SNAB A2 Revision Notes Unit 4: Environment and

Topic 5: On the wild side
A particular species can be identified using the features (the phenotype) which are characteristic to only that species. Species with similar phenotypes are likely to be related to each other. A key of characteristics is used to identify the species Organisms are classified into families according to similarity of features. The families start of large, but rapidly become smaller. This is the basis of a hierarchical classification system Kingdom Phylum Class Order Family Genus Species There are 5 kingdoms Animals, Plants, Fungi, Protoctists, Prokaryotes You need to know the main characteristics of each kingdom

Taxonomy: the science of classifying living things. Biodiversity: the variety of life on our planet, measurable as the variety within species, between species, and the variety of ecosystems If two organisms can interbreed to produce fertile offspring they are the same species. If not, they are different species Binomial System: (2 names)

Felix catus

Italics in print Underlined in hand

Genus: tells you what group the species is from (has a capital letter)

species: tells you the exact species (small case letter)

Distinguishing Characteristics of the Kingdoms

• • • •

Microscopic prokaryotic cells (2 - 5µ m long rather than 10-100µ m) Lack of a nucleus (DNA in cytoplasm) and possibly plasmids Lack of membrane-bound organelles Presence of 70s ribosomes No cytoskeleton

Protoctists • • Eukaryotic cell structure Simple body form, either unicellular, filamentous (chains), colonial (ball) or macroscopic (large and visible)

The Proctoctist’s kingdom tends to be full of organisms that do not fit into any other Kingdom e.g. algae and yeast Fungi • Heterotrophic nutrition (get food from eating, unlike plants) Made of a network of Hyphae, which form a 3D structure called a Mycelium. (look up Module 1 notes) Call walls containing chitin

Plants The distinguishing features of the Plants are; • • • • • Multicellular with eukaryotic structure Cell walls containing cellulose Complex body form Photoautotrophic nutrition (make food themselves through P/S) Presence of photosynthetic cells with chloroplasts 2 stages in the life cycle: a diploid spore-producing stage and a haploid gamete-producing stage.

Animals The distinguishing features of the Animals are; • • • Multicellular with eukaryotic cell structure Cells without cell walls Heterotrophic nutrition

• •


Highly organised organs and tissues including Genetic diversity nervous co-ordination The only haploid cells they have are gametes

Individuals in the same species look different (have different phenotypes). This is called variation Variation is caused by; The genotype of the individual (i.e. which alleles they have) 2. The environment

Genetic diversity describes the range of different genotypes within a species. If there are few genotypes the genetic diversity is small. If there are lots of genotypes the genetic diversity is large.
Advantages of little genetic diversity

Advantages of wide genetic diversity
• • Less chance of genetic disease Less chance of extinction when faced with disease (i.e. some individuals will have a phenotype that allows them to survive) Environment has less effect on phenotype Species more likely to survive environment change Species more likely to colonise Allows access to more niches, therefore less interspecific competition Natural selection & speciation can occur

All individuals have a preferential phenotype

• • • • •

Causes of Genetic Diversity: 1. Independent Assortment

Mutation 3. Chemicals (mutagens) and radiation can do this. by combining different gametes new variation occurs (random fusion). Therefore. This is caused by the orientation of homologous pairs of chromosomes during metaphase 2 of meiosis 2. Crossing Over Independent Assortment = which allele of each pair goes into which gamete. Each gamete is different. Random fusion 4. This usually occurs by DNA being improperly copied or damaged. This creates more variation by creating new combinations of alleles (crossing over) . Changes in the sequence of bases in codons (mutation) cause genetic variation. During meiosis sections of DNA are swapped between homologous chromosomes (pairs of chromosomes).

4. ♂ leaves ♀ Purple stem & Big Leaves AaDd Purple Stem & Big Leaves AaDd d = little Parent’s Phenotype: Parent’s Genotype: Gametes: AD Ad AD Ad aD F1 Genotype: AD ad aD ad Ad aD ad AD AADD AADd AaDD AaDd Ad AADd AAdd AaDd Aadd aD AaDD AaDd aaDD aaDd ad F1 Phenotype: AaDd Aadd aaDd aadd 9:3:3:1 A_B_ : A_bb : aaB_ : aabb Purple & Big : Purple & Little : Green & Big : Green & Little .5. D = Big Leaves. A = Purple stem.3 Dihybrid Cross Dihybrid Crosses are for crosses involving two different genes (2 loci). a = Green Stem.

• Too great an interval may mean that many species actually present are not noted. gives detail about species abundance down the line as well as range • Shows species dominance down the line What interval should be used? Transects can either be continuous with the whole length of the line being sampled. which affects the survival of organisms. Random Sampling (quadrats placed at randomly generated intervals) • Used where habitat is uniform • Removes observer bias • Used in a large area • Used if time is limited Systematic Sampling (quadrats placed at regular intervals) • Used to show zonation • Used where there is continuous variation • Used to sample linear habitats (e. competition. Examples include predation. which affects the survival of organisms. as well as obscuring zonation patterns for lack of observations. or samples can be taken at particular points along the line For both line and belt transects. the interval at which samples are taken will depend on the individual habitat.5. .g. a roadside) 2 types of systematic sampling technique. Line Transect: • Used where time is limited • Used to visually illustrate how species change along a line Belt Transect: • Produces more data. as well as on the time and effort which can be allocated to the survey. and pollution from excreted waste. Abiotic Factor: A non-living variable within the ecosystem. and water.4 Ecological Sampling Techniques Biotic Factor: A living variable within the ecosystem. light.4. Examples include temperature.

interspecific competition. food availability. temperature. grows slowly. salinity. water availability. predation. aspect. less temp range. dessication. pH etc Biotic Factors include.• 4. wave action. intense competition from same and other species Don’t learn this case study if your teacher gave you notes on a different habitat. usually submerged. An example of a Named Environment Is the British Rocky Seashore Abiotic Factors have more effect going up the beach Biotic Factors have more effect going down the beach Abiotic Factors include. but more predation from herbivores and carnivores Lower Shore: Kelp – constant environment. Middle Shore: Eggwrack – More water availability. presence of excreted wastes Species living in the Rocky Sea shore Splash Zone: Lichen – can survive dessication & temp variation. as well as yielding more data than is needed. Learn this study if you’re desperate . but is less tolerant to dessication than lichen. lower light levels.5 Too small an interval can make the sampling time consuming. intraspecific competition. substrate.5. requires little nutrient Upper Shore: Black Tar Lichen – can survive long periods without water.

Oystercatcher: Long pointed beak for opening shells and picking fish out of the water 2. Can bubble air through its gills and breathe out of water 3.4. Has a pair of canine teeth behind main teeth 4. so can survive out of water 2. Can shut down the circulation in its legs to stop them cooling the whole bird 3. creating a perfect fit with the rock Have no sex for their 1st year then change into males / females Dogwhelk: Has a adapted radula that bores through barnacle shells 2.6 Adaptations of Species in trophic levels Micro-algae Limpet Dogwhelk Crab Limpet: 1. 4. 5. Has bladders of N2 that allow it to float (to reach light) Tolerates fresh water Has specialised gonads (resceptacles) which release lots of sperm into the sea Has a specialised holdfast that anchors it to rocks Has fucoxanthin pigments that absorb more light than chlorophyll 3. Powerful jaws crush crabs 3. Vary in colour across species 4. which allows it to osmoregulate (it can cope with varying salinity) 2. Strong claws for snapping open dogwhelk shells 4. 2. Common Shore Crab: Has antennal glands. 3. Is intelligent and can learn techniques for opening shells 1. Young mature off-shore and then move back when mature 1. 5. Blenny Oystercatcher Micro-algae (Bladderwrack): 1. Carries eggs to be released in optimum conditions 1. Blenny: Retains water in its gill cavity. .5. 2. Has a mantle organ that makes the shell Has a radula covered in teeth that grind the microalgae off the rock Has gills and breathes through a hole in its head As the limpet clamps to the rock it grinds its shell. 4. Has natural anti-freeze in its blood to stop the legs from freezing 4. Has a very muscular foot to stop the effect of wave action 1. Has a grove in its shell that allows it to breath whilst boring 3.

4.7 Don’t learn this case study if your teacher gave you notes on a different habitat.5. Learn this study if you’re desperate Light Dependent Step of Photosynthesis .

ATP provides the energy for converting CO2 into glucose and NADPH provides the H for glucose. 4. 4. Electrons are received by electron carrier proteins in the thylakoid membrane (electron transport chain) Electron transport chain uses high energy electrons to power the following conversions. Chlorophyll emits electrons 3.8 Light Independent Step of Photosynthesis CO2 RuBP ADP + P ATP ATP NADPH GP ADP + P NADP GALP Glucose .Light Dependent Step: 1. Chlorophyll absorbs light (remember chlorophyll is the trap in the bottom of the photosystem) 2. H+ for the reduction of NADP and O2 which is excreted.5. 5. ADP + Pi ATP and NADP + H+ + eNADPH Water is split (photolysis) to produce replacement electrons for the photosystems. The purpose of the light dependent step is to produce ATP and NADPH.

