1 - Statistical Analysis

State that error bars are a graphical representation of the variability of data
Error bars show the spread of measurements around a central tendency (e.g. mean) on a graph
Error bars will usually show either:
The range of data (all the samples)
The standard deviation (68% of the sample)
The 95% confidence intervals (CI)

Calculate the mean and standard deviation of a set of values
Data can be measured in one of three ways:


Mean:
The average of a group of data entries
Calculation method = sum of data entries / total number of data entries

Standard Deviation:
Measures the variability (spread) in a set of data that is normally distributed (Gaussian)
In order to ensure normal distribution of the standard deviation, certain outliers may need to be
excluded from the data set (with justification)

State that the term standard deviation is used to summarise the spread of values around the
mean, and that 68% of the values fall within one standard deviation of the mean
Data which is normally distributed will exhibit a bell-shaped (Gaussian) curve which is symmetrical
around a central mean
68% of data values will fall within one standard deviation of the mean
95% of data values will fall within two standard deviations of the mean
99.8% of data values will fall within three standard deviations of the mean

Explain how the standard deviation is useful for comparing the means and spread of data
between two or more samples
Data sets that have the same mean may not have the same degree of variation in data
As standard deviation measures the spread of data, it can be used to compare data sets
The diagram below shows three sets of data with identical means but different spreads of data
A higher standard deviation means there is greater variation in the data set, whereas a lower
standard deviation means there is less






Graphical Representations of Data Spread


Deduce the significance of the difference between two sets of data using calculated values for
t and the appropriate tables
A t-test is a statistical test used to compare two means (e.g. between a control group and an
experimental group)
It can be used to compare a null hypothesis against an alternative hypothesis:
Null hypothesis: There is no significant difference between the means
Alternative hypothesis: There is a significant difference between two means
A t-test can be either one-tailed (difference only) or two-tailed (difference and direction)

Conducting a t-test:
A t-test is a statistical formula that calculates a t value based on a set of data
If there is a significant difference between the two means, then the t value will be greater than a
determined value for a given degree of probability
Scientists generally consider data to be statistically significant when there is less than a 5%
probability the results are due to chance
This 95% confidence level is a probability value of p<0.05
The reliability of a given t value will be affected by the size of the population used in the study (a
small population is less reliable)
The population size is reflected by the degrees of freedom, which is calculated as population size
minus two (df = n - 2)

Calculating significance:
Once a t-test has been conducted and a t value generated, statistical significance is determined by
completing the following steps:
Step 1: Determine degree of freedom (df = n - 2)
Step 2: Determine p value (p<0.05)
Step 3: Compare t value against value given for the conditions outlined in steps one and two
If the t value is greater than the value provided in the table, the data can be considered statistically
significant (reject the null hypothesis)




Table of t Values


Explain that the existence of a correlation does not establish that there is a causal relationship
between two variables
Correlation describes the strength and direction of a linear relationship between two variables
Is positive (x = y) or negative (x = - y)

Causation describes the relationship between two variables, where one variable has a direct effect on
another

Correlation does not automatically indicate causation just because two variables change in relation to
one another, does not mean they are linked
E.g. CO
2
levels and crime have both risen, but CO
2
levels don't cause crime

Types of Correlation


2.1 - Cell Theory
Wednesday, July 30, 2014
11:43 AM
2.1.1 Outline the cell theory
The cell theory states that:
All living things are composed of cells (or cell products)
The cell is the smallest unit of life
Cells only arise from pre-existing cells

2.1.2 Discuss the evidence for the cell theory
Microscopes:
Microscopes have increased man's ability to visualise tiny objects
All living things when viewed under a microscope have been found to be made of cells and cell products
(e.g. hair)
Note: Certain types of cells do not conform to the standard notion of what constitutes a cell
Muscle cells contain multiple nuclei
Fungal hyphae consist of multiple cells that share a continuous cytoplasm
Light vs Electron Microscopes

Experimental Evidence:
Cells removed from tissues can survive independently for short periods of time
Nothing smaller than a cell has been found to be able to live independently
Experiments by Francesco Redi and Louis Pasteur have demonstrated that cells cannot grow in sealed and
sterile conditions
History of the Cell Theory

2.1.3 State that unicellular organisms carry out all the functions of life
Unicellular organisms (such as amoeba, paramecium, euglena and bacterium) are the smallest organisms
capable of independent life.
All living things share 7 basic characteristics:
Movement: Living things show movement, either externally or internally
Reproduction: Living things produce offspring, either sexually or asexually
Sensitivity: Living things can respond to and interact with the environment
Growth: Living things can grow or change size / shape
Respiration: Living things use substances from the environment to make energy
Excretion: Living things exhibit the removal of wastes
Nutrition: Living things exchange materials and gases with the environment

2.1.4 Compare the relative sizes of molecules, cell membrane thickness, viruses, bacteria, organelles and
cells, using appropriate SI units
Relative sizes: Unit Conversion Table:

A molecule = 1 nm
Cell membrane thickness = 7.5 nm
Virus = 100 nm (range: 20 - 200 nm)
Bacteria = 1 - 5 um
Organelles = <10 um
Eukaryotic cells = <100 um

Diagram of the Relative Sizes and Scale of Biological Materials


2.1.5 Calculate the linear magnification of drawings
To calculate the linear magnification of a drawing the following equation should be used:
Magnification = Size of image (with ruler) Actual size of object (according to scale bar)

To calculate the actual size of a magnified specimen the equation is simply re-arranged:
Actual size = Size of image (with ruler) Magnification

2.1.6 Explain the importance of the surface area to volume ratio as a factor limiting cell size
The rate of metabolism of a cell is a function of its mass / volume
The rate of material exchange in and out of a cell is a function of its surface area
As the cell grows, volume increases faster than surface area (leading to a decreased SA:Vol ratio)
If the metabolic rate is greater than the rate of exchange of vital materials and wastes, the cell will
eventually die
Hence the cell must consequently divide in order to restore a viable SA:Vol ratio and survive
Cells and tissues specialised for gas or material exchange (e.g. alveoli) will increase their surface area to
optimise the transfer of materials










Microvilli increase surface area allowing for a more efficient exchange of materials / heat


2.1.7 State that multicellular organisms show emergent properties
Emergent properties arise from the interaction of component parts: the whole is greater than the sum of
its parts
Multicellular organisms are capable of completing functions that individual cells could not undertake - this
is due to the interaction between cells producing new functions
In multicellular organisms:
Cells may group together to form tissues
Organs are then formed from the functional grouping of multiple tissues
Organs that interact may form organ systems capable of carrying out specific body functions
Organ systems carry out the life functions required by an organism

Levels of Anatomical Organisation









2.1.8 Explain that cells in multicellular organisms differentiate to carry out specialised functions by
expressing some of their genes and not others

All cells of an individual organisms share an identical genome - each cell contains the entire set of genetic
instructions for that organism
The activation of different instructions (genes) within a given cell by chemical signals will cause it to
differentiate from other cells like it
Differentiation is the process during development whereby newly formed cells become
more specialised and distinct from one another as they mature
Active genes are usually packaged in an expanded and accessible form (euchromatin), while inactive
genes are mainly packaged in a condensed form (heterochromatin)
Differentiated cells will have different regions of DNA packaged as heterochromatin and euchromatin
depending on their function

Differential Gene Expression Leading to Specialisation of Cell Structure and Function





2.1.9 State that stem cells retain the capacity to divide and have the ability to differentiate along different
pathways
Stem cells are unspecialised cells that have two key qualities:
Self renewal: They can continuously divide and replicate
Potency: They have the capacity to differentiate into specialised cell types

Stem Cells

Outline one therapeutic use of stem cells
Stem cells can be derived from embryos or the placenta / umbilical cord of the mother; also minimal
amounts can be harvested from some adult tissue
Stem cells can be used to replace damaged or diseased cells with healthy, functioning ones
This process requires:
The use of biochemical solutions to trigger differentiation into desired cell type
Surgical implantation of cells into patient's own tissue
Suppression of host immune system to prevent rejection of cells
Careful monitoring of new cells to ensure they do not become cancerous

Examples of therapeutic uses of stem cells:
Retinal cells: Replace dead cells in retina to cure diseases like glaucoma and macular degeneration
Skin cells: Graft new skin cells to replace damaged cells in severe burn victims
Nerve cells: Repair damage caused by spinal injuries to enable paralysed victims to regain movement
Blood cells: Bone marrow transplants for cancer patients who are immuno-compromised as a result of
chemotherapy
















2.1 - Prokaryotes
2.2.1 Draw and label a diagram of the ultrastructure of Escherichia coli (E. coli) as an example of a prokaryote
2D Representation 3D
Representation

2.2.2 Annotate the diagram with the function of each of the named structures
Cell Wall: A rigid outer layer made of peptidoglycan that maintains shape and protects the cell from
damage or bursting if internal pressure is high
Cell Membrane: Semi-permeable barrier that controls the entry and exit of substances
Cytoplasm: Fluid component which contains the enzymes needed for all metabolic reactions
Nucleoid: Region of the cytoplasm which contains the genophore (the prokaryotic DNA)
Plasmid: Additional DNA molecule that can exist and replicate independently of the genophore - it can
be transmitted between bacterial species
Ribosome: Complexes of RNA and protein that are responsible for polypeptide synthesis (prokaryotic
ribosomes are smaller than eukaryotes - 70S)
Slime Capsule: A thick polysaccharide layer used for protection against dessication (drying out) and
phagocytosis
Flagella (singular flagellum): Long, slender projection containing a motor protein which spins the
flagella like a propellor, enabling movement
Pili (singular pilus): Hair-like extensions found on bacteria which can serve one of two roles
Attachment pili: Shorter in length, they allow bacteria to adhere to one another or to available surfaces
Sex pili: Longer in length, they allow for the exchange of genetic material (plasmids) via a process called
bacterial conjugation

2.2.3 Identify structures from 2.2.1 in electron micrographs of E. coli
Electron Micrograph of Escherichia coli


2.2.4 State that bacterial cells divide by binary fission
Binary fission is a form of asexual reproduction and cell division used by prokaryotic organisms
It is not the same as mitosis, there is no condensation of genetic material and no spindle formation
In the process of binary fission:
The circular DNA is copied in response to a replication signal
The two DNA loops attach to the membrane
The membrane elongates and pinches off (cytokinesis) forming two separate cells

The Process of Binary Fission






















2.3 - Eukaryotes
2.3.1 Draw and label a diagram of the ultrastructure of a liver cell as an example of an animal cell

2D Representation 3D Representation

2.3.2 Annotate the diagram from 2.3.1 with the functions of each named structure
Cell Membrane: Semi-permeable barrier that controls the entry and exit of substances
Cytosol: The fluid portion of the cytoplasm (does not include the organelles or other insoluble materials)
Nucleus: Contains hereditary material (DNA) and thus controls cell activities (via transcription) and
mitosis (via DNA replication)
Nucleolus: Site of the production and assembly of ribosome components
Ribosome: Complexes of RNA and protein that are responsible for polypeptide synthesis (eukaryotic
ribosomes are larger than prokaryotes - 80S)
Mitochondria: Site of aerobic respiration, which produces large quantities of chemical energy (ATP) from
organic compounds
Golgi Apparatus: An assembly of vesicles and folded membranes involved in the sorting, storing and
modification of secretory products
Lysosome: Site of hydrolysis / digestion / breakdown of macromolecules
Peroxisome: Catalyses breakdwon of toxic substances like hydrogen peroxide and other metabolites
Centrioles: Microtubule-organising centres involved in cell division (mitosis / meiosis and cytokinesis)
Endoplasmic Reticulum: A system of membranes involved in the transport of materials between
organelles
Rough ER: Studded with ribosomes and involved in the synthesis and transport of proteins destined for
secretion
Smooth ER: Involved in the synthesis and transport of lipids and steroids, as well as metabolism of
carbohydrates











2.3.3 Identify the structures in 2.2.1 in electron micrographs of a liver cell
Electron Micrograph of a Liver Cell


2.3.4 Compare prokaryote and eukaryote cells
Similarities:
Both have a cell membrane
Both contain ribosomes
Both have DNA and cytoplasm

Differences:













2.3.5 State three differences between plant and animal cells
Labelled Diagram of a Generalised Plant Cell




2.3.6 Outline two roles of extracellular components
Plants
The cell wall in plants is made from cellulose secreted from the cell, which serves the following functions:
Provides support and mechanical strength for the cell (maintains cell shape)
Prevents excessive water uptake by maintaining a stable, turgid state
Serves as a barrier against infection by pathogens

Animals
The extracellular matrix (ECM) is made from glycoproteins secreted from the cell, which serve the
following functions:
Provides support and anchorage for cells
Segregates tissues from one another
Regulates intercellular communication by sequestering growth factors
2.4 - Membranes
2.4.1 Draw and label a diagram to show the structure of membranes


2.4.2 Explain how the hydrophilic and hydrophobic properties of phospholipids help to maintain the structure
of cell membranes
Structure of Phospholipids
Consist of a polar head (hydrophilic) made from glycerol and phosphate
Consist of two non-polar fatty acid tails (hydrophobic)

Arrangement in Membrane
Phospholipids spontaneously arrange in a bilayer
Hydrophobic tail regions face inwards and are shielded from the surrounding polar fluid while the two
hydrophilic head regions associate with the cytosolic and extracellular environments respectively

Structural Properties of Phospholipid Bilayer
Phospholipids are held together in a bilayer by hydrophobic interactions (weak associations)
Hydrophilic / hydrophobic layers restrict entry and exit of substances
Phospholipids allow for membrane fluidity / flexibility (important for functionality)
Phospholipids with short or unsaturated fatty acids are more fluid
Phospholipids can move horizontally or occasionally laterally to increase fluidity
Fluidity allows for the breaking / remaking of membranes (exocytosis / endocytosis)

2.4.3 List the functions of membrane proteins

Transport: Protein channels (facilitated) and protein pumps (active)
Receptors: Peptide-based hormones (insulin, glucagon, etc.)
Anchorage: Cytoskeleton attachments and extracellular matrix
Cell recognition: MHC proteins and antigens
Intercellular joinings: Tight junctions and plasmodesmata
Enzymatic activity: Metabolic pathways (e.g. electron transport chain)

2.4.4 Define diffusion and osmosis
Diffusion:
The net movement of particles from a region of high concentration to a region of low concentration
(along the gradient) until equilibrium

Osmosis:
The net movement of water molecules across a semi-permeable membrane from a region of low solute
concentration to a region of high solute concentration until equilibrium is reached

2.4.5 Explain passive transport across membranes in terms of simple diffusion and facilitated diffusion


The plasma membrane is semi-permeable and selective in what can cross
Substances that move along the concentration gradient (high to low) undergo passive transport and do
not require the expenditure of energy (ATP)

Simple diffusion:
Small, non-polar (lipophilic) molecules can freely diffuse across the membrane

Facilitated diffusion:
Larger, polar substances (ions, macromolecules) cannot freely diffuse and require the assistance of
transport proteins (carrier proteins and channel proteins) to facilitate their movement (facilitated
diffusion)

2.4.6 Explain the role of protein pumps and ATP in active transport across membranes
Active transport is the passage of materials against a concentration gradient (from low to high)
This process requires the use of protein pumps which use the energy from ATP to translocate the
molecules against the gradient
The hydrolysis of ATP causes a conformational change in the protein pump resulting in the forced
movement of the substance
Protein pumps are specific for a given molecule, allowing for movement to be regulated (e.g. to maintain
chemical or electrical gradients)
An example of an active transport mechanism is the Na
+
/K
+
pump which is involved in the generation of
nerve impulses



Types of Membrane Transport


2.4.7 Explain how vesicles are used to transport materials within a cell between the endoplasmic reticulum,
Golgi apparatus and plasma membrane

Polypeptides destined for secretion contain an initial target sequence (a signal recognition peptide) which
directs the ribosome to the endoplasmic reticulum
The polypeptide continues to be synthesised by the ribosome into the lumen of the ER, where the signal
sequence is removed from the nascent chain
The polypeptide within the rough ER is transferred to the golgi apparatus via a vesicle, which forms from
the budding of the membrane
The polypeptide moves via vesicles from the cis face of the golgi to the trans face and may be modified
along the way (e.g. glycosylated, truncated, etc.)
The polypeptide is finally transferred via a vesicle to the plasma membrane, whereby it is either
immediately released (constitutive secretion) or stored for a delayed release in response to some cellular
signal (regulatory secretion = for a more concentrated and more sustained effect)











Overview of Vesicular Transport


2.4.8 Describe how the fluidity of the membrane allows it to change shape, break and reform during
endocytosis and exocytosis
The membrane is principally held together by the relatively weak hydrophobic associations between
phospholipids
This association allows for membrane fluidity and flexibility, as the phospholipids (and to a lesser extent
the proteins) can move about to some extent
This allows for the breaking and remaking of membranes, allowing larger substances access into and out
of the cell (this is an active process)

Endocytosis
The process by which large substances (or bulk amounts of smaller substances) enter the cell without
travelling across the plasma membrane
An invagination of the membrane forms a flask-like depression which envelopes the material; the
invagination is then sealed off forming a vesicle
There are two main types of endocytosis:

Phagocytosis
The process by which solid substances (e.g. food particles, foreign pathogens) are ingested (usually to be
transported to the lysosome for break down)

Pinocytosis
The process by which liquids / solutions (e.g. dissolved substances) are ingested by the cell (allows quick
entry for large amounts of substance)

Exocytosis
The process by which large substances exit the cell without travelling across the plasma membrane
Vesicles (usually derived from the golgi) fuse with the plasma membrane expelling their contents into the
extracellular environment

The Process of Exocytosis































2.5 - Cell Division
Wednesday, July 30, 2014
11:43 AM
2.5.1 Outline the stages in the cell cycle, including interphase (G
1
, S, G
2
), mitosis and cytokinesis
The cell cycle is an ordered set of events that culminates in cell growth and division into two daughter
cells
It can roughly be divided into two main stages:

