HG Biology Notes

Topic 5 : On the wild Side

1. PHOTOSYNTHESIS

"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."

a). Chloroplast

"Describe the structure of chloroplasts in relation to their role in photosynthesis."

Thylakoid: LDR (Light-dependent reaction) takes place, contains chlorophyll and other photosynthetic pigments, electron carriersGranum: A stack of thylakoids joined to one another - provides site for LDR. Large surface area. Stroma: Fluid surrounding thylakoids, site of the LIR (Light-independent reaction) + contains all enzymes for LIR (including RuBisCO)Thylakoid space: Fluid within the thylakoid membrane sacs, contains enzymes for photolysis of waterOuter Membrane: Smooth, freely permeable to molecules like Carbon Dioxide and Water, many open channel proteinsInner Membrane: Contain transporter molecules eg sugars and protein. Permeable to many substances which need to enter or leave the cell.

b). Redox

c). Light Dependent reaction

"Describe the light-dependent reactions of photosynthesis including how light energy is trapped by exciting elections in chlorophyll and the role of these electrons in generating ATP, and reducing NADP in photophosphorylation and producing oxygen through photolysis of water."

"Describe how phosphorylation of ADP requires energy and how hydrolysis of ATP provides an immediate supply of energy for biological processes."

d). Light independent reaction

"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)." InputsReduced NADPATPCO2Ribulose Bisphosphate

Outputs:GlucoseADP+PNADP

The Calvin Cycle is the process by which plants fix carbon to enable the conversion of 5 Carbon molecules (RuBP) and CO2 to become 6C molecules like Glucose. The first stage in the cycle is the fixing of CO2 and RuBP using the enzyme RuBisCo. This means there is now an unstable 6C molecule. This splits into two 3C molecules of Glycerate-3-Phosphate that both become reduced by two Reduced NADP (the product of the LDR). The energy required to do this is funded by 2 ATP molecules (also from LDR) and the new sugars are Glyceraldehyde-3-Phosphate (3C still). The final part of the cycle is very important to remember as it has 2 branches, the finished 6C Glucose and the original 5C Ribulose Bisphosphate which is used to repeat the cycle. Without recycling the RuBP the cycle can't continue and the Photosynthesis will stop.

Every 3 cycles produces a profit of 1 Triose Phosphate for use in

photosynthesis

2. PRIMARY PRODUCTIVITY AND ENERGY TRANSER

"Carry out calculations of net primary productivity and explain the relationship between gross primary productivity, net primary productivity and plant respiration."

"Calcaulate the efficiency of energy transfers between trophic levels."

The Gross Primary Productivity is the amount of energy produced by a plant while the Net Primary Productivity is the potential energy the plant has stored. The energy difference between the two is the energy spent by the plant to respire as the plant can't photosynthesise properly 24hrs a day. We can therefore summise that the Heat lost due to Respiration (thermal energy) = GPP - NPP. 

When calculating the energy transfer between trophic levels we focus on the NPP of the organisms. First subtract the respiration from the GPP to get the NPP of say a plant. Then you may be given either the energy gained by the (let's say it's a) antelope (they're pretty coo') or you could be given the efficiency of the animal. Using the efficiency as a percentage you can calculate how much of the NPP is stored by the antelope as opposed to how much is excreted or wasted. If you know the amount stored then you can now work out the efficiency by taking the Energy Stored / NPP of Plant x 100 = Efficiency (%)

Ecological pyramids

Pyramids of numbers

Total number of organisms in a food chain at each trophic level

Highest number at the bottom (usually producers, then consumers)

Pyramid will be inverted if lots of small animals are feeding off one large plant

Pyramids of biomass

Total biomass of organisms in a food chain at each trophic level

o Always pyramid shaped

Organisms multiplying rapidly may have biomass less than primary consumers

Dry mass is measured / H2O stores no energy and varies in different organisms

Pyramid of energy

Amount of energy transferred to each level of a food chain in an ecosystem

Always pyramid-shaped / no energy loss

Transfer of energy between trophic levels

Food chains and food webs

Energy is used to produce new cells / remains fixed in that organism

Energy is passed on to the next trophic level through feeding

Producers are photoautotrophs (plants)

o Transduce light energy into chemical P.E. by forming new tissues and storing organic compounds

(starch, glucose, lipids, proteins)

Consumers are herbivores, carnivores and omnivores

Decomposers are detritivores and saprophytes

o Break down dead complex organic molecules into simple inorganic molecules

Food chains are feeding relationships and linked with each other to form complex food webs

o Some organisms feed on different trophic levels / leaves and insects

o Some organisms feed on different foods when they are larvae (leaves) and when they are adult (nectar

produced by different flowers)

