IB Biology 2009 Syllabus Almost Complete Set of Notes

Biology Syllabus - Core
Saturday, January 24, 2009

9:06 PM
Topic 1: Statistical Analysis
4:33 PM
Topic 1.1: Standard Deviation
4:37 PM
Using Statistics to Measure Populations
• To calculate populations, we can use Statistics or Stats, to reach our answer.
• Statistics - The mathematics of the collection, organization, and interpretation of
numerical data, especially the analysis of population characteristics by inference from
sampling.
• There are several ways to interpret data, and we will look at a few.
1. Mean – is the average value obtained by dividing the total of a set of values by the
number of values.
2. Median – the middle value that separates the higher half of a data set from the lower
half of the data.
3. Mode – the most frequently occurring data observation.
4. Standard Deviation – is used to summarize the spread of variables around the mean.
68% of the values of a normal distribution fall within one standard deviation of the mean
(+/- 1)
• Standard Deviation (SD) can be used to compare populations. The closer the mean and
the SD, the more likely the populations studied are the same or similar. Smaller samples
create variation due to the random factors. Therefore, only considering the means may
give a distorted picture of the population and small samples are unreliable.
• Since the SD is the measure for the spread of variables, we subtract the mean from
each of the values. Then we square these numbers, add them and divide by the total
number of values, -1. The number acquired this way is called the variance.
• Using sample standard deviation assuming we have a sample and want to make
assumptions about the entire population. Since you are most likely to have missed the
extremes of the population in your sample, you are dividing by n-1 rather than n.
• A small SD indicates that the data is clustered closely around the mean value. A large
SD indicates a wider spread around the mean.
What does all this mean?

• When comparing two samples from different populations, the closer the means and SDs,
the more likely the samples are drawn from similar (or the same) population. The bigger
the difference, the less likely that this is so.
• Smaller samples will create a variation simply by random factors in the individual
values. A sample of population A or 3 plants may give the values of 10 cm, 20 cm, and
30 cm in height. A sample of population B may give the values of 20 cm, 20 cm and
20cm. The mean of the sample size will be the same for the populations but the SD’s,
will differ. However, if one of the plants in population B had measured 40 cm, the results
would have been very different.
• Two conclusions drawn from above are:
• Considering only the means may give a distorted picture.
• Small samples are unreliable.
Topic 2: Cells
8:42 AM
Topic 2.1: Cell Theory
8:43 AM
Calculating Linear magnification of drawings
1. Using a ruler measure the size of a large clear feature on the image
2. Measure the same length on the specimen
3. Convert to the same units of measurement
Magnification = measured length of the image /measured length of the
specimen
Length of the actual specimen = length on the image/ magnification ( e.g. rose
leaf = image length 4.2cm/ magnification 0.82 = 5cm real length
Scale Bars: images often carry a scale bar which is a horizontal line drawn on
the image. The scale bar shows how long the line is in the real specimen.
• This example shows a plant cell.
• The scale bar indicates the length of 10 microns = 10um
• Notice that 10 um is about the vertical length of the diameter of the nucleus.
• All other measurements from the image are made relative to this scale bar.
Cell Theory:
1. All organisms are made of one or more cells
2. Cells are the smallest units of life
3. Cells only arise from pre-existing cells
4. Cells form the building blocks of living things
5. Cells contain inherited info which controls their actions (DNA)
6. Given suitable conditions cells are capable of independent existence. (ex. heart
transplant)
Evidence for Cell Theory:

2. 1590 – Jansen invents compound microscopes -2 lenses, more magnification
2. Robert Hooke – he named the cellular organisms cells
3. Anton Van Leuwenhoek - made single lens microscope with amazing power.
a. 1675 – discovered uni-cellular organisms
4. Matthais Schleiden – 1838 – “all plants were made of cells”
5. Theador Schwann – 1838 –“all animals made of cells”
6. Johannes Purkinje – 1839 – “protoplasm” a jellylike material that fills the cell
7. Rudolph Virchow – 1855 – “all new cells arise from pre-existing cells”
Unicellular Organisms Functions of Life

3. Gas exchange
2. Taking in water
3. Regulation of wastes and water
4. Energy production
5. Movement and response to stimuli
6. Reproduction and growth
Surface Area to Volume Ratios
• As the size of a structure increases the surface area to volume ratio decreases.
• Therefore the rate of exchange (diffusion/radiation) decreases
• This is true for organelles, cells, tissues, organs and organisms. It is also true for
those structures that organisms build e.g. termite mound
• All organisms need to exchange substances such as food, waste, gases and heat
with their surroundings.
• These substances must be exchanged between the organism and its
surroundings.
• The rate of exchange of substances therefore depends on the organism's surface
area that is in contact with the surroundings.
• As organisms get bigger their volume and surface area both get bigger, but not
by the same amount.
Result:
• Large organisms the rate of exchange with their surroundings occurs more
slowly.
• Small organisms have the opposite problem of a rapid rate of exchange with the
environment.
Sizes of cells
Molecule - 1 µm
Membrane thickness - 10 µm
Viruses - 100 µm
Bacteria - 1 µm
Organelles - (up to) 10 µm
Most cells - (up to) 100 µm
Electron microscope vs. Light microscope

Electron microscope
• Can view most organelles and has high enough magnification for internal details
to be seen.
• Can view nucleus
• Uses an electron bean
• Smaller wave length which gives a greater resolution (5 nm)
Light microscope
• Can not view most organelle or inner details.
• Can view nucleus
• Uses a light beam
• Resolution 0.2 nm
Stem Cells
Therapeutic cloning: A procedure in which cells, typically skin cells, are taken
from a patient and inserted into a fertilized egg whose nucleus has been
removed. The cell that is so created is permitted to divide repeatedly to form a
blastocyst. Scientists then extract stem cells from it, and use those cells to grow
tissue that are a perfect genetic match for the patient.
1. It can create embryonic stem cells that are 100% compatible with the patient
• There would be presumable no danger of rejection of the transplant b/c organs
DNA would match the patients DNA exactly.
• For transplants involving kidney (or theoretically any other organ that is
duplicated in the body) another individual would not have to experience the
pain, inconvenience, and potentially shortened life span in order to donate
organ.
• The patient wouldn’t have to wait until an unrelated donor dies to obtain a
transplant. A new organ could be grown for them as needed.
• Wave lives which otherwise be lost waiting for a transplant that did not come in
time.
2. The supply of cells is unlimited
• Potential exists to cure, or at least treat, certain diseases and disorders that can
not be effectively handled today.
• Cells are totally rejuvenated independently of the ago of donor.
• Ex) Suppose a middle aged man suffers a serious heart attack while hiking in a
remote part of a national park. By the time he reaches the hospital, only a third
of his heart is still working, and it is unlikely he will be able to return to his
formerly active life. He provides scientist a small sample of skin cells.
Technicians remove the genetic material from the cells and inject it into the
donated human eggs from which the chromosomes have been removed. These
altered eggs (cloned, embryos) will yield stem cells that are able to form heart
muscle cells. Since they are a perfect genetic match for the patient, these cells
can be transplanted into his heart without causing his immune system to reject
them. They grow and replace the cells lost during the heart attack, returning
him to health and strength.
Multicellular Organisms and Specialized Cell Function

• Multi-cellular organisms are large and have to specialize parts of their structure
to complete the various functions that are characteristic of life.
• What is the benefit of differentiation and specialization of tissues rather than all
tissues carrying out all functions?
• An interesting parallel with economic theories is that the larger collective
economic group the greater the number of specialism's, a rough guide which is
found to hold true in living systems.
• Differentiation: Cells within a multi cellular organism specialize their function.
• Specialized cells have switched on particular genes (expressed) that correlate to
these specialist functions.
• These specific gene expressions produce particular shapes, functions and
adaptations within a cell.
• Therefore a muscle cell will express muscle genes but not those genes which are
for nerve cells.
• In a multi cellular organism specialization is more efficient than the generalized
plan when competing for a specific resource. Consider the role of water transport
through the plant. In higher plants we have specialization to for a tubular system
called the xylem. This is more efficient way of water transport than simply been
passed by the mass movement of water from cell to cell. In the xylem water can
be moved very efficiently from underground to the canopy of the highest trees at
very little cost to the plant. If there is no specialized tissue for carrying water
then the plant would rely on the movement of water by mass flow of diffusion
which is very slow. The plant is therefore limited in size and therefore cannot
compete with larger species.
• The study of how cells become specialized is called embryology. This study area
in biology has been developing very fast in recent time. Some of the discoveries
about why some embryonic cells become nerves, muscles or blood cells has led
to new ideas about the evolution of life. The new discipline is called evolutionary
developmental biology or 'Evo-devo'. The following text is a great introduction to
what will become one of the most important aspects of biology for this century
Multicellular Organisms
• Emergent properties arise from the interaction of component parts: the whole is
greater than the sum of its parts.
• Emergence is the occurrence of unexpected characteristics or properties in a
complex system. These properties emerge from the interaction of the ‘parts’ of
the system. Remember that biology insists on a population thinking so that we
know the interacting ‘parts’ vary in themselves and therefore their ‘emerging’
properties can only be generalised. One of the classic examples cited is to think
of the emergent properties of water (fluidity) that cannot be predicted from
knowledge of the constituent gases hydrogen and oxygen. On a biological scale
consider the current debate about the nature of human consciousness or the
origin of life itself.
Topic 2.2: Prokaryotic Cells
9:50 AM
Functions of Structures found in
prokaryotes:
1. Slime Capsule
• Protects cells against chemicals
• Drying out (keep moist)
• Can make cells stick together or other
surfaces
2. Cell Wall
• Made of amino (protein) sugars
• Protection
• Structural support
• Bursting due to hypotonic environment
3. Cell surface membrane (Plasma Membrane)
• Let things in and out "gatekeeper"
4. Cytoplasm
• Contains organelles
• Jelly-like fluid
5. Ribosome
• Make proteins using mRNA (messenger RNA)
6. Mesosome
• Pocket of cell surface membrane
• Aids in cell respiration (create
energy)
• Movement of DNA
• Making of cell wall
7. Circular DNA
• Naked DNA (no histones)
• Controls cells
• Found in nucleoid region
8. Plasmid
• Extra genetic material
• Can be exchanged with other cells
9. Flagellum
• Whip like thread used to move cell
10.Photosynthetic membrane
• Created from cell surface membrane
• Allows for photosynthesis
Prokaryotic cells:
• Before nucleus
• Oldest cells on planet
• Don’t have nucleus
• 3 distinct groups – eubacteria, cynobacteria, archaebacteria.
• Can be fond in virtually every environment
• Can obtain energy from fermentation, photosynthesis, & nitrogen fixations.
• Divide by binary fission
Topic 2.3: Eukaryotic Cells
9:50 AM
Eukaryotic Cell:
1. Ribosome’s – small organelle made
of 2 subunit, function make
protein, can be free or attached to
ER.
2. RER – system of membranes, forms
sheets continuous w/ nuclear
envelope.
3. Lithesome – contains digestive
enzymes (stomach), gets digested
afterwards along w/ food. (suicide
cell)
4. Golgi apparatus – system of
membranes for intracellular
transport & forms vesicles for
exoctosis. (stores and packages
cellular secretions for export out of
cell)
5. Mitochondrion – “power house”,
produce energy using cellular
respiration
6. Nucleus – largest cell organelle, contains chromatin, controls activities.
7. Cell membrane - protection, gatekeeper
8. SER - making energy and repair proteins
9. Cytoplasm - storage facility, holds organelles and allows them to move
10.Golgi vesicle - discharge cell membrane contents into exterior of cell
11.Microvillus - transportation
12.Pinocytotic vesicle - vesicle holding material came in threw process of
pinocytosis. Keep material in cell and transport it
13.Granules - storage
14.Chromatin - contain genetic information
15.Nuclear pore - let things in and out of nucleus
16.Nuclear envelope - satiability
17.Centrioles - forms spindle fibers to separate chromosomes during cell division.
Difference between plant and animal cells:
2. Plant have cell wall
2. Plant have chloroplast
3. Plant have larger vacuole
4. Animal is circular
5. Plant stores reserve food as starch (a complex carbohydrate)
6. Animal cells store glycogen, a modified form of the simple sugar glucose.
7. Size of vacuole –
a. Plants – generally filled with water, is quiet large and permanent.
b. Animal – vacuoles are small and temporary.
*Plant relies on cell wall for support, but cell wall alone can’t stabilize cell,
plant cell rely on vacuole to support cell.
• When vacuole is full it pushes itself towards cell membrane and against cell
wall, until inward moment of water is equal to amount being pressed out by
cell wall. This is called turgur pressure & is important for cell support.
• Plant cell walls made of cellulose micro fibrils – these are polysaccharides
which form long, straight chain with few covalent bonds from one chain to the
next. They also contain calcium and pectin.
• Animal cells secrete glycoprotein's that form the extracellular matrix. This
functions in support, adhesion and movement.
Similarities & differences between prokaryotes & eukaryotes:

Prokaryotes Eukaryotes
Form Unicellular/ Multicellular unicellular
Genetic Circular DNA (nucleus) Chromatin nuclide region
Material Naked DNA Associated with proteins
In cytoplasm Enclosed in nuclear envelope
Protein Ribosome’s Ribosome’s
Synthesis 70S 80S
Cell wall Cellulose fibers Amino sugars
Respiration/ Yes (complex) Yes (simple)
photosynthe
sis
Flagellum Yes Yes
Living area Specialized environment everywhere
Topic 2.4: Membranes

10:15 AM
Membrane
functions:
1. Transport raw
material into cell
2. Transport
manufactured
products & wastes
out of cell
3. Prevent entry of unwanted matter into cell
4. Prevent escape of matter needed to perform life functions.
Types of Membrane Proteins:
1. Integral Protein:
• Generally transmembrane with hydrophobic. (Across) regions that completely
span the hydrophobic region of the membrane.
• The ends of the integral membrane are hydrophilic and are exposed to the (aq)
or either sides of the membrane.
2. Peripheral proteins:
• Not embedded in the lipid bi-layer
• Instead they are loosely bounded to SM, often attached to parts of integral
proteins, or they are attached to bi-layer.
• Hydrophobic! – they don’t interact w/ hydrophobic core of bi-layer
• Like H20
• Glycolipids:
• Attached to the phosphor-lipid bi-layer are lips with carbohydrate groups
attached
• Functions are providing energy and also serve as markers for cell-to-cell
recognition.
• Glycoprotein's:
• which are carbohydrates attached to proteins.
• Functions are infinite. But main is mucins which are secreted in the mucus of
the digestive and respiratory tracts. Function is to lubricate and protect.
Diffusion – movement of
molecules from high
concentration
to low concentration.
• Happens
naturally, no
energy needed
• 3 different
molecules that diffuse into cells are oxygen, water, and CO2
Osmosis – the diffusion of a solvent across a particularly permeable membrane
from region of low conc. To high conc.
• Low solute concentration means high water concentration
• High solute concentration means low water concentration.
Facilitated diffusion – is passive movement of a substance in or out the cell,
along a concentration gradient through a carrier protein molecule.
• Facilitate
•to help small molecules
•to help carry glucose
Functions of proteins:
1. Hormone binding sites: (binding site with a specific shape that fits the shape of
a chemical messenger, hormones – cause a chare in the protein which then
sends the message to the inside of the cell.
2. Immobilized proteins: (stationary proteins are built into the membrane; active
site exposed to substances in the adjacent solution.
3. Cell adhesion: (membrane proteins of adjacent cells may be hooked
together in various kinds of junctions) “Cytoskeleton.

4. Cell to cell communication/ recognition: (some gyro proteins serve as a
recognition tag that is specifically recognized by other cells.
5. Pump s for active transport
6. Channels for passive transport (proteins that span membrane)
Endocytosis
Cells take up substances by enclosing them in a membrane.
2 types:
• Pinocytosis – cell drinking (fluids)
• Phagocytosis – cell eating (solids)
Transport
• Since the structure of the cell membrane is essentially the same as nuclear
envelope, the ER and the Golgi apparatus, it is possible to exchange materials
between them.
• Golgi apparatus: prepares substances for exocytosis (membrane bound
secretory vesicles). This involves wrapping it in a bit of membrane and this
membrane joins to the cell surface membrane during exocytosis.
• The connection between ER & the Golgi apparatus is not continuous; however
there is an indirect connection
1. Membrane bound secretory vesicle, bud off from the ER & more Golgi.
2. Membranes fuse and the contents are delivered for modification with Golgi.
3. Contents are then packaged in a membrane from the Golgi and exocytosis takes
place.
Passive transport
• No cell energy needed
• Move w/ concentration gradient (high – low)
• Diffusion – molecules from high to low concentration
• Osmosis – solvent from high to low concentration
• Facilitated diffusion – carrier proteins help substances move in & out of cells.
(subst. Moves down concentration gradient (high to low) therefore passive)
Active Transport: Membrane Pump
• Carrier proteins are selective and only allow certain things in cell based on
shape, size, and charge.
• Can move substances in or out by protein motion in membrane.
Ex) glucose (too big, insoluble in liquids, no charge)
• It lets into substance threw protein
• Goes to where less concentration of substance is.
Other examples:
• Kidney cells pump glucose and AA out of urine and back into cells
• Root cells pump in nutrients from gut
• Gill cells in fish pump out sodium (their extracellular fluid is less salty than
seawater)
Topic 2.5: Cell

Division
Saturday, January 24,
2009
11:20 AM
Cell Division
Stages:
1. Interphase – growth and replication (G1, S, G2)
2. Mitosis – division of nucleus (P, M, A, T)
3. Cytokenisis – cell division (after T)
2. Interphase (growth stage)

G1 – cytoplasm active
• New organelles formed
• Intense biochemical activity of growth cell.
S – DNA synthesis/ DNA replication (chromosomes copied)
G2 – more growth in cell
• Cell prepared for cell division (mitosis)
• Final checkpoint
*chromosomes are not easily seen, thin thread like structures, becoming
dispersed as chromatin.
2. Mitosis:
Prophase
• chromosomes coil and super coil to become visible
• Centrioles move to opposite poles
• Spindle fibers from spindle apparatus
• Nucleolus becomes invisible
• Nuclear membrane disappears
Metaphase: middle
• Chromosomes move to middle of cell
• Spindle fibers attach to Centromere of each chromosome
Anaphase: away
• Centromeres are split and chromatids are pulled to opposite poles
Telophase:
• Phase begins when chromatids have reached opposite poles
• Spindle apparatus disappears
• Centrioles replicate
• Nuclear membrane appears
• Nucleolus reappears
• Chromosomes uncoil & become less visible (thin)
• Cytokenisis (division of cytoplasm)

• In animal cell, division is by in-tucking of the plasma membrane at the equator
of the spindle, “pinching” the cytoplasm in half.
• Plant cell Golgi apparatus forms vesicles of new cell wall materials which collect
line of the equator of the spindle, known as cell plate. Here vesicles come
together forming new plasma membrane & cell walls between 2 cells.
• End up with 2 daughter cells
• Identical to parent cells (came genetic info & equal chromosomes)
Formation of two genetically identical nuclei:
• Exact copy of each chromosome made in a phase of Interphase, 2 chromatids
formed.
• Chromatids remain attached by their Centromere during metaphase;
Centromeres split in anaphase chromatids move to opposite poles of cell – one
copy of each chromosomes moves to each pole of the spindle.
• Chromosomes at the poles from the new nuclei – two to a cell at this point
• 2 cells are then formed by division of the cytoplasm at the middle of each cell,
each w/ exact copy of original nucleus
Interphase Significance:
Most of cell cycle life is spent in Interphase; a very active period in the life of a
cell, where many biochemical reaction, DNA transpiration and replication take
place.
• Mitosis is a small portion of cell cycle
• Duration of cell cycle varies greatly between different cells
• Increase in the number of mitochondria and/or chloroplasts
Uncontrollable Cell Division
• Cancer cells divide repeatedly through mitosis, without control of regulation,
forming an irregular mass of cells, called a tumor.
• Sometimes tumor cells break away and are carried to other parts of the body,
where they form a secondary tumor
• Unchecked, cancerous cells ultimately take over the body at the expense of
surrounding, healthy cells, leading to malfunction and death
• Benign (not harmful) but some may become malignant (cancerous)
Causes:
• Cancer is caused by the damage of DNA of chromosomes
• “Mistakes” of different types build up in the DNA of the body cells
• The accumulation of mistakes with time can explain why the majority of cancer
causes occur in older people.
• Different types of mistakes can occur, which explains why cancer is not just one
single disease.
• Another cause to cancer is damage to the gene that codes for a protein known
as p53 which stops the copying of DNA
• P53 protein and the gene that codes for it are called the “guardians of the
genome”
• Damage to DNA has many potential causes, include;
o The effects of X-rays, gamma rays & other rays
o Certain chemicals (components of tar in tobacco smoke)
o Certain forms of cancer are inherited
Treatment
• Surgery (removal)
• Radiation therapy (break chromosomes of dividing cells, killing them)
• Chemotherapy (destroying all rapidly dividing cells)
Why is mitosis necessary?
• Tissue growth and repair
• Asexual reproduction – involves the production of identical cells by mitosis which
are identical to the parent (ex. It’s a means of rapid & significant increase in #’s
of individual; bacteria & weeds)
Topic 3: The Chemistry of Life
11:43 AM
Topic 3.1: Chemical Elements of Water

11:43 AM
• Carbon is not only important elements required by cells. Oxygen, Nitrogen, and
Hydrogen are also very important elements.
• Other important elements needed by living organisms are sulphur, calcium,
phosphorus, iron, and sodium.
Thermal Properties of Water
• Def: Is the measure of the heat energy needed to increase the temperature of an
object y 1 degree Celsius.
• Water has a relatively high SHC; it needs a lot of energy to heat up. (more
energy to change temperature, it becomes hot slower)
• Can absorb and keep for a long time.
Element In Plants In Animals In prokaryotes
Sulphur - In some amino acids - In some amino acids and - In some amino acids and
and proteins. protein. proteins.
- In some vitamins. - In some vitamin. - In some vitamins.
Calcium - Cell wall formation - Constituent of bones - Co-factor for certain enzymes.
between dividing plant - Reacts in muscle fibre - Contributes to heat resistance of
cells. contraction, blood clotting, bacterial endospores.
- Co-factor for certain and synapses.
enzymes - Co-factor for certain
enzymes.
Phosphorus - Synthesis of nucleotides - Synthesis of nucleotides - Synthesis of nucleotides

- ATP - ATP - ATP
- Constituent of bones
Iron - Constituent of electron - Constituent of electron - Constituent of electron transport

transport molecules (e.g. transport molecules (e.g. molecules
cytochromes) cytochromes) - Chlorophyll synthesis in
- Chlorophyll synthesis - part of haemoglobin photosynthetic prokaryotes
Sodium - involved with Potassium - involved with Potassium in - involved with Potassium in
in membrane function membrane function and nerve membrane function
impulse transport
• Because hydrogen bonds must be broken to separate molecules and make
move further apart.
• Solvent Properties of Water
• Is a universal solvent.
• Substance (polar) can dissolve in water (hydrophilic) if its attractive forces are
equal to or stronger than the attractive forces of water.
• Substances cannot dissolve in water (hydrophobic) if its properties do not allow it
to overcome water’s strong attractive forces.
• Cohesive and Adhesion Properties of Water
• Cohesion refers to the ability of water to stick to itself.
• Due to polarity and subsequent attractions of water molecules to one
another.
• Results in high surface tension
• Adhesion refers to the ability of water to stick to other things.
Properties of Water
• Remains liquid over a wide temperature range, including temps where most
small molecules are gases.
• Dissolves most substances involved in living processes such as oxygen, carbon
dioxide, glucose, amino acids, and sodium chloride.
• Changes temperature gradually when heated or cooled
• It protects cells from rapid temperature changes and provides a stable
environment for cell reactions
• Is one of the only pure substances that expand when it becomes solid, which
makes it float when frozen.
• Transparent. Plants need for photosynthesis.
• Molecules with uneven charge distribution are polar (have oppositely charged
poles)
• (Even distribution of charges makes it nonpolar)
• Charge of water molecule is 0 (neutral).
• Water is a coolant
• Makes up sweat. Takes a lot of energy to turn into gas. It takes heat energy
from body cooling body.
Topic 3.2: Carbohydrates, Lipids, and Proteins

12:02 PM
Animals Plants
Monosacchari Glucose: Glucose:
de - Used as a respiratory substraight - First product of photosynthesis
for cellular respiration or converted Fructose:
to glycogen - produced in cellular respiration as
Galactose: an intermediate of glucose
- Used in production of lactose breakdown.
(milk, sugar) - used in production of sucrose
Disaccharide Lactose: Sucrose:
- Produced in mammary glands and - produced in green leaves, from
secreted into milk as an imp. glucose and fructose.
Component in the diet of very - transported in plant in solution, in
young mammals. the vascular bundles
Maltose:
- Breakdown product in the
hydrolysis of starch.
Polysaccharid Glycogen: Cellulose:
e - Storage carbohydrate formed from - manufactured in cells and laid
glucose in the liver and other cells. down externally in bundles of fibres
(but not brain cells) When glucose as the main component of the cell
not immediately required for cellularwalls.
respiration. Starch:
- storage carbohydrate
• Def: compounds containing carbon that are found in organisms.

