OCR Biology F212

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  • Created on: 27-05-13 10:46

Biochemistry and Metabolism

Carbohydrates: Energy storage and supply, structure (in some organisms)

Proteins: structure, transport, enzymes, antibodies, most hormones 

Lipids: Membranes, energy supply, thermal insulation, protective layers, electrical insulation in neurones, some hormones.

Vitamins and Minerals: Form parts of some larger molecules and take part in some metabolic reactions, some act as co-enzymes or enzyme activators

Nucleic Acids: information molecules, carry instructions for life

Water: Takes part in reactions, supports plants, solvent/medium for most metabolic reactions, transport

Metabolism: the sum total of all the biochemical reactions taking place in the cells of an organism.

Balanced diet: diet that contains all the nutrients in proportions that match the needs of the individual. Sufficient energy for metabolism, level of activity, water and fibre.

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Glucose is a monosaccharide with a hexose ring.

Alpha glucose: OH is down, down, up, down whereas Beta glucose has hydrogen on the bottom: OH is up, down, up, down.

Monosaccharides are joined together by glycosidic bonds. During condensation, a hydrogen atom on one monosaccharide and an OH from another, releases a molecule of water. 

During hydrolyis this glycosidic bond is broken and a water molecule is added to the monosaccharides.

Two alpha-glucose join together to make maltose, a disaccharide

Polysaccharides are formed when more than two monosaccharides are joined together by glycosidic bond.

When alpha glucose forms polysaccharides, every other glucose molecule is flipped upside down, whereas beta glucose forms straight chains.

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Carbohydrates 2

  • Starch: the main energy storage material in plants. 
    • Starch is made of two polysaccharides of alpha glucose: amylose and amylopectin.
    • Amylose is a long, unbranched chain that has a coiled structure, making it compact and good for storage.
    • Amylopectin is a long, branched chain. Side branches allow enzymes to break it down easily
    • Insoluble in water so does not cause water to enter cells by osmosis, causing swelling
  • Glycogen: main energy storage material in animals
    • Glycogen is a polysaccharide of alpha glucose
    • Long and branched. Many side branches allow stored glucose to release energy quickly
    • Compact molecule so is good for storage
  • Cellulose: major component of cell walls in plants.
    • Long, unbranched chains of Beta glucose
    • Bonds between sugars are straight so chains are also straight.
    • Cellulose chains are linked together by hydrogen bonds to form strong fibres called microfibrils. Strong fibres provide structural support for plants.
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Made mainly of carbon and hydrogen atoms and a few oxygen atoms, so hydrophobic and less dense than water. 

Glycerol (3-carbon compound which each C has -OH group which can react with FA and form ester bonds) and fatty acids (Long-chain hydrocarbon molecules, each has carboxyl group which reacts with -OH on glycerol, can very as length of hydrocarbon chain and number of double C=C bonds) are main components of lipid molecules.

Triglycerides - Made of 3-FA chains and glycerol molecule. Condensation reaction, has Ester bonds, can be Saturated (single bonds + solid at rtp) or Unsaturated (double bonds + liquid at rtp). Monounsaturated has 1 double bond, Polyunsaturated has 2 or more DB. Used in animals and plants for energy store, thermal insulators, buoyancy and protection.

Phospholipids - Similar to TG but 1 FA replaced by Phosphate group. PG hydrophillic so soluble in water, but FA hydrophobic so insoluble so overall form bilayers.

Cholesterol - Made of 4 hydrocarbon rings and hydrocarbon tail (non-polar) and -OH (polar) Arranged in bilayers and intreacts to control membrane fluidity.

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Water is a reactant in many molecules, a solvent, transport medium and helps with temperature control, as it carries away heat energy when it evaporates.

A molecule of water is made up of one atom of oxygen and two hydrogen atoms. The shared electrons are pulled towards the oxygen atom, making hydrogen delta positive and oxygen is delta negative, making water polar. 

