BIOL121 Lecture 1 2023-24 (1) PDF

Welcome to BIOL121: Impact of Microbes • • Module organiser: Muhammad Munir Teaching staff: Stephen Roberts, Jackie Parry, Roger Pickup • Overall and general aims of the module To illustrate the diversity of viruses, prokaryotes and fungi and their impact on life on earth • Specific aims • On c...

Welcome to BIOL121: Impact of Microbes • • Module organiser: Muhammad Munir Teaching staff: Stephen Roberts, Jackie Parry, Roger Pickup • Overall and general aims of the module To illustrate the diversity of viruses, prokaryotes and fungi and their impact on life on earth • Specific aims • On completion of this module a student should be able to: ☼ Outline beneficial and detrimental impacts of microbes. ☼ Outline the diversity of prokaryote lifestyles. ☼ Discuss the dynamics of bacterial growth. ☼ Describe the link between cell structures and the ability of bacteria to cause disease. ☼ Describe the structure of viruses and the ways they infect bacterial, plant and animal cells. ☼ Identify important protists, describe their life-cycles and outline their ecological roles. ☼ Describe the diversity, pathogenicity and exploitation of fungi. Module Overview Lectures are organised in subject blocks with all content relating to each lecture grouped by lecture The minimum expectation for all lectures on Moodle is: 1. Lecture slides/handout 2. Recording of the lecture recording from Panopto Then will be 1 Workshop and 3 Practical Visit: Moodle site for the Module Biol121: Impact of Microbes What is microbiology? • The study of organisms - too small to be seen clearly by the unaided eye, i.e. microorganisms (microbes): o Viruses: non-cellular o Prokaryotes: Bacteria/Archaea o Eukaryotes: Protists, Algae, Fungi In contrast to animal and plant, most microorganisms carry out their life processes independent of other cells In nature, microorganisms exist in populations • Mixed populations (microbial communities as seen in the image). • Bacteria interact with each other and with other organisms (competition/cooperation). • Activities – alter their environment. • Most of the biomass on earth is microbial. • An estimate of the total number of microbial cells on earth is 5  1030 cells. Disease • Infectious diseases are caused by pathogens • Vulnerable: LMIC, children • Still the major cause of death in many lower income countries (malaria, tuberculosis, cholera, COVID-19) • Controlled by combination of vaccination, antibiotics, personal hygiene, drastic control measures • Newly emerging diseases (COVID-19, Influenza, Monkeypox, Nipah etc.) Infographic about 20th century diseases Impact of microorganisms on humans • We are a human-centred world. • Microorganisms can be both beneficial and harmful to humans. • We tend to emphasize harmful microorganisms (as infectious disease agents = pathogens), but most microorganisms are beneficial. • Earth systems cannot exist with microorganisms Pros and Cons of Microbes: Food • • • Benefits: Food materials that benefit from or even require microbiological activity: yogurt, cheese, vinegar, sauerkraut, certain sausages, beer, wine … • Problems: Microbes grow well in food fit for human consumption: preservation to avoid – Food spoilage – Food borne disease Impact of Microbes BIOL121 Introduction and overview of prokaryotes and their cell structure Recommended reading : Campbell chapter 27 (unit 5 The Diversity of Life) Also Brock, chapter 2 Prof. Roger Pickup [email protected] Learning Objectives After this lecture and the further reading you should be able to: • • • • • • • • Distinguish the 3 domains List the relative sizes of microbes Describe basic bacterial cell structure Cell shapes and clusters Understand the Gram stain Name the main elements for movement Describe the main bacterial cell contents Name the characteristics of endospores Culture plate of bacteria (lake water) 100 ul of sample spread at a dilution of 10-1: Equates to Approx 60 bacteria x 10 (dilution) x 10 (1/10 of a ml) = 6000 culturable bacteria per ml Direct microscopic count of bacteria from lake water • Using microscopic direct counting method: 106 bacteria per ml = 1,000,0000 We cannot culture all bacteria form a sample • Lake water : 1000/1,000,0000 = 1/1000 • Therefore, we do not know the true diversity of a sample by culture. ??????? Three domains Prokaryotes “bacteria” Disease causing prokaryotes are all ‘Domain Bacteria’ Campbell Biology 11th ed. p535 Three domains • Eukaryote: • An organism that consists of one or more cells each of which has a nucleus and other well-developed intracellular compartments. • Eukaryotes include all organisms except bacteria, viruses, and certain (blue-green) algae which, by contrast, are prokaryotes. • Eukaryotes include fungi, animals, and plants as well as some unicellular organisms. Three domains: Bacteria • Bacteria are a type of biological cell. • They constitute a large domain of prokaryotic microorganisms. • Typically, a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. • Bacteria were among the first life forms to appear on Earth and are present in most of its habitats. Three domains: Archaea • are similar to bacteria in size and simplicity of structure but radically different in molecular organization. • constitute an ancient group which is intermediate between the bacteria and eukaryotes. • Characteristics: – (1) the presence of characteristic tRNAs and ribosomal RNAs; – (2) the absence of peptidoglycan cell walls, with in many cases, replacement by a largely proteinaceous coat; – (3) the occurrence of ether linked lipids built from phytanyl chains – (4) in all cases known so far, they occur only in unusual habitats. Properties of all cells From Brock Typical microbial cell sizes • Viruses 0.01-0.2 μm • Bacteria 0.2- 5 μm • Eukaryotes 5-100 μm Bacteria on human epithelial