Biology L3

1. Student book

  • UNIT 1: INTRODUCTION TO BIODIVERSITY
  • Key Unit Competence
    Explain how diversity is threatened by climate change and human activities

    Learning objectives
    By the end of this unit, I should be able to:
    –– Define the terms: species, ecosystem and niche.
    –– Explain that biodiversity is considered at three different levels
    –– Evaluate the consequences of loss of biodiversity.
    –– Characterize the biotic and abiotic components that define Rwanda’s ecosystems (example: freshwater, marine, and terrestrial).
    –– Apply Simpson’s Index of Diversity.
    –– Explain the importance of random sampling in determining the biodiversity of an area.
    –– Use suitable survey methods such as frame quadrats, line and belt transects to assess the distribution and abundance of organisms in a local area.
    –– Use Pearson’s linear correlation to analyze the relationships between the
    distribution and abundance of species and abiotic or biotic factors.
    –– Recognize that the biodiversity of the earth is threatened by human activities and climate change

    Introductory activity: Biodiversity of Rwanda

    Read the following text and answer the questions that follow

    Rwanda is located at the heart of the Albertine Rift eco-region in the western arm of the Africa’s Rift Valley. Habitats of Rwanda are equally varied, ranging from Afro-Montana ecosystems in the northern and western regions to lowland forests, savannah woodlands and savannah grasslands in the southern and eastern regions. There are other habitats around volcanic hot springs and old lava flows, especially in the northern and western part of the country.

    Rwanda also has several lakes and wetlands which are rich in different species. Though not yet well surveyed, all these ecosystems host a rich variety of fauna and flora and micro-organisms. This rich biodiversity is mainly conserved in protected areas including three national parks, natural forests and wetlands. These cover almost 10 percent of the national territory while the rest of the country is densely populated (507 people per square kilometer in 2018).

    Many tourists visit Rwanda for its beautiful environment and biodiversity made of different species of plants and animals such as Aloe vera (Igikakarubamba), Muringa oleifera (Muringa), Phaseolus vulgaris (common bean), Nymphaea thermarum (Endemic plant species that cannot be met elsewhere in the world, only found in Mashyuza minor locality harbors),
    Colobus polykoma (White-black colobus monkey), Gorilla gorilla (mountain
    gorilla) bird Laniarius mufumbiri (Bird species mainly found in Rweru- Mugera wetland),etc.

    The most attracting species in Rwanda is Gorilla gorilla whose habitat is the mountains of Birunga where they make a large population. Another natural forest, Nyugwe National Park is a terrestrial ecosystem that contains a large community of different plants and animals.

    Rwanda also has different lakes such as Muhazi and Rumira. They are aquatic ecosystems made of few species of fish, such as tilapias. Tilapias from Lake Muhazi are small, black and bony fish while those from Lake Rumira look red, big and soft. Tilapias from both lakes still belong in the same species but show variations.

    Many species of animals and plants have been discovered in Rwanda but some species also disappeared. Today the big garden snails known as Achatina achatina have become rare in Bugesera. Other people poached Rhinoceros alba living in Savanah of Akagera National Park.

    Honey bees, butterflies and grasshoppers are small in size but still important for different ecosystem services. Each organism is important for its niche in ecosystem. We need to identify and protect the biodiversity of our ecosystem. Many tourists enjoy visiting Rwanda for its biodiversity.
    1. Name the species not found elsewhere that attract the tourists and locate where it is found.
    2. Mashyuza is a minor locality in western province in Rusizi district that contributes to biodiversity of Rwanda. Give any other two locations.
    3. Define each of the following biological terms and give an example from the text
    abovesada) Species (b) Population (c) Community (d) Habitat (e) Ecosystem
    (f )Variation (g) Niche
    4. What causes some species to become extinct?
    5. What can be the consequences of the loss of some species from our
    biodiversity?
    6. Do you support tourism in Rwanda? Give a reason to justify your answer.

    1.1 Meaning of key ecological terms and biodiversity
    Activity 1.1
    1. What do you understand by the following terms: biodiversity, species, niche, population, and community?
    2. Differentiate between ecological niche and habitat.

    1.1.1 Key ecological terms
    Species is a group of closely related organisms which are capable of interbreeding to produce fertile offspring. Occasionally two organisms which are genetically closely related but not of the same species can interbreed to produce infertile offspring. For example:
    –– A cross between a donkey and a horse produces a mule, which is infertile. Thus, a donkey and a horse do not belong to the same species
    –– Lions and tigers belonging to different species. However, when a male tiger mates with a female lion they can have fertile offspring called tiglons, although the offspring of female tigers and male lions called ligers are not fertile

    Note that normally, tigers are forest dwellers and lions are plains dwellers and they are ecologically isolated. Breeding has only been observed in captivity. An ecological population is a group of individuals of the same species which live in a particular area at any given time.

    An ecological community consists of populations of different species which live in the same place at the same time, and interact with each other. A habitat is a specific area or place in which an individual organism lives. When a habitat is very small it is regarded as a microhabitat. Most ecosystems contain several habitats, and one species can have more than one habitat constituting its geographic range.

    An ecological niche is the status or the role of an organism in its habitat or the mode of life of an organism within its habitats. For example, insects are pollinating agents and preys of insectivores.

    Abiotic factor are non-living physical aspects of the environment such as the sunlight, soil, temperature, wind, water, and air. Biotic factors are the living organisms in the environment. They include organisms and their interactions with each other.

    An ecosystem is a natural unit consisting of biotic and abiotic factors through which energy flows and nutrients recycle. In an ecosystem, nutrients pass between different organisms in definite pathways. For example, nutrients in the soil are taken up by plants, which are then eaten by herbivores, which in turn may be eaten by carnivores and recycled by decomposers.

    A biome is a group of ecosystems that have the same climate and similar dominant communities. The highest level of organization is the entire biosphere.

    The Biosphere is the whole of the earth’s surface, the sea and the air that is inhabited by living organisms. The biosphere is made up of all ecosystems.

    1.1.2. Biodiversity



    Biodiversity is defined as the full range of variety and variability within and among living organisms and the ecological complexes in which they occur.

    Self-assessment 1.1
    1. Describe the two main components of an ecosystem.
    2. Hippopotamus has different habitats. It was found that the resting habitat is different from the mating habitat, and these two habitats are different from the area where this animal gets food. Explain the ecological term given to this set of habitats.

    1.2 Identification of biodiversity
    Activity 1.2
    Use books or other sources of information to answer the followings questions:
    1. What kinds of initiatives and incentive mechanisms are put in place by the Government of Rwanda to motivate local community in biodiversity conservation?
    2. Describe different ways used to identify biodiversity.
    3. Discuss the values of biodiversity and ecosystem services in Rwanda.
    4. Evaluate the contribution of biodiversity to human well-being.

    1.2.1. Categories of biodiversity
    Biodiversity can be categorized into three groups:
    –– Genetic diversity: the combination of different genes found within a population of a single species, and the patterns of variation found within different populations of the same species.
    –– Species diversity: the variety and abundance of different types of organisms which inhabit an area.
    –– Ecosystem diversity: the variety of habitats that occur within a region, or within the mosaic of patches found within a landscape.

    1.2.2. Importance of biodiversity
    Biodiversity contributes to ecosystem goods and services. The ecosystem goods and services include:
    –– Provision of food, air, fire wood, medicines(Fig.1.2), energy, fresh water.
    –– Nutrient cycling such carbon, water and nitrogen cycles by microorganisms and primary production by photosynthesis.
    –– Cultural or aesthetic service recreation, ecotourism, cultural andreligious inspiration.

    1.2.3. The threats and consequences of biodiversity loss
    1.2.3.1. Causes of biodiversity loss
    The main causes of biodiversity loss can be attributed to the influence of human activities on ecosystems. Threats to biodiversity include:

    a. Habitat loss and the degradation of the environment

    The habitat loss and the degradation of the environment occur in different ways.
    The most occurring, are tree cutting, agriculture and fires (Figure1.3). These human activities lead to the alteration and loss of suitable habitats for biodiversity. As a consequence, there is a loss of plant species as well as the decrease in the animal species associated to this plant diversity.

    b. Introduction of invasive alien species and genetically modified organisms

    Species originating from a particular area are harmful to native species also called endemic species when they are introduced into new natural environments. They can lead to different forms of imbalance in the ecological equilibrium, so that endemic species may fail to compete with introduced species, and they may affect the abundance and distribution in natural habitat.

    c. Pollution
    Human activities such as excessive use of fertilizers, and increased pollutants from industries and domestic sewage affect biodiversity. They contribute to the alteration of the flow of energy, chemicals and physical constituents of the environment and hence species may die as a result of toxic accumulation.

    d. Overexploitation of natural resources
    Increased hunting, fishing, and farming in particular areas lead to the decrease and loss of biodiversity due to excessive and continuous harvesting without leaving enough time for the organisms to reproduce and stabilize in their natural habitat.

    e. Climate change
    This is a change in the pattern of weather, related changes in oceans, land surfaces and ice sheets due to global warming resulting from man’s activities. Increasing global temperatures have resulted into melting of icebergs raising sea levels and so flooding coastal areas eventually affecting the niche.