  • Hydrogen bonds give water high specific heat capacity, a lot of energy is needed to raise the temperature of 1 gram of substance by 1C as H bonds can absorb a lot of energy, this is useful as it stops rapid temperature changes, temperature remains stable.
  • High latent heat of evaporation: lots of energy needed to break hydrogen bonds, lot of energy used up when it evaporates, allowing cooling.
  • Cohesion: attraction between molecules allows water to flow, making it good for transporting substances, such as in blood.
  • Good solvent: ionic substances can dissolve due to attractions to polar water molecules.
  • Freezing: water freezes, forming ice which is less dense and floats. Ice acts as an insulator allowing organisms below to survive.
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  •  A polypeptide is formed when more than two amino acids join together. 
  • Amino acids are made of a carboxyl group (COOH) and an amino group (-NH2) attached to a carbon atom, and an R group that varies.
  • Amino acids join together by peptide bonds, an OH from COOH and a H from NH2 is lost.
  • Primary structure is the sequence of amino acids in the polypeptide chain.
  • Secondary structure: hydrogen bonds form between amino acids in the chain, coiling into an alpha helix or folding into a beta pleated sheet.
  • Tertiary Stucture: 3D structure of the protein: ionic interactions, disulphide conds (between two cysteine), hydrogen bonds and hydrophobic and hydrophilic interactions.
  • Quaternary structure: way in which polypeptide chains are assembled together
    • Collagen is fibrous protein that forms supportive tissue in animals, so needs to be strong. It is made up of three polypeptide chains that are tightly coiled into a strong triple helix. Chains are interlinked by covalent bonds. Cross links are staggered to increase strength. Minerals can bind to triple helix to increase rigidity.
    • Haemoglobin is a globular protein with an iron-containing prosthetic group called a haem group. Hydrophilic side chains are outside and hydrophobic inside. Made of four polypeptide chains, two alpha helix and two beta sheets. It is soluble in water.
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Tests for Molecules

  • Reducing Sugars: Benedict's reagent is added to the sample and heated. If reducing sugars are present, the solution turns from blue to green to yellow to orange to brick red.
  • Non-reducing Sugars: Boil the solution with hydrochloric acid to break into monosaccharides. Neutralise with sodium hydrogencarbonate and carry out Benedict's test.
  • Starch: add iodine dissolved in potassium iodide. If starch is present, orange-brown solution turns to dark blue-black colour.
  • Proteins: add a few drops of sodium hydroxide solution. Add some copper (II) sulphate solution. If protein is present, a purple layer forms. If not, solution remains pale blue.
  • Lipids: shake the substance with ethanol then pour the solution into water. If lipid is present, solution turns milky. If not, solution remains clear and colourless.
  • Colorimetry is used to determine the concentration of a glucose solution. A calibration curve is made by making glucose solutions of known, different cocnentrations. Do benedict's test and remove any precipitate. Use a colorimeter to measure absorbance of Benedict's solution remaining in each tube. Use results to make a calibration curve.
    • The more concentrated the colour of the solution, the higher the absorbance is.
    • The higher the absorbance is of the solution, the lower the glucose concentration.
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DNA - Deoxyribonucleic Acid - A, G, C and T - sugar deoxyribose

RNA - Ribonucleic Acid - A, G, C and U - sugar ribose

Made of chains of nucleotides which make polynucleotides, joined by covalent bonds between phosphate and sugar molecules to form a 'backbone'.

Nucleotide - Made of pentose sugar (5 Carbon Atoms), Phosphate, Nitrogenous Base.

Bases - Purines (Adenine and Guanine, double ring of carbon and Nitrogen atoms) and Pyramidines (Thymine, Cytosine and Uracil, single ring...).

DNA is a Double Helix - Made of two polynuecleotides held togther by H bonds, arranged so Purine is opposite Pyramidine (A:T, G:C), A+T have 2 H bonds, G+C have 3 H bonds, the two polynucleotides are antiparallel.

DNA is stable info is stored for a long time, large molecule stores lots of info, two polynucleotides act as template for synthesis of new polynucleotide during replication.

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DNA Replication + Protein Synthesis

Half the parent DNA molecule is passed onto the daughter molecule.

  • Double helix unwinds, DNA 'unzips' so hydrogen bonds between polynucleotides are broken.
  • Original polynucleotides act as templates for assembly of nucleotides. 
  • Free nucleotides, made in cytoplasm, move towards the exposed bases of DNA.
  • Base pairing occurs and hydrogen bonds form between complementary bases.
  • Enzyme DNA polymerase forms covalent bonds between free nucleotides attached to each template.
  • Two daughter DNA molecules form seperate double helixes, each with one parent strand.

DNA contains genes which are instructions for proteins. 

  • A gene is a sequence of DNA nucleotides that codes for a protein. Different proteins have a different number and order of amimo acids. 
  • Order of nucleotides determines order of amino acids. Three bases code for an amino acid.
  • DNA is copied into RNA in the nucleus. RNA leaves nucleus through nuclear pores to ribosome as mRNA. Then tRNA bring amino acids to the ribosome in the correct order, according to base sequence. Amino acids are joined by peptide bonds to form proteins.
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Enzymes are biological catalysts.

