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These notes do not cover absolutely everything, but they do cover those major
topics and the wording you seem to have the greatest difficulty with.
Check the Specification and the Check Your Notes summary.
TOPIC 5
Topic 5 summary
Make sure your notes cover the following points. The points are listed in the approximate order they appear
within the topic. All the points are covered in the textbook but where there is supporting information within
the activities this is indicated.
There are suggestions on making notes and on revision in the Exam/coursework support.
You should be able to:
o Explain that the numbers and distribution of organisms in a habitat are controlled by biotic and abiotic
factors. (Activity 5.1 and 5.2) (Checkpoint question 5.4)
o Explain how the concept of niche accounts for distribution and abundance of organisms in a habitat.
(Activity 5.1 and 5.2) (Checkpoint question 5.1)
o Describe how to carry out a study on the ecology of a habitat to produce valid and reliable data
(including the use of quadrats and transects to assess abundance and distribution of organisms and the
measurement of abiotic factors, e.g. solar energy input, climate, topography, oxygen availability and
edaphic factors). (Activity 5.2)
o Describe the concept of succession to a climax community. (Activity 5.3) (Checkpoint question 5.2)
o Describe the overall reaction of photosynthesis as requiring energy from light to split apart the strong
bonds in water molecules, storing the hydrogen in a fuel (glucose) by combining it with carbon dioxide
and releasing oxygen into the atmosphere. (Activity 5.4 and 5.5) (Checkpoint question 5.3)
o Describe how phosphorylation of ADP requires energy and how hydrolysis of ATP provides an
immediate supply of energy for biological processes. (Activity 5.4 and 5.5)
o Describe the light-dependent reactions of photosynthesis including how light energy is trapped by
exciting electrons in chlorophyll and the role of these electrons in generating ATP and reducing NADP in
photophosphorylation and producing oxygen through photolysis of water. (Activity 5.4 and 5.5)
o Describe the light-independent reactions as reduction of carbon dioxide using the products of the light-
dependent reactions (carbon fixation in the Calvin cycle, the role of GP, GALP, RuBP and RUBISCO)
and describe the products as simple sugars that are used by plants, animals and other organisms in
respiration and the synthesis of new biological molecules (including polysaccharides, amino acids, lipids
and nucleic acids). (Activity 5.4, 5.5 and 5.6)
o Describe the structure of chloroplasts in relation to their role in photosynthesis. (Activity 5.4)
o Carry out calculations of net primary productivity and explain the relationship between gross primary
productivity, net primary productivity and plant respiration. (Activity 5.8)
o Calculate the efficiency of energy transfers between trophic levels. (Activity 5.8)
o Analyse and interpret different types of evidence for global warming and its causes (including records of
carbon dioxide levels, temperature records, pollen in peat bogs and dendrochronology) recognising
correlations and causal relationships. (Activity 5.9, 5.10 and 5.11)
o Outline the causes of global warming including the role of greenhouse gases (carbon dioxide and
methane, CH4) in the greenhouse effect. (Activity 5.12 and 5.13)
o Discuss the way in which scientific conclusions about controversial issues, such as what actions should
be taken to reduce global warming or the degree to which humans are affecting global warming, can
sometimes depend on who is reaching the conclusions. (Activity 5.14 and 5.15)
o Describe how data can be extrapolated to make predictions, that these are used in models of future global
warming, and that these models have limitations. (Activity 5.16)
o Describe the effects of global warming (rising temperature, changing rainfall patterns and changes in
seasonal cycles) on plants and animals (distribution of species, development and life cycles). (Activity
5.17 and 5.21) (Checkpoint question 5.5)
o Explain the effect of increasing temperature on the rate of enzyme activity in plants, animals and micro-
organisms. (Activity 5.18)
o Describe how to investigate the effects of temperature on the development of organisms (e.g. seedling
growth rate, brine shrimp hatch rates). (Activity 5.19 and 5.20)
o Describe how evolution (a change in the allele frequency) can come about through gene mutation and
natural selection. (Checkpoint question 5.6)
o Describe the role of the scientific community in validating new evidence (including molecular biology,
e.g. DNA, proteomics) supporting the accepted scientific theory of evolution (scientific journals, the peer
review process, scientific conferences). (Activity 5.22 and 5.23)
o Discuss how understanding the carbon cycle can lead to methods to reduce atmospheric levels of carbon
dioxide (including the use of biofuels and reforestation). (Activity 5.25) (Checkpoint question 5.7)
Demonstrate knowledge and understanding of the How Science Works areas listed in the table on page 13 of
the specification
Topic 5
Biotic and abiotic factors affect the distribution and abundance of
species in a habitat
When these factors are favourable organisms survive, grow and reproduce
successfully. When these conditions are unfavourable, organisms dont
survive, grow or reproduce as successfully.
