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 - 5µm long rather than 10-100µm) 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

This usually occurs by DNA being improperly copied or damaged. During meiosis sections of DNA are swapped between homologous chromosomes (pairs of chromosomes). Chemicals (mutagens) and radiation can do this. This creates more variation by creating new combinations of alleles (crossing over) . Each gamete is different. This is caused by the orientation of homologous pairs of chromosomes during metaphase 2 of meiosis 2.Mutation 3. by combining different gametes new variation occurs (random fusion). Changes in the sequence of bases in codons (mutation) cause genetic variation. Therefore. Crossing Over Independent Assortment = which allele of each pair goes into which gamete. Random fusion 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 . D = Big Leaves. A = Purple stem.3 Dihybrid Cross Dihybrid Crosses are for crosses involving two different genes (2 loci).5. a = Green Stem.4.

4 Ecological Sampling Techniques Biotic Factor: A living variable within the ecosystem. which affects the survival of organisms. • 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.g. and water.5. as well as obscuring zonation patterns for lack of observations. . 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. as well as on the time and effort which can be allocated to the survey. and pollution from excreted waste. a roadside) 2 types of systematic sampling technique. Abiotic Factor: A non-living variable within the ecosystem. Line Transect: • Used where time is limited • Used to visually illustrate how species change along a line Belt Transect: • Produces more data. Examples include predation. light. the interval at which samples are taken will depend on the individual habitat. Examples include temperature.4. or samples can be taken at particular points along the line For both line and belt transects.

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

3. 5. Oystercatcher: Long pointed beak for opening shells and picking fish out of the water 2. which allows it to osmoregulate (it can cope with varying salinity) 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. Young mature off-shore and then move back when mature 1. Carries eggs to be released in optimum conditions 1. Common Shore Crab: Has antennal glands. Has a pair of canine teeth behind main teeth 4. Strong claws for snapping open dogwhelk shells 4. Has a very muscular foot to stop the effect of wave action 1. Can bubble air through its gills and breathe out of water 3. Has natural anti-freeze in its blood to stop the legs from freezing 4. 5. .5. Powerful jaws crush crabs 3. 2. 4. 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. 2. so can survive out of water 2.4.6 Adaptations of Species in trophic levels Micro-algae Limpet Dogwhelk Crab Limpet: 1. 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. 4. Has a grove in its shell that allows it to breath whilst boring 3. Vary in colour across species 4. Blenny: Retains water in its gill cavity. Is intelligent and can learn techniques for opening shells 1. Can shut down the circulation in its legs to stop them cooling the whole bird 3. Blenny Oystercatcher Micro-algae (Bladderwrack): 1.

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

ADP + Pi ATP and NADP + H+ + eNADPH Water is split (photolysis) to produce replacement electrons for the photosystems. 5. The purpose of the light dependent step is to produce ATP and NADPH. 4.Light Dependent Step: 1.8 Light Independent Step of Photosynthesis CO2 RuBP ADP + P ATP ATP NADPH GP ADP + P NADP GALP Glucose .5. ATP provides the energy for converting CO2 into glucose and NADPH provides the H for glucose. Chlorophyll absorbs light (remember chlorophyll is the trap in the bottom of the photosystem) 2. 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. H+ for the reduction of NADP and O2 which is excreted.

1. Carboxylation: RuBP fixes CO2to form GP. 3. reverting to NADP) Regeneration: Some GALP is converted back into RuBP so the Calvin Cycle can continue.5.There are three steps in the Calvin Cycle. 2. A glucose molecule is generated every 6 turns of the Calvin Cycle 4.9 . 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. The rest of GALP is converted into glucose in a series of reactions.

