Grade 12 Biology Textbook PDF

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Biology Biology Biology Student Textbook Student Textbook Student Textbook Grade 12 Grade 12 Grade 12 Federal Democratic Republic of Ethiopia ISBN 978-99944-2-014-8 Federal Democratic Republic of Ethiopia FDRE Ministry of Education Price: ETB 36.00 MoE Ministry of Education  Biology Student Textbook Grade 12 Author: Steve Potter Adviser: Alemu Asfaw Evaluators: Solomon Belayneh Getachew Bogale Silas Araya Federal Democratic Republic of Ethiopia Ministry of Education Acknowledgments The development, printing and distribution of this student textbook has been funded through the General Education Quality Improvement Project (GEQIP), which aims to improve the quality of education for Grades 1–12 students in government schools throughout Ethiopia. The Federal Democratic Republic of Ethiopia received funding for GEQIP through credit/financing from the International Development Associations (IDA), the Fast Track Initiative Catalytic Fund (FTI CF) and other development partners – Finland, Italian Development Cooperation, the Netherlands and UK aid from the Department for International Development (DFID). MOE/GEQIP/IDA/ICB/001/09 The Ministry of Education wishes to thank the many individuals, groups and other bodies involved – directly and indirectly – in publishing the textbook and accompanying teacher guide. 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Cover images: Front: Alamy Images: bc; iStockphoto; Science Photo Library Ltd All other images © Pearson Education Every effort has been made to trace the copyright holders and we apologise in advance for any unintentional omissions. We would be pleased to insert the appropriate acknowledgement in any subsequent edition of this publication. © Federal Democratic Republic of Ethiopia, Ministry of Education First edition, 2002 (E.C.) ISBN: 978-99944-2-014-8 Developed, Printed and distributed for the Federal Democratic Republic of Ethiopia, Ministry of Education by: Pearson Education Limited Edinburgh Gate Harlow Essex CM20 2JE England In collaboration with Shama Books P.O. Box 15 Addis Ababa Ethiopia All rights reserved; no part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise without the prior written permission of the copyright owner or a licence permitting restricted copying in Ethiopia by the Federal Democratic Republic of Ethiopia, Federal Negarit Gazeta, Proclamation No. 410/2004 Copyright and Neighboring Rights Protection Proclamation, 10th year, No. 55, Addis Ababa, 19 July 2004. Disclaimer Every effort has been made to trace the copyright owners of material used in this document. We apologise in advance for any unintentional omissions. We would be pleased to insert the appropriate acknowledgement in any future edition Printed in Malaysia Contents Unit 1 Micro-organisms 1 1.1 Bacteria 3 1.2 The ecology and uses of bacteria 11 1.3 What are viruses? 26 Unit 2 Ecology 44 2.1 Cycling matter through ecosystems 45 2.2 Ecological succession 54 2.3 Biomes 58 2.4 Biodiversity 63 2.5 Populations 80 Unit 3 Genetics 101 3.1 Genetic crosses 102 3.2 Molecular genetics 128 3.3 Protein synthesis 142 3.4 Mutations 152 Unit 4 Evolution 170 4.1 The origin of life 171 4.2 Theories of evolution 183 4.3 The evidence for evolution 191 4.4 The processes of evolution 204 4.5 The evolution of humans 213 Unit 5 Behaviour 231 5.1 An introduction to behaviour 231 5.2 Innate behaviour 238 5.3 Learned behaviour 246 5.4 Examples of behaviour patterns 256 Index 271 Grade 12 iii Micro-organisms Unit 1 Contents Section Learning competencies 1.1 Bacteria Name, describe and give examples of (page 3) the different types of micro-organism. Describe the structure of a bacterial cell. Describe the shapes of different types of bacteria. Classify bacteria as Gram-positive and Gram-negative. 1.2 The ecology Appreciate that bacteria are found and uses of in many diverse locations. bacteria (page 11) Explain that bacteria are important disease-causing agents; are used in industrial processes and give examples of industrial processes that use bacteria; and are involved in the cycling of mineral elements such as carbon and sulphur. Describe the main groups of micro- organisms. Explain the roles of reservoirs of infection in the transmission of infectious diseases caused by bacteria. Explain the roles that bacteria play in every ecosystem. Explain how bacteria produce disease. Compare infectious disease with functional disease and state the germ theory. State the role of bacteria in recombinant DNA work. Define cloning and illustrate how foreign genes are inserted in bacterial pyramids, and how bacteria are used as vectors. Grade 12 1 Unit 1: Micro-organisms Contents Section Learning competencies 1.3 What are Describe the structure of a virus, draw viruses? and label it. Explain the different forms of viruses and diagram them. Classify viruses and give examples of RNA, DNA, and retroviruses. Discuss the reproductive cycles of viruses and compare the lytic and lysogenic cycles of viral reproduction. Draw and label a bacteriophage. Compare viruses with free-living cells. Draw, label and describe the structure of HIV, show the structure of glycoprotein-120 on its surface and tell that it is this protein that allows HIV to bind with CD4 lymphocytes. Explain the life cycle of HIV, show how it replicates. Explain how different anti-retroviral drugs work and tell why HAART is more effective than single drug treatment. State the social and economic impacts of AIDS. Demonstrate the life skills that lead to responsible sexual behaviour. 2 Grade 12  UNIT 1: Micro-organisms 1.1 Bacteria KEY WORDS micro-organism a very small By the end of this section you should be able to: organism, usually having just one cell Name, describe and give examples of the different types of fungus (plural fungi) a micro-organism. eukaryotic organism that Describe the structure of a bacterial cell. obtains its nutrition using Describe the shapes of different types of bacteria. extracellular digestion. A fungus is neither a plant nor Classify bacteria as Gram-positive and Gram-negative. an animal unicellular a unicellular organism has just one cell What different types of micro-organisms are there? multicellular a multicellular Any micro-organism is just what its name suggests – a very an organism has more than small organism. Most micro-organisms are unicellular (the whole one cell organism consists of just one cell), although some do contain more yeast a type of fungi used for than one cell. brewing and baking There are five main groups of micro-organisms, although each group can be subdivided. These groups are: protozoa some fungi some algae viruses bacteria Protozoa, fungi and algae Protozoa are unicellular organisms that lack a cell wall. Most of them are motile (able to move), and include organisms such as Amoeba, Plasmodium (the organism that causes malaria), and Paramecium. (a) (b) (c) The only unicellular fungi are the yeasts. These include brewer’s Figure 1.1 Some protozoa. yeast and baker’s yeast (Saccharomyces) as well as the yeast-like (a) Amoeba; (b) Plasmodium in organism that causes thrush in humans (Candida). blood cells; (c) Parameciu (a) (b) Figure 1.2 Some yeasts. (a) Saccharomyces; (b) Candida