Be prepared to answer questions on organisms and habitats you have not seen
before; the question and any data should give you sufficient information to be
able to interpret the factors, both biotic and abiotic, affecting the distribution
(i.e. where the species lives in the habitat) or abundance (how many there are
per unit area) of the organisms in question. Do not be afraid to think and
come up with biologically sensible ideas!
Sampling strategies
This produces a valid representative sample.
This allows us to estimate the abundance (i.e. how many) of species in a
particular area.
Succession
The initial environment is hostile and extreme. First colonisers are called
pioneer species
Pioneer plants are highly adapted to withstand hostile conditions
The abiotic factors in this environment mainly determine what species are
present since few species can tolerate such conditions so in the initial
stages the biodiversity will be low
The initial colonisers modify the environment to make it less extreme
pioneer plants die organic matter incorporated into developing soil/nitrate
content of soil increases
existing plants provide increasing dead organic matter and nitrates so soil
develops, they provide shade and shelter, reduce wind speed to reduce
transpiration etc so improve the environment so more plants now able to
establish and grow so early colonisers are outcompeted by later colonisers
(e.g. grasses shade out mosses, trees shade out grasses) so community
changes so more plants can grow so biodiversity increases
As number of different species present increases so there will be more
microhabitats for organisms to exploit/greater variety of food plants for
associated organisms/greater variety of feeding niches so biodiversity of
associated animal community will change too
In the latter stages biotic factors largely determine which organisms can
survive, e.g. predation, grazing, competition etc
The stable end point community is characteristic and is called the climax
community usually dominated by trees. It is in equilibrium with the
environment so undergoes little it any further change
Photosynthesis
Photolysis of water
electrons from water are used to replace the electrons lost from the chlorophyll
these are then excited when the chlorophyll absorbs light to be used to
make more ATP as before
oxygen is the valuable waste product of photolysis
Light independent stage
Not all the visible light energy coming in from the sun ever reaches a plant
Some is reflected by clouds and dust
Some will miss the leaves altogether
Some is not of the right wavelength to be absorbed by the photosynthetic
pigments
which absorb blue and red but not green
Some of this is then lost as heat by the reactions of p/s
What is left is fixed in the organic molecules which are the products of p/s; this
the gross primary productivity
In general less than 10% of the energy in the food taken in ends up in the
biomass
This ultimately limits the number of trophic levels. So much energy is lost
between levels that final level contains so little energy that, if only 10% of this
is transferred there simply isnt enough to support any further biomass.
All organisms contain DNA which is read in the same way, providing evidence
of evolution from a common ancestor.
DNA and proteins contain a record of genetic changes resulting from random
mutations over time, indicating gradual change within and between species.
Studying DNA and proteins allows these changes to be identified.
Genomics (the study of DNA); look at the sequence of bases in genes; the
more distantly related two species are the more differences there will be due to
the accumulation of mutations over time.
Analysed by DNA hybridisation, DNA profiling, DNA molecular clocks
In order for new evidence to be accepted as support (or rejection) for the
theory of evolution (or any other theory for that matter) it needs to be
regarded as VALID.
The evidence
Provides information back possibly as far as the last Ice Age (circa 12 000 years
ago).
