Biology Notes

Photosynthesis – 6CO2 + 6H20 + (Energy/ATP)  C6H12O6 + 6O2

Autotrophic organisms make their own food e.g. by photosynthesis.
Heterotrophic organisms eat other organisms as their source of food.

ATP – Adenosine triphosphate

ATP is the molecule that provides the energy that is needed within an organism to allow it to carry
out its metabolic reactions. It releases energy by breaking the third phosphate group to produce ADP
(Adenosine diphosphate) and an inorganic phosphate molecule. This is catalysed by the enzyme
ATPase.

The reaction is also reversible so energy can be used to produce ATP and the same enzyme catalyses
the reverse reaction.

Production of ATP
ATP is produced from ADP and an inorganic phosphate group. This requires energy which is
produced by many redox reactions throughout an electron transport chain. One electron
acceptor/carrier accepts an electron and is therefore reduced. It then passes on the electron to the
next acceptor so it is oxidised and the next acceptor is reduced. These reactions release a small
amount of energy each which is then used to produce the bond between ADP and phosphate to
produce ATP.

Structure of a chloroplast

 The thylakoids contain

chlorophyll which is a mix of 5 different
photosynthetic pigments which absorb
different wavelengths of light. This is
where the light dependent reaction
occurs.
 Stacks of thylakoids are called
granum (grana = plural). They are
connected to other grana by stroma
lamella which keeps the structure of the
chloroplasts rigid.
 The fluid matrix inside the
chloroplast is called the stroma and it
contains the enzyme RUBISCO (used in
independent stage). This is where the
light independent reaction occurs.
Chloroplast adaptations
 Chloroplast envelope keeps reactants very close to their reaction sites.
 Thylakoids have a large surface area to maximise light absorption.
 Stroma contains all the enzymes etc. for light independent reaction to take place.
 Lots of ATPase is present in the thylakoid membranes to produce ATP.

Light dependent reaction - first step in the production of glucose – takes

place on thylakoid membranes. These contain photosynthetic pigments
such as chlorophyll a, chlorophyll b and carotene.
It has a few main roles:

1. Produce ATP so that the energy can be used to produce glyceraldehyde 3-phosphate
from glycerate-3-phosphate in the light independent reaction.
2. Reduce NADP to NADPH so that it can reduce glycerate-3-phosphate to
glyceraldehyde 3-phosphate. NADP is a coenzyme. A coenzyme is a molecule that aids the
function of an enzyme. They work by transferring a chemical group from one molecule to
another, in this case the chemical group is H+.
3. Split water by the process of photolysis during non-cyclic photophosphorylation so
that PS2 stays stable.

A photosystem is a complex of proteins and the photosynthetic pigments and it plays a large role in
photosynthesis.

Cyclic photophosphorylation – in PS1 – produces ATP

1. Light hits the chlorophyll in photosystem 1 and excites the electrons.
2. Excited electrons move up an energy level and leave the chlorophyll molecule.
3. The excited electron is accepted/carried by electron acceptors and passed along a transport
chain through redox reactions.
4. This produces energy which is used to create ATP from ADP and phosphate.
5. The electrons return to photosystem 1 hence it is cyclic.

Non cyclic photophosphorylation – in PS1 – produces NADPH

1. Photons of light hit the chlorophyll and get excited.
2. Excited electrons are picked up by NAPD as well as H+ ions so it is reduced to NADPH.
3. NADPH is then used as a reducing agent in the light independent reaction to reduce
glycerate-3-phosphate to glyceraldehyde 3-phosphate.

Non cyclic photophosphorylation – in PS2 – photolysis occurs here

1. Electrons excited by photons of light.
2. Electron passes along an electron transport chain until it reaches PS1 so the electron that
PS1 lost is now replaced and the energy released is used to make ATP.
3. Now PS2 has one less electron (hence is unstable) so H2O is broken down by photolysis to
produce electrons so the electrons are replaced.
4. The remaining OH- molecules are used to produce water and O2 by the following
a. 4OH- - 4e- O2 + 2H2O
Light independent reaction – in the stroma – produces carbs, lipids, proteins, nucleic
acids.
1. CO2 reacts with a 5 carbon compound called RuBP to produce a 6 carbon compound. This
catalysed by the enzyme RUBISCO and is called carbon fixation.
2. This breaks down into 2 molecules of glycerate-3-phosphate almost immediately.
3. Glycerate-3-phosphate is reduced to glyceraldehyde 3-phosphate (a 3 carbon sugar) by
NADPH. Energy for this reaction is provided by ATP.
4. The sugar is then used to produce organic molecules such as glucose.
5. Glucose can then be used to produce starch so that it can be stored and doesn’t affect the
osmotic concentration of the cell (since it is insoluble).
6. 5 out of every 6 molecules of glyceraldehyde-3-phosphate (GALP) are used to regenerate
RuBP which also uses up the remaining ATP. This means the calvin cycle has to turn 6 times
to produce one molecule of glucose. This is because two molecules of GALP are made for 1
turn of the cycle so 3 turns produces 6 molecules of GALP. However, 5 of those 6 molecules
are used to regenerate RuBP so the cycle needs another 3 turns to produce 2 GALP
molecules that can be used to make glucose.

Ecosystems – definitions
 Ecosystem – all the organisms within a habitat as well as the abiotic factors.
 Habitat – the place where an organism lives.
 Microhabitat – a small section of a habitat.
 Population – all the organisms of the same species within a habitat at any one time.
 Community – all the populations of different species within a habitat at any one time.
 Niche – the role of an organism within its habitat.
 Abiotic factors – non-living factors in an ecosystem – e.g. light intensity and temperature.
 Biotic factors – living factors in an ecosystem – e.g. amount of predators.
 Biome – a major ecosystem.
 Biosphere – largest ecosystem in the world.

