Area of Study 1

Structure and function of membranes

Polar (Water) and non-polar (Methane) molecules:
Oxygen has an overall negative change of 2, so it attracts to hydrogen both with a
charge of +1
This causes the top of the oxygen to have an overall negative charge and the bottom
of the molecule to have a positive charge. That makes it a polar molecule negative at
one end positive on the other

Polar- Hydrophilic; Attracted to water

Non-Polar; Hydrophobic, repelled by water (Polar and non-Polar substances do not mix)

Plasma Membrane (Fluid Mosaic model) Phospholipid Biolayer

Made up of Phospholipid, Phospholipids are made of glycerol(head) and two fatty

tails.
The glycerol head is a polar molecule, hydrophilic.

The fatty tails ate non-polar, hydrophobic

Non polar molecules can pass through the plasma membrane

Phospholipid bilayer is used to separate the water that is inside the cell from the water outside the
cell, natural barrier

Protein Channels (Transport Proteins); Let things through the

plasma membrane that are ordinarily unable to get through the
phospholipid biolayer, e.g. molecules that are too large or polar or
charged ions (Can’t get past the fatty tails). (Transmembrane
protein as it goes from one side of the membrane to the other)

Glycoprotein; Has a carbohydrate chain, can complete a range of

purposes, often used in antigens in cells. Act as markers for cell to
cell communication. Used to tell the difference between self and
non-self

Cholesterol, Sits between the fatty tails in the phospholipid biolayer; helps regulate flexibility in the
plasma membrane, and creates stability

Called the fluid mosaic model as the phospholipid biolayer closely resembles a mosaic model, with
all the different colours and shapes. It is described as a fluid mosaic as although it looks similar to a
mosaic it is still a fluid and such it moves around.
Osmosis; the net diffusion of free water molecules through a semi-permeable membrane from a
region with a low solute(salt) concentration to a region with high solute(salt) concentration. Solvent
(water)

Diffusion is the passive net movement of molecules from a place of a high concentration to a place
of high concentration to a place of low concentration.

Facilitated Diffusion; The passive (no energy) net movement of a substance from a region with a
high concentration to a region of low concentration, through a membrane via a specific channel or
carrier protein.

Active transport; The active net movement of a substance from a region with a low concentration to
a region of high concentration through a membrane via a carrier protein.

The affect size and polarity have on transporting through the Plasma Membrane; Materials need to
cross the membrane.

Water entering the membrane; If there is a low concentration of the water in the cell then the water
outside the cell, water will just enter the cell through osmosis. This occurs as small gaps appear in
the phospholipid biolayer allowing for water to enter it.

If the water is of a very high the osmotic pressure may be so great that it can pass straight through
the phospholipid biolayer.

If there is a high concentration of CO2 in a cell it the CO2 can leave the cell through simple diffusion
down the concentration gradient.

Export of Proteins
The proteins are modified and packed within the Golgi Apparatus, ready to be exported from the
cell. When exporting proteins, a small vesicle buds off from the Golgi body, within which a protein is
contained. The vesical then reaches the membrane of the cell then joins to it causing the protein to
leave the cell. Called Exocytosis.

The endoplasmic reticulum that are covered in black dots called ribosomes become rough
endoplasmic reticulum. Acts as a system of networks that channels things around the cell.
Ribosomes, synthesis proteins, they are made up of proteins and rRMA
Some ribosomes float freely, they are used to synthesis proteins that the cell needs.
Ribosomes that are located on the rough endoplasmic reticulum, create proteins for exportation
from the cell

Building and moving proteins require energy from the mitochondria.

Cellular Engulfment
Endocytosis, bring in a molecule
Bringing a protein into the cell, the membrane raps around the object and engulfs it
Phagocytosis is a form of endocytosis
Pinocytosis, engulfing of a liquid object

Nucleic Acids and Protein

Proteome, all the proteins found in an organism

Protein structure

Primary structure: is a sequence of amino acids known as a polypeptide chain

Secondary Structure: After the polypeptide chain has been completed, it will naturally fold due to
reactions in the amino acids, as some are positive, and some are negative. This folding creates two
common shapes; alpha helixes and beta pleated sheets. Random coil or loops may also occur.

Tertiary Structure: A protein then bends and folds the polypeptide chain into a 3D shape that will be
used to complete a particular job. Changing the shape of a protein changes its function.

Quaternary Structure: Is a protein made up of more then one polypeptide chain.

Polypeptide synthesis

Amino acids are made up of 3 parts

Amine Group: NH2(NH3+) (Nitrogen and helium)

Carboxylic group: COOH (Carbon and Oxygen)
R group: Variable region

Condensation Polymerase:
Occurs on the formation of a polypeptide chain within which two adjacent amino acids join together
producing a bond called a polypeptide bond and causes one molecule of water to be released. (The
example here become amino acid residue bound to another amino acid residue, as they both are not
complete amino acids.)
Structure of DNA (Deoxyribose nucleic acid)
Chromosomes are made up of chromatin, chromatin is made of histones which is surrounded by
DNA.

Nucleotides: Nucleotide have 3 parts, Nitrogen base, 5 carbon sugar and phosphate group

Nucleosides: Is just the 5-carbon sugar and Nitrogen base.

The 5 carbons in a nucleotide can be numbered. Starting at

the carbon that is connected to the nitrogen base. This was
where the 5’ and 3’ of DNA is named after as the numbers
actually refer to 5th and 3rd carbon in the nucleotide.

4 different DNA nucleotides that exist in DNA

based on there nitrogen base
Guanine, Cytosine, Adenine and Thymine.
Guanine and Cytosine base bind via 3
hydrogen bonds
Adenine and Thymine bind via 2 hyrogen bonds

Guanine and Adenine has 2 rings on the nitrogen base, thus it is a

Purines
Uracil, cytosine and Thymine have 1 ring on the Nitrogen base, thus
are Pyrimidines

Nucleotide Polymerisation:
-a new nucleotide can only be added to the 3’ end of DNA via DNA polymerase
-When adding a nucleotide, it has 2 extra phosphates. These 2 phosphates are broken off the
nucleotide, in addition to an oxygen being removed from the OH group on the 3’ end of the DNA.
This reaction is simpler to condensation polymerisation but creates a molecule with two phosphates
and not water.

DNA and RNA are nucleic acids.

RNA (Ribose nucleic acid)

Single stranded, On the second carbon there is an oxygen and a hydrogen and not just a hydrogen
unlike DNA. Contains ribose instead of Deoxyribose

3 kinds all transcribed from the DNA, tRNA, mRNA and rRNA

Protein Synthesis Transcription and Translation

Transcription

RNA polymerase separates the DNA strands by breaking the hydrogen bongs connecting them.

It then adds complementary base pairs to the DNA strand, however it adds Uracil instead of Thymine
as in RNA Uracil is used.
In RNA it goes:
Guanine- cytosine
Adenine-Uracil

The strand that the RNA polymerase created is known as pre-messenger RNA or Pre-mRNA, the
strand then peels away from the DNA then the DNA reforms.

