General Biology I Notes PDF

Nile University Nigeria DEPARTMENT OF BIOLOGICAL SCIENCES Student’s Hand-out COURSE CODE: BIO 101 COURSE TITLE: General Biology I COURSE LECTURER: Mrs Chiadikobi, Esther Kelechi- Onyemata....

Nile University Nigeria DEPARTMENT OF BIOLOGICAL SCIENCES Student’s Hand-out COURSE CODE: BIO 101 COURSE TITLE: General Biology I COURSE LECTURER: Mrs Chiadikobi, Esther Kelechi- Onyemata. Abuja – 2016  BIO 101: GENERAL BIOLOGY I COURSE CONTENT: 1. Introduction: The Science of Biology. 2. Characteristics of Living Things. 3. Classification of Organisms. 4. Basic Biological Chemistry. 5. Cell Structure and Organization. 6. Functions of Cellular Organelles 7. Diversity of Living Organisms. 8. General reproduction 9. Heredity. 10.Evolution. 11.Interrelationship of Living Organisms. 12.Elements of Ecology and types of Habitat. 13.Human Ecology. RECOMMENDED BOOKS The following books are recommended but not compulsory text materials. You may use any other textbooks; provided it helps you achieve the objectives of the course and for assignments. 1. Prentice-Hall. Biology: the study of life (6th edition), 1995. 2. Roberts M.B.V. Biology: a functional approach (4th edition), 1986. 3. James L. Gould; William T. Keeton. Biological Science. (6th edtn), 1996. 4. Solomon; Berg; Martin. Biology (6th edition), 2002. 1  5. Starr and Taggart. Biology: the unity and diversity of life (11th edition). 6. Campbell; Reece. Biology (9th and 10th editions). 1. Introduction: The Science of Biology Biology: is the scientific study of life and living things. The word ‘biology’ comes from two Greek words: bio – which means ‘life’ and ‘logy’ – ‘the study of’. There is a wide diversity (biodiversity) of living organisms on this planet: some biologists estimate that there are between 10-30 million types of organisms, made up of plants, animals, bacteria, viruses etc. Most of these organisms are still undiscovered and unnamed. Life: A working definition lately used by NASA is that "life is a self- sustaining system capable of Darwinian evolution." The Origins of Modern Biology Although naturalists and collectors had been at work for centuries observing living things, the application of the scientific method to biology is a relatively recent innovation. The earliest scientific biologist was Andreas Vesalius (1514- 1564), who made the first serious studies of human anatomy by dissecting corpses. He discovered that the body is composed of numerous complex subsystems, each with its own function, and he pioneered the comparative approach, using other animals to work out the purpose and organization of these anatomical units. Important Biologists Anton van Leeuwenhoek (1632–1723): was born in Delft, Netherlands in 1632. His interest in lens making and curiosity led him to be the first to observe 2 single cell organisms. He is considered a biologist and microscopist which earned him the distinction of being the father of microbiology. Robert Hooke (1635–1703): born on 1635 in the Isle of Wight, England, Robert Hooke received his higher education at Oxford University where he studied physics and chemistry. His work included the application what is known today as Hooke’s law, his use of microscopy, and for the discovery of the “cell” in 1665 using cork and a microscope. Robert Brown (1773–1858): specializing in botany, Scottish born Robert Brown introduced the model that helps describe random movements of cells which is known as particle theory, or more aptly, Brownian motion. Among his contributions to the world of science was his description in detail of the cell nucleus in all living things. Charles Darwin (1809–1882): after attending the University of Cambridge and taking up medicine at the University of Edinburgh in Scotland, Darwin was considered a naturalist. As a biologist, he proposed the concept that “all species of life” came from a single source. His theory of evolution marked the beginning of the discussion on natural selection. Gregor Mendel (1822–1884): Austrian scientist / monk. When he wrote “Experiments on Plant Hybridization”, he paved the way for biology students to study genetic traits in peas. During his experiments, Gregor found that a specific trait would be dominant over other traits in the same species. This became recognized as the Mendelian inheritance. Louis Pasteur (1822–1895): a French chemist and biologist who proved the germ theory of disease and invented the process of pasteurization. He is best known for his work on the development of vaccines for rabies, anthrax, cholera, TB and smallpox. James D. Watson (b. 1928), and Francis Crick (1916–2004): jointly received the Nobel Prize in physiology / medicine for their 1953 determination of the structure of deoxyribonucleic acid (DNA). The double-helix model they 3 proposed provided a physical basis for Mendel’s genes, which are the basic units of Darwinian selection, has had a major impact on biology, particularly in the field of genetics enabling researchers to understand the genetic code. Branches of Biology Biological Sciences cover all aspects of the study of life and emphasizes both the unity and diversity of living things. Special emphasis is placed on the relationship between structure and function, progressing through molecular, cellular, organismic and ecological levels of complexity. Evolutionary relationships are explained and illustrated. Below is a list of major branches of biology with a brief description for each:  Anatomy - study of the animal form, particularly human body.  Physiology - the biological study of the functions of living organisms and their parts.  Zoology - the branch of biology that deals with animals and animal life, including the study of the structure, physiology, development and classification of animals.  Microbiology - the branch of biology that deals with microorganisms and their effects on other living organisms.  Botany - the scientific study of plants.  Ecology - the branch of biology that deals with the scientific study of the interactions among organisms and between organisms and their environment.  Genetics - the study of genes and heredity.  Paleontology - the study of fossils.  Taxonomy: The branch of biology that deals with the identification, nomenclature and classification of organisms. The above branches of biology are a few examples of the direct approach to the study of biological science, known as pure (basic) biological science. Applied 4 biology, which is the application of the knowledge of the pure biological sciences, includes branches such as: agriculture, medicine, veterinary science, biotechnology, etc. 1.1. The Scientific Method What is Science? Science is a methodical approach to studying the natural world. Science asks basic questions, such as how does the world work? How did the world come to be? What was the world like in the past, what is it like now, and what will it be like in the future? These questions are answered using observation, testing and interpretation through logical methods. The "Scientific Method" is a universal systematic approach to advancing knowledge. The scientific method may include some or all of the following “steps” in one form or another: observation, defining a question or problem, research (planning, evaluating current evidence); forming a hypothesis, prediction from the hypothesis (deductive reasoning); experimentation (testing the hypothesis); evaluation and analysis; peer review and evaluation, publication and in some cases formulation of theories. Many of the steps involved in a typical scientific investigation are discussed below: Observation & question: The first process in the scientific method involves the observation of a phenomenon, event, or “problem.” The discovery of such a phenomenon may occur due to an interest on the observer’s part, a suggestion or assignment, or it may be an annoyance that one wishes to resolve, or even by chance. Observation leads to a question that needs to be answered to satisfy human 5 curiosity about the observation, such as why or how this or that event happened. In order to develop this question, observation may involve taking measures to quantify it in order to better describe it. Scientific questions need to be answerable and lead to the formation of a hypothesis about the problem. Hypothesis: The next step in a scientific investigation is forming a hypothesis. A hypothesis is a possible answer to a scientific question, or an explanation to an observation, until it is tested. A hypothesis must be based on scientific knowledge, and it must be logical. A hypothesis also must be falsifiable. In other words, there must be a way to try to make the hypothesis fail. Science is often more about proving a scientific statement wrong rather than right. If it does fail, another hypothesis may be tested, usually one that has taken into consideration the fact that the last tested hypothesis failed. Hypothesis development depends upon a careful characterization of the subject of the investigation. Literature on the subject must be researched. Sometimes numerous working hypotheses may be used for a single subject, as long as research indicates they are all applicable. Experiment: An experiment is a test of the hypothesis. It is designed to prove or disprove the hypothesis. Testing and experimentation can occur in the laboratory, in the field, on the blackboard, or the computer. Results of testing must be reproducible and verifiable. The data should be available to determine if the interpretations are unbiased and free from prejudice. Experimental Design: The design of an experiment is critical to its success. In an experiment, the scientist sets up a situation in which a particular observation can be made. The scientist makes changes in the situation and observes the results or response. In biology, research often involves the use of controlled experiments. In a controlled experiment, a situation is set up in duplicate. A single factor, called a variable, is changed in one