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1 Laboratory techniques for biologists
(a) Health and safety
Substances, organisms, and equipment in a Hazards in the lab include toxic or corrosive Become familiar with standard laboratory
laboratory can present a hazard chemicals, heat or flammable substances, rules and with risk assessment.
pathogenic organisms, and mechanical
equipment.

Hazard, risk, and control of risk in the lab by Risk is the likelihood of harm arising from
risk assessment exposure to a hazard.

Risk assessment involves identifying control

measures to minimise the risk.

Control measures include using appropriate

handling techniques, protective clothing and
equipment, and aseptic technique.

(b) Liquids and solutions

Method and uses of linear and log dilution Dilutions in a linear dilution series differ by an Become familiar with the use of measuring
equal interval, for example 0·1, 0·2, 0·3 and cylinders, pipettes, burettes, autopipettes,
so on. and syringes.

Dilutions in a log dilution series differ by a

constant proportion, for example 10-1, 10-2,
10-3 and so on.

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Production of a standard curve to determine Plotting measured values for known
an unknown concentrations to produce a line or curve
allows the concentration of an unknown to be
determined from the standard curve.

Use of buffers to control pH Addition of acid or alkali has very small Practise making solutions using buffers and
effects on the pH of a buffer, allowing the pH measuring the pH with a meter or an
of a reaction mixture to be kept constant. indicator.

Method and uses of a colorimeter to quantify Calibration with appropriate blank as a Use a colorimeter or spectrophotometer to
concentration and turbidity baseline; use of absorbance to determine calibrate a known solution and determine an
concentration of a coloured solution using unknown using, for example, Bradford protein
suitable wavelength filters; use of percentage assay.
transmission to determine turbidity, such as
cells in suspension.

(c) Separation techniques

Use of centrifuge to separate substances of More dense components settle in the pellet;
differing density less dense components remain in the
supernatant.

Paper and thin layer chromatography can be The speed that each solute travels along the
used for separating different substances such chromatogram depends on its differing
as amino acids and sugars solubility in the solvent used.

Details of how to carry out these procedures

are not required.

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Principle of affinity chromatography and its A solid matrix or gel column is created with
use in separating proteins specific molecules bound to the matrix or gel.
Soluble, target proteins in a mixture, with a
high affinity for these molecules, become
attached to them as the mixture passes down
the column. Other non-target molecules with
a weaker affinity are washed out.

Principle of gel electrophoresis and its use in Charged macromolecules move through an Use protein electrophoresis to identify
separating proteins and nucleic acids electric field applied to a gel matrix. different muscle proteins.

Native gels separate proteins by their shape, Native gels do not denature the molecule so
size and charge that separation is by shape, size and charge.

SDS–PAGE separates proteins by size alone SDS–PAGE gives all the molecules an
equally negative charge and denatures them,
separating proteins by size alone.

Proteins can be separated from a mixture IEP is the pH at which a soluble protein has Determine the isoelectric point of a soluble
using their isoelectric points (IEPs) no net charge and will precipitate out of protein, such as casein.
solution.
If the solution is buffered to a specific pH,
only the protein(s) that have an IEP of that
pH will precipitate

Proteins can also be separated using their Soluble proteins can be separated using an
IEPs in electrophoresis electric field and a pH gradient. A protein
stops migrating through the gel at its IEP in

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the pH gradient because it has no net
charge.

Further details of electrophoresis are not

required.

(d) Detecting proteins using antibodies

Immunoassay techniques are used to detect
and identify specific proteins

These techniques use stocks of antibodies Knowledge of monoclonal antibody Research the use of monoclonal antibodies
with the same specificity, known as production is not required. in the diagnosis and detection of disease.
monoclonal antibodies

An antibody specific to the protein antigen is The ‘label’ is often a reporter enzyme Use the ELISA technique to identify the
linked to a chemical ‘label’ producing a colour change, but presence of specific antigens.
chemiluminescence, fluorescence and other
reporters can be used.

In some cases the assay uses a specific

antigen to detect the presence of antibodies.

Western blotting is a technique, used after

SDS–PAGE electrophoresis
The separated proteins from the gel are
transferred (blotted) onto a solid medium

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The proteins can be identified using specific
antibodies that have reporter enzymes
attached

(e) Microscopy
Bright-field microscopy is commonly used to Refresh skills in the use of microscopes and
observe whole organisms, parts of making slides.
organisms, thin sections of dissected tissue
or individual cells Discuss the ethics of dissection in an
educational context.

Fluorescence microscopy uses specific

fluorescent labels to bind to and visualise
certain molecules or structures within cells or
tissues

(f) Aseptic technique and cell culture

Aseptic technique eliminates unwanted Aseptic technique involves the sterilisation of Investigate methods of sterilisation of
microbial contaminants when culturing micro- equipment and culture media by heat or containers, equipment, and materials.
organisms or cells chemical means and subsequent exclusion of
microbial contaminants.

A microbial culture can be started using an Many culture media exist that promote the Culture bacterial, yeast, and algal cells using
inoculum of microbial cells on an agar growth of specific types of cells and aseptic technique.
medium, or in a broth with suitable nutrients microbes.

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Animal cells are grown in medium containing Growth factors are proteins that promote cell Investigate some of the different types of
growth factors from serum growth and proliferation. Growth factors are culture media and their uses.
essential for the culture of most animal cells.
In culture, primary cell lines can divide a
limited number of times, whereas tumour
cells lines can perform unlimited divisions

Plating out of a liquid microbial culture on

solid media allows the number of colony-
forming units to be counted and the density
of cells in the culture estimated

Serial dilution is often needed to achieve a

suitable colony count

Method and use of haemocytometer to Use a haemocytometer to make an estimate

estimate cell numbers in a liquid culture of cell count.

Vital staining is required to identify and count

viable cells

2 Proteins
(a) The proteome
The proteome is the entire set of proteins
expressed by a genome

The proteome is larger than the number of

genes, particularly in eukaryotes, because

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more than one protein can be produced from
a single gene as a result of alternative RNA
splicing
Not all genes are expressed as proteins in a Genes that do not code for proteins are
particular cell type called non-coding RNA genes and include
those that are transcribed to produce tRNA,
rRNA, and RNA molecules that control the
expression of other genes.

The set of proteins expressed by a given cell Some factors affecting the set of proteins
type can vary over time and under different expressed by a given cell type are the
conditions metabolic activity of the cell, cellular stress,
the response to signalling molecules, and
diseased versus healthy cells.
(b) The synthesis and transport of proteins
(i) Intracellular membranes
Eukaryotic cells have a system of internal Because of their size, eukaryotes have a
membranes, which increases the total area of relatively small surface area to volume ratio.
membrane The plasma membrane of eukaryotic cells is
therefore too small an area to carry out all the
vital functions carried out by membranes.

The endoplasmic reticulum (ER) forms a

network of membrane tubules continuous
with the nuclear membrane

The Golgi apparatus is a series of flattened

membrane discs

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Lysosomes are membrane-bound organelles
containing a variety of hydrolases that digest
proteins, lipids, nucleic acids and
carbohydrates

Vesicles transport materials between

membrane compartments

(ii) Synthesis of membrane components

Lipids and proteins are synthesised in the ER Rough ER (RER) has ribosomes on its
cytosolic face while smooth ER (SER) lacks
ribosomes.

Lipids are synthesised in the smooth

endoplasmic reticulum (SER) and inserted
into its membrane

The synthesis of all proteins begins in

cytosolic ribosomes

The synthesis of cytosolic proteins is

completed there, and these proteins remain
in the cytosol

Transmembrane proteins carry a signal A signal sequence is a short stretch of amino

sequence, which halts translation and directs acids at one end of the polypeptide that
the ribosome synthesising the protein to dock determines the eventual location of a protein
with the ER, forming RER in a cell.

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Translation continues after docking, and the
protein is inserted into the membrane of the
ER

(iii) Movement of proteins between

membranes
Once the proteins are in the ER, they are
transported by vesicles that bud off from the
ER and fuse with the Golgi apparatus

As proteins move through the Golgi Molecules move through the Golgi discs in Research post-translational modification and
apparatus they undergo post-translational vesicles that bud off from one disc and fuse activity in trypsinogen and trypsin.
modification to the next one in the stack. Enzymes
catalyse the addition of various sugars in
multiple steps to form the carbohydrates.

The addition of carbohydrate groups is the

major modification

Vesicles that leave the Golgi apparatus take

proteins to the plasma membrane and
lysosomes

Vesicles move along microtubules to other

membranes and fuse with them within the
cell

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(iv) The secretory pathway
Secreted proteins are translated in ribosomes Peptide hormones and digestive enzymes
on the RER and enter its lumen are examples of secreted proteins.