Post Transcription modifications

Within the pre-mRNA there is introns and exons. Exons are the regions of the mRNA that are used
for coding the amino acids into the protein. Introns are regions that don’t seem to contain useful
information. Thus, the introns are cut out and the remaining exons are joined together. Additionally,
a methyl cap is added to the 5’ end of the pre-mRNA and a poly-a tail (chain of adenine) is aided to
the 3’ prime end.
This becomes mRNA
This mRNA then leaves the nucleus then goes to a ribosomes often attacked to the rough
endoplasmic reticulum.
At the Ribosome the mRNA is read by tRNA have anticodon(3 bases
long) which will add corresponding amino acids depending on the
codon(3bases long) that the mRNA is presenting.

When going through a ribosome the methyl cap goes through first
and gives directionality. Every time the ribosome reads the mRNA it
will lose one of the As on the poly-a tail, eventually when they are
all gone it will stop being translated.

Genetic code table

Genetic code is called redundant as many genetic codes/codons can code for the same amino acid.
Genetic code is unambiguous as a particular codon will ALWAYS code for a particular amino acid
Genetic code is universal as it is the same for all species

Structural Genes and Regulator genes

Structural gene: Genes that produce proteins that don’t control other genes
Regulator gene: produce a product that controls other genes

Gene structure
Gene: a length of DNA that codes for the production of a polypeptide of protein
Open reading frame (ORF) is the main
part of the gene that contains the
coded instructions for the production
of the protein. Contains the Interns
and Exons.

5’ UTR (Untranslated region): Is where

the methyl cap will be added to it
important in enabling the mRNA to
enter the ribosome

3’UTR: Immediately after the stop

codon on the last codon and is
important for terminating translation.

UTRs are both transcribed but not

translated.

Promoter: RNA polymerase connects to the promoter and that is where transcription begins.

TATA box: Where the DNA polymerase binds too, There are molecule on the polymerase known as
transcription factors

Enhancers: Often many base pairs upstream from the open reading frame. Increases the rate of
transcriptions. An activator protein will bind to the promoter region and increase the rate of
transcription.

Silencers: Often many base pairs upstream from the open reading frame. Decreases the rate of
transcriptions. A repressor protein will bind to the silencer and decrease the rate of transcription.

Insulators: Prevent the RNA Polymerase from transcribed more then one gene at once and ensures
all genes must be transcribed separately, by almost walling off genes.

Gene Regulation the Lac Operon

Operons are not in Eukaryotic cells, only fond in prokaryotes, they are a serious of genes where
there all have a related function and work together so when they are transcribed they are
transcribed together.

Lac operon has to do with the digestion of

lactose. It transcribes 3 enzymes LacZ,
LacY and LacA all used in the digestion of
lactose.

The lac operon is controlled by an

operator which is a repressed by a
repressor protein that blocks the
transcription of LacZ, LacY and LacA.
Unless there is lactose present. If there is lactose is present it binds to the repressor protein causing
it to change shape causing it to no longer be able to fit in the operator causing it to disconnect.
Allowing the RNA polymerase to run down the DNA and transcribe the gene.
The repressor protein is created by the Regulatory gene
When there is no more lactose present then the repressor will once again slot into the operator
stopping the production of the enzymes.

Structure and regulation of biochemical pathways

Enzymes lower activation energy required for a reaction to occur

Enzyme, substrate active site product.

There are two kind of reactions that can occur. They are anabolic and catabolic reactions. An
anabolic reaction is a reaction that requires an input of energy and thus is endergonic and is when
an enzyme fuses two or more separate molecules together. A catabolic is when an enzyme slits a
substrate into two or more products causing a release of energy and thus is an exogenic reaction.

The lock and key model refers to when a substrate fits perfectly into the active site of an enzyme and
is very rare in nature.

The induced fit model is when the active site of an enzyme bends and changes in order to fit the
substrate into the active site.

Inhibitors are molecules that bind to the active site(Competitive) or other part of the enzyme(Non-
competitive) causing the active site of the enzyme to be changed or altered. This inhibits enzyme
activity as the active site has been altered casing the reaction rate to stop or slow.

Competitive inhibitors are inhibitors that can be overpowered if the concentration of the substrate
reaches a high enough level, as it pushed out the inhibiters from the active site of the enzyme. A
non-competitive inhibiter is an inhibitor that causes permanent irreversible altering of the active
sight.

Cofactors: are small molecules needed to help some enzymes complete their enzyme activity.
Cofactors are used to complete the active site of some enzymes allowing the substrate to fit better.
Can stay in active site indefinitely.

Co-enzymes: Are organic molecules that take up and unload substrate, to assist with enzyme
activity. However due to co-enzymes organic nature they are used up in the process meaning a new
co-enzyme will be needed for the reaction to occur again.

ATP is a co-enzyme, as when an endogenic reaction is needed, and ATP enters the active site of the
cell and is used as energy causing a phosphate to break off turning into ADP after the reaction.

NADH is a co-enzyme, as when an endogenic reaction is needed and NADH enters the active site of
the cell and is used causing a hydrogen to break off turning into NAD+ after the reaction.
NADPH is a co-enzyme, as when an endogenic reaction is needed, and NADPH enters the active site
of the cell and is used causing a hydrogen to break off turning into NADP after the reaction.

Denaturation from low/high pH is

reversable and does not occur in nature

Photosynthesis
12H2O + 6CO2 -> C6H12O2 + 6O2+6H2O

Purpose of photosynthesis is done to benefit the plant. Plants can not get glucose from easting
another organism, so they must synthesise it itself, so they can sue the glucose in cellular
respiration, oxygen is just a bi product.
A chloroplast is the same size and shape of a large
bacteria. The chloroplast has its own separate DNA
from the plant. The DNA is also circular like a
prokaryote; thus biologists assume that originally
Chloroplast derived from some kind of separate
bacteria.

Stack of thylakoids is a granum

Light dependent and Light independent stages are
known as the Calvin Cycle

Light Dependent Reaction of Photosynthesis

Occurs in the thylakoids.

12 H2O molecules enter the thylakoids. Within the thylakoids the energy from the sun is then used
to separate the hydrogen and the oxygen. The oxygen is then released and NADP molecules carry
the 24 Hydrogen molecules (Becoming NADPH+) into the stroma for the light independent stage,
additionally 18 ATP is created in this reaction. The ATP is then used as Co-Enzymes in the next stage.

Light Independent reaction

Occurs in the stroma.

The NADPH ions, ATP and 6CO2 at then added together and creates 6H20 molecules as well as
glucose C6H12012

Reaction Rate of Photosynthesis

If there is no light, or light levels are low then will be slower or not be able to occur, even if the other
conditions are ideal.
If there is no CO2 or low levels of CO2 the photosynthesis will slow down or not occur.
If the temperature is low then the enzymes will move much slower causing the rate of
photosynthesis to slow.