    1.2.3.2. Consequences of loss of biodiversity
    They are various consequences of loss of biodiversity that include:
    –– Desertification, is thought by scientists to be a consequence of climate change, has been considered to be related to deforestation. Disrupting water cycles and soil structure results into less rainfall in an area.
    –– Floods as a result of rising sea levels
    –– Habitat destruction for extensive farming, timber harvesting and infrastructure and settlement
    –– Decrease in food production as result of change in pattern of weather that affects productivity
    –– Large scale deforestation has a negative effect on nutrient recycling and can accelerates soil erosion
    –– Diseases that come as effects of floods and malnutrition due to famine

    Self-assessment 1.2
    1. Define the term Extinction.
    2. Suggest the causes of extinction of species in Rwanda.
    3. Discuss the benefits of biodiversity to humans
    4. Discuss the major factors leading to the degradation of ecosystems in Rwanda
    5. Discuss the contribution of ecosystems to cultural traditions in Rwanda.
    6. In Rwanda different plants are used in traditional medicine to treat different diseases. Conduct a research and list at least 20 medicinal plants and the diseases they treat. From the list above describe at least one medicinal plant and get ready to present your work. The project work should include: written content of 2 pages in minimum and 4 pages in maximum, a testimony of people that have used plant species.
    7. Pollution is one of the causes of aquatic biodiversity loss.
    a. What do you understand by water pollution?
    b. Outline human activities that contribute to water pollution
    c. Discuss how polluted water affects aquatic living organisms?

    1.3 Calculation of Simpson’s index
    Activity 1.3
    A survey on tree species was conducted in Gako forest by a group of students. Five tree species (A to E) were identified and counted. The numbers found during this exercise are summarized in the following table:
    1. Describe the relative abundance of species A to E.
    2. Based on the data in the above table, suggest how species diversity of tree species can be calculated.
    There are many ways to measure diversity. The Simpson diversity index among indices used to measure diversity. It is expressed in three related indices namely Simpson index, Simpson index of diversity and Simpson reciprocal index.

    a. Simpson index D
    Simpson index D can be expressed in two ways and takes into consideration the total number of organisms of a particular species and the total number of organisms of all species. It is calculated as follows:with n: the total number of organisms of a particular species and N: the total number of organisms of all species. When the index equals or is nearby 0 there is an infinite diversity of considered species. When it equals or is nearby 1, this means that there is no diversity. The bigger the value of D, the lower the diversity and small is D, the bigger is the diversity.

    b. Simpson index of diversity 1 – DThe value of this index ranges between 0 and
    1, but now, the greater the value, the greater the sample diversity. This makes more sense. In this case, the index represents the probability that two individuals randomly selected from a sample will belong to different species.

    c. Simpson reciprocal index 1 / D
    Another way of overcoming the problem of the counter-intuitive nature of Simpson’s index is to take the Simpson’s reciprocal index 1 / D. The value of this index starts with 1 as the lowest possible figure. This figure would represent a community containing only one species. The higher is the value of Simpson reciprocal index, the greater the biological diversity.

    Examples
    1. In woodland, a quadrat was sampled for ground vegetation. Data collected were recorded in the table 1.3.2. Find out the value of the Simpson index and draw the conclusion about the biological diversity of the sampled area.
    Table 1.3.2: Recorded data on the vegetation from a woodland
    Solution: Putting the figures into the formula for Simpson’s Index:


    Based on the meaning of Simpson index, the quadrat presents a low diversity because the value of D is near zero and zero and below 0.5.
    2. Calculate the value of Simpson’s Diversity Index (D) for a single quadrate sample of ground vegetation in woodland from which the following sampling date was obtained:

    Self-assessment 1.3
    1. Differentiate between species richness and species evenness
    2. Suggest precautions taken when measuring populations of aquatic animals or plants.
    3. Explain why a habitat with high diversity tends to be more stable than one with lower diversity.
    4. In a survey of trees in a tropical forest, students identified five tree species (A to E).
    They counted the numbers of trees in an area 100 m × 100 m and found these results:

    Calculate the Simpson’s Index diversity for identified species and explain the advantage of using data on species diversity and abundance when calculating an index of diversity.

    5. The Simpson’s Index of diversity for vegetation in an open area inhabited by grasslands was 0.8. For a similar sized area of vegetation beneath some conifer trees it was 0.2. What do you conclude from these results?

    1.4 Sampling techniques to assess the distribution and abundance of organisms
    Activity 1.4
    From your school garden, sample different flowering plant species and answer the following questions:
    1. Specify the techniques used for collecting flowers of different species.
    2. What are the advantages of the technique you used for data collection?
    3. Move around the school garden and collect different specimens of plant species. Name the collected species by using their names. In case you don’t know their names, use letters A, B, C ….
    Calculate Simpson index D, Simpson index of diversity and Simpson reciprocal index.

    To calculate Simpson’s index for a particular place:
    –– Identify the habitat to be studied.
    –– The number of individuals sampled for each species must be recorded.
    To analyze the distribution and abundance of organisms in an area of study, there are different sampling methods.
    Note that, sampling only one quadrat would not give reliable estimate of the diversity of the ground flora in the wood.

    a. Random sampling method
    A random sampling method is a sampling method where samples are taken from different positions within a habitat and those positions are chosen randomly.

    b. Quadrat sampling method
    A quadrat is a square area that is marked using a pre-made square of plastic, or stakes and string and it can range in size. Different species and their numbers within the quadrat are counted. Counting is repeated many times in different places in the habitat to get an accurate representation of biodiversity.

    c. Frame quadrats
    Frame quadrats are small plot used to isolate a standard unit of area for the study of the distribution of an item over a large area. While originally rectangular, modern quadrats can be rectangular, circular, and /or irregular. The quadrat is suitable for sampling plants, slow-moving animals such as millipedes and insect and some aquatic organisms.
    d. Transect sampling
    Transect sampling is done using a transect line, which is usually a rope or measuring tape that has been marked at set intervals, such as every meter. The line is unrolled within the habitat. At every interval, the type and number of species along the line are recorded. A measured line is laid across the area in the direction of the environmental gradient. The species touching the line can be recorded along the whole length of the line (continuous sampling) or at specific points along the line (systematic sampling).
    e. Belt transects method
    Belt transects method is the same as the line transects but widens the sampling area. The samples are taken and the abundance, percentage cover in a defined area determined. Samples can be taken within the belt.
    f. Netting
    Netting is a sampling method where fine mesh nets are used to capture different organisms that include insects, birds and bats. The technique is also used for sampling small aquatic organisms like daphnia, and water boatman.
    g. Capture -recapture technique
    This method is useful for sampling non-fixed population and is suitable for animal such as fishes, birds, lizards and insects. A sample of the population to be studied is first captured and each individual is marked with a spot for identification. These are then released and given enough time to mix up with the rest of the members in the habitat. After a certain period of time, another sample is taken. During the mark-release-recapture technique, the total population can be estimated by the use of the formula: where
    n1 is a number caught and marked in first sample,
    n2 is a number caught in second sample
    n3 is a number in the second sample that had been marked.
    To understand this application, let us use the following examples:

    1. A team of students used a sweep net to sample brown grasshoppers
    and each collect insect was marked with a very small spot of non-toxic waterproof paint and then they were released in the field. The next day, a second large sample was conducted and data were recorded as follows: number of caught and marked in first sample (n1) = 247, number of caught in second sample (n2) = 269, and the number in the second sample that had been marked (n3) = 16. What is the number of estimated population?
    2. A student collected 16 butterflies which he marked and released. For a second time he collected 18 butterflies among which 12 were already marked from the first sampling. Estimate the population size of butterflies in that area.
    Self-assessment 1.4
    1. Explain the advantages of the random sampling techniques.
    2. Use suitable methods, such as frame quadrats, line transects, and belt transects, to assess the distribution and abundance of insect species in a school garden. Record your data and use the Simpson index ofdiversity (D) to calculate the diversity of collected insects.
    3. Suggest the benefi ts of using the following sampling techniques:
    a. Quadrats
    b. Transect
    c. Mark-capture-recapture
    4. State the conditions in which quadrats, transect and mark recapture are
    suitable sampling methods.

    1.5 Pearson’s linear correlation
    Activity 1.5
    Some of the following fi gures indicate a positive, negative or non-correlation.


