BGY3100 Biology of Microorganism Lecture Notes (2024/2025) PDF

BGY3100 BIOLOGY OF MICROORGANISM Semester 1 2024/2025 Structure and Biology of Microorganisms Speaker DR. EDWARD ENTALAI BESI Department of Biology, Faculty of Science, UPM, Malaysia Member of IUCN Species Sur...

BGY3100 BIOLOGY OF MICROORGANISM Semester 1 2024/2025 Structure and Biology of Microorganisms Speaker DR. EDWARD ENTALAI BESI Department of Biology, Faculty of Science, UPM, Malaysia Member of IUCN Species Survival Commission (SSC) Content Structures and organelles in prokaryotic microbes Structures and organelles in eukaryotic microbes Prokaryotic cells vs Eukaryotic Cells Microbial locomotion Topic Learning Outcomes 1) Describe the basic structure of a typical prokaryotic microbes 2) Describe the basic structure of a typical eukaryotic microbes 3) Explain the different types of microbial locomotion  Basic Structures of Prokaryotic Cells Prokaryotes, found in both Domain Archaea and Bacteria Prokaryotes are unicellular organisms that lack organelles or other internal membrane-bound structures Prokaryotic cell structure: The features of a They do not have a nucleus typical prokaryotic cell are shown (Source: https://bio.libretexts.org/) Generally, they have a single chromosome: a piece of circular, double-stranded DNA located in an area of the cell called the nucleoid Most prokaryotes have a cell wall outside the plasma membrane  Basic Structures of Prokaryotic Cells Generally, they have a single chromosome: a piece of circular, double-stranded DNA located in an area of the cell called the nucleoid E. coli Nucleoids and Chromosomes. Bacterial chromosomes are located in the nucleoid, an area in the cytoplasm. (a) A color-enhanced transmission electron micrograph of a thin section of a dividing E. coli cell. The red areas are the nucleoids present in the two daughter cells. (b) Diagram illustrating the levels of chromosome organization within the nucleoid. [Source: (a) CNRI/SPL/Science Source, Image courtesy of The McGraw-Hill Companies, Inc.]  The Plasma Membrane of Prokaryotic Cells The plasma membrane is a thin lipid bilayer (6 to 8 nanometers) that completely surrounds the cell and separates the inside from the outside 6-8 nm Fluid Mosaic Model of Membrane Structure (Image courtesy of The McGraw-Hill Companies, Inc.)  The Plasma Membrane of Prokaryotic Cells Selectively-permeable nature - keeps ions, proteins, and other molecules within the cell, preventing them from diffusing into the extracellular environment, while other molecules may move through the membrane The general structure of a cell membrane is a phospholipid bilayer composed of two Plasma membrane structure: Archaeal phospholipids layers of lipid molecules differ from those found in Bacteria and Eukarya in two ways. First, they have branched phytanyl sidechains instead of linear ones. Second, an ether bond instead of an ester bond connects the lipid to the glycerol. (Image courtesy of The McGraw-Hill Companies, Inc.)  The Cell Wall of Prokaryotic Cells The cell wall is a protective layer that surrounds some cells and gives them shape and rigidity It is located outside the cell membrane and prevents osmotic lysis (bursting due to increasing volume) The chemical composition of the cell walls varies between archaea and bacteria It also varies between bacterial species Bacterial cell walls contain peptidoglycan composed of polysaccharide chains that are cross-linked by unusual peptides containing both L- and D-amino acids (e.g., D- Gram-positive bacterial cell wall (Image courtesy of The Willey JM: Prescott, Harley, & glutamic acid and D-alanine) Klein’s Microbiology, 7th edition. McGraw-Hill, 2008)  Basic Structures of Eukaryotic Cells Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes Many eukaryotic microbes does not have a cell wall However, unlike prokaryotic cells, eukaryotic cells have: ❑ a membrane-bound nucleus ❑ numerous membrane-bound organelles (including the endoplasmic reticulum, Golgi apparatus, chloroplasts, and mitochondria) The Structure of Two Representative Eukaryotic Microbes. Illustrations of (a) a yeast cell (fungus) and (b) the ❑ several rod-shaped flagellated protist Peranema. chromosomes (Image courtesy of The McGraw-Hill Companies, Inc.)  