Cellular Respiration
Aerobic respiration
Cellular respiration is a biochemical pathway that is to turn glucose into ATP, which is used as energy
in the body.
6O2 + C6H12O6 + 36-38 ADP + pi = 6CO2 + 6H2O + 36-38 ATP
Glycolysis
Occurs in the Cytosol.
Glucose is turned into 2 pyruvates.
2 ATP is produced (4 are produced by 2 are used up)
2NADH

Kerb Cycle (Citric acid cycle) (Don’t need to know the whole circle stuff just inputs and outputs)
-Occurs in the Matrix of the mitochondria.
-If oxygen is available in the cell the two pyruvates from glycolysis will diffuse into the matrix of the
mitochondria and start the kerb cycle.
-Inputs: 2 Pyruvate, Acetyl coenzyme is also used
-Outputs: 10 Loaded acceptors (8 NADH and 2 FADH) 6 C02

Electron transport
-Occurs in the Cristae(Inner membrane of mitochondria)
-Inputs; Loaded Acceptor molecules (Hydrogen ions), Electrons and 6O2 (Added in at the very end to
create water)
-Outputs: 6 H20, 32-34 ATP, Unloaded accepter molecules

Mitochondria (Single cellular chromosome) has its own separate DNA and ribosomes from the cell
that it is within. This has caused biologist to believe that the mitochondria was once a separate
prokaryotic cell that made a symbiotic relationship with primitive versions of our cells, hence
explaining why it has a separate DNA from the original cell. Inner membrane is known as the Cristae
and the liquid inside is known as the matrix
Anaerobic Cellular Respiration
Animal cells-
Inputs: 2 Pyruvate, 2 NADH molecules
Outputs: Lactic Acid, 2 ATP
Location: Cytosol

Plant cells-
Inputs: 2 Pyruvate, 2 NADH molecules
Outputs: CO2, Ethanol, 2 ATP
Location: Cytosol

Anaerobic cellular respiration creates ATP at a faster rate compared to Aerobic respiration, however,
aerobic is far more efficient in creating ATP.

Factors that affect the rate of cellular respiration

Oxygen and Glucose availability:
-both are inputs
-If there is no oxygen available the cell won’t be able to respire aerobically and will instead have to
respire anaerobically, will slow aerobic respiration

-If there is no glucose all stages of cellular reparation will slow down or stop, as glycolysis will not
begin, without glucose there is no cellular respiration

Temperature:
-If the temperature is low, rate of cellular respiration will slow as the biochemical pathway slows
down.
AOS 2
Signalling Molecules
Endocrine signalling is a signal from something like a hormone. Is a signalling molecule that travels
from one part of the body and travels some distance to its target cell.

Paracrine signalling, is a chemical signalling from one cell to an adjacent cell.

Autocrine signalling is when the cell produces a signalling molecule that then has an effect on itself.

Hormones: (secreted by endocrine glands distant to the target cell) Uses endocrine signalling,
meaning that a signal is created in one cell and is then transferred across the body to a target cell,
for an action to be performed.

Neurotransmitters: (secreted by neurons adjacent to the target cell) Held within vesicles within
axon terminals of neurons. After a wave of electrical depolarisation occurs, the neurotransmitters
will be released from the vesicles. It diffuses across the synapse as there is a lower concentration of
neurotransmitters in the adjacent neuron, it binds to the receptor and creates an action potential.
This a form of paracrine signalling.
Action potential:
-When the neuron is resting the inside of the cell is negatively charged and the outside of the cell
holds a positive charge
-During stimulation the charged K+ and Na+ ions exchange positions
-A series of exchanges results in an electrical impulse carried down the nerve- the “action potential”
-Important to note that when the K+ is outside, the only reason the inside in not positive is because
Chlorine ions are present

Cytokines: (secreted by and for immune cells) Used in the communication between white blood
cells. After a macrophage has engulfed a bacterium and has presented the foreign markers a helper
T cell will then bind to the MHC2 marker. Helper T cells then releases cytokines (insulins), which then
stimulates other white blood cells such as a cytotoxic T cell into action (Paracrine signalling). It also
activates the helper T cell itself (autocrine signalling).

Pheromones: (Secreted by glands in another organism to a target cell.) Ants follow pheromone trail;
an ant secretes a pheromone and the cells in other ants respond to it. A pheromone from a separate
species can have an effect on each other. Planets produce pheromones to attract bugs.
Plant hormones; sometimes known as planet grown regulators, as they have differences to
hormones in animals. Endocrine signalling.

Stimulus Response Model

A stimulus is a molecule that causes a response to occur in a cell

(Receptor and effector is known as Transduction)
-Receptor is a protein on the surface of the cell, that has a shape that makes it specific to a signalling
molecule, after receiving the stimulus the receptor will change shape causing other molecules to
change shape making them become Effectors
-The effector then produces a cellular response

Hydrophobic lipids in Signal transduction

Eg. Testosterone
Carried by carrier proteins
Due to the fact that it is hydrophobic it can pass through the phospholipid biolayer and get it it’s
receptor (intracellular receptor) that is located inside the cell. Causing effectors to activate, a thus
causing a response to occur.
Does not require a second messenger to produce a response.

Hydrophilic Ligand
Due to the hydrophilic nature they cannot pass through the cell membrane.
This means the receptor is on the outside of the cell
-When the ligand binds to the receptor it creates a second messenger, this second messenger
continues the reaction
-Often causes a much shorter response from the cell
Apoptosis
Programmed cell death
-Firstly, the cell receives a apoptotic signal, whether it be from an intrinsic or extrinsic pathway
-the cell shrinks in size (cell shrinkage)
-Blebbing: The cell’s membrane starts to form what is known as blebs that contain organelles and
cell fragments
-The Nucleus starts to break apart(Nuclear Fragmentation)
-The Chromosomes harden and condense, (Chromatin condensation)
-The DNA is fragmented and broken up into pieces. (Chromosomal DNA fragmentation)

Extrinsic Death Receptor Pathway

-a cytotoxic T cell signals a cell to undergo cell death, by secreting a death signalling molecule into
the death receptor on the surface of a cell.
-This receptor then activates caspase 8 which then activates caspase, 3,6 and 7 which then initiated
apoptosis

Intrinsic Mitochondrial Pathway

-The mitochondrial membrane breaks causing Cytochrome C to be released into the cell.
-This activates caspase 9, which then initiates caspase 3, 7 and 6 which then initiates apoptosis.

Malfunctions of Apoptosis
-when apoptosis fails to occur
-when forming as an embryo, certain parts of the forming body must be destroyed. For example, the
webbing between fingers and toes in the formation stay of foetal development need to be destroyed
before birth, and apoptosis insures that the process happens. If there is a problem with apoptosis it
can causes the webbing to not degrade causing the individual to have webbing between toes and
hands.

