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Heterotroph something which gets its food from other organisms Autotroph creates its own food Photoautotroph uses light & energy to create its own food ATP - Adenosine Triphosphate (3 phosphate groups) - Universal energy source. - Powers cellular processes by building and breaking bonds When we need energy, the third bond is broken by a hydrolysis reaction using ATPase enzyme. ATP The Electron Transport Chain ATP is made as a result of what is used in the electron transport chain. As electrons move along the chain, they lose energy which can be used to drive the synthesis of ATP to ADP & inorganic phosphate. Hydrogen molecules removed from compounds are picked up by other compounds and become reduced. OILRIG (oxidation is loss, reduction is gain) ADP + Pi + energy
Organelle which contains starch Extension of the Thylakoids (contain PSI) Organelle which contains chlorophyll (and PSI & PSII) found in the Stroma in stacks called Grana. Increase surface area for light capture and allows capture of photons with a wider range of wavelengths. Light Dependant Reactions occur in the Thylakoid Membrane. Stack of Thylakoid discs The space in a chloroplast surrounding the Thylakoids. Contains ribosomes and genetic materials so proteins required for photosynthesis can be synthesised. Also contains starch grains and lipid droplets. Organelle for synthesis of Polypeptides Permeable to most ions and metabolites. Highly specialised with transport proteins
Thylakoids
Ribosomes
Chlorophyll Pigments
There are 5 pigments: - Chlorophyll a - Chlorophyll b - Carotene - Xanthophyll - Phaeophytin
Carotenoids
All parts of the plant do not need to carry out photosynthesis and therefore do not have chloroplasts. The most abundant type of chlorophyll is chlorophyll a which is found in most places. The benefit of having different types is that it is most efficient as each of the pigments absorbs and captures light from particular areas, more energy from the light can be used and photosynthesis is maximised. Plant leaves appear green as all colours apart from green are absorbed so green is reflected back as chlorophyll a is most abundant.
Photosystem I Lamellae Photosystem II Granum Light dependent reactions Thylakoid Membrane Light independent reactions Stroma
Takes place on the thylakoid membranes of the chloroplasts. It has 2 main functions: 1. To produce ATP, supplying energy for the synthesis of carbohydrates 2. Split water molecules in a photochemical reaction providing hydrogen ions to reduce CO2 & produce carbohydrates The smallest unit of light energy is a photon. When a photon of light hits a chlorophyll molecule, the energy is transferred to the electrons of that molecule. Photoexcitation occurs & if an electron is raised to a sufficiently high energy level it will leave the chlorophyll molecule completely. The excited electron can be picked up by an electron acceptor (carrier molecule). This in turn results in the synthesis of ATP by one of two processes Cyclic & NonCyclic photophosphorylation.
CYCLIC PHOTOPHOSPHORYLATION
Cyclic photophosphorylation involves only photosystem I & drives the production of ATP. When light hits a chlorophyll molecule, a light excited electron leaves the molecule. It is taken up by an electron acceptor and passed directly along the electron transport chain to produce ATP. When an electron returns to the chlorophyll molecule in PSI, it can then be excited in the same Way.
LIGHT INDEPENDENT REACTIONS Carbon dioxide is converted to carbohydrates. These reactions occur in the Stroma of the chloroplasts, surrounding the grana. Carbon dioxide readily diffuses into the chloroplast where it is built up into sugars in a cyclic process called the Calvin cycle.