4. R is like income tax.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.e.5. lost as CO2 etc) Best analogy is a salary. GPP is the amount of stored chemical energy the plant earns through photosynthesis.5. heat. NPP = disposable income: what the plant has to spend after paying tax. 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.11 Energy in Primary Consumer Lost energy NPP in plant Lost energy . 4. i. The plant has to pay “respiration tax” because it can’t photosynthesis at night & not all parts of the plant are capable of photosynthesis.

passes through leaves. through movement. reflected light. There is variation in a species 2. Over a few generations the frequency of “fit” alleles increases and the frequency of “unfit” alleles decreases 6. energy still present in excreted materials etc Of the 100% sunlight energy that reaches plants. ~3% is converted into NPP. The fittest survive long enough to reproduce and pass their alleles onto the next generation. Energy is lost in the following ways.Energy in Sunlight Energy is lost between trophic levels. e.e. light of wavelengths not useful to plants. The individuals that survive tend to be those that have alleles which give them a selective advantage in their environment (i.g. which give new even better alleles . These are the “fittest” 4. Over this time new mutations occur. lost as heat etc 4. 3. camouflaged). lost in respiration. This process continues over many generations 8. Energy is lost in the following ways. energy still present in egested food. 5. Soon all / most individuals have the “fit” phenotype and the “unfit” phenotype is eradicated 7. through digestion.5. so some individuals must die. in respiration (mostly lost through heat). they are the best adapted to their environment. More individuals are born than the environment can sustain.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.

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

Other people believe in evolution. not a fact. creating rudimentary soil from their dead matter. but by mechanisms other than Natural Selection.g..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. . 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. even if you do not necessarily agree with them. Evolution is a theory. but reproduce at different times The species exist in the same area. Many people believe that species were created (creationism). In primary succession. 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. pioneer plants like mosses and lichen. You should respect the opinions of other people. but there are physical reasons which stop them from copulating In some species. hybrids are produces but they do not survive long enough to breed Hybrids survive to reproductive age. start to "normalize" the habitat. but do not respond to each other’s courtship behaviour Species coexist. a forest). 4. but cannot reproduce 4. 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.5.14 Isolation is important for evolution because it decreases the size of the gene pool.

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

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

Temperature is measured using a long thermometer with a wide range. 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.SNAB A2 Revision Notes Unit 4: Environment and Survival Topic 6: Infection. The initial plateau at 37˚C lasts 30 – 60 min.1 Time of death can be measured using the following factors.6. Immunity & Forensics 4. After 24hrs a body has usually finished cooling and temperature is no longer useful. . Temperature is usually taken rectally or using an abdominal stab.

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. This tends to happen in anaerobic conditions.g. Muscles stiffen because they run out of ATP. 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. 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. causing the actin and myosin muscle fibres to stick permanently to each other.The rate of cooling depends on the situation the body is found in e. 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. Muscles unstiffen because the muscle fibres begin to break down. body deflates & shrinks (one week +) . bacteria from the gut invade tissues and release more enzymes.

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

think about it. Fingerprints are unique and can be used to identify people. Genetic Fingerprint Identity Papers: This is very obvious.2 The identity of a dead person can be ascertained by.g. Genetic fingerprinting looks for the presence of repeated sequences of bases in the non-coding sections of DNA (introns). Dental Records: Can be used to identify age and to identify a person based on their dentist’s record of their teeth. This works because maggots of different species usually take a fixed number of days to pupate. whorls & loops). Identity papers 2. a corpse from a fire) Genetic Fingerprint: Used because DNA is unique to individuals (except identical twins and clones grown by mad scientists). toes etc is ridged into specific patterns (arches. 4.g. Fingerprinting process: 1.6. The satellites are repeated anything from 5 – 500 times and this produces a unique DNA signature. Dental records 4. Fingerprints: The skin on fingers. Sample is cut using a restriction enzyme . A sample of DNA is copied using PCR 2. Using aluminium powder or protein stain (e.must have been when they were taken from the body. The repeated sequences are called satellites and can be 2 – 4 bases long (Micro-satellite) or 5 – 20 bases long (Minisatellite). tented arches. Fingerprints 3. ninhydrin) fingerprints are revealed. 1. Sweat and sebum oil is left behind from our fingers on the things we touch. This is usually used when the body is damaged (e.