The proteins move through the Golgi

apparatus and are then packaged into
secretory vesicles

These vesicles move to and fuse with the

plasma membrane, releasing the proteins out
of the cell

Many secreted proteins are synthesised as Proteolytic cleavage is another type of post-
inactive precursors and require proteolytic translational modification. Digestive enzymes
cleavage to produce active proteins are one example of secreted proteins that
require proteolytic cleavage to become
active.

Specific names of digestive enzymes are not

required.

(c) Protein structure, ligand binding and

conformational change
(i) Amino acid sequence determines protein Use amino acid chromatography to
structure distinguish between different amino acids.
Proteins are polymers of amino acid
monomers

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Amino acids are linked by peptide bonds to Recognise the chemical structure of a
form polypeptides peptide bond from a diagram.

Amino acids have the same basic structure, R groups of amino acids vary in size, shape,
differing only in the R group present charge, hydrogen bonding capacity and
chemical reactivity.

Amino acids are classified according to their Classify amino acids according to the R Determine the isoelectric point of a protein
R groups: basic (positively charged); acidic group present. and explain the result using understanding of
(negatively charged); polar; hydrophobic protein structure.
Names and structures of individual amino
acids are not required.

The wide range of functions carried out by Carry out molecular modelling, for example
proteins results from the diversity of R groups computer-aided drug design.

The primary structure is the sequence in Carry out primary structure comparisons of
which the amino acids are synthesised into enzymes from different evolutionary
the polypeptide backgrounds, for example alcohol
dehydrogenase from different organisms.

Hydrogen bonding along the backbone of the

protein strand results in regions of secondary
structure — alpha helices, parallel or anti-
parallel beta-pleated sheets, or turns

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The polypeptide folds into a tertiary structure

This conformation is stabilised by interactions

between R groups: hydrophobic interactions;
ionic bonds; London dispersion forces;
hydrogen bonds; disulfide bridges Disulfide bridges are covalent bonds between
R groups containing sulfur.

Quaternary structure exists in proteins with Quaternary structure describes the spatial
two or more connected polypeptide subunits arrangement of the subunits.

A prosthetic group is a non-protein unit tightly The ability of haemoglobin to bind oxygen is Analyse haemoglobin dissociation curves.
bound to a protein and necessary for its dependent upon the non-protein haem group.
function

Interactions of the R groups can be Increasing temperature disrupts the

influenced by temperature and pH interactions that hold the protein in shape;
the protein begins to unfold, eventually
becoming denatured. The charges on acidic
and basic R groups are affected by pH. As
pH increases or decreases from the
optimum, the normal ionic interactions
between charged groups are lost, which
gradually changes the conformation of the
protein until it becomes denatured.

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(ii) Ligand binding changes the conformation
of a protein
A ligand is a substance that can bind to a
protein

R groups not involved in protein folding can

allow binding to ligands

Binding sites will have complementary shape

and chemistry to the ligand

As a ligand binds to a protein-binding site the

conformation of the protein changes

This change in conformation causes a

functional change in the protein

Allosteric interactions occur between spatially The binding of a substrate molecule to one
distinct sites active site of an allosteric enzyme increases
the affinity of the other active sites for binding
of subsequent substrate molecules. This is of
biological importance because the activity of
allosteric enzymes can vary greatly with
small changes in substrate concentration.

Many allosteric proteins consist of multiple

subunits (have quaternary structure)

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Allosteric proteins with multiple subunits
show co-operativity in binding, in which
changes in binding at one subunit alter the
affinity of the remaining subunits

Allosteric enzymes contain a second type of Investigate the action of aspartate

site, called an allosteric site transcarbamoylase as an example of an
allosteric enzyme of biological importance.

Modulators regulate the activity of the

enzyme when they bind to the allosteric site

Following binding of a modulator, the Positive modulators increase the enzyme’s

conformation of the enzyme changes and this affinity for the substrate, whereas negative
alters the affinity of the active site for the modulators reduce the enzyme’s affinity.
substrate

The binding and release of oxygen in Changes in binding of oxygen at one subunit
haemoglobin shows co-operativity alter the affinity of the remaining subunits for
oxygen.

The influence and physiological importance A decrease in pH or an increase in

of temperature and pH on the binding of temperature lowers the affinity of haemoglobin
oxygen for oxygen, so the binding of oxygen is
reduced. Reduced pH and increased
temperature in actively respiring tissue will
reduce the binding of oxygen to haemoglobin
promoting increased oxygen delivery to tissue.

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Effects of DPG are not required.

(iii) Reversible binding of phosphate and the

control of conformation
The addition or removal of phosphate can
cause reversible conformational change in
proteins

This is a common form of post-translational

modification

Protein kinases catalyse the transfer of a

phosphate group to other proteins

The terminal phosphate of ATP is transferred

to specific R groups

Protein phosphatases catalyse the reverse

reaction

Phosphorylation brings about conformational Research examples of proteins regulated by

changes, which can affect a protein’s activity phosphorylation, such as glycogen
phosphorylase.

The activity of many cellular proteins, such as

enzymes and receptors, is regulated in this
way

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Some proteins are activated by Adding a phosphate group adds negative
phosphorylation while others are inhibited charges. Ionic interactions in the
unphosphorylated protein can be disrupted
and new ones created.

3 Membrane proteins
(a) Movement of molecules across
membranes
Knowledge of the fluid mosaic model of cell Research the history of evidence-based
membranes models of membrane structure as an
example of refinement of scientific ideas.

Regions of hydrophobic R groups allow Integral membrane proteins interact

strong hydrophobic interactions that hold extensively with the hydrophobic region of
integral membrane proteins within the membrane phospholipids.
phospholipid bilayer

Some integral membrane proteins are

transmembrane proteins

Peripheral membrane proteins have

hydrophilic R groups on their surface and are
bound to the surface of membranes, mainly
by ionic and hydrogen bond interactions

Many peripheral membrane proteins interact

with the surfaces of integral membrane
proteins

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The phospholipid bilayer is a barrier to ions
and most uncharged polar molecules

Some small molecules, such as oxygen and

carbon dioxide, pass through the bilayer by
simple diffusion

Facilitated diffusion is the passive transport

of substances across the membrane through
specific transmembrane proteins

To perform specialised functions, different

cell types have different channel and
transporter proteins

Most channel proteins in animal and plant Channels are multi-subunit proteins with the
cells are highly selective subunits arranged to form water-filled pores
that extend across the membrane.

Some channel proteins are gated and Research CFTR mutation and cystic fibrosis.
change conformation to allow or prevent
diffusion

Ligand-gated channels are controlled by the

binding of signal molecules, and voltage-
gated channels are controlled by changes in
ion concentration

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Transporter proteins bind to the specific Transporters alternate between two Research glucose transporters in mammalian
substance to be transported and undergo a conformations so that the binding site for a cells.
conformational change to transfer the solute solute is sequentially exposed on one side of
across the membrane the bilayer, then the other.

Active transport uses pump proteins that Pumps that mediate active transport are
transfer substances across the membrane transporter proteins coupled to an energy
against their concentration gradient source.

A source of metabolic energy is required for

active transport

Some active transport proteins hydrolyse ATPases hydrolyse ATP.

ATP directly to provide the energy for the
conformational change required to move
substances across the membrane

(b) Ion transport pumps and generation of ion

gradients
For a solute carrying a net charge, the A membrane potential (an electrical potential
concentration gradient and the electrical difference) is created when there is a
potential difference combine to form the difference in electrical charge on the two
electrochemical gradient that determines the sides of the membrane.
transport of the solute

Ion pumps, such as the sodium-potassium

pump, use energy from the hydrolysis of ATP
to establish and maintain ion gradients

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The sodium-potassium pump transports ions
against a steep concentration gradient using
energy directly from ATP hydrolysis

It actively transports sodium ions out of the

cell and potassium ions into the cell

The pump has high affinity for sodium ions For each ATP hydrolysed, three sodium ions
inside the cell; binding occurs; are transported out of the cell and two
phosphorylation by ATP; conformation potassium ions are transported into the cell.
changes; affinity for sodium ions decreases; This establishes both concentration gradients
sodium ions released outside of the cell; and an electrical gradient.
potassium ions bind outside the cell;
dephosphorylation; conformation changes;
potassium ions taken into cell; affinity returns
to start

The sodium-potassium pump is found in most

animal cells, accounting for a high proportion
of the basal metabolic rate in many
organisms

In the small intestine, the sodium gradient In intestinal epithelial cells the sodium-
created by the sodium-potassium pump potassium pump generates a sodium ion
drives the active transport of glucose gradient across the plasma membrane.