The Plasma Membrane of Eukaryotic Cells Eukaryotic membranes are similar in structure and function to bacterial membranes but differ in lipid composition Plasma membrane of eukaryotes is a lipid bilayer (phospholipid) composed of a high Examples of Eukaryotic Membrane Lipids. (a) proportion of Phosphatidylcholine, a phospholipid. (b) Sphingomyelin, a sphingolipids and sphingolipid. The amine group is highlighted as this differentiates a sphingolipid from a phospholipid. (c) Cholesterol, a sterol. sterols (Image courtesy of The McGraw-Hill Companies, Inc.) In phospholipids and sphingolipids, the fatty acids are attached to glycerol with ester links  The Cell Wall of Eukaryotic Cells Eukaryotic microbes that have cell walls include photosynthetic protists (algae), cysts made by many types of protists, and most fungi Chemical composition of the cell walls of eukaryotic microbes varies Algal cell walls usually have a layered appearance and contain large quantities of the The cells of Chlamydomonas polysaccharides cellulose and pectin Fungal cell walls are rigid Usually chitin and glucan (a glucose polymer different from cellulose) are present.  The Nucleus & Its Structures One of the main differences between prokaryotic and eukaryotic cells is the NUCLEUS As previously discussed, prokaryotic cells lack an organized nucleus while eukaryotic cells contain membrane-bound nuclei (and organelles ) that houses chromatin (cell’s DNA + Proteins) in nucleoplasm ‘ ’ Eukaryotic nucleus: The nucleolus is a condensed region of chromatin where ribosome synthesis occurs. The boundary of the nucleus is called the nuclear envelope. It consists of two phospholipid bilayers: an outer membrane and an inner membrane. The nuclear membrane is continuous with the endoplasmic reticulum. Nuclear pores allow substances to enter and exit the nucleus. (Source: https://bio.libretexts.org/)  The Nucleus & Its Structures The nuclear envelope is a double- membrane structure that constitutes the outermost portion of the nucleus Both the inner and outer membranes of the nuclear envelope are phospholipid bilayers The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and cytoplasm. The Nucleus and Nuclear Pore Complex (Image courtesy of The McGraw-Hill Companies, Inc.) In the nucleus of each cell, the DNA molecule is packaged into thread-like structures called chromosomes Are chromosomes made of DNA? Or vice versa? Source: U.S. National Library of Medicine (https://www.nlm.nih.gov/)  Other Membrane-Bound Organelles of Eukaryotic cells Mitochondria are oval- shaped, double membrane organelles that have their own ribosomes and DNA - called the “energy factories” for making adenosine triphosphate (ATP) Endoplasmic reticulum modifies proteins and synthesizes lipids The Structure of Two Representative Eukaryotic Microbes. (Image courtesy of The McGraw-Hill Companies, Inc.)  Other Membrane-Bound Organelles of Eukaryotic cells Golgi apparatus is where the sorting, tagging, packaging, and distribution of lipids and proteins takes place Vesicles and vacuoles are membrane-bound sacs that function in storage and transport All of these organelles are found in each and every eukaryotic cell The Structure of Two Representative Eukaryotic Microbes. (Image courtesy of The McGraw-Hill Companies, Inc.)  Chromosome and DNA Eukaryotic cells have a true nucleus, which means the cell’s DNA is surrounded by a membrane In prokaryotes, DNA is organized into a single circular chromosome In eukaryotes, chromosomes are linear structures Prokaryotic DNA vs Eukaryotic DNA Source: https://www.majordifferences.com/ Eukaryotic chromosome vs Prokaryotic chromosome The graphical representation of the eukaryotic chromosome and prokaryotic chromosome. Note: the eukaryotic chromosome mentioned here not a plasmid DNA. (Source: https://geneticeducation.co.in/) Eukaryotic DNA vs Prokaryotic DNA The graphical representation of the eukaryotic DNA and prokaryotic DNA. (Source: https://geneticeducation.co.in/)  Eukaryotic DNA vs Prokaryotic DNA Prokaryotes have a circular single chromosome, whereas eukaryotes tend to have rod-shaped chromosomes (more than one) with the DNA wrapped around proteins called histones. (Source: https://the-science-of-life.blog/2023/04/10/prokaryotes-and-eukaryotes/)  Does plasmid really absent in an eukaryotic cell? “Plasmids (linear) are also found in higher organisms such as yeast and fungi. The 2 micron circle of yeast is a well- known example that has been modified for use as a cloning vector.” Clark, D. P., Pazdernik, N. J. & McGehee, M. R. (2019). Molecular