setup. The variable may be any factor, such as temperature or light intensity. In the other setup, no factor is changed. If any difference occurs in the results or response of the two setups, it can be assumed to 6 be caused by the changed factor. The set-up, in which no change was made, serves as a reference and is called the control. Conclusion & Evaluation: All evidence, data and conclusions must be analyzed to make sure bias or inadequate effort did not lead to incorrect conclusions. Qualitative and quantitative mathematical analysis may also be applied. Scientific explanations should always be made public, either in print or presented at scientific meetings. It should also be maintained that scientific explanations are tentative and subject to modification. Communication of results (Publication): When a research project has been completed, the investigator publishes his findings in scientific journals. Scientists generally do not regard information unless it has been published in a peer- reviewed or refereed journal. Typically, the scientist writes a report on the research and submits it to a journal editor. The editor distributes copies of the article to several peer reviewers that are recognized experts in the field. After reviewing the research, the peer reviewers recommend whether the paper should be published or not. After which the postulated hypotheses that have been tested by different investigators numerous times and have not been disproved become theory. Scientific Theory (or Law): is an integrated, comprehensive explanation of many “facts,” especially one that has been repeatedly tested or is widely accepted and can be used to make predictions about natural phenomena. A theory can often generate additional hypotheses and testable predictions. Theories can incorporate facts and laws and tested hypotheses. 7  Pic. 1. Steps of the scientific method SECTION REVIEW 1. Define biology 2. Which scientist contributed to the science of Microbiology? Bacteriology? Genetics? Medicine? 3. Name 5 branches of biology and what the specialists are known as? 4. What is pure and applied biology? 5. What is meant by the phrase ‘the scientific method’? Name 4 stages of the scientific method. 6. What is a hypothesis? Give an everyday example of a hypothesis. 7. At what stage of the scientific method is a hypothesis tested? Write a short note about that stage. 8. Scientific Method In Action:  The Strange Case of Beriberi. In 1887 a strange nerve disease attacked the people in the Dutch East Indies. The disease was beriberi. Symptoms of the disease included weakness and loss of appetite, victims often died of heart failure. Scientists thought the disease might be caused by bacteria. They injected chickens with bacteria from the blood of patients with beriberi. The 8  injected chickens became sick. However, so did a group of chickens that were not injected with bacteria. One of the scientists, Dr. Eijkman, noticed something. Before the experiment, all the chickens had eaten whole-grain rice, but during the experiment, the chickens were fed polished rice. Dr. Eijkman researched this interesting case and found that polished rice lacked thiamine, a vitamin necessary for good health. a) State the Problem b) What was the hypothesis? c) How was the hypothesis tested? d) Should the hypothesis be supported or rejected based on the experiment? e) What should be the new hypothesis and how would you test it?  How Penicillin Was Discovered. In 1928, Sir Alexander Fleming was studying Staphylococcus bacteria growing in culture dishes. He noticed that a mold called Penicillium was also growing in some of the dishes. A clear area existed around the mold because all the bacteria that had grown in this area had died. In the culture dishes without the mold, no clear areas were present. Fleming hypothesized that the mold must be producing a chemical that killed the bacteria. He decided to isolate this substance and test it to see if it would kill bacteria. Fleming transferred the mold to a nutrient broth solution. This solution contained all the materials the mold needed to grow. After the mold grew, he removed it from the nutrient broth. Fleming then added the nutrient broth in which the mold had grown to a culture of bacteria. He observed that the bacteria died which was later used to develop antibiotics used to treat a variety of diseases. i. Identify the problem. 9  ii. What was Fleming's hypothesis? iii. How was the hypothesis tested? iv. Should the hypothesis be supported or rejected based on the experiment? v. This experiment led to the development of what major medical advancement? 2. Characteristics of Living Things Living things are called organisms. Living organisms are comprised of the same chemical elements that make up nonliving things and both obey the same laws of physics and chemistry. We can better understand what distinguishes living from nonliving by examining the processes and characteristics that all living organisms have in common. Some of these characteristics are discussed below:  Living organisms are composed of cells. This is the single most fundamental difference between living and non-living things. Small 10  organisms such as bacteria and many protists are composed of a single cell. Larger organisms are composed of many cells; they are multicellular.  Living organisms are organized. The list below shows increasing levels of biological organization:  Atoms  Molecules  Cells  Tissues  Organs  Systems  Individual organism  Population  Community  Ecosystem  Biosphere Atoms: All substances are made up of matter and the basic unit of matter is the atom. The atom constitutes the smallest particle of an element. Molecules: A molecule is formed when atoms of the same or different elements combine. It is the smallest unit of a compound that can normally exist independently. Cells: a cell is the basic unit of life, it is considered to be the smallest structure alive. They are often too small to see without the aid of a microscope. Similar kinds of cells may be arranged together to form a tissue. Tissues have specific properties and functions. For example muscle tissue is composed of muscle cells. It functions to move body components. Two or more tissues that form a structure with a specific function are known as an organ. For example, the heart is an organ formed from muscle tissue, nervous tissue, connective tissue, and epithelial tissue. It functions to pump blood. An organ system consists of two or more organs which perform a specific task. Some organ systems are: the nervous, endocrine, skeletal, muscular, cardiovascular, immune, lymphatic, digestive, respiratory, excretory, and reproductive systems. 11  A population is an interbreeding group of organisms (the same species) that occupies a particular area. Two or more populations form a community. The word community refers to the organisms. The word ecosystem refers to the organisms of a community and also the nonliving environment. All of the ecosystems on earth form the biosphere.  Living organisms are sensitive and adapt to the environment: Living organisms are sensitive to things around them. They can sense changes in their surroundings, and respond to these changes. These changes known as stimuli (singular: stimulus) are of many types, such as changes in temperature, light intensity, sound, day length and the presence of chemicals. Sensitivity is the ability to detect or sense changes in the environment (stimuli) make responses and adapt.  Living organisms move: All organisms are able to move. Some, including most animals, are able to move their whole body from place to place, and this is called locomotion. But even seemingly non-moving organisms, such as plants, are able to move parts of their structures. By observing some living plant cells under a microscope, you may be able to see the tiny structures within each cell moving around. Movement is an action by an organism or part of an organism causing a change in position or place.  Living organisms use energy: All organisms need energy to carry out their activities. Energy used by most living things comes either directly or indirectly from the sun. The solar energy trapped from the sun is stored in food substances, which is then transferred from one organism to another through feeding patterns called food chains.  Living organisms have definite form and limited size.  Living organisms have limited life span.  Living organisms carry out various kinds of life processes, such as: 1. Nutrition 12  2. Synthesis and assimilation 3. Transport 4. Respiration 5. Growth 6. Excretion 7. Reproduction 8. Regulation These life processes are necessary for maintaining a fairly constant environment within an organism in spite of its constantly changing environment. The condition of a constant internal environment is known as homeostasis. Nutrition: Every organism takes in (ingest) substances from their external environment and convert them into useable forms. Nutrition is defined as the ingestion of nutrients (e.g. organic substances and mineral ions) containing the raw materials for growth and tissue repair, absorbing and assimilating them. Organisms such as green plants; cyanobacteria etc.; produce complex nutrients from simple substances (e.g. carbon dioxide; water) found in the environment, they are known as producers. Most animals on the other hand, obtain nutrients ready-made from the environment by consuming other organisms in their environment. Synthesis and assimilation: Organisms are able to combine simple substances chemically to form more complex substances. This process is called synthesis. Synthesis produces materials that can become part of the structure of an organism. In this way, the organism can repair or replace worn-out parts. These materials also allow the organism to grow. The incorporation of materials into the organism's body is called assimilation. Transport: The process by which substances enter and leave cells and become distributed within the