end of transcription; once RNA polymerase reaches the
termination sequence is the DNA molecule is wound up again into a double helix
2. RNA Processing: modifying the pre-mRNA molecule to produce m(mature)RNA

- the addition of 5’ methyl-G cap and a 3’ poly-A tail to stable the mRNA molecule,
preventing it from degrading and allowing it to bind to ribosomes during translation
- the removal of introns and splicing of exons; a spliceosome removes introns and
splices exons together
- Alternative Splicing: the removal of some exons of rearranging of exons to give rise
to many different mRNA strands that code for many different proteins
3. Translation: decoding and converting the mRNA strand into a polypeptide chain
- mRNA exits the nucleus through a nuclear pore and travels to a ribosome
either in the cytosol or attaches to the rough endoplasmic reticulum
- Initiation: the 5’ end of the mRNA molecule binds to the ribosome and is read
until a start codon (AUG) is recognised; a tRNA molecule with a
complementary anticodon (UAC) binds to the ribosome and delivers the
amino acids ‘met’ to signify the commencement of translation
- Elongation: the mRNA molecule is fed through the ribosome so that the next
codon can be matched to its complementary tRNA anticodon; amino acids
bind with peptide bonds via a condensation reaction; more tRNA-delivered
amino acids continue to grow the amino acid chain
- Termination: a stop codon is reached that ends translation because their is
no corresponding tRNA molecules; the polypeptide chain is released by the
ribosome into the cytosol or endoplasmic reticulum and begins to fold into a
protein
Trp Operon
● the basic elements of gene regulation: prokaryotic trp operon as a simplified example of a regulatory process
Gene Regulation: the control of gene expression, typically achieved by switching

transcription on and off

Structural Genes: responsible for producing proteins that are involved in the strucure and
function of a cell, found at the 3’ end of regulatory genes that control them
Regulatory Genes: responsible for the production of regulatory proteins such as repressor
proteins which inhibit or decrease the expression of structural genes; activator proteins
can initiate or increase the expression of structural genes; can turn gene expression off or
on to increase or decrease the rate of gene expression by promoting or hindering
transcription
Operon: a cluster of linked genes that all share a common promoter and operator and are
transcribed at the same time
- Operator Region: bound with repressor protein - then RNA polymerase cannot
move downstream and cannot transcribe the gene as usual; when not bound with the
repressor protein - RNA polymerase is free to move downstream, allowing
transcription of the gene as usual
Trp Operon: a series of genes that are involved in the production of the amino acid
tryptophan, which can subsequently be used in protein production
- found in certain species of bacteria include E.coli to regulate the expression of
structural genes that code for trp
- high levels of trp repress the transcription of trp structural genes to prevent
unnecessary production of trp (conserving energy); induces a conformational
change in the repressor protein so it can bind to the operator region and therefore
prevent transcription
- low levels of trp activate the transcription of trp to increase the amount of trp
available
Hair Pin Loop: the backup process to stop trp production
The Protein Secretory Pathway

● the role of rough endoplasmic reticulum, Golgi apparatus and associated vesicles in the export of proteins from a
cell via the protein secretory pathway
Exocytosis: the process by which the contents of a vesicle are released from a cell; a form
of bulk transport that allows for the movement of large substances (such as proteins) out
of cells; also a form of active transport that requires the input of energy
- a vesicle containing secretory products is transported to the plasma membrane
- the membrane of the vesicle fuses with the plasma membrane; which is allowed
because of fluid nature of the plasma membrane that has an ability to be mobile and
flexible
- the secretory products are released from the cell into the extracellular environment
1. Ribosome: synthesises proteins; assembles the chains of amino acids by translating

mRNA
2. Rough Endoplasmic Reticulum: folds and transports proteins;
3. Transport Vesicle: transports proteins; buds off the rough endoplasmic reticulum and
travels to the Golgi apparatus; it fuses with the Golgi and releases the protein into its
lumen

4. Golgi Apparatus: modifies and packages proteins; chemical groups are added or
removed from proteins; often packaged into secretory vesicles for export or released
directly into the cytosol to be used by the cell
5. Secretory Vesicle: transports proteins; bud off the Golgi apparatus and travel through
the cytoplasm, fusing to the plasma membrane; releases the proteins contained
within into the extracellular environment through exocytosis
Chapter 3 - Enzymes
Enzymes as Catalysts
● proteins as a diverse group of molecules that collectively make an organism’s proteome, including enzymes as
catalysts in biochemical pathways
- speed up biochemical reactions by lowering the activation energy required to
initiate a given reaction
- some chemical reactions include DNA replication, cell communication, cellular
respiration etc
Enzymes: organic catalysts that speed up chemical reactions

- enzymes are reusable, they are not broken down, used up or turned into a product,
and so can catalyse future reactions
- enzymes only bind to a specific substrate, meaning they only tend to catalyse just
one chemical reaction, although some are specialised
- most reactions are reversible and are often capable of building up larger molecules
(anabolic) or breaking down into smaller ones (catabolic)
- enzymes speed up, but don’t create new reactions, the reactions would otherwise
occur naturally
- enzymes are proteins
- all enzymes are catalysts, but not all catalysts are enzymes; hence they are a subset
of catalysts
- enzymes frequently influence entire biochemical pathways by catalysing each step
- typically end in ‘-ase’ Eg. polymerase, ligase, lactase
Substrate: the name given to the reactant undergoing an enzyme facilitated ration; upon
binding it undergoes a chemical reaction and forms a product that leaves the enzyme
Active Site: a pocket-like area of the enzyme’s tertiary structure where the substrate binds
to; the enzyme’s active site and substrate are ‘complementary’ in shape; there binding
together forms a enzyme-substrate complex; upon binds the active site undergoes a
conformational change to accommodate the substrate
Activation Energy: the energy required to initiate a reaction; the ‘minimum amount’ of energy
required to energies atoms so that they can undergo a chemical transformation
- Anabolic: when two or more smaller molecules combine to form a larger one
- Catabolic: a larger molecule turning into two or more smaller molecules
- lower activation energy of chemical reactions can bring reactants closer to the state
they need to be in order to react; therefore reactions can proceed at a much quicker
rate

Factors that Affect Enzymes
● the general role of enzymes and coenzymes in facilitating steps in photosynthesis and cellular respiration
● the general factors that impact on enzyme function in relation to photosynthesis and cellular respiration: changes
in temperature, pH, concentration, competitive and non-competitive enzyme inhibitors
Temperature: high temperatures denature an enzyme and stop functioning; low

temperatures reduce the speed of the reaction
- as temperatures increase, molecules have greater kinetic energy and collide with
one another more frequently, allowing reactions to occur faster
- at optimal temperatures (37°C for the human body) the activity is the greatest,
hence the enzyme and substrate collide and bind most frequently
- Denaturation: causes a conformational change in the active site of the enzyme,
and no substrate can fit; this is reversible
- low temperatures can cause enzymes to experience little to no activity and can
freeze, but they can regain functionality when reheated as significant denaturation
does not occur at low temperatures
- Tolerance Range: the wider range given to a condition for which an enzyme can
function; outside a tolerance range an enzyme is inactive Eg. an enzyme may have a
optimal temperature of 58-60°C but a tolerance range of 30-70°C
pH: can be measured on a scale based on the acidity or alkalinity of a solution; acids have
low pH and alkaline (basic) solutions have high pH values; if the enzymes becomes too
acidic or basic for the enzyme it can denature
Concentration: of either substrate or enzyme molecules influence the overall reaction rate
- Substrate Concentration: increase (with constant enzyme concentration) will
increase reaction rate; because there will be more reactants available to undergo the
reaction Saturation Point: a point will be reached when substrate molecules
continuously occupy all active sites making the enzymes saturated referred to as a
limiting factor before the plateau in the reaction because it prevent an increase in
reaction rate because of the presence of another factor such as pH, temperature or
enzyme concentration
- Enzyme Concentration: higher concentration will have a higher reaction rate; a large
number of active sites available for the substrate to bind to
- also has a saturation point in which there are more enzymes available then there is
other resources and therefore a greater amount of reactions cannot occur
Competitive Inhibition: impeded enzymes by blocking the active site so it can no longer
catalyse irs specific reaction; therefore reducing functioning; the competitive inhibitor will
have a shape that is complementary to the active site in some way (must share a shape
similar to the substrate)
Non-Competitive Inhibition: binds to a site other than the active site (allosteric site) and
induces a conformational change; prevents the substrate from binding to it, and prevents
the reaction from occurring
- inhibition has an important role biochemical pathways in the body; it can ensure
that the production of a substrate in slowed down when there is adequate supply;
creating a self-regulating pathway that conserves energy

Coenzymes: a subset of cofactors that are organic, non-protein molecules that assist
enzymes in catalysing reaction; integral to many biochemical processes
- the enzyme remains unchanged; but the structure of the coenzyme is changed
- during the reaction, the coenzyme binds to the active site, donates energy or
molecules, and then cannot be immediately reused; but can be recycle after
accepting more again to assist with more reaction
- ATP and ADP are involved in the main energy transfer of the cell; donating energy to
catalyse reactions; coenzymes are used so frequently that the same ATP molecule
can be cycled to ADP and back over 1000 times every day
Chapter 4 - DNA Manipulation

Enzymes to Manipulate DNA
● the use of enzymes to manipulate DNA, including polymerase to synthesise DNA, ligase to join DNA and
endonucleases to cut DNA
Endonuclease: cuts DNA sequence at a specific point; “molecular scissors”; cleave the
phosphodiester bond of the sugar-phosphate backbone that holds DNA nucleotides together
- Restriction Endonucleases: target specific recognition sites; often sourced from
bacteria, where they are naturally produced as a defence mechanism against
invading viral DNA that could harm the bacteria; the recognition site is usually four to
six nucleotides in length
- Sticky Ends: do not cut in the middle of the recognition site, resulting is staggered cut
with overhanging, unrepaired nucleotide; overhangs are attracted to a
complementary set of unpaired nucleotides which are easier to join together with
hydrogen bonds
- Blunt Ends: end in a straight cut and have no overhangs; harder to repair themselves
Ligase: “molecular glue” that joins two complementary fragments of DNA and RNA
together; hydrogen bonds naturally occur between complementary bases to catalyse the
formation of phosphodiester bonds between the sugar and phosphate backbone between
nucleotides; function as the reverse of endonucleases, but lack specificity like a restriction
endonuclease has
Polymerase: synthesises polymer chains from building blocks; adding new complementary
bases to growing DNA strands to copy entire genes; DNA becomes single-stranded
- RNA Polymerase: is primarily used in the transcription of genes
- DNA Polymerase: used in the replication or amplification of DNA
- Primer: a short piece of single-stranded (of nucleotide / DNA) that binds to the
template DNA and acts as a “starter” for the polymerase
- 6 base palindrome (read the same forwards as backwards) from 5’ to 3’
CRISPR-Cas9
● the function of CRISPR-Cas9 in bacteria and the application of this function in editing an organism’s genome
- naturally occurring sequence of DNA found in the bacteria that plays an important
role in their defence against viral attacks

