A2-LEVEL
A-LEVEL
BIOLOGY
BIOLOGY
NOTES
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INDEX
MODULE 5: COMMUNICATION,
HOMEOSTASIS AND ENERGY. . . . . . . . . . 6
TOPIC 1: COMMUNICATION AND HOMEOSTASIS. . . . . . . . . . . 8
1. The Need for Communication Systems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2. Cell Signalling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
3. Homeostasis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
4. Ectotherms and Endotherms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
TOPIC 2: EXCRETION AS AN EXAMPLE
OF HOMEOSTATIC CONTROL. . . . . . . . . . . . . . . . 14
1. The Importance of Excretion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2. The Mammalian Liver. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3. The Kidney. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
4. The Control of Blood’s Water Potential. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5. Kidney Failure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
6. The Use of Excretory Products in Medical Diagnosis . . . . . . . . . . . . . . . . . . . . . 24
TOPIC 3: NEURONAL COMMUNICATION . . . . . . . . . . . . . . . 26
1. Sensory Receptors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
2. Sensory, Relay and Motor Neurones. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3. Nerve Impulse Generation & Transmission. . . . . . . . . . . . . . . . . . . . . . . . . . . .27
4. Synapses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
TOPIC 4: HORMONAL COMMUNICATION . . . . . . . . . . . . . . 33
1. Endocrine Communication by Hormones. . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
2. The Adrenal Glands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
3. The Pancreas. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
4. Regulation of Blood Glucose Concentration. . . . . . . . . . . . . . . . . . . . . . . . . . 36
5. Diabetes Mellitus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
TOPIC 5: PLANT AND ANIMAL RESPONSES . . . . . . . . . . . . . . 40
1. Plant Responses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
2. Plant Hormones . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3. Experimental Evidence for The Role of Auxins. . . . . . . . . . . . . . . . . . . . . . . . . 43
4. The experimental evidence for the role of gibberellin. . . . . . . . . . . . . . . . . . . . . 43
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5. The Commercial use of Plant Hormones. . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
6. The Mammalian Nervous System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
7. The Human Brain. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
8. Reflexes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
9. Nervous and Endocrine Coordination. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
10. Regulation of Heart Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
11. The Neuromuscular Junction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
12. Mammalian Muscle and Muscular Contraction . . . . . . . . . . . . . . . . . . . . . . . . 54
TOPIC 6: PHOTOSYNTHESIS . . . . . . . . . . . . . . . . . . . . . . 60
1. Photosynthesis and Respiration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
2. Chloroplasts and Photosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
3. Factors Affecting the Rate of Photosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . 64
TOPIC 7: RESPIRATION. . . . . . . . . . . . . . . . . . . . . . . . . 67
1. The Need for Cellular Respiration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
2. The Mitochondrion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
3. Glycolysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
4. The Link Reaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
5. The Krebs Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
6. Anaerobic Respiration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
7. The Difference in Respiratory Substrates. . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
8. The Respiratory Quotient (RQ). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
9. Practical investigations into factors affecting the rate of respiration. . . . . . . . . . . . 73
MODULE 6: GENETICS, EVOLUTION AND ECOSYSTEMS. 74
TOPIC 1: CELLULAR CONTROL. . . . . . . . . . . . . . . . . . . . . 76
1. Types of Gene Mutations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
2. Gene Expression Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
3. The Genetic Control of Embryonic Development . . . . . . . . . . . . . . . . . . . . . . . 79
TOPIC 2: PATTERNS OF INHERITANCE . . . . . . . . . . . . . . . . 82
1. Phenotypic Variation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
2. Genetic Diagrams. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
3. Linkage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
4. Epistasis and Codominance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
5. The Chi-Squared (χ2) Test. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
6. Continuous and Discontinuous Variation. . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
7. Factors Affecting Species Variation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
8. The Hardy–Weinberg Principle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
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9. Isolating Mechanisms in the Evolution of New Species. . . . . . . . . . . . . . . . . . . . 90
10. Artificial Selection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
11. The Ethics of Artificial Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
TOPIC 3: MANIPULATING GENOMES. . . . . . . . . . . . . . . . . 93
1. DNA Sequencing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
2. Applications of DNA Sequencing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
3. DNA Profiling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
4. The Polymerase Chain Reaction (PCR) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
5. Electrophoresis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
6. Genetic Engineering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
7. The ethics of Genetic Manipulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
8. Gene Therapy in Medicine. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
TOPIC 4: CLONING AND BIOTECHNOLOGY . . . . . . . . . . . . . 102
1. Natural Clones in Plants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
2. Natural Clones in Animals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
3. Artificial Clones in Animals Produced by Artificial Embryo Twinning
or by Enucleation & SCNT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
4. Microorganisms in Biotechnological Processes . . . . . . . . . . . . . . . . . . . . . . . . 104
5. The advantages/disadvantages of using Microorganisms to Make Food
for Human Consumption . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
6. Aseptic Culture Technique for Microorganisms . . . . . . . . . . . . . . . . . . . . . . . . 106
7. Manipulating the Growing Conditions in Fermentation . . . . . . . . . . . . . . . . . . . 107
8. The Growth Curve of a Microorganism in a Closed Culture . . . . . . . . . . . . . . . . . 108
9. Immobilised Enzymes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
TOPIC 5: ECOSYSTEMS. . . . . . . . . . . . . . . . . . . . . . . . . 113
1. Ecosystems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
2. Biomass Transfer Through Ecosystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
3. Recycling Within Ecosystems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
4. Primary succession . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
5. Measuring the Distribution and Abundance of Organisms in an Ecosystem . . . . . . . 118
TOPIC 6: POPULATIONS AND SUSTAINABILITY. . . . . . . . . . . 120
1. The Factors that Determine the Size of a Population. . . . . . . . . . . . . . . . . . . . . 120
2. Conservation and Preservation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
3. Ecosystem Management for Sustainability. . . . . . . . . . . . . . . . . . . . . . . . . . . 122
4. The Management of Environmental Resources and the Effects of Human Activities. . . 123
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MODULE 5
COMMUNICATION,
HOMEOSTASIS
AND ENERGY
TOPIC 1
Communication
and
Homeostasis
Communication
and Homeostasis
1 The Need for Communication Systems
Keeping Cells Active
•• All organisms needs to maintain a limited set of conditions
•• Need to respond to changes in external and internal environments
•• This is because cellular activities rely on enzymes which require a specific set of conditions to
work effectively
•• Organs need to coordinate their activity to maintain optimal internal conditions that support
survival
2 Cell Signalling
When cells communicate by signalling, one cell releases a chemical
•• This chemical is detected by another cell
•• The second cell then responds to this signal
There are 2 major systems of communication:
Neuronal System
•• Network of neurons
•• Quick signals
•• Rapid responses
Hormonal System
•• Uses blood to transport signals
•• Endocrine organs secrete hormones directly into blood
•• Carried all over the body
•• Only recognized by specific target cells
•• Enables long-term responses to be coordinated
•• Specific target cells have receptors that have a shape that is complementary to the shape of
the hormone
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3 Homeostasis
Homeostasis is the regulation of internal environments independently of external
environments
These include:
•• Temperature
•• Blood glucose concentration
•• Blood salt concentration
•• Water content
•• Blood pressure
•• Blood carbon dioxide partial pressure (blood pH)
Negative Feedback
•• Reversal of a change in the environment to return to the optimum position
•• Receptor detects the change
•• Communication systems inform the effectors
•• The effector reacts to reverse the change
•• Eg: maintaining blood pressure
•• Pathway:
Positive Feedback
•• Response causes change to increase
•• Destabilizes the system
•• Usually more harmful
•• Does not lead to homeostasis
•• Can be useful in certain situation
•• Eg: childbirth - uterine contractions
•• Pathway:
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EXAM TIP
Know that conditions in the body never stay completely constant. Instead, they continually
‘bounce’ between the upper and lower thresholds of what is considered acceptable.
Stimulus and Response
•• What are they?
○○ A stimulus is any change in the environment that causes a response
○○ A response is a change in behavior or physiology as a result of a change in the
environment
•• External Environment
○○ Environment may change slowly
–– E.g. — Global Warming
○○ It may change quickly
○○ The changes must be monitored and the organism must respond to them
•• Internal Environments
○○ Some cells are not exposed to the external environment, but are protected by epithelial
tissues
○○ As cells undergo metabolic reactions there is a change in the environment
○○ Activities of the cells alter their own environments in this way
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4 Ectotherms and Endotherms
Changes in temperature can have a dramatic effect on enzyme action. Core temperature must
be maintained to ensure the functioning of vital organs.
Endotherms
•• Can maintain body temperature within strict limits
•• Independent of external temperatures
•• Internal sources of heat used to maintain body temperatures
•• Can increase respiration rates to generate heat
•• There are advantages:
○○ Constant body temperature regardless of external environment
○○ Activity possible in cooler temperatures
○○ Able to inhabit cooler parts of the world
•• There are also disadvantages:
○○ Significant part of energy intake used to maintain body temperature
○○ Moor food required
○○ Less energy from food can be used for growth
•• Physiological adaptations:
○○ Sweat glands in skin
○○ Hairs on skin
○○ Capillaries near skin surface
Sweat glands
Blood capillaries under
surface of skin
Erector muscles
controlling hairs on
skin
Hot
environment
Secrete sweat water has high
specific heat
capacity, therefore
heat escapes body
and converted into
evaporation of sweat
Capillaries dilate to
increase surface area
- heat from blood
transferred out of the
body and through the
skin more efficiently
Relax so hair is flat
against skin - air can
freely circulate over the
skin, cooling it down
Cold
environment
Sweat glands
inactive
Capillaries close to
reduce heat lost
through the skin
Contract so hair stands
on end - this serves to
trap air over the skin
which acts as a layer of
insulation
Ectotherms
•• Organism that relies on an external source of heat to regulate its body temperature
•• There are some advantages:
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○○ Less food used in respiration
○○ Less food required
○○ Greater proportion of energy derived from food can be used for growth
•• There are also disadvantages:
○○ Less active in cooler temperatures
○○ May not be capable of activity during cold winters
•• Physiological adaptations:
○○ Do not use internal energy source to maintain body temperature
○○ When they are active, increased respiration in muscles will generate some heat
○○ Temperature regulation relies on increasing the exchange of heat with their environment
–– When cold, they will change behavior to increase absorption of heat fro its
environment
–– When hot it will increase heat loss to the environment
○○ Warm-up by lying on a hot surface
EXAM TIP
Avoid calling ectotherms ‘cold-blooded’ as many, for example those living in the desert, are
able to maintain their internal body temperature at warm temperatures.
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TOPIC 2
Excretion
as an Example
of Homeostatic
Control
Excretion as an Example
of Homeostatic Control
1 The Importance of Excretion
Excretion = the removal of metabolic waste products from the body.
Metabolic waste = Unneeded byproducts produced as a result of normal metabolism. These
need to be removed from the body as they can become toxic in large quantities.
Carbon Dioxide
•• Excess carbon dioxide is toxic
•• High levels of carbon dioxide have many effects:
○○ Reduce the oxygen carrying capacity of the red blood cells
○○ Combines with haemoglobin to form carbaminohaemaglobin, which has a lower affinity
for oxygen
○○ Dissolve the blood plasma, causing respiratory acidosis
Nitrogenous Compounds
•• The body is unable to store amino acids or proteins
•• However, it is wasteful to excrete amino acids
•• Instead, they are transported to the liver and deaminated
•• The removed amino groups initially forms the very toxic ammonia
•• This is then converted to the less toxic urea, which is transported to the kidneys for excretion
•• The remaining keto acid can be directly respired, or converted to a carbohydrate or fat for storage
2 The Mammalian Liver
Blood Flow
•• Oxygenated Blood
○○ Travels from the aorta
○○ Hepatic artery
•• Deoxygenated Blood
○○ Travels from the digestive system
○○ Hepatic portal vein
○○ Rich in products of digestion
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•• Exit
○○ Blood exits via the hepatic vein
•• Sinusoids
○○ Oxygenated and deoxygenated blood mix
○○ Pass into special vessels called sinusoids
○○ Join together to form the hepatic vein
○○ Blood flowing along the sinusoids come into very close contact with the liver cells
Liver Cells
•• Called hepatocytes
•• Cuboidal shape
•• Microvilli
•• Many metabolic functions
Kupffer Cells
•• Specialised macrophages
•• Move in sinusoids
•• Break down and recycle old red blood cells
•• Haemoglobin is broken down into bilirubin
○○ This is the brown pigment in faeces
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The liver serves a range of functions that are critical to excretion. It metabolises many harmful
molecules that we might ingest and converts them into harmless molecules that we can then
excrete. One of the most important functions of the liver is the formation of urea:
Deamination
•• Amino acids broken down into keto acids and ammonia
•• Ammonia is highly toxic
Ornithine Cycle
•• Ammonia must be converted into a less toxic form
•• Ammonia is combined with carbon dioxide to produce urea
•• Urea is less soluble and less toxic
•• Urea is filtered out of the blood in the kidneys and concentrated in the urine
EXAM TIP
The process in which the liver metabolises toxic substances to render them harmless is
called detoxification. Using this keyword could gain you an extra mark in long answer
questions.
3 The Kidney
The kidney’s role is to filter blood and remove excess ions/water to produce urine. The
functional unit of the kidney is the nephron.
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The nephrons spread across the cortex and medulla of the kidney. Blood enters the organ via
the renal artery and exits via the renal vein. In between, it passes through tiny capillaries that
surround the continuous tube constituting the nephron.
Function
•• Filter out waste products
Structure
•• Bowman’s Capsule
○○ Ultrafiltration unit
○○ Filters blood
○○ Separates large particles from small particles
•• Proximal Convoluted Tubule (PCT)
○○ Involved in selective reabsorption
○○ Re-absorbs valuable substances, such as glucose
•• Loop of Henle
○○ Creates low water potential in the medulla
○○ Allows water to be reabsorbed
•• Distal Convoluted Tubule (DCT)
○○ Involved in osmoregulation
○○ Varies the amount of water reabsorbed into the blood
Blood vessels
•• Glomerulus
○○ Site of filtration
○○ Tight, knot-like, high pressure capillary bed
•• Afferent arteriole
○○ Brings blood from the renal artery
•• Efferent arteriole
○○ Narrow vessel that restricts blood flow
○○ Raises blood pressure
•• Peri-tubular capillaries
○○ Low pressure capillary bed
○○ Runs around the convoluted tubules
○○ Absorbs fluid from them
•• Vasa Recta
○○ Un-branched capillaries
○○ Similar in shape to the Loop of Henle
○○ Descending limb carries blood deep into the medulla
○○ Ascending limb brings blood back to the cortex
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•• Venule
○○ Carry blood to the renal vein
○○ Blood carried to the heart
Composition of Fluid through nephron
•• PCT
○○ In the PCT fluid composition is altered by reabsorption of all sugars, most salts and water
○○ 85% of water is reabsorbed here
•• Descending Limb
○○ In the descending limb the water potential is decreased
–– Salts added
–– Water removed
•• Ascending Limb
○○ In the ascending limb water potential is increased
○○ Salts are removed by active transport
•• Collecting Duct
○○ In the collecting duct water potential is decreased again
–– Water is removed
Ultrafiltration is the process by which substances in the blood enter the Bowman’s
capsule from the glomerulus:
•• Blood flows into glomerulus from the afferent arteriole
•• This is wider than the efferent arteriole
•• Difference in diameter ensures the blood remains under high pressure
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○○ Pressure in the glomerulus is higher than in the Bowman’s capsule
•• The barrier between the Bowman’s capsule and the capillary has three layers:
○○ Endothelium of capillary
–– Narrow gaps between cells
–– Blood plasma and dissolved substances can pass through
○○ Basement membrane
–– Fine mesh of collagen fibres and glycoproteins
–– Acts as a filter to prevent the passage of molecules with a RMM of over 69,000
–– Most proteins are held in the capillaries of the glomerulus
○○ Epithelial cells of the Bowman’s capsule
–– Podocytes
–– Specialized shape
ƒƒ Finger like projections called major processes
ƒƒ Ensure gaps between cells
ƒƒ Fluid from blood can pass into the lumen of the Bowman’s capsule
•• High pressure forces some water and solutes through the basement membrane and into the
Bowman’s capsule
•• This liquid is now known as the ‘glomerular filtrate’
What is left in the capillary?
