Micro Lecture 2 2024 Structure, Physiology, and Biochemistry of Microorganisms PDF

Lecture 2 Structure, Physiology and Biochemistry of Microorganisms Dr. Claire Atkinson  Today Lecture 2 Q&A Break Quiz Tutorial - lab book PollEv.com/valentinacap916  Learning objectives By the end of th...

Lecture 2 Structure, Physiology and Biochemistry of Microorganisms Dr. Claire Atkinson  Today Lecture 2 Q&A Break Quiz Tutorial - lab book PollEv.com/valentinacap916  Learning objectives By the end of the lecture you should be able to answer the following questions What is the cell structure and function ? What are the nutrition, culture and metabolic requirements of microorganisms? How do microbes grow? What is metabolic diversity? Revision Revision Revision  Cell Theory The cell is the basic structural and functional unit of all living organisms It is the smallest form of life All life is composed of 1 or more cells All cells come from preexisting cells Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition Alberts. Molecular Biology of the cell. (2014)  Prokaryotic vs. Eukaryotic Shared Properties Methods of reproduction by cell division, binary fission, mitosis, or meiosis Presence of DNA and RNA for protein synthesis Cellular metabolism organized in specific metabolic pathways Responses to external and internal stimuli to changes in temperature, pH, and nutrient levels All living cells are surrounded by a plasma membrane VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Prokaryotic vs. Eukaryotic Prokaryotic cells No nucleus No membrane-bound cell organelles Eukaryotic cells Nucleus Membrane-bound cell organelles VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Glycocalyx Extracellular matrix that surrounds cells Normally a network of polysaccharides, but the composition varies. Produced by some bacteria and epithelial cells Function: Cell-to-cell communication Binding of cells to the extracellular matrix Protection from pathogens Modulation of the immune response Attachment site for bacteria to inert surfaces (formation of biofilms). In bacteria the glycocalyx can form capsules which protect the bacteria against phagocytosis (being eaten) by white blood cells above Klebsiella adding to their pathogenicity pneumoniae below Streptococcus pneumoniae Pathogenicity = the ability of an organism to cause disease VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Cell Wall A cell wall is located below the glycocalyx surrounding the plasma membrane Bacteria, archaea, fungi, plants, and algae typically have cell walls, but not animal cells! Different chemical composition- and this can be used to differentiate between organisms Protect interior of cells from physical movements and hostile environments Contributes to the shape of the organism Algae Archaea Cellulose and a variety of glycoproteins Cell wall does not contain peptidoglycan Polysaccharide inclusions used in algal taxonomy Some contain pseudopeptidoglycan Plant cells Fungi Polysaccharides, mostly cellulose, Cellulose, glucosamine, and chitin hemicellulose, and pectin Not all fungi have cell walls  Bacterial Cell Wall Maintains the shape of bacteria Peptidoglycan Mixed polymer of sugars cross linked with peptides Cross linking peptidoglycan gives the cell wall its strength Identification of bacteria Gram-positive/ Gram-negative staining (lab 1) Differences in the cell wall composition are important in selecting the appropriate antimicrobial drug VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier. Gram+ Cell Wall Gram- Cell Wall Thick peptidoglycan layer (20 to 80 nm) Thin peptidoglycan layer (5 to 10 nm) External to the plasma membrane More complex Contains teichoic acid and lipoteichoic acid Outer membrane that provides cover and is anchored to Small Periplasmic space between plasma membrane the lipoprotein molecules of the peptidoglycan layer and cell wall The outer membrane is similar to plasma membrane Large periplasmic space *Basis of Gram staining Composition helps identification VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Gram staining Gram staining was invented in the 1880s by Danish scientist Hans Christian Gram. A bacterium’s ability to hold