Primary Succession – the process by which an ecosystem changes over time

This is when succession starts from barren land e.g. sand dunes or bare rocks that have been created
by volcanic eruptions or the formation of a new island.

1. Seeds from the pioneer species can be transported by the wind and animals and these
colonies the area. The pioneer species are able to live in the harsh conditions with no soil
(harsh pH, lack of minerals and lack of water). One example are lichens consisting of algae
and fungus which live symbiotically since the algae photosynthesises and provides energy
whilst the fungi break down bare rock to release minerals and create a small layer of humus
and a thin layer of soil.
2. Other plants with short roots colonise the area as they are able to grow in the thin layer of
soil e.g. ferns and grasses as the soil layer gets thicker and more nutrient rich. They out
compete the lichens for space and resources hence the lichens die out and the ferns and
grasses can grow.
 3. As the soil layer gets deeper more water and nutrients can be retained in the soil hence the
soil is less harsh and flowering plants and shrubs can outcompete the grasses and ferns and
grow on the land.
4. Then trees out compete the shrubs and plants and grow in the habitat producing a climax
community/final community of trees i.e. a forest.

Since more plants are present, there is a higher plant biodiversity and the plants are able to provide
for more animals hence the biodiversity of animals in the habitat also increases.

Secondary succession
Secondary succession is when succession occurs on land that already has soil but the previous
habitat was destroyed by a flood, forest fire etc. Since soil is already present, plants such as
flowering plants and shrubs can grow providing their seeds were preserved in the soil.

The secondary climax community depends on the plants and animals that are able to colonise the
area and survive in that area so the secondary climax community may differ from the primary climax
community.

Climax community
 This is the final community in natural succession and occurs if there are no human
influences.
 It has a high biodiversity of plants and animals.
 These species interact with each other.
 There is a balanced equilibrium of species.
 It is stable if there are no human influences and it is self-regulating.

Plagioclimax
This is a final community that is maintained by human interference and is not a typical climax
community as succession is prevented e.g. sheep grazing grass prevents woody parts of trees from
growing which is why the grass stays as it is.

Abiotic factors
 Light intensity – This is important for photosynthesis to occur but some plants have adapted
to low light conditions by having more chloroplasts or having chlorophyll that is more
sensitive to light.
 Temperature – Each organism has a range of temperatures it can survive between since too
high of a temperature will break intermolecular bonds in proteins, mess up their structure
and cause them to denature i.e. not function as they should. This is important during
enzyme controlled reactions as enzymes have an optimum temperature where they work
best at but if the temperature is too high they will denature and the shape of the active site
will change so the substrate will not be able to fit into it.
 Wind – wind increases water loss from the surface of plants and gale force winds can
destroy habitats.
 Water currents – If they are too strong they can physically destroy habitats.
 Water – it is needed for controlling body temperature, in the blood, intake minerals etc. so
sufficient amounts of water are required in the body of plants and animals.
  Oxygen – this is needed for respiration to produce energy in the form of ATP.
 Edaphic factors – these are factors that affect the soil – e.g. amount of water soil can retain
decided which plants can grow as well as amount of nutrients, pH etc. Sand is very loose so
will not retain water whereas soil with particles of different sizes will retain more water.

Biotic factors
 Predation – predators kill prey hence increased predators will cause a decrease in prey but if
the predator numbers increase too much they will compete (intraspecific competition) and
their numbers will decrease due to lack of food.
 Finding a mate – if a male can’t find a female they will not be able to reproduce and produce
offspring hence they will become extinct in extreme circumstances.
 Parasitism and disease – this kills the organisms or makes them disabled hence their
population size will decrease. A high population density promotes the rapid spread of
disease as members of the population live so close together.

Competition
1. Interspecific competition – competition between two different species for food, space and
other resources. The species that is best adapted to the habitat will outcompete the other
species, survive and reproduce to produce offspring whilst the less adapted species will
starve hence its population size will decrease and in extreme cases, become extinct.
2. Intraspecific competition – competition between organisms of the same species due to lack
of space, foo d and other resources.

Energy transfer in ecosystems

Energy is used to produce more body tissue and therefore increase the biomass of an organism.

Gross primary productivity (GPP)

This is the rate at which plants incorporate the suns energy into themselves and use it to increase
the plants biomass. Some of it is lost during respiration when energy is released in the form of ATP.
The energy that is stored in the plants biomass and is available to the next trophic level is known as
Net primary productivity (NPP).

NPP = GPP – respiratory losses

How does temperature affect NPP?

As the rate of enzyme controlled reactions are faster at higher temperatures the rate of plant
respiration increases and therefore NPP decreases since the amount of plant respiration subtracted
has increased. Conversely, if the temperature is decreased, the rate of plant respiration will decrease
since enzyme controlled reactions are slower therefore NPP will increase.

Energy transfer to higher trophic levels

Herbivores consume the plants and a lot of the energy is never assimilated by the herbivore. Instead,
it passes straight through the body into the faeces. The energy that is assimilated is used during
respiration, some is lost during various metabolic reactions and the remaining energy is incorporated
into the biomass of the herbivore. The energy that is used to make the biomass of the herbivore is
called the Net Productivity.
A similar type of energy loss occurs in each trophic level so very little energy is remaining for tertiary
consumers etc. However, if the number of trophic levels in a food chain was limited, more energy
would be available for each trophic level and energy transfer would be more efficient.

Investigating populations and abiotic factors

Abundance – the number of individuals of one species in an area. This can be measured by counting
the number of organisms of a species or by using percentage cover (for plants) i.e. the percentage of
area they cover.

Distribution – where the species is within a habitat.

Random sampling
1. Choose an area to sample within the entire area being investigated at random.
2. This can be done by dividing the area into 1m x 1m squares, numbering the rows and
columns and then using a random number generator to pick out coordinates.
3. Repeat the process as many times as possible so many samples are taken and the entire area
is represented fairly.
4. These samples can then be used to make an estimate of the entire area or percentage cover
can be calculated by simply calculating the mean of the results.

