Humans and the Microbial World PDF

Humans and the Microbial World (Chapter 1; Course Part 1) 12 What is Microbiology? 14 Microbiology is the study of the microbial world Figure 1.6 from McGraw Textbook (Nester’s Microbiology edition 2024)...

Humans and the Microbial World (Chapter 1; Course Part 1) 12 What is Microbiology? 14 Microbiology is the study of the microbial world Figure 1.6 from McGraw Textbook (Nester’s Microbiology edition 2024) 15  Major Groups of Microorganisms Bacteria Yeast Virus 3 Groups of Microorganisms: Prokaryotes Eukaryotes Acellular Infectious Agents Algae Protozoa Table 1.1 from McGraw Textbook (Nester’s Microbiology edition 2024) 16  Scientific Names Developed by Carl Linnaeus (1700s) Latin style, reflects a characteristic or honors a scientist Structure: 2-part naming system (Binomial system) Part 1 = Genus (capitalize the first letter) (e.g., Escherichia) Part 2 = species (all lowercase) (e.g., coli) Formatting: Online formats – use italics (e.g., Escherichia coli) Handwritten formats – underline (e.g., Escherichia coli) Abbreviate after first use to include only the first letter of the Genus (e.g., E. coli) 17  History of Microbiology See Figure 1.3 in Textbook (shown on the right) for a more detailed overview of major historical events (You don’t need to memorize this figure!) We are just going to review a brief history of microbiology 18  First Sights of Microbes Robert Hooke (1665) van Leeuwenhoek Microscope Used a crude microscope to view individual cells and Drawings: Called them “microscopical mushroom” (it was bread mold) Beginning of cell theory Cell theory = All living organisms are composed of cells Antonie van Leeuwenhoek (1674) Amateur lens grinder Built microscopes that could view living microorganisms He called them ‘little animalcules’ 19 Spontaneous Generation vs Biogenesis (1668 – 1800s) Spontaneous generation – belief that some forms of life can arise from non-living matter Biogenesis – living matter arises only from pre-existing living matter Louis Pasteur (1861) Used swan necked flasks to disprove the theory of spontaneous generation 20  Louis Pasteur’s Further Contributions It was believed that air was responsible for turning sugars into alcohol Pasteur showed that microscopic yeast (fungi) convert sugar to alcohol using a process called fermentation in the absence of oxygen – anaerobic Souring then occurs when bacteria turn the alcohol into vinegar in presence of air – aerobic Pasteur’s solution: Heat beer or wine after fermentation to kill the bacteria and prevent spoilage – this process is called pasteurization 21  The Germ Theory of Disease Previously, it was believed that disease was a punishment for crimes or misdeeds When whole towns got sick: It was the work of demons! Louis Pasteur’s work on fermentation showed that microbes were responsible for chemical and physical changes to their environment This prompted the speculation that microbes could also be responsible for disease Germ Theory of Disease = microorganisms cause certain diseases 22  Joseph Lister (1860s) Used phenol to clean surgical instruments and treat surgical wounds Drastically reduced the incidence of surgical wound infections Led to development of disinfectants and antiseptics 23  Robert Koch (1876) First proof that bacteria cause disease Investigated the cause of anthrax Isolated bacteria from the blood of infected cows Showed that a particular bacterium was present in all cases of the disease (now known as Bacillus anthracis) He injected the bacterium into healthy cows Those cows contracted anthrax and died Re-isolated bacteria from the injected cows and showed that they were identical to his first sample Showed that a specific microbe was the cause of a particular disease Established a sequence of experimental steps that could be used to find the causative agent of other diseases – Koch’s postulates 24  Edward Jenner (1796) Developed a vaccine to protect against the disease smallpox Observed that people who were previously sick with the mild disease cowpox did not get sick with smallpox He purposefully inoculated a young boy with cowpox The boy became mildly ill The boy recovered and became immune to smallpox 25  Paul Ehrlich (1909) Noticed that certain dyes stain bacteria differently than they stained animal cells Proposed that a chemical might be found that would harm disease causing microbes without harming the host. Selective toxicity → ability of the drug to targets sites that are relative specific to the microorganism responsible for infection. Sometimes these sites are unique to the microorganism or simply more essential to survival of the microorganism than to the