• Exceptions (non-organic forms of carbon):
• CO2 (carbon dioxide)
• Hydrogen carbonates (product when CO2 is dissolved in H20)
• Mineral Calcium Carbonate (CaCO3)
Types of Organic Compounds and Structural Features:
1. Carbohydrates (contain C, H, O)
• Largest group of organic compounds and include sugar, starch, glycogen,
and cellulose.
• Contain three elements: carbon, hydrogen, and oxygen with hydrogen and
oxygen always present in 2:1 ratio.
• Carbohydrates can be simplified by the following general formula: Cx(H2O)y
• These are thee common types of carbohydrates:
• Monosaccharide: simple sugars
• Ex) glucose, fructose (6-carbon sugar), ribose (5-carbon sugar)
• Disaccharide: 2 simple sugars together
• Ex) sucrose, lactose, maltose
• Polysaccharide: many simple sugars condensed
• Ex) starch, glycogen, cellulose
2. Lipids (fats and oils) (contain C, H, O)
• Contain carbon, hydrogen, and oxygen just like carbohydrates; however
the amount of oxygen in lipids is much less.
• Undergo condensation or hydrolysis reactions
• Compounds are called triglycerides
• Formed when a water molecule is removed (condensation reaction)
between fatty acids and an alcohol called glycerol.
• The bond formed is called an ester linkage.
• In cells, enzymes catalyze the formation of triglycerides and also in the
breakdown of glycerides by hydrolysis (addition of water)
3. Proteins (amino acids)
• Building block of peptides
• Contain nitrogen and usually sulphur, as well as carbon, hydrogen, and
oxygen
• Made up of a basic amino group (-NH2) and an acidic carboxyl group
(-COOH), attached to the same carbon atom.
• These are the reactive or functional groups of the molecule; they are
the groups that participate in the condensation reactions that form
peptide linkages.
4. Nucleic Acids (DNA and RNA)
Lipid Functions:
1. Subcutaneous fat as a buoyancy aid (and thermal insulation)
• Stored in animal tissues as adipose tissue, typically under the skin and is know
as subcutaneous fat.
• In aquatic mammals, subcutaneous fat is known as blubber; gives buoyancy to
the mammal b/c it is less dense than muscle or bone.
• Fat reserves like these usually have limited blood supply and if this happens the
heat of the body is not evenly distributed to the fat below the skin so the fat
layers serve as an insulation layer.
2. Water-proofing of hair and feathers

• The subcutaneous glands found in the skin secrete oily substances that act as a
water repellent – prevents fur and feathers from becoming saturated with water
(ex. Preen gland for the feather of birds)
• Electrical insulation
• Myelin lipid in the membrane of Schwann cells (neurons), forms the sheath
(protective covering) along nerve cells. Their function is to electrically isolate
the cell plasma membrane and to aid in the conduction of the nerve impulse
there.
Comparison of Lipids and Carbohydrates as energy sources:
Lipids Role Carbohydrates
More energy/gram Energy store Less energy/gram
Much metabolic water Metabolic water Less metabolic water is produced in
is produced in source oxidization
oxidization.
Insoluble so osmotic Solubility Sugars are highly soluble in H2 causing
water uptake is not osmotic water uptake.
caused.
Not quickly ‘digested’ Ease of More easily hydrolysed energy transferred
breakdown quickly.
Topic 3.3: DNA

Structure
12:24 PM
DNA Structure:
• Three parts; Pentose
Sugar, Phosphoric
Acid, Nitrogenous
Base
o Pentose Sugar:
Ribose or
Deoxribose
o Nitrogenous
Base: Guanine
(G) , Cytosine
(C) , Adenosine
(A) , Thymine (T)
o Phosphoric Acid
• Condensation reaction takes place to form a nucleotide
o Binding of OH group on phosphoric acid and OH group on pentose
sugar releases a water molecule
o Binding of second OH group on pentose sugar and Hydrogen
molecule on Nitrogenous base releases water molecule.
Formation of DNA (Double Helix):

• Nucleotides condense together, one nucleotide at a time, to form a huge
molecule called a nucleic acid or polynucleotide.
• Contain alternating sugar and phosphate molecules forming the
'backbone'.
• DNA molecule consists of two polynucleotide strands, paired together,
and held by hydrogen bonds.
• Links are relative to which two nitrogen bases are together
• Creation of two groups:
• Pyrimidines - cytosine and thymine
• Purines - adenine and guanine
• Opposite grouped nitrogenous bases are bonded together (a
pyrimidine is bonded to a purine)
• Two groups (Called complementary base pairing):
• Adenosine and Thymine
• 2 hydrogen bonds
• Guanine and Cytosine
• 3 hydrogen bonds
Topic
3.4: DNA
Replication
12:52 PM
DNA Replication:
1. DNA double helix unwinds:
• Hydrogen bonds are broken
o Enzyme helicase aids in breaking bonds which allows strands to
separate.
o Single strand binding proteins (SSB's) keep strand from joining back
together.
o Replication bubble formed.
2. Replication of Leading Strand (5" - 3")
• RNA primase synthesis the first nucleotides of the new strand in 3" to 5"
direction and RNA primer builds on RNA primase in 5" to 3". (adds a short
RNA primer)
• DNA polymerase III then turns RNA primer into DNA
• Replication of Lagging Strand (3" - 5")
• RNA primase builds section in 3" to 5" direction till it hits the RNA primer.
• RNA primase builds another and process continues creating
discontinuous sections called 'okasaki fragments'
• DNA polymerase III works in 5" to 3" direction adding succeeding free
nucleotides by complementary base pairing.
• DNA polymerase I changes RNA into DNA
• Ligase joins segments of DNA together
Semi-Conservative vs. Conservative:
• At end of DNA replication, each new pair of double strands winds up into a
double helix. One strand of each new double helix came from the original
chromosome and one is a newly synthesized strand.
• Arrangement known as semi-conservative replication because half
the original molecule is kept the same.
• If an entirely new double helix were formed alongside the original, then
one DNA double helix molecule would be conserved without unzipping, in
the next generation. (conservative replication.)
Significance of Base Pairing:
• Chargaff discovered significance of patterns in 1935.
o The numbers of purine bases (adenine and guanine) always equaled
the number of pyrimidine bases (thymine and cytosine)
o The number of adenine bases equaled the number of thymine bases,
and the number of guanine bases equaled the number of cytosine
bases.
• Means organic bases found in DNA are of two distinct types with
contrasting shapes:
o Cytosine and thymine are pyrimidines or singe-ring bases (smaller
structure)
o Adenine and guanine are purines or double-ring bases (bigger
structures)
• Only a purine will fit with a pyrimidine between the sugar-phosphate
backbones, when base pairing occurs. (one small structure with one big
structure)
• Because of the process of base pairing, the sequence of bases in one
strand exactly determines the sequence of bases in the other strand. This
makes the two strands complimentary.
Topic 3.5: Transcription and Translation
1:13 PM
DNA Transcription (Formation of mRNA):
Initiation: Preparation
• A promoter (15-300 base pairs long) serves a site where transcription takes
place, A TATA box helps in recognition.
• Transcription factors bind to box and help RNA Polymerase recognize and bind
to promoter.
• RNA polymerase II binds to promoter. It with the help of transcription factors
unwind this section of DNA.
2. Elongation: Creation of PremRNA
• RNA Polymerase II add base pairs. It uses Uracil instead of thymine. (sense
strand)
• Newly synthesized RNA strand separates from template. (antisense strand)
• Termination: Pre-mRNA released and DNA re-winds
• RNA polymerase II encounters a terminator (sequence of nucleotides that
signals end of transcription)
• Pre-mRNA strand released, DNA re-forms.
RNA Processing (Pre-mRNA to mRNA and release through nucleus):
• Mentholated Guanosine attached to 5" end
• Poly (A) Polymerase adds 100-200 adenine nucleotides to 3" end
• Introns are cut out by splicasomes and exons come together
o Introns - waste material, exons - wanted material
• mRNA released through nucleus
Translation (mRNA leaving Nucleus):
• Initiation: Preparation
• Small ribosomal sub unit binds to mRNA transcript
o Supports framework and is site for enzymes
• tRNA molecule attached to start codon "AUG"
• Larger ribosomal subunit binds to mRNA transcript, has "EPA" site
• Elongation: Forming polypeptide chain
• 3 nucleotides form a codon. Incoming tRNA contain a anti-codon
• Hydrogen bonds hold 2 together
• Peptide bond form between 2 amino acids held at the ribosome
• Used tRNA released from E (Exit) site, new tRNA molecule moves to P site
• Repeats forming long polypeptide chain
o Peptidyl transferase bonds formed by condensation reaction between
amino acids in chain.
• Termination: Releasing polypeptide chain and dismemberment of unit
• Stop codon reached
• Release factor binds and releases water through hydrolysis reaction
• Polypeptide chain released.
Structure of DNA vs. RNA:
DNA Feature RNA
Very long strands, several Length Relatively short strands, 100 to several
million nucleotides thousand nucleotides
Deoxyribose Sugar Ribose
C, G, A, and T Bases C, G, A, and U (not T)
Consists of two Forms Consists of single strands and in three
polynucleotide strands of functional units. Messenger RNA (mRNA)
complementary base pairs. Transfer RNA (tRNA) Ribosomal RNA
(C with G and A with T) held
by hydrogen bonds in the
form of a double helix
Nucleus Locatio Mostly Ribosomes in cytoplasm, some in
n nucleus
Theories:
• In 1940, Beadle and Tatum worked with a fungus which turned bread moldy. The
organism was cultured on laboratory agar plates containing minimal medium of
sugar, mineral ions, vitamin biotin, and a source of nitrogen. The fungus
naturally manufactured other organic compounds required, including all amino
acids.
• They exposed some of their cultures to x-rays that caused the formation of
mutants. A mutant organism has altered genetic material.
• Further investigation showed that the mutants most needed only one particular
amino acid added to minimal medium in order to grow and reproduce. Resulting
in the mutants to lose the ability to synthesize one particular enzyme.
• Results and discovery:
o A range of mutants were produced, each deficient in one of
o the enzymes needed to produce arginine.

o Arginine production in Neurospora with glutamic acid, involved two
intermediates and three enzymes.
o In different mutants, enzymes 1 2 or 3 were no longer produced.
• Conclusion: in an organism each gene coded for a particular enzyme. (one gene-
one enzyme hypothesis)
• As protein chemistry developed several proteins were found to consist of two or
more polypeptide chains. Also, not all proteins are enzymes so the hypothesis
was modified to one gene - one polypeptide.
• Another development has been the appreciation that in different parts of an
organism (or at different times) selected genes are switched on or off. The
existence of regulator genes which activate or suppress the action of
neighboring genes has been demonstrated in, prokaryotes.
• Ex. Human hemoglobin which consists of alpha chains and beta chains.
• Conclusion: genes have a range of roles, sometimes activated, but possibly
inactive at different times.
Genetic code in terms of Codons composed of triplets of bases:
• The sequence of bases in nucleic acid dictates the order in which specific amino
acids are to be assembled and combined to make proteins.
o This code is a three-letter or triplet code, meaning that each sequence of
three bases stands for one of the 20 amino acids, and is called a codon.
• Since there are 4 different bases (C, G, A, T) there are 64 possible different
triplet combinations.
o The genetic code has many more codons than there are amino acids - since
only 20 amino acids required coding.
• This type of code is described as degenerate since most amino acids have two or
three similar codons that code for them. A degenerate code has more than one
base triplet to code for one amino acid.
• Some codons stand for stop, signaling the end of a peptide or protein chain, or
signal start.
Topic 3.6: Enzymes

2:22 PM
Enzymes Specificity:
• They catalyze only one type of reaction or only a very small group of highly
similar reactions.
• This means that enzymes recognise a very small group of substrate molecules or
even only a single type of molecule. This is because the active site where the
substrate molecule binds has a precise shape and distinctive chemical
properties.
Lock and key hypothesis:
• Enzyme is the lock and the substrate is the key. The key fits into the lock, and
the point of link up is the active site on the enzyme.
• Enzymes control metabolism
• There is a huge array of chemical reaction that goes on in cells and organisms –
collectively the chemical reactions of life are called metabolism.
• Since the reactions of metabolism can only occur in the presence of a specific
enzyme, we know that if an enzyme is not present then the reaction it catalyses
cannot occur.
• Enzyme operation
An Enzyme is:
• Biological catalysts
• High temperatures, high pressures, extremes of pH, and maintaining high
concentrations of the reaction molecules create enzymes.
• Presence of enzymes enables the reactions to occur at incredible speeds, in an
orderly manner, yielding products that the organism requires.
• In a reaction catalyzed by an enzyme, the starting substance is called the
substrate, and what it is converted to is the product.
• An enzyme works by binding to the substrate molecule at a specially formed
pocket in the enzyme. The binding point is called active site.
An enzyme and substrate form a complex, the substrate is raised to a transition
state and instantly breaks down to products which are released, together with
unchanged enzyme. Process repeats.
Effects of External Factors on Enzyme Activity:
1. Temperature
• As temperature is increased, molecules have increased
active energy, and reactions between them go faster.
The molecules are moving more rapidly and more likely
to collide and react.
• Ever 10 C rise rate of reaction doubles
• Temperature Coefficient
• The rate of denaturation increases at higher
temperature. As the temperature rises the amount of
active enzyme progressively decreases.
• Gives an optimum temperature for an enzyme.
2. pH
• Each enzyme has a range of pH where it functions
efficiently. (around 7.0)
• The structure of a protein (and shape of active site)
is maintained by various bonds within the 3D
structure of a protein.
• A change in pH from optimal values alters the
bonding patterns, changing shape of molecule.
• Active site is quickly rendered inactive.
• Reversible
• Concentration
•
At lower concentrations the rate increases in direct
proportion to the substrate concentration
• At higher concentrations the rate of reaction becomes
constant and shows no increase.
• Works by forming a short-lived enzyme-substrate
complex. At low concentration of substrate, all
molecules can find an active site without delay.
Effectively, there is an excess of enzyme present.
Here the rate of reaction is set by how much
substrate is present – as more is made available the rate of reaction
increases.
• At higher substrate concentrations there comes a point when there is more
substrate than enzyme. No increase because adding more substrate
merely increases the # of molecules awaiting contact with an enzyme
molecule.
Denaturation
• Reactions catalyzed by enzymes are extremely fast. However the rate of an
enzyme catalyzed reaction is sensitive to environment conditions. 3 Factors
affect enzymes and therefore alter the rate of reaction. In extreme cases it
causes the protein to become denatured.
• Denaturation is a structural change in a protein that alters its 3-D shape and
causes the loss of its biological properties.
• This occurs when the bonds of the globular protein formed between
two amino acid residues break.
• Different bonds are formed
zyme use in production of Lactose free milk:

• Lactose is a disaccharide (glucose = Galactose)
milk sugar
• Around 90% of all humans show some kind of
lactose intolerance.
• People who are lactose intolerant can drink milk if
it is lactose free.
• Lactase is an enzyme extracted form a yeast that
can digest the milk sugar to glucose and
galactose.
Enzyme Immobolisation:
It is possible to make the process more efficient
by immobilising the lactose on a recoverable
surface such as alginate.
• First the Lactase is immobilised in alginate beads.

• Next the beads are placed in a container over which milk can be passed.
• The milk is collected and re-circulated (pump) to convert any remaining lactose
to glucose and galactose.
• The circulation is maintained until all lactose has been converted.
• This model of an industrial process allow the lactase to be recovered and re-used
(cheaper).
• Efficient conversion of lactose to glucose and galactose.
• reduced purification of milk since enzyme is retained and a high % lactose
conversion is achieved.
• All these factors reduce cost particularly on the downstream processing and
purification.
Topic 3.7: Cell Respiration

The sites of Cellular Respiration:
• The enzymes in cellular respiration occur partly in the cytoplasm )the enzymes
of glycolysis) and partly in the mitochondria (enzymes of pyruvate oxidation and
most ATP formation). After formation, ATP passes to all parts of the cells. Both
ADP and ATP pass through the mitochondrial membranes by facilitated diffusion.
Anaerobic Cellular Respiration - Fermentation:

• In the absence of oxygen, many organisms (and sometimes tissues in organisms,
when these have becomes deprived of oxygen) will continue to respire pyruvate
by different pathways, know as fermentation or anaerobic respiration, at least for
a short time.
• Many species of yeast (Saccaromyces) respire anaerobically, even in the
presence of oxygen. The products are ethanol and carbon dioxide. Ex. Alcohol
fermentation of yeast by humans in wine and beer production.
• In summary:
Glucose ------> Ethanol + Carbon Dioxide + ENERGY
• Vertebrate muscle tissue can respire anaerobically, too, but in this case it
involves the formation of lactic acid rather than ethanol. Once again, under
conditions in the cytoplasm, lactic acid is weakly ionized, and therefore exists as
the lactate ion.
• Lactic acid fermentation occurs in muscle fibers, but only when the demand for
energy for contractions is very great, and cannot be fully met by aerobic
respiration. In lactic acid fermentation the sole waste product is lactate
• In summary:
Glucose -------> lactate + ENERGY
• Must be noticed that both processes have no products of ATP

Sunday, March 22, 2009
5:30 PM
Is…When energy is transferred in cells by the breakdown of nutrients, principally
of carbohydrates like glucose. Also the process by which energy is made
available from nutrients in cells.
• Also known as the controlled release of energy from organic compounds, in cells
to form ATP, from organic compound cells.
Steps of Cellular Respiration:

• In the first steps of cell respiration, the glucose molecule (a 6-carbon sugar) is
split into two 3-carbon molecules. Then the products are converted to an organic
acid called pyruvic acid. Under conditions in the cytoplasm, organic acids are
weakly ionized, and therefore pyruvic acid exists as the pyruvate ion.
• Obviously, two molecules of pyruvate are formed from each molecule of glucose.
In addition, there is a small amount of ATP formed, using a little of the energy
that had been locked up in the glucose molecule. No molecular oxygen is
required for these first steps of cellular respiration.
• Because glucose has been split into smaller molecules, these steps are know as
glycolysis. The enzymes that catalyze these reactions are found in the cell
cytoplasm generally, but not inside an organelle. Throughout cellular respiration,
a series of oxidation-reduction reactions occur.
• In summary: (enzymes in the cytoplasm)
Glucose ------------------------------------------> pyruvate + small amount of
ATP
Aerobic Cellular Respiration:

• While no oxygen is required for the formation of pyruvate by cells in the early
steps of cellular respiration, most animals and plants and very many
microorganisms do require oxygen for cell respiration, in total. (they respire
aerobically)
• In Aerobic cellular respiration, sugar is completely oxidized to carbon dioxide and
water and much energy is made available.
• Equation:
(Glucose) + (Oxygen)  (Carbon Dioxide) + (Water) + (ENERGY)
C6H12O6 + 6O2  6CO2 + 6H2O
+ ENERGY
• The equation simply gives the inputs and outputs however it does not mention
pyruvate:
• If oxygen is available to cells and tissues, the pyruvate is completely oxidised to
carbon dioxide, water and a large quantity of ATP. Before these reaction take
place, the pyruvate first passes into mitochondria by facilitated diffusion. This is
because it is only in mitochondria that the required enzymes are found
• In summary: (enzymes in mitochondria)
Pyruvate -----------------------------------> Carbon dioxide + water + large
amounts of ATP
• In this phase of cellular respiration, the pyruvate is oxidised by:

o Removal of hydrogen atoms by hydrogen acceptors (oxidising agents)
o Addition of oxygen to the carbon atoms to form carbon dioxide
Topic 3.8: Photosynthesis
5:30 PM
• Plants use the energy of sunlight to produce sugars from the inorganic raw
materials carbon dioxide and water, by a process called photosynthesis.
The waste product is oxygen.
• Photosynthesis occurs in plant cells that contain the organelles called
chloroplasts. Here energy of light is trapped by the green pigment
chlorophyll, and becomes the chemical energy in molecules such as glucose
and in ATP.
• In summary: (chlorophyll in chloroplasts)
Carbon Dioxide + Water + Light Energy ------------> Organic Compounds
(sugars) + Oxygen
(raw materials) (Energy Source) (Products)
(Waste Products)
6CO2 + 6H2O + Light -------------> C6H12O6
+ 6O2
(Chlorophyll in Chloroplasts)
• Light energy ----> Chemical Energy
What is light?
• Light is a form of electromagnetic radiation produced by the sun. Visible light
forms only a part of the total magnetic radiation reaching the Earth. When the
visible 'white' light is projected through a prism, we see a continuous spectrum
of light - a rainbow of colors, from red to violet. Different colors have different
wavelengths.
• The significance of the spectrum of light in photosynthesis is that not all the
colors of the spectrum present in white light are absorbed equally by
chlorophyll. Some are even transmitted (or reflected), rather than being
absorbed.
Investigating Chlorophyll:
• Chlorophyll is the main photosynthetic pigment. This is where light energy is
trapped and turned into chemical energy.
• Some plant pigments are soluble in water, but chlorophyll is not. Chlorophyll
cannot be extracted from the leaves with water, but can be extracted by
dissolving in an organic solvent like propanone (acetone).
• With chlorophyll in solution, the colors of light it absorbs can be investigated. It
is known that white light consists of a roughly equal mixture of violet, blue,
green, yellow, orange, and red light. When these different colors are projected
through the chlorophyll solution in turn, the greatest absorption occurs in the
blue and red parts or the spectrum, whereas green light is transmitted or
reflected.
• The chemical structure of chlorophyll molecules allows absorption of the energy
of blue and red light.
What happens in Photosynthesis:

• Photosynthesis is a set of many reactions occurring in chloroplasts in the light.
However, these can be divided into two main groups:
1. Light energy is used to split water (photolysis)
• This releases the waste product of photosynthesis, oxygen, and allows the
hydrogen atoms released to be retained on hydrogen acceptor molecules. At
the same time, ATP is generated from ADP and phosphate, also using energy
from light.
2. Sugars are built up from carbon dioxide
• We say that carbon dioxide is fixed to make organic molecules. To do this, both
energy of ATP and hydrogen atoms from the reduced hydrogen acceptor
molecules are required.
Measuring the Rate of Photosynthesis:

• The rate can be estimated indirectly, by measuring the increase in biomass in
samples of illuminated leaves, since most of the sugar produced in the light is
immediately stored as starch in the cells.
• The rate can also be estimated using an oxygen sensor probe connected to a
data-logging device or, using a micro burette, measured as the volumes of
oxygen given out in the light by an aquatic plant. The experiment requires a
freshly cut shoot of a pondweed which, when inverted, produces a vigorous
stream of gas bubbles from the base. The bubbles tell us the pondweed is
actively photosynthesizing. The pondweed is placed in a very dilute solution of
sodium hydrogen carbonate, which supplies the carbon dioxide (as -HCO3 ions)
required by the plant for photosynthesis. The quantity of gas evolved in a given
time, say in 30 minutes, is measured by drawing the gas bubble that collects
into the capillary tube, and measuring its length. The length is then converted
into volume.
• Alternatively, the uptake of carbon dioxide in the light can be measured. Using
an aquatic plant, the dissolved carbon dioxide absorbed from the water will
cause the pH to rise and this may be monitored with a pH meter connected to a
data-logging monitor.
• Using this apparatus the effects of external conditions such as light intensity,
carbon dioxide concentration, and temperature on the rate of photosynthesis
have been investigated.
External factors and the rate of photosynthesis:

• Concentration of carbon dioxide, light intensity and temperature effect the rate
of photosynthesis.
• The concentration of carbon dioxide:
o When concentration is at zero there is no photosynthesis
o As concentration is steadily increased, the rate of photosynthesis, and the
rise of that rise is positively correlated with the increasing carbon dioxide
concentration.
o As much higher concentrations of carbon dioxide, the rate of
photosynthesis reaches a plateau - now there is no increase in rate with
rising carbon dioxide concentration.
• The effect of light intensity:
o When light intensity is low, the rate of photosynthesis is directly
proportional to light intensity.
o At much higher light intensities, there is no increase in rate with rising light
intensity - this rate had reached a plateau, too.
• Temperature:
o Rate of photosynthesis increases with an increase in kinetic energy
o Maximum rate of photosynthesis is at the optimal temperature
o Decrease rate of photosynthesis as the enzymes becomes less stable.
Topic 4: Genetics
5:37 PM
Topic 4.1: Chromosomes, genes, alleles, and
mutations
5:38 PM
Basics of Chromosomes
When the cell divides, the chromosomes are thick, compact structures, coiled
tightly. At all other times, the chromosomes are long, thin, uncoiled threads. The
granular appearance at this point means the chromosomes are called chromatin.
Review of DNA
• double helix, paired strands
• DNA runs the full length of the chromosome, supported by protein (histones)
• 50% built of protein
• some proteins are enzymes involved in copying and repair
• bulk of chromosome protein has a support and packaging role for DNA
Genetics – the study of inheritance and of variation of inherited characteristics
that chromosomes control.
Chromosomes hold the genetic blueprint, DNA (coded instructions) for the
organization and activities of cells and for the whole organism in the form of
genes.
Gene –
• a heritable factor that controls a specific characteristic.
Allele –
• one specific form of a gene, differing form other alleles by one or a few bases
only and occupying the same gene locus as other alleles of that gene.
Genome –
• the whole genetic information of the organism.
An example of substitution is Sickle Cell Anemia.