•• Proteins
•• Blood cells
•• Molecules bigger than 69,000 RMM will remain in the blood
Selective reabsorption
•• As fluid moves along the nephron, substances are removed
•• Sodium-Potassium pumps move sodium ions from the cells lining the PCT into the tissue
fluid
•• This reduced the concentration of sodium ions in the cytoplasm
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•• Sodium ions are transported into the cell, along with glucose or amino acids, by facilitated
diffusion
•• As the glucose and amino acid concentrations rise indies the cell, these substances diffuse
out of the opposite side of the cell into the tissue fluid
•• Process may be enhanced by the active removal of glucose and amino acids
•• Tissue fluids substances diffuse into the blood and are carried away
•• Reabsorption of salts, glucose and amino acids reduced the water potential in cells and
increases it in the tubule fluid
•• Water will enter cells
•• Larger proteins can be absorbed by endocytosis
Adaptions
•• Microvilli increase surface area
•• Membrane contains co-transporter proteins that transport glucose and amino acids with
sodium ions in facilitated diffusion
•• Many mitochondria
Reabsorption of Water
The Loop of Henle
•• Salts can be transferred from the descending limb to the ascending limb
•• Increases concentration of salts in the tubule fluid
•• Salts diffuse out into the surrounding medulla tissue
•• Medulla tissue has a very low water potential
•• Amount of water reabsorbed controls water potential of blood
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Process of water reabsorption
•• As the fluid moves down, the water potential falls
○○ Water is lost to surrounding tissue fluid
○○ Sodium and chloride ions diffuse into the tubule
•• As the fluid moves up the ascending limb, the water potential rises
○○ At the base, sodium and chloride ions diffuse out
○○ Sodium and chloride ions are actively transported out
○○ Wall of the ascending limb is impermeable to water
○○ Fluid loses salt, but not water, when moving up the ascending limb
Hairpin counter current multiplier
•• Close arrangement of the ascending and descending limb
•• Increases the efficiency of salt transfer from the ascending to descending limb
•• Salt concentrations build up in the surrounding tissue
•• Movement of salts into the medulla creates a low water potential
•• Removal of ions from the ascending limb means at the top, urine is dilute
•• Water is then reabsorbed, according to the needs of the body
The Collecting Duct
•• Fluid flowing in contains lots of water
•• Carries fluid back down the collecting duct to the pelvis
EXAM TIP
You’re sure to impress examiners if you are able to clearly recall the different processes
that happen in the descending and ascending limbs of the Loop of Henle.
•• Tubular fluid becomes highly concentrated as it travels through the descending limb
•• It becomes much more diluted as it travels back up the ascending limb
4 The Control of Blood’s Water Potential
The control of water content in the blood is regulated by a negative feedback loop:
•• Drop in Water in the Blood
•• Brain releases antidiuretic hormone (ADH)
•• ADH travels from the loop of Henle
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•• Cell have membrane bound receptors for ADH
•• ADH binds to receptors
•• Chain of enzyme controlled reactions occurs inside the cell
•• Aquaporins sent in vesicles to the cell surface membrane
•• Aquaporins inserted into cell surface membrane
•• Walls of collecting duct and DCT more permeable to water
•• More water moves into the medulla by osmosis
•• Water potential of the blood rises back to the set level
•• Brain stops releasing ADH
EXAM TIP
ADH is a really important hormone involved in regulation of blood’s water potential. Make
sure you remember what triggers its release and what its overall effect is.
•• Release caused by dehydration detected in the brain
•• Causes the kidney to reabsorb more water
•• It is subsequently released in smaller amounts because of the negative feedback
loop
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5 Kidney Failure
Causes of kidney failure:
•• Diabetes mellitus
•• Heart disease
•• Hypertension
•• Infection
Assessing kidney function/failure:
•• Estimate glomerular filtrate rate (GFR)
•• Achieved by measuring concentration of substances in urine
•• Presence of proteins indicates failure of the filtration of blood as they are normally too large
to enter the Bowman’s capsule
Treatment 1: Renal Transplants
•• Old kidneys usually left in place
•• Donor can be live or deceased
•• Kidney surgically attached to blood supply and bladder
•• Patient must take immunosuppressant drugs to prevent rejection
Treatment 2: Dialysis
•• Waste removed from blood by passing it over a dialysis membrane
•• Partially permeable membrane allows the exchange of substances between blood and
dialysis fluid
•• Any excess substances diffuse out of the blood and into the dialysis fluid
Treatment 3: Haemodialysis
•• Blood from an artery is passed into a machine and dialyzed
•• Heparin added to avoid clotting
•• Performed at a clinic
•• Three times a week
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Treatment 4: Peritoneal Dialysis
•• Uses filter in the abdominal membrane
•• Permanent tube implanted in the abdomen
•• Dialysis solution fills space between organs and membrane
•• Solution drained after several hours
•• Patient able to walk around
•• Can be carried out at home
6 The Use of Excretory Products
in Medical Diagnosis
Excretory products can serve as an excellent indication of what is happening in the body.
Therefore, urinalysis (analysis of urine composition) is a widely used tool in medical diagnosis.
Testing for anabolic steroids
•• Anabolic steroids increase protein synthesis
•• Results in build-up of cell tissue
•• Can give an advantage in sports, but have dangerous side effects
•• Anabolic steroids have a half-life of 16 hours
•• Remain in the blood for many days
•• Small molecules
•• Can enter the nephron easily
Gas Chromatography and Mass Spectrometry
•• Sample vaporized in the presence of a gaseous solvent
•• Passed down a long tube lined by an absorption agent
•• Each substance dissolved differently in the gas
•• Remains there for a unique and specific length of time
•• Eventually substance moves out of the gas and is absorbed into the lining
•• This is then analysed to create a chromatogram
•• Chromatograms of standard drugs and urine samples are taken, allowing unidentified
substances to be easily identified
Pregnancy
•• Once implanted, human embryos secrete a hormone called hCG
•• This is a small glycoprotein
•• Pregnancy tests contain monoclonal antibodies which bind to the hCG
•• Any hCG in the urine will attach to antibodies tagged with a blue bead
•• The hCG-antibody complex then moves up to the surface of the strip where it sticks to a
band of immobilised antibodies
•• All the hCG bound antibodies are held in one place, forming a blue line
•• There is always a control blue line to use as a comparison
•• 2 blue lines indicate pregnancy
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TOPIC 3
Neuronal
Communication
Neuronal Communication
1 Sensory Receptors
Sensory receptors are specialised tissues in the body that detect changes in the environment.
They work by converting energy — acting as transducers — from one form into electrical
energy, which relays a signal to another part of the body. Stimulus
Change in light
intensity
Sensory receptor
Rods and cones in
retina of eye
Energy change
Ultimate response
Light to electrical
Increased light intensity =
iris constriction
Change in temperature Heat receptors in skin
and hypothalamus
Thermal to electrical
Capillaries change
diameter, erector muscles
contract/relax, etc
Chemicals in food
Chemical receptors on
tongue
Chemical to electrical
Pleasure centres in brain
activated
Change in sound
Vibration receptors in
ear cochlea
Kinetic (sound wave) to Sound heard
electrical
Pacinian corpuscles
•• Pressure sensor in skin
•• Consists of concentric rings surrounding a nerve ending
•• Pressure causes the rings to apply pressure on the sensory nerve fibre
•• Nerve fibre detects change in pressure - not constantly applied pressure
2 Sensory, Relay and Motor Neurones
Sensory neurons
•• Carry AP from sensory receptor to CNS
•• Long dendron
•• Short axon
Relay neurons
•• Connect sensory and motor neurons
•• Many short dendrites
•• Short axon
Motor neurons
•• Carry AP from CNS to effectors (muscles, glands)
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•• Cell body is within CNS
•• Long axon
Myelinated and non-myelinated neurones
•• 1/3 of neurons are myelinated
•• Schwann cells create the myelin sheath
○○ Several layers of membrane
○○ Thin cytoplasm
•• Gaps in the sheath are called the nodes of Ranvier
•• Peripheral neurons in the CNS are non-myelinated
○○ Still associated with Schwann cells
○○ Several neurons wrapped in one loose Schwann cell
○○ Action potential moves along in a wave
Advantages of Myelination
•• Myelinated neurons can transmit action potential more quickly than non-myelinated neurons
○○ 100-120 m/s
•• Non-myelinated neurons tend to be slower
○○ 2-20 m/s
•• Myelinated neurons carry signals from sensory receptors, to the CNS and from CNS to effectors
•• Carry signals over long distances
•• Enables rapid response to a stimulus by saltatory conduction
3 Nerve Impulse Generation & Transmission
Generation of nerve impulses
•• At rest neurones have higher concentration of sodium outside the cell
○○ Steep concentration gradient across cell membrane
○○ Cell charge is -60mV compared to extracellular environment
•• Sodium can move into the cell by gated channels
○○ Causing cell to depolarise — become electrically charged
•• Gated channels stimulated to open by action of synapse
•• A few channels open — a few sodium ions move into the cell
•• The membrane depolarises
○○ Becomes less negatively charged compared to the extracellular environment
•• If the threshold potential is reached (enough sodium ions enter the cell to surpass
threshold), this initiates a positive feedback loop
○○ Threshold is -50mV
•• More sodium channels open
•• Cell becomes more depolarised
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•• Action potential has been established
○○ Charge is now +40mV
Transmission of nerve impulses along a neuron
•• Once the electrical impulse has been established, a local current exists in the cytoplasm of the neuron
•• This local depolarisation triggers neighbouring voltage-gated channels to open
•• Action potential travels in one direction along the cell
Refractory period
•• Almost immediately after the cell becomes depolarised, it begins to repolarise
•• When sodium channels open, potassium ion channels open as well
•• Potassium diffuses down the concentration gradient out of the cell
•• This outflux of positively charged ions makes the cell’s charge become more negative
•• Eventually the potential difference (difference in charge across the cell membrane) overshoots
○○ This is called hyperpolarisation
•• The original, resting potential (-60mV) is restored
•• Regions of the neuron that are in the refractory period cannot become re-charged
•• This ensures the action potential moves in a single direction
EXAM TIP
Remembering the resting charge, threshold potential and action potential charge of neurons
will show the examiner you understand the concept of depolarisation. Depolarisation is all
about the concentration of charged ions across a membrane potential. A depolarised cell is
full of Na+ ions - that’s why it has a ‘more positive’ charge than a resting cell.
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4 Synapses
A synapse is a junction between two neurons. The space between the neurons is called the
synaptic cleft and is about 20nm wide. An action potential travels from one neuron to the
next via the synapse via substances called neurotransmitters such as acetylcholine (ACh).
Cholinergic Synapse
•• Presynaptic action potential causes release of a transmitter substance
○○ Presynaptic = the first neuron with the action potential
○○ Postsynaptic = the neuron receiving the action potential
○○ Diffuses across the gap
○○ Generates a new action potential in postsynaptic neuron
•• Synapses that use acetylcholine as the neurotransmitter are called cholinergic substances
Synaptic Knob
•• Region at the end of the axon which is slightly bulged and stores neurotransmitter
•• Contains many mitochondria
○○ Active process
○○ Lots of ATP required
•• Large amount of SER
•• Vesicles of acetylcholine
○○ Transmitter substance
○○ Chemical
○○ Diffuses across the synaptic cleft
•• Voltage gated calcium ion channels in the membrane
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Postsynaptic Membrane
•• Contains specialized sodium channels that can respond to the transmitter substance
○○ 5 polypeptide molecules
○○ 2 have a receptor that is specific to acetylcholine
•• When acetylcholine binds, the sodium channels will open
Transmission Across the Synapse
•• Action potential arrives at synaptic knob
•• Voltage-gated ion channels open
•• Calcium ions diffuse into the synaptic knob
•• Calcium ions cause the synaptic vesicles to move to and fuse with the presynaptic membrane
•• Acetylcholine released by exocytosis
•• Acetylcholine diffuses across cleft
•• Acetylcholine binds to the receptor sites on the sodium ion channels in the postsynaptic
membrane
•• Sodium channels open
•• Sodium ions diffuse across post synaptic membrane into postsynaptic neurone
•• Excitatory postsynaptic potential (EPSP) is created
•• EPSPs can combine, reaching the threshold potential
•• New action potential created in the postsynaptic neurone
Acetylcholine esterase
•• Enzyme in the synaptic cleft
•• Hydrolyses acetylcholine to ethanoic acid and choline
•• Stops transmission of signals
•• Ethanoic acid and choline are recycled
•• Re-enter synaptic knob by diffusion
•• Recombined to acetylcholine using ATP from respiration in the mitochondria
•• Stored in synaptic vessels for future use
Action Potentials and Cell Signalling
•• All or nothing response
•• Does not vary in size or intensity
•• Process are the same in all neurons and cholinergic synapses
Role of Synapses
•• Several presynaptic neurons converge to one postsynaptic neuron
○○ Allows signals from different part of nervous system to create the same response
○○ Useful when different stimuli are warning us of danger
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One presynaptic nerve may diverge to many postsynaptic neurons
•• Allow one signal to travel to several parts of the nervous system
•• Useful in the reflex arc
Ensure signals are transmitted in the right direction
•• Only presynaptic knob contains vesicles of acetylcholine
Filter out low-level signals
•• Low-level stimuli may create action potentials
•• These are unlikely to pass across a synapse to the next neuron
•• Vesicles of acetylcholine will not be released
Summation
•• Low-level signals may be amplified
•• Persistent stimulus may cause several action potentials
•• May cause generator potentials to join together to produce an action potential
Acclimatisation
•• Synapses may run out of transmitter substance and become fatigued
•• No longer respond to stimulus
•• Helps to avoid over stimulation
The creation of specific pathways within the nervous system is the basis of conscious thought
and memory.
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TOPIC 4
Hormonal
Communication
Hormonal Communication
1 Endocrine Communication by Hormones
Hormones = molecules produced and secreted by endocrine glands directly into the blood.
They act as messengers and transport signals from one gland to a specific target tissue or
organ to produce a desired effect.
Endocrine glands
•• Release molecules directly into the blood
•• No duct involved
Exocrine glands
•• Secrete molecules into a duct
•• Molecules are then carried to where they are needed
Target Cells
•• Cells receiving the hormone must have a complementary receptor
•• Hormone binds to this receptor
•• Hormones bind to target cells
•• These cells are usually grouped together to form target tissues
Nature of Hormones
•• There are 2 types:
○○ Steroid hormones
○○ Protein and peptide hormones (Derived from amino acids)
•• Proteins are not soluble in the membrane
•• Steroid hormones can pass through and have a direct effect on DNA in the nucleus
EXAM TIP
You need to be aware of the difference between first messengers and second messengers.
First messengers are hormones that do not enter target cells. This includes all non-steroid
hormones. They exert their action by binding to signalling proteins on the cell surface
membrane, which triggers a change inside the cell, usually carried out by a second messenger.
cAMP is an exemplary second messenger. First messengers often trigger the action of a second
messenger via a G protein, which is a protein that spans the cell surface membrane and
enables communication between molecules outside the cell and molecules inside the cell.
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2 The Adrenal Glands
The adrenal glands are endocrine glands that are located just above the kidneys. They are
present on either side of the body.
