Lecture 1: The Microbial World PDF

LECTURE 1: THE MICROBIAL WORLD Domain – broad classification of life LECTURE OU...

LECTURE 1: THE MICROBIAL WORLD Domain – broad classification of life LECTURE OUTLINE B - bacteria  Microorganisms (foundations of life on Earth) A- archaea  Structure and Activities of Microbial Cells  Microscopy and the Origins of Microbiology E- eukarya (kingdom  The Impact of Microorganisms on Human Society Two Fundamental Types of Cell: plantae, protista, fungi, animalia) Eukaryotic and Prokaryotic Cell Microorganisms Each domain have Eukaryotic cell- multicelluar cells certain kingdoms,  also called microbes (domain eukarya) each kingdom have  life forms too small to be seen by the naked eye Prokaryotic cell- single-celled phylum  diverse in form and function organisms (bacteria and archaea)  typically live in complex microbial communities  their activities are regulated by interactions with each other, with their environments, and with other organisms STRUCTURE & ACTIVITIES OF MICROBIAL CELLS Microbial Cells are living compartments that interact with their environment and with other cells in dynamic ways. Elements of Microbial Structure? Both have ribosomes, these are structures that responsible for protein synthesis Both have genetic material: DNA Some of both have cell wall Not all eukaryotic cell have cell wall Differences: Both have cell membrane or cytoplasmic membrane Aside from the size and shape Cytoplasmic membrane- permeability barrier that P: simplier separates cytoplasm from the outside of the cell E: compartmentalized, complex (membrane bounded organelles) Cytoplasm- inside environment of the cell (mixture P: DNA inside nucleoid (not membrane bounded) no true nucleus of micromolecules: carbohydrates, proteins, nucleic acids DNA RNA, lipids, small organic molecules, E: true nucleus (nucleus is covered with nuclear membrane) DNA inside various inorganic ions, ribosomes nucleus  All living cells are capable Not all cells can form of metabolism spores. Viruses are not consiered Not all cells can living organism (obligate communicate. parasites) Not all cells can exchange genes. (horizontal gene transfer) All cells are able to grow Motile cells (sperm cells, and process nutrients from have ability to move, swim the environment, or glide) converting to new material to form new cells, capable Egg cells are not motile of evolution Microbes are the oldest life form on earth and has evolved (appeared 3.8 – 4.3 B years ago) fundations of life on earth Earth’s age: 4.6 B (estimation) Anoxic earth – atmosphere has no oxygen, anoxithropic bacteria are present Cynobacteria – able to carry out oxygenic photosynthesis (great oxygination event) Transition from AE to GOE --- modern eukaryotes evolved and life forms evolved continuously from then on LUCA: Last Universal Common Ancestor MICROSCOPY & THE ORIGINS OF MICROBIOLOGY Robert Hooke and Early Microscopy in 1664. The lens was fitted at the end of an adjustable belows (G) and light focused on the specimen by a separate lens. Coined the term “cells” Micrographia (the first book devoted to microscopic images) Antoni van Leeuwehoek Microscope in 1684. Several shapes of common bacteria: A, C, F, and G, rods; E, cocci; H, packets of cocci. The first person to see bacteria. LIGHT MICROSCOPE (depended on light to see specimen)  light is focused on the specimen by a glass condenser lens  image is then magnified by an objective lens and an ocular lens for projection on the eye 3 Important Paremeter in Microscopy to Consider  Magnification (ratio of object image size)  Resolution (measure of the clarity of the image)  Contrast (difference in brightest between the light and dark areas of the image) TO enhance contrast: staining, labeling cell components For magnification, different types of objective lens  Scanner  LPO (Low Power Objective)  HPO (High Power Objective)  OIO (Oil Immersiion Objective) --- highest magnification ELECTRON MICROSCOPE  beam of electrons is used instead of light  electron beam is focused