- the bacteria’s natural defence (immunity) system against a virus (bacteriophage);
CRISPR cuts up the viral DNA using the endonuclease called Cas9
1. Exposure: bacteriophage injects its DNA into a bacterium which identifies the viral
DNA as a foreign substance; a protospacer, or short section of the viral DNA is
made by the endonucleases (the ‘mugshot’) which is introduced into the bacterium’s
CRISPR gene and becomes a spacer (storing some of the viral genetic material
within the bacterium’s own genome)
2. Expression: the CRISPR spacers are transcribed along with a half palindrome from
the repeat either side of it and converted into an RNA molecule known as guide
RNA; gRNA binds to Cas9 to create a CRISPR-Cas9 complex which is directed to
any viral DNA inside the cell that is complementary to the gRNA; forms as hairpin
loop from the transcribed palindromic repeats either side of the spacer
3. Extermination: next time the virus invades, the bacterium transcribes the ‘mugshot’
DNA and attaches it to the Cas9 if the ‘mugshot’ is complementary to the viral DNA,
so that Cas9 only destroys the invading virus rather than any bacterial nucleic acids;
Cas9 cleaves the phosphate-sugar backbone to inactivate the virus and creates
blunt ends
- the viral DNA will naturally be repaired by enzymes within the bacterium, however,
these are prone to errors and can result in nucleotide additions, deletions or
insertions; mutations tend to render the viral genes non-functional
- can be used to precisely target and cut any piece of DNA which is not desirable
- genetic modifications can amend the deleterious mutations or introduce a
biologically advantageous allele to an individual’s genome; however, many gene
therapy techniques lack precision and may inadvertently insert and introduced piece
of DNA into the wrong part of the genome, interrupting healthy functioning of the
gene
- potentially increase crop productivity, eliminate genetic disease and better
understand the purpose of specific genes
- can induce genetic changes by cutting DNA at a location specifically chosen by
scientist; knockout, enhance or change the function of a gene
Gene Editing: CRISPR is currently the most precise and affordable option for genetic
engineering
1. synthetic gRNA is created in a lab that has a complementary spacer to target DNA
that scientists wish to cut
2. a Cas9 enzyme is obtained with an appropriate target PAM sequence
3. Cas9 and gRNA are added together in a mixture and bind together to create the
CRISPR-Cas9 complex
4. the gRNA-Cas9 mixture is then injected into a specific cell, such as a zygote
5. the Cas9 finds the target PAm sequence and checks whether the gRNA aligns with
the DNA
6. Cas9 cuts the selected sequence of DNA
7. the DNA has a blunt end cut that the cell will attempt to repair
8. when repairing DNA the cell can introduce new nucleotides into the DNA at the site;
scientists can inject a particular nucleotide sequence into the cell with the hope that it
will ligate into the gap

Limitations: it is difficult to achieve gene knock in or knock out with precision and may not be
consistently successful; to successfully complete a procedure scientists must treat embryos
prior to cells differentiating so that every cell in the organism is altered; use of embryos
may go against the sanctity of human life; there are unforeseen consequences and potential
harm to pregnant women and unborn babies;
- no-harm principle cannot be met because of the unknown consequences during
pregnancy
- Safety: there is a possibility that off-target cleavages
- Informed Consent: embryos cannot be asked permission to edit their DNA
- Inequality: wealthy people may be able to afford the technology but others cannot
- Discrimination: opens up judgement about ‘fixing’ defects or certain characteristics
making some people ‘biologicallty inferior’
Polymerase Chain Reaction

● amplification of DNA using polymerase chain reaction and the use of gel electrophoresis in sorting DNA
fragments, including the interpretation of gel runs for DNA profiling
- a DNA manipulation technique that amplifies DNA by making multiple identical
copies
- after undergoing this type of testing scientists can further analyse using paternity
testing, forensic testings of bodily fluid samples and analysis of fragments of genetic
diseases
- to make the process more efficient primers and restriction endonucleases are
used instead of a copy of the entire genome
- the necessary materials include a DNA sample that is denatured and amplified; Taq
polymerase for elongation; nucleotide bases; sequence specific primers to join to
the 3’ end of single-stranded DNA; all which are placed in a thermal cycler
Taq Polymerase: a heat-resistant DNA polymerase from the bacteria Thermus aquaticus
which amplifies a single-stranded DNA molecule by attaching complementary nucleotides
1. Denaturation: DNA is heated to approximately 90-95°C to break the hydrogen

bonds between the bases and separate the strands, forming single-stranded DNA
2. Annealing: the single-stranded DNA is cooled to approximately 50-55°C to allow the
primers to bind to complementary sequences on the single-stranded DNA
3. Elongation: the DNA is heated again to 72°C, which allow Taq polymerase to work
optimally; it binds to the primer, acting as a starting point, and begins synthesising a
new complementary strand of DNA
4. Repeat: the cycle is repeated multiple times to create more copies of DNA
Forward Primer: will bind to the start codon at the 3’ end of the template strand, causing Taq
polymerase to synthesise a new strand of DNA in the same direction as RNA polymerase
would function
Reverse Primer: will bind to the stop codon at the 5’ end of the coding strand; causing Taq
polymerase to synthesise new DNA strands in the reverse direction that RNA polymerase
would function

Gel Electrophoresis
● amplification of DNA using polymerase chain reaction and the use of gel electrophoresis in sorting DNA
fragments, including the interpretation of gel runs for DNA profiling
- a laboratory technique used by scientists to measure the size of DNA fragments;

typically used after a sample is cut up using restriction endonucleases or after a
short sequence of NDA has been amplified using the polymerase chain reaction
1. the DNA samples are placed in wells at one end of the gel using a micropipette; a
standard ladder of DNA fragments with known sizes is also typically loaded into one
well; the gel is made of agarose which is immersed in a buffer solution which helps
carry an electric current
2. an electric current is passed through the gel using two electrodes; the negative
electrode is positioned near the wells and the positive electrode is at the opposite
end of the gel; since DNA is negatively charged so it is attracted to the positive
electrode; when the electrical current is applied, DNA fragments will move from the
wells, through the tiny pores in the agarose gel towards the positive electrode
3. smaller DNA fragments move faster through the gel and so travel further than larger
fragments; which don’t move as easily through the pores in the agarose; when the
current is switched off and the DNA fragments stop moving in the fel and settle into
bands; now separated based on size
4. a fluorescent dye such as ethidium bromide, allowing the bands of DNA to be
visualised under an ultraviolet lamp; the dye can be included in the gel before the
experiment or applied after
Kilobases: a unit of measurement that corresponds to one thousand nucleotides (kb or kbp)
Molecular Size: indicates the length of a nucleic acid sequence and is measured in base
pairs
Standard Ladders: vital to gel electrophoresis because DNA fragments of the same size
don’t always travel the same distance; this can occur due to a number of factors
- the stronger the voltage and electric force generated by an electrode the further the
DNA travels towards the positive electrode
- gels with greater density (composition) and agarose concentration increase the
difficulty for larger fragments to move through
- the greater the concentration of ions in the buffer the more the electric current is
conducted through the gel, which causes DNA to move further down the lane
- the longer (more time) the electric current is applied, the further the DNA will travel
Genetic Testing: screening an individual’s DNA for anomalies that may make them
susceptible to a particular disease or disorder
- certain genetic disorders occur when individuals possess mutated alleles which
prevent parts of the body and its cells from functioning the way they should; these
mutations can be small as a change of a single nucleotide
- Eg. cystic fibrosis can be diagnosed using a combination of the polymerase chain
reaction and gel electrophoresis; a routine test called a heel prick test that is
performed using a blood sample is obtained from the heel of a newborn baby,

extracting their genetic material; the sample undergoes the PCR using specific
genetic material
DNA Profiling: the process of identification on the basis of an individual’s genetic information
- a crime scene may only contain small traces of DNA that can be amplified using
PCR until there is a large enough amount of testable genetic material
- Short Tandem Repeats: short, repeated sequences of nucleotides found in the non-
coding regions of nuclear DNA
- they’re found in non-coding regions that are not affected by natural selection and
many hundreds of variant STRs that can be found in the DNA of each person due to
their higher mutation rate (compared to other areas of DNA) that can give confidence
that two pieces of DNA that are similar belong to the same person
- particularly useful for paternity testing when the identity of one of the parents is not
known; the child must inherit half of the STRs from each one of their parents
Homozygous: having identical alleles for the same gene on homologous chromosomes; the
individual will have one thick band
Heterozygous: having different alleles form the same gene on homologous chromosomes;
the individual will have two bands
Recombinant Plasmids & Transformation

● the use of recombinant plasmids as vectors to transform bacterial cells as demonstrated by the production of
human insulin
Plasmid: a small, circular loop of DNA separate from the chromosome, typically found in
bacteria
- bacteria are simple prokaryotic organisms that replicate their plasmid DNA
independently from their circular chromosome
- bacteria possess independently replicating plasmids means that humans can
genetically modify bacteria to synthesise large amounts of protein in a simple
process
Recombinant Plasmid: a circular DNA vector that is ligated to incorporate a gene of interest
- plasmids are excellent cloning vectors because they can self-replicate, are small,
can be taken up by bacteria, and it is easy to include antibiotic resistance genes,
recognition sites, and expression signals
Gene of Interest: a gene scientists want to be expressed in recombinant bacteria; the gene
often encodes a protein that is wished to be produced in commercial quantities; the Dna
sequence is isolated and amplified using PCR because it can be inserted into a vector
Plasmid Vector: selected into which gene of interest will be inserted; includes restriction
endonuclease sites, antibiotic resistance genes, origin of replication, reporter gene
Restriction Endonuclease: the gene of interest and plasmid are both cut with the same
restriction endonuclease to generate identical sticky ends on either end of the DNA
sequence; the overhanging nucleotides on the plasmid vector can form hydrogen bonds so
that they stick together easily