Frame quadrats – 1m x 1m frame divided into 100 squares

1. Placed on the ground at random points.
2. Number of organisms is counted etc. in each quadrat
3. Percentage cover can be measured by counting the number of squares that the plant is in. If
its covering half a square, count it as a full square and 1 square = 1%.

Line transect
A tape measure is placed along a line and each species that touches it is counted and recorded.

Belt transect
This is a line transect with a frame quadrat placed at regular intervals and is used to count the
species. Taking recordings at regular intervals is called interrupted transect.

Point quadrat – a bar with two logs on either side with holes in the bar at regular
intervals.
1. Placed on the ground at random points.
2. Pins are dropped through each hole in the bar and if the pin touches a plant, it is recorded. If
the pin touches more than one plant, they’re all recorded.
3. Percentage cover can be measured by calculating the number of times a pin has touched a
species as a percentage of the total pins dropped.

This type of quadrat is especially useful when there is a lot of dense vegetation on the ground.
Global warming
Carbon cycle
Carbon is used to produce carbohydrates, proteins, lipids and nucleic acids which are the building
blocks of life.

This is the cycle by which carbon travels around the atmosphere through different organisms e.g.
animals eat plants and the carbon in plants biomass is released via respiration.

Carbon sinks – these are places where carbon is removed from the
atmosphere and locked up
Oceans – These are carbon sinks and they store a large proportion of the earth’s CO2.
Phytoplanktons use the CO2 to photosynthesise and crustaceans use it to make their shells. This
means there is always a higher concentration of CO2 in the atmosphere so more CO2 can be
dissolved into oceans continuously.

Fossils (fuels) – These are produced from dead organic matter and they contain carbon that was
once in the dead organic matter. They take millions of years to develop which means carbon can
be locked up in fossil fuels for millions of years. However, with human interference, these fossil
fuels are being burnt to release energy which is also releasing carbon dioxide into the
atmosphere and increasing the concentration of carbon in the atmosphere.

Plants and humans – plants take in CO2 to photosynthesise and create biomass and these plants
are eaten by animals so the carbon is therefore stored in the human for a certain period of time
before being released due to respiration.

Greenhouse effect
1. The sun radiates short wavelength infrared radiation to the earths surface.
2. Some of the radiation is reflected back to the sun.
3. Some of the radiation is absorbed by the earth and radiated back as long wavelength
infrared radiation.
4. This radiation is absorbed by greenhouse gases such as CO2 and CH4 and reradiated back
down to earth.
5. This keeps the earth warm but too many greenhouse gases has resulted in too much heat
being reradiated back to the earth hence global warming.

Methane, CH4
This is a much more potent/strong greenhouse gas compared to CO2 and it is created by the
digestion of ruminant herbivores such as cows and released as they belch. More human’s means
more cows are needed to eat and hence more CH4 is released.

Evidence of global warming

Dendrochronology
1. Trees produce 1 ring approximately each year. The ring effect is produced due to the fact
that during the winter, cells created are small and during the summer the cells are large
since it is warmer and the cells grow more to a larger size. This change in cell size produces a
 ring effect. However, if the temperature varies significantly during a year, the tree may
produce more than one ring. This means the date of the ring can be approximated and the
width of the rings can be used to suggest the temperature at the time.
2. By counting from the outside inwards, you can roughly estimate what year the ring was
made in.
3. If the rings are wide, this suggests that the year was particularly warm and vice versa for thin
rings. However, temperature isn’t the only thing that affects tree ring growth. If the ring is
wide, this could suggest better rainfall, CO2 levels, more sunlight etc. Not ONLY temperature.

Pollen in peat bogs

Peat bogs are made up of organic material and are cool, acidic and anaerobic hence they preserve
pollen as enzymes are not able to decompose them in these harsh conditions.

Mature plants produce and distribute their pollen into the soil around them hence the pollen can be
analysed to see which plants were mature at the time (i.e. which plants pollen is present) and
therefore we can see which plants were living successfully at the time.

After determining what species the pollen is from, you can determine the conditions at the time. If
the species normally prevails in warm conditions, then you can determine that the conditions were
particularly warm at that time and vice versa for species that prevail in cold conditions.

The number of layers of peat can also be used to determine the approximate time at which the
pollen grains were dispersed.

Temperature records
Temperature records can be used to see what the temperature was in a particular year. This could
include the ground temperature, atmospheric temperature, ocean temperature etc.

Predicting the future – extrapolation

Data can be extrapolated to estimate what the temperature will be like in the future but this is
unreliable as it doesn’t take into account the increased use of CO2 which may occur in the future as
well as other more unpredictable factors.

Effect of rising temperatures

 Changing rainfall patterns so animals will have to adapt to this change. Some areas will get
too much rain and hence become waterlogged whereas some areas will get too little rain
and have a drought.
 Changing species distribution as some species may have to move to a location which is more
suitable for them. If they are unable to migrate, they may become extinct or endangered.
 Increased enzyme activity in animals hence they will grow faster and will progress through
their lifecycles more quickly.
 Temperature may become too warm so enzymes may denature and therefore reactions will
be a lot slower and animals will progress through their lifecycles more slowly.
 Seasonal cycles will change such as seasonal temperatures, rainfall etc. so animals will have
to adapt to these changes. E.g. giving birth at an earlier point in the year so more food is
available.
Preventing increased carbon emissions
Biofuels – these are fuels made from renewable biological resources (biomass). They are carbon
neutral as they only release the carbon the plants took in during photosynthesis when the fuels
are burned. However, CO2 is released when the biofuels are transported hence they aren’t
completely carbon neutral.