Interphase
The stage in the development of the cell between two successive M phases
This phase of the cell cycle is a continuum of 3 distinct stages (G
1
, S, G
2
), whereby the cell grows and
matures (G
1
), copies its DNA (S) and prepares for division (G
2
)
Sometimes cells will leave the cell cycle and enter into a quiescent state (G
0
), whereby it becomes
amitotic and no longer divides

M phase
The periods of nuclear division (mitosis) and cytoplasmic division (cytokinesis)

The Cell Cycle M Phase


2.5.2 State that tumours (cancers) are the result of uncontrolled cell division and that these can occur in any
organ or tissue
The cell cycle is controlled by a complex chemical control system that responds to signals both inside and
outside of the cell
Tumor suppressor genes produce proteins which inhibit cell division, while proto-oncogenes produce
proteins that promote growth and division
Mutations to these genes result in uncontrolled cell division, resulting in the formation of a tumour
Tumours can grow in size which causes damage local tissue; they may also spread to other parts of the
body (malignant tumours)
Diseases caused by the growth of tumours are collectively known as cancers







2.5.3State that interphase is an active period in the life of a cell when many metabolic reactions occur, including
protein synthesis, DNA replication and an increase in the number of mitochondria and chloroplasts
Interphase is an active period in the life of a cell - many events need to occur before a cell can successfully
undergo division:
Protein synthesis: The cell needs to synthesise key proteins and enzymes to enable it to grow, copy its
contents and then divide
ATP production: The cell will need to generate sufficient quantities of ATP in order to successfully divide
Increase number of organelles: The cell needs to ensure both daughter cells will have the necessary
numbers of organelles needed to survive
DNA replication: The genetic material must be faithfully duplicated before division (this occurs during
the S phase)

As none of these processes can occur during the M phase, interphase contains growth checkpoints to
ensure division is viable
G
1
: A checkpoint stage before DNA replication during which the cell grows, duplicates organelles,
synthesises proteins and produces ATP
S: The stage during which DNA is replicated
G
2
: A checkpoint stage before division during which the copied DNA is checked for fidelity (mutations)
and final metabolic reactions occur

2.5.4 Describe the events that occur in the four phases of mitosis


Prophase
DNA supercoils, causing chromosomes to condense and become visible under a light microscope
As DNA was replicated during interphase, the chromosomes are each comprised of two genetically
identical sister chromatids joined at a centromere
The centrosomes move to opposite poles of the cell and spindle fibres begin to form between them (in
animals, each centrosome contains 2 centrioles)
The nuclear membrane is broken down and disappears

Metaphase
Spindle fibres from the two centrosomes attach to the centromere of each chromosome
Contraction of the microtubule spindle fibres cause the chromosomes to line up separately along the
centre of the cell (equatorial plane)

Anaphase
Continued contraction of the spindle fibres cause the two sister chromatids to separate and move to the
opposite poles of the cell
Once the two chromatids in a single chromosome separate, each constitutes a chromosome in its own
right


Telophase
Once the two sets of identical chromosomes arrive at the poles, the spindle fibres dissolve and a new
nuclear membrane reforms around each set of chromosomes
The chromosomes decondense and are no longer visible under a light microscope
The division of the cell into two daughter cells (cytokinesis) occurs concurrently with telophase

2.5.5 Explain how mitosis produces two genetically identical nuclei

During interphase (the S phase) the DNA was replicated to produce two copies of genetic material
These two identical DNA molecules are identified as sister chromatids and are held together by a single
centromere
During the events of mitosis (as described in 2.5.4), the sister chromatids are separated and drawn to
opposite poles of the cell
When the cell divides (cytokinesis), the two resulting nuclei will each contain one of each chromatid pair
and thus be genetically identical

2.5.6 State that growth, embryonic development, tissue repair and asexual reproduction involve mitosis
Growth: Multicellular organisms increase their size by increasing their number of cells through mitosis
Asexual reproduction: Certain eukaryotic organisms may reproduce asexually by mitosis (e.g. vegetative
reproduction)
Tissue Repair: Damaged tissue can recover by replacing dead or damaged cells
Embryonic development: A fertilised egg (zygote) will undergo mitosis and differentiation in order to
develop into an embryo




















3.1- Chemical Elements and Water

3.1.1 State that the most frequently occurring chemical elements in living things are carbon, hydrogen, oxygen
and nitrogen
The approximate proportions of the four main elements in living things are:
Carbon (19%) Hydrogen (10%) Oxygen (65%)
Nitrogen (3%)

3.1.2 State that a variety of other elements are needed by living organisms, including sulphur,
calcium, phosphorus, iron and sodium
Outside of the four main elements, living things may contain trace amounts of 20 or so other elements,
including:
Sulphur (0.25%) Calcium (1.5%) Phosphorus (1%)
Iron (0.7%) Sodium (0.15%)

3.1.3 State one role for each of the elements mentioned in 3.1.2
Sulphur (S): Found in certain amino acids (cysteine and methionine), allowing proteins to form
disulphide bonds
Calcium (Ca): Found in bones and teeth, also involved in neurotransmitter release in synapses
Phosphorus (P): Component of nucleic acids and cell membranes
Iron (Fe): Found in haemoglobin (animals), allowing for oxygen transport
Sodium (Na): Involved in the generation of nerve impulses in neurons

3.1.3 Draw and label a diagram showing the structure of water molecules to show their polarity and hydrogen
bond formation
Structure of a Water Molecule:

Water (H
2
O) is made up of two hydrogen atoms covalently bound to an oxygen atom
While this bonding involves the sharing of electrons, they are not shared equally
The oxygen atom, having more protons (+ve), attract the electrons (-ve) more strongly (i.e. the oxygen
has a higher electronegativity)
Thus the oxygen atom becomes slightly negative and the hydrogen atoms become slightly positive

Hydrogen Bonding between Water Molecules
Covalently bonded molecules that have a slight potential charge are said to be polar
The slightly charged regions of the water molecule can attract other polar or charged compounds
Water molecules can associate via weak hydrogen bonds (F/O/N bonding with H)





Structure and Bonding of Water Molecules


3.1.4Outline the thermal, cohesive and solvent properties of water
Thermal Properties
Water has a high specific heat capacity (the measure of energy required to raise the temperature of 1 g of
substance by 1C)
Water has a high heat of vaporisation (amount of energy absorbed per gram as it changes from a liquid to
a gas / vapour)
Water has a high heat of fusion (amount of energy required to be lost to change 1 g of liquid to 1 g of solid
at 0C)
These properties occur as a result of the extensive hydrogen bonding between water molecules - this
allows water to absorb considerable amounts of energy with little change in form (H-bonds need to be
broken first)

Cohesive Properties
Water molecules are strongly cohesive (they tend to stick to one another)
Water molecules will also tend to stick to other molecules that are charged or polar (adhesion)
These properties occur as a result of the polarity of a water molecule and its ability to form hydrogen
bonds with appropriate molecules

Solvent Properties
Water can dissolve many organic and inorganic substances that contain electronegative atoms (such as
fluorine, oxygen and nitrogen)
This occurs because the polar attraction of large quantities of water molecules can sufficiently weaken
intramolecular forces (such as ionic bonds) and result in the dissociation of the atoms

Other Properties
Water is transparent, allowing light to pass through it (important for photosynthesis)
Water expands when frozen, becoming less dense / lighter (important for life on earth - oceans don't
freeze)


3.1.5 Explain the relationship between the properties of water and its use in living organisms as a coolant,
medium for metabolic reactions and transport medium
Coolant
Both plants and animals use the evaporation of water from the surfaces of their bodies to facilitate
cooling (sweating and panting in animals, transpiration from leaves in plants)
Water can be used to carry heat to cooler places in our bodies (countercurrent exchange of thermal
energy)

Medium for Metabolic Reactions
Water can dissolve many organic and inorganic substances to facilitate chemical reactions
Water can also absorb thermal energy released as a by-product of many chemical reactions

Transport Medium
The forces of attraction between water molecules help facilitate the transport of water up the xylem of
plants
Water is an effective transport medium for dissolved substances (in plants, minerals from the soil and
sugars from the leaves can be transported in water through the xylem and phloem respectively; while in
animals, water in the blood is used to transport oxygen, glucose and urea)

Surface Tension
The force of attraction between water molecules makes water sufficiently dense for some smaller
organisms to move along its surface


































3.2 - Carbohydrates, Lipids and Proteins

3.2.1 Distinguish between organic and inorganic compounds
Organic compounds are compounds containing carbon that are found in living things - except hydrogen
carbonates (HCO
3
-
), carbonates (CO
3
2-
) and oxides of carbon (CO, CO
2
)
Inorganic compounds are all other compounds (there are less different inorganic compounds than organic
compounds)


Carbohydrates

Carbohydrates are organic compounds consisting of one or more simple sugars that as monomers follow
the general basic formula of (CH
2
O)
x

Note: Exceptions to this basic formula and the inclusion of other atoms (e.g. N) can occur

3.2.2 Identify glucose and ribose from diagrams showing their structure

Glucose (C
6
H
12
O
6
) Ribose (C
5
H
10
O
5
)


3.2.3 List three examples each of monosaccharides, disaccharides and polysaccharides
Monosaccharides: Glucose, galactose, fructose
Disaccharides: Lactose, maltose, sucrose
Polysaccharides: Cellulose, glycogen, starch

3.2.4 State one function of glucose, lactose and glycogen in animals and of fructose, sucrose and cellulose in
plants
Animals
Glucose: A source of energy which can be broken down to form ATP via cellular respiration
Lactose: A sugar found in the milk of mammals, providing energy for suckling infants
Glycogen: Used by animals for short term energy storage (between meals) in the liver

Plants
Fructose: Found in honey and onions, it is very sweet and a good source of energy
Sucrose: Used primarily as a transportable energy form (e.g. sugar beets and sugar cane)
Cellulose: Used by plant cells as a strengthening component of the cell wall




3.2.5 Outline the role of condensation and hydrolysis in the relationship between monosaccharides, disaccharides
and polysaccharides
Condensation (dehydration) reactions occur when molecules are covalently joined together and water is
formed as a by-product
In carbohydrates, the bond that is formed is called a glycosidic linkage
The opposite of a condensation reaction is a hydrolysis reaction, which requires a water molecule to break
a covalent bond between two subunits
Monosaccharides are single monomers that are joined to form disaccharides, while sugars containing
multiple subunits (more than 10) are called polysaccharides

A Condensation Reaction between Two Monosaccharides



Lipids

Lipids are a group of organic molecules that are insoluble in water but soluble in non-polar organic
solvents
Common lipids include triglycerides (fats and oils), phospholipids and steroids

3.2.6 Identify fatty acids from diagrams showing their structure

General Structure Saturated (no double bonds) Unsaturated (double
bonds)


3.2.7Outline the role of condensation and hydrolysis in the relationship between fatty acids, glycerol and
triglycerides
A condensation reaction occurs between the three hydroxyl groups of glycerol and the carboxyl groups of
three fatty acids
This reaction forms a triglyceride (and three molecules of water)
The bond between the glycerol and the fatty acids is an ester linkage
When one of the fatty acids is replaced by a phosphate group and phospholipid is formed
Hydrolysis reactions will, in the presence of water, break these molecules down into their constituent
subunits






Formation of a Triglyceride


3.2.8 State three functions of lipids
Structure: Phospholipids are a main component of cell membranes
Hormonal signalling: Steroids are involved in hormonal signalling (e.g. estrogen, progesterone,
testosterone)
Insulation: Fats in animals can serve as heat insulators while sphingolipids in the myelin sheath (of
neurons) can serve as electrical insulators
Protection: Triglycerides may form a tissue layer around many key internal organs and provide
protection against physical injury
Storage of energy: Triglycerides can be used as a long-term energy storage source

3.2.9 Compare the use of carbohydrates and lipids in energy storage
Similarities:
Complex carbohydrates (e.g. polysaccharides) and lipids both contain a lot of chemical energy and can be
used for energy storage
Complex carbohydrates and lipids are both insoluble in water - they are not easily transported
Carbohydrates and lipids both burn cleaner than proteins (they do not yield nitrogenous wastes)

Differences:
Lipid molecules contain more energy per gram than carbohydrates (about twice as much)
Carbohydrates are more readily digested than lipids and release their energy more rapidly
Monosaccharides and disaccharides are water soluble and easier to transport to and from storage sites
than lipids
Animals tend to use carbohydrates primarily for short-term energy storage, while lipids are used more for
long-term energy storage
Carbohydrates are stored as glycogen in animals while lipids are stored as fats (in plants carbohydrates
are stored as cellulose and lipids as oils)
Lipids have less effect on osmotic pressure within a cell than complex carbohydrates

Proteins

Proteins are large organic compounds made of amino acids arranged in a linear chain
The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code



3.2.10 Identify amino acids from diagrams showing their structure

Generalised Structure of an Amino Acid


3.2.11 Outline the role of condensation and hydrolysis in the relationship between amino acids and
polypeptides
A condensation reaction occurs between the amino group (NH
2
) of one amino acid and the carboxylic acid
group (COOH) of another amino acid
This reaction forms a dipeptide (plus a molecule of water) that is held together by a peptide bond
Multiple amino acids can be joined together to form a polypeptide chain
In the presence of water, polypeptides can be broken down into individual amino acids via hydrolysis
reactions

Formation of a Dipeptide











3.3. - DNA Structure

3.3.1 Outline DNA nucleotide structure in terms of a sugar (deoxyribose), base and phosphate



3.3.2 State the names of the four bases in DNA
The four bases in DNA are:
Adenine Guanine Thymine Cytosine

Adenine and guanine are purines (double ring bases)
Thymine and cytosine are pyrimidines (single ring bases)

3.3.3 Outline how the DNA nucleotides are linked together by covalent bonds into a single strand

Nucleotides a linked into a single strand via a condensation reaction
The phosphate group (attached to the 5'-C of the sugar) joins with the hydroxyl (OH) group attached to
the 3'-C of the sugar
This results in a phosphodiester bond between the two nucleotides and the formation of a water molecule
Successive condensation reactions between nucleotides results in the formation of a long single strand




3.3.4 Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds
Two polynucleotide chains of DNA are held together by hydrogen bonds between complementary base
pairs
Adenine pairs with thymine (A=T) via two hydrogen bonds
Guanine pairs with cytosine (G=C) via three hydrogen bonds

Thymine Adenine Cytosine Guanine


In order for bases to be facing each other and thus able to pair, the two strands must run in opposite
directions (i.e. they are anti-parallel)
As the polynucleotide chain lengthens, the atoms that make up the molecule will arrange themselves in
an optimal energy configuration
This position of least resistance results in the double-stranded DNA twisting to form a double helix with
approximately 10 - 15 bases per twist

3.3.5 Draw and label a simple diagram of the molecular structure of DNA












3.4 - DNA Replication

3.4.1 Explain DNA replication in terms of unwinding of the double helix and separation of the strands by helicase,
followed by the formation of the new complementary strands by DNA polymerase
Helicase
Unwinds the DNA and separates the two polynucleotide strands by breaking the hydrogen bonds
between complementary base pairs
The two separated polynucleotide strands act as templates for the synthesis of new polynucleotide
strands

DNA Polymerase
Synthesises new strands from the two parental template strands
Free deoxynucleoside triphosphates (nucleotides with three phosphate groups) are aligned opposite their
complementary base partner and are covalently bonded together by DNA polymerase to form a
complementary nucleotide chain
The energy for this reaction comes from the cleavage of the two extra phosphate groups

3.4.2 Explain the significance of complementary base pairing in the conservation of the base sequence of DNA
Each of the nitrogenous bases can only pair with its complementary partner (A=T ; G=C)
Consequently, when DNA is replicated by the combined action of helicase and DNA polymerase:
The new strands formed will be identical to the original strands separated from the template
The two DNA molecules formed will be identical to the original molecule

DNA Replication is a Semi-Conservative Process


3.4.3 State that DNA replication is semi-conservative
DNA replication is a semi-conservative process because when a new double-stranded DNA molecule is
formed:
One strand will be from the original molecule
One strand will be newly synthesised









3.5 - Transcription and Translation

3.5.1 Compare the structure of DNA and RNA


3.5.2 Outline DNA transcription in terms of the formation of an RNA strand complementary to the DNA strand by
RNA polymerase
Transcription is the process by which an RNA sequence is produced from a DNA template:
RNA polymerase separates the DNA strands and synthesises a complementary RNA copy from one of the
DNA strands
It does this by covalently bonding ribonucleoside triphosphates that align opposite their exposed
complementary partner (using the energy from the cleavage of the additional phosphate groups to join
them together)
Once the RNA sequence has been synthesised, RNA polymerase will detach from the DNA molecule and
the double helix will reform
The sequence of DNA that is transcribed into RNA is called a gene
Transcription occurs in the nucleus (where the DNA is) and, once made, the mRNA moves to the
cytoplasm (where translation can occur)

Three main types of RNA are predominantly made:
Messenger RNA (mRNA): A transcript copy of a gene used to encode a polypeptide
Transfer RNA (tRNA): A clover leaf shaped sequence that carries an amino acid
Ribosomal RNA (rRNA): A primary component of ribosomes

3.5.3 Describe the genetic code in terms of codons comprised of triplets of bases
The genetic code is the set of rules by which information encoded in mRNA sequences is converted into
proteins (amino acid sequences) by living cells
Codons are a triplet of bases which encodes a particular amino acid
As there are four bases, there are 64 different codon combinations (4 x 4 x 4 = 64)
The order of the codons determines the amino acid sequence for a protein
The coding region always starts with a START codon (AUG) and terminates with a STOP codon











The Genetic Code


The genetic code has the following features:
It is universal - every living thing uses the same code (there are only a few rare and minor exceptions)
It is degenerate - there are only 20 amino acids but 64 codons, so more than one codon may code for the
same amino acid (this allows for silent mutations whereby a change in the DNA sequence does not affect
the polypeptide sequence)