    1. What do you understand by the term correlation?
    2. Categorize the graphs given as positive, negative or weak or no correlation
    3. In which conditions results can indicate a positive correlation?
    4. Conclude about your results when there is no correlation.
    To decide if there is an association between collected data, a correlation coeffi cient is calculated and plot scatter graph drawn in order to make a judgment. The strongest correlation is present for studied items when all the points lie on a straight line. In this case, there is linear correlation, and the correlation coeffi cient equals

    1. If a given variable X increases so does another variable Y, the relationship is a positive correlation. If a variable X increases while the variable Y decreases, then the relationship is a negative correlation. A correlation coefficient of 0 means there is no correlation at all. These correlation coefficients are ways to test a relationship observed and recorded to see if the variables are correlated and, if so, to find the strength of that correlation.

    a. Pearson’s correlation coefficient
    Pearson’s correlation coefficient can only be used where there might be a linear correlation and when there are collected quantitative data as measurements (for example, length, height, depth, and light intensity, mass) or counts (for example number of plant species in quadrats). The data must be normally distributed.
    Where:
    r               is the correlation coefficient
    x              is the number of species in a quadrat
    y              is the number of species in the same quadrat
    n              is the number of readings (From1 to n)
    x              is the mean number of species
    y              is the mean number of species
    sx                  is the standard deviation for x
    sy                  is the standard deviation for y

    Self-assessment 1.5
    Use Pearson’s linear correlation to analyze the relationships between the distribution and abundance of species and abiotic or biotic factors.

    End of unit assessment 1

    Section A: Answer as true or false
    1. Abiotic factors are the non-living physical aspects of the environment.
    2. Capture –recapture is a method used to integrate the numbers of mobile animals in a particular place.
    3. A correlation coefficient of 0 means that there is no correlation at all.
    4. A sample is a portion, piece, or segment that is representative of a whole area of study.
    5. In the Simpson’s index, Nrepresentsthetotal number of organisms of a particular species

    Section B: Long and short answer based questions
    1. What do you understand by the term biodiversity?
    2. What do you think would happen to plants if there were no insects?
    3. Suggest different ways to conserve our forests.
    4. A student has randomly collected 5 types of species at the following frequencies.
    Calculate the Simpson’s diversity index of this community.
    5. A team of students conducted the capture- recapture sampling method of tilapia from lake Muhazi at different times of the day as recorded in the data below:
    a. Plot the graph for the date provided and describe the shape of the graph.
    b. From the graph, determine the appropriate time to have the most catch.
    6. What do you understand by term endangered species?
    7. Describe how diversity is threatened by climate change and human activities.

    URLs: 2Files: 2

  • UNIT 2: INTRODUCTION TO CLASSIFICATION

    Key Unit Competence
    Apply the basic knowledge of classification to group living organisms into the three domains.

    Learning objectives
    –– Describe the classification of species into the taxonomic hierarchy of domain, kingdom, phylum, class, order, family, genus and species.
    –– Outline the characteristic features of the three domains Archaea, Bacteria and Eukarya.
    –– Draw and label the structure of a typical bacterial cell.
    –– Identify common bacterial diseases in plants and animals.
    –– Outline the characteristic features of the kingdoms Protoctista, Fungi, Plantae and Animalia.
    –– Explain why viruses are not included in the three domain classification.
    –– Outline how viruses are classified limited to type of nucleic acid and their host.
    –– Describe the role of bacteria in the production of dairy products.
    –– Describe methods of preventing common bacterial diseases.
    –– Construct a dichotomous key for a group of organisms.
    –– Recognize that microorganisms can survive in hot springs

    Introductory activity
    Collect different fruits such as oranges, lemons, avocado, green paper, red paper, bananas, mangoes and tomatoes.
    1. Observe each of the above fruits and group them based on their external features.
    2. Based on groups made, which fruits are most closely related?
    For more than 3.5 billion years, life on earth has been constantly changing. Natural selection and other processes have led to a staggering diversity of organisms. A tropical rain forest, for example, may support thousands of species per meter square.
    Recall that a species is a population of organisms that share similar characteristics and breed with another to produce fertile offspring. Biologists have identified and named about 1.5 million species so far, and they estimate that between 2 and 100 million additional species have yet to be discovered.

    2.1 Taxonomic hierarchy
    Activity 2.1
    You are provided with cards written on a list of words such as continent, district,
    country, cell, province, sector, village and family.
    1. Arrange the above words in increasing size
    2. What is your opinion about the people of the same family and those in the
    whole country?
    3. Compare your arrangement above with 8 groups of the biological
    taxonomic hierarchy.

    Taxonomy is the study and practice of classification, which involves placing organisms in a series of taxonomic units, or taxa (singular: taxon). In biological classification, these taxa form a hierarchy. Each kind of organism is assigned to its own species, and similar species are grouped into a genus (plural: genera). Similar genera are grouped into a family, families into an order, orders into a class, classes into a phylum (plural: phyla) and phyla into a kingdom. The domain is at the top of this hierarchical system.

    The hierarchy classification starts from the largest group, the domain. The eight levels of classification are known as taxa (taxon in singular), these include: Domain, Kingdom, phylum, class, order, family, genus and species. As one moves down the taxonomic hierarchy, it follows that the number of individuals decreases but the number of common features increases. For example, there are numerous individuals in the domain Eukarya, with very few features in common.

    Binomial nomenclature
    When precision is not required one generally reverts to common names. The trouble is that an organism may be known by different common names, and sometimes the same name may be given to two quite different organisms because common names are not internationally recognized and they change from one region to another one, or from one country to another one. To solve this problem, the binomial system also known as scientific name was introduced and it was pioneered by the Swedish naturalist Carl Linnaeus (1707-1778).

    In this system, each organism is given two Latin names: a generic name beginning with a capital letter and a specific name beginning with a lowercase letter based on the physical characteristics of studied species. The scientific name is in italic when printed otherwise it is underlined, when hand written.

    For example, many cats belong to the genus Felis but there are many species of cats:
    A wild cat is Felis sylvestris while a domestic cat is Felis domesticus. These names are in
    italic because this book was written by the use of computer. Hierarchy taxonomy of human, earthworm and hibiscus plant are given in the table 2.1.

    Table 2.1 Taxonomic classification of human being, earthworm and hibiscus

    Scientific names present more advantages than common names.
    –– They are necessary whenever precise identification is required, and they enable scientists to communicate accurately with each other.
    –– They are used worldwide and have the merit that every biologist knows exactly which organism is being referred to.
    Currently, with DNA technology, it is possible to investigate relationships based on genes or DNA structure. As this new technology comes to greater use, it is possible to find that some species had to be reclassified into different taxa.

    Self-assessment 2.1
    1. An African bush elephant belongs to order Proboscidae and family Elephantae. Its scientific name is Loxodonta africana.
    a. Make a table indicating the hierarchy classification of African bush elephant
    b. Use the examples from table 2.1 to define the term “taxon”
    2. Classify each of the following organisms under the following kingdom, phylum and class taxa: honey bee, cockroach, maize, and spider.
    3. Describe the system of naming species that Linnaeus developed.

    2.2 Three domains: Archaea, Bacteria and Eukarya.
    Activity 2.2.
    Using text books and other sources identify the characteristics of each of the three biological domains
    Three domains are used by biologists to divide organisms into three large groups based on their cell structure. The domain is the highest taxon in the hierarchy. The prokaryotes are divided between the domains Bacteria and Archaea, while all the eukaryotes are placed into the domain Eukarya.

    a. Domain Bacteria
    Domain bacteria include prokaryotic organisms as their cells have no true nucleus. They are all microscopic that vary in size between 0.2 to 10 micrometres. The characteristic features of bacteria are:
    –– Cells with no true nucleus
    –– DNA exists in circular chromosome and does not have histone proteins associated with it
    –– No membrane-bound organelles (mitochondria, endoplasmic reticulum, Golgi body, chloroplasts)
    –– Contain mesosomes as infolding of membrane and acts as sites for respiration.
    –– Ribosomes (70 S) are smaller than in eukaryotic cells
    –– Cell wall is always present and contains peptidoglycans in place of cellulose
    –– Cells divide by binary fission
    –– Usually exist as single cells or colonies

    b. Domain Archaea
    This contains bacteria that live in extreme environments where few other organisms can survive. They are classified according to the environments they live in;
    –– Methanogenic bacteria that live in habitats deprived of oxygen and give off methane as a product of metabolism for example those that live in the guts of ruminant animals
    –– Halophilic bacteria live only in salty conditions
    –– Thermoacidophilic bacteria tolerate extreme acid and temperature that exceed boiling point of water and a pH below 2.

    c. Domain Eukarya
    All the organisms classified into this domain have cells with nuclei and membrane bound
    organelles. Their characteristic features are:
    –– Cells with a nucleus and membrane-bound organelles
    –– linear DNA associated with histones arranged within a chromosome in the nucleus
    –– Ribosomes (80S) in the cytosol are larger than in prokaryotes, while chloroplasts and mitochondria have 70S ribosomes, like those in prokaryotes.
    –– Chloroplast and mitochondrial DNA is circular as in prokaryotes suggesting an evolutionary relationship between prokaryotes and eukaryotes
    –– A great diversity of forms: unicellular, colonial and multicellular organisms
    –– Cell division is by mitosis
    –– Many different ways of reproduction including asexually and sexually.