Reforestation – replanting trees is a good way of decreasing carbon emissions as the trees will
then use CO2 to photosynthesise and produce biomass hence the carbon will be removed from
the atmosphere and locked up. However, since the replanted trees are smaller, they will not
take in as much CO2 as the fully grown trees that were chopped down.

Speciation and Evolution

Genome – all the DNA of an organism.
Proteome – all the proteins produced by the genome.

The proteins produced by the genome can vary due to post transcriptional changes during protein
synthesis or due to differential gene expression (when some genes are active and inactive).

Gene and allele frequency

A gene codes for a protein. The allele frequency is how often a particular allele is present in the gene
pool. Mutations are changes in the bases within genes and these lead to the production of new
alleles. Some mutations can be fatal where as some mutations such as point mutations may have no
effect at all since the DNA is degenerate.

If these new alleles are beneficial, their frequency will increase as the organisms with these alleles
are more successful hence they survive and reproduce to pass on the allele to their offspring. Vice
versa for non-beneficial alleles.

Species – a group of similar organisms that are able to reproduce to produce fertile offspring.

Speciation
Allopatric speciation
This is when speciation occurs due to a physical barrier between two groups of organisms such as a
mountain or a river.

Sympatric speciation
This is when speciation occurs even though there is no physical barrier between the two groups of
organisms. This occurs due to mutations.
Different types of sympatric speciation – pre-zygotic

Mechanical isolation – this is when the physical reproductive organs of two sets of organisms is
different hence they no longer fit together so reproduction is not possible.

Temporal isolation (time) – organisms may be fertile during different seasons. These seasons
may not be synchronised between two groups of organism and hence they are unable to
reproduce with each other.

Habitat isolation – this is when two sets of organisms choose different areas of the habitat
therefore they don’t come into contact with each other.

Behavioural isolation – this is when the mating call or ritual of an organism changes so they are
no longer seen as a potential mate so no one reproduces with them.

Gametic isolation - this is when the gametes of two organisms are no longer attracted to each
other or don’t function together properly. E.g. sperm cannot break through the zona pellucida
anymore.

Different types of sympatric speciation – post-zygotic

Low hybrid zygote vigour – the zygotes don’t survive or grow properly during their embryonic
stages and therefore they have abnormalities which prevent them from reproducing effectively.

Low hybrid adult viability – the do not thrive and grow properly into adults.

Hybrid infertility – they offspring produced are healthy but infertile/sterile hence they can
produce offspring. Like a mule or liger.

Step by Step speciation

1. Two groups of organisms are separated by geographical isolation e.g. a mountain in the
middle of them and they cannot get over it.
2. There are different selection pressures on either side of the mountain so different types of
organisms survive and reproduce to produce fertile offspring on either side therefore the
allele frequencies will be different. These are due to different climates on either side.
3. Random mutations occur independently on either side so different alleles may be present.
4. Through natural selection and evolution, this leads to reproductive isolation as the two
organisms are no longer able to reproduce to produce fertile offspring.
5. This means they are two different species now.
6. Could also be due to the founder effect where there is a small gene pool so a very acquired
set of animals grows and a new species is produced.

DNA Profiling

DNA
 Carries information in the body.
 Structure – Double helix, Bases (A, T, G, C), Phosphate group (PO43-).
  Sequence of base pairs is called a genetic code and it determines the proteins made during
protein synthesis.
 3 bases = 1 codon = 1 amino acid coded for.
 Introns are non-coding parts of DNA and exons are the coding parts of DNA.

DNA code is non-overlapping

For example, UUUAGC is not UUU, UUA, UAG, AGC, it is UUU, AGC. If the code was overlapping, it
would decrease the variety of codon that could proceed the previous codon since it would have to
start with the last two bases of the previous codon and this would therefore limit the combination of
amino acids that could come one after the other.

DNA is degenerate
DNA is degenerate meaning it carries more information than is needed. This is because one amino
acid is coded for by more than one codon and it’s usually the first two bases that determine the
amino acid so even if the last base in the codon changes, the same amino acid is produced. This is
important as it means that if a particular codon mutates and the last base changes, the same amino
acid will still be coded for hence the mutation will be neutral.

Protein synthesis
Transcription
1. RNA polymerase breaks the hydrogen bonds between the two strands of DNA.
2. RNA polymerase causes free RNA nucleotides to bond to their base pairs on the antisense
strand by complementary base pairing and bond to each other via phosphodiester bonds
creating a strand of mRNA.
3. T is replaced by U in mRNA.
4. When RNA polymerase has passed a section of DNA, that section of DNA coils back into a
double helix.
5. These mRNA molecules are small hence they are able to pass through the nuclear pores and
into the cytoplasm for translation to occur.

Post transcriptional changes – occur in the nucleus

1. The mRNA has introns and exons so the introns need to be cut out as they don’t code for an
amino acid.
2. These introns are cut out and the remaining exons are joined together.
3. The remaining exons can be joined together in any order e.g. ABC, ACB, BCA… so one gene
can code for many different proteins depending on the order that the bases are put back
into during the post transcriptional changes.
4. The mRNA then exits the nucleus through nuclear pores and attaches to a ribosome for
translation.

Translation
1. Translation starts at the start codon.
2. tRNA molecules carry free amino acids in the cytoplasm to the ribosome. Each tRNA
molecule only carries a specific amino acid based on its anticodon.
 3. tRNA molecules bond to their complementary base pairs on the mRNA molecules forming a
sequence of amino acids next to each other. These amino acids bond to each other by
forming peptide bonds and the tRNA molecule detaches from the amino acid and travels to
the cytoplasm to get another amino acid.
4. Once a stop codon is reached, the translation process stops, the amino acid chain detaches
from the ribosome and protein synthesis is complete.

DNA profiling – identifying relationships between the DNA of two people

Introns don’t code for proteins but exons do. Introns have repeating sequences which are called
STRs (Short Tandem Repeats) and these are of different lengths and different abundances. These
STRs are used to create DNA profiles to determine genetic relationships as more closely related
individuals will have more similar STRs.