Energy transfer and efficiency

2% of light energy is converted to chemical P.E. by photosynthesis

o Rest is lost reflection from leaves / heat loss / not all wavelengths are utilised / light strikes non-photosynthetic

structures

10% of that are passed on along trophic levels

o Rest is lost in respiration / as heat/faeces/urine

Chemical P.E. / generates heat / stores energy by forming organic matter (new cells)

o Mammals are homeothermic / must maintain constant body temp

o Warm environment / less energy maintains body temp / more organic matter stored / more transferred to

consumero Small organisms / large surface area:volume ratio / lose high amounts of energy

Carnivores fix organic matter more efficiently than herbivores

o Herbivores feed on plants

o Take up cellulose and lignin / difficult to digest

o More food passes through gut and is lost as faeces

Trout fix organic matter most efficiently, they are

o Poikilotherms → must NOT maintain constant body temp

o More energy is used to fix organic matter

o Carnivores are harvested while they are still young and grow rapidly

o Trout transfer most energy to consumer (human) in terms of food

[EXAM] Number of food chains is limited

o Due to energy losses (at each trophic level)

o In respiration/egestion/excretion/movement/as heat

o (Too) little energy is left to sustain higher trophic levels/to be passed on

3. ECOLOGY

"Explain that the numbers and distribution of organisms in a habitat are controlled by biotic and abiotic factors."

"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, eg solar energy input, climate, topography, oxygen availability and edaphic factors)."

4. THE CARBON CYCLE

"Discuss how understanding the carbon cycle can lead to methods to reduce atmospheric levels of carbon dioxide (including the use of biofuels and reforestation)."

The diagram below shows how the carbon compounds in the atmosphere and dissolved in water bodies is absorbed and is incorporated into the food chain by photosynthesis. The carbon dioxide is then returned to the atmosphere when the plants and animals respire or they die and the decay by microorganisms realeases more carbon dioxide back into the atmosphere. Left to itself the carbon cycle is self regulating as the amount of carbon dioxide released by respiration and other natural processes is the same as the amount absorbed by photosynthesis.

Human influence? In the past humans were probably fairly carbon-neutral however the increase in carbon dioxide produced by people since the industrial recolution joined with the manufactor of the car engine is threatening the balance of the carbon cycle.

Carbon sinksResevoirs where carbon is removed from the atmosphere and 'locked up' in organic or inorganic compounds. 

Carbon is stored in the bodies of organisms whilst they are alive.

The soil also contains humus (dead organic matter).

Rocks such as limeston and chalk and fossil fuels hold vast stores of carbon.

Oceans contain around 50 times more dissolved inorganic carbon than is present in the atmosphere. This carbon

dioxide is continually being exchanged at the air-water surface. Carbon dioxide in the water is taken up by

photosynthesising organisms. Large amounts of carbon is also stored in the shells as calcium carbonate of mairne

organisms. By lowering the amount of carbon dioxide in the water they make it possible for more carbon dioxide from

the air to be dissolved in the water.

5. NICHE

"Explain how the concept of niche accounts for distribution and abundance of organisms in a habitat."

6. SUCCESSION

"Describe the concept of succession to a climax community."

7. THE GREENHOUSE EFFECT

"Outline the causes of global warming - including the role of greenhouse gases (carbon dioxide and methane, CH4) in the greenhouse effect."

Greenhouse Effect

1. Radiation from the Sun reaches the Earth, some is reflected back into space by the atmosphere and by the Earth and

some is absorbed by the atmosphere.

2. Infrared radiation is felt as heat, when this reaches the Earth's surface it is absorbed by the Earth and reradiated at a

longer wavelength.

3. Some of the reradiated radiation is absorbed and again reradiated back to Earth's surface by the greenhouse gas

molecules in the atmosphere.

4. This maintains the surface temperature of the Earth at a higher level suitable for life. However the problem becomes

when extra greenhouse gas molecules reflect more radiation back to the Earth which heats the surface up even more

that the current temperatures. Greenhouse gases - Carbon dioxide, methane, water vapour

Methane: Has a 72 times greater effect on warming than carbon dioxide.

Main sources

Decay of organic material-bacteria in waterlogged paddy field soil- levels of rice production have been increasing so

more bacteria releasing methane.

Digestion of ruminant herbivores- Human population is growing so more food is required from herbivores..especially

cattle..therfore more methane from extra ruminants.

Naturally breaks down high in the atmosphere through a series of reactions in carbon dioxide and water.