Grade 12 3 Unit 1: Micro-organisms KEY WORDS Although the yeasts are the only unicellular fungi, other fungi are also classed as micro-organisms. Many fungi produce a mycelium mycelium the collection of of microscopic strands called hyphae. They release enzymes from very fine strands that makes these strands that digest whatever the fungus is growing on. The up a fungus. Each strand products of digestion are then absorbed into the fungus to help with is called a hypha (plural its growth and reproduction. Remember, fungi do not have true hyphae). The hyphae are not roots, stems and leaves. Some fungi live on or in living organisms, ‘compartmentalised’ into cells; as parasites. Others live on dead material as saprobionts, organisms each is ‘multinucleate’ – the that digest their food externally and absorb the products. cytoplasm contains many nuclei alga (plural algae) an alga is Algae are an important group of organisms. Many are large a single-celled organism that (the seaweeds are all algae), but some algae are unicellular. obtains its nutrition using The unicellular algae in figure 1.4 are part of the plankton, the photosynthesis. collections of small microscopic plant and animal organisms that float or drift in large numbers in fresh or salt water, providing food motile an organism that is for fish and other larger organisms. These unicellular algae in the able to move on its own oceans produce far more oxygen during photosynthesis than all the forests in the world together. hypha mycelium Figure 1.3 Fungal hyphae Figure 1.4 Unicellular algae are found in the ocean as plankton. Some unicellular algae are motile – they can move. Figure 1.5 shows an alga called Chlamydomonas, which has two flagella at one end to propel it through the water. Viruses are sometimes referred to as micro-organisms, although some biologists say that, strictly, they are not organisms at all. Viruses cannot independently carry out any of the processes common to all living organisms. They can only reproduce inside Figure 1.5 Chlamydomonas other cells. So they are all parasites. Some parasitise bacteria, some moves using its two flagella. parasitise plants and others parasitise animals. The basic virus is not even a cell – it has no nucleus and no cytoplasm – but it does have genetic material surrounded by a protein coat. A protein capsid B nucleic acid RNA core tail protein molecule tail fibres Figure 1.6 Some viruses. A Bacteriophages are viruses that parasitise bacteria; B Tobacco mosaic virus parasitises tobacco plants. 4 Grade 12  UNIT 1: Micro-organisms Activity 1.1: What micro-organisms do you know? Try to find one species of each type of micro-organism (bacteria, protozoa, algae, fungi and viruses) that is useful, and one that is harmful. You may not be successful for all types in both cases. Explain why. What are bacterial cells like? You already know about the structure of plant and animal cells. Figure 1.7 HIV is a virus that Biologists call these eukaryotic cells. Fungi and protoctistans (algae parasitises human white blood and protozoa) also have eukaryotic cells. cells, causing the symptoms of golgi apparatus AIDS. free ribosome cilia microvilli smooth KEY WORDS endoplasmic microtubule reticulum network eukaryotic cell a type of cell that has a nucleus. The word mitochondrion eukaryotic is derived from lysosome fusing Greek eu (true) and karyos with incoming phagocyclic vesicle (nuclear) prokaryotic cell a type of cell nucleus phagocyclic vesicle that does not have a nucleus. nuclear Only bacteria have prokaryotic envelope nucleolus cells. The word prokaryotic is derived from Greek pro vesicles (before) and karyos bacterium (plural bacteria) lysosome a micro-organism consisting of just one prokaryotic cell peroxisomes centrosome and centrioles cell membrane rough endoplasmic cytoplasm reticulum Figure 1.8 The structure of a eukaryotic cell Bacteria, however, have prokaryotic cells. In prokaryotic cells there is no true nucleus separated from the rest of the cell by a membrane. Instead, the DNA of the bacterium forms a continuous loop that is intermingled with the cytoplasm. Figure 1.9 shows the structure of a generalised bacterial cell. Not all bacteria have all the structures shown in the diagram. For example, not all bacteria have a capsule and many do not have a flagellum. All bacteria do have a cell wall (but it is not made from cellulose like plant cell walls and instead is made from a substance called peptidoglycan, which makes it rigid), a cell membrane, cytoplasm, ribosomes and DNA. Grade 12 5 Unit 1: Micro-organisms Activity 1.2 Work in small groups cytoplasm and brainstorm all the differences you can think of between eukaryotic and prokaryotic cells. Make a bacterial chromosome (DNA) table comparing the two different types of cells and plasmid (plasmid DNA) capsule share your ideas with the rest of the class. cell wall cytoplasmic membrane ribosomes pili flagella Figure 1.9 The structure of a bacterial cell Although bacterial cells vary a great deal in size, they are usually much smaller than eukaryotic cells. Bacterial cells are usually between 1 and 10 µm long, whereas eukaryotic cells are between 10 and 100 µm long. (1 µm is 0.001 mm, one-thousandth of one millimetre.) Did you know? The nucleus, mitochondria and chloroplasts found in eukaryotic cells are all surrounded by a double membrane. They are sometimes called ‘membrane-bound organelles’. So, biologists sometimes say that prokaryotic cells do not contain membrane-bound organelles. Because of this, photosynthesis and respiration are carried out differently in bacterial cells. Photosynthesis takes place in the plasma membrane or membranes in the cytoplasm. Many of the reactions of respiration take place in the cytoplasm, with some also occurring on the plasma membrane. 6 Grade 12  UNIT 1: Micro-organisms Are all bacteria the same shape? No – there are several shapes, sizes and arrangements. Bacterial cells come in three main shapes: cocci (singular, coccus) – spherical bacteria bacilli (singular, bacillus) – rod-shaped bacteria spirochaetes – spiral or corkscrew-shaped bacteria coccus (sphere) bacillus (rod) spirochaete pairs and singles pairs and singles borrelia chains chains treponema clusters flagellated bacilli spirilla Figure 1.10 Bacterial cells come in three main shapes. Whatever their shape, bacterial cells are sometimes found singly; sometimes two cells are stuck together; and sometimes the cells exist in chains. Activity 1.3: Finding out more about bacteria Streptococcus and Lactobacillus are two well-researched types of bacteria. Carry out a library search to find out what shapes these two bacteria have, and why they are so important to us. Also, try to find two diseases caused by spiral-shaped bacteria. Are there other ways of classifying bacteria? Bacteria can be classified in other ways, besides their shape. One of these ways is whether or not they are coloured by Gram’s stain. This test gives two categories: Grade 12 7 Unit 1: Micro-organisms Gram-positive – these bacteria are stained purple by Gram’s stain Gram-negative – these bacteria are stained pink by Gram’s stain Because Gram’s stain produces different results with different types of bacteria, it is called a differential stain. gram-positive