Chapter 1: The Living Organism and the Cell PDF

Université Saad Dahleb Blida-1 Faculté des sciences biologiques (SNV) Chapter I The living organism and the cell Livings beings  Introduction Living organisms have the ability to do: a) recover and produce energy from organic matter (glucose,...

Université Saad Dahleb Blida-1 Faculté des sciences biologiques (SNV) Chapter I The living organism and the cell Livings beings  Introduction Living organisms have the ability to do: a) recover and produce energy from organic matter (glucose, galactose...) Energy is produced either by fermentation (anaerobic environment) or respiration (aerobic environment). b) Able to reproduce, grow and differentiate c) Have genetic material encoding the enzymatic or non-enzymatic elements essential to their vital functions. d) Their fundamental unit of life is the cell, whether composed of a single cell (unicellular organisms) or several cells (multicellular organisms). e) Living beings are capable of catabolism (degradation of biomolecules) and anabolism (synthesis of biomolecules). Kingdoms of the living things Five kingdoms classification  I: Prokaryotic cell What is a Prokaryotic Cell? “Pro” means “before” and “kary” means ‘nucleus’. Prokaryotes are simple, single-celled organisms that are the most primitive life form on earth. It includes two domains: bacteria and archaeabacteria. Prokaryotes are free-living and photosynthetic (produce their food), parasitic (living inside other organisms), or saprophytic (feeding on the dead and decaying matter). Prokaryotes can be found almost anywhere on earth, from land to water bodies, atmosphere to hydrothermal vents, and even inside living organisms, including humans.  Structure and ultra-structure Prokaryotic cells have both essential and optional elements. Bacteria, as prokaryotic organisms, are characterized by the absence of the nuclear envelope, the endomembrane system (endoplasmic reticulum, Golgi apparatus...) and mitochondria.  I.1: Essential elements of the prokaryotic cell Cell wall : Outer covering of most cells that protects the bacterial cell and gives it shape. Two wall types have been described in bacteria, dividing them into two groups. Gram- positive bacteria (thick layer of peptidoglycan in the bacterial cell wall) and Gram- negative bacteria (Thin peptidoglycan layer).  Plasma membrane: Surrounds the cell's cytoplasm and regulates the flow of substances in and out of the cell. Cytoplasm: A gel-like substance composed mainly of water that also contains enzymes, salts, cell components, and various organic molecules. Nucleoid or nuclear area: Area of the cytoplasm that contains the prokaryote's single DNA molecule. Ribosomes: Cell structures responsible for protein production.  I.2: Optional elements of the prokaryotic cell Plasmid: is a small, circular piece of DNA that is different than the chromosomal DNA. Bacterial capsule: serves as a shield, giving protection from toxins, and from drying out. Capsules allow adhesion to surfaces and help enable the bacteria to evade the host immune system. Flagellum : is a motility organelle responsible for rapid movement of bacterial cells towards more desirable environments. Pili (singular pilus): are evaginations of the plasma membrane on the surface of the wall of many bacteria. Chromatophores: They are diffuse membrane systems in the cytoplasm, rich in specific pigments. They are found only in photosynthetic eubacteria. Gas vacuoles : are found almost exclusively in aquatic bacteria, where they provide buoyancy.  Prokaryotic reproduction Reproduction in prokaryotes is asexual and usually takes place by binary fission.  II. Eukaryotic cell II.1. Definition Eukaryotes are cells commonly identified by the presence of a nucleus. Eukaryota is one of the three domains of life (bacteria and archaea are the others and collectively referred to as prokaryotes) and encompasses single-celled organisms as well as all multicellular life. Eukaryotic cells are relatively larger (10 and 100 µm) and contain organelles with a well-developed endomembrane system, compared with prokaryotic cells. Organelles are membrane-bound compartments within the cytoplasm. These organelles perform specialized physiological functions to manage the cell's diverse metabolic reactions.  II.2.Structure and ultra-structure The great diversity of eukaryotic cells is reflected in their morphological and structural variety. 1. Nucleus The nucleus is an organelle found in the majority of eukaryotic cells. It is bounded by a double membrane called the nuclear envelope and contains the cell's genetic material in the form of a DNA-protein complex called chromatin.  2. Plasma membrane The plasma membrane of eukaryotic cells resembles that of prokaryotes.  3. Cytoplasme Cytoplasm is defined by the contents of a living cell: the entire cell volume bounded by the plasma membrane, with the exception of the nucleus. 4. Endoplasmic reticulum The endoplasmic reticulum (ER) is an organelle comprising a set of membrane-bound cavities. There are two types of ER: - Granular or rough endoplasmic reticulum, when its surface is covered with ribosomes. - Smooth endoplasmic reticulum without ribosomes. 5. Golgi apparatus Golgi apparatus, also named as Golgi complex, or Golgi body, is a series of flattened, stacked, membrane-bound cell organelle found in all animal and plant cells. 6. Mitochondria Mitochondria are organelles found in the majority of eukaryotic cells. They are responsible for the metabolic reactions of cellular respiration, leading to the production of energy in the form of Adenosine Tri-Phosphate (ATP). 7. Cytoskeleton The cytoskeleton is a network of protein filaments found in the nucleoplasm and hyaloplasm of eukaryotic cells. It is responsible, among other things, for the internal and external shape of the cell, cell movement and the transport of various organelles or vesicles within the cell.  8. Peroxysome Peroxisomes are cellular organelles surrounded by a simple membrane, containing enzymes that catalyze the production and decomposition of hydrogen peroxide (H2O2). 9. Lysosomes Lysosomes are cellular organelles that contain the hydrolase enzymes which breaks down waste materials and cellular debris.  II.3. Animal eukaryotic cell 1. Centrosoma They are small body located near the nucleus and has a dense center and radiating tubules. The centrosomes are the destination where microtubules are made.  II.4 Plant eukaryotic cell Compared with animal cells, they are larger (50 to 250 µm) and generally have an angular, geometric shape. Plant cells have a number of characteristic structures, including : 1. Cell wall It is the extracellular structure surrounding plasma membrane. The cell wall is composed of cellulose, hemicellulose, pectin and in many cases lignin. 2. Vacuole The vacuole is a compartment bounded by a simple membrane, filled with water and containing various inorganic and organic molecules. 3. Plastids Plasts are found in plants and algae. The best known are the chloroplasts in the cells of photosynthetic organisms, which are the site of photosynthesis. They also have their own genome. 4. Plasmodesmata Plasmodesmata are cytoplasmic bridges that link plant cells and enable intercellular communication.  III. Acaryotes (Viruses) A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea. Their genetic material is DNA or RNA. Organisation of virions Their size is generally between 10 and 100 µm, so they are invisible under an optical microscope. The electron microscope is therefore used. Viruses are essentially made up of three elements: the genome or genetic material, the capsid and, in some cases, the envelope. 1. Nucleic acid The viral genome is made up of one or more nucleic acid molecules, which may be DNA or RNA (never both at the same time) in single-stranded or double-stranded, circular or linear form. 2. Capsid The capsid is a protein box or shell which surrounds and protects the viral nucleic acid. It is made up of protein sub-units called capsomeres. 3. Envelope Many viruses are surrounded by an envelope obtained when they cross the host cell membranes. This envelope is a mixture of elements from the host cell membrane and elements of viral origin. Viruses with an envelope are called enveloped viruses, while those without an envelope are called naked viruses.