8. GLOBAL WARMING

"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."

a). Evidence for global warming

"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."

We only have recorded data of temperature from the mid-1800s so we look at temperature proxies such as tree rings, corals, ice cores and peat bog data to get a clearer idea of the temperature before records began.

Frozen Isotopes

Ice cores: from Antartic and Greenland scientists drill deep down into the ice.The air that is trapped in different layers is analysed which provides a good record that goes back thousands of years. Records of the oxygen isotopes in melted ice reflect the air temperature as the layer was laid down. Atmospheric carbon dioxide levels can also be measured.

Dendrochronology - The dating of past events using tree ring growth.

Trees increase in width as they get older by cell division of one particular layer in their trunks.

When conditions are good - plenty of moisture, warmer temperature - the new cells laid down are larger than when

conditions are tough.

It is the contrast between the small cells at the end of one year and the large ones produced the next spring which

give the appearance of rings.

Problems:

If conditions vary a lot within one year more than one ring may be produced.

Tree growth depends on many factors- amount of sunshine, temperature, carbon dioxide levels and the amount of

rainfall so it is hard to say what led to the large cells being laid down. Was it one of the above factors or was it a

combination of several of them?

Coral reefsData from coral reefs can be used to confirm the evidence of tree rings as the proportions of different isotopes taken up by the coral vary as the sea temperatures change and this gives another proxy for the climate.

Peat BogsPeat growth rate depends on prevailing conditions and varies widely. Therefore evidence from undisturbed peat body cna give a clear and unbroken record of the climate and has reulted in a continuous record from about 7500 BC which gives clear evidence of periods of warming and cooling.

Made: partly decomposed plant material, mainly Sphagnum mosses. The peat is very acidic, cool and aneorobic

which prevents bacteria from decomposing organic material. As a result, pollen grains, moss spores and even plant

tissues are preserved in the peat.

By sampling: we can look back in time at the plants and mosses growin gin and around that area from hundres of

years ago.

How helpful: As the types of plants that can grow in an area are affected by climate, the pollen/moss record can give

a clear reflection of how the climate has changed with time.

Increasing data reliability

Wiggle matching - Data from dendochronology and peat bog dating are used to confirm radiocarbon dating in a

process known as wiggle matching. For example data from wood of a known age and peat bog samples where the

age is known are dated from radiocarbon meausrements and the results are compared to give a form of calibration.

This gives scientists clear reference points which they can use to determine the accuracy of their estimates.

Evidence for increasing carbon dioxide levels

Mauna Loa curve : a series of reading taken regularly at Mauna Loa observatory on Hawaii. Air is continuously

sampled and the carbon dioxide concentration along with other readings are taken. The air in the area is relatively

free from local polutants and scientist believe it is representative of the air in the northern hemisphere.

The records that beagn in 1958 show that the level of atmospheric carbon dioxide has increased from 315.98 ppmv

(parts per million by volume of dry air) in 1959 to 381.74 in 2006.

The annual fluctuations are the result

of seasonal differences in the fixation of

carbon dioxide by plants as in

temperate regions plants lose their

leaves in winter so take up less carbon

dioxide.

What are ice cores?

Ice cores are cylindrical samples of ice removed from ice sheets and glaciers. Because ice cores are taken from regions which remain frozen year-round, they contain detailed information about the history of the Earth's climate, for those who know how to look. Paleoclimatologists often study ice cores extensively to gather data about major climate events and to piece together patterns in the Earth's meteorological history. Ice cores can be found in storage in numerous research facilities and archives.In order to take a core sample from ice, researchers must find an area with significant ice deposits, ideally an area where ice has been present for thousands of years. The polar ice caps are a prime location for taking ice cores, as are some permanent glaciers. The researchers drill into the ice with specialized equipment, using a liquid to maintain pressure so that the hole does not collapse, and they remove samples of ice from the hole and bag them for further study.These samples must be handled with care, to ensure that they are not contaminated by the modern climate. Because ice cores often experience radical pressure changes when they are pulled to the surface, researchers must first allow them to “relax” at extremely low temperatures so that they do not shatter. At all times, the ice cores must be kept scrupulously clean, and when the cores are finally ready for study, they are handled in a clean room to reduce the risk of contamination.