gram-negative gram-positive plasma membrane fixation periplasmic space peptidoglycan crystal violet iodine treatment plasma membrane periplasmic space decolorisation peptidoglycan outer membrane counter stain (lipopolysaccharide safranin and protein) gram-negative Figure 1.11 Gram staining The difference is due to the structure of the cell wall of the different KEY WORDS bacteria. Gram-negative bacteria have much less peptidoglycan Gram’s staining a test for in their cell walls. This is the part of the wall that absorbs the stain. classifying bacteria (named They also have a membrane outside the peptidoglycan cell wall, after Hans Christian Gram, which Gram-positive bacteria do not have. This outer membrane who developed the technique secretes endotoxins (a type of toxin that is a structural component in 1884) of these bacteria) and is also quite resistant to many antibiotics. This differential stain a test makes diseases caused by Gram-negative bacteria more difficult that uses staining to classify to treat. Gram-negative bacteria, on the whole, cause more serious organisms or organic material diseases, although there are exceptions – the bacterium that causes peptidoglycan a complex tuberculosis is a Gram-positive bacterium. molecule made from sugars Gram staining is used much less than it was in diagnosing disease, and amino acids. It has a as more advanced and more reliable biochemical techniques have mesh-like structure and is become available. found in bacterial cell walls endotoxins toxins found in Activity 1.4: Looking at bacteria in yoghurt some bacteria You will need: a microscope a slide and coverslip yoghurt water a dropping pipette 8 Grade 12  UNIT 1: Micro-organisms Method 1. Take a small sample of yoghurt using the pipette, and place it on a slide. 2. If the sample seems too thick, dilute it with a drop of water. 3. Lower a coverslip onto the yoghurt, taking care not to produce air bubbles. 4. First, observe the bacteria at low power (×100) to find a good place to start looking. The diaphragm setting should be very low (small) because these bacteria are almost transparent. 5. Switch to the highest power to identify the bacteria according to the shape of cells and arrangement of the cells (pairs, clusters, chains, etc.). 6. Make a drawing of the different bacteria you can see. Review questions Choose the correct answer from A to D. 1. Protozoa are: A multicellular organisms B one-celled animals C members of the group protoctista D unicellular plants 2. Micro-organisms include: A bacteria and some fungi B viruses C protozoa D all of the above 3. Viruses are sometimes not considered as living organisms because: A they do not have any of the organelles found in cells B they are incapable of independent reproduction C they cannot carry out any metabolic processes D all of the above Grade 12 9 Unit 1: Micro-organisms 4. Gram’s stain is called a differential stain because: A it stains bacterial cells, but not fungi B it stains some bacteria purple and others pink C it stains viruses, but no other organisms D it stains some fungal cells purple and others pink 5. Bacterial cells are different from animal cells because the bacterial cells: A are larger than animal cells B have no nucleus C have no DNA D have no cytoplasm 6. The three main shapes of bacterial cell are: A diplococci, staphylococci and bacilli B diplococci, streptococci and bacilli C diplococci, streptococci and staphylococci D cocci, bacilli and spirochaetes 7. Compared with Gram-positive bacteria, Gram-negative bacteria: A have an extra membrane outside the cell wall B are more resistant to antibiotics C produce more dangerous endotoxins D all of the above 8. Viruses can parasitise: A only animal cells B only plant cells C only bacterial cells D animal cells, plant cells and bacterial cells 9. It is true to say of bacterial cells that: A none can photosynthesise B only some can respire C none contain ribosomes D none contain chloroplasts 10. Membrane-bound organelles include: A the nucleus B chloroplasts C mitochondria D all of the above 10 Grade 12  UNIT 1: Micro-organisms 1.2 The ecology and uses of bacteria By the end of this section you should be able to: Appreciate that bacteria are found in many diverse locations. Explain that bacteria are important disease-causing agents; are used in industrial processes and give examples of industrial processes that use bacteria; and are involved in the cycling of mineral elements such as carbon and sulphur. Describe the main groups of micro-organisms. Explain the roles of reservoirs of infection in the transmission of infectious diseases caused by bacteria. Explain the roles that bacteria play in every ecosystem. Explain how bacteria produce disease. Compare infectious disease with functional disease and state the germ theory. State the role of bacteria in recombinant DNA work. Define cloning and illustrate how foreign genes are inserted in bacterial plasmids, and how bacteria are used vectors in the genetic engineering of plants. Where are bacteria found? Bacteria are found in every ecosystem – they are pretty well everywhere around you – and everywhere inside you as well! There are ten bacterial cells inside you for every one of your own cells. Most of these are found in the large intestine. Bacteria are important because they: cause diseases are used in many industrial processes recycle mineral elements such as carbon, nitrogen and sulphur through ecosystems Grade 12 11 Unit 1: Micro-organisms KEY WORDS Activity 1.5: Culturing micro-organisms from the germ theory says that environment infectious diseases are caused by micro-organisms pathogen the term describes any organism that causes disease infectious disease an infectious disease is caused 1 A wire loop is placed in a hot Bunsen burner flame for a few seconds, until by a living organism entering it glows red-hot. This sterilises the loop. It is then allowed to cool in the air. or infecting another living organism. They are sometimes called communicable diseases because they can be transmitted or communicated from one person to another 2 The lid of the Petri dish containing the mixture of colonies is lifted to an angle of about 45°, just enough to allow the wire loop to be used to collect a sample of the bacterium of interest. The lid is then replaced. Figure 1.12 Culturing micro-organisms. What is the role of bacteria and other microorganisms in infectious diseases? As we have already learned, the theory that some diseases are caused by the invasion of the body by micro-organisms was put forward by theon 3 The sample French the loopchemist andtomicrobiologist is transferred a fresh sterile agarLouis Pasteur. plate. The loop is moved in a zigzag pattern on the surface of the agar, just touching the jelly, The English surgeon Joseph Lister and the German physician but without letting the loop dig in. This is called ‘inoculating a plate’. RobertTheKoch were lid of the dishalso involved in the development of this theory. is replaced. In the mid-19th century, Pasteur showed that micro-organisms in the air caused wine to go ‘sour’. In the 1860s, Lister showed that carbolic acid (phenol) acted as a disinfectant, and prevented disease in bones following surgery. In 1880, Robert Koch identified the micro-organisms that cause tuberculosis and cholera. The theory that disease can be caused by micro-organisms is called the germ theory. Organisms that cause disease are called pathogens. A disease that is caused by a micro-organism infecting the body is an infectious disease. Koch’s postulates After considerable work on micro-organisms as the cause of disease, Robert Koch put forward the following ideas (or ‘postulates’) that should always apply if a certain micro-organism causes a disease. 