Systematic Biology PDF

Introduction Systematics is the name for the branch of biology concerned with the study of the kinds of organisms, their relationships to one another, and their evolutionary history. Two underlying goals of plant systematics, thus, are to:  Find, describe, give unique names to, and organize...

Introduction Systematics is the name for the branch of biology concerned with the study of the kinds of organisms, their relationships to one another, and their evolutionary history. Two underlying goals of plant systematics, thus, are to:  Find, describe, give unique names to, and organize into categories the species of plants of the world.  Organize plants and plant groups to reflect their evolutionary relatedness and their descent from a common ancestor. Systematics today is a vigorous and exciting field that has been given great impetus by the discoveries of molecular biologists, who now are describing organisms at their most fundamental level—the DNA sequences of the cells—and providing the systematists new data on which to base their phylogenetic trees. Phylogenetic trees are the graphic representation of the evolutionary divergences of organisms that put together on the same branches the organisms most closely related, with oldest ancestors near the base, youngest descendants near the top. 1 The binomial system of nomenclature The binomial system in use today gives a single name recognizable throughout the world to each individual kind of organism. The scientific name consists of two parts (in Latin): the name of the genus, plus the name of the particular species. The system originated with Carl Linnaeus in the middle of the eighteenth century as a shortcut to the cumbersome polynomial system then in use that required 12-word descriptions to be written as part of the name. In the binomial system, the scientific name is italicized in print and the genus is capitalized, but the species is not. Taxonomic hierarchy The Linnaean hierarchical system is a means to group similar organisms together in levels of increasing inclusiveness from the species at the bottom to the most inclusive—kingdom— at the top. Genera are groups of species, families are groups of genera, and so on up the hierarchy. Taxon is a general name given to the members of any level in the hierarchy. Major groups and current ways of grouping of organisms. 2 In the middle of the eighteenth century, Linnaeus’ ideas transformed biological classification. In the latter half of the nineteenth century, Darwin revolutionized biology with an irrefutable theory of evolution. At the end of the twentieth century, molecular sequencing is changing the phylogeny of the entire tree of life. Appropriately enough, a major adjustment has already been made at the roots of the tree: There appear to be three main lines of development from the primitive milieu. Biologists use the following features of organisms to identify the major groupings of current classifications: Features of identify and classify the organisms: 1. Presence or absence of a defined nucleus 2. Unicellular or multicellular with specialized organelles 3. Mode of nutrition 4. Presence or absence of a cell wall 5. Composition of the cell wall 6. Motility 7. Mode of reproduction 8. Kind of life cycle 3 Nucleus The most basic division of organisms separates the living world into two groups on the basis of those possessing and those lacking a defined nucleus (plural: nuclei). The nucleus is an organelle, which contains the major portion of the genetic material (DNA) of the cell and is surrounded by a nuclear membrane. Cellularity The form (morphology) of an organism can be unicellular (one- celled) or multicellular (many-celled). Some unicellular organisms form filaments (strings of cells), others form sheets of cells held together by pectins, and still others form colonies that give a superficial resemblance to multicellularity. Some organisms alternate a unicellular stage with a multicellular stage in their life cycles. Eukaryotic organisms have organelles, membrane-bounded structures within their cells specialized to perform certain functions. Nutrition All organisms need a source of energy to fuel their metabolism, the 4 chemical processes that maintain life. Organisms obtain their nutrients for metabolism in one of two basic ways: 1. Autotrophs are able to make the organic compounds they use for metabolism directly from inorganic materials. Some autotrophs are photoautotrophs. They use radiant energy from the sun in the process of photosynthesis to manufacture organic compounds. Chemoautotrophs use chemical energy in chemosynthesis, oxidizing inorganic compounds to manufacture organic nutrients. Chloroplasts are present in the photoautotrophs, absent in the chemoautotrophs. 