Viewed in cross-section, an ice core has a series of layers representing decades of snowfall. Each layer can be used to gather information about that year's climate. Ice can trap particulate materials like pollutants and ash, along with radioactive isotopes, and various levels of dissolved chemicals. Using ice cores, researchers can see what the oxygen and carbon dioxidelevels were like historically. They can also find clues like pollen and dust in ice cores which could be used to estimate the prevailing wind direction in any given year, and to learn more about what was happening on other parts of Earth.When examining ice cores, one of the key issues is accurate dating. Without a solid date to work with, the data is not terribly helpful. Dating can be accomplished by physically counting back layers, much like one does with tree rings. It can also be done by analyzing levels of isotopes in the ice and comparing the levels to known ice samples, or by looking for key layers in the ice which could be used to extrapolate. For example, when Krakatoa erupted in 1883, it distributed volcanic ash all over the world, leaving a tell-tale trace in ice cores from this era.

Visit this link http://oceanleadership.org/

b). Potential effects of global warming

"Describe the effects of global warming (rising termperature, changing rainfall patterns and seasonal cycles) on plants and animals (distribution of species, development and life cycles)."

"Explain the effect of increasing temperature on the rate of enzyme activity in plants, animals and micro-organisms."

"Describe how to investigate the effects of termperature on the develoopment of organisms (eg seedling growth rate, brine shrimp hatch rates)."

Risk of floodingAntarctic temperatures have increased by an average of 2.5 degrees in the past 50 years- faster than anywhere else on Earth. Many scientists believe that the thinning of the ice is a clear indication of global warming.As the antarctic ice melts the volume of water in the seas and oceans of the world will increase, causing sea levels to rise. As the water gets warmer its volume increases resulting in an even bigger impact on sea levels.The implications for human life as sea levels rise are immense- around 100 million people live less than 1 metre above current sea levels.

Climate changeRising temperatures affect weather and rainfall patterns. It is impossible to link any one weather event with global

warming but statistical evidence suggests that there is an increase in extreme weather events linked to the rise in global temperatures. Rainfall patterns are complex but they also seem to be changing.e.g. If the current trend of low rainfall continues in Africa it has been predicted that by the year 2020 between 75 and 250 million people will be short of water for their crops and to drink. In contrast, in some areas rainfall has been higher leading to flooding which causes devestation and carries away the vital topsoil.

Effect on organismsTemperature effects enzyme activity which in turn affects the whole organism. A 10 degree increase in temperature will double the rate of an enzyme controlled reaction. There is an optimum temperature for an enzyme controlled reaction and if the temperature increases past that point the enzymes denature and the reaction rate starts to fall.As a result an increase in temperature could have different effects on processes including the rate of growth and reproduction. If plants grow faster they will take up more carbon dioxide upto a certain temperature after which the enzymes will start to denature and the organism may die.

Global warming appears to be affecting the onset of season which affects both life cycles and the distribution of speacies. Insects may get through their life cycle more quickly and be ready to feed before the plants they feed on mature. For some animal species they may breed earlier in the year so they can fit in more than one breeding cycle per year which would increase the population.

Another problem would be within reptile species as the temperature affects the sex of the embryos. Warming could casue a change in sex ratios in these species which could ultimarely be the end of the species.

A change in climate could affect hte range of many different organisms. As animals can move more easily than plants they can often survive changed more eaily. So as areas become warmer some animals may be able to extend their ranges northwoards while becoming extinct at the southern end. Also species which cannot live in these areas now may move in (alien species) and out-compete native species rendering them extinct in the area. Additionally if organisms involved in disease are affected patterns of world health could change as well. The WHO (world health organization) has warned that global warming could be responsible for a major increase in insect-borne diseases in Europe.

c). Models for predicting the future

"Describe that data can be extrapolated to make predictions, that these are used in models of future global warming, and that these models have limitations."

The DebateA lot of evidence suggests a clear correlation between an increase in temperature and an increase in carbon dioxide levels. However, as the correlation is so close it is difficult to know if the increase in greenhouse gases are causing the increase in temperature or if the increase in greenhouse gases is the result of rising temperatures.

To say that there is a casual relationship we need a mechanism that explains how one factor changes the other. From our understanding of the greenhouse effect and from the timing of the industrial revolution, since when more carbon dioxide has been produced, it is logical to consider that humans are responsible for increasing carbon dioxide levels.However, some scientists have also proposed a mechanism where solar activity affects cloud formation and therefore surface temperature but the IPCC (intergovermental panel on climate change) have reached the conclusion that the sum of these activities over the past 50 years would have resulted in cooling rather than warming.

All these arguments are based on data that require detailed interpretation and the use of computer modelling to model a very complex system so proving a casual link is almost impossible. The IPCC now believe that there is sufficient evidence to state there is a casual link between anthropogenic carbon dioxide eissions and global warming. However it will probably turn out that global warming is multifactorial with many different inputs, not jsut carbon dioxide levels.