Peat formed when plant material dies but does not decompose
The peat accumulates in successive layers; lowest layers are the oldest: pollen
trapped in peat layers
Use of carbon dating techniques can establish the age of the layers
Trees produce a ring of new xylem each year = growth ring. Xylem vessels
produced in spring are wider than those produced in the summer and the
difference in vessel size from summer to the next spring is what demarcates
the ring.
Outer ring is current year; each ring can be dated by counting inwards
Width of ring reflects amount of xylem produced which reflects amount of
growth
Wide ring = lots of growth so by inference climatic conditions favoured
growth e.g. warm/wet
So, age of rings and widths provide clues about past climatic conditions
The Earth appears to have been warmer since 1980 than at any time in the last
18 centuries.
The Earth has warmed by 0.5oC over the last century and at least 0.2oC in the
last 20 years or so - the greatest amount by which it has warmed or cooled
over the space of a century in the past.
Temperature and other data shows mean global temperature is rising. Fact.
What is causing it? Several possible explanations (i.e. theories)
Greenhouse effect
light energy from the Sun reaches the Earths surface and is absorbed so the
Earth warms up
some of this energy is radiated back into space as longer wavelength
infrared radiation.
the atmosphere contains gases, including carbon dioxide, water vapour and
methane, which absorb some of this infrared radiation so stopping it leaving.
These are called greenhouse gases.
this causes the atmosphere to warm up which in turn warms up the Earths
surface.
Greenhouse gases absorb infra red radiation: the main greenhouse gases are:
water vapour
carbon dioxide
methane
Under normal circumstances the CO2 level will remain constant because the
processes which add CO2 are balanced by the processes that remove CO2 from
the atmosphere, i.e. in equilibrium
But the CO2 level will increase if the processes of the carbon cycle become
unbalanced.
Combustion
o burning fossil fuels e.g. coal. oil, petrol, natural gas
o burning of trees and tree debris (from felling operations) releases CO2:
trees contain a lot of biomass and are important carbon sinks (i.e.
CO2 used by p/s as the tree grows and the carbon atoms are removed
from the carbon cycle and locked away in the cellulose and lignin of
the wood biomass so a lot of extra carbon will be released by burning)
Deforestation:
o Loss of trees will result in loss of CO2 uptake by photosynthesis in the
short term so CO2 level will rise
o Increase in decomposition of dead organic matter in soil
loss of forest cover exposes soil to the sun so it warms up so the
rate of activity of the decomposers will increase so releasing
more CO2.
If we accept the CO2 levels are rising and are probably linked to rising global
temperatures, what can be done about it? How could we restore the CO2
balance?
Reafforestation:
o Replaces trees
o Young forests grow rapidly take up CO2 by p/s rapidly (especially if
climate is warmer!) and turn it into biomass (growing new wood)
faster than respiration occurs, so net CO2 absorption occurs
o As trees get bigger carbon taken up and locked away in biomass
of wood of tree so forests act as a carbon sink to keep carbon out of
the atmosphere (so there is less CO2 contributing to global
warming)
o May slow down further increase in atmospheric CO 2 so long as
reafforestation is a continuous process on a large scale worldwide
> deforestation
Limitations to reforestation :
o Mature forest has trees which are not growing so becomes carbon
neutral [CO2 uptake by p/s = CO2 release by respiration] so benefit
only lasts whilst forest grows
o Only a limited amount of land which can be used to grow forests
(land needed to live on, grow food on etc, plus trees dont grow
above the tree line)
1) Describe how DNA can be amplified using the polymerase chain reaction (PCR). (Activity 6.4)
2) Describe how gel electrophoresis can be used to separate DNA fragments of different length. (Activities
6.1 and 6.2)
3) Describe how DNA profiling is used for identification and determining genetic relationships between
organisms (plants and animals). (Activities 6.3 and 6.5) (Checkpoint question 6.1)
4) Describe how to determine the time of death of a mammal by examining the extent of decomposition,
stage of succession, forensic entomology, body temperature and degree of muscle contraction. (Activity
6.5) (Checkpoint question 6.2)
5) Describe the role of microorganisms in the decomposition of organic matter and the recycling of carbon.