Succession and forensic entomology also show if the body has been moved.g. 4. how old the corpse is. Sample is run on an electrophoresis gel.4 A typical prokaryote . a hair from the pathologist) the fingerprint will be exact. by the age and specific species living on a corpse. 4. it changes the body. which changes the body for the next group. often using a DNA sample of known length to act as a standardization. This change in turn makes the body attractive to another group of organisms. and so on until the body has been reduced to a skeleton. 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. A southern blot is taken 5.6. Assuming the original DNA sample has not been contaminated (by e.3. 4. This is a predictable process. This technique allows you to tell. with different groups of organisms occupying the decomposing body at different times. DNA is labeled using a DNA probe specific to the satellite 6.6.3 Succession on corpses: The idea that as each organism or group of organisms feeds on a body.

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

As a food reserve 3. Prokaryotic Cells Small cells (< 5 mm) Always unicellular No nucleus or any membrane-bound organelles DNA is circular. As protection against desiccation (drying out) and chemicals. and as protection against phagocytosis (being broken down by a white blood cell).2. A rotating tail used for propulsion. 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 . Flagellum.

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

HIV targets helper T cells. HIV) also inject the enzyme integrase. which helps insert the viral cDNA into the host’s DNA Be sure you can recall what the 3 viral enzymes do.5 & 4.6. usually through endocytosis using its lipid membrane. The cDNA copy is then inserted into the host cell’s DNA. these host cell may lyse (burst) and die. which makes a cDNA copy of the viral RNA.g.6 .attaches to a host cell ligand receptor it becomes anchored to the host cell. 4.g. DNA Polymerase: RNA Transcriptase: Integrase: Some viruses target specific tissues (e. Poliomyelitis virus targets motor neurones. Viruses without lipid membranes may have specialised proteins designed to help inject the viral genome into the cell cytoplasm. Other viruses (e. Other RNA viruses inject the enzyme Reverse Transcriptase. (i) (ii) (iii) Virus RNA enters host cell Virus may also inject RNA Polymerase into host cell as well.6. The virus attempts to get its viral genome into the host cell. 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. Influenza targets epithelial cells & rabies virus targets specific brain cells). If lots of new virus is being made.

which damage lung tissue & cause coughing. the lung heals 1. Course of infection for Tuberculosis: .7) 6. 10. Histamine release and inflammation occur (see 4. 3. where it reproduces causing the disease scrofula 9. The bacteria reproduce too rapidly for the body to destroy 12. TB can also spread to the lymph nodes in the body. which kills the bacteria. 4. Once the bacteria are dead. The macrophages engulf the TB bacteria in large groups. 7. When the immune system is weakened (by stress. which eventually leads to death.Course of infection for Tuberculosis: Tuberculosis (TB) is caused by the Mycobacterium tubercolusis bacterium. 13. The inside of the granuloma is starved of oxygen. 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. 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.6. TB begins to reproduce in the lungs. The lungs are progressively damaged. The body launches an immune response to the TB bacterium. malnutrition. The bacteria produce toxins. forming a mass of tissue called a granuloma. Mycobacterium tuberculosis is inhaled into the lungs in droplets of water & mucus from another person’s lung (droplet infection) 2. increasing the transmission of the disease. 8. 5. Macrophages enter the lungs in large numbers. 11.

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

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

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

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

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

2. B cells are recognise a specific foreign antigen using the antibody molecules on their surface. Killer and Helper Cells migrate to the site of infection Killer T Cells: attach to the infected / foreign cell and release the enzyme Perforin. Activated T Cell undergoes rapid mitosis forming a large number of identical clone T 3. 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. Memory or Suppressor T Cells.incorporated into the host cell surface membrane via MHC. Cell-Mediated Immune Response: 1. because they have the right T cell receptor to recognise the pathogen. B cells can also be activated by macrophages & Helper T cells. Helper. They will respond rapidly if the same pathogen invades the body again. These proteins are recognised as antigens. 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. 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. Cloned T Cells differentiate into Killer. 4.

g. 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. Signal causes action 2. Cloned B Cells differentiate into either Plasma or Memory cells Plasma Cells Memory Cells is Memory Cells continue to secrete antibody for many years.g. Action has effect 3. 1.10 Negative feedback systems aim to keep something (e. 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.macrophage’s membrane. any B Cells which come into contact with the antigen will then be activated 2. blood [glucose] or body temperature) at a constant level.6. insulin stimulates liver to take up glucose & convert it into glycogen stores . The activated B cell undergoes rapid mitosis and lots of clone B cells are produced 3. Effect removes original E. Negative feedback works as follows. High [glucose] in blood causes insulin release 2.