cells is known as transport. In the smallest and simplest organisms, materials are exchanged directly with the external 13 environment. Useable materials enter the cells directly from the environment; waste materials pass from cells directly into the environment. In larger, multicellular organisms, however, most cells are not in direct contact with the external environment. In many animals, for example, a circulatory system transports materials to, and wastes away from, the cells of the organism. The fluid, or blood, of the circulatory system is kept in motion, distributing these materials among the cells of the organism. In plants, specialized conducting structures transport substances from the roots and leaves to all parts of the plant. Respiration: All living organisms need energy. They get this by breaking down nutrients, such as glucose, inside their cells. This releases the energy from the nutrients. Respiration is the chemical reactions that break down nutrient molecules in living cells to release energy. Growth: Some of the nutrients that living organisms ingest are used to help cells to grow, and to help to make more cells. Growth can be defined as a permanent increase in size and dry mass by an increase in cell number or cell size or both. Excretion: Every organism produces waste substances that it cannot use and that may be harmful if accumulated in the body. These wastes are the products of many of the chemical / reactions that occur within cells. The removal of these wastes from the organism's body is called excretion. Reproduction: is the process by which living things produce new organisms of their own kind. Reproduction can take different forms of multiplication and division:  Asexual (e.g. microorganisms);  Sexual (e.g. humans). Regulation: All the activities that help to maintain an organism's homeostasis make up the process of regulation. In animals, systems such as the digestive, transport, excretory, nervous, and endocrine systems are involved in 14 some part of the process of regulation. Each of these systems contributes to maintaining homeostasis. Plants do not have nervous systems, but they do have parts that produce hormones. These hormones allow a plant to respond to various changes in its environment. SECTION REVIEW 1. What is homeostasis? 2. Define the term growth 3. How do organisms differ in the ways they obtain their energy source, or food? 4. Arrange these structures in ascending order: Cells; DNA; Genes; Chromosomes. 5. Explain the term biodiversity 6. The engine of a car uses petrol. Oxygen from the air combines with the petrol, releasing energy which is used to turn the wheels of the car. Waste gases from the burned petrol are given off in the exhaust fumes of the car. (a) Which characteristics of a car are similar to which characteristics of a living organism? (b) Explain why a car is not classified as a living organism. 3. Classification of Organisms All living organisms are classified and named according to an international system of criteria. The branch of biology that deals with the classification and naming of living things is called taxonomy. Classification helps us to impose order and a general plan on the diversity of living organisms. Classification can be defined as grouping organisms according to 15 their structural similarities. This means that organisms that share similar features are placed in one group. These groups are arranged from the largest group of organisms to the smallest group of organisms as follows: domain; kingdom; phylum (plural: phyla); class; order; family; genus (plural: genera) and species. Below is a classification of few animals as illustration (tab. 1). Table 1. Classification of living organisms Organism Group Name Human Lion House fly Domain Eukaryote Eukaryote Eukaryote Kingdom Animalia Animalia Animalia Phylum Chordata Chordata Arthropoda Class Mammalia Mammalia Insecta Order Primate Carnivora Diptera Family Hominidae Felidae Musciadae Genus Homo Panthera Musca Species sapiens leo domestica The group “species” is the most specific category available. Currently about 1.8 million species have been scientifically named, thousands more are added to the list every year as they are discovered. Domain: Until 1969 life was classified into two kingdoms: Plant and Animal Kingdoms. From 1969-1990 life was classified into 5 Kingdoms: Monera, Protista, Plantae, Fungi, Animalia, by R.H. Whittaker based on the methods of classification established by Carolus Linnaeus – a Swedish botanist, considered the father of modern taxonomy. Then in 1990 an evolutionary model of classification with a level higher than a kingdom was introduced. This latest version of classification using three domains based upon a new discovery in 1977 by Dr. Carl Woese, of a previously unknown group of prokaryotic organisms. These organisms lived in extreme environments (e.g. hot springs, acid lakes, salt evaporation ponds 16 etc). Based on biochemical characteristics; DNA and RNA sequence analyses these organisms where found to be different from previously known bacteria, and subsequently named archeabacteria classified under a new domain called Archaea. The three domains are as follows:  Archaea (Archeabacteria): consists of archeabacteria, bacteria which live in extreme environments. The name archeabacteria is derived from the Greek word archaio, which means “ancient”. The kingdoms of this domain include Archaea, Crenarchaeota, Euryarchaeota, Korarchaeota.  Eubacteria: members of this group consist of more typical bacteria found in normal conducive environments. The kingdom Eubacteria belongs to this group.  Eukaryote: members of this group include the kingdoms of Protista, Fungi, Plantae and Animalia. Kingdoms: According to the new hierarchical classification system there are six kingdoms under the three domains, as follows:  Animalia: consists of multicellular, eukaryotic, heterotrophic, motile organisms with highly specialized sense organs, e.g. humans, insects, fish, birds.  Plantae: consists of multicellular, eukaryotic, autotrophic, non-motile organisms, with cell walls made of cellulose. E.g., moss, ferns, flowering plants, trees, etc.  Protista: consists of mostly unicellular, eukaryotic organisms. Genetic similarities between organisms in this kingdom are largely unknown, due to their irregularities. Hence it is sometimes called the “odds and ends” kingdom for every organism that does not fit into the other four. E.g., amoeba, paramecium, euglena, algae, etc.  Fungi: consists of multicellular, eukaryotic, heterotrophic, non-motile organisms, with cell walls made of chitin and not cellulose. E.g. mushrooms, molds & mildews, yeast (unicellular). 17   Eubacteria (Monera): consists of unicellular, prokaryotic bacteria, e.g. Nitrogen-fixing bacteria, Blue-green Algae, Intracellular Parasites.  Archaebacteria (or Archaea): are bacteria which live in extreme environments. They possess unique properties and features such as special lipids that enable them to survive in extreme conditions. E.g., thermophiles, methanogens, halophiles, and hot springs microbes. Each kingdom is further divided into smaller groups called phyla, based on particular structural and functional properties shared by their common organisms. For example within the animal kingdom there are approximately 35 Phyla, some of which are: Platyhelminthes, Nematodes, Mollusca, Annelida, Arthropoda, Echinodermata, Chordata, etc. The Phylum Chordata containing the most familiar species, including humans, is further divided into 3 subphyla of: Cephalochordata, Tunicata (Urochordata) and Vertebrata based on their main features of the notochord, which is a rod that supports the nerve cord. It consists of a bundle of nerve fibers which connect the brain to the muscles and organs, and through which messages are passed from the brain. The subphylum vertebrata, which includes every animal with a backbone, is further divided into seven classes of which are: Amphibia, Reptilia, Aves, Mammalia, etc. Binomial nomenclature: Every recognized species on earth is given a two- part scientific name in Latin. This universal system is called "binomial nomenclature." Carl Linnaeus introduced the concept of binomial nomenclature in his great work called Systema Naturae (1st edition in 1735). The term binomial literally means two names – ‘bi’ means two and ‘nomial’ means name. Linnaeus derived scientific names from the genus and the species to which organisms belong. When writing a scientific name, the genus name is written first and starts with a capital letter, and the species name is written second 18 and starts with a small letter. The scientific name ought to be printed in italics when typed and underlined separately when handwritten, for example the tiger belongs to the genus called Panthera and the species called tigris, therefore its scientific name will be typed as Panthera tigris, or handwritten as Panthera tigris. The genus name can also be abbreviated with its first letter, followed by a period. This is usually done to avoid repetition when classifying species of the same genus, for example, oak trees of the same genus Quercus, and different species names: Quercus rubra and Quercus alba, can simply be written as Q. rubra and Q. alba. SECTION REVIEW 1. What is taxonomy? 2. An organism’s scientific name consists of? 3. Why do scientists organize living things into groups? 4. Which choice lists the groups in order of decreasing variety? a. species, genus, family, phylum b. family, order, phylum, class c. kingdom, order, genus, species. 