Microbiology Notes Chapter 1-9

Chapter One What is a microbe : A microorganism To see them use a microscope organism that cause disease Another word for bacteria is Prokaryotes they lack a nucleus Eukaryotic Have a true nucleus Eukaryotic microbes include some types of Fungi, Protozoa and Algae What is Protists A brain eating disease Causes malaria : transmitted by mosquitoes 5 Kingdoms 1.Animals 2.Plant 3.Monera (bacteria) 4.Fungi 5.Protista Microbes & Humans Organisms that are Pathogenic : Causes diseases Mutualistic: Probiotics Commeulustic: Dont help, just there, no harm or benefit 3 Domain System Eubacteria Archaea Eukaryota > - Prokaryotic Eukaryotic: plant, fungi,protist What are viruses : Noncellular Nonmetabolic The Cell Theory: All organism are comprised of cells The cell is the fundamental unit of life All cells comes from cells The Germ Theory of Disease Specific disease are caused by microscopic “germs” End of Notes Immunization : Building immunity Vaccination : DNA MRNA PROTEIN The Discovery of Viruses Viruses are non cellular agents of diseases Virus : Made up of DNA Retroviruses: made up of RNA: HIV, CORONA Chapter one End of Notes Chapter two Many areas of the human body are colonized with microbes called the HUMAN MICROBIOTA Parasites are microbes that cause harm-inducing infections Ectoparasites: such as a flea, that lives on the outside of its host Endoparasites : Inside the blood, inside the body Pathogens are bacterial parasites of humans Pathogenicity is the harm causing potential of a pathogen and depends on: Host Genetics & Physiology Virulence describes the level of harm caused by a pathogen following infection • Virulence is determined by Pathogen virulence factors that: promote attachment & colonization of host tissues ( invasion ) Primary Pathogens are likely to cause disease after infection in a healthy host • rapidly reproduce/ increase in numbers • Moderate to high virulence Opportunistic Pathogen are less likely to cause disease in a healthy host • Low Virulence Host Range: Some organism can infect only one type of host to produce disease Narrow : Salmonella enterica serovar Typhi infects human only Broad : Salmonella enterica serovar Typhimurium infects other animals in addition to humans Disease : A departure from a state of “ normal” health Infectious Disease: a disease caused by a microorganism (bacterial,viral or parasitic) that can be transferred from one host to another. Type of Diseases Acute Chronic Subacute Latent I Strep Throat Tuberculosis Bacterial Endocarditis Herpes Simplex Diseases are identified by characteristics Signs & Symptoms Signs: Can be observed by examination Symptoms: Are experienced by the person : Pain , Fatigue A Syndrome is a group of symptoms that consistently occur together & collectively characterized a condition Six Stages of Acute Infectious Diseases Incubation Prodromal Illness Decline Convalescent Long Term Morbidity is the rate of illness due to a disease Mortality is the rate of death due to a disease Indirect Cycles & Disease Transmission Indirect Transmission microbes can be transmitted indirectly by an inanimate objects ( fomites) , by vehicle transmission or by an insect vector Vehicle Transmission some microbes can be transmitted through contaminated fomites, food , water or air Direct Transmission microbes can be transmitted by direct contact or by aerosolization ( sneeze, influenza) Vertical Transmission transmission of an infectious agent from an insect to its offspring Insect Vectors microbes can be transmitted from animal to animal ( & to humans ) by insect vectors Vectors : ticks, mosquitoes Modes of Transmission Organisms may spread directly from person to person eg Touching, Kissing Direct contact transmission Endemic disease is one that is always present in a community at a low rate Epidemic disease is one in which the # of cases increases in a community in a short time Pandemic disease is an epidemic that spreads worldwide Zoonotic Disease are infections of animals that can be transmitted by humans Example: Lyme Disease- Tick Ebola Portals of Entry & Exit Fecal- Oral : Portal is the mucosa of the GI Tract Respiratory: Portal is the mucosa of the respiratory tract Urogential: Portal is the mucosa of genital & urinary tracts Parental: Portal is through breaks in skin Host Factors in Disease Host genetic makeup: host receptors to which