Structure
•• Adrenal Medulla
○○ Centre of the gland
○○ Manufacture and release adrenaline
○○ Effects include:
–– Relaxation of smooth muscle in the bronchioles
–– Increase volume of heart
–– Increase heart rate
–– Vasoconstriction
–– Dilation of pupils
–– Stimulate conversion of glycogen to glucose
–– Increase mental awareness
–– Cause body hair to erect
•• Adrenal Cortex
○○ Uses cholesterol to produce steroid hormones
○○ These have an important role in the body
–– Secretes mineralocorticoids which help to control the concentration of sodium and
potassium in the blood
–– Secretes glucocorticoids which help to control the metabolism of carbohydrates and
proteins in the liver
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Adrenaline
•• Adrenaline is an amino acid derivative secreted by the adrenal glands
•• Cannot enter target cell
•• Binds to target cell
•• Target cells is associated with adenylyl cyclase
•• Adrenaline is the first messenger molecule
•• First binds to specific receptor on cell surface membrane
•• Binding activates adenyl cyclase
•• This enzyme converts ATP to cyclic AMP (cAMP)
•• cAMP is a secondary messenger molecule
•• Causes an effect inside the cell by activating enzyme action
3 The Pancreas
The pancreas is an organ with both exocrine and endocrine functions. It is positioned just
below the stomach.
Structure
•• Lumpy appearance
•• Functional unit: islets of langerhans
•• Bile duct comes from liver and gall bladder
•• Exocrine enzymes are secreted into this duct
•• Endocrine hormones are secreted into surrounding blood vessels
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Secretion of Enzymes
•• Manufactures digestive enzymes
•• This is the exocrine function
•• Secrete enzymes into the pancreatic duct
•• Duct contains:
○○ Amylase
○○ Trypsinogen
○○ Lipase
○○ Sodium hydrogen carbonate
Secretion of Hormones
•• Areas in the pancreas called the Islets of Langerhans contain 2 types of cells
○○ Alpha cells
○○ Beta cells
•• Alpha Cells
○○ Secrete glucagon
•• Beta cells
○○ Manufacture and secrete insulin
4 Regulation of Blood Glucose
Concentration
Blood glucose is controlled by a negative feedback loop.
Blood glucose is too high
•• Detected by the beta cells
•• Target cells are hepatocytes
•• Respond by producing insulin
•• Insulin binds to adenylyl cyclase
○○ Converts ATP to cyclic AMP (cAMP)
•• cAMP causes:
○○ More glucose channels to open
○○ Glucose to be converted to glycogen
○○ Glucose converted to fats
○○ More glucose used in respiration
•• Activates a series of enzyme controlled reactions
•• Reduces blood sugar
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Blood glucose is too low
•• Detected by the alpha cells
•• Release glucagon
•• Target sites are hepatocytes
•• Glucagon causes:
○○ Glycogen to be converted to glucose (glycogenolysis)
○○ Fatty acids to be used in respiration
○○ Production of glucose by conversion of amino acids and fats (glycogenesis)
•• Overall effect increases the blood glucose concentration
Regulation of Insulin Secretion
•• Cell membrane of beta cells contain Ca and K ion channels
•• K ion channels normally open
•• Ca ion channels normally closed
•• K ions diffuse out, making the inside more negative
•• When glucose concentrations outside are too high, glucose molecules diffuse into the cells
•• Glucose used in the metabolism to produce ATP
•• Extra ATP causes K ion channels to close
•• K can no longer diffuse out
•• This alters the potential difference across the membranes, making the inside less negative
•• Change in potential difference opens the Ca ion channels
•• Ca ions enter the cell
•• Cause insulin containing vesicles to move to the cell surface
•• Exocytosis occurs
EXAM TIP
Insulin and glucagon are responsible for regulating blood glucose levels by a very complex
array of mechanisms. Remembering these mechanisms and the associated molecules
can be difficult because of how confusingly similar the words are (glycogen, glycogenesis,
glycolysis, etc) — but it’s worth learning the spelling and meaning of these as you’re
expected to know them.
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5 Diabetes Mellitus
The term ‘diabetes’ refers to any disease where the patient has uncontrolled blood glucose this usually manifests itself in the form of chronic hyperglycaemia. There are several types of
diabetes, and you need to know the disease mechanisms of Type 1 and 2 Diabetes Mellitus.
Type 1
•• Insulin-dependent
•• Caused by auto-immune disease
•• Body attacks its own beta cells
•• Body no longer able to manufacture sufficient insulin
•• Cannot store excess glucose as glycogen
Type 2
•• Non-insulin dependent
•• Sufferers can still produce insulin
•• Constantly high insulin levels due to too much sugar intake
•• Target cells’ sensitivity to insulin declines
•• Beta cells may become ‘exhausted’ and die — thereby producing less insulin in the long term
•• Certain factors can increase the likelihood of diabetes:
○○ Obesity
○○ Diet high in sugars
○○ Asian or Afro-Caribbean heritage
○○ Family history
Treatment
•• Type 1
○○ Insulin injections
○○ Blood glucose levels are monitored
•• Type 2
○○ Diet controlled and monitored
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TOPIC 5
Plant
and Animal
Responses
Plant and Animal
Responses
1 Plant Responses
Plants need to respond to their external environment in order to avoid stress, avoid being
eaten and ensure sufficiently long term survival.
Types of plant chemical defences:
•• Alkaloids
○○ Make plants taste bitter to deter herbivores
•• Pheromones
○○ Released from one plant and affect another
•• Tannins
○○ Toxic to microorganisms/herbivores
○○ Make the leaf taste unpleasant
Types of plant responses:
•• Tropism
○○ Directional growth responses
•• Phototropism
○○ Shoots grow towards light
○○ Enables them to photosynthesise
•• Geotropism
○○ Roots grow towards the pull of gravity
○○ Anchors them in the soil
○○ Helps them to take up water as a raw material
•• Chemotropism
○○ Occurs on flowers
○○ Pollen tubes grow down the style towards ovaries
○○ They are attracted by chemicals
•• Thigmotropism
○○ Shoots out of climbing plants wind around other plants
○○ Gain support
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Response to the Environment
•• Hormones co-ordinate plant response
•• Produced in a variety of cells
○○ Not in endocrine glands
○○ Often known as plant growth regulators
•• Hormones move around the plant
○○ Diffusion
○○ Active transport
○○ Mass flow in phloem and xylem
Nastic response = a non-directional response to stimuli, e.g. thigmonasty — Mimosa pudica
plant responds to touch by folding its leaves.
2 Plant Hormones
Plants are capable of producing a range of hormones. Some are synergic and amplify each
other’s’ effects. Others are antagonistic and oppose each other’s’ effects. There are many kinds
Auxins
•• Responsible for regulating plant growth
•• Inhibits the growth of side shoots
•• Inhibits leaf abscission
•• Action:
○○ Causes cell elongation
○○ Increases stretchiness of cell wall by increasing the AT of hydrogen ions
○○ ATPase enzyme moves more ions through the plasma membrane, into the cell wall
○○ Low pH allows wall loosening enzymes to work
○○ These break bonds in the cellulose, allowing the cells to expand
Cytokines
•• Promote cell division
Gibberellins
•• Promotes seed germination
•• Promotes growth of stems
Abscisic Acid
•• Inhibits seed germination
•• Causes stromal closure when the plant is water stressed
Ethene
•• Promotes fruit ripening
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Plant Growth
•• Growth occurs by 2 process in the meristem tissue
○○ Cell elongation
○○ Cell division
•• Apical Meristems are located behind shoots and are responsible for shoots getting longer
•• Lateral bud meristems are found in buds and give rise to shoots
•• Lateral meristems are found near the outside of shoots and root and make them wider
•• 2 cell walls are formed
○○ Primary does not have uniformly arranged fibres
○○ Secondary has uniformly arranged fibres
Auxin
•• Cell elongation
•• Inhibit growth of side-shoots
Cause of Phototropism
•• Shoot bends towards a light source
•• Shaded side elongates faster than the lit side
•• Light causes cells to actively unload IAA
•• Unloaded from cells in light, towards those in shade
•• Causes the shoot to bend
Leaf Loss
•• Cytokinins stop the leaves of deciduous plants from senescing (turning brown and dying)
○○ Makes sure the leaf acts as a sink from phloem transport
○○ Guaranteed to have a good supply of nutrients
•• If cytokinin production drops, so will the supply of nutrient and senescence will begin
•• Process:
○○ Leaf senescence causes auxin production at the top of the leaf to stop
○○ Makes abscission zone more susceptible to ethene
○○ Drop in auxin production causes an increase in ethane production
○○ Increases production of the enzyme cellulose
–– Digests walls of cells in the abscission zone
–– Causes petiole to separate from stem
EXAM TIP
Be clear about the exact roles of the key plant hormones. For example, auxins cause cell
elongation — not cell division. Ie, the number of cells remains the same.
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3 Experimental Evidence
for The Role of Auxins
The growth of the apical bud inhibits the growth of lateral buds. Therefore, if the apical bud
is broken off, dormant lateral buds will begin to grow. When auxin concentration in the shoot
decrease, the buds begin to grow.
Auxin paste applied to exposed tip
•• Buds did not grow
Auxin inhibitor applied below tip
•• Ensure it was auxin preventing the buds from growing
•• Lateral buds grew
Shoot tip cut off of kidney bean
•• Auxin concentration increased in lateral buds
•• Cytokinins can spread more evenly
•• Abscisic acid levels drop
•• Proved a causative effect
4 The experimental evidence
for the role of gibberellin
Gibberellin concentration in tall and dwarf pea plants compared
•• Higher in tall plants
Grafted a plant which has the enzyme, but no gibberellins onto a normal plant
•• Plant grows tall
•• Does not have its own gibberellins
•• Uses those from the normal plant and its own enzymes
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5 The Commercial use of Plant Hormones
Auxins
•• Used as a rooting powder for cuttings
•• Can promote the growth of seedless fruit in unpollinated flowers
•• Artificial auxins can be used as herbicides
•• Promote and inhibit fruit drop
Gibberellins
•• Fruit Production
○○ Delays senescence
○○ Make fruit last longer on shop shelves
•• Brewing
○○ Barley seeds germinate, with amylase breaking down stored starch into maltose
○○ Genes for amylase production are turned on by gibberellins
○○ Adding gibberellins can speed the process
○○ Malt is produced by drying and grinding the seeds
•• Sugar Production
○○ Sugar canes sprayed with gibberellins
○○ Stimulates growth between the nodes
○○ Sugar is stored in these internode cells
○○ Can increase sugar yield by up to 4.5 tonnes per hectare
•• Breeding
○○ Gibberellins speed up process
○○ Speed up seed production in young plants
○○ Inhibiting gibberellins can also make flowers short and stocky
Cytokinins
•• Delay leaf senescence
•• Prevent yellowing of lettuce leaves
•• Help mass produce plants
○○ Promote bud and shoot growth
○○ Produces short shoot with a lot of side branches
Ethene
•• Speeds up fruit ripening
•• Ethene can be inhibited to prevent fruit ripening
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6 The Mammalian Nervous System
The mammalian nervous system is commonly subdivided into 2 systems:
•• Central Nervous System (CNS)
•• Peripheral Nervous System (PNS)
CNS
•• Made up of grey matter and white matter
•• Myelin makes the fibres appear white
•• Involves only the brain and spinal cord
PNS
•• Contains all the nerves that are not in CNS
•• This includes motor nerves which can be subdivided:
○○ Somatic Motor Neurons
–– Carry impulses from CNS to skeletal muscles which are under conscious control
–– Voluntary - e.g. muscle locomotion
–– Most neurons are myelinated
–– Connections only ever consist of one neuron
○○ Autonomic Motor Neurons
–– Carry impulses from the CNS to cardiac muscle, smooth muscle in the gut wall, blood
vessels, glands and bladder
–– All of these are under unconscious control
–– Involuntary — e.g. intestinal smooth muscle contractions
–– Most neurons are non-myelinated
–– Connections can consist of more than one neuron
ƒƒ Connect at a ganglion
Autonomic Nervous System
•• Involuntary part of the PNS
•• Can be further subdivided:
○○ Sympathetic
–– Prepares us for vigorous activity
–– Fight or flight response
ƒƒ Involves noradrenaline
–– Motor neurons are connected by ganglia
ƒƒ Same signal can stimulate many motor neurons in different organs
○○ Parasympathetic
–– Relaxing responses
ƒƒ Involves acetylcholine
–– Maintains a suitable state for non-threatening conditions
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The sympathetic and parasympathetic nervous systems each have their own neurons. The two
systems are antagonistic.
•• They have opposite effects on an unconscious process
○○ Parasympathetic nerves increase blood flow to the gut wall
○○ Sympathetic nerves decrease blood flow to the gut during vigorous exercise
Effects on Heart
•• Parasympathetic
○○ Heart rate slowed
○○ Less blood needed
•• Sympathetic
○○ Heart rate increases
○○ Much more blood and oxygen needed
Effects on Salivary Glands
•• Parasympathetic
○○ Saliva production stimulated
○○ Food can be eaten in non-stressful situations
•• Sympathetic
○○ Saliva production inhibited
○○ Feeding not the main priority
Effects on Iris
•• Parasympathetic
○○ Circular muscles contract
○○ Pupil constricts the retina
•• Sympathetic
○○ Radial muscles contract
○○ Pupil dilates
○○ Better image
EXAM TIP
While the sympathetic nervous system stars in the fight or flight response, it is constantly
acting on a basal level to maintain homeostasis. In its total absence, we would have
dangerously low blood pressure, heart rate, and our muscles would have chronically
inadequate blood supply.
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7 The Human Brain
Cerebrum
•• Largest part
•• Involved in ‘higher’ brain activities
•• Divided into 2 hemispheres
○○ Left side controls muscles on the right side of the body
•• Connected via corpus callosum
•• Outermost layer is highly folded
○○ Consists of a thin layer of nerve cell bodies known as the cerebral cortex
Cerebral Cortex
•• Subdivided
○○ Sensory Areas
–– Receive impulses indirectly from receptors
○○ Association Areas
–– Compare input with previous experiences to interpret and judge response
○○ Motor Areas
–– Sends impulses to effectors
Cerebellum
•• Contains over half of all nerve cells
•• Inputs into the cerebral cortex
○○ Fine tunes the effectors response
•• Tensioning of muscles in order to manipulate tools effectively
•• Input is unconscious
○○ Muscle memory
•• Processes information from:
○○ Balance organs of the inner ear
○○ Retina
○○ Joints
○○ Muscle spindle fibres
•• Controls co-ordination of movement and posture
Medulla Oblongata
•• Controls:
○○ Action of smooth muscle in the gut
○○ Breathing movements
○○ Heart rate
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•• Regulatory centre for vital processes found here:
○○ Cardiac centre
○○ Respiratory Centre
Hypothalamus
•• Controls the autonomic nervous system and endocrine glands
•• Controls most of the homeostatic mechanisms
Pituitary Gland
•• Not part of the brain
•• Attached at the base
•• Endocrine gland
•• Secrete a variety of hormones
8 Reflexes
Reflex actions are responses to external stimuli that do not require conscious coordination.
They are immediate responses and their rapidity is achieved by bypassing the brain between
sensation and reaction. The brain is informed afterwards about the stimulus/reflex.
Sensory neurone
relay neurone in spinal cord
motor neuron
Blinking reflex
•• Passes through part of brain — is cranial reflex
•• Receptor and effector in same place
○○ Therefore called a reflex arc
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•• Stimuli:
○○ Foreign body touching eye (corneal reflex)
○○ Sudden increase in light intensity (optical reflex)
○○ Sudden movements close to eye
○○ Loud noise
Knee jerk reflex
•• Passes through spinal cord - is a spinal reflex
•• When tendons connecting quadriceps with patella are tapped, they stretch
•• When they stretch, they pull the quadriceps muscle
•• The quadriceps muscle senses risk of over-stretch
○○ Detected by muscle spindles
•• Reflex is to contract the muscle immediately
•• Causing knee jerk reaction
Significance for survival
•• Reflexes are key to survival
•• Provide effective protection from dangerous positioning/posture or incoming threats
•• E.g. when you touch a hot object, you withdraw your hand — this is a reflex that prevents
you from getting burnt
9 Nervous and Endocrine Coordination
The body frequently employs the use of both the nervous and endocrine systems to achieve
a common goal. The two systems can easily be used to amplify each other. The fight or flight
response is a good example of the body’s ability to do this.
