Molecules, Biodiversity, Food and Health

Biological Molecules
Proteins

Amino Acids
Structure Monomer of proteins Join to form backbone of polypeptide 20 types naturally occurring Differences caused by R-groups

Synthesis Plants: Convert nitrates into amino group and bond to organic part made from photosynthesis products Animals: Proteins broken down, 8 essential amino acids - cant be made from materials inside body - Can only store certain amount, amino group toxic if too many - Liver breaks amino acids down deamination urea Building proteins Reaction between carboxyl group and amino group Condensation reaction, bond broken by hydrolysis Forms peptide bond to make dipeptide Zwitterions Amino acid dissolves in water Carboxyl group disassociates and releases H+ Amino group receives H+ No net charge

Protein Structure
Primary structure Unique amino acid sequence of a polypeptide Secondary structure H-bonds form between amino acids Non-specific, polypeptides can take up same shape Alpha-helix H-bonds 4 along the chain Small parts of whole polypeptide can take up configuration Beta-pleated sheet Anti-parallel zigzagging chain Stronger and less elastic than Alpha-helix Tertiary structure 3D structure made in Golgi apparatus H-bonds, Ionic bonds, Disulphide bridges Globular proteins Irregular, compact shape Soluble hydrophilic outside, hydrophobic inside Fibrous proteins Long chains rich with hydrophobic amino acids Insoluble, unfolded, non-specific Quaternary structure How polypeptides link together (prosthetic group) Haemoglobin: 4 polypeptide chains and haem group

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Collagen

Structure 3 polypeptide chains wound around each other H-bonds between chains = strength Each collagen - strength Collagen fibril collagen fibre Function Arteries - collagen layer prevents bursting walls at high pressure Tendons mostly made of collagen Bones formed from collagen Cartilage and connective tissue made of collagen

Haemoglobin
Structure 4 polypeptide chains - 2 a-chains, 2 b-chains, 1 haem group Function Carries oxygen around the body Bonds to oxygen in lungs, releases in tissues Haem group contains Fe2+ - responsible for colour Haemoglobin + oxygen --> oxyhaemoglobin (purple-red) (bright red) One complete haemoglobin combines to four oxygen molecules

Monosaccharides

Carbohydrates

Structure General formula: CH2O - 3 carbon atoms = Triose - 4 carbon atoms = Tetrose - 5 carbon atoms = Pentose ribose - 6 carbon atoms = Hexose glucose, fructose Glucose can exist as two forms alpha and beta glucose

Disaccharides
2 monosaccharides joined together by condensation Monosaccharides broken by hydrolysis One monosaccharide loses H atom from C1 and other loses OH group from C4, creating a 1,4-glycosidic bond

Sucrose: glucose + fructose Used in plants to transport food reserves Lactose: glucose + galactose Sugar in the milk of mammals Maltose: glucose + glucose First product of starch digestion

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Polysaccharides

Polysaccharide Structure Starch Made of 2 polymers: Amylose: polymer of glucoses joined by a-1,4-glycosidic bonds. Forms helix with 6 molecules per turn & about 300 per helix

Function Storage in plants

Amylopectin: polymer of glucoses jonied by a-1, 4-glycosidic bonds but with branches of a-1,6-glycosidic bonds. Causes molecule to be branched

Glycogen

Similar to amylopectin but with many more branches which are shorter

Storage in animals and fungi

Cellulose

Adjacent chains of long, unbranched polymers of glucose joined with Structural 1,4-glycosidic bonds. The chains form hydrogen bonds with each other to constituent of form microfibrils which again pack together into macrofibrils plant cell walls

Lipids
Lipids: A diverse group of chemicals that dissolve in organic solvents but not water - includes fatty acids, triglycerides and cholesterol.

Roles of Lipids
Energy store Lipids stored in adipocytes Cell designed for continuous synthesis and breakdown of triacyglycerols Provide 9 kcal/gram Waterproofing The cuticle of plant leaves are protected against drying out by a lipid layer (waxy cuticle) , as lipids are hydrophobic - limits diffusion of water Allows release of volatiles (prevents pests, attracted pollinating insects) Insulation Mechanical support around soft organs Electrical insulation around long nerve cells E.g. Whale blubber is lipid that reduces heat loss & helps keep aquatic mammals buoyant Shock absorption Act as soft barrier to protect vital organs Prevent musculoskeletal system from easily breaking when hit

Molecules, Biodiversity, Food and Health Cell membranes All biological membranes are made of a phospholipid bilayer Phospholipids have a hydrophobic head and hydrophilic tail Partial permeability - substances don't move across the barrier indiscriminately Scents Most naturally occurring fats and oils are the fatty acid esters of glycerol Esters with a low molecular weight are used as fragrances and found in essential oils

Triglycerides
Structure 3 fatty acids attached to a glycerol molecule - Acids as they contain the carboxyl group -COOH General formula C3H8O3 Condensation reaction bonds the glycerol and fatty acids - Carboxyl group reacts with OH of glycerol - Forms ester bond

Phospholipid
Structure Like a triglyceride, but ne fatty acid is replaced by a phosphate group Phosphate heads are hydrophilic tiny ve charge - In water, phospholipid heads attracted to water and tails repelled, so they form a bilayer

Cholesterol and Steroids

Cholesterol and other substances that are formed from it are called steroids Huge number of different kind in the body testosterone and oestrogen Cholesterol helps regulate the fluidity of the membrane

Structure

Water

2 hydrogen atoms covalently bonded to one oxygen atom

Properties
High specific heat capacity Takes a lot of energy to raise the temperature of water Water temp fairly stable when air pressure changes rapidly High latent heat of evaporation A lot of energy needed to change water vapour Sweating, panting and transpiration effective cooling High density Maximum density at 4C expands upon freezing ice floats H-bonds form a lattice in ice crystals Water supports organisms with up thrust Cohesion Clingy water molecules rise up vascular tissue of plants in continuous column Surface tension pond skaters can walk on water Good solvent Water molecule polar other polar molecules attracted Transports substances in solution around body

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Carbohydrates

Tests

Starch Add solution of potassium iodide to sample If starch is present, the solution changes from yellowbrown blue-black

Reducing sugars Monosaccharide and disaccharide (molecule can react with other molecule by giving electrons to them When reducing sugar is heated to 80 with Benedicts solution, solution changes from blue orange-red Non-reducing sugars Sucrose would have no colour change Make sure there are no reducing sugars in sample boil with hydrochloric acid Hydrolyses any sucrose to glucose and fructose Cool solution and neutralise with sodium hydrogencarbonate Carry out Benedicts test again Should now give a positive result