Enzyme action can be intracellular (within cells) or extracellular.

Enzymes are globular proteins, with an active site, specific in shape to substrate.

Enzymes reduce activation energy.

Lock and Keysubstrate molecule may fit into the enzymes active site and are held in there for a short time which forms an enzyme-substrate complex

Induced Fit HypothesisEnzyme changes shape to mould itself around the substrate molecule. R groups of the polypeptide forming the active site move to form temporary bonds with the substrate. The active site of an enzyme decreases the activation energy of the enzyme so that the substrate has enough energy to react.

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Enzymes 2

pH - When the pH changes from the optimum the shape of the enzyme changes and the affinity of the substrate for the active site decreases.Change of pH means change in concentration of H+ ions, which cancels out the charge on the R groups and tertiary structure changes, so active site loses its specific shape.

Temperature - If low temperature, there will be slow reaction as theres little kinetic energy. So as the temp increases more kinetic energy is given to the substrate and enzyme so reaction rate increases. Once you go past the optimum temperature, the high temperature causes the bonds which hold the tertiary structure together to break, the tertiary structure changes, so the shape of the active site changes. The enzyme is denatured.

Substrate Concentration - Rate of reaction increases as substrate concentration increases, substarte conc. is the limiting factor, as at a certain point all the active sites are filled and the enzyme concentration is limited so rate of reaction stops increasing.

Enzyme Concentration - Rate of reaction increases as the concentration of enzyme increases, no limiting factor as the substrate can be used again.

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Enzymes 3

Cofactor - A non-protein component of an enzyme which can be organic or inorganic and is required my enzymes to carry a reaction out.

Coenzyme - An organic cofactor where many are involved in energy transfer reactions like photosynthesis and respiration.

Competitive Inhibitor - Molecular shape is similar to subtrate so it fits into active site, whichslows the rate of reaction as substrate can't get in. Eg statins which compete with cholesterol.

Non-Competitive Inhibitor - Molecule which binds to part of enzyme which is not active site and changes the enzyme's tertiary shape, so changes shape of active site, so substrate cannot fit and so slows the rate of reaction. Eg potassium cyanide which binds to haem which is part of enzyme cytochrome oxidase.

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Balanced Diet

Balanced Diet - Having all the components of the diet in correct proportions.

Obesity is defined as being 20% over the recommended body weight. Too much energy and too little exercise may cause obesity. This can lead to diabetes, arthritis, high blood pressure, CHD.

CHD is the result of reduced blood flow to coronary arteries in the heart, caused by atherosclerosis. Hypertension damages artery walls, encouraging atheromas to form.

Cholesterol is a lipid. It is transported as lipoproteins, composed of proteins and lipids.

  • High-Density Lipoproteins are mainly proteins. They transport cholesterol from body tissues to the liver. They reduce blood cholesterol when levels are too high.
  • Low-Density Lipoproteins are mainly lipid. They transport cholesterol from liver to blood. They increase blood cholesterol when levels are too low.
  • Diets high in saturated fat raises LDL level, so more cholesterol is transported to the blood, increasing risks of CHD.
  • Diets high in polyunsaturated fat raises HDL levels. More cholesterol is transported to the liver, decreasing risk of CHD.
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Food Production

Humans rely on plants which are the start of all food chains. Many modern farming methods aim to maximise productivity by increasing plant and animal growth.

Fertilisers: chemicals that increase crop yields by providing minerals. They replace minerals used up by plants so that lack of minerals does not limit growth of the next crop. Fertilisers can be natural (e.g. compost and manure) or artificial.

Pesticides: chemicals that increase crop yields by killing pests, fewer plants are damaged and destroyed. Pests include microorganisms, insects or mammals. Pesticides may be specific and kill only one species, or broad and kill a range of species. Some non-pests can also be harmed.

Antibiotics: chemicals that kill or inhibit growth of bacteria. Help to prevent diseases. Animals usually use energy fighting diseases, which reduce energy available for growth. They also help to promote growth of animals. However, bacteria may become resistant.

Selective breeding: select plants with good characteristics that will increase crop yield. Breed them together. Select offspring with best characteristics and breed. Continue over several generations until high-yielding plant is produced.

