1. Biology(Remedial) Duration: 5 months Credit hours: 4 Instructor: Markos K.

2. Unit Contents Unit 1: The science of biology (1 hrs.) 1.1. The methods of science 1.2. Tools of the biologist Unit 2: Biochemical molecules (6hrs.) 2.1. Inorganic molecules 2.2. Organic Molecules Unit 3: Cell biology (7 hrs.) 3.1. Cell theory 3.2. Types of cell 3.3. Parts of the cell and its function 3.4. The cell and its environment 3.5. Cellular respiration Unit 4: Microorganisms (7 hrs.) 4.1. Introduction to microorganisms 3 | P a g e 4.2. Beneficial microorganisms 4.3 Pathogenic microorganisms

3. Unit 5: Genetics (7 hrs.) 5.1. DNA and chromosome structure 5.2. DNA replication 5.3. Protein synthesis 5.4. Mitosis and meiosis 5.5. Mendelian inheritance 5.6. Mutations Unit 6: Evolution (2hrs.) 6.1. Theories of origin of life 6.2. Theories of mechanisms of evolution 6.3. Speciation through natural selection 6.4. Modern theories of evolution

4. Unit 7: Biotechnology (4 hrs.) 7.1. Scope and definition 7.2. Agricultural biotechnology 7.3. Medical biotechnology 7.4. Industrial biotechnology 7.5. Environmental biotechnology Unit 8: Human biology and health (10 hrs.) 8.1. Food and nutrition 8.2. Non communicable diseases 8.3. The digestive system 8.4 The respiratory system 8.5. The circulatory system 8.6. The nervous system 8.7. Sense organs 8.8. Endocrine glands 8.9. The reproductive system

5. Unit 9: Food making and growth in plants (4 hrs.) 9.1. Plant organs 9.2. Photosynthesis 9.3. Transport in plants 9.4. Response in plants Unit 10: Ecology and conservation of natural resources (5 hrs.) 10.1. Definitions 10.2. Cycling matter through ecosystems 10.3. Ecological succession 10.4. Biomes 10.5. Conservation and Biodiversity 10.6. Vegetation and wildlife 10.7. Global warming and air pollution

6. Unit 1: The Science of Biology

7. Biology is the science of life and living organisms. Living organisms are either unicellular or multicellular Areas of biological study  Astrobiologists  Astrobiologists: are engage in all kinds of research to try to find evidence of life on other planets in our Solar System and in galaxies elsewhere in the Universe.  Biomedical  Biomedical: help in the development of new drugs and vaccines treatment.

8.  Microbioloy  Microbioloy: study how micro-organisms of all kinds function. Some micro-organisms cause disease, and understanding how they work makes a treatment more likely.  Paleobiologyway in which life began on Earthhow it has evolved  Paleobiology: try to find out more about the way in which life began on Earth and how it has evolved from simple life forms into more complex ones.  Besides these biologists, there are others who are, perhaps, more recognizable. These include: Doctors, Dentists, Veterinary Surgeons, Nurses, Physiotherapists, Botanists, Zoologists, Physiologists, Biochemists, Agricultural Biologists, Ecologists, Ethologists, Oncologists, Neurobiologists,

9. 1.1 What is science? scientiaknowledge unique system of acquiring knowledge The word science comes from the Latin word scientia, which means ‘knowledge’. But science isn’t just about having knowledge. Rather it is a unique system of acquiring knowledge based on the scientific method. experimental science It is sometimes called experimental science, but unlike applied science, it depends very heavily on experimentation to obtain the information. However, it is often difficult to separate the two. ongoing effort new information and principles increase Science is an ongoing effort to find new information and principles which can increase human knowledge and understanding.

10. 1.2 Scientific method Is the process by which biologists and all other scientists approach their work scientifically. It depends on evidence. Steps of the scientific method

11. Disproving the theory of spontaneous generation ( S.G.) S.G. nonliving objects living organisms. S.G. suggests that nonliving objects can give rise to living organisms. Francesco Redi larger organisms o Preformed experiments that disproved theory of SG for larger organisms but not for microscopic o Utilized jars containing meat. Some were covered, some were not. uncovered jars. o Maggots appeared in uncovered jars. o Introduced experimental procedure for disproof S.G. o S. G. took another 200 years to disprove.

13. Louis Pasteur (1861) is a French microbiologist airwere not spontaneously produced. proved that microorganisms were present in the air and were not spontaneously produced. – Filtered air through cotton plug. – Placed plug in infusion broth, broth became cloudy - organisms present in the air. – Placed boiled infusion broths in “swan- necked” flasks unless tilted or neck broken. – Flasks remained sterile unless tilted or neck broken.

15. 1.2.1 Cause and Effect Scientific experiments try to establish cause and effect. This means that they try to prove that a change in one factor brings about a change in another factor. scientist changes, or manipulates independent variable The factor that the scientist changes, or manipulates, is called the independent variable (or IV for short). scientist measures dependent variable The factor that the scientist measures to see if it changes when the IV is changed is called the dependent variable (or DV for short). Q. Define the following phrases – Control group – Experimental group – Confounding variables – Fair test

16. 1.2.2 Accuracy, reliability and validity in scientific experiments precisely you measure Accuracy refers to how precisely you measure or count something. Validity is about whether or not our experiment measures what it says it is measuring. how dependable and consistent Reliability is measure of how dependable and consistent the results of an experiment are.

17. 1.3 Report writing on scientific experiments Any report must contain: – A title – A title states clearly what is being investigated – A hypothesis – A hypothesis often extended to a prediction for the particular experiment. – A procedure - clear – A procedure - clear description of the experimental results obtained – A results obtained is often helpful to summarize these (where appropriate) in graphs, charts and tables conclusions – A conclusions that have been drawn from the results – An evaluation – An evaluation of the procedure – An acknowledgement – An acknowledgement of the use of any other person’s work – References

18. 1.4. The tools of a Biologist Biologists use different biological lab equipment both in a laboratory and outside (in field) The following are some basic tools used in a laboratory. – Microscopes – Microscopes- are used to see objects that are too small to be seen with unaided eye – Dissecting equipment- – Dissecting equipment- are used to dissect different animals – Petri dishes- – Petri dishes- usually used to culture microbes – such as bacteria – Pipettes and syringes- – Pipettes and syringes- are devices used for measuring or transferring small volumes of liquid from one container to another with great precision. – Centrifuges- – Centrifuges- a device that is used to separate solids from liquids where simple filtration is not adequate for the task. – Measuring cylinders- is u – Measuring cylinders- is used to measure a precise volume of a liquid – Balances- is – Balances- is sed for measuring mass.