Proteins
Buiret Test Add buiret reagent to a sample Buiret reagent reacts with peptide bonds - pale blue lilac

Lipids
Ethanol emulsion test Mix sample with ethanol dissolves any lipid Pour liquid into water Cloudy white emulsion near top of water

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Nucleic Acids

DNA

Polynucleotides

Structure Deoxyribonucleic acid - Phosphate group - Deoxyribose - Organic base Base can be a purine two rings - Adenine - Guanine Base can be a pyrimidine one ring - Cytosine - Thymine These components link together to form long chains called polynucleotides Two chains of nucleotide lie side by side in antiparallel - Link by hydrogen bonds - Forms a double-helix Role of DNA A gene is a sequence of DNA that codes for a polypeptide A sequence of 3 bases on the DNA molecule codes for one amino acid Thus, the gene determines the primary structure of a protein

Complimentary base pairing Key to the ability of DNA to hold and pass on the code for making proteins There is just the right amount of space for a purine to link with a pyrimidine A only links with T, C only links with G The code can be copied over perfectly from generations Instructs proteins to construct the exact molecule

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RNA

Structure Ribonucleic acid - Phosphate group - Ribose sugar - Organic base Single stranded Contains uracil instead of thymine RNA uses information from the DNA to make proteins - Determines the primary structure of a protein

DNA replication
Semi-conservative replication DNA replication takes place during Interphase Each of the new DNA molecules are made of one old strand and one new strand of DNA 1. 2. 3. 4. Hydrogen bonds between bases are broken by DNA helicase Free nucleotides (present in the nucleus) pair up with complimentary exposed bases New strand is linked together by covalent bonds between phosphate and sugars by DNA polymerase 2 new DNA molecules, each contains one old strand and one new strand

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Enzymes

Structure
Structure Globular proteins - Specific tertiary structure Biological catalysts

Enzyme action

Location Intracellular - Catalyse reaction in the cell - E.g. hydrolases inside lysosomes Extracellular - Released from cells onto food - Break down organisms into nutrients - E.g. amylase which hydrolyses starch to maltose

How enzymes work

Reducing the required activation energy for a reaction Enzymes contain active sites which have a specific shape - Fits with the substrate molecules shape Enzymes can bind reactants to each other - Increases reaction chance Enzymes can break substrates apart Enzymes can expose the substrates bonds or create a water-free zone so non-polar reactants can react more easily The enzyme is unchanged by the process

Enzyme-substrate complex The theory that an enzymes active site fits perfectly to the substrate - Held by temporary bonds between R-groups The combined structure is called the enzymesubstrate complex Each type of enzyme will usually only fit to one type of substrate Induced-fit hypothesis The theory that when the substrate fits into the active site, the shape of the enzyme changes slightly Allows hold of the substrate in exactly the right position

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Changing conditions
Effect of changing concentration
Enzyme concentration As enzyme concentration increases, more active sites become available - A maximum reaction rate will be reached when all the occupy active sites The substrate concentration becomes the limiting factor Substrate concentration As substrate concentration increases, collisions increase - A maximum reaction rate is reached when all the active sites are occupied - Called Vmax

substrate molecules

Effect of changing temperature

Higher temp More kinetic energy more collisions higher rate of reaction When they do collide, a higher proportion of them will have the required activation energy Usually 10 temperature rise = double collisions However, increased vibrations put a strain on bonds in enzyme - Enzymes progressively and irreversibly denatured Each enzyme has an optimum temperature - Close to body temperature in warm-blooded animals - Optimum temp depends on length of time its expected to work

Effect of changing pH
Acids have a low pH high percentage of H+ ions - H+ interferes with negatively charged amino acids in active sites - H+ can also replace H-bonds and ionic bonds in structures like the alpha-helix Optimum pH varies between enzymes - pH range is usually very small Collect gas in a gas syringe, measure how much collected over a period of time - E.g. break down of hydrogen peroxide to water and oxygen using catalase To investigate the rate that amylase breaks down starch to maltose, measure how much starch disappears by taking samples at know intervals and using the iodine test - Use a colorimeter to measure the intensity of the blue-black colour - Plot a graph The beginning curve is the initial rate of reaction, it is quite steep as the reaction is fastest at the beginning as more un-reacted reactants are available

Measuring reaction rate

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Enzyme inhibitors

Inhibitors

A substance that slows down or stops an enzyme-controlled reaction It is possible for other molecules to bind with the active site is it is similar to the substrate Creates competition for it and the substrate for the site Inhibitors that seriously disrupt controlled reactions act as metabolic poisons - Death cap mushroom toxin called alpha-amanitin inhibits enzymes that catalyse production of RNA, cells are no longer able to synthesise proteins

Competitive inhibitors When the concentration of the inhibitor rises or that of the substrate falls, it becomes more likely that the inhibitor will bind with the enzyme, rather that the substrate Reversible if the concentration of the substrate is increased Irreversible if the inhibitor bonds permanently to the active site - Penicillin permanently binds to the active site of an enzyme essential for the synthesis of bacterial cell walls Non-competitive inhibitors When the inhibitor binds to another part of the enzyme Can seriously disrupt the normal arrangement of the bonds holding the enzyme in shape Enzymes function blocked no matter how much substrate is present Reversible if the inhibitor bonds briefly Irreversible if the inhibitor bonds permanently - Digitalis binds with the enzyme ATPase, resulting in increased contraction of the heart muscle

Cofactors and coenzymes

Some enzymes require the presence of another substance Briefly bind with the enzyme, some alter its shape so it can bind more effectively with the substrate Cofactor Simple molecule of inorganic ion Many made from vitamins - Vitamin B3 is required for the synthesis of coenzyme A Cl- cofactor in salivary glands change shape so starch molecules can fit into the active site Ca2+ cofactor for enzyme thrombin changes soluble, globular protein fibrinogen to insoluble, fibrous protein fibrin Coenzyme Larger molecules Coenzyme A needed in many metabolic pathways, including aerobic respiration

