Notes In MicroPara PDF

NOTES IN MICROPARA Lecture 1 - Microorganisms - Structure and Activities of Microbial Cells - Microscopy and the Origins of Microbiology - The Impact of Microorganisms on Human Society Microorganisms - Can also be called as microbes (sometimes called “germs”) - Life f...

NOTES IN MICROPARA Lecture 1 - Microorganisms - Structure and Activities of Microbial Cells - Microscopy and the Origins of Microbiology - The Impact of Microorganisms on Human Society Microorganisms - Can also be called as microbes (sometimes called “germs”) - Life forms too small to be seen by the naked eye (need microscope to see) - Has diversity in form and function (not only bacteria but also protozoans/fungi etc.) ❖ Single celled meaning they can live as one cell ❖ Can also be multicellular (Eukaryote) - Live in complex microbial communities - Activities regulated by interactions with each other, the environments and with other organisms ❖ Who they are and what they do Microbial Cells - Living compartments that interact with their environment and with other cells in dynamic ways - Two fundamental types of cell: Prokaryotic and Eukaryotic cell Domains of life (BAE) - broad classification - Bacteria - Eukarya - Achaea Prokaryotic - Single celled organisms - Bacteria and Archaea Eukaryotic - Multicellular Difference between Prokaryotic and Eukaryotic - Prokaryotic is much simpler than Eukaryotic (has compartments what we called membrane bounded organelles) - Shape and structure - Eukaryotic has true nucleus - Prokaryotic has a nucleus inside nucleoid (not true nucleus) - Eukaryotes have multiple origins of replication while prokaryotes don’t Similarities in Prokaryotic and Eukaryotic - Both have a cell membrane (cytoplasmic membrane) ❖ Cytoplasmic membrane separates inside of the cell - Both have cytoplasm ❖ Carbohydrates, lipids, inorganic ions - Both have ribosomes - Both have genetic material (DNA) - Metabolism, growth, evolution (which all cells have) Not all cells have: - Differentiation - Genetic exchange - Communication - Motility Brief History of Life on Earth - 4.6 billion years ago (Earth age)  - Microbial first to appear between 3.8 and 4.8 billion years ago ❖ Foundations of life on Earth - Anoxic Earth ❖ Atmosphere has no oxygen - Anoxygenic Phototrophic Bacteria ❖ Unable to carry out photosynthesis - Cyanobacteria (between 2 to 3 billion years ago) ❖ Can carry their own food and produce oxygen ❖ Great Oxygenation Event - Lost Universal Common Ancestor ❖ Where life begins to diverse from Microscopy and the Origins of Microbiology - Robert Hooke ❖ English mathematician and natural historian ❖ Illustrated and described sells ❖ Coined the term “cells” ❖ Published Micrography - Antoni Van Leeuwenhoek ❖ First person to see bacteria ❖ Made his own simple microscope ❖ Published a book about his findings ❖ Has a lot of contributions in microbiology and has evolved since his time - Light Microscope ❖ Light is focused on the specimen by a glass condenser lens ❖ Image is magnified by an objective lens and an ocular lens for protection on the eye Three Parameters to Consider in Microscopy: - Magnification ❖ Ratio of an object’s image size to its actual size - Resolution ❖ Clarity of an image - Contrast ❖ Difference of the light and darkness of an image Compound Microscope - LPO or Low Power Objective - HPO or High Power Objective - OIO or Oil Immersion Objective (highest magnification) Light Microscopy - Brightfield - Confocal - Phase-contrast - Deconvolution - Differential interference - Super-resolution - Fluorescence Electron Microscope - Beam of electrons is used instead of light - Focused on the specimen by a condenser lens - Has better resolution than light microscope Electron Microscopy - SEM or Scanning Electron Microscopy (3D image) - TEM or Transmission Electron Microscopy (cross section image) - If observing movement, do not use electron microscope Louis Pasteur - Father of Microbiology - Disproved theory of spontaneous generation (Abiogenesis) ❖ Living organisms could arise from nonliving matter Francesco Redi - Created a setup to disprove spontaneous generation Joseph Lister - Father of Modern Surgery - Introduced antiseptic techniques in surgery Robert Koch - Father of bacteriology - Koch’s postulates ❖ Organism should be regularly found in the lesions ❖ It be possible to isolate the organism in pure culture from lesions ❖ Inoculation of the pure culture into