Microbial Biology Past Paper PDF January 2025

1/6/2025 Biology 15:163/15:152 Microbial Biology January 2025 Dr Ellen Boudreau This Photo by Unknown Author is licensed under CC BY-NC-ND 1...

1/6/2025 Biology 15:163/15:152 Microbial Biology January 2025 Dr Ellen Boudreau This Photo by Unknown Author is licensed under CC BY-NC-ND 1 Email is best! [email protected] Contact info… Brodie Room 3-10 2 Module 1: Jan 7 – Jan 31 Chapter 6 (pp. 104-109; 119-120) A tour of the cell* Chapter 25 (pp. 562-565) The evolution of Module microorganisms* Chapter 26 (pp. 586-590) Phylogeny and systematics* outline… Chapter 27 (pp. 607-627) Bacteria and Archaea Chapter 28 (pp. 628-654) Protists Chapter 31 (pp. 698-716) Fungi *reviewing the important parts 3 1  1/6/2025 A review of the important bits about cells and how we look at them… Biologists use microscopes and tools of biochemistry to study cells Eukaryotic cells have internal membranes that compartmentalize their functions Mitochondria and chloroplasts change energy from one form to another, and have an interesting prokaryotic evolutionary origin 4 Microscopy… Biologists use Microscopes and the Tools of Biochemistry to Study Cells Though usually too small to be seen by the unaided eye, cells can be complex Microscopes are used to visualize cells In a light microscope (LM), visible light is passed through a specimen and then through glass lenses Lenses refract (bend) the light, so that the image is magnified 5 Figure 6.2 The size range of cells. 6 2  1/6/2025 Three important parameters of microscopy Magnification - ratio of an object’s image size to its real size Making something appear BIGGER  BIGGER Microscopy… Resolution - measure of clarity of the image Can you distinguish between two separate points on the image? Contrast - visible differences in parts of the sample Can you distinguish between a feature and the background? 7 LM magnifies effectively to about 1,000 times size of actual Exploring specimen Various techniques enhance Microscopy- contrast and enable cell Light Microscopy components to be stained or labelled (LM) Most subcellular structures, like organelles are too small to be resolved by standard LM 11 Light directly passes through specimen Little contrast, unless cells are Pigmented Light Stained Microscopy Example: Brightfield (Unstained) Figure 6.3a Exploring Microscopy 12 3  1/6/2025 Staining enhances contrast Cells are fixed and stained (and therefore killed) in most staining procedures. Light Microscopy Example: Brightfield (Stained) Figure 6.3b Exploring Microscopy 13 Useful for living, unpigmented cells Variations in density are amplified by manipulating the light (background light vs light scattered by the sample) Light Microscopy Example: Phase-Contrast Figure 6.3c Exploring Microscopy 14 Also called Nomarski Similar to phase contrast, works with interference and polarization principles Light Image almost 3-D Microscopy Example: Differential- Interference- Contrast Figure 6.3d Exploring Microscopy 15 4  1/6/2025 Specific molecules are visualized with fluorescently- labelled dyes or antibodies Allows for subcellular localization to be determined Nucleus - blue Light Mitochondria - orange Cytoskeleton - green Microscopy Example: Fluorescence Microscopy Figure 6.3e Exploring Microscopy 16 Recent advances in light microscopy Light Confocal microscopy and deconvolution microscopy provide Microscopy sharper images of 3-D tissues and cells Advances New techniques for labelling cells also improve resolution 17 Use of a laser produces sharper images, and allows 3-D image reconstruction Works by ‘optical sectioning’, then reconstructing images from different planes Figure compares images of labelled nerve cells captured by fluorescence microscope (left) and confocal microscope (right) Light Microscopy Example: Confocal Microscopy Figure 6.3f Exploring Microscopy 18 5  1/6/2025 Digital processing of fluorescence images Results in sharp 3-D image Light Microscopy Example: Deconvolution Figure 6.3i Exploring Microscopy 19 Digital processing Light of fluorescence images Microscopy Results in sharp 3-D image Example: Super- Resolution Microscopy Figure 6.3j Exploring