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Diet and food production

Nutrition

Balanced diets

A balanced diet contains a range of all of the different nutrients in the right proportions Food sources Animals are heterotrophs - Rely on organic substance that have been made by plants Plants are autotrophs - Use inorganic substances to build organic substances Nutrient Carbohydrate Proteins Lipids Vitamin A Vitamin C Vitamin D Iron Sodium Function Provides energy New cells, and components e.g. haemoglobin, collagen Cell membranes, steroids, provide energy Pigment rhodopsin in rod cells in eye Collagen Bones and teeth Haemoglobin Bones and blood clotting Sources Bread, rice, potatoes Meat, eggs, fish, dairy Dairy, red meat, oils Meat, egg yolks, carrots Citrus fruits, blackcurrants, potatoes Dairy, oily fish, egg yolks Meat, beans, chocolate, eggs, shellfish Dairy, fish Notes Includes sugars and starches 20 amino acids, 8 essential amino acids 2 essential fatty acids

Also made in skin exposed to sunlight Shortage = anaemia Shortage = osteoporosis

Malnutrition The result of any diet that is unbalanced Obesity, kwakiorshor, anorexia nervosa, marasmus

Cholesterol
Evidence shows that having high cholesterol levels increases CHD risk, diet high in saturated fats increases cholesterol levels, other evidence doesnt support this view Cholesterol insoluble - Carried in the blood plasma in the form of lipoproteins - Tiny balls made of lipids, cholesterol and proteins Come in several varieties - Different proportions of proteins and lipids - The more protein, the greater the density of the lipoprotein

High density lipoproteins HDLs A lot of protein with small amounts of lipids Usually pick up cholesterol from dying body cells and transport it to the liver Low density lipoproteins - LDLs More lipids and less protein than HDLs Usually carry lipids and cholesterol from liver to other parts of the body Chylomicrons Contain a lot of lipid and very little protein Formed in the wall of the ileum from digested fats Transport lipids from small intestine to liver

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Obesity

When BMI is over 30 (BMI = kg/m2) Constantly eating nutrients that contain more energy than you use - Spare energy stored as fat in adipose tissue - underneath skin and around body organs Increases risk of developing heart disease and type II diabetes

Coronary Heart Disease CHD Common disorder of coronary arteries - most common cause of death Cardiac muscles must have a continuous supply of oxygen to contract CHD is caused by atherosclerosis (hardening) in the coronary arteries Become blocked - Build up of materials inside walls - Makes the lumen narrower - Increases blood pressure - Can happen in arteries brain stroke Can occur naturally with old age Can become worse with tobacco chemicals and LDLs - CO damages endothelium of arteries - Repaired by WBC that encourage smooth muscle growth & deposit lipids - Deposits known as atheromas / atheromatous plaque Angina occurs when the artery cant keep up with oxygen requirements Blood clots can form - Coronary thrombosis CO sticky platelets, increased chance of blood clots - Platelets in blood come in contact with collagen in artery wall - Platelets secrete chemicals that clot the blood, thrombus - Narrows artery and may block vessel, can lead to stroke - Muscle cells die myocardial infarction Arteriosclerosis is the hardening of artery walls Myocardial Infarction Myocardial = heart muscle, infarction = loss of blood flow to tissue 90% of myocardial infarctions caused by coronary thrombosis Severe causes heart to stop beating Cardiac arrest can be very severe or may not even realise it, described as crushing burning Cholesterol and CHD LDLs deposit cholesterol in the damaged walls or arteries - Makes up a large proportion of atheromatous plaque HDLs protect from CHD - Remove cholesterol from tissues Saturated fats result in more LDLs Not directly linked cholesterol in blood doesnt all come from food Statins (drug) inhibits the enzyme in the liver cells which catalyses one of the reactions involved in cholesterol synthesis Hypertension Persons resting blood pressure is persistently high Increases risk of CHD - Causes arterial walls to thicken and stiffen - Developed atheromatous plaques - Heart has to pump blood at higher pressures High salt content in blood can increase risk - High salt concentration in blood draws water in by osmosis - Increases volume of blood and thus increases pressure People with hypertension may be given diuretics - Cause kidneys to excrete large amounts of fluid, reduces volume in body, reduces blood pressure

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Plants

Improving food production

Done mostly by specialist plant breeders, not farmers Give selectively bred seeds to farmers to grow May be genetically modified

Improving efficiency Improve growth rate of crops Increase yield Reduce losses from disease and pests Standardising plant size to make harvesting easier Improve responses to fertilisers

Animals
Selectively bred by farmers in farms Improving efficiency Improve growth rate Increase productivity Increase disease resistance

Selective breeding
Breeding animals with desirable traits leads to those traits becoming exaggerated Artificial selection is the intentional breeding of certain traits Three stages: - Isolation - Artificial selection - Inbreeding/ Line breeding 1. Selecting the pair of animals/plants that display the desired characteristics 2. Allowed to reproduce 3. Offspring sorted into those with best combination of characteristics 4. Offspring reproduce E.g. Chickens bred for egg production or meat production. Egg-layers can produce over 300 a year, while meat-producers have low fat content and a better colour and texture Modern methods Marker-assisted selection Section of DNA is used as a marker to recognise characteristic Offsprings DNA is checked for the marker - Allows selection at a very early stage E.g. Tomatoes a wild tomato variety with good resistance to yellow leaf curl virus was found, the allele responsible for the resistance was identified and bred into a domestic variety

Using chemicals
Fertilisers Replace minerals in the soil Contain nitrate, potassium, and phosphate Increase growth rate and overall size of crop Pesticides Designed to kill organisms that cause diseases in crops Include fungicides Broad-spectrum insecticides kill all insects, not just pests specific are more expensive Antibiotics For infected animals Reduce the spread of disease around animals that are intensively farmed and close to each other

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Food spoilage

Microorganisms

Microorganisms obtain nutrition by digesting organic matter around them They leave behind waste products

How microorganisms spoil our food Visible growth of microorganisms on food - Mouldy bread (Penicillium mould is blue-green) Releasing enzymes onto the food and absorbing the nutrients external digestion process - Food smells sweet sugars released from carbohydrate molecules - Food eventually reduced to mush Producing toxins - Clostridium botulinum produces toxin botulin one of the most toxic substances known Cause infection - Salmonella bacteria attacks the lining of the digestive system

Preventing food spoilage

Using food quickly while still fresh Longer kept food must be treated to prevent spoilage - Killing microbes already on the food - Preventing them from reproducing Food must then be packaged to prevent further contamination