1. Restriction endonuclease enzymes are used to cut up the DNA into fragments of STRs. They cut
the DNA at different points in the intron sequence. Specific restriction endonucleases cut the
DNA at specific points so they can be used to cut the DNA at either side of the STRs.
2. The DNA is amplified by a process called Polymerase Chain Reaction since there is not enough
DNA in one sample for DNA profiling to occur.
2.1. The DNA fragments, DNA polymerase, primers and free DNA nucleotides are placed in a
reaction vial.
2.2. The temperature is increased to 95oC to break the hydrogen bonds between the two
strands of DNA.
2.3. The temperature is then decreased to 50-65oC for annealing to occur. This is when the
primers attach to their complementary base pairs on the DNA strands.
2.4. The temperature is then increased to 72oC which is the optimum temperature for DNA
polymerase to function at. This enzyme causes the free nucleotides to bond to their
complementary base pairs on the DNA fragments.
2.5. One cycle of PCR forms two copies of the DNA fragments. This process is repeated many
times to produce millions of DNA copies which are needed for DNA profiling.
3. Fluorescent tags are added to the DNA fragments so that they can be viewed under UV light.
4. The DNA is then used to create a DNA profile using gel electrophoresis.
4.1. The DNA fragments are placed in a well in a slab of agarose gel which is in a buffer solution.
4.2. On one side of the well is the cathode and on the far side is the anode.
4.3. An electric current is passed through the gel and the DNA sample moves towards the anode
since it is negatively charged (PO43-). Smaller DNA fragments move further and faster than
larger fragments.
5. The gel is then viewed under UV light and the sample of DNA is shown as fluorescent bands.

Genetic mutation – Change in the order of bases in DNA which leads to a

change in the order of amino acids in proteins.

Microorganisms and disease

Infectious disease can be transmitted and are caused by the spread of pathogens (disease causing
microorganism) or natural flora (bacteria on skin and gut) mutating and becoming pathogenic.
Viruses – smallest type of microorganisms
 They are not cells; they are composed of viral DNA enclosed in a capsid (viral proteins).
Sometimes they have a lipid envelope surrounding them (taken from a host cell).
 They invade living organisms and manipulate the cells biochemistry to create more viruses.
 There are very few drugs that can kill viruses – anti viral drugs.
 They have a capsid (protein coat) composed of separate proteins called capsomeres. Each
capsomere is identical so minimal genetic
info is needed to create them and they can
be built easily.
 They contain genetic material
(DNA/RNA/single/double stranded) to create
the proteins and reproduce.
 They have receptors on their surface
to help them attach to hosts. Each antigen
only attaches to a specific host.
 They may have a lipid envelope taken
from a host cell which helps them move from
cell to cell.
 May contain DNA reverse transcriptase if it has RNA so DNA can be made by reverse
transcription. This is the case in HIV.

How viruses enter a cell

Some enter the cell by endocytosis and the host cell digests the capsid releasing the genetic
material.

Some enter the cell by fusing the lipid envelope with the phospholipid bilayer of a cell and releasing
its contents inside the cell.

Viral reproduction
 If the virus has DNA, the viral DNA is inserted into the host DNA and can be replicated by
DNA polymerase and then it can be used to make more viral proteins by protein synthesis.
 If the virus has RNA, DNA reverse transcriptase is used to translate the RNA into DNA. The
DNA then inserts itself into the hosts DNA and the host cell creates viral proteins during
protein synthesis. This is called reverse transcription.
 The new viruses then exit the cell by exocytosis and go on to infect other cells.

Viral infections are specific to tissues e.g. some viruses will only infect the respiratory tract.
Bacteria – prokaryotes – some are pathogens but most are harmless

 Bacteria have single stranded circular DNA as well as plasmids. The DNA is free floating in
the cytoplasm (i.e. they are prokaryotic, no nucleus).
 All bacteria have a cell wall to prevent them from bursting since they are hypertonic to their
environment most of the time so water moves into the cell by osmosis.
 Respiration occurs on parts of the cell membrane called mesosomes.
 Some bacteria have a slime capsule which protects them from phagocytosis by WBCs and
blocks their receptors so cells don’t recognise them as non-self so they are not recognised by
the host’s immune system.
 When mycobacterium tuberculosis is trapped in tubercules, some of them have slime
capsules so they are protected from being digested by the digestive enzymes in the
tubercules (tissue).
 Some bacteria have pilli which helps them attach to a host cell and are also used for sexual
reproduction.
 Some bacteria have a flagellum to help them move by rapid rotations such as sperm.
 Bacteria can be cocci (spherical), bacilli (rod shaped), spirilli (twisted) or vibrious (comma
shaped).

Bacterial reproduction – Asexual reproduction

The most common way in which a bacterium reproduces is by binary fission.

1. Once the bacterium gets to a certain size, its DNA is replicated.

2. Old cell wall breaks down.
3. Enzymes break open the circular DNA so it can be replicated.
4. New cell walls are laid down in the middle of the cell and a new cell membrane and cell walls are
created. The cell eventually divides to produce two identical cells.

Pathogens
Bacteria normally grows and reproduces in the body and produces toxins which make people feel
poorly.
Beneficial bacteria – skin and gut flora
 Skin and gut floras have various roles such as breaking down food in the gut. However, skin
and gut flora also outcompete pathogens for space and resources therefore the pathogens
die.
 Some bacteria are also decomposers meaning they break down organic material into simpler
inorganic material.

How bacteria enter the body

1. Open routes such as eyes, nose, ears, mouth, anus and penis.
2. Vectors – living organisms that transmit pathogens by biting e.g. mosquitos.
3. Travelling by an inanimate object e.g. sharing a towel.
4. Direct contact – e.g. shaking hands with another person.
5. Inhalation – coughing, sneezing or talking can spread bacteria from the respiratory tract of
someone with an infection as it can be inhaled by another person.
6. Ingestion – eating infected food or drinking infected drink.
7. Inoculation – entering the body through a cut or sharing needles.