The glucose transporter responsible for this Sodium ions enter the cell down their
glucose symport transports sodium ions and concentration gradient; the simultaneous

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glucose at the same time and in the same transport of glucose pumps glucose into the
direction cell against its concentration gradient.

Details of the apical and basal membranes

are not required.

4 Communication and signalling

(a) Co-ordination
Multicellular organisms signal between cells Steroid hormones, peptide hormones, and
using extracellular signalling molecules neurotransmitters are examples of
extracellular signalling molecules.

Receptor molecules of target cells are

proteins with a binding site for a specific
signal molecule

Binding changes the conformation of the

receptor, which initiates a response within the
cell

Different cell types produce specific signals Signalling molecules may have different Research examples of degenerative
that can only be detected and responded to effects on different target cell types due to diseases.
by cells with the specific receptor differences in the intracellular signalling
molecules and pathways that are involved.

In a multicellular organism, different cell

types may show a tissue-specific response to
the same signal

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(b) Hydrophobic signals and control of
transcription
Hydrophobic signalling molecules can diffuse
directly through the phospholipid bilayers of
membranes, and so bind to intracellular
receptors

The receptors for hydrophobic signalling Transcription factors are proteins that when
molecules are transcription factors bound to DNA can either stimulate or inhibit
initiation of transcription.

The steroid hormones oestrogen and

testosterone are examples of hydrophobic
signalling molecules

Steroid hormones bind to specific receptors

in the cytosol or the nucleus

The hormone-receptor complex moves to the The hormone-receptor complex binds to Research sex hormone disorders.
nucleus where it binds to specific sites on specific DNA sequences called hormone
DNA and affects gene expression response elements (HREs). Binding at these
sites influences the rate of transcription, with
each steroid hormone affecting the gene
expression of many different genes.

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(c) Hydrophilic signals and transduction
Hydrophilic signalling molecules bind to Peptide hormones and neurotransmitters are
transmembrane receptors and do not enter examples of hydrophilic extracellular
the cytosol signalling molecules.

Transmembrane receptors change

conformation when the ligand binds to the
extracellular face; the signal molecule does
not enter the cell, but the signal is transduced
across the plasma membrane

Transmembrane receptors act as signal

transducers by converting the extracellular
ligand-binding event into intracellular signals,
which alters the behaviour of the cell

Transduced hydrophilic signals often involve G-proteins relay signals from activated
G-proteins or cascades of phosphorylation by receptors (receptors that have bound a
kinase enzymes signalling molecule) to target proteins such
as enzymes and ion channels. Details of G-
proteins subunits are not required.

Phosphorylation cascades allow more than Phosphorylation cascades involve a series of

one intracellular signalling pathway to be events with one kinase activating the next in
activated the sequence and so on. Phosphorylation
cascades can result in the phosphorylation of
many proteins as a result of the original
signalling event.

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Binding of the peptide hormone insulin to its Binding of insulin to its receptor causes a Research data from glucose tolerance tests.
receptor results in an intracellular signalling conformational change that triggers
cascade that triggers recruitment of GLUT4 phosphorylation of the receptor. This starts a
glucose transporter proteins to the cell phosphorylation cascade inside the cell,
membrane of fat and muscle cells which eventually leads to GLUT4-containing
vesicles being transported to the cell
membrane.

Diabetes mellitus can be caused by failure to Research health effects associated with type
produce insulin (type 1) or loss of receptor 2 diabetes and the success rate of treatment
function (type 2) programmes.

Type 2 is generally associated with obesity Write a review of data from studies of health
and wellbeing, considering the importance of
Exercise also triggers recruitment of GLUT4, publishing negative results.
so can improve uptake of glucose to fat and
muscle cells in subjects with type 2

(d) Nerve impulse transmission

(i) Generation of a nerve impulse
Resting membrane potential is a state where
there is no net flow of ions across the
membrane

The transmission of a nerve impulse requires

changes in the membrane potential of the
neuron’s plasma membrane

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An action potential is a wave of electrical
excitation along a neuron’s plasma membrane

Neurotransmitters initiate a response by Neurotransmitter receptors are ligand-gated

binding to their receptors at a synapse ion channels.

Depolarisation of the plasma membrane as a Depolarisation is a change in the membrane Carry out Daphnia heart rate investigation.
result of the entry of positive ions triggers the potential to a less negative value inside. The action of chemical agonists can be
opening of voltage-gated sodium channels, assessed. This could provide an opportunity
and further depolarisation occurs to focus on aspects of experimental design
associated with pilot studies, measurement
accuracy, sample size and replication.
Inactivation of the sodium channels and the Binding of a neurotransmitter triggers the
opening of potassium channels restores the opening of ligand-gated ion channels at a
resting membrane potential synapse. Ion movement occurs and there is
depolarisation of the plasma membrane. If
sufficient ion movement occurs, and the
membrane is depolarised beyond a threshold
value, the opening of voltage-gated sodium
channels is triggered and sodium ions enter
the cell down their electrochemical gradient.
This leads to a rapid and large change in the
membrane potential. A short time after
opening, the sodium channels become
inactivated. Voltage-gated potassium
channels then open to allow potassium ions
to move out of the cell to restore the resting
membrane potential.

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Depolarisation of a patch of membrane
causes neighbouring regions of membrane to
depolarise and go through the same cycle, as
adjacent voltage-gated sodium channels are
opened

When the action potential reaches the end of

the neuron it causes vesicles containing
neurotransmitter to fuse with the membrane
— this releases neurotransmitter, which
stimulates a response in a connecting cell

Restoration of the resting membrane

potential allows the inactive voltage-gated
sodium channels to return to a conformation
that allows them to open again in response to
depolarisation of the membrane
Ion concentration gradients are re- Following repolarisation the sodium and
established by the sodium-potassium pump, potassium ion concentration gradients are
which actively transports excess ions in and reduced. The sodium-potassium pump
out of the cell restores the sodium and potassium ions back
to resting potential levels.

(ii) Initiation of a nerve impulse in response to Investigate vision experimentally.

an environmental stimulus: the vertebrate
eye

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The retina is the area within the eye that Rods function in dim light but do not allow Carry out a fish eye dissection.
detects light and contains two types of colour perception. Cones are responsible for
photoreceptor cells: rods and cones colour vision and only function in bright light.

In animals the light-sensitive molecule retinal

is combined with a membrane protein, opsin,
to form the photoreceptors of the eye

In rod cells the retinal-opsin complex is called

rhodopsin

Retinal absorbs a photon of light and

rhodopsin changes conformation to
photoexcited rhodopsin

A cascade of proteins amplifies the signal

Photoexcited rhodopsin activates a G- A single photoexcited rhodopsin activates

protein, called transducin, which activates the hundreds of molecules of G-protein. Each
enzyme phosphodiesterase (PDE) activated G-protein activates one molecule of
PDE.

PDE catalyses the hydrolysis of a molecule Each active PDE molecule breaks down
called cyclic GMP (cGMP) thousands of cGMP molecules per second.
The reduction in cGMP concentration as a
result of its hydrolysis affects the function of
ion channels in the membrane of rod cells.

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This results in the closure of ion channels in
the membrane of the rod cells, which triggers
nerve impulses in neurons in the retina

A very high degree of amplification results in

rod cells being able to respond to low
intensities of light

In cone cells, different forms of opsin

combine with retinal to give different
photoreceptor proteins, each with a maximal
sensitivity to specific wavelengths: red,
green, blue or UV

5 Protein control of cell division

(a) The cytoskeleton and cell division
The cytoskeleton gives mechanical support
and shape to cells

It consists of different protein structures Microtubules are hollow cylinders composed Research and consider the effects of
including microtubules, which are found in all of the protein tubulin. They radiate from the colchicine and paclitaxel on the cytoskeleton.
eukaryotic cells microtubule organising centre (MTOC) or
centrosome.

Knowledge of other cytoskeleton proteins is

not required.

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Microtubules control the movement of
membrane-bound organelles and
chromosomes

Cell division requires remodelling of the

cytoskeleton

Formation and breakdown of microtubules

involves polymerisation and depolymerisation
of tubulin

Microtubules form the spindle fibres that are

active during cell division

(b) The cell cycle

The cell cycle consists of interphase and Interphase involves growth and DNA Stain actively dividing plant meristem tissue
mitotic (M) phase synthesis including G1, a growth phase; S and calculate a mitotic index.
phase, during which the DNA is replicated;
and G2, a further growth phase.