DNA Ligase: is added to join together the gene of interest and the plasmid vector by forming
phosphodiester bonds in the sugar-phosphate backbone; not every plasmid will take up
the gene of interest
- the uptake of a recombinant plasmid involves the recombinant plasmid being

inserted into the cytoplasm of bacteria in a process known as bacterial
transformation Bacterial Transformation: the process by which bacteria takes up
foreign DNA from their environment
- can include large-scale production of the following proteins; insulin to manage
diabetes; interferons to treat some cancers; growth hormones to manage some
growth disorders; hepatitis B surface-antigen for use in the hepatitis B vaccine Heat
Shock: first requires bacteria and plasmids to be placed in a calcium ion solution on
ice; the positive calcium ions help make the plasma membrane more permeable to
the negatively charged plasmid DNA; the solution is then heated to around 37- 42°C
for 25 - 45 seconds before being returned to ice; the sudden change in temperature
makes the plasma membrane even more permeable and allows the plasmid vectors
to cross the phospholipid bilayer and enter the bacteria’s cytoplasm
Electroporation: an electric current is passed through the solution containing bacteria and
plasmid vectors; making the plasma membrane more permeable and allowing plasmid
vectors to cross the phospholipid bilayer
Antibiotic Selection: only transformed bacteria will contain the gene necessary for antibiotic
resistance, all untransformed bacteria will be killed of; this means that each colony visible on
the plate represents a transformation event whereby a single bacterium has taken up a
plasmid, allowing it to survive, multiply and form a colony of identical daughter cells
- Eg. gfp encodes for a green fluorescent protein which fluoresces green under UV
light when fully expressed; if taken up by the plasmid it will not glow
- the transformed bacteria are cultured and induced to produce the target protein, as
the bacteria makes lots of different proteins, the protein or interest is extracted and
purified
Insulin: an important hormone that is responsible for regulating blood glucose levels; people
with diabetes do not naturally produce or respond to insulin and require it to be administered
artificially into their body; can be produced by transformed bacteria
- insulin has a quaternary structure consisting of two polypeptide chains with alpha
and beta subunits
1. plasmid vectors are prepared which contain ampR gene to encode for antibiotic
resistance, and lacZ, which acts a reporter gene and has a specific recognition site
to restriction endonuclease
2. two plasmid vectors are used - one for insulin subunit A and another for subunit B;
both are cut to form sticky ends; DNA ligase is used to reestablish the sugar-
phosphate backbone and create two different recombinant plasmids
3. plasmids are added to a solution of E.coli and either heat shock or electroporation
is completed

4. the bacteria cultures are spread and incubated onto agar plates containing X-gal and
the antibiotic ampicillin; those that are colourless are determined as transformed, as
their lacZ gene is dysfunctional since the gene of interest in located inside it
5. recombinant plasmids will product the insulin subunit beta-galactosidase
6. transformed bacteria that contains the recombinant plasmid are placed in conditions
to exponentially reproduce before their membranes a broken down and the human
insulin is isolated and purified
7. the two insulin chains have their tails removed and are mixed together, allowing them
to connect via disulphide bonds and create a functional human insulin
Genetically Modified Organisms

● the use of genetically modified and transgenic organisms in agriculture to increase crop productivity and to
provide resistance to disease
Genetic Engineering: the process of using biotechnology to alter the genome of an
organism, typically with the goal of conferring some desirable trait Eg. increased size, higher
drought resistance, brighter colours; can use genetic recombination technologies
- genes may be silenced, inserted into the genome, removed from the genome or
altered by replacing nucleotides
- any organism altered this way is called a GMO; the organism that is altered is called
the host organism
Cisgenic Organisms: a GMO that has genes from the same species inserted into its
genome; involves transferring genes between organisms that could otherwise breed
together Transgenic Organisms: a GMO that has genes from a different species inserted
into its genome; the process is known as transgenesis that results in the organism having
foreign DNA transplanted from a different species; are able to produce proteins that were
not previously part of their species’ proteme
- the main purpose of GMOs in agriculture is to increase crop productivity and

increase disease resistance in crops
1. gene identification - a particular gene of interest must be identified and isolated
2. gene delivery - the isolated gene of interest must be delivered via cells of the host
organism; delivery may occur by direct insertion of NDA or use of a bacterial plasmid
that can successfully transfer DNA
3. gene expression - the transformed cell is grown repeatedly using plant tissue
cultures under sterile conditions before being applied in the field for agricultural use;
GM host organism is able to express the new transgene as a useful protein that can
regenerate itself
- crop productivity can be increased by increasing crop yield (how much is produced
on farming land) or the quality of crops could be better Eg. greater nutritional value
- disease resistance may mean a crop is less impacted by a certain pathogen that
may improve global food security and minimise crop destruction; environmental
damaging factors may decrease Eg. drought resistance/ pest resistance
Biological Implications: GM crops usually have been crop productivity so more food is
grown and land clearing is minimised; can be insect resistant which is better for the

environment; may have improved nutritional content to increase health of humans; BUT they
could lose their effectiveness to weed and pest resistance; widespread use could reduce
genetic diversity of crops; cross-pollination between GM crops could cause genes to spread
and lead to unforeseeable consequences
Social Implications: increased crop productivity reduced food insecurity; protect against
famine in adverse conditions because of resistance; weeds don’t need to be pulled because
of herbicide-tolerance; increased crop yields can increase profits; may have improved
flavour or texture increasing appeal; improved nutrient content can reduce nutritional
deficiencies; BUT buying new seeds can be costly; there are complex legal issues that can
cause stress and anxiety because of regulations; strict packaging and marketing
requirements may not be complied with
Ethical Implications: potential widespread benefits such as increased nutrition, wealth and
overall health is particularly good for developing nations; BUT some people consider GMOs
unnatural; they may be unsafe to eat and therefore people don’t eat them; modifying
animals may be considered inhumane; companies can own the rights to GM crops which
may be unfair for some farmers (cross-pollination and seeds can’t be reused)
Unit 3 AOS 2
Chapter 5 - Photosynthesis
C3 Photosynthesis
● the general structure of the biochemical pathways in photosynthesis and cellular respiration from initial reactant
to final product
- the main inputs are carbon dioxide and water to produce glucose, oxygen and water
- plants typically have a large surface area to maximise the amount of light hitting their
surface
Mesophyll Cells: are the main cells in the leaves of plants

Chloroplasts: are inside the mesophyll cells, and are the organelle that is the site of both
stages of photosynthesis
Chlorophyll: is the pigment that is directly responsible for initiating photosynthesis by
capturing and being energising by light energy
Stomata: are the tiny pores on the surface of leaves that allow carbon dioxide in the
atmosphere into the leaf and can close to prevent water loss from the leaf in dry conditions
Xylem: transport water that has been absorbed from the soil to photosynthesising cells
Light-Dependent Stage
inputs, outputs, and locations of the light-dependent and light-independent stages of photosynthesis in C3 plants
●
(details of biochemical pathway mechanisms are not required)
- occurs in the thylakoid membranes made up of grana inside chloroplasts

- the reaction is catalysed by various enzymes; with the purpose of generating
NADPH and ATP to power the second stage of photosynthesis
Inputs: 12 H2O molecules, 12 NADP+, 18 ADP + Pi (Note: sunlight is a catalyst, not a input)

Outputs: 6 O2 molecules, 12 NADPH, 18 ATP
1. inside the thylakoid, light energy excites electrons in the chlorophyll which move
along proteins in the thylakoid membranes, the energy in the electron (e-) powers the
pumping of H+ into the thylakoid lumen; water donates its electrons to chlorophyll to
replace the electrons causing water to split into oxygen and two H+ (photolysis)
2. the oxygen is released from the chloroplast; either diffusing out of the stomata and
into the environment or being used as an input into aerobic cellular respiration
3. the H+ ions from water generate NADPH, movement of H+ down the concentration
gradient generates ATP
4. ATP and NADPH coenzymes move on to the light-independent stage
- enzymes catalyse most reactions (Eg. ADP + Pi → ATP using energy flow from H+);
having enzymes to regulate each step in photosynthesis ensures reactions are sped
up and controlled, so plants can metabolise efficiently
- NADPH transfers hydrogen ions; ATP transfers energy
Light Independent Stage

inputs, outputs, and locations of the light-dependent and light-independent stages of photosynthesis in C3 plants
●
- occurs in the stroma

- the reaction is facilitated by enzymes that cycle through multiple reactions; therefore
also called the Calvin Cycle
Inputs: 6 CO2 molecules, 12 NADPH, 18 ATP

Outputs: glucose(C6H12O6), 6 H20 molecules, 12 NADP+, 18 ADP + Pi
1. carbon dioxide enters the Calvin cycle and undergoes initial reactions; CO2 combines
to a five-carbon molecule then splits into 2 three-carbon molecules
2. NADPH formed in the light-dependent stage donates into H+ and electrons and ATP
molecules break down into ADP + Pi to release energy that facilitates further changes
in carbon molecules
3. carbon molecules continue to change and rearrange; eventually one three-carbon
molecule is created that leaves the cycle to go on and produce glucose; the cycle
must occur six times in order to produce one glucose molecule
4. some of the leftover oxygen from breaking down CO2 in combined with hydrogen ions
from NADPH to create an output of water
Rubisco
● the role of Rubisco in photosynthesis, including adaptations of C3, C4, and CAM plants to maximise the efficiency
of photosynthesis