3.5.4 Explain the process of translation, leading to polypeptide formation
Translation is the process of protein synthesis in which the genetic information encoded in mRNA is
translated into a sequence of amino acids in a polypeptide chain
Ribosomes bind to mRNA in the cell's cytoplasm and move along the mRNA molecule in a 5' - 3' direction
until it reaches a start codon (AUG)
Anticodons on tRNA molecules align opposite appropriate codons according to complementary base
pairing (e.g. UAC will align with AUG)
Each tRNA molecule carries a specific amino acid (according to the genetic code)
Ribosomes catalyse the formation of peptide bonds between adjacent amino acids (via a condensation
reaction)
The ribosome moves along the mRNA molecule synthesising a polypeptide chain until it reaches a stop
codon, at this point translation stops and the polypeptide chain is released









The Process of Translation


3.5.5 Explain the relationship between one gene and one polypeptide
A gene is a sequence of DNA which encodes a polypeptide sequence
A gene sequence is converted into a polypeptide sequence via the processes of transcription (making an
mRNA transcript) and translation (polypeptide synthesis)
Translation uses tRNA molecules and ribosomes to join amino acids into a polypeptide chain according to
the mRNA sequence (as read in codons)
The universality of the genetic code means all organisms show the same relationship between genes and
polypeptides (indicating a common ancestry and allowing for transgenic techniques to be employed)
Some proteins may consist of a number of polypeptide chains and thus need multiple genes (e.g.
haemoglobin consists of four polypeptide subunits encoded by two different genes)
When a gene is mutated it may lead to the synthesis of a defective polypeptide, hence affecting protein
function












The 'One Gene - One Polypeptide' Rule


There are two exceptions to the 'one gene - one polypeptide' rule:
Genes encoding for tRNA and rRNA do not code for polypeptide sequences (only mRNA sequences code
for polypeptides)
A single gene may code for multiple polypeptides if alternative splicing occurs (the removal of exons as
well as introns)













3.6 - Enzymes

3.6.1 Define enzyme and active site
Enzyme: A globular protein that increases the rate of a biochemical reaction by lowering the activation
energy threshold (i.e. a biological catalyst)
Active Site: The site on the surface of an enzyme which binds to the substrate molecule

3.6.2 Explain enzyme-substrate specificity
Active site and substrate complement each other in terms of both shape and chemical properties (e.g.
opposite charges)
Binding to the active site brings the substrate into close physical proximity, creating an enzyme-substrate
complex
The enzyme catalyses the conversion of the substrate into a product (or products), creating an enzyme-
product complex
As the enzyme is not consumed in the reaction, it can continue to work once the product dissociates
(hence only low concentrations are needed)

Enzyme-Substrate Specificity


Lock and Key Model
Enzymes and substrates share specificity (a given enzyme will only interact with a small number of
specific substrates that complement the active site)
This explanation of enzyme-substrate interaction is described as the 'lock and key' model (a lock only
opens in response to a specific key)

3.6.3 Explain the effects of temperature, pH and substrate concentration on enzyme activity
Temperature
Low temperatures result in insufficient thermal energy for the activation of a given enzyme-catalysed
reaction to be achieved
Increasing the temperature will increase the speed and motion of both enzyme and substrate, resulting in
higher enzyme activity
This is because a higher kinetic energy will result in more frequent collisions between enzyme and
substrate
At an optimal temperature (may differ for different enzymes), the rate of enzyme activity will be at its
peak
Higher temperatures will cause enzyme stability to decrease, as the thermal energy disrupts the hydrogen
bonds holding the enzyme together
This causes the enzyme (particularly the active site) to lose its shape, resulting in a loss of enzyme activity
(denaturation)


pH
Changing the pH will alter the charge of the enzyme, which in turn will protein solubility and may change
the shape of the molecule
Changing the shape or charge of the active site will diminish its ability to bind to the substrate, abrogating
enzyme function
Enzymes have an optimum pH (may differ between enzymes) and moving outside of this range will
always result in a diminished rate of reaction

Substrate Concentration
Increasing substrate concentration will increase the activity of a particular enzyme
More substrate means there is an increased likelihood of enzyme and substrate colliding and reacting,
such that more reactions will occur and more products will be formed in a given time period
After a certain point, the rate of reaction will cease to rise regardless of further increases to substrate
concentration, as the environment has become saturated with substrate and all enzymes are bound and
reacting (V
max
)

Factors Affecting Enzyme Activity


3.6.4 Define denaturation
Denaturation is a structural change in a protein that results in the loss (usually permanent) of its biological
properties
Heat and pH are two agents which may cause denaturation of an enzyme

Denaturation









3.6.5 Explain the use of lactase in the production of lactose-free milk

Lactose is a disaccharide of glucose and galactose which can be broken down by the enzyme lactase
Historically, mammals exhibit a marked decrease in lactase production after weaning - leading to lactose
intolerance (incidence is particularly high in Asian / African / Native American / Aboriginal populations)
Lactose-free milk can be produced by purifying lactase (e.g. from yeast or bacteria) and binding it to an
inert substance (such as alginate beads)
Milk passed over this immobilised enzyme will become lactose-free

The generation of lactose-free milk can be used in a number of ways:
As a source of milk for lactose-intolerant individuals
As a means to increase the sweetness of milk (glucose and galactose are sweeter in flavour), thus
negating the need for artificial sweeteners
As a way of reducing the crystallisation of ice-creams (glucose and galactose are more soluble than
lactose)
As a means of shortening the production time for yogurts or cheese (bacteria ferment glucose and
galactose more readily than lactose)
















3.7 - Cell Respiration

3.7.1 Define cell respiration
Cell respiration is the controlled release of energy from organic compounds in cells to form ATP
(adenosine triphosphate)

3.7.2 State that, in cell respiration, glucose in the cytoplasm is broken down by glycolysis into pyruvate, with a
small yield of ATP
Glycolysis is the breakdown of one molecule of glucose (6C) into two molecules of pyruvate (2 x 3C) with a
small net yield of ATP (2 molecules of ATP)
This process also results in the reduction of two hydrogen acceptors (NAD
+
) to form 2 molecules of NADH
+ H
+


3.7.3 Explain that, during anaerobic cell respiration, pyruvate can be converted in the cytoplasm into lactate, or
ethanol and carbon dioxide, with no further yield of ATP
Anaerobic respiration occurs in the absence of a ready supply of oxygen (e.g. during intense physical
activity, when oxygen reserves are depleted)
In order to generate the small amounts of energy provided by glycolysis, the end product (pyruvate) must
be converted into another substance before more glucose can be used
This is because the conversion of pyruvate replenishes the levels of the hydrogen acceptor (NAD
+
) needed
for glycolysis to occur

Anaerobic Respiration


The conversion of pyruvate occurs in the cytoplasm of the cell and the products are:
Lactate (3C) in animal cells
Ethanol (2C) and carbon dioxide (CO
2
) in plants, fungi (e.g. yeast) and bacteria
The conversion of pyruvate into ethanol and CO
2
is also known as fermentation

3.7.4 Explain that, during aerobic cell respiration, pyuvate can be broken down in the mitochondrion into carbon
dioxide and water with a large yield of ATP
Aerobic respiration occurs in the presence of oxygen and takes place in the mitochondrion
Pyruvate is broken down into carbon dioxide and water and a large amount of ATP is formed (34 - 36
molecules)
Although this process begins with glycolysis (to break down glucose into pyruvate), glycolysis does not
require oxygen and is an anaerobic process

Anaerobic versus Aerobic Respiration






























3.8 - Photosynthesis

3.8.1 State that photosynthesis involves the conversion of light energy into chemical energy
Photosynthesis is the process by which plants synthesize organic compounds (e.g. glucose) from
inorganic compounds (CO
2
and H
2
O) in the presence of sunlight


Photosynthesis is a two-step process:
The light dependent reactions convert the light energy into chemical energy (ATP)
The light independent reactions use the chemical energy to synthesize organic compounds (e.g. glucose)
The organic molecules produced in photosynthesis can be used in cellular respiration to provide the
energy needed by the organism

3.8.2 State that light from the Sun is composed of a range of wavelengths (colours)

Sunlight is white light, made up of all the colours of the visible spectrum
Colours are different wavelengths of light and range from ~ 400 nm - 700 nm
The colours of the visible spectrum are (from longer to shorter wavelength):
Red Orange Yellow Green Blue Indigo Violet (R.O.Y.G.B.I.V)

3.8.3 State that chlorophyll is the main photosynthetic pigment
Chlorophyll is the main site of light absorption in the light dependent stage of photosynthesis
There are a number of different chlorophyll molecules, each with their own distinct absorption spectra
(the spectrum of light absorbed by a substance)
When chlorophyll absorbs light energy, they release electrons which are used to make ATP (chemical
energy)
Chlorophyll and Photosystems

3.8.4 Outline the difference in absorption of red, green and blue light by chlorophyll
The main colours of light absorbed by chlorophyll are red and blue light
The main colour of light not absorbed (it is reflected) by chlorophyll is green light
This explains why leaves are green - excepting when the presence of other pigmented substances (e.g.
anthocyanins) produces a different colour
Deciduous trees stop producing high amounts of chlorophyll in the winter (due to insufficient sunlight),
allowing other photosynthetic pigments (e.g. xanthophylls, carotenoids) to come to the fore, which
changes the colour of the leaf




3.8.5 State that light energy is used to produce ATP, and to split water molecules (photolysis) to form oxygen and
hydrogen

The first part of photosynthesis is the light dependent reaction, which uses light energy to make ATP

Light Dependent Reaction
Light stimulates chlorophyll to release electrons, which results in the production of ATP
Light energy also splits water molecules (photolysis), producing oxygen and hydrogen
The hydrogen is taken up by a hydrogen carrier (NADP
+
) to form NADPH
The splitting of water also releases electrons, which replace those lost by the chlorophyll
The ATP and hydrogen (NADPH) are taken to the site of the light independent reactions

3.8.6 State that ATP and hydrogen (derived from the photolysis of water) are used to fix carbon molecules to
make organic molecules
The second part of photosynthesis is the light independent reaction, which makes organic compounds
from the products of the light dependent reactions


Light Independent Reaction
ATP and hydrogen (carried by NADPH) are products of the light dependent reactions
They are used to fix carbon molecules together (add CO
2
to basic carbon compounds)
This allows for the production of more complex organic molecules (e.g. sugars)
These organic molecules can then be stored to use in cellular respiration as required

3.8.7 Explain that the rate of photosynthesis can be measured directly by the production of oxygen or the uptake
of carbon dioxide, or indirectly by an increase in biomass
The rate of photosynthesis can be measured by changes in the amounts of inputs (CO
2
) or outputs (O
2
or
glucose) of the photosynthesis equation
Water cannot be measured as it is involved in a number of essential processes besides photosynthesis
(e.g. condensation and hydrolysis reactions)


Measuring CO
2
Uptake
CO
2
uptake can be measured by placing a plant in an enclosed space with water
Carbon dioxide interacts with the water molecules, producing bicarbonate and hydrogen ions, which
increases the acidity of the resulting solution
The change in pH can therefore provide a measure of CO
2
uptake by a plant (increased CO
2
uptake = more
alkaline pH)

Measuring O
2
Production
O
2
production can be measured by submerging a plant in an enclosed space with water attached to a
sealed gas syringe
Any oxygen gas produced will bubble out of solution and can be measured by a change in water level (via
the position of the meniscus)

Measuring Biomass (Indirect)
Glucose production can be indirectly measured by a change in a plant's biomass (weight)
This requires the plant to be completely dehydrated prior to weighing to ensure the change in biomass
reflects a change in organic matter and not water content
An alternative method for measuring glucose production is to determine the change in starch levels in a
plant (glucose is stored as starch)
Starch can be identified via iodine staining (resulting solution turns purple) and quantitated using a
colorimeter

3.8.8 Outline the effect of temperature, light intensity and carbon dioxide concentration on the rate of
photosynthesis
Temperature
Photosynthesis is controlled by enzymes, which are sensitive to temperature
As temperature increases, the rate of photosynthesis will increase as reagents have greater kinetic energy
and are more likely to react
Above a certain temperature, the rate of photosynthesis will decrease as essential enzymes begin to
denature

Light Intensity
As light intensity increases, the rate of photosynthesis will increase up until a certain point, when
photosynthesis is proceeding at its maximum rate
Further increases to light intensity will have no effect on photosynthesis (the rate will plateau), as
chlorophyll are saturated by light
Different wavelengths of light will have different effects on the rate of photosynthesis (e.g. green light
will not be used)

CO
2
Concentration
As the concentration of carbon dioxide increases, the rate of photosynthesis will increase up until a
certain point, when photosynthesis is proceeding at its maximum rate
Further increases to carbon dioxide concentration will have no effect on photosynthesis (the rate will
plateau), as the enzymes responsible for carbon fixation become saturated





Factors Affecting the Rate of Photosynthesis











































4.1 - Chromosomes, Genes, Alleles, Mutations

4.1.1 State that eukaryotic chromosomes are made of DNA and protein
Eukaryotic chromosomes consist of DNA wrapped around histone proteins
This forms the basic structure of the nucleosome, which is packed together to form chromatin (in a
'beads on a string' arrangement)
Chromatin will supercoil and condense during prophase to form chromosomes that can be
visualised under a light microscope
Prokaryotic DNA is not wrapped around proteins and is thus considered to be 'naked'

Arrangement of DNA into chromosomes


4.1.2 Define gene, allele and genome
Gene: A heritable factor that controls a specific characteristic, consisting of a length of DNA occupying a
particular position on a chromosome (locus)
Allele: One specific form of a gene, differing from other alleles by one or a few bases only and occupying
the same locus as other alleles of the gene
Genome: The whole of the genetic information of an organism

4.1.3 Define gene mutation
Gene mutation: A change in the nucleotide sequence of a section of DNA coding for a particular feature

4.1.4 Explain the consequence of a base substitution mutation in relation to the process of transcription and
translation using the example of sickle cell anaemia
Cause of Sickle Cell Anaemia
A base substitution mutation is the change of a single base in a sequence of DNA, resulting in a change to
a single mRNA codon during transcription
In the case of sickle cell anaemia, the 6th codon for the beta chain of haemoglobin is changed from GAG
to GTG (on the non-coding strand)
This causes a change in the mRNA codon (GAG to GUG), resulting in a single amino acid change of
glutamic acid to valine (Glu to Val)
DNA: GAG to GTG (non-coding strand)
mRNA: GAG to GUG
Amino Acid: Glu to Val
The amino acid change alters the structure of haemoglobin, causing it to form fibrous, insoluble strands
This causes the red blood cell to adopt a sickle shape









Normal Red Blood Cell Sickle Cell


Consequences of Sickle Cell Anaemia
The insoluble haemoglobin cannot effectively carry oxygen, causing individual to feel constantly tired
The sickle cells may accumulate in the capillaries and form clots, blocking blood supply to vital organs and
causing a myriad of health problems
Also causes anaemia (low RBC count), as the sickle cells are destroyed more rapidly than normal red blood
cells
Sickle cell anaemia occurs in individuals who have two copies of the codominant 'sickle cell' allele (i.e.
homozygotes)
Heterozygous individuals have increased resistance to malaria due to the presence of a single 'sickle cell'
allele (heterozygous advantage)

Sickle Cell Anaemia










4.2- Meiosis

4.2.1 State that meiosis is a reduction division of a diploid nucleus to form haploid nuclei
Meiosis is the process by which sex cells (gametes) are made in the reproductive organs:
Most sexually reproducing animals are diploid - meaning they have two copies of every
chromosome (one of maternal origin, one of paternal origin)
In order to reproduce, these organisms need to make gametes that are haploid (have only one
copy of each chromosome)
Fertilisation of two haploid gametes (egg + sperm) will result in the formation of a diploid zygote
that will grow into a new organism

Meiosis consists of two cell divisions:
The first division is a reduction division of the diploid nucleus to form haploid nuclei
The second division separates sister chromatids (this division is necessary because meiosis is
preceded by interphase, wherein DNA is replicated)

4.2.2 Define homologous chromosomes
Homologous chromosomes are chromosomes that share:
The same structural features (e.g. same size, same banding pattern, same centromere position)
The same genes at the same loci positions (while genes are the same, alleles may be different)

4.2.3 Outline the process of meiosis, including pairing of homologous chromosomes and crossing over, followed
by two divisions, which results in four haploid cells
The process of meiosis involves two divisions, both of which follow the same basic stages as mitosis
(prophase, metaphase, anaphase and telophase)
Meiosis is preceded by interphase, which includes the replication of DNA (S phase) to create
chromosomes with genetically identical sister chromatids



Meiosis I
Homologous chromosomes must first pair up in order to be sorted into separate haploid daughter cells
In prophase I, homologous chromosomes undergo a process called synapsis, whereby homologous
chromosomes pair up to form a bivalent (or tetrad)
The homologous chromosomes are held together at points called chiasma (singular: chiasmata)
Crossing over of genetic material between non-sister chromatids can occur at these points,
resulting in new gene combinations (recombination)

The remainder of meiosis I involves separating the homologous chromosomes into separate daughter
cells
In metaphase I, the homologous pairs line up along the equator of the cell
In anaphase I, the homologous chromosomes split apart and move to opposite poles
In telophase I, the cell splits into two haploid daughter cells as cytokinesis happens concurrently

Meiosis II
In meiosis II, the sister chromatids are divided into separate cells
In prophase II, spindle fibres reform and reconnect to the chromosomes
In metaphase II, the chromosomes line up along the equator of the cell
In anaphase II, the sister chromatids split apart and move to opposite poles
In telophase II, the cell splits in two as cytokinesis happens concurrently

Because sister chromatids may no longer be genetically identical as a result of potential recombination,
the process of meiosis results in the formation of four genetically distinct haploid daughter cells