The enzyme Ribisco combines RuBP with CO to form a 6 carbon molecule (unstable) which then splits into 2 GP molecules which are 3 carbons each. These molecules are reduced using ATP energy & H+ from NADPH (from the light dependent reactions) to form 2 GALP molecules (3 carbons each). 1 carbon goes off to make complex molecules; glucose, lipids and amino acids & the other 5 start the process again converting back into RuBP. Products of the Calvin Cycle which pass from independent reaction to dependent reactions are: NADP, ADP & Inorganic Phosphate
ECOSYSTEM
- An ecosystem is a life supporting environment which includes all living organisms which interact together, the nutrients that cycle through the system, and the physical & chemical environment in which the organisms are living. Habitat place where an organism lives Population group of organisms of the same species Community all the populations of different species living in a habitat at any one time. Niche role of an organism, its way of life Abiotic factors non-living elements of the habitat of an organism e.g. sunlight, temperature, soil, ph. Biotic factors living elements of a habitat which affect the ability of a group of organisms to survive there e.g. the presence of suitable prey will affect the number of predators in the habitat
BIOMES
- Major ecosystems devised from the biosphere, distinguished by their similar climates and plant communities. Tropical Rainforest high humidity, warm and plenty of sunlight, rain all year. Savannah dry tropical grassland Tropical Woodland wetter than savannah, grassland with thornwoods, bushes and trees Desert very little rainfall, often extreme of temp. between day and night Taiga evergreen forests in cold subarctic & subalpine regions Tundra very cold, artic & high mountain regions The major biomes have developed over millions of years due to:
SUCCESSION Communities of animals and plants colonise an area, and over time are replaced by other, usually more varied communities
Primary Succession - Rock is uninhabited, due to poor conditions for growth such as no soil or moisture - Pioneer species such as algae or lichens penetrate the bare rock - The pioneer species break the bare rock, this is mixed with the remains of dead pioneer species organisms HUMUS, which creates the foundations of soil - Once soil is established, plants which require soil such as grasses and ferns colonise the area - Upon the death of primary colonisers, more humus is added to the soil, so the nutrient content develops. Roots hold the soil together and retain more water - Secondary colonisers more adapted to the new environment will then colonise the land - Larger trees block the growth of smaller plants, due to competition for sunlight & species diversity drops. - Climax community is self-sustaining & reached where the biodiversity is constant. Not many further changes occur. Secondary Succession
Occurs as rivers shift their courses after fires & floods and disturbances cause by humans. Due to primary succession, the soil is already formed and contains the seeds, tools and soil organisms, which means the number of plants and animals present right from the beginning of the succession, are much higher.
Light
EFFECT ON ECOSYSTEM IF IN MODERATION Plants depend on light for photosynthesis and must be able to cope in areas with low levels of light.
Temperature
Wind
Water
There is a range of temperatures which allow growth and reproduction for particular organisms. The temperature in an area also affects the rate of enzyme controlled reactions in plants Wind increases water and heat loss from the body ad adds to the environmental stress an organism has to cope with. Water is vital for living organisms
EFFECT ON ECOSYSTEM IF TOO MUCH/LITTLE Some plants are able to reproduce and thrive in low light levels, having extra chlorophyll or other chlorophyll pigments which are sensitive to lower light levels. Animals behaviour may be affected by seasonal light changes, as well as reproductive patterns. Above or below that range, reproduction does not occur, even if the organism survives. It is the extreme of temperature which determines where an organism can live, not the average. Few species can survive in areas with strong prevailing winds while occasional gales and hurricanes can devastate populations. So where the supply is limited it will cause severe problems. Organisms may die if the stress becomes too severe if like camels and cacti, the have adaptations to enable them to survive. The spaces between soil particles contain air so there is plenty of oxygen for the respiration of plant roots. In waterlogged soil, the air spaces are filled with water so plant roots may be deprived of oxygen and may die. Soil that contains high proportion of sand are light, easily worked and warmed. However, also easily drained so water passes through them rapidly, carry with it minerals needed for plants. The opposite occurs for soils made of predominantly tiny clay particles.
Oxygen Conc.
Oxygen can be in short supply in both water and soil. When water is cold sufficient oxygen dissolves in it to support life and vice versa. Soil is usually well aerated. Plant populations that are linked by massive root and rhizome networks, such as marram grass can survive in loose, shifting structures such as sand. They bind the sand together which makes it more suited for colonisation by other species.
EFFECT OF BIOTIC FACTORS HOW IT AFFECTS AN ECOSYSTEM Finding a mate Affects the finding a member of biodiversity the opposite sex to allows niches to reproduce with carry on. Larger allele/genetic diversity Territory an area Resources are occupied & defended defended making by an/a group of sure others can get organism (s) from them and continue the same or different reproducing species Parasitism & Disease Diseases can wipe biotic factors which out whole cause weakened populations within animal relationships. a biome Where 1 organism benefits at the others expense TERM & MEANING EXAMPLE A equine species becoming extinct due to reproduction isolation Lions dens
Competition - Intraspecific Competition competition for a limited resource between members of the same population or species. As a result of intraspecific competition, some individuals may not survive, or may not reproduce and so population growth slows. - Interspecific Competition occurs when different species within a community compete for the same resources. Competition will reduce the abundance of the competing species.