Mitotic phase involves mitosis and In mitosis the chromosomal material is

cytokinesis separated by the spindle microtubules. This
is followed by cytokinesis, in which the
cytoplasm is separated into two daughter
cells.

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Mitosis consists of prophase, metaphase, Prophase — DNA condenses into
anaphase and telophase chromosomes each consisting of two sister
chromatids. Nuclear membrane breaks down;
spindle microtubules extend from the MTOC
by polymerisation and attach to
chromosomes via their kinetochores in the
centromere region.

Metaphase — chromosomes are aligned at

the metaphase plate (equator of the spindle).

Anaphase — as spindle microtubules shorten

by depolymerisation, sister chromatids are
separated, and the chromosomes are pulled
to opposite poles.

Telophase — the chromosomes decondense

and nuclear membranes are formed around
them.

(c) Control of the cell cycle

Progression through the cell cycle is Checkpoints are mechanisms within the cell Use an online simulation of mitotic
controlled by checkpoints that assess the condition of the cell during checkpoint control.
the cell cycle and halt progression to the next
phase until certain requirements are met.

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Cyclin proteins that accumulate during cell Cyclins combine with and activate cyclin- Investigate cell cycle mutation in yeast
growth are involved in regulating the cell dependent kinases (CDKs). Active cyclin- Schizosaccharomyces pombe.
cycle CDK complexes phosphorylate proteins that
regulate progression through the cycle. If
sufficient phosphorylation is reached,
progression occurs.

At the G1 checkpoint, retinoblastoma protein

(Rb) acts as a tumour suppressor by
inhibiting the transcription of genes that code
for proteins needed for DNA replication

Phosphorylation by G1 cyclin-CDK inhibits This allows transcription of the genes that

the retinoblastoma protein (Rb) code for proteins needed for DNA replication.
Cells progress from G1 to S phase.

At the G2 checkpoint, the success of DNA

replication and any damage to DNA is
assessed

DNA damage triggers the activation of

several proteins including p53 that can
stimulate DNA repair, arrest the cell cycle or
cause cell death

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A metaphase checkpoint controls At the metaphase checkpoint, progression is
progression from metaphase to anaphase halted until the chromosomes are aligned
correctly on the metaphase plate and
attached to the spindle microtubules.

An uncontrolled reduction in the rate of the Research the role of cell cycle regulators in
cell cycle may result in degenerative disease degenerative diseases such as Alzheimer’s
and Parkinson’s.

An uncontrolled increase in the rate of the Research the types of mutations associated
cell cycle may result in tumour formation with cancer, for example the influence of
environmental factors and viruses, the
A proto-oncogene is a normal gene, usually conversion of proto-oncogenes into
involved in the control of cell growth or oncogenes, and mutations in
division, which can mutate to form a tumour- tumour-suppressing genes.
promoting oncogene

(d) Control of programmed cell death

(apoptosis)
Apoptosis is triggered by cell death signals The production of death signal molecules
that can be external or internal from lymphocytes is an example of an
external death signal. DNA damage is an
example of an internal death signal.

External death signal molecules bind to a

surface receptor protein and trigger a protein
cascade within the cytoplasm

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An internal death signal resulting from DNA
damage causes activation of p53 tumour-
suppressor protein

Both types of death signal result in the

activation of caspases (types of protease
enzyme) that cause the destruction of the cell

Apoptosis is essential during development of Research and consider apoptosis in

an organism to remove cells no longer development of tetrapod limbs.
required as development progresses or
during metamorphosis

Cells may initiate apoptosis in the absence of Research the challenges in overcoming
growth factors apoptosis in maintaining animal cell culture
lines.

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1 Field techniques for biologists
(a) Health and safety
Aspects of fieldwork can present a hazard Hazards in fieldwork include adverse weather Discuss standard rules for fieldwork safety.
conditions, difficult terrain, problems
associated with isolation, and contact with
harmful organisms.

Hazard, risk, and control of risk by risk Risk is the likelihood of harm arising from
assessment exposure to a hazard.

Risk assessment involves identifying control

measures to minimise risk.

Control measures include appropriate

equipment, clothing, footwear, and means of
communication.

(b) Sampling of wild organisms

Sampling should be carried out in a manner Participate in fieldwork, using a variety of
that minimises impact on wild species and techniques.
habitats

Consideration must be given to rare and Research protected species in Scotland.

vulnerable species and habitats that are
protected by legislation

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The chosen technique, point count, transect A point count involves the observer recording
or remote detection must be appropriate to all individuals seen from a fixed point count
the species being sampled location. This can be compared to other point
count locations or with data from the same
location gathered at other times.

Quadrats, of suitable size and shape, or

transects are used for plants and other
sessile or slow-moving organisms

Capture techniques, such as traps and nets,

are used for mobile species

Elusive species can be sampled directly

using camera traps or an indirect method,
such as scat sampling

(c) Identification and taxonomy

Identification of an organism in a sample can In the context of fieldwork, sample organisms
be made using classification guides, from a variety of habitats and attempt to
biological keys, or analysis of DNA or protein classify and catalogue them using keys,
guides, and other materials.

Organisms can be classified by both

taxonomy and phylogenetics

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Taxonomy involves the identification and Classic taxonomy classification is based on Research the taxonomic groups.
naming of organisms and their classification morphology.
into groups based on shared characteristics Visit a botanic garden to learn more about
the major divisions of plants.

Visit a zoological park to learn more about

the animal phyla.

Phylogenetics is the study of the evolutionary Phylogenetics uses heritable traits such as Read excerpts from Bryan Sykes’s book, The
history and relationships among individuals morphology, DNA sequences, and protein Seven Daughters of Eve.
or groups of organisms structure to make inferences about an [Sykes B. (2001), The Seven Daughters of
organism’s evolutionary history and create a Eve, New York: W. W. Norton & Company]
Phylogenetics is changing the traditional phylogeny (or phylogenetic tree) — a
classification of many organisms diagrammatic hypothesis of its relationships Research the evolution of the pentadactyl
to other organisms. Genetic evidence can limb.
reveal relatedness obscured by divergent or
convergent evolution.

Familiarity with taxonomic groupings allows Nematodes, arthropods and chordates are
predictions and inferences to be made about examples of taxonomic groups.
the biology of an organism from better-known
(model) organisms

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Model organisms are those that are either Model organisms, such as the bacterium
easily studied or have been well studied E. coli; the flowering plant Arabidopsis
thaliana; the nematode C. elegans; the
arthropod Drosophila melanogaster (a fruit
fly); mice, rats, and zebrafish, which are all
chordates, have been very important in the
advancement of modern biology.

Information obtained from them can be

applied to other species that are more difficult
to study directly

(d) Monitoring populations

Presence, absence or abundance of indicator Identify relevant indicator species to classify
species can give information of a habitat, using the British National
environmental qualities, such as presence of Vegetation Classification.
a pollutant

Susceptible and favoured species can be Absence or reduced population indicates a

used to monitor an ecosystem species is susceptible to some factor in the
environment. Abundance or increased
population indicates it is favoured by the
conditions.

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Procedure for the mark and recapture A sample of the population is captured and Carry out a mark and recapture experiment
technique as a method for estimating marked (M) and released. After an interval of using a wild species.
population size using the formula time, a second sample is captured (C). If
MC some of the individuals in this second sample Carry out a mark and recapture simulation in
N= are recaptured (R), then the total population
R the laboratory.
MC
N=
R

This method assumes that all individuals

have an equal chance of capture, that there
is no immigration or emigration, and that
individuals that are marked and released can
mix fully and randomly with the total
population.

Methods of marking animals such as:

banding, tagging, surgical implantation,
painting and hair clipping

The method of marking and subsequent

observation must minimise the impact on the
study species

(e) Measuring and recording animal

behaviour
Some of the measurements used to quantify Latency is the time between the stimulus
animal behaviour are latency, frequency and occurring and the response behaviour.
duration

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Frequency is the number of times a
behaviour occurs within the observation
period.

Duration is the length of time each behaviour

occurs during the observation period.

An ethogram of the behaviours shown by a An ethogram lists species-specific Use an ethogram and time sampling to
species in a wild context allows the behaviours to be observed and recorded in compare the behaviour of different individuals
construction of time budgets the study. Recording the duration of each of of a species.
the behaviours in the ethogram, together with
the total time of observation, allows the
proportion of time spent on each behaviour to
be calculated in the time budget.