Biology (3rd Edition). Academic Cell. 991 pp. DOI: https://doi.org/10.1016/C2015-0-06229-3 “The first plasmid detected in a eukaryote was discovered in 1967 in Saccharomyces cerevisiae (brewers yeast), the ‘2 μm DNA’. Plasmids have also been found in Zea mays (corn/maize), Podospora anserina (a filamentous fungus) and other fungi.” Meinhardt, F., Kempken, F., Kämper, J., & Esser, K. (1990). Linear plasmids among eukaryotes: fundamentals and application. Current genetics, 17(2), 89-95. DOI: 10.1007/BF00312851  Prokaryotic cells vs Eukaryotic cells Feature Prokaryotes Eukaryotes Size All unicellular, smaller – 1.5 um in diameter Unicellular/multicellular Membrane-bound No membrane-bound organelles Contain many membrane- organelles bound organelles Nucleus No nucleus, but have a free-floating Membrane-bound nucleus chromosome Plasmids Some prokaryotes have both small circular Fungi, yeast and some higher DNA (plasmids) in addition to the plants have linear plasmids bacterial chromosome Ribosomes 70s 80s Cell Surface Membrane Present Present Cell Wall Cell wall made out of peptidoglycan and Cell wall made of cellulose glycoproteins and chitin (fungi) Capsule Certain types of bacteria can also have a No capsule protective capsule surrounding the cell walls called lipopolysaccharide layer Motility Many prokaryotes are motile. Have cilia Some eukaryotes have cilia and flagella to help them swim. Many and flagella to drive bacteria have pili (hair-like processes) that movement help with motility and communication with other bacteria  Microbial Locomotion ‘Move in Response to Environmental Conditions’ Microorganisms, particularly bacteria and protists, have developed various modes of locomotion that enable them to move through their environment The way these microbes move/locomotion is essential for processes like nutrient acquisition, evasion from predators, and colonization of surfaces Five (5) major methods of movement by prokaryotic cells that have been observed: Prokaryotic Locomotion (Flagellar movement)  Prokaryotic Locomotion 1) Swimming: Bacteria Many bacteria possess flagella. The filament of a bacterial flagellum is a rigid helix. The cell moves when this helix rotates like a propeller on a boat Bacteria also have fine, hairlike-appendages that are thinner and shorter than flagella, called pili/fimbriae, involved in motility Flagella and Fimbriae. The long flagella and The Direction of Flagellar Rotation numerous shorter pili are Often Determines the Way a evident in this SEM of Bacterium Moves. Parts (a) and (b) Proteus vulgaris. describe the motion of bacteria with (Image courtesy of Thomas monotrichous, polar flagella. Parts (c) Deerinck, NCMIR/Science Source) and (d) illustrate the movements of bacteria with peritrichous flagella. (Image courtesy of The McGraw-Hill Companies, Inc.) (Source: https://stock.adobe.com/my/search?k=amphitrichous)  Prokaryotic Locomotion 2) Swarming: Bacteria Swarming motility is a type of group behavior in which cells move in unison across a moist surface Swarming requires flagella, and most swarming bacteria have peritrichous flagella Also required is the production of surfactant, a class of chemical that Swarming bacteria often produce lowers the surface tension of the distinctive patterns on a solid growth substrate to facilitate movement. medium. These bacterial cells swarmed from the center of the plate and produced a branching pattern called dendrites. Dr. Daniel Kearns (Image courtesy of The McGraw-Hill Companies, Inc.)  Prokaryotic Locomotion 3) Spirochete motility: Bacteria Spirochete motility is best described as the undulation of the entire cell Motility is conferred by periplasmic flagella that arise from each end of the cell and wind around the cell but are inside the cell wall Spirochete Flagella. (a) One or more These endoflagella rotate like the flagella arise from each end of the cell. These intertwine and wind around the cell, external flagella of other usually overlapping in the middle. (b) bacteria, causing the corkscrew- Electron cryotomographic image of the shaped outer membrane to spirochete Treponema denticola showing three flagella arising from the tip of the cell. rotate and move the cell through Jacques Izard the surrounding medium. (Image courtesy of The McGraw-Hill Companies, Inc.) Prokaryotic Locomotion (NON-flagellar movement)  Prokaryotic Locomotion 4) Twitching motility: Bacteria Twitching and gliding motility occur when cells are on a solid surface. However, unlike swarming, neither involves flagella Twitching motility is characterized by short, intermittent, jerky motions of up to several micrometers in length and is normally seen on moist surfaces Type IV pili alternately extend and retract to move cells during twitching motility. 