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Microorganisms and Food

  • Bread is made by mixing yeast, sugar, flour and water into a dough. Yeast turns sugar into ethanol and CO2, making bread rise.
  • Wine is made by adding yeast to grape juice. Yeast turns sugar in grape juice into ethanol (alcohol) and CO2.
  • Cheese is made by adding bacteria to milk. Bacteria turns sugar in milk to lactic acid, causing milk to curdle. Enzyme used to turn curdled milk into curds and whey. Curds are separated and left to ripen into cheese.
  • Yoghurt is made by adding bacteria to milk. Bacteria turns sugar in milk to lactic acid, causing milk to clot and thicken into yoghurt.
  • Salting and adding Sugar prevents microorganisms from taking in water, inhibiting their growth. Tinned foods are often preserved in brine.
  • Freezing slows growth of microorganisms, by slowing down reactions.
  • Pickling in acidic vinegar inhibits growth of microorganisms. Low pH reduces enzyme activity, inhibiting their growth.
  • Heat treatment kills microorganisms. Pasteurisation raises liquids to high temp.
  • Irradiation exposes food to radiation, killing any microorganisms.
    • Population of M grow rapidly, inexpensive, artificially controlled
    • high risk of food contamination, food poisoning, small chainges can kill M
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Infectious Disease

  • Health is a state of physical, mental and social well-being. Disease is a condition that impairs the normal functioning of an organism. Pathogen: organism that can cause damage to the organism it infects. Parasite: organism that lives in or on a host and causes damage.
  • Malaria: caused by plasmodium, a eukaryotic, single-celled parasite.
    • transmitted by mosquitoes (vector), insects that feed on blood of animals and humans.
    • mosquitoes spread infection by transferring parasite from one host to another.
    • mosquitoes transfer Plasmodium into human's blood when they feed on them.
    • Plasmodium infects liver and red blood cells, disrupt blood supply to vital organs.
  • AIDs: is caused by the HIV (Human Immunodeficiency Virus)
    • Infects human white blood cells. HIV can only reproduce in cells of infected organism.
    • Virus kills wbc as it leaves, leading to acquired immune deficiency syndrome.
    • Immune system deteriorates and fails - sufferer more vulnerable to other infections. 
    • HIV is transmitted via unprotected sex, through infected bodily fluids (e.g. sharing needles, blood transfusion) or from mother to fetus (through placenta/breast milk).
  • Tuberculosis is caused by a bacterium - Myobacterium tuberculosis
    • lung disease caused by bacterium. 
    • TB spreads by droplet infections. Passed due to overcrowding, poverty
    • Symptoms do not show; weakened due to disease/malnutrition activates it
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Infectious Disease 2

Malaria - Widely distributed throughout tropics and sub-tropics. More than 500 million people become ill with it each year. Mosquitoes resistant to insecticides, plasmodium is resistant to drugs. Control measures - Sleep in nets to prevent mosquitoes biting.

TB - Spread worldwide, 1/3 of human population carry the bacterium but for many it is inactive, more likely to spread in poverty-stricken and overcrowded conditions. Control meaures - cured by long course of antibiotics, BCG vaccine against it not very effective.

HIV/AIDS - 39.5mill people living with it, TB is an opportunistic disease associated with HIV. Control measures - use condoms, health education about safer sex, blood donations screened for HIV, blood donations heat treated fo kill viruses, needle exchange schemes.

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Immune System

  • Primary defences help to prevent pathogens and parasites from entering it.
    • Skin acts as physical barrier, blocking pathogens from enetering body. Acts as chemical barrier by producing antimicrobial chemicals that lower pH, inhibiting growth of pathogens
    • Mucous membranes protect body openings exposed to environments (e.g. nose). Some membranes secrete mucus that trap pathogens and contain antimicrobial enzymes
    • Eyes are protected by antibodies in the tear fluid
    • Ear canal is lined by wax, which traps pathogens
    • Vagina is protected by maintaining relatively acidic conditions
  • Secondary Defence consists of an immune response: specific response to a pathogen, which involves action of lymphocytes and production of antibodies.
    • Phagocytes engulf pathogens by carrying out phagocytosis. Phagocytes recognise antigens on pathogens. Pathogen is engulfed and held in a phagocytic vacuole. Lysosome fuses with vacuole. Enzymes break down pathogen. Present antigens to lymph nodes, by sticking antigens on its surface to activate other immune cells.
    • Neutrophils have multilobed nuclei and carry out phagocytosis. Macrophages are larger cells. They release chemicals such as histamine, attracting neutrophils and make capillaries more leaky. More tissue fluid passes into lymphatic system, leading pathogens to macrophages in lymph nodes. Macrophages activate lymphocytes.
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Immune System 2