(Checkpoint question 6.2)
6) Distinguish between the structure of bacteria and viruses. (Activity 6.6) (Checkpoint question 6.3)
7) Describe the non-specific responses of the body to infection, including inflammation, lysozyme action,
interferon, and phagocytosis. (Activity 6.7) (Checkpoint question 6.4)
8) Explain the roles of antigens and antibodies in the bodys immune response including the involvement
of plasma cells, macrophages and antigen-presenting cells. (Activity 6.8) (Checkpoint question 6.5)
9) Distinguish between the roles of B cells (including B memory and B effector cells) and T cells (T helper,
T killer and T memory cells) in the bodys immune response. (Activity 6.8) (Checkpoint question 6.5)
10) Explain how bacterial and viral infectious diseases have a sequence of symptoms that may result in
death, including the diseases caused by Mycobacterium tuberculosis (TB) and Human
Immunodeficiency Virus (HIV). (Activities 6.9, 6.11 and 6.17) (Checkpoint question 6.6)
11) Explain the process of protein synthesis (transcription, translation, messenger RNA, transfer RNA,
ribosomes and the role of start and stop codons) and explain the roles of the template (antisense) DNA
strand in transcription, codons on messenger RNA, anticodons on transfer RNA. (Activities 6.12
and 6.13)
12) Explain the nature of the genetic code (triplet code, non-overlapping and degenerate). (Activity 6.12)
13) Explain how one gene can give rise to more than one protein through post-transcriptional changes to
messenger RNA. (Activity 6.13)
14) Describe the major routes pathogens may take when entering the body and explain the role of barriers in
protecting the body from infection, including the roles of skin, stomach acid, gut and skin flora.
(Activity 6.14)
15) Explain how individuals may develop immunity (natural, artificial, active, passive). (Checkpoint
question 6.7)
16) Describe how to investigate the effect of different antibiotics on bacteria. (Activity 6.15)
18) Discuss how the theory of an evolutionary race between pathogens and their hosts is supported by the
evasion mechanisms as shown by Human Immunodeficiency Virus (HIV) and Mycobacterium
tuberculosis (TB). (Activity 6.17)
19) Describe how an understanding of the contributory causes of hospital acquired infections have led to
codes of practice relating to antibiotic prescription and hospital practice relating to infection prevention
and control. (Activity 6.17)
Demonstrate knowledge and understanding of the How Science Works areas listed in the table on page 13 of
the specification.
Table of Contents
Polymerase chain reaction...................................................................................18
Producing a DNA profile.......................................................................................18
Determination of the time of death.....................................................................19
Causes of decomposition......................................................................................20
Forensic entomology............................................................................................20
Non-specific responses to infection....................................................................22
TB..........................................................................................................................24
Antibiotics.............................................................................................................25
HIV.....................................................................................................................27
Nature of genetic code.........................................................................................27
HIV Infection and AIDS.................................................................................................................29
Topic 6
How to identify a dead body
Causes of decomposition
Autodigestion or autolysis due to action of hydrolytic enzymes (= self-
digestion!) begins about 4 mins after death!
In gut
from lysosomes in cells
Causes breakdown of body tissues
Action of bacteria
From gut especially, later those from outside which invade through
natural openings or wounds,
Initially aerobic bacteria but these use up oxygen so replaced by
anaerobic bacteria which cause putrefaction
Forensic entomolog
This is especially useful when the body has been dead for more than a few
days, because the features that are normally used to determine the time of
death, like temperature or rigor mortis, are no longer helpful
Many types of fly will lay their eggs in a dead body because it is a source of
food for the larvae (maggots). Eggs can be laid on the skin, in body openings,
e.g. nose, ears, mouth or in wounds
Structure of a bacterium
Bacteria Viruses
Prokaryotic cells No cellular structure
Cell wall, cell membrane, Protein coat surrounding nucleic
cytoplasm, no organelles, DNA acid molecule. May have outer
not in a membrane-bound envelope derived form host cell
nucleus. May have mucilage
capsule Typically up to 400 nm in size, so
Typically 10 mm in size very much smaller
(x 25 times bigger) Genetic material is DNA or RNA
Genetic material is DNA Reproduce by inserting nucleic
Reproduce by binary fission acid into host cell which reads
(asexual) the genes to synthesise new
virus particles which are
released
Defence against disease.