2. Heterotrophs are unable to do this and obtain their nutrients from the organic materials manufactured by autotrophs. Animals are heterotrophs; they ingest (swallow) their food and then digest it internally. Fungi are heterotrophs, which release digestive enzymes into their surroundings and then absorb the nutrients into their cells. Many protists use phagotrophy, a type of nutrition in which single cells ingest food particles. Some fungi (and other organisms) are saprophages, heterotrophs that break down the organic materials of dead organisms. 5 Cell wall Animals and the animal-like protists have no cell walls, but most other organisms (with a few exceptions) have some kind of wall made from a variety of materials. Almost all of the prokaryote cells have walls, and a major distinction between the Bacteria and the Archaea is the presence of peptidoglycans (glycoprotein polymers) in the Bacteria and their absence in the Archaea cell walls. Fungi cell walls are made of chitin, the substance that makes the exoskeletons of lobsters, crabs, cockroaches, and other arthropods hard. The basic material of plant cells (and those of many algae) is cellulose. Lignin, suberin, waxes, and many other substances may be deposited additionally. Motility Plants in general and some animals don’t move around; they are sessile (attached) to a substrate. But many plant and sessile animal cells are motile, and they move using a variety of techniques. The organelle that propels most cells is the flagellum (plural: flagella) or, in the terminology of some biologists, the undulipodium (plural: 6 undulipodia). A smaller, shorter flagellum is a cilium (plural: cilia). The flagella are long threads of protoplasm that extend outside of the cell and have the capability for limited movement. Type of reproduction Reproduction is the creation of new individuals from existing ones and can be either asexual—without special sex cells (gametes)—or sexual, in which gametes fuse to produce new individuals. Gametes are usually haploid (with a single set of chromosomes) and their fusion (fertilization) results in a diploid (with two sets of chromosomes) zygote (the cell formed by the fusion of two gametes). Variations of both sexual and asexual reproduction are legion throughout the living world. Asexual reproduction occurs in some members of all the kingdoms, whereas sexual reproduction is present in all but the Archaea. Many types of asexual reproduction exist. Fission, a splitting in two of the cell, is one type of asexual reproduction. In prokaryotes, division of the genetic material accompanies fission, whereas it does not accompany fission in the eukaryotes. Yeasts and some other organisms bud, simply by pushing out and breaking off pieces of the cell. Spore-formation is a widespread method of asexual reproduction in 7 which single-celled spores, formed in specialized structures called sporangia, are produced in large numbers. They may undergo a resting stage first, or produce new individuals directly. Sexual spores are produced in some organisms. Life cycle Three basic types of life cycles differentiate major groups of organisms. All are variations on a general theme in which haploid cells alternate with diploid in the stages of the life cycle. Thus, meiotic (reduction) cell divisions alternate with fertilization (fusion of gametes). The three life cycles are:  Zygotic meiosis: The individual organisms are haploid, and only the zygote is diploid. The zygote produced by fertilization immediately undergoes meiosis, producing more haploid individuals. This life cycle appears in all fungi and some algae.  Gametic meiosis: The mature, common individuals are diploid and produce haploid gametes that fuse. The zygote divides by ordinary mitosis, producing the adult diploid 8  individuals. Animals, some brown and green algae, and many other organisms maintain this type of life cycle.  Sporic meiosis: Also called alternation of generations because during the life cycle two kinds of individuals switch or alternate as the common individual, one diploid, one haploid. In plants the diploid individual, called the sporophyte, produces spore mother cells that divide by meiosis producing haploid spores. Life is currently classified as three major groups (sometimes called domains) of organisms: Archaea (also called Archaebacteria), Bacteria (also called Eubacteria), and Eukarya or eukaryotes (also spelled eucaryotes). The Archaea and Bacteria consist of small, mostly unicellular organisms that possess circular DNA, replicate by fission, and lack membrane bound organelles. The two groups differ from one another in the chemical structure