    Self-assessment 2.2
    1. What are the three domains of living things?
    2. Describe the ways in which a domain differs from a kingdom?
    3. It is confirmed that: “Some bacteria can survive in extreme temperatures such
    as hot springs”. Justify this statement.
    4. How is the information about evolutionary or phylogenetic relationships useful in classification of the living things?

    2.3 Five kingdoms of organisms
    Activity 2.3.
    Collect organisms from a habitat near your school including a housefly, spider, frog, gecko, bean/maize plant, moulds/mushroom, spirogyra (algae) and a hen. If there are small rapidly moving land animals such as insects, anaesthetise them by placing them in an ether/ethanol bottle for few seconds. Preserve the collected specimens for future use
    1. Examine each organism, using a hand lens.
    2. Make a table of the features observed and identify the kingdom to which each organism belongs.
    There are different ways of classifying the living world into kingdoms but the most common and recommended is the five kingdom classification. According to Kent (2000) the kingdoms are:
    –– Kingdom Monera or prokaryote
    –– Kingdom Protoctista
    –– Kingdom Fungi or kingdom mycota
    –– Kingdom Plantae
    –– Kingdom Animalia

    2.3.1 Kingdom Protoctista
    This kingdom is made up of a very diverse range of eukaryotic organisms, which
    includes those that are often called protozoans and algae. Any eukaryote that is not
    a fungus, plant or animal is classified as a protoctist. The characteristic features of
    protoctists are listed according to the different phyla due to their diverse range:
    –– Rhizopods that have pseudopodia for locomotion. Example, amoeba
    –– Flagellates which are hereorophic organisms with at least one flagellum for locomotion. Example, trypanosoma.
    –– Sporozoans which are mainly parasitic organisms that reproduces by multiple fission. Example plasmodium.
    –– Ciliates which are organisms with cilia. Example paramecium
    –– Euglenoid flagellates which are organisms with flagella but with a biochemistry quite distinct from that of flagellates. Example Euglena
    –– Oomocytes which are similar to fungi except that they have cell wall with cellulose. Example Phytopthora infestans; potato blight
    –– Green algae which are photsynthetic organisms with chlorophyll pigments similar to the ones of plants. Example chlorella
    –– Red aglae which are photosynthetic organisms with organelles with red pigment as well as chlorophyll. Example, chondrus
    –– Brown algae which are photsynthetic organisms with organelles which contain brown pigments as well as chlorophy. Example Fucus, sea weed Living things such as paramecium (a), amoeba (b), euglena (c) and plasmodia belong to the kingdom Protoctista.
    2.3.2 Kingdom Fungi
    Fungi have some similarities with plants, but none of them is able to photosynthesise. They are all heterotrophic, obtaining energy and carbon from dead and decaying matter or by feeding as parasites on living organisms. There is a vast range in size from the microscopic yeasts to what may be the world’s largest organisms. Other characteristic features of fungi are:
    –– Heterotrophic nutrition – they use organic compounds made by other organisms as their source of energy and source of molecules for metabolism
    –– Reproduce asexually by means of spores and sexually by conjugation
    –– Simple body form, which may be unicellular or made up of long threads called hyphae (with or without cross walls).
    –– Large fungi such as mushrooms produce large compacted masses of hyphae known as fruiting bodies to release spores
    –– Cells have cell walls made of chitin or other substances
    2.3.3 Kingdom Plantae
    Plants are all multicellular photosynthetic organisms. They have complex bodies that are often highly branched both above and below the ground. Characteristic features of plants are:
    –– Multicellular eukaryotes with cells that are differentiated to form tissues and organs.
    –– Few specialized cells
    –– Cells have large and often permanent vacuoles for support with cell walls made of cellulose
    –– Most plants store carbohydrates as starch or sucrose

    2.3.4 Kingdom Animalia
    Animals (Fig 2.3) are multicellular organisms that are all heterotrophic with different methods of obtaining their food. Organisms in this kingdom have other additional features.
    –– Different types of specialized cells
    –– Cells do not have chloroplasts and cannot photosynthesize (although some,
    such as coral polyps have photosynthetic protoctists living within their tissues)
    –– Cell vacuoles are small and temporary (for example lysosomes and food vacuoles)
    –– Cells do not have cell walls
    –– Communication is by the nervous system

    Activity 2.3
    Which feature do all animals (except sponges) have that distinguishes them from plants and fungi?

    2.3.5. Kingdom Monera
    Organisms in this kingdom have single cells that do not have a nucleus. They are prokaryotic. They are the smallest and simplest organisms. Examples are bacteria which form a diverse group with members that range widely in size and shape. Some of them stick together to form chains or clusters while others are single cells. The figure below (Figure 2.4) shows a typical structure of a bacterial cell which contains all the main features of prokaryotes
    Self-assessment 2.4
    1. The kingdom protoctista contains groups which do not appear to show an evolutionary relationship. On this basis, is the five kingdom classification a natural or artificial classification?
    2. What are the three methods that protists use to obtain food?
    3. Identify three characteristics of protists
    4. The following is a list of organisms belonging to various kingdoms: housefly (Musca domestica), maize (Zea mays), Frog (Rana spp), Bat and Eagle.
    a. Classify these organisms into their kingdoms
    b. Name any two organisms that are not closely related and give a reason.
    5. How are fungi different from members of kingdom plantae?

    2.4 Economic importance of bacteria
    Activity 2.4
    “Bacteria are both useful and harmful to humans”. Discuss the validity of the statement.
    Bacteria are economically important because they are essential in many beneficial biological and industrial processes. There exist some examples of bacteria that are pathogens as they cause disease and spoilage of food..

    2.4.1 Useful bacteria
    a. Biotechnology
    Bacteria are used in biotechnology and industry. They are used to manufacture products such as ethanol, acetone, organic acid, enzymes, and perfumes. In the chemical industry, bacteria are most important in the production of pharmaceuticals. For example, E. coli is used for commercial preparation of riboflavin and vitamin K.

    b. Genetic engineering
    Bacteria are used in genetic engineering through the manipulation of genes, also called recombinant DNA technology. In this case, bacterial cells are transformed and used in production of commercially important products for example, production of human insulin used in treatment of diabetes.

    c. Decomposition
    In addition, bacteria are important in decomposition of dead organisms and animal wastes such as feces to form organic matter. This process improves soil fertility and plays an important role in mineral recycling in an ecosystem.

    d. Fibre retting
    Some bacteria including Clostridium butyricum are used to separate fibres in a process called retting. In this process, fibres are formed to make ropes and sacks.

    e. Nitrogen fixation
    Some other bacteria are used to fix nitrogen in form of nitrates into the soil. For example, Rhizobium bacteria which live in root nodules of leguminous plants. Such bacteria help in improvement of soil fertility.

    f. Digestion
    Some bacteria living in the gut of ruminant animals such as cattle, horses and other herbivores secrete cellulase, an enzyme that helps in the digestion of cellulose of plant cell walls. Another example is Escherichia coli that live in the human large intestine which synthesizes vitamin B and releases it for human use.

    g. Biological control
    Some bacteria are used as biological agents in biological pest control such as Bacillus thuringiensis (also called BT) instead of pesticides. Because of their specificity to the
    host, these bacteria are regarded as environmentally friendly, with little effect on humans, wildlife, pollinators, or other beneficial insects.

    2.5 Common bacterial diseases in plants and animals
    Activity 2.5
    Suppose there is cholera outbreak in your village and the executive secretary invited you to sensitize people about preventive measures against cholera. Prepare a brief presentation for this purpose.

    The bacteria that cause diseases are harmful to humans and other animals and are referred to as pathogenic bacteria. The body is a home to many millions of bacteria both useful and harmful to humans.
    A bacterial disease is caused by entry of bacteria into a host where theycan grow, flourish then causing harm to the host. Bacteria e diseases include cholera, tuberculosis (TB), typhoid fever, pneumonia, tetanus, and diphtheria, and bacterial meningitis, tooth decay in humans and anthrax in cattle.