on the specimen by a condenser lens SEM: Surface structure TEM: Internal structure EM can kill cells SCIENTIFIC DEVELOPMENT OF MICROBIOLOGY LOUIS PASTEUR (1822- 1895)  known as the “Father of Microbiology”  disproved the theory of spontaneous generation SPONTANEOUS GENERATION (ABIOGENESIS) Aristotle  living organisms could arise from nonliving matter Francesco Redi John Needham (broth experiment, short duration of heating) & Lazaro Spallanzani (broth experiment, opposite) -Louis Pasteur accepted the challenge SCIENTIFIC DEVELOPMENT OF MICROBIOLOGY JOSEPH LISTER (1827- 1912) known as the “Father of Modern Surgery” applied Pasteur’s work andintroduced antiseptic techniques in surgery ROBERT KOCH (1843- 1910) known as the “Father of Bacteriology” EDWARD JENNER (1749- 1823) known as the “Father of Immunology” branches of microbiology BACTERIOLOGY: study of bacteria MYCOLOGY: study of fungi PHYCOLOGY: study of photosynthetic eukaryotes PROTOZOOLOGY: study of protozoa VIROLOGY: study of viruses THE IMPACT OF MICROORGANISMS ON HUMAN SOCIETY :MICROORGANISMS AS AGENTS OF DISEASE MICROORGANISMS, AGRICULTURE, & HUMAN NUTRITION Ruminants in the 4 stomach chambers MICROORGANISMS, AGRICULTURE, & HUMAN NUTRITION MICROORGANISMS AND FOOD MICROORGANISMS AND INDUSTRY Biofuels LECTURE 2: MICROBIAL Cell Structure & Function Contents: 1. Cells of Bacteria and Archaea 2 of the 3 domain: Archaea and 2. The Cell Membrane and Wall bacteria (prokaryotic organisms 3. Cell Surface Structures and Inclusions because they prokaryotic cells) 4. Cell Locomotion Humans belong to Eukarya 5. Eukaryotic Microbial Cells Microorganisms that are eukaryotic 1.Cells of Bacteria and Archaea cells like algae, protists, fungi WHAT IS MORPHOLOGY? In microbiology, the term morphology means cell shape. Rod (bacillus) Coccus form chains Poor predictor of other properties of cells: cell morphology Small cells have more surface area relative to cell volume than do large, kaya they have higher S/V ratio S/V ratio, the higher the S/V ratio of small cells, the faster rate of niutrient and waste exchange per unit cell (faster metabolism) Prokaryotic cells can grow faster and therefore can evolve rapidly than larger cells, such as bacteria AMR (Anti Microbial Resistance) bacteria in the body resistance against antibiotic, this bacteria evove (adapative mechanisms) faster because of their size as small SURFACE-T0-VOLUME RATIOS Small cells have more surface area relative to cell volume than do large cells and thus have a higher surface-to-volume ratio. S/V Ratio 1. The higher S/V ratio of small cells supports a faster rate of nutrient and waste exchange per unit cell. 2. Because of their small sizes, prokaryotic cells can grow faster and evolve more rapidly than can larger cells. 2. The Cell Membrane and Wall THE CYTOPLASMIC MEMBRANE surrounds the cytoplasm and separates it from the environment FUNC TIONS OF THE CYTOPLASMIC MEMBRANE (major function: selective permeability) the cytoplasmic membrane controls at least three critically important cellular functions ---- Permeability Barrier ---- Protein Anchor ---- Energy Conservation Bacteria and eukarya (prokaryotics) Archaeal Membranes structurally similar with B and E, phospolid layer but different in chemistry Bond between the Cytoplasmic membrane of all cells is tail and head: known as phospolipid bilayer through ether linkage  Hydrophobic region (water repelling) of repeating  Hydrophilic region (water isoprine units attracting) Some member of archaea’s tail have rings of hydrocarbon Bacteria and Eukarya: Hydrophobic component is composed of fatty acids (connected to the head which hydrophilic region) Blue: hydrophilic (glycerol molecule: phosphate and functional groups such as sugar) Yellow: hydrophobic (fatty acids) Through Ester linkage: fatty acids connected to the glycerol 2. The Cell Membrane and Wall Note: cytoplasm of prokaryotic cells contain high concetration of desolve solutes, that create significant osmotic pressure (if there is no protective layer, it may cause