A2 Biology

Joshua Cole F214
F214 - Communication, Homeostasis F215 - Controls, Genomes and

and Energy Environment
Module 1: Communication and Module 1: Cellular Control and Variation
Homeostasis 5.1.1 Cellular Control
4.1.1 Communication 5.1.2 Meiosis and Variation
4.1.2 Nerves Module 2: Biotechnology and Gene
4.1.3 Hormones Technologies
Module 2: Excretion 5.2.1 Cloning in Plants and Animals
4.2.1 Excretion 5.2.2 Biotechnology
Module 3: Photosynthesis 5.2.3 Genomes and Gene Technologies
4.3.1 Photosynthesis Module 3: Ecosystems and Sustainability
Module 4: Respiration 5.3.1 Ecosystems
4.4.1 Respiration 5.3.2 Populations and Sustainability
Module 4: Responding to the Environment
5.4.1 Plant Responses 5.4.2 Animal
Responses 5.4.3 Animal Behaviour
Joshua Cole F214 4.1.1
Communication
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Organisms need to respond to changing environments this can include those changes
outside the cells and
inside the cells
As organisms became multicellular this became more important and a effective communication method
needed to evolve:
From cells
Short Lasting
Fast Cells able to

communicate
Long lasting To cells
Good Communication System
Cover entire organism Specific Communications
Homeostasis - The maintenance of an constant internal environment despite external changes
- Works best if its controlled in both directions meaning

- Up
- Down
Negative Feedback- Reverses the effects of a change
It invokes maintaining
-Body Temperature (37.5C)

-Blood - Oxygen levels
-Blood - Carbon Dioxide Levels
-Blood - Sugar Levels
-Blood - Water - Salt Levels
3
Positive Feedback - Amplifies the Change
EVENTS IF HOMEOSTASIS
Stimulus
Receptor Cells detect Stimulus
Signal Sent to Processing Centre
Message sent to effector
Response
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Hand Movement
Movement
Muscles
Blinking
Good Communication System
Insulin
Glands
Substance Saliva
Response
There are 2 Communication systems in the Human Body
- Hormonal System
- Nervous System
Hormones are chemical messages carried around the body in the blood stream.
They monitor and control changes inside the body and they cause changes to take
place more slowly such as growth , sexual characteristics and blood - sugar levels
Neuronal Impulses are electrical signals carried along the nerves and allow the body
to sense change outside the body and enable quick responses
They are similar in that they both detect and then respond to changes in environments. They both involve
cell signalling and use Negative Feedback meaning that they both control homeostasis. They are different
because Nerves detect changes outside the cells whereas hormones detect intern changes. Nervous
impulses are also electrical rather than chemical as in Hormones. Hormones are also slower.
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ENDOTHERMY AND ECTOTHERMY
ENDOTHERMIC - Able to generate own body heat
ECTOTHERMIC - Rely on external temperatures to

maintain body heat
BEHAVIOURAL RESPONSES TO AN INCREASED EXTERNAL TEMPERATURE CAUSING THE BODY TO COOL

DOWN:
- Move into shade

- Hide in a Burrow
- Orientate body for a reduced surface area facing the sun
- Reduce Activity
- Remove coats
- Move into Water
BEHAVIOURAL RESPONSES TO A DECREASED EXTERNAL TEMPERATURE CAUSING THE BODY TO WARM UP:
- Move into Sun

- Orientate body for a increased surface area facing the sun
- Increase Activity
- Add warmer clothing / more layers
- Dry skin/Hair
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Endothermy Ectothermy
How Body Temperature is Generate and Conserve Own External Temperatures required to
Controlled body heat warm body
Relative Rates of Metabolism High metabolic rate to produce Low metabolic rate
heat
Amount of Food Eaten Lots of food required to drive high Little food required as low
metabolic rate metabolic rate
- Food for 1 cow would be enough
for 10 cow sized lizards
Advantages/Disadvantages Adv - Move easily in the cool/ Adv - Less food, much more effect
Night Dis - Needs a precise external
Dis - Lots of food temperature
Physiological Responses to Increased

Core Temperature
Sweat Glands activate (Latent heat of

Evaporation from skin)
Lungs, Mouth, Nose create panting (Latent
heat of evaporation)
Vasodilation - Arterioles to capillaries dilate
increasing radiation from surface
Liver cells reduce metabolic rate
Physiological Responses to Decreased

Core Temperature
Skeletal Muscles shiver

liver cells increase rate of metabolisms
Vasoconstriction
Hairs raise on skin to trap a warm layer of air
above the skin
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Nerves
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Sense Sense Organ Receptors sensitive to change

in:
Smell Nose Chemical changes in air
Taste Tongue Chemical changes in mouth
Touch Skin Pressure, Temperature and Pain
Sound Ear Vibrations and the position of the

head
Sight Eye Light, intensity and wavelength

(Colour)
TYPES OF NEURONES
There are 2 types of Neurone:-
Unipolar
(Sensory Neuron)
Multipolar
(Motorneuron)
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HOW DO NERVES WORK AND WHAT IS THE ELECTRICAL IMPULSE?
MAINTAINING A RESTING POTENTIAL
When not conducting an impulse, the potential difference across the membrane is -60mV. Sodium-
+ +
Potassium pumps actively transport 3Na ions out for every 2 K ions in.
The axon contains organic anions, which the membrane is impermeable to.
+
Slight loss of K ions through the permeable membrane.
+
Membrane impermeable to Na ions.
GENERATING A ACTION POTENTIAL
1. The membrane is at resting state; -60mV inside compared to outside. Polarised.
+ +
2. Na ion channels open and some Na ions diffuse out.
3. The membrane depolarises- it become less negative with respect to the outside and
reaches the threshold
potential of -50mV.
+ +
4. Voltage-gated sodium ion channels open and many Na ions enter. As more Na
ions enter, the more
positively changed the cell becomes, compared to outside.
5. The potential difference across the membrane reaches +40mV. The inside is now
positive compared to the
outside.
+ +
6. The Na ion channels shut and the K ion channels open.
+
7. K ions diffuse out of the cell, bringing the potential difference back to negative
compared with the outside-
repolarisation.
8. The potential difference overshoots slightly, making the cell hyperpolarised.
9. The original potential difference is restored, so the cell returns to its resting state.
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MYELINATED SHEATH
Areas of the axon
that are coated in a
fatty sheath. It is
made from Schwann
Cells. They get to
their peak
effectiveness around
adolescence which is
why teenagers have
the best response
times.
They wont allow any

sodium or potassium to
diffuse through it so the
action potential happens in
a jumping action.
At the nodes of Ranvier the
influx sodium and
potassium can happen as
usual but the diffusion will
be elongated along the
axon.
This benefits as it speeds up the time take for the impulse to travel down the axon. The jumping is
called saltatory Conduction (Jumping). Basically instead of possible thousands of influxes there is
only a few.
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SYNAPSES
Mitochondria Acetylcholine
Calcium ion Receptor Site
(Ca+) channel
Action
Potential
Axon of
presynaptic
neurone Vesicles
containing
Synaptic
acetylcholine Membrane of
Membrane of Cleft Sodium
postsynaptic Channel
Presynaptic
neurone
Neurone
SEQUENCE OF EVENTS AT THE SYNAPSE GAP
An action potential arrives at the presynaptic

knob
The action potential causes the uptake of
calcium ions
The calcium ions cause vesicles containing the

neurotransmitter acetylcholine to fuse with the
presynaptic membrane
Acetylcholine is relaxed by exocytosis and
diffuses across the synaptic cleft
Acetylcholine molecules bind with receptors on

protein channels in the postsynaptic membrane.
When acetylcholine molecules bind with receptor
sites on two protein subunits, the protein Sodium ions flood in through the open channels
changes shape, opening up the sodium channels in the postsynaptic membranes
between them
Acetylcholine (ACh) - Common

This depolarises the postsynaptic membrane and neurotransmitter, synapses with this are
causes an action potential known as Cholinergic Synapses. There are
other neurotransmitters such as Dopamine
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THE ROLE OF SYNAPSES IN THE NERVOUS SYSTEM
Synapses allow information to be dispersed or Amplified
- When one neurone connects to many neurones information

can be dispersed
This allows it to be dispersed to other parts of the body
Its called Synaptic Divergence
When many neurones connect to a single neurone the
information is amplified
- Its called Synaptic Convergence
Summation at the Synapses finely tunes the nervous response
Weak stimuli causes only a small amount of neurotransmitter to be

released into the cleft.
A small amount of neurotransmitter might not be enough to excite the
post synaptic membrane to the threshold level.
Summation is the effect of neurotransmitter from many neurone

is added together. This can also be when one neurone is
stimulated lots of time in a short period of time
Synapses make sure that impulses are transmitted one

way
Because the receptors are only in the postsynaptic membrane

it makes sure that impulses can only travel one way
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Hormones
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HORMONES ARE MOLECULES THAT ARE RELEASED BY ENDOCRINE SYSTEM.
- Hormones are released directly into the blood

- They have a slower response time than that of the nervous system
- Hormones act as messengers in the body
- Each hormone has a specific shape
There are 2 sorts of hormones:-
PROTEIN OR PEPTIDE HORMONES -
These proteins cannot enter cells so they bind to the cells and cause and effect inside the cells
These are like Insulin or Glucagon
STEROID HORMONES
These hormones pass straight into the cell and affect the DNA of the cell thats in the Nucleus.
Most sex hormones are steroid hormones
THERE ARE ALSO 2 SORTS OF GLANDS:-
Endocrine Gland Exocrine Gland
Glands secretes its product straight into the Secretes product into a duct
blood These are like salivary glands that have a
It has no duct duct to the mouth
Pancreas has both endocrine and exocrine functions
As hormones travel around the body in the blood they come in contact with lots of cells
Only cells with specific shape (receptor complimentary) will be affected
Some hormones have a widespread affect whereas others are much more specific
The target cells are those that possess a

specific receptor on their plasma (cell surface)
membrane. That shape of the receptor is
complementary to the shape of the hormone
molecule. Many similar cells together form a
tissue.
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ADRENALINE
The Adrenal Glands are at the top of the kidney
Adrenaline is manufactured in the adrenal medulla in the

centre of the Adrenal gland
ADRENALINE IS UNABLE TO ENTER CELLS BECAUSE IT IS A

POLYPEPTIDE DERIVATIVE.
Because of this it has to affect the cell from outside the cell.
It has a secondary messenger mechanism.
Process of Adrenaline
Primary Messenger -
Adrenaline released into
blood
Adrenaline binds to cell
Adenyl Cyclase Inactive
Once the adrenaline

binds the Adenyl Cyclase
becomes active
ATP changed into cAMP
cAMP ac'vates
other enzymes in the cell to
control changes
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Functions of Adrenaline The adrenal cortex uses cholesterol to

The adrenal medulla manufactures adrenaline in produce certain steroid hormones. These
response to stress such as pain or shock. It has a have a variety of roles within the body
Mineralocorticoids - Help to control
widespread affect, most cells have adrenaline
receptors. It prepares the body for activity:- concentration of sodium and potassium in
Relax muscles in the bronchiole blood (such as Aldosterone)
- To get more air in
Increase heart rate Glucocorticoids to help control
- Get adrenaline around body metabolism of carbohydrates and proteins in
Increase stroke volume of heart the liver (such as cortisol)
Cause general vasoconstriction
- to raise blood pressure
Stimulate conversion of glycogen to glucose
- Respiration energy
Dilate pupils
- More light
Increase mental awareness
Inhibit action of the gut
- Not needed when running away
Cause body hair to erect
PANCREAS AND CONTROL OF BLOOD GLUCOSE LEVELS
The pancreas is a small organ below the

stomach.
The pancreas is an unusual because it

has both endocrine and exocrine
functions.
The majority of cells in the pancreas

manufacture and release digestive
enzymes which is part of the exocrine
function
Other areas of the pancreas called the

islets of Langerhans secrete hormones,
this is the endocrine function
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DIAGRAM OF PANCREAS
Blood to receive hormones

from pancreas
Food moves from stomach

into small intestine
Pancreatic Duct carries

fluid from the pancreas and Islets of Langerhan where
liver. This includes:- hormones are produced
Digestive Enzymes
Bile from liver - This
neutralises the acid
from the stomach
ISLETS OF LANGERHANS
WHAT ENZYMES DOES THE PANCREAS MAKE?
The cells that produce the enzymes in the pancreas The islets langerhans are small patches of
are found in small groups that are surrounded by tissue that have the endocrine function in the
tiny tubules.
pancreas.
The tubules join up to make the pancreatic duct
which carries fluid containing the enzymes into the
first part of the small intestine.
These include: -
Amylase - Carbohydrase
Trypsinogen - Inactive protease
Lipase
Sodium Hydrogencarbonate is also included which

makes the solution alkaline. This (as well as bile)
help to neutralise the digestive system from the
stomach
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The Islets of Langerhans have 2 sorts of cells that produce different hormones that produce opposite results.
- - Cells (Alpha Cells) - these cells manufacture and secrete glucagon to increase glucose
concentration
- -Cells (Beta Cells) - These cells manufacture and secrete insulin to decrease the concentration of
glucose
CONTROL OF BLOOD GLUCOSE
The concentration of blood glucose is carefully regulated

The concentration is monitored by the islets of langerhans.
A healthy adult s about 90-100mg per 100cm3 of blood. This can also be expressed as between 4 and
6 mmol dm-3
When it strays from this precise measurement the cells in the Islets of Langerhans detect the change
and start to secrete the required hormone.
WHAT HAPPENS WHEN BLOOD GLUCOSE LEVELS GET TOO HIGH?
The -cells detect the change if the blood-glucose level gets too high. They then secrete insulin into the
blood. It targets certain cells, these cells are hepatocytes, muscle cells and some other cells in the body.
When insulin binds to the receptors, adenyl cyclase inside each cell which then converts ATP into cAMP.
(cyclic AMP).
WHAT HAPPENS WHEN THERE IS TOO LITTLE

Insulin has many different effects on the body? GLUCOSE?
More glucose channels are placed into the cell surface -Cells secrete glucagon
membrane It targets liver cells (hepatocytes)
More glucose enters the cells because they break down things
It has the following effects:-
Glucose is converted to glycogen for storage (Glycogenesis) Conversion of glycogen to glucose
More glucose is converted to fats (glycogenolysis)
Use more fatty acids in respiration
More glucose used in respiration
The production of glucose by
This take blood out of the blood which lowers the blood glucose conversion from amino acids and
levels fats (gluconeogenesis)
This increases the concentration of

glucose in the blood
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Glucose Concentration
Rises
-Cells in the
Liver cells convert
islets of Langerhan
glycogen to glucose and
Detect rise in Blood
releases it into the
Glucose
blood
Glucagon detected by -Cells secrete insulin

receptors in liver cells into the blood
-Cells secrete glucogon Insulin receptors on

into the blood liver and muscle cells
detect insulin
Those cells
-Cells in the islets of remove glucose from the
langerhan detect fall in blood and convert it into
glucose glycogen
Glucose Concentration
Falls
20
DIABETES MELLITUS
A condition where the blood glucose level of the body isnt controlled properly
TYPE 1 DIABETES TYPE 2 DIABETES
Also known as insulin-dependant diabetes Also known called non-insulin dependant

-Cells dont produce any insulin diabetes
When food has been ingested the blood- Occurs late in life - often linked to obesity
glucose level rises and stays high Happens because the -Cells don't produce
This is called hyperglycaemia (This can result enough insulin or the bodies cells don't
in death) respond to it properly
It usually develops in children to young adults This increases the blood-glucose level
USING GENETICALLY MODIFIED BACTERIA TO HELP PATIENTS WITH DIABETES

Years ago the insulin that diabetics required was extracted from the pancreases of animals such as pigs and
other cattle, for type 1 diabetics. As genetic modification improved human insulin can be made from
genetically modified bacteria.
GM INSULIN HAS MANY ADVANTAGES
Its cheaper than extracting from animals

Larger quantities can be manufactured
GM bacteria makes human insulin which is more effective than animal insulin and has a less
chance of triggering an allergic response
There are less ethical reasons as vegetarians and religions may object to the use of animals
for insulin
Using Stem cells could Cure Type 1 Diabetes
Stem cells are unspecialised and so have the ability to develop into any type of cell. The treatment is still in
development but if it works diabetics wont have the need for regular injection.
Stem Cells
are These cells
are implanted The patient
encouraged to
into patients makes insulin as
grow into -
pancreas normal
Cells
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REGULATION OF INSULIN LEVELS
Controlling insulin secretion happens in 8 steps
Cell membranes of the -cells

contain both calcium and potassium
ion channels
The potassium ion

channels are usually open and
the calcium channels are closed.
Potassium ions diffuse out of the cell
making in the inside more
negative (-70mv)
When the glucose concentration is

high enough, glucose molecules then
diffuse into the cell
The glucose is used to metabolise

ATP
The extra ATP causes the potassium

channels to close
Because of this the potential

difference is changed - it becomes
less negative (more positive although
still negative)
This change causes the calcium ion

changes to open
Calcium ions enter the
cell and cause the secretion of
insulin by exocytosis by making the
vesicles containing insulin to fuse
with the membrane
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CONTROL OF HEART RATE IN HUMANS
The heart pumps blood around the body,

Autonomic Nervous System - An automatic, this can is to supply the body with oxygen
self governing system in which the body
controls aspects of itself. and all the nutrients that the cells need.
Different cells require different amounts of
these at different time. For example when
you are exercising then the cells will be respiring more to create energy so needs more nutrients.
How the heart can change
1. How many contrac'ons there are in a minute
2. How strong the contrac'ons are
3. The stroke volume (how much blood is pumped with each stroke) - increase blood pressure
The control of Heart rate
The heart myogenic

it has its own pacemaker called the SAN (Sinoatrial Node) - it can ini'ate a ac'on poten'al
The atrioven'rcular node receives this ac'on poten'al holds it for a frac'on of 'me before con'nuing
down the purknye 'ssue
The heart is supplied by the medulla oblongata in the brain
The nerves connect to the SAN
They do ini'ate the ac'on poten'al but aect the frequency of it.
The blood can also react to adrenaline in the blood
Vagus nerve reduce the heart

rate
The accelerator nerve speeds up the heart rate
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Factors affecting the heart rate
Factor Explain
Stretch Receptors Detected by stretch receptors in muscles, the send

impulses to the cardiovascular centre informing it
that there may be a need for extra oxygen - this
increases heart rate
Change In the pH When exercising more CO2 is produced which

lowers the pH. Its picked up by chemoreceptors in
the carotid arteries, the aorta and the brain, this
increases heart rate
Stoping Excerising When stoping exercising the the concentration of

CO2 falls. Therefore the heart rate declines
Adrenaline Its secreted in response to stress, shock anticipation

or excitement. This increases heart rate to prepare
the body for work
Blood Pressure monitored by stretch receptors in the walls of carotid

sinus. This is a small swelling in the carotid artery, if
blood pressure is too highs the receptors detect it
and reduces the heart rate
Pacemakers)were)miniaturised)in)the)1950s.)
This)allowed)the)pa;ent)to)wear)a)small)
plas;c)box)with)wires)inserted)through)the)
skin)to)act)as)electrodes)on)the)heart)muscle.))
Modern)pacemakers)are)about)4cm)long)and)
are)implanted)under)the)skin)and)fat)on)the)
chest)(or)within)the)chest)cavity).))
They)are)able)to)respond)to)the)
))))needs)of)the)pa;ent.))
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Excretion
25
Excretion
Liver
Functions of Liver
Kidneys
Formation of Urine
Reabsorbing Water
Osmoregulation
EXCRETION - The removal of

metabolic waste from the body, that is
the removal from the body of by-
products or unwanted substances from
normal cell process
EGESTION - the removal of undigested

food by the process of defecation.
These substances have never been in
There are two mainly excreted products: cells and so cannot be excreted
- Carbon Dioxide (CO2)
Excreted through lungs
Produced by every cell in the body
- Urea
Excreted through the Urethra
Made in the liver from excess amino acids
THE LIVER
- One of the largest organs in the body
- 30% of pumped blood with each pump goes through the liver
- 450cm3 every minute
- Blood arrives in two locations which is different to every other organ
Why does the Liver have 2 blood supplies?
It has two blood supplies because 1 carries oxygenated blood. This is vitally important to the liver cells who
need oxygen to respire as well as every other cell in the body. This is the liver own blood supply. However
the livers main function is to clean blood, for this reason the liver actually receives 3 times as much
deoxygenated blood than oxygenated blood.
Describe how liver cell structure ensures that the blood flows past as many cells as possible
Cells are never more than 2 away from a blood source, this ensures that there is a large surface area of
cells in contact with blood
Suggest which organelles may be particularly common in the cytoplasm of liver cells
Lysosomes and mitochondria
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Structure of the Liver
HEPATIC PORTAL VEIN

- From small intestine
- Deoxygenated blood
- Lower pressure
- 3x as much blood
- Blood rich in absorbed nutrients
HEPATIC ARTERY
- Directly from aorta
- Delivers oxygenated blood
- High blood Pressure
HEPATIC VEIN
- Deoxygenated blood away
-Joins vena cava
-Allows amino acids to join circulation
BILE DUCT
-Bile secretion
-Digestion and excretory function
-Liver uses the gall bladder for
storage
-Aids fat digestion, acid neutralisation
in the small intestine
Hep - To do with liver
HISTOLOGY OF LIVER
- Made up of cylindrical lobules

Up to 100000 in a human
- In the middle there is a branch of
hepatic vein
- Between lobules are branches of
hepatic artery and branches of hepatic
portal veins
- Blood flows throw the lobules and into
the branches of the hepatic vein
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HEPATOCYTES (CELLS THAT MAKE UP THE LIVER)

- Radiate out from the middle lobule
- Not normally more than 2 cells away from blood SINUSOID
supply - Carries blood between rows of cells
- Close contact to blood - Blood from the hepatic portal vein
KUPFFER CELLS BILE CANALICULI

- Specialised Macrophages - Carry bile produced by some hepatocytes
- found in sinusoid - From centre to the lobule on the outside to enter
- Capture and destroy bacteria by phagocytosis branch of bile duct
- Breakdown, recycle old red blood cells
- Product of haemoglobin in bilirubin
- Excreted in bile
- Makes poo brown
NADs are required

to oxidise and break
down fatty acids. If
liver has to detoxify
too much alcohol
there isnt enough
NAD to deal with
the fatty acids so
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FUNCTIONS OF THE LIVER
Formation of Urea
Every day we need 40-60g of protein but most Deamination

people in world have more than this. Amino This produces ammonia which is very soluble
acids cant be stored as the Amine group is toxic and toxic. This cannot be allowed to
but they contain a lot of energy. It would be a accumulate. An organic compound (Keto Acid)
waste to just excrete them. Because of this it is also produced and passed into the blood to
undergoes treatment in the liver before the go straight into respiration
Amino is excreted. It consist of 2 processes
The Ornithine Cycle

The ammonia is highly toxic and soluble. It has
to be converted to a less toxic form very quickly.
Its combined with CO2 to produce urea in the ycl e
ornithine cycle. Urea is less soluble and and n eC
thi
toxic than ammonia. Its is passed back into the rni
blood and transported to the kidneys to be nO
t the
filtered out in urine. It can be stored in the
n firs
bladder. tio
ina
am
De
29
DETOXIFICATION IN THE LIVER
Liver can detoxify many compounds

Some are produced by the body (Hydrogen Peroxide) or can be consumed (Alcohol and Drugs)
Toxins can be rendered harmless by
Oxidation
Reduction
Methylation
Combination with another molecule
Liver cells contain many enzymes that refer toxins less toxic
Such as catalase with converts hydrogen peroxide to oxygen and water
It has a high turnover rate - over 5 million molecules a minute
Detoxification of Alcohol
Its broken down in the liver using the enzyme ethanol dehydrogenase to produce
ethanal. The ethanal is then broken down using the enzyme ethanal dehydrogenase to
produce ethanoic acid. This combines with coenzyme-A to produce acetyl coenzyme A
which can be used in respiration. The Hydrogen atoms released during this combine
with NAD to produce reduced NAD.
THE KIDNEY(S)
LOCATION OF THE KIDNEYS
2 kidneys lay at the back of the

abdominal cavity (Close to the
backbone)
EXTERIOR VIEW OF KIDNEY
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GROSS STRUCTURE OF A KIDNEY
Renal Pelvis
Renal Artery
Calyxes
Renal Vein
Ureter
Medullae Cortex
STRUCTURE OF THE NEPHRONS