External barriers to infection

1. Skin is impenetrable by pathogens as it is toughened by keratin unless it is cut in which case
pathogens have access to the blood stream and can infect the body.
2. Oily substance on skin called sebum contains chemicals that inhibit the growth of
microorganisms besides natural skin flora.
3. Skin and gut flora outcompete pathogens for space and nutrients so the pathogens die.
4. Surfaces that are not toughened by keratin e.g. mucous membranes such as reproductive
tracts, nose and respiratory system have mucus which traps microorganisms. The mucus
contains lysozymes which break down microbial cell walls.
5. Mucus is swept up the respiratory tract and into the stomach by cilia so it can be destroyed
by the pH2 hydrochloric acid and mucous in reproductive tracts is cleared out by the urine.
6. Saliva in the mouth can destroy the bacteria or slow down their growth as they have
antibacterial properties.
7. Acid in stomach is pH 2 which is not tolerable by most pathogens hence they die as their
enzymes denature at the harsh pH.
8. Vomiting – the contents of the stomach (including the pathogens) are removed via the
mouth. However, it can lead to loss of fluid and electrolytes which can be fatal for young
children and frail elderly people.

Non-specific responses – the same response is uses to deal with all sorts of
infections
Some of these responses rely on cell recognition systems. Each cell has a unique marker on its
surface such as a glycoprotein. These sites bind to each other if they are the same to form tissues.

These markers act as antigens that are recognised by white blood cells during specific responses. An
antigen is a substance that stimulates the production of antibodies (antibody generator = antigen) if
it is non-self. Toxins also make antigens.
Blood clotting
1. Thromboplastin is released from the damaged blood vessels.
2. This triggers the conversion of prothrombin into thrombin.
3. Thrombin catalyses the conversion of fibrinogen (soluble proteins) into fibrin which creates a
mesh of insoluble fibres.
4. Platelets as well as red blood cells get trapped in the mesh of fibres producing a blood clot.
The platelets tighten the clot.

Inflammation
1. Mast cells in the connective tissue and damaged white blood cells release chemicals called
histamines.
2. Histamines increase the permeability of the capillary walls (by making the cells separate
slightly) and allow fluid to enter the area of infection. This fluid includes plasma, white blood
cells, antibodies etc. so the specific responses can be carried out effectively e.g. WBC’s and
antibodies can kill pathogens. This causing swelling and pain in the area that is infected.
3. They also cause the blood vessels to dilate to increase blood flow to the infected area
causing redness and heat. The higher temperature also reduces the effectiveness of the
reproduction of pathogens.
4. Rash and red patches also occur as a result of inflammation.

Fever
The hypothalamus increases the body temperature causing a fever. This is because pathogens
cannot function as effectively at higher temperatures and they reproduce at slower rates. Also, the
specific response system works faster at higher temperature.

However, if the temperature gets too high, various proteins inside the body could denature as their
bonds brake and they change shape so this could be fatal. Enzymes, active site, enzyme substrate
complex etc.

Phagocytosis
1. Phagocytes recognise a certain cell as being non-self due to the antigens on the cell surface.
2. Phagocytes engulf the non-self cell by endocytosis.
3. The phagocytic vacuole fuses with the cells lysosomes and the lysozymes destroy the
pathogen leaving behind only the antigens of the pathogen.
4. These pathogenic antigens are presented on the cell surface of the phagocyte to produce an
antigen presenting cell which is destroyed during the specific response.

Interferons
 Invaded cells produce chemicals called interferons. These:
o Inhibit the production of viral proteins.
o Activate T and B lymphocytes.
o Activate other non-specific responses such as inflammation.

Specific response to infection

Antigens are used to identify a cell as self or non-self. The more antigens two people have in
common the more closely related they are and identical twins have exactly the same antigens. This
is why it is preferred to have a transplant from a close relative as the organ will not be rejected.
Characteristics of immune system:
1. Recognise self and non-self cells.
2. Specific – each lymphocyte only attacks and destroys specific pathogens.
3. Immunological memory – if a pathogen tries to re-invade the body, the immune system will
be able to react to it faster since it has T and B memory cells.
4. Diverse – recognises over 10 million different antigens.

B cells and T cells are the cells involved in the specific response. They are both made in the bone
marrow but T cells mature in the thymus whereas B cells mature in the blood.

B cells T cells
Made in the bone marrow Made in the bone marrow
Receptors on their cell surface are identical to T helper cells are involved in the humoral
the antibodies their plasma cells produce response
B effector and memory cells are involved in the T helper and killer cells are involved in the cell
humoral response mediated response

MHC proteins are the proteins that display antigens on the surface of cells to make them
antigen presenting cells.

Humoral response – this occurs when a pathogen is outside of the body’s

cells e.g. in the blood.
1. Pathogen is engulfed by a macrophage by endocytosis (phagocytosis). The macrophage fuses
the phagocytic vacuole with its lysosomes and the digestive enzymes in the lysosome
destroy the pathogens and leave the antigens behind. The antigen/MHC complex is then
presented on the cell surface so that macrophage has become an APC.
2. CD4 receptors on the T helper cell bind to their complementary antigens on the macrophage
3. This triggers the helper cells to produce clones. Most of these clones remain in the blood as
T helper cells but some become T memory cells (immunological memory).
4. There are millions of B cells in the body and some will be complementary to the antigens on
the pathogen.
5. The B cell that is specific to the antigen i.e. it has the specific antibody on its surface engulfs
the pathogen, fuses the vesicle with a lysosome and digests the pathogen leaving behind the
antigens. These antigens are presented on the surface of the B cell.
6. T helper cells produced earlier recognise the antigens and bind to them. They release
cytokines which cause the B cells to divide and form clones called B memory cells and B
effector cells.
7. The B effector cells differentiate into plasma cells and produce large amounts of antibodies
which circulate around the body in the blood and attack all the pathogens with the specific
antigen on their cell surface.