12 Grade 12  UNIT 1: Micro-organisms The micro-organism must always be present when the disease is present, and should not be present if the disease is not present. The micro-organism can be isolated from an infected person and then grown in culture. Introducing such cultured micro-organisms into a healthy host should result in the disease developing. It should then be possible to isolate the micro-organism from this newly diseased host and grow it in culture. The first postulate establishes a link between the micro-organism and the disease. The following three postulates prove that the metabolism of a specific living micro-organism, when transferred into a healthy host, causes the disease. Different micro-organisms cause disease in different ways, as shown in table 1.1. Table 1.1 How micro-organisms cause disease Type of How the micro-organism causes disease Examples of micro-organism diseases caused Bacteria Bacteria release toxins as they multiply. These toxins affect Pneumonia, cells in the region of the infection, and sometimes in other cholera, regions of the body as well. Bacterial diseases can be pulmonary treated with antibiotics, as each bacterium is a true cell tuberculosis (TB) with its own metabolic systems, and is capable of cell division. Some bacteria invade and grow in the tissues of organs, causing physical damage. Viruses Viruses enter living cells and disrupt the metabolic systems Influenza (‘flu), of the cell. The genetic material of the virus becomes AIDS, measles, incorporated with that of the cell and instructs the cell to common cold produce more viruses. Viruses cannot be treated with antibiotics as they are not true cells and are only active inside cells, which antibiotics cannot enter. Fungi When fungi grow in or on living organisms, their hyphae Athlete’s foot, secrete enzymes. These digest substances in the tissues, farmer’s lung and the substances produced are absorbed. Growth of hyphae also physically damages the tissue. Some fungi also secrete toxins. Others can cause an allergic reaction (e.g. farmer’s lung). Protozoa Protozoa cause disease in many different ways. Malaria, sleeping sickness Grade 12 13 Unit 1: Micro-organisms Figure 1.13 Types of disease-causing organism How are disease-causing micro-organisms transmitted? KEY WORD Table 1.1 looked at how bacteria cause disease. There must clearly be a source of infection. The origin of micro-organisms that reservoir of infection this infect other people is called the reservoir of infection. This is the is any person, animal, plant, principal habitat from which an infectious agent may spread to soil or substance in which cause disease. Reservoirs of infection include: an infectious agent normally lives and multiplies. The human beings – the reservoir for many diseases, including the reservoir typically harbours common cold, diphtheria and others the infectious agent without other animals – for example: chickens, the reservoir for showing symptoms of the salmonella infections; mosquito, the reservoir for malaria disease and serves as a source soil – the reservoir for tetanus and many other pathogens from which other individuals water – the reservoir for Legionnaire’s disease, amoeba, cholera, can be infected. People acting etc. as the reservoir of infection food – the reservoir for many diseases including typhoid are sometimes called carriers of the disease contaminated objects – contact infections such as HIV/AIDS and trachoma air – the reservoir for pneumonia, tuberculosis, etc. Figure 1.14 Airborne droplet infection 14 Grade 12  UNIT 1: Micro-organisms Because there are different reservoirs of disease-causing organisms, there are several different ways in which diseases can be transmitted, as shown in table 1.2. Table 1.2 How diseases can be transmitted Method of How the transmission route works Examples of transmission diseases Droplet Many of these diseases are ‘respiratory diseases’ – diseases Common cold, infection affecting the airways of the lungs. The organisms are carried in ’flu, pneumonia tiny droplets through the air when an infected person coughs or sneezes. They are inhaled by other people. Drinking The micro-organisms transmitted in this way often infect regions Cholera, contaminated of the gut. When unclean water containing the organisms is drunk, typhoid fever water they colonise a suitable area of the gut and reproduce. They are passed out with faeces and find their way back into the water. Eating Most food poisoning is bacterial, but some viruses are transmitted Salmonellosis, contaminated this way. The organisms initially infect a region of the gut. typhoid fever, food listeriosis, botulism Direct Many skin infections, such as athlete’s foot, are spread by direct Athlete’s foot, contact contact with an infected person or contact with a surface carrying ringworm the organism. Sexual Organisms infecting the sex organs can be passed from one sexual Candidiasis, intercourse partner to another during intercourse. Some are transmitted by syphilis, AIDS, direct body contact, such as the fungus that causes candidiasis gonorrhoea (thrush). Others are transmitted in semen or vaginal secretions, such as the AIDS virus. Some can be transmitted in saliva, such as syphilis. Blood-to- Many of the sexually transmitted diseases can also be transmitted AIDS, blood contact by blood-to-blood contact. Drug users sharing an infected needle hepatitis B can transmit AIDS. Animal Many diseases are spread through the bites of insects. Mosquitoes Malaria, vectors spread malaria and tsetse flies spread sleeping sickness. In both sleeping cases, the disease-causing organism is transmitted when the sickness insect bites humans in order to suck blood. Flies can carry micro- organisms from faeces onto food. Activity 1.6: Identifying sources of infection For each of the methods of transmission given in table 1.2, identify the reservoir of infection. Grade 12 15 Unit 1: Micro-organisms Did you know? What other types of disease are there? Eating too much food can Before we answer that question, we should really define what we result in obesity, which mean by ‘disease’. is regarded as a disease The World Health Organization’s definition of health is ‘a state of condition in itself, and can complete physical, mental and social well-being’. But disease is less also lead to other diseases easy to define. It doesn’t mean just the absence of perfect health. If such as coronary heart we are less fit than we might be, or if we are feeling depressed at the disease. thought of too much schoolwork, that doesn’t necessarily mean we have a disease. A useful definition of disease might be ‘a condition with a specific cause in which part or all of a body is made to function in a non- normal and less efficient manner’. This