5) Gliding motility: Bacteria In contrast to the jerky movement of twitching motility, gliding motility is smooth and requires no appendages It is only when the full set of protein complexes aligns across the entire cell envelope that they can exert the mechanical force to propel the cell.  Eukaryotic Locomotion (Flagellar and Ciliary movements)  Eukaryotic Patterns of Flagellar Movement. Locomotion To propel an organism, flagella (left illustration) move either from the base of the flagellum to its tip or in the opposite Eukaryotic Flagella and Cilia: direction. Flagella and cilia are the prominent external structures observed on eukaryotic cells – associated with motility Cilia are short hairlike structures, shorter than flagella, long whiplike filaments (Image courtesy of The McGraw-Hill Companies, Inc.) Flagellar and ciliary movement Patterns of Ciliary Movement. takes the form of waves The beat of a cilium (right illustration) may be divided into two phases. In the effective stroke, the cilium moves through the surrounding fluid like an oar, thereby propelling the organism. This is followed by a recovery stroke in which the cilium bends and returns to its initial position.  Chemotaxis The movement of cells toward chemical attractants or away from chemical repellents is called chemotaxis Chemotaxis is readily observed in Petri dish cultures Bacteria placed in the center of a dish of semisolid agar containing an attractant will swim outward following the attractant gradient they have created - resulting an Schematic representation showing chemotactic expanding ring of bacteria responses of Campylobacter jejuni to chemoattractant (serine), chemorepellent (arginine), When a disk of repellent is and a mix of chemoattractant/chemorepellent placed in a Petri dish of (serine/arginine). semisolid agar and bacteria, the bacteria swim away from (Source: Elgamoudi, B.A., Ketley, J.M., Korolik, V. 2018. New approach to distinguishing chemoattractants, the repellent, creating a clear chemorepellents and catabolised chemoeffectors for zone around the disk. Campylobacter jejuni. Journal of Microbiological Methods, 146, 83-91. DOI: 10.1016/j.mimet.2018.02.008) Viral Structure Fungi Structure Envelope Sporangia:  Double lipid layer holding the cells Spore producing body. genetic material. Sporangiophore: Glycoproteins Filamentous stalk on which the These serve 2 purposes sporangium forms.  Anchor the virus to the host cell. Rhizoids:  Transport genetic material from the The sub-surface hyphae are specialized virus to the host cell. for food absorption. Nucleic acid  Either DNA or RNA material, but virus cells rarely contain both. Most viral cells contain RNA material. 34 QUIZZES  REFERENCES 1) Berkeley, M.J. (1846). Observations, botanical and physiological, on the Potato Murrain. The Journal of the Horticultural Society of London, 1, 9-34. (reprinted as Phytopathological Classics number 8 by the American Phytopathological Society, 1948). 2) Clark, D. P., Pazdernik, N. J. & McGehee, M. R. (2019). Molecular Biology (3rd Edition). Academic Cell. 991 pp. DOI: 10.1016/C2015-0-06229-3 3) Elgamoudi, B. A., & Korolik, V. (2022). A Review of the Advantages, Disadvantages and Limitations of Chemotaxis Assays for Campylobacter spp. International Journal of Molecular Sciences, 23(3), 1576. DOI: 10.3390/ijms23031576 4) Elgamoudi, B.A., Ketley, J.M., Korolik, V. 2018. New approach to distinguishing chemoattractants, chemorepellents and catabolised chemoeffectors for Campylobacter jejuni. Journal of Microbiological Methods, 146, 83-91. DOI: 10.1016/j.mimet.2018.02.008 5) Meinhardt, F., Kempken, F., Kämper, J., & Esser, K. (1990). Linear plasmids among eukaryotes: fundamentals and application. Current genetics, 17(2), 89-95. DOI: 10.1007/BF00312851 6) Willey, J., Sandman, K. & Wood, D. (2023). Prescott’s Microbiology (12th ed.). McGraw-Hill Education. 7) Woese, C.R., Kandler, O., & Wheelis, M.L. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. 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