It can also lead to cancer, cancer is a uncontrolled process of cell division, continues to divide to
cause tumours. Regularly, apoptosis will cause cancerous cells to die, however if this fails the cancer
will grow nonstop.
-Changes in the cell could make it not respond to a death signal, causing it to grow uncontrollably

Responding to Antigens
All the cells in the human body have markers to be able to tell other cells that are self. They use
MHC1 and MHC2 markers (Self-antigen). MHC1 markers on all cells but red blood cells. MHC2 cells
are on some cells that are involved in the immune response; B Cells, Helper T Cells, dendritic cells
and macrophages.
Antigens: Is a substance that causes an immune response in the body. It may be a foreign substance
or originate from within the body.
Self-antigen: Self Antigens are normal body cells and substances that don’t usually stimulate an
immune response

Sterile: Free of pathogens

• flaming, steaming, boiling, autoclaving apparatus/equipment

• using antiseptic/antibacterial handwash

• using disposable gloves/equipment

Pathogens: Is an infectious diseases causing agent, it can be cellular (living) or non-cellular(nonliving)

Bacteria: Prokaryotes, single celled living organisms, cellular pathogen, don’t have membrane bell
organelles. E-coli

Viruses: Non-living, non-cellular pathogen. It still contains antigens. Viruses contain antigens, exist to
allow the virus to bind to certain receptors of the host cell. Viruses enter a cell and incorporates it’s
own DNA/RNA into the host cell causing the cell to produce more of the virus.
Structure consist of; Head, capsid, sheath, cone

Fungi: Generally rare in humans, they are a form of eukaryotic organisms

Prions: Are protein like structures that form plaques within the body, these proteins are able to
replicate even though they do not contain their own DNA (protein that has gone rouge)

First Line of Defence:

First line of defence refers to physical and chemical barriers that are always ready to defend the
body (or plant) from invading pathogens.
Animals:
-Intact skin; sebum (secretion from skin) is a weak antiseptic
-Ciliated mucous membranes; air ways are coated in mucous to protect it
-stomach acid; Low Ph thus strong acid
-Lysozyme in tears; enzyme in tears that digests the proteins in bacterial cell walls
-Expulsion reflexes; eg itching, vomiting, sneezing coughing
-Natural flora: Natural bacteria may engulf pathogens

Pants:
-Hairy leaves can stop entry of insects
-Some planets produce antibiotic chemicals
-In tact layer of cells over the surface of leaf (epidermis)
-Waxy cuticle over epidermis, to stop fungus

Innate Immune Response (Second line of defence)

-The second line of defence is an innate response to destroying invading pathogens in a generalised
non-specific way.
Phagocytes:
-Include a wide range of cells such as, Macrophages, Macrophage and Dendritic cells.
-Phagocytes engulf and digest foreign material via phagocytosis
- Phagocytes will also die in large numbers producing pus.

Monocytes:
Largen cells with an abnormally large nucleus. Monocytes are mainly inactive cells. However, when
they detect something foreign they begin to divide becoming Macrophages or Dendritic cells

Macrophages:
-Start off as monocytes which are largely inactive cells with a large nucleus, however when they
detect something foreign they begin to divide becoming Macrophages
-Macrophages are large phagocytes that engulf foreign material and present that foreign material’s
markers using MHC2 markers to other immune cells. Thus, becoming antigen presenting cells.
-They also secrete cytokines and complement proteins
-Act between cells, in the blood and in the lymph

Neutrophils:
-Phagocytes with an unusually shaped nucleus. They engulf foreign material but also secretes
cytokines which induces chemotaxis (movement of cells according to the concentration gradient)
and makes more histamine be released from mast cell at the sight of inflammation.

Dendritic Cells:
-Phagocytes with long membranous extensions. They engulf foreign material and precent the foreign
markers to other immune cells. Has a key role in the activation of the 3rd Line of defence. This is
because when a dendritic cell engulfs a pathogen it becomes activated and will enter the lymphatic
system, and the changes the surface receptor the B and T cells allowing them to activate.
-Act on the surfaces of the body eg, Eyes, mucous, skin, Intestine surface

Natural Killer cells:

-When it detects a foreign material it releases death ligands, (stimulates a cell to kill itself from
apoptosis). Is used to kill cells infected with virus or cancerous cells
-is a lymphoid cell (lymphocyte)

Mast Cells:
-Detect damage in nearby cells and produces histamine if damage is detected. This causes blood
vessels to dilate and makes cell walls more permeable, this allows white blood cells and plasma to
flow to the function site easily.
-Attracts phagocytes
-located in connective tissues
-Leukocytes

Inflammation Response:
- Bacteria invade cells, killing them or releasing harmful by-products.
-The bacteria is detected, and the surrounding mast cells releases histamine. Attracted phagocytes
and other cells secrete cytokines, which recruits other immune cells and causes chemotaxis.
-Histamine causes vasodilation & increases the permeability of capillaries, resulting in white blood
cells moving into surrounding tissue.
-Cytokines cause the migration of phagocytic cells and dendritic cells into the infection site, where
they become activated by the PAMPs
-Bacteria are engulfed by the phagocytes
-Redness, itchiness, pain

Interferons:
-Form of cytokine
-When a cell is infected by a virus it will releases the signalling molecules known as interferons
-These interferons make it so that surrounding cells are much less prone to viral attacks

Complement Protein (Complement protein)

-Is a system of 30 different blood proteins that act together to create three responses
1. Opsonize pathogens: Stick on the surface of a pathogen and make it easier for immune
cells(phagocytes) to identity the foreign material.
2. Attract phagocytes: Phagocytes are drawn to the source of the compliment bacteria
3. Create pores in bacterial membranes (MAC): This pore causes the bacteria to rupture.

Specific Immune Response (Adaptive Immune Response)

Lymphatic System:
-Drain fluid from the blood, and becomes lymph, It is sent through lymph vessels and lymph nodes
before being deposited back in the blood
-Lymph nodes contain large amounts of lymphocytes, key cells involved in the adaptive immune
response
-Secondary lymphoid tissue: Lymph nodes, tonsils, spleen
-Primary lymphoid tissue: is the bone marrow in the long bones of the arms and legs and
Thymies(Lymphocytes (T cells) mature in the Thymies) gland. Is where Leucocytes are produces.
-Tend to swell during times of infection as the lymphocytes attack the pathogens

Adaptive Immune Response:

Third line of defence: The third line of defence Is a highly specialised subsystem of the immune
system that is composed of highly specialised cells that are specific in eliminating particular
pathogens. It includes the process of Antibody Mediated Immunity and Cell mediated immunity.

-An antigen prestaining phagocyte (Macrophage, dendritic cells) engulfs a pathogen and presents
the foreign marker. It then becomes activated and travels in the lymphatic system until it reaches a
lymph node.
-Within the lymph node, by chance the antigen presenting phagocyte will find a helper T cell with a
matching receptor, this activates the T Helper cell
-Once bound the T helper cell is then stimulated to clone itself

Antibody Mediated Immunity

- A pathogen is taken into the lymphatic system, eventually it will reach a lymph node.
-Within the lymph node the pathogen will by chance bind with a B cell with matching receptors to
that specific pathogen.
-The B cell bound to the
pathogen will do nothing until a
T-Helper cell interacts with it
-A T helper cell that has been
activated by the same antigen,
interacts with the B cell and
releases interleukins, causing the
B cell to replicate many times,
otherwise known as clonal
expansion.
-Some of the daughter B cells become B memory cells, these cells are stored in the lymphatic tissue
and will mean that if the pathogen is encountered again the immune response will be stronger and
faster. B memory cells is what gives lasting immunity.
-The other daughter cells become Plasma cells. These plasma cells produce antibodies at a rapid rate
into the lymphatic system, which will then enter the circulatory system.
-These Antibodies will bind to the receptors of the specific antigen neutralizing it and allowing
nonspecific immune cells to destroy it, clumps of antibodies and pathogens activate the compliment
system (MAC, Opsonise)

-Naïve B cells are B cells that have not yet been exposed to an antigen once exposed they become
Plasma Cells or B memory cells