How do antibodies work?

 Agglutinate – they clump pathogens together to prevent them from functioning.
 Reduce pathogens ability to invade host cells.
  Antigen-antibody complex is readily engulfed by phagocytes.
 They may stimulate other reactions such as histamines being released so inflammation can
occur or the destruction of an antigen membrane if it has one.

Cell mediated response – this occurs when a pathogen has invaded a body
cell
1. The pathogen is digested by the cells lysosomes and the antigens along with the MHC
proteins are presented on the surface of the host cell.
2. T killer cells present in the blood that have complementary receptors binds to the APC host
cell.
3. If the T killer cells are exposed to cytokines from a T helper cell that is complementary to the
antigen, they divide by mitosis to form clones of identical T killer cells and T killer memory
cells which stay in the blood for use in the future if the same antigen is spotted.
4. These T killer cells bind to the antigens on infected body cells and release enzymes that
make pores appear in the membrane of infected cells hence water and ions can travel into
the cell and the cell dies or breaks down by lysis.
5. Any pathogens which are released intact are then attacked by the antibodies produced by B
effector cells.

6.3 – People versus pathogens

Pathogens reproduce inside the body and cause symptoms of disease.
Objective evidence – symptoms of infection that are visible on the outside e.g. a rash.
Subjective evidence – symptoms of infection that are felt by the patient e.g. headache

Asepsis – absence of pathogens e.g. aseptic techniques.

Antisepsis – disinfectants that are use directly on people.

Antibiotics work by selective toxicity i.e. they interfere with the metabolism or function of pathogens
with minimal damage to the host. Antibiotics do not work against all pathogens (e.g. HIV) hence
research is ongoing.

Bacteriostatic antibiotics – antibiotics that inhibit the growth and reproduction of pathogens.
Sufficient for most common infections as the immune system then kills the pathogens.
Bactericidal antibiotics – antibiotics that kill pathogens. Used for more serious infections or when the
immune system is supressed e.g. during a transplant or in a person with AIDS.

Broad spectrum antibiotics – kill a wide range of pathogens.

Narrow spectrum antibiotics – kill a limited range of pathogens.

Effectiveness of antibiotics
 Depends on the concentration of the drug that is in the area of the body that is infected i.e.
how quickly the drug gets to the infected area.
 pH – if it is wrong, the antibiotic could die.
 Susceptibility of pathogens – If they are sensitive they will be killed by a standard dose, if
they are moderately sensitive they will be killed by an increased dose and if they are
resistant they will not be killed by the antibiotic.
Creating drug resistant bacteria
Humans keep developing new medicines and pathogens keep evolving through natural selection to
develop resistance to these medicines. Antibiotics only work if the pathogen has the correct
receptor for the drug to bind to.

Mutations
 During the pathogens reproduction, a mutation could occur and these mutations may help
the pathogen develop resistance to an antibiotic by changing its receptors for example.
 The selection pressure of the antibiotic and natural selection will result in the resistant
antibiotics surviving, reproducing and passing on their viral DNA hence resistant pathogens
will become more common and sensitive ones will die.

Overuse or underuse of antibiotics

 People using their antibiotics for a limited time means that there will still be some
pathogens remaining and the immune system will not be able to cope with these so these
have a higher chance of mutating and developing resistance and then being spread to other
people as infected patients assume they have been cured.
 Different antibiotics are used to tackle resistant pathogens and this starts to shift the
selection pressure in favour of pathogens that are resistant to the new antibiotic resulting in
pathogens that are resistant to multiple antibiotics called ‘superbugs’.
 To prevent the creation of ‘superbugs’ antibiotics should only be used sparingly and as a last
resort when they are completely necessary as it limits the selection pressure and allows the
antibiotics to stay effective.

Hospital acquired infections

Superbugs are commonly found in hospitals and care homes where antibiotics are used much more
frequently. Patients who become infected with these resistant pathogens have to be kept in the
hospital for much longer.

MRSA – Methicillin Resistant Staphylococcus Aureus

Staphylococcus Aureus is on the skin and nasal passages of humans but is harmless unless it gets
into the blood where it can cause boils and abscesses. These can be treated by Methicillin but a
mutation has occurred which causes some of the SA to produce penicillinase, an enzyme which
breaks down methicillin so it’s called MRSA as it is resistant to methicillin.

This is able to infect frail patients in hospitals and these patients have to be treated with methicillin
or other antibiotics when methicillin doesn’t work. The result is MRSA, a superbug which is resistant
to multiple antibiotics. It can be treated with certain antibiotics but these are used sparingly to
prevent the MRSA becoming resistant to them as well.

Preventing and controlling the spread of infection

Codes of practice have been written for doctors, nurses and medical staff to prevent the spread of
pathogens in hospitals.

1. Using antibiotics sparingly – Using them sparingly prevents the likelihood of pathogens
evolving. They should only be used when absolutely necessary and the course of
prescription should be strictly followed. If not the pathogens will still remain in the body and
 the immune system will not be able to cope so the bacteria that have resistance will survive,
reproduce and spread to others. Using many different antibiotics has a very specific
selection pressure and encourages resistant bacteria to grow and multiply.
2. Hygiene – hands of medical staff as well as visitors should be washed using the correct
technique with hand wash or an alcohol based hand gel. Clothing such as ties and long
sleeved shirts should not be worn as they can carry pathogens and spread them. Hospital
wards, toilets etc. should be thoroughly cleaned as well.
3. Isolation of patients – patients who are infected with pathogens need to be isolated ASAP
and need to be given high hygiene rooms with infection control nursing so infections aren’t
spread.
4. Screening – Patients should be screened before being admitted into a hospital so that if
they are infected, they can be isolated immediately.
5. Monitoring levels of healthcare acquired infections – reports have to be made on the levels
of MRSA and c.difficile and the results have to be available to the public and government.