The term ‘fight or flight’ refers to a set of physiological changes which occur in the body
when danger is detected, and we need to either run away or fight it. It is a function of the
sympathetic nervous system and incorporates several hormones as well.
•• Combined nervous and hormonal response
○○ Pupils dilate, making retina more sensitive to e.g. motion
○○ Heart rate and blood pressure increase
–– Equips muscles with optimal oxygen supply and waste removal
○○ Arterioles to digestive system and skin constrict
–– Blood re-directed to muscles — prioritised organs during fight or flight
○○ Arterioles to muscles and liver dilate
○○ Blood glucose increases
–– Ready to deliver respiratory substrate to muscles
○○ Metabolic rate increases
○○ Erector pili muscles contract
–– Consequence of adrenaline — sign of aggression
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○○ Ventilation rate and depth increases
○○ Endorphins released by the brain
–– Higher pain threshold
○○ Sweat production increases
Co-ordination of Changes
•• Perception of threat comes from visual or auditory stimuli
•• Signals sent to the brain by sensory receptors
•• Information enters the cerebral cortex and person is consciously aware of the threat
•• Cerebral cortex activates the hypothalamus, stimulating activity in the sympathetic nervous system
•• Nervous impulse sent through sympathetic nerve to the adrenal glands, near the kidneys
•• Triggers the release of adrenaline — main hormone involved in fight or flight
○○ Medulla also secretes noradrenaline, which works with adrenaline
•• Hypothalamus also releases corticotropin releasing factor (CRF) into the pituitary gland
○○ Stimulates the release of adrenocorticotropic hormone (ACTH)
○○ Stimulates hormones which help the body to resist stressors
○○ These are stimuli that can cause a stress response
10 Regulation of Heart Rate
Cardiac (heart) muscle is myogenic. This means it can initiate its own contractions. It achieves
this with its own pacemaker: the sinoatrial node (SAN):
•• SAN initiates action potential independently of cranial input
•• Sends a wave of excitation over the atrial walls and through the AVN
•• Conducted down the Purkinje fibres to the ventricles
•• Causes ventricles to contract
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Supplied with nerves from the medulla oblongata
•• Found at the base of the brain
•• Region of the brain that co-ordinates the unconscious functions of the body
•• Nerves connect to the SAN
•• Nerves can affect the frequency of the contractions
Heart muscle responds to the presence of the hormone adrenaline
•• Beats faster
•• Beats stronger: myocytes contract with greater contractile force
Nodes
•• The heart has 2 main nodes that contain nerve cells
○○ Sinoatrial node
○○ Atrioventricular node
Controlling Heart Beat
•• SAN sends an electrical impulse over the atrial walls
•• Causes atria to contract
•• Conducted to AVN, where the electrical wave of excitation is conducted down the Purkinje fibres
•• Causes the ventricles to contract
•• Layer of insulation exists between the atria and ventricles to prevent the first wave of
impulse from the SAN from travelling all the way down
•• This layer causes a pause at the AVN
Rate of Initiation
•• Controlled by:
○○ Nerves that run from the brain
○○ Hormones in the blood
–– E.g. — Adrenaline
Nerves
•• Vagus Nerve
○○ Sends signals to decrease heart rate
•• Acceleratory Nerve
○○ Sends signals to increase heart rate
•• Both nerves connect to the medulla oblongata in the brain
Medulla Oblongata
•• Involved in many unconscious functions of the brain including breathing and heart rate
•• Specific regions of the medulla oblongata sense factors that require a change in heart rate
•• Cardiovascular centre can sense things like changes in carbon dioxide levels
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Interaction between control mechanisms
•• Resting conditions
○○ Heart rate controlled by SAN
○○ Set frequency
○○ Typically 60-80 beats per minute
○○ Frequency of excitation waves can be controlled by the cardiovascular centre in the
medulla oblongata
Factors affecting heart rate
•• Movement
○○ Limb movement is detected by stretch receptors in muscles
○○ Impulses sent to the cardiovascular centre
○○ Informs that oxygen is needed
○○ Increases heart rate
•• Exercise
○○ Muscles produce more carbon dioxide
○○ Carbon dioxide reacts with water in blood plasma, lowering the pH
○○ Drop in pH detected by chemoreceptors
○○ Chemoreceptors send impulses to the cardiovascular centre
○○ APs fired from chemoreceptors are passed to cardiovascular centre of the medulla oblongata
○○ Signals sent down the accelerator nerve to increase heart rate
○○ Heart rate increases
○○ When we stop exercising concentration of carbon dioxide falls
○○ Reduces activity of the accelerator pathway
○○ Heart rate declines
•• Adrenaline
○○ Secreted in response to stress, shock or excitement
○○ Presence increases heart rate
○○ Adrenaline binds to specific receptors on the membranes of cells in the SAN
○○ Helps to prepare body for activity
•• Blood Pressure
○○ Monitored by stretch receptors in the walls of the carotid sinus
○○ If blood pressure rises too high, signals are sent to the cardiovascular centre
○○ Signals sent through the vagus nerve to decrease the heart rate
○○ Heart rate is reduced
•• Artificial Pacemakers
○○ If the mechanism controlling heart rate fails, an artificial pacemaker can be fitted
○○ 1928
–– Needle electrode that is inserted into the heart wall
–– Not portable
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○○ Device further developed
○○ Modern pacemakers are only 4cm long
○○ They are implanted underneath the skin and at of the chest
○○ Deliver pulses to the ventricle walls
○○ Deals with conditions where the AVN is not functioning but the SAN may be
11 The Neuromuscular Junction
The neuromuscular junction is the site where action potentials carried by neurons are delivered to
muscle tissue to begin muscle contraction. Electrical energy is hereby converted into kinetic energy.
There are some similarities and differences between neural synpases and neuromuscular junctions:
Synapse
Neuromuscular Junction
•• Neurone to neurone
•• Neurone to sarcomere
•• Post synaptic stimulation leads to AP in
postsynaptic membrane
•• Postsynaptic stimulation leads to depolarisation
f sarcolemma and muscle contraction
•• Synaptic knob is smooth and rounded
•• End plate has a brush border
•• Vesicles located in presynaptic cytoplasm
•• Vesicles release neurotransmitter into cleft on stimulation
•• Neurotransmitter diffuses across the gap and binds to postsynaptic membrane
•• Binding of the neurotransmitter results in depolarisation
•• Enzymes are present to degrade the neurotransmitter
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12 Mammalian Muscle
and Muscular Contraction
Muscle Structure is highly specialised to achieve a specific function. Muscle tissue is composed of
many overlapping elongated cells which form fibres, and have the ability to contract and relax.
Muscle
•• Can be involuntary…
○○ Smooth muscle
○○ Cardiac muscle
○○ Controlled by autonomic nervous system
•• Or voluntary..
○○ Skeletal muscle
Smooth Muscle
•• Innervated by neurons of the ANS
•• Involuntary contraction
•• Does not have a striped appearance
•• Spindle shape cells contain bundles of actin, myosin and a single nucleus
•• Contracts and fatigues slowly
•• Involved in the movement of materials along a tube
Cardiac Muscle
•• There are 3 types:
○○ Atrial muscle
○○ Ventricular muscle
○○ Specialised excitatory and conductive fibres
•• Contract in similar way to skeletal muscle, but with longer duration of contraction
•• Some muscle fibres are myogenic
○○ Stimulate contraction without a nervous impulse
•• Innervated by the ANS
•• Sympathetic stimulation increases rate, parasympathetic decreases rate
•• Made of individual cells connected in rows
•• Dark areas are intercalated discs
○○ Cell membranes that fuses to form gap junctions
○○ Ions, and so Aps, are able to diffuse easily through this network of interconnections
•• Striated muscle
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Skeletal Muscles
•• Voluntary muscles
•• Action of these muscles leads to the movement of the skeleton
•• Ligaments connect bone to bone
•• Tendons connect muscle to bone
•• Form fibres with many nuclei
•• Cell surface membrane is the sarcolemma
•• Cell cytoplasm is the sarcoplasm
•• Sarcoplasm contains:
○○ Many mitochondria
○○ Extensive sarcoplasmic reticulum
○○ Myofibrils
–– Contractile elements
–– Contain smaller units called sarcomeres
–– Actin and myosin filaments
•• Called ‘striated muscle’ because of its striped appearance
Muscles contract using the Sliding Filament Model:
The Sarcomere
•• Span from one Z-line to the next
•• Z-lines closer together during contraction
•• I-band and H-band are reduced
•• A-band does not change in length
Structure
•• I Band
○○ Thin actin filaments
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•• Z line
○○ Region where actin myofilaments are anchored
•• A band
○○ Region containing the whole length of the myosin microfilament
•• M band
○○ Region where sarcomere connects to the skeleton
•• H band
○○ Thick myosin filaments only
Muscle protein Filaments
•• Thin Actin
○○ 2 strands of actin coiled around each other
○○ Composed of G actin subunits
○○ Tropomyosin molecules form around the actin, reinforcing it
○○ Troponin complex is attached to each tropomyosin molecule
–– Consists of 3 polypeptides
–– 1 binds to actin
–– 1 binds to tropomyosin
–– 1 binds to calcium ions
•• Thick Myosin
○○ Consists of myosin
○○ Shaped like a golf club, with 2 heads
○○ Heads stick out to form the cross bridge
○○ Many of these myosin molecules stick together to form a thick filament
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Process of contraction
•• When a muscle is at rest, Ca concentration surrounding the fibrils is very low
•• Under these conditions, tropomyosin sits in the myosin binding sites and the contractile
mechanism is ‘off’
•• When the muscle is stimulated, a wave of depolarisation passes in through the T system
•• When the impulse reaches the SR it causes the release of Ca ions
•• Ca concentration increases
•• Ca ions bind to troponin causing it to change shape
•• Tropomyosin moves out of the myosin binding site on the actin filaments
•• Actin is now ‘on’
•• ATP binds to the myosin and is hydrolysed to ADP and Pi, both of which remain bound to the
myosin head
•• Pi is released, changing the shape of the myosin head and allowing it to form cross-bridges
•• ADP is released causing the myosin head to tilt and pull the actin filament over the myosin
filament. This is the power stroke.
•• At the end of the power stroke, the ATP binds to the myosin head and the cross bridges are
broken
•• If Ca concentration remains high, the cycle will be repeated
End of Nervous Stimulation & muscle relaxation
•• ATP pump actively pumps Ca ions from the sarcoplasm to the cisternae of the SER
•• Ca ion concentration falls below the threshold level
•• Troponin is released and is bound back to Ca
•• This causes the tropomyosin to go back to the myosin binding sites
•• The muscle is now relaxes
ATP in Muscular Contraction
•• ATP provides the energy that allows binding, tilting and releasing on the myosin heads
•• It is the force that causes muscular contraction
Maintaining ATP Supply
•• Rate at which ATP is regenerate during respiration is dependent on oxygen
•• Aerobic respiration leads to increased levels of lactic acid in the blood, stimulating increased
blood flow to the muscles
•• Muscles contain small reserves of ATP
•• ATP can be formed from creatine phosphate
○○ Creatine phosphate can lose a phosphate group, donating it to ADP to form ATP
•• Glycogen is stored in the muscles, but when it has been used, the liver’s glycogen stores can
be respired
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Motor Unit
•• Some movements require a stronger contraction than others
•• Brain controls the strength of contractions
•• Many neurons can stimulate a single muscle
•• Each one branches to a neuromuscular junction, causing the contraction of a cluster of
muscle cells — the motor unit
•• The more motor units stimulated the greater the force of contraction
EXAM TIP
You need to know the structure and properties of the 3 types of muscle. Make sure you can
identify their unique features and how these make them adapted to their role.
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TOPIC 6
Photosynthesis
Photosynthesis
1 Photosynthesis and Respiration
Photosynthesis is the process by which plants and some other organisms convert light energy
into chemical energy. The chemical equation for photosynthesis is:
6CO2 + 6H2O + energy from photons
*chlorophyll*
C6H12O6 + 6O2
•• Autotrophic nutrition
○○ Generate nutrition from simple inorganic molecules
○○ Animals can’t do this
•• Takes place in chloroplasts
•• The sugar produced is glucose
○○ Monosaccharide
○○ Converted into starch for storage that doesn’t affect concentration
Respiration is a process that is carried out by all living organisms. It involves the oxidation of
glucose to produce carbon dioxide and water, as well as the ‘release’ of energy — often in the
form of generating ATP from ADP and Pi. It is a form of heterotrophic nutrition — deriving
nutrition from substances that contain organic molecules.
6O2 + C6H12O6
*mitochondria*
6H2O + 6CO2 + energy
The interrelationship between photosynthesis and respiration is highlighted in the fact that the
products of one are the raw materials of the other. The overall effect of the two reactions in
sync is the ability of life to convert sunlight into thermal/kinetic energy essential for life.
EXAM TIP
Plants are capable of photosynthesising and respiring. However, while respiration occurs round
the clock, photosynthesis requires light: it therefore only happens during daylight hours.
Compensation point is the term used to refer the state in which a plant is when the rate
of photosynthesis and the rate of respiration are equal. In other words, there is no net
change in carbohydrate content because it is being generated at the same rate that it is
being consumed.
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2 Chloroplasts and Photosynthesis
Photosynthesis is a 2 stage process which takes place in chloroplasts.
