Micro 2021 Lecture 1&part2 PDF

Module 1 - Microorganisms and Microbiology 1. Introduction to Microbiology 2. Historical Context 1  What are microorganisms? Organisms that cannot be seen clearly with the naked eye - typically 1 mm or less in diameter. Microorganisms or microb...

Module 1 - Microorganisms and Microbiology 1. Introduction to Microbiology 2. Historical Context 1  What are microorganisms? Organisms that cannot be seen clearly with the naked eye - typically 1 mm or less in diameter. Microorganisms or microbes can exist as single cells or cell clusters (basidiomycota, Streptomyces spp., cyanobacteria, Dictyostelium and many others) In contrast, majority of plant and animal cells exist as parts of multicellular organisms. 2 3  Major Groups of Microorganisms 1. Viruses -essentially nucleic acid enclosed in protein coat or envelope (retrovirus) -infectious agents that can only reproduce in other living cells -not considered cells because they lack certain characteristics of cells Figure 8.20 Phage T4- Virus that Infects E. coli 4  Major Groups of Microorganisms Continued 2. Bacteria -prokaryotic cells that usually have single chromosome -diverse group 3. Algae -very diverse group (not single phylogenetic group = polyphyletic); there are prokaryotic algae (e.g. cyano-bacteria or blue-green algae) and eukaryotic algae (e.g. green algae and red algae) -found mostly in marine & freshwater environments -photosynthesize (make energy using sunlight) and make O2 as by-product 5  Major Groups of Microorganisms Continued 4. Fungi -eukaryotes that make spores -yeast is a unicellular fungus -some fungi are molds that consist of hyphae - long, branched filaments spore Figure 17.19 Mould with hyphae and spores hypha 6  Major Groups of Microorganisms Continued 5. Protozoa -unicellular eukaryotes -generally colourless and motile (have cilia or flagella) -wide range of morphologies Fig 17.7 – Paramecium ciliated protist a) Phase contrast micrograph b) SEM 7  Major Groups of Microorganisms Continued 6. Archaea -prokaryotes that often live in extreme environments e.g. very high temps and extreme pH Methanogens Where do we find Archeae? Halophiles Thermoacidophiles Wikicommons & Pinterest 8 Summary: There are 5 basic groups of microorganisms: a. Bacteria & Archaea. b. Fungi: yeasts and molds. c. Viruses. d. Protozoa. e. Algae. 9  Pathways of Discovery in Microbiology - Historical Perspective van Leeuwenhoek -first person to see and describe microorganisms in the 1600s -developed microscope that could magnify 300X (recall from Cell Bio) Portret van Anthonie van Leeuwenhoek (1632-1723), natuurkundige te Delft. (source: wikimedia) 10  Pathways of Discovery in Microbiology - Historical Perspective Cohn -founder of bacteriology in 1800s Pasteur (1882-1895) -v. important in Microbiology -proved ‘spontaneous generation theory’ was false Studio portrait of Louis Pasteur Source: wikimedia 11 Figure 1.17 - Pasteur’s experiment showing spontaneous generation theory false 12 Koch -key figure in showing that microorganisms can be causes of human diseases (e.g. anthrax, tuberculosis) -developed criteria called Koch’s Postulates to prove a specific microbe is responsible for a specific disease -came up with the idea of growing bacteria on agar (solid medium) on flat plates -Petri modified Koch’s method and poured agar into sterile dishes that could be covered 13  KOCH’S POSTULATES Figure 1.20 Diseased Healthy The Postulates: Tools: animal animal 1. The suspected pathogen Microscopy, Red must be present in all staining blood Observe cases of the disease cell blood/tissue Red and absent from healthy under the blood Suspected microscope cell animals. pathogen 2. The suspected pathogen Laboratory Streak agar plate No must be grown in pure culture with sample from either organisms culture. diseased or present Colonies of healthy animal suspected pathogen Inoculate healthy animal with cells of suspected pathogen 3. Cells from a pure Experimental culture of the suspected animals pathogen must cause Diseased animal disease in a healthy animal. Remove blood or tissue sample and observe by microscopy 4. The suspected pathogen Laboratory Suspected Laboratory Pure culture reisolation pathogen culture (must be must be reisolated and same shown to be the same and culture organism as the original. as before) 14 Beijernick -worked in late 19th/early 20th century -developed enrichment method: -increase concentration of specific microbes from mixture -used specific nutrient and incubation conditions Winogradsky -showed that bacteria can be biogeochemical agents: -biological organisms that modify inorganic chemicals e.g. bacteria that fix atmospheric nitrogen (N2) 15 16  Tree of Life Phylogeny is the study of evolutionary relationships between organisms Phylogenetics uses the relatedness of DNA sequences to show evolutionary relationships. -the closer the DNA sequences of two different organisms, the smaller the evolutionary distance between them Phylogenetic tree of life is a diagrammatic way to show evolutionary distances between organisms. 