-
the key enzyme of the light-dependent stage of photosynthesis; sometimes binds to
carbon dioxide and facilitates further reactions in the photosynthesis process or
binds to oxygen to initiate the wasteful process of photorespiration
- uses 3 CO2 molecules and 3 five-carbon molecules to produce 6 three-carbon

molecules (or 3-PGA)
- the 3-PGA are converted by ATP and NADPH to make three-carbon molecules
(G3P)
- one G3P leaves the cycle to undergo further reactions to create glucose
- the remaining 5 G3P are recycled with the help of ATP to regenerate 3 RuBP which
start the cycle and the cycle begins all over again
Carbon Fixation: the conversion of CO2 and RuBP into 3-PGA; carbon from inorganic CO2 is
‘fixed’ into an organic compound; rubisco is responsible for taking carbon from an
inorganic, gaseous form and incorporating it into an organic compound (3-PGA)
Reduction: NADPH donates electrons to (‘reduces’) an intermediate three-carbon molecules
in the cycle to produce G3P
Regeneration: the RuBP molecule needed to start the cycle is reproduced again
Photorespiration: a wasteful process in plants initiated by rubisco that limits photosynthesis

- sometimes rather than using CO2 as a substrate it uses O2
- less photosynthesis means less glucose is produced which can negatively impact a
plant’s ability to grow, survive and reproduce - can dependent on some
enzymatic factors
- Substrate Concentration: more substrate allows easier reaction, rubisc ‘wants’
CO2 not O2
- Temperature: at regular temperature, rubisco’s affinity to CO2 is greater but at high
temperatures it general has a greater affinity to O2, leading to more binding to O2
C3 Plants: ‘normal’ plants; rubisco is responsible for fixing carbon dioxide and cycles in a
single mesophyll cell; have no adaptation to photorespiration; doesn’t consume extra
energy; moderate, or cool and wet environments Eg. most plants including wheat and rice
C4 Plants: minimises photorespiration by separating initial carbon fixation and the remainder
of the Calvin cycle (which occurs in bundle-sheath cells); hot, sunny habitats Eg. corn,
sugarcane, switchgrass
CAM Plants: minimises photorespiration by separating the initial carbon fixation and the
remainder of the Calvin cycle over time; at night they open their stomata to bring in CO 2
which prevents water loss; very hot, dry habitats Eg. cacti, pineapples, orchids
Factors that Affect the Rate of Photosynthesis

● the factors that affect the rate of photosynthesis: light availability, water availability, temperature, and carbon
dioxide concentration
in temperature, pH, concentration, competitive and non-competitive enzyme inhibitors
Light: required for the light-dependent stage of photosynthesis to occur; as light increase,
photosynthesis increases

-
the rate will reach a saturation point that causes the graph to plateau making light
a limiting factor when there isn’t enough light compared to other factors
- light affects C3, C4 and CAM plants the same way
Temperature: enzymes function at a optimum temperature; enzymes begin to denature at a

certain point and are unable to function, causing a steep drop off in photosynthesis rate pH:
enzymes function at an optimum pH; below the optimum pH enzymes will also denature;
however enzymes in the thylakoid can function well at a pH as low as 4
- between C3, C4 and CAM plants optimal temperatures and pH’s may differ
Carbon Dioxide: as an input of photosynthesis, it’s concentration impacts the rate of

photosynthesis
- C4 and CAM plants are less affected by this reduction than C3 plants are (as they
have no strategy to combat photorespiration
- a theoretical maximum of increasing CO2 is reached assuming light and water
availability are unlimited and temperatures are optimal
- another requirement may become a limiting factor and the rate of photosynthesis will
plateau
Water: influences the opening and closing of the stomata as it is an input for the light-
dependent stage of photosynthesis
- not typically a limiting factor
- with the stomata closed, O2 is more likely to be abundant compared to CO2, that
could initiate wasteful photorespiration
- C4 and CAM plants have evolved adaptations to ensure their plants are not affected
by water loss, C3 plants are more susceptible to water loss and can be impacted by
reduced water
Enzyme Inhibition: influence the function of enzymes and, as a result, the rate of
photosynthesis
- Competitive Inhibitors: bind to the active sites of enzymes to prevent the catalysis of
substrates
- Non-Competitive Inhibitors: bind to an allosteric site of an enzyme causing a
conformational change to the active site meaning the substrate can no longer bind
- the three types of plants are all susceptible to negative impacts of inhibitors
Agricultural Applications of CRISPR-Cas9

● potential uses and applications of CRISPR-Cas9 technologies to improve photosynthetic efficiencies and crop
yields
- one method to increase photosynthesis efficiency in agricultural plants using
CRISPR-Cas9 is to engineer crops that bypass photorespiration and somewhat
mimic the function of C4 and CAM plants
- rubisco’s function could be targeted directly or the function of chloroplasts could be
made more efficient or the stomata could be targeted to reduce water stress

-
- research is being done to assess how to the entire photosynthetic process of a target
crop species is undergone and the natural regulation of the photorespiration pathway
utilising high-level computers to model the photosynthetic pathway and identify
inefficiencies
- using CRISPR-Cas9 technologies to target and edit the genes responsible for the
identified inefficiencies
Chapter 6 - Cellular Respiration

Aerobic Cellular Respiration
● the general structure of the biochemical pathways in photosynthesis and cellular respiration from initial reactant
to final product
- allows cells to break down large molecules and produce substantial amounts of ATP
(slowly); is vital for all living organisms and occurs via two distinct biochemical
pathways
- cells require a constant supply of energy in order to perform crucial, life-sustaining
functions
- primarily involves the breakdown of glucose into ATP
Mitochondria: the sire of the second and third stages of aerobic cellular respiration; includes
an inner and outer membrane
- enzymes catalyse the reactions of cellular respiration to allow them to proceed at

significantly higher and biologically relevant rates
- the enzymes are under ‘tight regulation’ in order to ensure the correct amount of ATP
is being produced downstream and that the cell’s crucial cellular respiration
pathways are operating as efficiently as possible
Glycolysis
● the main inputs, outputs, and locations of glycolysis, Krebs Cycle, and electron transport chain including ATP yield
- occurs in the cytosol
- breaks down two pyruvate molecules into two ATP and two NADH molecules
Inputs: C6H12O6, 2 ADP + Pi, 2 NADH+, + 2 H+

Outputs: 2 pyruvate, 2 ATP, 2 NADH
- the 2 pyruvate molecules are transported to the mitochondria, where they will be
modified and broken down further into the Krebs cycle
Kreb’s Cycle
- occurs into the mitochondrial matrix
- generates lots of high-energy electron and proton carries; NADH and FADH2

-
- pyruvate is transported to the matrix and combines with coenzymeA (CoA) to from
acetyl-CoA

Inputs: 2 acetyl-CoA, 2 ADP + 2 Pi, 6 NAD+ + H+, 2 FAD + 4 H+
Outputs: 4 CO2, 2 ATP, 6 NADH, 2 FADH2
- by breaking down acetyl-Co, protons and electrons are released which are loaded on
NAD+ and FAD
- produces two CO2 molecules for every one acetyl-CoA molecule
- produces small amounts of energy in the form of 2 ATP molecules
Electron Transport Chain

- occurs in the inner membrane of the mitochondria known as the cristae
- energy is unloaded from NADH and FADH2 to generate a proton gradient that drives
ATP production
Inputs: 6 O2 + 12 H+, 32/34 ATP + Pi, 10 NADH, 2 FADH2

Outputs: 6 H2O, 32/34 ATP, 10 NAD+ + 10 H+, 2 FAD+ + 4 H+
Anaerobic Fermentation
● the location, inputs, and the difference in outputs of anaerobic fermentation in animals and yeasts
- involves the breakdown of glucose and ATP production (quickly) via glycolysis in the
absence of oxygen as well as allowing the replenishment of NAD+ for the continued
use of glycolysis
Lactic Acid Fermentation: occurs in animals, breaking down pyruvate into lactic acid and
cycling NADH back to NAD+ for reuse in glycolysis; lactic acid cannot accumulate
indefinitely, so once oxygen is present aain that lactic acid is metabolised back into pyruvate
for aerobic cellular respiration
Ethanol Fermentation: occurs in yeasts; converting pyruvate into ethanol and carbon
dioxide; often occurs to produce alcoholic drinks such as wine, beer and whiskey
Factors that Affect the Rate of Cellular Respiration

● the factors that affect the rate of cellular respiration: temperature, glucose availability, and oxygen concentration
in temperature, pH, concentration, competitive and non-competitive enzyme inhibitor
Temperature: the optimal temperature of an enzyme can increase the rate of respiration;
enzymes begin to denature above the optimal temperature and respiration rate drops due
to the loss of enzyme function (pH has a similar effect)
Glucose Availability: increasing glucose availability increases the rate of cellular respiration;
as glucose is an input for glycolysis it is necessary for both aerobic and anaerobic
respiration; enzymes will reach a saturation point
Oxygen Availability: increasing oxygen will increase the rate of aerobic respiration; however
it is not an input of anaerobic respiration and the presence of oxygen will automatically
cause aerobic respiration

Enzyme Inhibition: as in ‘photosynthesis’
- by matching respiration rates to their energy needs through end-product inhibition
and other feedback loops, cells are more efficient
Biofuel from Fermentation

● uses and applications of anaerobic fermentation of biomass for biofuel production
Biofuels: made from organic material known as biomass (plant or animal material) that can
be sourced from many existing industries and is renewable; they are also believed to be
carbon neutral
- used as an alternative to current fuels in many ways, including transport, heating,
energy and cleaning
- may help meet transportation needs that can be used as an alternative for traditional
fuels like petrol and diesel (already have E10, an alternative with 10% ethanol and
90% gasoline)
- can also be stored and used for energy generation; often used in backup systems
and generators
- could potentially be boiled down to two simple characteristics; renewability of
biomass as a fuel source and carbon neutrality of its combustion
First-Generation Biofuels: produced from edible food crops

Second-Generation Biofuels: produced from non-edible crops that competes less with
agricultural land
Strengths: less climate impact; greater energy security; provides localised energy
Weaknesses: become food vs fuel; could be costly and difficult to uptake; may have second
order environmental impacts
Unit 4 AOS 1
Chapter 7 - Dealing with Disease
Detecting Pathogens
● initiation of an immune response, including antigen presentation, the distinction between self antigens and non-
self antigens, cellular and non-cellular pathogens, and allergens
Pathogen: an agent that causes disease
- Cellular Pathogens: have a cellular structure and are living organisms
- Bacteria: unicellular pathogens that can infect almost any part of the body;
can cause disease through the production of toxins and enzymes which
either affect the functioning of cells or cause their death Eg. neisseria
meningitidis causing meningitis
- Fungi: eukaryotic organisms that include yeasts and moulds and contain
long, branching filaments called hyphae Eg. thrush, ringworm
- Worms: multicellular invertebrate parasites whose development include egg,
larval, and adult stages Eg. parasite, roundworm
- Protozoa: single-celled eukaryotes that can be free-living or parasitic Eg.