Cell Mediated Immune response

-An antigen presenting phagocyte (Macrophage, dendritic cells) engulfs a pathogen and presents the
foreign marker. It then becomes activated and travels in the lymphatic system until it reaches a
lymph node.
-A Cytotoxic T cell with match receptors binds to the pathogen
-A T Helper Cell then binds to the pathogen as well then sends interleukin through paracrine
signalling to the Cytotoxic T cell that causes it to multiply or proliferate.
-A portion of the cloned Tc cells become memory cells that are stored in the lymphatic tissue, so
when the antigen is encountered again the immune response will be stronger and faster
- The other portion of cloned Tc cells become Cytotoxic T cells that will signal cells infected with the
particular antigen to kill themselves via apoptosis by releasing cytokines into them.
-After the antigens have been exterminated Suppresser T cells turn the cell mediated immunity back
off.
Application of Immunity
Active (Memory B and T cells
are produced)
Natural -Once the body has suffered
from a disease and antibodies
and subsequent memory B and
T cells have been produced the
antibodies will be available for
the rest of the person’s life
Artificial -Body is deliberately infected
with a weekend or dead
pathogens
-Vaccines given in increasingly
stronger doses
-They stimulate the production
of antibodies
-This form of immunity
Passive (Memory B and T cells
are not produced)
The body is immune to disease
without previous exposure:
-If they body doesn’t have the
correct requirements for a
disease
-Sometimes occurs due to
inherited immunity/ inherited
ability to produce antibodies
-Babies receive antibodies
from the mother’s breast milk
that will protect them for 12
months, also antibodies from
the mother passes through the
placenta
Ready-made antibodies are
given:
-Antibodies are given via an
injection, that have been
harvested from a person or
animal that are specialised for
a disease.

Immunity: Having antibodies within the blood to fighter

Active immunity: Individuals produce their own antibodies in response to an antigen stimulating
their immune system

Passive immunity: Individuals receive antibodies from external source

Natural immunity: The individuals has antibodies without medical intervention

Artificial immunity: The individuals got antibodies with the aid of medical intervention

Vaccine: Stimulate the immune system to produce antibodies. It does this via give an individual the
antigen of a particular pathogen. It gives immunity to influenza the antigen of influenza must be
given.

-Inactivated Vaccine: The virus has been deactivated (Polio)

-Attenuated Vaccine: The virus is still active but has been made less virulent and no longer causes
the disease (Rubella)
-Toxoid Vaccine: The toxin of a bacterial infection is given but has been made harmless. Allowing for
antibodies for the toxin to be made (Tetanus)
-Virus like particle Vaccine: It is particle similar to a virus however, it does not contain DNA or RNA
and instead only contains the Antigens of the virus.
Vaccination Programs/Herd Immunity
Herd immunity is when there are enough people within a population who have been vaccinated
against a disease, that those few who are not vaccinated will still be protected as those who are
vaccinated will ensure the disease does not spread. Generally, occurs at 95% of the population

Malfunctions of the immune system

Autoimmune disorders:
-When the immune cells incorrectly identify self-cells as no self. Often caused by cytotoxic T cell
cause cells sending cytokines into self-cells thinking that they are non-self.
-Auto immune disorders occur during prenatal development, which causes T Cells to wrongly
identify self-cells as non-self.
-Multiple Sclerosis; is when the Cytotoxic T cells target the myelin sheath of motor neurons, causing
action potential to slow down.
-Eventually the blood brain barrier becomes damaged allowing uncontrolled entry of T Helper cells
and other white blood cells.
-This then causes more white blood cells to enter the brain as dendritic cells secrete cytokines to
attract more phagocytes

Immunodeficiency:
Is when the immune system does not work at it’s usual efficiency or has been compromised in some
way.
-HIV: is a virus that attacks Helper T cells causing the adaptive immune system to be compromised,
as it heavily relies on Helper T cells
Allergic Response:
-An allergy is an immune response characterised by class E antibodies production(usually very few
are produced by mast cells), travel around the body and when they find a mast cell they bind to it
with its antigen binding site pointing up. If the antibody detects a particular antigen it causes the
histamine to be released.
-However, when it comes allergies a large amount of class E antibodies are created. It makes it likely
for a small particle such as pollen to trigger all the histamine to be released from a mast cell causing
an allergic reaction as all the histamine is released, eg. Swelling and itchiness.

Monoclonal Antibodies for Treating Cancer

-Hybridoma: is when a cell is produced by fusing a B plasma cell and a tumour cell. This then creates
a Plasma cell that creates antibodies specific to the tumour cell
-Monoclonal antibodies: Antibodies that are produced by a hybridoma, these antibodies are specific
to a particular antigen.

Conjugated monoclonal antibodies: Are antibodies with an additional molecule added to them such
as a radioactive molecule
Non-conjugated: Are antibodies that have no additional molecules added to them

-The antibodies could be made radioactive and diver the radioactive substance straight to the cancer
cell
-The antibodies could hold the toxin used in chemo theory and deliver it directly to the cancer cell
meaning individuals wont have to suffer chemo theory
-The antibody and cancer cells make large clubs of antibodies and cancer cells that start the
compliment protein system causing a MAC causing pores to appear on the cancer cell membrane
killing it
-Making it so the antibodies bind to the FasR region to stimulate apoptosis
-Connect an antigen to the end to the antibody causing the phagocytes to engulf the antibody and
cancer cell
-Using antibodies to kill the blood vessels made by the cancer cells, cutting of the nutrients and
starving the tumour
AOS 3
Causes of Changing Allele frequencies
-Allele: is the expression of a gene within an organism

-Gene: segment of DNA in a chromosome that codes for a polypeptide

-Allele frequency: The amount of times an allele appears in a population

-Gene pool: Total genetic information contained in a population, the diversity in a population, eg
three alleles in a population (Yellow, brown and orange)

-A population with a large gene pool is not likely to go extinct. Lots of allele diversity. Thus they are
more likely to evolve through natural selection if there is a change in the environment. It allows
more phenotypes to exist.

-Genotype: An individual combination of alleles

for a particular gene

-Phenotypes: The expression of a feature trait

in an individual, based on the genotype

-Phenotypes that vary due to genetic

differences are called genetic polymorphisms.

-These arise from: mutations, immigration, emigration and the reproductive rate of various
individuals.

Mutations
-New alleles come from
mutation -
Mutation: Random and
unpredictable change in genetic
variation -
Occurs when DNA being copied

Spontanious mutations: Mutations that hapeen for no particlular reason were the DNA accidently
replicates an error.
1 in every 1000 genes will contain a a mutation

Induced Mutation: Mutations that is caused by an environmental factor, eg smoking, UV rays.

Germline mutation: Mutation that occurs in reproductive tissue and can be passed on to the
offspring. Eg mutation in a sperm
Somatic Mutations: Is a mutation that occurs in tissue other than reproductive tissue and can’t be
passed onto the offspring.

Polyploidy: Having 3 or more sets of chromosomes ( More then just 2 23 sets of chromosomes)

The sexy cell is diploid (2 sets of chromosomes) causing

What should happen; The sex cell is haloid
the resulting cell to have more then 2 sets of
chromosomes. Is common is some planets, fatal in
humans, This depicts Triploid

Aneuploidy: Having an extra or missing chromosome (Eg. Down Syndrome)

Monosomy is having only 1 chromosome

Block Mutations: Changes to a section of a chromosome.