17  Tree of Life Our current understanding of the tree of life indicates that three distinct lineages of cells have arisen through evolution Figure 1.6 – Tree of life based on comparative rRNA sequencing. 18  bacteria Hug et al 2016 Tree of Life 19  We are here We are related not only to every living thing, but also to everything that has ever lived on Earth. 20  Physiological Diversity of Microbes Groups of microbes can vary a great deal from each other in terms of morphology, size, physiology, motility, cell division mechanisms, pathogenicity, motility etc. First way we’re going to group microbes is through physiology (metabolism) i.e. mechanisms by which microbes obtain energy. 1. Chemoorganotrophs -break down organic (carbon-based) chemicals such as glucose and acetate to make ATP -aerobes require O2 to produce ATP while anaerobes do not use O2 to make ATP 21 Physiological Diversity of Microbes Continued 2. Chemolithotrophs -use inorganic chemicals (non-carbon based) such as H2, H2S, Fe2+, and NH4+ to make ATP -only Bacteria and Archaea capable of this -useful because this group doesn’t have to compete with chemoorganotrophs for organic compounds -also, inorganic chemicals such as H2 and H2S are actually waste products of chemoorganotrophs 22 Physiological Diversity of Microbes Continued 3. Phototrophs -capable of photosynthesis (use of light to make ATP) -again, don’t compete with other groups -oxygenic photosynthesis is photosynthesis where O2 is a byproduct; occurs in blue-green algae a.k.a cyanobacteria -anoxygenic photosynthesis - O2 is not a byproduct; occurs in purple and green bacteria 23 Figure 3.5 - Schematic diagram showing three physiological divisions of microbes. 24  Physiological Diversity of Microbes Continued All microbes require carbon for life. Heterotrophs require organic compounds (i.e. complex carbon containing compound such as glucose) as a carbon source. Chemoorganotrophs and some chemo- lithotrophs are heterotrophs. Autotrophs can use atmospheric CO2 as their carbon source. -Autotrophs are primary producers - produce organic compounds needed by themselves and by heterotrophs -group includes most chemolithotrophs and all phototrophs 25  Bacteria Diversity Proteobacteria are largest phylum (division) within bacteria - all are gram-negative Gram-positive bacteria -examples Bacillus, Streptomyces Cyanobacteria or blue-green algae are very impt. in evolution - first producers of O2 on Earth. See Pg 358 and Chapter 15 for descriptions of other groups. 26  Archaea Diversity Appear to be seven phyla within Archaea based on rRNA and other gene sequencing; Evolution of Archaea complex and ancestry of phyla not clear. They are mostly chemoorganotrophs or chemolithotrphs. Phyla include: i) Crenarchaeota – contain mostly hyperthermophiles (temp optimum > 80°C) ii) Euryarchaeota – more diverse group -includes methanogens (produce methane), extreme halophiles (requires ≥ 1.5 M NaCl for growth in lab), thermoacidophiles, and some hyperthermophiles 27  Archaea Diversity Continued iii) Thaumarchaeota – found in oceans, marine sediment, hotsprings, soil iv) Nanoarchaeota -one species (N. equitans) that has smallest known Archaeal genome (0.49 Mb) -can reproduce only when attached to host (species of Chrenarchaeota) ….others…See Pg 358 and Chapter 16. 28 Fig 16.1 – Phylogenetic tree of Archaea based on of life based on sequencing of ribosome proteins (vs. 16S rRNA) 29  Please complete Mini Quiz Module # 1 Attempts allowed 3 30 Module 2 – Cell Structure and Function, Macromolecules Chapters 1, 2 31  Cells Cells are the basic unit of life. Cell membranes and/or cell walls separate cells from each other. Each cell contains a variety of molecules that are contained in subcellular structures or regions. Question: What does compartmentalization allow? Answer (from Cell Bio) -incompatible rxns separated -increases efficiency of biochemical rxns e.g. by clustering substrates and enzymes in one spot 32 -allows for regulation of biochemical rxns  Cells Continued Extensive communication occurs within the cell, between the cell and the environment, and often between cells. Microbes (with the exception of viruses) are considered cells - possess the essential characteristics of cells. 33 Essential Characteristics of Cells - Present in Microbes Figure 1.3 34 Question: Which class of microorganisms are not considered cells? Answer: Viruses General Structure of Viruses Figure 22.3 from Human Biology, 9th edition by Sylvia S. Mader. Also see Fig 10.4. 35  General Structure of Viruses Continued Viruses are very small - 0.2 to 2 x 10-6 m (1/1000th of 1 mm). They are about 1/10th of the size of bacteria. Virus always has an outer coat called a capsid made of protein. Virus also has nucleic acid that is its genetic material - can be ds (double-stranded) DNA, ssDNA or even RNA. The genome (entire complement of genes) of the virus contains information for reproduction. 