    Table 2.2. Common bacterial diseases in humans



    2.5.1 Common Bacterial Diseases in Plants
    The table 2.3 common bacterial diseases in plants


    Self-assessment 2.5
    Mr. Green lives in one of the slums in a certain city. He prepares and sells chapattis on street. He is usually very clean, but one morning, he is late for work so he does not bother to wash his hands after visiting the toilet. That day he prepares 400 chapattis all of which are sold. Few hours later, his customer Sandra suffered from a disease with the following signs and symptoms: severe diarrhea, excessive loss of water leading to dehydration, and vomiting. Five dayslater, all his customers were rushed and admitted in hospital due to the same problem.
    1. Suggest the disease that Mr. Green’s customers were suffering from and what caused the disease
    2. Name three ways this disease might be spread around city.
    3. After reading this scenario, what message do you have for people who are like Mr. Green?
    4. Suppose you were the health officer for the area in town with such a
    problem. What steps would you take to prevent the disease from spreading further?
    5. House flies are described as vectors. Describe how houseflies transmit diseases to humans.

    2.6 Structure and classification of Viruses
    Activity 2.6
    Discuss the reasons why viruses are not classified in any of the five kingdoms of
    living organisms.
    Viruses are microorganisms whose structure is only visible with electron microscopes. Viruses are acellular and lack cellular structure. Viruses have none of the features that we traditionally use for classification. They are particles made of proteins and nucleic
    acids that are found in all cellular organisms, but show metabolism only once inside the host cell.
    When they infect cells, they use biochemical machinery and proteins of the host cell to copy their nucleic acids and to make proteins coats often leading to destruction of the host cells. The energy for these processes is provided by the ATP from the host cell.

    2.6.1. Structure of a virus
    A typical virus consists of DNA or RNA within a protective protein coat called capsid. The shape of the capsid may vary from one type of virus to another, as shown in Figure 2.5 below.
    Some viruses have an envelope of phospholipids and proteins. The envelope is made
    from portions of the host’s cell membrane. It surrounds the capsid and helps protect the virus from the host’s immune system. The envelope may also have receptor molecules that can bind with host cells and facilitate the virus to infect the cells.

    2.6.2. Characteristics of viruses
    An individual virus is called a virion. It is a tiny particle much smaller than a prokaryotic cell. Because viruses do not consist of cells, they also lack cell membranes, cytoplasm, ribosomes, and other cell organelles. Without these structures, they are unable to make proteins or even reproduce on their own.
    Instead, they must depend on a host cell to synthesize their proteins and to make copies of themselves. Viruses infect and live inside the cells of living organisms. They are also regarded as parasites since they depend entirely on living cells for their survival. Although viruses are not classified as living things, they share two important traits with living things: They have genetic material, and they can evolve.

    2.6.3. Classification of viruses
    Viruses can be classified according to:
    –– Type of nucleic acid molecules of DNA or RNA, forming the core of the capsid:
    Most animal viruses contain RNA while plant viruses contain DNA
    –– Type of host cell: plant or animal viruses as they are specific to their hosts
    –– Presence or absence of the envelope: Plant viruses’ bacteriophage are nonenveloped
    while animal viruses like HIV and influenza virus are enveloped.

    2.6.4. Viruses and human disease
    When viruses infect cells of their host, they cause disease. Examples of diseases caused by viruses include HIV/AIDS, influenza (flu), chicken pox, and the common cold. The human immunodeficiency viruses that causes AIDS is a retrovirus. Other viral diseases include rabies, measles, diarrheal diseases, hepatitis A, B and C, polio, and cold sores. One-way virus cause disease is by causing host cells to burst open and die. Viruses may also cause disease without killing host cells. They may cause illness by disrupting homeostasis in host cells.
    Some viruses live in a dormant state inside the body. The virus that causes chicken pox may infect a young child and causes the short-term disease chicken pox. Then the virus may remain latent in nerve cells within the body for decades. The virus may re-emerge later in life as the disease called shingles, where the virus causes painful skin rashes with blisters. Some viruses can cause cancer. Examples include the human papillomavirus (HPV) causing cancer of the cervix in females. Hepatitis B virus causes cancer of the liver. A viral cancer is likely to develop only after a person has been infected with a virus for many years.

    Self-assessment 2.6
    1. What is meant by the term virus?
    2. State the main components of a virus.
    3. Describe the two ways how viruses cause an infection.
    4. Differentiate between a bacteriophage and a retrovirus?
    5. Do you think viruses should be considered as a form of life? Give reasons for your answer.

    2.7 Dichotomous key of identification of organism
    Activity 2.7
    The figure below represents different types of plant leaves. Make a classification of these plants based on the external structure of the leaves.

    The dichotomous key is also referred to as biological identification key. It is made up of a series of contrasting statements called leads indicated by the numbers 1, 2, 3… where each lead deals with a particular observable characteristic. The characteristics used in keys should be readily observable morphological features which may be either qualitative, such as shape of abdomen, nature of legs, or quantitative, such as number of antennae, number of pairs of legs and length of the antennae in case of arthropods. It is essential to note that size and color are often less considered as both can be influenced by the environment, the season, the age or state of the organism at the time of identification.

    2.7.1. Guidelines used in construction of a dichotomous key:
    The following guidelines must be considered while constructing a dichotomous key.
    –– Use morphological characteristics which are observable as much as possible such as leaf venation, nature of margin, apex, lamina and nature or length of the petiole (leaf stalk).
    –– Start with a major characteristic that divide the organism or the specimen into two large groups such as the type of a leaf.
    –– Select a single characteristic at a time and identify it using a number for
    example: simple leaf………go to 2, compound leaf………go to 5. This means that in 2 you will deal with only simple leaves and 5 only compound leaves.
    –– Use similar forms of words for two contrasting statements for example at 2:
    leaf with parallel venation …………go to G and leaf with network venation ………go to 3.
    –– The first statement should always be positive.
    –– Avoid generalizations or overlapping variations, be specific and precise to the point.

    Example
    –– Collect leaves from the following plants: cassava, avocado, jacaranda, cassia, hibiscus bean, maize or paspalum grass,
    –– Label different leaves collected as, A, B, C, D, E, F and G
    –– Observe and familiarize with the specimens before starting the experiment to minimize errors during the identification process
    –– Make a table summarising the specimens and steps followed to identify each
    of them.
    –– Construct a dichotomous key based on the observable features (characteristics) and table of steps followed.

    Solution: The dichotomous key of specimens A, B, C, D, E, F and G.
    1. a. Simple leaves ---------------------------------------------------------------------go to 2
    b. Compound leaves ---------------------------------------------------------------go to 5
    2. a. Parallel venation ------------------------------------------------------------------------G
    b. Network venation --------------------------------------------------------------go to 3
    3. a.Simple digitate ---------------------------------------------------------------------------A
    b. Non simple digitate -------------------------------------------------------------go to 4
    4. a. Leaf with serrated margin -------------------------------------------------------------E
    b. Leaf with smooth margin -------------------------------------------------------------B
    5. a.Leaf with three leaflets (compound trifoliate)-------------------------------------F
    b. Leaves with more than three leaflets --------------------------------------go to 6
    6. a. Pinnate leaf ------------------------------------------------------------------------------ D
    b. Bipinnate leaf --------------------------------------------------------------------------- C

    2.7.2. Common features used for identification of animals
    Animals are classified based on the following features:
    –– Locomotory structures such as legs, wings and fins
    –– Antennae (presence, nature and number)
    –– Presence or absence of eye and eye type
    –– Number of body parts for example insects have three body parts
    –– Body segments (nature and number)
    –– Body surface structures such as fur, hair, feathers and scales
    –– Feeding structures such as mouth parts in arthropods for example in insects
    –– Type of skeleton present such as endoskeleton, exoskeleton and hydrostatic

    2.7.3. Common features used for identification of plants
    Plants can be classified basing on the following features:
    –– The leaf structure such as nature of apex, margin, venation, lamina and petiole
    –– The flower structure including inflorescence type, flower shape and number of floral parts
    –– The type of stem (woody, fleshy and herbaceous), shape (rectangular,
    cylindrical) and texture of the stem (smooth, spiny and thorny) …
    –– The type of root system, tap root, storage root, fibrous roots… Precaution
    –– Care must be taken while collecting and handling some organisms because
    some are poisonous, have thorns and others are able to sting
    –– Collection of specimen should be done a day or few days before the experiment
    depending on nature of the experiment
    –– Avoid and try to minimize where possible, uprooting, cutting down or plucking
    and pruning of plants as this may threaten the biodiversity as well as result
    into environmental degradation

    Activity 2.8
    Construct and interpret a dichotomous key of arthropods listed below.
    –– Collect the following litter arthropods: honey bee, spider, millipede, butterfly,
    sugar ant, centipede and mosquito and label each specimen as A, B, C, D, E, F and G respectively
    –– Observe and familiarize yourself with the specimens before starting the experiment.
    –– Use sharply contrasting external features of collected specimens /diagrams to construct a dichotomous key.