There are three steps in the Calvin Cycle. reverting to NADP) Regeneration: Some GALP is converted back into RuBP so the Calvin Cycle can continue. 2.5. 1. 3. This reaction is catalysed by the enzyme Rubisco Reduction: In a series of reactions GP reacts with ATP and NADPH reduced GP to form GALP (by reducing GP the NAHPH itself is oxidised. A glucose molecule is generated every 6 turns of the Calvin Cycle 4.9 . The rest of GALP is converted into glucose in a series of reactions. Carboxylation: RuBP fixes CO2to form GP.

heat. The plant has to pay “respiration tax” because it can’t photosynthesis at night & not all parts of the plant are capable of photosynthesis. lost as CO2 etc) Best analogy is a salary.e.5.5. R is like income tax.11 Energy in Primary Consumer Lost energy NPP in plant Lost energy .10 Thylakoid membrane = location of photosystems & electron transport chain Stroma = site of Calvin Cycle & photolysis of water Grana provide large surface area for absorbtion of light NPP = GPP – R NPP = Net Primary Productivity (amount of stored chemical energy the plant has to use for growth. GPP is the amount of stored chemical energy the plant earns through photosynthesis.4. i. This is directly proportional to biomass) GPP = Gross Primary Productivity (amount of stored chemical energy the plant earns through photosynthesis) R = Respiration (amount of energy lost through respiration. NPP = disposable income: what the plant has to spend after paying tax. 4.

Soon all / most individuals have the “fit” phenotype and the “unfit” phenotype is eradicated 7.Energy in Sunlight Energy is lost between trophic levels.g. Energy is lost in the following ways. Energy is lost in the following ways. in respiration (mostly lost through heat).e. Over a few generations the frequency of “fit” alleles increases and the frequency of “unfit” alleles decreases 6. through movement. Over this time new mutations occur. The individuals that survive tend to be those that have alleles which give them a selective advantage in their environment (i. light of wavelengths not useful to plants. These are the “fittest” 4. There is variation in a species 2.5. lost in respiration. e. lost as heat etc 4. More individuals are born than the environment can sustain. camouflaged). through digestion. which give new even better alleles . so some individuals must die. reflected light. they are the best adapted to their environment. energy still present in excreted materials etc Of the 100% sunlight energy that reaches plants. 3. The fittest survive long enough to reproduce and pass their alleles onto the next generation. This process continues over many generations 8. ~3% is converted into NPP.12 Evolution: the idea that one species changes into another over time Natural Selection: Darwin’s suggestion for the process by which evolution might occur Evolution by Natural Selection (Darwinian Evolution) 1. energy still present in egested food. passes through leaves. 5.

Over time the mutations accumulate in the phenotype until the organism is unable to reproduce (i. so Lamarck’s theory is easy to falsify. This means that the environment determines the phenotype of an organism Law 2: Changes are passed on to the next generation So a blacksmith. Malthus noticed that the human population was expanding exponentially.5. who uses his muscles all day.9. will the bigger muscles be passed onto his children? No.14) because this stops the influx of alleles from outside and allows new mutations to accumulate in the genotype more quickly 4. will grow bigger muscles. Darwin was influenced by this idea. He thought that the human population would outgrow its resources and that this would lead to famine and war. They were very similar to Darwin’s and this prompted Darwin to publish. At this point a new species has been produced (speciation) This process is speeded up by isolation (see 4.e. the population size is determined by the environment) 1809 Lamarck publishes a mechanism for evolution based on two laws Law 1: Organs / structures grow if they are used. .e. He publishes with Wallace who wrote to Darwin to discuss his own ideas about evolution.13 1798 Malthus publishes paper on population growth. because he noticed that animal populations grow exponentially and then plateau when they reach the limits the environment can sustain (i. 1859 Darwin publishes the Origin of species by means of Natural Selection. produce fertile offspring) with the original organisms. This works! But.5.

5. but reproduce at different times The species exist in the same area. You should respect the opinions of other people.4.15 Evolution is a theory. 4. .16 Primary succession is the first stage of the ecological succession of plant life from abiotic land with no soil to fully support plant ecosystems (e.14 Isolation is important for evolution because it decreases the size of the gene pool. not a fact. Many people believe that species were created (creationism). hybrids are produces but they do not survive long enough to breed Hybrids survive to reproductive age. but cannot reproduce 4.5. creating rudimentary soil from their dead matter. These pioneer plants create conditions for the start of plant growth and so more complex plants like grasses and shrubs begin to colonise the area. but there are physical reasons which stop them from copulating In some species. start to "normalize" the habitat. but by mechanisms other than Natural Selection. This stops new alleles coming in from breeding with original alleles and speeds the accumulation of new mutations (which is what leads to speciation) The different types of isolation. a forest).. pioneer plants like mosses and lichen. Method of isolation Ecological isolation Temporal isolation Behavioural isolation Physical incompatibility Hybrid inviability Hybrid sterility Description The species occupy different parts of the habitat The species exist in the same area. Other people believe in evolution. but do not respond to each other’s courtship behaviour Species coexist.g. even if you do not necessarily agree with them. In primary succession.5.

food web. which refers to succession after an environmental disaster (such as a forest Parent’s Phenotype: Red Red fire) primary succession occurs on the geologic timescale. The barren land is first colonised by simple pioneer plants which pave the way for more complex plants. Conducting research 2. By understanding the niche. feeding relationships etc scientists can suggest effective methods of conserving species. Running captive breeding programmes F1 Genotype: 3. after a few hundred years. A good example of primary succession takes place after a volcano has erupted. The large trees represent the climax community because succession stops at this point. over thousands Parent’s Genotype: Rr Rr of years ♂ ♀ 4. 1.Over time the grass area is colonised by small woody plants. which give way to small trees and finally. R = Red. Unlike secondary succession. Captive breeding programmes are used to reintroduce species to the wild. build up population numbers and maintain genetic diversity. such as hardwood trees by creating soils and other necessities. large trees take over.17 Gametes: Zoos can play a large role in conserving endangered species by. reproductive behaviour.g. r = white F1 Phenotype: 9:3:3:1 A_B_ : A_bb : aaB_ : aabb Purple & Big : Purple & Little : Green & Big : Green & Little . Reintroducing species into the wild 4. habitat. E. In a small population many alleles are lost between generations because an individual only passes on 50% of their alleles. Educating people Research enables scientists to understand the role of a species in an ecosystem.5.

a family tree for the captive animals) so that only non-related animals are bred with each other. the more advanced the species the more difficult reintroduction is. building roads with tunnels under them for badgers. how to reproduce. how / where to find shelter. but depends greatly on the species. As a general rule of thumb.18 If you get a question on this in the exam you’ll need to think.5. This is genetic drift and is a big cause of the loss of genetic diversity in an endangered species.R r R r If the parents only have 2 children and they are both Red (RR) then the r allele has been lost. Often just doing something slightly differently will have a big impact on conserving a species e. how to hunt. There are no set facts to learn. 4. Wild animals are often introduced to captive breeding programmes to avoid these problems Reintroducing species into the wild has some success.5. This is because animals need to learn specific behaviours e. 4.g.g. group behaviours. Breeding animals in captive environments that mimic the wild has more success because it allows some of these behaviours to be learned in captivity. This decreases the change of genetic drift and also decreases the change of genetic disease. Feeding the animals in the wild also helps survival rates. To avoid this studbooks are kept (basically. There are no set facts to learn. Educating people is essential to conservation. .19 If you get a question on this in the exam you’ll need to think.

SNAB A2 Revision Notes Unit 4: Environment and Survival Topic 6: Infection. Temperature is measured using a long thermometer with a wide range. Immunity & Forensics 4.6. The initial plateau at 37˚C lasts 30 – 60 min. o o o o Body temperature Extent of rigor mortis Level of decomposition Forensic entomology Body temperature: A body cools following an S-shaped (sigmoid) curve. . then the body cools quickly to ambient temperature. Temperature is usually taken rectally or using an abdominal stab. After 24hrs a body has usually finished cooling and temperature is no longer useful.1 Time of death can be measured using the following factors.

Level of decomposition: Autolysis is the break down of body tissues using the body’s own enzymes from the digestive system and from lysosomes After this. On page 80 of your text book is a little more detail about the sequence of events that causes muscles to run out of ATP. Small muscles stiffen first and unstiffen last. bacteria from the gut invade tissues and release more enzymes. causing the actin and myosin muscle fibres to stick permanently to each other. Muscles stiffen because they run out of ATP. This tends to happen in anaerobic conditions.The rate of cooling depends on the situation the body is found in e. which favours the growth of anaerobic bacteria Greenish discolouration of abdomen (36hrs) ↓ Spreads across rest of body (36 – 72hrs) ↓ Discolouration darkens to reddish green (36 – 72hrs) ↓ Discolouration darkens to purple-black (72hrs) ↓ Body becomes bloated with gas (one week) ↓ Gas is released. Clothing – slows cooling Found in water – speeds cooling Found indoors – slows cooling Air movements – speed cooling Extent of rigor mortis: Temperature of body Warm Warm Cold Cold Stiffness of body Not stiff Stiff Stiff Not stiff Approx time since death No more than 3 hrs 3 – 8hrs 8 – 36hrs > 36 – 48hrs Rigor mortis is the stiffening of joints and muscles.g. Muscles unstiffen because the muscle fibres begin to break down. body deflates & shrinks (one week +) .