Chloroplasts
•• Surrounded by an envelope
•• Outer membrane is permeable to small ions
•• Inner membrane is less permeable
○○ Folded into lamellae
○○ One granum consists of several stacked thylakoids
○○ Between grana is the intergranal lamellae
•• The stroma is the fluid filled matrix, which contains the necessary enzyme to carry out the
light dependent reactions
Chloroplast Adaptations
•• Many grana provide a large surface area for photosynthetic pigments
•• Photosynthetic pigments are arranged into photosystems
•• Proteins embedded in grana to hold the photosystems in place
Photosynthetic Pigments
•• A molecule that can absorb one or more specific wavelengths of light and reflect other
wavelengths
•• Each pigment can absorb on wavelength
•• A wide variety of these maximizes energy absorption
•• These are arranged in photosystems
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Primary Pigments
•• These are found at the centre of the PS
•• They can absorb energy from the sun or from accessory pigments
○○ E.g. Chlorophyll A (680,700,450)
Accessory Pigments
•• These are found at the edge of the PS
•• Absorb light from the sun and pass this onto the primary pigments
○○ E.g. Carotenoids, Chlorophyll B (500,640)
Chlorophyll
•• Head and a tail group
•• Head contain Mg atom
Light Dependent Stage
•• Photophosphorylation
○○ When a photon hits a chlorophyll molecule, the energy is transferred to 2 electrons
exciting them
○○ Electrons captured by electron carriers and passed along a series of electron carriers
○○ Energy is used to pump protons across the thylakoid membranes
○○ Proton gradient is formed and protons flow down the concentration gradients through
ATP channels
○○ This is chemiosmosis
○○ This produces a force which joins ADP and Pi to form ATP
–– ATP is used in the light independent stage of the reaction
–– The making of ATP using light energy is called photophosphorylation
•• Cyclic Photophosphorylation
○○ Only uses PS1
○○ Electrons pass to an electron acceptor, then return to the chlorophyll molecule from
which they were lost
○○ No photolysis of water
○○ No generation of reduced NADP
○○ Small amounts of ATP made
○○ This may be used in the light independent reaction to actively transport potassium into
the cell, lowering the water potential and causing ions to flow in by diffusion
○○ This causes the guard cells to swell and the stomata to open
•• Non-cyclic Photophosphorylation
○○ Involves both PS1 and PS2
○○ Light strikes PS2, exciting a pair of electrons
○○ Electrons leave the chlorophyll molecule from the primary pigment reaction centre
○○ Electrons pass along the chain of electron carriers
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○○ Energy is released, which is used to synthesize ATP
○○ Light strikes tPS1, causing the release of 2 electrons
○○ Electrons from oxidized PS2 replace those lost from PS1
○○ Electrons from photolysed water replace those lost from PS2
○○ Protons fro photolysed water take part in chemiosmosis, to make ATP
○○ They are captured in NADP in the stoma and used in the light-independent stage
Non light dependent stage
○○ This takes place in the stroma
○○ It is called the Calvin Cycle
○○ Although light is not used, the products of the light-dependent stage are used, so the
light independent stage will soon cease if light supply ceases
•• The Calvin Cycle
○○ Carbon dioxide from the air diffuses into the leaf
○○ Diffuses through air spaces and reaches the spongy palisade layer
○○ Diffuses through the cellulose cell walls and into the chloroplast envelope
○○ In the stroma, carbon dioxide combines with the 5C ribulose bisphosphate
○○ Reaction is catalysed by the rubisco enzyme
○○ Two 3C compounds, called glycerate phosphate (GP) are produced
–– Some GP is used to make amino acids and fatty acids
○○ GP is reduced and photophosphorylated to another 3C compound, triose phosphate (TP)
○○ ATP and reduced NADP are used in this reaction
○○ 5/6 TPs are recycled to ribulose bisphosphate
–– Pairs of TP combine to form hexose sugars
•• Conversion of Energy
○○ Light converted through cyclic phosphorylation and non-cyclic phosphorylation
○○ Both of which are light –dependent
○○ In Cyclic phosphorylation:
–– Light energy absorbed by PS1
–– Energy excites electrons, raising their energy level
–– This causes electrons to be transferred to carriers
–– As electrons drop down energy levels, they release energy
–– Energy is used to pump H+ ions through ATP synthase from thylakoid space to the
stroma
–– This is the process of chemiosmosis
–– In this process, ATP is produced
–– This process is used to make glucose
○○ In non-cyclic phosphorylation:
–– Light energy causes hydrolysis of water
–– This is photolysis
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–– 2 electrons are produced, which pass into the PS2
–– They are excited and transferred to the electron carriers
–– As they pass along the carriers, they release energy,
–– This is used to pump H+ ions into the stroma at the same time
Role of Water in the Light Dependent Stage
•• Photosystem 2 contain an enzyme that can split water into protons, electrons and oxygen
•• This is photolysis
•• Some of the oxygen is used in aerobic respiration
•• Water is a source of hydrogen ions, which are used in chemiosmosis
•• Protons are accepted by a coenzyme NADP, which is reduced to reduced NADP and used in
the light independent stage
Role of Carbon Dioxide in Light Independent Stage
•• Carbon dioxide is the source of carbon and oxygen for the production of all large organic
molecules
•• These molecules are used as energy stores for all life forms
EXAM TIP
Yes — it’s a lot — but you need to know the specifics listed above about the process of
photosynthesis in order to reach top marks
3 Factors Affecting
the Rate of Photosynthesis
The rate of photosynthesis is highly sensitive to 3 main factors:
Light Intensity
•• If light intensity was dramatically reduced:
○○ Levels of ATP and NADP would fall, as the light dependent reaction cannot occur
○○ Conversion of GP to TP requires ATP and reduced NADP, so this process will slow down
○○ As ATP is used to convert TP to ribulose bisphosphate, levels of this will also fall
○○ Reduction in ribulose bisphosphate means less carbon dioxide can react
○○ Eventually the whole cycle stops
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Carbon Dioxide
•• If carbon dioxide concentration was dramatically increased:
○○ More carbon dioxide fixation allows for more GP, TP and ribulose bisphosphate to be
created
○○ Stomata will be open more, causing an increased loss of water and wilting
○○ Stress response will close the stomata
○○ This will reduced carbon dioxide supply
○○ Photosynthesis rate will slow
Temperature
•• If temperature were raised:
○○ Below 25 degrees activity in light dependent stages is minimally affected
○○ Activity of molecules in the Calvin cycle are dramatically affected as they gain more
kinetic energy
○○ Higher temperatures will increase transpiration and cause the plant to wilt
○○ Stress reaction will cause the stomata to close, reducing carbon dioxide availability
○○ High temperatures may denature rubisco
○○ At higher temperatures, rubisco is more likely to bind to oxygen than carbon dioxide
○○ Photosynthesis rate will start to decrease
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TOPIC 7
Respiration
Respiration
1 The Need for Cellular Respiration
Respiration uses energy to make ATP. In living organisms, energy is the ability to do work. It is
needed to drive metabolic reactions:
•• Anabolic reactions (building large molecules)
•• Catabolic (breaking down molecules)
•• Active transport
•• Secretion
•• Endocytosis
•• Replication of DNA
•• Movement of organelles and of cells themselves
•• Activation of chemicals
ATP Consists of:
•• Ribose sugar
•• Adenine
•• 3 phosphate groups
Role of ATP:
•• Phosphorylated nucleotide
•• High — energy intermediate compound
•• Created after glucose is broken down
•• Stores energy, which can be released quickly and in small amounts
•• Called the ‘universal energy currency’
2 The Mitochondrion
The mitochondrion has also been called the ‘powerhouse of the cell’ because it is the main site
of respiration in the cell.
Structure
•• Inner membrane is folded into cristae, giving a large surface area
•• Matrix is enclosed by the membranes
○○ Link reaction and Krebs cycle occur here
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Shape
•• 2-5 micrometers long
•• Densely packed cristae
•• Moved within the cell by microtubules
3 Glycolysis
Glycolysis is the precursor to respiration and it takes place in the cytoplasm of the cell, not the
mitochondrion.
Stage 1 — Phosphorylation
•• Occurs in cytoplasm
•• 2 ATP molecules are hydrolysed, releasing phosphate group
•• Glucose 6-phopshate changes to fructose 6-phosphate
•• These sugars are then activated, forming hexose 1,6-biphosphate
Stage 2 — Splitting of hexosebisphosphate
•• Hexosebisphosphate is split into 2 triose phosphates
Stage 3 — Oxidation of Triose Phosphate
•• 2 hydrogen atoms removed from each triose phosphate
•• NAD combines with hydrogen, becoming reduced
•• Dehydrogenase enzymes used
Stage 4 — Conversion to pyruvate
•• Triose phosphate converted to a molecule of pyruvate
•• 2 molecules of ADP are phosphorylated to 2 molecules of ATP
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Net Products
•• 2 x ATP
•• 2 x NADH
•• 2 x Pyruvate
○○ 2 molecules produced per glucose molecule
○○ These are actively transported into the mitochondrial matrix for the next stage of aerobic
respiration
○○ In absence of oxygen, it is changed into lactate or ethanol in cytoplasm
4 The Link Reaction
The link reaction occurs in the matrix inside the mitochondrion, once pyruvate has been
actively transported there following glycolysis.
•• Pyruvate contains a carboxyl group
•• This disassociates to COO- and H+
•• Carboxyl group removed in decarboxylation
•• This also releases a molecule of CO2
•• Intermediate is then oxidised
•• H atom transferred to coenzyme NAD, producing NADH
•• Acetyl CoA is the final product
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5 The Krebs Cycle
The Krebs cycle Occurs in the mitochondrial matrix. It is a series of enzyme-catalysed reactions
that ultimately oxidise acetyl group of Acetyl CoA to 2 molecules of carbon dioxide.
1. Acetyl group and oxaloacetate join forming Citrate (6C)
2. Citrate is decarboxylated (carbon dioxide lost) and dehydrogenated (pair of hydrogen atoms
lost) by NAD+
3. 5C compound formed
4. Hydrogen pair accepted by NAD, reducing it
5. 5C compound is then decarboxylated and dehydrogenated, forming 4C compound and
another molecule of reduced NAD
6. 4C changed to another 4C compound, with ADP being phosphorylated to ATP
7. FAD becomes reduced and removing another hydrogen pair
8. 3rd 4C compound is further dehydrogenated, regenerating oxaloacetate
The Final Stages of respiration
•• Electron transport chain (ETC)
○○ Electron carriers are embedded in mitochondrial membrane
○○ Co-enzymes NAD and FAD are reoxidised when they donate H atoms to these carriers
○○ H atoms split into protons and electrons
○○ Electrons move down the chain
○○ They are finally donated to oxygen, the final electron acceptor
•• Chemiosmosis
○○ As electrons flow, energy is released
○○ This is used to pump protons into the matrix
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○○ This builds up a proton gradient (and electrochemical gradient)
○○ Potential energy builds up in the intermembrane space
○○ Hydrogen ions are only able to diffuse through ATP synthase
○○ This drives the reaction of ADP and Pi, forming ATP
•• Oxidative Phosphorylation
○○ As protons flow through ATP synthase, they drive rotation
○○ This joins ADP and Pi, forming ATP
○○ Electrons are finally passed to oxygen, reducing oxygen to water
EXAM TIP
Know the coenzymes involved in respiration and where they feature in the process:
•• NAD
•• FAD
•• Coenzyme A
6 Anaerobic Respiration
Anaerobic respiration is a type of respiration that takes place in the absence of oxygen. It
produces a byproduct called lactic acid — which builds up in our muscles when we exercise
for a long period of time, and makes them ache afterwards.
In Animals
•• Without oxygen, Link Reaction, ETC and Krebs cycle stop
•• Glycolysis can still occur
•• NAD+ is recycled
•• H atoms need to be removed from NADH molecules
•• Pyruvate is used as an H acceptor
•• In muscle cells, pyruvate is converted to lactic acid on accepting the H atom
•• Lactic acid is taken to liver
•• It is re-converted to pyruvate
•• This enters the link reaction in liver cells, where it is aerobically respired
In Yeast
•• NAD+ must be recycled
•• Pyruvate undergoes decarboxylation and reduction to form ethanol
•• If ethanol concentration increase to over 12%, the cells will be killed
•• Ethanol dissolves cell membranes, causing them to burst
ATP yield is much lower in anaerobic respiration because the majority of it is formed in the
oxidative phosphorylation — which requires oxygen as the final electron acceptor.
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7 The Difference in Respiratory Substrates
Respiratory substrate = an organic substance that can be used for respiration.
•• Majority of ATP produced in oxidative phosphorylation
•• More protons allows for more ATP to be produced
•• If a substrate has more hydrogen atoms, more ATP can be made
Carbohydrates
•• Glucose in main respiratory substrate
•• Brain and blood cells can only use glucose
•• Lowest mean energy value 15.8 kJ/g
Proteins
•• Excess amino acids may become deaminated
•• Rest of molecule is changed into glycogen
•• If an organism is starving, protein from muscle can be hydrolysed to amino acids
•• Some is converted to pyruvate and enters the Krebs cycle
•• Slightly higher energy yield than an equivalent mass of carbohydrates
•• Mean energy value 17.0 kJ/g
Lipids
•• Triglyceride hydrolysed to glycerol
•• Glycerol can be converted to glucose
•• Fatty acids can’t be converted into glucose
•• Fatty acids are long chain hydrocarbons
•• These can produce lots of ATP by chemiosmosis during oxidative phosphorylation
•• Each fatty acid must be combined with CoA, using energy
•• The acetyl groups enter the Krebs cycle
•• Lipids have the highest mean energy value 39.4 kJ/g
8 The Respiratory Quotient (RQ)
The respiratory quotient is an indication of how aerobic the respiration is that is taking place.
The formula for RQ:
RQ = CO2 produced ÷ O2 produced
A RQ value that is above 1 indicates that some aerobic respiration is taking place.
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9 Practical investigations into factors
affecting the rate of respiration
A good way to measure the rate of respiration of an organism is by using a respirometer.
Respirometers work because of the basic principle of respiration, wherein the respiring
organism uses up oxygen, and releases carbon dioxide. It follows that the rate of oxygen usage
and the rate of carbon dioxide production are direct indicators of the rate of respiration.
1. Set up the apparatus as shown
○○ Manometer contains liquid that moves as oxygen in tube A is used up
2. The germinating seeds release carbon dioxide
3. Carbon dioxide is absorbed by the sodium hydroxide
○○ Therefore has no effect on volume of air inside tube A
4. Germinating seeds use up oxygen
○○ This decreases volume of air in the tube
○○ Liquid in manometer is drawn up towards tube A
5. Rate of movement of liquid in manometer indicator of rate of respiration
6. Can change environmental conditions such as temperature, light intensity to observe how
these factors affect rate of respiration
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MODULE 6
GENETICS,
EVOLUTION
AND ECOSYSTEMS
TOPIC 1
Cellular
Control
Cellular Control
1 Types of Gene Mutations
Gene mutations are natural occurrences that come about during DNA replication. There are 3
categories of gene mutations:
Substitution = a nucleotide base is replaced with another
Insertion = an extra nucleotide base is inserted into the sequence causing ‘frameshift’ where
all the subsequent bases are shifted down 1 place relative to the twin DNA strand
Deletion = the absence of a nucleotide, causing ‘frameshift’ where all the subsequent bases
are shifted back 1 place relative to the twin DNA strand
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The effects of these mutations can be..
•• Neutral
○○ May occur in phenotypically insignificant strand of DNA
○○ May not result in change of polypeptide primary sequence (because DNA is degenerate)
○○ May result in a change of polypeptide primary sequence that does not affect secondary/
tertiary/quaternary structure of protein therefore protein function unaffected
○○ May results in a change of polypeptide secondary/tertiary/quaternary structure but
where active site of protein remains the same therefore function still unaffected
•• Harmful
○○ May result in change in final protein shape where protein and active site is deformed and
therefore cannot fulfil function
•• Beneficial
○○ May result in change in final protein shape where the protein performs its function
better than it would have without the mutation
○○ This is the basis of natural selection and evolution
○○ The individual is better suited to survival and will pass on the mutation to its offspring
○○ E.g. eye colour
–– Blue eyes was a mutation that occurred about 7000 years ago
–– In sunny areas, this would be harmful as the retina is more exposed
–– However in cloudy regions this was beneficial as it enabled people to see better
–– So the mutation was carried down generations and became widespread
Point mutation
•• Mutations can affect 1 nucleotide base, or more than one adjacent bases
•• A point mutation is where only one base is affected
•• There are 3 types: silent, nonsense, missense
•• Silent mutation
○○ No change in amino acid sequence of polypeptide
•• Missense mutation
○○ The mutation changes the code for 1 amino acid
○○ 1 amino acid in the sequence is changes
•• Nonsense mutation
○○ The mutation changes the code turning the triplet into a stop codon
○○ Instructs the end of polypeptide synthesis
○○ The polypeptide is shorter than it would normally be
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2 Gene Expression Regulation
Most genes that code for functional enzymes are transcribed constantly. The lac operon is an
example of a gene that is only transcribed in times of need. E.coli normally uses glucose as its
respiratory substrate. However in some environments, glucose is sparse and it needs to use
lactose instead. The lac operon represents the polypeptides that constitute the enzymes that
breaks down lactose.