    Self-assessment 2.7
    Read and interpret the dichotomous tree below and use it to answer the following questions.
    1. Specify the phylum of kingdom animalia represented by the above dichotomous tree?
    Give one observable reason to support your answer.
    2. According to this dichotomous tree, which characteristic feature was used to classify different insects?
    3. Which observable characteristic feature distinguishes between a spider and a mosquito?
    4. How does a millipede differ from a centipede?
    5. To which classes do a millipede and a centipede belong?
    6. Which class of arthropods is not represented on the dichotomous tree?
    d. Phylum
    3. Which one of the following is not a kingdom of living organisms?
    a. Monera
    b. Animalia
    c. Annelida
    d. Protoctista
    4. Which one of the following is a characteristic feature common to fish, reptiles and birds but absent in mammals?
    a. Possession of scales
    b. Has no limbs
    c. Possession of feathers
    d. Undergo internal fertilization
    5. Which one of the following statements about fish is not correct?
    a. Fish live both in water and on land and undergo external fertilization.
    b. Most fish have bones while others are cartilaginous
    c. Most fish have streamlined body, lateral line and swim bladder.
    d. Gills are organs for gaseous exchange in fish
    6 Which one of the following is not a characteristic of all insects?
    a. They have three body parts namely head, thorax and abdomen.
    b. They have three pairs of jointed legs attached on segment of the thorax.
    c. They have four pairs of jointed legs
    d. They have a pair of antennae attached on the head.
    7. The following are characteristics of all mammals except;
    a. They have mammary glands to secrete milk feed their young ones.
    b. Their skin is covered with hair.
    c. Undergo internal fertilization and internal development of the embryo.
    d. They have a pair of wings made up feathers.
    8. The point where the leaf joins the stem is called;
    a. Apex
    b. Margin
    c. Leaf base
    d. Lamina
    e. Length of petiole.
    9. Which of the following is less considered while identifying feature to construct
    a dichotomous key of leaves?

    End of unit assessment 2
    1. Which one of the following living organisms belongs to domain bacteria?
    a. Euglena
    b. Vibrio cholerae
    c. Paramecium
    d. moulds
    2. The group of classification where organisms resemble one another and are
    capable of interbreeding together to produce viable offspring is known as:
    a. Species
    b. kingdom
    c. Genus
    a. Nature of margin
    b. Nature of apex
    c. Size and color of leaf
    10. The following are characteristics of arachnids except;
    a. Four pairs of jointed legs
    b. Two body parts
    c. Three body parts
    d. Do not have wings
    11. Match the structures with the organisms which possess them.
    12. A group of S4 students drew a Venn diagram below to summarize the five kingdoms into which organisms are classified. Study the diagram and answer the questions that follow:
    a. Which kingdoms are represented by the letters x and y?
    b. State one characteristic that organisms of x may share with:
    i. Prokaryotes
    ii. Fungi
    iii. Plantae
    13. Complete the table to summarize the characteristics of each class of phylum Arthropoda.
    14. What is the significance of classification of living organisms?
    15. The binomial system of naming a blue monkey, Cercopithecus mitis, is provided below;
    Complete the table by filling the missing words.

  • UNIT 3: MICROSCOPY

    Distinguish between the types of microscopes and their principal uses.

    Learning objectives
    By the end of this unit, I should be able to:
    –– Describe the main features and functions of the components of a compound light microscope.
    –– Manipulate a compound light microscope to observe prepared slides.
    –– Show perseverance when using light microscopes.
    –– Pay attention when using a compound light microscope to avoid damage of the lenses, mirrors and slides.
    –– State that magnification is the increase in the apparent size of the object.
    –– State that resolution is the ability of the microscope to show two objects as separate.
    –– Appreciate the importance of magnifying instruments in Biology.
    –– Use of a microscope to determine the relationship between actual size of the specimen and the image.
    –– Calculate the approximate size of different biological structures using an appropriate unit of measurement
    –– State the advantages and disadvantages of using an electron microscope.
    –– State the principles and limitations of TEM (Transmission Electron Microscopy).
    –– State the advantages and disadvantages of using SEM (Scanning Electron Microscopy).
    –– Compare light and electron microscopes
    –– Acknowledge the use of electron microscopes in modern science with reference to electron micrographs.
    –– Observe and draw biological specimens under a light microscope.
    –– Prepare temporary slides for observation under light microscopes using different objective lenses
    –– Appreciate the importance of magnifying instruments in Biology

    Introductory activity
    Point out scientific activities that require the use of microscope in our daily lives.
    A microscope is used to produce a magnified image of an object or specimen.
    Anton Van Leeuwenhoek (1632-1723) was the first to invent a microscope powerful enough to explore the world of microbes. His discoveries stimulated an explosion of interest in scientific use of microscopes. Since the 18th century, many new types have been invented of which the most commonly used today are the compound light microscope and the electron microscope.1 (Kent, 2000, p. 58)).

    3.1 Compound Light Microscope
    Activity 3.1
    Some of the living things including protoctista and fungi have small size to be observed by naked eyes. Discuss the ways used by biologists to observe and identify different parts of these living organisms.
    The optical microscope, often referred to as light microscope is a type of microscope which uses visible light and a system of lenses to magnify images of small samples.
    The different parts of light microscope are described below:
    –– Base: supports and stabilizes the microscope on the table or any other working place
    –– Light source: It is made by lamp or mirror which provides light for viewing the slide.
    –– Stage: is a platform used to hold the specimen in position during observation.
    –– Stage clips: are pliers used to fix and hold tightly the slide on stage.
    –– Arm: supports the body tube of microscope
    –– Body tube: maintains the proper distance between the objective and ocular lenses
    –– Arm: used for holding when carrying the microscope and it holds the body tube which bears the lenses.
    –– Coarse focus adjustment: moves stage up and down a large amount for coarse focus
    –– Fine focus adjustment: moves stage up and down a tiny amount for fine focus
    –– Objective lenses: focuses and magnifies light coming through the slide
    –– Revolving nosepiece: rotates to allow use of different power objectives
    –– Slide: is a transparent pane on which a specimen is placed.
    –– Eye piece/ocular lens: magnifies image produced by objective lens
    –– Condenser: It will gather the light from the illuminator and focus it on the specimen lying on the stage. The function of the condenser is to focus the light rays from the light source onto the specimen.
    –– Iris diaphragm lever: This allows the amount of light passing through the condenser to be regulated to see the object.

    Activity 3.2
    Using the light microscope
    a. To observe under low power and low magnification, proceed as follows:
    –– Objects (specimens) to be observed under the microscope are first placed on a glass slide and covered with a cover slip.
    –– Place the specimen on the stage of your microscope; in other words, arrange it so that the specimen is exactly at the center of the hole at the stage.
    –– Fix the slide in place with two clips.
    –– Rotate the nosepiece so that small objective lens is immediately above the specimen.
    –– Set the angle of the reflector mirror so that light is directed up through the microscope.
    –– Look down the microscope through the eye piece. Adjust the iris diaphragm so that the field of vision is bright and not dazzling.
    –– Turn the course adjustment knob until the tip of the objective lens is close to the slide.
    –– Now look down the microscope again. Slowly turn the course adjustment knob in the other direction, so the tube gradually moves upwards. The specimen on the slide should eventually come into view.
    –– Use the course and fine adjustment knobs to focus the object as sharply as possible.
    –– If necessary readjust, the iris diaphragm so the specimen is correctly illuminated. You will get a much better image if you don’t have too much light coming through the microscope.
    b. To observe under high power at a greater magnification, proceed as
    follows:
    –– Rotate the nosepiece so that the large objective lens (with higher magnifying power) is immediately above the specimen. The nosepiece should click into position, as before.
    –– If the specimen is not in focus, focus it with fine adjustment knob. Be careful that the tip of the objective lens does not touch the slide.
    –– Readjust the illumination if necessary.

    Microscope uses transmitted light for observation. However, microscope uses specific light characteristics for specific samples, such as transparent specimens and samples that do not pass light. All parts of a microscope work together, the light from the illuminator passes through the aperture, through the slide, and through the objective lens, where the image of the specimen is magnified. Then the magnified
    image continues up through the body tube of the microscope to the eyepiece, which further magnifies the image the viewer can see.
    Light from the source is focused on the specimen by the condenser lens. It then enters the objective lens, where it is magnified to produce a real image. The real image is magnified again by the ocular lens to produce a virtual image that is seen by the eye.

