Unit 2 - Classification of Microorganisms PDF

www.udst.edu.qa Unit 2: Classification of Microorganisms What do we study when we study microbiology? How does microbiology relate to your field of study? Pharmacy, Denta...

www.udst.edu.qa Unit 2: Classification of Microorganisms What do we study when we study microbiology? How does microbiology relate to your field of study? Pharmacy, Dental hygiene, Respiratory theory, Environmental OHS Perspective… Human body: 30-50 Trillion cells Over 200 different cell types. On and in the human body: 40-65 Trillion cells Very diverse group of organisms Ratio: 1 human cell : 1.3 microorganisms.  Taxonomy and Classification Taxonomy is the study or science of classification. Provides an orderly method for naming as well as categorizing Panthera concolor organisms. Common names: Mountain lion, Cougar, Puma, Panther Yuma Categories are called taxons (pl. puma, Florida panther, Eastern cougar, Wisconsin puma, Texas panther. taxa) There are many more when different languages are considered. Binomial nomenclature Classification Systems Woese’s Three Domain System Classification is based on genetics and the evolution of cell types. Bacteria and Archaea are both prokaryotic, and Eucarya is eukaryotic. Classification Systems Whittaker’s 5 kingdom system. One of the most widely accepted system of classification of organisms. Organisms are grouped using the significant features presented in the figure. Humans as an example… Prokaryotic Vs. Eukaryotic Two basic cell types. All living things fall into these two cell types. Pro – Means before Eu – Means true Karyon – Nucleus Prokaryotic cells are all single celled organisms and are all bacteria Eukaryotic cells are bigger and more complex Eukaryotic Vs. Prokaryotic Cells. Characteristic Prokaryotic Eukaryotic Nucleus Absent Present Membrane bound Absent Present organelles Size ~5 – 10 um ~10 – 100’s um Internal Organization None Yes, division of labor DNA / Chromosomes Circular DNA and plasmids, no Linear DNA, proteins for folding proteins Ribosomes Present 70s Present 80s Reproduction Asexual, binary fission Sexual or Asexual Cell membrane Lipid bilayer, folding Lipid bilayer Motility If yes, only use flagella Yes, Flagella, Cilia, Pseudopods Capsule Present in some Absent Pilus (Pili) Present Absent What do we study in Microbiology? Bacteria Prokaryotic cells – all those characteristics from the table. Incredible diversity of metabolic pathways and ways and means of obtaining carbon and energy from the environment. No membrane-bound organelles, this means they have to be very small – single celled. Bacteria - Archea A group of prokaryotes, genetics and metabolic pathways are more similar to eukaryotic cells. Absorb nutrients from their environment Exist in extreme environments – extremophiles. Methanogens, Thermophiles, Barophiles, and Halophiles. Cellular reproduction Sexual reproduction – an exchange of genetics resulting in a genetically different organism than the parents. Asexual reproduction – cellular reproduction where new cells are not from combined genetics, involves only a single organism reproducing, new cells are clones. Eukaryotic Cells The rest of the groups we study as microorganisms are Eukaryotic cells. See the characteristics of these cells in the table earlier. These groups include: Fungi, Protists (including algae), and microscopic animals (or parts of their lifecycle). Why don’t we study plants? Protista Eukaryotic cells. Single celled organisms (for the most part – hard to say any absolutes for this group). Obtain food through ingestion or photosynthesis. Organisms can be plant-like, animal- like or fungi-like. Algae – Also Protists Microalgae – Phytoplankton, the basis for most food webs in the ocean. Provides more oxygen to the planet than plants. Macroalgae – seaweeds and kelps, significant habitat for marine fish and invertebrates. Study of algae – Phycology. Algae play huge roles ecologically as well as economically. Ecology – Algae! Algae is massively important from an ecosystem perspective. Algae Huge diversity of size and shapes, from microscopic to 10’s of meters. Contain various pigments giving them different colors. Can be motile or non-motile. Can reproduce sexually, asexually or both. All algae are photosynthetic. Similar to plants except they are aquatic or marine, and lack roots, shoots and leaves. Fungi Eukaryotic Cells Can be unicellular (Yeasts) but most are multicellular. Have a cell wall made of chitin. Are absorptive heterotrophs. Very important ecologically as decomposers. Very important economically as food or in food production – Alcohol. Animals Eukaryotic cells. Heterotrophic. Complex multicellular organisms. Often complicated lifecycles. Internal parasites are usually worms (Helminthes) and external parasite are usually insects (mites, lice, ticks, and flies). What is the worlds most dangerous