Computer models:

Factors to consider: 

rates of photosynthesis across the world

rates of carbon dioxide production by natural causes

the exchange of carbon dioxide between the atmosphere and the oceans

the effect of changing temperature on all of these

Predicting the future:We can extrapolate the data on greenhouse gases and use them in models to make predictions about what will happen to temperature in the future. These extrapolations can be used in other models to predict long term effects of increased temperature on the environment.These models are very helpful and can be used to plan international responses to the problems of rising carbon dioxide levels and global warming.

Limitations: 

It is impossible to tell the exact impact of global warming on particular aspect of the world climate

extrapolations form past data cannot take into account unknown factors in the fututre including how current trends in

the use of of resources and technologies may change.

9. EVOLUTION

"Describe how evolution (a change in allele frequency) can come about through gene mutation and natural selection."

The theory of evolution is about how and why organisms have changed over time. What actually changes is allele frequency (the relative frequency of a particular allele in the population). Gene mutations are changes in the

structure of DNA and these changes can increase the gene pool of a population by increasing the number of different alleles available, depending on the impact of the change. If a mutation results in an advantageous feature, the frequency of that allele in that population will increase in frequency due to natural selection. If the change is

disadvantageous, natural selection will usually result in its removal from the gene pool.

10. SPECIATION

"Explain how reproductive isolation can lead to speciation."

Speciation is the process by which new species arise. In order for a new species to form, part of an existing population needs to be reproductively isolated from the rest. At AS Level, allopatric speciation, when populations are separated by geographical isolation, was mentioned. However, speciation also occurs when there is no geographical barrier to interbreeding. This is sympatric isolation. 

Populations that have been isolated for millions of years can remain the same species, however. Species can be thousands of miles apart yet still be able to interbreed and produce viable offspring. Nevertheless, there are examples of populations that live quite close to each other that have become of two different species such as the Rhagoletis pomonella. Reproductive isolation is a type of sympatric isolation and occurs when fertilization is prevented or when the zygote is unable to breed. 

Types of isolation :

Presyzgotic reproductive barriers:

Habitat isolation - populations occupy different habitats in the same area so do not meet to breed

Temporal isolation - species exist in the same area but are active for reproduction at different times

Mechanical isolation - the reproductive organs don't fit together

Behavioral isolation - populations do not respond to each other's reproductive displays or signals

Gametic isolation - male and female gametes from two populations are simply incompatible with each other. In some

plants for example, the pollen of one species cannot form an effective pollen tube on the stigma of another species.

Postzygotic reproductive barriers:

Hubrid sterility - healthy individuals produced from the mating of two different species cannot themselves reproduce

(eg. a mule is the infertile offspring of a horse and a donkey)

Hybrid inviability - individuals produced from the mating of two different species are not healthy and do not survive

Low hybrid zygote vigour - zygots fail to develop properly, and die during the embryonic development or result in

offspring with severe abnormalities so they cannot reproduce successfully.

11. HOW NEW IDEAS GET ACCEPTED

"Describe the role of the scientific community in validating new evidence (including molecular biology, eg DNA, proteomics) supporting the accepted scientific theory of evolution (scientific journals, the peer review process, scientific conferences)."

Description:When a new scientific idea is created it must be submitted to a system called peer review which for more than a hundred years has been the systematic method scientists use to validate a claim made. It's always seen as important that the Scientist in question isn't overly criticised or supported so it is fair on the investigation.Conferences and discussions are held to peer review a new hypothesis before deciding whether it stands as a potential case. If it is a strong case then it can be publicised by the media and press with the supervision of scientists to ensure the public information is accurate.

Peer Review:Began in 18th Century, a paper of new ideas is submitted to a neutral journal editor who then forwards it to an expert in the field the idea is related to. The paper is reviewed for quality then revised and published as an article. Once published the community will take it more seriously and begin evaluating how useful it is and maybe use it in their own research to help with an ongoing investigation. Some questions asked during peer review:- Is the paper valid?- Is the paper significant? (The paper must make a useful addition to the existing body of scientific knowledge)- Is the paper original? (ie. has someone else already done the same work)

Validation:As the Peer Review system is only the first stage in making a concept proven and known there has to be some hard evidence backing it up and many neutral scientists will work to prove or disprove the theory. Many theories in the microbiology field will be alot harder to prove due to their size and difficulty for control.

There are thousands of scientific journals published worldwide and any research carried out and approved by other scientists is published in at least one of these so it can be read by other scientisits worldwide. 