19. The following are some basic tools used in a field to: – taking measurements of the abundance of organisms in the field Quadrats Quadrats are used to estimate abundance of organisms in an area Net Net to caught some insects. – taking samples of the environment (for example, soil, rocks, water) A flow meter A flow meter – this is used to measure the rate of flow of water – collecting specimens for identification and analysis in the laboratory. A pH kit A pH kit – this is used to measure the pH of soil or water

20. 1.5 The relevance and promise of biological science The science biology is related to food production, health and disease, conservation, control of the population and to genetic engineering and biotechnology. i. Biology and agriculture To alleviate food insecurity (how to produce crop plants that): adapted to the new conditions are capable of producing their crop quickly are disease resistant are drought resistant and environmental friendly

21. ii. Biology and medicine give advice on ways of reducing the rate of population growth. Biologists are also able to give advice on ways of reducing the rate of population growth. E.g. contraceptive iii. Biology and the environment monitoring the impact of global warming on the environment, conserve environments. Biologists are actively involved in monitoring the impact of global warming on the environment, conserve environments. iv. Biology and Biotechnology genetically modifying plants Producing genetically modifying plants to meet a specific need monoclonal antibodies production of monoclonal antibodies that can deliver a drug to only those cells that need treatment (for example, cancer cells) to repair damaged organs using stem cells to repair damaged organs and, ultimately, to grow whole new organs from just a few of a person’s stem cells…

22. 1.6. Biology and HIV/AIDS human immuno deficiency virus (HIV). AIDS (acquired immune deficiency syndrome) is caused by the human immuno deficiency virus (HIV). It infects cells in our immune systems called T-helper cells that enable us to fight other diseases. AIDS is usually fatal. AIDS is largely a sexually transmitted disease (STD), although there are four main ways in which HIV can be transmitted: infected person i.homosexual or heterosexual intercourse with an infected person ii.transfusion ii.transfusion of infected blood or blood products iii.sharing iii.sharing infected needles pregnancy iv.from mother to child during pregnancy

23. How can biology help in the fight against AIDS? transmission pathway i.Break the transmission pathway ii.Produce drugs ii.Produce drugs that kill the virus or at least stop it from reproducing. iii.Produce a vaccine iii.Produce a vaccine against the virus. How biologists combat the spread of the disease? spreadof AIDS: There are things we can do to help control the spread of AIDS: i.Restricting i.Restricting the number of sexual partners. circumcised ii.Men can elect to be circumcised. iii.Not sharing iii.Not sharing infected needles.

24. Unit 2:Biochemical Molecules

25. Biochemical Molecules Are molecules of life. They can be classified into two main types: o Inorganic molecules o Organic molecules

26. 2.1.Water The chemical formula for water – H 2 O. Covers three-quarters of the planet It is the only substance that exists in three states(solid, liquid and gas). Some of the importance of water are: – a place to live – a transport medium – a reactant in many chemical reaction – a place for other reactions to take place – water is a vital chemical constituent of living cells. – water is a vital chemical constituent of living cells. E.g. Most cells are about 70% water and some are as high as 90%.

27. 2.1.1 Properties of water Water: – is transparent – is transparent; light can pass through the water – has a high specific heat capacity – has a high specific heat capacity; it takes quite a lot of energy to heat water up. Water also loses heat quite slowly. has a high latent heat of vaporization – has a high latent heat of vaporization; it takes a lot of energy to turn liquid water into water vapor (or steam). has a high surface tension – has a high surface tension; the molecules at the surface are held together more strongly. – Ice is less dense than liquid water. ideal viscosity More viscous means less fluid. – Water has the ideal viscosity for a transport medium. Viscosity is a measure of how fluid a liquid is – how easily it flows. More viscous means less fluid.

28. 2.2 Organic molecules They always contain both carbon and hydrogen Most biological organic molecules contain oxygen in addition to carbon and hydrogen and some also contain nitrogen. most frequently Chemical elements that are found most frequently in living organisms are: Hydrogen (H) 59%, Oxygen (O) 24%, Carbon (C) 11%

30. 2.2.1 Carbohydrates carbon, hydrogen and oxygen. All carbohydrates contain the elements carbon, hydrogen and oxygen. For example, glucose, C 6 H 12 O 6, and maltose, C 12 H 22 O 11. the most abundant They are the most abundant organic molecules in nature. They are substances that yield aldehydes or ketones on hydrolysis. Aldose Aldose: Glucose Ketose Ketose: Fructose sugar units Based on the number of sugar units they contain, they are categorized into: i.Monosaccharaides ii.Disaccharides iii.Polysaccharides  Sugar molecules are bonded together through the glycosidic linkage

31. Carbohydrates have a range of functions: release energy – They are used to release energy. – Storage carbohydrates include: starch starch in plants glycogen glycogen in animals – Some carbohydrates are used to build structures; structural carbohydrates include: cellulose cellulose, which is the main constituent of the primary cell wall of plants chitin chitin, which occurs in the cell walls of fungi and in the exoskeletons exoskeletons of insects peptidoglycan peptidoglycan, which occurs in bacterial cell walls cell-cell recognition – Help for communication between cells (cell-cell recognition)

32. I.MONOSACCHARAIDES (SINGLE SUGAR) Are simplest carbohydrates (sugars) functional group Based on functional group that they possess, monosaccharaides can be classified: i.Aldoses- with aldehyde functional group (CHO). E.g. Ribose, Glyceraldehyde, Glucose, Galactose ii.Ketoses- with ketone functional group (C=O). E.g., Ribulose, Dihydroxyacetone, Fructose NB. Nearly all the polysaccharides found in living things are polymers of aldose monosaccharaides NB. Nearly all the polysaccharides found in living things are polymers of aldose monosaccharaides. Based on the number of carbon atoms are present in the molecule, monosaccharaides can be classified: i.Triose i.Triose - has three carbon atoms – formula C 3 H 6 O 3. E.g., Glyceraldehyde, Dihydroxyacetone, ii.Pentose ii.Pentose - has five carbon atoms – formula C 5 H 10 O 5. E.g., Ribose, Ribulose iii.Hexose iii.Hexose - has six carbon atoms – formula C 6 H 12 O 6. E.g., Glucose, Galactose, Fructose

34. 34 III. Polysaccharides: many sugar units Many simple sugars can be joined together by glycosidic bond to formpolysaccharides by dehydration. Examples: Starch(bread, potatoes), - a mixture of amylose and amylopectin. Glycogen (beef muscle)- β- glucose molecules, it is not a source of energy for humans. Cellulose (lettuce, corn)- made from β- glucose molecules, it is not a source of energy for humans. Chitin - exoskeleton of insects, cell wall of true fungi

35. 2.3 Lipids much less oxygen Like carbohydrates, nearly all lipids contain only the elements carbon, hydrogen and oxygen, but they contain much less oxygen than carbohydrates. Lipids are a varied group of compounds that include: i.Triglycerides i.Triglycerides = glycerol and three fatty acids joined by ester bonds. ii.Phospholipids ii.Phospholipids = glycerol+ two fatty acids + a phosphate group. There are two distinct regions to a phospholipid molecule: a hydrophilic (water-loving) region, consisting of the phosphate ‘head’ a hydrophobic (water-hating) region, consisting of the hydrocarbon ‘tails’ iii.Waxes iii.Waxes = fatty acids + long-chain alcohols

36. Lipids have a range of functions: o Waxesbirds’ feathers epidermis o Waxes for coating birds’ feathers and the epidermis of the leaves of plants (the waxy cuticle). o Phospholipidscomponents of all cell membranes. o Phospholipids are basic components of all cell membranes. o Triglycerides have several functions including o Triglycerides have several functions including: Respiratory substrate- Respiratory substrate- a molecule of triglyceride yields over twice as many molecules of ATP (twice as much energy) as a molecule of glucose Thermal insulation- Thermal insulation- adipose tissue contain large amounts of triglycerides, which give good thermal insulation Buoyancy- Buoyancy- lipids are less dense than water. Waterproofing- Waterproofing- the oils secreted by some animals onto their skin are triglycerides.

37. 2.3.1 Saturated vs. Unsaturated Fatty Acids. Unsaturated fatty acids: i. Unsaturated fatty acids: have at least one double bond between carbon atoms in the tail chain. Fats are solid at room temperature. liquid Oils are liquid at room temperature. ii. Monounsaturated fatty acids: one double bond have one double bond in the carbon chain. E.g., Butter, Olives, and Peanuts. iii. Polyunsaturated fatty acids: two or more double bonds. E.g., contain two or more double bonds. E.g., Soybeans, Safflowers, and Corn.