4.2.4 Explain that non-disjunction can lead to a change in chromosome number, illustrated by reference to Down
syndrome (trisomy 21)
Non-disjunction refers to the chromosomes failing to separate correctly, resulting in gametes with one
extra, or one missing, chromosome (aneuploidy)
The failure of the chromosomes to separate may either occur via:
Failure of homologues to separate during Anaphase I (resulting in four affected daughter cells)
Failure of sister chromatids to separate during Anaphase II (resulting in two affected daughter
cells)

Non-Disjunction



Individuals with Down syndrome have three copies of chromosome 21 (trisomy 21)
One of the parental gametes had two copies of chromosome 21 as a result of non-disjunction
The other parental gamete was normal and had a single copy of chromosome 21
When the two gametes fused during fertilisation, the resulting zygote had three copies of
chromosome 21, leading to Down syndrome

4.2.5 State that, in karyotyping, chromosomes are arranged in pairs according to their structure
A karyotype is a visual profile of all the chromosomes in a cell
The chromosomes are arranged into homologous pairs and displayed according to their structural
characteristics

Human Male Karyotype


Karyotyping involves:
Harvesting cells (usually from foetus or white blood cells of adults)
Chemically inducing cell division, then halting it during mitosis when chromosomes are condensed
and thus visible
The stage during which mitosis is halted will determine whether chromosomes appear with sister
chromatids
Staining and photographing chromosomes, before arranging them according to structure


4.2.6 State that karyotyping is performed using cells collected by chorionic villus sampling or amniocentesis, for
pre-natal diagnosis of chromosome abnormalities
Pre-natal karyotyping is often used to:
Determine the gender of an unborn child (via identification of sex chromosomes)
Test for chromosomal abnormalities (e.g. aneuploidies resulting from non-disjunction)

Amniocentesis
A needle is inserted through the abdominal wall, into the amniotic cavity in the uterus, and a
sample of amniotic fluid containing foetal cells is taken
It can be done at ~ 16th week of pregnancy, with a slight chance of miscarriage (~0.5%)

Chorionic Villus Sampling
A tube is inserted through the cervix and a tiny sample of the chorionic villi (contains foetal cells)
from the placenta is taken
It can be done at ~ 11th week of pregnancy, with a slight risk of inducing miscarriage (~1%)

Amniocentesis Chorionic Villus Sampling


4.2.7 Analyse a human karyotype to determine gender and whether non-disjunction has occurred
Every cell in the human body has 46 chromosomes (except anucleate red blood cells and haploid
gametes)
Males (X,Y) and females (X,X) can be differentiated on the basis of their sex chromosomes
Non-disjunction during gamete formation can lead to individuals with an abnormal number of
chromosomes (aneuploidy)
These disorders can be classified according to the chromosome number affected and the number of
chromosomes present






























4.3 Theoretical Genetics

4.3.1 Define genotype, phenotype, dominant allele, recessive allele, codominant alleles, locus, homozygous,
heterozygous, carrier and test cross
Genotype: The allele combination of an organism
Phenotype: The characteristics of an organism (determined by a combination of genotype and
environmental factors)
Dominant Allele: An allele that has the same effect on the phenotype whether it is present in the
homozygous or heterozygous state
Recessive Allele: An allele that only has an effect on the phenotype when present in the homozygous
state
Codominant Alleles: Pairs of alleles that both affect the phenotype when present in a heterozygote
Locus: The particular position on homologous chromosomes of a gene
Homozygous: Having two identical alleles of a gene
Heterozygous: Having two different alleles of a gene
Carrier: An individual that has one copy of a recessive allele that causes a genetic disease in individuals
that are homozygous for this allele
Test Cross: Testing a suspected heterozygote by crossing it with a known homozygous recessive

4.3.2 Determine the genotypes and phenotypes of the offspring of a monohybrid cross using a Punnett grid
A genetic cross is a means of determining the genetic characteristics of potential offspring based on the
genetic characteristics of the prospective parents
A monohybrid cross determines the allele combinations of offspring for one particular gene only (HL
students may refer to topic 10.2 for dihybrid crosses)


Monohybrid crosses can be calculated according to the following steps:
Step 1: Designate characters to represent the alleles
Capital letter for dominant allele, lower case letter for recessive allele

Step 2: Write down the genotype and phenotype of the parents
This is the P generation (parental generation)

Step 3: Write down the genotype of the parental gametes
These will be haploid as a result of meiotic division

Step 4: Use a Punnett grid to work out the potential gamete combinations
As fertilisation is random, all combinations have an equal probability

Step 5: Write out the genotype and phenotype ratios of potential offspring
This is the F
1
generation (first filial generation)
Subsequent generations through interbreeding labeled F
2
, F
3
, etc.

Note: The genotypic and phenotypic ratios calculated are only probabilities



4.3.3 State that some genes have more than two alleles (multiple alleles)
Some genes have more than two alleles for a given trait (e.g. the ABO blood group system)
The alleles which are not recessive may either:
Share codominance (be expressed equally in the phenotype)
Share incomplete dominance (neither is fully expressed in the phenotype, resulting in blending)
Demonstrate a dominance order (e.g. allele A > allele B > allele C)

4.3.4 Describe ABO blood groups as an example of codominance and multiple alleles
When assigning alleles for codominance, the convention is to use a common letter to represent dominant
and recessive and use superscripts to represent the different codominant alleles
I stands for immunoglobulin (antigenic protein on blood cells)
A and B stand for the codominant variants

The ABO gene has three alleles: I
A
, I
B
and i
I
A
and I
B
are codominant, wherease i is recessive (no antigenic protein is produced)
Codominance means that both I
A
and I
B
alleles will be expressed within a given phenotype

The genotypes and phenotypes of the ABO blood groups are:


The ABO Blood Group System


4.3.5 Explain how sex chromosomes control gender by referring to the inheritance of X and Y chromosomes in
humans
Humans have 23 pairs of chromosomes for a total of 46 (excluding instances of aneuploidy)
The first 22 pairs are autosomes - each chromosome pair possesses the same genes and structural
features
The 23rd pair of chromosomes are heterosomes (or sex chromosomes) and determine gender
Females are XX - they possess two X chromosomes
Males are XY - they posses one X chromosome and a much shorter Y chromosome

The Y chromosome contains the genes for developing male sex characteristic - hence the father is always
responsible for determining gender
If the male sperm contains the X chromosome the growing embryo will develop into a girl
If the male sperm contains a Y chromosome the growing embryo will develop into a boy
In all cases the female egg will contain an X chromosome (as the mother is XX)

Because the X and Y chromosomes are of a different size, they cannot undergo crossing over /
recombination during meiosis
This ensures that the gene responsible for gender always remains on the Y chromosome, meaning that
there is always ~ 50% chance of a boy or girl









4.3.6 State that some genes are present on the X chromosome and absent from the shorter Y chromosome

The Y chromosome is much shorter than the X chromosome and contains only a few genes
Includes the SRY sex-determination gene and a few others (e.g. hairy ears gene)

The X chromosome is much longer and contains several genes not present on the Y chromosome
Includes the genes for haemophilia and red-green colour blindness

In human females, only one of the X chromosomes remains active throughout life
The other is packaged as heterochromatin to form a condensed Barr body
This inactivation is random and individual to each cell, so heterozygous women will be a mosaic -
expressing both alleles via different cells



4.3.6 Define sex linkage
Sex linkage refers to when a gene controlling a characteristic is found on a sex chromosome (and so we
associate the trait with a predominant gender)
Sex-linked conditions are usually X-linked, as very few genes exist on the shorter Y chromosome

4.3.7 Describe the inheritance of colour blindness and haemophilia as examples of sex linkage
Colour blindness and haemophilia are both examples of X-linked recessive conditions
The gene loci for these conditions are found on the non-homologous region of the X chromosome (they
are not present of the Y chromosome)
As males only have one allele for this gene they cannot be a carrier for the condition
This means they have a higher frequency of being recessive and expressing the trait
Males will always inherit an X-linked recessive condition from their mother
Females will only inherit an X-linked recessive condition if they receive a recessive allele from both
parents

When assigning alleles for sex-linked traits the convention is to write the allele as a superscript to the sex
chomosome (usually X)
Haemophilia: X
H
= unaffected ; X
h
= affected
Colour Blindness: X
A
= unaffected ; X
a
= affected

Male and Female Genotypes for a Sex-Linked Condition


4.3.8 State that a human female can be homozygous or heterozygous with respect to sex-linked genes
As human females have two X chromosomes (and therefore two alleles for any given X-linked gene), they
can be either homozygous or heterozygous
Males only have one X chromosome (and therefore only one allele) and are hemizygous

4.3.9 Explain that female carriers are heterozygous for X-linked recessive alleles
An individual with a recessive allele for a disease condition that is masked by a normal dominant allele is
said to be a carrier
Carriers are heterozygous and can potentially pass the trait on to the next generation, but do not suffer
from the defective condition themselves
Females can be carriers for X-linked recessive conditions because they have two X chromosomes - males
(XY) cannot be carriers
Because a male only inherits an X chromosome from his mother, his chances of inheriting the disease
condition from a carrier mother is greater





4.3.10 Predict the genotypic and phenotypic ratios of offspring of monohybrid crosses involving any of the above
patterns of inheritance
Autosomal Dominance / Recessive
Choose a letter where the upper and lower case forms are easily distinguishable (e.g. E/e, A/a, B/b)
Use the capital letter for the dominant allele and the lower case letter for the recessive allele
Example:


Codominance
Choose a letter to denote the general trait encoded by the gene (capital = dominant, lower case =
recessive)
Use different superscript letters (capitals) to represent the different codominant alleles
Example:


X-linked Recessive
Use a capital "X" to denote the X chromosome
Choose a superscript letter to represent the trait (capital = dominant, lower case = recessive)
Example:


4.3.11 Deduce the genotype and phenotype of individuals in pedigree charts
A pedigree is a chart of the genetic history of a family over several generations
Males are represented as squares, while females are represented as circles
Shaded symbols means an individual is affected by a condition, while an unshaded symbol means they are
unaffected
A horizontal line between a man and woman represents mating and resulting children are shown as
offshoots to this line

Autosomal Dominance
All affected individuals must have at least one affected parent
If two parents are unaffected, all offspring must be unaffected (homozygous recessive)
If two parents are affected, they may have offspring who are unaffected (if parents are heterozygous)

Autosomal Recessive
If two parents show a trait, all children must also show the trait (homozygous recessive)
An affected individual may have two normal parents (if parents are both heterozygous carriers)

X-Linked Recessive
If a female shows the trait, so must all sons as well as her father
The disorder is more common in males











Identifying Modes of Inheritance

































4.4 - Genetic Engineering and Biotechnology

4.4.1 Outline the use of polymerase chain reaction (PCR) to copy and amplify minute quantities of DNA

PCR is a way of producing large quantites of a specific target sequence of DNA
It is useful when only a small amount of DNA is avaliable for testing
E.g. crime scene samples of blood, semen, tissue, hair, etc.

PCR occurs in a thermal cycler and involves a repeat procedure of 3 steps:
Denaturation: DNA sample is heated to separate it into two strands
Annealing: DNA primers attach to opposite ends of the target sequence
Elongation: A heat-tolerant DNA polymerase (Taq) copies the strands

One cycle of PCR yields two identical copies of the DNA sequence
A standard reaction of 30 cycles would yield 1,073,741,826 copies of DNA (2
30
)

4.4.2 State that, in gel electrophoresis, fragments of DNA can move in an electric field and are separated
according to their size
Gel electrophoresis is a technique which is used to separate fragments of DNA according to size

Samples of fragmented DNA are placed in the wells of an agarose gel
The gel is placed in a buffering solution and an electrical current is passed across the gel
DNA, being negatively charged (due to phosphate), moves to the positive terminus (anode)
Smaller fragments are less impeded by the gel matrix and move faster through the gel
The fragments are thus separated according to size
Size can be calculated (in kilobases) by comparing against a known industry standard

4.4.3 State that gel electrophoresis of DNA is used in DNA profiling
DNA profiling is a technique by which individuals are identified on the basis of their respective DNA
profiles
Within the non-coding region of an individual's genome, there exists satellite DNA - long stretches of DNA
made up of repeating elements called short tandem repeats (STRs)
These repeating sequences can be excised to form fragments, by cutting with a variety of restriction
endonucleases (which cut DNA at specific sites)
As individuals all have a different number of repeats in a given sequence of satellite DNA, they will all
generate unique fragment profiles
These different profiles can be compared using gel electrophoresis

DNA Profiling Using STR Analysis


4.4.4 Describe the application of DNA profiling to determine paternity and also in forensic investigation
A DNA sample is collected (blood, saliva, semen, etc.) and amplified using PCR
Satellite DNA (non-coding) is cut with specific restriction enzymes to generate fragments
Individuals will have unique fragment lengths due to the variable length of their short tandem repeats
(STR)
The fragments are separated with gel electrophoresis (smaller fragments move quicker through the gel)
The DNA profile can then be analysed according to need

Two applications of DNA profiling are:
Paternity testing (comparing DNA of offspring against potential fathers)
Forensic investigations (identifying suspects or victims based on crime-scene DNA)





4.4.5 Analyse DNA profiles to draw conclusions about paternity or forensic investigations
Paternity Testing: Children inherit half of their alleles from each parent and thus should possess a
combination of their parents alleles
Forensic Investigation: Suspect DNA should be a complete match with the sample taken from a crime
scene if a conviction is to occur

Paternity Test Forensic Investigation


4.4.6 Outline three outcomes of the sequencing of the complete human genome
The Human Genome Project (HGP) was an international cooperative venture established to sequence the
3 billion base pair (~25,000 genes) in the human genome
The outcomes of this project include:
Mapping: We now know the number, location and basic sequence of human genes
Screening: This has allowed for the production of specific gene probes to detect sufferers and carriers of
genetic disease conditions
Medicine: With the discovery of new proteins and their functions, we can develop improved treatments
(pharmacogenetics and rational drug design)
Ancestry: It will give us improved insight into the origins, evolution and historical migratory patterns of
humans

With the completion of the Human Genome Project in 2003, researcher have begun to sequence the
genomes of several non-human organisms

4.4.7 State that, when genes are transferred between species, the amino acid sequence of polypeptides
translated from them is unchanged because the genetic code is universal
The genetic code is universal, meaning that for every living organism the same codons code for the same
amino acids (there are a few rare exceptions)
This means that the genetic information from one organism could be translated by another (i.e. it is
theoretically transferable)

4.4.8 Outline a basic technique used for gene transfer involving plasmids, a host cell (bacterium, yeast or other
cell), restriction enzymes (endonucleases) and DNA ligase
DNA Extraction
A plasmid is removed from a bacterial cell (plasmids are small, circular DNA molecules that can exist and
replicate autonomously)
A gene of interest is removed from an organism's genome using a restriction endonuclease which cut at
specific sequences of DNA
The gene of interest and plasmid are both amplified using PCR technology



Digestion and Ligation
The plasmid is cut with the same restriction enzyme that was used to excise the gene of interest
Cutting with certain restriction enzymes may generate short sequence overhangs ("sticky ends") that
allow the the two DNA constructs to fit together
The gene of interest and plasmid are spliced together by DNA ligase creating a recombinant plasmid

Transfection and Expression
The recombinant plasmid is inserted into the desired host cells (this is called transfection for eukaryotic
cells and transformation for prokaryotic cells)
The transgenic cells will hopefully produce the desired trait encoded by the gene of interest (expression)
The product may need to subsequently be isolated from the host and purified in order to generate
sufficient yield

Treating Haemophilia via the Isolation of Human Factor IX Clotting Protein from Transgenic Sheep Milk


4.4.9 State two examples of current uses of genetically modified crops or animals
Crops
Engineering crops to extend shelf life of fresh produce
Tomatoes (Flavr Savr) have been engineered to have an extended keeping quality by switching off the
gene for ripening and thus delaying the natural process of softening of fruit
Engineering of crops to provide protection from insects
Maize crops (Bt corn) have been engineered to be toxic to the corn borer by introducing a toxin gene from
a bacterium (Bacillus thuringiensis)

Animals
Engineering animals to enhance production
Sheep produce more wool when engineered with the gene for the enzyme responsible for the production
of cysteine - the main amino acid in the keratin protein of wool
Engineering animals to produce desired products
Sheep engineered to produce human alpha-1-antitrypsin in their milk can be used to help treat individuals
suffering from hereditary emphysema





4.4.10 Discuss the potential benefits and potential harmful effects of one example of genetic modification
Example: Maize introduced with a bacterial gene encoding a toxin to the European Corn Borer (i.e. Bt
Corn)

Potential Benefits
Allows for the introduction of a characteristic that wasn't present within the gene pool (selective breeding
could not have produced desired phenotype)
Results in increased productivity of food production (requires less land for comparable yield)
Less use of chemical pesticides, reducing the economic cost of farming
Can now grow in regions that, previously, may not have been viable (reduces need for deforestation)

Potential Harmful Effects
Could have currently unknown harmful effects (e.g. toxin may cause allergic reactions in a percentage of
the population)
Accidental release of transgenic organism into the environment may result in competition with native
plant species
Possibility of cross pollination (if gene crosses the species barrier and is introduced to weeds, may have a
hard time controlling weed growth)
Reduces genetic variation / biodiversity (corn borer may play a crucial role in local ecosystem)

4.4.11 Define clone
A clone is a group of genetically identical organisms or a group of cells derived from a single parent cell

4.4.12 Outline a technique for cloning using differentiated animal cells
Somatic Cell Nuclear Transfer (SCNT) is a method of reproductive cloning using differentiated animal cells
A female animal (e.g. sheep) is treated with hormones (such as FSH) to stimulate the development of
eggs
The nucleus from an egg cell is removed (enucleated), thereby removing the genetic information from the
cell
The egg cell is fused with the nucleus from a somatic (body) cell of another sheep, making the egg cell
diploid
An electric shock is delivered to stimulate the egg to divide, and once this process has begun the egg is
implanted into the uterus of a surrogate
The developing embryo will have the same genetic material as the sheep that contributed the diploid
nucleus, and thus be a clone

Different Uses of Cloning



4.4.13 Discuss the ethical issues of therapeutic cloning in humans
Refer to Topic 2.1.10 for an outline of uses for therapeutic cloning in humans

Arguments for Therapeutic Cloning
May be used to cure serious diseases or disabilities with cell therapy (replacing bad cells with good ones)
Stem cell research may pave the way for future discoveries and beneficial technologies that would not
have occurred if their use had been banned
Stem cells can be taken from embryos that have stopped developing and would have died anyway (e.g.
abortions)
Cells are taken at a stage when the embryo has no nervous system and can arguably feel no pain

Arguments Against Therapeutic Cloning
Involves the creation and destruction of human embryos (at what point do we afford the right to life?)
Embryonic stem cells are capable of continued division and may develop into cancerous cells and cause
tumors
More embryos are generally produced than are needed, so excess embryos are killed
With additional cost and effort, alternative technologies may fulfil similar roles (e.g. nuclear
reprogramming of differentiated cell lines)





















5.1 - Communities & Ecosystems

5.1.1 Define species, habitat, population, community, ecosystem and ecology
Species: A group of organisms that can interbreed and produce fertile, viable offspring
Habitat: The environment in which a species normally lives or the location of a living organism
Population: A group of organisms of the same species who live in the same area at the same time
Community: A group of populations living and interacting with each other in an area
Ecosystem: A community and its abiotic environment
Ecology: The study of relationships between living organisms and between organisms and their
environment

5.1.2 Distinguish between autotroph and heterotroph
Autotroph: An organism that synthesises its organic molecules from simple inorgance substances (e.g.
CO
2
and nitrates) - autotrophs are producers
Heterotroph: An organism that obtains organic molecules from other organisms - heterotrophs
are consumers

5.1.3 Distinguish between consumers, detritivores and saprotrophs
Consumer: An organism that ingests other organic matter that is living or recently killed
Detritivore: An organism that ingests non-living organic matter
Saprotroph: An organism that lives on or in non-living organic matter, secreting digestive enzymes into it
and absorbing the products of digestion

5.1.4 Describe what is meant by a food chain, giving three examples, each with at least three linkages (four
organisms)
A food chain shows the linear feeding relationships between species in a community
The arrows represent the transfer of energy and matter as one organism is eaten by another (arrows point
in the direction of energy flow)
The first organism in the sequence is the producer, followed by consumers (1, 2, 3, etc.)