•• At first E coli is unable to metabolise the lactose, as there is a lack of appropriate enzymes:
○○ B-galactosidase
○○ Lactose permeate
•• After a few minutes, the synthesis of these 2 enzymes increases by about 1000 times
•• The presence of lactose is the trigger for the production of these enzymes
Lac system genes
•• Lac operon is a section of DNA within the bacterium DNA
○○ Structural genes code for the enzymes
○○ Operator region can switch the structural genes on and off
○○ Promoter region is a length of DNA which the RNA polymerase can bind to begin the
transcription of the genes
•• Regulator gene is not part of the operon and is some distance from it
Lac operon in the absence of lactose:
•• Regulator gene is expressed and the repressor protein is synthesized
○○ One site binds to lactose
○○ One site binds to the operator region
•• Repressor protein binds to operator region
○○ Covers part of the RNA polymerase binding site
•• RNA polymerase cannot bind to the promoter region
○○ Structural genes are not transcribed to mRNA
○○ Genes cannot pre translated
○○ Enzymes not produced
Lac operon in the presence of lactose:
•• Lactose inducer binds to the other side of the repressor, changing its shape
•• Repressor can now bind to the operator region
•• Repressor is now able to break away from the operator region
•• Promoter region is unblocked
•• RNA polymerase is now able to bind to this region
•• This system acts as a molecular switch
•• The enzymes can now be translated
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EXAM TIP
Make sure you understand that it is the presence of lactose that triggers the expression
of the lactase gene — not the absence of glucose (although both must be true for lactase
to be expressed)
3 The Genetic Control
of Embryonic Development
Homeobox Genes
•• Genes that turn on/off development of specific body parts
•• DNA sequence that is found within many genes
•• They are grouped together as homeotic genes in a ‘hox cluster’
•• These genes are involved in the regulation of anatomical development
○○ Very important therefore precisely conserved
•• More complex organisms have more hox clusters
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•• Homeobox genes expressed in specific patterns in certain stages of development
•• Activated and expressed from anterior to posterior
•• Very similar across species and highly conserved
○○ Indication that they first arose in early common ancestor
•• Regulate development of embryos along anterior-posterior axis
○○ Determine where limbs branch off
Apoptosis
•• Programmed cell death
•• Occurs in multicellular organisms
Sequence of events
•• Enzymes break down cell cytoskeleton
•• Cytoplasm becomes dense with organelles tightly packed
•• Cell surface membrane changes and blebs form
•• DNA breaks into fragments
•• Cell breaks into vesicles
•• These are taken up by phagocytosis
•• Very quick process
How is it controlled?
•• Controlled by a diverse range of cell signals
•• Nitric oxide can induce apoptosis
Development
•• Apoptosis causes limbs and appendages to separate
○○ E.g. separation of human fingers — rather than being webbed
•• Weeds out ineffective T-lymphocytes during the development of the immune system
Transcription factors
•• Can be proteins or noncoding pieces of RNA
•• Coded for by about 8% of genome
•• Attach/detach from DNA to control which genes are expressed
Introns and Exons
•• Post-transcriptional gene regulation
•• Regions of DNA that don’t code for genes are called introns — they separate…
•• Regions of DNA that are expressed, called exons
•• Both are transcribed, but resulting mRNA is modified to remove the introns
EXAM TIP
•• Homeobox genes are found across all multicellular organisms
•• Hox genes are a sub-type of Homeobox gene which are only found in animals
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TOPIC 2
Patterns
of Inheritance
Patterns of Inheritance
1 Phenotypic Variation
Genotype = genetic makeup of an individual
Phenotype = visual characteristics of an individual (not just external physical attributes — for
example, being affected by Diabetes Mellitus is a phenotype)
An individual’s phenotype is a result of its genotype and its phenotype. This is the basis of
the nature vs nurture debate. It explains why genetically identical twins may have diverging
phenotypes, especially as they get older and are exposed to more environmental stimuli.
Genetic factors
•• Genetic variation caused by mutations
○○ Those which are expressed in the phenotype contribute to phenotypic variation
○○ Caused by mutagenic agents eg…
–– X-rays
–– Benzopyrene found in tobacco smoke
–– Viruses
–– Gamma rays
○○ Caused by chromosomal mutations
–– Deletion: part of a chromosome is lost
–– Inversion: section of chromosome breaks off, then is re-inserted in the opposite
direction
–– Translocation: section of chromosome breaks off then is re-inserted on a different
chromosome
–– Duplication: part of a chromosome occurs twice
–– Non-disjunction: one pair of chromosomes fails to separate, so the gamete and
zygote has an extra chromosome (e.g. Down’s syndrome)
○○ Aneuploidy = chromosome number is not a multiple of the haploid number for that
organism
○○ Polyploidy = diploid gamete fertilised by a haploid gamete
○○ Resulting zygote is triploid (3n chromosomes)
○○ Caused by normal sexual reproduction
–– Meiosis produces genetically different gametes
–– Alleles shuffle around
–– Independent assortment of chromosomes
–– Contribute to genetic diversity
–– Random fusion of gametes at fertilisation
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Phenotypic factors
•• Variation caused by the environment alone
○○ E.g. losing a limb in an accident
•• Variation caused by the environment interacting with genes
○○ Environmental conditions can affect the expression of some genes
○○ This is called epigenetics
○○ Genes are put in certain ‘modes’ where they might behave in a certain way
○○ E.g. plants reacting to light
○○ It is thought that epigenetics can be passed vertically (from parent to offspring)
2 Genetic Diagrams
Genetic diagrams are used to illustrate the possible genotypes of offspring from two parents,
and the probability of occurrence of each.
If you are asked to draw a genetic diagram in the exam, your answer should include a punnett
square. You need to be able to draw monohybrid and dihybrid crosses.
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Monohybrid = investigations that examine the inheritance of a single characteristic:
Dihybrid = investigations that examine the inheritance of two characteristics:
EXAM TIP
Your genetic inheritance diagram should contain:
•• Parent phenotypes
•• Parent genotypes
•• Parent gamete genotypes
•• Punnett square
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3 Linkage
Linked genes more likely to be passed on together since their loci are close together on the
chromosome.
Linkage = when two or more genes are located on the same chromosome
Autosomal linkage = linked genes which are on non-sex chromosomes
Sex linkage = linked genes are on sex chromosomes — therefore specific characteristic is
more likely to be inherited in either male or female offspring
Sex linkage
•• Genes are more likely to be X-linked
○○ Found on X chromosome
•• This means female offspring will only show recessive genes if homozygous
•• Male offspring will show recessive X-linked genes even if only present on X chromosome
•• E.g. colour blindness more common in males
Autosomal linkage
•• Linkage of genes which are found on autosomal (non-sex) chromosomes
EXAM TIP
After drawing genetic diagrams to predict the phenotypes of F1 individuals — if the
expected vs observed phenotypes are significantly different, this could be because of
linkage. See the chi-squared page for more information on how to determine whether the
difference is significant.
4 Epistasis and Codominance
Epistasis = interaction of non-linked genes where one masks the expression of the other.
Recessive epistasis
•• Homozygous recessive alleles mask expression of another allele at different locus
•• E.g. flower colour in Salvia
•• Two gene loci: A/a, B/b
•• B = purple; b = pink; a = white
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•• Plant with genotype AABB is purple
•• Plant with genotype AAbb is pink
•• But any plant with genotype aa-- will be white — even if alleles at B/b are homozygous
dominant
•• Homozygous aa is epistatic to both alleles of the B/b gene
○○ Neither B nor b is expressed unless at least one dominant A is present
Codominance = when both alleles present in the genotype contribute to the phenotype.
•• I.e. phenotype of heterozygotes and homozygotes is different
•• E.g. human blood groups: example of codominance with multiple alleles
•• An individual possessing the A allele — with or without the O allele — expresses blood type A
•• An individual possessing the B allele — with or without the O allele — expresses blood type B
•• An individual possessing A and B alleles — express AB blood type
○○ Both A and B proteins are synthesised
•• Another example is coat colour in cattle
○○ Red allele AND white allele = roan coat, speckled white and red coat
○○ Both alleles are expressed
5 The Chi-Squared (χ2) Test
Chi-squared test = statistical test to find out whether the difference between observed vs
expected data is due to chance.
•• Genetic diagrams give us an indication of probable offspring genotypes
•• Due to the random nature of gamete fusion, these are rarely 100% accurate predictions
When to use the chi-squared test:
•• The data are in categories (i.e. discrete variation)
•• The sample size is large enough to be representative
•• The data indicate absolute numbers: not percentages
•• No data values are equal to null
How to apply the chi-squared test:
1. Define null hypothesis
a. States that there is no significant difference between observed/expected data
b. I.e. states that the difference is due to chance
2. Apply the test:
a. Use the equation to find x2
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3. Determine the number of degrees of freedom (number of categories — 1)
4. Determine value of p from distribution table
5. Decide whether the result is significant
EXAM TIP
No need to learn the formula for the chi-squared test as you will be provided with it in the
exam. However, you should find some practice questions to make sure you understand
how to apply the formula to your data, and how to relate your test statistic to p.
6 Continuous and Discontinuous Variation
Discontinuous variation
•• Phenotypes are in distinct categories
•• E.g. blood types or sex
○○ Cannot be ‘between’ blood type A and B
•• Determined by a single allele
•• Monogenic
•• Qualitative
Continuous variation
•• Phenotypes fall in a range
•• Smooth gradient between phenotypes, which are often distributed in a bell curve
•• Eg tail length in mice; birth weight; height; skin colour; heart rate
•• Controlled by more than one gene
•• Polygenic
•• Quantitative
EXAM TIP
Don’t get confused about what polygenic means. If a characteristic is polygenic, it is
determined by the interactions of several genes and the alleles at those loci — in that one
individual.
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7 Factors Affecting Species Variation
Evolution is driven by phenotypic variation. Some individuals will have phenotypic traits that
make them better adapted to their environment. They will live long and reproduce, passing on
the advantageous alleles. Over time these alleles will become more and more frequent in the
population. Allele frequency will change.
Directional selection
•• Environment favours individuals at one extreme of the bell curve
•• E.g. faster cheetahs are able to survive better
•• The mean changes
○○ Mean sprint speed of cheetahs becomes faster and faster over time
Stabilising selection
•• Environment favours individuals close to a specific value which doesn’t change
•• Individuals with extreme phenotypes are less likely to survive
•• E.g. birth mass
○○ Too heavy = birth problems
○○ Too small = developmental problems
•• The mean stays the same
•• Standard deviation becomes smaller over time
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Genetic drift
•• Occurs when population is small to begin with
•• Small gene pool
•• Chance mutations that are not beneficial or harmful might cause changes in allele frequency
•• The isolated population can ‘drift’ and become very different to the parent population
Genetic bottleneck
•• When a population shrinks and then increases again
•• E.g. when disease spreads through a population and few survive
•• The new population has reduced genetic diversity as their genes derive from a few
individuals
•• However in the case of disease, they will have acquired resistance to the disease which
allowed their ancestors to survive the epidemic
Founder effect
•• If a new population is established from very few ‘founding’ individuals, there will be little
genetic diversity
•• Small gene pool
•• Specific type of genetic drift
EXAM TIP
Be clear that genetic bottleneck and genetic drift occur as a result of random mutations —
not the other way round. Random mutations occur irrespective of the size of the
population, but if the population is notably small, they affect a larger proportion of it, and
therefore have a greater effect and are more likely to be carried into future generations.
8 The Hardy–Weinberg Principle
Hardy-Weinberg Principle predicts the ongoing frequencies of alleles and genotypes within a
closed, freely and randomly breeding population.
•• p + q = 1
•• P and q are the probability of 2 different alleles
•• P2 + q2 = 1
•• No change in the allele frequencies within a population
•• Assuming:
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○○ Large population
○○ No migration or immigration
○○ No mutation to new alleles
○○ Random mating, with respect to the genotype of the organism
EXAM TIP
No need to memorise the Hardy-Weinberg equation as it will be provided in the exam.
However, try out a few practice questions to make sure you know how to apply it.
9 Isolating Mechanisms
in the Evolution of New Species
Speciation = the formation of a new species.
•• Parent species must be split into 2 groups
•• Requires the isolation of one group which will go on to become new species
•• Different selection pressures on each group
•• Speciation occurs when individuals from the 2 groups have significant genetic differences
○○ Can no longer interbreed
Isolating mechanisms
•• Geographical isolation
○○ 2 groups separated geographically
○○ Eg. ocean/mountains/rivers
○○ 2 groups do not meet and cannot interbreed
○○ ‘Allopatric speciation’ = speciation in different countries
•• Reproductive isolation
○○ Biological/behavioural changes arise from mutation
○○ Mutation only affects some individuals in the species population
○○ E.g. mutation causes individuals to become active at night rather than in the day
–– Changes foraging behaviour
–– These individuals only meet/breed with individuals also active at night
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10 Artificial Selection
The agricultural revolution marked the beginning of man’s implementation of artificial
selection. This is where farmers and breeders select individuals from a population with
desirable traits — e.g. cereal with resistance to drought, or cows with high milk yields.
Natural selection = selection of genes which adapt a species to survival
Artificial selection = selection of genes for optimal economic yield
Hybrid vigour
•• Excessive selective cross-breeding can cause inbreeding depression
•• Breeding of related individuals
•• Gene pool diversity reduced
•• Chances of expression of recessive harmful gene increased
•• To avoid this problem, breeders must maintain a resource of genetic material
•• They outcross individuals from different varieties
○○ Often with wild types
•• The resulting F1 are heterozygous at many loci
•• This is hybrid vigour
•• Decreased genetic variety = increased widespread susceptibility to disease
11 The Ethics of Artificial Selection
•• Domesticated animals are less able to defend themselves against predators
•• They are also often less able to hunt prey
○○ E.g. dogs who became scavengers and were no longer under the selection pressure to be
able to hunt as a pack
•• Livestock animals are biomorphically different and this may not support a happy life
○○ E.g. chickens which grow too rapidly — bones unable to support weight
○○ Pigs vulnerable to low temperatures during the winter because of reduced fat percentage
•• Pedigree dogs subject to narrow gene pool and therefore often have higher susceptibility to
certain diseases
○○ E.g. Boxer: cancer, heart disease
○○ Labrador: abnormal hip and shoulder joints, lameness
○○ West Highland Terrier: dry eye, skin irritation
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TOPIC 3
Manipulating
Genomes
Manipulating Genomes
1 DNA Sequencing
DNA can be manipulated in several ways:
•• DNA profiling
•• Genomic sequencing
•• Genetic engineering
•• Gene therapy
Gene Sequencing Process:
•• Genomes mapped to identify which part of the genome they have come from
•• Microsatellites can be used to identify which region they are from
•• Samples of the genome are sheared into section around 100,000 base pairs long
•• Sections placed into separate bacterial artificial chromosomes (BACs) and transferred to
E-coli cells
•• As the cells grow in culture, many copies of the sections are produced
•• These are clone libraries
•• The cells containing the specific BACs are taken and cultured
•• DNA is extracted and cut up by restriction enzymes
•• Fragments separated using electrophoresis
•• Each fragment is sequenced using an automated process
•• Computer regions compare overlapping regions form the cuts made by different restriction
enzymes
Automated DNA sequencing
•• Reaction mixture contains:
○○ DNA polymerase
○○ Single stranded DNA fragments
○○ Free DNA nucleotides
–– Some have fluorescent markers
○○ Primers
•• If fluorescent markers are added to the chain, DNA polymerase is thrown off
•• The strand cannot have any more nucleotides
•• Process:
○○ Primer anneals at the 3’ end, allowing DNA polymerase to attach
○○ DNA polymerase adds free nucleotides, so the strand grows
○○ A modified nucleotide is added
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○○ Enzyme is thrown off
○○ Reaction stops
○○ In every strand the final nucleotide has a specific colour
○○ As these strands are run through a machine, a laser reads the colour sequence
–– Move in increasing size order
–– Sequence of colours and so bases can be displayed
High throughput sequencing = methods of rapid, inexpensive gene sequencing developed in
21st century
Pyrosequencing
•• Type of high throughput sequencing developed in 1996
•• Involves synthesising a single strand of DNA complementary to the one being sequenced
•• Process:
○○ DNA cut into fragments of 300-800 base pairs
○○ Fragments are degraded into single-strand DNA (ssDNA)
○○ Fragments incubated with primer, APS,luciferin, and several enzymes, including DNA
polymerase
○○ Nucleotides added are ATP, TTP, CTP, GTP
○○ Nucleotides form chains complementary to the DNA fragments
○○ They dephosphorylate: i.e. ATP -> adenosine; TTP
○○ APS + pyrophosphate
thymine, etc
ATP
○○ Visible light is released in this reaction and detected by a camera
○○ Light patterns detected indicate amount of ATP and therefore DNA sequence
○○ 10-hour run = 400 million bases are read
2 Applications of DNA Sequencing
Comparisons between species
•• Thanks to gene sequencing we can identify the presence of genes throughout many species
•• Humans share 99% of genes with chimpanzees
•• Few genes are unique to our species
•• Pigs have similar gene for insulin as humans
○○ Therefore pig insulin used to be used to treat diabetes in humans
•• FOXP2 is a gene found in humans, mice and chimpanzees
○○ However it is mutated in humans
○○ Allows speech
•• Identifying genetic similarities helps us track evolutionary paths/relationships of species
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Comparisons between individuals
•• Almost all humans share 99.9% similar DNA — the 0.1% makes us each unique
•• These 0.1% differences arise from substitutions
○○ Called ‘single nucleotide polymorphisms’ or ‘SNPs’
○○ Epigenetics is the study of how methylation of DNA causes changes in the expression of
some genes
•• E.g. parent/child genetic matching
Predicting amino acid sequences
•• Easier to sequence DNA than polypeptides
•• Can read amino acid sequence directly from DNA
•• According to triplets and codons
•• Need to know what part of DNA codes for introns/exons
Synthetic biology
•• = designing useful biological devices and systems
•• E.g. biomedicine, food production
3 DNA Profiling
DNA profiling refers to the practice of DNA analysis that confirms the identity of an individual.