38. 2.4. Proteins nitrogensulphur. They contain the elements carbon, hydrogen and oxygen (like carbohydrates and lipids), but they also contain nitrogen and most contain sulphur. amino acids which joined by peptide bonds. Protein molecules are polymers of amino acids which joined by peptide bonds. to form all living cells. Proteins are extremely important substances that are needed to form all living cells.

39. 2.4.1 Function of proteins Proteins are important in the: structure of plasma membranes: ion channelstransport proteins surface receptors structure of plasma membranes: protein form ion channels, transport proteins and surface receptors for hormones, neurotransmitters and other molecules immune system: immune system: antigen and antibody molecules are proteins control of metabolism: control of metabolism: all enzymes are proteins structure of chromosomes: structure of chromosomes: DNA is wound around molecules of the protein histone to form a chromosome.

40. 2.4. 2 Types of Proteins molecular shapes: Proteins are classified into two main groups, according to their molecular shapes: i.Fibrous proteins tertiary structurelong string or fiber. i.Fibrous proteins that have a tertiary structure that resembles a long string or fiber. E.g., Collagen And Keratin ii. Globular proteins globule or ball. ii. Globular proteins that have a tertiary structure that resembles a globule or ball. E.g., Enzymes And Receptor Proteins.

41. Amino acids: central carbon amino group(, carboxyl group, Hydrogen and R group consists of a central carbon atom bonded to amino group( –NH 2 ), carboxyl group (–COOH), Hydrogen and R group. common to all Amino group, carboxyl group, and Hydrogen are common to all amino acids. R group varies between amino acids and determine their identities and much of the chemical properties. But the R group varies between amino acids and determine their identities and much of the chemical properties.

42. 2.4.3. Structure of proteins 4 levels Proteins have 4 levels of organization or structure i. Primary structure: is the sequence of amino acids in the peptide chain.

43. ii. Secondary structure: is determined by the folding of the primary structure into either an α-helix or a β- pleated sheet; these structures are held in shape by hydrogen bonds coiled(spiral α-helix a coiled(spiral) secondary structure of a polypeptide folded(zigzag β-pleated sheet a folded(zigzag) secondary structure of a polypeptide.

44. . Tertiary structure: iii. Tertiary structure: is determined by the further folding of the secondary structure into either a fibrous or a globular shape; these structures are held in place by further hydrogen bonds, disulphide bridges and ionic bonds. These new bonds include: Hydrogen bonds- Hydrogen bonds- between the R-groups of some amino acids Disulphide bridges- Disulphide bridges- between amino acids that contain sulphur Ionic bonds- Ionic bonds- between amino acids with positively charged R-groups and those with negatively charged R-groups

45. iv. Quaternary structure: iv. Quaternary structure: three-dimensional It is the final three-dimensional structure of the protein. two or more polypeptide chains folded into a tertiary structure Structures formed when two or more polypeptide chains (folded into a tertiary structure) become associated in the final structure of the protein. E.g. Haemoglobin, Collagen quaternary structure (4  ) example: hemoglobin has 4 polypeptide chains

46. 2.5 Nucleic Acids Made up of elements of Carbon, Hydrogen and Oxygen, Nitrogen, and Phosphorus Made up of elements of Carbon, Hydrogen and Oxygen, Nitrogen, and Phosphorus nucleotides. are made up of smaller units called nucleotides. 3/1/202046

47. Nucleic Acidsare two types: DNA or Deoxyribonucleic Acid : i. DNA or Deoxyribonucleic Acid : DNA is the nucleic acid found in chromosomes. DNA is the genetic material. ii. RNA or Ribonucleic Acid: RNA is a nucleic acid found both in the nucleus and the cytoplasm. Q. Explain the difference between DNA and RNA

50. Unit 3: Cell biology

51. 3.1. Cell theory In 1839 Matthias Schleiden and Teodore Schwann introduced an idea known as the cell theory and In 1858 Rudolf Virchow, completes the first accepted version of the cell theory: i.All organisms are made up of one or more cells ii.All cells come from pre-existing cells iii.The cell is the unit of structure, and physiology in living things. iv.The cell retains a dual existence as a distinct entity and a building block in the construction of organisms.

52. Features of Living Organisms : Respiration – the process by which living organisms get the energy from their food. Excretion – getting rid of the waste products produced by the cells. Growth – living organisms get bigger. They increase in both size and mass, using chemicals from their food to build new material. Irritability – all living organisms are sensitive to changes in their surroundings Movement – all living organisms need to move to get near to things they need or away from problems. Animals move using muscles, plants move more slowly using growth. Reproduction – producing o ff spring is vital to the long- term survival of any type of living organism.

53. 3.2. Types of cell i. Prokaryotic: The first type of cells to be formed when life first evolved. A type of cell that does not have a nucleus. Are much smaller and simpler than eukaryotic cells. ii. Eukaryotic cells: A type of cell that has a nucleus. Have many more different individual structures, called organelles, Have many more membranes in the cell. Have membrane-bound organelles: endoplasmic reticulum, nucleus, mitochondria, chloroplasts (if present), lysosomes, Golgi apparatus.

54. Main differences between prokaryotic and eukaryotic cells

55. 3.3. Parts of the Cell and Its Function A cell contain small units called organelles. Many of these organelles contain enzymes and chemicals to carry out specialised jobs within the cell.Nucleus: Controls all the activities of the cell. Contains the instructions for making new cells or new organisms in the form of long threads known as chromosomes. Cell wall: is made mainly of a carbohydrate called cellulose, which strengthens the cell and gives it support. It is found outside the cell membrane.

56. Cytoplasm: Is a liquid gel in which most of the chemical reactions needed for life take place. About 70% of the cytoplasm of a cell is actually water! contains all the other organelles of the cell where most of the chemical reactions take place. Endoplasmic reticulum Endoplasmic reticulum: It links the nucleus with the cell membrane. Divided into: i. Rough endoplasmic has ribosomes on its surface and is responsible for the manufacture and transport of proteins. ii. Smooth endoplasmic reticulum. has no ribosomes on its surface. It is concerned with the synthesis of lipids.

57. Ribosomes: are found on the endoplasmic reticulum in your cells. are vital for protein synthesis, the process by which the body makes all the enzymes that control the reactions of the cells. Mitochondria Mitochondria: Are the powerhouse of the cell. Carry out most of the reactions of respiration. Golgi Complex: It is made up of a series of flattened, stacked pouches called cisternae. It processes the raw material into finished products. It is referred to as the manufacturing and the shipping center of the cell. It is responsible for transporting, modifying, and packaging proteins and lipids into vesicles for delivery to targeted destinations.

58. Vacuole: is a space in the cytoplasm filled with cell sap, a liquid containing sugars, mineral ions and other chemicals dissolved in water.Lysosomes: containing powerful hydrolytic enzymes They are membrane-enclosed sacs containing powerful hydrolytic enzymes capable of digesting and removing unwanted cellular debris and foreign materials such as bacteria that have been internalized within the cell. Peroxisome: oxidative enzymes and catalase It is membrane-enclosed sacs containing oxidative enzymes and catalase that detoxify various wastes (decomposing deadly hydrogen peroxide into harmless water and oxygen

59. Vesicles: They are membrane bound sacs that are used to store or transport substances around the cell. Lysosomes are actually Vesicles.Cytoskeleton: It is a complex protein network that act as the “bone and muscle” of the cell. This network has at least four distinct elements: Microtubules, Microfilaments, Intermediate filaments and Micro-tubular lattice Cell membrane: forms a barrier like a very thin ‘skin’ around the outside of the cell. controls the passage of substances. It is selectively permeable. i.e., it lets some substances through but not others.