BACTERIAL CELL WALL pressure which might cause the bursting cell, also known as osmotic lysis)  protection against osmotic lysis To withstand and prevent the pressure, most cells of bacteria and archaea have a layer  confer shape and rigidity on the cell of the cytoplasmic membrane called cell wall. Cell wall’s role is to protect the cell against osmotic lysis and to confer shape and rigidity on the cell Structure of Peptidoglycan PEPTIDOGLYCAN (major strengthening agent of cell wall)  rigid polysaccharide Most important structure of cell wall is Peptidoglycan  found in all Bacteria that contain a cell wall Cell’s bacteria can be divided into two major groups:  not present in the cell walls of Archaea or Eukarya gram positive and gram negative (the distinction is  To confer structural strength on the cell, very rigid based on gram staining reaction) Gram staining technique: type of method to Components of Peptidoglycan: distinguish if a bateria is gram positive and gram negative.  Composed of alternating repeats of two modified glucose residues: N-Acetylglucosamien (G) & N-Acetylmuramic acid (M)  G & M are connected through glycosidic bond (β-1,4-glycosidic linkage)  The linkage can destroyed by an enzime called lysozyme (if destroyed, peptidoglycan can be destroyed as well)  Lysozyme is present in human bodily fluids  If a bacteria sample is blue to purple, it is gram-positive. Gram-positive bacteria produced acidic moleculed called teichoic THE GRAM- POSITIVE CELL WALL (interbridge) acid. Functions as binding of divalent metal ions before they  many Gram + Bacteria form several layers of peptidoglycan stacked one upon another enter the cell.  produce acidic molecules called teichoic acids THE GRAM-NEGATIVE CELL WALL  only small amount of the total cell wall consists of peptidoglycan  most of the wall is composed of the outer membrane (LPS) Lipid A (Lipid portion of the LPS)  Toxicity is specifically linked to the LPS layer, in particular, to lipid A.  Endotoxin- toxic component of LPS. THE PERIPLASM AND PORINS PERIPLASM (space between of different classes of proteins like binding proteins and chemoreceptors) May contain several classes of protein --- Hydrolytic Enzymes --- Binding Proteins --- Chemoreceptors --- Proteins that construct extracellular structures PORINS are proteins that function as channels for the entrance and exit of solutes ARCHAEAL CELL WALL  variety of cell wall structures are found in Archaea, including walls containing polysaccharides, proteins, or glycoproteins or mixture of these macromolecules PSEUDOMUREIN (N-Acetylglocosamine (G) ---- N-Acetytalsaminoronic acid (P)) & OTHER POLYSACCHARIDE CELL WALLS Components of Pseudomurein:  Composed of alternating repeats of two modified glucose residues: N-Acetylglucosamien (G) & N-Acetytalosaminuronic (P)  G & P are connected through glycosidic bond (β-1,3-glycosidic linkage)  Lysozyme insensitive - Immune from the destruction of lysozymes and penicillin PSEUDOMUREIN  backbone is formed by alternating repeats of N- acetylglucosamine and N- acetyltalosaminuronic acid  glycosidic bonds between the sugar derivatives is -1,3  the amino acids are all of L stereoisomer  immune from destruction by both lysozyme and penicillin Cell walls of some other archaea lack pseudomurein and instead ocontain other polysaccharides. i.e. Methanosarcina species have thick polysaccharide walls composed of polymers of glucose, glucoronic acid, galactosamine uronic acid and acetate. S-Layer  paracystalline surface layer  most common type of cell wall in Archaea  consist of interlocking molecules of protein or glycoprotein  sufficiently strong to withstand osmotic pressures without any other wall components 3. Cell Surface Structures and Inclusions CELL SURFACE STRUCTURES  Capsules and Slime Layers (polysacharide or protein)  Fimbriae, Pili, and Hami  Capsule and slime layer CAPSULE functions as attachement of certain bacterium on the surface layer organized in a tight matrix that excludes small particles and is tightly attached