Different types of immunity caused by immunological memory

Vaccine – A vaccine consists of small amounts of viral antigens or neutralised/detoxified toxins or
inactivated viruses or dead bacteria. These substances will stimulate the body’s immune response
and therefore the production of T helper/memory cells, B memory/effector cells, plasma cells and
antibodies so the body can react to the vaccine and react to the pathogen quickly in the future if the
body becomes infected with it.

1. Natural active – this is when the body’s immune system comes into contact with a foreign
antigen and the immune response produces antibodies which destroy the pathogen.
2. Natural passive – this is when a baby receives antibodies through the placenta or through
breast milk from the mother. This occurs until the baby’s immune system is active and is not
a long term solution as the antibodies don’t live doe long periods of time.
3. Artificial active – This is when a vaccine is injected into someone and the body responds to
the vaccine with its normal immune response and leaves behind memory cells so the
immune response can be a lot quicker in the future.
4. Artificial passive – This is when antibodies from someone else are injected into another
infected person so that their body is able to fight off the pathogens. This is not long term as
the infected persons body will not be able to produce the antibodies to fight off the
infection in the future.

Tuberculosis – infection of the lungs and T cells in the lungs

Causes – caused by the spread of the pathogen mycobacterium tuberculosis which is spread in
water droplets when talking, coughing, sneezing etc.

Malnourished, ill or people with a weakened immune system after a transplant or HIV/AIDS are
more likely to develop tuberculosis.

Symptoms – coughing up blood, weakness, damaged lung tissue and supressed immune system
making the body more susceptible to infections.
Stages of TB
Primary infection – this mainly occurs in children and it is when the mycrobacterium tuberculosis is
reproducing slowly showing no obvious symptoms most of the time. If the person has a healthy
immune system, it will cause inflammation in the lungs and the dead bacteria and macrophages will
be locked up in mass of tissues called tubercules. After 8 weeks, the immune system has control
over the infection and inflammation goes down.

Later stage – In some people, the bacteria may survive since it has a thick waxy outer layer that
protects it from enzymes in the tubercules hence it will reproduce slowly or remain dormant in the
tubercules. This may occur for years and if the persons immune system weakens e.g. by AIDS the
bacteria may overcome the immune system and reproduce rapidly hence by natural selection the
best TB have reproduced. This is called active TB. They infect the lungs causing fever, weakness, lung
tissue damage and coughing up blood. Without treatment, the lungs breakdown and the alveoli
become inefficient air spaces.

The bacteria also target T cells hence reducing the production of antibodies. Fever occurs to kill the
bacteria but frail patients are at risk of death as proteins and enzymes in the body can denature at
temperatures about 40oC.

Opportunistic infections can also infect patients as the immune system is weakened and eventually
patients die due to lack of O2, infection or lack of nutrients.

Treatment and control

Chest x-rays may show an opaque area which suggests there may be a TB infection present although
it could actually be another chest infection.

Treatment involves a cocktail of different antibiotics so even if one doesn’t work (i.e. bacteria is
resistant), the others will work and kill the bacteria. This is followed by 4-7 months of taking 2
antibiotics and most people are free of TB after approximately 9 months.

HIV/AIDS
Symptoms: Fevers, diarrhoea, weight loss and secondary infections.

HIV positive: This is when people are infected with HIV but have no symptoms. Blood has
HIV antibodies in it. These can be tested for and if detected, the person is HIV positive.

How is HIV transmitted?

HIV relies on bodily fluids to survive. It is very fragile and will not survive in open air.
1. During sexual intercourse – i.e. in the sperm.
2. Sharing needles – in the blood.
3. Mother to foetus – in the placenta or during breast feeding in the milk.

How does HIV cause AIDS?

HIV attaches to the CD4 receptors on T helper cells and invades the cell. Once inside, it inserts the
viral DNA into the T helper c ells DNA and uses the cells protein synthesis mechanism to produce
more proteins and therefore produce more HIV. Once it leaves the cell, the T helper cell is killed and
whilst in the cell, T killer cells can kill some of the infected T helper cells. This causes the immune
system to become useless due to lack of T helper cells so opportunistic infections can occur.

Course of infection
Stage 1 – Acute HIV syndrome – This occurs during the first few weeks. Some people feel unwell and
some don’t feel unwell. 3-12 weeks after the infection, HIV antibodies are present in the blood
hence the person is HIV positive.

Stage 2 – Asymptomatic stage – There are no symptoms during this stage. During this stage, the
virus replicated but is controlled by T killer cells. This stage will last longer in healthy individuals who
have a stronger immune system.

Stage 3 – Symptomatic stage – Virus overpowers the immune system as the load gets too much and
the immune system starts to fail.

Stage 4 – Advanced AIDS – Major symptoms such as severe weight loss, dementia, cancer, TB etc.
occur and this leads to death.

Treating AIDS
AIDS is currently incurable so there are various ways to prevent infection.

1. Limit its spread

2. Provide education programmes for the public on the subject
3. Use protection, clean needles etc.

The HIV virus mutates very rapidly hence it is hard to make vaccines that destroy it. It is also hard for
the body to react to it as its antigens are always changing so when the body has made antibodies for
HIV, a mutation has already occurred which results in different antigens being present on the surface
of HIV so the antibody is useless.

Why is a mixture of antibiotics used for treatment?

 HIV has many different strains caused by their rapid rate of mutation and rapid rate of
reproduction.
 This means that some will be resistant to certain antibiotics.
 If only one antibiotic is used, some will be resistant and will survive.
 A mixture of antibiotics increases the likelihood of killing all the strains of HIV so it is
completely eradicated from the body.