plasmodium causing malaria
- Non-Cellular Pathogens: do not have a cellular structure and are non-living
- Viruses: an infectious agent composed of genetic material inside a protein
coat that may be surrounded by a lipid envelope; cannot independently
reproduce Eg. influenza, rhinovirus, ebola
- Prions: abnormally folded proteins that have the ability to induce normal
proteins nearby to become misfolded; only occur in mammals and affect only
the brain and other neural structures; currently only known infectious agents
that don’t contain nucleic acids Eg. Creutzfeldt-Jakob disease
Antigen: any molecule that may trigger an immune response

- Self Antigens: those located on the surface of cells that mark the cells of an
organism as ‘self’ so that the immune system doesn’t attack them
- MHC Proteins: the most important self markers in humans that enables the
immune system to distinguish it from non-self material
- MHC I: expressed on all nucleated cells in the body
- MHC II: found on specialised cells in the immune system
- Non-Self Antigens: a molecule from outside the body that is recognised by
the immune system and initiates an immune response; MHC I markers differ
between individuals, so if the another person cells (ie donated organ) enter
the body an immune response will occur
Autoimmune Disease: a disease in which an individual’s immune system initiates an

immune response against their own cells
Allergic Reaction: an overreaction of the immune system to a non-pathogenic antigen; in
severe cases a person may experience a constriction of airways, increased permeability of
blood vessels, difficulty breathing, and decreased blood pressure
- Allergen: a non-pathogenic antigen that triggers an allergic reaction
The First Line of Defence

● physical, chemical, and microbiota barriers as preventative mechanisms of pathogenic infection in animals and
plants
- a component of the innate immune system characterised by the presence of
physical, chemical and microbiological to keep pathogens out of the host
organism
Innate Immune System: a component of the immune system that is composed of

generalised and non-specific defences and/or responses to pathogens
Physical Barriers: a component of the first line of defence that features solid or fluid
obstacles that block pathogen entry such as skin or mucus
Chemical Barriers: a component of the first line of defence that features enzymes, toxins,
and acids to protect against pathogen invasion

- plants need to protect themselves from different types of pathogens including
being eaten by herbivores, but cannot move or run away like humans can
- Physical Barriers: Eg. thick bark, waxy cuticles on leaves, formation of galls,
presence of thorns and trichomes, closing of stomata
- Chemical Barriers: can repel insects or animals that may damage the plant
Eg. chitinases (enzymes that occur in a number of different plants and have
antifungal properties), phenols (secreted by wounded plants, repelling or
killing invading microorganisms)
- animals employ a range of first line defences against pathogens

- Physical Barriers: Eg. intact skin, mucous secretions
- Chemical Barriers: Eg. presence of lysozymes in tears and saliva, acidic
sweat, stomach acid, antibacterial compounds in earwax
- Microbiological Barriers: the presence of non-pathogenic bacteria in the body
that can prevent the growth of pathogenic bacteria as they compete for
resources and space Eg. presence of bacteria on the skin, the lower the
gastrointestinal tract (normal flora) etc.
The Second Line of Defence

● the innate immune response including the steps in an inflammatory response and the characteristics and roles of
macrophages, neutrophils, dendritic cells, eosinophils, natural killer cells, mast cells, complement proteins, and
interferons
- innate immunity
- all cells are leukocytes or white blood cells
Phagocytes: engage in phagocytosis in which they consume and destroy foreign or dead
material present in the body by engulfing it through the process of endocytosis;
lysosomes containing lysozymes present in the cell destroy the foreign or dead material
- Neutrophils: the most common leukocyte that engages in phagocytosis and releases
cytokines
- Macrophages: engages in phagocytosis and antigen-presentation
- Dendritic cells: engages in phagocytosis and antigen-presentation
Cytokines: a signalling molecule released by cells which aids communication between
immune cells and helps protect against pathogens
Natural Killer Cells: large granulated cells which target both abnormal and virally
infected cells; achieved by the killer inhibitory receptor and the killer activation receptor
Mast Cells: reside in connective tissues throughout the body, detecting injury; become
activated and degranulate, releasing histamines
Eosinophils: large granulated cells containing various toxic chemical mediators which help
destroy invading pathogens; typically target pathogens which are too large to be
phagocytosed by degranulating them on contact and releasing chemical mediators
contained within the granules
Interferons: a type of cytokine released from infected cells to make neighbouring cells less
susceptible to viral infection
Complement Proteins: proteins that reaction to cause a complement cascade

- Opsonisation: stick to the outside surface proteins of pathogens to make it easier for
immune cells to recognise them as foreign
- Chemotaxis: complement proteins gather near a pathogen and attract phagocytes to
it, making it more likely to be destroyed
- Lysis: join together on the surface of a pathogen forming a membrane attack
complex that creates pores in their membrane, destroying pathogens via a sudden
influx of fluid into the pathogen, causing it to burst; cannot occur to viruses
Fever: a temporary increase in body temperature; the body initiates a number of

countermeasures that increase core body temperature to reach this new setpoint, including
shivering and heat-conserving behaviours (putting on a jumper)
- in response to potential injection, as many pathogens cannot survive at the elevated
temperatures created by a fever; also thought to activate certain proteins in the body
that bolster the strength of the body’s defences
- prolonged fever can be detrimental to the body due to additional stress placed upon
our cells, which are no longer functioning at their optimal temperatures
Inflammatory Response: occurs to increase blood flow to the injured area, bringing an influx
of immune cells which may cause swelling, pain, heat and redness to the injured area
- Initiation: pathogens are introduced to the body because of the open wound or
infection that caused damaged cells to release cytokines and mast cells to
degranulate, releasing histamine
- Vasodilation: histamine travels to nearby blood vessels and binds to specific
receptors causing blood vessels to widen and increasing blood flow to the injury site
- Migration: immune cells can leave the bloodstream and enter the site of injury;
phagocytes miat be guided by cytokines to the damaged cells, and complement
proteins attract phagocytes
The Third Line of Defence

● initiation of an immune response, including antigen presentation, the distinction between self antigens and non-
self antigens, cellular and non-cellular pathogens, and allergens
● the characteristics and roles of the components of the adaptive immune response against both extracellular and
intracellular threats, including the actions of B lymphocytes and their antibodies, helper T, and cytotoxic T cells
- designed to combat and destroy pathogens that have breached the first and second
lines of defence
- has specificity as it is an adaptive immune response that responds to distinct
pathogens in a unique and tailored manner
- involves immunological memory that results in the production of cells that allow the
body to respond to future re-infections by previously encountered pathogens quickly
and effectively
Antigen-Presentation: a key process in the initiation of the adaptive immune response

involving the selection of a type of T lymphocyte called a T helper cell via the process of
antigen-presentation; those antigen-presenting cells are dendritic cells and macrophages
Humoral Immunity: an adaptive immune response in which extracellular pathogens are
targeted by specific antibodies produced by plasma cells

- B lymphocytes are the key mediators that’s surface is covered in antibodies that
travel around the body in the bloodstream
1. a pathogen with an antigen that is complementary to the shape of antigen-binding
site on the receptor of the B cell interacts with the B cell - selecting the B cell
2. a T helper cell selected through antigen-presentation, that is complementary to the
antigen which recognise the selected B cell and secrete cytokines that cause the B
cell to undergo clonal expansion; many copies of the B cell are produced in the
process of clonal selection
3. the T helper cell stimulare the selected B cell via cytokines to undergo
differentiation into B memory cells and plasma cells
4. plasma cells secrete antibodies in order to defend against a pathogen
- Antibodies: released by plasma cells are proteins; they are composed of four
polypeptide chains joined together that include two heavy (joined by a disulphide
bond) and light chains; they have two antigen-binding sites
- Agglutination: binding together antigens on two separate pathogens, forming large
antigen-antibody complexes that make it easier for phagocytes to recognise the
pathogens as foreign bodies and destroy them
- B Memory Cells: a differentiated B lymphocyte that is responsible for providing long-
lasting immunological memory of an antigen
Cell-Mediated Immunity: an adaptive immune response in which infected or abnormal cells

are destroyed by cytotoxic T cells
- Cytotoxic T Cells: a type of T lymphocyte that primarily carries out the role of
assessing MHC I markers for self and non-self recognition
1. at the same time as the selection of T helper cells, antigen-presenting cells
eventually come upon a naive T cells with a T cell receptor that matches the antigen
being presented, initiating clonal selection and stimulating the T cell with cytokines
to undergo the process of clonal expansion and differentiation
2. the clones of the selected T cells differentiate in cytotoxic T cells and T memory
cells; the majority become cytotoxic T cells and leave the lymph node and travel
throughout the body eventually to the site of infection
3. once a cytotoxic T cell finds a abnormal cell that is presenting complementary foreign
antigens on tis MHC I complex it binds via interactions between its T cell receptor
and antigen-MHC I complex; perforin and granzymes are released to stimulate
apoptosis of the infected cell
- T Memory Cells: are copies of originally selected T cells that reside in the body for
extended periods of time and help form immunological memory
Immunological Memory: remain in the blood for extended periods of time, allowing the body
to respond to pathogens it has previously encountered quickly and effectively
- B memory cells rapidly divide and form new antibody-producing plasma cells when
they encounter an antigen that matches their receptor; are also constantly secreting
low amounts of antibodies to keep the person immune to a pathogen
- T memory cells proliferate rapidly into T helper cells and cytotoxic T cells upon
stimulation by an antigen-presenting cell that is presenting a previously encountered
antigen