60. Figure 4.22 The current fluid mosaic model of membrane structure

61. The components of the membrane are: i.Phospholipid bilayer: is the basis for the membrane ii. Integral proteins: Are intrinsic proteins and transmembrane proteins that span the membrane. The main types of these transport proteins are: Channel proteins: these proteins have a channel through them along which a specific ion can pass Carrier proteins: these proteins transport larger molecules through the membrane by facilitated diffusion or active transport.

62. iii. Peripheral proteins: Are extrinsic proteins that span only one layer (or sometimes less) of the membrane. They have a range of functions; some are enzymes, others anchor integral proteins to the cytoskeleton iv.Glycoproteins and glycolipids: often serve as signals to other cells. act as receptor sites for hormones and drugs. allow identification of the cell by the immune system. v. Cholesterol: reduces the fluidity of the membrane.

63. Fig: Animal cell

64. Fig.: Plant cell

65. 3.4. The cell and its environment Diffusion: of high concentration to an area of low concentration is movement of particles from an area of high concentration to an area of low concentration along a concentration gradientOsmosis: water moves a partially permeable membrane. is the process by which water moves across a partially permeable membrane. a high water potential to a system with a low water potential is the movement of water from a system with a high water potential to a system with a low water potential across a partially permeable membrane. Pure liquid water Pure liquid water has a higher water potential than any other system.

66. When comparing the water potential of a solution to that of a cell, we could describe it as: same water potential i.Isotonic: having the same water potential as the cell lower (more negative) water potential ii.Hypertonic: having a lower (more negative) water potential than the cell higher (less negative) water potential iii.Hypotonic: having a higher (less negative) water potential than the cell.

67. hypotonic environment turgidcytoplasm of a plant cell is pushed hard against the cell wall The plant cell in hypotonic environment will be turgid when the cytoplasm of a plant cell is pushed hard against the cell wall by the vacuole which is filled with water hypertonic environment flaccidvacuole shrinks plasmolyzedcytoplasm shrinks The plant cell in hypertonic environment will be flaccid when the vacuole shrinks and the cell becomes plasmolyzed when the cytoplasm shrinks away from the cell wall due to osmotic movement of water.

68. Facilitated transport: assistance of transmembrane proteins without the expenditure of cellular energy. material moves across the plasma membrane with the assistance of transmembrane proteins down a concentration gradient (from high to low concentration) without the expenditure of cellular energy. Active transport: against a concentration gradientusing energy Is the movement of substances against a concentration gradient using energy from respiration.

69. Endocytosis In this process, large particles are engulfed by a cell. large particles whole organisms smaller particles Can be phagocytosis (ingestion of large particles or even whole organisms outside the cell.), pinocytosis (the ingestion of smaller particles). Exocytosis: In this process, substances are moved from the inside to the outside of the cell.

70. 3.5. Cellular Respiration ATP: is Adenosine Tri-Phosphate a phosphorylated nucleotide is sometimes described as a phosphorylated nucleotide. pentose sugar, nitrogen base(adenine), and phosphate group. is essentially the adenine nucleotide that contains pentose sugar, nitrogen base(adenine), and phosphate group. Figure 5.1 A nucleotide containing base adenine Figure 5.2 structure of the ATP molecule

71. The processes that require energy from ATP: macromolecules synthesis of macromolecules-E.g., proteins active transport active transport across a plasma membrane. muscle contraction muscle contraction conduction of nerve impulses conduction of nerve impulses initial reactions of respiration. initial reactions of respiration. There are two main pathways by which respiration can produce ATP by using ATP synthase enzyme : i.aerobic pathway (aerobic respiration) presence of oxygen i.aerobic pathway (aerobic respiration) – this requires the presence of oxygen, and ii.anaerobic pathway (anaerobic respiration absence of oxygen. ii.anaerobic pathway (anaerobic respiration) – this can take place in the absence of oxygen.

72. Stages of aerobic respiration of glucose There are four stages: i.Glycolysis ii.Link Reaction iii.Krebs Cycle iv.Electron Transport and Chemiosmosis Glycolysis: Anaerobic Anaerobic respiration Occurs in the cytosol (both in prokaryotes and eukaryotes) under both aerobic and anaerobic conditions It does not take place inside the mitochondria because: the glucose molecule cannot diffuse through the mitochondrial membranes, and there are no carrier proteins to transport the glucose molecule across the membranes.

73. In ten steps, glycolysis produce a net yield of: i. 2 ATP, ii. 2 NADH, iii. 2 pyruvate(3C) iii. 2 pyruvate(3C) molecules

74. The following reactions take place in glycolysis: i.two molecules of ATP are used to ‘phosphorylate’ each molecule of glucose. This makes the glucose more reactive. glucose ii.In the phosphorylation process, glucose is converted fructose 1,6-bisphosphate. two molecules iii.The fructose 1,6-bisphosphate is split into two molecules of the three-carbon sugar glyceraldehyde-3 phosphate (GP) GP pyruvate one molecule of reduced NAD. iv.Each molecule of GP is then converted into pyruvate, with the production of two molecules of ATP (by substrate level phosphorylation) and one molecule of reduced NAD.

76. Link reaction: In the reaction: pyruvate coenzyme A (CoA) acetyl coenzyme A (acetyl CoA). A molecule of pyruvate reacts with a molecule of coenzyme A (CoA) to form a molecule of acetyl coenzyme A (acetyl CoA). Hydrogen is lost () reduced NAD Hydrogen is lost (dehydrogenation) and reduced NAD is formed. A carbon atom carbon dioxide. A carbon atom is lost(decarboxylation) to form carbon dioxide.

77. Krebs Cycle: 1)1Acetyl coenzyme A (2C) oxaloacetate (4C) citrate (6C) 1)1Acetyl coenzyme A (2C) reacts with the oxaloacetate (4C) to form called citrate (6C). 2)Citratefive- carbon compound and CO 2 is produced. 2)Citrate then loses a carbon atom (decarboxylated) to form a five- carbon compound and CO 2 is produced. 3)The five-carbon compound a four-carbon compound and CO 2 is again produced ATP by substrate level phosphorylation 3)The five-carbon compound is then further decarboxylated to form a four-carbon compound and CO 2 is again produced; 1ATP is also produced by substrate level phosphorylation. 4)The four-carbon compound regenerate(oxaloacetate) complete 4)The four-carbon compound undergoes several molecular transformations to regenerate(oxaloacetate) and the cycle is complete and can begin again with oxaloacetate reacting with another molecule of acetyl CoA. 5)Inseveral reactions reduced NAD, in just one reaction, reduced FAD 5)In several reactions in the cycle, reduced NAD is produced and, in just one reaction, reduced FAD is produced.

78. The main stages of the Krebs cycle

79. Electron Transport Chain and Chemiosmosis oxidative phosphorylation In these process oxidative phosphorylation will occur. in the fluid matrix of the mitochondrion, on the inner mitochondrial membrane. The link reaction and Krebs cycle take place in the fluid matrix of the mitochondrion, the reactions of the electron transport chain and chemiosmosis take place on the inner mitochondrial membrane. cristaefold On the cristae (is a fold in the inner membrane of a mitochondrion.), the following events take place: split into protons (hydrogen ions) and electrons. o The hydrogen atoms carried by reduced NAD and reduced FAD are released and split into protons (hydrogen ions) and electrons. a series of electron carriers transport chainthey lose energy o The electrons pass along a series of electron carriers that form the transport chain; they lose energy as they pass from one carrier to the next.