Bowmans Capsule Proximal
Convoluted Tube
Efferent Arteriole
Glomerulus
Afferent Arteriole
Distal Convoluted
Tube
Renal Artery
Renal Vein
Collecting Duct
Loop of Henle
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WHERE ARE THE NEPHRONS?
HOW DO THE NEPHRONS WORK?
Ultrafiltration The endothelium of the capillaries -

contains narrow gaps between the cells
Blood flows into the glomerulus through the which allows so blood plasma and the
afferent arteriole. This is wider than the efferent dissolved substances can pass through
arteriole. This ensures that the blood in the
glomerulus is under increased pressure. The The Basement Membrane - Consists of a
pressure in the glomerulus is higher than that fine mesh of collagen fibres and
in the bowmans capsule. This pushes fluid glycoproteins. This acts as a filter to
from the blood to the bowman's capsule. molecules with a molecular mass (Mr) of
over 69000. This keeps blood and most
There are 3 levels of the barrier between the proteins in the capillaries.
blood of the capillaries and the bowman's
capsule.
Epithelial cells of the of Bowmans
The pressure pushes out blood plasma Capsule (Podocytes) - They have a very
containing dissolved substances into the lumen particular shape. They have finger-like
of the bowman's capsule. This includes the projections called major processes. This
following: keeps space between the cells. This allows
fluid to enter the lumen of the Bowman's
- Water capsule
- Amino Acids
- Glucose
- Urea
- Inorganic Ions
Sodium
Chloride
Potassium
32
The blood cells and proteins are left in the capillary. The presence of proteins lowers the water potential
greatly. This is important at a later stage as some water and fluid is kept in but not enough.
The total volume of fluid filtered out by both kidneys is 125cm3min-1. This equates to about 180dm3day-1. So
much of the water is needed to be reabsorbed.
Selective Reabsorption
The filtrate flows along the lumen of the bowman's 1. On cell surface membrane closest to
capsule to the proximal convoluted tubule. Here 85% blood capillary sodium potassium pumps
of the filtrate is reabsorbed. This includes: (Actively) Na+ out of cell and K+.
All glucose
All Amino Acids
Some salts
Some Water
Happens in a few stages:
2. As Sodium ions are pumped out the

concentration of sodium inside the cell falls
3. This causes them to diffuse back into

the cell through co-transporter proteins which
couple the movement with amino acids and
glucose (Facilitated Diffusion)
Cell Adaptions to achieve Reabsorption
- Cell Surface Membrane is highly folded

to create Microvilli (increases Surface
area to volume)
- Contains loads of co-transporter 4. This causes the concentration of
proteins for facilitated diffusion these substances inside the cell to rise. This
- Contains loads of Mitochondria to causes them to diffuse out into the capillary by
supply ATP for active transport via facilitated diffusion.
- Membrane to the blood capillaries is
also highly folded and has lots of
sodium-potassium pumps to pump the
Na+ and K+
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REABSORPTION OF WATER
The role of the loop of Henle is to create a low which means very negative water potential in the tissue of the
medulla. This allows even more water to be reabsorbed.
HOW IS A WATER POTENTIAL GRADIENT CREATED?
The descending limb is highly

permeable to water - This means
water is lost and reabsorbed back
into capillaries
At the bottom of the loop the

concentration gradient allows
Sodium Chloride ions to diffuse out
into the medulla
At the top of the ascending

limb Sodium Chloride is actively
transported out - This lowers the
water potential outside the defending
limb to encourage the water to
leaver by osmosis
Some of the sodium chloride

The Loop Of Henle ions diffuse back into the ascending
limb - They cannot leave the
- Consists of an: ascending limb though
- Descending Limb that goes into the
Medulla
- Ascending Limb that goes into the
Cortex
- This arrangement allows Salts to be to
be transferred from the ascending limb
to descending limb
- Tissue fluid in the medulla has a very
low water potential
34
OSMOREGULATION
Urine
Food Sweat
Water
Drink Water Water Vapour in
Gained
Metabolism Lost By: Exhaled Air
(Respiration) from:
Faeces
How Does it Happen?
The walls of the collecting duct can respond

to the hormone ADH or anti-diuretic
hormone. It ca cause a chain of enzyme
reactions to happen in the cell.
The end result causes vesicles containing
water-pearmable channels into the cell
membrane. These are called aquaporins.
More ADH means that more water is
absorbed in the collecting duct, whereas
less ADH causes less water to be
reabsorbed.
HOW IS THE CONCENTRATION OF ADH ALTERED?
The water
potential is monitored in The cells respond to the effects of
the brain by osmoreceptors osmosis from the blood. When the blood
in the hypothalamus has low WP the shrink
They cause
neurosecretory cells to release and produce ADH.
It is manufactured in the cell body and travels down the axon
to the terminal bulb in the posterior pituitary gland
and stored until needed
It then enters the blood and

travels around the capillaries till its used. It is
slowly broken down and has a half life of 20
minutes
35
WHERE IS ADH MADE?
Low water potential of the blood causes the

osmeoreceptros to trigger neurosecretory cells in the
hypothalamus
These are specialised neurones that produce and release
ADH
ADH is manufactured in the cell bodies of these
neurones
It then flows down the axon to the terminal bulb in the
posterior pituitary gland - Its stored here until its needed
When the neurosecretory cells are stimulated they send
an action potential down the their axons which realises the
ADH into the blood
KIDNEY FAILURE
When the Kidneys fail the body cannot remove excess water and
waste products. This leads to a build up of the substances which
can quickly lead to death.
TREATMENT OF KIDNEY FAILURE
Dialysis
- Most common type of treatment
- It removes waste, excess fluid and salt from the body by passing the blood over a dialysis membrane.
This is a partially permeable membrane that allows the exchange of substances between blood and the
dialysis fluid
- The Dialysis fluid contains the correct amount of salts, urea water and other certain substances. This
means that anything thats too high in the blood diffuses out of it and anything thats not got enough of
in the blood diffuses from the dialysis fluid
It needs a careful diet
HAEMODIALYSIS PERITONEAL DIALYSIS

The filter is in the bodes own own abdominal
blood from a vein is passed through a machine membrane. 1st a Surgeon implants a permanent
that contains the artificial dialysis membrane. tube in the abdomen. Dialysis solution is poured
Heparin is added to avoid clotting and any through the tube and fills the space between the
bubbles are removed before retiring to the blood. abdominal wall and organs. After several hours
Its usually carried out 3 times a week at a clinic the solution is removed. Its usually done several
but can be done at home consecutive sessions daily. Can be done whilst
walking about
36
KIDNEY TRANSPLANT
During the procedure the old kidneys are usually led in place unless they are cause infectious or are
cancerous. The donor is usually a living relative who is happy to donate a kidney. Is major surgery. After the
operation the patient will feel better although the immune system will recognise it a foreign object. Patients
are given immunosuppressant drugs to prevent this.
Advantages Disadvantages
Freedom from time consuming dialysis Need immunosuppressants for life of kidney
Diet is less limited Need major surgery under a general anaesthetic
Feeling better physically Risks of surgery include infection, bleeding and

damage to surrounding organs
A better quality of life - Able to travel Frequent checks for signs of organ rejection
No longer seeing oneself as chronically ill Side effects: anti-rejection medicines cause fluid
retention and high blood pressure;
immunosuppressants increase susceptibility to
infection
TESTING FOR PREGNANCY
These tests detect the hormone human chorionic gonadotropin (hCG) thats only found in
pregnant women:
1. A stick is used with an application area that contains antibodies for hCG bond to coloured
bead (Blue)
2. When urine is applied to the application area any hCG will blind to the antibody on the beads
3. The urine moves up the test strip, carrying the beads with it
4. The test strip has antibodies to hCG attached (Immobilised)
5. If there is any hCG present the test strip turns blue because the immobilised antibodies bind
to any hCG attached to the blue beads, concentration the blue beads in that area. If no hCG
is present the beads will pass through the test area without binding to anything and so wont
go blue
TESTING FOR STEROIDS
1. Anabolic steroids are drugs that build up muscle tissue

2. Testosterone is an anabolic steroid as well as Nandrolone
3. Some athletes are banned from taking anabolic steroids. This is to try to stop the misuse of
steroids that can have dangerous side effect such as liver damage. Also. its considered
unfair to the athletes that dont use them
4. Steroids are removed from the blood in the urine
5. Urine is tested using gas chromatography
6. The urine is vaporised and passed through a column containing liquid. Different substances
move through the liquid at different speeds.
37
KEY TERM DEFINITION
EXCRETION The removal of Metabolic waste from the body
METABOLIC WASTE Consists of waste substances that may be toxic or

are produced in excess by the retains inside cells
DEAMINATION The removal of amine group from an amino acid to

produce ammonia
HEPATIC PORTAL VEIN Is an unusual blood vessel that has capillaries at

both ends - it carries blood from the digestive
system to the liver
FUNCTION OF KUPFFER CELLS appears to be the breakdown of and recycling of old

blood cells
BILIRUBIN One of the waste products from the breakdown of

haemoglobin
UREA is an excretory product formed from the breakdown

of excess amino acids
ORNITHINE CYCLE The process in which ammonia is converted to urea.

It occurs partly in the cytosol and partly in the
mitochondria, as ATP is used
DETOXIFICATION Is the conversion of toxic molecules to less toxic or

non-toxic molecules
NEPHRON Is the functional unit of the Kidney. It is microscopic

tubule that receives fluid from the blood capillaries
in the cortex and converts this into urine, which
drains into the ureter
GLOMERULUS Is a fine network of capillaries that increases the

local blood pressure to squeeze fluid out of the
blood. It is surrounded by a cup-or-funnel-shaped
capsule which collects fluid and leads into the
nephron
SELECTIVE REABSORPTION useful substances are reabsorbed from the nephron

into the blood stream while other excretory
substances remain in the nephron
AFFERENT VESSELS AND EFFERENT VESSELS Afferent vessels bring blood into the organs.
Similarly, efferent vessels carry blood away from the
organ. In the glomerulus the efferent vessel is an
arteriole which is muscular to change the blood
pressure.
ULTRAFILTRATION is the filtration at a molecular level - as in the

glomerulus where large molecules and cells are left
in the blood and smaller molecules pass into the
bowman's capsule
PODOCYTES Specialised cells that make up the lining of the

Bowman's capsule
MICROVILLI Microscopic folds of the cell surface membrane that

increase the surface area of the cell
38
CO-TRANSPORTER PROTEINS Protein in the cell surface membrane that allow the
facilitated diffusion of simple ions to be
accompanied by transport of a larger molecule such
as glucose
SODIUM-POTASSIUM PUMPS Diffusion that is enhanced by the action of proteins

in the cell membrane
HAIRPIN COUNTERCURRENT MULTIPLIER is the arrangement of a tubule in a sharp hairpin so

that one part of the tubule passes close to another
part of the tubule with fluid flowing the other way.
This arrangement can be used to create a very high
concentration os solutes
OSMOREGULATION the control and regulation of the water potential of

the blood and body fluids - in humans the kidney
control the water potential of the blood
DISTAL CONVOLUTED TUBE Is coiled portion of the nephron between the

collecting duct and loop of Henle
DIALYSIS The use of a partially permeable membrane to filter

blood
DIALYSIS MEMBRANE Partially permeable membrane that separates the

dialysis fluid from the patients blood in a dialysis
machine
DIALYSIS FLUID A complex solution that matches the composition of

the body fluids
HAEMODIALYSIS Blood is taken vein and passed through a dialysis

machine so that exchange can occur across an
artificial partially permeable membrane
PERITONEAL DIALYSIS Dialysis fluid is pumped into the body cavity so that
exchange can happen across the peritoneal
membrane
HUMAN CHORIONIC GONADOTROPHIN (hCG) is a hormone released by human embryos;

its presence in the mothers urine confirms
pregnancy
MONOCIONAL ANTIBODIES are identical because they have been produced by

cells that are clones of the original cell
ANABOLIC STEROIDS are drugs that mimic the action of steroid hormones
that increase muscle growth
GAS CHROMATOGRAPHY is a technique used to separate substances in a

gaseous state. A chromatogram is a chart produced
when substances are separated by movement of a
solvent along a partially permeable material such as
paper or gell
39
Photosynthesis
40
Its thought that this process first evolved
OVERVIEW OF PHOTOSYNTHESIS in prokaryotes at least 2500 million years
ago. Its an important process because
nearly all life on Earth rely depend on it.
Its a two part process
It requires light, Carbon Dioxide and Water It transforms light energy into chemical
The actual equations go as follows:- potential energy thats available to
consumers and decomposers. This
Carbon Dioxide + Water Glucose + Water +Oxygen
process release oxygen from water which
6CO2 +12H2O C6H12O6 + 6O2 + 6H2O allows other forms of processes and
organisms such as humans to respire and
evolve.
Some Key Words
Autotrophs Organisms that make their own food using

simple organic compounds
Photoautotrophs Organisms that use light as a source of

energy
Chemoautotrophs Organisms that use chemical energy (this

includes some bacteria)
Heterotrophs Organisms that gain its nutrients from

complex organic molecules. They digests
them to simpler, soluble molecules and then
respire some of them to obtain energy -
these are considered consumers in food
chains
THE STRUCTURE OF CHLOROPLASTS
They are usually disc shaped and 2-10 long

They have a double membrane called an envelope
The inter membrane space is about 10-20nm wide which is between the inner and outer membrane
The outer membrane is permeable to many
small ions
The inner membrane is less permeable and
has transport protein embedded it
Its folded into lamalle (thin plates)
which are stacked up
Each stack is called a granum (plural
= Grana)
Intergranal Lamellae Connect the Grana
Each compartment is called a Thylakoid
The fluid surrounding the grana is called the
stroma
Starch, DNA and Ribosomes are all found in
the stroma matrix which are all used to make
proteins
41
PHOTOSYNTHETIC PIGMENTS AND PHOTOSYSTEMS
Photosynthetic Pigments are embedded in the thylakoid membrane and absorb the light energy
Each pigment absorbs a certain range of wavelengths

This means they have their own unique peak of absorption
They appear as the colour they are reflecting
Lots of pigments work together to absorb as much light as possible
They are funnelled shaped and held in place by proteins
ACCESSORY PIGMENTS - Surround the

Primary Pigment Reaction Centres
and supply light energy to them
PRIMARY PIGMENT REACTION CENTRES -

This is where the light energy collected
from the accessory pigments excites
electrons. They contain chlorophyll
Peak Absorption wavelength

Pigment Colour Function In Photosynthesis
(nm)
Chlorophyll a Yellow-Green 430662

Absorbs Red and Blue-
Chlorophyll b Blue-Green 453642 Purple Light
Carotene Orange 450 Absorb Purple light, protect

Chlorophylls from damage
Xanthphyll Yellow 450-470 from light and oxygen
42
Chlorophyll - A special Pigment
Is a mixture of pigments that have similar

molecule structure
They all have a long hydrocarbon (phytol)
chain and a porphyrin which is similar to
haem but has magnesium instead of iron
When light hits chlorophyll a pair of electrons
get excited
There are two types of Chlorophyll and they
both appear yellow green colour
Chlorophyll a - P680
Chlorophyll b - P700
They are both found at the primary pigment
reaction centre
The number refers to the peak absorption in Accessory Pigments -
nm
Chlorophyll a also absorbs blue light around - Contain Carotenoids which reflect yellow and
wavelength 450nm orange light
Chlorophyll b absorbs light of wavelengths - They Absorb Blue light
around 500nm and 640nm and appears blue- - They dont contain a porphyrin group and
green arent directly involved with the LDR
- They absorb light energy thats not absorbed
very well by the chlorophyll and then pass the
energy to the chlorophyll at the bottom of the
photosystem
- Carotene (Orange) and Xanthophyll (yellow)
are the main carotid Pigments
The wavelengths that the pigments absorb can

be summarised with a graph
43
THE LIGHT DEPENDENT STAGE
1. Light is absorbed by the pigments in photosystem II (PSII)

a. This energy is then transferred to other pigment molecules until it reaches chlorophyll a
b. This excites a pair of electrons from the photolysis of water at the primary pigment reaction
centre
c. The Equation for this is
2. The Primary Electron Acceptor captures these excited electrons

3. The Excited electrons pass from the primary acceptor down an Electron Transport Chain
a. They pass through 3 carriers
THE LIGHT DEPENDENT STAGE
b. They release energy as they pass through them

c. This energy is used to pump H+ ions through to the thylakoid space (Chemiosmosis)
4. The flow of protons back through ATP synthase adds phosphorous grow to ADP to make ATP
5. Photosystem I (P700) also absorbs light energy. Just like with PSII
a. This is used to excite electrons in the primary pigment reaction centre
b. Those electrons then travel down another electron transport chain
c. The de-energised electron from the previous step now passes through to PSI to the same place
in PSII to be re-energised
6. The second electron transport chain contain Ferrodoxin
7. The target is NADP Reductase The diagram below shows the journey of
a. This reduced NADP+ to NADPH Electrons (Blue Line) and Protons/H+ ions
(Red Line)
This is non-cyclic
phosphorylation.
This is because
there is no cycle.
We want to
make 18 ATP
and 12 NADPH.
If we do this
process 12 times
we only get 12 of
each. To account
for this another
process called
cyclic
phosphorylation.
44
CYCLIC PHOSPHORYLATION
Only happens in photosystem I (P700)

It can only occur if there is plenty of light and water
The Electrons are reenergised in photosystem I cary on as usual but if there is plenty of light and
water is lots of energy and electrons.
To avoid wasting this extra energy there is a clever way to use it
Extra electrons are taken by the PSI and energised, but instead of going down the usual Electron
transport chain they go back into the cyctochome complex on the first electron transport chain and
continue down like before
This pumps extra H+ ions into he lumen to then flow through the ATP synthase to make ATP
The box below shows the process which loops as electrons can go round and round
Its important to note that the original non-cyclic phosphorylation is still going on whilst this cycle is
occurring
THE LIGHT INDEPENDENT STAGE
This stage involves the Calvin Cycle
Its like the krebs cycle whereby it is a cycle of enzyme controlled reactions
The ATP and NADPH that were made in the LDR are now used to provide the energy required to make
glucose
The process of making organic compounds from inorganic ones is called fixation. In this case Carbon
Dioxide is Fixed into glucose so its called Carbon Fixation
Carbon Dioxide + ATP + NADPH Glucose
6CO2 + 6 RuBP + 18 ATP + 12 NADPH C6H12O6 + 6 RuBP
Recycled
45
1. Carbon Dioxide from the Air Binds to a Five Carbon Compound in the Stroma called Ribulose
Biphosphate (RiBP)
The Reaction is catalysed by RuBP Carboxylase or Rubisco. This 6 carbon molecule is unstable and the
reaction can be summarised as
The black
circles
THE LIGHT INDEPENDENT STAGE

represent
carbon atoms
2. The unstable 6 carbon compound splits in half to form two carbon chains called glycerate-3-
phosphate.
At This point the Carbon Dioxide is considered fixed
3. ATP and NADPH from the first stage of photosynthesis turn the glycerate-3-phosphate into trios
phosphate (TP)
12 Glycerate-3-phosphate + 12 ATP + 12 NADPH 12 Triose Phosphate + 12 ADP + 12 Pi + 12 NADP+
+ Reduced 12
Triose Phosphate
Glycerate-3-Phosphate
12 ATP + 12 Reduced 12
NADPH ADP + 12 Pi +
12 NADP+
4. The Triose Phosphate made can now either be recycled and turned back into RuBP or used to
make sugar based compounds needed by the plant
12 Triose Phosphate Sugar Phosphate + Pi + 10 Triose Phosphate
12 Triose Sugar Phosphate + Pi 10 Triose Phosphate

Phosphate
This shows that 1 glucose molecule is made from 6 Carbon Dioxide Molecules entering the cycle
46
5. The 10 trios Phosphate Molecules are turned back into 6 RuBP molecules to enter the cycle at the
start again. This requires ATP.
10 Triose Phosphate 6 Ribulose Biphosphate
6ATP 6ADP
THE CYCLE IS CALLED THE CALVIN CYCLE
Products of the Calvin Cycle
g3p can be used to make amino acids and

fatty acids
pairs of TP can be combined to make
hexose sugars such as glucose
glucose can be Isomerismed to make other
hexose sugars such as fructose
glucose and fructose molecules can be
combined to make disaccharide sugar such
as sucrose
hexose sugars can be polymerised into
carbohydrates such as starch or cellulose
TP can be converted into glycerol and then
this can combine with fatty acids to form
lipids
Calvin'cycle:' CO2
Rubisco
Amino acids
RuBP 6 (G3P)
Reduced Fatty acids
ADP ATP
NADPH
ATP NADP ADP + Pi
Starch Triose
phosphate
Hexose
Glycerol Lipids
e.g Glucose
Cellulose
Sucrose
Fructose 47
LIMITING FACTORS
3 things limit the rate of photosynthesis
Light Intensity
Carbon Dioxide Levels
Temperature
LIMITING FACTORS ARE THINGS THAT LIMIT HOW FAST A METABOLIC PROCESS (OR REACTION) CAN GO
At any given time the limiting factor will be the one that is the least favourable
Effect of Light on Rate of Photosynthesis
When light is the limiting factor the rate of photosynthesis is directly

proportional to the light intensity
There are 3 effects of light

EFFECT OF LIGHT
Stomata in the leaf get opened so CO2 can get

into the leaf
Causes the enzyme to split water, releasing H+

and e-leading the production of O2 (Photolysis)
Light is absorbed by the chlorophyll, exciting

electrons in the light dependent stage of
photosynthesis
48
Effect Of Carbon Dioxide
The concentration of CO2 in the atmosphere is around 0.039% by volume or 0.058 by mass, it varies
depending on location
EFFECT OF CARBON DIOXIDE

Increasing the Carbon Dioxide Levels will make more raw material available and so can increase the rate
as levels increase if it is the limiting factor
History of Carbon Dioxide Levels -
Levels fell during the carboniferous period as

fossil fuels were formed and CO2 was trapped
inside
It rose during the Triassic and Jurassic Period

before falling to preindustrial levels
Levels have been increasing since the industrial

revolution due to bring fossil fuels
Greenhouse levels are typically lower at about

0.02% as many plats growing in close proximity
will be absorbing it
EFFECT OF TEMPERATURE
Effect of Temperature
as temperature increases, the rate of photosynthesis increases but only to a certain point
The temperature mostly effects the light independent stage
The rate doubles for every 10C rise from 0 to 25C as the enzymes in the calvin cycle can work faster
After 20C the rate levels off as the enzymes become less efficient
This is partly due to the increased competition between CO2 and O2 in the active site of rubisco (Rubisco
can also carry out the reverse reaction called photo-respiration)
Temperature can also sweat the plant causing it loose water and close the stomata letting less gas in
49
Photosynthometer - apparatus used to measure the

rate of photosynthesis under various conditions
HOW DO LIMITING FACTORS EFFECT THE CALVIN CYCLE ?
EFFECT OF LIGHT ON THE CALVIN CYCLE
When light increase the levels of NADPH and ATP increase

This supplies energy and hydrogen for the light
independent stage
ATP and NADPH are used to convert GP into TP and
regenerate RuBP from TP
If there is no light then the levels of ATP and NADPH fall
This means that GP cannot be converted into TP as there
is No ATP or NADPH
Therefore the levels or GP will increase and TP and
RuBP will fall as they are not being made
GP levels will level off as there is no more RuBP to make
more
EFFECT OF CARBON DIOXIDE LEVELS ON THE CALVIN CYCLE
If there is lots of carbon dioxide then carbon fixation will

continue so long as nothing else is limiting the rate
Therefore the levels of GP, TP and end products will
increase
Opening stomata to let more CO2 in can let water vapour
out causing the plant to wilt and stress which causes them
to close stopping CO2 enter
If levels fall below 0.01% RuBP will accumulate (as little
CO2 is available to be added to make GP etc)
EFFECT OF TEMPERATURE ON CALVIN CYCLE
At first increased temperature will increase the rate of photosynthesis as the enzymes work more
efficiently and photolysis occurs more frequently
Above 25C oxygenate activity of rubisco increases over carboxylase dissipating the ATP and
NADPH
Very high temperatures can also damage the enzymes so they don't work
Increase temperature cause stomata to close allowing less CO2 in
50
Respiration
51
WHY DO LIVING ORGANISMS NEED TO RESPIRE
THE ROLE OF ATP
Its a phosphorylated nucleotide. Its considered a high energy intermediate in the cell. It carries
energy around the cell to where its needed. Its synthesised from ADP and a inorganic phosphate
(Pi) from energy releasing reactions. ATP
WHAT IS ENERGY? diffuse to the part of the cell that its needed.
When it gets to where its needed it is broken
It exists as potential and kinetic energy, there are back down into ADP and (Pi). Chemical
a few things to remember with energy. energy is released form the phosphate bond
and used by the cell. It catalysed by ATPase.
Energy :- The ADP and Inorganic phosphate are
recycled an the process starts again.
cannot be deterred but converted from one
form to another
Measured in joules or kilojoules
has many forms such as sound, light, heat,
electrical and atomic
The overall equation for Aerobic Respiration
C6H12O6 + 6O2 6CO2 + 6H2O + Energy
MITOCHONDRIA
There are 4 stages in respiration.