The Lymphatic System
● the role of the lymphatic system in the immune response as a transport network and the role of lymph nodes as
sites for antigen recognition by T and B lymphocytes
- a large network of vessels and tissues throughout the body that form an important
component of the circulatory and immune systems
- transportation of antigen-presenting cells (and pathogens to serve as the local for
clonal selection) to secondary lymphoid tissues for antigen recognition and
initiation of the adaptive immune response
- production of leukocytes, including lymphocytes in primary lymphoid tissues
- removal of fluid from tissues around the body
- absorption of fatty acids from the digestive system
Lymph: the pale fluid that flows through the lymphatic system and has a high concentration
of leukocytes
Primary Lymphoid Tissues: responsible for the creation and maturation of lymphocytes;
bone marrow and thymus
- B and T lymphocytes are produced in the bone marrow; B lymphocytes remain in the
bone marrow to mature, while T lymphocytes move to the thymus to mature
Secondary Lymphoid Tissues: responsible for remaining mature lymphocytes and
initiating the adaptive immune response; lymph nodes and the spleen
- mature lymphocytes cluster together and ‘scan’ passing lymph for the presence of
pathogens or antigen-presenting cells; foreign antigens cause clonal selection and
differentiation; B and T cells are created causing the characteristic swelling of lymph
nodes
- blood vessels constantly leak into tissues around the body; this is increased by the
inflammatory response to allow movement of leukocytes; lymph vessels drain this
fluid
Lymphatic Capillaries: extremely small vessels that exist throughout the tissues of the body,
collecting fluid in tissues as well as any pathogens that might be present
- small lymphatic capillaries slowly join together to form larger vessels that contain an
increasing amount of lymph; the vessels have small thin walls that rely on
surrounding muscle movements to squeeze lymph fluid through the system; they
feature one-way valves that flow lymph in one direction only - away from tissues and
into lymph nodes
- fluid drained from tissues arrived at lymph nodes via afferent lymphatic vessels to
find a cluster of B and T cells; antigen-presenting cells and pathogens are most likely
to meet with a lymphocyte that matches the antigen-binding site and stimulate clonal
selection and surveillance
- an adaptive immune response is initiated which antibodies and cytotoxic T cells
being transported by lymph away from lymph nodes in efferent lymphatic vessels
to return in the circulation near the heart where blood is returning to the body
Chapter 8 - Immunity
Acquiring Immunity
● the difference between natural and artificial immunity and active and passive strategies for acquiring immunity

● vaccination programs and their role in maintaining herd immunity for a specific disease in a human population
Natural Immunity: protection against disease that has developed without any medical
intervention
- Passive: an individual acquires antibodies from a ‘natural’ non-medical source
- breastfeeding is a way to give nutrients and proteins that are essential for human
growth and development through breastmilk; any antibodies generated from the
mother’s own immune system is absorbed into the baby’s bloodstream and protect
them against pathogens
- placenta transfer during pregnancy as any antibodies produce by the mother are
able to cross the placenta and enter the foetus’ bloodstream via the umbilical cord;
confer the child protection during pregnancy to compensate for the baby’s weak
immune system
- Active: an individual’s own immune system encounters a pathogen and mounts a
response against it, creating antibodies and memory cells specific to that pathogen
- the next time the person encounters the pathogen it’s cells will rapidly be recognised
by memory cells which will proliferate and differentiate so the pathogen can be
neutralised without causing disease in the body
Artificial Immunity: protection against disease formed as a result of medical intervention

(induced)
- Passive: created when an individual acquires antibodies from an external source via
a medical intervention; people who have been bitten by a snake are given
antivenom which contains antibodies designed to neutralise the venom
- Active: created when an individual’s own adaptive immune system produces
antibodies and memory cells due to a mental intervention
- Vaccines: medical treatments that contain components that resemble a certain
pathogen’s antigens, but these components are not able to cause disease;
sometimes the components are attenuated (weakened) or inactivated pathogens or
toxoids that allows the person’s immune system recognises these components as
foreign and mounts a response to them
- Booster Vaccines: a vaccine given to a person later in time after they have
completed their initial vaccination program to enhance their existing immunity against
the disease
Primary Immune Response: the reaction of the adaptive immune system to an antigen it has
not previously been exposed to
Secondary Immune Response: the heightened reaction of the adaptive immune system to
an antigen it has previously been exposed to
Herd Immunity: protection against a disease conferred to non-immune individuals when a

high percentage of a population is immune to the same disease; often achieved through
high rates of vaccination
- one of the most effective ways to comprehensively protect everyone in a population
from a disease
- more contagious diseases require more people to be immune to achieve herd
immunity

Emergence of Pathogens
● the emergence of new pathogens and re-emergence of known pathogens in a globally connected world, including
the impact of European arrival on Aboriginal and Torres Strait Islander peoples
- can depend on how contagious a pathogen is and how virulent the pathogen is
Emerging: diseases that currently circulate around the human population and have occurred
previously but only affected particular populations in isolated places, or have occurred
through history and have only recently been recognised as caused by pathogens Re-
Emerging: diseases that were once major public health problems but then declined
dramatically in incidence, but are once again becoming health problems for a large number
of people
Zoonosis: an infectious disease that is caused by a pathogen that has transferred form an
animal to a human
Epidemics: a dramatically increased occurrence of a disease in a particular community at a

particular time
Pandemics: an epidemic that has spread across multiple countries and/or continents
- some major diseases in Europe were smallpox, syphilis, tuberculosis, influenza and
measles that were spread to Indigenous populations upon European arrival in
Australia
- there was a lack of immunity amongst the Indigenous population; Europeans had
some form of natural active immunity already
- there was a lack of knowledge and experience with European diseases; they didn’t
no how to avoid or treat these infections
- the disruption that colonisation caused meant that the indigenous populations that
were one spread out and uncrowded had become more crowded making infections
easier and access to food or water being restricted or denied; the general health
status of the Aboriginal’s declined as a result
Controlling Pathogen Spread

● scientific and social strategies employed to identify and control the spread of pathogens, including identification of
the pathogen and host, modes of transmission, and measures to control transmission
Identifying Pathogens: to assess how virulent, and contagious they are
- Physical: use microscopes to determine structure
- Phenotypic: selective media to allow certain pathogens to grow; biochemical test
panels to specify a sample’s genus and species
- Immunological: diagnose a disease based on the presence of anitbodies and
antigens in a person’s serum
- ELISA: antibodies specific to a certain pathogen are attached to a plate; the serum
and sample to be tested is applied to the plate, resulting in any pathogen antigens to
attach to antibodies; a second detection antibody with a colour-linked enzyme is
added to the plate, binding to the antigen-antibody complex present; a substrate is
added to react to the enzyme on the second antibody and change colour and emit a
signal that the pathogenic antigens are present

- Molecular: hybridisation-based detection to label segments of the genetic material
that are complementary to the pathogens genetic material; whole genome
sequencing
Transmission: the passing of a pathogen from an infected host to another individual or group
- Airborne: small particles that stay in the air for long periods which can be inhaled Eg.
influenza, COVID-19
- Droplet: respiratory droplets containing pathogens remain suspended in the air; if a
person touches the surface of a person can infect them Eg. rhinovirus
- Direct Physical Contact: spread when the host physically touches another individual
Eg. HIV and tinea
- Indirect Physical Contact: can be spread through fomites or a vector Eg. malaria
- Faecal-Oral: pathogens excreted in faeces that are consumed by another person or
via contamination of food or water Eg. rotavirus, cholera
Controlling Transmission: the ways of managing a disease is complex and can depend on
the pathogen
- Prevention: improving hygiene, sterilising using antiseptics and disinfectants;
ensuring clean food and water; vaccination; lockdowns
- Screening: routine testing; observing medical sales
- Quarantine & Isolation
- Identification of a Pathogen
- Identification and Control of Modes of Transmission: wearing masks for airborne
diseases
- Treating Infected Individuals: use of medications such as antibiotics and antivirals
to target the pathogen; unfortunately this can lead to antimicrobial resistance
Immunotherapy
● the development of immunotherapy strategies, including the use of monoclonal antibodies for the treatment of
autoimmune diseases and cancer
- a form of medical treatment that modulates the functioning of the immune system in
order to treat disease
Monoclonal Antibodies: laboratory-made proteins that can be used to treat a number of

different diseases as they bind to a specific antigen
- Activation Immunotherapies: aim to induce or amplify an immune response
1. scientists isolate an antigen
2. scientists vaccinate an animal with an antigen to result in the selection and
proliferation of a B lymphocyte that matches the antigen
3. scientists extract the B lymphocyte from the spleen
4. the lymphocyte is fused with a cancerous human plasma cells to create a myeloma
cell which has the ability to grow indefinitely and produce large quantities of
antibodies
5. hybridomas are screened so cells with an appropriate antibody is selected; these are
cloned to result in a mass production of antibodies
6. antibodies are collected and purified before being administered to the patient

- Cancer: an incredibly complex group of diseases caused by the uncontrolled
and unregulated replication of cells that then invade other sites of the body;
cancerous cells have developed mutations that allow them to evade the
immune system and suppress immune responses against them
- Naked Monoclonal Antibodies: don’t have any molecules attached to them
- Conjugated Monoclonal Antibodies: have other molecules attached to them
Eg. chemotherapy drugs or radioisotopes
- natural killer cells may be able to recognise the cancer cell as forgien and kill
it
- may interact with complement proteins to destroy cancerous cells using
MAC or enhance the function of other immune cells
- Some methods do not use immunotherapy; blocking cell growth by blocking
the connection between cancer cells and proteins that promote cell growth;
triggering apoptosis
- Autoimmune Disease: a disease in which an individual’s immune system

initiates an immune response against their own cells; brought about by both
B and T cells responding to self-tissues as if they were forgien, B cells
release autoantibodies and T cells become autoreactive
- Suppression Immunotherapies: aim to prevent or reduce an immune
response
- cytokines can be inhibited to reduce the immune response
- B and T cells can be depleted or inhibited; monoclonal antibodies bind to the
autoreactive B and T cells and inhibit these cells or stimulate other immune
cells to destroy them
- prolonged immunosuppression can lead to immunodeficiency and make a
person more susceptible to developing infections and cancer
Unit 4 AOS 2
Chapter 9 - How Species Evolve
The Gene Pool
● causes of changing allele frequencies in a population’s gene pool, including environmental selection pressures,
genetic drift and gene flow, and mutations as the source of new alleles
- the total aggregation of all the genes and alleles present within a particular
population or species
Allele Frequencies: the proportion of certain alleles in the gene pool
Genotype: the genetic composition of an organism at a particular gene locus