80. pump protons from the matrix of the mitochondrion to the inter-membrane space. o Three of the electron carriers that pump protons from the matrix of the mitochondrion to the inter-membrane space. These are: i.Reduced NAD dehydrogenase i.Reduced NAD dehydrogenase (also a proton pump) ii.Ubiquinone (also a proton pump), and iii.Cytochromes (the third proton pump). o Electrons from reduced NAD make this happen at all three pumps. o At the end of the electron transport chain, the electrons combine with protons and with oxygen to form molecules of water. Because of this, oxygen is known as the terminal electron acceptor.

81. The carrier molecules in the electron transport chain on the inner membrane of a mitochondrion

83. Anaerobic Pathway: No oxygen No oxygen involvement. cannot take place Electrons and protons react with oxygen to form water, cannot take place halt. The link reaction, Krebs cycle and electron transport chain come to a halt. Different organisms produce different fermentation end products: Animallactate (lactic acid) Animal cells produce lactate (lactic acid) when they ferment glucose. Yeast cells ethanol (ethyl alcohol). Yeast cells produce ethanol (ethyl alcohol).

85. Unit 4: Micro-organisms

86. 4.1. Introduction to microorganisms Micro-organisms: tiny living organisms too small to be seen seen with the aid of a microscope are tiny living organisms that are usually too small to be seen with the naked eye or can only be seen with the aid of a microscope. five main groups There are five main groups of micro- organisms: – Protozoa, some fungi, some algae, Viruses, bacteria

87. Bacteria: single-celled – are single-celled organisms. – have prokaryotic cells cell membrane, cytoplasm, ribosomes and cell wall peptidoglycangenetic material (DNA), – Its cell is made up of a cell membrane, cytoplasm, ribosomes and cell wall (peptidoglycan), genetic material (DNA), but this is not contained in a nucleus. flagella move slime capsules – Some bacteria have flagella to help them move, or protective slime capsules. – Have di ff erent shapes and sizes: spherical Cocci (singular, coccus) – spherical bacteria rod-shaped Bacilli (singular, bacillus) – rod-shaped bacteria spiral or corkscrew-shaped Spirochaetes – spiral or corkscrew-shaped bacteria

89. Gram’s stain Whether or not they are colored by Gram’s stain, bacteria are classified in to two: – Gram-positive purple – Gram-positive – these bacteria are stained purple by Gram’s stain – Gram-negative pink – Gram-negative – these bacteria are stained pink by Gram’s stain.

90. Viruses: smaller than bacteria are even smaller than bacteria. regular geometric usually have regular geometric shapes protein coat genetic material are made up of a protein coat surrounding genetic material containing relatively few genes. do not carry out reproduction They do not carry out any of the functions of normal living organisms except reproduction, and they can only reproduce by taking over another living cell. all disease. all naturally occurring viruses cause disease.

91. nature of their genetic material Based on the nature of their genetic material and the way in which it is expressed, viruses are grouped into: cold sores i.DNA viruses – for example, Herpes simplex (causes cold sores) swine flu ii.RNA viruses – for example, H1N1 virus (causes swine flu) AIDS iii.Retroviruses – for example, HIV (causes AIDS) type of organism they infect Based on the type of organism they infect, viruses can also be classified in to: i.animal-infecting viruses ii.plant-infecting viruses iii.bacteria-infecting viruses iii.bacteria-infecting viruses – these are called bacteriophages

92. life cycles There are three different life cycles in viruses: i.Lytic life cycle: host cell to burst release new viruses. – infection causes the host cell to burst and release new viruses. ii.Lysogenic life cycle a latent state DNA is reproduced no new viruses – infection causes the virus to enter a latent state where its DNA is reproduced with the host DNA, but no new viruses are formed iii.Chronic release life cycle released without killing the host cell. – infection causes viruses to be released without killing the host cell.

93. Protozoa: unicellularlack a cell wall are unicellular organisms that lack a cell wall. motile most of them are motile (able to move) Amoeba, Plasmodium, and Paramecium. include organisms such as Amoeba, Plasmodium, and Paramecium. Fungi: dead or living organisms living organisms which obtain their food from other dead or living organisms. decomposers decomposers, breaking down animal and plant material and returning nutrients to the environment. E.g. moulds and yeasts. do not do not have true roots, stems and leaves.

94. Yeast Yeast: single-celled Is a single-celled organisms. nucleus, cytoplasm, a membraneand a cell wall Has a nucleus, cytoplasm, a membrane. and a cell wall. budding Reproduces by asexual budding – splitting to form new yeast cells. yeast-like thrush The yeast-like organism that causes thrush in humans (Candida). Figure 4.3 Yeast cell structures

95. Moulds: threadlike hyphae cell wall, cytoplasm nuclei. are made up of minute, threadlike structures called hyphae. Hyphae are tubes consisting of a cell wall, cytoplasm and nuclei. Mycelium is the collection of very fine strands that makes up a fungus. fruiting bodies spores reproduce asexually by producing fruiting bodies containing spores.

96. Alga (plural algae): photosynthesis is an organism that obtains its nutrition using photosynthesis. large unicellular Many are large (seaweeds), but some algae are unicellular. The unicellular algae: plankton – are part of the plankton: are collections of small microscopic plant organisms that float or drift in large numbers in fresh or salt water, are providing food for fish and other larger organisms. far more oxygen all the forests in the world – in the oceans produce far more oxygen during photosynthesis than all the forests in the world together. – Some unicellular algae are motile – they can move. E.g. Chlamydomonas.

97. Control of micro-organisms SterilizationSterilization is the killing of all micro-organisms in a material or on the surface of an object, making it safe to handle without fear of contamination. There are a number of di ff erent ways we can sterilize things: High temperatures or heat i. High temperatures or heat E.g. Autoclaving, Ultra high temperature (UHT), Pasteurisation, ii. Disinfectants inactivate ii. Disinfectants: is a chemical substance or compound used to inactivate or destroy microorganisms on inert surfaces. fast actingfast acting e ff ective against all types of infectious agentse ff ective against all types of infectious agents able to easily penetrate material to be disinfected without damaging or discoloring it. iii. Antiseptics -slows or stops external surfaces iii. Antiseptics - is a chemical agent that slows or stops the growth of microorganisms on external surfaces of the body and helps to prevent infection.

98. Germ theory: micro-organisms Is the theory that disease can be caused by micro-organisms. pathogens. – Organisms that cause disease are called pathogens. infectious disease – A disease that is caused by a micro- organism infecting the body is an infectious disease. one type – Infectious disease is just one type of disease.

100. other factors. Disease can be caused by a number of other factors. person’s lifestyle 1)Human induced diseases are diseases that arise as a result of a person’s lifestyle. ageing process 2)Degenerative diseases often result from the ageing process during which the affected tissues deteriorate over time due to simple ‘wear and tear’. mutated genes. 3)Genetic diseases are diseases that result from the action of mutated genes. lack of a nutrient 4)Deficiency diseases are diseases that result from a lack of a nutrient in our diet. socially unacceptable behaviour. 5)Social diseases are conditions that result from social activities and may lead to socially unacceptable behaviour. many factors. 6)Multifactorial describes a condition that is affected by the interaction of many factors.

