BIOD 171 MICROBIOLOGY NOTES. COMPLETE (100%) LATEST UPDATE.

BIOD 171 MICROBIOLOGY NOTES. COMPLETE (100%) LATEST UPDATE. 1.1 : Introduction What is Microbiology? As the name suggests, it is the study of biological processes at the micro (microscopic) level. These microorganisms usually consist of a single cell, so they are too small to study with just your eyes. Examples would include bacteria, archaeons, fungi, protozoa, and algae. Although they are also microscopic, viruses are not living, so they are not considered microorganisms—a point that will be expanded later in this course. However, viruses can be classified as microbes, a more general term that includes microorganisms and viruses. Taken together, microbiology is the study of microbes. Despite being invisible to the naked eye, microbes play a complex role in our world. For instance, microbes can be beneficial in a variety of ways ranging from aiding in food digestion to protecting us when we are exposed to potentially harmful foreign invaders to helping crops grow. However, microbes can also be detrimental, as harmful strains of bacteria, fungi, protozoa, and viruses kill millions of people each year and sicken even more. Indeed, microbes can be just as harmful as they can be advantageous. 1.2 : Classification of Cells: Prokaryotic vs Eukaryotic Although all four macromolecules described (proteins, nucleic acids, lipids and sugars) exist in all living organisms, distinct differences in the organization of the cellular materials are also possible. For this reason, not all organisms are classified in the same way. The most common distinction between living organisms is to define whether their cells are prokaryotic or eukaryotic. Prokaryotic is derived from Greek, meaning “before kernel,” whereas eukaryotic means “true kernel.” The kernel described the appearance of what is now called the nucleus of a cell—a membrane enclosed region within a cell that contains the genetic material. Thus, prokaryotic cells lack a nucleus, whereas eukaryotic cells have a defined nuclear region. It is also important to simply note that as of 1990 biologists further expanded the characterization and specification of the classifications of life into three categories: Bacteria, Archaea, and Eukarya. The first two categories are all comprised of prokaryotic microorganisms lacking a membrane-bound nucleus. The distinction made between prokaryotes (Bacteria vs. Archaea) is based mainly on the differences in cellular composition and is briefly described below. The Eukarya (eukaryotic) classification remained unchanged and still consists of all nuclear-bound microorganisms. 1. Bacteria Bacteria (sometimes referred to as Eubacteria, meaning ‘true bacteria’) constitute a large cohort of prokaryotic microorganisms. They can be considered the everyday bacteria and are common in human daily life. They have a variety of shapes by which they can be further classified. Bacteria display many distinct morphologies (shapes), the most common include: coccus (round/spherical), bacillus (rod), vibrio(curved rod), or spirillum (spiral/corkscrew). Aside from the shape of the bacterial cell, consider the cellular organization—cells may appear as isolated (individual) cells, in chains, or in clusters. Certain bacteria may also demonstrate motility (swimming movements), while others do not. Examples of Eubacteria are: Streptococcus, which have the appearance of round chains; E. coli, which have the appearance of rod; and Mycobacterium tuberculosis, a unicellular bacterium. 2. Archaea Archaea , the other prokaryotic class of microorganisms, have similar characteristics and shapes as Bacteria (Eubacteria) and yet remain genetically and compositionally distinct. Most notably, they can survive in extremely harsh environmental conditions, such as high salt levels, acid conditions, high temperatures, and oxygen-poor conditions. As such, Archaeons may also be referred to as extremophiles, based on the extreme or atypical environments in which they can be found. 3. Eukarya Eukarya is a diverse category and consists of a wide range of microorganism. Due to high diversity and complexity, eukaryotes can be subdivided into multiple categories, a process still debated today. However, the unifying characteristic of all eukaryotic cells is the presence of a membrane-bound nuclear region within the cell. For the purposes of this course, eukaryotic microorganisms will be classified as either: Animalia, Plantae, Fungi, and Protista. Animalia consists of multicellular eukaryotic organisms, and, as the name suggests, includes animals, as well as humans (and their cells) in their classification. All microorganisms in this category are heterotrophic , meaning they are incapable of producing their own energy, must absorb (consume) nutrients from the environment, and have the general characteristic of motility (the ability to move). Plantae are also multicellular eukaryotes, but, unlike Animalia, they can obtain most of their energy from sunlight via photosynthesis—a process that converts light energy (sunlight) into chemical energy (sugars) within the organism and fuels its activities. Fungi can be either multicellular or unicellular microorganisms, and, like Animalia, they are heterotrophic. A defining characteristic of fungi is the presence of chitin, a derivative of glucose, in their cell walls. Common examples of multicellular fungi are molds and mushrooms, while perhaps the most common unicellular fungus is yeast. Protista are unicellular microorganisms