onto a stain is dependent on the structure of their cell wall - Gram negative organisms predominate in the bowel (eg. E. coli and other coliforms, Bacteroides species etc) - Gram positives (Staphs. and streptococci) predominate on the skin, upper respiratory tract and oropharynx. - Gram negative bacteria generally more resistant to antibiotics http://static.diffen.com/uploadz/0/0e/cell-wall-gram-bacteria.png  Staining in microbiology Mosby items and derived items © 2010 by Mosby, Inc., an affiliate of Elsevier Inc. Mosby items and derived items © 2010 by Mosby, Inc., an affiliate of Elsevier Inc. Gram staining method Exotoxin and Endotoxin  Surface Appendages Present in both prokaryotic and eukaryotic cells functions include motility, absorption and attachement Eukaryotes: Cilia, microvilli, flagella Microvilli Absorption/secretion/adhesion/motility Cilia Cilia and eukaryotic flagella are structurally identical —cilia are shorter in movement on surface; flagella are longer and move the whole cell. Move fluid over the surface (goblet cells) Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Surface Appendages Prokaryotes: pili (fimbriae) Pili, are hair-like appendages found on the surface of many bacteria and archaea. Made up of protein subunits called Pili have several functions, including: Cell-to-cell interactions Motility DNA uptake. Adhesion There are different types of pili, including ordinary pili and sex pili Ordinary pili are found all over the bacterial cell surface, while sex pili (pilus) are longer and thicker and each bacterial cell can have up to four of them Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier. Bacterial Flagella Surface Appendages Long helical filaments about 12 to 30 nm in diameter 3 parts : Long filament external to the cell surface Hook located at the end of the filament Basal body to which hook is anchored Basal body consists of a rod and one or two pairs of discs Structure of a prokaryotic flagellum- Gram negative bacterium VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier. Types of Bacterial Flagella Mono = one Lopho = crest of tuft on head Amphi = on both sides Amphibian: An animal that lives in both water and on land Peri = all around ‘ perimeter’  Organisation: Biofilms Collection of surface-associated microbes Enclosed by extracellular mostly polysaccharide matrix Can include non-cellular material—mineral crystals, corrosive particles, blood, and other substances First colony adheres to surface and anchor permanently if not removed immediately New incoming cells then attach Concern in the food industry Biofilm grows through cell division and recruitment Cleansers used on surfaces will kill single cells Cell’s behavior changes with thickness of the film Biofilms provide ideal environment for plasmid exchange Positive use: bioremediation of contaminated soil or water They form on a variety of surfaces Indwelling medical devices, aquatic systems, etc. VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Cell Organelles- ribosomes Ribosomes: Proteins (ribosomal proteins) and RNA (rRNA) Eukaryotes— 80s Prokaryotes— 70s Production of proteins for cell maintenance and repair (translation) Alberts, B., Et al Molecular Biology of the Cell. 6th Ribosomal subunit – used to ID bacteria and fungi at molecular level Bacteria 16S Fungi 18S VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier. Factors Influencing Microbial Growth Nutritional requirements Temperature Osmotic pressure Other atmospheric conditions Metabolic diversity Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition  Metabolic diversity All living things undergo metabolism and may be classified according to: 1. The method by which they obtain their carbon 2. The method by which they derive their energy 3. The method by which they generate reducing equivalents Carbon source Autotrophs: Organism that can biosynthesize all cell material from CO2 Heterotrophs: Organism that can biosynthesize all cell material from complex organic substances Energy source Phototroph: uses light as a source of energy (photosynthetic bacteria and plants) Lithotroph: uses energy derived from oxidation of minerals Organotroph: uses energy derived from the metabolism of organic compounds from complex (polysaccharides) to smaller (glucose or pyruvate).  