of certain cellular components. Eukaryotes are unicellular or multicellular organisms that possess linear DNA (organized as histone-bound chromosomes), replicate by mitotic and often meiotic division, and possess membrane-bound 9 organelles such as nuclei, cytoskeletal structures, and (in almost all) mitochondria. The three-domain system was first introduced by Carl Woese in 1990 that is called Carl Woese’s Classification. This classification system also is known as the Six Kingdoms and Three Domains Classification because it divides the life forms into three domains and six kingdoms. The three-domains of Carl Woese’s Classification system include archaea, bacteria, eukaryote, and six kingdoms are Archaebacteria (ancient bacteria), Eubacteria (true bacteria), Protista, Fungi, Plantae, Animalia. This classification system divides the life based on the differences in the 16S ribosomal RNA (rRNA) structure and as well as the cell’s membrane lipid structure and its sensitivity to antibiotics. The main difference from earlier classification systems is the splitting of archaea from bacteria. The prokaryotic Monera continue to comprise the bacteria, although techniques in genetic homology have defined a new group of bacteria, the Archaebacteria, that some biologists believe may be as different from bacteria as bacteria are from 11 other eukaryotic organisms. The eukaryotic kingdoms now include the Plantae, Animalia, Protista, and Fungi. The protists are predominantly unicellular, microscopic, nonvascular organisms that do not generally form tissues. Exhibiting all modes of nutrition, protists are frequently motile organisms, primarily using flagella, cilia, or pseudopodia. The fungi, also nonvascular organisms, exhibit an osmotrophic type of heterotrophic nutrition. Although the mycelium may be complex, they also exhibit only simple tissue differentiation, if any at all. Their cell wall usually contain chitin, and they commonly release spores during reproduction. The plants are multicellular, autotrophic organisms with cellulose-containing cell walls. The vascular plants possess roots, stems, leaves, and complex reproductive organs. The non-vascular plants life cycle shows an alternation of generations between haploid (gametophyte) and diploid (sporophyte) generations. The animals are multicellular, heterotrophic organisms whose cells are not surrounded by cell walls. Animals generally are independently motile, which has led to the development of organ and tissue systems. The 11 monerans, the only prokaryotic kingdom in this classification scheme, is principally made up of the bacteria. They are generally free-living unicellular organisms that reproduce by fission. Their genetic material is concentrated in a non- membrane-bound nuclear area. Motility in bacteria is by a flagellar structure that is different from the eukaryotic flagellum. Most bacteria have an envelope that contains a unique cell wall, peptidoglycan, the chemical nature of which imparts a special staining property that is taxonomically significant (i.e., gram-positive, gram-negative, acid-fast). Non-cellular micro-organisms Viruses 12 Viruses are not living things. Viruses are complicated assemblies of molecules, including proteins, nucleic acids, lipids, and carbohydrates, but on their own they can do nothing until they enter a living cell. Without cells, viruses would not be able to multiply. Therefore, viruses are not living things. Three main properties distinguish viruses from their various host cells: size, nucleic acid content and metabolic capabilities. The largest of the human pathogenic viruses, the poxviruses, measure only 250 nm along their longest axis, and the smallest, the poliovirus, is only 28 nm in diameter. 13 In general, viruses contain only a single type of nucleic acid, either DNA or RNA. Virus particles have no metabolic machinery of their own. They cannot synthesize their own protein and nucleic acid. They are obligatory intracellular parasites, only growing within other living cells whose energy and protein-producing systems they redirect for the purpose of manufacturing new viral components. Virus particles are composed of a core of genetic material, either DNA or RNA, surrounded by a coat of protein. Which protects the viral genes from inactivation by adverse environmental factors, such as tissue nuclease enzymes. Properties common to all viruses  Viruses have a nucleic acid genome of either DNA or RNA.  Compared with a cell genome, viral genomes are small, but genomes of different viruses' range in size by over 100-fold.  Small genomes make small particles – again with a 100-fold size range.  