Haemoglobin is made up of 4 polypeptide chains, 2 alpha and 2 beta. Normal red
blood cells are flexible and donut shaped (binoconcave). This allows them to carry
four O2 molecules per RBC. They are said to have Hb, which is regular.
Sickle Cell is a base substitution in the gene coding for the 6th amino acid in the
beta chain. This causes glutamic acid to be inserted instead of valine, resulting in
abnormally shaped haemoglobin molecules. They are said to have HbS, or sickle cell
haemoglobin.
The shape and rigidity of the sickle shape cause the RBC to bunch together,
blocking the capillaries and the cells cannot carry as much oxygen. This can cause
death due to lack of oxygen to major organs. (See above)
But… the gene has survived for years. Why?
The sickle cell trait is co-dominant with the gene coding for regular haemoglobin
(meaning that it is not found more often in individuals, than regular haemoglobin).
This means that individuals will be heterozygous (meaning the person will have both
types of RBC), with more being normal. They will be mildly anemic.
A person who is homozygous (only contains the sickle cell trait), will die of anemia.
An advantage of having sickle cell anemia is the sickle shape of the RBC cannot be
infected by the protest, Plasmodium, that causes malaria. In areas where malaria is
a problem, have HbS is an advantage. Natural selection has ensured that the sickle
cell trait is more common among people living in malaria infected areas, such as
West Africa.
Gene Mutations
The sequence of base pairs for the production of amino acids is changed.
Two types of Gene Mutations:
1. Point Mutations – where only one base pair is affected
2. Base Substitution Mutations or Insertion / Deletion – where a base is inserted or
deleted from a gene
If only one base is changed, it may not have any effect. The reason is that
amino acids are coded for three bases. If the change only takes place in the
third (or second base), the AA may not change or change may not affect the
structure, since the genetic code is degenerate.
Also, with point mutations, the part of the DNA involved might not be used by
that cell, or may involve part of the sense strand that is not transcribed.
With insertion and deletion, the codon is definitely altered. An extra base is
deleted from a gene or is added. This causes the AA to change from this point
on, which causes major changes in the protein.
Topic 4.2: Meiosis

Wednesday, March 25, 2009
10:44 PM
The purpose of meiosis is to produce gametes. It only occurs in diploid cells and
reduces the number of chromosomes per cell. The gametes contain half the number
of chromosomes than the original cell. This means it goes from diploid to haploid.
When the two gametes meet in the process of fertilization, the original number of
chromosomes is restored.
Homologous chromosomes – also called a homologous pair. They are two

chromosomes that look the same. They are the same size and show the same
banding pattern in a karyotype. They carry the same genes but not necessary the
same alleles. For example both chromosomes will carry the gene for eye colour, but
one may have the allele for brown and the other may have the allele for blue.
The only way to get genes that are not identical is to have a mix of genetic
material. This is done by crossing over, or synapsis.
Cross Over
• During Prophase I, the chromatids of the bivalent are close together. During the
coiling and shortening process, breakages of the chromatids occur frequently.
Breakages are common in non-sister chromatids.
Process of Cross Over

• Broken ends rejoin more or less immediately, but where it rejoins are between
non-sister chromatids, swapping pieces of the chromatids. This is why it is
called crossing over.
• The point where the pieces join is called a chiasma (plural – chiasmata).
• Every pair of homologous chromosomes forms at least one chiasma, and
sometimes having two or more in the same bivalent is very common.
• The new combinations are called recombinants.
• Recombination is the re-assortment of genes or characters into different
combinations from those of the parents.
• As a result, meiosis results in an infinite number of variations in gametes during
Prophase I and randon orientation in Metaphase I.
• The number of different types of gametes produced by random orientation is
represented by 2n, where n is the haploid number in a gamete. Throw in the
affect of crossing over, and you have a lot of genetic variety.
• For example, the human has 23 chromosomes. Therefore, the possible
combinations of genetic material, would be 223. This works out to
• A pea plant has 4 genes, so the possible combinations would be
• In order for a gamete to have exactly the same genetic make-up as the parents
would occur every 246 or 7 x 10 13.
• When the chromosomes separate during anaphase, this is called disjunction
(junction – joined). If the chromosomes do not separate properly, there can be a
problem with the amounts of chromosomes in the gametes, and as a result,
more or less than the required 46 chromosomes in a human. This is called non-
disjunction.
• During each of the cell divisions, the chromosomes are pulled to opposite ends
of the cells. Sometimes the chromosomes do not separate properly, leading to a
condition known as aneuploidy.
Aneuploidy is either an extra or missing chromosome. This only happens in 9
cases, with Down’s Syndrome being the most common. In some cases, total non-
disjunction takes place, which is called polyploidy.
Stages of Meiosis
Meiosis consists of two stages – Meiosis I and Meiosis II
1. Meiosis I
a. Interphase
• the DNA replicates
b. Prophase I
• Chromosomes condense
• Nucleolus becomes visible and the spindle forms
• Synapsis – when the homologous chromosomes are side by side
( now called a bivalent) and they cross over at a point called a
chiasmata)
• Nuclear membrane disappears
• Metaphase I
• Homologous pairs (tetrads or bivalents) move to the middle of the
cell
• Anaphase I
• Homologous pairs split up
• One chromosome goes to each pole
• Telophase I
• Chromosomes arrive at poles
• Spindle disappears
• Cell / Egg rests.
2. Meiosis II
• Prophase II
• New spindle forms at right angles to the previous spindle
• Metaphase II
• Chromosomes move to the equator
• Anaphase II
• Chromosomes separate, chromatids move to opposite poles
• Telophase II
• Chromatids arrive at poles
• Spindle disappears, nuclear membrane reappears
• Nucleolus reappears, chromosomes become chromatin
Summary – It takes one cell that is diploid and creates 4 haploid cells –
this is a reduction division.
Karyotyping
Karyotyping is a “map” of chromosomes that have been paired up according to
their structures.
The chromosomes can be dyed to show banding, and the arranging can be done
easier.
Why is this done?

Often used to determine if there are any genetic abnormalities, like missing or
extra chromosomes, or deformity, due to a non-disjunction (homologous pairs do
not separate properly during mitosis or meiosis).
Examples are Down’s syndrome, Turner (X), and Klinefelter (XXY)
Karyotyping is done following these steps: (Diagram 5)
• extract a cell sample from the placenta (amniocentesis)
• add colchine to stop cell division
• add water to burst cell
• apply stain to chromosomes
• create a photographic image of scattered chromosomes
• cut out and pair the chromosomes by their length and position of the centromere
• observe deviation from a “normal” chromosome set.
Topic 4.3: Theoretical Genetics
11:00 PM
Co-dominance
• Co-dominance is when both alleles are expressed simultaneously rather than one
being dominant and the other being recessive in the phenotype.
• For co-dominance, the gene is the main letter and the allele is the superscript.
Both are expressed in capital letters.
• Then we go through the test cross just like a monohybrid cross before.
• The pink colouration of the alleles occurs because both alleles are being
expressed in the heterozygote and two pigment systems are present, rather than
just the dominant allele only. When third type of phenotype appears, and blends
the phenotype to produce a heterozygous offspring it is called incomplete
dominance.
Multiple Alleles
• The genes introduced so far have two forms, or alleles. For example, tall or
dwarf, red or white, wrinkled or smooth. This is what Mendel identified.
• When the gene for one trait exists as only two alleles, and the alleles play
according to Mendel’s Law of Dominance, there are 3 possible genotypes and 2
possible phenotypes.
• If you remember from earlier, if there are only 2 alleles, but three possible
phenotypes, there must be co-dominance or incomplete dominance occurring.
• With some genes, there are more than two possible alleles. Then there are 4 or
more possible phenotypes for a particular trait. These are called multiple alleles.
BUT, VERY IMPORTANT: There may be multiple alleles within a population, but
individuals have only two of the alleles. WHY?
Example of Multiple Alleles – Blood Type

As we discussed earlier, there are 4 blood types: A, B, AB, and O.
There are three alleles the gene that determines blood type.
(With multiple alleles, we choose a single capital letter to represent the locus at
which the alleles may occur. The individual alleles are then represented by an
additional single letter (usually a capital) in a superscript position.)
If you notice, the allele for O is recessive (i).
If you look at the three alleles, the possible combinations are as follows:
GENOTYPES PHENOTYPES
IAIA / IAi Type A / Type A
IBIB / IBi Type B / Type B
IAIB Type AB
ii Type O
Genotype - The alleles possessed by an organism
Phenotype - All of the characteristics of an organism.
Homozygous - Having the two identical alleles of a gene.
Heterozygous - Having two different alleles of a gene.
Dominant Allele - An allele which has effect on a phenotype wherever present.
Recessive Allele - An allele which only has partial effect on the phenotype when
present.
Co-dominant Allele - Individual that has partial effect on the phenotype present in
heterozygous and homozygous.
Carrier - An individual that had a recessive allele of a gene that has no effect on the
phenotype.
Test Cross – testing a heterozygous genotype versus a homozygous genotype, by
theoretically mating them, called crossing over.
Locus - The particular position on homologous chromosomes of a gene.
Introduction and Monohybrid Crosses:
• Based upon how organisms look, we can deduce what genes the zygote
developed from. In theory, each organism should have a set of genes from the
male and a set of genes from the female.
Test Crosses in Theoretical Genetics:
How do we get the above? We need to cross the gametes and see what we get.
We will use Mendel’s Monohybrid Cross for pea plants as an example.
Monohybrid – investigation of the inheritance of single contrasting characteristic
There are several parts to a test cross. As we saw earlier, in our definitions, the
terms will be used now.
1. Constructing a Punnett Grid
• A Punnett Grid or Square, is used to find the ratio of the offspring, given
parental phenotypes.
• It is like the multiplication tables you did way back when.
2. Figuring out the parental phenotypes and genotypes. (P)

• Plants showed two phenotypes, tall and dwarf.
• Mendel found that tall plants were dominant and dwarf plants were
recessive, because when the plants were self-fertilized, they produced all
tall plants. Therefore, the homozygous tall plant was either TT, or Tt
(genotypes). The homozygous dwarf plants had to be genotype (tt). What
would be the possible gametes?
First Filial Offspring (F1) from the cross of parental (P)

• Mendel found that the offspring were all tall plants. This lead him to
conclude that tall was a dominant phenotype, but the plants also had to
have some of the characteristics of the dwarf plants also.
• He concluded that the genotypes were Tt, based upon the original parental
genotypes.
• Could Mendel have made an error here?
Second Filial Offspring (F2) from the self-pollination of the F1 generation.

• Mendel found that when the offspring were crossed, the majority of the F2
generation was tall, but there were some dwarf plants as well. The ratio
was 3:1.
• He was able to conclude that the dominant trait was the tall, and those tall
plants had a genotype of Tt or TT, depending on the gametes that fused. In
the case of the dwarf plants, they cannot have T as a genotype, as the
dwarf phenotype is recessive, or t. Therefore, all dwarf plants must be tt for
their genotype.
Human X and Y Chromosomes and the Control of Gender
• Initially, male and female embryos develop identically in the uterus. At the
seventh week of pregnancy, the sexes are starting to be determined. This is
shown by the development of male genitalia, only if a Y chromosome is present.
• Why is XX female and XY male? On the Y chromosome is the prime male-
determining gene. This gene codes for a protein, the testis-determining factor
(TDF). TDF functions as a molecular switch; on reaching the embryonic gonad
tissues, TDF initiates the production of a relatively low level of testosterone. The
effect of this hormone at this stage is to inhibit the development of female
genitalia, and to cause the embryonic genital tissue to form testes scrotum and
penis.
• In the absence of a Y chromosome, the embryonic gonad tissue forms an ovary.
Then, partly under the influence of hormone from the ovary, the female
reproductive structures develop.
• In order for this to happen, the X and Y chromosomes have to pair up. We know
that homologous chromosomes pair up during meiosis. Since the female has XX,
the two are similar, containing the same genes, but maybe different alleles.
• With the X and Y chromosomes, only a very small part of the X and Y have
complimentary alleles and pair up during Meiosis. The two only pair up at a very
small portion of the chromosome.
• In summary, the short Y chromosome carries genes specific for male sex
determination, for coding for TDF and sperm production. The X chromosome
carries an assortment of genes, very few of which are concerned with sex
determination.
Sex linkage and Sex Linked Traits
Although most of our traits are carried on our autosomes, there are some traits that
are located on the sex chromosomes – however, because the Y chromosome does
not code for all the traits on the X, we have an interesting situation. Therefore, the
genes present on the sex chromosomes are inherited with the sex of the individual.
They are said to be sex linked characteristics or traits.
Sex linkage - In a special case of linkage occuring when a gene is located on a sex
chromosome (usually the x-chromosome)
The difference between inheritance of genes on autosomal chromosomes and
sex-linked genes
• The inheritance of sex-linked genes is different from the inheritance of genes on
autosomes, because the X chromosome is much longer than the Y chromosome
and many of the genes on the X chromosome are absent from the Y).
• In a female, if the X chromosome carries a recessive form of a gene (one allele),
the pair X chromosome will often carry the dominant allele. As a result, the
recessive allele will not be expressed.
• In a male (XY), an allele present on the X chromosome is most likely to be on its
own, and will be apparent even if it is recessive. In other words, it does not have
a pair, dominant allele to “override” the recessive allele.
• In conclusion, a human female can be homozygous or heterozygous with respect
to sex-linked characteristics, whereas males will have only one allele.
• An individual with a recessive allele of a gene that does not have an effect on
the phenotype (ie. heterozygous) is known as a carrier. They carry the allele but
it is not expressed. Therefore, female carriers are heterozygous for sex-linked
recessive characteristics.
•
Examples of Genotypes for Sex Linkage
• NB: A female has one of three possible genotypes for a sex-linked trait:
homozygous dominant, heterozygous and homozygous recessive.
• Human males cannot be heterozygous, since they only have one copy of the
allele.
Heterozygous females are carriers.
Example 1 – Colour Blindness

Existing XB for normal Normal vision but a Xb for colour
Alleles vision carrier blindness
A female can XB XB XB Xb Xb Xb
be:
A male can XBY XbY
be:
Example 2 – Haemophilia
Existing XH for normal blood Normal but a Xh for
Alleles clotting carrier haemophilia
A female can XH XH XH Xh Xh Xh
be:
A male can XHY XhY
be:
* Xh Xh is homozygous lethal, meaning that the individual would not exist.

Haemophilia is largely a male disease. The only way for a female to be a
haemophiliac is to be homozygous recessive. When this happens, the condition
is usually fatal in the uterus, typically resulting in a natural abortion. If the
female was born with this condition, she would bleed to death during her first
menstrual cycle.
Mendel’s Conclusion from the Monohybrid Test Cross:
1. Within an organism, there are breeding factors controlling characteristics such

as “tall” and “dwarf”
2. There are two factors in each cell.
3. One factor comes from each parent
4. The factors separate in reproduction and either can be passed on to an offspring
5. The factor for “tall” is an alternative form of the factor for “dwarf”.
6. The factor for “tall” is an dominant over the factor for “dwarf”.
Steps to solving Genetics Problems 1 – Monohybrid Cross
2. Figure out the genotypes of the parents

2. Figure out the kinds of gametes the parents can produce
3. Set up a Punnett Grid for your mating
4. Fill in the babies inside the table by matching the egg allele at the top of the
column with the sperm allele at the head of the row.
5. Figure out the genotypic ratio for your predicted babies
6. Figure out the phenotypic ratio for your predicted babies
Answer the questions you have been asked
Co-dominance and Multiple Alleles

We saw in the previous section that if we take one trait, with different alleles, and
cross the two, we will get a 3:1 ratio in terms of the phenotypes and a 1:2:1 ratio for
the genotypes.
These are very broad generalizations, and can be affected by numerous factors.
In some cases, there are multiple alleles, that can be expressed and some traits are
co-dominant. Some traits are linked to sex (male or female). Using these as a guide,
we can determine a pedigree, or the inheritance of several traits over several
generations. We will explain these next.
Pedigree Charts
• A pedigree can be represented as a diagram showing the phenotypes of a trait
that is inherited from generation to generation. The genotypes can then be
determined or predicted from these charts. Look at the following example of a
simple pedigree diagram.
• The squares represent males and the circles represent females. A horizontal line
joining a male and a female indicates that the couple is married or is capable of
having children. A shaded square or circle means that this person has the trait
being studied.
• The Roman numerals represent the generation. Each person in a generation can
be numbered to show birth order (e.g., 1, 2, 3 and so on). For example, II-3
represents the third child born in the second generation. Moving up in the
diagram shows ancestors; moving down shows descendants.
5 Rules for Pedigree Analysis
1. Every gamete carries exactly one allele for every gene. The exceptions are sex
linked genes in males.
2. Any individual with the recessive phenotype (appearance) must be homozygous
recessive.
3. Any individual with a homozygous recessive offspring must have at least one
recessive allele.
4. Any individual with a homozygous recessive parent must have at least one
recessive allele.
If you don’t know, don’t guess. Use the Punnett Square.
Topic 4.4: Biotechnology

11:37 PM
Polymerase Chain reaction
1. A DNA sample (called target DNA) is obtained. It is denatured (DNA strands are
separated) by heating at 98 degrees Celsius for 5 minutes.
2. The sample is cooled to 60 degrees Celsius. Primers are annealed (bonded) to
each DNA strand. In PCR, the primers are short strands of DNA, they provide the
starting sequences for DNA extension.
3. Free nucleotides and the enzyme DNA polymerase are added. DNA polymerase
binds to the primers and, using the free nucleotides, synthesizes
complementary strands of DNA.
4. After one cycle, there are now two copies of the original strand.
5. Repeat this cycles until enough copies of the target DNA have been produced.
Gel Electrophoresis
• Gel electrophoresis is a method that separates large molecules (including nucleic
acids or proteins) on the basis of size, electric charge, and other physical
properties. Such molecules possess a slights electric charge.
• To prepare DNA for gel electrophoresis the DNA is often cutup into smaller
pieces. This is done by mixing DNA with restriction enzymes in controlled
conditions for about an hour. Called restriction digestion. It produces a range of
DNA fragments of different lengths.
• During electrophoresis, molecules are forced to move through the pores of a gel,
when the electrical current is applied. Active electrodes at each end of the gel
provide the driving force. The electrical current from one electrode repels the
molecules while the other electrode simultaneously attracts the molecules. The
frictional force of the fel material resists the flow of the molecules, separating
them by size.
• Steps:
1. A tray is prepared to hold the gel matrix
2. A gel comb is used to create holes in the gel. The gel comb is placed in the
tray.
3. Agarose gel powder is mixed with a buffer solution (the liquid used to carry
the DNA in a stable form). The solution is heated until dissolved and poured
into the tray and allowed to cool.
4. The gel tray is placed in an electrophoresis chamber and the chamber is
filled with buffer, covering the gel. This allows the electric current from
electrodes at either end of the gel to flow through the gel.
5. DNA samples are mixed with a "loading dye" to make the DNA sample
visible. The dye also contains glycerol or sucrose to make the DNA sample
heavy so that it will sink to the bottom of the well.
6. A safety cover is placed over the gel, electrodes are attacked to a power
supply and turned on.
7. When the dye marker has moved through the gel, the current is turned off
and the gel is removed from the tray.
8. DNA molecules are made visible by staining the gel with ethidum bromide
which binds to DNA and will fluoresce in UV light.
DNA profiling using PCR
• In chromosomes, some of the DNA contains simple, repetitive sequences. The
noncoding nucleotide sequences repeat themselves over and over again and
are found scattered throughout the genome.
• Some repeating sequences or short (2-6 base pairs) called microsatellites or
short tandem repeats (STRs) and can repeat up to 100 times.
• The human genome has numerous different microsatellites. Equivalent
sequences in different people vary considerably in the numbers of the repeating
unit. This phenomenon has been used to develop DNA profiling, which identifies
the natural variations found in every person's DNA. Identifying such differences
in the DNA of individuals is a useful tool for forensic investigations.
• DNA profiling can also be used to establish genetic relatedness (e.g.. Paternity
or pedigree disputes), or when searching for a specific gene.
• Process:
1. Extract DNA from sample
• A sample collected from the tissue of a living or dead organism is treated with
chemicals and enzymes to extract the DNA, which is separated and purified.
2. Amplify microsatellite using PCR
•
Specific primers that attach to the flanking regions either side of the
microsatellite are used to make large quantities of the microsatellite and
flanking regions sequence only.
• Visualize fragments on a gel
• The fragments are separated by length, using gel electrophoresis. DNA, which is
negatively charges, moves toward the positive terminal. The smaller fragments
travel faster than larger ones.
The Human Genome Project
• The human genome project (HGP) is a publicly funded venture involving many
different organizations throughout the world.
• Aims:
• identify all the approximate 30,000 genes in human DNA.
• determine the sequences of the 3 billion chemical base pairs that make up
human DNA.
• store this information in database.
• improve tools for data analysis.
• transfer related technologies to the private sector.
• address the ethical, legal, and social issues (ELSI) that may arise from the
project.
• To help achieve these goals, researchers also are studying the genetic
makeup of several nonhuman organisms. These include the common human
gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse.
Medical Benefits Non-Medical Benefits Possible Ethical Issues
-Improved diagnosis of -greater knowledge of -it is unclear whether third
disease and family relationships parties, e.g. health insurers,
predisposition to disease through genetic testing have rights to genetic test
by genetic testing. -Advances forensic results.
-better identification of science through analysis -If treatment is unavailable
disease carriers, through of DNA at crime scenes. for disease, genetic
genetic testing -Improved knowledge of knowledge about it may
-Better drugs can be the evolutionary have no use.
designed using relationships between -Genetic tests are costly, and
knowledge of protein humans and other there is no easy answer to
structure (from gene organisms, which will who should pay for them.
sequence information) help to develop better, -Genetic information is
rather than by trial and more accurate hereditary so knowledge of
error. classification systems. an individual's own genome
-Greater possibility of has implications for
successfully using gene members of their family.
therapy to correct
genetic disorders.
Genetic Code:
• The genetic code is universal.
• All known organisms use the same genetic code.
• Therefore in principle if we transfer a gene from one species to another it should
still be transcribed and translated into the same protein.
Gene Cloning Using Plasmids:
• Gene cloning is a process of making large quantities of a desired piece of DNA
once it has been isolated.
• The purpose of the process is to yield a large quantity of either an individual
gene or its protein product.
• Methods have been developed to insert a DNA fragment of interest into the DNA
of a vector, resulting in a recombinant SNA molecule or molecular clone.
• A vector is a self-replicating DNA molecule used to transmit a gene from one
organism Into another. All vectors must be able to replicate inside their host
organism, they must have one or more sites at which a restriction enzyme can
cut, and they must have some kind of genetic marker that allows them to be
easily identified. (plasmid or viral DNA)
• The hose (bacterium) may go on to express the gene and produce the desired
protein after gene is replicated inside.
• Process:
1. A gene of interest (DNA fragment) is isolated from cells that have been grown in
laboratory culture. Process of preparing a gene for cloning is as follows:
a. Double stranded DNA of a gene from eukaryotic contains introns is
collected.
b. As a normal part of the cell process of gene expression, transcription
created a primary RNA molecule.
c. The introns are removed by splicing enzymes to form a mature mRNA (now
excluding the introns) that codes for the making of a single protein.
d. The mRNA is extracted from the cell and purified
e. Reverse transcriptase is added which synthesizes a single stranded DNA
molecule complementary to the mRNA.
f. The second DNA strand is made by using the first as a template, and
adding the enzyme DNA polymerase.
2. An appropriate plasmid vector is isolated from a bacterium cell.
3. Both the human DNA and the plasmid are treated with the same restriction
enzyme to produce identical sticky end.
4. The restriction enzyme cuts the plasmid DNA at its single recognition
sequences, disrupting the tetracycline resistance gene.
5. The DNA fragments are mixed together and the complementary sticky ends are
attracted to each other by base-pairing. The enzyme DNA ligase is added to
bond the sticky ends.
6. The recombinant plasmid, or molecular clone, is introduced into a bacterial cell
by adding the DNA to a bacterial culture. Under the right conditions, some
bacteria will take up the plasmid from solution by the process of transformation.
7. The actual gene cloning process (making multiple copies of the human gene)
occurs when the bacterium with the recombinant plasmid is allowed to
reproduce.
8. Colonies of bacteria that carry the recombinant plasmid can be identified by the
fact that they are resistant to ampicillin but sensitive to tetracycline.
Example of GMOS:
• Genetic manipulation are now widely applied in food and enzyme technology,
modern biotechnology, and in agriculture and horticulture.
1. Extending shelf life
• Some fresh produce, ex tomatoes, have been genetically engineered to have an
extended keeping quality. In the case of tomatoes, the gene for ripening has
been switched off, delaying the natural process of softening in the fruit.
2. Livestock improvement using transgenic animals
• Transgenic sheep have been used to enhance wool production in flocks. The
keratin protein of wool I is largely made of a single amino acid, cysteine.
Injecting developed sheep with the genes for the enzyme that generated
cysteine produces woollier transgenic sheep. In some cases, transgenic animals
have been used as biofactoires. Transgenic sheep carrying the human gene for
a protein, alpha-1-antitrypsin produce the protein in their milk. The antitrypsin is
extracted from the milk and used to treat hereditary emphysema.
Ethics of GMO Technology:
Issue Problem Solution
Accidental Recombinant DNA Legislation to control the
release of may be taken up by production and release of
GMO's into bon-target,, GMOs varies in different
the organisms. e.g. countries. These controls are
environmen weeds may take up usually rigorous and strictly
t a gene for enforced. GMOs may have
herbicide specific genes deleted so
resistance. These that their growth
unintended GMOs requirements can only be
may have the met under particular
potential to laboratory environments.
become pests or
cause disease.
Ethics of Therapeutic cloning:

• May lead to human cloning
• A somatic nucleus being transplanted into a human egg that has or will
undergo fertilization.
• Where the embryos are gotten from and what is given in return for them from
donor
• Payments for embryos
• Donors rights
• How old are the stem cell lines that the embryos are gotten from
• New research could give development of new ways to prevent, treat, and even
cure specific diseases
• Embryonic stem cells are 100% compatible with the patient
• To create “designer cells” for transplantation. When ever one organ is
transplanted from a human to another the recipient’s immune system sees
the new material as foreign material and tries to reject the transplant.
Therapeutic cloning may offer a solution, by cloning and not using someone
else’s embryo than your immune system will not kill the embryonic cells.
• Embryonic stem cells offer the possibility of a renewable source of replacement
cells and possibly tissues to treat a variety of diseases, conditions, and
disabilities.
• Non-Hodgkin’s Lymphoma
• Parkinson’s Disease
• Type 1 diabetes
Clone:
• Are genetically identical individuals produced from one parent.
• Process of Cloning using Nuclear Transfer:
1. Donor cells are taken from the udder; cells from the udder of a Finn Dorset ewe
are in low nutrient medium for a week. The nutrient deprived cells stop dividing,
have active genes switched off, and become dormant.
2. Unfertilized egg has nucleus removed; In preparation for the nuclear transfer,
an unfertilized egg cell is taken from another ewe. Using micromanipulation
techniques, the nucleus containing the DNA is removed. This leaves a recipient
egg cell with no nucleus, but an intact cytoplasm and the cellular machinery for
producing an embryo.
3. Cells are fused; The two cells (the dormant donor cell and the recipient egg cell)
are placed next to each other and a gentle electric pulse causes them to fuse
together (like soap bubbles)
4. Cell division is triggered; A second electric pulse triggers cellular activity and
cell division, effectively jump-starting the cell into production of an embryo. This
reaction can also be triggered by chemical means.
5. After six days, the resulting embryo is surgically implanted into the uterus of the
surrogate mother.
6. Birth; After a gestation of 148 days the pregnant ewe gives birth to the lamb
(Dolly), a genetically identical lamb to the original donor.
Topic 5: Ecology and Evolution
2:40 PM
Topic 5.1: Communities and Ecosystems
2:41 PM
Food Chains:
• The feeding relationship in which a carnivore eats a herbivore, which itself has
eaten plant matter, is called a food chain.
• Energy from the sun is the initial energy source. The arrows go from producers
to consumers to represent the energy flow. Depending on the ecosystem, the
food chains are different.
• There are two types of food chains:
Grazer food chain – a producer that is fed on by a herbivore, who is in turn
eaten by a carnivore.
Detritus food chain – food for decomposers come from plant and animal waste
and remains. This is where scavengers are located.
Food Web:
• In an ecosystem, food chains are not isolated. They interconnect with one
another, as a predator may have several species of prey, or a primary consumer
that eats several species of plants.
• Food webs are advantageous as they allow predators and prey alternative food
choices when one source becomes scarce. It also allows the consumers to take
full advantage of some food sources when they become plentiful as well.
Trophic Level:
• Trophic Levels refer to the position or level of an organism during its energy
seeking activities.
For example, if it is a producer, it is the first trophic level. Plants are said to
belong to the first trophic level since the chemical energy they store and use is
one step from the original energy source, the sun. When an organism eats
another, it is one step further removed, or one trophic level up.
• Note that there is not a fixed number of trophic levels to a food chain, but there
are usually three to five levels only.
Also important, is that food chains tell us about the feeding relationships of
organisms in an ecosystem, but they are entirely qualitative relationships rather
than providing quantitative data (numbers of organisms).
Habitat - The locality or physical area in which individuals of a certain species can
be found. If the area is extremely small, we call it a microhabitat. The insects that
inhabit the crevices in the barks of a tree, are in their own microhabitat, and the
conditions will be different than the surrounding habitat
Population - All the living organisms of the same species in a habitat at any one
time. The members of a population have the chance to interbreed. The borders of
populations are often hard to define, but, for example, the limit of a population of
aquatic organisms are limited by the boundary of the pond.
Community - All the living things in a habitat or ecosystem; the total of all the
populations. They all interact with each other in the habitat. For example, the
community of a well-stocked pond would have populations of rooted, floating and
submerged plants, bottom living animals, fish, invertebrates of the open water and
the population of surface living organisms.
Species – A group of individuals of common ancestry that closely resemble each
other and are capable of interbreeding and producing fertile offspring.
Ecology – The study of relationships between living organisms and their
environment
Ecosystem – a settled unit of nature consisting of a community of organisms,
interacting with each other and the abiotic (non-biological) environment.
Autotrophs:
• Organisms that synthesize its organic molecules from simple inorganic
substances. Green plants make their own organic nutrients form an external
supply of inorganic molecules, using energy from sunlight in photosynthesis. The
nutrition of the green plants is described as autotrophic (meaning self-feeding)
and in ecology green plants are known as producers.
Heterotrophs:
• Organisms that obtain organic molecules from other organisms. Most of the
organisms use only existing nutrients, which they obtain by digestion and then
absorb into their cells and tissues for use. All animal nutrition is dependent upon
plant nutrition directly or indirectly. Animal nutrition is described as heterotrophic
(meaning other nutrition) and in ecology, animals that ingest other organic
matter that is living or recently dead is called a consumer.
Consumers:
• Animals that ingest other organic matter that is living or recently dead.
o Herbivores – feed exclusively and directly on plants and plant material.
Herbivores are primary consumers.
o Carnivores – feed exclusively on other animals. Carnivores that feed on
primary consumers (herbivores) are called secondary consumers.
Carnivores that feed on secondary consumers are called tertiary consumers,
and so on.
o Omnivores – feed on both plant and animal matter. Therefore, they are a
blending of a consumer. An example would be a black bear.
Saprotrophs:
• Organisms that feed on dead plants and animals, and on the waste matter of
animals (meaning ‘putrid feeding’). In ecology, these feeders are known as
detritivores and decomposers.
o Decomposer – an organism that feeds on dead organic matter using
extracellular digestion. These are specialized saprotrophs, which consume
cellulose and nitrogenous waste. Examples include fungi and bacteria.
• Feeding by saprotrophs releases inorganic nutrients from the dead organic
matter, including carbon dioxide, water, ammonia, and ions, such as nitrates and
phosphates. The inorganic nutrients are absorbed by green plants and re-used.
Detritivore:
• Organisms that ingest dead organic matter, like large scavengers and
earthworms.
Ecological Pyramids:
• Ecological pyramids are practical means of analysing ecosystems. They can be
used to express seasonal changes in one ecosystem or to compare different
ecosystems at comparable times.
Pyramids of numbers
• All the organisms at each trophic level were counted.
• The results were presented as rectangular blocks, stacked on top of each other,
representing the numbers of organisms at each trophic level in a bar diagram.
The organisms can be observed and not damaged with this approach.
• The problem with this approach was that it did not allow for differences in size of
organisms. Also, some organisms are so numerous it was hard to make the levels
of the pyramid.
Pyramids of biomass
• To find biomass, the numbers of organisms or each type in a trophic level are
estimated and then the dry weight of the organisms is found by using a sample
of a representative size. A pyramid of biomass will have a shape close to the
ideal model. Based upon seasonal changes or the amount of nutrients available
at each trophic level, the pyramid can change shape.
• The problem with a pyramid of biomass is the organism is destroyed to find its
dry mass. More mass is on the bottom due to the amount of flow of nutrients.
Also pyramids of biomass measure the matter in different organisms at a certain
point. It does not allow for matter being added (births, growth) or for matter
consumed.
Pyramid of energy
• Looks at the inflow of energy in each trophic level.
• A pyramid of energy will never be inverted since it looks at figures of the amount
of energy per unit area (or volume) that flows through the trophic level in a given
period of time. There are a few examples of the pyramid, but they destroy the
observed organism and the data is hard to obtain. They still provide the most
accurate tool to analyze an ecosystem based upon the populations of organisms.
• Pyramids of biomass can be converted to pyramids of energy. The amounts of
energy are converted into kJ (kilojoules) and are measured in square meters or
area occupied by the community per year. (kJ m-2 year-1).
The Flow of Energy
• Light is the initial source for almost all communities. While materials cycle
through the ecosystem, energy enters with autotrophs and is used or changed
into other forms of energy and leave the ecosystem again.
• The problem is that every time energy is transferred from one level to another,
some is lost, mostly as heat.
o Some is reflected, some transmitted, and some lost as heat energy. Heat is
also a waste product of the reactions of respiration and of the plant’s
metabolism, as sugar is converted into lipids and amino acids. Some of the
metabolites are used in the growth and development of the plant, and by
these reactions energy is locked up in the organic molecules of the plant
body.
• When the plant is eaten, the stored energy is passed on to the consumer. When
the plant dies, the remaining energy passes on to the detritivores and
decomposers. When the consumer eats the producer, the energy is passed on.
The consumer transfers some of the energy into muscular movements and to
maintain its metabolism. Some remains undigested and goes through the
consumer unchanged. If the consumer is caught and eaten by another
consumer,
the energy is again transferred.
• In general, the higher the trophic level, the more food you must consume to
maintain a desired level of energy. Only 10% - 20% of what is eaten by a
consumer is built into the body of an organism to be potentially available for a
predator or browsing. There are two consequences of this:
The energy loss at transfer between trophic levels is the reason why food
chains are short. Few transfers can be sustained when so little of what is eaten
by one consumer is potentially available to the next step in the food chain. That
is why most food chains have 5 levels at the most.
2. Feeding relationships of a food chain may be structured like a pyramid. At the
start of the chain is a very large amount of living matter (biomass) of green
plants. This supports a smaller biomass of primary consumers, which in turn
supports and even smaller biomass of primary consumer, which in turn supports
and even smaller biomass of secondary consumers.
In other words, there is a huge loss of energy at each stage and an ecosystem
can only support a limited number of higher trophic level organisms.
For example:
Only 1.2% of sunlight is used for photosynthesis, a loss of 98.8%. Of the 1.2 %,
a deer only will get 16.2 % of the energy out of plants. Of this energy, a wolf
only gets 11.4% of useful energy from the deer.
Recycling:
• Energy enters ecosystems as light energy, is transferred to chemical energy in
the nutrient molecules that sustain the growth of tissues of producers and
consumers, but is lost to space as heat and light. Energy continuously flows
through ecosystems in this way. The energy from the sun is constantly received.
• On the other hand, nutrients of an ecosystem are not lost. They are recycled and
reused. The process of this cycle needs energy. Nutrients provide the chemical
elements that make up the biochemical molecules of cells and organisms. All
organisms are made of carbon, hydrogen and oxygen, together with mineral
elements nitrogen, calcium, phosphorus, sulphur, and potassium, with other
trace minerals.
• Plants obtain their essential nutrients as carbon dioxide and water to
manufacture sugars, through photosynthesis. With the addition of mineral
elements absorbed as ions from the soil solution, plants build the complex
organic molecules they need.
• Animals obtain nutrients as complex organic molecules of food, which they
digest, absorb and assimilate into their own cells and tissues.
• When organisms die, their bodies are broken down to simpler substances (CO2,
H2O, NH3 and ions). The waste products are also broken down. This is all done by
the detritivores, decomposers and saprotrophs.
• All organisms depend on micro-organisms to release the nutrients in the final
stage to be re-used.
Topic 5.2: The Greenhouse Effect

3:14 PM
Carbon dioxide:
• Carbon dioxide is present in the atmosphere at about 0.038% by volume (which
represents 0.057% by mass). The amount of atmospheric carbon dioxide is
maintained by a balance between the fixation of the gas during photosynthesis
and the release of carbon dioxide into the atmosphere by respiration,
combustion and decay of micro-organisms.
• This process is required for the building of all organic compounds and involves
the participation of many of the earth’s key forces. Much of the earth’s carbon is
contained in the atmosphere, which serves as a reservoir. Much of the carbon is
in the form of carbon dioxide and has two major sinks: terrestrial ecosystems
and marine ecosystems. Both deal with photosynthesis as a part of assimilation
and respiration as a release. In other words, Photosynthesis withdraws about as
much carbon dioxide during the daylight each day as is released into the air by
all the other processed day and night, or nearly so.
• We all hear that the amount of carbon dioxide is increasing in our atmosphere.
Carbon dioxide is a normal component of our atmosphere, because it maintains
a favourable environmental temperature on Earth, known as the Greenhouse
Effect. But, the affects of carbon dioxide levels beyond what is needed to
maintain a normal surface temperature have contributed to an increase in global
warming.
1. Ice Core Samples from Antarctica and Greenland
The best long-term records of changing levels of greenhouse gases are
based upon evidence obtained from ice cores drilled in the Antarctic
and Greenland ice sheets.
For example, data from the Vostok ice core in East Antarctica, show
that methane and carbon dioxide levels have varied over no less than
400 000 years. This is taken from the bubbles of gas trapped in the ice.
Variations in the concentration of oxygen isotopes from the same
source indicate how temperature has changed during the same period.
Clearly the levels of greenhouse gases in the atmosphere can be
closely correlated with global temperature. Environmental conditions
on Earth have changed as a consequence, and we may anticipate
further changes unless the current, rising levels of atmospheric carbon
dioxide are reversed by internationally agreed action.
• As carbon dioxide increase, temperature increases. Thus, the
temperature will rise over time
• Or we have cycles. Thus, in a high period we have an increase in
temperature.
Atmospheric CO2 levels being measured – Mauna Loa Observatory
For millions of years, the lower part of the atmosphere has contained
approximately 0.03% CO2. The recent problems are largely caused by
the rapid increase of CO2 in the atmosphere.
• Increase in temperature
Greenhouse Effect
• The greenhouse effect is exactly what it says. The atmosphere behaves the
same as a greenhouse.
The heat is caught inside the greenhouse because its radiation cannot travel out
through the glass, and is reflected back into the greenhouse. Therefore on a
bright, sunny winter day, your greenhouse will be a lot warmer than the outside
temperature, even without additional heating systems.
• The atmosphere, like the glass of the greenhouse, holds in the radiant energy of
the sun. The radiant energy from the sun reaches the Earth in the form of visible
light, ultraviolet light (UV) and infra-red radiation, which warms up the sea and
the land. As it is warmed, the Earth radiates infra-red radiation back towards
space. However, much of this heat does not escape from our atmosphere. Some
is reflected back by clouds and much is absorbed by gases, in the atmosphere
which, are warmed. Keep in mind, that normal levels of greenhouse gases are
important, as the greenhouse effect keeps the surface temperature at a level
that can sustain life.
• The higher the concentration of gases, the more heat is prevented from leaving
the Earth. Greenhouse gases include:
• Carbon dioxide – complete combustion
• Carbon monoxide – incomplete combustion
• Water vapour - precipitation
• Nitrogen oxides – burning fossil fuels/ refining processes
• Methane – gas/farming
• Chlorofluorocarbons (CFC’s) and ozone in the troposphere. – Coolant
Is the enhanced greenhouse effect leading to Global Warming?

The composition of the atmosphere has changed over time. That is beyond
dispute. The global issue is that human actions are contributing to an increase in
greenhouse gases which presumably cause global warming. Keep in mind, not all
scientists agree with this conclusion.
What is needed is evidence that the increase in the gases have caused an
increase in atmospheric and surface temperatures.
Global Warming and the Precautionary Principle

• The Precautionary Principle is summed up by the expression ‘Better Safe than
Sorry’.
• The most common definition is: When an activity raises threats of harm,
measures should be taken, even if a cause and effect relationship has not been
established scientifically.
In order to take strong action, areas of concern need to be identified to justify
changes to be made.
2. The consequences that may result from failure to slow down the rising level of
atmospheric carbon dioxide and then reduce it to earlier values
3. The actions needed to deliver the measures that enable us to achieve this.
• The Intergovernmental Panel on Climate Change (IPCC) was set up in 1988 to
find out if human activities have an impact on climate. In February 2007, their
forth report came to some of the following conclusions:
o Global Temperatures are increasing; global warming is not a hypothesis but
a confirmed reality
o There is over a 90% chance that the cause of this increase in temperature
is die to the production of greenhouse gases by human activity. The chance
that these fluctuations could be caused by natural phenomena alone is less
than 5%
o Within the coming century, sea level is expected to rise between 18 cm
and 59 cm
o It is likely that severe weather events such as heat waves, drought or
heavy rains will increase The IPCC’s report cannot say what specific impact
these consequences will have on the world’s ecosystems or on specific
economic activities such as the fishing industry.
• Observers are predicting mostly negative impacts, no one knows precisely
where, what or how severe they may be.
• This is where the precautionary principle comes in. Make changes, even without
the data to back it up.
Human Impact on Arctic Ecosystems
The Arctic consists of those parts of North America, Greenland, Iceland, Norway and
Russia, which are north of the Arctic Circle. It also includes the Arctic Ocean, which
is covered in ice surrounding the North Pole.
Arctic Ecosystems consist of areas of permanent ice desert and huge areas of low-
lying treeless land with environment and vegetation described as tundra.
The few plants present all through the year are sedges, lichens, and sometimes
dwarf willows. Trees do not grow as the growing season is too short, the winters are
too long and dry and the soil does not allow for normal root development.
Most of the year the temperatures are well below freezing point, so the moisture,
soil and organic strata remain frozen (permafrost). Dead organic matter
accumulates, because the periods of the year when bacteria and fungi might decay
this to humus are too short. The bulk of nutrients are locked away and few are
released in growing periods.
Photosynthesis will reduce the amount of carbon dioxide available but

deforestation reduces the amount of photosynthesis. On land, plants fix about
3.50 x 1026 kg per year. Plants and animals respire 1.00 x 1013 kg and the
decomposers release 2.50 x 1013 kg every year. Some scientists estimate that
deforestation decreases the carbon fixation by about 5.00 x 1012 yearly.
2. Earlier in history, processes like volcanic eruptions and the weathering of chalk
and limestone added to the extra carbon dioxide. Today, the release of carbon
dioxide, due to volcanic eruptions is only 1% of the amounts released by human
activities.
The burning of fossil fuels has contributed to the atmospheric carbon dioxide.
Scientists estimate 5.00 x 1012 kg are added yearly, the same decrease as
deforestation.
Topic 5.3: Populations

4:23 PM
There are four factors that influence the size of a population
Natality – birth rate
Mortality – death rate
Immigration – moving in
Emigration – moving out
• The growth of the number of individuals in a population usually follows
a sigmoid (S shaped) curve. The curve can be divided into four phases:
• Lag phase – organisms become adapted to the medium
• Exponential Growth or log phase – growth occurs at an exponential
rate
• Linear or transitional growth phase – growth proceeds at a more
steady rate
• Plateau phase – growth slows down and stops
• To explain each phase, we will use a population of rabbits.
• A group of new, young rabbits moves into a meadow in which all other
rabbits are excluded. After familiarizing themselves with the new
territory, and establishing burrows, they have unrestricted access to
food supplies and breeding starts.
• The population of rabbits would increase exponentially, but eventually
because of the very large number of rabbits, the vegetation would be
used up faster than it grew. Increases in population would stop and
the population enters a plateau or stationary phase. The supply of
food would be a limiting factor in the growth of the rabbit population
• The food supply would be used up to a point where it would no longer
sustain reproduction.
In the transition or linear growth phase, the increase will slow down
until it reaches zero. This occurs when the environment suddenly
changes and only a few individuals survive. Interspecies competition
results, where the strong survive.
• This is when the habitat has reached its carrying capacity. Carrying
Capacity is the number of individuals in the population has reached
the maximum, which can be supported by the environment. As a
population increases, it begins to experience environmental
resistance, because space and resources are reduced and competition
for space and resources increases.
If the numbers start to increase above carry capacity, shortage of
resources reduces the numbers of offspring produced and the
population regulates itself at the carry capacity.
• If the population is reduced, by heavy predation, for example, the
additional resources that then become available lead to an increase in
reproductive rate, and the carrying capacity is again reached. In other
words, the populations tend to be self-regulating.
Limiting Factors
• Populations fluctuate in the wild. There are times of boom and bust. Why does
this occur?
There are several factors that can limit populations.
1. Density Dependent – affect the proportion of the population as the density
increases. Examples are predation, disease or intra-species competition. The
effects of these factors increase with increasing population numbers.
2. Density Independent – affect the proportion of the population regardless or size,
and affect the overall size of the population or reducing the birth and death
rates. Examples are death due to weather, earthquakes, drought.
3. Extrinsic Regulatory Mechanisms – originate outside the population and include
biotic as well as physical factors. For example food supplies, natural enemies,
disease, weather.
4. Intrinsic Regulatory Mechanisms – originate in the anatomy, physiology and
behaviour. Competition is the main regulating mechanism for large groups.
Topic 5.4: Evolution
Thursday, March 26, 2009
5:54 PM
Evolution – the process of cumulative change in the heritable characteristics of a
population. If we accept not only that species can evolve, but also that new species
arise by evolution from pre-existing ones, then the whole or life can be seen as
unified by its common origins. Variation within our species is the result of different
selection pressures operating in different parts of the world, yet this variation is not
so vast to justify a construct such as race having a biological or scientific basis.
Mechanism of Evolution - The Idea behind Evolution and Neo Darwinism
• Darwin and Wallace suggested a process. This process is known as natural
selection. It works by over production of offspring and the presence of natural
variation.
Too many offspring

• Populations tend to produce more offspring than the environment can support.
The production of offspring involves the expenditure of energy and resources.
This over production of offspring leads to intra-species competition and survival
of the individuals best suited to that particular environment. Example, trees have
active compounds that ward off insects. Competition can also lead to adaptive
behaviours.
Natural Variation within a Population

• Sexual Reproduction promotes variation in species. Darwin knew nothing of
Mendel’s work, like most scientists of the time. They believed in blended
inheritance, which would lead to less variation. Neo-Darwinism restates the
essential concepts of evolution in terms of Mendelian and Post-Mendelian
Genetics.
• Creating gametes by meiosis involves the separation of the homologous pairs of
chromosomes. Since this process is random, a gamete has a mixture of paternal
and maternal chromosomes. Two gametes from different individuals fuse to
create a new organism. Since gametes from one individual differ, this mixing will
lead to further variation.
• To summarize, variation arise via:
o random assortment of chromosomes
o crossing over of segments of chromosomes result in new combinations of
genes, different than the parental combinations
o random fusion of gametes in sexual reproduction
o additional variations arise due to mutations, either chromosomal or gene
• As a result of all of these, the individual offspring of parents are not identical and
show variations in their characteristics. If the variations are successful, the
organism will be successful.
• Variety may be caused by:
• Mutations
• Sexual Reproduction – random splitting of cells during meiosis will
determine the genetic variety.
Natural Selection and Favourable Heritable Variations
• Sexual reproduction and/or mutations, leads to variations of a species. Variation
is non-directional or random. The selection process is dictated by the
environment and leads to differential survival.
• The result is that the individuals best adapted to a particular environment will
survive. They will be able to get the most food, find the best shelter, find a
mate, reproduce and care for their offspring as well as not be eaten by other
species.
• Since most environments are different, the “best adapted” may be different too.
Also, environments may change. This can happen gradually or suddenly, due to
a natural disaster, for example. As a result, the criteria for the “best adapted
will also change.
• This process of natural selection can lead to changes in the species. It can also
lead to speciation. When two groups of a species are in different environments
and they cannot interbreed, selection pressure will be different and eventually
they will become different species (adaptation) due to their natural
environment. This is what Darwin noticed in the many species of finches in the
Galapagos Islands. Sometimes the idea of natural selection is summarized in
the phrase “survival of the fittest”, and not “the strong survive”, although these
words were not used by Charles Darwin.
Natural Selection Summarized