Phenotype: the physical and biochemical characteristics of an organism that are the result of
gene expression and the environment
Mutation: a permanent change to a DNA sequence; responsible for introducing new alleles
into a population via changes to DNA

- can involve the substitution, addition or deletion of single nucleotide bases or larger
blocks of DNA
- the mutation can be classified as advantageous, neutral or deleterious
- will be heritable if it occurs in the germline cells; but if it occurs in a somatic cells it
is not heritable
Point Mutation: a mutation that alters a single nucleotide in a DNA sequence

- Silent Mutation: has no effect on the resulting amino acid sequence, due to the
degenerate nature of the genetic code
- Missense Mutation: codes for a different amino acid; altering the primary structure of
the polypeptide; affects the folding of the polypeptide and could alter the functioning
of the protein
- Nonsense Mutation: prematurely ends the translation of a gene’s mRNA; the affected
codon may become a stop codon so that gene will not be completely translated,
leading to a polypeptide that is too short to function as intended (considered the most
dangerous)
- Frameshift Mutation: addition or deletion of one or two nucleotides that alters the
reading frame of the following nucleotides; causes major disruptions
Block Mutation: a mutation that affects a large chunk of DNA, or an entire gene; involve
alterations of the structure of a chromosome by inserting, deleting, duplicating, or swapping
a cluster of nucleotides, potentially involving multiple different genes
Mutagen: an agent that can cause mutations in DNA
Environmental Selection Pressures

● biological consequences of changing allele frequencies in terms of increased and decreased genetic diversity
- factors in the environment that impact an organism’s ability to survive and reproduce
Eg. predation, disease, competition, climate change
Natural Selection: can occur through these factors, as certain phenotypes are more suited to
overcome certain environmental selection pressures
- organisms more suited to a particular environment are considered to have a higher
genetic fitness due to the present of their advantageous phenotype which arises
due to the presence of certain alleles
- overtime, fitter organisms with an advantageous phenotype have a selective
advantage and are more likely to pass on their alleles to the next generation,
increasing this allele frequency of those alleles that code for the advantageous
phenotype
- natural selection relies on the heritability of a trait and the presence of variation
within the existing population to ensure that the allele confer the advantages are
present within the environment
- ultimately, the four basic conditions are; variation, selection pressure, selective
advantage and heritability

- the environmental selection pressures determine which phenotypes are considered
fitter and advantageous and, consequently, which traits are more likely to be passed
on to the next generation
- as advantageous traits become more common in the population, the allele
frequencies of the population changes, with the frequency of the advantageous allele
increasing, eventually the evolution of a new species will occur
- due to the generational increase in the frequency of the advantageous allele, the
genetic diversity of the population will also decrease as the phenotypes of the
population a driven towards a specific allele
- the survivability of a species relies on having large genetic diversity; this is because
a population with great variation in alleles has a higher change of possessing a
favourable allele that will help them survive if a new selection pressure arises
Genetic Drift & Gene Flow

Genetic Drift: a random event that dramatically alters a population’s gene pool
- Bottleneck Effect: the reduction in genetic diversity that occurs when a large
population is removed due to a chance event; many unique allele may be lost
- Founder Effect: the reduction in genetic diversity that occurs when a population is
derived from a small unrepresentative sample of the original population
- inbreeding may occur which keeps harmful alleles in the gene pool
- the lower adaptive potential makes populations more vulnerable to new selection
pressures that could challenge and potentially wipe out the entire population due to
the absence of advantageous alleles
Gene Flow: the flow of alleles in and out of a population due to the migration or
interbreeding of individuals between two populations
- Immigration: the movement into a population that increases genetic diversity
- Emigration: the movement out of a population that decreases genetic diversity
- Interbreeding: when two individuals living in different populations mate and have
offspring that increases genetic diversity
Speciation
● evidence of speciation as a consequence of isolation and genetic divergence, including Galápagos finches as an
example of allopatric speciation and Howea palms on Lord Howe Island as an example of sympatric speciation
- the process by which populations genetically diverge until they become distinct
species
Species: a group of individuals who are able to breed with each other and produce viable
and fertile offspring
Isolating Mechanisms: prevent species from interbreeding to produce fertile and viable
offspring

- Pre-Reproductive: geographical Eg. a body of water; ecological, habits that don’t
interact; temporal, the time of day which they breed; behavioural, type of mating
behaviours; structural, physically characteristics that may be drastically different
- Post-Reproductive: gamete mortality, sperm cannot penetrate the ovum for
fertilisation; zygote mortality; hybrid sterility, may survive into adulthood but not be
fertile
Allopatric Speciation: the geographical separation of a population from a parent population

resulting in the formation of a new species
- genetic differences can accumulate due to the presence of different selection
pressures, driving the geographically separated populations towards different
phenotypes; sufficient differences result in a new species
1. geographical barrier isolates the populations
2. environment subjects different selection pressures
3. speciation occurs and the two populations can no longer produce viable and fertile
offspring
- Galapagos Finches: the 19 islands served as a geographical barrier preventing gene
flow; there are 18 known species of the finches; they have a vast array of beak
shapes and sizes tailored towards species food sources on the different islands
- it is hypothesised that these changes have occurred largely due to allopatric
speciation
Sympatric Speciation: the divergence of a species from an original species without the
presence of a geographical barrier
- can also arise from genetic abnormalities that occur during gamete formation,
producing polyploid variants; while these errors in humans usually result in death of
embryos, plants are genetically tolerant to changes in the set of chromosomes
- Howea Palms: the two species H. forsteriana and H. belmoreana have different
breeding times; the difference in soil acidification is hypothesised to be the catalyst
for the speciation
- a difference in flowering times occurred; becoming a reproductive isolating
mechanism; as the differences accumulated, the two species of palm could no longer
interbreed to produce viable and fertile offspring
Selective Breeding
● manipulation of gene pools through selective breeding programs
- the changing in a population’s gene pool due to humans altering the breeding
behaviour of animals and plants to develop a selected trait
- shares similarities to natural selection except for the difference in selective
pressure
- described in the process of; variation, selection pressure (intervention of artificial
selection for a desirable trait) and heritability
- reduces genetic diversity leading to a smaller gene pool and overexpression of

deleterious alleles, which can reduce adaptability and fitness within a population

- referred to as an human-induced genetic bottleneck because it restricts interbreeding
between populations
- reduced genetic diversity can lead to increased inbreeding, which can increase the
prevalence of deleterious alleles and lower an adaptive potential
Evolving Pathogens
● consequences of bacterial resistance and viral antigenic drift and shift in terms of ongoing challenges for
treatment strategies and vaccination against pathogens
Antibiotic Resistance: natural selection has occurred because of the exposure to antibiotics
on bacteria, acting as an environmental selection pressure; bacteria resistant to particular
antibiotics are conferred a selective advantage and replicate within their host, increasing
their allele frequency
- largely facilitated by mutations that allow new alleles to arise in bacteria and may
increase a bacteria's resistance to an antibiotic
- occurs due to the inappropriate compliance of treatment (prematurely stopping a
course of antibiotics); inappropriate use of antibiotics (prescribed when not required);
widespread use of antibiotics
- viruses are constantly adapting and changing, allowing their to increase their y and
resistance against the immune system
Viral Antigenic Drift: involves small gradual changes in the genes encoding for viral surface
antigens; previous memory cells may be able to recognise them initially, but after another
change the virus will no longer be memorised
Viral Antigenic Shift: sudden and significant changes in the genes encoding viral surface
antigens; commonly occurs when two or more different strains of a virus combine to co-
infect the same host (viral recombination), natural immunity is uncommon, making the
virus extremely induction and could result in an epidemic or pandemic
Chapter 10 - How We Are Related

The Fossil Record
● changes in species over geological time as evidenced from the fossil record: faunal (fossil) succession, index and
transitional fossils, relative and absolute dating of fossils
- information derived from fossils, is arranged in chronological order and helps map
the history of life on Earth, placing species in appropriate geological time frames
- emergence of prokaryotes - widespread photosynthesis - first eukaryotes - first
multicellular organisms - the Cambrian explosion - animals on land - mammals
flowering plants
Fossilisation: an organism is rapidly covered in sediment; sediment builds in layers

to form fossils must be physically protected from scavengers, experience constant
cool temperatures, have low oxygen availability and low light exposure; all which
reduce decomposition
Relative Dating: a dating technique used to determine the relative age of a fossil by
comparing the position to other fossils or rocks in surrounding rock strata
- Law of Fossil Succession: the accumulation of sediment layers on top of each other
means those fossils found below other fossils are older than those above (which are
younger)
- Index Fossils: a group of widespread fossils which have existed for short period of
time and have a known age; act as a reference for other fossils
- must be physically distinctive, have had a large population; have existed in many
geographical areas (widespread) and have lived for a short period of time
- Transition Fossils: a fossil that shows traits that are common in both its ancestral
group and its descendant group and can help demonstrate the evolutionary
relationship between the two
Absolute Dating: an estimate of the age (in years) of a fossil or rock

- compares radioactive isotopes found in a fossil relevant to the stable amount of
that which is found in the atmosphere
- radioisotopes are unstable elements that will break down over time into a more
stable amount
- the average rate of breakdown is constant and can be modelled to calculate a half-
life
- Radiocarbon Dating: uses the radioisotope carbon-14 as it returns to its stable form
nitrogen-14
- all living things contain carbon and when an organism dies carbon-14 will start to
decay
- carbon-14 has a half-life of 5,730 years; it’s dating period is up to 50,000 years
- other forms of radioisotopic dating require igneous rock or materials containing that
isotope; generally this makes it hard to date fossils that may be older than 50,000
years as the rock would have to be dated rather than the fossil themselves
Evidence of Relatedness
● evidence of relatedness between species: structural morphology – homologous and vestigial structures; and
molecular homology – DNA and amino acid sequences
Structural Morphology: the study of physical structures to establish relatedness

- Homologous Structures: features found in different species that may look and
function very differently from one another but can be shown to be derived from a
common ancestor Eg. humans carry things with their arms, cats walk with their
legs, whales swim with flippers and bats fly with wings, yet they all have similar
bone structures
- depicts divergent evolution in which two or more populations of a single
species accumulate enough genetic differences to be classified as a different
species; which can occur as a result of different selection pressures or genetic
drift