Examples of Food Chains


5.1.5 Describe what is meant by a food web
A food web is a diagram that shows how food chains are linked together into more complex feeding
relationships within a community
There can be more than one producer in a food web, and consumers can occupy multiple positions
(trophic levels)

5.1.6 Define trophic level
An organism's trophic level refers to the position it occupies in a food chain
Producers always occupy the first trophic level, while saprotrophs would generally occupy the ultimate
trophic level of a given food chain or food web
The trophic levels in a community are:


5.1.7 Deduce the trophic levels of organisms in a food web and food chain
The trophic level of an organism can be determined by counting the number of feeding relationships
preceding it and adding one (producer always first)
Trophic Level = Number of arrows (in sequence) before organism + 1
In food webs, a single organism may occupy multiple trophic levels

5.1.8 Construct a food web containing up to 10 organisms, using appropriate information
Hint: When constructing a food web, always try to position an organism relative to its highest trophic
level (to keep all arrows pointing in same direction)

Food web (trophic levels in red)


5.1.9 State that light is the initial energy source for almost all communities
All green plants, and some bacteria, are photo-autotrophic - they use light as a source of energy for
synthesising organic molecules
This makes light the initial source of energy for almost all communities
Some bacteria are chemo-autotrophic and use energy derived from chemical processes (e.g. nitrogen-
fixating bacteria)

5.1.10 Explain the energy flow in a food chain
Energy enters most communities as light, where it is absorbed by autotrophs (e.g. plants) and converted
into chemical energy via photosynthesis
Energy then gets passed to the primary consumer (herbivore) when they eat the plant, and then gets
passed to successive consumers (carnivores) as they are eaten in turn
Only ~10% of energy is passed from one trophic level to the next, the rest is lost
Because ~90% of energy is lost between trophic levels, the number of trophic levels are limited as energy
flow is reduced at higher levels

Summary of Energy Flow in a Food Chain


5.1.11 State that energy transformations are never 100% efficient
When energy transformations take place in living organisms the process is never 100% efficient
Typically, energy transformations in living things are ~10% efficient, with about 90% of the energy lost
between trophic levels
This energy may be lost as heat, be used up during cellular respiration, be excreted in faeces or remain
unconsumed as the uneaten part of food

5.1.12 Explain the reason for the shape of pyramids of energy

A pyramid of energy is a graphical representation of the amount of energy of each tropic level in a food
chain
They are expressed in units of energy per area per time (e.g. kJ m
2
year
-1
)
Pyramids of energy will never appear inverted as some of the energy stored in one source is always lost
when transferred to the next source
This is an application of the second law of thermodynamics
Each level of the pyramid of energy should be approximately one tenth the size of the level preceding it,
as energy transformations are ~10% efficient

5.1.13 Explain that energy enters and leaves ecosystems, but nutrients must be recycled
The movement of energy and matter through ecosystems are related because both occur by the transfer
of substances through feeding relationships
However, energy cannot be recycled and an ecosystem must be powered by a continuous influx of new
energy from an external source (e.g the sun)
Nutrients refer to material required by an organism, and are constantly being recycled within an
ecosystem as food (either living or dead)
The autotrophic activities of the producers (e.g. plants) produce organic materials from inorganic sources,
which are then fed on by the consumers
When heterotrophic organisms die, these inorganic nutrients are returned to the soil to be reused by the
plants (as fertiliser)
Thus energy flows through ecosystems, while nutrients cycle within them

5.1.14 State that saprotrophic bacteria and fungi (decomposers) recycle nutrients
In order for organisms to grow and reproduce, they need a supply of the elements of which they are made
The saprotrophic activity of decomposers (certain bacteria and fungi), free inorganic materials from the
dead bodies and waste products of organisms, ensuring a continual supply of raw materials for the
producers (which can then be ingested by consumers)
Thus saprotrophic bacteria and fungi play a vital role in recycling nutrients within an ecosystem
































5.2 - The Greenhouse Effect

5.2.1 Draw and label a diagram of the carbon cycle to show the processes involved
There are four main 'pools' of carbon in the environment:
Atmosphere Biosphere Sediments Ocean

There are a number of processes by which carbon can be cycled between these pools:
Photosynthesis: Atmospheric carbon dioxide is removed and fixed as organic compounds (e.g.
sugars)
Feeding: In which organic carbon is moved from one trophic level to the next in a food chain
Respiration: All organisms (including plants) metabolise organic compounds for energy, releasing
carbon dioxide as a by-product
Fossilization: In which carbon from partially decomposed dead organisms becomes trapped in
sediment as coal, oil and gas (fossil fuels)
Combustion: During the burning of fossil fuels and biomass
In oceans, carbon can be reversibly trapped and stored as limestone (storage happens more readily
at low temperatures)

The Carbon Cycle


5.2.2 Analyse the changes in concentration of atmospheric carbon dioxide using historical records
Recent Trends:
Atmospheric carbon dioxide concentrations have been measured at the Mauna Loa atmospheric
observatory in Hawaii from 1958 and has since been measured at a number of different locations
globally
The data shows that there is an annual cycle in CO
2
concentrations which may be attributable to
seasonal factors, but when data from the two hemispheres is incorporated, it suggests that
atmospheric CO
2
levels have risen steadily in the past 30 years




Long Term Estimates:
Carbon dioxide concentration changes over a long period of time have been determined by a
variety of sources, including analysing the gases trapped in ice (and thus providing a historical
snapshot of atmospheric concentrations)
Data taken from the Vostok ice core in Antarctica shows that fluctuating cycles of
CO
2
concentrations over thousands of years appear to correlate with global warm ages and ice
ages
It is compelling to note that CO
2
levels appear to be currently higher than at any time in the last
400,000 years

Recent and Long-term Changes in Carbon Dioxide Concentration

Mauna Loa CO
2
Data (last 50 years) Vostok Ice Core Data - CO
2
vs Temperature (last
400,000 years)

5.2.3 Explain the relationship between the rises in concentrations of atmospheric carbon dioxide, methane
and oxides of nitrogen and the enhanced greenhouse effect
The greenhouse effect is a natural process whereby the earth's atmosphere behaves like a greenhouse to
create the moderate temperatures to which life on earth has adapted (without the greenhouse effect,
temperatures would drop significantly every night)
The incoming radiation from the sun is short-wave ultraviolet and visible radiation
Some of this radiation is reflected by the earth's surface back into space as long-wave infrared
radiation
Greenhouse gases absorb this infrared radiation and re-reflect it back to the earth as heat,
resulting in increased temperatures (the greenhouse effect)
The Greenhouse Effect

The enhanced greenhouse effect refers to the suggested link between the increase in greenhouse gas
emissions by man and changes in global temperatures and climate conditions
The main greenhouse gases are water vapour, carbon dioxide (CO
2
), methane (CH
4
) and oxides of
nitrogen (e.g. NO
2
)
While these gases occur naturally, man is increasing greenhouse gas emissions via a number of processes,
including:
Deforestation (less trees) Industrialisation (more combustion) Increased
farming / agriculture (more methane)
With increases in greenhouse gas emission, it is thought that the atmospheric temperature may increase
and threaten the viability of certain ecosystems, although this link is still being debated

5.2.4 Outline the precautionary principle
The precautionary principle states that when a human-induced activity raises a significant threat of harm
to the environment or human health, then precautionary measures should be taken even if there is no
scientific consensus regarding cause and effect
Because the global climate is a complex phenomena with many emergent properties, and is based
on time frames well beyond human lifespans, it is arguably impossible to provide appropriate
scientific evidence for enhanced global warming before consequences escalate to potentially dire
levels
According to the precautionary principle, the onus falls on those contributing to the enhanced
greenhouse effect to either reduce their input or demonstrate their actions do not cause harm -
this makes it the responsibility of governments, industries, communities and even the individual
The precautionary principle is the reverse of previous historical practices whereby the burden of
proof was on the individual advocating action

5.2.5 Evaluate the precautionary principle as a justification for strong action in response to the threats posed
by the enhanced greenhouse effect
Arguments for Action
Risks of inaction are potentially severe, including increased frequency of severe weather
conditions (e.g. droughts, floods) and rising sea levels
Higher temperatures will increase the spread of vector-borne diseases
Loss of habitat will result in the extinction of some species, resulting in a loss of biodiversity
Changes in global temperature may affect food production, resulting in famine in certain regions
The effects of increased temperatures (e.g. rising sea levels) could destroy certain industries which
countries rely on, leading to poverty
All of these consequences could place a far greater economic burden on countries than if action
were taken now
These factors would increase competition for available resources, potentially leading to increased
international tensions

Arguments for Inaction
Cutting greenhouse emissions may delay economic growth in developing countries, increasing
poverty in these regions
Very difficult to police - what level of action would be considered sufficient on a global scale in the
current absence of scientific consensus?
Boycotting trade with non-compliant countries could negatively effect economies and create
international tensions
No guarantee that human intervention will be sufficient to alter global climate patterns
Money and industrial practices that may be used to develop future technologies may be lost due to
restrictions imposed by carbon reduction schemes
Carbon reduction schemes will likely result in significant job losses from key industries, retraining
workers will require significant time and money

5.2.6 Outline the consequences of a global temperature rise on arctic ecosystems
Increases in global temperature pose a credible threat to arctic ecosystems, including:
Changes in arctic conditions (reduced permafrost, diminished sea ice cover, loss of tundra to
coniferous forests)
Rising sea levels
Expansion of temperate species increasing competition with native species (e.g. red fox vs arctic
fox)
Decomposition of detritus previously trapped in ice will significantly increase greenhouse gas
levels (potentially exacerbating temperature changes)
Increased spread of pest species and pathogens (threatening local wildlife)
Behavioural changes in native species (e.g. hibernation patterns of polar bears, migration of birds
and fish, seasonal blooms of oceanic algae)
Loss of habitat (e.g. early spring rains may wash away seal dens)
Extinction and resultant loss of biodiversity as food chains are disrupted


















5.3 - Populations

5.3.1 Outline how population size is affected by natality, immigration, mortality and emigration
The change in population size over a given period of time can be summarised by the following
equation: Population Size = ( N + I ) - ( M + E )


Natality: Increases to population size through reproduction (i.e. births)
Immigration: Increases to population size from external populations
Mortality: Decreases to population size as a result of death (e.g. predation, senescence)
Emigration: Decreases to population size as a result of loss to external populations

5.3.2 Draw and label a graph showing the sigmoid (S-shaped) population growth curve
Population Growth Curve





5.3.3 Explain reasons for the exponential growth phase, the plateau phase and the transitional phase
between these two phases
Initially, population growth may be slow, as there is a shortage of reproducing individuals which may be
widely dispersed
As numbers increase and reproduction gets underway, three stages of population growth are seen:

Exponential Growth Phase
There is a rapid increase in population size / growth as the natality rate exceeds the mortality rate
This is because there is abundant resources (e.g. food, shelter and water) and limited
environmental resistance (disease and predation uncommon)

Transitional Phase
As the population continues to grow, eventually competition increases as availability of resources
are reduced
Natality starts to fall and mortality starts to rise, leading to a slower rate of population increase

Plateau Phase
Eventually the increasing mortality rate equals the natality rate and population size becomes
constant
The population has reached the carrying capacity (K) of the environment
Limited resources, predation and disease all contribute to keeping the population size balanced
While the population size at this point may not be static, it will oscillate around the carrying
capacity to remain relatively even (no net growth)

5.3.4 List three factors that sets limits to population increase
Every species has limits to the environmental conditions it can endure and must remain within
appropriate levels for population growth to occur
Some of these factors are density-dependent, while others are unrelated to the density of the
population

Factors affecting population growth:







5.4 - Evolution

5.4.1 Define evolution
Evolution is the cumulative change in the heritable characteristics of a population

5.4.2 Outline the evidence for evolution provided by the fossil record, selective breeding of domesticated
animals and homologous structures
Something provides evidence for evolution when it demonstrates a change in characteristics from an
ancestral form

The Fossil Record

A fossil is the preserved remains or traces of any organism from the remote past
Fossil evidence may be either:
Direct (body fossils): Bones, teeth, shells, leaves, etc.
Indirect (trace fossils): Footprints, tooth marks, tracks, burrows, etc.

The totality of fossils (both discovered and undiscovered) is known as the fossil record
The fossil record reveals that, over time, changes have occurred in features of organisms living on
the planet (evolution)
Moreover, different kinds of organisms do not occur randomly but are found in rocks of particular
ages in a consistent order (law of fossil succession)
This suggests that changes to an ancestral species was likely responsible for the appearance of
subsequent species (speciation via evolution)
Furthermore, the occurrence of transitional fossils demonstrate the intermediary forms that
occurred over the evolutionary pathway taken within a single genus

While fossils may provide clues regarding evolutionary processes and ancestral relationships, it is
important to realise that the fossil record is incomplete
Fossilization requires a unusual combination of specific circumstances to occur, meaning there are
many gaps in the fossil record
Only the hard parts of an organism are preserved and often only fragments of fossilized remains
are discovered

Selective Breeding

Selective breeding of domesticated animals is an example of artificial selection, which occurs when man
directly intervenes in the breeding of animals to produce desired traits in offspring
As a result of many generations of selective breeding, domesticated breeds can show significant variation
compared to the wild counterparts, demonstrating evolutionary changes in a much shorter time frame
than might have occurred naturally
Examples of selective breeding include:
Breeding horses for speed (race horses) versus strength and endurance (draft horses)
Breeding dogs for herding (sheepdogs), hunting (beagles) or racing (greyhounds)
Breeding cattle for increased meat production or milk
Breeding zebras in an attempt to retrieve the colouration gene from the extinct Quagga

Homologous Structures
Comparative anatomy of groups of animals or plants shows certain structural features are basically
similar, implying a common ancestry
Homologous structures are those that are similar in shape in different types of organisms despite
being used in different ways
An example is the pentadactyl limb structure in vertebrates, whereby many animals show a
common bone composition, despite the limb being used for different forms of locomotion (e.g.
whale fin for swimming, bat wing for flying, human hand for manipulating tools, horse hoof for
galloping, etc.)
This illustrates adaptive radiation (divergent evolution) as a similar basic plan has been adapted to
suit various environmental niches
The more similar the homologous structures between two species are, the more closely related
they are likely to be


Homologous Structures (Pentadactyl Limb)


5.4.3 State that populations tend to produce more offspring than the environment can support
The Malthusian dilemma states that populations tend to multiply geometrically, while food
sources multiply arithmetically
Hence populations tend to produce more offspring than the environment can support

5.4.4 Explain that the consequence of the potential overproduction of offspring is a struggle for survival

When there is an abundance of resources, a population can achieve a J-curve maximum growth
rate (biotic potential)
However, with more offspring there will be less resources available to other members of the
population (environmental resistance)
This will lead to competition for available resources and a struggle for survival
Intraspecific competition occurs when members of the same species compete for the same
resources in an ecosystem (e.g. light, food, water)
It is density dependent, as the available resources must be shared among members of the species
Competition that occurs between different species for resources is interspecific
The result of this competition will be an increase in the mortality rate, leading to an S-curve
growth rate as the population approaches the carrying capacity (K)