definition could include diseases of all organisms – including plants. It could also include physical, mental and social aspects of disease in humans. Infectious disease is just one type of disease. Disease can be caused by a number of other factors. A person’s lifestyle and working conditions may result in human-induced diseases. Examples include many cancers, together with some forms of heart disease and fibrosis. KEY WORDS Degenerative processes are often the result of ageing. Arthritis Human induced diseases are and atherosclerosis are examples of degenerative diseases. diseases that arise as a result Our genes may lead to disease. Haemophilia and sickle-cell of a person’s lifestyle disease are examples of genetic diseases. Degenerative diseases often result from the ageing process Lack of nutrients in our diet may lead to deficiency diseases, during which the affected including scurvy (caused by a lack of vitamin C) and tissues deteriorate over time kwashiorkor (caused by a lack of protein). due to simple ‘wear and tear’ Social activities can lead to disease. Social diseases, including Genetic diseases are diseases alcoholism and drug addiction, may result in dependency on that result from the action of the drug, isolation, clinical depression and various levels of mutated genes antisocial behaviour. Deficiency diseases are diseases that result from a Categorising diseases lack of a nutrient in our diet. In many cases, it is an oversimplification to place a disease in just Social diseases are one category. For example, atherosclerosis (laying down fatty conditions that result from substances in arteries) increases as we age, so it can be classified as social activities and may a degenerative disease. But our diet influences this process. If we lead to socially unacceptable eat more saturated fat, more fatty substances are laid down in our behaviour arteries. There is also a genetic component – some people are at Multifactorial describes a increased risk of this disease because of genes inherited from their condition that is affected parents. Stress and high blood pressure increase the rate at which by the interaction of many atherosclerosis develops, and these can be the result of our lifestyle. factors Clearly, atherosclerosis does not fit neatly into any one category. It is best to consider such conditions as multifactorial. 16 Grade 12  UNIT 1: Micro-organisms Functional diseases In some cases, there is an obvious ‘malfunction’ of an organ or system, without there being any obvious damage or physical sign of disease in the organ. Because of the malfunction, these diseases are called functional diseases, for example, heart disease. Several intestinal conditions fall into this category. In many forms of Irritable Bowel Syndrome (IBS), there is no sign of damage or disease in the large intestine, yet the large intestine does not function normally. Myalgic Encephalopathy (ME or Chronic Fatigue Syndrome) is another functional disease. In this condition, for no apparent reason, the sufferer is drained of all energy and the simplest task can be an extreme effort. However, some biologists believe that there must be some kind of abnormality in the organs involved in functional diseases. For example, there is some evidence to suggest that, in ME, many of the mitochondria (which release energy in respiration) are abnormal. If this is true, then it may be that functional diseases are really just like other forms of disease, but the precise cause is yet to be discovered. The role of bacteria in an ecosystem The role of bacteria in recycling minerals through ecosystems Many bacteria are decomposers. When organisms die, these bacteria break down the complex molecules that are found in the bodies of the dead organisms into much simpler molecules. The bacteria use some of these for their own metabolism, but in the process they release some minerals, in various forms, into the Did you know? environment. Many elements are recycled in this way, including: carbon We describe the nitrogen conversion of ammonium sulphur ions to nitrate ions as phosphorus oxidation because in the process oxygen is gained Here we will look at how nitrogen and sulphur are recycled. and hydrogen ions are lost. The nitrogen cycle The element nitrogen is found in many important organic molecules in all living organisms. These include: proteins Activity 1.7 DNA Plan a presentation which RNA you can give to younger ATP students explaining the and many others. different ways they can It is important that once organisms die, the nitrogen they contain is catch infectious diseases, made available again to other organisms. Several different types of and suggesting ways to bacteria are involved in this recycling of nitrogen. avoid the spread of disease. Grade 12 17 Unit 1: Micro-organisms The nitrogen cycle will be treated in detail in Unit 2, but table 1.3 below shows the main bacteria involved and the roles they play. Table 1.3 The role of bacteria in the nitrogen cycle Micro-organism Process Nitrogen-fixing bacteria, Nitrogen gas is fixed into forms other organisms can use e.g. Rhizobium (e.g. ammonium). Ammonifying bacteria The decomposers break down proteins in dead organisms and animal (decomposers) waste releasing ammonium ions, which can be converted to nitrates. Nitrifying bacteria, Nitrification is a two-step process. Ammonia or ammonium ions e.g. Nitrosomonas and are oxidised first to nitrites (Nitrosomonas) and then to nitrates Nitrobacter (Nitrobacter) which is the form most usable by plants. Denitrifying bacteria, Nitrates are reduced to nitrogen gas, returning nitrogen to the air e.g. Pseudomonas and reducing the amount of nitrogen in the soil. Figure 1.15 Root nodules The sulphur cycle Sulphur is found in fewer types of organic molecule than nitrogen, but it is found in many proteins. The sulphur cycle will will be covered in detail in Unit 2, but table 1.4 below shows the bacteria involved in the cycle and the roles they play. Table 1.4 The role of bacteria in the sulphur cycle Reaction Bacteria involved Conditions Process needed Decomposition Desulphovibrio Anaerobic Sulphur is released from proteins of dead matter as hydrogen sulphide (giving the ‘rotten eggs’ smell). Oxidation of Photosynthetic Anaerobic Hydrogen sulphide is oxidised to release hydrogen sulphide sulphur bacteria sulphur. Oxidation of Non-photosynthetic Aerobic Sulphur is oxidised to sulphate ions. sulphur sulphur bacteria 18 Grade 12  UNIT 1: Micro-organisms natural causes human causes volcanic eruptions burning fossil fuels and lightning sulphur dioxide water vapour and nitrogen oxides from clouds sulphuric and nitric acids rain acid rain death of conifers acidification of lakes (death of bacteria and acidification of soil algae; death of fish and (leaching of some ions into lakes amphibian eggs; change kills fish; root hairs less effective at in ecosystem) absorbing minerals so tree growth slowed) Fig_1520_A Figure 1.16 Acid rain has many serious effects on living organisms, and can also corrode stone and metal over a long period. If the populations of bacteria that are involved in the nitrogen cycle and the sulphur cycle were reduced, then the cycling of these Activity 1.8 elements could not occur, and all life would be impossible