[glucose] falls 4. which is the optimum temperature for human enzymes. Body Temperature: Body temperature is carefully regulated to maintain a steady 37.3.11 Homeostasis is the maintenance of the body’s internal environment. 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 . which aim to keep conditions at a stable controlled level. Sensors (thermoreceptors) in the hypothalamus continually monitor blood temperature and activate warming / cooling processes to keep the temperature as stable as possible.6. This is carefully controlled by a series of systems.5˚C.

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

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

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

and several orders of magnitude higher levels of antibody are produced. Epithelial cells secrete mucus.4. Mucus also directly prevents pathogen attachment 5. which remain in our lymph nodes and wait until we are re-exposed to the same pathogen. 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 . However. Mucus contains lysozyme 4. When we are exposed to a new antigen it takes us about a week to be able to make new antibody. The memory cells provide active immunity. a second exposure to antigen produces a much faster response. which is trapped by cilia. 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.13 Both T and B Cells differentiate into Memory Cells.6.

So how has HIV evolved to beat us? . which means it is partially protected against lysozyme 5. It is spread by droplet infection. non-speficif defence mechanisms and specific ones. 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 .vaccination Artificial Passive Immunity – antibody injection 4.Passive Immunity is immunity to a pathogen without Memory cells. It does not kill immediately. consisting of barriers. when inhaled. why do we still get ill? Answer: pathogens are evolving as well.6. It has a very thick waxy cell wall. which means that. This means that it has a large window of opportunity to spread to others 4. it is exactly where it wants to be 3. It can survive inside macrophages and lie dormant until the immune system is weakened. So how has TB evolved to beat us? 1. when it can re-infect.14 We have evolved a very effective immune system. It specifically targets epithelial cells. which is the most effective method of infection 2. If we’re so good at fighting infections.

16 The effectiveness of antibiotics can be measured using a disc diffusion technique. It specifically targets Helper T cells 4. A clear circle of dead bacteria will form around the disc .6. Bacteriostatic antibiotics stop bacteria reproducing. Penicillin can be taken in large doses by humans because it has no effect on our cells (we have no cell walls). It is spread by sexual contact.1. they do not kill bacteria Bacteriocidal antibiotics kill bacteria 4.15 Antibiotics work by targeting prokaryotic features not found in eukaryotic cells. 2. It weakens the immune system to increase its chance of survival 2. A disc of blotting paper is soaked in antibiotic of known concentration and placed in the centre of the plate. so it is easily spread 4. It stays in the body for years. or by using a pour plate). e.6.g. so it can spread 3. A bacterial lawn is grown on an agar plate (either by spreading the bacteria over the plate. 1. penicillin targets the cell wall and breaks it down. 3.

as long as the same concentration of antibiotic is used. This can be compared to other antibiotics. 1. Bacteria reproduce very quickly (they divide every 20min) so a bacterium with a beneficial mutation will spread quickly 3. That might sound like a small amount. Mutating the structure of the bacterium so that the antibiotic no longer works This problem is very serious. One in every million bacteria contains a mutation. The diameter / radius of the circle of dead bacteria is proportional to the effectiveness of the antibiotic 5. but consider that one E coli bacterium can reproduce to form a colony of 2 million bacteria in two hours. even others in different species. In addition. So a mutation in one bacterium can quickly be copied to others. A bacteria can mutate and develop resistance by.6.4. Bacteria become resistant because.17 Bacteria are becoming resistant to antibiotics. Having a protein which pumps antibiotic out of the cell 3. one can also compare the effectiveness of an antibiotic with a disinfectant or sanitiser (e.g. Bacteria develop resistance through mutation. Having an enzyme that breaks the antibiotic down 2. Bacteria mutate very easily. Bacteria have the ability to pass copies of plasmids from one to another (conjugation). 1. . some of which will be beneficial 2. Phenol coefficient) 4. months and years that’s a lot of mutations. Over weeks.