The importance of avoiding Anthropomorphism can lead to invalid

anthropomorphism when analysing behaviour conclusions.

2 Evolution
(a) Drift and selection
Evolution is the change over time in the
proportion of individuals in a population
differing in one or more inherited traits

During evolution, changes in allele frequency

occur through the non-random processes of
natural selection and sexual selection, and
the random process of genetic drift

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Natural selection acts on genetic variation in Variation in traits arises as a result of
populations mutation. Mutation is the original source of
new sequences of DNA. These new
sequences can be novel alleles. Most
mutations are harmful or neutral, but in rare
cases they may be beneficial to the fitness of
an individual.

Populations produce more offspring than the

environment can support

Individuals with variations that are better Selection results in the non-random increase
suited to their environment tend to survive in the frequency of advantageous alleles and
longer and produce more offspring, breeding the non-random decrease in the frequency of
to pass on those alleles that conferred an deleterious alleles.
advantage to the next generation

Sexual selection is the non-random process

involving the selection of alleles that increase
the individual’s chances of mating and
producing offspring

Sexual selection may lead to sexual

dimorphism

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Sexual selection can be due to male-male Male-male rivalry: large size or weaponry
rivalry and female choice increases access to females through conflict.
Female choice involves females assessing
the fitness of males.

Genetic drift occurs when chance events

cause unpredictable fluctuations in allele
frequencies from one generation to the next

Genetic drift is more important in small

populations, as alleles are more likely to be
lost from the gene pool

The importance of bottleneck and founder Population bottlenecks occur when a

effects on genetic drift population size is reduced for at least one
generation.

Founder effects occur through the isolation of

a few members of a population from a larger
population. The gene pool of the new
population is not representative of that in the
original gene pool.

A gene pool is altered by genetic drift

because certain alleles may be under-
represented or over-represented and allele
frequencies change

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Where selection pressures are strong, the Selection pressures are the environmental Study cladograms of MRSA and primate
rate of evolution can be rapid factors that influence which individuals in a evolution to compare the effect of generation
population pass on their alleles. time on rates of evolution.

They can be biotic: competition, predation,

disease, parasitism; or abiotic: changes in
temperature, light, humidity, pH, salinity.

The Hardy-Weinberg (HW) principle states The conditions for maintaining the HW
that, in the absence of evolutionary equilibrium are: no natural selection, random
influences, allele and genotype frequencies mating, no mutation, large population size
in a population will remain constant over the and no gene flow (through migration, in or
generations out).

The HW principle can be used to determine Use the HW principle to calculate allele, Research the application of the HW principle
whether a change in allele frequency is genotype and phenotype frequencies in in medical research.
occurring in a population over time populations.

p 2 + 2 pq + q 2 = 1

Changes suggest evolution is occurring p = frequency of dominant allele

q = frequency of recessive allele
p2 = frequency of homozygous dominant
genotype
2pq = frequency of heterozygous genotype
q2 = frequency of homozygous recessive
genotype

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(b) Fitness
Fitness is an indication of an individual’s Fitness is a measure of the tendency of some
ability to be successful at surviving and organisms to produce more surviving
reproducing offspring than competing members of the
same species.

It refers to the contribution made to the gene

pool of the next generation by individual
genotypes

Fitness can be defined in absolute or relative

terms

Absolute fitness is the ratio between the frequency of a particular genotype

frequency of individuals of a particular after selection
genotype after selection, to those before frequency of a particular genotype
selection before selection

If the absolute fitness is 1, then the frequency

of that genotype is stable. A value greater
than 1 conveys an increase in the genotype
and a value less than 1 conveys a decrease.

Relative fitness is the ratio of the number of number of surviving offspring per
surviving offspring per individual of a individual of a particular genotype
particular genotype to the number of number of surviving offspring per
individual of the most successful genotype
surviving offspring per individual of the most
successful genotype

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(c) Co-evolution
Co-evolution is the process by which two or
more species evolve in response to selection
pressures imposed by each other

A change in the traits of one species acts as

a selection pressure on the other species

Co-evolution is frequently seen in pairs of Symbiosis: co-evolved intimate relationships Research examples of co-evolved symbiotic
species that have symbiotic interactions between members of two different species. relationships.

The impacts of these relationships can be

positive (+), negative (-) or neutral (0) for the
individuals involved

Mutualism, commensalism, and parasitism Mutualism: both organisms in the interaction

are types of symbiotic interactions are interdependent on each other for
resources or other services. As both
organisms gain from the relationship, the
interaction is (+/+).

Commensalism: only one of the organisms

benefits (+/0).

Parasitism: the parasite benefits in terms of

energy or nutrients and the host is harmed as
the result of the loss of these resources (+/-).

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The Red Queen hypothesis states that, in a Read excerpts from Matt Ridley’s book, The
co-evolutionary relationship, change in the Red Queen: Sex and the Evolution of Human
traits of one species can act as a selection Nature.
pressure on the other species [Ridley M. (2003), The Red Queen: Sex and
the Evolution of Human Nature, London:
Harper Perennial]
This means that species in these
relationships must adapt to avoid extinction

3 Variation and sexual reproduction

(a) Costs and benefits of sexual and asexual
reproduction
Costs of sexual reproduction: males unable Research how the evolutionary importance of
to produce offspring; only half of each sexual reproduction influences experimental
parent’s genome passed onto offspring, design in the life sciences. The natural
disrupting successful parental genomes variation generated means that biologists
have to take care when sampling a
population and analysing data to make sure
that they can distinguish this ‘noise’ from any
experimental result or ‘signal’.

Investigate the paradox of the existence of

males.

Benefits outweigh costs due to an increase in

genetic variation in the population

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Genetic variation provides the raw material
required for adaptation, giving sexually
reproducing organisms a better chance of
survival under changing selection pressures

The Red Queen hypothesis to explain the

persistence of sexual reproduction

Co-evolutionary interactions between Hosts better able to resist and tolerate

parasites and hosts may select for sexually parasitism have greater fitness. Parasites
reproducing hosts better able to feed, reproduce and find new
hosts have greater fitness.

If hosts reproduce sexually, the genetic

variability in their offspring reduces the
chances that all will be susceptible to
infection by parasites

Asexual reproduction can be a successful In asexual reproduction, just one parent can
reproductive strategy as whole genomes are produce daughter cells and establish a
passed on from parent to offspring colony of virtually unlimited size over time.

Maintaining the genome of the parent is an

advantage particularly in very narrow, stable
niches or when re-colonising disturbed
habitats

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Vegetative cloning in plants and Parthenogenesis is reproduction from a
parthenogenesis in lower plants and animals female gamete without fertilisation.
that lack fertilisation are examples of asexual
reproduction in eukaryotes

Offspring can be reproduced more often and

in larger numbers with asexual reproduction

Parthenogenesis is more common in cooler Examine reproduction in a parthenogenic

climates, which are disadvantageous to organism, such as the laboratory stick insect
parasites, or regions of low parasite density Carausius morosus (in which offspring are
or diversity female), and compare with the Komodo
dragon (in which offspring are male).

Asexually reproducing populations are not

able to adapt easily to changes in their
environment, but mutations can occur that
provide some degree of variation and enable
some natural selection and evolution to occur

Organisms that reproduce principally by Prokaryotes can exchange genetic material

asexual reproduction also often have horizontally, resulting in faster evolutionary
mechanisms for horizontal gene transfer change than in organisms that only use
between individuals to increase variation, for vertical transfer.
example the plasmids of bacteria and yeasts
Mechanisms of horizontal gene transfer are
not required.

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(b) Meiosis Names of stages are not required. Use microscopy to examine gamete
formation or gametes in plants or
invertebrates.

Meiosis is the division of the nucleus that

results in the formation of haploid gametes
from a diploid gametocyte

In diploid cells, chromosomes typically Homologous chromosomes are

appear as homologous pairs chromosomes of the same size, same
centromere position and with the same
sequence of genes at the same loci.

Meiosis I
The chromosomes, which have replicated
prior to meiosis I, each consist of two
genetically identical chromatids attached at
the centromere

The chromosomes condense and the

homologous chromosomes pair up

Chiasmata form at points of contact between Linked genes are those on the same
the non-sister chromatids of a homologous chromosome. Crossing over can result in
pair and sections of DNA are exchanged new combinations of the alleles of these
genes.

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This crossing over of DNA is random and
produces genetically different recombinant
chromosomes

Spindle fibres attach to the homologous pairs

and line them up at the equator of the spindle

The orientation of the pairs of homologous Each pair of homologous chromosomes is Breed model organisms in the laboratory (for
chromosomes at the equator is random positioned independently of the other pairs, example Drosophila or rapid-cycling
irrespective of their maternal and paternal Brassica) to demonstrate independent
origin. This is known as independent assortment or, if possible, recombination.
assortment.