1. The favourable characteristics are expressed in the phenotypes of some of the
offspring
2. These offspring may be better able to survive and reproduce in a particular
environment; others will be less able to compete successfully to survive and
reproduce.
The three areas we will look at to provide evidence for the theory of
evolution by natural selection are:
1. Fossil Records
• Fossil – any form of preserved remains from a living organism.
• Some examples are:
o Mammoths frozen in Siberia
o Mummies in acidic swamps in Scandinavia
o Insects in amber
o Bones in rock
• Fossils are only formed in some circumstances. Most individuals do not
leave a fossil after death.
• A fossil has to be formed when an organism dies and gets buried in
sedimentary silt. It will decay slowly and leave a space in the silt. The
gap becomes solid and is filled the exactly the same as the organism
left behind. The silt may solidify, becoming sedimentary rock and in it
is the fossil.
• To see how old fossils are and their forms, carbon dating is used,
usually Carbon 14 and potassium 40, which are isotopes.
• Palaeontologists have discovered the following:
o Overall, life, which existed more than 500 million years ago, was
very different from life today.
o Although the planet Earth has had extensive oceans for most of its
existence, fish fossils have only been found in rocks 500 million
years old or younger (less than 15 % of the history of life)
o Although most of the top predators today are mammals such as
bears, orca whales, big cats wolves and the like, none of them
existed at the time of the dinosaurs or before
o Apart from organisms such as certain types of sharks, cockroaches
or ferns, many living organisms today have no identical form in
the fossil record.
• One conclusion that can be drawn from observing fossils is that life on
Earth is constantly changing. For example, in some cases, as for the
example of the horse, we see macroevolution. The first fossils of the
ancestors of the modern horse are 53 million years old. They had 4
toes on the front foot and 3 toes on the back. Their eyes were halfway
up their head, between the nose and ears and the teeth structure
showed it ate leaves, not grass. This early horse was known as
Eohippus, which means dawn horse.
• Fossils in the upper strata of sedimentary rocks (younger fossils) show
the horse grew larger, one of its toes grew bigger and the others
reduced. We also see that the vegetation changes from thick forests to
grasslands, due to fossils of early vegetation. The eyes grew closer to
the back of the head, closer to its ears, to improve its peripheral vision
to be able to watch for predators while they grazed. The teeth also
became bigger and stronger to promote grazing.
• Many fossils of horses that do not have these features have been
found, but the evidence is that they became extinct (ie. they could not
outrun predators, attain food, etc.). They were eventually replaced by
species that were better suited to the environment. The only line that
continued into our time, was Equas, the modern horse.
2. Artificial Selection
• The fossil record is not complete, but breeding domesticated animals
provides a good record of recent changes in heritable characteristics.
• By watching mating of males and females, and the offspring, breeders
select the desirable traits they want. After practicing selective
breeding for hundreds of dozens of years, certain varieties of animals
had unique combinations of traits not seen before. The evidence is
that small changes are occurring over time, which is driven by humans
or is artificial. If evolution can be controlled artificially, then it could
also be natural.
• Homologous Structures
• Comparative Anatomy concentrates on studying homologous
structures. Two structures are homologous if they come form the same
origin though they may look different now and have different
functions.
• Analogous structures are those that have the same functions, but
come from differ origins. For example, the wing of a bird and a wing of
an insect are both used for flying, but the wing of the bird used to be a
limb and the wing of the insect comes from a fold in the skin. This tells
us that there is not a common ancestor.
• Examples of homologous structures are the arm of a human, the wing
of a bat and flipper of a seal. They all have the same pentadactyl limb.
This means they have the same basic patterns of bones, including five
digits. The pentadactyl limb is used differently in different mammals,
but the common structure could lead to the conclusion that there is a
common ancestor.
• We can also look at physiological evidence, by looking at the functions
of parts of organisms or rudimentary structures (ie. pelvis in a whale).
• We have seen that the wastes from birds and reptiles have the same
chemical makeup and the hormones from sheep and pigs are also
present in humans!!
• We can also look at Embryology, which is the study of organisms in
early stages of development.
• Scientists have discovered a similarity between the embryos of
different species and it is theorized that this similarity is due to their
evolution from a common ancestor. There is also a theory that every
organism repeats its own evolutionary development as the embryo
develops.
Examples of Evolution in response to Environmental Change
• If a species cannot adapt to the changing environment, then the species will die
out. As the dinosaurs did not find a way to deal with the climate becoming
colder, they did not survive. Their place was taken by the homeothermic, or
warm-blooded mammals.
1. Multiple Antibiotic Resistance in Bacteria

• Penicillin is not effective over the entire field of micro-organisms pathogenic to
humans. During the 1950’s, the search for antibiotics to fill this gap resulted in
a steady stream of them, some with a much wider antibacterial range than
penicillin (broad spectrum antibiotics). Some were capable of coping with those
micro-organisms that are inherently resistant to penicillin or that have
developed resistance through exposure to penicillin.
• Many diseases caused by bacteria have been successfully treated with penicillin
and other antibiotics. However, since WWII, when the use of antibiotics became
widespread, many disease-causing bacteria have developed resistance against
antibiotics. There are strains of bacteria causing tuberculosis, which are
resistant to all known antibiotics. The same applies for cholera, as there is only
one effective antibiotic available. This means that is you become infected with
these bacteria, treatment with antibiotics will not cure you and the disease may
become fatal.
• Staphylococcus aureus is a common bacterium found living on the skin. This
species is usually harmless but, in certain circumstances, can invade your blood
stream, infect tissues in the kidneys or bones and could become fatal. These
days, strains of S. aureus exist which are resistant to all known antibiotics.
These MRSA bacteria (methycillin-resistant Staphylococcus aureus) are of grave
concern to hospitals all over the world.
• The resistance to antibiotics is probably caused by spontaneous mutation. As a
result, the bacterium produces penicillinase, for example, an enzyme, which
breaks down penicillin. If the bacteria are exposed t penicillin, the one without
resistance will be killed. However, those with resistance will survive and, due to
lack to competition, grow rapidly.
• The genetic information for antibiotic resistance is often found on plasmids,
which can be spread rapidly over a population and can even cross into other
species of bacteria. This is likely to occur when a small dose of antibiotics is
used for a short time. It will kill some of the bacteria, but not all and may lead to
the creation of some bacteria that have some resistance. The next time
antibiotics are used, these bacteria are less vulnerable and some more may
survive. Repeated use of small doses of antibiotics can produce very resistant
strains. This explains why doctors always insist on patients finishing the course
of antibiotics even if they are feeling better.
• Overuse of antibiotics in medicine, the cattle industry and antibiotic soaps have
led to a rise in antibiotic strains.
2. The Peppered Moth (biston betularia)

• This moth is found in England, near Manchester (boo United!!!). Before 1848,
trees on which they rested were covered with off-white lichen. The moths were
white, and therefore camouflaged from predation by birds. Occasionally a black
moth would appear, and due to its high visibility, would have a high possibility
of falling prey.
• Due to coal base industry, the trees became covered with soot and the white
moths were easily spotted and eaten. The dark (melanic) form now had an
advantage and became predominant (95%) in certain areas in 1950. Reduce
use of coal has now made the trees green (covered in algae) and both forms are
common. This is called balance polymorphism. This is a short termed example
of evolution.
Topic 5.5: Classification

5:54 PM
The Binomial System:
The first part of the name is the genus or the generic name based upon a noun.
It is given with an upper case letter. E.g.. Homo. The second name is the species,
or the specific name, based upon an adjective. It is written with a lower case
letter. E.g.. sapiens.
• If written by hand should be underlined
• If typed name should be in italics.
• Often name will be followed by another in brackets which refers to the first
person to scientifically identify the species.
The Scheme of Classification
• The science of classification is taxonomy. “Taxa” is the general word for groups
or categories. Biological classification is the invention of biologists, based upon
the best evidence at the time.
• There are 7 categories for naming:
• Kingdom – largest and most inclusive grouping
• Phylum / division – organisms constructed on a similar plan
• Class – a grouping of orders within a phylum
• Order – a group of apparently related families
• Family- a group of apparently related genera
• Genus - a group of similar and closely related species
• Species – a group of organisms capable of interbreeding to produce fertile
offspring
There are 5 kingdoms to classify organisms. They are:

Prokaryotes – unicellular organisms lacking nuclei and other membrane bound
organelles. DNA is mainly circular and is not organized in chromosomes.
Examples are bacteria and cyanobacteria
Protista – unicellular and multicellular eukaryotic organisms that may be
autotrophic or heterotrophic and may live in salt or fresh water. Examples are
Euglena and Paramecium
Fungi – Eukaryotic filamentous or unicellular. Filamentous fungi grow a
mycelium from which mushrooms or toadstools grow. They are heterotrophic
and they feed by absorption of nutrients. Their cells have chitin in the cells
walls, as opposed to cellulose. Examples are yeasts and mushrooms.
Plantae – Eukaryotic, multicellular, phosynthetic organisms. The cells walls
contain cellulose, and most cells contain chlorophyll. Examples are mosses,
ferns, flowering plants.
Animalia - Eukaryotic, multicellular, heterotrophic organisms that are often
motile, and feed by ingestion. Examples are humans and jellyfish.
Topic 6: Digestion
4:38 PM
Topic 6.1: Digestion

4:38 PM
Purpose of Digestion:
• Digestive System, series of connected organs whose purpose is to break down,
or digest, the food we eat.
• Food is made up of large, complex molecules, which the digestive system
breaks down into smaller, simple molecules that can be absorbed into the
bloodstream. The simple molecules travel through the bloodstream to all of the
body's cells, which use them for growth, repair, and energy.
• Is an essential step because the bulk of the food taken in consists of insoluble
molecules that are far too large to cross the gut wall and enter the blood stream.
• Food consists of carbohydrates, lipids, and proteins. These must be hydrolysised
to monosaccharides, fatty acids and glycerol, and free amino acids before they
can be absorbed and later used by our body.
Types of Digestion:
Digestion generally involves two phases:
• Mechanical phase - teeth or other structures physically break down large pieces
of food into smaller pieces.
• Chemical phase - digestive chemicals called enzymes break apart individual
molecules of food to yield molecules that can be absorbed and distributed
throughout the body. These enzymes are secreted (produced and released) by
glands in the body.
o Digestive enzymes are protein catalysts produced in specialized cells in
glands.
o Action of enzymes greatly speed up the breakdown of insoluble food
substances.
• Work efficiently at relatively low temperatures the body is maintained
at
o To complete digestion processes enzymes secreted onto the food work
together with those held in the plasma membranes of cells of the gut lining.
Small Intestine
• Most digestion, as well as absorption of digested food, occurs in the small
intestine. Over a period peristalsis moves chyme through the duodenum into the
next portion of the small intestine, the jejunum, and finally into the ileum, the
last section of the small intestine.
• During this time, the liver secretes bile into the small intestine through the bile
duct. Bile breaks large fat globules into small droplets "emulsification", which
enzymes in the small intestine can act upon.
• Pancreatic juice, secreted by the pancreas, enters the small intestine through the
pancreatic duct. Pancreatic juice contains enzymes that break down sugars and
starches into simple sugars, fats into fatty acids and glycerol, and proteins into
amino acids.
• Glands in the intestinal walls secrete additional enzymes that break down
starches and complex sugars into nutrients that the intestine absorbs. Structures
called Brunner’s glands secrete mucus to protect the intestinal walls from the
acid effects of digestive juices.
• The small intestine’s capacity for absorption is increased by millions of fingerlike
projections called villi, which line the inner walls of the small intestine. Each
villus is covered with a single layer of cells. Even tinier fingerlike projections
called microvilli cover the cell surfaces. This combination of villi and microvilli
increases the surface area of the small intestine’s lining, multiplying its capacity
for absorption. Beneath the villi’s single layer of cells are capillaries (tiny
vessels) of the bloodstream and the lymphatic system. These capillaries allow
nutrients produced by digestion to travel to the cells of the body. Simple sugars
and amino acids pass through the capillaries to enter the bloodstream. Fatty
acids and glycerol pass through to the lymphatic system.
Absorption:
• Soluble products of digestion absorbed into blood circulation system. (into
lymphatic system if fat droplets)
Assimilation:
• Products of digestion absorbed from blood into body cells and used and stored.
Stomach:
• The stomach, located in the upper abdomen just below the diaphragm, is a
saclike structure with strong, muscular walls.
• The stomach can expand significantly to store all the food from a meal for both
mechanical and chemical processing. The stomach contracts, churning the food
and mixing it with gastric juice. This fluid, secreted by thousands of gastric
glands in the lining of the stomach, consists of water, hydrochloric acid, an
enzyme called pepsin, and mucin (the main component of mucus). Hydrochloric
acid creates the acidic environment that pepsin needs to begin breaking down
proteins. It also kills microorganisms that may have been ingested in the food.
• Mucin coats the stomach, protecting it from the effects of the acid and pepsin.
• After a meal, food processed by the stomach, called chyme, begins passing a
little at a time through the pyloric sphincter into the duodenum, the first portion
of the small intestine.
Large Intestine
• A watery residue of indigestible food and digestive juices remains unabsorbed.
This residue leaves the ileum of the small intestine and moves by peristalsis into
the large intestine. The large intestine forms an inverted U over the coils of the
small intestine.
• The large intestine serves several important functions. It absorbs water daily—as
well as dissolved salts from the residue passed on by the small intestine.
• In addition, bacteria in the large intestine promote the breakdown of undigested
materials and make several vitamins, notably vitamin K, which the body needs
for blood clotting.
• The large intestine moves its remaining contents toward the rectum. The rectum
stores the feces—waste material that consists largely of undigested food,
digestive juices, bacteria, and mucus—until elimination.
• Then, muscle contractions in the walls of the rectum push the feces toward the
anus. When sphincters between the rectum and anus relax, the feces pass out of
the body.
Enzyme Source Substrate Product pH

Amylas Salivary Starch Maltose 6.5-7.5
e glands
Pepsin Gastric glands Protein Polypeptides 2.0
Lipase Pancreas Triglyceride Fatty acids and 7.0
glycerol
Topic 6.2: Transport System
6:27 PM
Coronary Arteries:
• Blood Vessels that bring blood
and oxygen to the heart muscle
Blood Flow through Heart:
• Blood enters the right atrium
from the vessels called inferior
vena cava
• Blood pumped through
atrioventricular valve (tricuspid
valve) into the right ventricle.
• Then pumped upwards through
the semilunar value (pulmonary
valve) into the vessel called
pulmonary artery, which takes it
into the lungs. (Here picks up
oxygen)
• The blood returns to the heart,
entering left atrium through
pulmonary vein.
• It is pumped down through an
antrioventricular valve (mitral valve) and into the left ventricle.
• Then blood is pumped up through the semilunar valve (aortic valve) and out of
the heart through the aorta. It is sent to all the body cells to drop off oxygen and
pick up carbon dioxide.
Control of Muscle Heart Beat:
• Bundle of muscle tissues on the wall of the right atrium control heart rate.
• These fibers are called the sinoatrial node (S-A-node) or pacemaker. The SA node
signals the atriums to contract
• The AV node which is just between the atrium and ventricle, picks up this signal
and amplifies it, sending it down the septum through the bundle of HIS and
purkinje fibers, when in turn causes the ventricles to contract.
o Bundle of HIS is a collection of heart muscle cells specialized for electrical
conduction that transmits the electrical impulses from the AV node (located
between the atria and the ventricles) to the point of the apex of the
fascicular branches. The fascicular branches then lead to the Purkinje fibers
which innervate the ventricles, casing the cardiac muscle of the ventricles
to contract at a paced interval.
Heart Beat:
• "lub" is caused by closing of antrioventricular valves closing.
• "dub" is caused by closing of semilunar valves in arteries.
1. Blood enters atria; the antrioventricular valves open when atria pressure is
greater than ventricular pressure. This resting period is called diastole.(blood
flowing into ventricles)
2. Two atria contract (systole) causing blood to move into ventricles
3. Ventricles contract (ventricular systole - lub), increasing pressure in ventricle so
valves close which in turn opens semilunar valves in arteries, closing AV valve.
4. Ventricles relax (ventricular systole - dub) and semilunar valves close because
some blood tries to flow back.
• Lub sound (softer) is Antrioventricular valves closing and dub sound (louder) is
semilunar valves closing.
Arteries, Capillaries, and Veins:
• Artery - high pressure, carries blood away from heart, thick muscular walls which
pump blood.
• Arterioles - same as arteries but smaller and more branched
• Capillaries - site of exchange between blood and cells, 1 cell thick, have low
blood pressure due to their numbers, and connect arteries and veins
• Venules - smaller version of vein
• Vein - thick walled, low blood pressure, tube that takes blood back to the heart,
valves prevent backflow of blood.
• Veins and Arteries have strong elastic walls due to collagen fibers present and
elastic and involuntary muscle fibers.
• Capillaries have endothelium only.
Blood:
• Plasma - transport nutrients, excretory products such as urea, hormones,
dissolved proteins, dissolved proteins which are antibodies, and heat distribution
to all tissues
• Erythrocytes (RBC) - transport of oxygen and carbon dioxide
• Lymphocytes (WBC) - important in the immune system because they form
antibodies
• Phagocytes - ingest bacteria or cell fragments
• Platelets - play a part in the blood clotting mechanism
Topic 6.3: Defence Against Infections Disease
7:24 PM
Pathogen:
• Anything that can cause a disease/sickness
HIV:
• Human Immunodeficiency Virus
• HIV is a retrovirus - uses RNA to make DNA
• Uses lysogenic cycle to produce the virus (replicate it) and may sit dormant in a
person.
• Hard to get rid of:
o It kills only HTC cells which conduct immune responses. Thus don't have
enough HTC to recognize pathogen and immune system becomes
depressed.
• B-cells not activated effectively - have limited AMI response
• Limited activation of KTC - have limited CMI response
• Limited amount of B-cells activated, less memory B cells produced
o If immune system is depressed, the smallest virus can kill a person.
How antibiotics work:
• Antibiotics only work on prokaryotic cells and the cells in our bodies are
eukaryotic cells.
• Both fungi and bacteria act as decomposers and sometimes compete with one
another for food. Some microorganisms produce chemicals called antibiotics to
inhibit growth of their competition.
• Antibiotics interfere with bacterial metabolic processes such as DNA replication,
transcription, translation, ribosome function and cell wall formation. This is why
antibiotics can be used in the human body. Protein synthesis is similar in both
types of cell, but not exactly the same. Prokaryotic cells have a cell wall and
eukaryotic cells do not. Some antibiotics block biochemical pathways in the
bacterium, causing death – usually blocking protein synthesis. Some stop the
reproduction of the cells and allows the white blood cells to catch up, while
others kill the bacterial cells by dissolving the cell walls and membranes.
• Viruses are not living cells, only live within a host cell. Viruses are DNA and RNA
in a capsule. They do not reproduce on their own, do not produce energy, and
don't produce enzymes on own. They take over a host cell by drilling and
inserting DNA and RNA inside. This causes the cell to reproduce inside while
killing the host cell itself.
AIDS:
• Acquired immune deficiency syndrome
• Social Implications:
o Gay disease (bisexual targeted disease)
o Individual who has AIDS is shunned, people think if come in contact with
person they will get it
o Fear
• Positive Social Implications:
o More research on disease
o Public awareness of safe sex
o Drug users provided with needles to make processes safer
o Screen blood with blood transfusions
o People with HIV can have drugs and treatments
Role of phagocytic leucocytes:

• Leucocytes, or white blood cells, are the cells in our blood stream that help us
fight off pathogens that enter our bodies and also provide us with an immunity
for many pathogens we encounter a second time. All of the leukocytes, along
with the erythrocytes (RBC) and platelets are produced on the bone marrow.
• One type of leucocyte that gets involved very early in the process of fighting off
pathogens is a macrophage. They are large white blood cells that are able to
change their shape a surround an invader to take it in by phagocytosis, like an
amoeba. Since they can change their shape, they are able to squeeze their way
in and out. This allows them to move in and out of the blood stream to go after
pathogens.
• When a macrophage does meet a cell, it recognizes whether the cell is a natural
part of the body, “self” or a foreign invader, “not self”. The macrophage
recognizes and reads the proteins and other molecules on the surface of the
pathogen. If it is “not self”, it will be ingested, regardless of the protein on the
cell. This is an example of CMI Response.
Preventing pathogens from entering our body - Lines of Defence
• The ability to resist infection by a disease is termed immunity. Non-specific
immunity allows the body to resist infection by a wide range of pathogens. An
example is the skin.
• The best line of defense is to prevent the pathogen from entering the body. This
is done in many ways:
Skin:
• If there is not a cut or an opening of any kind, it is impossible for pathogens to
penetrate. Our skin has two layers, the dermis and the epidermis. The dermis is
alive and contains the sweat glands, capillaries, sensory receptors and dermal
cells that give structure and strength to our skin. The epidermis is constantly
being replaced, as underlying dermal cells die and move upwards. This layer is
effective as a barrier because it is not truly alive.
• The skin oil, sebum, is secreted by the sebaceous glands in the skin. The sebum
is a protective film over the skin. It maintains skin moisture and lowers the skin
pH.
Perspiration flushes microbes away and contains Lysosome, an enzyme, which
breaks down bacterial cell walls.
Mucous:
• On the epithelial layers, the fluid is emitted which traps bacteria and prevents
further entry in internal cavities that are exposed to the external environment.
Mucous membranes secrete mucous. They are found in the: Trachea, Nasal
Passages, Urethra, Vagina.
• The sticky mucous traps the bacteria, as do tiny hairs. Cilia in the bronchial
tubes, sweep the mucous to the digestive system, through the mouth and throat,
or trigger a spasm of the bronchioles, called coughing. In addition, the cells that
secrete mucous also secrete an enzyme called lysazome (same as the
perspiration). The enzyme does chemical damage to the pathogen.
1. T-Cells (stored in the thyroid gland, around the
throat) are inactive. When an antigen enters the
body, they are off, constantly moving through your
body, in search of the harmful antigen.
When the pathogen is found, the T-Cell acts like a
macrophage, engulfing the invader. This happens
through the process of Phagocytosis.
The T-Cell breaks down the antigen and continues to
track the pathogen to destroy it. This is CMI
response.
Some T-Cells do not destroy the antigen or parts of
the cell membrane, but pushes them to the outside
of their own cell membrane. As a result, the T-Cell
now becomes an Antigen Presenting Cell (APC), and
forms the Major Histocompatibility Complex (MHC)
proteins found on the macrophage.
MHC binds with the markers. MHC goes to outside of
cell by exoctosis to present itself.
6. The T-Cell, now an APC, travels to the lymph node,
where the antigen it has is presented and read by a
Helper T-Cell.
7. HTC binds with the matching receptor for the
antigen.
HTC brings the antigen complex inside. The HTC
becomes activated. This is known as colonel
selection.
The Helper T-Cells divide by mitosis, forming clones
of themselves, and Memory T-Cells.
The Helper T-Cells clones release a chemical (IL2)
that activates B-Cells, which have surface receptors
complimentary to the antigen. This is AMI
response.
11.The B-cell is activated by the T-Cell showing the
antigen.
12.B-Cells find and recognize the original Antigen.
The B-Cells produce clones, by a process called
Clonal Expansion. The B-Cells differentiate into
plasma cells and memory cells.
14.The memory cells serve to remember the antigen,
as the infection progresses.
15.The plasma cells make large amounts of antibodies,
and the antibodies are then attached to the surface
of the pathogen, to be identified by the Killer T-Cells.
16.The Helper T-Cells send signals to activate the Killer T-Cells, called
Cytotoxic T-Cells, which search out the antibody covered pathogens.
KTC perforates the cell membrane releasing perferin.
18.Cytotoxic T-Cells either destroy the invading cell, or, if it is an invading
virus, destroy the cell it has entered into.
Antigen– a molecule or particle recognized as foreign by the immune system

that can trigger an immune response.
Antibody - Immunoglobulin, A globular protein that recognizes an antigen.
• Antibodies have a T or Y shape made from polypeptide chains. The antibody is a
globular protein, that belong to a group of glycoprotein (remember the
glycoprotein on the cell membrane?)
Topic 6.4: Gas Exchange