These are glycolysis, the link
reaction, the Krebs cycle and
oxidative Phosphorylation.
The first 3 stages are a series of
reactions, the products of which
are used in the final stage to
make loads of ATP. The first
stage takes place in the
cytoplasm of the cell the other 3
stages take place in the
mitochondria. All cells use glucose to respire, but organisms can also break down other complex
organic molecules. Which can then be respired.
How are Mitochondria Specialised to carry out its function?
The matrix is the place where the link reaction and Krebs cycle happen. It contains:-
all the required enzymes
SUMMARY OF RESPIRATION Molecules of coenzyme NAD
Oxalacetate - the 4 carbon compound that accepts acetate from the link reaction
Mitochondrial DNA, codes for mitochondrial enzymes and proteins
Mitochondrial ribosomes where the proteins are accepted
52
Key CO2
Cytoplasm O2
Mitochondrial Matrix ATP
Inner Membrane of Mitochondria Reduced NAD (NADH)
Pyruvate Reduced FAD
Acetyl Co A
Glycolysis -
This happens in the cytoplasm of all cells
that respire. Its an ancient biochemical
pathway. It doesnt need oxygen and can
take place in aerobic or anaerobic
conditions. During it a glucose (six carbons)
is broken down into two molecules of pyrite
(3 carbons)
Link Reaction -
This happens in the matrix of mitochondria.
Pyruvate is dehydrogenated (hydrogen
Removed) and decarboxylated (carboxyl
removed) and converted to acetate
Krebs Cycle -
Also takes place in the matrix of
mitochondria. Acetate is carboxylated and
dehydrogenated
Oxidative Phosphorylation (Electron Transport Chain) -

Takes place in the folded inner membrane (cristea) of the mitochondria. Here ADP is
phosphorylated to ATP
53
GLYCOLYSIS
STAGE 1 - PHOSPHORYLATION
Glucose is a hexose sugar meaning that it contains six carbons. Its

stable and so needs to be activated before it can be spilt
1. 1 ATP is hydrolysed and a phosphate group group is released.

ATP ADP
This joins the glucose at the carbon 6 (Glucose-6-Phosphate)
2. This is changed into Fructose-6-Phosphate
3. Another ATP is hydrolysed and the phosphate group and
ATP attaches to Fructose-6-Phosphate at carbon 1. This is a ADP
activated hexose sugar called Fructose 1,6-bisphosphate
4. The energy realised from the ATPs is used to activate the
hexose sugar and prevents it from leaving the cell. Its referred
to as hexose 1,6-bisphosphate
5. 2 Molecules of ATP are used
STAGE 2 - SPLITTING HEXOSE 1,6-BISPHOSPHATE
Each molecule of Hexose 1,6-Bisphosphate is split into two

molecules of a triose phosphate (3 carbon Sugar) with each one
having a phosphate group attached
STAGE 3 - OXIDATION OF TRIOSE PHOSPHATE

NAD NADH
1. Although anaerobic and oxidation process is needed
2. Two hydrogen atoms with electrons are removed from each
NAD trios phosphate molecule NADH
3. Its aided by coenzyme NAD (nicotinamide adenine
dinuceotide) - Its a hydrogen acceptor
4. NAD combines with hydrogen atoms and becomes reduced
ADP NAD or NADH
5. So here 2 molecules of NAD are reduced per molecule of ATP
glucose and 2 molecules of ATP are formed by substrate-level
ADP phosphorylation ATP
54
STAGE 4 - CONVERSION OF TRIOSE PHOSPHATE TO PYRUVATE
1. 4 Enzyme controlled reactions convert each triose phosphate ATP

ADP
molecules to a molecule of pyruvate
2. Pyruvate is a 3 Carbon molecule
3. During the process another 2 molecules of ADP are ATP
ADP
phosphorylated to two molecules of ATP by substrate level
phosphorylation
THE LINK REACTION
Ultimately the link reaction is the carboxylation and dehydrogenation of pyruvate to acetate by
enzyme controlled reactions.
Pyruvate decarboxylase
Pyruvate Dehydrogenase
Removes hydrogen atoms Removes a carboxyl group,

from pyruvate which eventually becomes
Carbon Dioxide (CO2)
COENZYME NAD - ACCEPTS HYDROGEN ATOMS
COENZYME A ACCEPTS ACETATE AND BECOME ACETYL COENZYME A - THIS CARRIES ACETATE TO THE
KREBS CYCLE
No ATP is Produced,
The following equation summarises the link reaction:-
however each NADH
will take a pair of
hydrogen atoms to 2pyruvate+2NAD++2CoA 2CO2 + 2reduced NAD + 2acetyl CoA
the inner
mitochondrial
membrane where The reaction accounts for the 2 molecules of pyruvate from one
they will be used molecule of glucose
during oxidative
phosphorylation to
make ATP
55
Acetyl CoA CoA
THE KREBS CYCLE
Acetate
Oxalacetate Citate (6C)
Reduced
NAD
CO2 Reduced NAD
4C Compound
5C Compound
Reduced
FAD
4C Compound
Co2
Reduced NAD
4C Compound
ATP
STEP 1
Acetate is offloaded from coenzyme A

The acetate can then join a 4-carbon compound called oxalacetate
This forms a 6 Carbon compound called Citrate
STEP 2
Citrate is decarboxylated (Removes a molecule of carbon dioxide)

Its then dehydrogenated (removes a pair of hydrogen atoms)
This forms a 5 carbon compound
the hydrogen atoms are accepted by NAD and becomes reduced
STEP 3
The 5 Carbon compound is decarboxylated and dehydrogenated

This forms a 4 Carbon compound and another molecule of NAD is reduced
STEP 4
The 4 carbon compound is then changed into another 4 carbon compound

During this a molecule of ADP is Phosphorylated into ATP (By substrate Level Phosphorylation)
STEP 5
This 4 Carbon compound is then changed into another 4 Carbon compound

A molecule of reduced FAD is released
STEP 6
The third 4 Carbon molecule is is further dehydrogenated and regenerates oxalacetate

A molecule of NAD is reduced
56
For each molecule of acetate there is one turn of the cycle, therefore there is
two whole cycles per molecule of glucose because a molecule of glucose
makes 2 molecule of pyruvate
Product per molecule of Link Reaction Krebs Cycle

glucose
Reduced NAD 2 6
Reduced FAD 0 2
Carbon Dioxide 2 4
ATP 0 2
Both of these reactions occur in the mitochondrial matrix
Oxygen isnt used in these reactions, THE FINAL STAGE OF AEROBIC RESPIRATION
however they wont occur in the absence
It involves electron carriers embedded in the
of oxygen:- mitochondrial membranes
The membranes are folded into cristae
Glucose isnt the only food substrate increasing the surface area
that can be respired Reduced NAD and FAD are deoxidised
Fatty acids can be broken down into when they donate their hydrogen atoms
acetate and enter the Krebs cycle by which get split into protons and electrons
CoA The first electron carrier accepts electrons
Amino groups can be deaminated and from reduced NAD is called complex I, called
then the molecule can enter the Krebs NADH - Coenzyme Q reductase (Or NADH
cycle or be changed to acetate or dehydrogenase)
pyruvate The protons go into solution in the matrix
CHEMIOSMOSIS AND OXIDATIVE PHOSPHORYLATION
NB - ALWAYS REFER TO PROTONS BEING

PUMPED INTO THE INTER MEMBRANE SPACE.
DONT SAY THAT THEY ARE ACTIVELY
TRANSPORTED AS THIS IMPLIES ATP IS USED
Oxidative Phosphorylation - is the
AND, IN THIS CASE, ITS THE ENERGY FROM
formation of ATP by adding a phosphate
THE ELECTRON FLOW, NOT ATP
group to ADP, in the presence of oxygen
which is the final electron acceptor
57
STEP 1
The molecules of Reduced NAD

and Reduced FAD are deoxidised
by donating 2 hydrogen atoms to
the electron carriers
One hydrogen is split into a proton
and electron so each NADH2 and
FADH2 donate 2 protons and 2
electrons
STEP 2
The electrons from the reduced NAD are accepted by the first electron carrier
It a protein complex called Complex I or reduced NAD Dehydrogenase
The electrons are passed along the chain to the next carrier Complex II
This flow of electrons along the chain releases energy which complex I uses to pump protons
through to the inter membrane space
STEP 3
Two more electrons from the hydrogen

atoms of a reduced FAD molecule are
accepted by Complex II (making there four
present electrons in Complex II)
STEP 4
These four electrons are passed along to

complex III (Transported by coenzyme-Q) -
This releases energy
This energy is not used by Complex II as
Complex II doesnt transport protons
The four electrons are accepted in pairs
by complex III, here they are transported
to Complex IV (Coenzyme cytochrome C)
This is used to pump a proton into the
inter membrane space
58
STEP 5
The four electrons are then donated

one by one to molecular oxygen , this
also accepts 4 protons
two from the deoxidised FAD
and 2 which are pumped back
through the membrane using the
enzyme at the end of the ETC to form
water - a waste product
STEP 6 - CHEMIOSMOSIS AND OXIDATIVE

PHOSPHORYLATION
As electrons are passed along the

chain energy is released
This is used to pump protons over the
membrane
This creates a proton gradient where
there is a high concentration down the
gradient towards the matrix - this is
chemiosmosis
At the end of the ETC is a enzyme
called ATP Synthase - this is where
oxidative phosphorylation happens
Overall equation is ADP + Pi ATP
The concentration gradient of the protons flow through the ATP synthase
This drives the ATP synthase rotational part outside the membrane
This allows a molecule of ADP to join with a phosphate group (Pi)
59
EVIDENCE FOR CHEMIOSMOSIS
It was already clear by the 1940s that there was a link between the oxidation of sugars and the
formation of ATP
Before the 50s scientists knew that Reduced NAD linked metabolic pathways such as the krebs
cycle and the production of ATP
What wasnt known was the mechanism for ATP production
It was thought that the energy associated with the Reduced NAD was stored in a high energy
intermediate before producing ATP
This high energy intermediate could not be found
By the 60s scientists were extracting mitochondria and examining them with electron microscopes
and special staining techniques. They were able to identify: -
- An outer and Inner membrane with a space in-between
- The inner membrane was folded into cristae
- The inner surface was covered with mushroom shaped particle (small, 9nm)
PETER MITCHELL
Peter Mitchells theory was not greeted with
- The year was 1961 when Peter Mitchell, A content by the scientific community because
British Biochemist, realised that a build up of it was radically different to that of the high
Hydrogen Ions on one side of a membrane energy intermediate. However by 1978 there
could be a source of energy was lots of evidence to support tis theory
- He proposed the idea that the movement of and he was awarded the nobel prize for
hydrogen ions down a electrochemical chemistry.
gradient could provide the energy needed to
form ATP from ADP and Pi
- He called it the chemiosmosis theory
This would make the inner membrane a energy-

transducding membrane.
He also suggested that the movement of

electrons along the ETC would release energy to
pump hydrogen ions
to create the gradient.
These hydrogen ions

would then diffuse a
protein channel
attached to an enzyme
(ATP synthase
although not named
yet) and the kinetic
energy would drive the
formation of ATP. Its
called the Proton
Motive Force
60
EVIDENCE FROM OTHER STUDIES

Experiments used to Work out mechanism
Placing mitochondria in solution with very for ATP production
low water potential causes the outer
membrane to rupture. This releases the 1. Electron Transfer in mitoblasts doesnt
contents of the inter-membrane space to be produce ATP so inter membrane space
studied. Further treatment of the mitoblasts must be involved
(these are mitochondria without an outer 2. If the mushroom shape was removed
membrane) by using a strong detergent from the stalk ATP was not produced so
could rupture the inner membrane and that must be involved
release the contents of the matrix. 3. In the presence of oligomycin (An
antibiotic that blocks the flow of protons)
This was key in discovering where the krebs ATP was not produced so proton
cycle and link reaction happen. It was movement is involved.
possible because they could look at what In intact Mitochondria
enzymes where present. This also enabled
them to discover that the electron transport There was a potential difference of -200mv
chain happens in the inner membrane as across the membrane so matrix was more
thats where the enzymes where. negative. And pH was higher in the matrix
ANAEROBIC RESPIRATION
When there is no oxygen the electron transport chain cannot function properly because its the final
electron acceptor, and therefore the krebs cycle and link reaction stop.
This leaves only glycolysis as a source of ATP.
However this needs NAD+ to keep working. This means that there needs to be a way to keep
supplying the NAD to be oxidised.
There are two anaerobic pathways.
Fungi such as Yeast use ethanol (Alcohol) fermentation (Plant Cells, such as root cells under
waterlogged conditions can also use this pathway)
Animals Use lactate fermentation
61
LACTATE FERMENTATION
This occurs is mammalian muscle tissue during

vigorous activity, such as running to escape a
predator when the demand for oxygen is high
and there is a oxygen deficit.
Reduced NAD must be re-oxidised to NAD+

Pyruvate is Hydrogen acceptor
It accepts hydrogen atoms from reduced NAD
This can then re-enter glycolysis so that ATP
can continue to be produced
Its catalysed by lactate dehydrogenase
The lactate is carried away in the blood away

from the muscles. When more oxygen is
available lactate can be converted back to
pyruvate to re enter the krebs cycle or be
recycled to glucose and glycogen.
The build up of lactate doesnt cause fatigue but

the reduction of pH. With the correct pH buffers
the body can still continue in the presence of
lactate.
ALCOHOLIC FERMENTATION
Under anaerobic conditions in yeast cells:-
Each pyruvate molecule looses a carbon

dioxide molecule because its decarboxylated
and becomes ethanal
This reaction is catalysed by the enzyme
pyruvate decarboxylase (this isnt present in
animals).
It has a coenzyme (thiamine diphosphate)
bound to it
Ethanal accepts hydrogen atoms from reduced
NAD which becomes re oxidised as ethanal is
reduced to ethanol.
The reaction is catalysed by the enzyme
ethanol dehydrogenase
The reduced NAD can now reenter the
glycolysis
It does die when ethanol builds up to 15%. The rate

of growth is faster under aerobic condi'ons if there's
equal levels of glucose
62
RESPIRATORY SUBSTRATES
The majority of ATP made during oxidative phosphorylation hen hydrogen ions flow through
channels associated with ATP synthase enzymes.
A respiratory substrate is an organic substrate that can be used for respiration
Respiratory Substrate Mean Energy Value /KJ g-1
Carbohydrate 15.8
Lipid 39.4
Protein 17.0
FATS AND PROTEINS CAN ONLY BE RESPIRED AEROBICALLY BECAUSE THEY CANNOT UNDERGO
GLYCOLYSIS
63
Cellular Control
64
WHAT IS A GENE?
Genes are lengths of DNA, this essentially means that it is a sequence of nucleotide bases which code for
one or more polypeptide chains.
There are 2 types of nucleic acid, DNA and RNA. Essentially there are 3 differences between the two:
DNA = Deoxyribose RNA= Ribose
RNA = Uracil instead of Thymine
RNA is single helix whereas DNA is Double Helix
The Genetic Code
The sequence of bases on a gene (length of

DNA) provides a code can be used as
instructions. The Code itself has some useful
characteristics that enable it to work:-
Its a triplet code - IE 3 bases code for an

amino acid, 4 bases arranged in groups of 3 so
43 = 64 combinations and there are only 20
amino amino acids so more than enough
A Degenerate Code - All amino acids apart

from methionine have more than one code
Some codes dont correspond to a amino aid

but indicate STOP at the end of a chain
Its widespread but not universal - most but not

all animals use the same code
The process of Protein Synthesis happens in 4 stages: -
DNA in the
Nucleus
Polypeptide
T
DN rans
A t crip
o M tio
ak n of of e a
eR n
NA mRN l a tio mak
A ns to
from moves tra NA eptid
e
Nu
Cytop cleus to mR olyp
lasm p
Amin
o
Activ Acid
ation
65
1. TRANSCRIPTION OF DNA TO MAKE RNA
For a gene to be
transcribed a
section of the
DNA enters the
nucleolus. Here
the hydrogen
bonds between
complementary
bases break.
Activated RNA nucleotides bind using hydrogen bonds to the exposed bases
complementary. However, unlike normal DNA U binds with A the rest is the same. It
catalysed by RNA polymerase.
2 extra phosphoryl groups / phosphate groups are released which provide the energy for
bonding of the adjacent nucleotides.
When it finishes the mRNA is released from the DNA and passes out through pores in the
nuclear envelope
2. TRANSLATION OF MRNA TO MAKE A POLYPEPTIDE
Transfer RNA is another kind of RNA also

known as tRNA. These are made in the
Ribosomes nucleus and pass into the cytoplasm. They
fold into hairpin shapes and have three
Assembled in the nucleolus of eukaryotic cells exposed bases at the end of where a
from Ribosomal RNA and protein. Its made of particular amino acid can join. The other end
2 subunits and there is a groove into which the has a anticodon pair which binds
length of mRNA and hence the code can slide complementary to the triplet codon
into, here is it easy to read the code.
Sequence of amino acids in a protein is critical

because:-
Forms primary structure of protein
Primary determines the tertiary structure
because of the bonds formed
The tertiary structure is what allows the
proteins to work
The active site may not work for example in
enzymes due to specificity
66
ASSEMBLING THE POLYPEPTIDE CHAIN
1. mRNA binds to a ribosome. Six bases (2 codons) attach to the small subunit of
the ribosome. The first mRNA codon is always AUG. Using ATP energy and a
enzyme a tRNA binds with methionine and the anticodon UAC forms hydrogen
bonds with this codon
2. A second tRNA with the next complementary codon binds with different amino
acids
3. Peptide bonds form between 2 adjacent amino acids with an enzyme catalysing
the reaction
4. The ribosome now moves along the mRNA reading the next codon, the next
tRNA binds as the first one leaves to collect another amino acid
5. The polypeptide chain keeps growing until a stop codon is reached. There are
no corresponding tRNA for these codes and so the chain is now complete,
UAA,UAC,UGA
Some proteins are activated by chemical cyclic AMP like ATP is a nucleotide
derivative, it activates proteins by changing their shape so they can fit their
complementary molecules.
67
MUTATIONS
A mutation is a random change in the genetic material. There are a number of ways
this can happen. A chromosome mutation is a change in the structure of a
chromosome. The following are all forms of DNA mutations.
It can happen when DNA is replicating before nuclear division, either by mitosis or
meiosis.
there are 2 main types of mutations:
Insertion/Deletion
Point Mutations - -
where one base pair Where one or more
replaces another these nucleotide pairs are
are also called inserted or deleted
substitutions (these are also called
frameshift
Not all mutations actually make a change in the protein produced. For example
point mutations may change only base pair but still code for the same amino acid
so there is no overall change - these are called silent or neutral mutations. Some
change the DNA for better - this allows natural selection
68
THE LAC OPERON
Escherichia coli (E. coli) is a bacterium that can synthesise around 3000 different
polypeptides. There are however, a great variation in the number of polypeptides in
each cell. It usually respires glucose but when lactose is present it can use that as
a respiratory substrate.
When placed in a culture medium with lactose the E. coli cannot metabolise it
initially because it only has tiny amounts of the required enzymes. These are:-
-galactosidase (Cataylses the hydrolysis of lactose to glucose and

galactose)
Lactose Permease (Transports lactose into the cell)
Once added to the culture the cell increases the production of these enzymes by
about 1000 times. Lactose must trigger the production of these enzymes and is
therefore considered the inducer.
The lac operon is a section of DNA within the bacteriums DNA. It consists of
a number of parts : -
The Structural Genes - Z codes for -galactosidase and Y codes for lactose
permease. Each consists of a sequence of base pairs that can be transcribed into a
length of mRNA
The operator regions - O is a length of DNA next to the structural genes. It can
with them on and off
The Promotor Region - P is a length of DNA tow which the enzymes RNA
polymerase binds to begin transpiration of the structural genes
The regulatory gene (I) is not part of the operon and is actually some distance away
from it
69
HOW THE LAC OPERON WORKS
When Lactose is absent
1. The regulatory gene is expressed and so

the repressor protein is synthesised (it has
2 binding sites - one for the lactose and one
for the operator region)
2. It binds to the operator region- this covers
part of the promoter region where RNA
polymerase normally attaches and
therefore cannot produce the enzymes
because RNA polymerase cannot attach
When lactose is present
1. Lactose (inducer molecules) bind to the

other site of the repressor molecule - This
causes the molecules to change shape so it
can no longer bind to the operator region
and breaks away from it
2. The promoter region is now unblocked
3. RNA binds to the promoter region and
begins transpiration
4. the operator-repressor-inducer system acts
as a molecular switch
5. The result means that E. coli can respire
using the sugars thus gaining energy from
lactose
The advantage of not producing the enzymes when the lactose isnt present is
simply to not waste useful resources as the enzymes are unnecessary as they
wouldn't be doing anything.
USING HOMEOBOX GENES IN BODY PLANS
Drosophila help to show the different sections

or segments that the homeobox genes help
produce and regulate. This is the key to
specialisation.
This is a very old process and is common in
lots of different organisms, even humans
supporting the theory of evolution.
70
BODY PLANS AND GENES
Drosophila
When they lay eggs a series of mitotic

divisions are triggered. They happen at
about 1 every 6-10 minutes which is the
fastest known for a eukaryotic organism
Initially no new cell membranes form and a

multinucleate syncytium is formed
After the 8th division the 256 nuclei migrate
to the outer part of the cell and by the 11th
division they have formed a layer around the
central yolk filled core
Now the division rate slows with the 14th
one taking 60 minutes
The plasma membrane folds inwards
(invaginate) around 6000 nuclei leaving the cell with a single outer layer
After 2-3 hours the embryo divides into a series of segments which correspond to the
body plan
At metamorphosis when the larval form becomes an adult legs, wings and antennae
develop
Homeobox genes code for transcriptional factors. These regulate the expression of other
genes important in development
Maternal Effect Genes - Determine the embryo

Homeobox Genes control the development of the
polarity (Which end has the tail and the other the
body plan of an organism including the polarity
head)
(head and tail needs) and the positioning of the
Segmentation genes - Determine the polarity of organs
each segment (What part of the head is the brain
and what is the mouth)
Homeotic Selector Genes specify the identity
of each segment and the development of each segment. These are considered the
master genes and are separated into 2 families
- Complex that regulates development of thorax and abdomen segments
- Complex that regulates development of head and thorax segments
71
HOMEOBOX GENES IN OTHER ORGANISMS
Homeobox genes are found in the genomes in many different organisms that are
considered segmented from annelids (worms) all the way to vertebras such as
humans.
- They contain a sequence of 180 pairs known as the homeobox which produces a
polypeptide of around 60 amino acids
- Sometimes these polypeptides are transcription factors and bind to genes further
upstream to initiate transcription and hence regulating the expression of other
genes
- They work in a similar way in most organisms for example when a cutting is
taken from a plant they grow based on the polarity i.e. roots at the end closest to
the roots before the cutting
Homeobox genes are arranged in clusters known as Hox Clusters
The increase in the number of clusters probably arose due to the duplication of a
single complex in the worms and allowed more complex arthropods to evolve from
simple annelids . They are expressed in specific patterns along the different stages
of development. They are activated in the same order as they are expressed along
the body of an organisms from anterior (head) to posterior (tail).
Homeobox genes and Birth Defects