suitable laboratory animals should reproduce the lesion or disease ❖ It should possible to reisolate the organism in pure culture from the lesions produced in the experimental animals Edward Jenner - Father of Immunology Branches of Microbiology - Bacteriology - Protozoology ❖ Study of bacteria ❖ Study of protozoa - Mycology - Virology ❖ Study of fungi ❖ Study of viruses - Phycology ❖ Study of photosynthetic eukaryotes Impact of Microorganisms on Human Society - Microorganisms are agents of diseases - Agriculture and Human Nutrition ❖ Legumes in relationship with nitrogen fixing bacteria ❖ Probiotics (good bacteria) - Food ❖ Fermentation of microorganisms (cheese, pickles, wine, etc.) - Industry ❖ Biofuels Lecture 2 - Cells of Bacteria and Archaea - The Cell Membrane and Wall  - Cell Surface Structure and Inclusions - Cell Locomotion - Eukaryotic Microbial Cells Morphology - Shape - Cannot fully identify a microorganism Bacteria and Archaea Morphology - Plural form of bacterium - Long thin wavy body (spirochete) - Spherical (coccus/cocci) - Appears to have budding and - Rod (bacillus has this shape) appendaged - Curved or spiral (spirillum/spirilla) - Filamentous Cell Size and Volume Surface to Volume Ratio - Small cells have more surface area - Higher S/V ratio of small cells supports a faster rate of nutrient and waste exchange per unit cell ❖ Because of its small size, prokaryotic cells can grow faster and evolve more rapidly than larger cells - AMR or Antimicrobial Resistance Cytoplasmic Membrane - Surrounds the cytoplasm and separates it from the environment Functions of the Cytoplasmic Membrane - Three critical cellular functions ❖ Selective barrier (decides which comes in and out/permeability barrier) ❖ Protein Anchor ❖ Energy Conservation Structure of Cell Membrane and Wall - Cytoplasmic Membrane ❖ Phospholipids (by layer) ❖ Hydrophobic (water repelling) region found in inner area ❖ Hydrophilic (water attracting) region found in outer area ❖ Glycerol connected due to ester linkage - Cell Wall ❖ Phospholipids by layer as well but connected is by ether linkage ❖ Tail is made of repeating of isoprene ❖ Hydrocarbon rings Archaeal Membranes - Lipid mono layer Bacterial Cell Wall - Protection against osmotic lysis (bursting of the cell) - Shape and rigidity on the cell Peptidoglycan - Rigid polysaccharide - In all Bacteria that have cell wall - Not present in the cell walls of archaea or eukarya - Confer structural strength - Glycan tetrapeptide ❖ Basic unit of peptidoglycan - Glycosylic bond can be destroyed by enzyme lysozyme ❖ When destroyed, a possibility that the peptidoglycan will also be destroyed Structure of Peptidoglycan - Gram Positive - Gram Negative Gram Positive Cell Wall - Gram positive bacteria form several layers of peptidoglycan stacked one upon another - Produces acidic molecules called teichoic acids - Also appears blue to purple - Teichoic acid ❖ Attached to the peptidoglycan ❖ Bind divalent metal ions - Lipoteichoic acid ❖ Attached to the lipids Gram Negative Cell Wall - Only small amount of the total cell wall consists of peptidoglycan - Most of the wall is composed of the outer membrane (Lipopolysaccharide/LPS) ❖ Consists of Core Polysaccharide and O-specific Polysaccharide ❖ Ketodeoxyoctonate (KDO), heptoses, glucose, and galactose, are what consists of the polysaccharide in the salmonella species - Toxicity is primarily linked to the LPS layer (lipid A) ❖ Endotoxin is the toxic component - Periplasm and Porins ❖ Space between the outer and inner cytoplasm ❖ Has several types of proteins (binding, etc.) ❖ Porins are proteins that function as channels for the entrance and exit of solutes Archaeal Cell Wall - Variety of cell wall (includes polysaccharides, proteins, glycoproteins, or a mixture of these macromolecules) - Cell walls of some other archaea may lack pseudomurein and might only have polysaccharide Pseudomurein - Backbone formed by alternating repeats of N (acetylglucosamine) and N (acetyltalosaminuronic acid) - Glycosidic bonds between the sugar derivatives is B-1,3 - Amino acids are all L stereoisomer - Immune from destruction by both lysosome and penicillin Difference of Pseudomurein and Peptidoglycan - B-1,4 for peptidoglycan while B-1,3 for Pseudomurein - Acetylglucosamine is attached to a different acid S Layer  - Most common type of cell wall in archaea - Procrystalline surface layer - Interlocking of molecules of protein or