5.4.5 State that members of a species show variation
Members of a species show variation, which can manifest itself in one of two forms:
Discontinuous variation: A type of variation usually controlled by a single gene, which leads to
distinct classes (e.g. ABO blood group in humans)
Continuous variation: A type of variation controlled by many genes, which leads to a range of
characteristics (e.g. skin pigmentation in humans)

There are three primary sources of variation within a given population
Gene mutations (a permanent change to the genetic composition of an individual)
Gene flow (the movement of genes from one population to another via immigration and
emigration)
Sexual reproduction (the combination of genetic materials from two parental sources)

5.4.6 Explain how reproduction promotes variation within a species
There are three primary ways by which sexual reproduction promotes variation within a species:

Independent Assortment
During metaphase I, when homologous chromosomes line up at the equator, the paired
chromosomes can randomly arrange themselves in one of two orientations (paternal left /
maternal right OR maternal left / paternal right)
When the chromosomes separate in anaphase I, the final gametes will differ depending on
whether they got the maternal or paternal chromosome
Independent assortment of chromosomes creates 2
n
different gamete combinations (n = haploid
number of chromosomes)



Crossing Over
During prophase I, when homologous chromosomes pair up as bivalents, genetic information can
be exchanged between non-sister chromatids
The further apart two genes are on a chromosome, the more likely they are to recombine
Crossing over greatly increases the number of potential gamete variations by creating new genetic
combinations



Random Fertilisation
Fertilisation results from the fusion of gametes from a paternal and maternal source, resulting in
offspring that have a combination of paternal and maternal traits
Because fertilisation is random, offspring will receive different combinations of traits every time,
resulting in near infinite genetic variability

5.4.7 Explain how natural selection leads to evolution
The theory of natural selection was postulated by Charles Darwin (and also independently by Alfred
Wallace) who described it as 'survival of the fittest'
There is genetic variation within a population (which can be inherited)
There is competition for survival (populations tend to produce more offspring than the
environment can support)
Environmental selective pressures lead to differential reproduction
Organisms with beneficial adaptations will be more suited to their environment and more likely to
survive to reproduce and pass on their genes
Over generations there will be a change in allele frequency within a population (evolution)

5.4.8 Explain two examples of evolution in response to environmental change; one must be antibiotic
resistance in bacteria
Example 1: Staphylococcus aureus (associated with a variety of conditions, including skin and lung
infections)
Variation: Antibiotic resistance (some strains have a drug-resistant gene ; other strains do not)
Environmental change: Exposure to antibiotic (methicillin)
Response: Methicillin-susceptible S. aureus (MSSA) die, whereas methicillin-resistant S. aureus (MRSA)
survive and can pass on their genes
Evolution: Over time, the frequency of antibiotic resistance in the population increases (drug-resistant
gene can also be transferred by conjugation)




Example 2: Peppered Moth (Biston betularia)
Variation: Colouration (some moth have a light colour, while others are a darker melanic colour)
Environmental change: Pollution from industrial activities caused trees to blacken with soot during the
Industrial Revolution
Response: Light coloured moths died from predation, whereas melanic moths were camouflaged and
survived to pass on their genes
Evolution: Over time, the frequency of the melanic form increased (with improved industrial practices,
the lighter variant has become more common)






















































5.5 - Classification
Wednesday, July 30, 2014
11:46 AM
5.5.1 Outline the binomial system of nomenclature
The binomial system of nomenclature was devised by Carolus Linnaeus as a way of classifying organisms
that was globally recognised and could demonstrate evolutionary relationships between organisms (and
thus allow for the prediction of features closely related organisms may share)
According to the binomial system of nomenclature, every organism is designated a scientific name with
two parts:
Genus is written first and is capitalised (e.g. Homo)
Species follows and is written in lower case (e.g. Homo sapiens)
Some species may also have a sub-species designation (e.g. Homo sapiens sapiens)
Conventions: When typing, the name should be in italics; whereas when hand writing, it should
be underlined

5.5.2 List the seven levels in the hierarchy of taxa - kingdom, phylum, class, order, family, genus and species
- using an example from two different kingdoms for each level
When classifying living things, organisms are grouped according to a series of hierarchical taxa - the more
similar their characteristics, the closer the grouping
Classification of Animals and Plants


5.5.3 Distinguish between the following phyla of plants, using simple external recognition features:
bryophyta, filicinophyta, coniferophyta and angiospermophyta




5.5.4 Distinguish between the following phyla of animals, using simple external recognition features:
porifera, cnidaria, platyhemlnthes, annelida, mollusca and arthropoda




5.5.5 Apply and design a key for up to eight organisms
A dichotomous key is a method of identification whereby a group of organisms are sequentially divided
into two categories until all are identified

Example of a Dichotomous Key:
Organism is a plant ...................................................................................... Go to Q2
Organism is not a plant (animal) ................................................................ Go to Q5
Has no 'true' leaves or roots ....................................................................... Bryophyta
Has leaves and roots ................................................................................... Go to Q3
Has no seeds (sporangia) .......................................................................... Filicinophyta
Has seeds ..................................................................................................... Go to Q4
Has no flowers ............................................................................................. Coniferophyta
Has flowers ................................................................................................... Angiospermophyta
Asymmetrical body plan ............................................................................. Porifera
Symmetrical body plan ............................................................................... Go to Q6
Has radial symmetry ................................................................................... Cnidaria
Has bilateral symmetry ............................................................................... Go to Q7
Has no anus ................................................................................................. Platyhelminthes
Has an anus ................................................................................................. Go to Q8
Has a segmented body .............................................................................. Go to Q9
Has no visible body segmentation ........................................................... Mollusca
Have an exoskeleton ................................................................................. Arthropoda
Have no exoskeleton ................................................................................. Annelida

Dichotomous Key as a Flowchart























7.1 - DNA Structure

7.1.1 Describe the structure of DNA, including the antiparallel strands, 3' - 5' linkages and hydrogen bonding
between purines and pyrimidines
The carbon atoms in deoxyribose are numbered, with the nitrogenous bases attach to C
1
and the
phopshate group is attached to C
5

Nucleotides are joined by a covalent phosphodiester bond between the C
5
phosphate group and
the C
3
hydroxyl group
Hence one nucleotide strand runs 5' - 3'
The nitrogenous bases interact via hydrogen bonding (complementary base pairing)
Adenine (A) and thymine (T) share 2 hydrogen bonds
Guanine (G) and cytosine (C) share 3 hydrogen bonds
In order for the bases to associate (i.e. face each other), one strand must run antiparallel to the
other (this antiparallel strand runs 3' - 5')
Double stranded DNA forms a double helix, with 10 nucleotides per turn and the structure
containing both major and minor grooves

Structural Organisation of DNA


7.1.2 Outline the structure of nucleosomes

The DNA double helix contains major and minor grooves on its outer diameter, which
expose chemical groups that can form hydrogen bonds
The DNA of eukaryotes associates with proteins called histones
DNA is wound around an octamer of histones (146 bases and 1.65 turns of the helix per octamer)
The octamer and DNA combination is secured to a H1 histone, forming a nucleosome







7.1.3 State that nucleosomes help to supercoil DNA and help to regulate transcription
Nucleosomes serve two main functions:
They protect DNA from damage
They allow long lengths of DNA to be packaged (supercoiled) for mobility during mitosis / meiosis
When supercoiled, DNA is not accessible for transcription
Cells will have some segments of DNA permanently supercoiled (heterochromatin) and these
segments will differ between different cell types

7.1.4 Distinguish between unique or single copy genes and highly repetitive sequences in nuclear DNA


7.1.5 State that eukaryotic genes contain introns and exons
Intron: A non-coding sequence of DNA within a gene (intervening sequence) that is cut out by enzymes
when RNA is made into mature mRNA
Exon: The part of the gene which codes for a protein (expressing sequence)
Eukaryotic DNA contains introns but prokaryotic DNA does not













7.2 - DNA Replication

7.2.1 State that DNA replication occurs in a 5' - 3' direction
DNA replication is semi-conservative, meaning that a new strand is synthesised from an original
template strand
DNA replication occurs in a 5' - 3' direction, in that new nucleotides are added to the C3 hydroxyl
group such that the strand grows from the 3' end
This means that the DNA polymerase enzyme responsible for adding new nucleotides moves
along the original template strand in a 3' - 5' direction

Direction of DNA Replication


7.2.2 Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA
polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates
DNA replication is semi-conservative and occurs during the S phase of interphase
Helicase unwinds and separates the double stranded DNA by breaking the hydrogen bonds
between base pairs
This occurs at specific regions (replication origins), creating a replication fork of two
polynucleotide strands in antiparallel directions
RNA primase synthesises a short RNA primer on each template strand to provide an attachment
and initiation point for DNA polymerase III
DNA polymerase III adds deoxynucleoside triphosphates (dNTPs) to the 3' end of the
polynucleotide chain, synthesising in a 5' - 3' direction
The dNTPs pair up opposite their complementary base partner (adenine pairs with thymine
; guanine pairs with cytosine)
As the dNTPs join with the DNA chain, two phosphates are broken off, releasing the energy
needed to form a phosphodiester bond
Synthesis is continuous on the strand moving towards the replication fork (leading strand)
Synthesis is discontinuous on the strand moving away from the replication fork (lagging strand)
leading to the formation of Okazaki fragments
DNA polymerase I removes the RNA primers and replaces them with DNA
DNA ligase joins the Okazaki fragments together to create a continuous strand





Overview of DNA Replication


7.2.3 State that DNA replication is initiated at many points in eukaryotic chromosomes
Because eukaryotic genomes are (typically) much larger than prokaryotic genomes, DNA
replication is initiated at many points simultaneously in order to limit the time required for DNA
replication to occur
The specific sites at which DNA unwinding and initiation of replication occurs are called origins of
replication and form replication bubbles
As replication bubbles expand in both directions, they eventually fuse together, two generate two
separate semi-conservative double strands of DNA
Origins of Replication

















7.3 - Transcription

7.3.1 State that transcription is carried out in a 5' - 3' direction
Transcription is carried out in a 5' - 3' direction (of the new RNA strand)

7.3.2 Distinguish between the sense and antisense strands of DNA
DNA consists of two polynucleotide strands, only one of which is transcribed into RNA
The antisense strand is transcribed into RNA
Its sequence will be complementary to the RNA sequence and will be the "DNA version" of the
tRNA anticodon sequence
The sense strand is not transcribed into RNA
Its sequence will be the "DNA version" of the RNA sequence (identical except for T instead of U)

7.3.3 Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA
polymerase, nucleoside triphosphates and the terminator
A gene is a sequence of DNA which is transcribed into RNA and contain three main parts:
Promoter: Responsible for the initiation of transcription (in prokaryotes, a number of genes may
be regulated by a single promoter - this is an operon)
Coding Sequence: The sequence of DNA that is actually transcribed (may contain introns in
eukaryotes)
Terminator: Sequence that serves to terminate transcription (mechanism of termination differs
between prokaryotes and eukaryotes)

Transcription is the process by which a DNA sequence (gene) is copied into a complementary RNA
sequence and involves a number of steps:
RNA polymerase binds to the promoter and causes the unwinding and separation of the DNA
strands
Nucleoside triphosphates (NTPs) bind to their complementary bases on the antisense strand
(uracil pairs with adenine, cytosine pairs with guanine)
RNA polymerase covalently binds the NTPs together in a reaction that involves the release of two
phosphates to gain the required energy
RNA polymerase synthesises an RNA strand in a 5' - 3' direction until it reaches the terminator
At the terminator, RNA polymerase and the newly formed RNA strand both detach from the
antisense template, and the DNA rewinds
Many RNA polymerase enzymes can transcribe a DNA sequence sequentially, producing a large
number of transcripts
Post-transcriptional modification is necessary in eukaryotes











Overview of Transcription


7.3.4 State that eukaryotic RNA needs the removal of introns to form mature mRNA
Euakaryotic genes may contain non-coding sequences called introns that need to be removed
before mature mRNA is formed
The process by which introns are removed is called splicing
The removal of exons (alternative splicing) can generate different mRNA transcripts (and different
polypeptides) from a single gene















7.4 - Translation

7.4.1 Explain that each tRNA molecule is recognised by a tRNA-activating enzyme that binds a specific amino
acid to the tRNA using ATP for energy

Each different tRNA molecule has a unique shape and chemical composition that is recognised by
a specific tRNA-activating enzyme
The enzyme (aminoacyl-tRNA synthetase) first binds the amino acid to a molecule of ATP (to form
an amino acid-AMP complex linked by a high energy bond)
The amino acid is then transferred to the 3'-end of the appropriate tRNA, attaching to a terminal
CCA sequence on the acceptor stem and releasing the AMP molecule
The tRNA molecule with an amino acid attached is thus said to be 'charged' and is now capable of
participating in translation
The energy in the bond linking the tRNA molecule to the amino acid will be used in translation to
form a peptide bond between adjacent amino acids

7.4.2 Outline the structure of ribosomes, including protein and RNA composition, large and small subunits,
three tRNA binding sites and mRNA binding sites
Ribosomes are made of protein (for stability) and ribosomal RNA (rRNA - for catalytic activity)
They consist of two subunits:
The small subunit contains an mRNA binding site
The large subunit contains three tRNA binding sites - an aminacyl (A) site, a peptidyl (P) site and an
exit (E) site
Ribosomes can be either found freely in the cytosol or bound to the rough ER (in eukaryotes)
Ribosomes differ in size in eukaryotes and prokaryotes (eukaryotes = 80S ; prokaryotes = 70S)

7.4.3 State that translation consists of initiation, elongation, translocation and termination
Translation occurs in four main steps:
Initiation: Involves the assembly of an active ribosomal complex
Elongation: New amino acids are brought to the ribosome according to the codon sequence
Translocation: Amino acids are translocated to a growing polypeptide chain
Termination: At certain "stop" codons, translation is ended and the polypeptide is released



7.4.4 State that translation occurs in a 5' - 3' direction
The start codon (AUG) is located at the 5' end of the mRNA sequence and the ribosome moves
along it in the 3' direction
Hence translation occurs in a 5' - 3' direction

7.4.5 Draw and label a diagram showing the structure of a peptide bond between two amino acids


7.4.6 Explain the process of translation, including ribosomes, polysomes, start codons and stop codons
Pre-Initiation:
Specific tRNA-activating enzymes catalyse the attachment of amino acids to tRNA molecules,
using ATP for energy

Initiation:
The small ribosomal subunit binds to the 5' end of mRNA and moves along it until it reaches the
start codon (AUG)
Next, the appropriate tRNA molecule binds to the codon via its anticodon (according to
complementary base pairing)
Finally, the large ribosomal subunit aligns itself to the tRNA molecule at its P-site and forms a
complex with the small ribosomal subunit

Elongation:
A second tRNA molecule pairs with the next codon in the ribosomal A-site
The amino acid in the P-site is covalently attached via a peptide bond to the amino acid in the A-
site

Translocation:
The ribosome moves along one codon position, the deacylated tRNA moves into the E-site and is
released, while the tRNA bearing the dipeptide moves into the P-site
Another tRNA molecules attaches to the next codon in the newly emptied A-site and the process is
repeated
The ribosome moves along the mRNA sequence in a 5' - 3' direction, synthesising a polypeptide
chain
Multiple ribosomes can translate a single mRNA sequence simultaneously (forming polysomes)

Termination:
Elongation and translocation continue until the ribosome reaches a stop codon
These codons do not code for any amino acids and instead signal for translation to stop
The polypeptide is released and the ribosome disassembles back into subunits
The polypeptide may undergo post-translational modification prior to becoming a functional
protein



Overview of the Process of Translation


7.4.7 State that free ribosomes synthesise proteins for use primarily within the cell, and that bound ribosomes
synthesise proteins primarily for secretion or for lysosomes
Ribosomes floating freely in the cytosol produce proteins for use within the cell
Ribosomes attached to the rough ER are primarily involved in producing proteins to be exported
from the cell or used in the lysosome
These proteins contain a signal recognition peptide on their nascent polypeptide chains which
direct the associated ribosome to the rough ER




















7.5 - Proteins

7.5.1 Explain the four levels of protein structure, indicating the significance of each level
Primary (1) Structure
The order / sequence of the amino acids of which the protein is composed
Formed by covalent peptide bonds between adjacent amino acids
Controls all subsequent levels of structure because it determines the nature of the interactions
between R groups of different amino acids

Secondary (2) Structure
The way the chains of amino acids fold or turn upon themselves
Held together by hydrogen bonds between non-adjacent amine (N-H) and carboxylic (C-O) groups
May form an alpha helix, a beta-pleated sheet or a random coil
Secondary structure provides a level of structural stability (due to H-bond formation)

Tertiary (3) Structure
The way a polypeptide folds and coils to form a complex molecular shape (e.g. 3D shape)
Caused by interactions between R groups; including H-bonds, disulphide bridges, ionic bonds and
hydrophilic / hydrophobic interactions
Tertiary structure may be important for the function of the enzyme (e.g. specificity of active site in
enzymes)

Quaternary (4) Structure
The interaction between multiple polypeptides or prosthetic groups that results in a single, larger,
biologically active protein
A prosthetic group is an inorganic compound involved in protein structure or function (e.g. the
heme group in haemoglobin)
A protein containing a prosthetic group is called a conjugated protein
Quaternary structure may be held together by a variety of bonds (similar to tertiary structure)

Levels of Protein Organisation








7.5.2 Outline the difference between fibrous and globular proteins, with reference to two examples of each
protein type


7.5.3 Explain the significance of polar and non-polar amino acids
Polar amino acids have hydrophilic R groups, whereas non-polar amino acids have hydrophobic R
groups
For water soluble proteins, non-polar amino acids tend to be found in the centre of the protein
(stabilising structure) while polar amino acids are found on the surface (capable of interacting with
water molecules)
For membrane-bound proteins, non-polar amino acids tend to be localised on the surface in
contact with the membrane, while polar amino acids line interior pores (to create hydrophilic
channels)
For enzymes, the active site specifically depends on the location and distribution of polar and non-
polar amino acids as hydrophobic and hydrophilic interactions can play a role in substrate binding
to the active site