Block Inversion: A chromosome that is looped, breaks then re-joins and a section of chromosome is
flipped upside down

Block Deletion: When a chromosome breaks an re-joins an a section of the Chromosome is lost.

Block Duplication: In a pair of chromosomes a portion of one chromosome breaks off and attacks
itself to the parallel chromosome creating a duplication of bases. Generally has no effect, unless it is
a germline mutation. Assuming the egg was normal it would mean then individual would only have
one copy of J-K-L and not the usual two, or may have three copies of J-K-L

Block Translocation: When there is a pair of chromosomes and a part of a completely different
chromosome re-joins on of the pair. Once again has no effect on an individual unless it is germline as
it could cause a child to have three copies of the added sequence.

-Beloved to be important part of evolution; Our chromosome 2 has the same bases as a
chimpanzees Chromosome 12/13 but added together.

Point Mutations: Changes to a single base of a chromosome, or small number of nucleotides.

Silent substitution point: Occurs as a result of a copying error a nucleotide base changes causing one
of the bases to change. However, during transcription the codon of the change nucleotide is apart of
still produces the same amino acid.
eg. TTC produces Lys -> TTT but still produces Lys

Nonsense Substitution point: Occurs as a result of a copying error a nucleotide base changes causing
one of the bases to change, the resulting codon that the changed nucleotide is apart of codes for
STOP. Meaning translation will stop and causing
the protein to not finish.

Missense Substitution point: Occurs as a

result of a copying error a nucleotide base
changes causing one of the bases to
change, the resulting codon produces a
different amino acid then the one that is
meant to be coded for.
Conservative: The resulting polypeptide
still folds the same and produces the same
protein, this no affect
Non Conservative: Produces a polypeptide that folds differently and thus does not act the same as
the desired protein causing serious adverse effects.

Missense deletion frameshift: A single nucleotide has been deleted causing all the nucleotides to
move up one, completely changing the codons resulting in a completely different polypeptide.

Mechanisms of Evolution
Natural selection:
-Natural selection involves environmental factors that act on
phenotypes so that some survive and reproduce and others do not,
resulting in changing populations over time. Selects the individuals, that
survive within set environmental conditions.
-Selective advantage; is a phenotype that gives asm advantage in it’s
given environment eg a green beetle on grass vs yello bettles

Homozygous: Is have two identical alleles on both chromosomes eg BB or bb

Heterozygous: Is having two different alleles on each chromosome eg Bb

Process of natural selection

1. There is variation within a population, some of which is genetic.

2. Some individuals are better suited to a particular environment.
3. Individuals better suited to the environment are more successful at survival and
reproduction.
4. Over time there is an increase in particular characteristics in the population.

Gene Flow:
-refers to the migration of an organism from one population to another, causing that organism to
breed with the other (can appear in a population overtime)
Genetic Drift:
-Chance events that occur in a population causing some alleles to not be pass on thus effecting the
gene pool. (The smaller the population the more susceptible it is to change)

Founder effect:
-A small population of a particular organism colonises a new area through a chance event eg.
Tornado blowing them over there. (Organisms are known as founders)
-Causes the gene pool of the new population to be very different from the original due to the alleles
that may be present.

Genetic Bottleneck: An intensive selective pressure or natural disaster the can dramatically reduce
the gene pool, can drastically reduce variation in a population as prior generations cannot come
back.

Outcomes of Natural selection

Allopatric speciation:
Species: A species is a group of organisms that can mate and produce fertile off-spring
-Not always as simple as that:
-Yellow rosellas and Orange rosellas can breed and produce fertile offspring
-Crimson rosellas and orange rosellas can breed
-However, crimson rosellas and yellow rosellas cannot breed, these are considered subspecies and in
the process of speciation.
-Species, definition does not work for bacteria as they do not mate

Allopatric speciation:
-Due to geographic location species are separated
1. A parent population divided by geographic barrier (Desert, mountains)
2. No or little gene flow between the two daughter populations
3. Mutations arise within each population
4. Different selective pressures in each population causes particular mutations to be favoured in
each population
5. Even if the geographic barrier is removed, the two populations are reproductively isolated,
meaning they can no longer breed and produce fertile offspring causing them to be different species

Isolating mechanisms; stop the species from breeding

-Temporal isolation: Planets flower at a certain time can’t breed with a tree that does not, Mismatch
in breeding cycles
-Animal calls
-Behaviour, mating ritual (dance
-Structural isolation; a large sub species cannot breed with a small sub species

Selective breeding
-Similar to natural selection, however, traits that are selected are traits are traits that we want to see
in a species.
-starts with a high variety in the gene pool, however humans breed for particular trait thus reducing
the variation in alleles as humans only breed the animals with the desired trait

Changes in Biodiversity overtime

-3800 MYA, simple cellular life began
-2000 MYA Eukaryotes first appeared
-1000 MYA Multicellular organisms
-600 MYA animals appeared
-500 MYA vertebrates appeared
-315 MYA reptiles
-225 MYA Triassic period
-200 MYA Jurassic Period
-145 MYA Cretaceous begins
-65 MYA Mass extinction (meteor)
-50 MYA Rise of mammals
-14 MYA Great Apes
-2.4 MYA Genus homo
-200,000 years ago Homo sapiens
Evidence of Evolution
Fossil Record
Process of fossilisation:
-For a fossil to form it needs to be buried by sediment, generally happens underwater
-The quick burial prevents the decomposing process, by decomposers
-Generally has to be hard tissue eg bone
-Then needs to be left undisturbed for a long period of time

Mineralised Fossil:
-Sediments form around the bone
-Minerals from surrounding sediments, enter the bone, eventually the bone is made completely
from minerals
-This forms a fossil completely made of minerals (not bone)

Mould Fossil:
-Sediment forms around the bone
-The bone then decomposes slowly under the sediment
-This will leave a mould of the bone

Cast
-When a mould fossil is filled with some kind of different sediment such as volcanic rock

Fossil Record:
-From rock layers
-Simpler organisms are generally older (Fossils lower in the layers are older)
-Many species that have existed are now extinct
-Many extant species (exist now) don’t seem to have existed in the past, due to them not sharing
rock layers with older organisms

Fossil Dating:
Absolute dating: Get an actual age of the fossil, by looking at the fossil directly
-Radio metric dating: Uses an elements/radioactive isotopes present within the fossil, to date a fossil
-Radio Carbon dating: Uses the measures the half-life of carbon 14 (the radioactive version of
carbon) which is 5730 years. This is then used to date fossils as if a fossil is found to have ¼ of the
original amount of carbon 14 then the fossil must be 22,920 years old, only works for 50,000 years
-Radio Uranium 238 dating can be used for 4.47 billion years as it turns into lead
-Hard to date old fossils

Relative dating:
Stratigraphy: Makes a key assumption. The law of superposition; that is the bottom rock layers are
older than the ones at the top
-Fossils would be the same age as the rock layer, and other organisms within the rock layer
-Uses volcanic ash within rock layers to date the layers above it as volcanic rock can be dated

Index fossils:
-Fossils that is used to date other fossils in the same rock layers
-The fossils must be distinctive, abundant, wide geographic distribution, need to exist for a short
period in geologic history
Fossil Structure
Transition fossil
-Is a fossil that shows an intermediate link between one species of animals and another. Often it will
show vestigial structures. For example; a bird with reptilian features.