Autolysis is increased by mild heat and slowed by intense heat. a maggot 3mm long found growing at 28˚C will be roughly 0. Corpse succession: e.g. Using the life-cycle of the maggot to identify age 3. mummies) stop it completely. in some cases (e. it is sometimes possible to work backwards from the pupation date and work out hold the maggots .3 days (8 hrs old) 2. If maggots are taken from the body. the clothing the person was wearing and the combination of gases released during decomposition also have an effect. allowed to grow and the time taken to pupate is recorded. If the temperature of the body has remained relatively constant the age of the maggots growing in it can be determined by their starting length and the temperature of the part of the body they grew in. Humidity has a big involvement as well – dry conditions slow autolysis and.g. 1. Forensic entomology: The insects found in a dead body can help identify time of death in 3 ways. The presence of wounds.

Genetic fingerprinting looks for the presence of repeated sequences of bases in the non-coding sections of DNA (introns). Fingerprints 3. 1. Sample is cut using a restriction enzyme .must have been when they were taken from the body. This works because maggots of different species usually take a fixed number of days to pupate. Fingerprinting process: 1.2 The identity of a dead person can be ascertained by. This is usually used when the body is damaged (e. tented arches. a corpse from a fire) Genetic Fingerprint: Used because DNA is unique to individuals (except identical twins and clones grown by mad scientists). 4. Genetic Fingerprint Identity Papers: This is very obvious. toes etc is ridged into specific patterns (arches. Fingerprints are unique and can be used to identify people. whorls & loops). A sample of DNA is copied using PCR 2. The satellites are repeated anything from 5 – 500 times and this produces a unique DNA signature.6.g. Using aluminium powder or protein stain (e. Identity papers 2. ninhydrin) fingerprints are revealed. Dental Records: Can be used to identify age and to identify a person based on their dentist’s record of their teeth. think about it.g. Fingerprints: The skin on fingers. Sweat and sebum oil is left behind from our fingers on the things we touch. Dental records 4. The repeated sequences are called satellites and can be 2 – 4 bases long (Micro-satellite) or 5 – 20 bases long (Minisatellite).

by the age and specific species living on a corpse. Assuming the original DNA sample has not been contaminated (by e.4 A typical prokaryote .6. A southern blot is taken 5. and so on until the body has been reduced to a skeleton. Sample is run on an electrophoresis gel. which changes the body for the next group. with different groups of organisms occupying the decomposing body at different times. This change in turn makes the body attractive to another group of organisms. Succession and forensic entomology also show if the body has been moved. This is a predictable process. 4. a hair from the pathologist) the fingerprint will be exact. 4. it changes the body.3. 4.g.6. DNA is labeled using a DNA probe specific to the satellite 6.3 Succession on corpses: The idea that as each organism or group of organisms feeds on a body. This technique allows you to tell. how old the corpse is. An X-ray is taken to reveal the location of the bands of DNA The fingerprint is the pattern of bands on the electrophoresis gel. often using a DNA sample of known length to act as a standardization.

Nuclear Zone. The region of the cytoplasm that contains DNA. There is no nuclear membrane. Cell Wall. DIFFERENT from plant cell wall. containing non-esential genes. Sticking cells together . Cell membrane. Very small circles of DNA. DNA. Same function as eukaryotic cells (protein synthesis). Can be exchanged between different bacterial cells. Thick polysaccharide layer outside of the cell wall. Always circular.Ribosomes. made of phospholipids and proteins. 1. Tightly-folded region of the cell membrane containing all the proteins required for respiration and photosynthesis. There are two kinds of cell wall. which can be distinguished by a Gram stain: A: Gram positive bacteria have a thick cell wall and stain purple B: Gram negative bacteria have a thin cell wall with an outer lipid layer and stain pink. Capsule (or Slime Layer). Mesosome. Made of murein (a protein). Used for. but are smaller (70s rather than 80s). like eukaryotic membranes. and not in chromosome form. Plasmid.

As a food reserve 3. without proteins Ribosomes are small (70S) No cytoskeleton Cell division is by binary fission Reproduction is always asexual Eukaryotic cells Larger cells (> 10 mm) Often multicellular Always have nucleus and other membrane-bound organelles DNA is linear and associated with proteins to form chromatin Ribosomes are large (80S) Always has a cytoskeleton Cell division is by mitosis or meiosis Reproduction is asexual or sexual A typical virus . Prokaryotic Cells Small cells (< 5 mm) Always unicellular No nucleus or any membrane-bound organelles DNA is circular. and as protection against phagocytosis (being broken down by a white blood cell). As protection against desiccation (drying out) and chemicals.2. A rotating tail used for propulsion. Flagellum.

The genetic material is either DNA or RNA. or a cylindrical shape (e. and can be single or double-stranded. from about 20 in the polio virus to more than 200 in the herpes virus (human genome contains ~80. whilst others can range from 20 – 3000nm. Some viruses are about 100nm in diameter. The virus genetic material (the viral genome) contains only a few genes. which contains genetic material. which allows the virus to penetrate the host cell membrane by endocytosis.g. The capsomeres can be arranged into an icosahedral shape (e. In addition. some viruses also have an outer membrane envelope. HIV and measles virus all have membrane envelopes.Viruses have a wide range of different structures.g. polio & herpes). All viruses have a protein coat (the capsid). measles & influenza).g.000 genes). The protein capsid is made from identical subunits (called capsomeres). Influenza. The viral genome codes for the proteins required to manufacture the virus. (ligands) Viral Damage – What do Viruses actually do to us? . TMV & rabies) or a loose containment structure (e.

. HIV targets helper T cells. viruses have protein ligands on their capsid that attach to ligand receptors on eukaryotic cells. which helps insert the viral cDNA into the host’s DNA Be sure you can recall what the 3 viral enzymes do. HIV) also inject the enzyme integrase. If lots of new virus is being made.Like bacteria. Other viruses (e.g. Viruses without lipid membranes may have specialised proteins designed to help inject the viral genome into the cell cytoplasm.g. (i) (ii) (iii) Virus RNA enters host cell Virus may also inject RNA Polymerase into host cell as well. usually through endocytosis using its lipid membrane. Influenza targets epithelial cells & rabies virus targets specific brain cells). Viral RNA and RNA Polymerase enter host cell nucleus via nuclear pores (iv) Viral RNA is copied in nucleus (v) Viral RNA is transcribed using viral RNA Polymerase (vi) Viral mRNA is translated in the cytoplasm (vii) New Virus proteins formed (viii) Viral proteins associate with copied RNA forming new complete viruses (ix) New viruses leave host cell to infect other cells Viruses that have a DNA code instead of an RNA code often insert their viral DNA into the host cell’s DNA. DNA Polymerase: RNA Transcriptase: Integrase: Some viruses target specific tissues (e. After a virus ligand attaches to a host cell ligand receptor it becomes anchored to the host cell. Other RNA viruses inject the enzyme Reverse Transcriptase. these host cell may lyse (burst) and die. The cDNA copy is then inserted into the host cell’s DNA. which makes a cDNA copy of the viral RNA. Poliomyelitis virus targets motor neurones. The virus attempts to get its viral genome into the host cell.

BUT TB bacteria can survive inside macrophages as the cell wall of the bacterium is very thick and waxy and is resistant to the macrophage enzymes. When the immune system is weakened (by stress. 4. 5.6. Course of infection for Tuberculosis: . which eventually leads to death. The bacteria reproduce too rapidly for the body to destroy 12. 8. forming a mass of tissue called a granuloma. Macrophages enter the lungs in large numbers. The macrophages engulf the TB bacteria in large groups. The body launches an immune response to the TB bacterium. Histamine release and inflammation occur (see 4. TB begins to reproduce in the lungs. 10. or another disease – HIV is a common cause) the TB bacterium breaks out and re-infects the body.The bacterium can survive and reproduce inside the macrophage for many years without causing infection. malnutrition. increasing the transmission of the disease. the lung heals 1.6 Course of infection for Tuberculosis: Tuberculosis (TB) is caused by the Mycobacterium tubercolusis bacterium.7) 6. TB can also spread to the lymph nodes in the body. 13. Mycobacterium tuberculosis is inhaled into the lungs in droplets of water & mucus from another person’s lung (droplet infection) 2.5 & 4. 3. 11. 7. which damage lung tissue & cause coughing.6.4. The inside of the granuloma is starved of oxygen.6. The lungs are progressively damaged. where it reproduces causing the disease scrofula 9. Once the bacteria are dead. which kills the bacteria. The bacteria produce toxins.

2. through sexual intercourse. The acute phase. HIV rapidly infects Helper T cells and the virus population increases quickly. Another problem is that HIV attacks Helper T cells. which slows the replication of the virus. 1. which eventually leads to Acquired Immunodeficiency Syndrome (AIDS) HIV is spread by direct contact i. The chronic phase. The person will die quickly from the secondary infection and this is the AIDS disease state. The huge problem with HIV is that it mutates very quickly. because the immune system is weakened other bacteria and viruses are more likely to infect the person (TB may reactivate at this point) The disease phase. 3. Eventually a second pathogen will infect the person (an opportunistic infection) which cannot be fought off. As the numbers of virus increase and the numbers of Helper T cell fall the immune system becomes weaker and weaker. HIV virus has a ligand (GP120). but the Killer T cells keep the numbers in check. Once inside the body the viral antigens change and the (already damaged ) immune system can’t keep pace with the changes. which attaches to a receptor (CD4) on the membrane of a type of white blood cell called a Helper T cell. Once inside the bloodstream an HIV infection occurs in 3 distinct phases. However. The acute phase ends when the Killer T cells begin to recognise infected Helper T cells and kill them. which are crucial for activating the B cells and also play a role in activating . blood-to blood transfer (tattoos. piercing & cut-tocut transfer). This can last for many years. needle sharing.HIV is the Human immunodeficiency Virus.e. At the same time the population of Helper T cells falls rapidly. The virus continues to replicate.

