BIO102: General Biology II Lecture Notes PDF

Students are allowed to reproduce for their own use NOT FOR SALE BIO102: GENERAL BIOLOGY II MODULE 1: BASIC CHARACTERISTICS, IDENTIFICATION AND CLASSIFICATION OF VIRUSES AND BACTERIA Introduction The sci...

Students are allowed to reproduce for their own use NOT FOR SALE BIO102: GENERAL BIOLOGY II MODULE 1: BASIC CHARACTERISTICS, IDENTIFICATION AND CLASSIFICATION OF VIRUSES AND BACTERIA Introduction The science of identifying, naming and classifying organisms on the basis of their degree of similarity and arranging them in an order on the basis of their evolutionary relationship is called taxonomy. Taxonomy is considered as a man made and multidisciplinary science. It owes its progress on the advancement made in other branches of sciences like morphology, histology, physiology, cell biology, biochemistry, genetics, molecular biology, computational biology etc. A taxonomic system therefore classifies every species of living thing on earth. One important aspect of taxonomy is taxonomic classification, which is the grouping of different organisms on the basis of shared features into different categories called Taxa (singular=Taxon). Different taxa are then arranged in a hierarchical manner (either in ascending or descending order) starting from lower to higher ranks. The basic categories in a taxonomic system, beginning with the lowest are: species, genus, family, order, class, phylum, kingdom and domain (the largest category/taxon). No single classification system is completely accepted by all biologists. One of the most widely accepted is the five kingdom system. The five kingdom system of classification was proposed by an American taxonomist, R. H. Whittaker in 1969 (also called Whittaker’s system of classification). In this classification, cellular organisms have been divided into five kingdoms namely, Monera, Protista, Fungi, Plantae and Animalia. Whittaker delimited the five kingdoms on the basis of three main criteria viz. cell structure type, degree of cellular organization and mode of nutrition. Besides these major characteristics he has also given importance to characters of ecological role-played and mode of reproduction. Page 1 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE The Five Kingdom System of Classification of Living Things Kingdoms Monera/Proka Protista Fungi Plantae Animalia Criterion ryotae Cell type Prokaryotic Eukaryotic Eukaryotic Eukaryotic Eukaryotic Noncellulosic Present (made of Present in Present with Cell wall with no Absent polysaccharides & some cellulose cellulose amino acids Multicellula Unicellular, Unicellular Multicellular, r, existing Unicellular, but but may occur Cell / existing as as existing as in organization multicellula tissues/organs tissues/org colonies/groups colonies/grou r /organ systems ans/organ ps systems Variable: Heterotrop Autotrophic Heterotrop Phototrophic/ Phototrophic/ hic Nutrition (photosynthesi hic heterotrophic/ heterotrophic (absorption s) (ingestion) chemo-autotrophic ) Asexual & Asexual & Asexual & Primarily Reproductio Sexual without Sexual with Sexual with sexual with Primarily Asexual n embryonic spore embryonic embryonic stage formation stage stage Ecological Decompose Variable Variable Producer Consumer role r Definition of Some Common Terms  Diploblastic: describes an invertebrate animal with adult tissues derived from two layers of embryonic germ tissue (endoderm & ectoderm)  Triploblastic: describes the development of a multicellular animal body from three basic embryonic cell layers (endoderm, ectoderm & mesoderm) Page 2 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE  Body Symmetry: mutual arrangement of various parts of an animal body which gives rise to a proportionate, balanced form (regularity in the arrangement of the parts of an organism).  Asymmetry: an irregular body form in which body parts are not arranged orderly on opposite sides of around a central point of the body of an animal.  Radial symmetry: is the proportional arrangement of similar parts of a body around a central axis. Body is usually cylindrical/disk shaped with body parts radiating from a central hub.  Bilateral symmetry: is a type of arrangement of the parts and organs of an animal in which the body can be divided into two halves that are mirror images of each other along a linear plane. Body is long and narrow, with a distinct head and tail end.  