Homologous Structure:
-Bones that are similar in structure, as proof of evolution, showing that they
evolved from some kind a common ancestor

Analogous Structures:
-Animals that have differing bone structures but still complete the same
purpose

Comparative Embryology:
-Is the tendency for a developing embryo off all species looks
similar, and is used for proof of evolution

Biogeography
-Wattles in Australia looks very different in
Africa
-Emu’s and ostriches, This is due to the
movement of continents (continental drift) and
then each species of emu evolved to their
environment
-This is because these large flightless birds and
Wattles both lived in the south side of Pangea
hence why they are not on some continents

Patterns of evolution
Divergent evolution:
-Is when a species evolves in different direction, they diverge from each other

Adaptive Radiation
-Is a form of revolution in which organisms rapidly diversify from an ancestral species into a multiple
of forms. Eg Darwin’s finches

Convergent evolution
-Is when two entirely different species, evolve similar adaptations, and features due to having the
same selective pressures. Although the two species may look and act similar, they would not be
closely related

Transitional form:
-The form between two separate species
Extinction:
-When the variation within a species, is insufficient for some individuals to be favoured by a
selection pressure
-A higher variation allows for selective advantages
-If there is a rapid change in the selective pressure there may be not individuals that are able to
survive the selective pressures

-Mass extinction; when lots of species go extinct in the same period of time. This could be due to
major selective pressure, eg. The meteor that hit earth in the cretaceous period
-Human caused extinction: Due to human deforestation and other industries it has caused the
extinction of a range of species

Molecular Homology as Evidence of Relatedness

DNA Sequencing:
-If DNA have similar sequences then they, those organisms will be related
-Molecular homology is the use of DNA strands to view the relatedness between species
-Comparative Genomics: Is a field of biology in which the genomic features of species are compared

Sanger Method
-Method for sequencing DNA
-First PCR is used to clone the DNA
sequences, however Dideoxynucleotides
are added. These nucleotides have been
edited so that no nucleotides can be
placed after it. The Dideoxynucleotides
have also be edited so that they glow so
the researcher can tell the length of the
sequence
-This PCR then occurs millions of times
eventually creating a sequences of DNA
ta every length
-The DNA strands are then put into a gel
electrophoresis machine so that the
strands can be compared
-This process is very time consuming
DNA Hybridisation (More important)
-First the DNA is heated to 87C to make the strands of DNA separate.
-The DNA is then cooled to 55C this causes the DNA sequences to join back together
-This may cause the strand of DNA of one species to join the other strand of DNA from the other
species
-However, these new strands will not have the exact matching base pairs, meaning the hydrogen
bonds are weaker. Causing them to separate at a lower temperature.
-The two strands are then gradually heated up until the strands separate again, generally is far lower
than the usual 87C
-The degrees difference between the temperate needed to separate the hybrid DNA and the original
strand of DNA shows the % difference in the base pairs. 1degree= 1% difference in the sequences

Mitochondrial DNA
-Mitochondria always comes from the mother
-Due to the mitochondria nor requiring cutting and shuffling due to it only coming from the mother
-This means that scientist can measure the mitochondrial mutations as they happen at a consistent
rate in order to see the relatedness between species

Molecular clock
-Technique that uses that rate of biomolecules to deduce the time it has taken for two or more
species to diverge
Phylogenetic Tree

-Phylogenetic trees are individuals’ interpretation of the quantitative and qualitative data of a
species. The tree shows how related the species are by placing them on a tree format. The closer the
species are the more closely related they are.

Mutations to Master Genes

-Master genes control large phenotypic shapes, controls large number of genes
-BMP4 controls the size and thickness and shape of beaks of beaks
-The amount of BMP4 determines whether a finches beak is big and heavy or small and slender
-The more BMP4 the bigger and thicker the beak
-These changes occur in the embryo
-Gene for producing a protein that makes beaks better

Primate Classification
-Primates: Primates is a classification of organisms that covers a range of physical characteristics. For
example, apposable thumbs, relatively large brain, social groups, relatively long gestation period,
large forward-facing eyes.

-Hominoids: Refers to the great ages, such as gorillas, chimpanzee and humans
-Hominin: Refers to the homo genus, and the bipetal ancestors.
Trends in Hominin Evolution
-A more vertically sloped face
-Larger brain capacity
-The jaw bane is more slender
-Smaller teeth, no canines
-Smaller brow ridge
-Smaller zygomatic arch

-Parabolic jaw not box shaped

-Foramen magnum is almost central on the skull

-Knees can sit parallel to the spine

-Longer leg to arm ratio
-Have a distinct heel, due to the bipedal nature

-The birthing cannel of the pelvis is much larger

Cultural Evolution
Refers to how customs and language are used transfer information across generations. It refers to
the conscious behaviours and learnt information that gets used to better adapt to the environment
and build effective survival mechanisms.
Biological evolution: Refers to changes that happen within a population due to genetic variation and
reproduction.
-Use of tools
-Hunting tactic
-Language
-Cave painting
-art
-Occurred due to our lager brain size, the ability to move further distances and encounter other
hominins due to the bipedal nature and their ability to communicate

Fossil Record of Humans

-A large amount of gaps in the human evolution record
-The fossil record takes the qualitive data and make an interpretation of how past hominins looked
in the past. Not all interpretations are the same
-Due to the culture of humans, not allowing bodies to be buried in water
-Humans have also not existed for long so fossils have had time to develop

-The only information that is available when making these phylogenetic trees, is the dating of the
fossils and the qualitative data of the fossils themselves
-However, it is very open to interpretation
DNA Manipulation
Use of Enzymes
Biotechnology: The utilisation of scientific methods and technique to manipulate DNA to complete a
range of purposes

Restriction enzymes:
-Are enzymes that are used to cut a DNA sequence at a particular base sequence that acts as a
recognition site, it is usually 4-8 base pairs long
-Most restriction enzymes Binds to paranoiac base recognition sites meaning that the basses read
the same way but backwards on the complimentary base

Blunt ends: Is cut in a way where there are no complimentary bases and thus cannot easily create
hydrogen bonds. Requires additions enzymes to re-bond

Sticky ends: Is cut in such a way that if complimentary base pairs are added it will easily form a
hydrogen bond

-Often originates from bacteria, where the enzyme is used to cut up strands of DNA Viruses have
injected into them, works on any DNA

Ligase
-Helps create to sugar phosphate binds in DNA strands. Acts as a glue to “stick” strands of DNA
together

DNA Polymerase/Taq Polymerase

-Ads complimentary base pairs to sequences of DNA
-Taq Polymerase was sourced from a bacterium found it hot springs and thus can withstand very
high temperatures

Reverse polymerase: Does the opposite of mRNA into DNA

PCR
-Is a process used to amplification of DNA strands

-Requires; Taq Polymerase, DNA strand for amplification, free nucleotides and primers

1.Denaturation: Heat the solution to 95C allowing the hydrogen bonds in the DNA to break causing
them to separate or denature. This creates 2 single strands of DNA

2.Annealing: The solution is then cooled to 50-60C allowing for short primers to attach or hybridise
to the 3’end of the DNA strands