Lysozyme
Enzyme found in tears, nasal secretions, saliva
first line of defence against bacteria entering body through eyes, nose or
mouth
breaks down bacterial cell wall
Inflammation
Damage/infection causes damaged mast cells (cells found in connective
tissue) to release hisamine
causes vasodilation of the arterioles nearby so more blood flows to area
of infection
also increases permeability of capillaries so more tissue fluid forced out
-> localised swelling
Phagocytes can squeeze out of capillaries into the tissues to destroy the
bacteria to limit infection.
Phagocytosis
Non-specific first line of defence mechanism if any pathogens have got
into the blood or tissues
phagocytes recognise antigens on surface of pathogen as foreign; engulf
pathogens (phagocytosis a form of endocytosis); killed by hydrogen
peroxide produced and digested by enzymes from lysosomes
Interferon
Cells infected with virus secrete a protein called interferon (a type of
cytokine)
attaches to membranes of surrounding cells.
this triggers the cells to make their own antiviral proteins which inhibit
synthesis of viral proteins so no new viruses can be produced, so limiting
infection.
Also stimulates virus-infected cells to self-destruct
Significance
Interferon system reacts very quickly to viral infection
This limits the infection until the slower acting specific immune response
kicks in to take over.
This is immunity.
Active immunity
the body produces antibodies in response to an antigen following infection
artificially acquired by injection of vaccines containing dead or weakened
forms of a pathogen
Passive immunity
Ready-made antibodies pass from mother across placenta and in milk
Artificially acquired by injection of serum containing antibodies e.g. anti-
venom. Tuberculosis (TB) is a contagious disease caused by the
bacterium Mycobacterium tuberculosis. Respiratory or
Herd immunity pulmonary TB is the most common form.
Achieved when enough people in a community are immunized against
certain diseases so it is more difficult for that disease to get passed between
those who aren't immunized.
Infection may occur when M. tuberculosis bacteria are
inhaled and lodge in the lungs. Here they start to multiply.
TB
Tuberculosis is causedTheby
firstthe
phase (primary infection)
bacterium can last for several tuberculosis.
Mycobacterium Course
months; it may have no symptoms.
of the disease.
Some M. tuberculosis bacteria may survive inside macrophages. The bacteria have
very thick waxy cell walls, making destruction inside the macrophages very
difficult. The bacteria can lie dormant for years.
The second phase (active tuberculosis) occurs if there are too many bacteria for the
immune response to deal with, or if an old infection breaks out because the
immune system is not working properly.
The lung damage will eventually kill the sufferer if they are
not treated with an appropriate antibiotic.
Active TB
Diagnosis of TB
Skin test (Heaf test and Mantoux test); uses protein tuberculin derived from
dead bacteria; detects whether body has anti-TB antibodies inflammation
reponse
Culture of TB bacteria from sputum
Prevention of TB
Use of specific antibiotics to kill the bacteria (a course can last more than 6
months and must be completed to ensure all the bacteria are killed)
Antibiotics
Active TB bacteria are killed by using a combination of antibiotics
An antibiotic is a drug that kills or prevents the growth of bacteria.
