Biological Classification 1st Course PDF

Biological classification Taxonomy Introduction The classification of the living world, also known as taxonomy, is a science that aims to organize and categorize living organisms into hierarchical groups based on their common characteristics. Traditional classification relies on systemat...

Biological classification Taxonomy Introduction The classification of the living world, also known as taxonomy, is a science that aims to organize and categorize living organisms into hierarchical groups based on their common characteristics. Traditional classification relies on systematic approaches, which encompass nomenclature (naming) and phylogeny (reconstruction of evolutionary relationships). The classification of the living world includes several levels, ranging from the most general to the most specific. Here are the main hierarchical levels in biological classification 1-Domain: The three domains of life are as follows: Archaea (archaea) Bacteria (bacteria) Eukaryota (eukaryotes) 2-Kingdom: Each domain is divided into kingdoms. For example, the domain of eukaryotes is subdivided into several kingdoms, including: Animalia (animals) Plantae (plants) Fungi (fungi) Protista (protists) 3- Phylum: Phyla are even more specific groups within kingdoms. For instance, in the animal kingdom, arthropods (such as insects and arachnids) and chordates (such as vertebrates) are two distinct phyla. 4- Class: Classes group similar animals or plants within a phylum. For example, in the phylum of chordates, the class of mammals is a group that includes animals like humans, dogs, and cats. 5- Order: Orders are even more specific groups within classes. For instance, in the class of mammals, the order of primates includes monkeys, chimpanzees, and humans. 6- Family: Families are even more restricted groups, grouping species that are very similar. 7- Genus: Genuses are very close groups, grouping very similar species. 8- Species: This is the lowest level of classification. A species is defined as a group of individuals capable of reproducing with each other and producing fertile offspring. It's important to note that the classification of the living world is constantly evolving as new genetic and anatomical information is discovered. Taxonomy is an essential tool for biologists and ecologists because it allows them to understand the relationships between organisms and study the evolution of life on Earth.  The cell The cell (from the Latin cellula, meaning small chamber or room) is a compartment partitioned (a closed structure) by a biomembrane containing genetic material plus a viscous fluid called cytoplasm. The cell represents the structural, functional, and reproductive unit constituting all (bacteria) or part of a living organism (animal or plant).  I- Prokaryote In biology and taxonomy, a prokaryotic cell (from the Latin pro, meaning 'before,' and the Greek karyon, meaning 'nucleus') is a unicellular organism lacking a nucleus and intracellular organelles (except for ribosomes). Its DNA is in the form of a circle or helix. For example, a bacterium.  Regardless of their form, size, specialization, and lifestyle, all living cells (Eukaryotes or Prokaryotes) exhibit a fundamental structure characterized by the presence of the following three elements: 1- Cell membrane or plasma membrane, without which intracellular biomolecules would be diluted in the surrounding environment. 2- Region containing genetic material, located inside the cell with molecules capable of reading and copying hereditary instructions. 3- Cytoplasm: the region between the nucleus (or DNA) and the cell membrane.  - Caracteristics The prokaryotes are unicellular organisms belonging to the kingdoms of bacteria and archaea. Prokaryotic cells are much smaller than eukaryotic cells, All prokaryotic cells are surrounded by a cell wall. Many also have a capsule or slimy envelope made of polysaccharides. Prokaryotes often have appendages (protrusions) on their surface. The flagellum and certain pili are involved in locomotion, fimbriae allow the cell to adhere to a substrate, and sex pili are used for DNA exchange. Most prokaryotic cells have a single circular chromosome. They also sometimes contain smaller circular DNA elements called plasmids.  Lack of Nucleus: Unlike eukaryotes, prokaryotes do not have a nucleus enclosed by a membrane. The DNA is located in a region known as the nucleoid, which is not surrounded by a membrane. Absence of Organelles: Prokaryotes lack membrane-bound organelles such as mitochondria or chloroplasts, which are found in eukaryotes. Diverse Metabolism: Prokaryotes exhibit diverse metabolism. They can be aerobic (using oxygen) or anaerobic (thriving in the absence of oxygen). Some are autotrophic (producing their own food), while others are heterotrophic (obtaining their food from the environment).  Reproduction: Prokaryotes primarily reproduce through binary fission, a process where a mother cell divides into two genetically identical daughter cells. Horizontal Gene Transfer: Prokaryotes can exchange DNA fragments through conjugation, transformation, and transduction, promoting genetic diversity. Resistance: Some prokaryotes develop resistance to antibiotics and harsh environmental conditions through mechanisms such as mutation and plasmid transfer. Ecological Importance: Prokaryotes play a crucial role in terrestrial and marine ecosystems as decomposers, nitrogen fixers, producers of greenhouse gases, and perform various other functions.  Domain of bacteria A bacterium is a unicellular prokaryotic organism of very small size (1 to 10µm). Bacteria can live individually or grouped in colonies. They have various shapes, such as rod-shaped, spherical, cylindrical, etc. Bacteria reproduce through binary fission or constriction. The bacterial cell is composed of both constant (essential) and variable structures. (a)Bacillus megaterium; (b)Tetracoccus canadensis Staphylococcus aureus Morphology of some bacterial cells Constant structures: Constant structures are mandatory organelles found in all bacteria. A living and functional bacterial cell cannot be devoid of any of these organelles. The constant structures are: 1- Nucleoid Material: This is the bacterial chromosome, composed of a single double-stranded circular DNA molecule of approximately 1mm. It is free in the cytoplasm, not separated by a nuclear envelope to form a true nucleus, hence the name Prokaryote. 