Process:
•• DNA obtained from individual — e.g. mouth swab
•• DNA cut by restriction enzymes at specific sites
•• Fragments are separated by gel electrophoresis
•• Banding pattern can be seen
•• Banding pattern compared to another individuals’ which has been treated with the same
restriction enzymes
•• Related individuals will have more similar banding patterns
DNA profiling in forensic science
•• Establish innocence of suspects
•• Identify Nazi war criminals hiding in South America
•• Identify victims’ body parts after air crashes/terrorist attacks
DNA profiling in analysis of disease
•• Protein electrophoresis can identify type of Hb produced by an individual
•• Diagnose sickle cell anaemia
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EXAM TIP
DNA profiling and DNA sequencing is not the same thing. DNA profiling doesn’t necessarily
involve the reading of individual nucleotides or genes.
4 The Polymerase Chain Reaction (PCR)
PCR = The polymerase chain reaction, a technique used to amplify DNA which makes it more
suitable for analysis. Millions of copies of sample of DNA are made and the base sequence is
retained.
Principles
•• DNA consists of 2 antiparallel chains
•• Each strand has 3’ end and 5’ end (according to direction of phosphate backbone)
•• DNA only grows from the 3’ end
•• Complementary base pairs
Process
•• DNA Replication in Test Tube
○○ Needed:
–– DNA to be replicated
–– DNA polymerase
–– Excess of A/T/G/C bases
–– Primers
•• Separating DNA strands
○○ Heated to 95c
○○ Causes strands to separate
•• Primers
○○ Cooled to 55c
○○ Primers are able to attach
•• DNA replication
○○ Heated to 72c
○○ DNA replication can now occur
•• Thermostable DNA polymerase
○○ Taq polymerase used
○○ Thermus aquaticus
○○ Bacteria that lives in deep, warm oceans
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•• Overall Process
○○ Everything added
○○ Heated to 95c
–– H bonds broken
○○ Cooled to 40c
–– Allows primers to join
○○ Increase temperature to 72c
–– Allow DNA to replicate
○○ DNA is replicated
○○ Heated again and process repeated
•• Difference between PCR and normal DNA replication
○○ Strand separation
–– In the cell DNA helicase separates DNA strands
–– In PCR, heat and temperature do this
○○ Primers
–– Required to allow DNA polymerase to begin
–– In cells, they are made by DNA polymerase
–– In PCR they are synthesised separately and added
Problems
•• Any contamination will be amplified
Uses
•• Cloning
•• Electrophoresis
•• Gene Probes
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5 Electrophoresis
Electrophoresis = uses electric currents through agarose gel to separate DNA fragments
according to size
•• DNA samples treated with restriction enzymes to cut them into fragments
•• DNA samples placed into wells of the gel
•• Gel is immersed in a tank of buffer solution
•• Phosphate groups make DNA negatively charged, so DNA diffuses through the gel towards
the positive electrode
•• Shorter lengths of DNA move faster than longer lengths, so move further
•• Position of fragments can be shown by a dye that stains DNA molecules
DNA Probes = short, single-stranded pieces of DNA
•• DNA fragments are complementary to the piece of DNA that is being investigated
•• Probe is labelled:
○○ Using a radioactive marker
○○ Fluorescent marker that emits a colour on exposure to UV light
•• Copies of the probe will anneal to any complementary single strand
•• Probes are useful in locating specific sequences, for example:
○○ Locate a desired gene for genetic engineering
○○ Identify the same gene on different genomes
○○ Identify the presence or absence of an allele
EXAM TIP
Electrophoresis uses agarose gel — which is similar to agar. The main differences are
that agarose is chemically more simple, and also has a neutral charge, and is therefore
preferred for this technique as it is less likely to interfere with the DNA structure.
6 Genetic Engineering
Genetic engineering = recombinant DNA technology = genetic modification = involves the
manipulation and combination of genes from different organisms.
1. Specific gene is isolated and copied
2. Gene is placed inside vector (e.g. plasmid)
3. Vector carries gene to target cell
4. Recipient cell now has recombinant DNA and expresses newly acquired gene
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Isolating a required gene
•• mRNA coding for the specific gene is obtained
•• Reverse transcriptase forms a single strand of complementary DNA (cDNA) based off the mRNA
•• Adding primers and DNA polymerase catalyses the formation of double stranded DNA
•• Gene is then synthesised
○○ Automated polynucleotide synthesis if gene sequence known
○○ PCR if gene sequence unknown
•• DNA probe used to locate gene
•• Gene isolated by restriction enzymes
Placing the gene inside a vector
•• Cut plasmid at specific site using restriction enzymes
•• Cuts made by restriction enzymes match the ends of the isolated gene
○○ The complementary ends are called sticky ends
•• DNA ligase catalyses insertion of gene into plasmid
•• Gene can also be sealed in an attenuated virus
Vector carries gene to target cell
•• Several methods of achieving this
•• Heat shock
○○ Bacteria subject to fluctuating temperatures between 0C and 42C
○○ Cell walls and cell membranes become more permeable
○○ Recombinant DNA enters cell more easily
•• Electroporation
○○ High voltage applied to cell and the membrane becomes more permeable
•• Electrofusion
○○ Electrical fields cause DNA to enter cells
•• Transfection
○○ Gene inserted into bacteriophage which infects bacterial cell
7 The ethics of Genetic Manipulation
Modified organism
Pathogens
Benefits
Hazards
•• GM viruses which have no •• In gene therapy, gene
harmful effect can be used
modification can increase risk
to make vaccines.
of cancer
•• Gene therapy
Mice
•• GM mice used for medical
research, e.g. breast and
prostate cancer
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Modified organism
Benefits
Hazards
Golden Rice
•• GM rice contains beta
carotene to reduce rates
of blindness in children
suffering from Vit A
deficiency
•• Originally there were concerns
that new seeds would have to
be bought each year but the
manufacturers have developed
schemes so farmers can keep
and re-sow seeds
Plantains
•• GM plantain has higher
zinc content as local
consumers have low-meat
diet making them zinc
deficient
•• People fear artificially present
DNA can harm our own
genomic sequence — however
DNA that we ingest orally is
digested by lytic enzymes
Microorganisms
•• GM E. coli makes human
insulin to treat diabetics
and human growth
hormone
•• GM microorganisms must be
carefully contained, as if they
are released into the wild,
their genes will spread and
will affect entire ecosystems
8 Gene Therapy in Medicine
Gene therapy is the use of gene technology to treat genetic disorders, which usually involves
adding a functional copy of a gene to cells which only contain a dysfunctional copy
Somatic Cell Gene Therapy
•• During growth, cells become specialized
•• In these specialised cell, genes are switched on and off
•• Although the cell has a full genome, not all of it is active
○○ Adding Genes
–– Some diseases caused by faulty alleles
–– Engineering a functional copy of that gene into the cell means that the polypeptide
can be produced
–– Functional gene product created
○○ Killing Cells
–– Cancerous cells can be made to express certain genes and create proteins
–– These can make the cells vulnerable to attack by the immune system
–– Targeted cancer treatments
Germ line Cell Therapy
•• Gene engineered into sperm or egg
•• Ensures all cells in the adult organism will have a copy of it
•• Illegal in humans
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TOPIC 4
Cloning
and
Biotechnology
Cloning and Biotechnology
1 Natural Clones in Plants
Cloning = process leading to the formation of a clone
Clones = genetically identical copies of an organism
Advantages of natural cloning
•• Same environment suitable for parent and
offspring
•• Rapid
•• Reproduction doesn’t require two parents
or sexual reproduction
Disadvantages of natural cloning
•• Offspring overcrowding
•• No genetic diversity/variation
•• Therefore selection is impossible
•• Entire population vulnerable to
environmental changes
Reproductive Cloning
•• Cloning that makes another organism
Non-reproductive Cloning
•• Therapeutic cloning
•• Goal is to produce embryonic stem cells
•• Stem cells taken from blastocysts
Cloning in Plants: Natural Vegetative Propagation
•• Generation of multiple offspring from one plant without sexual reproduction
Advantages
•• Only one parent required
•• Saves resources
Disadvantages
•• One disease can affect the whole population
Process
•• Many plants can reproduce asexually following damage to the parent plant
•• Root sucker, or basal sprouts, appear within 2 months
•• These grow from meristem tissue, where damage is least likely to have occurred
•• The offspring are genetically identical to the parent plant
Micropropagation and tissue culture = the use of plant cuttings to produce clones. This
process produces many genetically identical plants from just one plant, e.g. Elm trees
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Process
•• Cells taken from shoot tip with sterile forceps
•• These are explants
•• Explants placed in nutrient agar
•• Cells proliferate to form a big ball of cells, called a callus
•• Cells are then treated with shoot stimulating hormones
•• Cells grow into plantlets
•• Treated with root-stimulating hormones
•• Plants grow
•• Plants are planted into compost
Advantages
•• Farmers know what the crop will be like
•• Reduced costs as all crop is ready for harvest at the same time
•• All crop has ideal features
•• Faster than selective breeding
•• Horticulture and agriculture
Disadvantages
•• All plants susceptible to the same pest or disease
EXAM TIP
If you’re asked to define a clone, explicitly state that the two clones are genetically identical.
2 Natural Clones in Animals
Natural cloning does not happen as frequently in animals as in plants because most animals
reproduce sexually, creating genetic variation and diversity. However there are a few
exceptions:
•• Identical twins
○○ Zygote divides early in development to form 2 separate cells
○○ Each cell is genetically identical and grows into an individual organism
•• D. pulex and A. pisum
○○ Species which reproduce asexually to produce clones
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3 Artificial Clones in Animals Produced
by Artificial Embryo Twinning
or by Enucleation & SCNT
•• Making a genetically identical copy of an organism
•• Copying its genome
○○ Conservation
○○ Exploitation
○○ Experimentation
Embryo Twinning
•• Cleaving of embryo is repeated
•• Used in artificial cloning in animals
•• All organisms produced are genetically identical
○○ E.g. Cloned herds of cattle in America
Somatic Cell Nuclear Transfer
•• Nucleus of an adult egg placed in an enucleated egg
•• Organism produced is genetically identical to that from which the nucleus was taken
•• This is how Dolly the Sheep was created
Advantages
•• High-value animals can be cloned in large numbers
•• Rare animals can be cloned to preserve the species
•• Genetically modified animals can be quickly produced
Disadvantages
•• Animal welfare may be forgotten
•• Reduced genetic diversity may decrease ability to cope with change
•• Long term health of cloned animals is still unclear
4 Microorganisms in Biotechnological
Processes
Microorganisms have many features that are useful in biotechnology
•• Grow rapidly in favorable conditions, with generation time of less than 30 minutes
•• Metabolites can be harvested
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•• Can be genetically engineered to produce specific products
•• Can grow well at low temperatures
•• Can be grown anywhere in the world and are not dependent on climate
•• Tend to generate more pure products
•• Economic considerations
Example uses of microorganisms
•• The Production of food
○○ Cheese and yoghurt
○○ Quorn
○○ Soya Sauce
•• Production of drugs
○○ Penicillin
○○ Insulin
•• Production of enzymes
○○ Pectinase
○○ Calcium citrate
○○ Bio-gas fuel production
•• Bioremediation of waste products
○○ Waste water treatment
5 The advantages/disadvantages of using
Microorganisms to Make Food
for Human Consumption
Advantages
•• Protein produced faster than animals/plants
•• Production easily increased or decreased according to demand
○○ Easy to regulate speed of generation/growth
•• Protein contains no fat or cholesterol — health benefits
•• Requires small land surface area
•• Microorganisms easier to GM than animals or plants
•• Independent of seasons
Disadvantages
•• Unappetising
•• Protein needs to be isolated from the growth substrate
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•• Protein needs to be purified
•• Amino acid profile different from animal protein
•• Risk of infection of growth tank
•• Poor palatability
6 Aseptic Culture Technique for
Microorganisms
Microorganisms are very versatile and can survive in a range of environments. However to be
grown for scientific purposes, a culture needs to be preserved aseptically.
Aseptic technique
•• Microorganisms grown on agar jelly in petri dishes
•• Hands always washed
•• Working area disinfected
•• Nearby bunsen burner warms air and causes airborne microbial contaminants to rise away
from work area
•• Place neck of any open test tubes/containers over the bunsen burner to prevent bacteria in
surrounding air from entering the vessel
•• Avoid removing petri dish lid entirely
•• Sterilise any equipment in the burner before making contact with the microorganism
Growing microorganisms on agar plates consists of:
1. Sterilisation
a. Agar and equipment must be sterile
b. Achieved by using an autoclave — 121 degrees C — for 15 minutes
c. All organisms are killed
d. Keep lid on petri fish to maintain sterility
2. Inoculation
a. Microorganisms introduced to sterile medium
b. Streaking — wire loop with microorganism on it is dragged across agar surface
c. Seeding — pipette used to drop liquid medium on agar
d. Spreading — glass spreader used to spread the drop across the agar
3. Incubation
a. Petri dish placed in warm environment
b. Place upside down to prevent condensation falling on the surface of the agar
c. Do not open petri dish
d. Observe culture growth after 24-48 h
e. Wash petri dish after use
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7 Manipulating the Growing
Conditions in Fermentation
Scaling-Up Growth
•• Conducted in a fermenter
•• Culture bacteria in an aqueous environment
•• High pressure steam
○○ Sterilizes environment
•• Sparger
○○ Delivers oxygen
•• Waste products removed
•• Incoming air filtered
•• Outlet at the top
•• Respiration increase temperature
○○ Lowered by a water jacket
•• pH may become more acidic
○○ Alkali can be added to neutralize this
Continuous Culture
•• Useful and waste products continually removed
•• Some bacteria are removed
•• Useful for maintaining the culture in the log phase
•• Difficult to set up
•• More efficient as the fermenter operates continuously
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Batch Culture
•• Closed environment
•• Competition for limited resources
•• Useful for maintaining culture in stationary phase
•• Must know the end of log phase and the end of stationary phase
•• Easy to set up and maintain
•• Less efficient as the fermenter is not in operation full time
•• Useful for producing secondary metabolites
8 The Growth Curve of a Microorganism
in a Closed Culture
Lag Phase
•• Cells increase in size
•• Enzymes synthesized
•• No cell division
•• Gives time to ensure a stable environment
•• Cells taking in water
•• Population remains fairly constant
Log Phase
•• Exponential growth due to high metabolic activity and reproduction
•• Cells are most vulnerable to anti-microbial during this period
•• Exponential growth
Stationary Phase
•• Nutrient levels decrease
•• Toxic metabolites build up
•• Growth rate slows
•• Population stabilizes
•• Organisms die at the same rate at which new individuals are being produced
Death Phase
•• Nutrient exhaustion
•• Increased levels of toxic metabolites
•• Microbial death exceeds numbers produced
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Primary Metabolites
•• Substances produced by an organism as part of its normal growth
•• Vital for cell growth
○○ Amino acids
○○ Lipids
○○ Vitamins
•• Produced during log phase
Secondary Metabolites
•• Substances produced that are not part of normal growth
•• Produced once the colony has reached its maximum sustainable size
○○ Antibiotics
○○ Penicillin
•• Produced during stationary phase
Serial dilutions = repeated dilutions of a solution in order to reduce its concentration
•• Useful technique for identifying rate of growth of a colony
•• Original solution may contain high numbers of microorganisms
•• Need to dilute the broth in order to clearly see starting density of colonies and determine
growth
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9 Immobilised Enzymes
Immobilised enzyme = an enzyme that is fixed and unable to move freely throughout a solution.