Lysozyme is also made by the skin. This causes local oedema (the swelling associated with inflammation). causing them to lyse and die. It also causes holes to open between endothelial cells in capillary walls. Macrophages engulf pathogens using pseudopodia (“fake feet”). the immune system cannot communicate effectively and this increases the ability of HIV to survive in the body.6. which engulf and destroy foreign bodies and pathogens.7 Non-specific immune responses: Inflammation: damaged white blood cells and mast cells release histamine at the site of infection. Lysozyme is made in lysosomes inside phagoctyes and is responsible for digesting engulfed bacteria. epithelial cells. 4. . With low numbers of Helper T cell. It blocks RNA synthesis and therefore stops virus replication Phagocytosis: the process in which a pathogen is engulfed and destroyed. Lysozyme: an enzyme that breaks down bacterial cell walls. The bacterium is taken into the macrophage by endocytosis and enters the macrophage inside a vacuole. and is present in tears Interferon: a protein made by virus-infected cells. increasing the blood supply to the area.Killer T cells. Lysosomes containing lysozyme fuse with the vacuole and digest the bacterium inside. Eventually phagocytes arrive and complete the job. Dead monocytes and pathogen form pus. Histamine causes local arterioles to vasodilate. It allows monocytes and neutrophils into the infected area.

B cells & Macrophages all have the ability to recognise an antigen and once this has happened. tissue fluid. They are found in blood plasma. mucus and milk. T cells.4. They are then incorporated into the cell membrane of the Macrophage. Antibodies (also called Immunoglobulins) are proteins produced by B cellls.8 Pathogens have proteins on their surface that our immune system has learned to recognise as foreign. macrophages have the ability to present foreign antigens to T and B cells. Antigen-binding site . In addition to this. they will trigger an immune response. Once a pathogen has been engulfed and destroyed MHC proteins inside the Macrophage stick to the pathogenic antigen. so it can present the foreign antigen and activate the T and B cells responses. These proteins are called antigens. lymph. tears.6.

bind 2 antigens at one time. hence the name.also known as γ -globulin). therefore you have the ability to recognise and react to a million different antigens. There are 5 different families of immunoglobulin molecule in the human body (G. A. D & E. IgG . .Two light chains Each pair of chains is held together by disulphide bridges (hydrogen bonds would be too weak).Two heavy chains . Each variable region is different. Each immunoglobulin molecule has 2 antigen binding sites and can. The families can be distinguished from each other by slight differences in the constant region of the protein Each antobody molecule contains two pairs of proteins. The variable region of the immunoglobulin protein is what recognises & binds to the antigen. which . therefore. There are over a million different B cells in your body. M. This means that a single antibody molecule can bind to 2 pathogens at the same time.Variable Region Disulphde Bridges Constant Region Each B cell produces a different immunoglobulin molecule which recognises and binds to a specific antigen.

6. when viruses invade host cells. .Makes it easier for T cell activation as more antigens are presented in one area 4. . A B NB: Cell-mediated Immune Response Antibody-mediated Immune Response.9 There are two different types of Immune Response.Isolates pathogens so they cannot infect other host cells . Isolated viruses do not present antigens and therefore do not trigger either the Cell. viral proteins are expressed which become .or Antibody-mediated immune Response. Antibody Pathogen Antigen The formation of the Antibody-Antigen Complex is important because it.causes pathogens to clump together and form the Antibody-Antigen Complex.Makes it easier for macrophages to engulf & destroy the pathogens.Stops the pathogen from entering a host cell . However.

Cloned T Cells differentiate into Killer. B cells can also be activated by macrophages & Helper T cells. Cell-Mediated Immune Response: 1. Helper. These proteins are recognised as antigens.incorporated into the host cell surface membrane via MHC. which makes holes in the pathogen’s cell membrane causing it to die Helper T Cells: stimulate B cells to start producing antibody and attract macrophages to the site of infection Memory T Cells: remain in the lymph nodes. When a macrophage digests a pathogenic cell antigens from the cell membrane get stuck in the . Competent T Cells recognise a specific foreign antigen using its T cell receptor. Activated T Cell undergoes rapid mitosis forming a large number of identical clone T 3. B cells are recognise a specific foreign antigen using the antibody molecules on their surface. Memory or Suppressor T Cells. They will respond rapidly if the same pathogen invades the body again. Killer and Helper Cells migrate to the site of infection Killer T Cells: attach to the infected / foreign cell and release the enzyme Perforin. 2. 4. This means that the body can mount an immune response before infection becomes serious Suppresor T Cells: stop the immune reaction after about a week Antibody-mediated Immune Response: 1. because they have the right T cell receptor to recognise the pathogen.

1. so that if the body is infected by the same pathogen the Memory B cells can produce an instant supply of antibody before the infection becomes serious a) Plasma cells antibody. 1. Action has effect 3. Negative feedback works as follows. any B Cells which come into contact with the antigen will then be activated 2.6. Effect removes original E. blood [glucose] or body temperature) at a constant level. insulin stimulates liver to take up glucose & convert it into glycogen stores . which specific for one antigen only b) Antibody is transported via the lymph to the site of infection c) Antibody attaches to the specific antigen d) An antigen-antibody formed complex is 4. The activated B cell undergoes rapid mitosis and lots of clone B cells are produced 3.g. High [glucose] in blood causes insulin release 2.macrophage’s membrane. Cloned B Cells differentiate into either Plasma or Memory cells Plasma Cells Memory Cells is Memory Cells continue to secrete antibody for many years.10 Negative feedback systems aim to keep something (e. Signal causes action 2.g.

Sensors (thermoreceptors) in the hypothalamus continually monitor blood temperature and activate warming / cooling processes to keep the temperature as stable as possible. Body temperature is normal Exercise Body temperature rises Detected by thermoreceptors in hypothalamus Hair erector muscles cause body hairs to lie flat Peripheral arterioles vasodilate More heat radiated away from skin Sweat glands release sweat onto skin Sweat evaporates carrying heat away .11 Homeostasis is the maintenance of the body’s internal environment.3. [glucose] falls 4. Body Temperature: Body temperature is carefully regulated to maintain a steady 37.5˚C. This is carefully controlled by a series of systems. which aim to keep conditions at a stable controlled level.6. which is the optimum temperature for human enzymes.

The hypothalamus now thinks body temperature is too low and triggers a system of responses which aim to generate heat (thermogenesis) and raise body temperature. viral proteins and substances produced by necrotic tissue may also trigger fever. 4. bacterial toxins. which causes fever. which elevates the thermoregulatory set point. The general class of hormones that lead to fever are called pyrogens (interleukin is a natural pyrogen). vasoconstriction and the production of thyroxine hormone (which makes respiration less efficient. therefore producing more heat). i. Pyrogens travel in the blood to the hypothalamus in the brain.12 .e. These mechanisms include. They bind to receptors there and trigger a complex set of reactions that lead to the production of PGE2 hormone. The cytokines have hundreds of different roles and many more are yet to be discovered. shivering. Fever can be induced by many factors. How does fever work? All white blood cells communicate with each other and the rest of the immune system using a class of hormones called cytokines. One class of cytokine is the hormone interleukin.Less insulating air trapped next to skin Body temperature returns to normal Tuberculosis bacterium (Mycobacterium tuberculosis) causes fever.6. it re-sets the body’s natural thermostat to a higher temperature. However. increased muscle tone.

A Outer cornified layer. composed of compacted dead dry cells filled with indigestible keratin protein (which also forms nails and hair) . • Skin • Stomach Acid • Normal Flora • Epithelial cells Skin Adaptations for defence: The skin is made from 2 layers. .Barrier Mechanisms include.Inner dermis layer The epidermis provides a physical barrier to invading pathogens.Outer epidermis layer . There are 2 layers in the epidermis.