Microscopy 20 Exploring Microscopy- Electron Microscopy (EM) Two types of electron microscopes (EMs) are used to study subcellular structures Scanning electron microscopes (SEMs) focus a beam of electrons onto surface of a specimen, providing 3-D images. The surface is usually covered in a thin film of gold, and the electron beam excites the surface electrons. Most SEMs you see are artificially coloured. Transmission electron microscopes (TEMs) focus a beam of electrons through a specimen, to study internal structures. TEM specimens are usually stained with heavy metals, which attach to different structures and change the electron density. Both types focus a beam of electrons (not light!) using electromagnets rather than lenses. 21 6  1/6/2025 Electron Microscopy Example: Scanning Electron Microscopy 3-D imaging of surface of tracheal cilia Figure 6.3j SEM showing the surface of a cell 22 Electron Microscopy Example: Transmission Electron Microscopy Profile of a thin section of cilia specimen Figure 6.3j TEM of a specimen 23 The cell is the basic structural and functional unit of every organism Eukaryotic Cells There are two types of cells: Have Internal prokaryotic and eukaryotic Membranes that Two of the three domains of life Compartmentalize (Bacteria and Archaea) are comprised entirely of prokaryotic cells Their Functions… Protists, fungi, animals, and plants all are eukaryotic cells 28 7  1/6/2025 Comparing Basic features of all cells Prokaryotic Plasma membrane Semifluid substance called and cytosol Eukaryotic Chromosomes (carry genes) Ribosomes (make proteins) Cells… 29 Comparing Prokaryotic and Eukaryotic Cells… Prokaryotic cells are characterized by having: No nucleus DNA in an unbound region called the nucleoid No membrane-bound organelles Cytoplasm bound by plasma membrane Figure 6.5 A prokaryotic cell. 30 Comparing Eukaryotic cells are characterized by having Prokaryotic DNA in a nucleus bounded by a membranous nuclear envelope and Membrane-bound organelles Cytoplasm between plasma membrane Eukaryotic and nucleus Cells… Eukaryotic cells are generally much larger than prokaryotic cells 31 8  1/6/2025 The plasma membrane is a selective barrier Allows passage of sufficient amounts of oxygen, nutrients, and waste to support the cell volume Comparing General structure of a biological membrane is a phospholipid bilayer Prokaryotic and Eukaryotic Cells… Figure 6.6 The plasma membrane. 32 Surface Area to Volume of Cells Surface area to volume ratio of cells is critical Metabolic requirements set upper limits on the size of cells As a cell increases in size, its volume grows faster than its surface area: Figure 6.7 Geometric relationships surface area increases by a factor of n2, between surface area and volume. volume increases by a factor of n3 Small cells have a greater surface area relative to volume 33 Exploring Eukaryotic Cells: Animal Cells Eukaryotic cells have internal membranes that partition the cell into organelles Compare to some unicellular eukaryotes (e.g. fungi) Figure 6.8 Exploring Eukaryotic Cells 34 9  1/6/2025 Exploring Eukaryotic Cells: Plant Cells Plant and animal cells have mostly the same organelles Unique plant cell structures: Chloroplasts Large central vacuoles Cell walls Plasmodesmata Compare to some unicellular eukaryotes (e.g. photosynthetic Figure 6.8e Exploring protists) Eukaryotic Cells 35 Mitochondria are the site of cellular respiration, a metabolic process that uses Mitochondria oxygen to generate ATP and Chloroplasts, found in plants and algae, are the site of photosynthesis, a chloroplasts metabolic process that uses the energy from sunlight to fix carbon (from CO2) change energy and uses it to generate energy-rich from one form organic molecules such as glucose Peroxisomes are oxidative organelles, to another… using oxygen for some molecular breakdown, forming peroxides but also converting those peroxides into water, protecting other cellular components. 