  • Macrophages activate T lymphocytes. Their surface is covered in receptors. Receptors bind to antigens presented by phagocytes. Each TL has different receptor. When complementary antigen bind to receptor, TL is activated. T Helper cells release chemicals to activate BL. T Killer cells attach to antigens and kill. T Memory cells retain.
  • T Lymphocytes activate BL, divide into plasma cells, covered in antibodies, bind to antigens to form an antigen-antibody complex. Each BL has a different shaped antibody. When complex forms, BL divide into plasma cells and memory cells.
  • Cell Signalling: communication between cells. Cell may release a substance that binds to receptors on another cell, causing a response. Helps to activate w.b.c when needed. 
  • Plasma cells make more antibodies specific to antigens. Antibodies have variable regions that is complementary to an antigen. Variable region differs. Hinge region allows flexibility when antibody binds to antigen. Constant region allows binding to receptors on immune system cells. Disulphide bridges hold polypeptide chains together.
    • Agglutination: each antibody has two binding sites. Antibody can bond to two pathogens at the same time. Pathogens become clumped together, easing phagocytosis.
    • Neutralising toxins: antibodies bind to toxins, complex also phagocytosed.
    • Prevent pathogen binding to human cells: block cell surface receptors that pathogens need to bind to host cells. 
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Immune System 3

  • Primary response is slow
    • When pathogens enter the body, antigens on surface activate the immune system
    • This is the primary response. Not many B lymphocytes to bind. 
    • Eventually body produces enough of the right antibody to overcome the infection. 
    • Host still shows symptoms of disease
    • T and B memory cells are produced. 
    • The person is now immune and can respond quickly to second infection.
  • Secondary response is faster
    • Immune system produces a quicker, stronger, larger response
    • Memory B lymphocytes divide into plasma cells that produce the right antibody to antigen. 
    • Memory T lymphocytes kill the cell carrying the antigen
    • The secondary response often gets rid of pathogen before host begins to show symptoms.
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Immunity and Vaccinations

  • Active Immunity: Immune system makes own antibodies after being stimulated by antigen
    • Natural: after catching disease, body makes its own antibodies
    • Artificial: immunity after vaccination containing harmless dose of antigen
  • Passive Immunity: antibodies given by a different organism
    • Natural: baby becomes immune, antibodies from mother through placenta + breast milk
    • Artificial: injected with antibodies from someone else, e.g. for snake venom
  • Vaccines contain antigens that cause your body to produce memory cells against a particular pathogen, whithout causing disease. Body is immune, without symptoms. 
    • Herd vaccination: if most people are vaccinated in a community, disease becomes rare.
    • Ring vaccination: vaccinate all in immediate vicinity of new cases
    • Oral vaccines may be broken down by enzymes or may be too large to be absorbed.
  • Influenza: influenza virus causes influenza (flu). Memory cells produced from vaccination with one strain of flu will not recognise other strains with different antigens. Due to mutations, there are different strains each year. New vaccines are chosen each year. 
  • Possible sources of drugs such as plants need to be protected.
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Smoking and Disease

Smoking damages the cardiovascular system:

  • Atherosclerosis: caused by nicotine, causes hypertension
    • Damage occurs to lining of artery. White blood cells move into area. 
    • Over time, fatty deposits build up and harden to form a fibrous plaque (atheroma).
    • Restricts blood flow by narrowing lumen. 
  • Coronary Heart Disease: carbon monoxide and nicotine; may cause heart attack
    • Carbon monoxide prevents oxygen transport to coronary arteries
    • Nicotine causes hypertension, which leads to atherosclerosis
    • Nicotine causes platelets to become sticky, increasing chances of blood clots
  • Stroke: nicotine and carbon monoxide
    • Stroke is rapid loss of brain functioning due to disrupture in blood supply to brain
    • Blood clot in artery leading to brain reduces oxygen that reaches the brain
    • Nicotine increases risk of clots forming (hypertension, sticky platelets)
    • Carbon monoxide reduces O2 to brain, preventing Hb from binding
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Smoking and Disease 2