Coelom: is a fluid-filled cavity that forms the main body cavity of most animals, formed due to splitting of the mesoderm.  Acoelomate: describes any animal that lacks a coelom.  Pseudocoelomate: describes any invertebrate with a pseudocoel/pseudocoelom (a cavity between the gut and outer body wall) as its body cavity.  Coelomate: describes animals with cavity between the body wall and the digestive tract (coelom).  Parazoa: a sub-kingdom comprising of animals that lack tissues in their body organization,  Metazoa (Eumetazoa): a sub-kingdom comprising all multicellular animals that possess cells that are separated into different parts such as tissues and organs (specialized cells that form true tissues). Page 3 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE Diagramatic Representation of Animal Body Organization Page 4 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE VIRUSES The Russian botanist D.I. Ivanosky (1852) reported the existence of viruses as organisms causing the tobacco mosaic disease. The causal organism was too small and was able to pass through a filter that can prevent bacteria from passing. These organisms were named ‘virus’ (Latin for poison) by another scientist called Beijerink in 1898. They can only be studied with an electron microscope. Classification Viruses can be classified based on a number of characteristics: A. Host Specificity: The scientist Frobischer divided viruses into four groups in 1957. 1. Plant viruses e.g. Tobacco mosaic virus 2. Insect viruses e.g Reoviridae, Poxviridae 3. Mammalian viruses e.g. Ebola virus 4. Bacterial viruses e.g. Bacteriophage B. Envelope: Viruses are divided based on the presence or absence of envelop. 1. Enveloped viruses e.g. HIV, Influenza virus. 2. Non-enveloped viruses e.g. TMV. C. Nuclear material: Viruses are also classified based on the presence of DNA or RNA. 1. DNA viruses e.g. Herpes simplex. 2. RNA viruses e.g. TMV, Phages. Characteristics i. Viruses have no cellular structures (e.g. cell wall, cytoplasm, nucleus, chromosomes etc.) ii. Viruses are parasitic and they are not capable of reproducing outside the living cell of the host. Page 5 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE iii. Viruses are on the boundary between what is regarded as living and non-living iv. Viruses are specific to their host i.e. they can only recognize and infect certain types of cells. v. They range in size from the smallest which causes foot and mouth diseases (20nm) to the largest animal virus i.e. smallpox virus which measure (300nm) in diameter. On the average viruses are about 1/100 times smaller than bacteria (m = 10-3 and n = 10-9). vi. Viruses have a simple structure consisting of a nucleic acid (DNA or RNA) surrounded by a protein or lipoprotein coat called CAPSID. The capsid is formed from identical protein subunit called CAPSOMERS. Viruses can have a lipid envelope derived from the host cell membrane. Morphologically, there are four main types of virus based on the shape of viral capsid.  Helical  Icosahedral  Prolate (envelope)  Complex vii. There are about 2000 viruses known, about 400 are said to attack plants. Example of such include, mosaic virus (e.g tobacco mosaic virus, turnip yellow mosaic virus, cow pea mosaic virus), wound tumor virus, tobacco ring spot virus. Bacteriophage These are a group of viruses that attack bacteria. They are small in size and can reproduce rapidly. There are seven strains coded T1 – T7. An example of this virus is the T4 bacteriophage which parasitizes on Escherichia coli (E. coli), a bacterium. It consists of a polyhedral head, a neck, a collar, the core (the genetic material, either DNA or RNA, which may be single or double, stranded), sheath, endplate and six tail Page 6 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE fibers. The sheath is specialized in function and is contractile permitting the penetration of the core into the bacterium cell. Structure of a Bacteriophage T4 Bacteriophage Infesting a Bacterium Tobacco mosaic virus (TMV) This is an example of a virion structure that was first discovered by Bawden and Pirie (1937). It has a structure made up of nucleoproteins (protein and nucleic acid). They are rod shaped and measure 300nm in length and 15nm in diameter. Structure of TMV Page 7 