7:51 PM
Ventilation:
• System which includes a pumping mechanism that moves air into and out of the
lungs efficiently, thereby maintaining the concentration gradient for diffusion.
o Significance - a pumping system that moves air into and out of the lungs
efficiently, thereby maintaining high concentration gradients for diffusion
(high to low) in the alveoli.
Gas Exchange:
• Is the exchange of gases between an organism and its surroundings, including
the uptake of oxygen and the release of carbon dioxide in animals and plants.
Cell Respiration:
• Is the controlled release of energy in the form of ATP from organic compounds in
cells. IT is a continuous process in all cells.
Inspiration and Expiration (Ventilation):
Inspiration
• External intercostal muscles contract
• Internal intercostal muscles relax
• Diaphragm moves down (contract)
• Ribs move up and out (volume increase in the thoracic cavity)
• Process :
o Air is drawn into the alveoli when the air pressure in the lungs is lower than
the atmospheric pressure, and it is forced out when pressure is higher than
atmospheric pressure. Since the thorax (chest cavity) is an air tight
chamber, pressure changes in the lungs occur when the volume of the
thorax changes
o Volume of the thorax (chest cavity) increase when the ribs move up and out
and also when the diaphragm moves down; creating a low pressure space
so that "air" can rush in from the high pressure outside the body
Expiration
• External intercostal muscles relax
• Internal intercostal muscles contract
• Ribs move down and in
• Diaphragm moves up
• Process:
o Volume of the thorax (chest cavity) decreases when the ribs move down in
and also when the diaphragm moves up; creating a high pressure space so
that "air" can rush out of the lungs.
Alveoli features:
• Film of moisture on the surface so that oxygen can dissolve (lipoprotein based
lubricating film)
• Thin membrane (alveoli) - single layer of flattened cells (1 cell thick)
• Dense capillary network (site of exchange of oxygen and carbon dioxide and
transport in blood)
• Large total surface area; concentration gradient
Topic 6.5: Nerves, Hormones, and Homeostasis
8:21 PM
The Nervous System consists
of the Central Nervous System
(spinal cord, brain) and the
peripheral nerves, called
neurons. Their function is to
transport messages in the form
of electrical impulses to
specific sites. For example,
breathing rate is controlled by
the Nervous System.
Thermoregulation is one of the
processes carried out by the Nervous System and the Endocrine System.
The Motor Neuron
• The Motor Neuron is a nerve cell, which transmits impulses from the brain to a
muscle or gland.
• The cell body contains a nucleus, rough ER, smooth ER, Golgi bodies, ribosomes,
lysosomes, mitochondria, which are also found in the axon.
• The axon is an extension of the cell body, and contains axoplasm, which is the
cytoplasm of the axon. The plasma membrane extends the entire length of the
axon.
• Around the axon, are Schwann cells, which provide a multi-layered lipid and
protein coating, called a myelin sheath. The sheath electrically insulates the
axon and increases the speed of electrical impulses.
• The nodes of Ranvier, are gaps between the myelin sheath. These help conduct
the electrical impulses.
• The axon terminates at a motor end plate, or axon terminal. These have synaptic
end bulbs that join to a muscle or gland.
• A nerve is a bundle of many nerve fibers that travel along the same path, in the
PNS. Nerve cell bodies that are clustered together form ganglia. It is along the
axon that nerve impulses travel.
• Together, the sensory neurons and motor neurons make up the peripheral
nerves. A neuron is an individual cell, which carries electrical impulses from one
point to the other very quickly. A group of neurons in a single structure is called a
nerve.
• Nerve impulses are conducted from receptors to the CNS by sensory neurons,
within the CNS by relay neurons and form the CNS to effectors by motor neurons.
The Process of Thermoregulation or Keeping Cool or Hot!:
• Body Heat is the heat produced by the biochemical reactions of the body.
• The rate at which body heat is produced is called Metabolic Rate and is
measured in kilocalories.
• The factors that affect metabolic rate are: Exercise, Nervous System – stress –
release norepinepherine, Hormones – testosterone and HGH, Body Temperature,
Ingestion of Food, Age, Others – Females, etc.
• In the body of a mammal or a bird, there are thermoreceptors in the skin. The
theromreceptors monitor the shell temperature, temperature on the skin. The
core temperature, is the body’s temperature below the skin’s surface, in the
body’s structures. The core temperature is a little higher than the shell
temperature.
• The theromreceptors monitor changes in the environment as well as changes in
the blood temperature (core). Cells in the hypothalamus, a region of the brain,
detect changes in the core temperature. If the core temperature goes too high,
the heat kills by denaturing body proteins (like frying an egg). If the core
temperature goes too low, it can cause cardiac arrhythmias (due to the slowing
down of biochemical reactions) or hypothermia.
HOT!!! :
If you get too hot, you need to cool down. This can be done in several ways:
• vasodilatation – blood vessels in the skin become wider, increasing blood flow,
causing the skin to become warmer, increasing the heat loss to the environment
• sweating – for fluid to evaporate, it requires energy, which is takes from the heat
of your skin
• decreased metabolism – all reactions produce waste heat – by slowing reactions
you decrease heat production
• behaviour adaptations – many animals change their behaviour to release heat –
e.g. birds bathe, dogs pant, then dig holes in the ground to allow heat from belly
to be absorbed by the earth, humans get into AC, put on cooler clothes
COLD!!! :
If you become cold:
• vasoconstriction – blood vessels in skin contract, decreasing blood flow and heat
loss
• *shivering – is when the muscles undergo tiny contractions. The muscle
contraction requires energy from ATP and this has to be made from cellular
respiration. Heat is produced that warms the blood.
• increased metabolism – break down of energy stores and more heat produced
• fluffing of hair or feathers – increases the insulating air layer around the
organism
• thickening of brown fat or blubber – adding insulation for those long winter
months
• special hair structure – polar bear hair absorbs UV light
• Heat is not produced or released equally from all parts of the body. Thus blood is
very important in moving heat around your body, and compensating for heat
losses in certain areas.
Nerve Impulse:
There are two main ideas to an impulse:
1. Resting Potential – an electrical impulse across a cell membrane when not
propagating an impulse.
2. Action Potential – the localized reversal and then restoration of electrical
potential between the inside and outside of a neuron as the impulse passes
along it.
The Neuron at rest- Resting Membrane Potential:

• The resting membrane potential occurs because there is a small build-up of
negative charge just
inside the membrane and an equal build-up of positive charge on the outside.
• The separation of the + and – charges is a form of potential energy. It is
measured in mill volts. A membrane that exhibits a membrane potential is
considered to be polarized.
• This resting state has a resting membrane potential of –70 mV. The negative
means that the inside is negative compared to the outside.
• The resting membrane potential (RMP) is like voltage stored in a battery. If you
connect a wire,
the electrons will flow. In a cell, ions carry out the flow of current.
The two main factors that contribute to the RMP are:

• Distribution of Ions across the plasma membrane
• Outside the cell, there is a greater concentration of Na+ and inside the cell there
is a greater concentration of K+.
• Both have a charge of +1 and this does not create a potential difference. The
distribution of Cl- and other negatively charged organic ions are responsible for
the RMP.
• The selectively permeable membrane
• The plasma membrane is 50 to 100 x more permeable to potassium that
sodium.
• As potassium leaves, the sodium does not leak in to replace it as fast as the
potassium leaks out.
• To maintain the electrochemical gradient, the membrane pumps out sodium and
brings back in potassium to maintain the negative RMP.
Action Potential – Impulse:

• The action potential is generated by a stimulus of a receptor or from an action
potential from another neuron. Information travels down the neuron.
• The impulse travels by the depolarization of the membrane and the
repolarization of the membrane to its RMP. The entire phase lasts about 1 m sec
(1/1000 s)
• The action potential generated acts according to the all-or-none principle. If the
depolarization reaches a threshold of about –55 mV (40 – 60 mV), the action
potential arises. If not, the action potential fades out. Every action potential has
a constant and maximum strength. It does not matter how strong or weak the
start of the impulse is. The action potential will travel regardless.
The action potential progresses as follows:

• The sodium pores in the membrane open. Due to the difference in
concentration, and the electromagnetic forces, the sodium flows into the axon.
• The inside of the axon, that was a negatively charged environment, is now more
positive. The potential difference is reduced, to about 0 mV. This is called
depolarization.
The sodium continues to go into the cell, driven by diffusion. This magnifies the
original impulse.
• The inside of the axon is now more positively charged than the outside. When
the value has reached +40 mV, the sodium pores shut and the potassium pores
open. This is the end of the depolarization phase.
• The potassium (K+) moves out of the axon, due to diffusion and electromagnetic
forces.
• The potential difference across the membrane will decrease. This is called
repolarization.
• Once the potential difference falls below 0 mV, the K+ is driven out by diffusion.
• Once the potential difference is back at –70 mV, the potassium pores close.
• What about the Na+ and K+?
They are in the wrong place. The sodium / potassium pump will return them to
their original position by active transport.
Hormone Secretion:
• Hormones are secreted by the Endocrine System through a series of endocrine
glands. The endocrine glands are ductless glands. They simply secrete hormones
into the blood, which transports it around the body. As the hormones pass cells,
only the cells with special receptors will react to the presence of hormones.
These cells are called target cells.
Controlling Blood Glucose Levels or That Sugar Rush! :
• The endocrine system is responsible for glucose levels in your blood. If the
concentration deviates from the set point of 5 mmol dm-1, then the homeostatic
mechanisms involving the pancreatic hormones insulin and glucagon are
initiated.
• The pancreas (which has exocrine glands, see digestion) also has endocrine
glands, which are clustered together in groups called the Islets of Langerhans.
• Cells in the islets have chemoreceptors, which are sensitive to levels of glucose
in the blood. Glucose is absorbed from digested food but can also be converted
to glycogen and stored. Levels of glucose can fluctuate. After a meal the levels
can rise and after exercise, the levels can lower. This is where the control
mechanisms come into place.
• If blood glucose levels are too low, the a cells in the islets in the pancreas will
secrete glucagons. Glucagon is a protein hormone and is secreted into the blood.
It will travel to all parts of the body, but its target cells are in the liver.
Hepatocytes (cells in the liver) will respond to glucagon’s presence by converting
glycogen to glucose and releasing it into the blood. The can also convert amino
acids into glucose (indirectly).
• If blood glucose levels are too high, the b cells in the islets will secrete insulin.
Insulin is a protein hormone that acts on the muscle cells. Its presence makes
muscle cells absorb glucose, and the muscle cells and Hepatocytes convert
glucose into glycogen. In adipose tissue (fat tissue), glucose is converted to fat
in the presence of insulin.
To summarize:
Blood Glucose is lowered by:
• Increased uptake into cells
• Increased conversion to glycogen in liver and muscles
• Increased conversion to fat
• Increased rate of cellular respiration
Blood Glucose is raised by:
• Increased breakdown of liver glycogen
• Synthesis of glucose from fats and amino acids
Homeostasis:
• Maintenance of a constant internal environment despite possible changes in the
external environment.
1. Oxygen and Carbon Dioxide Concentrations
•
As you saw in Gr. 11, the concentrations of the two gases are maintained with
the aid of the chemo detectors in the walls of the aorta and carotid artery, along
with the medulla oblongata
2. Blood Glucose – glucagons, insulin and the pancreas play a role here.
Body Temperature – generally around 37-38oC
4. Water Balance – maintained by the kidneys and large intestine.
5. Blood pH – maintained within 7.2 – 7.6, with the average being 7.4. As you
discussed in Gr. 11, the CO2 causes fluctuations in the pH and buffers to
minimize the change. The slight decrease is good, because it causes the O2 to
be released at the cell, called Bohr Shift.
The Process and Negative Feedback
• Is the control of a process by the result or effect of the process in such a way
that an increase or decrease in the results or effects is always reversed.
• The entire process requires certain elements to be present:
1. Sensors are required to measure the current conditions.
2. The sensors need to pass on the information to a centre, which knows the
desired value (the norm) and compares the current situation to the norm.
3. If the two are not the same, the centre activates a mechanism to bring the
current value closer to the norm.
• The whole point is that the action taken, aims at changing the situation so that
the action no longer is required.
Synaptic Transmission:
Electrical synapses are where two neurons may have their membranes pressed
close together with minute pores through them (called gap junctions).
• An impulse can travel from one membrane to the other causing a second action
potential in the second neuron.
For example, vertebrate fish have electrical synapses to activate tail flip, which
is used for quick starts for escape or catch prey.
Chemical synapses are two neurons close together, but do not touch. They are
separated by a synaptic cleft. Impulses cannot jump the cleft. The impulse is
transferred by chemicals. They are slower than electrical synapses.
• In the synapse, the action potential causes a change in the membrane
permeability for Ca+2. The Ca+2 flows into the synaptic knob.
• The surface releases a neurotransmitter substance in vesicles by exocytosis. The
neurotransmitter then diffuses across the synaptic cleft (20 nm) and attaches to
receptors in the post-synaptic membrane.
• When the neurotransmitter causes depolarization, the receptor sites change and
open Na+ channels. This causes an action potential to develop in the neuron.
This is called an excitatory synapse.
• If the neurotransmitter causes K+ and Cl- to open, is called an inhibitory synapse.
The potassium moves out and the chloride moves in, increasing the polarization
of the neuron and increasing the distance from the threshold value.
• After the post-synaptic membrane has been affected, enzymes break down the
neurotransmitter, some diffuse out of the synaptic cleft, some are taken back
into the cells.
What is diabetes?
• Diabetes mellitus is a group of disorders that all lead to an elevation of glucose
in the blood. - Type I Diabetes means there is an absolute deficiency of insulin.
(Also called Insulin Dependent Diabetes.) This condition requires regular
injections of insulin. In some cases, the Immune System attacks and destroys the
b Cells (autoimmune disease). As a result insulin is not present to aid the entry
of glucose into the cell. The cells use fatty acids, which leads to the creating of
ketones as a by-product. This can lead to ketoacidosis, a build up of ketones in
the blood, which lowers the pH of the blood and can lead to death. Other
complications are artherosclerosis, heart disease, poor wound healing
(gangrene), vision loss caused by cataracts, and damage to the renal blood
vessels in the kidney.
• Type II Diabetes is more common. The disease is caused by the body’s cells
becoming less sensitive to the insulin present, due to the excess insulin in the
system, due to diet and lifestyle. There is insulin present and produced and this
is why it is called Non – Insulin Dependent Diabetes. Therefore the body cannot
process the sugars, causing an imbalance.
Topic 6.6: Reproduction

5:55 PM
Roles of Testosterone in Males:
1. Week 7 of embryonic development, testosterone initiates the development of
male genitalia.
2. Around mid teens, testosterone initiates the development of secondary sexual
characteristics
• increase in muscle mass
• increase in the length of the long bones (height)
• increase in the length of the vocal cords (voice deepens)
• spermatogenesis
• growth of the penis and testis.
• Post puberty testosterone maintains the production of sperm cells and the male
sex drive.
In vitro Fertilization:
• “In vitro” means “in glass”. In this procedure, the egg and sperm cells meet
outside the body of the female. A successful procedure produces the test tube
baby. The first test tube baby was Louise Brown, born in 1978.
• IVF is usually used for women who have blocked oviducts or who cannot sustain
a pregnancy. The original eggs can be used or donor eggs can be used. In both
cases a women is given hormones to allow more than one follicle to ripen. A
needle is placed in the follicle and the egg is sucked out. This is repeated until all
the eggs are harvested.
• The egg cells are then mixed with sperm cells. The fertilized egg cells are
cultivated and either placed in the uterus or frozen to be used later. One embryo
can be placed or many can be placed depending on the rate of success of the
implantation.
• Hopefully, the implanted embryo completes gestation.
Ethical Issues:
• Advantages of IVF: there are as many reasons for this treatment as there are
people seeking this treatment. As examples
• over comes infertility
• allow families for people who must be sterilized e.g. radiography/chemo
therapy cancer patients
• Disadvantages of IVF:
• what happens to unwanted embryo's
• what happens to orphaned embryo's
• should infertility be by-passed
Hormones and the menstrual cycle:
In the female there are four hormones at work:
1. Follicle Stimulating Hormone (FSH)
2. Luteinizing Hormone (LH)
3. Progesterone
4. Estrogen
FSH – is produced in the anterior pituitary and starts off the cycle by ripening the
follicle.
Estrogen – is released from the growing follicle. It increases the thickness of the
endometrium and inhibits the production of FSH. In turn it stimulates the production
of LH. It also promotes the development of secondary female sex characteristics
and the inhibition of mild secretion. High levels of estrogen can cause nausea
(morning sickness?).
LH – is released from the anterior pituitary. It stimulates ovulation and the formation
of the corpus luteum. The corpus luteum produces progesterone.
Progesterone – keeps the endometrium intact and inhibits both FSH and LH. It also
will inhibit milk secretion and ovulaltion.
If fertilization does not occur, the corpus luteum breaks down and the pituitary
produces more FSH to stimulate another follicle.
Biology Syllabus - HL
8:36 PM
Topic 7 - Nucleic Acids and Proteins
9:10 PM
Topic 7.1: DNA Structure
9:10 PM
Structure of a Nucleosomes:
• Coiled DNA looped around protein beads
• The packaging protein of the nucleosomes, called a histone, is a basic (positively
charged) protein containing a high concentration of amino acids residues with
additional base groups (-NH2), such as lysine and arginine. In nucleosomes, eight
histone molecules combine to make a single bead. Around each bead, the DNA
double helix is wrapped in a double loop.
• Whole beaded thread is itself coiled up, forming the chromatin fiber. The
chromatin fiber is again coiled, and the coils are looped around a 'scaffold'
protein fiber, made of non-histone protein. The whole structure is folded
(supercoiled) into the much condensed metaphase chromosome.
• Nucleosomes are the key structures that facilitate supercoiling of these
phenomenal lengths of DNA that are packed in the nuclei. Also, they facilitate
access to selected lengths of the DNA (particular genes) during transcription.
Topic 7.5: Proteins

9:25 PM
• Structure of
Proteins:
• Differ in the variety,
number, and order of
their constituent
amino acids.
Primary Structure (1st
o)
• The order of their
amino acid residues
attached by peptide
linkages.
• Proteins differ in
variety, number, and order of their constituent amino acids. (Order matters)
Secondary Structure (2nd o)
• Develops when parts of the polypeptide chain take up a particular shape,
immediately after formation at the ribosome. Result, chain becomes folded or
twisted, or both, in various ways.
• Most common shapes are formed either by coiling to produce a helix or folding
into sheets.
• These shapes are permanent, held in place by hydrogen bonds.
Tertiary Structure (3rd o)
• The precise, compact structure, unique to that protein, which arises when the
molecule is further folded and held in a particular complex shape.
• The result shape is permanent by 4 different types of bonds, established
between adjacent parts of the chain.
• Hydrogen bond
• In a hydrogen bond a hydrogen atom is shared by two other atoms
• Are weak but common in many polypeptide chains, they help to
stabilise the protein molecule.
• Van der Waals forces (specialised hydrogen bonding)
• These come into play when two or more atoms are very close
• Disulphide bond
• Strong covalent bonds formed by the oxidation of -SH groups of two
cysteine side chains
• Ionic bond
• Electrostatic interaction between oppositely charged ions; may often
be broken by changing pH
• Some proteins in 3rd o structure that is long, much-coiled, and narrow shaped
called Fibrous Proteins.
• Ex. Keratin (nails), Collagen ( bones)
• More spherical structured proteins called Globular Proteins.
• Highly soluble in water
• Ex. Catalyst or Insulin (hormones)
Quaternary Structure (4th o)
• Arises when two or more proteins become held together, forming a complex,
biologically active molecule.
• Each subunit is a conjugated protein, consisting os a protein chain (globin)
attached to a prosthetic group (haem). A prosthetic group is a 'helper' molecule
to be biologically active.
• Ex. Haemoglobin, 4 polypeptide chains help around a non-protein haem group.
Polar/ Non-Polar Properties of Amino Acids
• Amino Acids with Polar R group are hydrophilic
• Make bulk of protein hydrophobic which is compatible with hydrocarbon tail of
phospholipid molecules of bilayers.
Function Role/Examples
Biological Alter the speed of the chemical reactions, making possible
catalysts biochemical changes of organisms under the normal conditions of
enzymes life. (ex. Digestive enzyme pepsin and carbonic anhydrase of red
cells.
Defence Antibodies secreted by B-lymphocytes (a type of white cell) in
against response to non-self substances (antigens) that may invade the
disease body. Antibody proteins are known as immunoglobulin.
Transport Haemoglobin in red cells – a conjugated protein which combines
of with oxygen in the lungs and frees the oxygen in respiring tissues.
respiratory
gases
Muscle Myosin and actin proteins of voluntary muscle myofibrils bring
movement about muscle contraction by reaction with ATP, triggered by
calcium ions.
Chemical Hormones are chemical messengers produced and secreted by
Messenger cells of endocrine glands. Some are polypeptides or proteins
s others are hormones or steroids.
Structural Fibrous Proteins (ex. Collagen in bone, keratin or hair)
Support
Topic 7.6: Enzymes

9:48 PM
Enzymes:
• Metabolic pathways consist of chains and cycles of enzyme-catalyzed reactions
Induced Fit:
• Enzymes are highly specific in their action which makes them different than most
inorganic catalysts.
• Specific because of the way enzymes bind with their substrate at the active site,
which is a pocket or crevice, in a protein.
• The necessity of binding the substrate at the active site of the enzyme before
catalysis explained why changed in temperature and pH affected enzyme action
since these changes often cause the shape of the enzyme molecule to change.
• However, the lock and key model does not fully account for the combined events
of binding and simultaneous chemical change observed in most enzyme-
catalyzed reactions.
o At the active site, the arrangement of certain amino acids residues in the
enzyme matches certain groupings of the substrate molecule, enabling the
enzyme-substrate complex to form. As the complex is formed, it seems an
essential, critical change of shape is induced in the enzyme molecule. It is
the shape change that is important in momentarily raising the substrate
molecule to the transitional state in which it is able to react.
o With a transitional state achieved, other amino acid residues of the active
site bring about the breaking of particular bonds in the substrate molecule,
at the point where it is temporarily held by the enzyme. Because different
enzymes have different arrangements of amino acids in their active sites,
each enzyme catalyses either a single chemical reaction or a group o
closely related reactions.
• In conclusion, induced fit also accounts for the broad specificity of some
enzymes (that is, the ability of some enzymes to bind to several substrates).
Competitive Inhibitors Non-competitive Inhibitors
Inhibitor chemically resembles the Inhibitor chemically unlike the substrate
substrate molecule and occupies molecule, but reactions with bulk of
(blocks) the active site enzymes, reducing accessibility of active
site
With a low concentration of inhibitor With low concentration of inhibition,
increasing concentration of increasing concentration of substrate
substrate eventually overcomes cannot prevent binding – some inhibition
inhibition as substrate molecules remains at high substrate concentration
displace inhibitors.
02 competing with CO2 for active Cyanide ions blocking cytochromo
site of rubisco oxidase in terminal oxidation in cell
aerobic respiration
Control of Metabolic Pathways
• Metabolic pathways are switched off by a process known as allosteric inhibition.
• Enzyme has two sites, one is active site and other is an additional site.
• Once a substrate has locked into one, the whole enzyme is rendered
inactive.
• The enzyme machinery of cells plays a part in the control of the pathways of
metabolism. Achieve this by:
• Specificity.
• Reaction occurs only in the presence of a specific enzyme.
• Because enzymes are effective in very small amounts
• Production of a specific enzyme leads to immediate reactions and the
formation of products.
• Where enzyme compete for the same substrate molecules, the amount of
each enzyme present, and how readily each forms its enzyme-substrate
complex.
• Decides the extent to which pathways operate
• Enzyme production only in the presence of the substrate.
• Substrate molecule triggers the synthesis machinery by which
enzymes are produced.
Inhibitors of enzymes
• Certain substances present in cells (and some which enter from the
environment) may react with an enzyme altering the rate of reaction. These
substances are called inhibitors.
• Their effects are to generally lower the rate of reactions.
• They have helped our understanding of
• Chemistry of the active site of enzymes
• Natural regulation of metabolism and which pathways operate
• Ways certain commercial pesticides and some drugs work, namely by
inhibiting specific enzymes and preventing particular reactions.
• Two types:
• Competitive inhibitors
• Molecules that sufficiently resemble the substrate in shape may
compete to occupy the active site.
• These are not acted on by an enzyme and turned into products, as
normal substrate molecules are, they tend to remain attached.
• Non-competitive inhibitors
• An inhibitor may be unlike the substrate molecules and yet still
combine with the enzyme.
• The attachment occurs at some other part of the enzyme probably
quite close to the active site. Here the inhibitor either partly blocks the
access to the active site by substrate molecules or it causes the active
site to change shape and thus be unable to accept the substrate.
Metabolism
• Totality of enzyme catalyzed chemical reactions of life. Molecules involved called
metabolites.
• Metabolites are made in organisms and imported from the environment.
• Chemical energy exists in the structure of the molecules. Every molecule
contains a quantity of stored energy equal to the amount of energy needed to
synthesise it. Chemical energy does not exist in the chemical bonds of
molecules, but rather in the structural arrangement of the molecules.
• When energy is no longer in store but on the move it is active energy.
• Stored energy in the molecule that is available to do work is called free
energy.
• Two types;
• Anabolic reactions
• larger molecules are build up from smaller molecules
• Endergonic reactions
• Energy requiring reactions.
• Energy has to be put in b/c the products have more stored energy
than he reactants.
• Catabolism reactions
• larger molecules are broken down
• Exergonic reactions
• Energy releasing reactions
• Products have less stored energy than reactants
• Metabolism – anabolism + catabolism
• Endergonic reactions are made possible by being coupled to Exergonic reactions
• Coupling occurs through ATP
• ATP is referred to as the energy currency molecule.
• Work in metabolism by linking energy-requiring reactions and energy
yielding reactions.
Exothermic Reactions (Catabolism and Anabolic reactions):