Ingested bacteria are quickly killed by the low stomach pH and digestive proteases. Commensual bacteria are adapted to live the environment of the skin and the gut and the and compete with invading pathogens for the limited supply of nutrients. Cilia also beat in the GI tract. which is an oil with pH 3 – 5. Epithelial cells have cilia. This makes the skin acidic sebaceous glands also secrete the enzyme lysozyme. respiratory tract and gut are covered with commensual bacteria. where they are swallowed. Epithelial cells are closely packed & connected by tight junctions forming a continuous impermeable layer 2. Normal Flora: The skin. The skin also has chemical defence mechanisms. Cilia ‘beat’ in waves. . which form a direct physical barrier preventing pathogen attachment 3. which are part of the normal flora of the body. Lysozyme destroys bacterial cell walls. which helps clear bacteria out of the lungs and into the throat.B Inner Malpighian layer. Epithelial cell Adaptations for defence: 1. - sweat & sebaceous glands secrete sebum. which is a natural antibiotic. Stomach Acid: Is made from HCl at pH 1 – 2. site of rapid mitosis and keratinisation. it is a very effective barrier.

which is trapped by cilia. Mucus also directly prevents pathogen attachment 5. When we are exposed to a new antigen it takes us about a week to be able to make new antibody. Epithelial cells secrete mucus. a second exposure to antigen produces a much faster response. Plasma B cells make lots of antibody on re-exposure Antibody made by memory B cells provides active immunity Without immunity the level of antibody produced by plasma cells is much less .13 Both T and B Cells differentiate into Memory Cells. However. When the Memory B cell is activated by the old antigen it makes large quantities on antibody quickly and kills the pathogen before it can infect us properly. and several orders of magnitude higher levels of antibody are produced. The memory cells provide active immunity.6. which remain in our lymph nodes and wait until we are re-exposed to the same pathogen.4. Mucus contains lysozyme 4.

when inhaled. It can occur through antibody injection or from drinking breast milk (breast milk contains high [antibody]) Active Natural Immunity – the process above Passive Natural Immunity – beastfeeding (antibody in milk) Artificial Active Immunity . If we’re so good at fighting infections. It can survive inside macrophages and lie dormant until the immune system is weakened. So how has HIV evolved to beat us? .14 We have evolved a very effective immune system. which means it is partially protected against lysozyme 5. which means that. when it can re-infect. non-speficif defence mechanisms and specific ones. It does not kill immediately. So how has TB evolved to beat us? 1. why do we still get ill? Answer: pathogens are evolving as well. It is spread by droplet infection. It has a very thick waxy cell wall. it is exactly where it wants to be 3. This means that it has a large window of opportunity to spread to others 4. It specifically targets epithelial cells.Passive Immunity is immunity to a pathogen without Memory cells. which is the most effective method of infection 2. consisting of barriers.vaccination Artificial Passive Immunity – antibody injection 4.6.

g. It specifically targets Helper T cells 4. Penicillin can be taken in large doses by humans because it has no effect on our cells (we have no cell walls).1. so it is easily spread 4. 2. It weakens the immune system to increase its chance of survival 2. 3. penicillin targets the cell wall and breaks it down. A clear circle of dead bacteria will form around the disc .6. A bacterial lawn is grown on an agar plate (either by spreading the bacteria over the plate. Bacteriostatic antibiotics stop bacteria reproducing.15 Antibiotics work by targeting prokaryotic features not found in eukaryotic cells. It is spread by sexual contact. 1. or by using a pour plate). so it can spread 3.6. A disc of blotting paper is soaked in antibiotic of known concentration and placed in the centre of the plate.16 The effectiveness of antibiotics can be measured using a disc diffusion technique. It stays in the body for years. they do not kill bacteria Bacteriocidal antibiotics kill bacteria 4. e.

Mutating the structure of the bacterium so that the antibiotic no longer works This problem is very serious. Bacteria reproduce very quickly (they divide every 20min) so a bacterium with a beneficial mutation will spread quickly 3. So a mutation in one bacterium can quickly be copied to others. months and years that’s a lot of mutations.6. Bacteria develop resistance through mutation. but consider that one E coli bacterium can reproduce to form a colony of 2 million bacteria in two hours. This can be compared to other antibiotics. one can also compare the effectiveness of an antibiotic with a disinfectant or sanitiser (e. as long as the same concentration of antibiotic is used. even others in different species. One in every million bacteria contains a mutation. Having a protein which pumps antibiotic out of the cell 3. Bacteria have the ability to pass copies of plasmids from one to another (conjugation). some of which will be beneficial 2. 1. That might sound like a small amount. Over weeks. A bacteria can mutate and develop resistance by. Having an enzyme that breaks the antibiotic down 2. Phenol coefficient) 4. 1.4.g.17 Bacteria are becoming resistant to antibiotics. . The diameter / radius of the circle of dead bacteria is proportional to the effectiveness of the antibiotic 5. In addition. Bacteria become resistant because. Bacteria mutate very easily.

Exercise and Coordination Topic 7: Run for your life 5. If a bacterial population is continually exposed to antibiotic all bacteria will die. There are over 100 different types of antibiotic and in the 40years since their development 4 species of bacterium have developed resistance against all of them.g. 4. E. SNAB A2 Revision Notes Unit 5: Energy.e.4. they have viral infections) or to people who don’t bother to complete the course of antibiotic. tipped against humans. They are often given to people who don’t need them (i.e. at the moment.7. 5. Methicillin Resistant Staphyloccus Aureus (MRSA) has been named the Superbug.1 .6. now the field is open for the mutated bacterium to grow without competition. As soon as a bacterium mutates the rest of the bacteria will be killed off by the latest dose of antibiotic.18 The evolutionary arms race between bacteria and drug developers is. another way of targeting prokaryotic structures without damaging eukaryotic ones) there may well be a global pandemic of resistant bacteria. Humans have been reckless with use of antibiotics. The use of antibiotics speeds the rise of immunity. Unless drug developers discover another branch of antibiotics we’re not currently using (i. because we have do drugs left that can kill it.

therefore. Muscles which cause a joint to extend are called extensors. which are extremely long. muscles which cause a limb to retract are called flexors. which protects bone ends A muscle: an organ that produces movement by contraction A joint: the junction between two bones A tendon: joins muscle to bone A ligament: joins bone to bone to stabilise a joint Muscles work in pairs. A Synovial Joint Bone Ligament Muscle Cartilage Synovial Fluid Synovial membrane Tendon 5. Arrangement of myofibrils into a muscle fibre Muscle cells (Myofibrils) .7. the pairs are called antagonistic pairs. Each fibre is made from bundles of myofibrils.2 Muscles are made from muscle fibres arranged into bundles. cylindrical muscle cells. One muscle produces the opposite movement from the other muscle.Cartilage: a tissue made from collagen.

The actin is. protein move position in the thin filament A sacromere. This is called striation. Repeat stages 7 to 13 until the [Ca2+] falls too low. Ca bids to Troponin protein in the contain many sarcomeres arranged in parallel. The muscle cell is depolarised 3. when contraction stops . A nerve impulse arrives at the neuromuscular junction 2. ADP diffuses away from the myosin head leaving the ATPbinding site empty New ATP binds & the myosin head & causes the myosin head to detach from the actin. 10. The myosin is often head) is hydrolysed causing the called myosin headfilamentforwards in the thick to pivot because the the powerstroke myosin heads make it appear thick. thick thin 9. on a characteristic banded appearance because of the regular 5. The muscle cell takes thin filament. Troponin protein and Tropomyosin arrangement of the sarcomeres. Ca2+ is released from the sarcoplasmic reticulum inside muscle cells The functional unit of contraction is the sarcomere. ATP (already bound to overlapping actin and myosin. The head rebinds further up the myosin. It is how muscles contract. Myosin heads of the thick filament stick to actin Cross-Bridge Cycling: The sarcomere contains the myosin 8. 11. Myosin binding sites are exposed striated 7. Muscle cells 2+ 4. 12. The myosin head re-cocks 13. filament the on the thin Note appearance of the muscle 6. As the head pivots the the filament filament moves across the thin filament – muscle contraction The process by which the thin filaments are pulled in towards each other by occurs the myosin is called cross-bridge cycling. therefore. 14.Muscle Fibre 1.

If ATP levels drop (assuming Ca2+ is present) the myosin stays attached to the actin and the muscle stays permanently 5. This is what causes rigor mortis Adenosine TriPhosphate (ATP) is made from three components. A base (a group consisting of linked rings of carbon and nitrogen atoms). These phosphates are the key to the activity of ATP Adenine base 3 x phosphate Ribose .3 contracted. in this case the base is adenine. Up to 3 phosphate groups.7.Key Point: ATP is required to release myosin from actin. - Ribose (the same sugar that forms the basis of DNA).

By breaking the 3rd phosphate from the ATP molecule energy is released. For example a runner uses ~84kg of ATP in a marathon (more than their total body weight). which can be used to power intracellular reactions. The recycling of ATP is crucial for life.6kJ/mol) (13.The energy used in all cellular reactions comes from ATP. photosynthesis).8kJ/mol) ATP + H2O → ADP + Pi (30.g. The ATP is then regenerated by recombining the phosphate and ADP in respiration (or another process e. yet there are only 50g of ATP in the entire body! This means each that each molecule of ATP has been recycled 1676 times during the race! Adenosine P ATP = one adenosine molecule with 3 phosphate groups attached “Energy rich bond” Less energy rich bond(30.6kJ/mol) “Energy rich bond” How the energy in ATP is liberated: Energy Adenosine ADP + H2O → AMP + Pi P Energy Adenosine P AMP + H2O → Adenosine + Pi .

as soon as ATP has been converted into ADP + Pi it is converted back into ATP using energy from Step respiration. in Respiration: a process x CO2 (mitochondria 3 x NADH series molecules into 38 glucose molecules is used to convert 38 ADP of steps the 6C molecule matrix) 1 FADH 2 releases the two C atoms ATP molecules. 1 x Glucose 2 x ATP 2 x Pyruvate 4 x ATP 2 x NADH (cytoplasm) 2. Oxygen xis required and Carbon Dioxide andas CO2 Water are produced as waste products. However. As Respiration occurs in 4 distinct steps. which is attached to a CoA enzyme to form Acetyl CoA.Energy Adenosine 1.eventually re-forming the starting 4C compound. Link Reaction (mitochondria matrix) 3. Oxidative Phosphorylation (mitochondria christae) 10 x NADH 2 x FADH2 6 x O2 34 x ATP 6 x H2O The electron transport chain uses the NADH and FADH2 made in previous steps to make lots of ATP Respiration . Products exercise ADP may be Reactants Summary during converted into AMP or even Adenosine to provide energy. The cycle is then ready to repeat itself. the cycle turns ATP. Some ATP is used to split the glucose molecule in the first part of glycolysis 3C Pyruvate is split into a 2C molecule. Krebs’ Cycle 1 x Acetyl CoA 1 x Pyruvate 1 x CoA A 6C glucose molecule is split into two 3C pyruvate molecules. The remaining carbon atom is used to form CO2 1 x Acetyl CoA 1 x CO2 1 x NADH 1 x CoA CoA enzyme gives its 2C atoms 1 x ATP to a 4C molecule to form a 2 in which the chemical bond energy In a temporary 6C molecule. Glycolysis Normally. NADH & FADH2 are formed 4.