3.Primers are Extended: The solution is then heated to 72C which is the optimal temperature for Taq
DNA polymerase. This will allow the Taq polymerase to extend the primers by adding complimentary
base pairs at its most effective rate. Thus, creating two identical DNA strands

Gel Electrophoresis
Is a technique that separates fragments of DNA according to their size and charge.
-Due to the DNA’s overall negative charge it will move from the negative end to the positive end

The marker can be known as the Molecular Weight Ladder as each piece of DNA is at a particular
length so the length of the other DNA strands can be measured

Buffer solution: allows for an electric current

STR
A gel electrophoresis uses STRs(Short tandem repeats) when comparing DNA
-STR are regions of DNA that contain 2-5 base pairs and repeat over and over again
-STRs are found in nuclear non coding DNA and non-coding sections of mitochondrial DNA
-STRs are considered hypervariable regions of DNA, as they vary greatly among people
-STRs can be inherited thus it can be used for paternity testing, however rarely some individuals may
have matching STRs
-Everyone will have the same STR but the amount of times it is repeated will vary

Recombinant Plasmids (Gene cloning)

Plasmid: Is a small circular piece of DNA found naturally in bacteria
-Plasmids are often used as vectors is biotechnology
-A plasmid that has taken up a piece of DNA becomes a recombinant plasmid
1. The DNA strand of interest and the plasmid are cut with the same restriction enzyme
2. Ensure the Plasmid has resistance to two antibiotics
3. Insert the gene of interest into one of the resistances to one of the antibiotics splitting it up
4. Use DNA ligase to stick the gene to the plasmid Creating a recombinant plasmid
5. These recombinant plasmids are then mixed with some bacteria, this will cause some of the
bacteria to take up a plasmid
6. To separate the transformed bacteria to the other bacteria, the bacteria will need to be exposed
to the first antibiotic resistance
7. This will leave only recombinant bacteria
8. To separate bacteria with a plasmid from to those with a recombinant plasmid all the surviving
plasmids should be separated and grown
9. Then, once of each of the separated bacteria will be added to an agar plate containing antibiotic 2
10. The plasmid that dies is the recombinant plasmid, thus the group will continue to be grown, and
the human gene’s product will be harvested

Applications of DNA knowledge

DNA Profiling:
-refers to matching and comparing individuals on the basis of their DNA
-STRs are used in DNA Profiling
-The likelihood that two people have the same allele is very small
-In DNA profiling when comparing DNA the same 9 STRs are used

Paternity Test:
-Children and parents will share some alleles

This alleged father is not the actual father as, although they have a matching band it would have
come from the mother not him

Gene Therapy: This involves the insertion of a healthy allele into a virus that is inserted into the
individual with the unhealthy allel and the healthy allele is then inserted
Genetic Screening:
-Testing somebody for the presence of an allele that can cause a genetic disease
-All babies will receive genetic screening
-PKU; is one of the illness screened. It means that an individual cannot breakdown phenylalanine. If
an individual knows they have PCU it means that they will suffer from not ill health as they will not
eat foods containing phenylalanine
-PCR and gel electrophoresis can be sued in the diagnosis for cystic fibrosis and Huntington’s disease
Issues with Genetic testing
Pre-Symptomatic screening:
-E.g. getting screened for Huntington’s disease before it develops
Discrimination-
Insurance: If you have Huntington’s disease insurance companies will not insure you
Employment: The issue of if someone should tell their employer of their disease

Family planning-
-After being diagnosed people may have to make a decision whether to have children. Some people
may prefer not knowing

Information only or treatment-

-Should genetic screening just be used for treatment, e.g PKU or whether it should be used for
information as well e.g for a disease that does not have a treatment such as Huntington’s disease

Emotional impact:
-Some people may feel as if they need to know, while others may feel as if they would rather not
know
-A screening may also have an emotional impact and children and other family members

Prenatal screening
-Is the screening of a foetus to see if it will have a genetic disease

Abortion-
Some people get screened to that if the child may have a particular disease, they can be tested for it,
and if they do The pregnancy may be terminated. This may be considered unethical

Support-
Will allow people to get support if their child does have a disease

Incomplete information about severity-

The information about how serious the disorder would be is not disclosed so a child may have down
syndrome, but it only affects them mildly

Pre-Implantation screening
-Is a form if screening that involves artificially inseminating and egg and then genetically screening it
to ensure it has not got a genetic disease before implantation

Changing the gene pool-

Removes variation as an embryo is chosen specifically, although for a good thing

Waste Embryos-
Some embryos are disposed of and individuals are not happy about it

What traits do we allow to be tested-

This could turn into people choosing specific genetic characteristics that they like, this sparks some
controversy
Genetically Modified Organisms
Transgenic organism: An organism that contains DNA from an unrelated species

Genetically modified organism (GMO): AN organism that had its DNA artificially modified to produce
a desired characteristic

In agriculture:
-Cannola in Australia has been genetically modified so that it would be immune to pesticides
-Plants have been modified to be salt resistant so they can be grown in dirt with high salt content

Ethical problems
-Some individuals feel as if GMOs are evil, unnatural or even harmful to the body
-Often GMOs that produce more yield, this is an unfair advantage on those farmers that do not use
genetically modified organisms.
-If all famers use the new GMO seeds then gene pool will reduce in size

Strategies to deal with the mergence of new diseases

Outbreak: Sudden appearance in a restricted locale or restricted population

Epidemic: Is a large portion of a population within a country has a disease

Pandemic: When an outbreak of a disease spreads from one country to another

Zika Virus epidemic: In response, countries told their population to not go to effected country
-modification of ones behaviour, e.g. putting on insect replant
-Killing of mosquitoes in large number

For other pandemics:

-Quarantine
-Sanitation

Rational Drug Design

-Rational drug design: Is a drug design technique that involves determining the structure of a target
molecule and then designing a drug with a complementary shape that will bind to and block or
inactivate the target molecule.

Relenza: Is an Australian made anti-viral drug

-Used on the influenza virus, it is an inhibiter
-When a virus has infected a cell an reproduced itself enough it will use the enzyme neuraminidase
(found on the virus surface) to exist the cell
-Relenza acts as an inhibiter to the activate site of the neuraminidase meaning that the virus may be
able to get into cells but will not be able to break the cell body to then infect other cells.
-The inhibiter has a complimentary shape to the neuraminidase
Chemical Agents against Pathogens
Antibiotics
-Antibiotics, are generally naturally occurring compounds from other organisms such as fungi
Antibiotics can have 3 affects:
1.Interfere with Bacteria’s ability to repair damage DNA
2.Weaken cell wall, meaning the cell wall will be less stable and make the bacteria more likely to die
to die
3.Stop bacteria from building new cell walls, meaning that new bacteria cannot form

Narrow Spectrum Antibiotic:

-Only specific to a particular bacterium
-Is generally more effective against specific bacteria

Antiviral Drugs
-Is a drug used against viruses.
Antiviral Drug has several affects:
-Prevents viruses from binding to host cell
-Preventing the virus from entering the host cell
-Prevents transcription of viral components in host cell
-Targets virus DNA/RNA and cutting it into pieces

Specific Antiviral drugs

-Only work on a specific virus
-Is more effective against certain virus