    Care of the compound microscope
    The microscope is an expensive instrument that must be given proper care. Always
    general instructions have to be respected when using a microscope. These include:
    –– Carry the microscope with both hands, one hand under the base, and the other on the arm.
    –– When getting ready to put the microscope away, always return it to the low power or scanning power setting.
    –– When setting the microscope on a table, always keep it away from the edge.
    –– It is generally better to clear your lab table of items that are not being used.
    –– Never clean lenses with anything other than lens paper, don’t use towels and
    other paper tissues because they scratch the lens.
    –– Inform the instructor or the biology lab technician if there is any microscope
    damage or irregularity in its operation as soon as possible. Do not return a
    faulty microscope without first informing the instructor or lab technician.
    –– You are responsible for the microscope while using it treat it with care!

    Self-assessment 3.1
    1. Complete the table below:
    2. What is the importance of a light microscope?
    3. Suggest a reason why it is not advisable to clean the objective and eye piece
    lens with a wet cloth or towel?

    3.2 Magnification and resolution of a compound light microscope.
    Activity 3.2
    Work out the following equivalent measurements:
    1. 1 millimetre (mm) =........... metre (m)
    2. 1micrometre (μm) =............mmetre (m)
    3. 1 nanometre (nm) =..............metre (m)
    4. 1 metre (m) = .............mm =.......... μm =........nm,
    5. 1 kilometre (km) = .............m

    a. Magnification
    Magnification refers to increase in the apparent size of the object, while resolution of a microscope is the ability to show two close objects as separate. The maximum magnification of an ordinary light microscope is about x1500. Magnification must be written on the right side and below the biological drawing and it does not have units. The size of the image is measured in mm but converted into micrometres or nanometres to work out the actual size. It is calculated as follows:
    Example
    Calculate the magnification if the actual size is 5μm and the measured image of the specimen has the size of 40mm.

    Answer:
    –– Make the size of the image and the actual size in the same units by converting mm in μm. This is done by multiplying 40mm by 1000 so that 40mm = 40000 μm
    Note that the magnification of the specimen under a light microscope is calculated by multiplying the magnification of the objective used to that of the eyepiece.
    For example: 10x (objective) 10x (eyepiece) = x100.

    b. Microscopic observation
    Activity 3.3
    Using prepared slides of microorganisms such as a bacterium, amoeba, and paramecium. Observe, draw and label the visible parts under a light microscope. Avail these materials before you start: Petri-dishes, plate covers, pencil, transparent tape, microscope, agar powder, and permanent slide of bacteria, amoeba, and paramecium, Bunsen burner or any other source of heat.

    Procedure
    –– Prepare agar medium by boiling a mixture of 10g of agar powder with 50ml of water
    –– Label a control and exposed petri dishes in which you pour prepared agar medium.
    –– Cool both plates for 20 minutes until the medium hardens.
    –– Tape closed the cover of the control plate and removes the cover of the exposed plate.
    –– Leave both plates for 5 minutes, and do not touch or breathe on the agar. After five minutes, tape closed the lid of the exposed plate and store both plates upside down in a warm place and draw your observations
    –– Repeat the observation by using mounted slides of amoeba and paramecium and make a comparison between bacteria, amoeba and paramecium: what is your conclusion?
    For this experiment, light microscope allows to observe organisms of small size including bacteria, amoeba and paramecium. Some other parts of macroscopic organisms such as cells and tissues of plants and animals or some parts of these living organisms such as stems and roots can also be observed under light microscope.
    Some specimens can be observed directly after collection and preparation. However, some of the details might not be clearly observed because specimens are not colored. Also, some material distorts when you try to cut the specimen into thin sections. To overcome this challenge, slides can be prepared in advance by the use of the following steps:

    –– Staining: colored stains are chemicals that bind to chemicals on or in the specimens. This allow the specimen to be seen. Some stains bind to specific cell structures. For example, acetic orcein stains DNA dark red, while gentian violet stains bacterial cell walls.
    –– Sectioning: specimens are embedded in wax, where thin sections are then cut without distorting the structure of the specimen. This is particularly useful for making sections of soft tissue, such as brain. Safety measures might be taken. Make sure that hands are washed with soap and warm water after the
    experiment. Use a disinfectant to wipe down all surfaces where bacteria may
    have been deposited for example. Be sure that some substances and animals
    might be harmful to the life.

    Activity 3.4
    Preparing of temporary slides and observation under light microscope
    Make temporary preparation of slides of epidermis of onions young stems by fixing, staining and mounting. Observe under low and high power of a light microscope.

    Preparation and procedures
    –– Add a drop of water at the center of the microscopic slide to flatten the membrane
    –– Pull of a thin membrane from the onion layer and lay it at the center of the microscopic slide
    –– Add a drop of iodine solution or methylene blue on the onion membrane
    –– Gently lay a microscopic cover slip on the membrane and press it down gently using a needle to remove air bubbles.
    –– Touch a blotting paper on one side of the slide to drain excess iodine/water solution,
    –– Place the slide on the microscope stage under low power to observe.
    –– Adjust focus for clarity to observe.
    –– Make another slide without adding the stain to see the difference between a stained slide and a non- stained slide.
    –– Draw and label the observed parts of each of the two slides and compare a drawing of a stained slide and that of a non-stained slid.

    c. Measuring cells
    Cells and organelles can be measured with a microscope by means of an eyepiece called graticule. This is a transparent scale, usually having 100 divisions (Figure 3.4, A). The eyepiece graticule is placed in the microscope eyepiece so that it can be seen at the same time as the object to be measured (Figure 3.4, B). At this figure (Figure 3.4, B), the cell lies between 40 and 60 on the scale, so that it measures 20 eyepiece units in diameter (60 – 40 = 20).
    To calibrate the eyepiece graticule scale, a miniature transparent ruler called a stage micrometer scale is placed on the microscope stage and is brought into focus. This scale may be fixed onto a glass slide or printed on a transparent film. It commonly has subdivisions of 0.1 and 0.01 mm. The images of the two scales can then be superimposed (Figure 3.4, C). If in the eyepiece graticule, 100 units measure 0.25
    mm, the value of each eyepiece unit equals  By converting mm to μm, the value of eyepiece equals  The diameter of the cell shown superimposed (Figure 3.4, B) measures 20 eyepiece units. Its actual diameter equals 20 × 2.5 μm = 50 μm. This diameter is greater than that of many human cells because the cell is a flattened epithelial cell.
    Use the following instructions to measure the length of one cell

    –– Measure the distance in millimetre from the start of one cell to the end of 10 cells
    –– Divide by 10 to find the length of one cell in the specimen.
    –– Convert this length in millimetre to micrometer by multiplying by 1000.
    –– Find the actual length of a cell by dividing this length by the magnification of thespecimen got from the product of eye piece and objective lens used.

    Self-assessment 3.2.
    1. Calculate the magnification of an image with 50mm, and the objectmeasuring 5μm. in length.
    2. If a nucleus measures 100mm on a micrograph, with a magnification of X10 000, what is the actual size of the nucleus?

    3.3 Electron microscopes
    Activity 3.3
    Suggest the form and source of energy used by electron microscope. How does this differ from that used by a compound microscope?
    An electron microscopes use a beam of accelerated electrons as a source of illumination.
    Electron beams have a much smaller wave length than light rays and therefore have greater resolving powers and can produce higher effective magnifications than light microscopes. There are two types of electron microscopes;
    –– Transmission electron microscope (TEM)
    –– Scanning electron microscope (SEM)
    Electron microscopes are used to study the details of internal structures (the ultrastructures)
    of cells. Most modern TEMs can distinguish objects as small as 0.2nm.
    This means that they can produce clear images magnified up to 250,000 times. Formation of an image by the TEM:
    –– Extremely thin samples of the specimen are needed and are cut by using diamond or glass knives as they are supported in resin block to prevent them from collapsing
    –– The section is then impregnated with a heavy-metal stain
    –– As the beam passes through the specimen, electrons are absorbed by the heavily stained parts but passes readily through the lightly stained parts.
    –– Electro magnets bend the electron beam to focus an image onto the florescent screen or photographic film to form an electron micro graph
    Scanning electron microscope (SEM)
    The SEM is used to produce 3D images of surfaces of the specimens. Electrons are reflected from the surface of the specimen stained with a heavy metal. This enables the SEM to produce images of all specimens, cells, tissues, or even organisms
    a. Advantages of the electron microscope over light microscope
    Electron microscope has a higher resolution and istherefore able of a higher effective magnification estimated at up to 250,000 million times compared to the light microscope which can show a useful magnification only up to 1000-2000 times. This is because a light microscope uses a beam of light with a longer wave length while Electron microscopes use a beam of electrons that have a short wave length.

    b. Disadvantages of electron microscope
    Despite the advantages, electron microscope presents a number of setbacks and limitations.
    –– They are extremely expensive and the maintenance costs are high.
    –– Sample preparation is often much more technical requiring special training.
    –– Samples must be dead, exposed to high radiation and are placed in a vacuum so that it is impossible to observe living specimens
    –– It is not possible to observe colors because electrons do not possess a color. The image is only black-white, even if sometimes the image is colored artificially to give a better visual impression.
    –– They require more training and experience in identifying artifacts that may have been introduced during the sample preparation process.

    c. Comparison between light and electron microscopes
    Light and electron microscope presents the following similarities and differences. The following are some of the similarities:
    –– Both light and electron microscopes form larger (magnified) and more detailed (highly resolved) images of small objects or small areas of larger objects
    –– Both light and electron microscopes are used in biology study, research and medical sciences particularly histology, material sciences such as metallurgy and other aspects of science.
    –– Specimens must be carefully prepared using techniques appropriate for both the equipment and the sample including slicing, staining, and mounting.