4 Respiration: Step 1 .7.Glycolysis Glucose 2ATPs are required Glyceraldehyde Phosphate Glyceraldehyde Phosphate 2ATPs are made (4 overall) 1 NADH is made (2 overall) .5.

2NADH are made and 2ATPs are used. In anaerobic conditions [H+] rises in the mitochondria as there are no available oxygen molecules to mop it up with and form water. each 3C Glyceraldehyde Phosphate molecule is converted into a 3C Pyruvate molecule. Acetyl CoA levels build-up. [CoA] falls and the Link Reaction stops. This means [NAD] falls. enzyme controlled reactions are reversible and depend on [reactants] and [products]). In the process of converting one Glyceraldehyde Phosphate to one Pyruvate. Then. This leads to saturation of the electron transport chain and a build-up of NADH and FADH2. which stops the Krebs’ Cycle. 2ATPs are required for this to happen. Pyruvate levels start to rise… Muscle cells turn pyruvate into lactate to stop rising [pyruvate] from stopping Glycolysis (remember. enough energy is released to convert one NAD molecules into one NADH molecules and also to make two ATP molecules. Net gain: 2ATP and 2NADH Pyruvate Lactate NADH NAD . 4ATP are made. Overall.Pyruvate Pyruvate Glycolysis takes place in the cytoplasm of a cell In Glycolysis a Glucose molecule (6C) is split into 2 molecules of Glyceraldehyde Phosphate (3C).

which is the basis of the “Oxygen Debt” Respiration: Step 2 – Link Reaction Pyruvate 1 NADH is made (2 overall) 1 CO2 is made (2 overall) CoA enzyme Acetyl CoA Link Reaction takes place in the matrix of the mitochondria In the Link Reaction a Pyruvate molecule (3C) is split into a 2C molecule and a CO2.5 Respiration: Step 3 – Krebs’ Cycle Net gain: 2NADH CoA enzyme 2 NADH are made (4 overall) 1 ATP is made (2 overall) 1 FADH2 is made (2 overall) 2 CO2 are made (4 overall) . 2NADH and 2 CO2 are made.In the liver the lactate is converted back into pyruvate. Remember. two molecules of Pyruvate were made at the end of Glycolysis. therefore the Link Reaction happens twice. The 2C molecule is attached to a CoA enzyme. forming Acteyl CoA. Overall.7. 5. This requires oxygen.

Each NADH makes 3ATP and each FADH2 makes 2 ATP. Succinyl – CoA is converted back into Oxaloacetate and this releases enough energy to make one NADH. 2FADH242CO2 and 2ATP Phosphorylation Oxidative Phosphorylation uses the NADH and FADH2 produced in the previous steps of respiration to make ATP.6 Respiration: Step . The Oxaloacetate can then be used in the cycle again. . – Oxidative are made. therefore the Krebs’ Cycle happens twice. The 6C molecule breaks down into a 4C compound (Succinyl – CoA) releasing enough energy to make one NADH. 5. 4NADH.7. Overall. Remember. two molecules of Acetyl CoA were made at the end of the Link Reaction. one FADH2 and one ATP.Krebs’ Cycle takes place in the matrix of the mitochondria In the Krebs’ Cycle the Acetyl CoA gives its 2C atoms to a 4C molecule (Oxaloacetate) forming an unstable 6C molecule (Citric Acid). The two spare C atoms are released as two CO2 molecules.

Carrier NAD ATP FADH ATP ATP ½ O2 + 2H+ 2e - Oxidative Phosphorylation takes place using enzymes embedded in the inner membrane of cristae of the mitochondria Hydrogen atoms from the NADH and the reduced FADH2 are passed onto 2 the first 2 enzymes of the Electron Transport Chain. but crucial. At the end of the Electron Transport Chain. part of respiration to involve oxygen. Electrons. which made up the chemical bond between the hydrogen atoms and the NADH / FADH2 are passed onto 3 Electron Carrier enzymes further down the Electron Transport Chain. These enzymes are Hydrogen Carriers and they accept the H atoms from the NADH and the FADH2.Carrier e.Carrier e. This is the only. to form water.ATP NADH FADH2 ADP ADP H2O H+ Carrier H+ Carrier e. the electrons are recombined with the H+ atoms and oxygen. .

it generates 2 ATPs Where does the 38 ATP come from? Glycolysis produces. H+ ions are actively pumped into the mitochondrial envelope. Kreb’s Cycle produces.NADH starts at the first Hydrogen Carrier and has enough energy to phosphorylate 3ADP. This is done by the proteins in the electron transport chain. using the energy stored in NADH and FADH2. Link Reaction produces. FADH2 has less energy and starts at the second Hydrogen Carrier. . 2ATP Total 4 ATP 2ATP 2NADH 2NADH 6NADH 2 FADH2 10NADH 2 FADH2 Each NADH produces 3ATP ∴ total production is 30ATP from NADH Each FADH2 produces 2ATP ∴ total production is 4ATP from FADH2 Grand Total 4ATP + 30ATP + 4ATP = 38ATP Chemiosmosis of H+ ions from the mitochondrial envelope into the matrix through ATP Synthetase proteins is what actually generates the ATP in respiration The electron transport chain uses the process of chemiosmosis (the diffusion of ions across a membrane).

7 In anaerobic respiration lactate is taken via the blood to the liver. H+ cannot escape because it is charged (hydrophilic) and therefore cannot move through the phospholipid bilayer in the envelope membranes. where it is broken down into pyruvate using oxygen and NADH. . 5. 5. 1. In summary. The potential energy of the H+ is used to phosphorylate ATP as the H+ moves out of the envelope 3. However.7. 4. 2.The [H+] builds up to very high levels in the envelope. NADH and FADH2 contain stored chemical energy The energy is used to pump H+ into the mitochondrial membrane against the concentration gradient H+ trapped in one place represents a store of potential energy H+ ions leave the envelope through ATP Synthetase proteins. Whenever an H+ ion moves through the ATP Synthetase protein an ADP is phosphorylated by the ATP Synthetase. Special proteins called ATP Synthetase do allow H+ to pass through them and escape into the mitochondrial matrix.

7.9 .7.8 c h e m o r e c e p t o r s in c h e m o r e c e p s o t rr es t ci n h t r e c e p t oc r o s r t e x a o r t ic a n d c a r o t i d m e d u l la in m u s c l e s( v o l u n t a r y b o d ie s c o n t r o l) R in E S P I R A T O C E N T R E m e d u l la o f R Y b r a in in t e r c o s t a l p h r e n i nc e r v e v a g u s n e r v e n e r v e s t r e t cnh t e r c o s t a l i r e c e p m t o u r ss c l e s d ia p h r a g m p r e s s u r e c h e m o r e c e p t o t er s m i p e r a t u r e n r e c e p t o r s i n a o r t ic s t r e t c h r e c e p t o a o r t ic a n d c a r r o e t ci d e p t o r s i n a n d c a r o t id in m u s c le s b o d ie s m u s c le s b o d ie s C in A R D I O V A S C U L A C E N T R E m e d u l la o f b r a in t ic m p a t h e t i c e r v e c c e le r a t o r ) t r ia l R p a r a s y m p a t h e s y n e r v e n ( in h ib it o r ) ( a s in o a n o d e v a s o c o n s t r ic t io n a n d v a s o d il a t io n 5.5.

if CO2 is removed. Muscle type in humans is predominantly one or the other due to inherited alleles. whereas the muscle of a camel or an elephant will be predominantly slow twitch. O2 is replaced proportionally with CO2.7.7.10 & 5. As the person respires. joggers need slow twitch. Therefore. .TV A spirometer is used to plot breathing patterns Vital Capacity: The maximum amount of air a person can exhale after inhaling the maximum possible volume of air The volume of air inhaled & exhaled in one breath The rate of respiration Tidal Volume: Basal Metabolic Rate: The spirometer can be used to plot VC and TV directly. You are not expected to know how the spirometer works… although its not very difficult to understand. The total volume should stay constant. The spirometer has fixed volume and is filled with 100% O2 before the experiment begins. 5. BMR can be worked out if a CO2 scrubber is used. However. The rate at which the volume decreases is proportionaly to BMR. different training programmes can cause the % of either type to change slightly.11 Sprinters need lots of fast twitch muscle. However. the total volume will slowly fall as O2 is used. the muscle type of a cheetah or a gazelle will be predominantly fast twitch.