Advantages of immobilising enzymes in biotechnology:
•• Enzymes don’t mix with product — lower purification cost
•• Enzymes can be re-used
•• Cells containing enzymes are replaced with immobilised enzymes, therefore no need to deal
with cellular demand for nutrients or release of waste products
•• Enzymes are fixed within immobilising matrix which protects them from harsh environments
○○ High temp/extreme pH more feasible
Disadvantages of immobilising enzymes in biotechnology:
•• Expensive to set up
•• Immobilised enzymes are less active than free enzymes so process is slower
Methods of immobilising enzymes:
•• Adsorption
○○ Enzymes bound to e.g. clay surface by hydrophobic interactions and ionic links
○○ Weak bonds — some enzymes break loose
•• Covalent bonding
○○ Enzymes bound to e.g. clay surface by covalent bonds
○○ Sharing electrons = strong bonds
○○ Can be expensive and reduce enzyme action
○○ But enzymes unlikely to break free into reaction mixture
•• Entrapment
○○ Enzymes trapped in matrix
○○ Enzymes fully active
○○ Substrate diffuses into matrix
○○ Product diffuses out of matrix
○○ E.g. calcium alginate beads
•• Membrane barrier
○○ Semi-permeable membrane around enzymes
○○ Substrate small enough to pass through membrane to meet enzymes
○○ Limits rate of reaction
EXAM TIP
Make sure you’re aware about the benefits of using immobilised enzymes over cellular
microorganisms in biotechnology
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Example of use of immobilised enzymes:
•• Lactase
•• Converted glucose to galactose
○○ Hydrolysis reaction
•• Used to make lactose-free milk
•• Makes calcium-rich milk available to people who are lactose intolerant
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TOPIC 5
Ecosystems
Ecosystems
1 Ecosystems
Ecosystem = dynamic system of interactions involving a community of living organisms and
the abiotic factors of their environment. Ecosystems can range in size:
•• Large scale e.g. African grassland
•• Medium scale e.g. football field
•• Small scale e.g. a single tree
Habitat = the place where an organism lives
Population = a group of organisms of the same species who live in the same place at the same
time and can breed
Community = all the populations of different species living in the same place at the same time
Ecosystems are said to be dynamic:
•• Populations constantly rise and fall
•• This is because of interactions between living things and their ecosystem
•• Any small changes can have a large effect
•• Subject to change due to biotic and abiotic factors
Abiotic
•• Effects of non-living components
•• pH
•• Temperature
•• Soil type
Biotic
•• Effects of living components
•• Food supply
•• Predation
•• Disease
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2 Biomass Transfer Through Ecosystems
Biomass = the combined total weight of a defined set of organisms. Biomass revolves around
the idea that energy is created by producers in the food chain, which are then eaten. Energy and
materials (such as amino acids and glucose) thereby travel up the food chain or trophic levels.
Pyramid of Biomass
•• Indicates biomass at each trophic level
•• Area of bars is proportional to the dry
mass of all organisms at that trophic level
•• Ecologists put organism in an oven,
evaporating all of the water
•• In order to be less destructive, wet mass
can be calculated, using previous data to
calculate dry mass
•• However, these do not take the variation
in energy released per unit into account
Pyramid of Energy
•• This pyramid indicates the energy
contained within the biomass of
each trophic level
•• Organisms are burnt in a calorimeter
•• This calculates the energy released
per gram
•• This is both time consuming and
destructive, so is rarely used
•• However, these only take a
‘snapshot’ of the organisms and
may provide a distorted view due to
fluctuation in population
Productivity
•• Ecologists often look at the rate that energy passes through each trophic level
•• This gives an idea of how much energy is available to organism
•• It is measured in megajoules of energy per square meter per year
•• At the base of the food chain, productivity is called primary productivity
•• Gross primary productivity is the rate at which plants convert light energy into chemical energy
•• However, some energy is lost when the plant respires
•• Remaining energy is called net primary productivity
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Efficiency of Transfer
•• At each level, some energy is lost
•• Less energy is therefore available for organisms at the next level
•• At each level organisms need energy to carry out life process
•• Respiration releases energy, some of which is converted to what
•• Energy remains stored in dead organisms and waste material, which is only available to
decomposers
•• Waste material also includes parts that cannot be broken down and digested by consumers
•• Higher up in food chains, less energy is available to sustain living things so less tissue can be
kept alive
•• This means that if organism are the same size, fewer can be sustained higher up the food chain
EXAM TIP
Check out a pyramid of numbers — it’s similar to a pyramid of biomass, but indicates the
number of individuals at each trophic level. Be aware that some pyramids of numbers are not
pyramid-shaped. For instance, a single tree can be eaten by thousands of bugs and insects.
Human manipulation of biomass transfer:
Improving Primary Productivity
•• Plants grown earlier or under light banks to maximise light exposure
•• Plants are irrigated to maximise water supply
•• Warmer temperatures, often in form of greenhouses, are used to increase speed of chemical
reactions
•• Nutrient levels in soil are maintained
•• Pests are sprayed with pesticides to prevent loss of biomass from crops
•• Fungal diseases are limited through the use of fungicides
•• Herbicides used to kill weeds which provide the corps with unnecessary competition
Improving Secondary Productivity
•• Manipulation of energy transfer from producer to consumer
•• Animals harvested young, when most of their energy is used for growth
•• Steroid used to increase growth
•• Selective breeding used to produce breeds with higher growth rates
•• Animals treated with antibiotics to prevent loss of energy due to pathogens
•• Limiting movement reduces energy loss due to heat, maximising the mass
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3 Recycling Within Ecosystems
In an ecosystem, materials must be recycled. Nitrogen and carbon are in high demand in all
aspects of an ecosystem and their recycling occurs in the Nitrogen and Carbon cycles, aided by
decomposers.
Role of Decomposers
•• Dead and waste organic material is broken down by decomposers
•• Bacteria and fungi feed in a different way to other organisms, they are saprotrophs:
○○ Secrete enzymes onto dead waste material
○○ Enzymes digest material into small molecules
○○ Molecules then absorbed into the body
○○ Molecules are stored or respired to releases energy
Nitrogen Cycle
•• Living things require nitrogen to make proteins and nucleic acids
•• Nitrogen is cycled between biotic and Abiotic components
•• Bacteria is involved in ammonification, nitrogen fixation, nitrification and denitrification
•• Nitrogen Fixation
○○ Nitrogen is incredibly uncreative when in the atmosphere
○○ Plants need a supply to be ‘fixed’
○○ Nitrogen fixation can occur when:
–– Lightning strikes
–– Haber process
–– Nitrogen fixing bacteria (Rhizobium) fixes it
○○ Bacteria has a mutualistic relationship with the plant providing in with nitrogen and
receiving carbon compounds in return
•• Nitrification
○○ Chemotropic bacteria absorbs ammonium ions
○○ Ammonium ions are released in putrefaction of proteins
○○ Nitrosomonas bacteria oxidise ammonium to nitrates
○○ Nitrobacteria oxidise nitrites to nitrates
○○ As reaction requires oxygen, it only occurs in well aerated soil
•• Denitrification
○○ Bacteria can convert nitrates back to nitrogen gas
○○ When bacteria involved are growing under anaerobic conditions, they can produce
nitrogen gas and nitrous oxide
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Carbon Cycle
4 Primary succession
•• Over time gradual and directional changes occur in an ecosystem
•• The development of communities from bare ground is known as primary succession
•• It occurs like so:
○○ Pioneer community of algae and lichens grow on bare rock
○○ Pioneer species = first species to colonise an abiotic area, which begin the process of
succession
○○ The rock is eroded and dead organisms build up
○○ This produces soil for larger plants to grow. These plants succeeds the algae and lichens
○○ Larger plants continue to succeed smaller plants until a final stable community is
reached. This is the climax community
○○ Deflected succession = when succession stops or is interfered with
–– E.g. when mowing grass
Climax Community
•• Final, stable community
•• Larger plants replace smaller plants in process of succession
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EXAM TIP
Primary succession can occur in a wide range of environments — bare rock, sand dunes, etc.
Secondary succession is the sequential community changes that happen following
deflection, when the environment is altered somehow
5 Measuring the Distribution
and Abundance of Organisms
in an Ecosystem
Measuring Distribution
Sampling
•• Small portions of the habitat are studied
•• These are taken as representative for the larger habitat
Quadrats
•• Quadrats are used to enable sampling of a small space in the habitat
•• The square frame is used to define the sample area
•• Randomly place quadrats across the habitat
•• Or take samples at regular intervals across the habitat (systematic)
Transects
•• More systematic approach
•• Looking for changes in distribution or abundance
•• A line is taken along a habitat and sample are taken along this line
•• Line transect = regular intervals — record species making contact with the tape
•• Belt transect = regular intervals — place quadrat next to the line and study quadrat results
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TOPIC 6
Populations
and
Sustainability
Populations
and Sustainability
1 The Factors that Determine
the Size of a Population
A population cannot increase exponentially and infinitely. The size of a population naturally
fluctuates but is usually within a certain range, which is determined by a few limiting factors.
○○ Availability of resources
○○ Nesting sites
○○ Shelter
○○ Predation
○○ Parasites
•• The carrying capacity is the upper limit that these factors place on the population size
Carrying Capacity
•• The maximum population size that can be maintained over a period of time in that particular
habitat
○○ Lag Phase
–– Few individuals
–– Acclimatising to habitat
–– Reproduction and growth slow
○○ Log Phase
–– Resources plentiful
–– Reproduction fast
○○ Stationary Phase
–– Population levels out at the carrying capacity
–– Habitat cannot support a large population
–– Rates of reproduction and mortality are equal
–– Population size stays stable
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Predator and Prey
•• Predators can act as a limiting factor on prey’s population size
•• When population gets bigger, more prey are eaten
•• Prey population shrinks, leaving less food available
•• Less food, so less predators survive and population size reduces
•• Fewer predators, fewer prey eaten, population size increases
•• More prey, so predator population rises again
Competition
•• If resources are in short supply, competition will always exist
•• It occurs when resources are not present in adequate amounts to satisfy the needs of all
individuals who depend on those resources
○○ Intraspecific
–– Happens between individuals of the same species
○○ Interspecific
–– Happens between individuals of different species
–– Can affect both population size and distribution
EXAM TIP
Consider which population limiting factors are dependent and independent of the size
of the existing population. For example, cold temperatures can decrease the size of a
population irrespective of its size. On the other hand, the availability of nesting sites for
birds will only become a limiting factor when the population becomes dense enough.
2 Conservation and Preservation
Conservation = Maintenance of existing biodiversity, including interspecies, genetic,
intraspecies, habitat and ecosystem diversity. Often involves management and reclamation
Preservation = Maintenance of habitats and ecosystems in their present condition by
minimising human impact.
Reasons for conservation
•• Ethical
•• Economic
○○ Many plant and animal species are rich food source
○○ Genetic diversity in wild strains needed for hybrid vigour
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○○ Natural predators can drive out pests
○○ Conservation of wild/rare species can boost local tourism
•• Social
○○ Microorganisms and plants can be a source of medicinal drugs
Methods of conservation
•• Protected areas like National Parks
•• Ex situ protection e.g. zoos, botanical gardens
•• Increase habitat carrying capacity by increasing available food
•• Control predators and poachers
•• Vaccinate individuals against disease
•• Preserve habitats by reducing waste/pollution
3 Ecosystem Management
for Sustainability
Small-scale Timber Production
•• Coppicing involves cutting a tree trunk close to the ground to encourage growth
•• It is a traditional supply to obtaining a sustainable supply of wood
•• Once cut, new shoots grow from the stems
•• Woodland managers divide trees into 3 sections, cutting one section a year until all the trees
have been cut
○○ This is rotational coppicing
•• In each section some trees are left un-cut
•• These standards supply larger pieces of timber
•• Rotational coppicing is very good for biodiversity
•• It allows different habitats to thrive and presents succession
Large-scale timber production
•• Often involves clear-felling of trees
•• If done altogether, this can destroy areas of woodland
•• Leaving each section to mature for 50-100 years allows biodiversity to increase
•• Felled trees are replaced
•• Selective cutting involves felling only the largest and most valuable trees, which has little
impact on the ecosystem
•• In order to sustainably manage the forest, foresters must:
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○○ Control pests and pathogens
○○ Only plant plants that will grow well
○○ Position trees an optimal distance apart
Fish Farming
•• Fishing takes place in a way that allows it to be continued indefinitely
•• Stocks are not depleted
•• Over-fishing therefore not possible
•• Ecosystem structure, production and function is preserved
4 The Management of Environmental
Resources and the Effects of Human
Activities
Habitat Disturbance
•• Increase in population size has placed huge demands on water, energy and sanitation
services
•• Demand for oil has increased
•• Conversion or land for agriculture has resulted in the fragmentation of habitats
○○ Forests of scalesia trees and shrubs have almost been eradicated to make way for
agricultural land
Terai Region
•• Southern Nepal
•• Over-exploited for the past 10 years by agricultural pressures
•• Forests provide source of fuel for local people
•• WWF and Nepalese government focused on conservation of the area
•• Local people could exploit the forest but had responsibility to look after it
•• Developing waterholes, forest corridors to enable animal migrations
•• Tiger population are using forest corridors
○○ Population is growing
Maasai Mara
•• Savannah region in Kenya
•• Surrounding communities suffer poverty and rely heavily on tourism for wildlife watching
•• Conservation maintains biodiversity of the region whilst helping local people financially
•• In 1986 the security of the land was threatened and Maasai people claimed parts of it for themselves
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•• Land use became progressively more agricultural
•• Mobility of livestock was reduced
•• Density of wildlife dropped 65% over last 30 years
•• In 2005, some land-owners unionised and turned their land into conservancies to generate
tourism income
•• Conservancies are now paid by tourism operators for land set aside for conservation
•• However the the landowners must move their livestock out of the designated conservancies
during tourism season
•• There are constraints on how they can use the land
Human Activity on the Galapagos Islands
Over-exploitation of resources
•• Giant tortoises historically taken on ships as a food source
•• 200,000 taken in less than half a century
•• Depletion of sea cucumber populations
•• The shark fin market has led to the deaths of 150,000 sharks each year
•• 14 species are listed as endangered
Introduced Species
•• Alien species deliberately brought to the islands
•• These have eradicated native species
•• The goat has been one of the most damaging species
○○ Eats Galapagos rock purslane
○○ Outcompetes giant tortoise in grazing
•• Cats hunt a number of species including the lava lizard and young iguanas
•• The Charles Darwin Research Station has introduced many measures to prevent and limit this:
○○ Quarantine system
○○ Culling of dominant alien species
○○ 36% of coastal areas designated as ‘no take’ zones
•• It is essential to find a balance between the environmental, social and economic concerns
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