7.5.4 State four functions of proteins, giving a named example of each
Structure: Support for body tissue (e.g. collagen, elastin, keratin)
Hormones: Regulation of blood glucose (e.g. insulin, glucagon)
Immunity: Bind antigens (e.g. antibodies / immunoglobulins)
Transport: Oxygen transport (e.g. haemoglobin, myoglobin)
Movement: Muscle contraction (e.g. actin / myosin, troponin / tropomyosin)
Enzymes: Speeding up metabolic reactions (e.g. catalase, lipase, pepsin)










7.6 - Enzymes

7.6.1 State that metabolic pathways consist of chains and cycles of enzyme-catalysed reactions
Most chemical changes in a cell results from chains and cycles of reactions, with each step
controlled by a separate specific enzyme
This allows for a far greater level of control and regulation of metabolic pathways (such as
photosynthesis and cell respiration)

7.6.2 Describe the induced fit model
When enzymes and substrates bind, the active site is not completely rigid and may undergo a
conformational change in shape to better fit the substrate
This conformational change may increase the reactivity of the substrate and be necessary for the
enzyme's catalytic activity
The induced fit model explains how an enzyme may be able to bind to, and catalyse, several
different substrates (broad specificity)

The Induced Fit Model


7.6.3 Explain that enzymes lower the activation energy of the chemical reactions that they catalyse
Every reaction requires a certain amount of energy to proceed - this is the activation energy (E
a
)
Enzymes speed up the rate of a biochemical reaction by lowering the activation energy
If more energy is in the products than the reactants, energy is lost from the system (endergonic)
These reactions are usually anabolic (building things up), as the energy is being used up in bond
formation between two substrate molecules
If more energy is in the reactants than the products, excess energy is released into the system
(exergonic)
These reactions are usually catabolic (breaking things down), as the energy is released from the
broken bonds within molecules

Reaction Pathway of a Typical Exergonic / Exothermic Reaction


7.6.4 Explain the difference between competitive and non-competitive inhibition, with reference to one
example of each
Competitive Inhibition
A molecule (inhibitor) which is structurally / chemically similar to the substrate and binds to the
active site of the enzyme
This serves to block the active site and thus prevent substrate binding (competes for the active
site)
Its effect can be reduced by increasing substrate concentration
Example: Relenza is a competitive inhibitor of neuraminidase (influenza virus enzyme), preventing the
release of virions from infected cells

Non-competitive Inhibition
A molecule (inhibitor) which is not structurally or chemically similar to the substrate and binds to a
site other than the active site (allosteric site)
This causes a conformational change in the active site, meaning the substrate cannot bind
Its effect cannot be reduced by increasing substrate concentration as it is not competing for the
active site
Example: Cyanide (CN
-
) inhibits enzymes (cytochrome oxidase) in the electron transport chain by
breaking disulphide bonds within the enzyme

Competitive versus Non-competitive Inhibition


7.6.5 Explain the control of metabolic pathways by end-product inhibition, including the role of allosteric sites
End-product inhibition is a form of negative feedback in which increased levels of product decrease the
rate of product formation
Because metabolic pathways usually consist of chains (e.g. glycolysis) or cycles (e.g. Krebs cycle),
the product can regulate the rate of its own production by inhibiting an earlier enzyme in the
metabolic pathway
The product binds to an allosteric site of an enzyme, causing a conformational change in the active
site (non-competitive inhibition)
As the enzyme can not currently function, the rate of product formation will decrease (and with
less product there is less enzyme inhibition)

End-Product Inhibition


An example of end-product inhibition is the regulation of ATP formation by phosphofructokinase (an
enzyme in glycolysis)
ATP inhibits phosphofructokinase, so that when ATP levels are high, glucose is not broken down
(but instead can be stored as glycogen)
When ATP levels are low, phosphofructokinase is activated and glucose is broken down to make
more ATP


























8.1 - Cell Respiration

8.1.1 State that oxidation involves the loss of electrons from an element, whereas reduction involves a gain
of electrons and that oxidation frequently involves gaining oxygen or losing hydrogen, whereas reduction
frequently involves losing oxygen or gaining hydrogen

Redox (reduction-oxidation) reactions are chemical reactions that involve the transfer of electrons
(gain or loss) between species
Mnemonics for redox reactions include:
OIL RIG: Oxidation Is Loss (of electrons), Reduction Is Gain (of electrons)
ELMO: Electron Loss Means Oxidation
LEO goes GER: Loss of Electrons is Oxidation, Gain of Electrons is Reduction
In metabolic reactions, a species that has been reduced has the ability to reduce other species (this
is the predominant role of hydrogen carriers)

The differences between oxidation and reduction can be summarised by the following table:


8.1.2 Outline the process of glycolysis, including phosphorylation, lysis, oxidation and ATP formation

Glycolysis is the first stage of cell respiration and involves the breakdown of glucose into two
molecules of pyruvate
It is an anaerobic reaction (does not require the presence of oxygen) and occurs in the cytoplasm

There are four main parts in glycolysis (not including intermediary steps):
Phosphorylation: A hexose sugar is phosphorylated by two ATP to become hexose biphosphate
Lysis: The hexose biphosphate splits into two triose phosphates (3C sugars)
Oxidation: Hydrogen removed from the triose phosphates via oxidation (NAD is reduced to NADH + H
+
)
ATP Formation: Four ATP molecules are released as the triose phosphates are converted into pyruvate
Overall: One molecule of glucose results in 2 pyruvate, 2 (NADH + H
+
) and 2 ATP (net gain)

8.1.3 Draw and label a diagram showing the structure of a mitochondrion as seen in electron micrographs
2D Representation 3D Representation Electron Micrograph

8.1.4 Explain aerobic respiration, including the link reaction, the Krebs cycle, the role of NADH + H
+
, the
electron transport chain and the role of oxygen
Aerobic respiration takes place in the mitochondria, using the pyruvate produced via glycolysis
It produces large amounts of ATP in the presence of oxygen via three main processes:


The Link Reaction
Pyruvate is transported from the cytosol to the mitochondrial matrix in a reaction that produces
(one) NADH + H
+
via oxidation
The pyuvate loses a carbon (as CO
2
) and the remaining two carbons are complexed with coenzyme
A (CoA) to form acetyl CoA

The Krebs Cycle
In the matrix, acetyl CoA combines with a 4C compound to form a 6C compound
Over a series of reactions the 6C compound is broken back down into the original 4C compound
These reactions result in the formation of 2 CO
2
molecules, 1 ATP molecule and multiple hydrogen
carriers, specifically 3 (NADH + H
+
) and 1 FADH
2


The Electron Transport Chain
The hydrogen carriers (NADH + H
+
and FADH
2
) provide electrons to the electron transport chain
on the inner mitochondrial membrane
As the electrons cycle through the chain they lose energy, which is used to translocate H
+
ions to
the intermembrane space (creating a gradient)
The hydrogen ions return to the matrix through the transmembrane enzyme ATP synthase,
producing multiple ATP molecules (via chemiosmosis)
Oxygen acts as a final electron acceptor for the electron transport chain, allowing further electrons
to enter the chain
Oxygen combines the electrons with H
+
ions to form water molecules
The electron transport chain produces the majority of the ATP molecules produced via aerobic
respiration (~32 out of 36 ATP molecules)

8.1.5 Explain oxidative phosphorylation in terms of chemiosmosis
Oxidative phosphorylation describes the production of ATP from oxidised hydrogen carriers (as
opposed to substrate level phosphorylation)
When electrons are donated to the electron transport chain, they lose energy as they are passed
between successive carrier molecules
This energy is used to translocate H
+
ions from the matrix to the intermembrane space against the
concentration gradient
The build up of H
+
ions creates an electrochemical gradient, or proton motive force (PMF)
The protons return to the matrix via a transmembran enzyme called ATP synthase
As they return they release energy which is used to produce ATP (from ADP and Pi)
This process is called chemiosmosis and occurs in the cristae
The H
+
ions and electrons are combined with oxygen to form water, allowing the process to be
repeated anew











Overview of Chemiosmosis


8.1.6 Explain the relationship between the structure of the mitochondria and its function
Inner membrane: Folded into cristae to increase surface area for electron transport chain
Intermembrane space: Small space between inner and outer membranes for accumulation of
protons (increases PMF)
Matrix: Contains appropriate enzymes and a suitable pH for the Krebs cycle to occur
Outer membrane: Contains appropriate transport proteins for shuttling pyruvate into the
mitochondria


















8.2 - Photosynthesis

8.2.1 Draw and label a diagram showing the structure of a chloroplast as seen in an electron micrograph
2D Representation 3D Representation Electron Micrograph

8.2.2 State that photosynthesis consists of the light-dependent and light-independent reactions
Photosynthesis is a two-step process:
The light dependent reactions convert the light energy into chemical energy
The light independent reaction uses the chemical energy to make organic molecules

Overview of Photosynthesis


8.2.3 Explain the light dependent reactions
The light dependent reactions occur on the thylakoid membrane and may occur by either cyclic or
non-cyclic processes
In both processes, light excites chlorophyll (clustered in photosystems) which release electrons
that pass through an electron transport chain, making ATP (photophosphorylation)

Non-Cyclic Photophosphorylation
Chlorophyll in photosystems I and II absorbs light, which triggers the release of high energy
electrons (photoactivation)
The electrons from photosystem II pass along a series of carriers (electron transport chain),
producing ATP via chemiosmosis
The electrons from photosystem I reduce NADP
+
to generate NADPH + H
+

Electrons lost from photosystem I are replaced by electrons from photsystem II
Electrons lost from photosystem II are replaced by electrons generated by the photolysis of water
(oxygen is produced as a by-product)

Cyclic Photophosphorylation
Only photosystem I is involved in cyclic photophosphorylation
The high energy electrons released by photoactivation pass along an electron transport chain
(producing ATP) before returning to photosystem I
Cyclic photophosphorylation does not produce NADPH + H
+
, which is needed for the light
independent reactions
Thus while cyclic photophosphorylation can make chemical energy (ATP) from light, it cannot be
used to make organic molecules

Non-Cyclic versus Cyclic Photophosphorylation


8.2.4 Explain photophosphorylation in terms of chemiosmosis
As the electrons (released from chlorophyll) cycle through the electron transport chains located on
the thylakoid membrane, they lose energy
This free energy is used to pump H
+
ions from the stroma into the thylakoid
The build up of protons inside the thylakoid creates an electrochemical gradient (or proton motive
force)
The H
+
ions return to the stroma via the transmembrane enzyme ATP synthase, which uses the
potential energy from the proton motive force to convert ADP and an inorganic phosphate (Pi)
into ATP
This process is called chemiosmosis











Photophosphorylation via Chemiosmosis


8.2.5 Explain the light independent reaction
The light independent reaction occurs in the stroma and uses the ATP and NADPH + H
+
produced
by the light dependent reaction (non-cyclic)
The light independent reaction is also known as the Calvin cycle and occurs via three main steps:

Carbon Fixation
The enzyme rubisco (RuBP carboxylase) catalyses the attachment of CO
2
to the 5C compound
ribulose bisphosphate (RuBP)
The unstable 6C compound that is formed immediately breaks down into two 3C molecules called
glycerate-3-phosphate (GP)

Reduction
Each GP molecule is then phosphorylated by ATP and reduced by NADPH + H
+

This converts each GP molecule into a triose phosphate (TP) called glyceraldehyde phosphate

Regeneration of RuBP
For every six molecules of TP produced, only one may be used to form half a sugar molecule (need
two cycles to form a complete glucose)
The remaining TP molecules are reorganised to regenerate stocks of RuBP in a reaction that
involves ATP
With RuBP regenerated, this cycle will repeat many times and be used to construct chains of
sugars (e.g. sucrose) for use by the plant









The Light Independent Reaction (Calvin Cycle)


8.2.6 Explain the relationship between the structure of the chloroplast and its function
Thylakoids: Small lumen means small changes in proton concentration have a large effect on the
proton motive force
Grana: Thylakoids arranged in stacks to greatly increase surface area available for light absorption
(chlorophyll located in thylakoid membrane)
Stroma: Contains appropriate enzymes and suitable pH for the light independent reaction to
occur

8.2.7 Explain the relationship between the action spectrum and absorption spectrum of photosynthetic
pigments in green plants
Pigments absorb light as a source of energy for photosynthesis
The absorption spectrum indicates the wavelengths (frequency) of light absorbed by each pigment
The action spectrum indicates the rate of photosynthesis for each wavelength / frequency
There is a strong correlation between the cumulative absorption spectrum of all photosynthetic
pigments and the action spectrum
Both display two main peaks - a larger peak at ~450 nm (blue) and a smaller peak at ~670 nm (red)
with a decrease in between (green)










Absorption Spectrum versus Action Spectrum


8.2.8 Explain the concept of limiting factors in photosynthesis, with reference to light intensity, temperature
and concentration of carbon dioxide
The law of limiting factors states that when a chemical process depends on more than one
essential condition being favourable, its rate will be limited by the factor that is nearest its
minimum value
Photosynthesis is dependent on a number of favourable conditions, including:

Light Intensity
Light is required for the light dependent reactions (photoactivation of chlorophyll and photolysis
of water molecules)
Low light intensities results in insufficient production of ATP and NADPH + H
+
(both needed for
the light independent reaction)

Temperature
Primarily affects the light independent reaction (and to a lesser extent the light dependent
reactions)
High temperatures will denature essential enzymes (e.g. rubisco), whereas insufficient thermal
energy will prohibit reactions from occurring

Concentration of Carbon Dioxide
Carbon dioxide is required for the light independent reaction to occur (carbon fixation of RuBP by
rubisco)
At low levels, carbon fixation will occur very slowly, whereas at higher levels the rate will peak as
all rubsico are being used

Factors Affecting the Rate of Photosynthesis




9.1 - Plant Structure and Growth

9.1.1 Draw and label plan diagrams to show the distribution of tissues in the stem and leaf of a dicotyledonous
plant
Stem Tissue Leaf Tissue


9.1.2 Outline three differences between the structures of dicotyledonous and monocotyledonous plants


9.1.3 Explain the relationship between the distribution of tissues in the leaf and the function of these tissues
Upper Epidermis
Function: Main function is water conservation (secretes cuticle to create a waxy outer boundary)
Distribution: On top of leaves where light intensity and heat are greatest

Palisade Mesophyll
Function: Main photosynthetic tissue (cells contains many chloroplasts)
Distribution: Upper half of leaf where light intensity is greatest (upper epidermal cells are
transparent)

Spongy Mesophyll
Function: Main site of gas exchange (made of loosely packed cells with spaces)
Distribution: Lower half of leaf, near the stomatal pores (where gases and water are exchanged
with the atmosphere)

Vascular Tissue
Function: Transport of water (xylem) and the products of photosynthesis (phloem)
Distribution: Found in middle of leaf (allowing all cells optimal access)




9.1.4 Identify modifications of roots, stems and leaves for different functions: bulbs, stem tubers, storage roots
and tendrils
A storage organ is a part of a plant specifically modified to store energy (e.g. carbohydrates) or
water
They are usually found underground (better protection from herbivores) and may result from
modifications to roots, stems or leaves:
Storage roots: Modified roots that store water or food (e.g. carrots)
Stem tubers: Horizontal underground stems that store carbohydrates (e.g. potato)
Bulbs: Modified leaf bases (may be found as underground vertical shoots) that contain layers
called scales (e.g. onion)
Some plants (called succulents) have modified leaves or stems (thickened, fleshy and wax-
covered) to enable water storage (e.g. cacti)
Other plants (e.g. vines) have modifications to their leaf or stem to enable climbing support and
attachment - these are called tendrils

Modifications to Plant Structure


9.1.5 State that dicotyledonous plants have apical and lateral meristems
A meristem is a tissue in a plant consisting of undifferentiated cells (meristematic tissue) and are
found in zones where growth can take place
Meristematic cells are analogous to stem cells in animals, however have specific regions of growth
and development (unlike stem cells)
Dicotyledonous plants have apical and lateral meristems

9.1.6 Compare growth due to apical and lateral meristems in dicotyledonous plants
Similarities:
Both are composed of totipotent cells (able to divide and differentiate)
Both are found in dicotyledonous plants

Differences:





9.1.7 Explain the role of auxin in phototropism as an example of the control of plant growth
Phototropism is the growing or turning of an organism in response to a unidirectional light source
Auxins (e.g. IAA) are plant hormones that are produced by the tip of a shoot and mediate
phototropism
Auxin makes cells enlarge or grow and, in the shoot, are eradicated by light
The accumulation of auxin on the shaded side of a plant causes this side only to lengthen, resulting
in the shoot bending towards the light
Auxin causes cell elongation by activating proton pumps that expel H
+
ions from the cytoplasm to
the cell wall
The resultant decrease in pH within the cell wall causes cellulose fibres to loosen (by breaking the
bonds that hold them together)
This makes the cell wall flexible and capable of stretching when water influx promotes cell turgor
Auxin can also alter gene expression to promote cell growth (via the upregulation of expansins)

The Role of Auxin in Phototropism




9.2- Transport in Angiosperms

9.2.1 Outline how the root system provides a large surface area for mineral ion and water uptake by means of
branching and root hairs
Plants take up water and essential minerals via their roots and thus need a maximal surface area in
order to optimise this uptake
The monocotyledon root has a fibrous, highly branching structure which increases surface area for
maximal absorption
The dicotyledon root has a main tap root which can penetrate deeply into the soil to access deeper
reservoirs of water and minerals, as well as lateral branches to maximise surface area
The root epidermis may have extensions called root hairs which further increase surface area for
mineral and water absorption
These root hairs have carrier proteins and ion pumps in their plasma membrance, and many
mitochondria within the cytoplasm, to aid active transport