animal? Virus Non-living, not considered a living cell, can be called Acellular pathogen. Pathogen is an organism that causes disease. Extremely small. No metabolism or reproduction without a host cell. Motile?? The Typical Bacterial Cell Cell Glycocalyx membrane Biofilm Cell Wall Pili Cytoplasm Fimbriae Ribosomes Flagella Nucleoid Bacterial Plasmids cytoplasm Endospores Bacterial Structure and Function When we first consider bacteria we look at size, shape and arrangement. Size: Smallest of all organisms range in size from 0.5 – 2 µm in diameter. Bacterial Structure and Function Shape: Bacteria typically identify into three shapes. Cocci – Circular Bacilli – Rod shaped Spirilli – Spiral Shaped Vibrio, Spirillium, Spirochaete. Bacterial Structure and Function Arrangement: Groups of cells that form when cells divide but don’t separate. Arrangement depend on the cells shape. Cocci, being circular can divide in more planes than bacilli, and spirillum bacteria are very limited. Mono-, Diplo-, Tetrad, Sarcina, Staphylo-, Strepto-. Cell Membrane: A living Bacterial Structure and Function boundary between the cell and the environment. Function: Controlling what enters and leaves the cell. Very Dynamic – Remember the Fluid Mosaic Model. Made up of phospholipids, and integrated proteins and carbohydrates. Bacterial Structure and Function Cell Membrane In bacteria the cell membrane is more involved than eukaryotic CM. In bacteria the CM synthesizes cell wall components, helps in DNA replication, secretes proteins, carries out respiration, captures energy (ATP). Cell transport. Bacterial Structure and Function Cell Wall: Structural boundary outside the CM, gives cell its shape and prevents the cell from bursting under osmotic pressure. Made up of peptidoglycan (Murein), components are referred to as NAG and NAM, has peptide cross-links. Use the cell wall to classify bacteria into Gram-positive and Gram-negative groups.  Bacterial Structure and Function Gram Positive bacteria have a thick layer of peptidoglycan in their cell walls. Gram Negative bacteria have a small amount of peptidoglycan, but have an outer membrane, much more complex cell wall. Mycobacteria or Acid Fast bacteria have barely any peptidoglycan but have a thick wall made up of lipids. Bacterial Structure and Function Bacterial cytoplasm: Makes up the largest part of the inside of the cell. Made up of 4/5 water, and 1/5 dissolved substances including enzymes, proteins, carbohydrate, lipids and inorganic ions. Many metabolic reactions will take place in the cytoplasm. Bacterial Structure and Function Ribosomes: non-membrane bound organelles, the site of protein synthesis. They are found throughout the cytoplasm of bacteria. Bacterial ribosomes are smaller than eukaryotic ribosomes but perform the same function. Referred to as 70s ribosomes, based on sedimentation rates – Svedberg units (s). Bacterial Structure and Function Nucleoid: The area in the cytoplasm where the mostly DNA, some RNA and some proteins are located. This is NOT membrane-bound. Bacterial chromosome are circular, there is usually 1, but there may be exceptions. Bacterial Structure and Function Plasmids: Small extrachromosomal DNA molecules. Carry genes that are not essential for survival, genes that carry out nonessential cellular functions. Plasmids can be exchanged between cells during a process called conjugation, which allows for genetic transfer. Bacterial Structure and Function Endospores: A resting stage, a means of survival when conditions are unfavorable. NOT the same as fungal spores. Can survive very harsh conditions, high temps, radiation, dehydration, very difficult to kill spores. Can survive for thousands of years. Bacterial Structure and Function Glycocalyx: a layer outside the cell wall mostly made up of polysaccharides. Can be as thin as a layer of slime, or very thick and called a Capsule. Capsule: a thick layer secreted by the cell over the cell wall that serves a protective (desiccation, chemicals) as well as an Bacterial Structure and Function Flagella: Long, thin helical appendage used for mobility. About half of known bacteria are motile. Arrangement of flagella can be used to classify bacteria Different structurally than eukaryotic flagella, much simpler. Bacterial Structure and Function Pili (Pilus): Tiny hollow projections that help the bacteria adhere (Stick) to surfaces, they are NOT involved in movement. Fimbriae: Short attachment pili. (Pathogenicity). Sex pili: Long, modified for transfer of genes between cells in a process called conjugation. Bacterial Structure and Function Biofilm: A layer of living cells that exist on a surface. The cells can stick to a surface or each other, often they develop an extracellular matrix. This is a living entity and results in a microbiome, comprising of many different species or can be a single species. Example: Dental plaque.