- Temporal Isolation
Species exist in the same area but are reproductively active at different times of the year
- Behavioural
Isolation Speciation populations do not respond to each others mating calls
Low Hybrid Zygote Vigour Zygote fails to develop and dies or produces offspring with severe disability
- Mechanical Isolation
Reproductive organs do not fit together with all potential members of the same species
- Hybrid Infertility
Offspring of two different species are not fertile
INVESTIGATING TIME OF DEATH A number of changes take place in the place of any mammal after death which can be helpful in estimating the time of death. - The normal human body temp is 37C, at death the metabolic reactions which have created the body heat slow down and eventually stop. Although body temp. Starts to fall straight after death, it plateaus for a while before dropping steadily to room temp. As a result, the temp. of a body will give some indication of how long they have been dead. Rigor Mortis a stiffening effect caused by lack of ATP in the muscles & muscle fibres becoming permanently contracted and locked solid. On average rigor mortis starts about 2-4 hours after death, begins in the face & neck and works its way down the body.
Stages of Succession The first colonisers are anaerobic bacteria, which do not need oxygen and thrive in the lactic acid rick environment of the muscles after death. As enzymes break down cells, the bacteria spread & are joined by several species of flies mostly blowflies. These insects can arrive on the body within minutes of death as they are attracted to the moisture and smell of natural orifices of the body as well as open wounds. The main attraction of the body is a site to lay eggs. Maggots begin to hatch and feed on the tissues, breaking them down. The maggots pupate, turn into flies, mate & start the cycle again. As the tissues of the body liquefy, adult flies can feed on this too. Beetles then begin to lay eggs on the carcass & parasitic wasps arrive to lay their eggs in the larvae. As the body is digested it also dries out, which doesnt suit the early colonisers. Different species such as the cheese flies and coffin flies move in. As the body becomes too dry for maggots, carcass beetles, ham beetles and hide beetles feed on the remains of the muscles and connective tissues At the very end, mites and other larvae will feed on the hair until only dry bones are left.
Viruses - Viruses are the smallest of all microorganisms. They are not cells, but arrangements of genetic material and protein that invade other living cells & take over their biochemistry to make more viruses. - Most scientists class viruses as obligate intracellular parasites meaning they can exist and reproduce as parasites only in the cells of other living organisms. The Structure of Viruses The protein coat or capsid is made up of simple repeating protein units known as capsomeres, arranged in different ways. In some viruses, the genetic material and protein coat are covered by a lipid envelope, produced from the host cell. The presence of the envelope makes it easier for the viruses to pass from cell to cell but it does make them vulnerable to substances such as ether which will dissolve the lipid membrane. Viral genetic material can be
DNA or RNA, and nucleic acid can be single or double stranded. Viral RNA directs the synthesis of a special enzyme called reverse transcriptase which proceeds to make DNA molecules corresponding to the viral genome. Viruses attach to their host cells by means of specific proteins (antigens) known as Viral attachment particles (VAPs) which target proteins in the host cell surface membrane.
Bacteriophages inject their genome into the host bacterial cell but the bulk of the viral material remains outside the bacterium. The viral DNA forms a plasmid within the bacterium. The viruses that infect animals get into the cells in several ways. Some types are taken into the cell by endocytosis & the host cell then digests the capsid, releasing the viral genetic material. The viral envelope fuses with the host cell surface, releasing the rest of the virus inside the cell membrane. Plant viruses usually get into the plant cell using a vector (often an insect) to pierce the cellulose cell wall. 2 routes of infection - Lysogenic Pathway Many viruses are non-virulent when they first get into the host cell. They insert their DNA into the host DNA so it is replicated every time the host cell divides. This inserted DNA is called a provirus. During this period of lysogeny, when the virus is part of
the reproducing host cells, the virus is said to be dormant. - Lytic Pathway Sometimes the viral genetic material is replicated independently of the host DNA straight after entering the host. Mature viruses are made & eventually the host cell bursts, releasing large numbers of new virus particles to invade other cells. The virus is said to be virulent (disease causing) & the process of replicating & killing cells is known as the lytic pathway. 1. Bacteriophage attracts bacterium 2. Phage DNA is injected into host cell. It brings about the synthesis of viral enzymes 3. A. Viral DNA is incorporated into host cell DNA & replicated each time the bacterium divides, without causing any damage. B. OR Phage DNA inactivates the host DNA and takes over the cell biochemistry 4. Phage DNA is replicated. New phage particles are assembled as new protein coats are made around phage DNA. The enzyme lysozyme is synthesised or released 5. Lysis the bacterial cell bursts due to the action of lysozyme, releasing up to 1000 phages to infect other bacteria & the cycle begins again.