-
- Analogous Structures: features present two or more species that fulfil the same
function but do not originate from a common ancestor Eg. bat or insect wings
- evidence for convergent evolution through which two distantly related species
can be seen to have independently evolved similar traits to adapt to similar
environments or selection pressures
- Vestigial Structures: features that have lost all or most of their usefulness as a
result of evolution by natural selection Eg. the human coccyx (tailbone) that may
have balanced ancestors bodies but it still retained OR the whale’s and snakes
pelvis that is present despite them not having legs
Molecular Homology: the study of the similarities in the nucleotide sequences of DNA or
amino acid sequences in proteins between organisms to establish relatedness
- Amino Acid Sequences: similarities are determined based on conserved genes
which are found in a number of different species
- haemoglobin carries oxygen from the lungs to cells and it found in the bodies on
many different species; consists of 146 amino acids
- cytochrome c is an enzyme present in mitochondria that consists of 104 amino
acids which are encoded into the conserved gene of mitochondrial DNA
(mtDNA)
- DNA Sequences: similarities in a DNA sequence can determine the relatedness
between different organisms; the higher the similarity the closer the relatedness
- uses nucleotide base differences to compare relatedness and is generally more
specific than amino acid sequencing because of the degenerate nature of the
genetic code
Phylogenetic Trees
● the use and interpretation of phylogenetic trees as evidence for the relatedness between species
Phylogenetics: the study of the relatedness between organisms
- can be useful for displaying the timeline of lineages; relatedness between taxa;
shared characteristics of different taxa
- may have many different components including a root, branch, nodes, and leaves
- when constructing these trees, the presence or absence of homologous structures

are assessed
- the exchange of genetic material between groups can be shown by a linking line
called an ‘interbreeding event’
Chapter 11 - Hominin Evolution

Defining Human
● the shared characteristics that define mammals, primates, hominoids, and hominins
Mammals: warm-blooded vertebrates belonging to the taxonomic class Mammalia that have
mammary glands, hair/fur, three middle ear bones and one lower jawbones
also include a variety of teeth

Primates: the highest order of mammals, comprised of about 400 different living species
who share a number of features including opposable digits and binocular vision
- 3D colour vision and forward facing eyes
- a large number of touch receptors in their fingertips
- prehensile hands
- flexible spines and a large degree of rotation in hips and shoulders
Hominoids: include greater and lesser apes

- shorter spine between rib cage and pelvis
- broader rib cage and pelvis
- lack of tail
- typically longer arms
- distinctive molar teeth in the lower jaw
Hominins: humans are separated here from all other species in the animal kingdom
- Bipedalism: using two legs for walking upright
Hominin Evolution
● evidence for major trends in hominin evolution from the genus Australopithecus to the genus Homo: changes in
brain size and limb structure
Brain Size: include higher cognitive processes such as planning, speech and abstract
thinking
- cerebrum of hominins is more folded, increasing the total surface area of the brain,
resulting in more neurons and an increase in the number of connections between
brain cells
- a more centralised foramen magnum
- shrinking of the sagittal crest
- lessening of the brow ridge
- flattening of the face
- less protruding chin
- more domed skull
- smaller teeth
Limb Structure: arm-to-leg ratio decreased over time in response to increased reliance on
bipedal motion
- Shorter Arms: movement through trees used to be required; but forelimbs were no
longer in contact with the external environment so arms were freed up to carry
children, prepare food and build tools
- Longer Legs: positively affect stride length and made upright walking more energy
efficient; longer legs lessen intensity of rising and falling motion of the body’s centre
of mass
- Pelvis Shape: shorter and more bowl-shaped over time; give support to the upper
body while standing and being upright; also changed with the demands of childbirth
as the cranial capacity of hominins increased

-
The Human Fossil Record

● the human fossil record as an example of a classification scheme that is open to differing interpretations that are
contested, refined, or replaced when challenged by new evidence, including evidence for interbreeding between
Homo sapiens and Homo neanderthalensis and evidence of new putative Homo species
- not all individuals die in conditions that promote fossilisation Eg. an organism might
decompose or be eaten by scavengers when they die
- rock layers and fossils that are contained may erode and disappear over time
- many rock layers are still inaccessible to palaeontologists not all fossils have been
found
- hominin behaviours may include burial rituals and not leaving the dead behind
Neanderthals: around 1-4% of some human genomes are made up of Neanderthal DNA;
100,000 year old DNA from Neanderthal fossils found in Siberia in 2016 contained
significant amounts of ancient human DNA not found in other Neanderthal populations
Homo Denisova: only a few small teeth were uncovered and a partial jawbone; thought to
have interbred with a particular group of ancient humans from Melanesia; share 4-6% of
their DNA with Denisovans making an interbreeding event likely occurred between 15,000
and 44,000 years ago
Homo Luzonensis: originally stemmed from a ‘long foot bone’ but includes now two more
two bones, seven teeth, two finger bones and part of a femur; the fossil showed a mix of
both ancient and modern human traits
Human Migration
● ways of using fossil and DNA evidence (mtDNA and whole genomes) to explain the migration of
● modern human populations around the world, including the migration of Aboriginal and Torres Strait Islander
populations and their connection to Country and Place
- according to the fossil record the earliest known Hominins first evolved in Africa
approximately 4 million year ago
Multiregional Hypothesis: suggests that the evolution of modern humans, from Homo
erectus to Homo sapiens was actually an ongoing process across all regions of the world
with gene flow between different continental populations
- Homo sapiens evolved form several different geographically separate groups of
Homo erectus who had migrated out of Africa and Eurasia in the million years prior to
the emergence of humans
- there is limited evidence to this hypothesis but some morphological clades
demonstrate this
Out Of Africa Hypothesis: the more generally accepted model for human migration;
suggests that the Homo sapiens evolved in Africa 200,000 years ago, long after the
departure of Homo erectus into Eurasia, and remained there for an extended period of time
before emigrating in waves and replaced existing hominin species in different parts of
Europe and
Asia

large-scale analysis of mitochondrial DNA of modern humans to demonstrate
mitochondrial lineage traced back to a common ancestor in Africa between 140,000
and 290,000 years ago
- very little genetic diversity in modern-day humans compared to other species; could
be due to relatively short existence (-200,00 years) and origins from a small,
centralised population
- fossil record of Homo sapiens is limited however the short time frame of existence
models the first migratory wave of early fossilised remains found also the east coast
of Africa (160,000 years ago) and those in the Middle East (100,000 years ago)
- artefacts found in the far north-west and deeper parts of Europe, including stone
tools, carvings, cave paintings to indicate the increased complexity and cultural
evolution that can be dated further following migratory patterns into Eurasia
- Aboriginal Australians are the longest continuous population of earth

- it is thought that around 50,000 and 65,000 years ago a wave of migrants reached
Sahul (Australia/New Guinea that wasn’t separated yet) and because geographically
and genetically isolated; making them one of the world’s oldest surviving civilisations
Connection to Country: a reciprocal relationship between First Nations people and
their ancestral lands and seas
Country: the area that is traditionally owned and looked after by an Aboriginal group or
certain people in that group; encompasses spiritual meaning and feelings of deep
connection and attachment associated with that area
- kinship terms are used to describe the mutual responsibility of caring, transfer of
knowledge and shared growth in the community and to the land
Dreaming: an Aboriginal philosophy that describes the time when Ancestral Sprites moved
over the land and created life and important geographical sites; explains the origins of the
universe as well as the relationship between humans, animals and the land; passed down
through generations

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Is VCE Biology Unit 3 & 4

Chapter 1 - General Skills

Controlled Experiment: an investigation into the effect of an independent variable on a

Random Error: variation in results caused by uncontrollable conditions between replications,

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Integrity: encourages a full commitment to knowledge and understanding as well as honest

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

- polypeptide chains have to fold carefully into the correct shape

Deoxyribonucleic Acid: consists of two strands of nucleotides bonded together via

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Protein Synthesis & Gene Expression

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

1. Transcription: copying DNA into pre-mRNA

2. RNA Processing: modifying the pre-mRNA molecule to produce m(mature)RNA

Gene Regulation: the control of gene expression, typically achieved by switching

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Hair Pin Loop: the backup process to stop trp production

The Protein Secretory Pathway

1. Ribosome: synthesises proteins; assembles the chains of amino acids by translating

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Enzymes: organic catalysts that speed up chemical reactions

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Temperature: high temperatures denature an enzyme and stop functioning; low

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Chapter 4 - DNA Manipulation

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Polymerase Chain Reaction

1. Denaturation: DNA is heated to approximately 90-95°C to break the hydrogen

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

- a laboratory technique used by scientists to measure the size of DNA fragments;

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Recombinant Plasmids & Transformation

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

- the uptake of a recombinant plasmid involves the recombinant plasmid being

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Genetically Modified Organisms

- the main purpose of GMOs in agriculture is to increase crop productivity and

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Mesophyll Cells: are the main cells in the leaves of plants

- occurs in the thylakoid membranes made up of grana inside chloroplasts

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Light Independent Stage

- occurs in the stroma

Inputs: 6 CO2 molecules, 12 NADPH, 18 ATP

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

- uses 3 CO2 molecules and 3 five-carbon molecules to produce 6 three-carbon

Photorespiration: a wasteful process in plants initiated by rubisco that limits photosynthesis

Factors that Affect the Rate of Photosynthesis

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Temperature: enzymes function at a optimum temperature; enzymes begin to denature at a

Carbon Dioxide: as an input of photosynthesis, it’s concentration impacts the rate of

Agricultural Applications of CRISPR-Cas9

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Chapter 6 - Cellular Respiration

- enzymes catalyse the reactions of cellular respiration to allow them to proceed at

Inputs: C6H12O6, 2 ADP + Pi, 2 NADH+, + 2 H+

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Electron Transport Chain

Inputs: 6 O2 + 12 H+, 32/34 ATP + Pi, 10 NADH, 2 FADH2

Factors that Affect the Rate of Cellular Respiration

Eowyn Bowles - VCE Biology Unit 3 & 4 Study Guide - 2022

Biofuel from Fermentation

Biology Revision Notes - Unit 3 & 4

Biology Revision Notes - Unit 3 & 4