4. Basic Biological Chemistry Matter makes up everything in the universe, including all living organisms. Matter is composed of elements. An element is a pure substance that cannot be 19 broken down into simpler substances using ordinary chemical or physical techniques. The smallest particle of an element is an atom. Elements differ from one another in their atomic structure. Atoms often bind to each other chemically in fixed numbers and ratios to form molecules. For example, the oxygen gas we breathe is formed from the chemical combination of two oxygen atoms. Living organisms are composed primarily of carbon, hydrogen, oxygen, as well as nitrogen (organic compounds). There are about 21 other elements found in living organisms, but these four elements make up 96% of the weight of a living organism (Tab. 2). Seven other elements make up most of the other 4%: calcium, phosphorus, potassium, sulfur, sodium, chlorine, and magnesium. These elements often occur as ions or in inorganic compounds within living organisms. The rest of the elements that are required by organisms are found in such small amounts (< 0.1 %) that they are called trace elements, e.g., Iodine, iron, etc. Table 2. Some chemical elements found in human body Atomic % by mass in Element Symbol number humans Hydrogen H 1 10.00 Carbon C 6 18.00 Nitrogen N 7 3.00 Oxygen O 8 65.00 Sodium Na 11 0.010 Magnesium Mg 12 0.010 Phosphorus P 15 1.20 Sulfur S 16 0.20 Chlorine Cl 17 0.20 Potassium K 19 0.20 Calcium Ca 20 1.50 Iron Fe 26 0.05 Iodine I 53 0.05  Atomic structure: The atom is the basic unit of matter, made up of three particles:  Protons (+) and neutrons form the nucleus. 20   Electrons (-) orbit the nucleus.  All the mass is in the nucleus (protons + neutrons).  Atoms have equal numbers of electrons and protons.  Overall no net charge. A chemical element is a pure substance made up of only one type of atom.  Atomic number: the number of protons in an atom of an element.  Different numbers of neutrons in an atom create isotopes.  Atoms possess the same chemical properties because of the same number of protons & electrons. A chemical compound is a stable combination of different elements that are held together by chemical bonds, e.g. H2O or NaCl. The main types of chemical bonds are:  Ionic bonds - form when electrons are transferred from one atom to another, e.g. the chemical reaction between Na & Cl.  Covalent bonds - form when electrons are shared between atoms, e.g. H2O.  Properties of water: Water molecules (H2O) are neutral, yet charged. This is due to the oxygen end that has a slight negative charge, while the hydrogen end has a slight positive charge. Hence a water molecule is known as a polar molecule – an uneven distribution of charges between atoms in a molecule. Polar molecules can attract one another in different forms, such as in:  Hydrogen bonds -formed when the H atom on one water molecule is attracted to the O atom on another water molecule.  Cohesion forces - is an attraction between molecules of the same substance, e.g. surface tension of water.  Adhesion forces - is an attraction between molecules of different substances 21  Mixtures: a mixture is formed when two or more elements or compounds are physically combined together, but not chemically joined, e.g. salt and iron fillings. Two types of mixtures can be made with water:  Solution – in this mixture all the components are evenly spread out, water is the solvent while the substance dissolved is the solute.  Suspension – is a mixture of insoluble materials that separates on standing.  pH scale: A water molecule can split to form a hydrogen ion (H +) and a hydroxide ion (OH–). The pH meter indicates the concentration of H+ ions in a solution on a scale of 0–14. Pure water has a pH value of 7, acids forms H+ ions in solution. Acidic solutions have higher concentrations of H + ions than pure water and possess pH values below 7. Bases form OH– ions in solution. Basic, or alkaline, solutions have lower concentrations of H+ ions than pure water; hence possess pH values above 7 (fig. 1). Fig. 1. Diagram of an illustrative pH scale  Carbon Compounds: Organic chemistry is the study of compounds with bonds between carbon atoms. Carbon compounds are also known as organic 22  compounds. Living organisms are made up of molecules of various sizes and complexity; very large molecules are called macromolecules. Macromolecules are formed through a process called polymerization; this process involves the joining of smaller units called monomers, to form macromolecules, called polymers. There are four major groups of organic compounds found in living organisms: 1. Carbohydrates (starch and sugar) – are compounds of C, H, & O. Living organisms use carbohydrates as their main energy source, plants and some animals also use carbohydrates for structural purposes. Simple sugars are called monosaccharides, e.g. glucose, fructose. Sugar molecules can be bonded together by an anabolic process known as dehydration synthesis - chemical bonding of molecules through the use of enzymes and a loss of water. When two monosaccharides join they form a disaccharide, e.g. maltose; and when several simple sugars join they form a polysaccharide. Organisms store excess sugar in the form of polysaccharide. In plants this form of stored sugar is called starch and in humans – glycogen. Other examples of polysaccharides are cellulose and chitin. 2. Lipids (fats, oils, waxes) – are made mostly of C, H, & to a lesser extent - O. Molecules of lipids are made up of compounds of fatty acids and glycerol. Lipids are used to store energy, they hold twice as much energy in sugar or protein; they forms parts of cell structures. 3. Nucleic acids (DNA & RNA) – are compounds that contain H, O, N, C & P. They store and transmit hereditary, or genetic, information. 4. Proteins – are compounds made up of N, C, H, O and in some cases P & S. Proteins are polymers of amino acids. The bond between two amino acids is called a peptide bond, several chains of amino acids bonded together are known as polypeptides. Proteins control the rate of reactions and regulate 23  cell processes. They help form bones and muscles; carry substances into or out of cells, are present in antibodies and help fight diseases.  Chemical Reactions and Enzymes: All metabolic processes in living organisms are based on chemical reactions. A chemical reaction is a process that changes one set of substances into another set of substances. The elements / compounds involved in these reactions are called reactants. The elements / compounds produced by the reaction are the products Chemical reactions always involve breaking the bonds in reactants and forming new bonds in products. Some chemical reactions release energy; others absorb energy. Reactions that release energy often occur spontaneously (fig 2b), while reactions that absorb energy require a source of energy (fig 2a). Every reaction needs energy to get started, called activation energy. a b Fig. 2. Chemical reactions Chemical reactions of some life processes occur slowly and hence need a catalyst - is a substance that speeds up the rate of a chemical reaction. They work by lowering the activation energy. Enzymes are proteins that act as biological catalysts. They speed up reactions that take place in cells (fig. 3). In a reaction catalyzed by an enzyme, the reactants (substrates) bind to a site on the enzyme called an active site. The fit is so specific, like a lock and key, so that only particular 24  substrates can bind with a specific enzyme. Enzymes are affected by pH, temperature, enzyme and substrate concentration, presence of inhibitors/activators. Fig.3. effects of Enzymes SECTION REVIEW 1. Negatively charged particles in an atom are called a) neutrons. b) electrons. c) protons. d) elements. 2. Substances that cannot be broken down into simpler substances by ordinary chemical reactions are called a) atoms. b) compounds. c) elements. d) molecules. 3. A particle with a negative or positive charge is referred to as a) electron. b) proton. c) ion. d) isotope. 4. A chemical bond where electrons are transferred from one atom to another is a(n) a) hydrogen bond b) ionic bond. c) covalent bond. d) none of the above 5. The bond which is found between water molecules is a(n) a) hydrogen bond. 25  b) ionic bond. c) covalent bond. d) none of the above 6. A chemical bond in which one pair of electrons is shared between atoms is a(n) a) hydrogen bond. b) ionic bond. c) covalent bond. d) none of the above 7. All of the following are organic compounds EXCEPT a) nucleic acids. b) water. c) proteins. d) carbohydrates. 8. Energy needed for chemical reactions in the body is provided by the breakdown of a) ribonucleic acid (RNA). b) deoxyribonucleic acid (DNA). c) adenosine triphosphate (ATP). d) adenosine diphosphate (ADP). 9. Which of the following describes the most acidic solution? a) pH 4 b) pH 5 c) pH 7 d) pH 14 10. The building blocks of proteins are a) fatty acids. b) nucleic acids. c) amino acids. d) monosaccarides. 11. A carbon atom has six protons but has 7 neutrons, this carbon atom would be called a(n): a) cation b) acid c) compound d) isotope 12. What are enzymes? What factors affect the action of enzymes? 13. What is hydrolysis? 14. Name 2 types of nucleic acids. 15. List the elements found in both proteins and nucleic acids. What additional element is found in proteins? 26  5. Cell Structure and Organization. All organisms are made up of one or more cells, and all cells have many of the same structures and carry out the same basic life processes. A cell is the basic unit of life. They are often too small to see without the aid of a microscope. The cell concept: In 1665, Robert Hooke, a British scientist was the first to discover and coin the word “cell” after examining thin slices of cork under a microscope. Soon after the discovery of cells Anton van Leeuwenhoek’s interest in lens making and curiosity led him to be the first to observe single cell organisms. Two German scientists, named Matthias Schleiden and Theodor Schwann in 1838 and 1839 respectively, proposed that cells are the basic building blocks of all living organisms, after having observed the cells of many different plants and animals. In 1855, Rudolf Virchow a German doctor proposed that living cells arise only from other living cells, after observing cell division and formation under a microscope. The ideas of all three scientists (Schleiden, Schwann and Virchow) led to the cell theory, which is one of the fundamental theories of biology. The cell theory states that:  All living organisms are composed of one or more cells.  