Treatment methods Cooking denatures proteins and kills microorganism Pasteurising heating to 72C for 15 seconds and cooling rapidly to 4C, killing harmful microbes Drying, slating, coating in sugar dehydrate microbes Smoking - develops dry hardened outer surface, smoke contains antibacterial chemicals Pickling uses acid pH to kill microorganisms by denaturing enzymes and other proteins Irradiation ionising radiation kills microorganisms by disrupting DNA structure Cooling and freezing retard enzyme activity so metabolism, growth and reproduction is slow Packaging methods Canning heated and sealed in air tight containers Vacuum wrapping air excluded so microbes cannot respire aerobically Plastic or paper packaging

Making food
Types of food made with microorganisms Yoghurt - Lactobacillus uses lactose sugar in milk to make lactic acid causes milk proteins to curdle Cheese - Made from curdled milk, acted upon by Lactobacillus, additional flavour by other bacteria Bread - Made to rise by yeast, respires anaerobically to release CO2, bubbles of gas collect in dough Alcohol - Another product of anaerobic respiration of yeast, cereal grains with maltose can be used to brew beer, as the yeast respires the sugar - Yeast respires fructose and glucose in grapes Quorn Single-cell protein, mycoprotein made by fungus, vegetarian, healthy, cholesterol-free Advantages Fast protein production Production increased and decreased on demand No animal welfare issues Source of protein for vegetarians No animal fat or cholesterol Combined with removal of waste products Disadvantages Many dont want to eat fungal protein Microorganisms need to be grown in huge fermenters Must be purified Care to prevent infection Not as tasty as traditional protein sources

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Health and Disease

Parasites and pathogens

Getting infected
Health: A state of complete physical, mental & social well being and not merely the absence of disease of infirmity. Disease: A departure from good health caused by a malfunction of the mind of body Pathogen An organism that causes disease Live by taking nutrients from their host but damage it in the process Parasite An organism that lives in or on another living things, causing harm to the host Usually cause harm by taking nutrition from the host External parasite: Live on the host - Head lice Internal parasite: Live in the host - Tapeworm Most can go unnoticed for a long time before they cause considerable damage - Can cause damage that allows other organisms to invade the host and cause secondary infections Transmission of disease A pathogen must be able to - Travel between hosts - Get into tissues - Reproduce - Cause damage to tissues Most common form of transmission - Means of a vector - Physical contact - Droplet infection

Malaria
Transmission Cause by eukaryote Plasmodium Spread by vector - Female Anopheles mosquito Mosquito feeds on blood Plasmodium live in red blood cells and feed on haemoglobin 1. The mosquito will suck the parasite gametes into its stomach 2. Zygotes form in the mosquitos stomach 3. Infective stages move to the mosquitos salivary glands 4. Mosquito injects saliva into another person as an anticoagulant 5. Infective stages enter liver, multiply and enter blood again 6. Enter red blood cells, where gametes are formed Global impact Kills 3 million a year, 300 million infected 90% of sufferers live in sub-Saharan Africa

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HIV/AIDS

Transmission The Human Immunodeficiency Virus enters the body and remains inactive - HIV positive When the virus becomes active it destroys T-lymphocytes - T helper cells prevent infection - Ability to resist infection is reduced Subject will catch a range of opportunistic infections Acquired Immune Deficiency Syndrome Transmitted via: - Exchange of bodily fluids (not saliva) - Unsterilized surgical equipment - Unprotected sex - Across the placenta - During childbirth - During breast feeding Global impact Pandemic Half of sufferers in sub-Saharan Africa 2005 45 million people living with HIV/AIDS

Tuberculosis
Transmission Mycobacterium tuberculosis Mycobacterium bovis Usually found in lungs - Its inactive in many people or controlled by their immune system Droplet infection - Contained in tiny droplets of liquid released when an infected person coughs, sneezes, talks - Takes very close contact with an infected person to contract the disease Contraction more likely in - Overcrowding - Poor ventilation - Poor health - Poor diet - Homelessness - Living or working with infected people Global impact WHO declared TB to be a public health emergency in 1993 Most common in South-east Asia and sub-Saharan Africa Increasing threat of new strains of Mycobacterium being resistance to most of the drugs available

WHO
Health organisations use epidemiology to study the spread of disease They identify risk factors, incidence, prevalence, mortality, morbidity Endemic regularly found among particular people in a certain area, epidemic spreading rapidly over a large area, pandemic worldwide epidemic They educate, raise awareness, screen people, provide health centres, provide vaccinations, target research for cures

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Defence
Immune response
Immune response: A specific response to a pathogen which involves the action of lymphocytes

Primary defences
Skin Pathogens need to enter the body of the host The primary defences are those that prevent pathogens entering the body

Epidermis consists of layers of cells, mostly called keratinocytes Cells reproduce at base of epidermis, then migrate to surface - Cytoplasm dries out and is replaced by keratin keratinisation - Keratinised layer of dead cells acts as a barrier to pathogens

Mucous membranes Potential for infection high where air and food enters airways, lungs, digestive system Protected by epithelial layer containing goblet cells that secrete mucus Mucus lines passages and traps pathogens Ciliated cells waft layer of mucus to top of trachea where it is swallowed - Most pathogens killed by acidity of the stomach, as the pathogens enzymes are denatured Mucous membranes found in gut, genitalia, anus, ears and nose Other primary defences Eyes protected by antibodies in tears Ear canal lined by wax, traps pathogens Vagina is protected by acidic conditions

Secondary defences
Many trapped pathogens are not killed by conditions in the body Phagocytes kill the pathogens before they reproduce and cause symptoms

Neutrophils Most common Multi-lobed nucleus Made in bone marrow Squeeze out of capillaries in tissue fluid Short lived, released in large numbers as a result of infection Macrophages Larger cells manufactured in bone marrow Travel in blood as monocytes Settle in body organs, particularly lymph nodes - Develop into macrophages Specific response to invading pathogens Long-lived Antigen-presenting cells - Break particles up into their component molecules and place some molecules in their plasma membrane