Retinoic Acid - Is a derivative of
vitamin A. It activates genes in Thalidomide
- Taken by mothers in the 1950s to help
vertebrates in the correct order they morning sickness
should be. Its a morphogen as it - Affected homeobox genes stopping legs and
governs the pattern of tissue arms forming properly
development. The amount of this in the
body is crucial to proper development.
Too much taken by pregnant women
causes deformities particularly cranial deformities.
72
APOPTOSIS
Apoptosis literally means means programmes cell death. The process is essentially
a series of small biochemical events which lead to a tidy and clean cell death which
causes no harm to the overall organism. Before this happens the cell should have
gone through around 50 mitotic divisions which is known as the Hayflick
constant.The opposite to Apoptosis is cell necrosis which is an untidy and
damaging cell death that occurs after trauma and releases hydrolytic enzymes.
Stages of Apoptosis
HOW IS IT CONTROLLED?
Enzymes break down
cells cytoplasm It happens very quickly. Its
controlled by a diverse
range of cell signals both
from within the cell and
outside the cell
(intercellular and
Cytoplasm extracellular). These
becomes densely signals could be cytokines
packed as all the tiny made by the immune
system, hormones and
organelles bundle
nitric oxide. Nitric Oxide
together
can induce apoptosis by
making the inner
mitochondrial membrane
more permeable to
Cell hydrogen ions hence
surface membrane dissipating the proton
alters in shape giving the gradient thus messing with
appearance of a flaccid cell - chemiosmosis.
The parts sticking out are
called blebs Proteins can be released
into the cytosol and these
bind with apoptosis
inhibitor proteins and allow
Chromatin from the process to take place.
within the nucleus
condenses and the
nuclear envelope
breaks down
DNA breaks
into fragments which Vesicles are taken up by
even then they break phagocytes and the cellular
down even smaller to debris disposed of, no other
enter vesicles cells are harmed
73
APOPTOSIS AND DEVELOPMENT
Apoptosis is a integral part of development in plants and animals. The importance is

enhanced due the higher number of mitotic divisions occurring.
Excess cells shrink and fragment before

getting phagocytksed and reused so that Cancer
no harmful hydrolytic enzymes are When cells stop responding to certain signals
released into the surrounding tissue. that control mitosis, due to DNA damage or
During development this is highly mutation, cancer can form. They do not
regulated and there are different tissue undergo apoptosis and keep dividing by
mitosis to form a tumour. If part of the tumour
signals for controlling it. It can weed out breaks of and enters the blood stream or
harmful T lymphocyte or ineffective lymph system then they can travel and form a
during the development of the immune secondary cancers. This is called metastasis.
system.
Apoptosis is responsible for the development of toes or digits such as fingers to

separate from each other.
Between the ages of 8 and 14 there are 20-30 billion cells that undergo apoptosis.
In 1 year this is equates to the a mass of cells the same as the total body mass. In
adults this number is reduced to 50-70 million and the now the number of cells
dying should balance the number of cells produced from mitosis.
74
Meiosis and
Varation
75
THE SIGNIFICANCE OF MEIOSIS
There are four ways in which meiosis and fertilisation lead to variation
Crossing Over - during prophase I which reshuffles the alleles

Genetic Reassortment - due to the random distribution and subsequent
segregation of the maternal and paternal chromosomes in the homologous pairs in
meiosis I
Genetic Reassortment - due to the random distribution and segregation of the
sister chromatids at meiosis II
Random Mutation
Crossing Over
Occurs during prophase I. The homologous
chromosomes pair and come and pair together to
form bivalents. There are on average between 2 and
3 cross over events
Non-sister chromatids wrap around each other very

tightly and attach at points called chiasmata
The chromosomes may break at these points and
the broken sections may rejoin to the ends of the
non-sister chromatids in the same bivalent
This leads to similar sections sections of non-sister
chromatids being swapped, they contain the same
genes but different alleles
These new combination become chromosomes in
new daughter cells
Chiasmata remain in place during metaphase
An allele is a version of an gene, where a gene Reassortment of Chromosomes

is a length of DNA that codes for one or more
polypeptides. An allele is of the gene has a
The reassortment is a consequence of random
difference in DNA that is expressed as a slightly
different polypeptide
distribution of maternal and paternal chromosomes
on the spindle equator metaphase I and
subsequent segregation into two daughter cells
The locus is the position of a gene on a Each gamete acquires a different mixture of
chromosome maternal and paternal chromosomes
Crossing over is when lengths of dan are

The process alone can theoretically produce 2n
swapped from one chromatid to another gametes where n= the number of haploid number of
chromosomes, in reality its much greater because of
the other methods of genetic variation
76
Reassortment of Chromatids
Maternal chromosomes are the set of
The result of random distribution on the spindle chromosomes in an individuals cells
equator of sister chromatids at metaphase II that were contributed by the egg
Paternal chromosomes are the set of

Crossing over means that sister chromatids are no
chromosomes in an individual cells
longer genetically identical that were contributed from the sperm
How they align at metaphase II determines how they

segregate at anaphase II
Fertilisation
Mutation In humans only one ovum is
released from the ovary at a time.
DNA mutation may also occur during interphase
when DNA replicates. This is not peculiar to meiosis There are bout 300 million
as it can happen during mitosis and binary fission. spermatozoa that are all genetically
different but only one of them can
Chromosomes mutation may also increase genetic fertilise the ovum. This is a
variation, if it happens in a sex cell then every cell in incredibly small number with a huge
the new organism will have the mutation number of possible outcomes
77
VARIATION
Some key terms : -

The genotype refers to the number precise genetic makeup of an organism in terms of the
alleles it contains.
The alleles are expressed and what they express is called the phenotype
Where an organism has two identical alleles its considered homozygous or a
homozygote
Where an organism has two different alleles its considered heterozygous or a
heterozygote
RECESSIVE AND DOMINANT ALLELES

Dominant
Alleles
Dominant alleles are always expressed in the phenotype regardless of whether or not
another another allele for the same gene is present
The characteristic in question and inheritance pattern are also considered dominant
Recessive alleles are only expressed in the phenotype if another identical allele is
Recessive
Alleles
present or an absence of a dominant allele.

For example if somebody who has Cystic Fibrosis (Recessive Allele (cf)) then they must
have cfcf to suffer from it. However if they have CFcf they are symptomless carriers
CODOMINANT ALLELES
Using the rules above falls

short if there are two
dominant alleles. Dominant
alleles are always
expressed so what happens
when two alleles have to be
expressed?
An example of how this

works can be the colour of snapdragon plants. They have two alleles that are both
dominant. They are shown as capitol letters because they are still dominant but have
another superscript letter to show what they code for. As the table shows they are still
shown because they are both dominant so combine to make a pink flower.
LINKAGE
Sex Linkage
This refers to two or more genes located on
A characteristic is sex linked if the gene that
the same chromosome. The linked alleles are codes for it is found on one of the sex (X and Y
usually inherited as they aren't independently chromosome). Because the Y chromosome is so
segregated during meiosis unless chiasmata small most of them are found on the X one. X
are formed between them. contains about 2000 genes where Y contains
Most linked genes are found on the fewer than 100. Females are homogametic (XX)
autosomes (Not sex determining meaning and males are heterogametic (XY). Because part
there are 22 autosomes in humans) some of the X chromosome doesn't have a
however can be sex-linked homologous section on the Y it is always
78
Take the example
shown in the
diagram: an
organism has two
alleles on each
chromosome for
linked genes, AB
and ab. Most of its
gametes produced
by meiosis will obviously be AB or ab. Usually, linked genes do not allow alleles to
independently assort as unlinked genes can do, so most of the gametes stay either AB or
ab. However, where chiasmata form cross-links between the two genes on a chromosome,
and crossing-over takes place, recombinants are produced: cells which contain genotypes
which dont belong to either of their parents. The recombinants are shown in the red
meiotic cells above, although in reality linked genes prevent this happening too often.
Linkage therefore reduces the number of phenotypes of the organism.
79
A monohybrid cross involves involves one gene and therefore only one characteristic or
phenotype. However sometimes there are two genes involved and therefore two
phenotypes.
80
EPISTASIS
The homozygous presence of a recessive allele may prevent the expression of another
unrelated allele from another allele at a second locus.
If this is the case the allele at the first locus is considered epistatic to the alleles at the
second locus. The allele at the second locus is called hypostatic.
Epistasis is not inherited, it is an interaction between two gene loci as it reduced

phenotypic variation
Antagonistic Epistasis
Recessive Epistasis
The inheritance of colour in the flower Salvia is

an example of recessive epistasis.
It involves two gene loci (A/a, and B/b) on

different chromosomes
So if a pure-breeding pink-flowered variety of
Salvia with genotype AAbb was crossed with a
pure-breeding white-flowered variety with a
genotype aaBB
The F1 generation all had AaBb and purple
flowers
Interbreeding the F1 to F2 resulted in purple,
pink and white flowers in the ratio 9:3:4
This shows that the homozygous aa is epistatic
to both alleles of the gene B/b
Neither the allele B nor the allele b can be
expressed if their is no dominant allele A Dominant Epistasis
present
This is when a dominant allele at one locus
masks the expression of the alleles at another
locus
Two gene loci D/d and E/e are involved here -

the presence of D results in white regardless of
the alleles at the other locus
In homozygous individuals with dd the
presence of E means its yellow and the
presence of two ee produces green plants
If two DdEe are crossed the offspring show
phenotype ratio : -
12 White (D - E or D- ee
3 Yellow (ddE)
1 Green (ddee)
81
Complementary Epistasis
William Bateson and Reginald Punnet (Punnet Square Guy) crossed two strains of white-
flowered sweet peas which brought some unexpected results that the two scientists had to
create another form of epistasis to explain.
They crossed two strains of white-flowered sweet peas which means ccRR X CCrr
Unexpectedly all the F1 plants had purple flowers

The F1 were interbreed and resulted in an F2 variation of purple and white flowers in the
ratio 9:7
This suggests that at least one dominant allele for both gene loci (C-R-) are present for
the flowers to be purple
All other genotypes such as ccR- or C-rr produce white flowers
This is because the homozygous recessive condition at either locus masks the
expression of the dominant allele at the other locus
In other words for the purpler flowers to be shown the first gene needs to be shown
The way the two gene loci may produce purpler flowers is if they complement each other
So if one gene codes for an intermediate colourless pigment and the second one codes
for a an enzyme that converts the intermediate pigment purple
This means both dominant alleles are needed to express the purple flower
The Chi-Squared (X2) Test
The x2 test is a statistical test to find out if the

The formula for calculating x2 is: -
difference between the observed categorical
data (Data in categories) and expected data is
small enough to be due to chance
ITs used to:
For categorical data
Strong biological theory that can use to Which Simplifies to -
predict expected values
Other criteria must also be met ; -
Sample must be relatively large

Only raw counts, not percentages or ratios
can be sued
No zero scores
82
The equation looks complicated but has a simple basis. There a few factors that are taken
into account : -
The differences can be negative or positive so they are squared to stop any negative
values cancelling out the positive values
Dividing by E takes into account the size of the numbers
The sign takes into account the number of comparisons being made
CALCULATING CHI SQUARED

The Best way to calculate the value of x2 is by using a table
Class/Catogory Observed (O) Expected (E) O-E (O-E)2 (O-E)2 / E
Yellow Round 169 162 7 49 0.30
Green Round 54 54 0 0 0.00
Yellow Wrinkled 51 54 -3 9 0.17
Green Wrinkled 14 18 -4 16 0.88
X2 = 1.35
The bigger the value of X2 the more certain we are that there is a significant difference
between the observed and expected values
The smaller the value of X2 the more certain we are that there difference between the
observed and expected results is by chance and there is no significant difference
The result is then looked up on a distribution table showing values of X2.
The critical value of X2 for 3 degrees of freedom and Probability 0.05 is 7.82. This
means that is could happen 1 in 20 times or 5 in 100.
If the value is smaller than the critical value then we say that the difference is due to
chance and not significant , if its bigger then its probably significant and we need to
rethink out explanation for the results
Number Degrees of X2
of Freedom
Classes
2 1 0.00 0.10 0.45 1.32 2.71 3.84 5.41 6.64
3 2 0.02 0.58 1.39 2.77 4.61 5.99 7.82 9.21
4 3 0.12 1.21 2.37 4.11 6.25 7.82 9.84 11.34
5 4 0.30 1.92 3.36 5.39 7.78 9.49 11.67 13.28
6 5 0.55 2.67 4.35 6.63 9.24 11.07 13.39 15.09
Probablity that 0.99 0.75 0.50 0.25 0.10 0.05 0.02 0.01
deviation is due to (99%) (75%) (50%) (25%) (10%) (5%) (2%) (1%)
chance alone
Accept Null Hypothesis (Any difference is Reject null hypothesis -

due to Chance and not significant accept experimental
hypothesis - Difference is
83 significant and not due to
Critical Value - This is the level at which we are 95% sure that chance
the result is not due to chance (Agreed by statisticians )
VARIATION
Both types of variation may be the result of more than one gene. However in discontinuous
variation if there more than one gene involved they work in a epistatic way where one
gene masks or suppresses the expression of another gene.
Situations where only one gene is involved are known as monogenic and when more than
one are involved called polygenic situations.
Discontinuous Variation Continuous Variation
This describes qualitative differences This describes quantitative differences

between phenotypes between phenotypes
Qualitative differences fall into clearly Phenotypic Differences where there is a

distinguishable categories wide range of differences within the
There are no immediate categories you are population
either male or female No distinct categories
Causes Causes
Different alleles at a single locus have large Traits exhibiting continuous variation are
effects on the phenotype controlled by two or more genes
Different gene loci have quite different Each gene provides an additive component
effects on the phenotype to the phenotype
Examples include Different alleles at each gene locus have
- Codominance small effect on the phenotype
- Dominance A large number of different genes ay have
- Recessive patterns of inheritance combined effect on the phenotype
The genes are unlinked - on different
chromsomes
HOW DOES ENVIRONMENT CONTRIBUTE TO VARIATION IN PHENOTYPE
A plant with a genotype of AABBCC has the genetic potential to be 12cm in length of grain.
This is because each dominant allele adds 2cm of length to the grain. However some
plants with this potential wont produce grains of 12cm. The usual factors affecting growth
can cause this difference. These environmental factors can limit the expression of genes.
Intelligence in humans is partly determined by both environmental and genetic factors.

This potential can only be realised when a stimulating learning environment is used both at
home and school.
The expression of polygenic traits is influenced more by the environment than is the
expression of monogenic traits.
84
WHAT IS A SPECIES?
Biological Concept of A species is a group of similar organisms that can interbreed

and produce fertile offspring and is reproductively isolated from other such groups
Problems with this concept
Sometimes scientists want to classify organisms that don't sexually reproduce

Some members of the same species may look very different from each other
Males look different to females and some species such as ants have castes which look
very different from one another
Some isolated populations may appear to be very different from each other
As all living organisms have DNA,

RNA and proteins, scientists have
been able to notice that closely related
The phylogenetic species concept is group of organisms have similar molecular
organisms that have similar:- structures for these substances. With
Morphology (Shape) improved DNA sequencing techniques
Physiology (Biochemistry)
biologists have been able to compare
Embryology (stages of development)
particular base pair sequences
Behaviour
Whether or not they occupy the same (haplotypes) on chromosomes of
ecological niche specific organisms. Analysis of of base
pair sequence is carried out and the
difference, caused by base pair
substation are expressed as %
divergence.
The organisms with halotypes that are similar to each other than those in any other group
are called clades. Hence the use of molecular systematics (analysis) is a cladistic
approach to classification. It assumes that classification of living organisms corresponds to
their phylogenic descent and that all valid taxa
(groups) must be monophyletic.
Monophyletic Groups are ones that include
A clade is a taxonomic group comprising a ancestral organisms and its decedent species.
single ancestral organism and all its
descendants. For this reason its described as
a monophyletic group
Cladistics is the hierarchical classification of species based on their evolutionary ancestry.

It is different from taxonomic classification systems as:-
It focuses on evolutionary (phylogenetic relationships) rather than similarities between species
It places great importance on using objective and quantitative (molecular) analysis
Uses DNA and RNA sequencing
Uses computer programmes and the data obtained from nucleic acid sequencing to generate
dendrograms or cladograms that represent the evolutionary tree of life
It makes no distinction between extinct and extant species and both may be included in
cladograms
85
A german entomologist (studier of insects) Willi Hennig called it phylogenetic systematics,
the term cladistics comes from a greek word meaning branch
Its different from Linnaean classification

because it does not use the kingdoms, A paraphyletic group includes the most recent
phylum or class as it regards evolutionary ancestor but not all its descendants.
tree as very complex, as such it is not helpful Its a monophyletic group with one or more
to use a fixed number of levels in the clades excluded
classification of living organisms E.G the group of reptiles is paraphyletic as it
excludes birds which are descendants of
Linnaean system also reflects the
reptiles
phylogenies between the different species of
The group Prokaryotes is paraphyletic as it
organisms, however unlike cladistics it shows
comprises Bacteria and Archaea but excludes
both monophyletic and paraphyletic groups o the eukaryotes
taxa
The cladistic approach is often used to
confirm the Linnaean classification of organisms but sometimes led to reclassification
It help biologists to understand the evolutionary relationships between species
POPULATION GENETICS
A population is a group of individuals of the same species that can interbreed. Populations
are dynamic - They can expand or contract due to changes in birth or death rates or
migration
Gene Pool The Hardy-Weinberg Principle
Total information from all the genes and allele of Mathematical model used to calculate
the breeding individuals in a population at a the allele frequency of traits with
particular time dominant and recessive alleles
If there is constant change in allele frequency For the model to work a few factors are
then the population is evolving assumed to be true: -
The Population is large These imply that the
Gene pools composition changes rom one Random Mating
generation to the next as relative proportions of population remains
No natural selection stable over time
genes change
No Random Mutations
The principle requires the knowledge of two equations with skills of substitution.
In this equation: -
Equation 1 p = Frequency of Dominant alleles
q = Frequency of Recessive alleles
p+q=1
The frequency will always be between 1-0 and refer to a percentage
Equation 2
p2 + 2pq + q2 = 1
86
THE ROLES OF GENES AND ENVIRONMENT IN EVOLUTION
Variation and Natural Selection Environmental Resistance -
The set of alleles in a population is its gene Environmental factors that limit the
pool growth of population offer environmental
Each individual can have any combination of resistance
alleles in the gene pool
Producing variation
The factors can be biotic (caused by
Some individuals are more likely to survive
The reproduce and pass genes onto
other living things) or abiotic (caused by
offspring non-living components of the
Advantageous alleles become more environment
frequent in the population
87
Selection Pressures
An environmental factor that selects for some

members of a population over others
Confers an advantage onto certain individuals
Stabilising Selection
If the environment stays stable

The Same alleles will be selected for
successive generations
If nothing changes from generation to the
next then stabilising selection is
occurring
Directional Selection
Change in the environment resulting in

change in the selection pressures on the
population
Previously disadvantageous alleles may
be selected for
Change in the genetically determined
characteristics of subsequent generations of the species
Also known as evolution
Genetic Drift - A change in the gene pool and characteristics within the population
which occurs by chance rather than the result of natural selection
Genetic Drift is thought to happen relatively frequently in populations on islands
Because of small populations

They are geographically separated from other members of their species
This is supported by the fact that many isolated islands have their own endemic species
of plants and animals
Effects of Genetic Drift
Reduces genetic variation

Reduce the ability of the population to survive in a new environment
May contribute to the extinction of populations or species
Could lead to the production of a new species
88
Isolation - Splitting apart of a
Reproductive isolation occurs in many ways
splinter group
Ecological Barriers
Ecological barriers exist where two species live

in the same area at the same time, but rarely
meet
For example two different species of crayfish
both live in freshwater habitats in North
America
Temporal Barriers
Two species live in the same place, and may

even share the same habitat
Do not interbreed as they are active at different
times of the day, or reproduce at different times
of the year
Example, flowering shrubs in Western Australia
Reproductive Barriers
Even if species share the same habitat and are

reproductively active at the same time, they
may not be able to interbreed
- Different courtship behaviours
- Mechanical problems with mating
- Zygote inviability
- Hybrid Sterility
89
Speciation
The formation of a new species.
In the production of a new species, some

individuals must Species - A group of organisms with similar
morphology and physiology, which can
- Become morphology or physiology
interbreed with one another to produce fertile
different from members of the original species
offspring
- No longer be able to breed with the
members of the original species to produce
fertile offspring
Natural and Artificial Selection
Natural Selection Artificial Selection
Mechanism for Evolution Humans elect the favourable

Organisms best adapted to their characteristics
environments are more likely to survive Humans allow those organisms to
to reproductive age breed
Favourable characteristics are passed Produced populations that show on
on characteristic to an extreme
Produces organisms that are well Other characteristics may be retained
adapted to their environment that are disadvantageous
Artificial Selection and Modern Cows
Breeds of cows with higher milk production have Disadvantages to high milk yields
been artificially selected for
Health costs for artificially selected cows is
1. Milk yield from each cow is measured and higher due to
recorded
2. Test progeny of bulls - Mastitis (Inflammation of mamary
3. *Elite cows given hormones to produce many glands)
eggs - Ketosis (Fatal Bacteria infection)
4. Eggs fertilised in vitro
- Milk Fever (Metabolic disorder where
there isn't enough energy for milk
5. Embryos implanted into surrogate mothers
production which causes low blood
glucose levels)
*A few elite cows produce more offspring than - Lameness
they would naturally - Respiratory Problems
90
Artificial Selection of Bread Wheat
Polyploidy - Nuclei contain more than one diploid set of chromosomes
Wild species of wheat have a diploid number (2n) of 14

Modern bread wheat is hexaploid (6n), it has 42 chromosomes in the nucleus of every
cell, this gives them a larger nucleus and hence cell size is larger
Winter Wheat - Soft, low protein

grains that are suitable for biscuits
and usually grown in the UK
Spring Wheat - Harder, high protein

grains that are suitable for bread
Breeder are continuing to try and

improve wheat varieties to
- Resistance to fungal
infections
- high protein content
- Straw stiffness
- Resistance to lodging
- increase yield
91
Cloning in Plants
and Animals
92
A clone is an exact copy, in biology this fundamentally means that they are
derived from the same original DNA (Identical DNA)
TWINS - TWO TYPES OF CLONES
Identical twins are produced when a zygote

splits in two. These are natural clones and
are also known as dizygotic twins.
Non-Identical twins are produced when two

sperm cells join two different egg cells. They
are no different to normal brothers and
sisters but grow simultaneously. They are
not clones.
ASEXUAL REPRODUCTION
Plants are reproduce via asexual methods. They produce runners which in turn
grow into new plants but they are exact clones.
Bacteria (single celled organisms) divide asexually via binary fission producing
multiple clones
Binary Fission is a method of asexual reproduction that involves splitting the parent
cell into approximately two equal parts
Prokaryotes divide by binary fission - there DNA replicates and the cell divides into
two separate haves so the new cells are identical to the parent cell
Eukaryotes use Mitosis as the basis of Asexual Reproduction
Single celled
Genetic material
Eukaryotes cells split to
replicates to form two identical
produce two daughter offspring
daughter nuclei before dividing
cell that are cloned
into to two identical cells
organisms
93
Binary Fission in
Prokaryote
1.Initially the DNA is tightly

coiled
2.DNA has replicated
3.DNA pulled to separate
poles of the bacterium as
it increases in size
4.New cell wall grows
5.Cell wall fully devoples
and a split occurs and the
DNA is coiled tightly again
Advantage and Disadvantages of asexual reproduction
Its quick so organisms can reproduce rapidly to take There isnt any genetic variation so weaknesses are
advantage of resources in an environment passed on to offspring
Can occur when sexual reproduction isnt possible Changes in the environment can wipe out entire
organisms
Can occur is sexual reproduction fails Adaptions are reduced and natural selection
between species cannot occur
Offspring have the required genetic information to

enable survival in their environment
NATURAL VEGETATIVE PROPAGATION

Vegetative Propagation - The production of
A number of plant species such as
structures in an organism that can grow into a
new individual organisms. These offspringthe English Elm Tree have adapted
contain the sam genetic information makingto reproduce asexually following
them clones of the parent.
damage to the parent, this allows
the species as a whole to survive
catastrophes such as disease and damage. They have new growth in the form of
root suckers or basal sprouts and they appear within 2 months of the destruction of
the main trunk. They grow from meristem tissue in the trunk close to the ground
where least damage would occur.
Another method of vegetative propagation in plants is runner, these are small

shoots that run along the ground and cause buds to grow which develop roots.
94
Vegetative Propagation by using runners
ADVANTAGES AND DISADVANTAGES TO THE ELM OF VEGETATIVE