bacteria and viruses bind Host genetics: Genetic variants in immune system genes that may influence course of infection Pre- existing conditions: Chronic infections, autoimmune disease, cancer, innate or acquired immunosuppression End of Notes Chapter two Chapter three Microscope is a system of lenses that creates an enlarged image of an object, making it visible to the human eye. Monocular: has one lenses, that you look through with one eye Binocular: has two lenses that you look through with both eyes The resolution limit (size of the smallest object that can be clearly seen) of the human eye is 150um or 1/7th of a millimetre Types of Microscope Light microscope: stained samples use light Phase contrast mircroscope: stained or unstained samples, can look at tissues Fluorescence microscopy : samples are stained with a fluorescent dye Electron microscopy Scanning electron microscopy (SEM) Transmission electron microscopy (TEM) Advance Microscopy Phase contrast microscopy : exploits small differencesmin refractive index between the cytoplasm & the surrounding medium or between organelles Dark field microscopy :special condenser blocks transmitted light, only reflected light is observered.Object is light, background is dark Interference microscopy : enchnances contrast by superimposing the image of the specimen in a second beam of light that generates an interference pattern Electron microscopy : illuminating source is a beam of evidence of electrons ( very short wavelength light) . Transmission electron microscopy ( TEM) : Electron beams penetrate a very thin slice of tissue with a very high resolution Scanning electron microscopy (SEM) : electron beams scan the specimen & are reflected by the stain molecules to reveal the contours of its 3D surface. Optics & Properties of Light Light interacts with an object & then travels to the eye to be seen Absorption: the object blocks part of the light.Heat increases Reflection :The wavelength of the light bounces off the surface Refraction the light bends when it enters a substance that changes speed Scattering :a small fraction of the incident light is sctattered in all directions.Object dimensions are close to the wavelength of incident light The Compound Brightfield Microscope Optical system with two leases • Objective lens magnifies the object either 4x, 10x, 40x or 100x Depth of field : decreases as magnification increases Gram Stain Method Gram positive Gram negative Cells are fixed to slide surface Cells are fixed to slide surface Crystal Violet stains cells reversibly Crystal Violet stains cells reversibly Stained Samples Staining adds contrast to microscopic images • Simple stain: one stain, single step Methylene blue Giema stain • Diffrential staining methods : staining & destaining steps Chapter 4 : Living Chemisrty: From Atoms to Cells Cholera • severe dehydration Vibrio cholera ORT : Oral rehydration therapy • Treatment Life at the Chemical Level • Matter - anything that takes up space and has mass Atoms- the smallest unit of matter Elements - pure form of matter composed of atoms of single type Molecules - compound of atoms Compounds contain at least 2 different elements Organic compounds contain at least carbon & hydrogen Bio molecules are organic compounds found in cells/ organisms 3 types of matter ( molecules) Elements Compounds Macromolecules Carbohydrates (Polar) (Polar) Proteins Nucleic acids Mixture Lipids (Polar) (non polar) Water is the Solvent of Life Polar covalent bonds in a single water molecule • Water moderates Temperature A hydrogen bond is an attraction between the positive end of one water molecule to the negative end of another The universal Solvent Compounds that are mostly non polar do not dissolve in water & are termed hydrophobic ( water feeding ) Hydrophilic Amphipathic Hydrophilic dissolves in water Hydrophopic Amphihatic both hydrophobic & hydrophilic Organic molecules make up cells • Organic molecules contain carbon (C) and hydrogen (H), at least. • Biomolecules are organic compounds that include other elements • oxygen (O) • Nitrogen (N) • Sulfur (S) • Phosphorus (P) • Others Biomolecules are polymers constructed from smaller molecules (monomers). • Lipids (triglycerides, steroids, phospholipids) Monomer - fatty acids • Carbohydrates . • Monomer - simple sugars Nucleic acids Monomer - nucleotides • Proteins Monomer- amino acids Monomer