Cells are the basic units of structure and function in an organism.  Cells originate from pre-existing cells by the process of cell division. Cells contain a variety of internal structures called organelles. An organelle is a cellular component that performs specific functions in the cell. The various functions of cell organelles help maintain the life of the Cell. 27  Types of cell: There are two basic types of cell: Prokaryotic - means ʺwithout nucleus” and Eukaryotic cells – means ʺtrue nucleus”. Apart from their structural differences, both cells are fundamentally alike: they are both surrounded by a membrane that helps keep their internal environment constant and different from their external environment; both Prokaryotic and Eukaryotic cells carry out the same life processes, using the same kinds of organic compounds – carbohydrates, fats, proteins and nucleic acids. Prokaryotic cell: is a type of cell lacking a membrane enclosed nucleus and other membrane-enclosed organelles found in eukaryotic cells, such as nucleus; mitochondria; chloroplast; Golgi apparatus; etc. It is found mostly in unicellular organisms, e.g. in the domains of Archaea and Eubacteria. The diameter of prokaryotic cells can range between 1 and 10 micrometers (fig. 4). Fig.4. Prokaryotic cell Eukaryotic Cell: is a type of cell that has a membrane enclosed nucleus and other organelles enclosed within membranes. All organisms except bacteria are composed of eukaryotic cells, i.e. organisms in the kingdoms of the eukarya domain - Protista, Fungi, Plantae, and Animalia. Eukaryotic cells are on the average, about 10 times larger, with diameters that can range between 10 and 100 micrometers (fig. 5). 28  Fig.5. Eukaryotic cell Table 3. Comparison between Prokaryotic and Eukaryotic Cells Characteristics Prokaryotes Eukaryotes Typical Bacteria Protists, fungi, plants, animals examples Typical size Small cells (1-10 μm) Larger cells (10-100 μm) Type of nucleus Nuclear body; No nucleus Real nucleus with nuclear envelope Linear molecules (chromosomes) DNA Circular without proteins with histone proteins Ribosomes Small ribosomes (70S) Large ribosomes (80S) Cytoplasmatic Highly structured by membranes; Very few structures; no cytoskeleton structure has a cytoskeleton Cell movement Flagellae/cilia made of flagellin Flagellae and cilia made of tubulin Mitochondria None Present Chloroplasts None In algae and plants Organization Usually unicellular Unicellular; multicellular Cell division Binary fission Mitosis; Meiosis Cellular organization: Cells in multicellular organisms are organized as follows: Cell Tissue Organ System Organism (tab 4.). Table 4. Human cellular organization 29  Cell Tissue Organ System Organism Epithelial; Epithelial; Red & white Connective; Skin Integumentary Human blood cells; Nerve; Nerve Muscle; 6. Functions of Cellular Organelles Table 5. Functions of cellular organelles CELL LOCATION DESCRIPTION FUNCTION STRUCTURE  Support Plant, Fungi, &  Outer layer  Protection Cell Wall Bacteria, but  Rigid & strong  allows H2O, O2, not animal cells  Made of cellulose CO2 to diffuse in & out of cell  Support  Plant - inside cell wall  Protection  Animal - outer layer;  Controls movement Cell cholesterol of materials in/out of membranes All cells  Double layer of cell phospholipids with  Barrier between cell proteins and its environment  Selectively permeable  Maintains homeostasis  Controls cell  Large, oval activities Nucleus All cells except  May contain 1 or  Contains the prokaryotes more nucleoli hereditary material  Holds DNA of the cell Nuclear  Surrounds nucleus  Controls movement All cells except membrane  Double membrane of materials in/out of prokaryotes  Selectively permeable nucleus  Clear, thick, jellylike material (cytosol)  Supports and Cytoplasm  Organelles found All cells protects cell inside cell membrane organelles  Contains the cytoskeleton fibers 30   Network of tubes or membranes  Smooth w/o  Carries materials Endoplasmic ribosomes through cell reticulum (ER) All cells except  Rough with  Aids in making prokaryotes embedded ribosomes proteins  Connects to nuclear envelope & cell membrane  Small bodies free or Ribosome attached to ER All cells  Synthesizes proteins  Made of rRNA & protein  Peanut shaped  Breaks down sugar  Double membrane (glucose) molecules All cells except  Outer membrane to release energy Mitochodrion prokaryotes smooth  Site of aerobic  Inner membrane cellular respiration folded into cristae Plant cells have  Store food, water, a single, large metabolic & toxic vacuole  Fluid-filled sacs Vacuole wastes  Largest organelle in  Store large amounts Animal plant cells of food or sugars in cells have small plants vacuoles Plant -  Breaks down larger Lysosome uncommon  Small and round with food molecules into Animal - a single membrane smaller molecules common  Digests old cell parts  Green, oval containing chlorophyll (green pigment)  Double membrane  Uses energy from with inner membrane sun to make food modified into sacs (glucose) for the Plants and Chloroplast called thylakoids plant algae  Stacks of thylakoids  Process called called grana & photosynthesis interconnected  Release oxygen  Gel like innermost substance called stroma  Found inside the cell's nucleus Nucleolus All cells except  May have more than  Make ribosomes prokaryotes one  Disappear during cell division  Have a cis & trans face Golgi All cells except  Stacks of flattened  Modify proteins Apparatus prokaryotes sacs made by the cells  Package & export proteins 31   Have a 9-2 arrangement of Cilia Animal cells,  Movement microtubules Protozoans  Short, but numerous  Have a 9-2 arrangement of Flagellum Bacterial cells microtubules  Movement & Protozoans  Long, but few in number  Paired structures  Separate Centrioles near the nucleus Animal cells chromosome pairs  Made of a cylinder of during mitosis microtubule pairs  Strengthen cell & Cytoskeleton  Made of microtubules maintains the shape All cells 7 microfilaments  Moves organelles within the cell SECTION REVIEW 1. What instrument led to the discovery of cells? 7. Cell organelles are located within the ____ of the cell. 2. State the cell theory A. nucleus 3. How many cells make up an B. cytoplasm organism? C. cell membrane D. lysosomes 4. What is the function of the cell membrane? 8. The endoplasmic reticulum functions to: 5. This organelle functions in cellular A. transport materials respiration: B. destroy old cell parts A. lysosome C. make ribosomes B. endoplasmic reticulum D. package proteins C. mitochondrion D. golgi apparatus 9. Genetic material is contained within the ___ of the cell. 6. The organelle functions to package A. ribosomes and deliver proteins: B. cytoplasm A. lysosome C. nucleus B. endoplasmic reticulum D. nucleolus C. mitochondrion D. golgi apparatus 32 10. This organelle is responsible for 15. What part of the cell is responsible destroying worn-out cell parts: for breaking down and digesting A. lysosomes things? B. mitochondrion A. ribosomes C. golgi apparatus B. lysosomes D. ribosomes C. endoplasmic reticulum D. vacuole 11. The _____ controls what enters 16. Which of the following would you and leaves the cell. NOT find in a bacterial cell? A. DNA A. mitochondrion B. cell membrane B. golgi apparatus C. Golgi apparatus C. nucleus D. Ribosomes D. cell membrane 17. Which of the following is found in 12. The rough endoplasmic reticulum plant cells, but not animal cells? has ____ located on it. A. cell wall A. lysosomes B. vacuole B. cytosol C. mitochondria C. ribosomes D. endoplasmic reticulum D. proteins 18. Which of the following scientists 13. Located within the nucleus, it is was not involved in the formation responsible for producing of the cell theory? ribosomes: A. Luis Pasteur A. centrosome B. Robert Hooke B. nucleolus C. Anton van Leeuwenhoek C. lysosome 19. Which combination of organelles D. endoplasmic reticulum below could only be found in a plant cell? 14. Which structure is directly A. nucleus, ribosomes, endoplasmic responsible for the formation of reticulum proteins within the cell? B. ribosomes, centrioles, cytoplasm, A. lysosomes cell membrane B. vacuoles C. nucleus, cell membrane, Golgi C. centrioles bodies, mitochondria D. ribosomes 33 D. endoplasmic reticulum, A. nucleic acids chloroplasts, mitochondria, cell B. proteins wall C. lipids D. carbohydrates 20. Which of the following organic compounds is not part of cell membrane? 6.1. Passive and Active Transport Substances move in and out of cells through the cell membrane. The cell membrane helps organisms maintain homeostasis by controlling the entrance of necessary nutrients and the exit of waste products from the cell. Hence it is crucial that membranes be selectively permeable, for example, the movement of ions across membranes is important in regulating vital cell characteristics such as cellular pH and osmotic pressure. 