    Despite the similarities, light and electron microscope presents differences such as these summarized in the following table:
    Table 3.1. Differences between light and electron microscopic



    Self-assessment 3.3
    1. How is magnification varied in;
    a. A light microscope
    b. An electron microscope?
    2. Why is the resolving power of an electron microscope such better than that of a light microscope?
    3. Make a comparison between light and electron microscope, highlighting the advantages and disadvantages for each type of microscope. Summarise the similarities and differences between light and electron microscopes

    End of unit assessment 3
    Section A. Multiple choice questions
    1. Which ranges can be viewed using a light microscope?
    a. 4 only
    b. 1 and 2 only
    c. 2 and 3 only
    d. 3 and 4 only
    2. The figure below shows a mitochondrion drawn from an electron micrograph. Study it carefully and answer the following questions.
    If the length of the mitochondrion line X Y is 3000 nm. What is the magnification of the drawing of the mitochondrion?
    a. ×100
    b. ×1000
    c. ×10 000
    d. ×100 000
    3. A light microscope is used to observe two membranes that are 200 nm apart. How far apart are the membranes when the objective lens is changed from low power (×40) to high power (×400)?
    a. 2 μm
    b. 20 μm
    c. 200 nm
    d. 2000 nm
    4. The electronmicrograph below is that of a chloroplast.

    The length of the chloroplast along the line shown is 80 mm. The actual length of the chloroplast is 10 μm. What is the magnification of the chloroplast?
    a. ×8 × 102
    b. ×8 × 103
    c. ×8 × 104
    d. ×8 × 106
    5. The following diagram below is drawn from an electron micrograph of an animal cell.
    Which represents the same cell, seen under a light microscope at ×400 magnification?

    Section B:
    6.

    The micrograph above shows a transverse section of part of an animal cell.
    a. Identify organelles labelled X and Y
    b. The maximum actual diameter of Y is 2um. Calculate the magnification of this organelle in the electron micrograph.
    c. Determine with two reasons whether the cell is prokaryotic or eukaryotic.
    d. From evidence in the electron micrograph, deduce two substances that were being synthesised by large quantities by this cell.
    e. The dark granules in the cell are glycogen. Explain the conclusion that you draw from this information



  • UNIT 4: CELL STRUCTURE AND SPECIALIZATION

    Key Unit Competence
    Describe the structure and function of cells in an organism.

    Learning objectives
    By the end of this unit, I should be able to:
    –– Identify plant and animal cell structures visible under a light microscope.
    –– State functions of cell structures as seen under an electron microscope.
    –– Describe the nature of artefacts.
    –– State the importance of freeze fracturing for examining membrane structure.
    –– Explain how cell organelles can be isolated by cell fractionation.
    –– List the functions of cell membranes.
    –– Describe the fluid mosaic structure of cell membranes.
    –– Explain the role of the different components of a cell membrane.
    –– Explain cell specialization as the differentiation of a cell or process to do a particular function.
    –– Interpret charts and micrographs to relate the structure of specialized cells to their functions.
    –– Prepare, observe and draw diagrams for specimens on temporary slides for:
    Wandering Jew, in plants and cheek cells under a light microscope.
    –– Distinguish between ultra-structures of plant cells and animal cells.
    –– Compare ultra-structures of prokaryotic and eukaryotic cells
    –– Show resilience and be aware of artefacts when preparing temporary slides.
    –– Appreciate the importance of cell specialization in multicellular organisms.

    Introductory Activity
    1. Differentiate between prokaryotic and eukaryotic cells.
    2. By using charts for the two cells, identify different organelles of eukaryotic cell that may perform functions similar to those of a prokaryotic cell.

    Cytology is the study of the structure and function of cells. A Cell is the basic unit of life. All living organisms are made up of cells.
    Living organisms are classified into:
    –– Unicellular organisms are made of only one cell, such as bacteria,
    –– Multicellular organisms are animals and plants composed of many cells. In
    multicellular organisms, cells divide and then undergo differentiation or
    specialisation for specific functions.

    Cell theory.
    The cell theory states that all living organisms are made up of cells, and cells are the basic unit of structure function in all living organisms.
    The main principles of cell theory are based on the following ideas.
    –– All known living organisms are made up of one or more cells,
    –– All cells come from pre-existing cells by division
    –– Cells contain the hereditary information that is passed from cell to cell during
    cell division.
    –– Metabolism takes place in cells
    –– Given suitable conditions, cells are capable of independent existence

    4.1 Ultra-structure of a cell
    Activities 4.    1
    1. Observe the chart given for Ultra structure of a cell and identify parts that are easily recognizable when compared with a photomicrograph form a light microscope.
    2. Identify the se mitochondria and ribosomes and state their roles in the life of the cell.
    When viewed under light microscope, the most obvious features observed are the very large nucleus and a clear cytoplasm surrounded by a cell membrane. However, under electron microscope, it is possible to identify a range of organelles in plant and animal cells. Ultrastructure is the detailed of cell as revealed by the electron microscope.

    4.1.2 Similarities between animal cell and plant cell
    –– Both have a cell membrane, a cytoplasm and a nucleus.
    –– Both animal and plant cells have mitochondria, Golgi apparatus, Reticulum endoplasmic, lysosome, big ribosomes (80S), peroxisome, microtubules.
    Table 4.1: Differencied between animal and plant cell


    Self-assessment 4.1
    1. What structures do both animal and plant cells have in common?
    2. State any five principles of the cell theory.
    3. Give the major difference between a plant and animal cell. Which organelles does this difference relate to?

    4.2 Prokaryotic cells
    Activities 4.2
    Under microscope, observe mounted slides of bacteria, and plant cells. Draw and label the parts that are common in both plant and bacterial specimens

    A typical bacterial cell has a cell surface membrane enclosing the cytoplasm that contains enzymes, ribosomes and food granules. The membrane is surrounded by the cell wall and this may in turn be enclosed in a capsule. A bacterial cell lacks high level of organization compared to animal or plant cell. It has no Golgi apparatus or endoplasmic reticulum. The genetic material is a single strand of DNA usually
    coiled up into the center of the cell to form a nucleoid. This nucleoid has no double membraned nuclear envelope so is often described as an ‘ill-defined nucleus’.
    –– Some bacterial cells contain plasmids with additional DNA.
    –– Respiration generally takes placein mesosomeswhich is an in-folding of the
    cell surface membrane but lack mitochondria
    –– Photosynthesizing bacterial cells such as cyanobacteria(blue green algae) have a special form of chlorophyll but it I not enclosed in a double membraned chloroplast

    4.4.1. Comparison between prokaryotic and eukaryotic cells
    Table 4.2 Comparison between prokaryotic and eukaryotic cells


    Self-assessment 4.2
    Organisms such as bacteria are known as prokaryotes.
    1. Which structure in a bacterial cell resembles a nucleus?
    2. How does it differ from the nucleus of eukaryotic cells?

    4.3 Cell organelles
    Activities 4.3
    By using iodine solution, methylene blue, a piece of onion leaf, a scalpel, forceps, light microscope, slides and cover slips, clean cotton wool bud, and onion bulbs. Observe cells from onion epidermis under light microscope. Observation of a plant cell
    –– Add a drop of diluted iodine solution on the slide.
    –– Remove a transparent layer of onion epidermis from the inner side that you will mount on the slide and add iodine solution.
    –– Cover your preparation with a cover-slip and mount it on the stage.
    –– Observe the preparation under the low power and thereafter under high magnification.
    Why did you use iodine solution in this experiment?
    What main parts of a plant cell are easily observed from a light microscope?

    Observe animal cells from mouth cheek epithelium
    –– By using a clean cotton wool bud, wipe over inside of your cheek.
    –– Smear cells over surface of a clean grass microscope slide containing a drop of methylene blue stain
    –– Carefully put the cover-slip on the preparation and mount it on the stage to observe.
    Draw both plant and animal cell and label the cell wall, nucleus and vacuole.