PROPAGATION
Healthy elm
with root sucker
Advantages
Root suckers help the elm to spread as they can

grow all around the original trunk
Suckers grow in circles of new elms called

Elm colonial patch - this puts out new suckers
starting to
show symptoms New suckers keep the patch expanding
of Dutch elm
Disease
Disadvantages
No genetic variation - no natural selection
The new trees get infected easily because they

Main
are clones of the old ones
stem is dead
but the roots are No resistance to the fungal attack leaves the Elm
alive and Tress vulnerable
producing
suckers
Root
suckers grow
but the largest one
shows symptoms
of disease
95
ARTIFICIAL VEGETATIVE PROPAGATION
Farmers and growers are able to artificially propagate valuable plants using two
main methods , taking outings and grafting. These allows them to keep their
valuable traits
Taking cuttings Grafting
Section of stem is cut between leaf joints called A shoot section of a woody plant such as a fruit
nodes and the cut end is then treated with plant tree or rosebush is joined to an already growing
hormones to encourage root growth and root and stem known as a rootstock and the graft
planted - this allows many clones to be will grow being genetically identical to the parent
produced quickly despite having a different rootstock
TISSUE CULTURE
Tissue Culture refers to the separation of cells
Used to generate huge numbers or of any tissue type and their growth in or on a
genetically identical plants from a very small nutrient medium. In plants, the undifferentiated
amount of plant material callus tissue is grown in nutrient medium
It is the cloning of isolated cells or small containing plant hormones that stimulate
amounts of plant tissue in special culture development development of a complete plant
solutions
Scientists take small groups of cells from a
part of a plant and put them into a special
liquid or jelly
Special chemicals are added to promote the development of these cells into root cells,
stem cel and leaf cells so the new plant grows
Micropropagation - The most common method of large scale cloning
The
Small pieces The explant Single cells plants can
of tissue is can be Shoots begin now be placed
cells divide but
taken called an removed from to grow and in a green
not differentiate
explant and this and placed then placed on a house to
and form a mass
placed on a on a different different acclimatise
of cell called a
nutrient growth medium with medium to before being
callus
medium hormones grow roots planted
outside
96
CLONING ANIMALS
Only animal embryonic cells are able to go through the stages of development into a new
individual. These cells are known as totipotent stem cells because they are able to
differentiate into any type of adult cell in the organism. In other words they are able to
switch on any of the genes on the genome.
There are two methods of artificially cloning animals
Splitting Embryos - Artificial Identical Twins
- Cells in a developing embryo can be

Eggs$obtained$from$
separated out and each cell can then Sperm$ the$best$female$
obtained$
produce a separate genetically identical from$the$best$
male$
organism Fer5lised$in$a$dish$
- It was developed in 1979 and has been used Embryos$are$split$

to clone multiple animals
Nuclear Transfer New$embryos$develop$and$are$placed$in$surrogate$mums.$

Calves$are$all$gene5cally$iden5cal$to$each$other.$
A differentiated cell is taken from an adult cell
and the nucleus placed in an egg cell that
has had the nucleus removed. The egg goes
through the stages of development using the Dolly the Sheep
genetic information inserted.
- Named after Dolly Parton
- The cell was taken from the mammary gland
of a 6 year old ewe, its nucleus transplanted
into a cell from a second sheep and then
inserted into the uterus of a third sheep, and
then a fourth sheep, to develop. This was
the only success in 277 attempts.
- She was put down in 2003 due to a tumour
caused by a virus at the age of 6
- Her premature death was initially blamed on
the clone but the post morton revealed
nothing unusual
97
High-value animals that give a high milk yield can High value animals are not produced with animal
be cloned in large numbers welfare in mind - sometimes chickens are unable to
walk
Rare animals cloned to preserve species lack of gene pool makes them susceptible to
changes in environment
Gentically modified animals that produce bi- It is still unclear whether animals cloned using the
products can be cloned quickly in large numbers nuclear material of adult cells with remain healthily
in the long term, like in the case of dolly the sheep
NON-REPRODUCTIVE CLONING
The above show methods of reproductive cloning as they are generating new organisms
hence increasing the population.
Non-Reproductive cloning involves the use of cloned cells to produce new cells, organs
and tissues. It is a new field of research and is showing promising advances in the
treatment of helping humans, particularly after trauma injuries. It could be used to repair
damaged tissues and organs such as:
- Regenerating heart muscle cells after a heart attack

- Repairing nervous tissue destroyed by diseases such as multiple sclerosis
- Repairing the spinal chords of those paralysed by an accident that resulted in a
broken back or neck
98

Biotechnology
99
Biotechnology refers to technical processes which involve the use of living organisms.
Biotechnology today is used is a very wide range of fields. It can be used to help produce
foodstuffs, drugs and many more products. It has been happening for 1000s of years but
the term was first used around 100 years ago by Karl Ereky.
Purpose of Biotechnological Examples Organisms involved

Process
Cheese and yoghurt-making Bacterial growth in milk changes

the flavour and texture to
generate different foods, and the
bacteria prevents the growth of
other bacteria which would cause
the food to spoil
Food Production Mycoprotein Growth of a specific fungus in a

culture : the fungal mycelium
produced is separated and
processed as food
Naturally brewed soya sauce Roasted soya beans are

fermented with yeast or fungi
such as Aspergillus
Penicillin Penicillium fungus is grown in

culture to produce the antibiotic
as a by-product of its metabolism
The production of drugs or other Insulin E. Coli can be genetically
pharmaceutical chemicals modified to carry the human
insulin genes so they can
manufacture and secret the
hormone
Pectinase - Used in fruit The fungus, A. Niger is grown in

extraction certain conditions that make it
produce and secrete pectinous
enzymes
Calcium Citrate (used in The Fungus A. Niger produces

Production of Enzymes or other
Detergents) citric acid as a by-product of
chemicals for commercial use
normal metabolism
Bio-Gas fuel production Methanogenic bacteria, grown on

concentrated sewage, respire
anaerobically and generate gases
that can be used as fuel
Bioremediation of waste products Waste water treatment A variety of bacteria and fungi use
organic waste in the water as
nutrients and make the water
unharmful.
100
THE STANDARD GROWTH CURVE WITH RESPECT TO CULTURES
Cultures are populations of one type of microorganism that is or has been grown under
controlled conditions.
Closed cultures refers to a culture that is in an environment that all conditions are fixed in
and contained. No new materials are added nor are products removed.
Lag Phases -
e
adjusting to th
Organisms are co uld
d in g co nditions. This
su rr o u n ansion,
lv e ta ki n g in water, cell exp
invo
n and enzyme
gene activatio ce lls are active
but
s. H e re th e
synthesi ulation
re p ro d u ci ng so the pop
n o t of this
a in s co n sta nt - the length
rem
ndent on the
period is depe
environment.
Log (exp
onential)
phase -
Populati
on size d
generati ou
on as ev bles every
enough ery indiv
spa idual
reproduc ce and nutrients has
e. This c to
minutes an
dependin be around 20-3
microorg g 0
anism. It on the
their is s go
FERMENTATION AND FERMENTERS pace and es as long as
nutrients
Fermentation initially only referred to the use of aerobic

hase -
respiration to substance, particularly the production of Stationary P
aste
alcohol through yeast. ls d e c rease and w
Nutrient le v e other
Now it refers to the culturing of microorganisms both k e c a rb o n dioxide and
anaerobically and aerobically in fermentation tanks. products li ild up. Indiv
idual
b u
meta b o li te s te as new
These are treated too produce a desired product is m d ie a t the same ra duced
organ eing intro
isms are b
microorgan
Death
(declin
e ) Phas
e -
Nutrien
ts are e
of toxic xhaust
w ed
metabo aste produc and the leve
lit ts ls
increas es lead to the and
in d
Eventu g above repr eath rate
ally, all oductio
culture or nr
will die ganisms in a ate.
closed
101
Metabolism is a process with metabolites being the products
Primary and secondary metabolites are used to describe the metabolic processes of a
microorganisms
Primary metabolites are Secondary metabolites are

substances produced by an substances produced by an
organisms as part of it normal organism that are not part of its
growth. normal growth.
These can include -

- Amino Acids These are usually antibiotic
- Proteins chemicals produced as
- Enzymes secondary metabolites. Because
- Nucleic Acids they begin after the main growth
- Ethanol period of the organism they don't
- Lactate match the growth population of
the organism
They usually match the growth in
population of the organism
When growing conditions are favourable which is usually during the log phase, primary
metabolites are usually produced as they are often essential for normal growth. When
those conditions are less favourable usually during the stationary phase, secondary
metabolites are produced. These are not essential for normal growth but useful in other
ways.
102
USING BIOTECHNOLOGY COMMERCIALLY
Commercial use of biotechnology involves the growth of certain microorganisms on an

enormous scale. This is done in a large fermentation, this is basically a huge tank with
capacity of tens of thousands of litres. The special quality of fermenters is that the internal
conditions can be manipulated to provide the best possible yield of the product.
Many things affect what conditions are best for the microorganism that is being
grown. The conditions can also be altered depending on whether a primary
metabolite or secondary metabolite is being produced.
o Hot
m p e r a t ure - To Type an
d time
Te s w ill Growth of add it
ion of
d t h e enzyme of micro
organis
nutrien
t -
an er if its
nutrien
t supply ms requ
e howev , in ires a
r carbon, clu d ing
d e na t u ime nitroge so urces
t h e g rowth t vitamin n and a
ny esse
of
d
to o co l
s and m ntial
add ing in erals. T
he timin
slowe d this can g of
w ill be depend
ing whe
be man
ipulate d
designe th er the pro
d to pro cess is
seconda duce a
r y meta primar y
bo lite or
Oxygen
concentr
applicati ation -
ons use mos t co
growth m mercia
under a o f organ l
erobic c isms
sufficie o nd it ion, the
nt oxyg refore
e n mu s the pH
A lack
of oxyg t be ma
de avail - c ha nges in
pro ducts en w ill
lead to able. pH entation
of aero unwante he fer m
re duce bic con
d itions d w ithin t e the ac
tivity
the gro and n re d u c
tank ca
wth rate
d hence
z ymes an
of e n rates
growth
re duce
There are different parts of a fermenter to

ensure that these conditions are maintained.
- pH is monitored via a pH probe
- The water jacket inlet allows circulation of
water around the fermenter to regulate
temperature
- Paddles move to make sure that microbes
are in constant supply of fresh nutrients
- Sterile air is pumped in to keep the levels
of oxygen correct
- The vessels need to be sterilised with
steam that has been super heated to kill any
unwanted organisms
103
USING A FERMENTER
There are two ways of using a fermenter, batch cultures and continuous cultures.
Batch Cultures Continous Culture
In this scenario the microorganism is Nutrients are added to the tank at

mixed with a set amount of nutrient and regular intervals and products removed
allowed to grow for a fixed period of at regular intervals.
time.
At the end of this time the products are This is how insulin is produced
removed and the tank emptied
Batch Culture Continous Culture
Growth Rate is slower because nutrient level Growth rates is higher as nutrient are constantly
decline with time added to the tank to keep levels high
Set up is more difficult, maintenance of required

Easy to set up and maintain
growing conditions can be difficult to achieve
If contamination occurs then more of the product is

If contamination occurs it only affects one batch
lost
Less efficient as the tank isnt use all of the time More efficient as the tank is in constant use
Very useful for processes involving the production of Useful for processes involving the production of
secondary metabolites primary metabolites
ASEPTIC CONDITIONS
The nutrient that helps the microorganisms grow can also help other organisms grow
inside the tank as well. The growth of unwanted microorganisms in the product is called a
contaminant. They are unwanted because -
Aseptic
techniques
are measures taken at
Asepsis is the
any point during a
absence of
process to
unwanted
prevent unwanted
microorganisms
104 contamination
INDUSTRIAL ENZYMES
Enzymes are biological catalysts for metabolic reactions, both anabolicaly and
catabolicaly. The reason they are so useful in industry is that they are so specific. They
can also work well at low temperatures, there optimum being around 40C.
It is more efficient to isolate enzymes to do the reactions rather than growing the whole
organism with the catalyst. Isolating enzymes happens on a large scale. Extracting an
enzyme from the fermentation mixture is known as downstream processing.
For the product of an enzymes controlled reaction, the enzyme and substrate need to
collide and form a enzyme-substrate complexes.
The product then needs to be extracted from the mixture, usually a costly process
It is possible to immobilise the enzyme so they can continue to catalyse the reaction but
not mix with the substrate as they would normally. This has advantages and
disadvantages
Enzymes are not present with the products so Immobilisation requires additional time, equipment
purifications/downstream processing costs are low and materials and so is expensive to set up
Enzymes are immediately available for reuse. This

Immoblised enzymes can be less active because
is particularly useful in allowing for continuous
they do not mix freely with substrate
processes
Immobilised enzymes are more stable because the Any contamination is costly to deal with because the
immobilising matrix protects the enzyme molecules whole system has to be stopped
There are four methods of immobilising enzymes : -
Adsorption (emphasise AD) - Enzymes molecules

are mixed with the immobilising support and bind to
it due to a combination of hydrophobic interaction
and ionic links. These are usually clay, resin and
glass beads. These forces are weak and some
leaking (enzymes detaching) ca occur - it still gives
high reaction rates regardless
105
Covalent Bonding - Enzymes are covalently

bonded to a support, this usually involves
bonding enzymes to enzymes and then them
tho an insoluble material such as clay particles.
A cross linking agent can be used, this is
something like gluteraldehyde or spharose.
This doesnt bond large numbers of enzymes
but is much stronger than adsorption so less
leakage occurs.
Entrapment - Enzymes can be trapped things

such as gel beads or cellulose fibres. This allows
them to be trapped in their natural state as they
are not bound to another molecule so their active
sties are not affected. Reaction rates can be
reduced as substates need to be able to get
through the trapping barrier. Hence meaning that
the active site is less easily available than with
other methods.
Membrane Separation - Enzymes can be

separated from the substrate by a partially
permeable membrane. Put simply the
enzyme solution is held in one side of a
membrane whilst substate solution is passed
along the other side. Substrate molecules are
small enough to fit through the membrane so
the reaction can take place and the product is
also smaller enough to fit through. The
enzymes are too big so stay on one side.

106
Genes and Gene

Technology
107
DNA - contains some three billion base pairings which is the equivalent of 3 gigabytes of DNA.
The genome of a species is the entire DNA sequence of an organism and can therefore be
considered the entirety of an organism hereditary information.
DNA is composed of smaller lengths called genes which code for the production of certain
polypeptide and proteins, the rest is junk and called non-coding DNA
There isn't much coding DNA, only 1.5% of the genome is actually coding so the rest in non-coding
DNA
Since DNA was discovered in 1953 there have

been major advances insouciance thanks to it.
The Genomic Age These include : -
The term junk DNA is misleading when talking DNA profiling (Genetic Fingerprinting) which
about coding and non-coding DNA. This junk is used in forensic science for analysis and in
DNA carries out allot of regulatory functions of maternity and paternity tests
which, many are still unknown. Genomic Sequencing and comparative
genome mapping is used in the research of the
functions of genes and regulatory DNA
Genomics is the study of genomes - this is sequences
basically mapping the whole genome of an Genetic Engineering - Is used in the
increasing number of organisms. Comparing production of pharmaceutical chemicals,
genes and regulatory sequences will help to genetically modified organisms and
understand the role of genetic information in a xenotransplantation
range of areas such : Gene Therapy - can be used to treat
Health condition such as cystic fibrosis
Behaviour
Evolution relationships Genome maps allows identification of the
location that the bacterial artificial chromosome
(BAC) sample has come from
SEQUENCING THE GENOME OF AN ORGANISM - AN OUTLINE
Genome Sequencing - The technique used to give the base

sequence of DNA of a particular organism
Sequencing can only operate on a length of DNA of about 750

base pairs so the genome is broken up into sections before
sequencing
1. Genome are mapped to identify which part of the genome
they have come from. Information that is already known is
used (microsatellites which are short runs of 3-4 base
pairs found in several thousand sites of the genome)
2. Samples of the genome are sheared (mechanically
broken) int smaller sections of around 100000 base pairs.
This is called the shotgun approach
3. Those sections are placed into separate BACs and
transferred to E.coli cells. As the cells grow in the culture
many copies of the sections are produced. These are
called clone libraries
108
SEQUENCING A BAC SECTION
1. Cells contain specific BACs are

taken and cultured. The DNA is
extracted from the cells and restriction
enzymes are used to cut it into smaller
fragments. The use of different
restriction enzymes on a number of
samples give different fragment type
2.The fragments are separated using
electrophoresis
3. Each fragment is sequenced
4.Computer programmes then compare
overlapping regions from the cuts made
by different restriction enzymes in order
to reassemble the BAC segment
sequence
COMPARING GENOMES
Knowing and comparing the genes for the same or similar proteins across a range of
organisms is known as comparative gene mapping. Here are some of the applications of
this technique:-
Identification of genes for protein found in all or many living organisms gives clues the
relative importance of such genes to life
Comparison can show evolutionary relationships
Modelling the effects of changes to DNA can be carried out
Comparing genomes from pathogenic and similar but non-pathogenic organisms can
be used to identify the genes or base pair sequences that are most important in
causing the disease. This can lead to development o more effective drugs and
vaccines
Individual DNA can be analysed to reveal mutant alleles or the presence of alleles
associated with increased risk of a particular disease such as heart disease or cancer
BACKGROUND OF ELECTROPHORESIS
Electrophoresis is used to separate DNA fragments based on their size. The process is
accurate enough to be able to separate fragments that are different by only one base in
length. Its used in gene technology to separate DNA fragments for identification and
analysis.
The technique uses a gel plate or slab containing agarose (a type of sugar) which is
covered in buffer solution. Electrodes are attached to each end of the gel so that a current
can be passed through it. The separation occurs because the longer strands get caught up
in the agarose when travelling through it. The shorter strands can move further through.
109
PROCESS OF ELECTROPHORESIS
1. DNA samples are treated with restriction

enzymes to cut them into fragments
2. The DNA samples are placed into wells cut
into one end of the gel - the wells are at the end
of the negative electrode
3. The gel is immersed in a tank of buffer
solution and an electric current is passed
through the solution for a fixed period of time -
usually around 2 hours
4. DNA is negativly charged because of many
phosphate groups which makes them attracted
to the positive electrode
5.Shorter lengths of DNA move through the gel
faster than longer lengths so move further in the
fixed amount of time
6.The position of the DNA is shown using a dye
that stains DNA molecules
DNA PROBES
There are two types of DNA probes:-
Radioactively labelled with isotope 32P.

This is identified with photographic plates
DNA Probe - Short single stranded section of
DNA (50-80 nucleotides) that has some sort of
label attached to it. There are two sorts of DNA
probes with different labels.
Fluorescently labelled Probes - Identified
when they emit light
Copies of the probe can be added to any sample of DNA fragments and, because they are
single stranded, they will bind to any fragment where a complementary base sequence is
present
Bonding between Base pairs is called ANNEALING. It involves hydrogen bonding
110
HOW DO PROBES IDENTIFY GENES?

Disease Diagnosis and DNA Probes
- Probes are complementary to DNA
sequence Diagnosis of some genetic diseases and
- DNA gets separated into two strands identification of symptomless carriers can be
- Separated strands are mixed with the made by analysing patients DNA using DNA
probes which bind with the probes. The probes are made using
complementary bases - This is called complementary sequences found in the faulty
DNA Hybridisation alleles of a particular gene. Different probes
- can be placed on a DNA microarray and once
The site as which the probe binds can be
the DNA sample is applied it can reveal the
identified by the radioactively or the presence of faulty or mutated alleles that
fluorescence that the probe emits when match the fixed probes because the sample
its bonded DNA will anneal to any complementary fixed
probes.
PCR - POLYMERASE CHAIN REACTION
In order to anneal the sample DNA must be
The whole point of PCR is to make copies broken into smaller fragments. It may also be
of DNA. Its important in crime scene amplified using PCR so that many copies of
analysis where DNA samples can be taken the chain are made
and multiplied known as amplification. This
produces enough copies for genetic
profiling. Kary Mullis proposed the idea in
1983 and won a nobel price in 1993.
PCR is a Cyclic Reaction
1. DNA sample is mixed with a supply of nucleotides and DNA polymerase