Polymer Bond Function Lipids Fatty acid Triglyeide Ester- linkage Makes up cell Carbohydrates Monomer Monosaccharide - Simple sugar Polyscaccharides Polymer Gylcosidic linkage Bond Provide energy Function membrane All cells are made up of carbohydrates Made up of carbons Composition Composition Carbon, hydrogen & oxygen & hydrogen Proteins Nucleic Acid Nucleotides Monomer Amino acid Monomer Polynucleotide Polymer Polypeptide Polymer Peptide bond Phosphodiester bond Bond Bond Does everything Transfer genetic info from Function Function one generation to the next Composition carbon, hydrogen, oxygen, Compostion nitrogen; plus phosphorous (C, H, O, N, and P) PH = measures the level of acidity Levels of protein folding Primary structure Secondary structure Tertiary structure Quaternary structure 6 catabolic Exergonic Energy + A + O B (spontaneous ) AB Monomers Endergonic anabolic 68 Polymers ( non- spontaneous ) Membranes and Transport Diffusion – movement of solute from high to low concentration Osmosis – movement of water across a membrane from high to low concentration Endocytosis Pinocytosis Cell Transport in Eukaryotic Cells Two types of endocytosis : pinocytosis & phagocytosis ⑫ Gin Phagocytosis Receptor-mediated endocytosis: looking for something specific Exocytosis Cell membrane - are made up of phospholipids Membranes are selectively permeable Chapter 5 : Cell Biology of Bacteria & Eukaryotes Prokaryotic cells: cells without a true nucleus ( no nuclear membrane ) Two domains : Bacteria & Archaea Eukaryotic cells: cells with nucleus & other organelles One domain : Eukaryota All other organisms ( animals, plants, fungi, & protist ) On the outside Everything on the inside In the cytoplasm any region that has the DNA The Cell Membrane defines a cell Cell (plasma) membrane separates the cytoplasm from the outside environment Phospholipid bilayer with proteins Bacterial Membrane Protein Functions • Support for structures that protrude from the cell ( flagella, pili) • Signaling & communication • Export of toxins & other virulence factors • Transport of substances in/out of the cell across the membrane • Establish concentration gradients for energy transfer The cell wall is a single, interlinked molecule that encloses the entire cell Bacterial Cell Wall Types Gram-positive: thick cell wall, multiple layers of peptidoglycan Gram-negative: thin cell wall, single layer of peptidogylcan, enclosed by am outer membrane Gram-positive cell wall Gram-negative cell wall Murein lipoprotein: inner leaflet of the outer membrane that forms a peptide bond with peptidoglycam Lipopolysaccharide : outer leaflet Other Cell Wall Types Acid-Fast Cell Wall • complex cell wall with peptidoglycan & mycolic acid • Resistant to staining Mollicutes are bacteria without a true cell wall Bacterial DNA is organized in a nucleoid Bacterial Cell Division • DNA replication • Protein synthesis & expansion of cytoplasm causes cell to elongate • Septum forms & the Septum formation ( separation) & motility determines the microscopic arrangement of cells • Cells form pairs ( diplo- ), chains ( strepto-), or Palisades when they separate in parrel planes • Cells form packets of 4 or 8 when they septate in alternating parrel planes • Cells form clusters if they septate in random orientations Attachment Pili ( singular, pilus) are made of pilin protein. • Fimbriae ( attachment pili) attach cells to surfaces • Conjugation (sex) pilus facilitates transfer of DNA between cells • Stalks are membranous extensions of cytoplasm that secrete adhesion factors Flagella enable motility & chemotaxis Flagella filament is made of flagellin protein Rotation of flagella propels the cell in response to stimuli * Motile organisms are made up of Flagella Adaptive Structures for Diverse Environmnets Thylakoid membranes Photosynthetic bacteria Gas vesicles Aquatic bacteria inflate/deflate for buoyancy Storage granules Storage of nutrients such as sulfur, phosphate, or PHA Magnetosomes Store magnetite (iron oxides) for magnetotaxis The Eukaryotic Cell The Endomembrane System •Rough endoplasmic reticulum (rough ER) •Smooth endoplasmic reticulum (smooth ER) •Lysosomes •Golgi apparatus The nucleus organizes DNA • Nucleus • Nuclear membrane • Nucleolus Mitochondria and Chloroplasts •Mitochondria and chloroplasts have bacterial genomes and ribosomes. •Evolved early in the history of