as a Investigate the negative result. It is worth thinking about. We are made from atoms and effects of acid rain and molecules that have been in many other bodies before they were in ways in which it can be ours. The micro-organisms that recycle carbon, nitrogen, sulphur prevented or the effects on and all the other minerals make them available again … and again the environment reduced. … and again … How are bacteria used in industrial processes? Food and beverage fermentation Bacteria and other micro-organisms have been used in manufacturing processes for thousands of years. They have been used to make: bread alcohol irgo or yoghurt vinegar as well as many other products. They have also been used in key processes such as sewage treatment. Grade 12 19 Unit 1: Micro-organisms Did you know? Production of vinegar Vinegar is a dilute solution of ethanoic acid in water. It also contains Acetobacter gets its name other substances that give the vinegar its flavour. Vinegar is used in from the old name for two main ways: ethanoic acid, which used to be called acetic acid. to flavour foods to preserve foods Vinegar is too acidic for most micro-organisms to grow and multiply, so keeping foods in vinegar is a good way of preserving KEY WORD them. We call this method of preserving food pickling. Vinegar is produced by fermenting beer, wine or cider for a second antibiotic a drug that kills time. A culture of a special bacterium called Acetobacter is used. bacteria The alcohol in the beer, wine or cider is oxidised to ethanoic acid. This takes place in a special fermenter. The fermenter is filled with wood shavings and the alcohol source is sprayed in from the top. It trickles down through the wood shavings, which are covered with Acetobacter bacteria. As the liquid flows past them, the bacteria oxidise the alcohol to ethanoic acid. Air is blown in at the bottom to supply the oxygen the bacteria need. The vinegar drips out at the bottom of the wood shavings and is tapped off. ethanol source air outlet spray head air inlet wood shavings vinegar outlet sampling port cooling system Figure 1.17 Vinegar production Fig_2217_A This type of production is called continuous production, as alcohol is continuously being fed in and ethanoic acid is continuously dripping out at the bottom of the fermenter. Producing antibiotics The first antibiotics all came from fungi. Today, they are increasingly being made using genetically modified bacteria in huge fermenters. The stages in the process are shown in figure 1.18 overleaf. 20 Grade 12  UNIT 1: Micro-organisms motor steam inlet steam outlet inlet exhaust outlet At the start of the process, nutrients are fed in through pipes which can be opened and closed using valves. cold water outlet Fermentation produces heat, so temperature to prevent the contents from and pH probes overheating, the fermenter is surrounded by a water jacket The pH of the contents can be through which cold water adjusted by adding acid or alkali circulates, keeping the to keep it constant. temperature at the best level for growth. cold water inlet stirring paddles water jacket Stirring paddles mix up the contents. This keeps the micro-organisms in air inlet suspension in the liquid, so that they get more exposure to the nutrients, If the organisms respire and helps to keep the temperature aerobically, filtered air is even throughout the vessel. Some supplied through this inlet. fermenters use jets of air to mix the The air is filtered to contents instead of paddles. prevent contamination. filter harvesting Many micro-organisms produce outlet acidic waste products, so fermenters have to be made of materials which will not corrode, such as stainless = valves steel or special alloys. Genetically modified bacteria are also used to produce: Fig_2205_A Figure 1.18 Production of insulin antibiotics human growth hormone antibiotics enzymes for washing powders human vaccines, such as the vaccine against hepatitis B Sewage treatment All types of sewage treatment rely on the action of a range of micro- organisms to oxidise the organic matter present in sewage. There are two main methods: the percolating filter method the activated sludge method In the percolating filter method: sewage is screened to remove large pieces of debris it stands in a large settlement tank to allow suspended matter to settle out it is then allowed to trickle through a bed of stones, each of which is covered in a layer of micro-organisms (bacteria, fungi and protozoa) as the sewage trickles through the filter bed, the micro- organisms digest the organic matter and absorb the products by the time the liquid reaches the bottom of the filter bed, the polluting organic matter has all been removed Grade 12 21 Unit 1: Micro-organisms Figure 1.19 Percolating filter In the activated sludge method: sewage is screened and allowed to stand in settlement tanks, as in the percolating filter method it is then pumped into treatment tanks, where: – activated sludge, rich in micro-organisms, is added – oxygen is blown through the mixture in the oxygenated mixture, the micro-organisms from the added activated sludge oxidise the polluting organic matter, reproducing as they do so some of the sludge formed is recycled to ‘seed’ new tanks. sewage air bubbles – oxygenate and mix sewage and sludge t reated activated sewage sludge – rich in micro-organisms air sludge Activity 1.9 treated and sold We use bacteria in many different ways in industry. Make a poster to show as Figure 1.20 The activated sludge method many of these different industrial uses of bacteria as you can. Make your poster clear and colourful so people enjoy learning from it. 22 Grade 12  UNIT 1: Micro-organisms How are bacteria genetically modified? KEY WORDS You have already been introduced to genetic engineering. genetic engineering the Genes are sections of the DNA of an organism that code for a practice of transferring genes particular protein. So if a gene can be transferred successfully from from one organism to another one organism into a bacterium, the genetically modified bacterium organism (either belonging to will now make the protein that its ‘new gene’ codes for. the same species or belonging The development of three main techniques made genetic to a different species). This is engineering possible. done by taking DNA from the The discovery that genes can be ‘cut’ out of a DNA molecule first organism and transferring using enzymes called restriction endonucleases. it to the second organism. The discovery that genes can be inserted (‘tied’) into another Genetic engineering has only been practised since 1980 DNA molecule using a ligase enzyme. Genes can be transferred into other cells using vectors. These are vector a means of transferring something. In genetic usually either plasmids (small pieces of circular DNA found in engineering, viruses are used bacteria), or viruses. as vectors to transfer genetic Once the gene has been inserted into the new bacterium, the information between different bacterium becomes a genetically modified or transgenic organism. organisms bacterial chromosome plasmids Figure 1.21 The main stages of genetic engineering plasmids isolated Plasmids are isolated from a bacterium. The gene to be transferred is cut from the donor