Unless drug developers discover another branch of antibiotics we’re not currently using (i.4. Methicillin Resistant Staphyloccus Aureus (MRSA) has been named the Superbug.e. Exercise and Coordination Topic 7: Run for your life 5. SNAB A2 Revision Notes Unit 5: Energy. because we have do drugs left that can kill it. They are often given to people who don’t need them (i.18 The evolutionary arms race between bacteria and drug developers is. 4.7.e. Humans have been reckless with use of antibiotics. If a bacterial population is continually exposed to antibiotic all bacteria will die. E.1 . now the field is open for the mutated bacterium to grow without competition. they have viral infections) or to people who don’t bother to complete the course of antibiotic. 5.6. 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. at the moment. As soon as a bacterium mutates the rest of the bacteria will be killed off by the latest dose of antibiotic. The use of antibiotics speeds the rise of immunity. tipped against humans. another way of targeting prokaryotic structures without damaging eukaryotic ones) there may well be a global pandemic of resistant bacteria.

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

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

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

By breaking the 3rd phosphate from the ATP molecule energy is released. The ATP is then regenerated by recombining the phosphate and ADP in respiration (or another process e. photosynthesis).8kJ/mol) ATP + H2O → ADP + Pi (30.The energy used in all cellular reactions comes from ATP. The recycling of ATP is crucial for life. which can be used to power intracellular reactions. 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.g. For example a runner uses ~84kg of ATP in a marathon (more than their total body weight).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 .6kJ/mol) (13.

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

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.

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

The 2C molecule is attached to a CoA enzyme. therefore the Link Reaction happens twice.7. 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.In the liver the lactate is converted back into pyruvate. Remember. Overall. 5. forming Acteyl CoA. 2NADH and 2 CO2 are made. This requires oxygen.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) . two molecules of Pyruvate were made at the end of Glycolysis.

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

part of respiration to involve oxygen. 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. the electrons are recombined with the H+ atoms and oxygen.Carrier e. These enzymes are Hydrogen Carriers and they accept the H atoms from the NADH and the FADH2.ATP NADH FADH2 ADP ADP H2O H+ Carrier H+ Carrier e.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. At the end of the Electron Transport Chain. but crucial. This is the only.Carrier e. Electrons. to form water. .

Link Reaction produces. Kreb’s Cycle produces. H+ ions are actively pumped into the mitochondrial envelope. This is done by the proteins in the electron transport chain. using the energy stored in NADH and FADH2. FADH2 has less energy and starts at the second Hydrogen Carrier.NADH starts at the first Hydrogen Carrier and has enough energy to phosphorylate 3ADP.2ATP Total 2ATP 2NADH 2NADH 6NADH 2 FADH2 10NADH 2 FADH2 4 ATP 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). . it generates 2 ATPs Where does the 38 ATP come from? Glycolysis produces.

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. 1. Whenever an H+ ion moves through the ATP Synthetase protein an ADP is phosphorylated by the ATP Synthetase.The [H+] builds up to very high levels in the envelope. Special proteins called ATP Synthetase do allow H+ to pass through them and escape into the mitochondrial matrix. 2. The potential energy of the H+ is used to phosphorylate ATP as the H+ moves out of the envelope 3. where it is broken down into pyruvate using oxygen and NADH. H+ cannot escape because it is charged (hydrophilic) and therefore cannot move through the phospholipid bilayer in the envelope membranes. 4.7. However. 5. . In summary. 5.7 In anaerobic respiration lactate is taken via the blood to the liver.

9 .7.5.8 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 5.7.

different training programmes can cause the % of either type to change slightly. the muscle type of a cheetah or a gazelle will be predominantly fast twitch. Therefore. The total volume should stay constant. whereas the muscle of a camel or an elephant will be predominantly slow twitch. 5. The rate at which the volume decreases is proportionaly to BMR. The spirometer has fixed volume and is filled with 100% O2 before the experiment begins. O2 is replaced proportionally with CO2. if CO2 is removed. BMR can be worked out if a CO2 scrubber is used. .11 Sprinters need lots of fast twitch muscle. However. Muscle type in humans is predominantly one or the other due to inherited alleles. the total volume will slowly fall as O2 is used.7.10 & 5. As the person respires. However. joggers need slow twitch.7.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.