34  Structure of cell membrane: Substance move in and out of cells as a result of the semi permeable nature of the plasma membrane (cell membrane) - is a fine fluid film with thickness of about 8 nm, made up of mainly lipids (phospholipids) and proteins arranged in a bilayer of phospholipids embedded with proteins. This structural model of the plasma membrane is known as the fluid-mosaic model. Fig. 6. Fluid-mosaic structural model of plasma membrane The phospholipid molecule has a water-soluble, polar “head” and two fat- soluble, nonpolar “tails.” The hydrophobic tails always try to avoid water and face the inside of the bilayer, whereas the hydrophilic head faces the exterior and the interior. Within the phospholipid bilayer are many different types of embedded proteins and cholesterol molecules that can move sideways throughout the membrane, meaning the membrane is not solid, but more like a fluid. The membranes also have glycoproteins attached to their surface, which aid in their location and identification of food, water, waste, and other membrane traffic. Each cell has a particular glycoprotein structure based on its need to attract or repel membrane traffic. The proteins embedded in the membrane serve many of the membrane functions, such as holding the membrane in a regular, identifiable structure for easy bonding. They also have a specific and unique shape that allows them to function 35 as receptors and receptor sites for attachment to the appropriate raw materials needed for cellular functions. In some cases, the receptor protein is also a signal transducer that begins a series of enzyme-catalyzed reactions to stimulate a particular reaction or function within a cell. Finally, the transport proteins, which are of two classes known as carrier and channel proteins, help substances move across membranes through the hydrophobic interior of the bilayer. Passive Transport: Is the movement of substances across the membrane without energy input from the cell, e.g., lipid-soluble molecules, water, and gases. The concentration gradient is the driving force for passive transport because of the kinetic energy of the molecules, which are in constant motion. The following are the classes of passive transport:  Diffusion (Simple diffusion): Is the movement of molecules from an area of high concentration to an area of low concentration until equilibrium of the substance is attained, e.g., Oxygen diffuses out of the lungs and into the blood for transport to all of the cells. The rate of diffusion depends on the temperature, size and the type of the diffusing molecules.  Facilitated Diffusion: This is a special type of diffusion that is useful because substances are sometimes too large to move freely through a membrane, or they need to move against a concentration gradient so transport (carrier) proteins embedded in the membrane assist with the passage. In most cases, the transport protein creates a chemical channel for the passage of a specific substance. Because no energy is expended, the rate of facilitated diffusion depends on the number of transport proteins embedded in the membrane. As an example, glucose is moved by a glucose-transporter protein as it passes through the red blood cell into a body cell.  Osmosis: Is the diffusion of water across a semi-permeable membrane from a weak solution to a strong solution. This is similar to diffusion except that it refers only to water diffusing through a permeable membrane. Water as a solvent moves from an area of low to high concentration. The solution that has 36  a high-solute concentration is a hypertonic solution relative to another lower- solute concentration or hypotonic solution. Osmosis will continue until both sides of the solution are isotonic, or equal. Animal cells placed in a hypotonic solution will swell and often burst because of osmosis. The bursting of cells is called cytolysis. Plant, fungal and bacterial cells do not burst because of their cell wall. Conversely In a hypertonic environment, water leaves the cells by osmosis, the cell membrane shrinks away from the cell wall, and turgor is lost. This condition is called plasmolysis, and is the reason plants wilt. Osmoregulation is a struggle for all organisms as we continually adjust our cellular water balance for optimal conditions.  Ion channels. These are membrane proteins that allow the passage of ions that would ordinarily be stopped by the lipid bilayer of the membrane. These small passageways are specific for one type of ion, such that a Ca 2+ ion could not pass through an fe2+ ion channel. The ion channels also serve as gates because they regulate ion flow in response to two environmental factors: chemical or electrical signals from the cells and membrane movement. Active Transport Cell Membrane Pumps (Sodium Potassium pump): Cells often move molecules across the membrane against the concentration gradient, i.e. from an area of low concentration to an area of high concentration. This requires energy (uses ATP), and is known as active transport. Active transport involves the use of carrier proteins, similar to those of facilitated diffusion, but these carrier proteins acts as pumps, using the energy from splitting ATP to pump specific molecules against the concentration gradient. These carrier proteins are known as membrane pumps, and are particularly important in maintaining the Na+ / K+ ion balance between Eukaryotic cells and their external environment. The sodium / potassium (Na+ / K+) pump maintains a 37 high concentration of Na+ ions outside the cell, and a high concentration of K + ions inside the cell. This is particularly important in muscle contractions, nerve impulses and the absorption of nutrients from the gut. The Na + / K+ ion pump moves Na+ ions out of the cell and K+ ions into the cell, against their concentration gradient, using ATP to supply the energy needed. In plants, active transport enables roots to absorb mineral ions from the soil, which are therefore more concentrated inside plant cells than in the soil. This requires ATP energy from aerobic respiration, and therefore roots need oxygen to allow mineral uptake and a waterlogged (thus anaerobic) soil will kill most roots. The following steps demonstrate an active transport mechanism: 1. Sodium ions inside the cell bind to the transport (carrier) protein as a phosphate is added from an ATP, which changes the shape of the transport protein. 2. The new transport protein structure carries and deposits the sodium to the exterior and bonds with a potassium ion, loses the phosphate group (which again changes the shape of the transport protein), and allows for the return trip. 3. The potassium is deposited inside the cell, and a sodium ion and a phosphate are attached to a transport protein to repeat the process. Endocytosis and exocytosis (Bulk Transport): Some molecules, such as large proteins, are too large to cross the cell membrane, and enter by bulk transport. Other examples include food particles and bacteria (phagocytes). Endocytosis means substances entering the cell; exocytosis means substances leaving the cell. During endocytosis the cell membrane folds into a pouch that encloses the particles, before pinching itself off to form the vesicle or vacuole. The vesicle often then fuses with a lysosome, which releases its contents to digest the contents of the vesicle. There are three types of endocytosis: 38   Pinocytosis occurs when the cell absorbs fluid from the exterior, creating a fluid vacuole.  Receptor-mediated endocytosis is a special type of pinocytosis that is activated by the identification of a receptor protein sensitive to the specific substance.  Phagocytosis is the engulfing and digesting of substances, usually food, by vacuoles with a lysosome attached (a lysosome is an organelle that contains digestive enzymes). Exocytosis is the opposite of endocytosis and can be used for secretion (e.g. hormones, and enzymes, packaged in the Golgi apparatus) or for excretion of waste products (indigestible parts of food from Amoeba). SECTION REVIEW 1. If a plant cell contains more solutes than 3. The concentration of calcium in a cell is its surrounding environment: 0.3%. The concentration of calcium in the a) There will be no net movement of fluids surrounding the cell is 0.1%. How water could the cell obtain more calcium? b) Water will leave the cell a) osmosis c) The cell will burst b) active transport d) Water will enter the cell c) diffusion 2. When two solutions that differ in solute d) facilitated diffusion concentration are placed on either side of a 4. Which of the following pieces of evidence semi-permeable membrane and osmosis is would suggest that a substance entered a cell allowed to occur, which of the following via active transport as opposed to passive will happen? transport? a) The solute will move from the area a) the substance moved from a high of high concentration to an area of concentration to a low concentration low concentration b) the substance moved across the b) Water will move from an area of low membrane via a carrier protein solute concentration to an area of c) ATP was required for transport high solute concentration d) none of the above c) There will be no net movement of 5. Which statement is correct concerning the water sodium-potassium pump? d) Water will move from an area of a) it is used in order to generate ATP high solute concentration to an area for cellular activities of low solute concentration 39  b) sodium ions are pumped out of the a) die cell b) take on water c) an equal concentration of sodium c) lose water and potassium ions are exchanged d) divide d) the ions move directly through the 8. Which of the following is NOT a type of phospholipids of the plasma passive transport? membrane a) diffusion 6. What will happen to an animal cell placed b) osmosis in a salt water solution? c) endocytosis a) The cell will shrink d) facilitated diffusion b) the cell will expand 9. Describe the Fluid-mosaic structural c) the cell will burst model of plasma membrane. d) the cell will shrink and then expand 10. Explain the mechanism of the sodium and then shrink again potassium pump. 7. An animal cell placed in a hypotonic solution will: 40  7. Diversity of Living Organisms Scientist estimate that there are about 10-30 million organisms living on planet earth today, of which only about 18 % (1.8 million) have been identified and named. Tropical forests e.g., the Amazon and deep oceans like the Pacific and Atlantic oceans likely hold the highest population of still unknown species. The total population of living organisms in a particular habitat is known as biodiversity. According to the hierarchical classification system, biodiversity on earth have been grouped into 3 domains of: Archaea; Eubacteria and Eukarya. These domains are further divided into 6 kingdoms of: Archaea; Eubacteria; Protista; Fungi; Plantae and Animalia. For the purpose of this study this unit will focus on the kingdoms of Animalia and Plantae. The Animal Kingdom: The animal kingdom consists of a diverse range of organisms which share common properties that define animals as a distinct group of life forms. Animals are multicellular; eukaryotic; aerobic; heterotrophic organisms; capable of reproducing sexually or asexually; mostly motile and live on land or water habitats. Animals are classified based on some certain fundamental features and similarities, such as cellular arrangement; body symmetry, segmentation, presence or absence of notochord etc. These features help to identify and organize the various animals into specific groups. Below are some of the fundamental features:  Levels of organization: The patterns of organization of cells vary in animals in spite of their multicellular nature. The patterns of cellular organization seen in animals are: 1. Cellular level of organization - In these animals, the cells of the body form loose aggregates e.g., Sponges. 