2. The mixture is heated to 96C to break the hydrogen bonds between bases. This
makes the complementary strands separate
3. Primers (short lengths of 10-20 base pairs long) are added to the mixture
4. The temperature is reduced to 55C which allows the primers to hydrogen bond
(anneal) - this means there are short strands of double strands at either end of the
sample.
5. The temperature is now heated to 72C to allow DNA polymerase to bind to the double
stranded sections and extend them using the free nucleotides
6. When the DNA polymerase reaches the other end a new double stranded DNA
molecule is produced
111
The sequencing relies on
the fact that DNA:-
Is made up of antiparallel
backbone strands
Is made up of strands
that have a 5 and a 3 end
Grows from the 3 end
Base pairs pair up
according to
complementary base-
pairing rules
It can only
replicate relatively short The addition of the primer
sequences of DNA (a few molecules is required for the
hundred rather than a process to start
whole chromosome)
PCR is not
the same as
DNA replication
A cycle of heating
and cooling is used in PCR to
separate and bind strands - DNA
helices enzyme separates strands
in the natural process
Primers
Short, single stranded sequences of DNA

around 10-20 base pairs in length. They are
needed in sequencing reactions and
polymerase chain reactions to bind to a section
of DNA because the DNA polymerase
enzymes can not directly bind to single
stranded DNA fragments.
112
AUTOMATED DNA SEQUENCING
This was initially carried out using a slow and inefficient method involving radioactive
nucleotides. By improving this technology and the development of automated DNA
sequencing there has been a large increase in the number of organisms genomes
sequenced and published.
The reaction mixture contains :-
- DNA polymerase
- Copies of the single stranded template DNA fragment
- Free DNA nucleotides
- Primers
This is almost identical to the PCR reaction mixture. The only difference is that some of the
DNA free nucleotides have a florescent marker. These modified nucleotides also throw the
DNA polymerase of the chain therefore stopping any more addition of nucleotides.
How it Works:-
1. The primer anneals at the 3 end allowing the DNA polymerase to attach
2. DNA polymerase adds free nucleotides according to base pair ruling
3. If a modified nucleotide is attached the polymerase is thrown off and the reaction stops
4. As the reaction proceeds,
many molecules of DNA
are made. Fragments vary
in size - some are only one
nucleotide long as the
polymerase is thrown off in
others the strand could be
completed
5. In each case the final
nucleotide is tagged with a
specific colour
6. AS these strands move
through the machine a
laser reads the colour
sequence, from the strand
with only a single
nucleotide added to the
one with 2 , 3 , 4 etc
7. The sequence of colours
and so the sequence of
bases can then be
displayed
113
The process involved in genetic engineering is known recombinant DNA
technology, because these processes involve combining DNA from different
organism or from different sources, in a single organism
There a few steps involved in Genetic Engineering
The required
gene is obtained
Vector - Carrier agent of a piece of DNA from one
cell into another such as a bacterial plasmid
A
copy of the
gene is placed
Protein synthesis - The creation of proteins by
(packaged and
cells that uses DNA, RNA and various enzymes
stabilised) in
a vector
Stage in Methods Possible
Engineering
Process
Obtaining The The mRNA produced from transcription of the gene can be obtained
The vector genes to be from cells here that gene is expressed. For example, the mRNA for
engineered insulin is obtained from cells in islets of langerhan in the pancreas.
carries the gene The mRNA can be used as a template to make a copy of the gene.
to the recipient They use an automated polynucleotide sequencer.
A DNA probe can be used to locate the gene on DNA fragments and
the gene can be cut from a DNA fragment using restriction enzymes
Placing the gene in Gene can be sealed into a bacteria plasmid using the enzyme DNA
a vector ligase. This is the most common method of using vectors in genetic
The engineering
recipient Genes can also be sealed into virus genomes or yeast cell
chromosomes
expresses the
Vectors often have to contain regulatory sequences of DNA, these
gene though ensure that the inserted gene is transcribed in the host cell
protein
synthesis Getting the gene Vectors can often be too large to fit through membranes easily so
into the recipient there are multiple methods to help solve this problem : -
cell Electroporation - High voltage pulse used to disrupt the membrane
Microinjection - DNA is injected ising a very fine micropipette into
the host nucleus
Viral Transfer - The vector is a virus and so the DNA is inserted
using the virus mechanism
Ti plasmids used as vectors can be inserted into the soil bacterium
Agrobacterium tumefaciens . Plants can be infected with the
bacterium which inserts the DNA into the plants genome
Liposomes - DNA is wrapped in lipid molecules which are fat
Restriction Enzymes soluble and can therefore cross the bilayer
act like scissors
Ligase Enzymes act

as glue
114
Isolation Insertion Transformation Identification Growth/

Cloning
Stage 1 - Using Restriction Enzymes
- The enzyme restriction endonuclease are

used to cut thorough DNA as specific points
Restriction Enzymes -
- The enzymes are extracted from bacterial
bacterial cells where they preform a defence - Recognition sites are usually palindromic
function against viruses which means the sequence and its
- Bacteria contain enzymes to defence against complement are the same but reversed
invading viruses - GAATTC and complement CTTAAG
- There are more than 50 commonly used - In most cases the enzyme catalyses a
restriction enzymes hydrolysis reaction which breaks the
- Specific enzymes cut DNA wherever a phosphate sugar backbone
specific base sequence occurs and only when - This gives a staggered cut which leaves some
that sequence occurs exposed bases called sticky ends
- This means they have a highly specific active
sites
- Usually cut DNA as specific sites (around 4-8 bases long) which are called recognition
sites
Sticky Ends -
Most restriction
enzymes make a
staggered cut
forming sticky ends
Srticky ends have a

strand of single
stranded DNA which
are complementaryy
to each other
They will join with
another sticky end
only if it has been cut with the same restriction
enzyme.
DNA from different sources can be joined together if they have the same sticky ends i.e.
the same recognition sites
In order to have the same sticky ends they must have been cut using the same restriction
enzyme. The sticky ends of joined together using DNA ligase to join the sugar phosphate
back bone together
115
Blunt Ends -
Some restriction enzymes cut straight across

both chains forming blunt end
Endonuclease can produce blunt ends
Stage 2 - Using Ligase Enzymes
When enzymes need to be stuck together DNA ligase (an enzyme) is used to catalyse a
condensation reaction which joins the phosphate-sugar backbones of the DNA double
helix together
This is the same enzyme that is used in natural DNA replication to seal DNA nucleotide
together
In order to join DNA fragments from different sources both need to have been cut with
the same restriction enzymes
This makes the sticky ends complementary
If the ends art complementary the bases to bond together
DNA ligase can then seal the backbone
When DNA from different organisms is joined together in this way its
called RECOMBINANT DNA
Vector
Used to Plasmid
Insertion of DNA into a Vector - transport DNA The most common vector.
into a host cell A circular piece of DNA
found in bacteria, useful
because they contain
One of the Antibacterial resistant genes is antibiotic residence
disrupted when the enzymes cut the plasmid
open
The other antibiotic resistant gene is used in
selection of the correct host gene
116
Bacterial Cells and Plasmids
-Once a gene has been

identified to be placed into
another organism, it can be
cut from DNA using
restriction enzyme and then
placed into a vector
-Bacterial plasmids are
often used as the vector in
cases of genetic
engineering
-Plasmids often carry genes
that code for resistance to
antibiotics
-If plasmids are cut with the
same restriction enzyme
they will have
complementary sticky ends
- Mixing quantities of
plasmid and gene in the
presence of ligase enzymes
means that some plasmids
will combine with the gene,
which then becomes sealed
in the plasmid as
recombinant plasmid
-It is important to note that
many cut plasmids will, in
the presence of Ligase enzymes simply reseal to reform the original plasmid.
Transgenic and Transformed (Stage 3)
Large quantities of the plasmid are mixed with the bacterial cells, some of which will
take up the recombinant plasmid
The addition of calcium salts and Heat shock (The culture is lowered to
around freezing then quickly risen to 40C increase the rate at which
plasmids are taken up bacterial cells) attempt to increase the The
efficiency but the process is still extremely inefficient process is
Bacteria that take up DNA from their surroundings are so inefficient that
transformed less than 1% of
The transformation results in bacteria with new DNA bacterial cells take
Organisms are described as transgenic when it contains up the
DNA that has been added to its cells as a result of genetic plasmid
engineering
So bacteria are considered transformed when they first take up the plasmid
and then transgenic once they contain the DNA
117
Identification of Bacteria containing the plasmid with the DNA fragment (Stage 4)
Gene markers are used to identify which plasmids have taken up the DNA fragment
Gene markers can be : -

Resistance to an antibiotic
A fluorescent protein Usually the gene
An enzymes whose action can be identified marker is disrupted causing
a change if the DNA
fragment is present
Antibiotic-resistance Markers
The second antibiotic resistance (resistance to ampicillin)

is used to identify those plasmids with a DNA fragment in
them
Replica Plating
If the DNA fragment has been inserted into the ampicillin
resistance gene it will no longer grow on mediums
containing ampicillin
Its no longer resistant to ampicillin
A process called replica plating is used to identify these

bacteria.
The green plate (right) contains the plasmid as some of

them haven't grown (because they ant resistant to
ampicillin anymore
The bacteria which d not grow in the green plate contain a

plasmid with the DNA fragment
Cloning the Bacteria (Stage 5)
If there has been successful identification of the bacteria containing the plasmid and the
DNA fragment the bacteria are cloned
As the bacteria are cloned, the plasmid contain the DNA fragment are cloned also.
The type of cloning is considered in vivo which means cloned within a living organism
The opposite of in vivo is in vitro meaning non-living
118
BACTERIAL CONJUGATION
Bacteria are capable of a process known as conjugation, where genetic material may be
exchanged
In this process, copies of the plasmid DNA are passed between bacteria. Since plasmids
often carry genes associated with resistance to antibiotics., this swapping of plasmids is of
concern because it speeds the spread of resistance between bacterial populations.
Resistant strains of bacteria such as MRSA are causing health care problems because the
bacterium is usually found on human skin where it is not a problem. The transfer of this
bacterium to a wound however leads to a very serious infection. Scientists are continually
looking for new antibiotics to target these disease-causing organisms.
The advantage to the bacteria is that it may contribute to genetic variation and, in the case
of antibiotic resistance genes, survival in the precedes
MANUFACTURE OF INSULIN
Type 1 diabetes is when people cant produce their own insulin, a hormone.
Initially people would use insulin taken from the pancreatic tissue of slaughtered pigs (until
around the 1980s), there are however some issue with this : -
Its not identical to human insulin, this makes it less effective

Its very expensive since there isn't that much of it in the pancreatic tissue and
because its so ineffective more is needed
There is a sense of ethical reasons to not do this as well although the pigs
were slaughtered for other reason apart from the insulin
By the 1970s it was known that insulin is a polypeptide, consisting of 51 amino acids. The
DNA code for a polypeptide is very small (less than 200 base pairs long)
This makes it difficult to find in a genome of 300 million bases
1. Scientists focused their attention on finding the mRNA for the gene
2. Once they found the mRNA, the enzymes reverse transcriptase was used to synthesis
the complementary DNA strand (DNA template strand)
3. Adding DNA polymerase and a supply of DNA nucleotides to these single strands
means that the second strand is built using copied DNA as a template
4. This process produces a copy of the original gene called a cDNA - unpaired
nucleotides are added at each end to give sticky ends complimentary to those cut on
the plasmid
5. Plasmids are then cut open and mixed with cDNA genes
119
Some of the plasmids take up the gene

1. DNA taken from a DNA ligase enzyme then seals up the
Human cell plasmids which are now called
recombinant plasmids because they
contain the new piece of DNA
The plasmids are then mixed with bacteria,
2. Use some of which take up the recombinant
a restriction plasmids
enzyme to cut out the The bacteria are then grown on agar plate,
gene for insulin from where each bacterial cell grows to produce
the DNA a mound of identical (Cloned) cells, called
a colony
3. Use a
lysosome enzyme to
cut the plasmid out of
a bacterial cell
Using Reverse Transcriptase
4. Use the same 1. - cells from islets of langerhans in the

restriction enzyme to
cut a section of DNA Human pancreas
from the plasmid
2. Extract mature mRNA coding fro Insulin
3. A single stranded complimentary copy of

5.
DNA (cDNA) is formed using reverse
Insert the Gene for
insulin into the transcriptase on the mRNA template
plasmid
4. Single stranded cDNA is used to form
double stranded DNA using DNA

6. Use a ligase
enzyme to join the ends polymerase
of the DNA
5. This forms a double stranded copy of
the human insulin gene which is then

7.
Put the plasmid genetically engineered into a bacteria
with the insulin gene
back into a bacterial
cell
8. Leave the
9. Insulin
bacterial to divide to
removed and purified
make multiple copies of
so ready for use in
the bacteria that
humans
produce insulin
120
Not all bacteria take up the plasmid
There are 3 possible colonies that may grow during this process:-
Some from bacteria that did not take up a
plasmid
Some from bacteria that have taken up a
plasmid that has not sealed in a copy of the
gene but has sealed up on itself to reform the
original plasmid
Some - the desired ones - that have taken up
the recombinant plasmid, we call these the
transformed bacteria
IDENTIFICATION OF TRANSFORMED BACTERIA BY

REPLICA PLATING
To identify the transformed bacteria, radio-

labelled antibodies which specifically bind to the
insulin are used
Modern methods of identification use plasmid vectors with genetic markers
Antibiotic Resistance Genes

Replica Plating
Process of growing bacteria on an agar plate,

then transferring a replica of that growth to other
plates, usually containing different growth
promoter or inhibitors
Analysis of growth pattern on the replica plate

gives information about the genetic properties of
growing bacteria
121
Process of Replica Plating
1. The bacteria are grown on

standard nutrient agar, so all bacterial
cells grow to form colonies
2. Some cells from the colonies are
transferred onto agar that has been
made with ampicillin, so only those
that have taken up a plasmid will
grow
3. Some cells from these colonies are
transferred onto agar that has been
made with tetracycline so only those
that haven't taken up the plasmid will
grow
4. By keeping track of which colonies
are which, we know that any bacteria
that grow on the ampicillin agar, but
not on the tetracycline agar, must
have taken up the plasmid with the
insulin gene
5. We can identify the colonies we
want and grow them on a large scale,
these bacteria then produce insulin
on a large scale which can be
harvested for use
6.
GOLDEN RICE
There is a serious vitamin A

deficiency in up to 120 million people
with the majority of these around
Africa and South East Asia
500,000 people become blind as a
result of Vitamin A deficiency each
year
Vitamin A in the diet only comes from animal sources, if not then its taken from beta
carotene which is converted to Vitamin A in the Gut
Function Reason
Eyesight Forms part of the visual pigment, rhodopsin
Cell Growth and Development Involved in the synthesis of glycoproteins
Epithelial Cells Needed for maintenance and differentiation of

epithelial cells which reduces the risk of infection
Bones Essential for growth of Bones
122
Rice plants contain the code for the Golden Rice Mk 2
production of beta-carotene, which - because
its photosynthetic its required in the green In 2005 UK scientist developed a new variety
parts of the plant called golden rice 2
Unfortunately this part isn't eaten but only the The variety accumulates around 20 times more
endosperm (grain) beta-carotene in the endosperm than the
In 2000 genetically engineered rice was original version
created that accumulated beta-carotene in the If successfully grown this variety could deliver
grain the required amounts of beta-carotene within a
The accumulation of the molecule made the daily intake of 200-300g of rice
rice grains a yellow-orange in colour and they
named in Golden Rice
Benefits of Golden Concerns regarding Golden Rice
Reduce Vitamin A deficiency in areas Reduces genetic diversity/ variation

Reduce eye protection The clone may suffer disease
Provide a more stable diet The Seeds are expensive
Rice may not grow in all the areas that need it
Some ideas of doubt that they contain sufficient
vitamin A
GENE THERAPY
In humans gene therapy refers to any

therapeutic technique where the functioning
An experimental technique used to treat
or prevent by correcting faulty genes
allele of a particular gene is placed in the
cells of an individual lacking functional alleles
This is so that, in the future a gene can - the technique is not invasive
be inserted into a patients cell instead of
using surgery or drugs It can be used to treat some recessive
conditions but not dominant conditions such
as Huntington Disease
If you can get the working copy of a gene into cells that contain only dysfunctional copies
of that gene, then transcription of the working gene mean that the individual may no
longer have the symptoms associated with the genetic disorder (The working gene
overrides the faulty one)
The Human Genome project has helped to bring about further therapeutic possibilities
including the use of RNA which could silence genes binding to mRNA - this is only used
with AIDS patients as for the minute
The main point of gene therapy is to get the functioning protein into the body, this
helps the body to no longer express the symptoms of genetic diseases
123
Increasingly difficult and

approaching genetic
There are a multiple approaches to Gene Therapy :-
engineering
1. Replacing a mutated gene that causes disease with a healthily copy of the gene
2. Introducing a new gene into the body to fight off the disease and replace with a non-
functional gene
3. Inactivating a mutated gene that isnt functioning properly
4. Repairing the abnormal gene through selective reverse mutation
Somatic Cell Gene

Theory
Involves placing the gene in Germline Cell Gene Theory

adult differentiated cells such
as CTFR genes into Involves placing the gene into
respiratory systems cells of embryonic cells
cystic fibrosis sufferers
Somatic Cell Gene Therapy

As cells grow these cells become specialised to preform a specific function within the
body. On these specialised cells certain genes are switched on whilst others turned off.
Although the cell contains a full genome only a few will be actively producing proteins
Gene therapy by adding genes (augmentation) Gene therapy by killing specific cells
Some conditions are caused by the inheritance of Cancers can be treated by eliminating certain
faulty alleles leading to the loss of a functional gene populations of cells
product (polypeptide) Using genetic techniques to make cancerous cells
Engineering a functional copy of the gene into the express genes to produce proteins (surface
relevant specialised cells means that the antigens) that make the cells vulnerable to attack
polypeptide is synthesised and the cells can from the immune system which could lead to
function normally targeted cancer treatments
Germline Cell Gene Therapy
Each cell of an early embryo is a stem cell which means it can divide and become
specialised and potentially become a new being, hence why the cells are called germline
cells
Sperm and Egg - zygote contains copies of engineered genes
Some transgenic animals have been genetically engineered and the allele they have
received may be passed onto their offspring which is not the case with somatic
techniques
An individual who has had gene therapy for an genetic illness may still pass that disorder
to their offspring
124
Legal Issues and Ethics surrounding

Germline Gene Therapy
Although widely implied in experimental

animals, germline gene therapy in humans is
illegal and ethically unacceptable
The Ethics committee such as the Clothier

Committee would say that : -
An inadvertent modification of DNA

introduced into the germline could create a
HOW DOES IT WORK?
new human disease or interfere with human
A liposome is an artificial vesicle. Genes
evolution in an unexpected way
can be enclosed in the liposome and so
are able to pass through the plasma
OR
membrane of the target cell. This is a
form of gene therapy
Permanent modifications to the human
genome in this way raises difficult moral,
ethical and social issues that need to be fully
debated
Lipid Molecules pass easily through the

plasma membrane Possible Problems with This Technique
Normal CTFR genes isolated from human
cells and inserted in plasmids Liposomes might not be small enough to pass
Plasmids are placed back into bacteria. into the lung cells through the bronchioles
Gene markers pick up the cells that contain Poor Expression of the CFTR gene
the plasmid with the CFTR gene Adenoviruses may cause infection or patients
Bacteria is then cloned may develop an immunity to them making
Plasmids taken and wrapped in lipid them useless in future treatments
molecules (forming a liposome)
Liposomes sprayed into patients nostrils
125
Essentially what is happening is that a normal gene is inserted into the genome to replace
a abnormal disease-causing gene. A vector is used to deliver the normal gene and this is
normally a virus which has had its DNA altered. Vectors deliver the normal gene to the
target cell. The target cells such as liver or lung cells are infected with the vector. The
genetic information is unloaded to the target cell.
Now the cell produces a functional protein and restores to target cell to a normal
state.
Problems with this Technique
The technique is still risky and still under Ethical Considerations

study to make sure it is safe and effective
Only being tested for treatment of disease Are disabilities diseases? Should they be cured
that currently have no cure - Creating or prevented?
treatments for untreatable diseases Does searching for cures demand the lives of
The approach is limited in application as its those who are presently affected by disabilities
used only with certain tissues and requires It is very expensive so who'll have access to
large amounts of DNA these? And who'll pay?
Patients have to undergo multiple rounds of
gene therapy
May trigger and Immune Response
Problems with Viral response
GENE THERAPY FOR SCID (SEVERE COMBINED IMMUNODEFICIENCY)
There are 10 different forms of this condition, which leads to complete dysfunction of the immune
system.
In 1972, one of the forms was found to be due to the presence of a defective gene for the
enzyme adenosine deaminase (ADA)
The lack of ADA leads to an accumulation of metabolites toxic to T lymphocytes, so complete
loss of T lymphocytes occurs
This form of the condition has a recessive inheritance pattern
Gene Therapy trials in Began in 1990
A retrovirus, which is capable of transferring its DNA into Eukaryotic Cells, is engineered to
contain the normal human ADA gene
Bone marrow, containing T cells is removed from the patient and exposed to the retrovirus in
cell culture. Viral Infection leads to uptakes of the ADA gene
The transgenic cells formed are placed back into the patients bone marrow where they
establish a line of cells with functional ADA
126
Xenotransplantation - The transplantation of

Allotransplantation - The transplantation
cell tissues or organs between animals of
between animals of the same species
different species
Advantages and Disadvantages of Genetic Manipulation
Organim Example of benefit Example of Drawback
Humans Gene therapies have been Ethical Consideration : -

developed and further research is Effects of gene transfer are unpredictable
occurring to help treat genetic Individuals resulting from gremlin therapies would
disorders have no say in whether their own genetic material
should be modified
Not only might gremlin therapies be used to
eliminate disease but also breed designer children
as parents become able to choose and enhance
favourable characteristics
Animals Pharmaceutical chemicals can be Animal Welfare issues arise due to the treatment,
produced for example in milk suffering and genetic manipulation of animals
Increased milk production Sometimes such research may contradict strong views
held by some religious groups
Production of compatible organs
is becoming possible for
transplantation
Plants Accumulation of beta-carotene ins Genetic variation may be reduced as inserted genes
the endosperm of golden-rice can be passed to wild relatives
Devolping crops which are Favourable genes may be transferred to unwanted

resistant to pesticides allows the weeds and other crops which damages agriculture
use of weedkillers and
insecticides to increase yields Modified plants may be toxic to other organisms or
cause allergic reactions in humans
Microorga Genetically modified Micro-organisms may escape from containment and

nism microorganisms such as bacteria pass on their modified genes to other pathogenic
can be used to produce useful organisms with unknown effects
products such human insulin or
growth hormones Techniques often involve using genetic markers of
antibiotic resistance which can be passed on increasing
widespread resistance to antibiotics
127
Ecosyestems
128
ECOSYSTEMS
A group of living organisms and Component of Ecosystem Definition

non-living things occurring
Abiotic - together, and the Habitat The place where an organism
Effects of non interrelationships between lives
living things on them is thought of as an Population All of the organisms of one
an ecosystem ecosystem. species, who live in the sam
The size of ecosystems can place at the same time, and
vary greatly from huge african can breed together
grassland to small scale pond life. Community All the populations of different
species who live in the same
Biotic- The role that each organisms place at the same time, and
Things such as plays in the ecosystem is can interact with each other
food supply, called its niche.
prediction and The niche includes both the living and non-living and therefore it is
disease (living impossible to define its niche entirely.
things
ECOLOGY - COMES FROM THE GREEK WORD FOR HOUSE
Ecosystem
An Ecosystem is a part of a biome.
Biomes themselves are far too large to study so ecology work tends to be based around a
par'cular ecosystem.
ach ecosystem has a characteris'c set of plants, animals and microbes.
E
The organisms in an ecosystem form a self-sucient unit in balance with their environment.
Ecosystems are dynamic, con'nually changing as the organisms within them interact with one
another, and the ever changing environment.
Energy and nutrients generally ow between organisms within the same ecosystem, and liTle is
lost to the outside.
Biospere
The volume of the earths surface where organisms can be found.
It extends from the depths of the ocean (11km below sea level) to at least the highest plant
communi'es (6.2km)
Includes areas of polar ice and volcanic hot springs and undersea thermal vents
Huge diversity of organisms living in the biosphere
Some extremely specialised and adapted to the environment they are found in
Biome
The biosphere is made up of several types of biome.
These are classied due to their major vegeta'on types, for example
TUNDRA or TROPICAL RAINFOREST.
Community
All the organisms, of all the dierent species, living in a habitat
This is a group of species that occurs at the same place at the same 'me.
The word is oben used to refer to organisms of a par'cular kind, such as the plant community on
a lawn.
Eg the woodland community contains all the plants, trees, fungi microorganisms, invertebrates
and larger animals which live in the wood
129
Popula'on
Ecosystems and communi'es contain popula'ons of species.
A popula'on is made up of all the members of a species living together in the same place at the
same 'me and can interbreed with each other.
n example would be all the oak trees in a wood
A
Note that if oak trees in a nearby wood can interbreed with the trees in the rst wood, they are
part of the same popula'on
Individual
Finally each popula'on is made up of many individuals.
The gene'c and physiological adapta'ons of an individual organism to its environment is an
important aspect of ecology.