However. Increased BMR 1. it is detected. over-training can result in the opposite effect. Decreased blood pressure 2. Decreased LDL . in this case 37.7.13 A moderate level of exercise improves health & well-being.7. This is the phenomenon known as “burn-out” Positive effects of exercise include. Increased HDL 3. holds systems at a set point. The thermoregulatory process (and most homeostatic systems) are controlled by negative feedback processes. which aims to return the system to its original level. therefore.6. If a system changes.11 for mechanisms of thermoregulation. Negative feedback.Slow twitch fibres Red (lots of myoglobin) Many mitochondria Little sarcoplasmic reticulum Low glycogen content Numerous capillaries Fatigue resistant 5.5˚C. a homeostatic response is activated.12 Fast twitch fibres White (little myoglobin Few mitochondria Lots of sarcoplasmic reticulum Lots of glycogen Few capillaries Fatigue quickly See 4. 5.

. Maintaining healthy BMI 5.Decreased risk of CHD 11. Less stress 10. Increased cortisol levels. Tendinitis 8. Decreased levels of Natural Killer Cells. Muscle tears and sprains 3. Improved well being 8. Increased stress 6. There is also less chance of infection. Decreased adrenaline levels 9. Because the incisions are small and only the damaged area is targeted. Increased adrenaline levels 4. 1.7. The surgeon makes a small incision (a “key-hole”) and uses a fibre-optic camera to view the damaged area. Phagoctyes and B & T Cells. If required. Moderate exercise increases levels of Natural Killer cells. Increased bone density 7. the patient recovers quickly. the surgeon can make a second incision and use a number of small.4. which also decreases the immune response 5. Swollen bursae 5. Ligament damage 9. which secrete apoptosis-inducing chemicals in response to non-specific viral or cancerous threat Negative effects of exercise (over-training) include. This decreses immune response. Increased muscle inflammation 2.14 Key-hole surgery is a technique which allows doctors to conduct surgery with the minimum possible damage to the patient. remote operated tools to repair the damage. Damaged cartilage 7. Decreased risk of diabetes 6.

7. vomiting. such as actin & myosin. Prosthetics allow people with amputations to participate in many activities. Agression. Creatine combines with Because ATP is re-generated phosphate to form Creatine without using the respiratory Phosphate (CP). acne. re. expensive equipment and can only be used on certain types of surgery. infirm etc) Arguments for not using drugs. the procedure requires a high degree of training. It also decreases proteins (growth proteins) recovery time. shrunken testicles Why should we allow use of drugs. This increases the level of work the body can sustain through aerobic respiration (aerobic threshold).Unfortunately. 5. • Dangerous (obviously) • May be pushed onto athletes by trainers • Effects are permanent .should increase the maximum generating ATP. Creatine Testosterone EPO causes the bone marrow Extra blood cells mean the to generate extra red blood blood can carry extra oxygen. infertility. which in target cells and increases makes the athlete more transcription of anabolic powerful. theoretically it phosphorylate ADP. liver damage and kidney damage. power of muscles and decrease recovery time Binds to androgen receptors Muscle mass increases. cells. • • • • • 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. This causes strain on the heart and can lead to infarction Diarrhoea . including sports. skin problems. decreased sex drive. CP can pathways.15 Drug Erythropoietin (EPO) Effect on physiology Effect on performance Side-effects Increased haemocrit increases blood viscosity.

• 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. but make sure you can back up your opinion with some sensible. just think for yourself in the context of the question. You can argue the toss either way.

these are called Nodes of Ranvier.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.8. creating a thick layer of membrane. Also relays message to the brain. Exercise and Coordination Topic 8: Grey matter 5.2 .8. which insulates the nerve and allows for much faster conduction speed. wrap around the axon of the long nerves.SNAB A2 Revision Notes Unit 5: Energy.