101. Reservoirs of infection Reservoirs of infection: 1)Human beings 1)Human beings – the reservoir for many diseases, including the common cold, diphtheria and others 2)Other animals 2)Other animals – for example: chickens, the reservoir for salmonella infections; mosquito, the reservoir for malaria 3)Soiltetanus 3)Soil – the reservoir for tetanus and many other pathogens 4)Water 4)Water – the reservoir for Legionnaire’s disease, amoeba, cholera, etc. 5)Food 5)Food – the reservoir for many diseases including typhoid 6)Contaminated objects 6)Contaminated objects – contact infections such as HIV/AIDS and trachoma 7)Air 7)Air – the reservoir for pneumonia, tuberculosis, etc.

103. 4.2. Beneficial Microorganisms i. Recycling minerals through ecosystems: Many bacteria are decomposers and recycle many elements, including: Carbon, Nitrogen, Sulphur and Phosphorus. The nitrogen cycle: The element nitrogen is found in proteins, DNA, RNA, ATP

104. The sulphur cycle: Sulphur is found in fewer types of organic molecule than nitrogen, but it is found in many proteins.

105. ii. Industrial importance Food and beverage fermentation Bacteria and other micro-organisms have been used to make: Bread. Alcohol, irgo or yoghurt, vinegar, sewage treatment Production of vinegar Vinegar is a dilute solution of ethanoic acid in water. Vinegar is used in two main ways: to favour foods, and to preserve foods

106. Producing antibiotics the first antibiotics all came from fungi. Genetically modified bacteria are also used to produce: insulin, human growth hormone, antibiotics, enzymes for washing powders and human vaccines, such as the vaccine against hepatitis B. Sewage treatment Sewage treatment All types of sewage treatment rely on the action of a range of microorganisms to oxidise the organic matter present in sewage. there are two main methods: i.the percolating filter method and ii.the activated sludge method Read How Do the Methods Work!

107. Unit 5: Genetics

108. Definitions of terms Gene a section of DNA that determines a specific feature. Histone the core of a chromosome around which the chromosome’s DNA is wrapped. Chromosome a long strand of DNA on which a large number of genes is stored. Allele a version of a gene that determines a particular trait. Locus (plural loci) the position of a particular gene on a chromosome. Codominant or incomplete dominant alleles the pattern of inheritance where both alleles of a gene are equally expressed and determine which trait occurs in a heterozygous organism.

109. Homozygous Homozygous an organism is homozygous for a particular gene if it has the same allele for that gene on each of the chromosomes in the homologous pair. Heterozygous Heterozygous an organism is heterozygous for a particular gene if it has different alleles for that gene on each of the chromosomes in the relevant homologous pair. Genotype Genotype a genotype describes the pair of alleles for a particular gene possessed by a organism. Phenotype Phenotype a phenotype describes the trait or traits determined by a particular genotype.

110. 5.1. DNA and chromosome structure Inside the nucleus of every cell there are thread-like structures called chromosomes. A chromosome is a structure in the nucleus of a cell consisting of genes. A gene is a unit of hereditary material located on the chromosomes. Chromosomes are made from two chemicals: DNA (deoxyribonucleic acid) and Histones (a set of globular proteins) Chromosomes come in pairs known as homologous pairs. Homologous chromosomes a pair of chromosomes having the same gene sequences, each derived from one parent. Karyotype map of the chromosomes in the nucleus of a single cell.

111. Human have 23 pairs, tomatoes have 12 pairs and elephants have 28 pairs of chromosomes. 22 pairs of chromosomes in human are known as the autosomes. The remaining (1Pair) is sex chromosomes because they determine whether you are male(XY) or female(XX). Chromosomes are made up of the genetic material DNA in a DNA–protein complex. humans have 46 chromosomes and tomatoes have 24, while elephants have 56. DNA nucleic acid containing the genetic instructions used in the development and functioning of all known living organisms and some viruses

112. The two DNA strands are linked by the bases: adenine, thymine, guanine and cytosine. Adenine is a base that comprise DNA which pairs with thymine. Guanine is a base that comprise DNA which pairs with cytosine. Nucleotide is a building block of DNA or RNA which consists of a sugar, a phosphate, and one of the four bases. Polynucleotide is long chains of linked nucleotides.

113. The basic unit of a DNA strand is a nucleotide. There are four types of nucleotides: i.Adenine-containing nucleotide ii.Guanine-containing nucleotide iii.Cytosine-containing nucleotide, and iv.Thymine-containing nucleotide (in DNA, or Uracil-containing nucleotide in RNA)

115. 5.2. DNA Replication DNA molecule replicates in such a way that: each new DNA molecule formed contains one strand from the original DNA both new DNA molecules formed are identical to each other and to the original molecule The process of DNA molecule replication involves several enzymes and proteins, but the key stages are as follows: i. Molecules of the enzyme DNA helicase break hydrogen bonds and ‘unwind’ part of the helix of the DNA molecule, revealing two single-stranded regions. ii. Molecules of DNA polymerase follow the helicase along each single-stranded region, which acts as a template for the synthesis of a new strand.

116. iii. The DNA polymerase assembles free DNA nucleotides into a new strand alongside each of the template strands. e base sequence in each of these new strands is complementary to its template strand because of the base-pairing rule, A-T, C-G. iv. The processes of unwinding followed by complementary strand synthesis progresses along the whole length of the DNA molecule. v. The result is two DNA molecules that are identical to each other (and to the original molecule); each contains one strand from the original DNA molecule and one newly synthesized strand that is complementary to this.

118. Cloning and Genetic Engineering A clone of an organism is a group of organisms that are genetically identical to each other and to the organism from which they were derived. Gene cloning means making multiple copies of a gene. There are several ways in which this can be done. The principal methods are divided into two main categories: i.In vivo cloning – the gene is introduced into a cell and is copied as the cell divides. ii.In vitro cloning – this does not take place in living cells but the DNA is copied many times over using the polymerase chain reaction (PCR). It is a process mimics the natural semiconservative replication of DNA in a machine called a PCR machine.

119. Genetic engineering Genetic engineering is a process in which the genome of an organism is altered, usually by having an extra gene from a different organism added. The organism is then a genetically modified or a transgenic organism. Transgenic organism a genetically modified organism that contains a gene or genes transferred from another organism belonging to a different species.

120. Genetic engineering has many potential benefits: to treat infectious diseases by implanting genes that code for antiviral proteins specific to each antigen. to give increased growth rates and reduced susceptibility to disease. This would reduce the use of fertilizers and pesticides and the chemical pollution that results from their use. to absorb more CO 2 and reduce the threat of global warming. to increase genetic diversity, and produce more variant alleles which could also be crossed over and implanted into other species. Genetic engineering is a much quicker process than traditional selective breeding.

121. 5.3. Protein synthesis mRNA (messenger RNA) is a nucleic acid that transmits the genetic code from DNA to ribosome. Transcription the process that converts genetic information from a DNA code into an mRNA code. tRNA (transfer RNA) transfers individual amino acids during translation Translation the process in which the mRNA code is converted into a sequence of amino acids.

122. Events occur during protein synthesis : – The DNA code for the protein is rewritten in a molecule of messenger RNA (mRNA); this rewriting of the code is called transcription. – The mRNA travels from the nucleus through pores in the nuclear envelope to the ribosomes. – Free amino acids are carried from the cytoplasm to the ribosomes by molecules of transfer RNA (tRNA). – The ribosome reads the mRNA code and assembles the amino acids carried by tRNA into a protein; this is called translation.

124. Genetic code: It is the sequence of bases in the nucleotides of the DNA that makes up a gene that codes for the protein and that each amino acid in the protein is coded for by a triplet (sequence of three) of bases. A gene is a sequence of base triplets in the DNA molecule that carries the code for a protein. With four different bases to work with (adenine, thymine, cytosine and guanine), there are 64 possible triplet codes, but only 20 amino acids are used to make all the different proteins. In DNA there is coding strand or the sense strand and non-coding or antisense strand.