life through endosymbiosis •Convert energy from food to ATP Flagella and cilia are constructed of microtubules. Contractile vacuole removes water from cells. Chapter 6 : Bacterial Growth, Nutrition, and Differentiation Essential nutrients are substances bacterial cells require for growth but must acquire from their environment. Many bacteria require only elemental building blocks to produce all chemical compounds required for life. Elements Carbon (C) Sulfur (S) •Magnesium (Mg2+) •Nitrogen (N) •Phosphorus (P) •Hydrogen (H) •Iron (Fe2+) •Potassium (K+) •Trace elements such as cobalt, copper, and zinc •Oxygen (O) Culture media provides essential nutrients for bacteria. •Chemically defined (minimal) media •Complex media Nutritional needs of some bacteria, such as Rickettsia, are unknown or are very complex, and they cannot be grown in culture. Carbon (organic) compounds are an essential need for all forms of life. Carbon compounds (simple and complex) are used as food, which stores energy and is a source of cellular building material for making biomass. • Autotrophs make their own carbon compounds starting with C02 • Heterotrophs obtain carbon compounds from other organism Energy is an essential need for all forms of life. Light or chemical compounds may be used as a source of energy by living things. •Phototrophs use light as an energy source. •Chemotrophs use potential energy stored in chemical compounds as an energy source. • Lithotrophs use inorganic chemical compounds. • Organotrophs use organic chemical compounds Nitrogen is needed by cells to make proteins and nucleic acids. Converting inorganic to organic nitrogen is a bacterial process. The Nitrogen Cycle: Involves different communities of bacteria Rhizohium is a nitrogen-fixing plant symbiont that forms bacteria-filled nodules on roots Growing Bacteria in Culture Culture is an artificial growth environment. • Bacteria will grow in culture if the natural environment can be provided : Nutrition: provided in culture medium Permissive growth temperature Environmental variables such as pH, pressure, & osmotic balance Solid Media Bacterial cells from colonies on solid media with agar added to make a firm surface Streak plate method allows for the separation of colonies into pure cultures e Selective Media: Compounds in the media prevent some types of bacteria from growing, favoring the growth of one specific type. Differential Media: Compounds in the media are metabolized Bacterial growth is measured at the population level Growth rate is a measure of the # of cells in a population over time Most bacteria reproduce by Binary Fission ( one parent cell divides& forms 2 offspring cells ) Binary fission may be symmetrical or asymmetrical Eukaryotic microbes divide by mitosis Chapter 7: Bacterial Metabolism Phototrophy : light - energy absorption makes high-energy no A molecule that donates electrons to the acceptor Chemotrophy: high-energy food molecule donates electron to acceptor • In biology enzymes control chemical reactions • Enzymes lower the activation energy of chemical reactions do they will proceed • Energy-releasing reactions (catabolism) are coupled with energy- capturing reactions ( anabolism) • All heterophs are catabolic • Catabolic : releases energy • Anabolic: requires energy • Oxidation: substance donates electrons • Reduction: substrate accepts electrons Biomolecules donate electron ( oxidation) electron carries (NAD, FAD, ATP) accepts electrons ( reduction) Glycosis ‘splits’ sugar molecules & energy is transferred to ATP Glycolysis occurs in 2 phases : Phase 1 consumes energy (2 ATP) Phase 2 releases energy, which is Glycolosis transferred to 2 ATP & 2 NADH ↑So Energy investment Hexose sugar Pyruvate ( pyruvic acid) DPR Takes place in the cytoplasm ( cytosol) Substrate level phosphorylation (ATP) synthase Phase 2 Energy production ADD P, ATP TP Fermentation Electrons removed from donor molecule (glucose) reduce NAD to NADH; 2 ATP also produced. NADH returns electrons to pyruvate, forming organic acids or alcohols as end products (Phase) Respiration investment energy ATP Glycolosis Hexose NAD + ADP + P , Sugar - NADH Takes place in the cytoplasm (cytosol) Pyruvate (Phase 2) energy production App + P, - ATP 4(ATP) Electrons removed from donor molecule reduce NAD to NADH. NADH “carries” hydrogen atoms to membrane-associated redox enzymes and drops them