RETROVIRUSES Retroviruses have a more complex life cycle. Their genetic material is viral RNA. This cannot be used as mRNA but is translated into DNA using reverse transcriptase. 1. The retrovirus attacks an animal cell 2. Viral RNA enters the host cell. This RNA cannot be used as mRNA. 3. Viral RNA is translated into viral DNA by reverse transcriptase in the cytoplasm 4. Viral DNA is incorporated into the host DNA in the nucleus. It directs the production of new viral genome RNA, mRNA and coat proteins. 5. New viral particles are assembled and leave the host cell by exocytosis. Viral DNA remains in the nucleus so the process is repeated. 6. The host cell continues to function as a virus making factory, while the new viruses move on to infect other cells.
Bacteria
Flagella & Pilli Flagella are rigid protein strands that arise from basal bodies in the plasma membrane in some bacteria. They bring about movement by rotating from their base, driven by the basal body. Pilli are tiny tubular structures that arise from the cell membrane of some bacteria. They enable bacteria to attach to surfaces and to other bacteria.
Cytoplasm - About 75% water in which are dissolved proteins (mainly enzymes) Lipoproteins, sugars, amino acids and fatty acids, inorganic salts, and the waste products of metabolism.
Cell Wall Protects against rupture due to osmosis and keep shape. Rigid wall containing giant molecules consisting of amino sugars and peptidogylcan
Capsule A slime layer or capsule is made up of additional materials that are laid down on the outer surface of the wall. Capsules are firmly attached, whereas slime layers may diffuse into the surrounding medium.
Ribosomes - Sites of protein synthesis. Bacterial ribosomes are known as 70S ribosomes because they are smaller than those in the cytoplasm of plant and animal cells and fungi (called 80S ribosomes)
Plasmids Additional hereditary material small rings of DNA, present in the cytoplasm of some but not all bacteria.
Mesosomes Infoldings of the plasma membrane found in some bacterial cells. In the photosynthetic bacteria, they are where the photosynthetic pigments are housed.
Plasma Membrane - Consists of phospholipids and proteins arranged in the fluid mosaic model. Carbohydrates attach to some lipids forming glycolipids and some proteins forming glycoproteins on the outer surface membrane.
There are two different types of bacterial cell walls which can be distinguished by Gram Staining. Gram positive bacteria have a thick layer of peptidoglycan containing chemicals such as teichoic acid. The crystal violet in the stain binds to the acid & resists decolouring, leaving the positive PURPLE/BLUE in colour. Gram negative bacteria have a thinner layer of peptidogylcan with no teichoic acid. Any crystal violet which does bind is readily decolourised & replaced with red safranine in the stain, so the cells appear RED in colour.
Classifying Bacteria
- by shape Cocci (spherical) Bacilli (rod shaped) Spirilla (twisted/spiral) Vibrios (comma shaped)
Reproduction of Bacteria Bacteria can reproduce in two main ways. The most common is Asexual Reproduction (binary fission) splitting into two. One the bacterium reaches a certain size, the DNA is replicated and the old cell wall begins to break down around the middle of the cell. Enzymes break open the circular piece of DNA allowing the strands to unwind and be replicated.
Another form of reproduction is Sexual reproduction. In very rare conditions, bacteria can reproduce using what appear to be different forms of sexual reproduction. There are 3 ways in which genetic material from one bacterium cab be taken in and used as part of the DNA of another bacterium.
Transformation A short piece of DNA is released by a donor and actively taken up by a recipient where it replaces a similar piece of DNA. Only occurs in certain types of bacteria. Transduction Takes place when a small amount of DNA is transferred from one bacterium to another by a bacteriophage. Bacteriophage attaches to the bacterial cell wall. Enzymes are released to break down the cell wall. New bacteriophage forms and some bacteria DNA is included by mistake
Conjugation genetic information is transferred from one bacterium to another by direct contact. The donor cell is similar to a male cell and this produces a sex pillus, a cytoplasmic bridge between the two cells through which DNA is transferred to the recipient cell, similar to the female cell
Endotoxins - Lipopolysaccharides (part of the outer layer of gram negative bacteria) - Rarely fatal - Tend to cause symptoms such as fever, vomiting & diarrhoea - E.g. Salmonella & E.coli - However symptoms may indirectly lead to death Exotoxins - Soluble proteins produced & released into the body by bacteria as they metabolise and reproduce. - There are many different types; some damage cell membranes causing internal bleeding, some act as competitive inhibitors to neurotransmitters, whilst others directly poison cells. - Rarely cause fevers but so include some of the most dangerous bacterial diseases. - E.g. Clostridium botulinum produces one of the most toxic substances known, botulinum toxin
BENEFICIAL BACTERIA
- Many bacteria in the body is beneficial, helping to break down food and keeping pathogens at bay by outcompeting them. The normal growth of bacteria on your skin or in your gut is referred to as the skin flora or gut flora Probiotic drinks and foods contain cultures of these good bacteria to help support the normal healthy bacterial flora of the gut. - Bacteria also play a vital role in the ecosystems of the natural world. The majority of bacteria are decomposers. They break down organic material to produce simple inorganic molecules such as CO2 and water. - They release inorganic nitrogen which returns to the soil in the nitrogen cycle, and also sulphur compound which returns to the soil or water. - Another important aspect of bacteria is in the carbon cycle is the fact that some microorganisms produce the enzyme cellulase. This enzyme breaks down the cellulose produced in plant cell walls to give sugars which can then be used as food by a wide range of other microorganisms.