glycoprotein Cell Surface Structures - Capsules and slime layers ❖ Functions to attachment of surface and bacterium - Fimbriae, Pili, and Hami ❖ Can be found in prokaryotic organisms ❖ Fimbriae and Pili are filamentous Capsule - Layer organized in a tight matrix that excludes small particles and is tightly attached - Visible by light microscope if cells are treated by India ink Slime Layer - Layer that is easily deformed, loosely attached and does not exclude particles Fimbriae and Pili - Enable cells to stick to surfaces, but Pili is much longer than the fimbriae - Pili facilitates genetic exchange (conjugation/conjugative or sex pili) Hami - Unique attachment structure that resembles a grappling hook - Functions to attach cells to the surface and to one another Virulence Factors - Molecules that contribute to the pathogenicity of a bacterial pathogen Cell Inclusions - Carbon Storage Polymers - Magnetic Storage inclusions ❖ Polyphosphate, Sulfur, and ❖ Magnetosomes Carbonate Minerals ❖ Gas Vesicles ❖ Endospores Poly-Beta-Hydroxyalkanoate (PHA) - Synthesized by cells when there is an excess of carbon and are broken down as carbon energy Glycogen - Polymer of glucose; reservoir of both carbon and energy (produced when carbon is in excess) Polyphosphate Granules - Formed when phosphate is in excess and can be drawn as a source of phosphate Sulfur Storage Products - Oxidized reduced sulfur compounds Carbonate Minerals - Gloeomargarita ❖ Forms intracellular granules of bensonite Magnetosome - Enable some bacteria to orient themselves within a magnetic field - Biomineralized particles of magnetic iron oxides, magnetite, and greigite - Magnetotaxis ❖ Process of migrating along Earth’s magnetic field Gas Vesicles  - Structure that conveys buoyancy and allow cells to position themselves in regions of water Endospores - Highly differentiated cells that are extremely resistant to heat and harsh chemicals - Function as survival structures and enable the organism to endure unfavorable growth conditions Endospore Formation and Germination - Vegetative Cell ❖ Converted into a non-growing, heat-resistant, and light-retractive structure - Sporulation ❖ Occurs when a key nutrient becomes limiting - Can remain dormant for years but can come back to vegetative cell instantly - Activation, germination, and outgrowth (the three steps) ❖ Activation occurs when they are heated for several minutes at an elevated sublethal temperature ❖ Germination is typically a rapid process; loss of retractility ❖ Outgrowth involves visible swelling - Exosporium ❖ Thin protein covering - Spore coats ❖ Layers of spore-specific proteins - Cortex ❖ Loosely cross-linked peptidoglycan - Core ❖ Contains core wall, cytoplasmic membrane, cytoplasm, nucleoid, ribosomes, and other cellular essentials Differences Between Endospores and Vegetative Cells Cell Locomotion - Flagella, archaella, and swimming - Mobility Bacterial Flagella (plural of flagellum) - Long thing appendages (free at one end and anchored to the cell on the other) - Can rotate up to 1000 revolutions per second Flagella Structure and Activity - Filament ❖ Main part; composed of many copies of flagellin - Hook  ❖ Connects filament to flagellum motor - Flagellum motor ❖ Rotor and stator ❖ Rotor has central rod and the L, P, C, and MS rings ❖ Stator consists of Mot proteins that surround the rotor and function to generate torque - Rotation of flagellum occurs at the expense of the proton motive force Archaella (plural of archaellum) - Found in archaea - Structure bears resemblance to type 4 - Impart movement to the cell by rotating pili - Filament is made up of several different - Rotations is driven by hydrolysis of ATP proteins - Methanocaldococcus ❖ Fastest organism on Earth Gliding Movement - Some bacteria are motile but have no flagella - Gliding requires that cells be in contact with solid surface Eukaryotic Microbial Cells - Nucleus and cell division - Mitochondria, hydrogenosomes, and chloroplasts The Nucleus - Contain chromosomes of the eukaryotic - Nucleolus cells ❖ Sito of rRNA synthesis - Histones ❖ Protein that are tightly pack Cell Division - Mitosis ❖ Unique only to eukaryotic cells ❖ During mitosis, chromosomes condense, divide, and are separated into two sets - Meiosis ❖ Converts diploid cell into several haploid cells Mitochondria - Respiration site (aerobic) - Enclosed by double membrane system Hydrogenosomes - Present in anaerobic