125. Different amino acids have different codes: one triplet – Methionine and tryptophan have one triplet each two triplets – Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Histidine, Lysine, Phenyl -alanine and Tyrosine have two triplets each four triplets – Alanine, Glycine, Proline, Threonine, Valine have four triplets each six triplets – Arginine, Serine and Leucine have six triplets each. three triplets – Isoleucine and Stop have three triplets each ‘Stop’ codes(TAA, TAG and TGA): – do not code for amino acids at all degenerate code. – signals the end of protein manufacturing inside the cell, like a period at the end of a sentence. Because there is this extra capacity in the genetic code, over and above what is essential, it is said to be a degenerate code.

126. DNA code is a: – Non-overlapping code. This means that each triplet is distinct from all other triplets. The last base in one triplet cannot also be the first base (or second base) in another triplet. – Universal code. This means that the triplet TAT is the DNA code for the amino acid tyrosine in a human, a giant redwood tree, a bacterium or in any other living organism

127. Figure 3.47A The genetic code

128. Transcription in eukaryotic cells During this process, the coded information in the DNA of one gene is used to synthesize a molecule of mRNA that will carry the code to the ribosomes. To form the single-stranded mRNA when transcription takes place, only the antisense strand of DNA is transcribed. mRNA is similar to DNA in that it is built from nucleotides; however, it is different from DNA in a number of ways: – it is a much smaller molecule – it is single stranded – the base thymine is replaced by uracil – the sugar in the nucleotides is ribose, not deoxyribose. The triplets of bases in mRNA that code for amino acids are called codons.

129. In eukaryotic cells, transcription takes place in the following way: – The enzyme DNA-dependent RNA polymerase (RNA polymerase) binds with a section of DNA next to the gene to be transcribed. – Transcription factors activate the enzyme. – The enzyme begins to ‘unwind’ a section of DNA. RNA polymerase moves along the antisense strand, using it as a template for synthesizing the mRNA. – The polymerase assembles free RNA nucleotides into a chain in which the base sequence is complementary to the base sequence on the antisense strand of the DNA. This, therefore, carries the same triplet code as the sense strand (except that uracil replaces thymine). – The completed molecule leaves the DNA; the strands of DNA rejoin and re-coil.

131. Translation Translation Translation of the mRNA code into a protein depends on the interaction within a ribosome between mRNA and tRNA. The tRNA is has an anticodon loop and amino acid acceptor end. – The anticodon loop makes bases complementary to the codes on the mRNA and amino acid end has an attachment site for the amino acid that is specified by the mRNA codon.

132. Within the ribosome, there are three sites that can be occupied by a tRNA molecule, called the A, P and E sites.

133. The following events take place during translation: – The first two codons of the mRNA enter the ribosome. – Transfer RNA molecules (with amino acids attached) that have complementary anticodons bind to the first two codons of the mRNA. A site. – A peptide bond forms between the amino acids carried by these two tRNA molecules and the dipeptide is transferred to the tRNA in the A site. P site. – The ribosome moves along the mRNA by one codon, bringing the third codon into the ribosome; at the same time the ‘free’ tRNA exits the ribosome and the tRNA with the dipeptide moves into the P site. – A tRNA with a complementary anticodon binds with the third codon, bringing its amino acid into position next to the second amino acid. – A peptide bond forms between the second and third amino acids. – The ribosome moves along the mRNA by one codon, bringing the fourth mRNA codon into the ribosome, and the whole process is repeated until a ‘stop’ codon is in position and translation ceases.

135. Protein synthesis different in prokaryotic cells The process is essentially similar in both types of cells, with DNA being transcribed to mRNA, which is then translated to a polypeptide chain. However, there are some differences and these are linked to the fact that: – prokaryotic cells do not have a nucleus – prokaryotic mRNA does not need post-transcriptional processing – Prokaryotes: transcription and translation are coupled; mRNA can be translated by ribosomes at one end of its molecule while it is still being transcribed from DNA at the other end – Eukaryotes: transcription and translation are separated transcription occurs in the nucleus translation occurs in the cytoplasm eukaryotic mRNAs are modified before leaving the nucleus

137. Gene expression All genes aren’t active all the time. For examples: the genes that control the color of your iris are present in all your cells, but all your other cells aren’t this color – just the iris. Genes switch on: very often, genes are switched on by ‘transcription factors’ that are present in the cell. E.g. Protein Gene transcription factors operate in the following way: The transcription factors bind to a promoter sequence of DNA near to the gene to be activated. RNA polymerase binds to the DNA/ transcription factor complex. The RNA polymerase is ‘activated’ and moves away from the DNA/transcription factor complex along the gene. The RNA polymerase transcribes the antisense strand of the DNA as it moves along; the gene is now being expressed.

138. Genes switched off short interfering RNA(siRNA). gene itself posttranscriptional interference Besides transcription factors that promote the expression of genes, other factors can act to repress gene action. E.g. short interfering RNA(siRNA). Short interfering RNA is a short sequence of RNA which can be used to silence gene expression. They don’t act on the gene itself, but they ‘interfere with’ or ‘silence’ the mRNA once it has been transcribed from the DNA. This is called posttranscriptional interference.

139. Biologists think that the action of siRNA is as follows: – Double-stranded RNA (dsRNA) is produced in the nucleus from a range of genes. – It is then split into the very short lengths that characterize siRNA by an enzyme called ‘Dicer’. – The antisense strand of the siRNA then binds with a complex of molecules called RISC. – The siRNA binds with mRNA and allows RISC to degrade/ cleave the mRNA into small fragments.

140. 5.4. Mitosis and meiosis Mitosis Body cells divide by mitosis to produce more identical cells for growth, repair, replacement and, in some cases, asexual reproduction. Mitosis is division of the somatic cells to make identical daughter cells. Before a cell divides, It produces new copies of the homologous pairs of chromosomes in the nucleus. Each chromosome forms two identical chromatids. Then the chromatids divide into two identical packages, and the rest of the cytoplasm divides as well to form two genetically identical daughter cells. Once the new cells have formed, the chromatids are again referred to as chromosomes. Mitosis is one continuous process.

141. There are four stages in mitosis: interphase, prophase, metaphase, anaphase and telophase..

142. The cell cycle The cells in your body divide on a regular basis to bring about growth. They divide in a set sequence, known as the cell cycle, which involves several di ff erent stages. A period of active cell division: o this is when mitosis takes place and the number of cells increases. A long period of non-division: o when the cells get bigger, increase their mass, carry out normal cell activities and replicate their DNA ready for the next division.

143. Meiosis The cells in the reproductive organs (germ cells) divide to make sex cells. The cell division that takes place in the reproductive organ cells and produces gametes is known as meiosis. Meiosis is a special form of cell division where the chromosome number is reduced by half. When a cell divides to form gametes, meiosis is divided into two divisions. In the first meiotic division: The chromosomes are copied so there are four sets of chromatids. The cell then divides to form two identical daughter cells. The first meiotic division is very similar to mitosis.