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE Cultivation Viruses can only be cultivated in-vivo (inside a living thing) in developing chick embryo, in bacteria, in laboratory animals, etc. Economic significance Viruses cause many diseases of plants and animals such as mosaic disease of apple, bean, cabbage, cauliflower, groundnut, potato, tobacco, tomato. Barley yellow dwarf disease of wheat barley oats and rye etc., in plants, while mumps, smallpox, chickenpox, measles, herpes, polio, yellow fever, influenza, common cold, cancer, AIDS, etc., in humans. KINGDOM MONERA The term “Monera” includes those unicellular organisms without a nuclear membrane (i.e. prokaryotes) such as the bacteria and the cyanobacteria. The kingdom comprises of the most abundant micro-organisms commonly known as Bacteria which occur almost everywhere. Hundreds of bacteria are present in a handful of soil. They also live in extreme habitats such as hot springs, deserts, snow and deep oceans where very few other life forms can survive. BACTERIA Bacteria are a diverse group of (usually) single-celled prokaryotic microorganisms, mostly free-living, occurring in soil, on plants, in various aquatic habitats and even in antarctic snow. Some are also found as symbionts (beneficial relationship) in plants, animals and certain microorganisms. They can cause a number of major and minor diseases in both plants and animals, however many are used in a number of commercial and manufacturing processes. Discovered by Anthony Von Leuwenhook in 1683 using magnifying glasses (first crude microscope), where he first called them “tiny animacules”. Later Ehrenberg (1929) was the first man to establish genus ‘Bacteria’. They possess the following characteristics: - Unicellular, achrolophyllous (non chlorophyllous) minute organisms. Page 8 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE - The leading autotrophic (using CARBON DIOXIDE and light for most or all of the energy requirements), saprophytic (obtaining nutrients from non-living or decaying plant and animal matter) and parasitic (benefiting at the expense of the other) lives. - May be motile or non-motile and if motile, it is due to the presence of flagella. - Structurally, each bacterial cell is primitive and lacks nucleus and nuclear membrane in the cell hence called prokaryotic. - The method of propagation is by binary fission, sexual reproduction is absent but recently reported in Escherichia coli. - Bacteria grow under all possible environments on earth. They occur in air, in fresh and marine waters, petrol and related products, dust particles, in plants and animals. Some bacteria survive in heat (thermophiles) and cold (psychrophiles). - They are microscopic and vary in size, ranging from 0.5µm - 10µm. The smallest are about 0.2µ, approximately the size of the largest virus. But a few reach up to 100µ (1 micron (µ) = 1/1000 millimeter). - Shape and form of bacteria varies considerably which may be influenced by environment. Cohen divided bacteria into the following four forms: 1. Cocci or spherical: are spherical or ellipsoidal (near-spherical) forms. Cocci (sing: coccus) may occur singly, in pairs , in regular groups of four or more, in chains, or in irregular clusters and are more draught resistant owing to their spherical shape. These forms are divided on the basis of cell arrangement into: a. Micrococci: Such forms grow singly as they separate immediately after cell division. b. Diplococci: They are found in pairs due to characteristic cell division in a single plane forming two cells e.g. Diplococcus pneumoniae. Page 9 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE c. Streptococcus: Cells are found arranged in chains looking like beaded structure. Cell division occurs in one place and daughter cocci remain attached e.g. Streptococcus pyogenes. d. Staphylococcus: These appear like bunches of grapes because of irregular cell division in more than two planes e.g. Staphylococcus aureus. e. Sarcinae: These show a cubiodal structure (occur in three-dimensional cube) and many form definite geometrical figures. The cell division is in three planes at right angle to each other e.g. Sarcina lutea. f. Tetracocci/Gaffkya: Such bacteria occur in groups of four cells due to characteristic cell division in two planes but right angle to each other and are called Gaffkya. 