Molecules, Biodiversity, Food and Health How phagocytes work Engulf and destroy pathogens 1. Pathogen recognised by chemical markers on its outer membrane Markers are antigens Specific to the organism 2. Proteins in the blood called antibodies attach to foreign antigens 3. Phagocytes have membrane-bound proteins that act as receptors Binds to antibody already attached to pathogen Process may be assisted by other organisms called opsonins 4. Phagocytes envelop pathogen by folding in its membrane Pathogen trapped inside vacuole called phagosome Lysosomes fuse with phagosome and release enzymes called lysins digest bacterium Ends up as harmless nutrients that can be absorbed by the cytoplasm 5. Neutrophils die after digesting a few pathogens and may collect in an area to form pus Role of macrophages Initiate the specific response to disease immune response - Activation of lymphocytes Infected cells release histamines attract neutrophils - Histamine also makes capillaries more leaky - More fluid leaves the capillary in infected area swelling and redness More tissue fluid passes into lymphatic system Pathogens towards macrophages waiting in lymph nodes

Antibodies
Antigen A molecule that stimulates an immune response Any molecule can act as an antigen Detected by immune system, stimulates production of antibodies specific to the antigen and pathogen Antibody A protein that can identify and neutralise antigens (aka immunoglobulin) Produced by lymphocytes in response to infection Specific to antigen Attach to antigens and render them harmless Structure 4 polypeptide chains held together by disulphide bridges Constant region enables antibodies to attach to phagocytic cells Variable region has specific shape that ensures antibody attaches to correct antigen Hinge region allows flexibility and branches to move apart for attachment to more than one antigen How they work Attaching to antigens on pathogen When the antibody blocks the binding site, the pathogen cant bind to its host cells neutralisation Each variable region can act as a binding site to bind antigen to pathogen - Can attach to a number of pathogens at the same time agglutination When the pathogens are stuck together they cannot enter host cells Producing antibodies When an infecting agent is detected, the immune system produces antibodies May take a few days for numbers to rise enough to combat the infection successfully primary immune response If the body is infected a second time, the immune system can act more quickly secondary immune response

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Lymphocytes

Small white blood cells B-lymphocytes - Form in bone marrow T-lymphocytes - Develop in thymus gland during childhood - Gland in neck, disappears in teen years Stimulated to act when in contact with antigens Each lymphocyte is specific to one antigen Produce antibodies

Cell signalling Achieved through cell surface molecules and through release of cytokines Target cell has receptor B lymphocytes and T lymphocytes have receptors that are complimentary to the antigen - Detection = lymphocyte activated 1. Identification Pathogen carries antigens on its cell surface Act as markers that say it is foreign Detected by body cells 2. Distress signals Internal cell organelles e.g. Lysosomes will attempt to fight invader Parts of pathogen cell damaged End up attached to plasma membrane - Act as signals that can be detected by immune system - Act as markers to indicate host cell is infected T killer lymphocytes destroy infected cell 3. Antigens Macrophages in lymph nodes engulf and digest pathogen Separate out antigens and incorporate them into the cell surface membrane Antigen presenting cell Finds lymphocytes that can neutralise that antigen 4. Instructions Cytokines released by cells - Act as instructions to target cells by binding to specific receptors on target cell Cause release of messengers inside cell which alter its behaviour through gene expression Macrophages release monokines that attract neutrophils - Movement by chemotaxis (movement of cells towards a chemical) Macrophages release monokines to stimulate B cells to differentiate and release antibodies T and B cells release interleukins that stimulate proliferation and differentiation of T and B cells Many cells release interferon which inhibits virus replication and stimulates activity of T killer cells

Memory cells: cells that circulate the blood after a specific immune response. They speed up the response to a subsequent attack by the same pathogen.

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How lymphocytes respond to antigens

B lymphocytes T lymphocytes

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Immunity
Vaccinations
Vaccination: A deliberate exposure to antigenic material, which activates the immune system to make an immune response and provide immunity. Controlling disease A person that is vaccinated will have artificial active immunity - Deliberate exposure to antigenic material rendered harmless Immune system treats the antigenic material ad a real disease Immune system manufactures antibodies and memory cells that provide long-term immunity Herd vaccination Using a vaccine to provide immunity to almost all of the population at risk If enough people are immune, the disease can not spread To eradicate smallpox, 80-85% of the population had to be vaccinated UK, vaccination programme to immunise children of many diseases - TB, diphtheria, tetanus, whooping cough, polio, meningitis, measles, mumps, rubella Ring vaccination Used when a new case of disease is reported Involves vaccinating all the people in the immediate vicinity of the new case Such as vaccinating people in the surrounding houses, or a whole town or village Used to control the spread of livestock disease Type of vaccines Whole, live organisms - Not as harmful as real disease, but with similar antigens - Smallpox vaccine Harmless version of pathogenic organism - Measles and TB vaccine Dead pathogen - Typhoid and cholera vaccines Preparation of the antigens from the pathogen - Hepatitis B vaccine Harmless toxin called a toxoid - Tetanus vaccine Immunity Active immunity: Immunity achieved through activation of the immune system. Lymphocytes in body manufacture antibodies and release them from the blood - may last for many years or even lifetime. Passive immunity: Provided by antibodies that havent been manufactured by stimulating immune system, provided by mother across placenta or breast feeding or intravenous injection, short-lived. Natural immunity: Gained through normal living, result of infection that stimulates immune response Artificial immunity: Gained by deliberate exposure to antibodies of antigens

Possible threats

Many pathogens can mutate and form new strains resistant to drugs and vaccines Influenza Virus that affects the respiratory system People over 65 and with a respiratory tract infection are most at risk Immunisation programme for all those over 65 New strains are used each year, and research determines which strains are most likely to spread

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Finding new drugs

Need for new drugs New diseases are emerging Some diseases have no treatment Diseases mutate and evolve which makes antibiotics ineffective, as the new drugs gives the microorganism a selection pressure, so strains of microorganism that are resistant of less susceptible to the drug will survive and reproduce, so the next generate will be resistant Discovery Accidentally, e.g. Alexander Flemings discovery of penicillin Traditional medicines such as plants - 80% of the world relies on traditional medicine Anaesthetics - Opium, to chloroform Wildlife observation - Monkeys and bears rub citrus oils on their coat as antiseptics - Chimpanzees swallow leaves folded in a way to remove parasites from their digestive tract - Elephants use clay to counteract dietary toxins - Birds line their nest with medicinal leaves to protect chicks from blood sucking mites Modern research Antibiotics developed over the last 50 years come from Streptomyces - Pharmaceutical companies make us of receptors, as if it can be blocked then the pathogen cannot gain access to the cell - Genomic by sequencing the genes of microorganisms, we should find a range of candidates from which vaccines can be made