2-Plasmids: Plasmids are double-stranded circular DNA fragments. They are extrachromosomal and located in the cytoplasm. A plasmid can be present in multiple copies within a single bacterial cell. They encode for the synthesis of various enzymes that enable the bacterium to utilize certain substrates or resist antibiotics. 3-Ribosomes: Grouped in clusters forming polyribosomes. Their synthesis does not require the presence of a nucleolus. 4-Plasma Membrane: Composed of lipids and proteins. It does not contain cholesterol and is low in carbohydrates. It facilitates the transport of nutrients. 5-The cell wall: Thick, ranging from 20 to 80 nm, it externally delimits the bacterium and determines its shape. It plays a protective role: a bacterium without a cell wall dies. It is separated from the plasma membrane by the periplasmic space. The ultrastructure of the cell wall subdivides bacteria into two main groups :  Gram-positive bacteria : their wall is dense and composed of thick peptidoglycan. Gram-positive bacteria retain the dye, appearing violet in color. Their cell walls have a single layer of peptidoglycan resting on the plasma membrane, and both together constitute the cell wall. Examples of Gram-positive bacteria include staphylococus. Gram-negative bacteria : their wall is composed of a loose peptidoglycan layer. Gram-negative bacteria are much more permeable to the dye, resulting in a pink coloration. Their walls consist of a thin layer of peptidoglycan resting on the plasma membrane, surrounded by an outer membrane, making a total of three layers. A pertinent example would be Escherichia coli. Bacteria replicate rapidly through cell division or binary fission. They can be either pathogenic or non-pathogenic. Optional Structures: Optional structures are organelles that may or may not be present in the bacterium. They are found in certain groups and are absent in others, depending on the species and their environments. These include: 1-Capsule: Often polysaccharide or polypeptide in nature, the capsule primarily plays a protective role. Its presence is a sign of virulence as it shields the bacterium from phagocytosis. 2-Mesosomes: Exclusive to aerobic bacteria, mesosomes are membranous invaginations that penetrate the cytoplasm. They contain enzymes of the respiratory chain, thus serving a role similar to that of mitochondria. 3-Flagella: These are mobile membranous extensions, ranging from 1 to 8, located in different positions. Flagella are composed of a contractile protein known as flagellin, and they facilitate the bacterium's locomotion. 4-Pili (Fimbriae): Similar to flagella but shorter, pili are membranous extensions that facilitate the adhesion of bacteria to substrates. They are composed of a protein called pilin. 5-Cytoplasmic Inclusions: This includes reserve granules or gas vacuoles, allowing the vertical movement of the bacterium that contains them. Figure : Representative diagram of the ultrastructure of a bacterial cell (Prokaryote)  Archaea domain The prokaryotes are divided into two major taxonomic groups, EUBACTERIA and ARCHAEBACTERIA. Eubacteria are the most common forms of bacteria. As of now, no pathogenic strain of archaebacteria has been identified. Archaebacteria are typically found in extreme environments (they are also called extremophiles), such as hot springs (~100°C), the deep ocean floor, salt-saturated waters and other environments previously thought to be inhospitable to life. They can metabolize unusual substances like methane, sulfur, and hydrogen gas. The origins of this group and its relationship with eubacteria and eukaryotes are currently hotly debated among microbiologists. However, some of their characteristics place them closer to eukaryotes than eubacteria. Figure: archaea colony  Viruses The term "virus" is derived from the Latin word for poison. Viruses are the causative agents of numerous viral diseases, some of which remain fatal and incurable to this day. Viruses are not considered living beings because they lack a cellular structure, have no independent metabolism, and can only be reproduced by infecting living cells to ensure their multiplication cycle (absolute parasitism) 1-Definition and Characteristics of Viruses: Viruses are obligatory parasites of specific hosts (either eukaryotic or prokaryotic). They consist of genetic material (either DNA or RNA, but not both), a capsid with variable symmetry, and potentially an envelope. Devoid of cytoplasm and a nucleus, viruses lack their own metabolism and replication capabilities. Their size ranges from 15 to 300 nm. Being devoid of cellular organelles, viruses do not constitute a true cell; they are merely internal particles incapable of autonomous evolution. They parasitize living cells, introducing their genetic material and utilizing the host's organelles for their own benefit. Viruses are very simple, with a relatively short piece of genetic code inside a packaging of protein called a capsid. When the virus infects a cell, it inserts its genetic code into the cell and takes over the machinery of the host cell to make lots of copies of its genetic code and proteins for its capsid. The new viruses are then assembled inside the host cell and eventually burst the cell and kill it. Viral destruction of cells causes disease. 2-Classification of Viruses: Viruses can be classified based on various criteria, as follows: 1-Nature of Nucleic Acid: Adenovirus (DNA) or Retrovirus (RNA). 2-Capsid Symmetry: Helical or Cubic. 3-Presence or Absence of Envelope: Enveloped or Non-enveloped viruses.