Viral genomes are associated with protein that at its simplest forms the virus particle, but in some viruses this nucleoprotein is surrounded by further protein or a lipid bilayer.  Viruses can only reproduce in living cells. 14   The outermost proteins of the virus particle allow the virus to recognize the correct host cell and gain entry into its cytoplasm.  They have a component—a receptor-binding protein—for attaching or ‘docking’ to cells so that they can commandeer them as virus production factories. Virus proteins may be carried out by structural proteins, and some by non-structural proteins (proteins synthesized by the virus in an infected cell but they are not virion components). The structural proteins have to carry out a wide range of functions, including, protection of the virus genome, attachment of the virion to a host cell and fusion of the virion envelope to a cell membrane. The coat of viruses may also play an important part in the attachment of the virus to receptors of susceptible hosts. In many bacterial viruses the coat is further modified to facilitate the insertion of the viral genome through the bacterial cell wall. The viral protein coat, or capsid, is composed of a large number of subunits, called capsomeres. In addition to the capsid, many animal virus particles are surrounded by a lipoprotein envelope which has generally been derived from the cytoplasmic membrane of their host 15 cell, and sometimes another layer of protein, surrounds this structure, which is referred to as a nucleocapsid. Capsids are constructed from many molecules of one or a few species of protein. A capsid is the protein shell of a virus. It consists of several oligomeric structural subunits made of Protein called protomers. It is the smallest unit composed of at least two different protein chains that form a larger hetero-oligomer by association of two or more copies of this unit. These three-dimensional morphological subunits are called capsomeres. The individual protein molecules are asymmetrical, but they are organized to form symmetrical structures. The majority of viruses 16 the capsid symmetry is either helical or icosahedral in addition to the rod and cone shape. The most common are helical and icosahedral symmetries. 1. Helical symmetry capsid: The capsids of many ssRNA viruses have helical symmetry; helical nucleocapsids consist of a helical array of capsid proteins (protomers) wrapped around a helical filament of nucleic acid. The length of the capsid is determined by the length of the nucleic acid. 17  2. Icosahedral symmetry Capsids The icosahedral shape has 20 equilateral triangular faces, approximates a sphere. This means the icosahedron is an object with, 20 faces, each an equilateral triangle; 12 vertices, each formed where the vertices of five triangles meet; 30 edges, at each of which the sides of two triangles meet. Each icosahedron has five, three- or two- fold axes of rotational symmetry. Each vertex has three protein molecules per triangular face, giving a total of 60 for the icosahedron. 18 The capsid surfaces vary in their topography; there may be canyons, hollows, ridges and/or spikes. Some icosahedral viruses have a structure such as a knob, projection or fiber at each of the 12 vertices of the capsid. An elongated icosahedron is a common shape for the heads of bacteriophages. Such a structure is composed of a cylinder with a cap at either end. The cylinder is composed of 10 elongated triangular faces. 19  3. Conical and rod-shaped capsids HIV-1 and baculoviruses have capsids that are conical and rod shaped, respectively. Inside each capsid is a copy of the virus genome coated in a highly basic protein. Both of these viruses have enveloped virions. The virus genome is one or more molecules of nucleic acid. The virus genome is composed of either RNA or DNA. Each nucleic acid molecule is either single-stranded (ss) or double-stranded (ds), giving four categories of virus genome: dsDNA, ssDNA, dsRNA and ssRNA. The dsDNA viruses encode their genes in the same kind of molecule as animals, plants, bacteria. The most fungal viruses have dsRNA genomes, most plant viruses have ssRNA genomes and 21 most prokaryotic viruses have dsDNA genomes. Generally, the most fungal viruses have dsRNA genomes, most plant viruses have ssRNA genomes and most prokaryotic viruses have dsDNA genomes. The largest virus genomes, such as that of the mimivirus, are larger than the smallest genomes of cellular organisms, such as some mycoplasmas. The genomic RNA strand of single-stranded RNA viruses is called sense (positive sense, plus sense) in orientation if it can serve as mRNA, and antisense (negative sense, minus sense) if a complementary strand synthesized by a viral RNA transcriptase serves as mRNA. 21