Smoking
Effects
Short term Tar settles in the lining of the airways and alveoli - Increases diffusion distance for gas exchange Chemicals in the tar may cause an allergic reaction - Smooth muscles contract, lumen narrows, flow or air restricted to alveoli Tar paralyses and destroys cilia - Unable to move mucus up the trachea - Stimulates more mucus to form - Trapped bacteria is not removed, so they multiply and block bronchioles - Lungs more susceptible to infection Long term Smokers cough - Attempt to shift bacterial mucus - Delicate lining of airways becomes damaged, and will be replaced by scar tissue thicker and less flexible - Smooth muscle thickens reduces lumen, flow of air permanently restricted Frequent infections will inflame lining of airways and attracts white blood cells - White blood cells release enzymes that digest part of the lining in order to pass through into the air spaces of the lungs - Enzyme elastase is used, that breaks down the elastic tissue in the lining of the lungs - Reduce elasticity of the alveoli - Exhaling alveolus walls do not recoil enough to push the air out, the bronchioles collapse, trapping air in the alveoli - Alveoli may burst as pressure in lungs increases

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Diseases

Bronchitis Inflammation of the lining of the airways Damage to cilia and overproduction of mucus Mucus collects in the lungs, which causes irritation, continual coughing up mucus filled with bacteria and white blood cells Increased risk of lung infection Emphysema Loss of elasticity in the alveoli, causing them to burst Lungs have reduced surface area for gas exchange Shortness of breath, harder to exhale, breathing will be shallow and rapid Blood less well oxygenated with causes fatigue Chronic obstructive pulmonary disease COPD Combination of diseases that includes chronic bronchitis, emphysema and asthma Lung cancer Cigarette smoke contains carcinogens in the tar such as benzopyrene Carcinogens enter nucleus of the cells of the lung tissue and cause a mutation, which may cause uncontrolled cell division Continual coughing and shortness of breath Pain in chest and blood coughed up in sputum

Nicotine and carbon monoxide

Increase the risk of: - Atherosclerosis - Coronary heart disease - Stroke

Nicotine Chemical in smoke that causes addiction Body becomes used to the affects over time and smoker no longer feels wells without nicotine Mimics the actions of transmitters in the nerve synapses - Makes nervous system more sensitive, smoker feels more alert Causes release of adrenaline - Increases heart and breathing rate - Causes constriction of arterioles raises blood pressure - Decreases blood flow to extremities Makes platelets more sticky - Increases risk of blood clot or thrombus Carbon monoxide Enters red blood cells, combines with haemoglobin more readily that oxygen carboxyhaemoglobin - Reduces oxygen concentration in the blood Damages the lining of arteries Risk factor Changes in body leads to serious diseases such as the multifactoral coronary heart disease Increases chance of blood clots because of sticky platelets People in less economically developed countries will be less at risk of developing CHD - Eat less fatty foods, less likely to be obese - Less likely to smoke - Shorter life expectancy, wont live long enough to develop CHD - More likely to die from other diseases such as malaria, HIV/AIDS and tuberculosis Epidemiology: study of the distribution of a disease in populations, and the factors that influence the spread

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Biodiversity

Habitats and species

Definitions
Species: A group of individual organisms very similar in appearance, anatomy, physiology, biochemistry and genetics, whose members are able to interbreed freely to produce fertile offspring Habitat: The place where organisms lives, with a specific set of conditions that those organisms are adapted to live in Biodiversity: The variety of life, the range of living organisms to be found. Biodiversity may be considered at different levels The range of habitats in which different species live The difference between species; structural and functional Genetic variation between individuals in the same species

Sampling
Plants
Random sampling To measure the biodiversity of a habitat - observe all species, identify and count Too many to count, select small portion and study carefully, multiply to estimate whole habitat - Take samples at regular distances - Use random coordinates generated by a computer, use GPS The number of samples depends on the time you have and the size of the habitat Record results on a table Measures Use quadrat to define the size of the sample area Hard to count small herbs and grasses, so measure percentage ground cover - Plants that you see but arent found in random sample recorded as present with no abundance - Measure percentage using a point frame, frame holding a number of long needles or pointers ACFOR abundance scale: Abundant, common, frequent, obvious, rare Can use a transect line long rope, take samples along line in habitat

Animals
Animals move, so you need to catch the small animals and estimate numbers Sweep netting Walking through a habitat with a net, sweeping through vegetation in wide arcs Empty the contents on a white sheet to identify them Collecting from trees Spread a white sheet under the branch and knock the branch Dislodged animals drop onto the sheet, count them before they fly away Pitfall trap Small container buried in soil to rim is just below surface Animals moving through the plants will fall into the container, with little water or paper to stop them crawling out Tullgren funnel Place leaf litter in a funnel, light above litter drives animals downwards as litter dries out Fall through mesh screen to be collected in jar underneath Light trap To collect flying insects at night Ultraviolet light attracts insects, under light is collecting vessel containing alcohol Moths and insects attracted to light and fall into alcohol

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Measures of biodiversity
Species richness and evenness
Species richness Number of species present in a habitat Make observations within habitat and record all different species you see Not a measure of diversity Species evenness A measure of the relative abundance of individuals of a species Habitat with even numbers is more diverse than when one species outnumber all the others Plants: use the sampling technique, then measure percentage cover Animals: mark and recapture technique - Number captured first x number captured second time / number recaptured

Simpsons Index of Diversity

Measure of diversity in a habitat Takes into account species richness and evenness

D = 1 [(n/N)2]
n is the total number of a particular species N is the total number of all individuals of all species High value indicates diverse habitat - Place for many different species and organisms - Small change to the environment may affect a species - Total number of individuals affected is a small proportion so the effect is small on the whole habitat Low value = habitat dominated by a few species - Habitat dominated by a few species - Small change to environment affects one of those species could destroy whole habitat

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Classification

Definitions

Types of classification

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, reflecting evolutionary relationships Taxonomy Taxonomy: the study of the principles of classification The study of differences between species Species usually grouped by physical similarities Modern classification has come to reflect the evolutionary distance between species - Any two species will have a common ancestor at some point - The more recent to common ancestor, the more closely related the two species Phylogeny Phylogeny: The study of the evolutionary relationships between organisms The study of how closely different species are related Humans and gorillas are monophyletic they belong to the same phylogenetic group as they have a common ancestor, thus they can be placed in the same taxonomic group The thrush is more closely related to snakes than mammals as they have a common ancestor, thus the thrush must be placed in a different group from mammals