Increased BMR 1. over-training can result in the opposite effect. in this case 37. Increased HDL 3.5˚C.Slow twitch fibres Red (lots of myoglobin) Many mitochondria Little sarcoplasmic reticulum Low glycogen content Numerous capillaries Fatigue resistant 5. therefore. If a system changes.11 for mechanisms of thermoregulation.13 A moderate level of exercise improves health & well-being. 5. a homeostatic response is activated.7.12 Fast twitch fibres White (little myoglobin Few mitochondria Lots of sarcoplasmic reticulum Lots of glycogen Few capillaries Fatigue quickly See 4. Decreased LDL . holds systems at a set point. which aims to return the system to its original level. This is the phenomenon known as “burn-out” Positive effects of exercise include. Decreased blood pressure 2. it is detected. The thermoregulatory process (and most homeostatic systems) are controlled by negative feedback processes. However.7. Negative feedback.6.

1. remote operated tools to repair the damage. Phagoctyes and B & T Cells.7. Increased adrenaline levels 4. This decreses immune response.4. There is also less chance of infection. Increased muscle inflammation 2. Increased bone density 7.14 Key-hole surgery is a technique which allows doctors to conduct surgery with the minimum possible damage to the patient. Decreased risk of diabetes 6. the surgeon can make a second incision and use a number of small. the patient recovers quickly. If required. Decreased levels of Natural Killer Cells. Swollen bursae 5. Improved well being 8. which also decreases the immune response 5. Increased cortisol levels. Decreased adrenaline levels 9. Moderate exercise increases levels of Natural Killer cells. Tendinitis 8. Damaged cartilage 7. Muscle tears and sprains 3. Maintaining healthy BMI 5. Because the incisions are small and only the damaged area is targeted. Ligament damage 9.Decreased risk of CHD 11. The surgeon makes a small incision (a “key-hole”) and uses a fibre-optic camera to view the damaged area. Less stress 10. which secrete apoptosis-inducing chemicals in response to non-specific viral or cancerous threat Negative effects of exercise (over-training) include. . Increased stress 6.

It also decreases proteins (growth proteins) recovery time. expensive equipment and can only be used on certain types of surgery. infirm etc) Arguments for not using drugs. 5. including sports. which in target cells and increases makes the athlete more transcription of anabolic powerful. This causes strain on the heart and can lead to infarction Diarrhoea . power of muscles and decrease recovery time Testosterone Binds to androgen receptors Muscle mass increases.Unfortunately. Agression. shrunken testicles Why should we allow use of drugs. skin problems. vomiting. re. Creatine Creatine combines with Because ATP is re-generated phosphate to form Creatine without using the respiratory Phosphate (CP). the procedure requires a high degree of training.should increase the maximum generating ATP. theoretically it phosphorylate ADP. liver damage and kidney damage.15 Drug Effect on physiology Effect on performance Side-effects Increased haemocrit increases blood viscosity. • Dangerous (obviously) • May be pushed onto athletes by trainers • Effects are permanent . Prosthetics allow people with amputations to participate in many activities.7. decreased sex drive. cells. This increases the level of work the body can sustain through aerobic respiration (aerobic threshold). acne. Erythropoietin EPO causes the bone marrow Extra blood cells mean the (EPO) to generate extra red blood blood can carry extra oxygen. infertility. such as actin & myosin. CP can pathways. • • • • • Gives people a chance to be as good as their potential allows Removes “unfair” genetic advantages Controlled use of drugs is less risky People should have the right of choice Legalising drugs makes their distribution controllable (no use by under-age.

just think for yourself in the context of the question.• Not used under doctor’s supervision • Often cut with other drugs • Exposes athletes to criminals (danger of using other drugs) The list goes on. logical arguments. You can argue the toss either way. but make sure you can back up your opinion with some sensible. .

which insulates the nerve and allows for much faster conduction speed. creating a thick layer of membrane. wrap around the axon of the long nerves.2 . these are called Nodes of Ranvier.8.1 Sensory nerve: Motor nerve: Relay nerve: Schwann cells: carries electrical message from receptor to spine carries electrical message from spine to effector connects sensory and motor nerves. 5. The thick layer of membrane has gaps in it between adjacent Schwann cells. Exercise and Coordination Topic 8: Grey matter 5. Also relays message to the brain.SNAB A2 Revision Notes Unit 5: Energy.8.

High light intensity Circular muscles: contracted Radial muscles: relaxed Pupil diameter: small Low light intensity Circular muscles: relaxed Radial muscles: contracted Pupil diameter: large 5.3 The Action Potential Voltage-Gated K+ Channels open Voltage-Gated Na+ Channels open Nerve is hyperpolarised and inactive (refractory period) Sequence of events in an action potential.8. .

5.4 A synapse is the junction between two nerves. The 3Na+/2K+ ATPase (Na+/K Pump) restores the ion concentrations 9. but over 2000 other transmitters have been discovered .1. Voltage-gated K+ Channels open 6.e. 3. passes a message to another). Nodes of Ranvier speed this conduction process up. Na+ diffuses into the next section of the nerve.8. i. one nerve synapses with another (meaning. A stimulus depolarises the nerve to threshold (-50mV) Voltage-gated Na+ Channels open 4. This causes the action potential to “jump” between nodes of ranvier. which depolarises the nerve to threshold. Potassium floods out of the cell and the membrane potential falls to -90mV 7. It is also a verb. The neurotransmitter on your syllabus is Ach. The nerve is ready to fire again As one part of the nerve fires off. Nerve is at resting membrane potential (-70mV) 2. When one node depolarises it induces the next section of the nerve to depolarise by forming a mini-circuit between nodes. This sequence is repeated like a tiny Mexican wave down the axon of the nerve. making conduction speed much faster. Sodium floods into the cell and the membrane potential depolarises to +30mV 5. The nerve is in the refractory period and cannot conduct another action potential 8.

3 1 2


5 7 6


The wave of depolarisation arrives at the synaptic knob. The membrane in the presynaptic neuron is depolarised to –50mv (threshold potential) and the voltage-gated Na+ channels open, letting Na+ into the cell. The membrane is depolarised to +30mV and voltage-gated K+ channels open. The membrane potential falls to –90mV and the cell goes into its refractory period, where the 3Na+/2K+ATPase restored the ion concentrations. Unlike axons, presynaptic nerves also contain a Voltagegated Ca2+ channel. As the presynapstic membrane depolarises these channels open and let Ca2+ into the cell. The Ca2+ causes vesicles in the presynaptic nerve to migrate and fuse with the presynaptic membrane, where they spill neurotransmitter chemical into the synaptic cleft.





The neurotransmitter (Acetyl Choline) diffuses across the cleft and binds to receptors on the postsynaptic membrane. The receptors let a little Na+ into the postsynaptic neuron, which is enough to initiate another action potential in the postsynaptic nerve. The ACh is broken down by an enzyme called Acetyl Choline Esterase (AchE), which allows the postsynaptic receptors to be freed ready for a second synapse.



In a neuromuscular junction the sequence of events in the synapse is exactly the same. The only difference is that the posysynaptic nerve is a muscle cell and, instead of being flat, the postsynaptic membrane has deep grooves (t tubules) which allow the depolarisation to spread quickly through the muscle so all parts of the muscle contract at the same time. Some neurotransmitters can hyperpolarise postsynaptic nerves, which essentially switches them off. An example of this type of inhibitory neurotransmitter is GABA 5.8.5
Visual transduction is the process by which light initiates a nerve impulse. The structure of a rod cell is:

The detection of light is carried out on the membrane disks in the outer segment. These disks contain thousands of molecules of

rhodopsin, the photoreceptor molecule. Rhodopsin consists of a membrane-bound protein called opsin and a covalently-bound prosthetic group called retinal. Retinal is made from vitamin A, and a dietary deficiency in this vitamin causes night-blindness (poor vision in dim light). Retinal is the light-sensitive part, and it can exists in 2 forms: a cis form and a trans form: In the dark retinal is in the cis form, but when it absorbs a photon of light it quickly switches to the trans form. This changes its shape and therefore the shape of the opsin protein as well. This process is called bleaching. The reverse reaction (trans to cis retinal) requires an enzyme reaction and is very slow, taking a few minutes. This explains why you are initially blind when you walk from sunlight to a dark room: in the light almost all your retinal was in the trans form, and it takes some time to form enough cis retinal to respond to the light indoors. Rod cell membranes contain a special sodium channel that is controlled by rhodopsin. Rhodopsin with cis retinal opens it and rhodopsin with trans retinal closes it. This means in the dark the channel is open, allowing sodium ions to flow in and causing the rod cell to be depolarised. This in turn means that rod cells release neurotransmitter in the dark! However the synapse with the bipolar cell is an inhibitory synapse, so the neurotransmitter stops the bipolar cell making a nerve impulse. In the light everything is reversed, and the bipolar cell is depolarised and forms a nerve impulse, which is passed to the ganglion cell and to the brain.