36  General Structure of Viruses Continued Host cell machinery is also required for virus cell reproduction. Some viruses also have an envelope -envelope contains host proteins and viral glycoproteins called spikes – used to attach to host cell. 37 Question: What are the two groups that comprise prokaryotes? Answer: Bacteria and Archaea Structure of Prokaryotic Cells Prokaryotic cells are simpler and smaller than eukaryotic cells. -lack membrane-bound nucleus and organelles 38  Structure of Prokaryotic Cell Continued Figure 1.2 a – Prokaryotic Cell Structure) Cell wall - found in most prokaryotic microorganisms (but not eukaryotic microorganisms -gives microbial cell structural reinforcement -cell wall is selectively permeable 39  Structure of Prokaryotic Cell Continued Nucleoid - nucleoid - region where nucleic acid (usually DNA) lies -Bacteria may have one or multiple nucleoids and therefore, may be haploid or polyploid (multiple incompletely replicated chromosomes/cell) -chromosome often circular; can be linear -DNA is highly compacted Plasmid -extrachromosomal DNA that is often found in bacteria nucleoid -plasmids are small in size and circular -plasmids typically confer special properties (e.g. selective drug resistance, ability to synthesize 40 certain molecules) to the bacteria  Structure of Eukaryotic Cell Eukaryotic cells are larger and more complex than prokaryotic cells Fig 2.13 from Brock Biology of Microorganims, 12th ed. - Schematic diagram showing relative sizes of a virus, prokaryotic cell and eukaryotic cell Defining feature is the presence of a membrane- bound nucleus. 41  Structure of Eukaryotic Cell Continued Figure 2.11b from Brock Biology of Microorganisms, 13th ed. - Structure of eukaryotic cell See also Figure 1.2 in 14th edition. 42  Structure of Eukaryotic Cell Continued Mitochondria -certain microbes have mitochondria that produce ATP through cellular respiration Chloroplast -other microbes have chloroplasts allowing for photosynthesis 43  Structure of Eukaryotic Cell Continued Nucleus -surrounded by nuclear membrane continuous with ER -double phospholipid bilayer -nucleus contains DNA that is typically linear -DNA is highly compacted and organized into chromosomes -nucleolus is subcompartment of nucleus where ribosomal RNA (rRNA) is made -nuclear pores in envelope allow certain molecules to pass in and out Should know rest of cell structures from Cell Biology. Go over notes and review if necessary. 44  Glycosidic Bonds in Microbes Polymers of glucose are used as an energy storage form by some microorganisms (and macroorganisms). Starch – can be found certain microbes (algae, some protozoa) Cellulose - found in the cell wall of certain algae. Glycogen – found in many bacteria and fungi. 45  Lipids in Microbes Simple lipids or fats e.g. fatty acids (most microbes) or isoprene (Archaea). Complex lipids - simple lipids plus P, N, S, or small hydrophilic compounds. Phospholipids are key complex lipids. 46  Levels of Protein Structure Modern view of protein is that there are six levels of structure: -Primary -Secondary -Motifs -Tertiary -Domains -Quaternary Structure determines function! 47  Primary Structure 1 Primary structure R H H O R H H O R H H C C N C C N C C N C C N C C N C H O R H H O R H H O R Figure 3.8 - Biology, Raven, 7th ed. Primary structure refers to the amino acid sequence of a protein. Sequence of amino acids is written from left to right corresponding to the order from the amino (N) terminus to the carboxy (C) terminus. e.g. Met-Ala-Val-Ser-Cys-Thr etc. 48  Secondary Structure 1 Primary structure R H H O R H H O R H H C C N C C N C C N C C N C C N C H O R H H O R H H O R 2 Secondary structure b pleated sheet a helix Figure 3.8 - Biology, Raven, 7th ed. Secondary structure results from the way that amino acids interact with their neighbours. Hydrogen bonds play key roles in secondary structure. 49  Motifs Figure 3.8 - Biology, Raven, 7th ed. 2 Secondary structure b pleated sheet a helix 3 Motifs b a b motif a turn a motif Motifs are characteristic interactions between secondary structural elements. Motifs are also called “supersecondary structure.” 50  Tertiary Structure 4 Tertiary structure Figure 3.8 - Biology, Raven, 7th ed. Tertiary structure is final folded globular shape of a protein (or a protein domain). 51  Domains 5 Domains Domain 1 6 Quaternary structure Domain 2 Domain 3 Figure 3.8 - Biology, Raven, 7th ed. Some proteins consist of multiple domains. Domains are independently folding units of a protein. 52  Quaternary Structure 6 Quaternary structure Figure 3.8 - Biology, Raven, 7th ed. Certain proteins are made up of more than one polypeptide (subunit). Quaternary structure refers to the arrangement of multiple subunits. 53  Denaturation of Proteins Proteins can denature when exposed to extreme pH, high heat, or denaturing chemicals. Denaturation means that the polypeptide (protein) unfolds and higher order structure is lost. Since structure determines function, function is also lost with denaturation. Some disinfectants (e.g. ethanol) kill microbes by denaturing their proteins. 54 For next week: 1. Read relevant Chapters in book. 2. Blended learning 3. Completing Module 2 and Moving to Module 3 Microbial Nutrition