Fibriae and Pili and hami (found readily visible by light microscope if cells are treated with India ink in prokaryotic organisms) SLIME LAYER Fibrae and pili are made up of layer that is more easily deformed, loosely attached, and does not exclude particles protein. Fimbriae enable cells to stick to surfaces, in case of animal tissues in the case of pathogenic bacteria, or to form pellicles (thin sheets of cells on a liquid surface) or biofilms on surfaces Pili similar to fimbriae but are typically longer and only one or a few pili are present on the surface of the cell facilitate genetic exchange between cells in the process called conjugation (conjugative or sex pili) enable the adhesion of pathogens to specific host tissues that they subsequently invade (type IV and other pili; twitching motility (type IV) Hami unique attachment structure that resembles a tiny grappling hook structurally resemble type IV pili except for their barbed terminus, which functions to attach cells both to surfaces and to each other Virulence Factors molecules that contribute to the pathogenicity of a bacterial pathogen i.e. the case of Bacillus anthracis Cell Inclusions  Carbon Storage Polymers  Polyphosphate, Sulfur,  and Carbonate Minerals  Magnetic Storage Inclusions: Magnetosomes  Gas Vesicles  Endospores CARBON STORAGE POLYMERS Poly-B-hydroxyalkanoate (PHA) synthesized by cells when there is an excess of carbon and are broken down as carbon energy sources when conditions warrant Glycogen polymer of glucose; reservoir of both carbon and energy and is produced when carbon is in excess POLYPHOSPHATE, SULFUR, AND CARBONATE MINERALS Polyphosphate Granules formed when phosphate is in excess and can be drawn as a source of phosphate for nuclei acid and phospholipid biosynthesis when phosphate is limiting Sulfur Storage Products oxidized reduced sulfur compounds Carbonate Minerals Gloeomargarita: forms intracellular granules of bensonite MAGNETIC STORAGE INCLUSIONS: MAGNETOSOMES  enable some bacteria orient themselves within a magnetic field  biomineralized particles of of the magnetic iron oxides magnetite and greigite  Magnetotaxis: the process of migrating along Earth’s magnetic field GAS VESICLES  structures that confer buoyancy and allow cells to position themselves in regions of water column that best suit their metabolism (foating bacteria) Endospores  highly differentiated cells that are extremely resistant to heat, and harsh chemicals  function as survival structures and enable the organism to endure unfavorable growth conditions Endospore Formation and Germination (i.e. hibernation)  a vegetative cell is converted into a non growing, heat- resistant, and light- refractive structure  sporulation occurs when a key nutrient becomes limiting  an endospore can remain dormant for years but can convert back to vegetative cell rapidly  three steps: activation, germination, and outgrowth  activation: occurs when endospores are heated for several minutes at an elevated but sublethal temperature  germination: typically a rapid process; loss of refractility  outgrowth: involves visible swelling Structure of Bacterial Endospore  exosporium: thin protein covering  spore coats: layers of spore- specific proteins  cortex: loosely cross- linked peptidoglycan  core: contains core wall, cytoplasmic membrane, cytoplasm, nucleoid, ribosomes, and other cellular essentials  endosprotein: two functions--- bind tightly the dna to the core and to protect from potential damage such UV radiation, dry heat Cell Locomotion  Flagella, Archaella, and Swimming Motility  Gliding Motility FLAGELLA AND FLAGELLATION Bacterial Flagella  sing. flagellum  long- thin appendages; free at one end and anchored into the cell at the other end  flagella can rotate up to 1000 revolutions per second to support a swimming speed of up to 60 celllengths/ second Flagella Structure and Activity  filament: main part; composed of many copies of flagellin  hook: connects filament to flagellum motor  flagellum motor: has two main components: rotor