cell • Yeast 5-10 μm • Algae 10-100 μm • Protists 50 -1000 μm 1 μm = 0.001mm = 0.000001m = 1 x 10-6 m Importance of cell volume • Higher surface/ volume ratio of smaller cells leads to faster rate of nutrient exchange compared to large cells • Smaller cells = faster growth • Evolution/mutation rates, more cells/growth > more mutations may lead to greater evolutionary possibilities Eukaryotic cell structure Nucleus – membrane enclosed (contains DNA) Endoplasmatic Reticulum (ER; protein glycosylation, membrane factory, lipid synthesis) Cytoplasmic membrane (separates cytoplasm from the outside) Cell wall (plants & fungi; gives structural strength) Mitochondrion (respiration) Golgi apparatus (modifies, stores, routes products of the ER) Chloroplast (plants & algae; photosynthesis) Ribosomes (protein synthesis) Diagram of a eukaryotic cell (simplified!) Bacterial cell structure Nucleoid Flagellum S-layer Ribosome Inclusions Cytoplasmic membrane Capsule/Slime layer Cell wall Membrane structure in bacteria - + Functions of the bacterial cell membrane Barrier function: separation of cell from its environment Selectively permeable barrier – controls movement of molecules into or out of the cell (transport proteins) • site of respiration and photosynthesis • energy conservation (proton motive force) Active transport Dilute nutrients still taken up efficiently Transport vs diffusion. In transport, the uptake rate shows saturation at relatively low external concentrations. Bacterial cell structure Cell wall • determines & maintains the shape of bacteria • protects the cell from osmotic lysis Vibrio Bacterial cell clusters diplococci Neisseria meningitidis streptococci clump of cocci Streptococcus pneumoniae Staphylococcus aureus Gram-positive cell wall Gram-negative cell wall Mycobacterial/Archaeal cell walls The Gram Stain Bacteria are divided into two major groups based on their response to the ‘Gram-stain’ Gram positive bacteria Peptidoglycan structure • Peptidoglycan only found in Bacteria. • Cell wall antibiotics such as Penicillin prevent cell wall formation and are bacteriolytic • LYSOZYME breaks G-M bonds. ‘bursts the cell’ • Defence against bacteria G = N-Acetylglucosamine M = N-Acetylmuramic acid MG polymer chains linked via peptide bridges Archaea cell walls • Why doesn’t lysozyme lyse Archaea? • Why doesn’t penicillin kill Archaea? • They lack peptidoglycan • They have a variety of cell walls including a pseudo-peptidoglycan Components external to cell wall Nucleoid S-layer Flagellum Ribosome Inclusion bodies Cytoplasmic membrane Capsule Cell wall Capsule (made of polysaccharides) • Protection from host defences (phagocytosis) • Protection from harsh environmental conditions (desiccation) • Attachment to surfaces Fimbriae and Pili • Fimbriae (singular = fimbria) – short, thin, hair-like, proteinaceous appendages (up to 1,000/cell) – recognition and attachment to surfaces • Pili (s., pilus; sometimes called sex pili) – similar to fimbriae except longer, thicker, and less numerous (1-10/cell), required for mating Locomotion: Patterns of flagella arrangement • • • • • polar flagellum monotrichous amphitrichous lophotrichous peritrichous – flagellum at end of cell – one flagellum – one flagellum at each end of cell – cluster of flagella at one or both ends – spread over entire surface of cell The Proton turbine - proposed model • Protons flowing through Mot proteins exert forces on charges present in ring Bacterial cytoplasm cytoplasm Gelatinous material inside the cell contains - ribosomes (for protein synthesis) & nucleoid - cellular inclusions (sometimes) - macromolecules (proteins, RNA etc) - organic molecules such as carbohydrates & lipids - inorganic ions The Nucleoid Irregularly shaped region. Is location of single chromosome sometimes two. Electron micrograph of sectioned cells showing nucleoid nucleoid Electron micrograph of an isolated nucleoid Plasmids Usually small, closed circular DNA molecules Exist and replicate independently of chromosome Not required for growth and reproduction EM picture of isolated plasmids May carry genes that confer selective advantage (e.g., drug resistance) Cellular inclusions Granules of organic or inorganic material that are reserved for future use – glycogen - polymer of glucose units – poly-β-hydroxybutyrate (PHB = polymers of β-hydroxybutyrate) – polyphosphate granules – sulphur granules PHB granules Cellular inclusions Specialist bacteria with magnetosomes – Contain iron in the form of magnetite - Use is to orient cells in magnetic fields Cellular inclusions Gas vesicles:Used for buoyancy in some aquatic bacteria. Eg. Cyanobacteria that perform photosynthesis and need sunlight. Gas vesicles are arranged in bundles. Show in transverse and longitudinal section in the top picture. Endospores • made by some Gram-positive bacteria Advantages of Endospores • Can survive for hundreds or even thousands of years - produced under unfavourable conditions; perhaps when cells run out of nutrients. • Highly resistant to heat, drying, radiation, & chemicals very low water content. • Contain calcium dipicolinate – binds free water and helps dehydrate cell • Special proteins protect DNA Can endospores live forever?! A) Clostridium spores from 1947 B) Halophilic bacteria (including Archaea) in a ¼ billion (250 million) year old salt crystal Differences between prokaryotic and eukaryotic cells Feature Prokaryote Eukaryote Cell size Nucleus? No. of Chromosomes mostly small <5 μm no commonly one larger than 5 μm yes more than one Mitosis Membranous organelles? no no Cell wall thin and usually peptidoglycan 70 S none no yes mitochondria, Golgi apparatus, chloroplasts, ER, etc. thick or absent Cytoplasmic ribosomes Ribosomes in organelles Cilia? Flagella ? yes, helical arrangement 80S 70S yes yes, 9:2 fibril arrangement