GUT
- Saliva in the mouth has bacterial properties. Some polypeptides produced in the salivary glands destroy bacteria while others slow down bacterial growth. - Acid in the stomach destroys the majority of ingested microorganisms. - The natural flora in the gut usually competes successfully for both nutrients and space with any microorganisms which manage to get through the stomach & produces anti-microbial compounds - VOMITING is effectively removing many of the microorganisms physically from the system when the body is infected.
T Cells
B Cells
Helper Cells
Killer Cells
T cells - made in the bone marrow but mature and become active in the thymus gland - Surface of each T cell displays thousands of identical T-cell receptors. There are 2 main types of T-cells; T killer cells produce chemicals that destroy pathogens & T helper cells involved in the process which produces antibodies against the antigens on particular pathogen. The working of these cells depend on special proteins known as major histocompatibility complex (MHC) proteins, which display antigens in the cell surface membranes
ANTIBIOTICS
- Bacteriostatic the antibiotic used completely inhibits the growth or the microorganism - Bactericidal the antibiotic used will destroy almost all of the pathogens present
Artificial Passive Immunity occurs when antibodies are formed in one individual, extracted & injected into another individual. Artificial Active Immunity is when small amounts of antigen (vaccine) are used to produce immunity in a person
CORE PRACTICALS 1. Studying The Ecology On An Area - Techniques such as taking a transect can be used to study the topography of an area the shape, height & depth of the land surface. - Quadrats can be used to give valid & reliable measures of the numbers and types of plants. - The animal communities can be investigated by many methods, including quadrats, nets, pitfall traps & taking soil samples. - The abiotic factors which affect a habitat such as rainfall & temperature & edaphic factors such as soil type & pH are also measured & recorded to give as much information as possible about the ecology of the area.
2. Effect of temperature on a living organism - It is possible to model the effect of increasing temperature on the development of living organism in the laboratory. - There are many different experimental procedures which can be used such as germination of seeds, the growth rate of young seedlings, or the hatching rate of brine shrimps. - The temperature differences for the investigation need to be controlled very carefully
3. Gel Electrophoresis - Gene probes are short DNA sequences that are complementary to specific sequences which are being sought. Each probe is labelled, either with a radioactive element or with a fluorescent molecule - Large amounts of the gene probes are added to the filter and bind with complementary DNA strands in a process known as hybridisation - Excess probes are washed away & either X-ray pictures are taken of the filter, or the filter is placed under UV light to show up the DNA regions
4. Polymerase Chain Reaction (PCR) - Amplifying the DNA - Adapts the natural process in which DNA is replicated in the cell, making it possible to produce enough DNA for a profile from tiny traces of biological material - Primers (small sequences of DNA which must join to the beginning of the separated DNA strands before copying can begin) & a good supply of the four nucleotide bases are mixed together in a PCR vial and placed in a PCR machine. - The mixture is heated to 90-95C which causes hydrogen bonds to break so DNA strands separate - The mixture is then cooled to 55-60C so the primers bind to the single DNA strands - The mixture is then heated again to 75C which is the optimum temperature for DNA polymerase enzyme to build the complementary strands of DNA. - The process is repeated about 30 times to give approx. 1 billion copies of the DNA.
5. Effect Of Different Antibiotics On Bacteria - The effect of different antibiotics on bacteria can be investigated using standard microbiological techniques. - An agar plate is seeded with a known bacterial culture - Filter paper discs containing different antibiotics, or different concentrations of the same antibiotics, are placed in the agar & the plate is sealed. - A control culture of microorganisms with known sensitivity to the antibiotic is grown at the same time under the same conditions - The level of inhibition of bacterial growth gives a measure of the effectiveness of the dr ugs.