Bacteriocidal
o Kill bacteria e.g. penicillins
Bacteriostatic
o Prevent the multiplication of bacteria
Antibiotics are used to kill or slow the reproduction of a pathogen to give the
immune system the chance to respond and catch up so it can deal with the
infection e.g. by phagocytes or antibody production
Antibiotics target processes in bacterial cells but do not affect mammalian cells
because:
they are eukaryotic
do not have cells walls
have larger ribosomes and subtle differences in the mechanism of protein
synthesis
have different enzymes
Antibiotic resistance
Antibiotics are often over-prescribed or used when not really needed e.g. for
colds, flu, other viral infections
Patients stop taking them before the course in ended when they feel better
but not all the bacteria are killed)
Antibiotics used in low doses in diet of farm animals to make them grow
faster so get passed to humans in the food chain
The consequence is that the antibiotic is now ineffective so there is a need to:
HIV
HIV infection occurs when blood or the body fluids containing the virus of an
infected person gets transferred directly into the body, and subsequently the
blood, of an uninfected person by:
Unprotected sex
Direct blood to blood contact e.g.cuts, grazes, oral sex via gum
damage/intravenous drug abusers sharing needles
Mother to child across placenta, during birth or via breast feeding
Viruses reproduce by inserting their nucleic acid into the host cell
which is then translated into proteins to build new viruses.
Each DNA molecule (which makes up a chromosome) contains the genetic code
for a large number of proteins.
A gene is a region of a DNA molecule which codes for the synthesis of one
particular protein.
HIV infection occurs when the body fluid (blood, vaginal secretions and semen, but not saliva
or urine) of an infected person is transferred directly into the body of an uninfected person.
This can occur This can occur when This can occur with This can occur from
through unprotected sharing needles, whether direct blood-to-blood mother to child across the
sex. used illegally or legally. transfer through cuts and placenta or in breast milk.
grazes.
HIV invades T helper cells and macrophages. The HIV gp120 molecules attach to their CD4 receptors allowing the virus
envelope to fuse with the host cell surface membrane, enabling the viral RNA to enter the cell.
Once inside, the virus uses reverse transcriptase to produce DNA from its RNA. The DNA is integrated into the hosts
DNA by another HIV enzyme, integrase. The viral DNA is transcribed and translated to produce new viral proteins and
assemble new viruses.
The new virus particles bud out of the T cell, taking some of the surface membrane with them as their envelope, and
killing the cell as they leave.
When a person is first infected by HIV, there is an acute phase of infection. There is rapid replication of the virus and loss
of T helper cells.
As the number of viruses increases, the number of host T helper cells decreases. Macrophages, B cells and T killer cells
are not activated and the infected persons immune system becomes deficient.
The infected person may experience symptoms such as fever, sweats, headache, sore throat and swollen lymph nodes, or
they may have no symptoms.
The virus continues to reproduce rapidly, but the numbers are kept in check by the immune system.
T killer cells recognise the infected T helper cells and destroy them.
There may be no symptoms during this chronic phase, but there can be an increasing tendency to suffer various
infections which are slow to go away. Dormant diseases such as TB and shingles can reactivate. The chronic phase can
last for years, especially if combined with drug treatment.
An increased number of viruses in circulation (viral load) and a declining number of T helper cells indicate the onset
of AIDS, the disease phase.
The weakened immune system makes the patient more prone to opportunistic infections such as pneumonia and TB.
There may also be significant weight loss, dementia (memory and intellect loss) and the cancer Kaposis sarcoma.
AIDS is usually fatal.
Course of the disease
Acute phase
May suffer fever, sweats, headache, sore throat, swollen lymph nodes
similar to flu. (Some people have no symptoms)
Lasts 3-12 weeks after infection
Rapid viral multiplication + loss of T helper cells.
Increase in HIV antibodies now HIV positive
T killer cells destroy infected T helper cells, keeping numbers in check, so
reducing rate of viral multiplication, but numbers of helper T cells decreases
as they are destroyed
Hopefully start to feel better!
Treating HIV
A number of new drugs are being designed to block fusion of HIV with its
host cell to prevent infection.
Inhibitors of reverse transcriptase, such as AZT, were the first anti-HIV
medications, and are still a critical part of treating infection.
Inhibitors of integrase are under study as a new way to block HIV replication
HIV protease inhibitors, one of the most potent types of anti-viral
medications, block the processing of other HIV proteins into their functional
forms essential for virus maturation before release
For this reason, based on our current knowledge, patients must remain on anti-
viral therapy for life. The drugs are very expensive and need to be taken for
extensive periods of time so they are not available to the vast majority of
infected people