2. Tissue level of organization: In these animals, cells of the animal carrying out the same function are arranged in tissues e.g., Coelenterates. 41 3. Organ system level of organization: In these animals, tissue are grouped together to form organs, each specialized for a particular function e.g., members of Platyhelminthes and other higher phyla.  Body symmetry: The arrangement of body parts around a central point or line determines symmetry. Some animals are asymmetrical which cannot be divided into two equal halves along any plane passing through the centre e.g., sponges. Some exhibit radial symmetry where the animal can be divided into two equal halves along any plane passing through the central axis e.g., Coelenterates, Echinoderms (fig. 7a), etc. Others exhibit bilateral symmetry where the body can be divided into identical left and right halves along only one plane. e.g., Annelids, Arthropods, Chordates etc., (fig. 7b). In most bilateral animals nerve cells are concentrated at the head end; this process is known as cephalization - concentration of nerve cells at one end of the body. a b Fig. 7. (a) Radial symmetry (b) Bilateral symmetry.  Polarity: Is the front-to-back axis of animal body, with an anterior or leading end and a posterior (trailing) end.  Body wall: The body wall of the animal may be arranged in two or three embryonic layers. Accordingly the animals are called diploblastic (having outer ectoderm and inner endoderm and undifferentiated mesoglea in between them) animals. E.g., Coelenterates, and triploblastic (having outer 42  ectoderm, middle mesoderm and inner endoderm) animals. E.g., Platyhelminthes to Chordates. Fig. 8. Body layers (a) Diploblastic (b) Triploblastic.  Coelom: The presence or absence of a cavity called coelom in between body wall and gut is important for classification. Animals are group into 3 types based on the presence or absence of a coelom: 1. Acoelomates: Body cavity in this group of animals is absent e.g. Platyhelminthes. 2. Pseudocoelomates: Body cavity in this group of animals is not lined by a mesoderm e.g. Aschelminthes. 3. Eucoelomates: Animals in this group possess true coeloms lined by a mesoderm e.g., from Annelids to Chordates. Fig. 9. Cross sectional view of (a) Eucoelomate; (b) Pseudocoelomate; (c) Aceolomate. 43  Segmentation: Also called metamerism. The body is externally and internally divided into repeated, linear series of body units called metameres or somites, e.g., Earthworms.  Notochord: Is a supporting rod-like structure derived from mesoderm. It may be present in embryonic or adult stages. The animals which possess notochord are called chordates, e.g. Chordata. The animals in which notochord is absent are called non chordates, e.g., Porifera to Hemichordata. Fig. 10. Classification outline of the animal kingdom The animal kingdom is further divided into groups of approximately 35 Phyla, below are the 10 major phyla of the animal kingdom:  Porifera: These are the salt-water sponges, approximately 8,000 exists today. Below are the features of this group:  all aquatic – mostly marine, some freshwater;  sessile;  asymmetrical;  no true tissues (no mouth, no digestive cavity, no muscles, no nervous system); hence known as the Parazoans;  epithelial, collar, and amoeboid cells; 44  asexual and sexual reproducers;  most are hermaphrodites;  food and shelter for many organisms;  endoskeleton – made of CaCO3 or silica;  Cnidaria: Organisms in this group include jellyfish, anemone, sea corals etc., and approximately 15,000 species exist today. Features include:  radial symmetry;  two layers of tissue – endoderm and ectoderm with a jellylike mesoglea layer in between;  specialized nerve, muscle, digestive, and reproductive tissue;  tentacles with nematocysts;  many species considered at risk;  most have 2 life cycle stages – polyp (asexual) - mostly sessile; and medusa (sexual) - free swimming.  Platyhelminthes: These are flatworms e.g., tapeworm, fluke worm, etc., approximately 15,000 species exist today. Features include:  Flattened;  Un-segmented;  bilateral symmetry;  hydrostatic skeleton;  three cell layers;  3 cell layers but acoelomates;  no circulatory or respiratory systems;  degree of cephalization;  Mainly parasites.  Nematodes: These are the round worms, consists mainly of parasitic worms e.g., hook worm, trichenella, etc., there are about 80,000 known species. Features include: 45  Round / cylindrical shapes;  soil and aquatic ;  un-segmented;  separate mouth and anus;  3 cell layers but pseudocoelomates;  no circulatory or respiratory systems ;  hydrostatic skeleton;  scavengers, parasites;  Rotifers: These are microscopic freshwater and moist soil invertebrate animals. There are about 1,800 known species. Features include:  bilateral symmetry;  body has more than two cell layers, tissues and organs;  body cavity is a pseudocoelom;  body possesses a through gut with an anus;  body covered in an external layer of chitin called a lorica;  Has a nervous system with a brain and paired nerves;  has no circulatory or respiratory organs;  reproduction mostly parthenogenetic, otherwise sexual and gonochoristic;  feed on bacteria, and protista, or are parasitic;  free swimming or attached organisms.  Mollusca: This group includes organisms such as snails, clams, squids and octopus. Over 100,000 species are known today. Features include:  most are marine and live freely;  some swim, some creep slowly, some are terrestrial;  body plan contains a foot (muscular, used for motion), mantle (covers gills and secretes shell), and visceral mass (contains organs);  varying degrees of cephalization;  bilateral symmetry;  3 cell layers; coelomates; 46  possess radulas used for scraping and burrowing.  Annelida: these are the segmented worms; organisms in this group include earthworms, leeches, etc. Features include:  segmented;  terrestrial, marine, freshwater;  3 cell layers; coelomates;  grow larger than non-segmented worms;  hydrostatic skeleton;  bilateral symmetry;  complete digestive and circulatory system;  some are hermaphrodites;  Arthropoda: This large group consists of insects, spiders, crustaceans, etc; scientists estimate that there are more than 1 million species of insects. Features include:  segmented body with jointed appendages;  aquatic and terrestrial;  3 cell layers; reduced coelom;  most dominant animals on Earth;  exoskeleton made of chitin;  efficient gas exchange allows rapid supply of oxygen to muscles;  well-developed sensory (some with antennae), nervous, and circulatory systems.  Echinodermata: Organisms in this group include star fish, sea urchins, etc., there about 6,000 known species, features include:  Spiny-skinned;  larvae are bilaterally symmetrical, adults are radial;  digestive and circulatory systems, but no respiratory or excretory systems;  endoskeleton;  3 cell layers, coelomates; 47  sexual reproduction;  move using ‘hydraulics’;  no head (no cephalization).  Chordata: This group consists of animals that are classified based on the 3 common embryological features: dorsal nerve cord; notochord (supportive structure); and pharyngeal gill pouches. The phylum chordate is further divided into 3 subphyla as follows: 1. Tunicata (Urochordata): large group of unusual invertebrates that start life as larvae with notochord in the tail region, while adult life is sedentary (attached) forms without notochord. Eg: - Ascidia, Doliolum. 2. Cephalochordata: Animals of this subphylum have fish-like appearance with notochords extending from the head to tail region. They lack bones, brains, eyes, and most organs associated with the brain. eg: - Brcmchiostoma (Amphioxus or Lancelet). Subphyla Urochordata and Cephalochordata are called protochordates and are all marine organisms. 3. Vertebrata: The largest subphylum composed of members which possess notochord only in the embryonic stages. In adults it is replaced by Vertebral column. All vertebrates have a skeleton of either bone or cartilage, with brains protected by a boney cranium. They have ventral heart with 2-4 chambers; a closed circulatory system; kidney for excretion; and paired appendages which may be fins or limbs. There are 7 classes within the subphylum Vertebrata: 1. Agnatha: These are ancient animals similar to fish, but noticeably different. They have suctorial and circular mouth without jaws, lack paired fins and scales. E.g. Lamprey, Hag fish, etc. 2. Chondrichthyes: They are marine fishes with cartilaginous endoskeleton. The exoskeleton has placoid scales. E.g. Shark, Saw fish, Sting ray, Electric ray, etc. 48  3. Osteichthyes: The largest class of vertebrates with over 20,000 species. They are marine or freshwater fishes with bony endoskeleton. The exoskeleton has cycloid or ctenoid scales. Ovoviviparous reproduction – hatched egg birthing, e.g. Sardine, Mackerel, Flying fish. 4. Amphibia: They are the vertebrates adapted to land and water. The word ‘amphibian’ is derived from two Greek words amphi (double) and bios (life), which refers to the two phases in the life cycle of most amphibians: an acquatic larval stage and a terrestrial adult stage. They do not possess exoskeleton. E.g. Frog, Toad, Salamander. 