The Five Kingdoms

Kingdoms

Prokaryotes No nucleus looped and naked DNA - evolved before nucleus became the place for DNA Smaller ribosomes Respiration from mesosomes Protoctists Include all organisms that dont fit into the other four kingdoms Many are single-celled, some are Multicellular Eukaryotes Mostly free living Autotrophic or heterotrophic Fungi Plants Organisms that are mostly saprophytic (cause decay of organic matter) They consist of mycelium Walls made from chitin Network of numerous strands called hyphae Has several nuclei Multicellular Autotrophic Surrounded by cell wall made of cellulose Multicellular embryos from fertilised eggs

Animals Multicellular Heterotrophic Fertilised eggs that develop into a blastula

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How organisms are classified

System of Classification
The binomial system Two names are used to identify each species - Genus and species Typed as Genus species Handwritten as Genus species Latin names, common for every country Dichotomous key Way of identifying and naming a specimen you found Each question has yes or no, leading to another question and eventually leads you to the name of the specimen Helps to identify what species are present when doing an Environmental Impact Assessment - As it is illegal to cause some animals harm or death if they are endangered

Modern classification
Early classification Based on observable features - No microscopes More information from electron microscopes help classify Aristotle classified things as plants or animals Animal kingdom and plant kingdom had single-celled organisms that had features of animals and plants Recent classification We now use physiology and biochemistry to help classification systems DNA can be used to classify The more similar the sequence, the more closely related the two species Three domains 1990, Carl Woese suggested a new classification system based on a detailed study of DNA Bacteria - Different cell membrane structure - Different enzymes - Flagella with internal structure - No proteins bound to genetic material Archeae - Similar mechanisms to Eukaryotae: - Similar enzymes - Building RNA Eukaryotae

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Evolution
Variation

Types of variation

Intraspecific variation: differences between individuals within a species Discontinuous variation Discontinuous variation: variation in which each organism belongs to one of a few clearly defined groups e.g A persons blood group Almost always caused by genes with no environmental input Continuous variation Continuous variation: variation in which there is a continuous range of values between two extremes e.g. human skin colour, eye colour, leaf length May be caused by genes or the environment - Eye colour caused by genes with hundreds of possible combinations of alleles - Skin colour caused partly by genes, partly by the environment - Leaf length caused entirely by environment

Causes of variation
Genetic variation Different varieties of a gene for a particular characteristic are called alleles In sexually reproducing organisms, alleles shuffle when a new organism is produced - Caused by gamete formation, when meiosis mixes up chromosomes - When fertilisation occurs, an infinite number of possible combinations of alleles can be forms when a sperm fuses with an egg Also possible for new alleles to be produced occasionally by a mutation - When a mistake is made as DNA is replicated - A nucleotide may be missed out, or an extra one slipped it Environmental variation Two people with the same combinations of alleles may end up differently because of their environment - People with naturally fair skin may have different colours because of sunbathing - Alleles that allow people to grow tall may not have the same effect because of different environments - Plants with identical genes may differ as one may grow in the shade, or with different nutrients Arise during an individuals lifetime Cannot be inherited

Types of adaptations

Adaptations

Adaptation: a variation that helps an organism to survive Behavioural adaptations An aspect of an organisms behaviour that helps it to survive in the conditions it lives in E.g. touching an earthworm makes it contract, earthworms have no eyes Physiological adaptations

One that ensures the correct functioning of cell processes E.g. yeast can respire sugars anaerobically or aerobically, depending on oxygen level

Anatomical adaptations A structural variation that enhances the survival of the organism

E.g. Legionellla bacteria have flagella so they can move independently

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Theory of natural selection

Charles Darwin

1856, Charles Darwin (and independently, Alfred Russel Wallace) put forward a new theory - Darwin perhaps more known because he developed the ideas more and wrote On the Origin of Species - He developed logical theories about how and why different areas of biology happened

The four observations All organisms over-reproduce Populations tend to remain fairly constant over long time periods Organisms within a species vary Some of the variations are inherited The three deductions Theres competition for survival Individuals with the best adapted characteristics for their environment are more likely to survive and reproduce If the characteristics can be inherited, the organisms will pass the characteristic to their offspring The characteristics of a species would gradually change, as better adapted individuals are more likely to survive and pass characteristics on. Species would become better and better adapted to their environment.

Selection pressures
Selection pressure: an environmental factor that decreases or increases the chance of survival of organisms with particular variations Results in natural selection If an individual has beneficial characteristics, it will be selected to survive and pass on its characteristics Examples of selection pressures: - Availability of suitable food selected organisms will be able to eat the available food - Predators selected organisms can avoid being seen and eaten, or can escape - Diseases - selected organisms will survive a disease - Physical and chemical factors selected organisms will be able to grow in extreme conditions

New species

Speciation

Speciation: the production of a new species A species is a group of organisms that can interbreed to produce fertile offspring To produce a new species, a group needs to be produced that can no longer breed with the original species - The population must become reproductively isolated Speciation is difficult to study as it takes a long time to happen, but we can look at patterns that tell us what may have happened in the past Allopatric speciation Two populations of the same species may become separated by a geographical barrier, such as water or mountains The environments that they live in are different, so they will have different selection pressures - Different adaptations will occur - Eventually, the differences may become so great that the populations can no longer interbreed Sympatric isolation No geographical isolation Possibly a reproductive barrier within the population, from a biochemical change; behavioural change e.g. a courtship dance being unrecognisable; physical change, sexual organs incompatible

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Fossils

Evidence for evolution

Fossils are the preserved remains of organisms that lived and died long ago - Many form from hard part of organisms e.g. bone and shells, become mineralised - Soft parts can also become fossils, as well as droppings and worm burrows Tiny proportion of organisms fossilise Enough fossils of some organisms give us an idea of how they evolved

Horse fossils Many, dating 55 million years ago to almost present Organised according to age shows changes sequence From the type of rocks found, can deduce environment that the species lived, and trace the changes - Early species, toes lived in swamps - Modern horses single toes can run fast Changes - natural selection favoured characteristic over another Environment changed, the selection pressures caused different selected characteristic - succession of different species We cant say this evolved into that, only that they are related

Molecular evidence
Look at molecular structure of genes, not features they produce - fundamental evidence for evolution Some ancient bones are in such good condition that DNA can be extracted E.g. DNA in mitochondria in bones of woolly mammoths found similar to elephant mitochondrial DNA Common ancestor about 6 million years ago

