Microbiology Post-Lecture Summaries PDF

Post Lecture Summaries Week 1 L1 (T 9/3): Intro to microbiology Outline Introduction to microbes! ○ What are microbes? ○ How do we grow them? ○ Intro to main lineages of microbes ○ Overview of beneficial and harmful contributions of microbes main poi...

Post Lecture Summaries Week 1 L1 (T 9/3): Intro to microbiology Outline Introduction to microbes! ○ What are microbes? ○ How do we grow them? ○ Intro to main lineages of microbes ○ Overview of beneficial and harmful contributions of microbes main points Microbes are life forms too small to be seen by human eye (oldest form of life) ○ Single-celled ○ Live in microbial communities How big are things? ○ Atom = 100pm ○ Virus 10-100 nm ○ E coli = 1-10 um ○ Skin cell = 10-100 um Growing microbes ○ (2 common methods) is required to study them Streaking to single cells on agar plate Inoculating and growing in liquid culture ○ Isolating Common features of all cells: ○ Cytoplasmic membrane ○ Cytoplasm ○ DNA, RNA, proteins ○ ribosomes There are 3 subdivisions of life: ○ bacteria (most primitive) ○ archaea (combo & poorly characterized) ○ prokaryotes (most complex) Similarities / differences between eukaryotes and prokaryotes: ○ Prokaryotes Eukaryotes No nucleus or secretory pathway Contains membrane-enclosed membranes organelles DNA is in circular chromosomes DNA in linear chromosomes; inside membrane-bound nucleus  Small compact genomes (.5-1 million Larger genomes (billions of bp) bp) ○ Streaking (on agar plate) vs. growing in liquid culture Isolating a single strain from a community of multiple strains L2 (Th 9/5): Microscopy & cell morphology Outline Microscopy basics ○ Light microscopy and the discovery of microorganisms ○ Improving contrast in light microscopy ○ Electron microscopy Cell morphology overview main points Robert Hooke ~1665 made first description of microorganisms using a microscope Modern microscopes ○ multiple lenses to achieve magnification ○ light source and a condenser lens Magnification: how much a microscope enlarges an image Resolution: ability to distinguish two adjacent objects as distinct Contrast: ability to distinguish between the sample and background Scattering: collision process between incoming light particles and particles in the sample; light microscopy utilizes scattering to create contrast ○ Sample particles attenuate light going in its original direction and redirect that light, producing faint light going in all directions Light microscopy ○ Brightfield Light source shines light on sample Unscattered light reaches the objective lens image is formed by scattering of light by the dense areas of the sample Specimen appears darker on a brighter background ○ Darkfield Light that passes through the specimen never reaches the eyepiece ONLY the light that is scattered by the sample reaches the objective Specimen appears brighter on a darker background ○ Fluorescence Samples absorb light at one wavelength and re-emit light at a longer wavelength  Used to visualize specimens that fluoresce Autofluorescence = natural fluorescence due to cell pigments Samples can also fluoresce after staining Achieve high contrast by using filters that block out excitation light and only image the re-emitted light ○ Confocal Uses a pinhole to decrease out of focus light - blocks light from above or below focal plane Used to obtain z-slice images that can be compiled into a 3D reconstruction of specimen Electron microscopy ○ Uses electrons instead of photons to image samples ○ Much greater resolving power ○ Electromagnets function as lenses ○ Operates in a vacuum ○ Camera takes electron micrograph SEM - visualizes surface of objects ○ Specimen coated with a thin film of heavy metal which scatters electrons ○ Electron beam scans the object ○ Scattered electrons are collected to produce an image ○ Large specimens can be observed TEM - electrons travel through the sample ○ Sample is either a thin slice of specimen or individual macromolecules on a surface ○ Can be at room temp Sample stained with high atomic weight substances that scatter electrons ○ Or can be at cryogenic temp Sample is flash-frozen and usually not stained Cryo EM single-particle reconstruction uses images of thousands of individual molecules to reconstitute the 3D structure of protein complexes ○ i.e. RuBisCO (CO2-fixing enzyme) bound to a RuBisCO binding peptide was uncovered using this method Cryo-electron tomography allows visualization of cellular structures at high resolution Cell Morphology Overview: Morphology typically does not predict physiology, ecology, phylogeny or other properties of a prokaryotic cell Selective forces influence morphology ○ Optimization for nutrient uptake Small cells and high surface-to-volume ratio, such as appendaged cells ○ Swimming motility in viscous environments or near surfaces Helical or spiral shaped cells ○ Gliding motility filamentous bacteria  Surface-to-volume ratio ○ Much greater S-t-V ratio in smaller cells compared to larger ones ○ Smaller cells exhibit better nutrient and waste product exchange per unit cell volume ○ Allows for faster growth than larger cells when transport across the membrane is limiting bacterial growth Largest bacteria ○ Compensates for their small S-t-V ratio by having a large vacuole inside cell which pushes cytoplasm to the periphery and artificially mimics a larger ratio Lower limit to bacteria cell size ○ Unlikely to have microorganism