36 Energy-transducing mitochondria and The chloroplasts are not part of the endomembrane system, and are derived evolutionary from prokaryotes origins of Endosymbiotic theory Mitochondria and chloroplasts resemble mitochondria bacteria in numerous ways and Contain free ribosomes and circular DNA molecules chloroplasts… Grow and reproduce independently in cells using prokaryotic-like mechanisms 37 10  1/6/2025 The endosymbiotic theory suggests that an early ancestor of eukaryotes engulfed The an aerobic (oxygen-using) nonphotosynthetic prokaryote evolutionary The engulfed prokaryote was origins of maintained within the host cell and became an endosymbiont, eventually mitochondria evolving into a mitochondrion and A second endosymbiotic event involved a photosynthetic prokaryote being engulfed chloroplasts by a eukaryote containing mitochondria This endosymbiont evolved into a chloroplast 38 The Endosymbiont Theory of the Origin of Mitochondria and Chloroplasts Figure 6.16 The endosymbiont theory of the origin of mitochondria and chloroplasts in eukaryotic cells. More on this in a little bit…. 39 The geologic record is divided into the Key Events in Archaean, the Proterozoic, and the Life’s History Phanerozoic eons Include Origins The Phanerozoic includes the last half billion years, and encompasses of Organisms and multicellular eukaryotic life Colonization of The Phanerozoic is divided into three eras: the Paleozoic, Mesozoic, and Land Cenozoic 40 11  1/6/2025 Table 25.1 The Geologic Record 41 The Geologic Record… Table 25.1a The Geologic Record 42 The Geologic Record – we’re concerned with the earliest cells and atmospheric oxygen… Table 25.1b The Geologic Record 43 12  1/6/2025 The Geologic Record Figure 25.8 Visualizing the Scale of Geologic Time Major boundaries between geological divisions correspond to major extinction events in the fossil record 44 The First Single- Celled Organisms… This Photo by Unknown author is licensed under CC BY-NC-ND. The oldest known fossils are stromatolites, rocks formed by the accumulation of sedimentary layers on bacterial mats Stromatolites date back 3.5 billion years ago Prokaryotes were Earth’s sole inhabitants from 3.5 to about 2.1 billion years ago This Photo by Unknown author is licensed under CC BY. 45 Most atmospheric oxygen (O2) is of biological origin O2 produced by oxygenic photosynthesis reacted with dissolved iron and precipitated out to form banded iron Photosynthesis formations By about 2.7 billion years ago, O2 began and the Oxygen accumulating in the atmosphere and Revolution rusting iron-rich terrestrial rocks This “oxygen revolution” from 2.7 to 2.3 billion years ago caused extinction of many prokaryotic groups Some groups survived and adapted using cellular respiration to harvest energy 46 13  1/6/2025 Photosynthesis and the Oxygen Revolution The initial rise in O2 was likely caused by ancient cyanobacteria Later increases in atmospheric O2 might have been caused by the evolution of eukaryotic cells containing Figure 25.9 The rise of atmospheric oxygen. chloroplasts 47 The oldest fossils of eukaryotic cells date back approximately 1.8 billion years Eukaryotic cells have a nuclear The First envelope, mitochondria, endoplasmic reticulum, and a Eukaryotes cytoskeleton The endosymbiont theory states that mitochondria and plastids (chloroplasts and related organelles) were formerly prokaryotes living within larger host cells 48 An endosymbiont is a cell that lives within a host cell Prokaryotic ancestors of mitochondria and plastids probably The First gained entry into host cell as undigested prey or internal Eukaryotes parasites In the process of becoming more interdependent, the host and endosymbionts became a single organism 49 14  1/6/2025 A Hypothesis for the Origin of Eukaryotes Through Serial Endosymbiosis Serial endosymbiosis supposes that mitochondria evolved before plastids through a sequence of endosymbiotic events Figure 25.10 A hypothesis for the origin of eukaryotes through serial endosymbiosis. 50 Key evidence supporting the endosymbiotic origin of mitochondria and plastids includes: Inner membranes are similar to plasma membranes of prokaryotes Division and DNA structure are Endosymbiont similar in these organelles and prokaryotes theory These organelles transcribe and translate their own DNA Their ribosomes are more similar to prokaryotic than eukaryotic ribosomes 51 15