144. In the second meiotic division: o identical daughter cells divide to form four gametes, each with a single set of chromosomes. o The second is again similar, but there is no more replication of chromosomes i.e., without the chromatids doubling again. There is no crossing over in prophase The chromosomes line up side by side in metaphase Chromatids are separated in anaphase

145. Figure 2.8 Tis simple diagram sums up the main stages of meiosis – see figure 2.9 for the details.

146. Meiosis occurs as part of a process known as gametogenesis, or gamete formation. In females this is called oogenesis (forms the ova). In a baby girl, the first stage of meiosis is completed before she is even born. The second stage occurs as the eggs ripen during the menstrual cycle and is completed after fertilization of the egg. In males, meiosis doesn’t start until puberty, when the testes start to produce sperm. The production of sperm is called spermatogenesis, and carries on throughout a man’s life.

147. Figure 3.20 Meiosis I

148. Figure 3.21 Meiosis II

149. Comparison of mitosis and meiosis Table 2.1 Comparing mitosis and meiosis

150. 5.5. Mendelian inheritance Inheritance is the science of how information is passed from parents to their children. Mendel used seven clearly di ff erent, pure-breeding traits (homozygotes) of the pea plant for his experiments. They are shown here in both their dominant and recessive forms. if only one copy Dominant allele is an allele where the characteristic is expressed in the phenotype even if only one copy of the allele is present Recessive allele is an allele where the characteristic is only expressed in the phenotype if two copies of the allele are present.

152. Mendel observed, for example, that the round shape of peas seemed to dominate the wrinkled shape, but that the information for a wrinkled shape continued to be carried and could emerge again in later generations – in other words there were unique units of inheritance that were not blended together.

153. Figure 2.16 A cross between a pea plant homozygous for the round pea allele, and a plant homozygous for the wrinkled pea allele, through the F1 and F2 generations.

154. The first generation of any cross is called the F1 (first filial generation) and they all have: the same heterozygous genotype and they also all have the same phenotype (the round pea shape) because the round allele is dominant. There is no sign of the wrinkled pea allele. If we then cross members of the F1 generation we call the next generation the F2 (second filial generation). The genotypes of F2 will be: one homozygous round pea, two heterozygous round peas and one homozygous wrinkled pea. The recessive trait for the wrinkled pea has become visible again, after being ‘hidden’ in the F1 generation.

155. Some genes have more than two alleles, and then the pattern of inheritance is a little more complex. We call this situation multiple allele inheritance. E.g., ABO blood groups There are three alleles involved in the inheritance of these blood groups: i.I A, which determines the production of the A antigen ii.I B, which determines the production of the B antigen iii.I O, which determines that neither antigen is produced Alleles I A and I B are codominant, but I O is recessive to both. The possible genotypes and phenotypes (blood groups) are shown below. GenotypeBlood group Genotype Blood group I A I A, I A I O A I B I B, I B I O B I A I B AB I O I O O

156. How inheritance works? The chromosomes we inherit carry our genetic information in the form of genes. Many of these genes have di ff erent forms, known as alleles. An allele is the particular form of information in an individual chromosome. There are genes that decide whether: your earlobes are attached closely to the side of your head or hang freely your thumb is straight or curved you have dimples when you smile you have hair on the second segment of your ring finger. Figure 2.14 These are all human characteristics that are controlled by a single pair of genes, so they can be very useful in helping us to understand how sexual reproduction introduces variety and how inheritance works.

157. Heredity and breeding selective breeding i.In selective breeding, only the animals or plants with the characteristic you want are allowed to breed. In time, every member of the breed shows that characteristic. ii.Cross–breed (Combination of traits) ii.Cross–breed (Combination of traits) between two different breeds. This gives you a combination of traits from the two different breeds – the best of both can be used to develop a new breed. Breeding animals and plants is very important for society: to enable us to make the best possible use of our resources, to feed our population, to maintain our genetic diversity and to provide new and useful genes for the international community.

158. 5.6. Mutations A mutation is any spontaneous change in the genetic material of an organism. There can be: – whole chromosomes changes or – parts of chromosomes changes, or – only a single base changes. The changes involving only a single base are called point mutations. There are several types of point mutation: i.Substitution ii.Addition iii.Deletions – These mutations occur quite randomly when DNA is replicating and each involves a change to just one base, but the change to the gene can be dramatic and the result can be that: the protein the gene should code for is not made at all or a different protein is made.

159. Figure 3.56 A substitution mutation Substitution

161. Addition and deletion In a deletion mutation a base is ‘missed out’ during replication, whilst in additions, an extra base is added. Both these are more significant mutations than substitutions.

163. Causes of Point Mutations The rate of mutation can be increased by a number of factors including: – carcinogenic chemicals, for example, those in tobacco smoke – high-energy radiation, for example, ultraviolet radiation, X-rays Consequences of Gene Mutations Mutations that occur in a normal body cell (a non- sex cell) will have one of four possible consequences: – It will be completely harmless. – It will damage the cell. – It will kill the cell. – It will make the cell cancerous, which might kill the person.

164. Genes called proto-oncogenes and tumour suppressor genes play important roles in regulating cell division and preventing the formation of a tumour. – When proto-oncogenes mutate, they often become active oncogenes, which stimulate the cell to divide in an uncontrolled manner. – Tumour suppressor genes recognize uncontrolled cell division and act to suppress cell division. If these genes mutate and become inactive, a tumour will form as uncontrolled cell division continues. A tumour is a mass of cells created when cell replication gets out of control. Tumours cause the disease cancer.

165. Mutations benefit an organism Mutations are the raw material of evolution. It is the only process that creates new genes. It gives bacteria resistance to a specific antibiotic, such as penicillin or ampicillin.

166. Chromosome mutations These occur: – when there is any change in the arrangement or structure of the chromosomes. – occur most often during meiosis at crossing over in prophase I. – They are much bigger events than point mutations and usually result in the death of a cell, may abort a fetus.

167. Inversion: occurs when an area of DNA on a chromosome reverses its orientation on the chromosome. Just one inversion on chromosome 16 can cause leukemia. An inversion can cause the embryo to miscarry, fail to grow, or be born with substantial medical problems. Chromosome 21 Chromosome 16 is one of the 23 pairs of chromosomes in humans. It spans about 90 million base pairs and accounts for nearly 3% of DNA in cells. Chromosome 21 is one of the 23 pairs of chromosomes in humans. It is the smallest of the chromosomes.

168. Deletion: a large section occurs due to the deletion of a large section of a chromosome. Prader-Willi syndrome can result in a variety of genetic disorders, such as Prader-Willi syndrome. This results from a malfunction of the hypothalamus (a small endocrine organ at the base of the brain), which plays a crucial role in many bodily functions, including hunger and satiety, temperature and pain regulation, fluid balance, puberty, emotions and fertility.

169. Insertion: is type of mutation describes an increase in the number of genes caused when an unequal crossover happens during meiosis. The chromosome may become abnormally long or short and stop functioning as a result.

170. Duplications: – When genes are duplicated it results in them being displayed twice on a single chromosome. This is usually harmless as the chromosome still has all its genes. However, duplication of the whole chromosome is more serious. Having three copies of chromosome 16, known as trisomy 16, leads to babies being born with a range of medical issues, such as poor foetal growth, muscular and skeletal anomalies, congenital heart defects and underdeveloped lungs.

171. Chromosome non-disjunction – When homologous chromosomes do not separate successfully to opposite poles during meiosis, the result is one of the gametes lacking a chromosome and the other having an extra chromosome. If this happens with chromosome 21, Down’s syndrome results. Those with the condition will have 47 chromosomes in every cell (because they have three copies of chromosome 21) as opposed to 46 like normal. Down’s syndrome is characterized by mental retardation, heart defects and stunted growth. –

172. Translocations A piece of one chromosome is transferred to another non-homologous chromosome. This type of chromosome mutation is often responsible for chronic myelogenous leukemia.