DNA using the same restriction endonuclease enzyme. DNA to be transferred two strands of plasmid DNA The plasmids are opened sticky ends with a specific restriction on plasmid endonuclease enzyme. donor cell sticky ends on DNA being transferred The opened-up plasmids and the isolated gene are mixed with a DNA ligase enzyme to create recombinant plasmids. Bacteria are incubated with the recombinant plasmids. recombinant plasmid Some bacteria will take up the plasmids. bacterium containing recombinant plasmid The bacteria that have taken up the plasmid now contain the gene from the donor cell. This could be a gene controlling the production of human insulin. Fig_2305_A Grade 12 23 Unit 1: Micro-organisms Bacteria aren’t the only organisms that have been genetically modified. Many crop plants have also had foreign genes inserted into them. These give the plants new properties, such as: resistance to infectious disease resistance to animal pests a longer shelf-life before decaying Genetic engineering of plants posed problems for biologists, as plant cells will not accept plasmids in the same way as bacterial cells do. However, they discovered that one particular bacterium, called Agrobacterium tumefaciens, regularly infects plant cells. This bacterium can act as a vector to carry genes that have been inserted into a genetically modified Agrobacterium into plants. Figure 1.22 shows how this is done. DNA from another species plasmid isolated DNA cut with restriction enzyme to isolate plasmid cut open Agrobacterium desired gene with restriction tumefaciens enzyme cut plasmid joined to desired gene using ligase Figure 1.22 Genetic modification leaf discs leaf discs floated on of plants using Agrobacterium obtained from liquid containing the plant to be plasmids; some will modified take up the plasmid. leaf discs cultivated on a nutrient medium (micro propagation) plantlets grown into whole plants whose cells now contain the foreign gene However, Agrobacterium can’t Fig_23.06 be used to genetically modify all types of plant. It will not infect cereals such as maize, for example. To solve this problem, biologists developed the gene gun. This literally shoots the genes into cells of plants, using as ‘bullets’ tiny pellets of gold that are covered in DNA. You could think of it as the ‘golden gun’. The gene gun has made it possible to genetically modify plants such as maize, tobacco, carrots, soybean and apple. For example, maize has had genes inserted into it that cause it to: Figure 1.23 A scientist working produce a pesticide that makes it resistant to some insect pests with a gene gun be resistant to some fungal diseases 24 Grade 12  UNIT 1: Micro-organisms Review questions Choose the correct answer from A to D. 1. Sources of infectious organisms that spread to infect others are called: A hosts of infection B sources of infection C reservoirs of infection D sites of infection 2. Disease-causing bacteria can be transmitted by: A sexual intercourse B droplet infection C eating contaminated food D all of the above 3. Which of the following is not an infectious disease? A tuberculosis B AIDS C coronary heart disease D the common cold 4. Which if the following statements are NOT true about nitrogen-fixing bacteria? A They are often found in nodules on the roots of legumes B They convert nitrogen gas into ammonium ions C They break down nitrate ions into ammonium ions D They play a vital role in the nitrogen cycle in nature 5. In the sulphur cycle, the main source of sulphur for plants is: A sulphur in rocks B sulphates in the air C sulphur in water D sulphates in soil 6. In the percolating filter method of sewage treatment: A the sewage is screened to remove large pieces of waste B the sewage trickles through stones covered in micro- organisms C the micro-organisms oxidise the organic matter in the sewage D all of the above 7. DNA can be transferred into maize using: A plasmids B the gene gun C Agrobacterium D viruses Grade 12 25 Unit 1: Micro-organisms 8. In genetic engineering, a section of DNA is removed from a DNA molecule using: A ligase enzymes B plasmids C restriction enzymes D polymerase enzymes 9. Which of the following is NOT a term used to describe organisms that have had foreign genes added to them? A transgenic organisms B genetically modified organisms C pathogenic organisms D genetically engineered organisms 10. Which of the following were important in developing the germ theory of disease? A Louis Pasteur, showing that excluding micro-organisms from wine prevented it from going sour B Joseph Lister, showing that using carbolic acid, which killed bacteria, reduced infection during surgery C Robert Koch, identifying specific micro-organisms associated with specific diseases D all of the above 1.3 What are viruses? By the end of this section you should be able to: Describe the structure of a virus, draw and label it. Explain the different forms of viruses and diagram them. Classify viruses and give examples of RNA, DNA, and retroviruses. Discuss the reproductive cycles of viruses and compare the lytic and lysogenic cycles of viral reproduction. Draw and label a bacteriophage. Compare viruses with free-living cells. Draw, label and describe the structure of HIV, show the structure of glycoprotein-120 on its surface and tell that it is this protein that allows HIV to bind with CD4 lymphocytes. Explain the life cycle of HIV, show how it replicates. 26 Grade 12  UNIT 1: Micro-organisms Explain how different anti-retroviral drugs work and tell why KEY WORD HAART is more effective than single drug treatment. virus some genetic material State the social and economic impacts of AIDS. contained in a protein coat. Demonstrate the life skills that lead to responsible sexual It is not usually regarded as a behaviour. living organism Introducing viruses Did you know? We have already looked a little at viruses and we have seen that The particle of a virus there are reasons to consider them not to be living organisms – a is called a virion. All virus particle (sometimes called a virion) is nothing like either a virions contain at least two prokaryotic cell or a eukaryotic cell. components: Viruses are much smaller than even the smallest bacterium. Most a protein shell or capsid are between 0.01 and 0.1 µm in length or diameter. This makes DNA or RNA as the them at least 1000 times smaller than the smallest bacterium and genetic material 1 000 000 times smaller than most human cells. Some also have: The characteristics of viruses are shown in table 1.5. a membrane made from lipids and proteins outside Table 1.5 Characteristics of viruses the capsid other proteins and Feature Virion (virus particle) enzymes inside the capsid Size 0.01–0.1 µm Nucleus Absent DNA Tiny amount of linear DNA in some; others contain RNA but no chromosomes Other cell Absent organelles Because they do not have the major organelles that are present DNA or RNA envelope (membrane from in living cells, virus particles can’t carry out any of the normal host cell) metabolic processes of cells, such as: respiration protein synthesis DNA replication photosynthesis active transport protein coat facilitated diffusion any other process requiring control by enzymes or the presence 0.01 to 0.1 µm of proteins Figure 1.24 The structure of a Fig_2111_A typical virus Grade 12 27 Unit 1: Micro-organisms As a result, all viruses are parasites. The only way they can reproduce is to invade cells, ‘hijack’ the normal metabolic processes of those cells, and make the cells produce more virus. Once produced, the viruses escape from the cell and infect other cells. Figure 1.25 shows how this happens in two different types of viruses. Other viruses adopt different strategies. (1) enveloped DNA virus attachment non-enveloped RNA virus (2) entry uncoating entry DNA uncoating RNA nucleus replication replication assembly cell assembly membrane ruptures budding through host cell membrane new viral RNA particle is released new viral DNA particle is released Figure 1.25 Stages of virus infection of cells. 