  • Lung cancer: cigarette smoke contains carcinogens
    • Carcinogens may cause mutations in DNA of lung cells, leading to uncontrolled cell growth and formation of a malignant tumour.
    • Tumours block air flow to areas of lungs, decreasing gas exchange, leading to shortness of breath as body struggles to take in oxygen.
    • Tumour uses energy and nutrients to grow, leading to weight loss.
  • Chronic bronchitis: inflammation of the lungs
    • Cigarette smoke damages cilia and cause more mucus to be produced
    • Mucus accumulates, increased coughing to try and remove mucus
    • Microbes multiply, cause lung infections, inflammation, decreases gas exchange
    • Type of chronic obstructive pulmonary disease, permanent airflow reduction
  • Emphysema: lung disease caused by smoking/air pollution
    • Particles become trapped in alveoli, inflammation, encourages phagocytes to area
    • P produce enzyme, breaks down elastin, alveolar walls destroyed, elasticity lost
    • Reduces surface area of alveoli, rate of gas exchange reduced
    • Shortness of breath, wheezing, increased breathing rate
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  • Species: group of similar organisms able to reproduce to give fertile offspring
  • Habitat: area inhabited by a species, including physical factors (soil, temp.) and living biotic factors (availability of food, presence of predators)
  • Biodiversity: variety of living organisms in an area
    • Habitat diversity: no. of different habitats in an area e.g. coastal has beaches, sand dunes, salt marshes
    • Species diversity: no. of different species and abundance of each in an area
    • Genetic diversity: variation of alleles within species or population of species
  • Species richness: number of different species in an area. The higher the number of species, the greater the species richness. It is measured by taking random samples of a habitat and counting the number of species.
  • Species evenness: measure of the relative abundance of each species in an area. The more similar the population size of each species, the greater the species evenness. It is measured by taking random samples of a habitat, and counting the number of individuals of each different species.
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Biodiversity 2

  • Choose an area within habitat to sample
  • Count number of individuals of each species
    • Plants: use quadrat, point frame, transect
    • Flying Insects: sweepnet, white sheet and stout stick
    • Ground Insects: pitfall trap, tullgren funnel, light trap
    • Aquatic Animals: net
  • Repeat process to take as many samples as possible, better indicant of whole habitat
  • Use results to estimate total no. of individuals or total no. of different species in habitat
  • Diversity is measured using Simpson's Index of Diversity
  • Simpson's index of diversity takes into account both species richness and evenness
  • D = 1 - (sum of (n/N)^2)
    • n = total number of individuals of one species
    • N = total number of organisms of all species
  • Closer to 1 the index is, the more diverse the habitat.
  • Greater the species richness and evenness, the greater the number.
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Global Biodiversity

  • Global biodiversity is the total number of species on Earth
  • Climate change can affect biodiversity:
    • Most species need a particular climate to survive
    • A change in climate may mean an inhabitable area becomes uninhabitabe or vice versa
    • This may increase or decrease range of species in that habitat
    • Some species may be forced to migrate to a more suitable area, causing a change in species distribution. If there is no suitable area for migration, or chang is too fast, species may become extinct. This will decrease biodiversity.
  • Climate change may also contribute to spread of disease:
    • Ranges of some insects that carry disease might become greater. E.g. warmer and wetter areas are more habitable for insects such as mosquitoes spread into previously uninhabitable areas
    • Warmer and wetter areas also encourages spread of fungal diseases
  • Changes in temperature, rainfall, timing of seasons, frequency of flood and drought will all affect patterns of agriculture
    • previously unsuitable land may become habitable
    • different crops require different conditions; different conditions = different crops grown
    • Disrupts food chains; extreme weather events and unexpected conditions such as flooding may result in crop failure
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Importance of Biodiversity

  • Economic reasons:
    • Plants and animals are the source of almost all food and some drinks
    • Clothing - lot of fibres and fabrics are made from plants and animals
    • Drugs - many are made from plants e.g. morphine made from poppies
    • Fuels - renewable fuels, including biogas and ethanol
    • Other industrial materials - wood, paper, dyes, adhesives, oils, rubber
  • Ecological reasons:
    • Disruption of food chains and recycling of nutrient cycles
    • regulation of atmosphere and climate
    • purification and retention of fresh water
    • formation and fertilisation of soil; crop pollination
    • detoxification and recycling of wastes
  • Ethical reasons:
    • Organisms have a right to exist - cannot become extinct because of human activities
    • Religious and spiritual reasons - harmony with natural world
    • Moral responsibility - humans exist on every continent and mechanise
  • Aesthetic reasons:
    • hospitals and schools have gardens, shown to improve mentality
    • regular wildlife treks, zoos, etc
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Importance of Biodiversity 2

Maintaining biodiversity is also important to agriculture:

  • Pollinators: Many fruit and vegetable crops are pollinated by insects such as bees and butterflies. The higher the diversity, the more pollinators
  • Source of Food: Many species are used as food sources for humans and livestock. More different species there are, the more possible sources there are to choose from
  • Pest Control: A number of animals like frogs, birds and gedgehogs are natural predators of crop pests like slugs. The more of these organisms, the less pests.
  • Protection against disasters: majority of our food comes from only a few species of plants. If a disease or pest affects these few, our food supply is at risk. E.g. in 1845 only two varieties of potato were planted in Ireland. A disease destroyed both types, causing famine. The more crop varieties that are used, the less chance there is that all crops will be destroyed. 
  • New Varieties: Plant varieties are needed for cross-breeding. Wild plants can be bred with domesticated plants to produce new varieties with improved characteristics, e.g. increased disease resistance or faster growth. New varieties of crops can also be bred to cope with climate change. The more varieties of crop there are, the more characteristics there are to choose from.
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  • In situ conservation keeps species in their natural habitats:
    • Establishing protected areas such as national parks and nature reserves - restricts urban development, industrial development and farming
    • Controlling or preventing introduction of species that threatens local biodiversity
    • Protecting habitats e.g. controlling water levels, allowing organisms to continue living in their natural habitat.
    • Restoring damaged areas, such as coastline polluted by an oil spill
    • Promoting particular species, by promoting food sources or nesting sites
    • Giving legal protection to endangered species e.g. law preventing hunting/trading
  • Ex situ conservation removes species from their natural habitat:
    • Relocating an organism to a safer area
    • Breed organisms within captivity then reintroduce them to wild when strong enough
    • Botanic gardens are controlled environments used to grow a variety of rare plants for the purposes of conservation, research, display and education. Reintroduced into habitat
    • Seed banks - seeds can be frozen and stored without losing their fertility. Seed banks provide useful source of seeds if natural reserves are destroyed, e.g. by disease or other natural disasters.
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Conservation 2

  • Advantages of in situ: both the species and habitats are preserved. Larger populations protected. Less disruptive that removing organisms completely. Chances of population recovering are greater than with ex situ methods. 
  • Disadvantages of in situ: difficult to control some factors that are threatening a species (poaching, predators, climate change)
  • Advantages of ex situ: controlled environment. Predation and hunting controlled more easily. Reintroduce species that have left an area. 
  • Disadvantages of ex situ: difficult and expensive to create and sustain the right environment. Usually less successful than in situ. Many cannot breed successfully in captivity. May not adapt to new environment when moved to new location.
  • Environmental Impact Assessments used to inform planning decisions
    • Estimating biodiversity on project site and evaluating how development might affect it
    • Identifying ways that biodiversity could be conserved
    • Identifying threatened or endangered species on project site snd laws relating to conservation
    • Deciding on planning stipulations - measures that will have to be implemented if project proceeds, e.g. relocating or protecting endangered species
  • International laws such as CITES agreement - designed to increase international cooperation in regulating trade in wild animals and plant specimens.
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  • Biological classification is the process of sorting living things into groups. Natural classification does this by grouping things according to how closely related they are. Natural classification reflects evolutionary relationships.
  • Taxonomy is the study of the principles of classification.
  • Phylogeny is the study of the evolutionary relationships between organisms. All have evolved from a common ancestor. More recent relative = more closely related
  • Monophyletic: belong to the same phylogenetic groups
  • Taxonomic hierarchy: Domain, Kingdom, Phylus, Class, Order, Family, Genus, Species
  • Autotrophic Nutrition: organism makes its own food from simple inorganic molecules
  • Heterotrophic Nutrition: gains nutrients from complex organic molecules 
  • Prokaryotae: e.g. bacteria: prokaryotic, unicellular, no nucleus, less than 5 micrometres, naked DNA chromosomes, no membrane-bound organelles, smaller ribosomes
  • Protoctista: e.g. algae: eukaryotic, mostly single-celled, wide variety of forms, plant and animal features, mostly free-living, autotrophic and heterotrophic nutrition
  • Fungi: eukaryotic, mycelium with hyphae, cell walls made of chitin, multinucleate
  • Plantae: eukaryotic, multicellular, cellulose cell wall, autotrophic nutrition
  • Animalia: eukaryotic, multicellular, heterotrophic nutrition, fertilised eggs, usually mobile
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Classification 2