host. Eventually discovered salvarsan – an arsenic derivative that could be used to treat syphilis (first antimicrobial medication to treat syphilis) 26  Alexander Fleming (1928) Noticed that mold inhibited bacterial growth on contaminated plates Produced a natural compound called penicillin The first antibiotic A compound naturally produced by molds or bacteria that inhibits the growth of or kills other microorganisms Image from: https://jpabs.org/misc/the-first-antibiotics.html 27 Fun Fact: What Can Microbes Do? Make vitamins Make antibiotics Make chocolate Make cement 28  Fun Fact: Microbes can degrade explosives Trinitrotoluene, TNT, is a problematic explosive that contaminates the soil in areas where ammunition is kept Bacteria named Clostridium bifermentans can break down this contaminant 29  Fun Fact: Bacteria are used to make chocolate Chocolate comes from the seeds of the Cacao tree The seeds come in pods and the only way to retrieve the seeds are to ferment them with yeasts and Lactobacilli and Acetobacter Fermentation of pulp by microbes promotes flavour development of the resulting chocolate 30  Fun Fact: Microbes can make plastics Ralstonia eutropha (formerly Alcaligenes eutrophus) is a useful bacterium having the capability of making plastics The plastic it produces is biodegradable! Strong hopes for medical purposes (e.g., slow release drug delivery) Polyhydroxbutyrate (PHB) 31  Fun Fact: Bacteria are used for biofinishing jeans! Cellulase from an alkalothermophilic bacterium, Thermomonospora sp., reduces hairiness and increases softness of denim in alkaline conditions with the right fade (“worn look”) Better alternative to stone-washing (and other cellulases) and more environmentally friendly! 32  More Fun Facts: Microbes can… Convert atmospheric nitrogen into a form that humans and animals can use (i.e., nitrogen fixation) Aid in digestion (e.g., degrade cellulose) Degrade pollutants (i.e., bioremediation and biodegradation) Make food (e.g., bread, beer, yogourt, chocolate, cheese, etc.) Make antibiotics Make biofuels Make cement Make vitamins Make insecticide Genetically engineered to make insulin Be important research tools 33  Who runs the world….Microbes!! Your body is half human and half microorganism ~ 1:1 ratio of microbial cells : human cells You have tens of trillions of microbes (our normal microbiota!) We CANNOT survive without microbes Research on animals suggests our microbiome can affect brain chemistry and behaviour (microbiome may also play a role in depression – currently being researched to determine if it is a cause-and-effect relationship or a consequence of something else) 35  Not all microbes cause disease! Microbes are an essential component of a healthy human! Human Microbiome (or normal microbiota or normal flora) Group of microorganisms that live in and on your body and don’t usually cause disease Prevent disease by competing with pathogens Aid with digestion Promote immune system development (“Old Friends” hypothesis; become better at identifying friends vs foes with more diverse microbiomes) 36  But, the dark side of microbes Pathogens = disease-causing microbes Microbes have “killed far more people than have ever been killed in war” (direct quote from our McGraw textbook) In Canada (2008 data), communicable disease cost $8.3 billion (Government of Canada, 2016, “Economic burden of communicable diseases in Canada) In 2008, it was estimated that the total cost due to antibiotic-resistant infections in the United States was $55 billion (Antibiotic Resistance Threats in the United States Centers for Disease Control and Prevention (CDC) 2013 Report) 37  What do Microbiologists do? Work in almost every industry: food, agriculture, bioremediation, biotechnology, pharmaceuticals, health, government agencies and labs, education, research, etc. Microbiology is a HUGE field, and we can’t focus on everything so there are different specialties: bacteriologists (bacteria), virologists (viruses), mycologists (fungi), epidemiologists (spread of diseases), immunologists (immune system and body’s defence against microbes), etc. 38  The Molecules of Life (Chapter 2; Course Part 1) 1  Chemical Building Blocks Atom = The smallest chemical unit of matter Element = Matter composed of one type of atom (e.g. Carbon [C], nitrogen [N], oxygen [O], sodium [Na]) Molecule = formed by combining two or more atoms Either same type of atom (e.g. N2) Or different (e.g. CO2) – called a compound 3  Structure of Atoms Every atom has a centrally located nucleus Nucleus = Protons (+ charge) & Neutrons (neutral charge) Overall, the nucleus bears a net positive charge Nucleus is stable and does NOT