5. Reptilia: They are the creeping or crawling vertebrates having dry-cornified skin without skin glands; ectothermic – need outside source of heat to generate adequate body heat. The exoskeleton has horny scales or scutes. E.g. Tree lizard (Chameleon), Garden lizard, Turtle, Tortoise, Cobra. 6. Aves: They are animals with wings and are adapted for flight. They have feathers as exoskeleton and their jaws are modified into beaks. They are oviparous – egg-laying. E.g. Crow, Pigeon, Peacock, Parrot, Ostrich, Penguin. 7. Mammalia: Represent only about 9% of the known vertebrates. They possess breast glands (mammary glands) and majority of them are viviparous – live birthing. They have hair as exoskeleton. E.g. Platypus, Kangaroo, Camel, Monkey, Humans, Elephants, Dogs, Cats. SECTION REVIEW 1. Name the fundamental features which are considered in the classification of animals? 2. Name the phylum in which the members possess pseudocoelom. 3. The members of which phylum have chitinous exoskeleton? 4. Which chordates do not possess vertebral column in adults? 5. Dry, cornified skin is the feature in the members of what animal class? 49 6. In which group of animals are beaks present? 7. Members of which class are generally viviparous. 8. Repetition of body parts is known as segmentation. Which of these phyla does NOT display segmentation? a) Annelida b) Echinodermata c) Chordata d) Arthropoda 9. Most animal phyla show some type of body symmetry. Which of the following show radial symmetry? a) Cnidaria b) Echinodermata c) Mollusca d) Both A and B are correct. e) A, B, and C are correct. 10.Some animals are said to be "hermaphroditic." To what does this term refer? a) a species with the ability to reproduce both by sexual and asexual means b) a state in which one animal possesses both female and male sex organs c) a state in which a single species has one type of symmetry as an embryo and a different symmetry as an adult d) a state in which a single species has both a sessile and motile stage 50  7.2. Plant Kingdom Scientists estimate that there about 315 thousand species of plant today, that evolved from a small group of aquatic green algae called Charophytes to modern terrestrial plants roughly 500 million years ago. Plants are multicellular; eukaryotic; autotrophic organisms, that reproduce through spores or seeds. Their cells possess cell walls made of a carbohydrate called cellulose and store food in the form of starch. They have chloroplasts containing chlorophyll and other pigments. Most plants are terrestrial although there are some exceptions. Plant life cycles have two alternating phases, a haploid (n) phase and a diploid (2n) phase. The diploid phase is called the sporophyte and produces spores, while the haploid is called the gametophyte and produces gametes. Plants are classified based on some common characteristics and similarities, such as differentiated body parts; presence of vascular tissues; method of reproduction; seed forms and availability; the presence of Chlorophyll a & b, and Carotenoid pigments; alternation of generations (Gametophyte > Sporophyte > Gametophyte); etc. These characteristics help to identify and organize the diverse range of plants into specific groups; some of the fundamental characteristics are discussed below: Plant body plan: The plant body may be thalloid e.g., algae; fungi; lichens (Thallophyta) or differentiated into root, stem and leaves. 51  Presence of vascular tissue: a vascular tissue is a complex conducting tissue composed of xylem and phloem, which function in the transport of water and dissolved substances. All plants are classified using the availability of the vascular tissue and could be: i. Non-vascular - plants (e.g., mosses) that have no system for transporting water or nutrients. ii. Vascular - plants that have a system through which they can transport water and nutrients throughout the plant, e.g., ferns, maize, oaks, etc. Seeds: Plants could either be seedless plants (Cryptogamae), examples include ferns, moss, etc., - though some (ferns) have a vascular system, they reproduce using spores; or seed plants (Phanerogamae) – flowering plants that reproduce using seeds, and based on their morphology can be further divided into two types: 1. Gymnosperms (e.g., pine) have seeds that are not enclosed, i.e., naked seeds. 2. Angiosperms (i.e., flowering plants) have seeds that are enclosed in fruits. Angiosperms are further arranged into two groups:  Monocotyledons: examples are grasses, palms, etc., characteristics include:  Leaves have parallel venation;  Embryos have one cotyledon;  Fibrous root system;  Flowers are in multiples of three.  Dicotyledons: examples are trees and most common plants, characteristics include:  Leaves have netlike venation;  Embryos have two cotyledons;  Tap-root system;  Flowers are in multiples of four or five. 52  Fig. 11. Classification outline of the plant kingdom The plant kingdom is further grouped into 10 divisions (Phyla), which are discussed below:  Division Bryophyta: Plants in this division include liverwort, hornwort and mosses. There are approximately 20,000 species. Bryophytes are nonvascular plants. Mosses have minute "leaves" and stalks bearing a terminal capsule (sporangium) containing spores; moss sex organs (male antheridia and female archegonia) are typically produced on the leafy gametophytes of separate male and female plants; liverworts have a dorsi- ventrally flattened thallus with tiny palm-like stalks bearing male and female sex organs; the gametophyte thallus of some species also bears small, cuplike structures called gemmae cups; the cups contain lens-shaped buds called gemmae which can grow asexually into new thallus plants; there are aquatic and terrestrial forms of mosses and liverworts, some of which have a flattened, thallus that superficially resembles certain forms of green algae. The bryophytes are divided into three classes: Hepaticopsida (Liverworts) e.g. Riccia, Marchantia; Anthocerotopsida (Hornworts) e.g. 53  Anthoceros, Notothylas; Bryopsida (Mosses) – e.g. Funaria, Sphagnum, Polytrichum.  Division Psilophyta (Psilotum): These are primitive leafless vascular plants bearing 3-lobed sporangia on branches, e.g., whisk ferns (Psilotum nudum).  Division Lycophyta: Plants in this group include Club Mosses, there are approximately 12,000 species. They possess minute "true" leaves superficially resembling a moss; terminal, stalked spore-bearing strobilus in Lycopodium; in Selaginella male and female sporangia are produced in the leaf axils; examples also includes the quillworts (Isoetes) and many fossil forms (some tree-like) dating back 300 million years ago.  Division Sphenophyta (Horse tail): This is a primitive vascular plant group of the Carboniferous Period (300 million years ago) with jointed stems, whorls of tiny scale-like leaves at the nodes, and a terminal spore cone (strobilus); some species with dense branches at nodes called horse tail, examples include species of the genus Equisetum.  Division Pterophyta: These are ferns that have leaves (fronds) with sporangia clusters (sori) on the underside; fronds arising from subterranean, non-vascular plants, reproduce by spores, examples includes the orders Filicales (true ferns - Adiantum, Pteridium, Dryopteris, Polypodium, Polystichum, Pellaea, etc.); Marsileales (clover-leaf ferns Marselia, Pillularia); Ophioglossales (Ophioglossum); and Salviniales (water ferns Azolla and Salvinia).  Division Cycadophyta: These are cycads, the largest of all living cone- bearing plants. They are palm-like plants with large seed and pollen cones; flourished during the days of the dinosaurs and undoubtedly were a major food supply for herbivorous dinosaurs; cycads were so numerous in Mesozoic times that this era is often called the Age of Cycads and Dinosaurs; cycads are dioecious species with pollen cones and seed cones produced on separate male and female individuals. 54  Division Ginkgophyta: Plants in this division include the Maidenhair Tree. They produce seeds borne in pairs on dwarf shoots (gymnosperms); have leaves similar in shape to the maidenhair fern (Adiantum); a true living fossil dating back 185 million years; only one living representative Ginkgo biloba.  Division Gnetophyta: A remarkable plant division including Ephedra, Gnetum and Welwitschia; stems of Ephedra are jointed with small scale-like leaves at the nodes; the bizarre, shredded, wind-blown leaves of Welwitschia arise from a woody caudex on the desert floor; this division includes species with vessels and other characteristics typically found in flowering plants.  Division Coniferophyta: Plants in this group include cone-bearing trees and shrubs. Have seeds borne on the surface of woody scales (gymnosperms), the overlapping scales forming a cone; examples includes pine (Pinus), fir (Abies), spruce (Picea), hemlock (Tsuga), larch (Larix), juniper (Juniperus), and cypress (Cupressus); also includes the tallest (redwood) and most massive (giant sequoia) living organisms; some species (especially pines) require fire for seed germination and regeneration. Fig. 12. Classification of the major divisions of kingdom plantae  Division Anthophyta (Magnoliophyta): These are flowering plants or Angiosperms. Flowering plants are similar to non-flowering seed plants 55  (Gymnosperms) in having advanced vascular tissue, a dominant sporophyte stage, a markedly reduced gametophyte stage, and production of seeds. However angiosperms differ from gymnosperms by the production of a derived organ, the fruit. Angiosperm ovules are enclosed in a carpel. After fertilization, the ovule develops into the seed and the carpel develops into the fruit. Angiosperms also produce flowers, which are structures containing the reproductive organs of the sporophyte. The flower functions t