NB - (From spec) Genomics = study of DNAProteomics = study of proteinsThe study of DNA and amino acids and comparing them in different species can show how closely related species are in evolutionary terms. The more similar the sequence, the more closely related the speces.

TOPIC 6: Infection, immunity and forensics

1. DNA

a). Genetic code

"Explain the nature of the genetic code (triplet code, non-overlapping and degenerate."

b). Protein synthesis

"Explain the process of protein synthesis (transription, translation, messenger RNA, transfer RNA, ribosomes and the start and the role stop codons) and explain the roles of the template (antisense) DNA strand in transcription, codons on messenger RNA, anticodons on transfer RNA."

c). 1 gene many proteins

"Explain how one gene can give rise to more than one protein through post-transcriptional changes to messenger RNA."

d). DNA profiling

"Describe how DNA profiling is used for identification and determining genetic relationships betwen organisms (plants and animals)."

e). PCR

"Describe how DNA can be amplified using the polymerase chain reaction (PCR)."

f). Gel electophooresis

"Describe how gel electrophoresis can be used to separate DNA fragments of different length."

2. MICROORGANISMS

a). Bacteria

"Distinguish between the structure of bacteria and viruses."

b). Mycobacterium Tuberculosis

"Explain how bacterial and viral infectious diseases have a sequence of symptoms that may result in death, uncluding the diseases caused byMycobacterium tuberculosis (TB) and Human Immunodeficiency Virus (HIV).""Disucss 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)."

Tuberculosis:The Bacteria, Mycobacterium Tuberculosis, infects a host when the host breathes in infected sputum. In high density populations therefore it is very easy for the spread of TB to increase. Fortunately only 30% of people exposed get infected and very few people, partucularly not children, suffer beyond the primary stage of infection. It is however incredibly deadly with a mortality rate of 50% if left untreated. This is because after the initial infection the body bombards the bacteria with macrophages to try and kill it quickly. Any bacteria left after the primary stage begin

learning how to evade the immune system. Often this is by covering itself in a waxy outer layer which protects them from macrophage enzymes. This is then countered by the body trying to break through the layer so the TB adapts and forms new ways to defend itself, forming the "evolutionary arms race" the spec requires you to know.

People most at risk of infection are:AIDS patientsInner City DwellersAlcoholics (malnourished)

Symptoms:Coughing up blood, fatigue, respiratory failures, fever, weight loss and loss of appetite.

Mycrobacterium Bovis:A similar strain of bacteria to TB which affects cattle. This pathogen can infect humans through contaminated milk, uncooked beef etc. and people working on farms are at risk of infection through direct contact.

Treatment:For the first part the patient is asked to take a multitude of antibiotics, this course must last between 6 and 24 months, unlike other less dangerous bacterial infections. This is because the mycobacteria cell wall has a greater resistance to antibiotics. If a wide range of antibiotics is used then it's unlikely to become immune to all of them so eventually they will decrease in number. Once a strain of TB becomes resistant to the most popular treatments (rifampicin & isoniazid) they become known as MDR-TB (Multi Drug Resistant) and the treatment becomes far more expensive and lengthy. 

http://www.healthscout.com/ency/68/123/main.html

c). Viruses

Structure of Viruses

Viruses are very simple things and it's widely disputed as to whether they are alive or not. They are not cells unlike bacteria as they do not have a cell membrane or wall. Instead they possess an outer layer called a capsid made from repeating proteins called capsomeres. They do contain Genetic Material but they do not have a nucleus. They Reproduce by infecting a cell and using it's ribosomes and energy to duplicate itself and survive (if it is alive). It holds on to the host cell using a tail or receptor hooks on it's outer layer. It then injects the DNA/RNA into the host cell and begins reproducing. When it's ready it can leave the cell and infect other cells. It's difficult for the body to kill because it infects host cells which the immune system doesn't usually target.

Features

Roughly 0.02 to 0.3 micrometers across, 50 times smaller than BacteriaUsually geometrically shaped

d). HIV

"Explain how bacterial and viral infectious diseases have a sequence of symptoms that may result in death, including the diseases caused byMycobacterium tuberculosis (TB) and Human Immunodeficiency Virus (HIV)."

"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)."

3. DECOMPOSITION

"Describe the role of micro-organisms in the decomposition of organic matter and the recycling of carbon."

4. IMMUNE SYSTEM

a). Innate defenses

ANATOMICAL BARRIERS

"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."

b). Non-specific immune response

"Describe the non-specific responses of the body to infection, including inflammation, lysozyme action, interferon and phagocytosis."

c). Specific immune response

"Explain the roles of antigens and antibodies in the body’simmune response including the involvement of plasma cells,macrophages and antigen-presenting cells."