participate in chemical reactions 5  Electrons Circle the nucleus and are negatively charged Stabilize the positive charge of the nucleus An equal number of electrons and protons will give a net charge equal to neutral Unlike protons and neutrons, which are densely packed in the nucleus, the lighter electrons orbit the nucleus in “shells” Electron shells correspond to different energy levels 6  Chemical Bonds Chemical bonds form between atoms through 8e- interactions of electrons in their outer shells 8e- The goal of every atom is to become 2e- chemically stable, which is achieved by filling its outermost shell with electrons + 1st = 2 e- maxium 2 2nd = 8 e- maximum 8 electrons 3rd * = 8 e- 8 electrons (in this course) *only if it’s the valence shell valence shell is the outer shell(?) Atoms achieve a full complement of electrons by combining together to form molecules https://manoa.hawaii.edu/exploringourfluidearth/chemical/chemistry-and-seawater/ionic-compounds 7 3 Types of Chemical Bonds in Living Organisms Hydrogen Bond Ionic Bond Unbalanced Opposites attract attraction two different molecules that are inbalanced but are attracting Covalent Bond Sharing is caring 8  Ions Ion = An atom (or group of atoms) that has a positive or negative charge If an atom loses an electron, it has an overall positive charge Cation thinks Cats are positive If an atom gains an electron, it has an overall negative charge Anion Cation Anion Images: From Pearson Textbook 9  Ionic Bonds Result from attraction between ions of opposite charges Anions and cations can form ionic bonds to neutralize their charges Attraction holds the ions together to form a compound E.g., NaCl salt 10  Covalent Bonds (/)basically opossite of ion (/) Covalent bonds form when atoms share pairs of electrons Found in many compounds, especially those that contain carbon Carbon atoms can form up to 4 covalent bonds (e.g., CH4) methane Very strong bonds 11  Polarity for Hydrogen Bonds Occur between covalently bonded molecules polarity: a uneaqually sharing that display polarity δ- E.g., the water molecule H2O δ+ When hydrogens are bonded to oxygen, the larger oxygen atom tends δ+ partial negative (the delta sympbol) to pull the electrons closer to itself Creates a region with partial negative charge δ- (O) And a region with partial positive charge δ+ (H) These regions can now participate in hydrogen bonding 12  intra molecular forces (just look that up lol) Hydrogen Bonds Loose attraction between oppositely charged regions need polarity, 2 different molecules, and hydrogen to make a hydrogen bond of different molecules (intermolecular force) the hyrdogen and oxygen bonds are on δ- 2 different molecules Weaker than ionic and covalent bonds δ+ Serve to bridge separate molecules together δ+ E.g., In water (H2O), the H’s of one molecule are attracted to the O’s of other molecules Occurs when hydrogen is covalently bonded with oxygen, nitrogen, or other electronegative atoms (typically those with large nucleus) and attracted to another molecule (oxygen, nitrogen, or other electronegative atom) 13  Water as the Solvent of Life Approx. 75% of cell weight is water solvent is something that u use to dissolves something and the solute it the thing that gets dissolved Water has an unequal charge distribution (water is a polar solvent) Unequal charge distribution allows it to dissolve many ionic compounds and polar substances (dissociation) Positive portion of solute molecule surround negative O Negative portion of solute surround positive H Therefore, salts like NaCl tends to separate into cations and structure of water molecules in liquid anions (holds ions in solution; solution = solute + solvent) E.g., NaCl easily dissolves into Na and Cl in water + - Aqueous solution = a solution where water is the solvent Each water molecule can form up to four hydrogen bonds with other water molecules → GIVES WATER ITS UNIQUE PROPERTIES structure of wwater molcules in ice 14  Polar Nature of Water Gives it the Following Characteristics (Part 1): High boiling point (100°C) Strong attraction between water molecules means more heat is required to separate water molecules Exists in liquid state on most of the Earth’s surface Hydrogen bonding between water molecules affects density of water Ice = hydrogen bonds in the crystalline structure of water takes up more space than in liquid form (therefore ice floats) 15  Polar Nature of Water Gives it the Following Characteristics (Part 2): Hydrogen bonds of water provide surface tension (this is how lighter insects can walk on water) Water is key for many digestive processes Large molecules broken down into smaller For synthetic reactions, water