.8.3 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.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.

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

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 Voltage-gated 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.

This gives us colour vision. except that they contain the pigment Iodopsin. Bleaching occurs and trans retinal is formed Trans retinal blocks Na+ channels 4. . The bipolar cell is no longer inhibited and depolarises 6. Photon hits rhodopsin 2.8. which carries the message to the brain Cones work in exactly the same way. 3. The ganglion cell is activated.Hormone responses give responses over weeks – months . 1.Nerve reflexes give immediate responses . redsensitive. The rod is hyperpolarised and stops releasing inhibitory neurotransmitter 5.Summary for light. 5.6 Homeostasis is the maintenance of the internal environment. blue-sensitive and green-sensitive. which is found in 3 different forms.

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

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

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

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

which proves the illusion is caused by learned visual processing. because it must be close). because it must be far away) and line A as a corner (therefore. rather than an innate function of the eye / brain. We live in a “carpentered world” of straight lines and we interpret line B as a corner (therefore larger than it appears. 5.8. our brains will become “fixed” with tangled columns and won’t be able to process stimuli properly. smaller than it appears. If we miss the window.10 The Muller-Lyer illusion. Hubel & Wiesel’s experiments prove this. yet look different – why? The answer is that you have learned to process this kind of stimuli in a certain way. 5.8.11 Association (classical conditioning): US → UR (Food → Salivation) .younger for visual processing). Lines A and B are the same length. These optical illusions do not work on Zulus.

if a neutral stimulus (CR) is played with the US. If a nerve is frequently stimulated.e. Eventually. it becomes associated with the US and begins to elicit the same response. Wolfgang Kohler performed insight experiments on chimpanzees. but all the time. This means no neurotransmitter is released. The animal learns the bell signals nothing and it ignores the CS totally. the amount of Ca2+ that enters the pre-synaptic nerve gradually diminishes. the animal learns CS → CR (Bell → Salivation) Pavlovian conditioning occurs by synapses between nerves growing together. Kohler showed that the chimpanzees sometimes (pushing a level → food) . 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). which triggers the CR. This is called habituation. that the stimulus is ignored. The effect is. essentially. Insight Learning: In the early 1900s. the animal learns to ignore the CS. which results in no post-synaptic depolarisation. until it is no longer enough to trigger vesicles to fuse with the pre-synaptic membrane.Over time. Operant Conditioning: This is very similar to classical conditioning except the animal learns by doing something i.

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

Group 3 are blindfolded in one eye (monocular deprivation) 3. Hubel & Wiesel’s Method: 1.Permanently blind monkeys? Hubel & Wiesel investigated the critical window. 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 2 are blindfolded in both eyes. They used monkeys and kittens in their studies Their work permanently blinded some animals and can be argued to be unethical. Test the sensitivity of retinal cells 5. All could see. Raise monkeys from birth in three groups for 6 months Group 1 are the control (no blindfold). 2. . Test the monkeys to see whether they can see using each eye 4.

which causes difficulty in movement and limb shaking. In depression neurons in the brain that secrete serotonin neurotransmitter stop working properly and serotonin levels fall. in some cases. therefore. . and does.14 Animals are often poorly cared for in labs In Parkinson’s disease neurons in the brain die. All these neurons secrete dopamine neurotransmitter. because of events happening in the brain.Why not use computer simulations in Without animals we would not be able Clinical trials instead? to discover new drugs Animal physiology is different to human Animal testing is better than nothingphysiology. avertunhelpful potential loss of human life Utilitarian argument: Animal testingAnimals have rights too. You need to know about these experiments because they all use animals 5.8. not the eye. which requires stimulus from the eye. Testing on animals when the potential side-effects are unknown is immoral.13 Arguments For Arguments Against Clinical Trials Stage 1 involves animals.The Conclusion: There is a critical window for visual neural development. Animal testing is.8. is for the greater good Animals have no informed consent Machines like the MRI were unvested using animals. If this window is missed the monkey is blind. Animal testing has advanced our understanding of human physiology Animals can’t tell you when they are suffering 5.

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

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

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