The chromosomes of each homologous pair

are separated and move towards opposite
poles

Cytokinesis occurs and two daughter cells

form

Meiosis II
Each of the two cells produced in meiosis I A total of four haploid cells are produced.
undergoes a further division during which the
sister chromatids of each chromosome are
separated

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(c) Sex determination Examine data on sex determination in a
variety of organisms.

The sex of birds, mammals and some insects Use Drosophila to investigate sex-linked
is determined by the presence of sex inheritance patterns.
chromosomes

In most mammals the SRY gene on the Y Examine data on inheritance patterns of
chromosome determines development of tortoiseshell cats.
male characteristics

Heterogametic (XY) males lack most of the Research X-linked agammaglobulinemia and
corresponding homologous alleles on the colour vision defect.
shorter (Y) chromosome

This can result in sex-linked patterns of

inheritance as seen with carrier females
(XBXb) and affected males (XbY)

In homogametic females (XX) one of the two X chromosome inactivation is a process by

X chromosomes present in each cell is which most of one X chromosome is
randomly inactivated at an early stage of inactivated.
development

X chromosome inactivation prevents a

double dose of gene products, which could
be harmful to cells

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Carriers are less likely to be affected by any
deleterious mutations on these X
chromosomes

As the X chromosome inactivated in each cell

is random, half of the cells in any tissue will
have a working copy of the gene in question

Hermaphrodites are species that have Compare the flowers of hermaphroditic and
functioning male and female reproductive unisexual plants.
organs in each individual

They produce both male and female gametes

and usually have a partner with which to
exchange gametes

The benefit to the individual organism is that

if the chance of encountering a partner is an
uncommon event, there is no requirement for
that partner to be of the opposite sex

For other species, environmental rather than Environmental sex determination in reptiles is
genetic factors determine sex and sex ratio controlled by environmental temperature of
egg incubation.

Sex can change within individuals of some

species as a result of size, competition, or
parasitic infection

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In some species the sex ratio of offspring can
be adjusted in response to resource
availability

4 Sex and behaviour

(a) Parental investment
Comparison of sperm and egg production in
relation to number and energy store

Greater investment by females Female investment in the egg structure in

non-mammals or in the uterus and during
gestation in mammals.

Parental investment is costly but increases

the probability of production and survival of
young

Classification of r-selected (r-strategists) and Characteristics of r-selected species: smaller;

K-selected (K-strategists) organisms based have a shorter generation time; mature more
on level of parental investment in offspring rapidly; reproduce earlier in their lifetime,
and number of offspring produced often only once; produce a larger number of
smaller offspring, each of which receives only
a smaller energy input; limited parental care;
most offspring will not reach adulthood.

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Characteristics of K-selected species: larger
and live longer; mature more slowly; can
reproduce many times in their lifetime;
produce relatively few, larger offspring; high
level of parental care; many offspring have a
high probability of surviving to adulthood.

r-selection tends to occur in unstable

environments where the species has not
reached its reproductive capacity, whereas K-
selection tends to occur in stable environments

Comparison of costs and benefits of external External fertilisation

and internal fertilisation  benefits: very large numbers of offspring
can be produced
 costs: many gametes predated or not
fertilised; no or limited parental care; few
offspring survive

Internal fertilisation
 benefits: increased chance of successful
fertilisation; fewer eggs needed; offspring
can be retained internally for protection
and/or development; higher offspring
survival rate
 costs: a mate must be located, which
requires energy expenditure; requires
direct transfer of gametes from one
partner to another

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(b) Reproductive behaviours and mating
systems in animals
Mating systems are based on how many
mates an individual has during one breeding
season

These range from polygamy (polygyny and Monogamy: the mating of a pair of animals to
polyandry) to monogamy the exclusion of all others.

Polygamy: individuals of one sex have more

than one mate.

Polygyny: one male mates exclusively with a

group of females.

Polyandry: one female mates with a number

of males in the same breeding season.

Many animals have mate-selection courtship Courtship in the field: create an ethogram
rituals observing the ritualised courtship displays of
water birds, such as grebes or ducks.

Successful courtship behaviour in birds and

fish can be a result of species-specific sign
stimuli and fixed action pattern responses

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Sexual selection selects for characteristics Courtship in the laboratory: observe
that have little survival benefit for the stickleback or Drosophila courtship;
individual, but increase their chances of investigate sexual selection in different
mating Drosophila varieties.

Many species exhibit sexual dimorphism as a Females are generally inconspicuous; males
product of sexual selection usually have more conspicuous markings,
structures and behaviours.

Reversed sexual dimorphism occurs in some

species

Female choice involves females assessing Honest signals can indicate favourable Research honest signalling in lekking
honest signals of the fitness of males alleles that increase the chances of survival species.
of offspring (fitness) or a low parasite burden
suggesting a healthy individual.

In lekking species, males gather to display at Some bird species exhibit lekking behaviour.
a lek, where female choice occurs Dominant males occupy the centre of the lek,
with subordinates and juveniles at the fringes
as ‘satellite’ males. During the display,
female choice occurs.

Success in male-male rivalry through conflict Males will fight for dominance and access to
(real or ritualised), increases access to females, often using elaborate ‘weapons’
females for mating such as antlers, tusks, horns.

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5 Parasitism
(a) (i) Niche
An ecological niche is a multi-dimensional
summary of tolerances and requirements of a
species

A species has a fundamental niche that it

occupies in the absence of any interspecific
competition

A realised niche is occupied in response to

interspecific competition

As a result of interspecific competition,

competitive exclusion can occur, where the
niches of two species are so similar that one
declines to local extinction

Where the realised niches are sufficiently

different, potential competitors can co-exist
by resource partitioning

(ii) The parasite niche

Parasitism is a symbiotic interaction between Research the niche of C. difficile and the use
a parasite and its host (+/-) of faecal transplants.

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A parasite gains benefit in terms of nutrients Research the ecology, evolution,
at the expense of its host reproduction, and physiology of a selected
human parasite.

Unlike in a predator–prey relationship, the

reproductive potential of the parasite is
greater than that of the host

Most parasites have a narrow (specialised)

niche as they are very host-specific

As the host provides so many of the

parasite’s needs, many parasites are
degenerate, lacking structures and organs
found in other organisms

An ectoparasite lives on the surface of its

host, whereas an endoparasite lives within
the tissues of its host

(b) Parasitic life cycles

Some parasites require only one host to
complete their life cycle

Many parasites require more than one host to The definitive host is the organism on or in
complete their life cycle which the parasite reaches sexual maturity.
Intermediate hosts may also be required for
the parasite to complete its life cycle.

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A vector plays an active role in the
transmission of the parasite and may also be
a host

The human disease malaria is caused by An infected mosquito, acting as a vector,

Plasmodium bites a human. Plasmodium enters the
human bloodstream. Asexual reproduction
occurs in the liver and then in the red blood
cells. When the red blood cells burst
gametocytes are released into the
bloodstream. Another mosquito bites an
infected human and the gametocytes enter
the mosquito, maturing into male and female
gametes, allowing sexual reproduction to
now occur. The mosquito can then infect
another human host.

Schistosomes cause the human disease Schistosomes reproduce sexually in the

schistosomiasis human intestine. The fertilised eggs pass out
via faeces into water where they develop into
larvae. The larvae then infect water snails,
where asexual reproduction occurs. This
produces another type of motile larvae, which
escape the snail and penetrate the skin of a
human, entering the bloodstream.

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Viruses are parasites that can only replicate Specific examples of viral life cycles are not Investigate the effects of a phage virus on
inside a host cell required. bacterial growth.

Viruses contain genetic material in the form

of DNA or RNA, packaged in a protective
protein coat

Some viruses are surrounded by a

phospholipid membrane derived from host
cell materials

The outer surface of a virus contains

antigens that a host cell may or may not be
able to detect as foreign

Viral life cycle stages: infection of host cell

with genetic material, host cell enzymes
replicate viral genome, transcription of viral
genes and translation of viral proteins,
assembly and release of new viral particles

RNA retroviruses use the enzyme reverse

transcriptase to form DNA, which is then
inserted into the genome of the host cell

Viral genes can then be expressed to form

new viral particles

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(c) Transmission and virulence
Transmission is the spread of a parasite to a Investigate the spread of a plant pathogen in
host a variety of planting densities and humidities.