and stator  rotor: central rod and the L, P, C, and MS rings  stator: consists of Mot proteins that surround the rotor and function to generate torque  rotation of flagellum occurs at the expense of the proton motive force ARCHAELLA  sing. archaellum  impart movement to the cell by rotating  filament is made up of several different proteins  overall structure bears resemblance to type IV pili   rotation is driven by hydrolysis of ATP  Methanocaldococcus swims nearly 500 cell lengths per second, which makes it the fastest organism on Earth! GLIDING MOTILITY  some bacteria are motile but lack flagella  these non swimming yet motile cells move by gliding  gliding bacteria are typically filamentous or rod- shaped in morphology  gliding process requires that the cells be in contact with a solid surface Eukaryotic Microbial Cells  The Nucleus and Cell Division  Mitochondria, Hydrogenosomes, and Chloroplasts  Other Eukaryotic Cell Structures THE NUCLEUS AND CELL DIVISION The Nuclues (control center)  contains the chromosomes of the eukaryotic cell  histones: proteins that tightly pack the DNA to form nucleosomes  nucleolus: site of rRNA synthesis Cell Division THE NUCLEUS AND CELL DIVISION  mitosis: unique to eukaryotic cells PMAT  during mitosis, chromosomes condense, divide, and are separated into two sets, one for each daughter cell  meiosis: converts a diploid cell into several haploid cells MITOCHONDRIA, HYDROGENOSOMES, & CHLOROPLASTS Mitochondiria (cellular respiration)  site of respiration (aerobic eukaryotic cells)  enclosed by a double membrane system Hydrogenosomes  present in anaerobic eukaryotic microorganisms  lack citric acid cycle enzymes and cristae  metabolism is strictly fermentative (no citric acid cycle enzymes)  oxidation of pyruvate to hydrogen, carbon dioxide, and acetate Chloroplasts  chlorophyll- containing organelles of phototrophic microbial eukaryotes that carry out photosynthesis  Feature/Structure Bacteria Archaea Eukarya Cell Type Prokaryotic Prokaryotic Eukaryotic Phospholipid bilayer with Phospholipid bilayer with Phospholipid bilayer Cell Membrane fatty acids linked via ester isoprene units linked via ether with fatty acids linked Composition bonds bonds via ester bonds Pseudomurein or other No peptidoglycan, Peptidoglycan (contains N- Cell Wall polysaccharides (contains N- may contain cellulose acetylglucosamine and N- Composition acetylglucosamine and N- (in plants) or chitin (in acetylmuramic acid) acetyltalosaminuronic acid) fungi) Peptidoglycan Yes, in most bacteria No No Presence Fatty acids linked by ester Isoprene units linked by ether Fatty acids linked by Lipid Composition bonds bonds ester bonds Gram-positive or Gram- Gram Staining negative based on Not applicable (no peptidoglycan) Not applicable peptidoglycan layer Present in some Capsules and Slime Present in some (polysaccharide (polysaccharide or protein Absent Layers or protein layer) layer) Cilia or flagella (whip- Flagella/Locomotion Flagella (rotation driven by Archaella (rotation driven by ATP like movement, Structures proton motive force) hydrolysis) powered by ATP) Present, aid in attachment Fimbriae and Pili Present, similar to bacteria Absent and conjugation Present (highly resistant Endospores Absent Absent dormant structures) Magnetosomes Present (some species) Absent Absent Present (membrane- Nucleus Absent Absent bound nucleus) Linear DNA, organized into Chromosomes Circular DNA Circular DNA chromosomes within a nucleus Mitochondria Absent Absent Present Present in photosynthetic Chloroplasts Absent Absent organisms (e.g., plants, algae) Respiration in Respiration or fermentation Respiration or fermentation (no mitochondria, Energy Generation (no mitochondria) mitochondria) photosynthesis in chloroplasts Capsules/Slime Present in some bacteria Present in some Absent Layers for protection/adhesion Mitosis and meiosis Cell Division Binary fission Binary fission (for sexual reproduction)  Feature/Structure Bacteria Archaea Eukarya Protein Synthesis 70S ribosomes 70S ribosomes 80S ribosomes (Ribosomes) Important Terms and Definitions 1. Morphology o Refers to the shape of a cell in microbiology (e.g., rod-shaped, spherical). 