Nutritional Requirements Photoautotrophs Photoheterotrophs Use sunlight as the energy source Use sunlight for energy Use CO2 as their carbon source Use organic compounds as carbon source Photosynthetic bacteria, algae, green plants Chemoautotrophs Chemoheterotrophs Use chemical compounds as the source of Use organic compounds for both the source energy of energy and a carbon source Use CO2 as their carbon source Mosby items and derived items © 2010 by Mosby, Inc., an affiliate of Elsevier Inc.  Other Nutritional Requirements Nitrogen Some bacteria can obtain nitrogen from inorganic compounds such as nitrates Sulfur and phosphorus Can be met by organic compounds or inorganic salts of sulfates, sulfides, and thiosulfates Minerals Required in trace amounts Slonczewski J.L,.Microbiology: An Evolving Science. 5th Edition  Temperature Psychrophiles (cryophiles) Cold-loving—can grow at 0° C or lower Thermophiles Optimal growth around 15° C Heat-loving organisms Arctic and Antarctic regions Grow best at temperatures of 45°-60° Psychrotrophs Hyperthermophiles Grow very slow at 0° C but have an optimal growth range of 25° C to 30° C Heat-loving organisms Abundant in nature Grow best at temperatures of 65° C or higher Hot springs, deep sea hydrothermal vents, tropical soil composts (rotting), hay stacks Mesophiles Optimal growth in moderate temperatures Generally between 25° C and 40° C Habitat: soil, human body, animals Most bacteria fall into this classification Brock Biology of Microorganisms, Global Editiony Michael T. Madigan; Kelly S. Bender; Daniel H. Buckley; W. Matthew Sattley; David A. Stahl 2018  Temperature Psychrotrophs – food spoilage in a fridge Listeria monocytogenes Food hygiene danger zone, most bacteria will grow in this zone Brock Biology of Microorganisms, Global Editiony Michael T. Madigan; Kelly S. Bender; Daniel H. Buckley; W. Matthew Sattley; David A. Stahl 2018  Osmotic Pressure Microorganisms with cell walls can withstand some osmotic pressure— osmotolerant Osmophiles—require high solute concentration in the environment for optimal growth Obligate Present in salt lakes (Halococcus and Halobacterium) Oceans at 3.5% NaCl Facultatives can live up to 10% NaCl (Staphylococcus aureus and Enterococcus faecalis) Most microbes do not tolerate hypertonic environments Mosby items and derived items © 2010 by Mosby, Inc., an affiliate of Elsevier Inc.  Hydrostatic Pressure Pressure that a fluid exerts in a confined space, this pressure is applied to aquatic microorganisms because of the weight of water surrounding them. Barotolerant Microbes that can survive in increased hydrostatic pressures. Halomonas salaria Up to 200- 600 atmospheres Barophiles Grow best under high hydrostatic pressure Occur only in the deepest part of oceans Mosby items and derived items © 2010 by Mosby, Inc., an affiliate of Elsevier Inc.  Atmospheric conditions - Cellular Respiration Anaerobic cellular respiration:In the absence Aerobic cellular respiration: Requires O2 of O2 Aerobic vs. anaerobic bacteria venn diagram Stock Illustration | Adobe Stock  Fermentation Fermentation is a way bacteria can produce ATP to meet their energy needs without oxygen A single molecule of glucose is broken down into 2 molecules of pyruvate), as well as additional fermentation reactions that produce a variety of end products (acids, alcohols, gases). 1.22: Fermentation - Biology LibreTexts  Fermentation Fermentation is a way bacteria can produce ATP to meet their energy needs without oxygen A single molecule of glucose is broken down into 2 molecules of pyruvate), as well as additional fermentation reactions that produce a variety of end products (acids, alcohols, gases). 