Eye gene DNA analysis can sometimes give unexpected results - Animals eyes have structural differences - assumed separate evolution - Insect eyes evolved in line leading to insects, while vertebrate eyes evolved in line leading to vertebrates E.g. the gene ey from a fruit fly was found to have similarities to the gene Pax6 in vertebrates. - Ey is a gene that controls the development of the fruit flys compound eye - Pax-6 is a gene that turns on other genes that cause an eye to develop - Researchers injected Pax-6 into a cell in a larval fruit fly that would develop into the wing - The wing grew a compound eye Seems as there is a common origin of eyes in all animals, despite different looks

Antibiotic resistance

Resistance

Antibiotic: a substance that kills bacteria without harming animal cells Example of natural selection - We change the selection pressures by changing the bacteriums environment Bacteria become resistant to antibiotics by adapting to produce enzymes that inactivate the antibiotic - Tremendous selective advantage, as those not resistant are killed - Bacteria reproduce very quickly producing huge numbers of resistant descendants - Bacteria can also transfer resistant plasmids from different species E.g. MRSA Methicillin-resistant staphylococcus aureus, is very harmful to those with weak immune systems

Insecticide resistance
Natural selection led to development of insects resistant to insecticides Almost 20% of insecticides used are aimed at getting rid of insects that damage cotton plants - Species of moth caterpillar that damage plant have become resistant to many insecticides - Led to use of toxic chemicals that also kill harmless or beneficial organisms

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Maintaining Biodiversity

Humans affect nature

Conservation of species

We use the environment to our advantage We have grown in numbers We are using more and more of the Earths resources Loss of biodiversity and extinction many occur We hunt for food and over harvest We kill for protection We cause pollution We destroy habitats

Extinction: When the last living member of a species dies and the species ceases to exist Loss of biodiversity Extinction reduces biodiversity Humans have cleared huge amounts of vegetation to make food Replace with a crop of low diversity a monoculture

Why we should conserve species

Economic reasons Evolution has provided us with answers to many technological problems Provide medicines and furniture Grown timber, food and fuel Ecological reasons Rainforests regulate the atmosphere Purify fresh water Form and fertilise soil Recycle nutrients Pollinate crops Ethical reasons All organisms have a right to survive and live in the way that they have adapted to Human groups still live in natural habitats Aesthetic reasons We experience joy and wellbeing when we observe the infinite variations of nature Patients recover more rapidly from stress and injury when they are exposed to pleasing natural environments

Importance of genetic diversity

It is important to maintain the diversity of wild plants and animals because of the potential that exists in the wide range of species currently alive Without genetic diversity, species will be unable to adapt to changes in the environment A higher proportion of species will get a new disease A reduction in variation because of human activity reduced the gene pool and hinders a species ability to evolve Wild animals and plants may hold the answers to problems caused by climate change as they have adapted to these problems We would be able to breed new varieties that can cope with conditions Genetic engineering can produce transgenic organisms New medicines can be found in wild plants Range of possible vaccines

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Climate change
Movement of species
Species with little genetic variation will be less able to evolve when there are changes in temperature Only alternative would be for a species to move Slow migration of populations, communities and whole ecosystems towards the poles Migration obstructed by developments, agricultural land, water and humans

Effect of agriculture Domesticated plants and animals are at potential risk of extinction if the climate changes as they have been selectively bred to provide the best yield - We have developed crops and animals with little variation - These species will be unable to evolve Effect of diseases Crops grown in new areas will not be resistant to new diseases and pests Higher temperatures will provide a longer growing season but pests will have more time to increase in numbers More diseases and pests will be able to cause greater infestation the next year after the winter as they are able to survive - Less yields for humans Human diseases will migrate to new areas, such as malaria being able to move to hotter areas as the world heats up

Types of conservation
In situ
Conserving a species in its normal environment Conservation parks Possible to stop unacceptable activities by establishing areas specially for conservation of a species In the UK, we have - 14 National Parks - National Nature Reserves - Sites of Special Scientific Interest - Local Nature Reserves Advantages Permanently protects biodiversity and ecosystems Protects natural and cultural heritage Opportunity for ecological sustainable land uses Facilitates scientific research Maintains ecological integrity Disadvantages Protected animals raid local crops People continue to hunt Illegal harvesting of timber and other plants Tourists feed protected animals

Repopulation Possible to rebuild lost biodiversity if crops and animals are reintroduced to their habitats Large areas for grazing are being helped to turn back into traditional meadows

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Ex situ
Conserving an endangered species by activities that take place outside its normal environment Zoos

Many now prefer to be known as wildlife parks Concentrate on breeding endangered species Enable repopulation into the wild Advantages Sperm freezing, artificial insemination used to reproduce Reproductive physiology specific Research on domestic species helps the whole population Saves rare individuals from experiments Disadvantages Many fail to successfully breed Decrease genetic diversity Species less able to adapt Species have to survive reintroduction to the wild Difficulties with accepting wild members

Seed banks Many botanical gardens e.g. Kew Gardens Collection of seed samples Seeds stored in dry and freezing conditions Seeds tested at regular intervals to see if they can germinate - Seeds planted in petri dishes of nutrient agar in controlled conditions - Germination rate measures - Enabled scientists to monitor the condition of the seeds Advantages Seeds can be collected without harm to the ecosystem Seeds are a natural part of a plants life cycle Can be stored in huge numbers without taking up too much space Plants can often breed asexually Provides large sample for research Can be easily replanted Can remain viable for decades Disadvantages Collection of wild seeds may cause some disturbance Collected samples may not be representative of genetic diversity Seeds may not be viable after a very long time Plants breed asexually so offspring will be genetically identical Conclusions reached from research may not be valid for whole species

International problem

International cooperation

CITES Convention on International Trade of Endangered Species 1973 to ensure international trade of wildlife does not threaten their survival Regulates and monitors international trade Trade in wild plants is prohibited for commercial purposes Less endangered species allowed to be traded Hard to enforce Convention on Biological Diversity Promotes sustainable development for our need of food, medicines, shelter and a healthy environment Encourages cooperation between countries and states to share genetic resources and technologies EIA Environmental Impact Assessment Procedure to assess the likely effects that a proposed development may have on the environment Provide improvements in the planning and design of development, so it is more environmentally acceptable