Virulence is the harm caused to a host

species by a parasite

Ectoparasites are generally transmitted

through direct contact

Endoparasites of the body tissues are often

transmitted by vectors or by consumption of
intermediate hosts

Factors that increase transmission rates:

 the overcrowding of hosts when they are

at high density
 mechanisms, such as vectors and
waterborne dispersal stages, that allow
the parasite to spread even if infected
hosts are incapacitated

Host behaviour is often exploited and Alteration of host foraging, movement, sexual
modified by parasites to maximise behaviour, habitat choice or anti-predator
transmission behaviour.

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The host behaviour becomes part of the
extended phenotype of the parasite

Parasites often suppress the host immune

system and modify host size and
reproductive rate in ways that benefit the
parasite growth, reproduction or transmission

(d) Defence against parasitic attack

Immune response in mammals has both non-
specific and specific aspects

Non-specific defences
Physical barriers, chemical secretions, Epithelial tissue blocks the entry of parasites;
inflammatory response, phagocytes, and hydrolytic enzymes in mucus, saliva and
natural killer cells destroying cells infected tears destroy bacterial cell walls; low pH
with viruses are examples of non-specific environments of the secretions of stomach,
defences vagina and sweat glands denatures cellular
proteins of pathogens.

Injured cells release signalling molecules.

This results in enhanced blood flow to the
site, bringing antimicrobial proteins and
phagocytes.

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Killing of parasites using powerful enzymes
contained in lysosomes, by engulfing them
and storing them inside a vacuole in the
process of phagocytosis.

Natural killer cells can identify and attach to

cells infected with viruses, releasing
chemicals that lead to cell death by inducing
apoptosis.

Specific cellular defences

A range of white blood cells constantly
circulate, monitoring the tissues

If tissues become damaged or invaded, cells

release cytokines that increase blood flow
resulting in non-specific and specific white
blood cells accumulating at the site of
infection or tissue damage

Mammals contain many different Specific lymphocyte names are not required.
lymphocytes, each possessing a receptor on
its surface, which can potentially recognise a
parasite antigen

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Binding of an antigen to a lymphocyte’s
receptor selects that lymphocyte to then
divide and produce a clonal population of this
lymphocyte

Some selected lymphocytes will produce

antibodies, others can induce apoptosis in
parasite-infected cells

Antibodies possess regions where the amino

acid sequence varies greatly between
different antibodies

This variable region gives the antibody its

specificity for binding antigen

When the antigen binds to this binding site

the antigen-antibody complex formed can
result in inactivation of the parasite, rendering
it susceptible to a phagocyte, or can
stimulate a response that results in cell lysis

Memory lymphocyte cells are also formed Initial antigen exposure produces memory
lymphocyte cells specific for that antigen that
can produce a secondary response when the
same antigen enters the body in the future.
When this occurs antibody production is

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enhanced in terms of speed of production,
concentration in blood and duration.

(e) Immune evasion

Parasites have evolved ways of evading the
immune system

Endoparasites mimic host antigens to evade

detection and modify host immune response
to reduce their chances of destruction

Antigenic variation in some parasites allows Compare antigenic variation in trypanosomes

them to change between different antigens with antigenic variation in the influenza virus.
during the course of infection of a host

It may also allow re-infection of the same

host with the new variant

Some viruses escape immune surveillance

by integrating their genome into host
genomes, existing in an inactive state known
as latency

The virus becomes active again when

favourable conditions arise

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(f) Challenges in treatment and control Research how attempts to disrupt the
lifecycle of Plasmodium in the control of
malaria have resulted in the loss of apex
predators due to bio-magnification of the
organochloride insecticide, DDT.

Epidemiology is the study of the outbreak

and spread of infectious disease

The herd immunity threshold is the density of

resistant hosts in the population required to
prevent an epidemic

Vaccines contain antigens that will elicit an

immune response

The similarities between host and parasite

metabolism makes it difficult to find drug
compounds that only target the parasite

Antigenic variation has to be reflected in the

design of vaccines

Some parasites are difficult to culture in the Research the problems associated with the
laboratory making it difficult to design development of successful vaccines for HIV
vaccines and malaria.

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Challenges arise where parasites spread Overcrowding can occur in refugee camps Research the decline of effectiveness of
most rapidly as a result of overcrowding or that result from war or natural disaster or chemical treatments over time.
tropical climates rapidly growing cities in LEDCs.

These conditions make co-ordinated

treatment and control programs difficult to
achieve

Civil engineering projects to improve

sanitation combined with co-ordinated vector
control may often be the only practical control
strategies

Improvements in parasite control reduce child Research parasitism and childhood.

mortality and result in population-wide
improvements in child development and Research the impact of parasitism on child
intelligence, as individuals have more mortality rates in different parts of the world.
resources for growth and development
Consider the benefits of intervention
programmes in terms of childhood
development and intelligence.

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1 Scientific principles and process
(a) Scientific method
Scientific cycle — observation; construction In science, refinement of ideas is the norm, Research Karl Popper’s concept of
of a testable hypothesis; experimental and scientific knowledge can be thought of as falsifiability as the basis for scientific thinking.
design; gathering, recording, and analysis of the current best explanation, which may then
data; evaluation of results and conclusions; be updated after evaluation of further
the formation of a revised hypothesis where experimental evidence.
necessary

The null hypothesis proposes that there will Failure to find an effect (a negative result) is Research recent examples of scientific
be no statistically significant effect as a result a valid finding, as long as an experiment is breakthroughs to identify any examples of
of the experiment treatment well designed. Conflicting data or conclusions unexpected results, conflicting data, or
can be resolved through careful evaluation or creative experimentation.
can lead to further experimentation.

If there is evidence for an effect, unlikely due

to chance, then the null hypothesis is
rejected

Scientific ideas only become accepted once Effects must be reproducible; one-off results
they have been checked independently are treated with caution.

(b) Scientific literature and communication

The importance of publication of methods, Common methods of sharing original
data, analysis, and conclusions in scientific scientific findings include seminars, talks and
reports so that others are able to repeat an posters at conferences, and publishing in
experiment academic journals.

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The importance of peer review and critical Most scientific publications use peer review. Compare the dispassionate approach taken
evaluation by specialists with expertise in the Specialists with expertise in the relevant field in presenting scientific results with the
relevant field assess the scientific quality of a submitted passionate reality of scientific investigation,
manuscript and make recommendations described in Frederick Grinnell’s book,
regarding its suitability for publication. The Everyday Practice of Science: Where
Intuition and Passion Meet Objectivity and
Logic.
The use of review articles, which summarise [Grinnell F. (2008), The Everyday Practice of
current knowledge and recent findings in a Science: Where Intuition and Passion Meet
particular field Objectivity and Logic, Oxford: Oxford
University Press]

Critical evaluation of science coverage in the

wider media

Increasing the public understanding of

science, and the issue of misrepresentation
of science

(c) Scientific ethics

Importance of integrity and honesty — While judgements and interpretations of Discuss excerpts from Ben Goldacre’s book,
unbiased presentation of results, citing and scientific evidence may be disputed, integrity Bad Science
providing references, avoiding plagiarism and honesty are of key importance in Goldacre B. (2008), Bad Science, London:
science. The replication of experiments by Fourth Estate
others reduces the opportunity for dishonesty
or the deliberate misuse of science. Use a standard system, such as Harvard or
Vancouver, to make appropriate citations in a
piece of scientific writing and to construct a

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reference list that allows another investigator
to locate your source material.

In animal studies, the concepts of

replacement, reduction, and refinement are
used to avoid, reduce or minimise the harm
to animals

Informed consent, the right to withdraw, and Discuss the implications of the British
confidentiality in human studies Psychological Society’s ethical guidelines on
school-based investigations on humans.

The justification for scientific research and The value or quality of science investigations
the assessment of any risks must be justifiable in terms of the benefits of
its outcome, including the pursuit of scientific
knowledge. As a result of the risks involved,
many areas of scientific research are highly
regulated and licensed by governments.

The risk to and safety of subject species,

individuals, investigators and the
environment must be taken into account

Legislation, regulation, policy and funding Legislation limits the potential for the misuse
can all influence scientific research of studies and data.

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2 Experimentation
Validity, reliability, accuracy and precision Validity: variables controlled so that any
measured effect is likely to be due to the
independent variable.

Reliability: consistent values in repeats and

independent replicates.

Accuracy: data, or means of data sets, are

close to the true value.

Precision: measured values are close to each

other.