that may form as colonies. However, the colonies (seemingly multicellular) do not form tissue layers and thus retain the unicellular classification. Protista is often used as a classification for any microorganism that does not clearly fit the criteria for being considered animal, plant, or fungi. Common examples range from amoeba, known for its motility; algae, known for its plant-like characteristics; and mold, known for its fungi-like properties. Viruses , although they are considered neither prokaryotic nor eukaryotic, do play a large role in microbiology. Viruses are not considered living and do not replicate on their own, meaning they must replicate within a host. Outside of a host cell viruses have no metabolism and are essentially dormant—the virus takes up neither energy nor nutrients. Although viruses contain similar structures to the microorganisms described above, they are not cellular, and, as such, they do not fall within one of the categories described above. For instance, viruses contain a capsid , a membrane-like structure that contains genetic material, similar to the nucleus of a eukaryotic cell. 1.3 : Parts of a Cell Although there are key differences between the prokaryotic and eukaryotic cells, many similarities also exist in the basic organization of the cell. Below is a description of cellular structures found within a cell. Cell Membrane The cell membrane encloses the main body of the cell. The cell membrane may also be referred to as the plasma membrane and/or the cytoplasmic membrane. Both names are descriptive derivations of its function: to surround the plasma/cytoplasm of the cell. The cell membrane is a semi-permeable barrier surrounding the cytoplasmic space of a cell. Semi-permeable means that it allows certain substances to pass through while excluding others. It acts as a barrier to the outside environment while also retaining and preventing the intra (within) cellular components from being lost to the surrounding environment. The cell membrane is a bilayer composed primarily of amphipathic phospholipids, meaning they contain a polar hydrophilic (water loving) head group and a non-polar hydrophobic (water fearing) tail region. The lipid bilayer is situated with the non-polar tail groups facing inward, orienting the polar head groups to interact with water both outside and inside of the cell, as shown in Figure 1.6 (see lesson 1.4: Macromolecules). It is also important to note that the membrane has a relatively high degree of fluidity, meaning lipids can move freely within the two layers. How freely the lipids move is largely dependent on the types of lipids present, the temperature of the environment (lipids are slower at lower temperatures and faster at high temperatures), and the presence of any additional molecules (proteins). A key distinction between prokaryotic and eukaryotic cell membranes is the absence of sterol lipids (such as cholesterol), which play a major role in eukaryotic membrane composition. Cell Walls Cell walls (or outer membrane) are found in bacteria, plants, fungi, and algae and help to form the shape of the cell. The cell wall is an additional layer surrounding the cell membrane; it is rigid and for the most part cannot change its shape. As the outermost layer, the cell wall plays an important role in providing support, structure, and protection. The combination of the cell membrane and the outer membrane (cell wall) are referred to as the cell envelope. The composition of cell walls is also very diverse. The bacterial cell wall contains peptidoglycan, a peptide-polysaccharide matrix, which can vary in thickness. The peptidoglycan layer is essential for bacterial survival as it protects the cell from potentially damaging environmental stresses. Interestingly, despite the harsh conditions in which they are found, organisms in the class Archaea lack peptidoglycan in their cell walls. Instead, the cell wall is composed primarily of surface-layer proteins (called an S- layer) that provide both a physical and chemical protective barrier to the harsh surrounding environments in which they are often found. The specific type of protein comprising the S-layer varies from organism to organism. Diversity also exists among the various subgroups of eukaryotic cells. Some cell walls may contain polysaccharides, like cellulose and pectin, whereas fungi have cell walls containing cellulose and chitin. Yeasts have cell walls composed of mannoproteins— highly glycosylated polypeptides called mannan and mannose. Diatoms, a type of algae, have thick cell walls containing silica (the main component found in glass), making them very rigid. Note: For the following organelles listed below, please reference Figure 1.1, 1.2 and 1.3 found at the end of this page. Cytoplasm The cytoplasm constitutes the open volume within a cell. It is comprised mostly of water containing dissolved substances important to the functioning of the cell. Within the cytoplasm are organelles, membrane-enclosed structures that perform specific functions, as described below. All of these organelles, with the exception of the ribosomes, are exclusive to eukaryotic cells. Nucleus The nucleus is the defining organelle of all eukaryotic cells and is defined by a porous double lipid bilayer that contains the genomic content of the cell (DNA). The nucleus is thus the command center of the cell. In contrast, the genomic material of prokaryotic cells is found within the cytoplasm. Within the nucleus is the nucleolus, the site of ribosome synthesis.