off. Hydrogen atoms split into protons and electrons, generating a proton motive force for ATP Respiration Electrons removed from substrates in glycolysis and TCA cycle are carried by reduced NAD and FAD to membrane-associated chain of redox enzymes called the electron transport system (ETS). Flow of electrons through redox chain powers proton pumps, which generate a proton motive force (PMF) across the membrane. Electron transport requires a strong oxidizing agent, like oxygen. Respiration completes catabolism of sugars and other biomolecules. ger Glycosis Fermentation 8 oxygen Aerobic respiration = Pyruavic acid Bacteria have many cell processes that use the PMF directly Not all respiration is aerobic Some bacteria can use alternative electron acceptor to complete respiration instead of oxygen Lithropy : Is an alternative route to get electrons for ETS & PMF generation An organic, reduced molecule serves as the electron donor instead of an organic compound Chapter 8 : Bacterial Genetics & Biotechnology transcription (gene expression) nucleoid region MRNA DNA genome plasmids 1. peptidyl transferase (protein sytnthesis) 3 PROTEIN Ribosomes Nucleoid ( cytoplasm ) Bacterial Genome translation 2 trna (amino acids) 2. 1 Chromosome 4. Circular 5. 1 million - 100 million 3. Extra- chromosal ( plasmids) Bacterial genomes are organized diffrently from those of eukaryotic organism Bacteria may have chromosomes & plasmids Some bacteria may have DNA molecules in addition to chromosomes called plasmids Plasmids are smaller tahn chromosomes & carry genes not truly essential but generally very useful The directional of DNA is always the same Genomes evolve through mutation & natural selection Mutations are random changes in the nucleotide sequence of a gene Natural selection chooses which mutattion will become established in a genome DNA replication is bidirectional & semiconservative Stages of DNA replication Initiation: Helicase opens helix into 2 strands Elongation: DNA polymerase copies old strands Any permanent, heritable change in a DNA sequence is called a mutation What causes mutation? • replication errors,physica agents: X-rays,UV radiation Most DNA damage is repaired • Base exicision repair - SOS (Save our Ship) repair • Methyl mismatch repair - recombinational repair Tods of Biotechnology Plasmids are small extrachromosal DNA molecules in baacterial cells that carry genes.All ci genes Restriction enzymes (endonuclease) recognizes specific base sequence & cut DNA Biotechnology: Making DNA from RNA cDNA is made when mRNA is rverse transcribed into DNA Reverse transcriptase is an anenzyme from retroviruses, such as HIV , which reverse copies mRNA molecules into 2 strands of DNA Transfer RNA ( tRNA) molecules transport amino acids to mRNA transcripts for aassembly into protein Chapter 9 : Bacteral Genomes & Evolution Transformation Modes of Horizontal Gene Transfer - Competent bacterial cells can bind & import DNA from their surroundings Conjugation - Conjugation involves cell to cell contact - DNA donor cells produce a protein tube called conjuation (sex) pilus - Donor sends DNA through tube to recipeint cells Transduction -Viruses that infect bacteria are called bacteriophage (phage) -Infection cylce by virus can transfer DNA from one bacterial cell to another Recombination -Generalized (homologus) recombination * Requires that the 2 recombining molecules have long stretches of sequence homology - Site specific recombination * Short DNA sequence recognized by a special recombination enzyme * Example is integration of beta pahge of C. diptheriae Composite transposons include gene sequence in addition to insertion sequences. Molecular Clocks * Random mutations with neutral effects accumulate at a stead rate over generations.In population that do not interbreed, genetic drift causes genome sequences to diverge over time. A gene in which random mutatins accumulate at a constant rate is called a molecular clock. Evolution of Endosymbionts *Pathogens can evolve specific traits that enhance their ability to colonize a host. *A pathogen can also evolve by losing cellular functions that are supplied by the host cell *Loss of traits in the absence of selection pressure is called degenerative or reductive eveolution. * Endosymbosis is a mutualistic relationship between the host & the symbiont where each is required for normal growth &.