ENERGY AND ECOSYSTEMS
Ecosystems are Dynamic
Matter is constantly recycled within an
Most population sizes go up and down, either
ecosystem - through nutrient cycles such as
slightly or noticeably. This is because of the way the nitrogen cycles and carbon cycle.
the community interacts with its self. Energy however, is not recycled it flows
Any small changes can affect others through the ecosystem.
If a predators population goes up then the
population size of the prey goes down All living things need energy. Via respiration,
The nitrogen levels in soil can affect plants they release energy from organic molecules
growing there. If it falls plants growing there such as glucose in their food. The energy
attempt to increase it which causes other here originally came from the sun. For this
plants to grow there reason the start of every food chain is a
plant as they can get energy from the sun
and convert it to organic matter.
Producer The plant in the food chain - they make food from photosynthesis
Primary Consumer Animals that eat the producer
Secondary Consumer Usually eat animal matter (carnivores)
Tertiary Consumer Eat Secondary consumers
Omnivore Eats both plants and meat
Trophic Level Position occupied by a group of organisms in a food chain
Food Chain Describes a feeding relationship between organisms
Food Web Many food chains linked together
Carnivore An animal that eats other animals and may therefore be 2 or 3

consumers
Decomposers Living things such as bacteria, fungi and some animals that feed on
waste material or dead organisms
130
FOOD CHAINS SHOW HOW ENERGY IS TRANSFERRED FROM ONE LIVING THING TO ANOTHER
Within an ecosystem, living organisms are usually

members of more than one food chain, and often
feed at different trophic levels in different chains.
Refer to When they are combined they form a food web rather
the arrows as than a food chain.
showing the
direction of
energy transfer
EFFICIENCY OF ENERGY TRANSFER
At each trophic level, living organisms need energy to

carry out life processes. Respiration releases energy from
organic molecules like glucose - some of this energy is
converted to heat
Energy remains stored in dead organisms and waste
material, which is then only available to decomposers,
such as fungi and bacteria. This waste material includes
animal parts and plants that cannot be digested by
consumers.
This means theres less energy avertible to sustain life at

higher levels of the food chain so less tissue is kept alive.
131
When organisms in a food chain are about the same sizer then there will be fewer
consumers at the higher levels. Ecologists use pyramid of numbers to represent this idea.
The area of each bar is proportional to the number of individuals.
Pyramids can be drawn for individual food chains or for an ecosystem as a whole
Pyramids of Biomass
Counting the number of organisms does

not always show the amount of tissue at
each level. For that reason a better
approach is to draw a pyramid of biomass,
where the area is proportional to the
amount of dry mass (gm2) of all the
organisms at each trophic level. They
represent the amount chemical potential
stored energy in organic matter.
To do this properly an ecologist would need
to collect all the organisms and put them in an oven at 80C until all the water in them has
been evaporated which makes it a very destructive method.
Pyramids of Energy
Pyramids of biomass still present

problems, as different species release
more energy per unit mass. Because of
this ecologists sometimes prefer to
construct a pyramid of energy. This
involves burning organisms in a
calorimeter to determine how much energy
is released per gram. This is very time
consuming an extremely destructive again so ecologists ofter revert back to biomass
pyramids
Pyramids of Productivity
Even pyramids of energy have limitations

They only take a snapshot at one
moment in time
Because population sizes can fluctuate
over time, this may provide a distorted idea
of the efficiency of energy transfer
As such ecologists look at the rate at

which energy passers though each trophic
level, drawing a pyramid of energy
flow .The rate of energy flow is called productivity.
Productivity gives an idea of how much energy is davalaiable to organisms at a
particular trophic level, per unit area (usually meter squared) in a given amount of time
(usually a year) Its measured in kilojoules or megajoules per square metre per year
At the base of the food chain, the productivity of plants is called the primary productivity
The gross primary productivity is thew rate at which plants convert light energy into
chemical energy. However, because energy is lost when the plant respires, less energy
is available to the primary consumer, remaining energy is called the net primary
productivity (NPP)
132
TYPE OF PYRAMID EXPLANATION ADVANTAGES DISADVANTAGES
Biomass Amount of tissue is Gives and idea into how Destructive to the
available at each level - much available tissue is ecosystem due to having
the dry mass of all the at each level to kill the organisms
organisms at each level
Energy Burning the organisms in Accounts for the fact that Very destructive to the
a calorimeter to different species release ecosystem - only takes a
determine how much different amounts of snapshot at one moment
energy is available per energy per unit mass in time - doesn;t give any
gram reference to energy
transfer
Productivity Looks at the amount of Gives much more detail

energy transferred to into the ecosystem
each level
MANIPULATING ENERGY TRANSFER
Primary Productivity is the total amount of energy fixed by photosynthesis. It is the net flux
of carbon from the atmosphere to plants, per unit time. It is a rate and may be measured
terms of energy per unit time, such as MJ m-2 yr-1.
Net primary productivity is the rate at which carbohydrate accumulates in the tissue of
plants of an ecosystem and is measured in dry organic mass such as kg ha-1 yr-1
Net Primary productivity = Primary Productivity - Respiratory heat loss
Improving Primary Productivity Improving Secondary Productivity
Scientists have found that the occult NPP in the Transfer of energy from primary consumers to
field is actually between 1% and 3% - Humans secondary consumers etc
can manipulate this
light levels can limit the rate of photosynthesis Young animal invests a larger proportion of its
- Plant crops early energy into growth than adults - Harvest
Lack of water is important in many countries animals just before adult hood
- Irrigating crops , drought resistant strains of Treat animals with steroids to make them grow
bred even more quickly - now outlawed in the EU
Temperature can limit speed of reactions Selective breeding used to produce breed with
- Green Houses faster growth rates- increased egg production
Lack of nutrients - Crop rotation/ fertiliser and increased milk production
Pests such as insects eat crops - Pesticides Animals may be treated with antibiotics to
Fungal disease - fungicides avoid unnecessary loss of energy to pathogens
Competition from weeds - herbicides and parasites
Mammals and birds waste energy through
moving about so are giving small enclosures to
minimise this
Enclosures kept at constant temperatures and
given food so energy isn't wasted keeping
temperature constant and looking for food
133
SUCCESSION
Succession is a directional change in a community of organisms over time
How Does Succession Occur?
The island of Surtsey in Iceland was formed by a volcanic eruption in the 1960s and is now
home to a new community of plants.
Development of a new community from bare ground is known as primary

succession, its brought about by the following : -
Algae and lichens begin to live on the bare Sand Dunes

rock - they make a pioneer community
Erosion of the rock and build up of the dead Useful as they show all the stages of succession
and rotting organisms produces enough soil in one place at the same time.
for plants, mosses and ferns to grow which
succeed (replace) the algae and lichen Looking at the beach and sand dunes you can
Similarly, larger plants succeed the smaller see the different sections. Sand is deposited on
plants until a final, stable community is the beach by the sea and so we know that the
reached that is called the climax community areas of sand closest to the shore are more
recent that those further inland.
Secondary succession occurs where This means that just above the level of high tide
is the process of succession, those more inland
previously colonised but damaged or disturbed
have reached their climax community
habitat is recolonised - Secondary succession
Eventually a sand dunes community may develop into a grassland community, and then a
woodland community, although this takes much longer is is usually a fair bit inland. This is
representative of the UK as a whole, as most climax communities in the UK are grassland
ecosystems.
134
The following steps outline the succession process for a sand dune, showing the the
diagram on the previous page
Pioneer plants such as sea rocket and prickly

snakeroot colonise the sand just above the
high water mark - these can tolerate the little
salt water spray and the lack of freshwater
and the unstable sand - only pioneer plants
exist here
Wind-blown sand builds up around the base

of these plants, forming a mini-dune and as
plants die and decay, nutrients accumulates
in this mini dune. As the dune gets bigger
and bigger plants like sea couch and marram
grass colonise there - root systems stabilise
environment
With more stability and further accumulation

of nutrients, plants like Hares foot clover and
Birds foot Trefoil start to grow
As the sand dune and nutrients continue to

build up and other plants may colonise the
sand
Eventually the dune areas far inland may

become grassland and overtime woodland
allowing much larger species of plants
including large trees to grow
135
STUDYING ECOSYSTEMS
Ecologists study ecosystems to find out the abundance and distribution of a species in
relation to other species. It can also be related to soil pH, light intensity or other
environmental factors.
Sampling Techniques
Used because it is impossible to count every single organism in a habitat so small section
are used to represent the whole area
Quadrats
- Makes it able to compare the abundance and

distribution of plant species in two different Transects
fields - using small samples of a field and Useful in showing change in variation across a
scale them up to estimate the abundance habitat. It could show changes in abundance and
- Quadrats can give you two different types of distribution of species. For example across a
data sand dune and beaches, environmental
conditions are recorded as well. There are two
Presence or absence of individuals approaches to using this method : -
(Distribution)
Estimate or count the number of individuals Line Transect - At regular intervals, make a not
(Abundance) of which species is touching the tape
- This is difficult so they usually estimate a
percentage cover Belt Transect - At regular intervals, place a
- Percentage cover quadrat next to the line (interrupted belt
Difficult to predict transect) studying each as you normally would.
Could use smaller squares on quadrat but Can also have continuous belt transect
still very in accurate
Frame points are a little more accurate
Sampling
- If you take samples from one corner of a field, the soil could be particularly rich in
nitrates and these species differ significantly to those in other areas of the field
- Should randomly select different samples by randomly positioning the quadrants
using random number generator on a grid reference system or take samples at
regular intervals
- Rather than looking at one quadrat which isn't enough or 20000 which is too many,
by taking random samples across the whole habitat and making a cumulative
frequency against the quadrat number, when the point where the curve levels off
tells them how many quadrants to use, ecologists double this number
- A similar method is used to decide how big the quadrants should be. Count the
number of species in larger and larger quadrants, plot quadrat area on x axis
against the number of species , optimal quadrat size is where they level off
The following equation shows you how to estimate the size of each species population in
the habitat
136
DECOMPOSERS AND RECYCLING
If decomposers did not break down dead

Lots of energy is lost through waste material and
organisms organisms, energy and
dead matter. To help preserve some of this
energy, decomposers such as bacteria and fungi. valuable nutrients would remain trapped
within the dead organisms. By digesting
Bacteria and fungi involved in decomposition dead and waste material, microbes get a
feed in a different way from animals, they feed supply of energy to stay alive, and the
saprotrophically so are described as trapped nutrients are recycled.
saprotrophs. Microorganisms have a particularly
Saprotrophs secrete enzymes onto dead and important role in the cabin and nitrogen
waste material cycles within ecosystems.
These enzymes digest the material into small
molecules, which are absorbed into the
organism body
Having been absorbed, the molecules are
stored or respired to release energy
NITROGEN CYCLE
Living things need to make proteins and nucleic acids. Nitrogen is used in this process and
cycled between the biotic and abiotic components of an ecosystem.
137
STEPS OF THE NITROGEN CYCLE
NITROGEN FIXATION
Nitrogen in the atmosphere is very unreactive so its impossible for plants to use it directly
(even though its abundant, 78%). This means they need a supply of fixed nitrogen such as
ammonium ions (NH4+) or nitrate ions (NO3-). Nitrogen fixation can occur when lightening
strikes or through the barber process. However these only account for about 10% or the
nitrogen that gets fixed around the world.
The other 90% is carried out by nitrogen fixing bacteria. Some of there live freely in the soil
and fix nitrogen gas by using it to manufacture amino acids.
Nitrogen-fixing bacteria such as Rhizobium, also live inside root nodules inside plants such
as peas, beans and clovers - all members of the bean family
They have a mutualistic relationship with the plant; the bacteria provide the plant with
fixed nitrogen and receive carbon compounds such as glucose in return
Proteins, such as leghaemoglobin, in the nodes absorb oxygen and keep the conditions
aerobic. Under these conditions the bacteria use an enzyme, nitrogen reductase, to
reduce nitrogen gas to ammonium ions that can be used by the host plants
NITRIFICATION
Happens when chemoautotrophic bacteria in the soil absorb ammonium ions
Ammonium ions are released by bacteria involved in the putrefaction of proteins found
in dead or waste material organic matter
Rather than getting their energy from sunlight (like photoautotrophic bacteria, algae
and plants), chemoautotrophic bacteria obtain it by oxidising ammonium ions to nitrites
to nitrates (nitrobacter)
Because oxidation requires oxygen, these reactions only happen in well-aerated soils
Nitrates can be absorbed from the soil by plants and used to make nucleotide bases
(for nucleic acids) and amino acids (for proteins)
DENITRIFICATION
Other bacteria convert nitrates back to nitrogen gas. When bacteria involved are growing
under anaerobic (without oxygen) conditions, such as in water logged soils, they use
nitrates as a source of oxygen for their respiration and produce nitrogen gas (N2) and
nitrous oxide (N2O)
138
AFFECTING POPULATION SIZE
Carrying Capacity And Limiting Factors
In most ecosystems, the population of different species changes over time. This isn't
however always the case, sometimes they will remain fairly stable.
The size of a population is determined by the difference between the birth rate
reproductive race) and the mortality rate (death Rate)
Lag Phase
During the lag phase there may only be a few individuals, still acclimatising to their habitat,
and at this point the reproductive rate (r) is low and the growth rate of the population is
slow
Log Phase
During log phase, resources are plentiful and

conditions are good. The reproductive rate
exceeds the mortality rate, and the population Carrying Capacity
size increases dramatically
The maximum population size that can be
Stationary phase maintained over a period of time in a particular
habitat
The habitat itself cannot support a larger
population, this means the population size has
levels out and reaches what is known as the carrying capacity
The factors that resist the habitat growing any larger are called limiting factors, which
include the availability of resources and the intensity of competition
The carrying capacity is the upper limit that these factors place on the population size
139
Predators and Prey
Predators Hunt Prey

Predation can be a limiting factor on a preys population size
This in turn affects the predators population size
When a
predator
population gets
bigger more
prey is eaten
With more The prey

prey, the population gets
Predator Prey Relationship

predator smaller, leaving
population gets less food for
predators
Cycle
bigger
With
With less
fewer
food, fewer
predators,
predators can
fewer prey are
survive and their
eaten and their
population
population
decreases
increases
140
COMPETITION
Competition happens when resources (like food and or water) are not present in adequate
amounts to satisfy the needs of all the individuals who depend on those resources
There are two different types of Competition - Intra and Inter specific Competition
Intraspecific Competition
This happens between individuals of the same species. Factors include food supplies, that become
limiting so individuals need to compete for them. This slows down population growth and the
population enters the stationary phase.
Although there are slight fluctuations in population size during the stationary phase, intraspecific
competition keeps the population relatively stable
If population size drops, competition reduced and the population size then increases
If the population size increases, competition increases, and the population size then drops
Interspecific Competition
This happens between individuals of different species. It can affect both the population size of
species and the distribution of species in an ecosystem. If two species are competing for the same
resource then one of them will be more superior than the other and so the weaker one will be
excluded.
Species can avoid Interspecific by niche specialisation, by using different resources to avoid
competition or to use resources in a different way. For example rather than just eating different
plant change the time of the day when the plant is eaten.
Sessile (non-mobile) organisms pose a problem when space is the factor in question. This can be
shown with the organisms on a beach as shown on the
left
For example, say species 1 (S1) was one species of
barnacle, existing only at high tide and is covered for a
part of the day by the high tide; and species 2 (S2)
was another species which lives only at low tide. When
S2 is removed, the other species, S1 thrives both at high
tide and low tide, so why when S2 is present does S1
141
only exist at high tide? We can decipher from this that S1 is able to survive in the whole range, as
it can resist desiccation (drying out when the high tide goes down), however, it does not
outcompete S2 at low tide.
We can also tell that S2 is quick to colonise and so competes well for space at the low water
mark, where it is constantly wet and so does not suffer desiccation, and so survive there but do
not outcompete S1 at high tide regions because that barnacle simply cannot survive there, allowing
S1 to thrive.
142
Populations and
Sustainability
143
Conservation is a dynamic process in which positive action is taken to maintain and
enhance biodiversity
This includes: -
Active breeding programmes
Importing individuals from captive breeding programmes or from other more
stable ecosystems to increase population size
Removal of excess predators
Prevention of poaching
Monitoring health and carrying out vaccination to reduce disease
Provision of food to reduce competition
Preservation is maintaining or protecting an area in its current state, and is best

applied to areas that have not yet been affected by humans. If the area has already
been altered it may have not have the suitable environmental conditions to enable
survival of the ecosystem. It may allow succession to occur or the ecosystem may
become unstable.
Sustainable Woodland Management
A sustainable harvest is one that can be carried out indefinitely without damaging
the ecosystem.
Suitable management systems can actually achieve a whole range of
achievements in a an environment that at first, may seem to conflict. There are a
number of simple techniques that can be used to allow amenity use and maintain
biodiversity.
Never clear fell - use selective thinning or selective felling so that the ground is
never fully exposed over a large area. Could also
use strip felling
Replace felled trees using fast-growing native
species
Protect young trees from browsing animals
Harvest timber from a part of the woodland each
year and rotate the are used to avoid clearing
one huge area. This is also means that a wide
range of habitats are maintained whilst new ones
are simultaneously created
Coppicing (Cutting the plans at ground level leaving the roots so that the soil
isn't disturbed) - Encourages more growth and produces a variety of different
types of timber
Pollarding - Has the same advantages of coppicing
Use standards, these are tall trees left to grow between coppicing to protect the
soil - these can be cut down once tall enough
Include fire breaks to protect crops from fires - these
double as walking an cycle tracks
Include touristy areas of use for the land
144
Reasons for Conservation
Ethical Every species has its own value and right to survive. As many
Considerations species are endangered as a result of human activities we
have an ethical responsibility to protect them
Economic Many species have an economic value when harvested as a
Considerations food source or fuel supply
Pollination of crops is carried out by insects and some animals
provide a natural predator to pests so help with pest control
Ecotourism can help bring wealth to places that don't have
much to offer
Social Ecotourism and recreation in the countryside also have a
Considerations significant social and financial value, which derives from the
aesthetic value of living things. Ecotourism depends on the
maintenance of biodiversity, and this of course links into the
economic reasons, as there is a sizeable commercial side to
ecotourism
Management Systems
Effective conservation requires consideration of the social and economic costs to the local
community, as well as effective education and liaison with the community. It can involve
establishing protected areas, such as SSSIs (sites of special scientific interest) or National
Parks, and can provide legal protection for endangered animals or plants. Conservation
can also take place ex-situ in places such as zoos or botanical gardens
The system thats put in place depends on which system would best benefit the
environment.
- raise carrying capacity (see 7.5 Populations) by providing extra resources, mainly food
- move individuals to enlarge populations, encourage natural dispersion of individuals
between fragmented habitats
- restrict dispersion of individuals by fencing

- control predators and poachers
- vaccinate individuals against disease
- preservation of habitats by protecting against pollution or disruption
145
HUMAN IMPACT ON THE GALAPAGOS ISLANDS
Since Charles Darwins discoveries made the Galapagos Islands famous, they have been
severely affected by human activities
Habitat Disturbance
Increase in population increases
demand of water, energy and sanitation
services
More waste and pollution and therefore
increase demand of oil
Oil spills such as the on in 2001 have
had adverse affects on marine and
coastal ecosystems
Increased demand for land and
buildings means that habitats have
been destroyed
Some species have been completely
destroyed or nearly destroyed such as
the forests of Scales Trees
Lonesome George is the last surviving
individual of his kind.
Exploitation of Resources
Species have been harvested quicker than they can be replenished
Giant tortoises were taken because they could survive on little food in the hold of a ship
for a longtime - they were then killed an eaten, the population dropped 200000 in less
than 50 years
There are 14 registered endangered species as result of human intervention
Introduced Species
As humans populated the islands many non-native
species were brought with them
Alien species can : -
Eat native species
Destroy native species
Bring diseases
Goats
Most damaging to the ecosystem

It eats Galapagos rock purslane which is unique to
the islands
The tortoises are out competed for grazing and
tramples the food supple and eats it all
They change the habitat and reduce the available nesting sites available for tortoises
In some places they have managed to transform forest into grassland causing soil
erosion
Conservation Efforts in The Galapagos
Introduced species are now centre of conservation. Strategies have been adopted to help
sort the issue .
Quarantine System - Search arriving boats and tourists
Natural Predators are exploited to remove damage as pest control
Culling has been successful against feral goats and pigs
146
Plant Responses
147
STIMULI THAT PLANTS RESPOND TO
As expected, plants can respond to biotic (living) and abiotic (non-living) components of
their environment.
Responding to the environment means that the plant may have a greater chance of
survival by avoiding stress or avoiding getting
eaten. This means it may survive long enough
to reproduce. Tropisms are directional growth responses of
plants
Type of Tropism Response
Phototropism Shoots grow towards the light

Positively phototropic
Enables photosynthesis
Geotropism Roots grow towards pull of gravity
Enables the roots to anchor to the soils and take up water
This improves support and makes the plant turgid
Cools the plant
Water contains minerals such as nitrates, which are needed to synthesis amino
acids
Chemotropism On a flower, pollen tubes grow down the style, attracted by chemicals, towards
the ovary where fertilisation can take place
Thigmotropism Shoots of climbing plants

Plants such as ivy wind around other plants or solid structures and gain support
CONTROLLING PLANT RESPONSES
Hormones coordinate plants responses to the environmental stimuli

They are similar to animal hormones, chemical messengers that target specific cells
In plants however, some cells produce hormones for use in the same cell, these are
often referred to plant growth regulators rather than hormones because , unlike animals
they are not produced in the endocrine gland and rather by a variety of cells in a variety
of tissues of the cell
Hormone Effect
Auxins Promote cell elongation; inhibit

growth of side shoot; inhibit leaf
abscission (leaf fall)
Cytokinins Promote cell division

Hormones move
around the plant by: - Gibberellins Promote seed germination and
- Active Transport growth of stems
- Diffusion
- Mass flow in the phloem Abscisic Acid Inhibits seed germination and
growth; causes stomatal close
sap or xylem vessels when the plant is stressed by low
water availability
Ethene Promote fruit ripening
148
PLANT GROWTH
The cell wall around plant cells limits their ability to divide and expand. This means that
growth can only happen in certain places in. This happens in groups of immature cells that
are still capable of dividing called meristems.
Meristem Location Function
Apical Tips or apices (apex) of roots and Responsible for roots and shoots
shoots getting longer
Lateral Bud Found in buds Gives rise to side shoots
Lateral Found in a cylinders near the Responsible for roots and shoots
outside of roots and shoots getting longer
Intercalary Located between the nodes Growth between the nodes is

(where leaves and buds branch responsible for the shoot getting
from the stem) longer
Cell divisions happens

closest to the apex and
then cell elongation
happens just behind the
apex.
Auxins are produced at
the apex and then the
auxins travels to the cells
in zone of elongation,
causing them to elongate
and hence making the
shoot grow

The extent to which cells elongate is due to the concentration of auxins and is
proportional.
Auxins increase the stretchiness of the cell wall by promoting the active transport of
hydrogen ions, by ATPase enzyme on the plasma membrane , into the cell wall. The
resulting lower pH provides optimum conditions for wall loosening enzymes to work
These enzymes break bonds between cellulose causing the walls to become less rigid
and can expand as the cell takes in water
149
WHAT CAUSES PHOTOTROPISMS
Phototropism - Growth Towards Light
Shoots bend towards the light because the shaded side elongates faster than the lit side
Evidence from experiments involving cereal seedlings in particular, suggests that the light
shinning on one side of the shoot cases auxins to be transported to the shaded side where
they promote elongation of those cells so the shoot grows towards the light.
Two enzymes that have been associated with this are phototropin 1 and phototropin 2
which are activated by blue light (wavelength 400-540 nm) so lots of activity on one side
and progressively less away from the light which causes the redistribution of auxins
Shedding Leaves
Cytokines stop the leaves of
deciduous trees sensing (turing
brown and dying) by making sure the
leaf acts as a sink for phloem
transport - if cytokine levels fall then
the supply of nutrients drops and the
leave may fall
Normally auxins inhibit abscission by

acting on cells i the abscission zone
Leaf senescence causes auxin
production at the tip of the leaf to
drop
This causes the cells in the
abscission zone more sensitive to
another substance called ethene
A drop in auxin also causes a
increase in ethene production
Then this increases the production
of the enzyme cellulose which
digests the walls of cells in the
abscission zone eventually for
separating the petiole from the stem
AUXIN ROLE IN APICAL DOMINANCE
In most plants the apical tip inhibits the growth of lateral buds which is known apical
dominance
If the tip of the plant is removed then the lateral buds will elongate and grow
Auxins are also thought to play a role in apical dominance
150
Auxins exert their influence in an unknown In tall unbranched species of the sunflower,
way, possible by attracting nutrients to the apical dominance is strict and extents over the
apex entire stem
As auxins move down the other parts of
there plant they stimulate elongation of cells
just behind the apical meristem, but inhibit IN shooter plants the tomato plant, apical
the growth of the lateral buds dominance may extend only as far as the first
Apical dominance is a classical example of few lateral buds
one part of a plant controlling another, by
the influence of a growth substance
This is a CORRELATION
The degree of dominance of the apical bud is however very variable between species
When the apical bud is removed the source of the IAA is removed making the
concentration of auxin is much lower the lateral buds can now grow
Imposed by the young leaves of the apical buds

These synthesise indoleacetic acid (IAA)
IAA inhibits the growth of buds below
If the apical bud is removed, one or more of the lateral buds takes over
If the apical stump is treated with IAA, the growth of the lateral buds is suppressed
COMMERCIAL USES OF HORMONES
Taking Cuttings Seedless Fruit

Dipping the end of a cutting in rooting Treating un-pollinated flowers with
power before planting it encourages auxin can promote growth of
root growth. Rooting powder contains seedless fruit. Auxin promotes ovule
auxins, a fungicide and talcum growth, which triggers automatic
powder production of auxin tissues in
developing fruit
Commercial Uses of Auxins
Herbicides
Artificial auxins are used as herbicides to kill weeds. They
are transported in the phloem to all parts of the plant and
they can act within the plant for longer because they are not
a close fit to the enzymes that break them down. They
promote growth of shoots so much that the stem cannot
support itself, buckles and then dies
151
GIBBERELLIN HAS MULTIPLE COMERCIAL USES
Fruit Production Synthesised in the apical proteins of roots and