"Distinguish between the roles of B cells (including B memoryand B effector cells) and T cells (T helper, T killer and T memory cells) in the body’s immune response."

The humoral Response:

Consists of two main stages: T helper activation and effector stage.

T Helper activation stage occurs when pathogen enters body, the non-specific immune response will

bring it in contact with macrophages. The following process then occurs:

1. Bacterium with antigens on its surface is engulfed by a macrophage through phagocytosis

2. The vesicle contianing the bacterium combines with a lysosome, and enzymes from the lysosome break

down the bacterium releasing the Anitgens. this process is known as ANTIGEN PROCESSING.

3. These Antigens then combine with major histocompatibility complexes (MHCs) forming complexes

(antigen/MHC protein complexes). These complexes are displayed on the cell surface and the cell is now

aantigen presenting cell (APC), and is also referred as a CD4 macrophage APC in step 4).

4. A CD4 macrophage APCbinds to a T-helper cell

ADAPTIVE DEFENSES

a). T CELLS

"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 body's immune response."

b). B cells

"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 body's immune response."

c). Antibodies

"Explain the role of antigens and antibodies in the body's immune response including the involvement of plasma cells, macrophages and antigen-presenting cells."

d). Immunity

"Explain how individuals may develop immunity (natural, artificial, active, passive)."

5. HELP AND TREATMENT

"Distinguish between bacteriostatic and bactericidal antibiotics.""Describe how to investigate the effect of different antibiotics on bacteria.""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."

Bacteriostatic: the type of antibiotic or dose used completely inhibits the growth of the microorganism

Bactericidal: the type of antibiotic or dose used destroys all the microorganisms present (useful in more severe infections or when the immune system is suppressed such as HIV and transplant patients). Bacteriocidal drugs only kill cells which are actively growing.

Broad spectrum antibiotic: destroys a wide range of pathogens. Narrow spectrum antibiotic: targets a few specific pathogens. 

Different types of antibiotics1. Antimetabolites - interrupt metabolic pathways (e.g. sulphonamides) - BACTERIOSTATIC 2. Prevent peptide cross-linking between the polysaccharid chains in peptidoglycan molecules so affect the formation of bacterial cell walls (e.g. penicillin, glycopeptides) - BACTERIOCIDAL 3. Cell membrane agents damage the cell membrane so metabolites leak out or more water moves in and kills bacteria by lysis. (e.g. some penicillins, cephalosporins) - BACTERIOCIDAL 4. Protein synthesis inhibitors prevent transcription or translation (e.g. tetracylines, chloramphenicol) - BACTERIOSTATIC 5. DNA gyrase inhibitors stop bacterial DNA coiling so it doesn't fit within the bacterial cell anymore (quinolone) - BACTERIOCIDAL

Investigating the effect of different antibiotics on bacteria using standard microbiological techniques

1. An agar plate is prepared with a known bacterial culture (lawn of bacteria) 2. Filter paper discs soaked in different antibiotics or different concentrations of antibiotics are placed on the agar. Another method would be to create wells in the agar and antibiotic solutions can be poured into them. 3. The plate should be sealed and aseptic techniques should be employed to minimise the exposure of the agar plate to air-borne microorganisms. 4. A control agar plate with the same microorganism with known sensitivity to a particular antibiotic can be grown as well as a comparison. 5. By measuring the inhibition zone around the filter paper discs (measure radius or trace the zone on graph paper so area can be calculated), the antibacterial effect of different types of antibiotics or different concentrations can be seen. 6. For each type of antibiotic or concentration, the experiment should be repeated three times so an average of the three inhibition zone sizes can be calculated. This increases reliability. 7. Variables to be controlled include temperature, volume of antibiotic solution, area of filter paper discs, distribution of bacterial lawn, pH and time kept in the incubator. 

Conclusion: The susceptibility of a pathogen to a particular antibiotic is determined through dosage. If the standard dose (prescribed by a doctor) destroys pathogens successfully, the pathogen is sensitive to the antibiotic. However, if the pathogen is only affected by a higher dose, then it is moderately sensitive. In some cases, the pathogen will not be affected at all and is resistant to the antibiotic. 

Healthcare-acquired infections: arise from drug-resistant bacteria (superbugs). Through natural selection, the bacteria with mutations that prevent antibiotics from binding to them are likely to survive and the bacteria with the useful mutations divide to produce more bacteria which are resistant to the drug. Over time, the bacterial population becomes increasingly resistant to antibiotics. 'Superbugs' are commonly found in places where antibiotic use is highest and during surgery where the protective layer of the skin is breached (like hospitals) and are known as hospital-acquired infections. MRSA and C. difficile are two of the most common hospital-acquired infections in the UK.