• Releases energy in the form of heat
• Temperature of the reaction increases
• A + B = C + D + heat
• As molecules react they become unstable.
• This is called transition state because the products are formed immediately.
The products have a lower level of energy that the substrate molecules.
• The minimum amount of energy needed to raise substrate molecules to
their transition state is called activation energy.
• Enzymes work by lowering the amount of energy required to activate the
reacting molecule.
• Boulder on hillside model.
• Boulder (substrate) is perched on a slope, prevented from rolling down hill
by a small hump (activation energy) in front of it. The boulder can be
pushed over the hump or the hump can be dug away (= lowering the
activation energy) allowing the boulder to roll down hill and shatter at a
lower level (products).
Topic 8.0: Cell Respiration and Photosynthesis

5:57 PM
Topic 8.1: Cell Respiration
5:59 PM
Topic 8.2: Photosynthesis
6:00 PM
Topic 9: Plant Science
10:20 PM
Topic 9.1: Plant Structure and Growth
10:20 PM
Plant Tissues:
• A leaf consists of a leaf blade
connected to the stem by a
leaf stalk. It grows from the
apical meristem at the tips of
the stem. Leaves must have
a large surface area and a
small space between the upper and lower surfaces. The leaf is an organ
specialized for photosynthesis.
The leaf is composed of:
1. The outer structure - Epidermis
It is a tough, transparent layer.
a. The upper epidermis has an external waxy cuticle on its surface. The
cuticle is impervious and effectively reduces water vapour loss from the
leaf surface.
b. The lower epidermis has a thinner
cuticle, with specialized
epidermal cells called guard cells
and pores called stomata
(stoma).
They are the sites of inward diffusion
of carbon dioxide. Within the inner
structures are air spaces that enhance
the diffusion of carbon dioxide to the
cells.
2. Inner part of the Leaf
The inner part of the cell consists of
mesophyll cells that are spread out
over a wide area, so the amount of
light absorbed is maximized.
b. In the upper layer, the mesophyll
cells are called palisade
mesophyll cells and are tightly
packed close to the upper surface of the epidermis. They are packed with
chloroplasts.
b. In the lower half, there are spongy mesophyll cells. These are loosely
packed in the lower portion of the leaf, with large air spaces in between
and fewer chloroplasts.
c. Between the mesophyll cells lies a network of vascular bundles or the
veins.
i. The vascular bundles contain xylem and phloem. This brings water
(xylem) to the cells and transports the sugars made (phloem).
ii. Also; support the leaf. Mesophyll tissue is supported by the turgidity of
all its cells, contained in the non-elastic epidermis and reinforced by
the network of bundles.
Main functions:
2. Purpose of waxy cuticle - keeps water from evaporating from the leaf surface
(water conservation)
2. Leaf Epidermis is transparent - Allows photosynthesis (absorption of light)
3. Leaves are broad and flat - Gives a large surface are for gas exchange (gas
exchange)
4. Large air spaces in the leaf tissue - Enhances the diffusion of carbon dioxide into
cells, which enhance the transportation of water and products of photosynthesis
out of cell
5. Inner cell contains mesophyll cells that are spread out - light absorbed is
maximised.
6. Xylem tissue - supports the leaf, and transports water
7. Phloem tissue - transports photosynthetic products around cells
Plant Growth
Meristems
• Plants grow throughout their lifetime. This pattern of growth is called
indeterminate. Plants, of course, will die, based upon their life cycle. Annuals
complete their life cycle in one year, whereas perennials live many years and
usually die due to a disease or environmental factor.
Indeterminate growth is due to the meristematic tissue. In dicots, there are:
1. Apical Meristems
Sometimes referred to as primary meristems, these occur at the tips of roots
and stems. Primary tissue is produced and causes primary growth. In the root
this allows the structure to extend through the soil. In the stem, it allows the
stem to grow longer and increases the exposure to light and carbon dioxide.
This type of growth results in herbaceous, non-woody stems and roots.
• Monococotyledonous plants
2. Lateral Meristems
• Lateral meristems allow growth in thickness of plants. This is referred to as
secondary growth. Most trees and shrubs have active lateral meristems. These
plants have two types of lateral meristems:
o Vascular Cambium produces secondary vascular tissue. It lies between the
xylem and phloem in the vascular bundles. On the inside is produces
secondary xylem, which is a major component of wood. One the outside it
produces secondary phloem.
o Cork cambium occurs within the bark of a plant and produces the cork cells
of the outer bark.
• Dicotyledonous plants
Modifications and Adaptations of roots, stems and leaves:
• The structures of the root, leaf and stem are very similar, with some differences.
As the principle plant organs, they are used to build the structures that they
need for water and mineral absorption, support and photosynthesis.
• Other functions can be carried out if the principle structures are modified.
Roots- Roots can be modified, based upon the needs of the plant.
Besides tap roots and lateral (fibrous) roots there are:
• Storage Roots – specialized cells within the roots store large quantities of
carbohydrates and water. Ex. Carrots and Beets.
Stems - Stems are capable of great modification.
• Bulbs – vertical, underground stems consisting of enlarged bases of leaves that
store food. Ex. Onions
• Tubers – horizontally growing stems below ground that are modified as
carbohydrate- storage structures. Ex. Potatoes
Leaves - They still function as photosynthesizing factories, but can adapt.
• Tendrils – structures that coil around objects to aid in support and climbing. Ex.
Pea plants
Monocots Dicots
Number of Cotyledons 1 2
Numbers of Organs in the 3 or 6 4 or 5
Flowers
Meristems Apical only – stems Apical and lateral so stems can
cannot grow wider widen
Leaf Attachment Around the whole stem To one side of the stem by a leaf
circumference stalk
Method of Formation of By formation of roots By branching from other roots
new roots from the stem
Vascular Tissue in the Vascular Bundles Branching to form a network
Stem spread throughout
Leaf Veins Parallel Branching to form a network
Growth and Phototropism

• Plants use hormones to control the growth of stems and roots. Rate and
direction are controlled. Both light and gravity influence growth. In light they
grow towards the brightest source and in the dark, grow in the opposite
direction to gravity. The responses are called tropisms. The growth towards light
is called phototropism.
• The steps of phototropism are:
1. Photoreceptors (proteins called phototropins) absorb light.
2. Light of an appropriate wavelength is absorbed which stimulates the
photoreceptors to bind in the cells and transcribe glycoproteins which will aid in
the transport of a plant hormone called auxin where it is needed.
a. Auxin does many things in the plant:
i. It promotes the elongation of cells in stems, by loosening the
connections between the cell walls and cellulose microfibrils
ii. Is synthesized in the tips of growing stems and transported down to
stimulate growth.
iii. If phototropins detect a greater light intensity on one side of the stem
than the other, it is transported to the shadier side. This promotes the
stem to grow more on the shadier side and go towards the light.
Which allows the leaves on the sunny side to get more light and
photosynthesize at a greater rate.
Topic 9.2: Transport in Angiospermophytes

10:55 PM
Transpiration:
• Transpiration – the loss of water vapour from the leaves and stems of plants.
• As water is lost, the amount of water in the plant decreases. A pull is created in
the plant to “pull” water up the plant. This is similar to maintaining
homeostasis.
• Water is taken up the stem from the roots by many processes:
1. Mass Flow or Apoplast Pathway, into the xylem.
• In the root, the xylem is centrally located, in the stem, the xylem occurs in the
ring of vascular tissue. Xylem, therefore runs from the roots to stem and then to
leaf.
• Xylem begins as elongated cells with cellulose walls and living contents,
connected end to end. During development, the end walls dissolve away, and
the mature xylem is a long hollow tube. As the tubes extend, the tissue dies.
Therefore, xylem is dead tissue, and is composed of two elements:
o Tracheids – narrow cells arranged in columns, overlapping at tapered ends
giving some support to the plant. The ends have pits for water to move
rapidly from one cell to the next. Due to their structure, they are less
efficient that xylem vessels.
o Xylem vessels – larger columns of cells. When the dead cell walls
disappear, they become wider and transport water more efficiently. Since
they are so wide, they are reinforced by ligin for support of the plant. This
only occurs in angiosperms.
2. Transpiration Pull
Transpiration controls the flow of water. But, how does water move against
gravity?
• First, in the leaf are stomata. These open and close to control the amount of
water present in the leaf. Around each stomata are guard cells, which open and
close, depending on the turgor of the cells.
• When the plant is well hydrated, the guard cells are swollen, causing them to
open, due to the pressure on the cells walls. When the plant dries out, the guard
cells sag and the stomata close. Water loss is stopped and gas exchange is
halted.
• Other external factors that affect the opening and closing of stomata are:
o Light causes stomata to open
o Low CO2 levels in the air spaces in the cause the stomata to open
o Shortage of water causes the stomata to close
• When leaves are deficient in water, they synthesize a hormone called abscisic
acid. This closes the stomata and overrides any external stimuli – the stomata
close. This allows the plant to avoid dehydration and death.
When the stomata are open, water evaporates out of the leaves, diffusing water
vapour out. This maintains a concentration gradient that requires more water.
• The water in the stem, which is connected by xylem, moves up to replace the
water lost by transpiration. As a result, the water is pulled up the plant.
• Cohesion and adhesion:

• The transpiration pull is assisted by the special cohesive and adhesive
properties of water.
• Water is polar and is held together by its cohesive forces. Therefore, the water
molecules stick together and flow up the stem together.
• Water molecules are pulled through the plant and they adhere to the walls of
the xylem. This creates one unbroken column of water through the plant. The
upward pull on the cohesive sap creates a tension (a negative pressure.) This
facilitates water uptakes and movement through the plant.
• Root pressure:
• Water entering the stele from the soil creates a root pressure; a weak 'push'
effect for the water's upward movement through the plant. Root pressure can
force water droplets from some small plants under certain conditions
(guttation), but generally it plays a minor part in the ascent of water.
Root Systems
• One of the earliest stages in the development of an embryo plant is the
formation of a root. When seeds germinate, the embryonic root grows out of the
seed coat and downwards into the soil.
• Two main types:
Tap Roots – Roots that go deep into the soil and anchor the plant. They are the
site of absorption of water and ions from the soil.
2. Lateral roots - When the roots branch out to the side. They search for water
outside their canopy.
The seedling root develops branches in some plants and hairs, which absorb
more water in dry soil. The branching helps with absorption by increasing the
surface area. The water flows in by osmosis.
• Roots have an epidermis that forms a protective outer layer. The inner layer is
called the cortex. This is used for conducting water and can be modified to store
nutrients. There is an endodermis that surrounds the vascular layer that
contains xylem and phloem.
Uptake of Minerals in Root:
• There are three ways that minerals can move from the soil to the root.
• Active Transport using protein pumps in the plasma membranes of root cells. As
the concentration outside the cells decreases, a concentration gradient is built
up and then the ions flow in by diffusion.
• Mass Flow or the water carrying the ions goes into the root.
• Fungal hyphae – fungus grows on the surface of roots and sometimes into the
cells of the roots. The hyphae grow into the soil and absorb minerals ions and
phosphate from the surface of soil particles. The ions are supplied to the roots
and allow the plant to grow in mineral poor soil. Some plants supply sugars, and
other nutrients to the fungus. This is an example of a mutualistic relationship.
Factors affecting Transpiration
• The rate of transpiration is the amount of water vapour that a plant loses from
its leaves and stems per unit of time. The rate depends on the:
o Size of the plant
o The thickness of the cuticle
o How widely spaced the stomata are
o Whether the stomata are open or closed
• These are the biotic factors. These are the factors the plant can control. There
are four abiotic factors that affect the rate of transpiration.
Temperature – affects the rate at which water evaporates from the surfaces
inside the leaf. At higher temperatures, evaporation increases. The higher
temperatures also increase the rate of diffusion between the inside of the leaf
and the outside. The increase in temperature allows the air to hold more
moisture and reduces the relative humidity of air outside the leaf. The
concentration gradient increases, doubling the rate for every 10oC increase in
temperature.
Humidity – is the water vapour content of the air. It is measured as a percentage
of the maximum amount of water vapour the air can hold. The humidity inside
the leaf is always around 100%. The lower humidity outside the leaf causes the
evaporation to be higher, increasing transpiration. Evaporation is much higher
in dry air, so on hot / cold, dry days, transpiration increases dramatically.
Wind – air currents take water vapour away from the leaf surface, keeping the
concentration gradient large, and increasing the rate of transpiration. On calm
days, the humidity around the leaf increases, slowing down transpiration.
Light – in light, photosynthesis increases and stoma open to allow CO2 in, but
also water out. Therefore, transpiration increases. In darkness, there is no need
to absorb CO2, and water can be conserved, as the stoma close and
photosynthesis decreases.
Sources Sinks
Photosynthetic tissues: Roots that are growing or absorbing
• Mature green leaves mineral ions using energy from cell
• Green stems respiration
Storage organs that are unloading Parts of the plant that are growing
their stores: or developing food stores:
• Storage tissues in germinating seeds • Developing fruit
• Tap roots or tubers at the start of the • Developing seeds, Growing leaves
growth season
Translocation:
• Phloem transport may occur in either direction in stem leaves and roots, and is
believed to move by mass flow. How this works is:
o Solutes are loaded into the phloem sieve tubes, requiring ATP and then the
solutes flow through the phloem from a region of high hydrostatic pressure
to low hydrostatic pressure.
o Hydrostatic pressure is high around photosynthetic cells in the light
(mesophyll of the leaf), and in the phloem sieve tubes nearby. It is the
presence of the sugars, which concentrate the fluid and creates a high
osmotic pressure. Water flows in, raising the hydrostatic pressure further.
This is called a source area.
o Hydrostatic pressure is low in cells where sugar is converted to starch and
stored. Areas of storage are the cortex of the root, stem, seeds and in the
nearby phloem tissue. Here the removal of sugars lowers the osmotic
pressure, and water flows away. These storage areas are called sink areas.
(Diagram 9)
• Sometimes sinks turn into sources and visa versa, and therefore, phloem must
be able to transport in both directions. Unlike the vessels in animals, there are no
valves or a central pump. However, they are similar because in both, fluid flows
inside tubes due to pressure gradients. Energy is needed for both, and therefore,
both are active processes. The movement of substances in phloem is called
active translocation for this reason.
Adaptations of xerophytes:
• Xerophytes are plants that have adapted to arid climates. Examples are cacti are
an example.
In order to adapt to dry climates, xerophytes must decrease water loss due to
transpiration. Therefore, the plants have adapted by:
o Small, thick leaves reducing the water loss by deceasing surface area
(needles or green stems)
o Reducing the number of stomata
o Having the stomata located in crypts or pits on the leaf surface, which
causes higher humidity near the stomata
o Having a thickened, waxy cuticle
o Having hair-like cells on the surface to trap water vapour
o Becoming dormant in the dry months
o Storing water in the fleshy stems and restore the water in the rainy season
o Using alternative photosynthetic processes called CAM photosynthesis
(Crassulacean acid metabolism) and C4 photosynthesis. CAM plants close
stomata during the day and incorporate carbon dioxide at night. C4 plants
have stomata open during the day, but take in carbon dioxide more rapidly
than non-specialized plants.
Support of Terrestrial Plants:
• Thickened Cellulose - Cellulose located in the walls
• Cell Turgor - Cells which are almost rigid because of their high pressure
• Lignified Xylem - Making it woody and hard
Topic 9.3: Reproduction in Angiospermophytes

11:35 PM
Pollination, Fertilization, Seed Dispersal:
• Pollination is the transfer of pollen from a
mature anther to a receptive stigma.
• The pollen may come from the anthers or the
same flower or flowers of the same plant,
which is called self-pollination. When pollen
comes from flowers on a different plant of the
same species, which is transferred, is called
cross-pollination.
• Transfer of pollen is usually by insects,
wind, birds or bats. Flowers that attract
insects usually produce nectar.
• Fertilization occurs after the pollen grain has
landed on a stigma, and germinated there. It is the fusion of the male and
female gametes.
• The pollen produces a tube, which grows down between the cells of the
style, and through the ovule. The pollen tube delivers two male nuclei. One
of these male nuclei then fuses with the egg nucleus in the embryo sac,
forming a diploid zygote. The other fuses with the other nucleus, which
triggers formation of the food store for the developing embryo.
• Seed formation and dispersal; The seed develops from the fertilized ovule and
contains and embryo plant and a food store. After fertilization:
• The zygote grows by mitosis. The cells form the embryonic plant, consisting
of an embryo root and stem.
• A seed leaf or cotyledon forms. The seed leaf has two forms, as
angiosperms have two classes.
• Monocotyledons – have a single seed leaf
• Dicotyledons – have two seed leaves
• The formation of stored food reserves is triggered. In many seeds the food
store is absorbed into the cotyledons.
• As the seed matures, the outer layers of the ovule become the protective
seed coat, or testa. The micropyle is a small hole through the testa, where it
was attached to the parent plant. The whole ovary develops into the fruit.
The water content decreases and the seed moves into a dormancy period.
Water only makes up 10 –15% or the seed weight.
• Dispersal of the seed is needed to make sure there are not many seeds
close together, as they will compete for resources. Therefore they travel
long distances from then parent plant.
• The type of seed dispersal depends on the structure of the fruit; dry and
explosive, fleshy and attractive for animals to eat, leathery and winged to
catch the wind, or covered in hooks to catch the coats of animals.
The parts of flowers:
Sepal (together called the calyx) – enclose and protect the flower in the bud, and
are small, green and leaf like.
Petals (together called the corolla) – coloured and used to attract insects or other
small animals to pollinate the flower.
Stamen – male part of the flower, which consists of:
Anthers – produces the male sex cells house the pollen grains
Filament or stalk – holds up the anther
Carpels – female part of the flower, and they may be on their own or fused together.
Each carpel consists or:
Ovary – at the base of the carpel which contains the female sex cells (containing
many ovules)
Stigma – sticky top of the carpel (to receive the pollen)
Connecting style – supports the stigma
Control of Flowering in Angiosperms

• Light is required for photosynthesis and controls aspects of growth and
development. Plants are able to detect the presence of light, its direction,
wavelength and intensity.
• Photoperiodism is the plant’s response to light involving the lengths of day and
night. It is the length of day and night that controls flowers.
• When the plant is young and structures, such as leaves, stem and roots grow,
this is called the vegetative phase. When the plant is ready to reproduce, this is
called the reproductive phase and flowers form. As mentioned before, flowers
are very important, as they attract pollinators.
• It is actually the length of night that controls the flowering process in the long-
day and short-day types. The control by light is brought about by a special blue-
green pigment called phytochrome.
o Phytochrome is a large protein that is not a plant growth hormone, but a
photoreceptor pigment.
• There are two forms of phytochrome:
o inactive form Pr
o active form Pfr
• When red light (600 nm) is present in available light, the Pr is converted to Pfr. It
is done rapidly. The active phytochrome can absorb far-red light (730 nm). Pfr is
rapidly converted back to the inactive form in daylight. In darkness, the active
form slowly converts back to Pr. The slow conversion allows the plant to time the
dark period and controls the flowering in short-day and long-day plants.
What does this all mean?
• In long-day plants, the remaining Pfr at the end of a short night, stimulates the
plant to flower. It acts as a promoter in these plants. The long day, long period of
daylight, causes the accumulation of Pfr.
In short-day plants, enough Pfr acts as an inhibitor. It has been converted to Pr,
to allow flowering to occur. In other words, the very long nights required by
short-day plants allow the concentration of Pfr to fall to a low level, removing the
inhibition.
Plant Type Flowering and Light Examples
Long-day plants Bloom when days are longest Radishes, spinach and
and nights are shortest lettuce
(midsummer)
Short-day plants Bloom in spring, late summer Poinsettias,
and autumn when days are chrysanthemums and
shorter asters
Day-neutral plants Flower without regard to day Roses, dandelions, and
length tomatoes
The metabolic processes during the germination of a seed are as
follows:
1. The seed absorbs water.
2. Gibberellin, or gibberellic acid, is released after the uptake of water and is a
plant hormone.
3. Gibberellin triggers the production of amylase.
4. Amylase causes the hydrolysis of starch into maltose. The starch is present in
the seed’s endosperm or food reserve.
5. Maltose is then further hydrolysed into glucose that can be used for cellular
respiration or may be converted into cellulose by condensation reactions.
6. Cellulose is used to produce the cell walls of new cells.
7. The seed coat cracks and out comes the plant.
• The seedling develops and functional leaves appear. Photosynthesis takes over
and becomes less dependent on the maltose.
• The seed will eventually become a mature plant and produce seeds of its own,
starting the whole process over again.
The conditions that are essential for germination are:
1. Water – hydrates plant and activates amylase and removes the abscisic acid
2. Oxygen – for Cellular respiration
3. Period of warm temperatures as this is important for enzyme production.
Topic 10: Genetics

6:01 PM
Topic 10.1: Meiosis
6:01 PM
Topic 10.2: Dihybrid Crosses and Gene Linkage
6:02 PM
Topic 10.3: Polygenetic Inheritance
6:03 PM
Topic 11: Human Health and Physiology