9.2.2 List the ways in which mineral ions in the soil move into the root
Minerals move into the root system via the following pathways:
Diffusion: Movement of minerals along a concentration gradient
Mass Flow: Uptake of mineral ions by means of a hydrostatic pressure gradient
Water being taken into roots via osmosis creates a negative hydrostatic pressure in the soil
Minerals form hydrogen bonds with water molecules and are dragged to the root, concentrating
them for absorption
Fungal Hyphae: Absorb minerals from the soil and exchange with sugars from the plant
(mutualism)

9.2.3 Explain the process of mineral ion absorption from the soil into roots by active transport
Minerals that need to be taken up from the soil include K
+
, Na
+
, Ca
2+
, NH
4
+
, PO
4
3-
and NO
3-

Fertile soil invariably contains negatively charged clay particles to which positively charged
minerals may attach
Root cells contain proton pumps that actively pump H
+
ions into the surrounding soil, which
displaces the positively charged minerals allowing for their absorption (the negatively charged
minerals may bind to the H
+
ions and be reabsorbed with the proton)

Mineral Ion Absorption

This mode of absorption is called indirect active transport - it uses energy (and proton pumps) to
establish an electrochemical gradient by which mineral ions may be absorbed via diffusion
Alternatively, the root cells may absorb mineral ions via direct active transport - using protein
pumps to actively translocate ions against their concentration gradient

9.2.4 State that terrestrial plants support themselves by means of thickened cellulose, cell turgor and lignified
xylem
Three ways by which terrestrial plants may support themselves are:
Thickened cellulose: Thickening of the cell wall provides extra structural support
Cell turgor: Increased hydrostatic pressure within the cell exerts pressure on the cell wall, making
cells turgid
Lignified xylem: Xylem vessels run the length of the stem and branches, lignification of these
vessels provides extra support

9.2.5 Define transpiration
Transpiration is the loss of water vapour from the leaves and stems of plants



9.2.6Explain how water is carried by the transpiration stream, including the structure of xylem vessels,
transpiration pull, cohesion, adhesion and evaporation

Some of the light energy absorbed by leaves changes into heat, converting water in the spongy
mesophyll into vapour
This vapour diffuses out of the stomata and is evaporated, creating a negative pressure gradient in
the leaf
New water is drawn from the xylem (mass flow), which is replaced by water from the roots (enters
from soil via osmosis)
The flow of water through the xylem from the roots to the leaf is called the transpiration stream
Water rises through xylem vessels because of two qualities:
Cohesion: Water molecules are weakly attracted to each other via hydrogen bonds
Adhesion: Water molecules form hydrogen bonds with the xylem cell wall
These properties create a suction effect (or transpiration pull) in the xylem
The xylem has a specialised structure to facilitate transpiration:
The inner lining is composed of dead cells that have fused to create a continuous tube
These cells lack a cell membrane, allowing water to enter the xylem freely
The outer layer is perforated (contains pores), allowing water to move out of the xylem into the
leaves
The outer cell wall contains annular lignin rings which strengthens the xylem against the tension
created by the transpiration stream



9.2.7 State that guard cells can regulate transpiration by opening and closing stomata
The transpiration pull is generated by the negative hydrostatic pressure created by the
evaporation of water vapor from the leaf
Guard cells line stomata and regulate transpiration by controlling how much water vapor can exit
the leaf
When stomata are open the rate of transpiration will be higher than when they are closed

9.2.8 State that the plant hormone abscisic acid causes the closing of the stomata
When a plant begins to wilt from water stress, dehydrated mesophyll cells release the plant
hormone abscisic acid (ABA)
Abscisic acid triggers the efflux of potassium from guard cells, decreasing the water pressure
within these cells and making them flaccid
This causes the stomatal pore to close

Opening and Closing of Stomata by Abscisic Acid


9.2.9 Explain how the abiotic factors light, temperature, wind and humidity, affect the rate of transpiration in a
typical terrestrial plant
Light
Increasing the intensity of light increases the rate of transpiration
Light stimulates the opening of stomata (gas exchange required for photosynthesis to occur)
Some of the light energy absorbed by leaves is converted into heat, which increases the rate of
water evaporation

Temperature
Increasing the temperature increases the rate of transpiration
Higher temperatures cause an increase in water vaporisation in the spongy mesophyll and an
increase in evaporation from the surface of the leaf
This leads to an increase in the diffusion of water vapour out of the leaf (via the stomata) which
increases the rate of transpiration

Wind
Greater air flow around the surface of the leaf increases the rate of transpiration
Wind removes water vapour (lower concentration of vapour on leaf surface), increasing the rate of
diffusion from within the spongy mesophyll



Humidity
Increasing the humidity decreases the rate of transpiration
Humidity is water vapour in the air, thus a high humidity means there is a high concentration of
water vapour in the air
This reduces the rate of diffusion of water vapour from inside the leaf (concentration gradient is
smaller resulting in less net flow)

9.2.10 Outline four adaptations of xerophytes that help to reduce transpiration
Xerophytes are plants that can tolerate dry conditions (such as deserts and high altitudes) due to a
number of specialised adaptations:
Reduced leaves: Reducing the surface area of the leaf will reduce the area for water loss and thus
reduce transpiration
Rolled leaves: Rolling up leaves (lower epidermis inside) reduces exposure of stomata to air and
thus reduces transpiration
Thick waxy cuticle: A thickened cuticle prevents water loss from the surface of the leaf and thus
reduces transpiration
Stomata in pits: Having stomata in pits, surrounded by hairs, concentrates water vapour near the
stomata, reducing the rate of transpiration
Low growth: Plants located near the ground are less exposed to wind and may be shaded,
reducing the rate of transpiration
C
4
/ CAM physiology: Plants with C
4
or CAM physiology require less amounts of CO
2
, meaning
stomata can stay closed for longer

9.2.11 Outline the role of the phloem in active translocation of sugars (sucrose) and amino acids from source
(photosynthetic tissue and storage organs) to sink (fruits, seeds, roots)
Organic molecules (sugars, amino acids) move from their source (photosynthetic tissue or storage
organs) into a tube system called the phloem
Sugars are transported as sucrose (because it is soluble but metabolically inert) in the fluid of the
phloem (called the sap)
They are actively loaded into the phloem by companion cells, creating a high concentration which
draws water from the xylem via osmosis
The sap volume and pressure consequently increase to create mass flow which drives the sap
along the phloem
The organic molecules are actively unloaded by companion cells and stored in the sink (fruits,
seeds, roots)
Sucrose is stored as starch (insoluble), while the water in the phloem is released (now that solute
concentration is low) and returned to the xylem












Active Translocation in the Phloem





















9.3 - Reproduction in Angiosperms

9.3.1 Draw and label a diagram showing the structure of a dicotyledonous animal-pollinated flower

Structure of a Flower

9.3.2 Distinguish between pollination, fertilisation and seed dispersal
Pollination: The transfer of pollen grains from the anther to the stigma (usually of another plant), often
facilitated by animals, wind or water movement
Fertilisation: Fusion of the male gamete nuclei (in the pollen grain) with the female gamete (in the ovule)
to form a zygote
Seed Dispersal: Fertilised ovules form seeds which move away from the parental plant before
germination, reducing competition for resources
There are a variety of seed dispersal mechanisms, including fruit, wind, water and animals

9.3.3 Draw and label a diagram showing the external and internal structures of a named dicotyledonous seed
Structure of a Pea Seed (Pisum sativum)



9.3.4 Explain the conditions needed for the germination of a typical seed
Germination is the process by which a seed emerges from a period of dormancy and starts to sprout
For germination to occur, a seed requires a combination of:
Oxygen: For aerobic respiration (need ATP in order to grow)
Water: To metabolically activate the cells
Temperature: For the optimal function of enzymes

In addition, particular seed species may require other specialised conditions, such as:
Fire
Light or darkness
Freezing
Prior animal digestion
Erosion of the seed coat
Washing (to remove inhibitors)

9.3.5 Outline the metabolic processes during germination of a starchy seed

The first step in the germination process is the absorption of water, which causes gibberellin - or
gibberellic acid (GA) - to be produced
Gibberellin causes the synthesis of amylase, which breaks down starch into maltose
Maltose is transported to the embryo, where it is either hydrolysed to glucose (for energy) or
polymerised to cellulose (for cell wall formation)
Stored proteins and lipids will also be hydrolysed by the addition of water to form enzymes,
triglycerides and phospholipids
Germination uses the food stored in cotyledons as an energy source until the developing shoot
reaches the light and can begin to photosynthesise

9.3.6 Explain how flowering is controlled in long day and short day plants, including the role of phytochrome
Flowering is controlled by phytochrome, which is affected by light (photoperiodicity)
Phytochrome exists in two forms:
A red (P
r
) form absorbs red light (~660 nm) and is converted into a far red form (P
fr
)
A far red (P
fr
) form absorbs far red light (~730 nm) and is converted into a red form (P
r
)
The P
fr
form is the active form of phytochrome, while the P
r
form is the inactive form of
phytochrome
Sunlight contains more red light, so the P
fr
form is predominant during the day, with the gradual
reversion to the P
r
form occurring at night
In long day plants, the active P
fr
form is a promoter of flowering and so flowering is induced when
the night period is less than a critical length and P
fr
levels are high
In short day plants, the active P
fr
form is an inhibitor of flowering and so flowering is induced when
the night period is greater than a critical length and P
fr
levels are low

The Control of Flowering in Plants























10.1 - Meiosis

10.1.1 Describe the behaviour of the chromosomes in the phases of meiosis
Interphase: Cell growth and DNA replication (duplication of DNA creates sister chromatid chromosomes)

Meiosis I
Prophase I: DNA supercoils and chromosomes condense, nuclear membrane dissolves,
homologous pairs form bivalents, crossing over occurs
Metaphase I: Spindle fibres from centrioles (at poles) attach to centromeres of bivalent, bivalents
line up along the equator of the cell
Anaphase I: Spindle fibres contract and split the bivalent, homologous chromosomes move to
opposite poles of the cell
Telophase I: Chromosomes decondense, nuclear membranes may reform, cell divides
(cytokinesis) forming two haploid daughter cells

Interkinesis: An optional rest period between meiosis I and meiosis II, no DNA replication occurs in this
stage

Meiosis II
Prophase II: Chromosomes condense, nuclear membrane dissolves (if reformed), centrioles move
to opposite poles (perpendicular to previous poles)
Metaphase II: Spindle fibres from centrioles attach to centromeres of chromosomes,
chromosomes line up along the equator of the cell
Anaphase II: Spindle fibres contract and split the chromosome into sister chromatids, chromatids
(now called chromosomes) move to opposite poles
Telophase II: Chromosomes decondense, nuclear membrane reforms, cells divide (cytokinesis)
resulting in four haploid daughter cells

Summary
Meiosis is the division of a cell to form four haploid gametes, all of which may be genetically
distinct if recombination occurs in prophase I

Overview of Meiosis


10.1.2 Outline the formation of chiasmata in the process of crossing over
Crossing over involves the exchange of segments of DNA between homologous chromosomes
during Prophase I of meiosis
The process of crossing over occurs as follows:
Homologous chromosomes become connected in a process called synapsis, forming a bivalent (or
tetrad)
Non-sister chromatids break and recombine with their homologous partner, effectively
exchanging genetic material (crossing over)
The non-sister chromatids remain connected in an X-shaped structure and the positions of
attachment are called chiasmata
Chiasma hold homologous chromosomes together as a bivalent until anaphase I
As a result of crossing over, chromatids may consist of a combination of DNA derived from both
homologues - these are called recombinants

Crossing Over in Prophase I




10.1.3 Explain how meiosis results in an effectively infinite genetic variety in gametes through crossing over
in prophase I and random orientation in metaphase I
During anaphase I, homologous chromosomes separate, such that each resultant daughter cell
(and subsequent gametes) contains a chromosome of either maternal or paternal origin
The orientation of these homologues in metaphase I is random, such that there is an equal
probability of the daughter cell having either the maternal or paternal chromosome
As humans have a haploid number of 23 chromosomes, this means that there is 2
23
potential
gamete combinations (over 8 million combinations)
Crossing over in prophase I results in entirely new chromosome combinations, as recombination
through gene exchange produces wholly original chromosomes containing both maternal and
paternal DNA, resulting in near infinite genetic variability
Other sources of genetic variation include random fertilisations, DNA mutations, chromosome
mutations and non-disjunction

10.1.4 State Mendel's law of independent assortment
Gregor Mendel was a 19th century Moravian monk who demonstrated that the inheritence of traits (i.e.
genes) followed particular laws:
Law of Segregation: Each hereditary characteristic is controlled by two alleles, which segregate
and pass into different reproductive cells (gametes)
Law of Independent Assortment: The separation of alleles for one gene will occur independently
of the separation of alleles for another gene
According to the law of independent assortment, different allele combinations should always be
equally possible
However this law only holds for genes that are on different chromosomes - the law of independent
assortment does not apply to linked genes

10.1.5 Explain the relationship between Mendel's law of independent assortment and meiosis
The law of independent assortment relates to the random orientation of homologous
chromosomes in metaphase I of meiosis
Because the orientation of a homologous pair is random, and does not affect the orientation of
any other homologous pair, any one of a pair of alleles on a chromosome has an equal chance of
being paired with, or separated from, any one of a pair of alleles on another chromosome
This means the inheritance of two different traits will occur independently of each other (provided
the genes aren't linked)















Linked versus Unlinked Genes













10.2 - Dihybrid Crosses and Gene Linkage

10.2.1 Calculate and predict the genotypic and phenotypic ratio of offspring of dihybrid crosses involving
unlinked autosomal genes
A dihybrid cross determines the allele combinations of offspring for two particular genes that are unlinked
(not on the same chromosome)
Because there are two genes with two alleles per gene (multiple alleles not required), there can be up to
four different gamete combinations
To work out gamete combinations remember FOIL:
First (AaBb = AB) Outside (AaBb = Ab) Inside (AaBb = aB) Last (AaBb =
ab)
When calculating genotype, always pair alleles from the same gene (e.g. ABab should be AaBb) and
always write capitals first

Calculating genotypic and phenotypic ratios from a dihybrid cross


10.2.2 Distinguish between autosomes and sex chromosomes
Autosomes: Pairs of chromosomes that are identical in appearance (e.g. same size, same gene loci, etc.)
and are not involved in sex determination
Sex chromosomes: Pairs of chromosomes involved in sex determination and are not identical in
appearance (e.g. X and Y chromosome in humans)




10.2.3 Explain how crossing over between non-sister chromatids of a homologous pair in prophase I can
result in the exchange of alleles
During crossing over in prophase I, non-sister chromatids of a homologous pair may break and
reform at points of attachment called chiasmata
As these chromatids break at the same point, any gene loci below the point of the break will be
exchanged as a result of recombination
This means that maternal and paternal alleles may be exchanged between the maternal and
paternal chromosomes, creating new gene combinations
The further apart two gene loci are on a chromosome, the more likely they are to be exchanged

The Formation of Recombinant Chromosomes via Crossing Over


10.2.4 Define linkage group
A linkage group is a group of genes whose loci are on the same chromosome and therefore do not
follow the law of independent assortment
Linked genes will tend to be inherited together - the only way to separate them is through
recombination (via crossing over during synapsis)



10.2.5 Explain an example of a cross between two linked genes
When two genes are linked, they do not follow the expected phenotypic ratio for a dihybrid cross
between heterozygous parents
Instead the phenotypic ratio will follow that of a monohybrid cross as the two genes are inherited
together
This means that offspring will tend to produce the parental phenotypes
Recombinant phenotypes will only be evident if crossing over occurs in prophase I and would thus
be expected to appear in low numbers (if at all)
An example of a cross between two linked genes is the mating of a grey bodied, normal wing fruit
fly with a black bodied, vestigial wing mutant






10.2.6 Identify which of the offspring are recombinants in a dihybrid cross involving linked genes
Recombinants of linked genes are those combinations of genes not found in parents
For example, in a test cross of a heterozygous fruit fly (grey bodied, normal wings) with a homozygous
recessive mutant (black bodied, vestigial wings), the recombinants would be the grey bodied, vestigial
winged offsprings and the black bodied, normal winged offspring


Linked genes that have undergone recombination can be distinguished from unlinked genes via a test
cross because the frequency of the recombinant genotypes will always be less than would occur for
unlinked genes (crossing over does not happen every time)
For example:
Heterozygous test cross of unlinked genes = 1 : 1 : 1 : 1 phenotypic ratio
Heterozygous test cross of linked genes = 1 : 1 : 0.1 : 01 phenotypic ratio (uncommon phenotypes
are recombinants)

















10.3 - Polygenic Inheritance

10.3.1 Define polygenic inheritance
Polygenic inheritance refers to a single characteristic that is controlled by more than two genes
(also called multifactorial inheritance)
Polygenic inheritance patterns normally follow a normal (bell-shaped) distribution curve - it shows
continuous variation
By increasing the number of genes controlling a trait, the number of phenotype combinations also
increase, until the number of phenotypes to which an individual can be assigned are no longer
discrete, but continuous

10.3.2 Explain that polygenic inheritance can contribute to continuous variation using two examples, one of
which must be human skin colour
Human Skin Colour
The colour of human skin is determined by the amount of dark pigment (melanin) it contains
At least four (possibly more) genes are involved in melanin production; for each gene one allele
codes for melanin production, the other does not
The combination of melanin producing alleles determines the degree of pigmentation, leading to
continuous variation

Grain Colour in Wheat
Wheat grains vary in colour from white to dark red, depending on the amount of red pigment they
contain
Three genes control the colour and each gene has two alleles (one coding for red pigment, the
other coding for no pigment)
The most frequent combinations have an equal number of 'pigment producing' and 'no pigment'
alleles, whereas combinations of one extreme or the other are relatively rare
The overal pattern of inheritance shows continuous variation

Polygenic Inheritance of Grain Wheat Colour