8. The rod is hyperpolarised and stops releasing inhibitory neurotransmitter 5. except that they contain the pigment Iodopsin.Summary for light. which carries the message to the brain Cones work in exactly the same way.6 Homeostasis is the maintenance of the internal environment. redsensitive. This gives us colour vision. Bleaching occurs and trans retinal is formed Trans retinal blocks Na+ channels 4. The bipolar cell is no longer inhibited and depolarises 6.Nerve reflexes give immediate responses . 5. . 3. which is found in 3 different forms. The ganglion cell is activated.Hormone responses give responses over weeks – months . blue-sensitive and green-sensitive. Photon hits rhodopsin 2. 1.

controls vital ‘housekeeping’ functions. blood pressure and peristalsis. . The hormone is carried all over the body. such as heartbeat. which release hormone into the blood. It binds to hormone receptors on cell membranes and initiates responses in those cells.8.7 Midbrain Cerebrum Cerebellum Medulla Brainstem Hindbrain Brainstem – Uppermost part of the spine.Hormones are released from glands. 5. where the spine joins the brain Medulla .

g. like how to ride a bike.e. which control the initial processing of visual information. learning.controls muscle co-ordination & learns motor programmes (e. their cortex is much. The Superior Colliculi control object tracking. However. Premotor (Speech motor Auditory area)association area Somatosensory Visual association area . Other animals have roughly similar size hind.Cerebellum . This is the part of the brain that actually “thinks. much smaller. i. Contains homeostatic centres. The thalamus contains the Superior Collicului. personality and memory. Midbrain: Thalamus – a relay station that carries sensory information from the sense organs to the correct part of the cortex and hypothalamus. The hypothalamus is connected to the Pituitary gland and therefore the hypothalamus can stimulate the release of a great number of pituitary hormones Forebrain: Cortex – processes sensory information and controls the body’s voluntary behaviour.and midbrains.” The cortex is very large in humans and is folded to increase the surface area further. or write). spatial position and partial recognition (i. whether a stimulus is food or a threat) Hypothalamus – receives sensory information from the thalamus. which control factors like body temperature and blood osmolarity.e.

planswater organises thought. pain.processes & source. eyes The rays are collected on the However. This shows up all the areas in the brain where oxygen is being used As above. This is the only technique. is involved with up a align protons in and molecules out by protons we can build in the patients brain. give “frozen” from theimages. the types of tissues inside the brain. lets us and out touch. MRI Scan 5. This can tell us a lot about the function of the brain. Temporal lobe . When the sequence short term memory and puts speech together. such as their strength measured. they are very useful other side of the head and for picking up diseases. which can be detected. except that the magnetic fields are tuned to excite deoxygenated haemoglobin. but whether they are active. stroke and oedema.CT Scans show brain structures. brain.processes & interprets information from the C T Scan density of the tissue the Xray ears and processes language and the meaning of words passes through decreases the strength of the signal. that shows brain activity. of thin pictures of the fields are switched off. This can be fed into a computer. taste.Technique What it allows us to see The patient can tell the doctor what he/she is feeling as the doctor stimulates parts of Surgery his/her brain. but the doctor not only knows what the tissues look like. Magnetic fields are used to By recording the energy given Frontal lobe . heat and commands.8 protons give out a little energy.type of tissue is in the cold. This allows the surgeon to ask the patient questions as he operates on their brain fMRI Scan . The cancer. How it works During brain surgery a local anaesthetic is often used. They also only head from a rotating interprets information still Occipital lobe . Also initiates motor what pressure. (Understanding language) Thousands of narrow-beam X.8. rays pass through the patient’s not brain activity. and Parietal lobe – processes work interprets information about therefore. which uses the picture to build up a 3D image of the inside of the head Very similar to above.

When we are born. .9 How to process stimuli correctly must be learned.8. which no longer overlap. the cells organise themselves into discrete columns. There is a “critical window” for this to happen (usually before puberty. As we learn to process stimuli.5. the columns overlap and are tangled. The cortex is split into column of cells.

8. These optical illusions do not work on Zulus. yet look different – why? The answer is that you have learned to process this kind of stimuli in a certain way. 5. 5.11 Association (classical conditioning): US → UR (Food → Salivation) . which proves the illusion is caused by learned visual processing. We live in a “carpentered world” of straight lines and we interpret line B as a corner (therefore larger than it appears. Hubel & Wiesel’s experiments prove this. because it must be far away) and line A as a corner (therefore. smaller than it appears. Lines A and B are the same length. our brains will become “fixed” with tangled columns and won’t be able to process stimuli properly.younger for visual processing).8.10 The Muller-Lyer illusion. rather than an innate function of the eye / brain. If we miss the window. because it must be close).

that the stimulus is ignored. Eventually. the animal learns CS → CR (Bell → Salivation) Pavlovian conditioning occurs by synapses between nerves growing together.Over time. if a neutral stimulus (CR) is played with the US. Wolfgang Kohler performed insight experiments on chimpanzees. the animal learns to ignore the CS. Kohler showed that the chimpanzees sometimes (pushing a level → food) . until it is no longer enough to trigger vesicles to fuse with the pre-synaptic membrane. The animal learns the bell signals nothing and it ignores the CS totally. Operant Conditioning: This is very similar to classical conditioning except the animal learns by doing something i. which triggers the CR. This means no neurotransmitter is released. The effect is. it becomes associated with the US and begins to elicit the same response. but all the time. which results in no post-synaptic depolarisation. If a nerve is frequently stimulated. essentially. This is called habituation. Insight Learning: In the early 1900s.e. This means that the sensory nerve carrying the message of the CS will always lead to the firing of the motor nerve. it learns that an action has a certain outcome A →O Habituation: If the neutral stimulus is continuously present (not just before the US). the amount of Ca2+ that enters the pre-synaptic nerve gradually diminishes.

Kohler's experiments showed that primates can both see and use the relationships involved to reach their goals. food causes salivation. The food is. This type of learning is very difficult to explain using the Pavlovian model of conditioning. CS → CR Hubel & Wiesel .e. therefore. i. When a banana was placed high out of reach. even if no food is presented. the dog has learned that the bell signals food. a chimp balanced a stick on end under a bunch of bananas suspended from the ceiling.8. unconditioned. In this case.used insight instead of trial-and-error responses to solve problems. What Pavlov discovered was that if a neutral stimulus. This is not learned and is.12 Pavlov’s Dogs Pavlov had observed that an unconditioned stimulus causes an unconditioned response. US → UR US + CS → UR Eventually. They also realized that they could use sticks to knock the banana down. such as a bell is rung just before the food is given for a few occasions. the animals discovered that they could stack boxes on top of each other to reach it.e. It is also difficult to explain using neuronal models of learning (i. a conditioned stimulus and it prompts a conditioned response. the dog will salivate every time the bell is rung. then quickly climbed the stick to obtain the entire bunch intact and unbruised (a better technique than the researchers themselves had in mind). synapses growing together through use) developed through studies on Aplysia. How insight learning occurs is unknown at the moment. 5. In another experiment. therefore.

Hubel & Wiesel’s Method: 1. Test the monkeys to see whether they can see using each eye 4. Test the sensitivity of retinal cells 5. Test the activity of nerves in the visual cortex in response to stimuli The results: − − − − − Monkeys in Group 2 (both eyes blindfolded) had impaired vision Monkeys in Group 3 (monocular deprivation) were blind in the deprived eye Retinal cells were responsive in all groups Cortical activity was reduced in parts of the brain that process information from the deprived eye Adults undergoing the same tests showed no difference between groups. Group 3 are blindfolded in one eye (monocular deprivation) 3. . 2. All could see. Raise monkeys from birth in three groups for 6 months Group 1 are the control (no blindfold). Group 2 are blindfolded in both eyes.Permanently blind monkeys? Hubel & Wiesel investigated the critical window. They used monkeys and kittens in their studies Their work permanently blinded some animals and can be argued to be unethical.

All these neurons secrete dopamine neurotransmitter. You need to know about these experiments because they all use animals 5. Testing on animals when the potential side-effects are unknown is immoral. which causes difficulty in movement and limb shaking. is for the greater good Animals have no informed consent Machines like the MRI were unvested using animals.8.8. Animal testing has advanced our understanding of human physiology Animals can’t tell you when they are suffering 5. avertunhelpful potential loss of human life Utilitarian argument: Animal testingAnimals have rights too. therefore. which requires stimulus from the eye. because of events happening in the brain.The Conclusion: There is a critical window for visual neural development.Why not use computer simulations in Without animals we would not be ableClinical trials instead? to discover new drugs Animal physiology is different to human Animal testing is better than nothingphysiology. and does.13 Arguments For Arguments Against Clinical Trials Stage 1 involves animals. Animal testing is. In depression neurons in the brain that secrete serotonin neurotransmitter stop working properly and serotonin levels fall. .14 Animals are often poorly cared for in labs In Parkinson’s disease neurons in the brain die. in some cases. not the eye. If this window is missed the monkey is blind.

BUT. when these channels are blocked.g.8. continuous variation is more complex. This binds to protein pumps on the pre-synaptic membrane of nerves that secrete serotonin. which helps alleviate some of the symptoms of the disease. 5. height) Discontinuous variation: phenotypes fall into discrete categories (e. therefore reducing firing in post-synaptic nerves. giving greater post-synaptic activation and a sense of euphoria.g.15 Drugs that affect synapses can drastically alter the functioning of the brain. serotonin builds up in the cleft. blood type) Discontinuous variation tends to be coded for by one gene with a few different alleles. L-Dopa: This is a precursor of dopamine. MDMA: Active ingredient in ecstasy.In both cases treatments that increase the levels of neurotransmitter might prove successful in relieving the symptoms of these diseases 5. This is usually coded for by many genes (polygenes). with many alleles.8. The pumps would normally take serotonin up after it had been released. . which produces the much greater range of possible phenotypes. However. When given to Parkinson’s sufferers it is turned into dopamine.16 Continuous variation: there is a wide range of phenotypes (e.

Diseases that are both genetic and environmental are called multifactorial 5. .17 Brain development is a combination of nature and nurture. usually with an environmental trigger.8.Polygenes can give rise to susceptibility to disease.

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