Brewing stems
Plant Breeding play a leading role in controlling stem
Delays Senescence elongation in the growing stems of mature
Improve Shape trees and shrubs- promotes internode
elongation
Its effect is enhanced when Auxin is present
One classic effect of gibberellins is their
Applying them to draw mutants is known to
ability of breaking the dormancy of certain restore normal growth and development
seeds partially cereal. The germination is Induce plants to grow out of the rosetta stage
triggered by soaking the seeds in water. This and flower early during first year
because water softens the testa-pericarp Speeds up seed germination
covering and enters the rest of the cell
Gibberellins In Fruit Production Gibberellins in Brewing
Delay senescence in citrus fruits - extending Malt is needed to make beer, which is usually
the time that fruits can be left unpicked and produced in a malthouse in the brewery
therefore making them available in shops for When barley germinates, the aleurone layer of
longer the seed produces amylase enzymes that
Gibberellins acting with cytokines can make break down stored starch into maltose. Usually,
apples elongate to improve shape the genes for amylase production are switched
Without cytokines grape bunches are very on by naturally occurring gibberellins
compact, this limits the growth of the grapes. Adding gibberellins can speed up the process
With gibberellins, the stalks elongate and less Malt is then proceed by drying and grinding up
compact and so the grapes are much bigger the seeds
Gibberellins in Sugar Production Gibberellins in plant Breeding
Spraying sugar cane with gibberellins Speed up the process of producing trees with
stimulates growth between the nodes, which desirable characteristics by inducing seed
make the stems elongate formation in young trees
Sugar cane stores sugar in the cells of the Seed companies who want to harvest seeds
internode, with more internode cells the more from plants which only flower in their second
sugar is available in each plant year of life (biennial) can add gibberellins to
Spraying with gibberellins increases the yield induce seed production in the first year
of sugar by up to 4.5 tonnes per hectare Stopping plants producing gibberellins can be
useful as it keeps some plants short and sticky
(poinsettias)
It also keeps the internodes of crop plants
short, helping to prevent lodging. Lodging
happens in wet summer where stems bend
over because of the weight of water
152
Cytokinins
Delay leaf senescence, they are sometimes used to

prevent the yellowing of lettuce leaves after they
have been picked Ethene
Cytokinins are used in tissue cultures to help Speeds up ripening
mass produce plants because they promote Promotes Fruit Drop
bud and shoot growth from small pieces of Female Sex expression in
tissue taken from a parent plant. This produces cucumbers
a short shoot with a lot of side ranches, which Promotes lateral growth
can be split into lots of small plants
Each small plant is then grown
153
Animal
Behaviour
154
RESPONDING TO THE ENVIRONMENT
A very complex nervous and

Fight or Flight? endocrine system monitor internal
and external environments using
If a threat is perceived a whole host of changes
receptors throughout the body. They
take place though the body to prepare an
appropriate response - to run away or to fight coordinate responses to any change
in these environments. They are
A number of responses ensure that an organism coordinated to ensure survival,
is ready to fight or flight (run away) including short term responses to
temperature and longer term to
ensure reproductive behaviour.
The brain decides the best response of both nervous system

and controlling endocrine gland through the hypothalamus
and therefore the pituitary gland.
The perception of the threat can come from various stimuli -

normally visual or auditory
The cerebral processing of a potential threat activates the

hypothalamus, which stimulates increased activity in the
sympathetic nervous system (speedy one)
This in turn encourages the release of adrenaline from the

adrenal medulla into the blood
The hypothalamus also releases

Corticotropin Releasing Factor
(CRF) into the pituitary gland, which
releases Adreno-corticotrpic
hormone (ACTH) from the anterior
pituitary gland
Adreno-corticotropic hormone
stimuates the release of a whole
range of corticostreiod hormones
from the adrenal cortex. Some of
these help the body resist stressor
(stimulus that
causes a stress response. The combined
CRF
effects of the sympathetic nervous system
and the release of hormones and other
ACTH
hormones cause the physiological response
155
Adrenaline
INNATE BEHAVIOUR
The features of innate behaviour include the following:
Genetically determined and passed on

via reproduction
All members of a species show the Innate behaviour always has a survival value.
behaviour This may be survival of the individual or the
Stereotyped meaning there is a fixed species through ensuring reproduction occurs.
action pattern
Usually inflexible so it cannot change as
a result of changing stimulus around it
Unintelligent - No sense of purpose of the behaviour
There is two sorts of innate behaviour. Both are present at birth and not learnt or
taught.
- Taxis = A Directional response (similar to a tropism although refers to a

movement rather than growth)
- Kinesis - An increased movement in a random direction
The main difference between the two is that Taxis (like the car transport) move to a
specific place in direction whereas Kinesis increases random movement until
desired conditions are found.
Type of Innate Behaviour Example Survival Value
Reflex - usually an escape The escape refuse when To avoid predation - not get
response that takes the earthworms are touched or eaten
body or part of the body out the rapid movement of a
of harms way very quickly squid
Taxis - A directional A shark is attracted to a To find more food or to get
response. The animal source of blood in water, so away from an unpleasant
moves away or towards a it swims up the stimulus
stimulus concentration gradient
Kinesis - This is an Woodlice move about more To spend more time in the
increased movement that quickly in the light or in dry right conditions where there
has no defined direction. conditions is no unpleasant stimuli
The animal moves more
quickly in repose to an
undesired condition and
slows down when reaches a
desired condition.
156
LEARNED BEHAVIOUR
Learned behaviour develops as a result of experience. The features of learned

behaviour include : -
It is not present at birth

Not all members of the species show it
The behaviour can be adapted according Learned behaviour is behaviour that is altered
to experience by experience
It can be passed on to other members of
the species through observation
Learned behaviour usually has a survival value.
Type of Behaviour Example
Habituation - the animal learns to ignore repeated Birds learn that a scarecrow is no risk
stimuli that causes no harm, there is no reward or
punishment from stimuli
Imprinting - young animals associate with another Lorenz showed that young geese recognise their
organism, usually a parent own kind because they imprint on the first things
they see move - usually a parent
Classical Conditioning - An animal learns to Pavlov trained dogs to salivate at the sound of a
associate two related stimuli through repetition bell.
Operant Conditioning - Animals can be trained to Dogs learn to sit or shake hands if given a reward
preform an act to receive a reward. The reward is such as a friendly pat
reinforcement
Latent Learning - An animal that can explore its Rats and mice can be trained to run through a
surroundings learns the surroundings and may be maze. If they have done a maze before they learn it
able to make use of that knowledge to escape much quicker
predators or find food - exploring their surroundings
Insight Learning - Use of previous experience to A chimp trying to reach a banana that is out of reach
solve a problem - Higher level thinking skill may stack boxes to climb higher to reach the food
157
PRIMATE BEHAVIOUR
Social behaviour refers to that of organisms of a particular species living together in

groups with relatively defined roles for each member of the group
Social Organisation
- Mountain gorillas live in stable groups of around 10 individuals called a troop
Silverbacks
These are the main dominant

mature male of a group. He
protects the other members of
the group and leads them in
search for food. He is the only
male that mates with the
mature females.
As younger males reach sexual

maturity they leave the group to
live alone until they are mature
enough to attract females. As females mature they remain in the same group or join
another
Social Behaviour Hierarchy within a group exists where

individuals have a place in the order of
Grooming - One individual picks the importance within the group.
Those higher up to hierarchy show power and
parasites from the fur of another. This
position by often receiving more food, or
occurs between all members of the group having rights of access to mate with other
reinforcing relationships between individuals as shown with silverback gorillas
individuals
Care Of The Young - this is the role of the mother. During the first five months the
infant remains in constant contact with the other , suckling at hourly intervals. At 12
months, infants venture as far as 5m from the mother.
The mother protects the young gorilla as it learns social behaviour and how to live
independently.
At the age of 2 further learning takes place and juvenile gorillas play together, as
they become adults they begin to forage for food and get interment. The silverback
is important for development of young gorillas, both in terms of protection and as a
source of learning
158
Communication systems - a variety
Advantages of Social behaviour
of calls, displays and grunts are used to
Hunting as a group enables successful hunts signal danger to other members of the
for larger animals as food group, to issue threats to predators or
Many individuals searching for new sources of other groups and in play fighting
food can cover a wider area
displays as juveniles learn how to
Food Sources such as tree in fruit can be
protected behave like adults.
Many eyes watching for predators will be
more likely to spot one coming or individuals Facial Expressions - important
can take it turn to act as a lookout allowing especially in terms of recognition
others to feed in peace
Many individuals together can protect each
other and fight off a predator Most primates are social animals living
Social grooming can help to rid the family of in groups of families. Typically the
parasites group has a hierarchal structure in
Care of young can be shared between a
number of closely related individuals
which different individuals have
The young members of the group can learn different status and roles. There are
through observation and play many advantages to living in groups
HUMAN BEHAVIOUR, DOPAMINE AND DNA
Dopamine is a chemical found in the Structure and Activity of Dopamine

brain. Its a neurotransmitter associated
with the release of adrenaline and Acts as a neurotransmitter and hormone
Is a precursor in the production of adrenaline
noradrenaline. and noradrenaline
Low levels of adrenaline are associated with
There are at least 5 different dopamine Parkinson's which is treated with the precursor
receptors. These are called DRD1 to L-dopa
High levels of dopamine is also associated with
DRD5. Each one mediates a different mental health conditions such as schizophrenia
response , the range of responses - this means people treated for parkinsons are
include: often prone to random behavioural changes
such as compulsive gambling
- INcreases general arousal and decreases
Increase General Arousal inhibition making people more creative
- Decreasing inhibition
- Controlling Motivation
- Controlling Learning
DRD4 Receptor Gene
There are over 50 different variants of this gene. They differ in a specific sequence
known as variable number tandem repeat. It has around 20 different alleles. The
receptor therefore differs from person to person. Particular variants have been
associates with behavioural disorders such as ADHD.
159
A number of studies have shown that some of these variant are implicated in
certain human behavioural conditions. It is thought that the inheritance of particular
variants of the DRD4 gene affects the levels and action of dopamine in the brain
Attention-deficit hyperactivity disorder Addictive and Risk Behaviours

(ADHD)
Some people are more likely to display
Drugs such as methylphenidate (Ritalin) are addictive behaviour than others
used to treat ADHD by affecting levels of This may be because of the levels of
dopamine in the brain. adrenaline released when leaving in a
One version of the DRD4 receptor are certain way, such as gambeling
shown to be more frequent in individuals
suffering ADHD
Other Neurotransmitters and behavioural conditions
OCD is thought to be a result of low levels of serotonin. In 2007 genome wide

search in to DNA sequences found 8 genetic markers linked with OCD. They looked
at DNA from 1008 people and 219 families were included
160
Animal
Responses
161
THE BRAIN
Structure of the Brain
There are four main sections of the brain
CEREBELLUM - The largest part of the brain and most recognisable part of the brain. It is
responsible for the elements of the nervous system that are associated with being human
CEREBELLUM - Controls the coordination of movement and posture
HYPOTHALAMUS - Controls the autonomic nervous system and the endocrine glands
MEDULLA OBLONGATA - Controls the action of smooth muscle in the gut wall and controls
breathing movements and heart rate
Parietal Lobe
Orientation
Frontal Lobe Movement
Higher brain Sensation
functions Calculation
Decision thinking Recognition
Planning Memory
Emotions
Motor Cortex
Occipital Lobe
Visual Cortex
Processing
Temporal Lobe information from the
Processing auditory eyes such as
information colour, shape and
Sound perspective
Recognition of
speech
Also involved in Cerebellum
memory Co-ordinates
movement
Balance
Cerebrum
Corpus Callosum
Hypothalamus
Cerebellum
Brain Stem
Pituitary Gland
162
REGION OF THE BRAIN OUTLINE OF FUNCTIONS
Medulla oblongata Controls non-skeletal muscles (cardiac and involuntary muscle). This means
that is effectively in control of the autonomic nervous system. Regulatory
centres for a number of vital processes are found in the medulla oblongata
including:
the cardiac centre (heart rate)
Respiratory centre (breathing rate etc)
Hypothalamus Controls homeostatic mechanisms. Sensory input from temperatrue receptors
is received and causes an automatic response. It contains the pituitary gland
and therefore most of the endocrine system
How do neuroscientists know so much about the brain?
Pathological Specimens
Examining damaged areas
Animal Studies
Studying during surgery
Non-invasive techniques
By studying the results of injuries to the brain it is possible to identify which parts of the
brain control what by working backwards. If the back of the brain is damaged and vision is
impaired then its possible to deduce that that part of the brain is responsible for vision and
processing images received from the eyes
163
ORGANISING THE NERVOUS SYSTEM
It coordinates the actions of the body through elliptical impulses

It is structurally functionally divided into subsystems
It works in conjunction with the endocrine system
The nervous system is divided into 2 systems
Central Nervous System Peripheral Nervous System
Brain and spinal cord. Made up of grey Made up of the neurones that carry
matter (billions of non-mylelinated nerve impulses into and out of the CNS.
cells) and white matter (billions of longer
mylelinated axons and dendrons).
Subdividing the Nervous System
Sensory neurones carry impulses from many receptors, in and around the body to the
CNS.
Motor neurones carry impulses from the CNS to the correct effector organs. Nerves are
formed from many neurones bundled together in connective tissue.
The motor system is further divided beyond this :
Somatic motor neurones carry impulses from the CNS to skeletal muscles - This is
voluntary
Autonomic motor neurones carry impulses from the CNS to the cardiac muscle, to
smooth muscle in the gut wall and to glands, these are involuntary
164
Autonomic Nervous System
Autonomic translates to self-governing referring to the fact that system operates to a large
extent independently of conscious mind
The system is responsible for the majority of homeostatic mechanisms

The system is also capable of controlling the heightened responses associated with the
stress receptors
Differs from the somatic nervous system in a number of ways
Autonomic neurones are un-myelinated whereas the somatic neurones are

Autonomic connections to effectors always consist of two neurones whereas somatic
have one
There are two types of autonomic neurones, sympathetic and parasympathetic
- They differ in structure and action (speed)

- Under normal resting conditions impulses are passing along at a relatively low rate
- The balance of stimulation is controlled by subconscious parts of the brain
- Changes to internal environment leas to an altered balance of stimulation which leads to
an appropriate response
Parasympathetic Sympathetic
Most active in sleep and relaxation Most active in times of stress
The neurones of a pathway are linked at a ganglion The neurones of a pathway are linked at a ganglion
within the target tissue. So pre ganglionic neurones just outside the spinal cord. So pre-ganglionic
vary considerably in length neurones are very short
Post-ganglionic neurones secrete acetylcholine as Post-ganglionic neurones secrete noradrenaline in

the neurotransmitter at the synapse between the the synapses between the effector and the neurone
neurone and effector
Effects of action include: decreased heart rate, pupil Effects of action include: Increased heart rate, pupil
constriction, decreased ventilation rate and sexual dilation, increased ventilation rate and orgasm
arousal
165
MUSCLES
Muscles are composed of elongated cells that form fibres. These cells are able to contract
and relax.
Filaments are mad up of the proteins actin myosin which cause the contractions
There are 3 types of muscle in the body :
Voluntary (Skeletal) muscle - Which leads to the movement of the skeleton at the joints
in the body
Cardiac Muscle - Forms the muscular part of the heart
Involuntary (Smooth) Muscle - controlled by the autonomic nervous system therefore

meaning that its not voluntary movement
Voluntary Muscle Involuntary Muscle Cardiac Muscle
Striated, multinucleate, organised Smooth muscle consists of Organised as single cells joined
in parallel bundles of microfibrils, individual cells by intercalated discs; parallel
fibres all parallel microfibrils similar to striated
muscle, cross bridges present
between fibres
Skeletal muscle attachted to Found in walls of blood vessels, Found only in the heart
bones by tendons digestive system and airways
Supplied by nerves from the Supplied by nerves from the Supplied by nerves from the
peripheral somatic nervous autonomic nervous system autonomic nervous system
system
Skeletal/Voluntary Muscle
The fibres formed are about 100m

in diameter
Each fibre is surrounded by a cell
surface membrane called a
sarcolemma
A sarcoplasm is the cytoplasm in
a muscle cel, it has specialised
organelles to help preform its
function
Many mitochondria
Extensive sarcoplasmic
reticulum (special ER)
Number of microfibrils - the
contracting elements of
muscle- each contain a
smaller unit called a sarcomere
166
Involuntary/smooth muscle
Initiated by neurones of the autonomic nervous system. This type of muscle are not under
voluntary control
Not striated like voluntary and cardiac muscle
Considered spindle-shaped
single nucleus
Contraction is relatively slow
Tires really slowly
Location Arrangment of muscle cells Action
Walls of the intestine Circular and longitudinal bundles Peristalsis - moves food along the
intestine
Iris of the eye Circular and radial bundles Controls the intensity of light
entering the eye
Contraction of radial muscles
dilates the pupil
Wall of arteries and around Circular bundles Important in temperature

arterioles; wall of cervix and regulation, regulation of local
uterus blood pressure and the
redirecting of blood to voluntary
muscles during exercise
Contraction of muscle narrows
vessel diameter os reducing
blood flow
Relaxation causes dilation,
increasing the blood flow
Cardiac Muscle
There are 3 types of cardiac muscle

Atrial muscle
Ventricular Muscle
Specialsed excitatory and conductive muscle fibres
Some of the muscle fibres are able to stimulate contraction without a nerve impulse. These
are considered myogenic.
167
MUSCLE CONTRACTION - THE SLIDING FILAMENT MODEL
The Sarcomere
The sarcomere spans from one Z-Line to another Z-line

During contraction the H-zone and I-band are made smaller to bring the Z-lines closer
together - the A-Band does not change size during this contraction
Thin Filament Structure (yellow Above) Thick Filament Structure
Consists of two strands of G-actin (a globular Bundles of protein myosin

protein) wrapped around each other Each protein consists of a tail and 2 protruding
Each strand is called an F actin heads
Tropomyosin ( a rod shaped proetin) coils Overall there is many myosin molecules whose
around the f actin to reinforce it heads stick out from opposite ends of the
Troponin is attachee to each tropomyosin, one filament
binds to actin, another to tropomyosin and
another to calcium ions
Tropomyosin
Troponin G-Actin
168
The Power Stroke
1. Myosin head groups attach to the surrounding actin filaments forming a cross-bridge
2. The heads then bend, causing the thin filament to be pulled along and so overlap with
the thick filament - this is the power stroke and ADP and a Pi are released
3. The cross bridge is then broken as new ATP attaches to the myosin head
4. The head moves backs as the ATP is hydrolysed to ADP and Pi - it now forms another
cross-bridge with the thin filament further along and the process looks
Calcium Ions
The binding site for the Myosin on the actin is covered by tropomyosin subunits so binding
is impossible in this state and contraction wont occur. When an action potential arrives
calcium ions are released which bind to the tropomyosin which uncover the binding sites
so cross bridges can occur.
When stimulation stops the calcium ions are actively transported back into the
sarcoplasmic reticulum by carrier protein so the muscles can relax.
ATP
When the myosin heads bend the molecules are in their most stable form. Energy from
ATp is needed to break the crop-bridges and re-set the myosin heads. The head group can
then rebind and bend again
Maintenance of ATP supply
There is only around 1-2 seconds of contraction energy available in the muscle fibre. This
means energy is needed and regenerated very quickly There are 3 ways this is done
Aerobic Respiration in muscle cell mitochondria - dependant on oxygen supply

Anaerobic Respiration - Quick but produces lactic acid
Transfer from creatine phosphate in the muscle cell sarcoplasm. The phosphate group
from creatine phosphate can turn ADP to ATP very quickly using the enzyme
phosphotransferase = another 2-4 seconds of contraction
169
ACTION OF MUSCLES
Movement requires the coordinated action of voluntary muscles. Skeletal muscles can only
contract but they cant elongate without the action of an antagonistic muscle. Thats why
skeletal muscles are always in antagonistic pairs.
Muscles are stimulated by motor neurones

leading from the motor area of the brain called a
Antagonistic means that muscles oppose each
motor unit. Individual motor neurones are
other
attached to one or more muscle fibres by a motor
end plate or neuromuscular junction. Similar to a
synapse the can stimulate muscle fibre
membranes.
Synovial Joints - The Elbow
The arm contains 3 bones:

- The Humerus
- Radius
- Ulna
These join at the elbow.

The elbow is considered a
hinge joint.
Biceps are a flexor muscle

that bends the joint when
it contracts.
Triceps are extensor that

straightens the joint when
it contracts.
These are an antagonistic

pair that work together.
The synovial fluid acts as an lubricant for the joint. It eases the movement of the bones at
the joint.
170
Events that occur in a striated muscle
fibre Following stimulation by a motor
neurone
1.Action potentials travel down the

motor neurone
2.They stimulate calcium ions to enter
the presynaptic swelling
3.The vesicles of neurotransmitter
fuse with the membrane releasing
acetylcholine into the cleft
4.Acetylcholine binds to receptors,
causing an inflow of sodium ions that
depolarise the sarcolemma (an end
plate potential)
5.If above threshold, action potentials
are transmitted along the sarcolemma
6.Action Potentials are also
transmitted down into the transverse system (T-system) tubules . These membranes
have the same channel proteins and pumps found in neurones
7. The impulse is coupled to the contraction mechanism. Depolarisation of T-system
tubules causes calcium channels in the sarcoplasmic reticulum. These act as a second
messengers to stimulate movement of muscle myofibrils
171

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Joshua Cole F214

F214 - Communication, Homeostasis F215 - Controls, Genomes and

Fast Cells able to

Long lasting To cells

Good Communication System

Cover entire organism Specific Communications

Homeostasis - The maintenance of an constant internal environment despite external changes

- Works best if its controlled in both directions meaning

Negative Feedback- Reverses the effects of a change

-Body Temperature (37.5C)

Positive Feedback - Amplifies the Change

Receptor Cells detect Stimulus

Signal Sent to Processing Centre

Message sent to effector

Good Communication System

There are 2 Communication systems in the Human Body

ENDOTHERMIC - Able to generate own body heat

ECTOTHERMIC - Rely on external temperatures to

BEHAVIOURAL RESPONSES TO AN INCREASED EXTERNAL TEMPERATURE CAUSING THE BODY TO COOL

- Move into shade

- Move into Sun

Physiological Responses to Increased

Sweat Glands activate (Latent heat of

Physiological Responses to Decreased

Skeletal Muscles shiver

Sense Sense Organ Receptors sensitive to change

Smell Nose Chemical changes in air

Taste Tongue Chemical changes in mouth

Touch Skin Pressure, Temperature and Pain

Sound Ear Vibrations and the position of the

Sight Eye Light, intensity and wavelength

There are 2 types of Neurone:-

HOW DO NERVES WORK AND WHAT IS THE ELECTRICAL IMPULSE?

MAINTAINING A RESTING POTENTIAL

GENERATING A ACTION POTENTIAL

1. The membrane is at resting state; -60mV inside compared to outside. Polarised.

8. The potential difference overshoots slightly, making the cell hyperpolarised.

They wont allow any

SEQUENCE OF EVENTS AT THE SYNAPSE GAP

An action potential arrives at the presynaptic

The calcium ions cause vesicles containing the

Acetylcholine molecules bind with receptors on

Acetylcholine (ACh) - Common

THE ROLE OF SYNAPSES IN THE NERVOUS SYSTEM

Synapses allow information to be dispersed or Amplified

- When one neurone connects to many neurones information

Summation at the Synapses finely tunes the nervous response

Weak stimuli causes only a small amount of neurotransmitter to be

Summation is the effect of neurotransmitter from many neurone

Synapses make sure that impulses are transmitted one

Because the receptors are only in the postsynaptic membrane

HORMONES ARE MOLECULES THAT ARE RELEASED BY ENDOCRINE SYSTEM.

- Hormones are released directly into the blood

There are 2 sorts of hormones:-

PROTEIN OR PEPTIDE HORMONES -

THERE ARE ALSO 2 SORTS OF GLANDS:-

Endocrine Gland Exocrine Gland

Pancreas has both endocrine and exocrine functions

The target cells are those that possess a

The Adrenal Glands are at the top of the kidney

Adrenaline is manufactured in the adrenal medulla in the

ADRENALINE IS UNABLE TO ENTER CELLS BECAUSE IT IS A

It has a secondary messenger mechanism.

Adrenaline binds to cell