is an important source of H and O atoms that are incorporated into numerous organic compounds in living cells Makes water resist rapid changes in temperature Heat absorption by molecules tends to increase kinetic energy and their rate of motion With water, heat first results in breaking Hydrogen bonds rather than increasing rate of motion. Consequently, it doesn’t heat and cool as fast as other liquids ex. an ocean don't have extereme temperatures fluctuations it's just moderate constantly 16  Water and pH don't memorize this Water’s polarity facilitates the splitting and joining of hydrogen ions (H+) and hydroxide ions (OH-) Makes these ions available for chemical reactions pH scale describes the concentration of H ions in a + solution Measure of acidity pH 7 = neutral (pure water) pH below 7 = acidic pH above 7 = basic or alkaline 17  Organic Molecules Any molecule that contains both carbon and hydrogen Because each C atom can participate in 4 covalent bonds, carbon carbon can be used to build an enormous variety of compounds Four major classes of organic molecules make up the building blocks of life: 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic Acids 18  1. Carbohydrates Large group of compounds including sugars and starches All contain the elements C, H and O often in the ratio C H O E.g., glucose = C H O 1 2 1 6 12 6 carbon, hydrogen, oxygen Generally polar (so they dissolve in water) Functions: A type of sugar (deoxyribose) is the building block of DNA Some types of sugars needed for the cell wall Simple carbohydrates are needed for synthesis of amino acids and fats Main function: Ready source of energy for cells 3 major groups: monosaccharides, disaccharides, and polysaccharides all ends in chardes 19  Types of Carbohydrates Monosaccharides: mono = one Basic units of carbohydrates Simple sugars, e.g., Glucose Disaccharides: di = two Two monosaccharides joined by a covalent bond E.g., Sucrose (table sugar) = Glucose + Fructose Polysaccharides: poly = many Composed of long chains of monosaccharides Often not soluble in water Complex sugars, e.g., Cellulose Cellulose is the most abundant carbohydrate on Earth (found in plant cell walls) Only digested by certain microbes and fungi 20  2. Lipids Includes fats, complex lipids (e.g., phospholipids), and steroids Essential to the structure and function of membranes Used for energy storage Non-polar molecules = Hydrophobic = water-hating Fats: Made from a glycerol backbone + 1 or more fatty saturated bond v acids: Monoacylglycerides: 1 fatty acid Diacylglycerides: 2 fatty acids Triacylglycerides: 3 fatty acids Fatty acids can be: Saturated = no double bonds or unsaturated = double bonds unsaturated bond^ (typucally liquird) 21  Complex lipids such as Phospholipids Contain glycerol, 2 fatty acids, and a phosphate group The phosphate group is polar: Hydrophilic waterloving The fatty acid tails are non-polar: Hydrophobic Allows phospholipids to form membranes in water Saturated fatty acids tend to form membranes that are more solid Unsaturated fatty acids – more fluid. 22  Biological membranes Are made from a phospholipid bilayer Are semi-fluid (contain a mix of saturated and unsaturated fatty acids) Separate the watery inside of the cell from the watery environment. (hydropphobicfatty acid tails 23  Steroids (or sterols) Structurally different from other lipids Built on a hydrophobic 4 ring structure Generally found in eukaryotes (not in prokaryotes) E.g., Cholesterol, ergosterol and vitamin D. https://pubmed.ncbi.nlm.nih.gov/12519197/ 24  3. Proteins proteins this part can change > Made up of building blocks: amino acids All contain: C, H, O, N (and some have S) required in all aspects of cell structure and function Some are structural speeds things up But most act as enzymes – increase the rate at which chemical reactions take place in living organisms Proteins typically contain: 20 different amino acids have at least one amino (-NH2) and one carboxyl (-COOH) group side groups determine properties. 25  3. Proteins – Continued Amino acids are joined to make proteins by covalent peptide bonds Protein = polypeptide = chain of amino acids shape and function of the protein is determined by the sequence of amino acids. (this is the joining process) 26  4. Nucleic Acids DNA = deoxyribonucleic acid RNA = ribonucleic acid Built of building blocks called nucleotides – Nucleotides are joined together by covalent bonds to form a strand of nucleic acid Each nucleotide has 3 parts: this is one nulueotide – 1. Nitrogenous Base: Purine → 2 rings = Adenine (A) or Guanine (G) Pyrimidine → 1 ring = Thymine (T), Cytosine (C), Uracil (U) pentose means 5 (C,U