28 Grade 12  UNIT 1: Micro-organisms Classifying viruses KEY WORDS It is difficult to classify viruses because, even though they have a DNA virus contains genetic basic structure, there is a great deal of variation in their shape and information stored in the form the way in which they infect cells. However, they can be classified of DNA into three main groups, based on the nature of their genetic RNA virus contains genetic material and the way in which it is expressed. These groups are: information stored in the form DNA viruses – for example, Herpes simplex (causes cold sores) of RNA RNA viruses – for example, H1N1 virus (causes swine flu) retrovirus an RNA virus retroviruses – for example, HIV (causes AIDS) that converts its genetic information from RNA into DNA viruses DNA after it has infected a host When a DNA virus infects a cell, the viral DNA can replicate itself and can also control the synthesis of virus proteins, so that the new bacteriophage a virus that DNA and new protein can be assembled into new virus particles. uses a bacteria to replicate its genetic information RNA viruses When an RNA virus infects a cell, its RNA can be used to synthesise more viral proteins, including an enzyme that controls the synthesis Did you know? of more RNA. The new RNA and new proteins can be assembled into new virus particles. We say that the RNA is reverse-transcribed because, With the exception of the RNA viruses, all organisms store their in cells, DNA is normally permanent information in DNA, using RNA only as a temporary transcribed into RNA messenger for information. DNA is quite a stable molecule, is not as part of the process of very reactive with other molecules, and replicates very accurately. In protein synthesis. Carrying contrast, RNA is quite unstable and makes frequent mistakes during out the process in the copying. opposite direction is reverse But these very properties make RNA ideal for the storage of transcription. viral information. Once the host’s immune system has learned to recognise an infecting virus and create antibodies against it, it can quickly destroy it, and the virus needs to change its nature so that the host’s immune system will no longer recognise it – it must mutate. The unstable nature of RNA allows RNA viruses to evolve far more rapidly than DNA viruses, frequently changing their surface structure. DNA protein coat Retroviruses Retroviruses also contain RNA, but replicate in a different way. When they infect cells, they release into the cells their RNA and an head enzyme that causes it to be ‘reverse-transcribed’ into DNA. This then controls the formation of more viral protein and RNA that can be assembled into new virus particles. Viruses can also be classified by the type of organism they infect: tail animal-infecting viruses plant-infecting viruses tail fibres (six) bacteria-infecting viruses – these are called bacteriophages 0.1 μm Bacteriophages have a really unusual shape – they look rather like a Figure 1.26Fig_2114_A Structure of a lunar landing module! bacteriophage Grade 12 29 Unit 1: Micro-organisms Virus multiplication Much of our knowledge about how viruses are reproduced comes from work on bacteriophages. One bacteriophage in particular, called T4, has been studied more than any other. Its reproductive cycle is shown in figure 1.27. bacterium 1 Attacking virus (bacteriophage) attaches to host cell wall. bacterial chromosome 2 Virus injects its DNA into bacterium. 3 Virus DNA controls production of more virus DNA and protein coats. bacterial chromosome is ‘switched off’ or even destroyed 4 DNA and protein coats assembled into new virus particles. 5 Host cell bursts open, releasing new virus particles. Figure 1.27 The reproductive cycle of bacteriophage T4 Fig_2115_A This type of life cycle is called a lytic cycle because it causes the rupture (lysis) of the host cell. From research on bacteriophages, we know that this is not the only type of reproductive cycle in viruses. Sometimes, instead of causing the cell to burst and release the viruses all at once, a few at a time are released by exocytosis through the plasma membrane. This type of life cycle is called a chronic release cycle, because release of new viruses is ongoing (chronic). In other cycles, the virus’s DNA becomes incorporated into the DNA of the host cell. Each time the cell divides, the DNA is replicated, and each daughter cell gets a copy of the cell’s DNA, which now includes the virus DNA. This can continue for many generations until some factor in the environment triggers the 30 Grade 12  UNIT 1: Micro-organisms virus DNA to start producing virus proteins. Then whole viruses Activity 1.10 are assembled, which then leave the cell either by causing cell lysis (splitting), or by chronic (ongoing) exocytosis from the plasma You have now studied membrane. This type of life cycle is called a lysogenic cycle. viruses and bacteria as well as plant and animal cells. These different reproductive strategies are summarised in figure Brainstorm the similarities 1.28. and differences between them and then produce a large, Virion clear table comparing viruses, Infection bacteria, plants and animals. Host cell Disease of host cell Genetic alteration of host cell PRODUCTIVE INFECTION LATENT STATE More virus produced Nucleic acid of virus becomes part of host cell DNA Lysis of cells – Release of virions – release of virions non-lysis of cells Host cell multiplies – Host cell dies continuous leakage Host cell is often modified of virions and continues to multiply Lytic cycle Figure 1.28 Reproductive Chronic release cycle strategies of viruses: lytic cycle, chronic release cycle and Lysogenic cycle lysogenic cycle Modes of virus transmission As well as having different reproductive strategies inside the host cell, different viruses also enter cells in different ways. The bacteriophage injects just its DNA; the rest of the virus remains outside the cell. Many (but not all) animal viruses manage to get the whole virus inside the cell. This is done by tricking the cell into bringing the virus into the cell in the same way as it would with any large protein molecule – using the process of endocytosis. Grade 12 31 Unit 1: Micro-organisms HIV and AIDS What is HIV like? Human Immunodeficiency Virus or HIV is one of the retroviruses. It has RNA as its genetic material. This is transcribed to DNA by the enzyme reverse transcriptase, which HIV contains together with the RNA. lipid membrane enzyme molecule antigen central core