2. Bacilli or rod shaped bacilli (Sing: Bacillus): Bacillus is a Latin word which means ‘Stick’. These bacteria are cylindrical or rod shaped. They may be found in pairs (Diplobacilli), in chains (Streptobacilli) or showing palisade arrangement e.g. Tubercle bacilli appearing in groups of three. 3. Sprilla or spirals: These are spirals of helical structures. Spirillum means “coils’. The spirals may be short and tightly coiled or long with many coils. E.g. Leptospira and Treponema 4. Vibrio or comma: These are comma shaped and called vibrio e.g. Vibrio cholerae. Morphological Representatives Bacteria Page 10 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE Flagellation Bacteria may be motile and non-motile. The motile forms have flexible whip like structure called flagella. Each flagellum is a long delicate protoplasmic elongation consisting of single protein fibril. Depending upon number and position of attachment of flagella, the following types of bacteria are recognized: i. Monotrichous: Each cell has a single flagellum at one end e.g. Vibrio cholerae. ii. Lephotrichous: A cell has many flagella but present only at one pole e.g. Spirillum undulla. iii. Amphitrichous/Multitrichous: A cell bears many flagella in two tufts, one at both ends e.g. Spirilla pseudomonas. iv. Petritrichous: A cell has a larger number of flagella attached all round the surface e.g. Salmonella typhosa. A = Monotrichous, B = Lophotrichous, C = Amphitrichous, D = Peritrichous A few species of bacteria are capable of movement due to their cellular contraction as in the case of spirochaetes or due to creeping motion as in sulphur bacteria. Myxobacteria move due to characteristic ‘swelling of the slime’. Page 11 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE Cell structure A typical bacterial cell is found enveloped by three distinct layers i.e. the capsule or slime layer, the cell wall and the cell/plasma membrane. 1. Capsule (sheath) or slime layer: Capsule is found present only in a few types of bacteria. It is formed at a particular stage of life cycle. When the outer covering around the cell wall is diffused and loosely arranged, it is called slime layer and when it is thick, mucilaginous and compactly arranged it is called capsule. Capsule bearing bacteria are pathogenic to animals e.g. Bacillus anthracis and Mycobacterium tuberculosis. Capsule is an outer protective covering against adverse conditions and chemicals. 2. Cell wall: The bacteria cell wall is a strong rigid structure that protects and supports the weaker and biochemical more active parts of the cell. Its thickness varies from 10-25nm, depending on the species of the organism. The bacterial cell wall is a heteropolymer consisting of two amino acid sugars (N – acetylglucosamine and N-acetyl muramic acid) and amino acids such as glutamic acid, alanine, glycine and either diaminopimelic acid or lysine. In certain cases, the cell wall may contain chitin or cellulose e.g. Acetobacter xylinum. Gram positive bacteria have thicker cell wall than gram negative bacteria. Page 12 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session) Students are allowed to reproduce for their own use NOT FOR SALE 3. Cell membrane: The protoplasm bounded by a thick cell membrane present beneath the cell wall. Chemically, it is composed of phospholipids and proteins. Some polysaccharides are also found. Besides its function as a selective membrane, it plays a significant role during respiration. 4. Cytoplasm: It is a granular and viscous substance found between nucleic region and plasma membrane and comprises of salts, sugars, amino acids, vitamins, glycogene e.t.c. Ribosomes are freely found in the cytoplasm. In photosynthetic bacteria chromotophore are found which contain photosynthetic pigments associated with electron carriers. 5. The nucleic region: Bacterial nucleus is quite primitive in nature (simple) and consists of only diffused nucleic acid, that occur as single circular chromosome containing DNA and Protein. The DNA is concentrated in structures called chromatic bodies that is capable of dividing. They may also have additional nuclear materials called plasmids. There may be 1 – 100 plasmids per bacterium. Organelles like nucleolus, nuclear membrane, nuclear sap are not seen. Page 13 of 13 Faculty of Life Sciences BIO102 Lecture Note (2023/2024 Session)