2. Surface-to-Volume Ratio (S/V Ratio) o The ratio of a cell’s surface area to its volume. Smaller cells have a higher ratio, allowing for faster nutrient exchange and waste elimination, contributing to faster growth and evolution. 3. Cytoplasmic Membrane o A phospholipid bilayer that surrounds the cytoplasm and separates it from the environment. It is responsible for selective permeability, protein anchoring, and energy conservation. 4. Peptidoglycan o A rigid polysaccharide that is the main component of the bacterial cell wall, providing structural strength and preventing osmotic lysis. It is composed of alternating units of N-acetylglucosamine (G) and N-acetylmuramic acid (M). 5. Gram-Positive Bacteria o Bacteria with a thick layer of peptidoglycan in their cell walls, which retain the purple-blue stain in Gram staining. They also produce teichoic acids. 6. Gram-Negative Bacteria o Bacteria with a thin layer of peptidoglycan and an additional outer membrane composed of lipopolysaccharides (LPS). The LPS contains Lipid A, which is toxic (endotoxin). 7. Lipopolysaccharide (LPS) o A component of the outer membrane of Gram-negative bacteria. It consists of a lipid component (Lipid A) and polysaccharides. Lipid A is responsible for the toxicity of the bacteria. 8. Periplasm o The space between the cytoplasmic membrane and the outer membrane in Gram-negative bacteria. It contains various proteins such as enzymes and transport proteins. 9. Capsules o A tightly organized, structured layer made of polysaccharides or proteins that surrounds some bacteria, protecting them from desiccation and helping them adhere to surfaces. 10. Slime Layer  o A more loosely attached and easily deformed layer than the capsule, which does not exclude particles and provides protection and adhesion. 11. Fimbriae o Short, hair-like structures that help bacteria attach to surfaces, form biofilms, and interact with host tissues. 12. Pili o Similar to fimbriae but longer, pili are involved in conjugation (the exchange of genetic material between bacteria) and also aid in adhesion. 13. Endospores o Highly resistant, dormant structures formed by certain bacteria (e.g., Bacillus species) under unfavorable conditions. Endospores allow bacteria to survive extreme environments. 14. Flagella o Long, thread-like appendages that allow bacterial motility. Bacterial flagella are driven by the proton motive force, allowing rotation. 15. Archaella o Similar to bacterial flagella but found in archaea. Their movement is powered by ATP hydrolysis. 16. Magnetosomes o Particles of magnetic iron oxides found in certain bacteria, allowing them to orient themselves in a magnetic field (a process known as magnetotaxis). 17. Pseudomurein o A polysaccharide similar to peptidoglycan found in the cell walls of some archaea, providing structural strength but resistant to destruction by lysozyme and penicillin. 18. Teichoic Acids o Acidic molecules found in Gram-positive bacteria that contribute to the structural integrity of the cell wall and bind metal ions for cell function. 19. Mitosis o A process of cell division in eukaryotes, where chromosomes condense, separate, and are divided into two identical daughter cells. 20. Meiosis o A form of cell division that produces haploid cells from a diploid cell, important for sexual reproduction in eukaryotes. 21. Hydrogenosomes o Organelles found in anaerobic eukaryotes that generate energy by fermenting pyruvate to hydrogen, carbon dioxide, and acetate. 22. Chloroplasts o Organelles in photosynthetic eukaryotes that carry out photosynthesis, containing chlorophyll. 23. Gliding Motility o A form of movement in some bacteria that lack flagella but move along solid surfaces using different mechanisms. 24. Conjugation o A process by which bacteria transfer genetic material between cells through specialized structures called sex pili.