  • Binomial Naming System: two names to identify each species: genus and species. Genus is capitalised. The name is writtenin italics.
  • Dichotomous key: series of qus with two alternative answers to help identify specimen
  • Early classification systems only used observable features:
    • Molecular evidence - similarities in proteins and DNA. More closely related organisms will have more similar molecules. Sequence of DNA bases, sequence of amino acids in proteins from different organisms. More similar = more related
    • Embryological evidence - similarities in early stages of organism's development
    • Anatomical evidence - similarities in structure and function of different body parts
    • Behavioural evidence - similarities in behaviour and social organisation of organisms
  • Three domains: Cells that contain a nucleus are placed in the domain Eukarya. Organisms that were in Prokaryotae are separated into to new kingdoms: Archaea and Bacteria.
    • New evidence, mainly molecular, reclassified as two domains showed large differences between Archaea and Bacteria.
    • Molecular = enzyme RNA polymerase is different in Archaea and Bacteria. 
    • Archaea have similar histones to Eukarya
    • Cell membrane evidence - bonds in B and A different. Composition of flagella different
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  • Variation is differences that exist between individuals. Even clones such as identical twins can show some variation.
  • Intraspecific variation: variation within a species, e.g. eye colour, hair colour
  • Interspecific variation: variation between different species, e.g. size
  • Variation can be continuous or discontinuous (distinct categories).
  • Variation can be caused by genetic factors, environmental factors or both.
    • Genetic factors: different species have different genes. Individuals of same species have same genes but different alleles. Genes make up genotype. Differences in genotype result in variation in phenotype (characteristic displayed by an organism), e.g. blood group, antibiotic resistance. Genes are inherited.
    • Environmental factors: differences in the environment can also cause variation. These characteristics can change over an organism's life, e.g. accents.
    • Both: Environmental factors can affect how some genetic characteristics develop, e.g. height can be affected by genes but also by nutrient availability and diet.
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  • Adaptations increases an organism's chances of survival, reproduction and chances of its offspring reproducing successfully. 
  • Adaptations develop due to evolution by natural selection.
  • In each generation, best-adapted individuals are more likely to survive and reproduce, passing their adaptations on their offspring. 
    • Behavioural adaptations: Organisms act that increase its chances of survival, e.g. possums 'play dead' to escape attack by a predator, scorpions dance before mating.
    • Physiological adaptations: processes inside an organism's body that increases chance of survival, e.g. brown bears hibernate and lower metabolism over winter to conserve energy, some bacteria produce antibiotics, killing other species, reducing competition.
    • Anatomical (structural) adaptations: structural features  that increases chances of survival, e.g. otters have streamlined shape and whales have thick layer of blubber.
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  • Organisms produce more offspring than survive.
  • There's variation in characteristics of memebers of same species.
  • Some of these characteristics can be passed on from one generation to the next.
  • Individuals that are best adapted to their environment are more likely to survive.

Theory of evolution by natural selection is based on these observations: 

  • Individuals within a population show variation in their phenotypes.
  • Predation, climate change, disease and competition act as selection pressures and create a struggle for survival.
  • Individuals with better adaptations (characteristics that give a selective advantage) are more likely to survive, reproduce and pass on their advantageous adaptations to their offspring.
  • Over time, number of individuals with advantageous adaptations increases.
  • Over generations this leads to evolution as the favourable adaptations become more common in the population.
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Evolution 2

Speciation is the formation of a new species. A species is defined as a group of similar organisms that can reproduce to produce fertile offspring.

Speciation occurs by reproductive barriers. This means that variation causes some organisms unable to breed. Variations are passed on, so if changes only occur in one part of the group only that part will benefit. The groups become so different they cannot interbreed. Reproductive barriers include: allopatric speciation (geographical) and sympatric speciation within the populationdue to a biochemical or physical change.

In some situations a group of individuals will evolve into another species if

  • a population migrates to a new environment
  • an environmental change effects only some of the popualiton
  • there is a reproductive barrier such as physically unable to mate due to size, mating patterns, hibernating patters, sleeping patterns, or biochemically unable to produce fertile offspring with wrong numbers of chromosomes.
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Evolution 3

  • Fossil record evidence: fossils are the remains of organisms preserved in rocks. By arranging fossils in chronological order, gradual changes in organisms can be observed that provide evidence for evolution.
  • DNA evidence: evolutio suggests that all organisms have evolved from shared common ancestors. Closely related species diverged (evolved) more recently. Evolution is caused by gradual changes in base sequence of DNA. Organisms that diverged away more recently have more similar DNA, as less time has passed for changes in DNA to occur.
  • Molecular evidence: similarities in other molecules also provide evidence. Sequence of amino acids in proteins, e.g. cytochrome c enzyme.

Populations of bacteria can evolve resistance to antibiotics. 

    • There is variation in a population of bacteria. Random genetic mutations make some bacteria naturally resistant to an antibiotic.
    • If population is exposed to antibiotic, only individuals with resistance will survive to reproduce. Antibiotic is selection pression.
    • Alleles which cause resistance is passed on to offspring. Over many generations, resistance is developed.
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