MRSA: How MRSA WorksC. difficile: How Clostridium Difficile Works

Infection Prevention and Contol Guidelines

1. To prevent resistant bacteria from evolving, antibiotics should be used carefully and every course of antibiotics should be finished. Multi-drug therapy with antibiotics can also lead to faster evolution of some bacteria so doctors should prescribe treatments with care. 2. Hygiene measures: simples hygiene measures like washing hards, using alcohol-based gels between patients and not wearing long ties or white coats can prevent cross-infection. The NHS website   outline some hygiene measures that can be taken by doctors, patients and visitors to minimise infections3. Isolation of patients: patients with signs or symptoms of the infection should be isolated as quickly as possible from the other patients and they should only be transferred around the hospital if it is absolutely necessary. 4. Prevention of infection coming into the hospital: all patients coming in to the hospital for any procedure should be tested for common infections so they can be immediately isolated and treated. 5. Monitoring levels of healthcare-acquired infections: hospitals should keep records of all infections so more targets can be set for the following years. 

Useful Links:

A new 'superbug'   – NHS

6. FORENSICS

"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.""Describe how gel electrophoresis can be used to seperate DNA fragments of different length""Describe how gene profiling is used for identification and determining genetic relationships between organisms""Describe how DNA can be amplified using the polymerase chain reaction (PCR).

INVESTIGATING TIME OF DEATHRigor Mortis:- Happens after death when ATP begins to run out. ATP is created by respiration, this requires oxygen. When the person dies to oxygen is taken into the body so no more ATP can be made, therefore it runs out. -ATP is required to kep the muscles relaxed so when it does get low the body's muscles contract and the body becomes stiff- Begins acout 2-4 hours after death, full effect is at about 6-8 hours. It passes at about 36-48hours after death- The bodies stage in rigor mortis can give a rough outline of the time of death.

Body temperature:- Core temperature used, from either rectal or more commonly liver temperature- Body cools slowly to room temperature with time. If the temperature of the room the body was killed in is known it is possible to create a cooling curve with time ant therefore discover the time of death.- This only works for a freshly killed person, as the body reaches room temperature at about 18hours

Forensic entomology:-This is insects in the body, there are 2 main ways that forensic entamologists can discover time of death

1. Succession:

A dead body is a newly exposed habitat

First anaerobic bacteria thrive in the oxygenless and acidic (due to lactic acid) conditions in the body

Then certain flies, such as blowflies, arrive, they are attracted to the moisture and smeell around the

natural orifices as well as open wounds. These flies then lay eggs on the carcass

The eggs hatch and maggots eat the skin and tissue of the body, this liquidises certain parts which then

the adult flies feed on.

Beetles then are attracted to the carcass, they lay eggs and the grub that hatch eat the maggots mainly.

Parasetic wasps then lay eggs in the beetle and fly larvae

Eventually the body dries out and species such as cheese flies and coffin flies are more prevelent.

Dehydration continues and maggots cant survive any longer, beetles with strong mandibles, such as

carcass and ham beetles, move in and eat the remaining muscles and connecting tissues.

Finally ,ites and moth larvae digest feed on the hair

-Forensic entomomlogists can see what species are living in the body and therefore know how long down the line of succesion of insects the body is. Using this they can estimate a time of death.

2. Insect lifecycles

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Insects go from eggs, which hatch to larvae, these go through 3 stages, they then turn into a pupa and

back to an adult

When a forensic entamologist finds a body, they collect eggs and larvae and pupa and let them grow into

adults.

From the stage the insect was found and the fact that insects have different life cycles for each stage the

forensic entamologist can tell how long the insects have been in the body. This linked with the insect

succession can give a much more accurate time of death.

Using forensic entomology the date of death can be confirmed to a few days or theorised to a few months, however it is mostly used for bodies that are 4-14 days old.

GENETIC IDENTIFICATION-Find DNA at the crime scene-Amplify it using PCR:

1. Place a mixture of enzymes, primers, the DNA and other reactants in a vial

2. Place vial in a PCR machine

3. They will be heated to 90-95 degrees celcius for about 30s, this seperates strands of DNA

4. heated to 50-60 degrees celcius for about 20s, this bnds primers to DNA strands

5. heated to 75 degrees celcius for at least a minute, DNA build complementary DNA strand6. Repeat steps 3-5 as much as wanted