1.22: Fermentation - Biology LibreTexts  Atmospheric Conditions Aerotolerant anaerobes Obligate aerobes Can grow in the presence of oxygen but Grow only in the presence of oxygen cannot use oxygen for energy requirements Aerobic cellular respiration Fermentation only (obligate fermenters) Obligate anaerobes Facultative anaerobes Grow only in the absence of oxygen Grow either in the absence or presence of Inhibited or killed by the presence of oxygen oxygen Aerobic respiration with oxygen—fermentation in the absence of oxygen Microaerophiles Require a low concentration of oxygen Approximately 2% to 10% less than atmospheric oxygen Capneic Require more carbon dioxide than present in regular atmosphere  Atmospheric Conditions * Humans Pathogen/ Nonpathoge Aerotolerant anaerobes Obligate aerobes Can grow in the presence of oxygen Grow only in the presence of oxygen Fusobacterium spp/ Bifidobacterium spp Mycobacterium leprae/ Pseudomonas fluorescens Obligate anaerobes Facultative anaerobes Grow only in the absence of oxygen Grow either in the absence or presence of Clostridium botulinum/ Clostridium oxygen sporogens Escherichia coli/ Staphylococcus Microaerophiles epidermidis Require a low concentration of oxygen Campylobacter jejunae/ Thiovuhlum majurs Capneic Require more carbon dioxide than present in regular atmosphere Neisseria gonorrhoeae/ Mannheimia succiniciproduccccens Oxygen requirements  pH pH of natural environments ranges from approximately 0.5 in acidic soils and approximately10.5 in alkaline lakes Optimal pH range varies for microbes Acidophils—best pH below 5.5 Helicobacter pylori Neutrophils—range: 5–8 Alkaliphiles—best pH above 8.5 Vibrio cholerae Many archaea are thermoacidophiles Brock Biology of Microorganisms, Global Editiony Michael T. Madigan; Kelly S. Bender; Daniel H. Buckley; W. Matthew Sattley; David A. Stahl 2018  Helicobacter pylori Cause peptic ulcers by weakening the gastric mucosa Allows acid to penetrate the tissue and aids bacteria spread Produces gastric urease which allows the organism to colonize the acidic stomach Gastric urease serves as a biomarker for the presence of H. pylori Molecular Biology  Molecular Biology Follows the central dogma Flow of genetic information DNA  RNA Protein DNA Replication Prokaryotic – in cytoplasm Eukaryotic – in nucleus Transcription Prokaryotic – in cytoplasm Eukaryotic – in nucleus Translation- Translation of mRNA into amino acids via transferRNA in the ribosome Prokaryotic – in cytoplasm Eukaryotic – Cytoplasm and endoplasmic Reticulum (ER)  Replication DNA replication is the process by which a cell makes an identical copy of its DNA. This process is performed at the beginning of every cell division (S phase) Each consisting of a new and an old strand The whole DNA is replicated only once every cycle. Bacteria—circular DNA Plasmids- small circular pieces of DNA VanMeter, K.C, VanMetter W.G and Hubert RJ. Microbiology for the healthcare professional. Elsevier.  Binary Fission Form of asexual reproduction – primary method of reproduction in bacteria Single cell separates into two identical daughter cells, each containing the identical copy of the parental DNA Bacterium elongates, followed by DNA replication Central transverse septum forms—divides cell into two daughter cells Similar to mitosis in multicellular organisms but with a different purpose multicellular organisms, mitosis causes the organism to grow larger or replaces old cells with new ones. In bacteria, cell division is how the bacteria reproduce and add more bacteria to the population Alberts, B., Et al Molecular Biology of the Cell. 6th Translation/Transcription as a drug target Please note you do not need to know this in detail for the exam. You will learn about antimicrobials in the last lecture and this is covered in L6 Clinical Micro!  Alberts, B., Et al Molecular Biology of the Cell. 6th  More to follow in following lectures Questions BREAK  MCQ Questions True of false? Eukaryotic cells do not have a nucleus Prokaryoric cells are smaller than eukaryotic cells The cell is the smallest form of life The glycocalyx is found inside the plasma membrane Eukaryotes have a cell wall True of false? Gram positive bacteria have a thick peptidoglycan layer Gram negative bacteria have a thick peptidoglycan layer True of false? Flagellum Are membrane extensions Can move Are also called cilia Can be up to 50nm in diameter  Group depending on the Types of Bacterial Flagella D A B C F E G Binary fission is a form of reproduction used by Viruses Bacteria Animal cells Plants cells