11:55 PM
Topic 11.1: Defence against Infections disease
11:56 PM
Monoclonal Antibodies:
• Monoclonal Antibodies are highly specific, purified antibodies that are produced
by a clone of cells, derived from a single cell, and they recognize only one
antigen. As was mentioned before, polyclonal immune response means many
different kinds of antibodies are produced. Scientists have developed a
technique to form many antibodies of the same type.
How to do it?
• You take an antigen and inject it into a mammal, like a mouse. The mammal’s
plasma cells produce antibodies through a primary response. This response is
polyclonal. After an appropriate period of time, the spleen of the animal is
harvested. The B-cell for that antibody is isolated. In order to keep the B-cells
alive, they are fused with cancerous myeloma cells. A few of the cells fuse
together and become a cell called a hybridoma. The hybrid cells have the
characteristics of both cells; they produce antibodies of a particular type and are
very long lived. The hybrid plasma cells are put in an environment in which they
can only survive, and those cells that did not fuse together die.
• The hybridoma cells are cultured in separate containers. Each container is tested
for the presence of a particular antibody, called an ELISA (enzyme-linked
immunosorbent essay). The pure colony of B-cells are identified. As a result of
the hybridization, the cells are virtually immortal.
• The pure antibody can be used to determine drug levels in blood, allergies, and
diseases such as rabies, hepatitis and STD’s.
• A pregnancy test, looks for HCG (human chorionic gonadotropin). The embryo
produces HCG early in pregnancy. The hormone shows up in the urine and blood
of the female. You produce antibodies to recognize HCG as an antigen. You take
the antibodies, and chemically bond them to an enzyme which catalyzes a color
change and put them on a testing strip. HCG is present in urine of a pregnant
female. If the HCG is present, it will attach to the antibodies, changing color and
giving a positive test. They are also used to detect the presence of HIV.
• Monoclonal antibodies can be used for treatment also. Anthrax is a disease
caused by a bacterium that produces toxins. It is often lethal, even when
antibiotic treatments are given. Monoclonal antibodies are being developed to
neutralize one of the toxins and therefore doctors can sustain the patient’s life
until their body produces the toxin naturally. Another possible treatment is for
cancer. If the monoclonal antibodies can carry a toxin specific to the cancer cell,
we might be able to pin-point the cancer cell and not have to use broad
treatment techniques.
Blood Clotting
• Since fluid loss is a one way ticket to the morgue, it is very important to stop
the escape of blood from a cut or wound. It is equally important the blood does
not clot at other times inside the veins and arteries. Also, we need to seal off
the break to prevent pathogens from entering our body.
Blood clotting goes like so:
1. Within a matter of seconds, the process begins. The blood will react with the air
and substances from the damaged cells. The damaged cells release chemicals
which stimulate platelets to adhere to the damaged area.
2. The traumatized tissue, releases a tissue protein called thromboplastin, which
initiates the formation of prothrombinase, along with coagulation factor VII and
X.
3. Once factor X is activated, it combines with Ca+2 ion and factor V. This will
change the prothrombinase (or prothrombin) to thrombin.
4. The thrombin will hydrolyse soluable fibrinogen to insoluable fibrin molecules.
These form a network to catch the erythrocytes and form a clot.
5. The epithelial tissue can grow under the build up of clot tissue and repair the
area.
Immunity and Vaccination:
• Some people are immune to certain diseases. We take the “flu shot” to become
immune to this year’s strain of flu. How does it work?
• When we contact a pathogen for the first time, this is called the primary
infection. This is called a polyclonal response. This is because the pathogen is
typically being recognized as many antigens and not just one. For example, a
virus might have many types of proteins on its capsid, and therefore, several
immune responses. Several types of B-Cells undergo clonal selection and several
antibodies are produced. There are now several Memory cells made also.
• Your body might be able to fight off the infection, perhaps with the help of
antibiotics, but the pathogen may be causing damage and disease. But if you
come in contact with the pathogen again, a second time, the memory cells will
respond to the pathogen quickly. These long-lived cells are in large numbers and
live for a long time.
• The following principles apply for all types of infection.
o Challenge and response – The immune system must be challenged by an
antigen during the first infection in order to develop an immunity. All cellular
events are part of the response, which leads to immunity to the pathogen.
o Clonal selection – your immune system selects the type of cell that will be
useful and initiates the cloning of that cell.
o Memory Cells (as mentioned above)
Cell immunity:
• Immunity is the acquisition of antibodies to fight off a secondary infection.
There are two types of immunity:
1. Active Immunity
• Immunity due to the production of antibodies by the organism itself after the
body’s defence mechanisms have been stimulated by the invasion of
pathogens. Due to the Memory B and T-Cells, people who have had the disease
(chicken pox, measles) are not likely to become reinfected.
2. Passive Immunity
• Immunity due to acquisition of antibodies from another organism, in which
active immunity has been stimulated. Included in this are antibodies received
via the placenta or colostrum from the mother. This means the person is
immediately protected from the disease.
• These two types of immunities can also be classified in two different ways –
natural and artificial immunity
o Natural Active – antibodies as a result of infection.
o Natural Passive – made antibodies from the placenta and passed on to the
fetus or through the colostrums
o Artificial passive – obtained from another organism through biotechnology
o Artificial active – vaccination
Vaccinations:
What is a vaccination? Why do we vaccinate?
• We need to develop immunity in individuals, but more importantly, to develop
“herd immunity”.
• Herd Immunity is when you vaccinate the majority of the people, and the rest
have a very low chance of coming in contact with the disease. After herd
immunity is achieved, society must ensure the disease is completely eradicated.
For discussion – Is this possible?
• Vaccines are basically dead viruses, weakened or a similar vaccine (cowpox for
smallpox) that is injected into the body. The T-Cells go through the whole process
and develop Memory cells to make antibodies in the case of infection. In all
cases, when someone is vaccinated, the second response is faster and stronger
than the first. Vaccines are a huge help to people because, for example the MMR
vaccine (Measles, Mumps and Rubella), vaccinates against two potentially lethal
childhood diseases, measles and mumps. They can cause blindness, loss of
hearing and mental incapacitation, if contracted. Rubella, if contracted by
pregnant mothers, can have babies born with the same conditions as mentioned
above.
• With vaccinations, there is a possible total elimination of the disease (ex.
Smallpox). Epidemics can be prevented from spreading. As a result, preventative
medicine is a cost-effective approach to health care. Lastly, as herd immunity is
developed, an individual does not have to experience the full effect of the
disease to promote immunity.
• There are some proposed dangers with vaccines. First, there are some side-
effects. Some people develop the disease as a result of exposure to the antigen.
The pathogen can be passes through feces and infect others. Some people may
not develop the antibodies, due to malnutrition and other problems (AIDS).
• The overloading of the immune system, may cause other reactions, which are
not known. Allergic reactions have been documented.
• Prior to 1999, many vaccines contained thimerosal, a mercury based-
preservative. Mercury has been shown to be a neurotoxin.
• The MMR vaccine may have a link to Autism.
• The other problem is that some diseases are changing, and the vaccine used
today, is not effective tomorrow. There are several strains of the flu, so every
year, the new vaccine is added to the shot. Now, Avian flu has mutated to not
only affect birds, but also humans. It is now possible to get chicken pox twice,
Fifth’s Disease and the common cold will keep everyone coughing for years to
come.
Topic 11.2: Muscles and Movement

The Human Elbow Joint
• Humerus – rigid structure for muscles to anchor to.
• Ulna – create a fulcrum at joint, insertion for triceps
• Radius – insertion point for biceps
• Biceps – flexor muscle-bends joint and lessens the angle of a joint
• Triceps – extensor muscle-straightens joint and increases the angle of the joint
• Cartilage – smooth, strong covering on articulating surfaces of a joint
• Synovial Fluid – lubricates articulating surfaces of cartilage; acts like a shock
absorber. Contains nutrients and Oxygen for the cartilage.
• Spongy Bone – end of bones that are light and strong.
• Band Ligaments – tough elastic structures holding bones of a joint together.
• Capsular Ligaments – encloses joint to protect it.
Sunday, January 25, 2009
12:09 AM
Skeletal Muscle Fibers

• A skeletal muscle is made up of bundles of thousands of muscle fibers, or muscle
cells.
• The muscle fibers lie parallel to one another and range from 10 to 100 um in
diameter. The typical length is 100 um, but some can be as long as 30 cm.
• Each muscle fiber is surrounded by a sarcolemma (sarco – flesh, lemma –
sheath). This is the muscle fiber’s cell membrane.
• The muscle fibers are developed from the fusion of smaller cells during
development, and therefore, have many nuclei and mitochondria.
• Each muscle fibers contains many myofibrils. The cytoplasm, called sarcoplasm,
contains mitochondria packed between the myofibrils. In between the myofibrils
is a transverse tubular endoplasmic reticulum, called the sarcoplasmic reticulum.
Hip Joint Knee joint
Freely moveable Freely moveable
Angular motion in many directions and Angular motion in one direction
rotational movement
Motions possible are flexion, extension, Motions possible are flexion and
abduction, adduction, circumduction and extension
rotation
Ball-like structure fits into a cup-like Convex surface fits into a concave
depression called the acetabulum surface
Roles of Necessary Locomotive Factors:
• A person needs the nerves to signal movement, muscles connected to bones, to
act as levers, tendons to attach to the bones and ligaments to hold the bones
together.
In order to move, skeletal muscles are involved. Muscles in the body not
attached to bones are the cardiac muscle and the muscles of the gut and
reproductive system.
Nerves
• Carry impulses to and from the brain to co-ordinate muscular activity
• Motor neuron impulses stimulate the muscles to contract
• Nerve impulses control timing and speed of muscular contraction
Muscles
• Contain receptors that send information via sensory neurons to the brain about
the position of the muscle
• Contract to bring movement to the joint
• Work in muscles pairs on each side of a joint
o Muscles have a belly (gaster) and a tendon.
• Belly (Gaster) – is the fleshy portion of the muscle between the
tendons.
• Tendon – a white fibrous cord of dense, regularly arranged connective
tissue that attaches muscle to bone. They have the tensile strength of
steel.
• Each muscle has an insertion and an origin.
• Insertion is the attachment of the muscle tendon to the moveable bone
• Origin is the attachment of the other muscle tendon to the stationary
bone.
• The biceps inserts on the radius and originates on the scapula. The
triceps inserts on the ulna and originates on the humerus and the
scapula.
• Based upon the insertion and origin, you can figure out what the
muscle moves.
Bones
• Bones meet at a joint and act as levers
• Different types to joints between bones control the range of movement
• Provide rigid anchorage for muscles through tendons
• Form blood cells in the bone marrow
• Provide a hard framework to support the body
• Allow protection of vulnerable softer tissue and organs
• Allow for the storage of minerals, especially calcium and phosphorus
As well...
Band Ligaments – tough elastic structures holding bones of a joint together.
Capsular Ligaments – encloses joint to protect it.
Contraction of Striated Muscle:
• When muscles contract, it was discovered that the actin and myosin filaments
slide past one another. The A band, myosin, is the same length in contracted
and relaxed muscles. This lead to the sliding filament theory.
• The contraction of muscles occurs in a series of steps, sometimes described as
a ratchet mechanism. Lots of ATP is used in the process.
• Along the actin filament are binding sites for the heads of the myosin filament.
Actin filaments contain actin as well as tropomyosin and troponin. Tropomyosin
forms two strands which wind around the actin filament, covering the binding
site. The tropomyosin is held in place by the troponin. This is how the actin
filament remains at rest.
• The thick filaments are composed of myosin molecules, each with a bulbous
head. The head protrudes from the length of the myosin filament. The head,
when the muscle cell contracts, binds to the site on the actin filament. This is
what causes movement of the filaments, and eventually the movement of the
whole muscle.
• The contraction of the sarcomere is best described in four steps:
1. The myofibril is stimulated to contract by the arrival of an action potential. This
triggers the release of calcium ions from the sarcoplasmic reticulum, to
surround the actin molecules. The calcium ions react with the troponin. When
the troponin is activated, it triggers the removal of the blocking molecule,
tropomyosin. The binding sites are now exposed.
2. Each bulbous head has an ADP and Phosphate group attached to it (called a
charged bulbous head). It reacts with a binding site on the actin molecule
beside it. The phosphate group detaches.
The ADP molecule is then released from the head, and this is a trigger for the
rowing movement of the head. The head tilts 45o and pushes the actin filament
along. This step is called the power stroke and the myofibril contracts.
4. A molecule of ATP binds to the head. The protein, ATPase, catalyses the
hydrolysis of ATP. The result is ADP and Phosphate is attached to the bulbous
head, and it is said to be charged again. The charged head detaches from the
binding site and straightens.
• The cycle of movement repeats itself many times per second, with thousands of
heads working along each myofibril. ATP is used up and the muscle may shorten
by about 50% of its relaxed length.
When no more impulses arrive, calcium ions are moved back into the vesicles of
the sarcoplasmic reticulum by active transport. The binding sites are covered by
the tropomysin and the muscle relaxes.
Topic 11.3: The Kidney

12:51 AM
The Loop of Henle:
• The Loop of Henle is an extension of the proximal tubule, but it extends into the
medulla of the kidney. There are two sections, the descending loop and the
ascending loop. It creates a hypertonic environment in the medulla.
• In the descending loop, water leaves by osmosis due to the increasing
concentration of salt. The water immediately passes into the blood and is
removed from the area. Some salt diffuses out as well.
• The ascending loop in impermeable to water and salt is lost from the filtrate by
active transport. The amount of salt lost here is greater than in the descending
loop. The salt remains near the loop, in the tissue, to maintain a concentration
gradient in the medulla.
• The fluid that leaves the Henle’s Loop is less concentrated than the tissue fluid
around it.
• The concentration gradient is maintained by the vasa recta, the blood vessels
that run along the loop of Henle. There is no direct exchange to the blood and
substances must pass through the tissue of the medulla. The tissue maintains a
concentration gradient, called the vasa recta countercurrent exchange.
• Therefore, as the blood, from the afferent vessel enters the medulla, and from
the descending capillary, it will lose water by osmosis and gain salt and urea by
diffusion.
• In the ascending capillary, the reverse happens. The concentration of the blood
does not change and since all processes are passive, energy is not needed, to go
from tissue to capillary. All the salts and urea are recycled in the medulla.
ADH:
• The wall of the distal convoluted tubule is permeable to water and the water can
pass from the ultrafiltrate into the blood vessels, to be carried away. The same
happens in the collecting duct. This area is controlled by ADH.
• ADH increases the permeability of the walls of the distal convoluted tubule and
the collecting duct.
• When there is a lack of water, as we saw before, ADH is released. The dilute
filtrate coming from the Henle’s Loop can then lose water from the distal
convoluted tubule and the collecting duct. The water is reabsorbed by the blood.
• When ADH is absent, the walls are impermeable, and the urine is dilute (ie. Lots
of Water)
Excretions:
• The elimination of wastes
products through
metabolic processes
The Process of
Ultrafiltration:
• Blood carries the particles
left to be absorbed. It is
from the blood that
passes through the
kidney, that the last of the
nutrients the body needs
is taken.
1. The renal artery supplies
the kidney with blood.
2. It splits into many smaller
blood vessels and each
nephron has an afferent
vessel, which carries the
blood to the glomerulus, which is a bundle of specialized capillaries.
3. The blood eventually returns to the efferent vessel, which carries the blood
around to the other parts of the nephron.
4. Blood that has been filtered passes out into larger vessels and becomes the
renal vein.
• Connected to the glomerulus is the Bowman’s Capsule.
blood in the glomerulus is under high pressure and this is where ultra filtration
takes place.
• Reason – The efferent vessel (e = exit), is narrower than the afferent vessel
going in, and therefore, the blood pressure is much higher. Particles and
fluid are pushed into the Bowman’s Capsule.
• Bowman ’s capsule - In order for the filtrate to pass into the capsule from
the glomerulus, is has to pass a barrier. There are three layers which the
blood fluid must pass through to enter the nephron:
• Wall of the glomerulus – which contains small pores that allows
plasma to mover through. It is said to be fenestrated. There are small
slits along with the pores to filter the fluid.
• Basement membrane of the glomerulus – protein membrane outside
the cells; it contains no pores and serves as a filter during
ultrafiltration. Its main job is to stop the blood cells and large proteins.
(Acts like a dialysis membrane, made of negatively charged
glycoproteins).
• Inner wall of the Bowman’s Capsule – made of specialized cells called
podocytes. They have many folds that surround the blood vessels and
a network of filtration slits that hold back the blood cells.
Osmoregulation and reabsorption:
• Osmoregulation – the control of water balance of the blood, tissue and cytoplasm
of a living organism.
The Proximal Convoluted Tubule:
• The Bowman’s capsule is the first part of the nephron. This is where the filtrate
goes.
• From the Bowman’s capsule, the filtrate goes to the proximal convoluted tubule.
Most of the re-absorption takes place here. The fluid is similar to plasma, as it
contains glucose, amino acids, vitamins, hormones, urea, salt, ions and water.
• All of the glucose, amino acids, vitamins, hormones and most of the sodium
chloride and water are reabsorbed into the peritubular capillaries. Osmosis
drives the re-absorption of the water. Sodium, glucose, and salts are absorbed by
active transport. Chloride follows the actively transported sodium, based upon
an electrochemical gradient. The water follows the salts, because in the proximal
tubule, the salts create a concentrated environment. Water flows out of the
tubule to the vessels to dilute the salts.
• To facilitate the movement of across the wall of the PCT, the lumen of the tube is
covered with microvilli, similar to the small intestine. In the microvilli, are
mitochondria to provide energy (ATP) for the active transport.
Topic 11.4: Reproduction

6:04 PM
Topic H: Further Human Physiology
1:08 AM
H4: Function of the Liver
11:06 AM
Structure of the Liver:
• The liver is the heaviest and the second largest organ in the body, after the
skin. It is located under the diaphragm, on the right side of the body.
• The liver has excellent blood supply. The hepatic artery delivers blood from the
heart, and the hepatic portal vein deliver blood from the organs. The hepatic
vein takes away the blood from the liver to the heart.
• The liver is connected to the gall bladder, which is connected to the small
intestine (duodenum) and the pancreatic duct, by the common hepatic duct.
The common bile duct and the pancreatic duct enter the duodenum by a
common duct called the hepatopancreatic ampulla (ampulla of Vater)
• The liver is made of several lobules. Each lobule consists of specialized
epithelial cells called hepatic liver cells or hepatocytes. The cells are arranged in
irregular branches, and irregular plates around the central hepatic vein. In
between the lobules you find branches of the hepatic artery and hepatic portal
vein and bile tubules. All of these together form the functional unit of the liver,
called an acinus.
• Rather than capillaries, the liver has sinusoids. These are larger spaces lined by
the epithelium. This is where the blood passes.
• The sinusoids differ from capillaries in three ways:
1. They have a dilated, irregular lumen.
2. Between the lining endothelial cell are spaces that facilitate exchange between
the sinusoids and adjacent tissues.
3. The basement membrane-like material is not continuous but forms barrel,
hooplike rings around the endothelial walls.
• Lining the sinusoids are also stellate reticuloendothelial cells, commonly called
Kupffer Cells. They are phagocytes that destroy worn out white and red blood
cells, bacteria and toxic substances.
• Liver synthesises plasma proteins and cholestrol
• Lives has a role in detoxification
Functions:
1. Carbohydrate storage
• We have talked about this: see insulin and glucagon talk in homeostasis section.
• The liver maintains a healthy blood glucose level in blood. Generally it is
constant at 90 mg glucose /100 mL blood. The liver converts all
monosaccharides into glucose. Fructose and galactose are all converted. The
surplus is stored as an insoluable polysaccharide, glycogen.
• The following steps are involved in glucose metabolism.
• Glycogenesis – for storing glucose
• The liver can store up to 100 g of glycogen and muscles also store
glycogen.
• Glycogenolysis – breaking down glycogen
• Phosphorylase is activated by hormones (glucagon, adrenalin, and nor
adrenalin)
• Since muscles lack some of the enzymes to convert glycogen directly to
glucose, the muscles convert glycogen to pyruvate for respiration. We will learn
more about this in Cellular Respiration.
• Gluconeogenesis – glucose from AA and glycerol in times of stress and
hypoglycemia.
Storage of Iron
Iron is a very important component of haemoglobin, but is very hard to absorb
from foods. After the erythrocytes (RBC) have been broken down, the iron is
carefully stored.
The breakdown is done by phagocytosis in the liver by the Kupffer Cells, spleen
and bone marrow. The iron is packed and broken down into haem and globin.
Haem is an iron containing group. The iron is stored in the liver and the
remainder of the group becomes biliverdin (a green bile pigment), which
becomes bilirubin, which we talked about earlier.
Globin is a protein and is broken down to its amino acids. These are then
treated like other amino acids and can be used to make other proteins, or trans-
aminated or de-aminated for energy.
The iron will be used again to make new haemoglobin. It is stored in the liver in
the form of ferritin, a complex of iron and B-globulin. Liver contains approx 1 mg
of iron per dry gram
2. Storage of retinol and calciferol

• The Liver is capable of storing water soluble vitamins but main vitamins stored
are the fat soluble ones – retinol (Vitamin A) and calciferol (Vit. D)
• Retinol (dairy and carrots) is part of a visual pigment and a deficiency can lead
to night blindness.
• Calciferol (cod liver oil and dairy, or made by skin under UV light) helps in
uptake of calcium – deficiency can lead to rickets as a child.
• Protein Metabolism
• Without the role of the liver, death would occur in a few days. The liver de-
aminates (removes the amino group NH2) amino acids, so they can be used for
ATP production or used as an energy source. It converts the resulting ammonia
(NH3) to the less toxic urea.
• It is also involved in the production of plasma proteins. The most common type
are proteins found in the blood. One is albumin, which transports a variety of
molecules, calcium, amino acids and hormones. Other examples are alpha and
beta globulin, prothrombin, and fibrinogen.
• The process of transamination is done by the liver. It is when one amine group is
transferred to convert one amino acid to another.
• Lipid Metabolism
• The liver stores some triglycerides and breaks down fatty acids to acetyl
coenzyme. The coenzyme is further broken down to ketones (called
ketogenesis). It also synthesizes cholesterol to make bile salts.
• Removal of Drugs and Hormones

• The liver can detoxify or excrete into bile, drugs such as penicillin,
erythromycin, and sulfonamides. It can alter or excrete thyroid hormones and
steroids.
Bile and Bile Secretion:
• The hepatic cells secrete about 1L of bile each day.
Bile is a yellow, brownish or olive green liquid, with a pH of 7.6 – 8.6. Bile
contains water, bile salts, bile pigments, inorganic salts and cholesterol. Bile is
produced by the hepatocytes and travels via the bile canaliculi to the bile duct,
which empties into the gall bladder. When the duct to the duodenum closes, the
bile is pushed back and stored in the Gall Bladder.
• Bile salts are derivatives of cholesterol and sodium and potassium. The salts
have a hydrophobic side, which will attach to a lipid and a
hydrophilic side which will stick out and interact with the water. This emulsifies
the fat, or makes into little fat droplets, making it easier to digest and absorb.
Too little bile salts in the bile will raise the concentration of the cholesterol and
may cause them to precipitate, forming gall stones.
Bicarbonate (HCO3-) in the bile, helps neutralize the acid of the stomach as the
food enters into the duodenum.
• The principle bile pigment is bilirubin. It is a product of the breakdown of red

blood cells. When they break down, iron, globin and bilirubin, which is derived
from the heme, are released. The yellow, brown bilirubin is released into the
small intestine and is broken down. The action of bacteria breaks it down to
urobilinogen, which give feces its normal brown color.
• Bile secretion is stimulated by both nervous and hormonal factors. When acid
chyme come in contact with the wall of the duodenum, it will secrete a hormone
CCK (cholecystokinin). CCK promotes the release of bile, by causing the wall of
the gall bladder to contract, and a relaxing of the spincter of the ampulla of
Vater. The bile will flow through the bile duct, joining the pancreatic juice before
emptying into the duodenum.
Regulation of Nutrients:
• A regulating mechanism, which keeps the nutrient levels in the blood constant, is
needed. This is where the liver comes in.
• The liver regulates the levels of nutrients in the blood. This is especially
important, as large spikes in levels of some nutrients (i.e. glucose) can be
harmful and in times of need, nutrients must be used.
• Since the liver receives all of the blood from the small intestine and other
organs, it can store the excess or breakdown energy stores to be used.
In the example of blood glucose, the liver, under the influence of insulin, will
store the excess as glycogen. When blood glucose levels are low, the glucagons
stimulates the breakdown of glycogen to glucose in the blood.
• Proteins are broken down by proteases and the amino acids are used to build
proteins, but also other amino acids can be made from existing ones in a process
called trans-amination. Amino acids can also be used as an energy source after
de-amination. This is done by the liver.

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Biology Syllabus - Core

Saturday, January 24, 2009

What does all this mean?

Evidence for Cell Theory:

Unicellular Organisms Functions of Life

Electron microscope vs. Light microscope

Multicellular Organisms and Specialized Cell Function

Similarities & differences between prokaryotes & eukaryotes:

Topic 2.4: Membranes

together in various kinds of junctions) “Cytoskeleton.

Topic 2.5: Cell

2. Interphase (growth stage)

• Cytokenisis (division of cytoplasm)

Topic 3.1: Chemical Elements of Water

Phosphorus - Synthesis of nucleotides - Synthesis of nucleotides - Synthesis of nucleotides

Iron - Constituent of electron - Constituent of electron - Constituent of electron transport

Topic 3.2: Carbohydrates, Lipids, and Proteins

• Def: compounds containing carbon that are found in organisms.

2. Water-proofing of hair and feathers

Topic 3.3: DNA

Formation of DNA (Double Helix):

o the enzymes needed to produce arginine.

Topic 3.6: Enzymes

zyme use in production of Lactose free milk:

• First the Lactase is immobilised in alginate beads.

Topic 3.7: Cell Respiration

Anaerobic Cellular Respiration - Fermentation:

• Must be noticed that both processes have no products of ATP

Steps of Cellular Respiration:

Aerobic Cellular Respiration:

• In this phase of cellular respiration, the pyruvate is oxidised by:

What happens in Photosynthesis:

Measuring the Rate of Photosynthesis:

External factors and the rate of photosynthesis:

An example of substitution is Sickle Cell Anemia.

Topic 4.2: Meiosis

Homologous chromosomes – also called a homologous pair. They are two

Process of Cross Over

Why is this done?

Example of Multiple Alleles – Blood Type

2. Figuring out the parental phenotypes and genotypes. (P)

First Filial Offspring (F1) from the cross of parental (P)

Second Filial Offspring (F2) from the self-pollination of the F1 generation.

Example 1 – Colour Blindness

* Xh Xh is homozygous lethal, meaning that the individual would not exist.

1. Within an organism, there are breeding factors controlling characteristics such

Steps to solving Genetics Problems 1 – Monohybrid Cross

2. Figure out the genotypes of the parents

Co-dominance and Multiple Alleles

Wednesday, March 25, 2009

Ethics of Therapeutic cloning:

Saturday, January 24, 2009

Is the enhanced greenhouse effect leading to Global Warming?

Global Warming and the Precautionary Principle

Photosynthesis will reduce the amount of carbon dioxide available but

Topic 5.3: Populations

Saturday, January 24, 2009

Too many offspring

Natural Variation within a Population

Natural Selection Summarized

1. Multiple Antibiotic Resistance in Bacteria

2. The Peppered Moth (biston betularia)