(a) Pilot study

Integral to the development of an Follow a multi-step protocol, such as protein
investigation, a pilot study is used to help electrophoresis, mitotic index, or cell cycle
plan procedures, assess validity and check mutation in yeast, to appreciate the need to
techniques practise difficult techniques.

This allows evaluation and modification of

experimental design

The use of a pilot study can ensure an Use a pilot study to establish ranges for
appropriate range of values for the variables in an investigation, such as enzyme
independent variable activity or Daphnia heart rate.

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In addition, it allows the investigator to
establish the number of repeat
measurements required to give a
representative value for each independent
datum point

(b) Experimental design

(i) Independent and dependent variables An independent variable is the variable that is
changed in a scientific experiment.

A dependent variable is the variable being

measured in a scientific experiment.

Independent and dependent variables can be

continuous or discrete

Experiments involve the manipulation of the

independent variable by the investigator

The experimental treatment group is

compared to a control group

The use and limitations of simple (one The control of laboratory conditions allows
independent variable) and multifactorial simple experiments to be conducted more
(more than one independent variable) easily than in the field. However, a drawback
experimental designs of a simple experiment is that its findings may
not be applicable to a wider setting.

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A multifactorial experiment involves a
combination of more than one independent
variable or combination of treatments.

Investigators may use groups that already

exist, so there is no truly independent
variable

Observational studies are good at detecting In observational studies the independent Carry out an observational study in which the
correlation, but since they do not directly test variable is not directly controlled by the investigator groups the independent variable,
a hypothesis, they are less useful for investigator, for ethical or logistical reasons. such as a study of the effect of gender in a
determining causation human study.

(ii) Confounding variables

Due to the complexities of biological systems, Design and carry out a simple laboratory true
other variables besides the independent experiment, such as an enzyme experiment,
variable may affect the dependent variable where confounding variables are tightly
controlled.

These confounding variables must be held Design and carry out a field observational
constant if possible, or at least monitored so study, such as an environmental transect,
that their effect on the results can be where the independent variable is not under
accounted for in the analysis direct control and where confounding
variables cannot be tightly controlled.

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In cases where confounding variables cannot Randomised blocks of treatment and control
easily be controlled, a randomised block groups can be distributed in such a way that
design could be used the influence of any confounding variable is
likely to be the same across the treatment
and control groups.

(iii) Controls
Control results are used for comparison with
the results of treatment groups

Negative and positive controls may be used The negative control provides results in the Design an experiment with positive and
absence of a treatment. A positive control is negative controls, such as a laboratory
a treatment that is included to check that the investigation using an enzyme.
system can detect a positive result when it
occurs.

Use of placebos and the placebo effect Placebos can be included as a treatment
without the presence of the independent
variable being investigated.

Placebo effect is a measurable change in the

dependent variable as a result of a patient’s
expectations, rather than changes in the
independent variable.

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(iv) In vivo and in vitro studies
In vitro refers to the technique of performing Examples of in vitro experiments: cells
a given procedure in a controlled growing in culture medium, proteins in
environment outside of a living organism solution, purified organelles.

In vivo refers to experimentation using a

whole, living organism

Advantages and disadvantages of in vivo and

in vitro studies

(c) Sampling
Where it is impractical to measure every
individual, a representative sample of the
population is selected

The extent of the natural variation within a

population determines the appropriate
sample size

More variable populations require a larger

sample size

A representative sample should share the

same mean and the same degree of variation
about the mean as the population as a whole

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Random, systematic and stratified sampling In random sampling, members of the In ecological studies, use random numbers to
population have an equal chance of being select quadrats for sampling.
selected. In systematic sampling, members
of a population are selected at regular Establish sample size by determining a
intervals. In stratified sampling, the travelling mean or the cumulative total of
population is divided into categories that are species in quadrats.
then sampled proportionally.
Use line or belt transects to systematically
sample an environment.

Use stratified sampling to sample habitats

that are not uniform, using a standard
formula to calculate the number of samples
from each area.

(d) Reliability
Variation in experimental results may be due
to the reliability of measurement methods
and/or inherent variation in the specimens

The precision and accuracy of repeated The reliability of measuring instruments or Determine the precision of a measuring
measurements procedures can be determined by repeated procedure by repeated measurements, and
measurements or readings of an individual the accuracy of a measuring procedure by
datum point. The variation observed indicates calibration against a known standard.
the precision of the measurement instrument
or procedure but not necessarily its accuracy.

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The natural variation in the biological material
being used can be determined by measuring
a sample of individuals from the population

The mean of these repeated measurements

will give an indication of the true value being
measured

The range of values is a measure of the

extent of variation in the results

If there is a narrow range then the variation is

low

Independent replication should be carried out Overall results can only be considered
to produce independent data sets reliable if they can be achieved consistently.

These independent data sets should be

compared to determine the reliability of the
results

(e) Presentation of data

Discrete and continuous variables give rise to Qualitative data is subjective and descriptive.
qualitative, quantitative, or ranked data
Quantitative data can be measured
objectively, usually with a numerical value.

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Ranked data refers to the data transformation
in which numerical values are replaced by
their rank when the data are sorted from
lowest to highest.

The type of variable being investigated has

consequences for any graphical display or
statistical tests that may be used

Identification and calculation of mean,

median and mode

Use of box plots to show variation within and Median, lower quartile, upper quartile and
between data sets inter-quartile range.

Interpret error bars on graphical data

Correlation exists if there is a relationship Correlation is an association and does not

between two variables imply causation. Causation exists if the
changes in the values of the independent
variable are known to cause changes to the
value of the dependent variable

Positive and negative correlations A positive correlation exists when an

increase in one variable is accompanied by
an increase in the other variable.

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A negative correlation exists when an
increase in one variable is accompanied by a
decrease in the other variable.

Strong and weak correlations Strength of correlation is proportional to

spread of values from line of best fit.

Correlation values are not required.

3 Reporting and critical evaluation of

biological research
(a) Background information
Scientific reports should contain an Background information should be clear,
explanatory title, an abstract including aims relevant and unambiguous. A title should
and findings, an introduction explaining the provide a succinct explanation of the study.
purpose and context of the study including An abstract should outline the aims and
the use of several sources, supporting findings of the study.
statements, citations, and references
An aim must link the independent and
dependent variables.

The introduction should provide any

information required to support: choices of
method, results, and discussion. An
introduction should explain why the study has
been carried out and place the study in the
context of existing understanding. Key points
should be summarised and supporting and

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contradictory information identified. Several
sources should be selected to support
statements, and citations and references
should be in a standard form. Decisions
regarding basic selection of study methods
and organisms should be covered, as should
the aims and hypotheses.

(b) Reporting and evaluating experimental

design
A method section should contain sufficient
information to allow another investigator to
repeat the work

Experimental design should address the The validity and reliability of the experimental
intended aim and test the hypothesis design should be evaluated. An experimental
design that does not address the intended
aim or test the hypothesis is invalid.

Treatment effects should be compared to

controls

Any confounding variables should be taken

into account or standardised across
treatments

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The validity of an experiment may be
compromised when factors other than the
independent variable influence the value of
the dependent variable

The effect of selection bias and sample size Selection bias is the selection of a sample in
on representative sampling a non-random way, so that the sample is not
representative of the whole population.
Selection bias may have prevented a
representative sample being selected.

Sample size may not be sufficient to decide

without bias whether the change to the
independent variable has caused an effect in
the dependent variable.

(c) Data analysis

The appropriate use of graphs, mean, In results, data should be presented in a
median, mode, standard deviation and range clear, logical manner suitable for analysis.
in interpreting data Consideration should be given to the validity
of outliers and anomalous results.

Statistical tests are used to determine Knowledge of specific statistical tests is not Explore error bars showing standard
whether the differences between the means required. deviation, standard errors, or range. These
are likely or unlikely to have occurred by could be used in project work, where
chance appropriate.

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A statistically significant result is one that is
unlikely to be due to chance alone

Error bars indicate the variability of data

around a mean

If the treatment mean differs from the control

mean sufficiently for their error bars not to
overlap, this indicates that the difference may
be significant

(d) Evaluating results and conclusions

Conclusions should refer to the aim, the
results and the hypothesis

The validity and reliability of the experimental

design should be taken into account

Consideration should be given as to whether

the results can be attributed to correlation or
causation

Evaluation of conclusions should also refer to Meaningful scientific discussion would

existing knowledge and the results of other include consideration of findings in the
investigations context of existing knowledge and the results
of other investigations. Scientific writing
should reveal an awareness of the
contribution of scientific research to

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increasing scientific knowledge, and to the
social, economic and industrial life of the
community.

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