eukaryotic microorganisms - Lack citric acid cycle enzymes and cristae - Metabolism is strictly fermentative - Oxidation of pyruvate to hydrogen, carbon dioxide, and acetate Chloroplasts - Chlorophyll - Containing organelles of phototrophic microbial eukaryotes that carry out photosynthesis Lecture 3 - Microbial Taxonomy Taxonomy - Science of classification - Provides orderly basis for the naming of organisms and for placing them into categories ❖ Taxa (plural of taxon)  - Diversity of microorganisms with the aim of organizing and prioritizing in an orderly manner Three Components of Taxonomy - Identification ❖ Process of characterizing organisms - Classification ❖ Process of arranging organisms into similar or related groups - Nomenclature ❖ The system of assigning names to organisms Criteria for Classifying Bacteria Carolus Linnaeus - Founding the science of taxonomy - Originated binomial nomenclature (two name system) - Established a hierarchy of taxonomic ranks Binomial Nomenclature Using a Taxonomy Key - Dichotomous Key ❖ Paired statements describing characteristics of organisms Lecture 4 - Flow of Genetic Information - Replication, transcription, and translation in prokaryotes DNA Replication - Gene (plural form of genome) - Nucleic acid (informational macromolecules) - Difference between DNA and RNA ❖ DNA is double stranded while RNA Is single stranded ❖ RNA pentose sugar is ribose while DNA pentose sugar is deoxyribose ❖ Absence of Thymine and is replaced by Uracil in RNA - Purines are Adenine and Guanine - Pyrimidines are Thymine and Cytosine - Nucleic acid backbone is a polymer of alternating sugar and phosphate molecules ❖ Linked by phosphate by 3 carbons, 1 sugar, and 5 prime carbons of the next sugar ❖ Sugar phosphate backbone - Adenine always pairs with Thymine while Guanine always pair with Cytosine Chargaff’s Rule - A = T/U, G = C DNA Replication in Prokaryotes - Semiconservative ❖ Each of the two progeny double helices have one parental and one new strand - Always proceeds from the 5’ end to the 3’ end Origins of Replications - Prokaryotes only have introns while eukaryotes have both introns and exons ❖ Introns are non-coding Leading Strand - DNA synthesis begins at the origin of replication prokaryotes - Replication fork ❖ Zone of unwound DNA where replication occurs - DNA polymerase III ❖ Primary enzyme replicating chromosomal DNA ❖ Requires a primer (primer made from RNA by primase) - Finds 5’ to 3’ strand - Topoisomerase ❖ Prevent supercoiling of the DNA strand ❖ DNA gyrase - Primer is a guide Logging Strand - Occurs continuously on the leading strand - Moving away the replication fork - Due to Okazaki fragments, you may need a lot of primers Bidirectional Replication - Will create to leading and logging strands - 2 replication forks moving in opposite directions - Replisome ❖ Complex multiple proteins involved in replication Proofreading in DNA - Proofreading helps to ensure high fidelity - Occurs in prokaryotes, eukaryotes, and viral DNA replication systems - Polymerase can detect mismatch through incorrect hydrogen bonding - DNA replication is extremely accurate - Mutation rates in cell are 10 to the negative 5 to 10 to the negative 11 per base Transcription - DNA to RNA - RNA polymerase uses DNA as a template - RNA precursors are ATP, GTP, CTP, and UTP - Chain growth is 5’ to 3’ - Initiation, elongation, termination Termination - Hairpin structure - Termination of RNA is governed by a specific DNA sequence - Intrinsic terminators ❖ Transcription is terminated without any additional factors - Rho-dependent termination ❖ Rho protein recognizes specific DNA sequences and causes a pause in the RNA polymerase Unit of Transcription - Unit of chromosomes bounded by sites where transcription of DNA to RNA is initiated and terminated - Some RNAs are not translated - 16s, 23s, and 5s (three types of rRNA) - mRNAs have short half-lives (a few minutes) Transcription in Archaea and Eukarya - Archaea has a much more simpler transcription apparatus than eukaryotic - Archaeal introns excised by special endonuclease - Eukaryotic RNA processing  ❖ Many RNA molecules are altered before they carry out their role in the cell - RNA splicing ❖ Takes place in the nucleus ❖ Removes introns from RNA transcripts ❖ Performed by the spliceosome - RNA capping ❖ Addition of methylated guanine to 5’ end of mRNA - Poly (A) tail ❖ Addition of 100-200 adenylate residues ❖ Stabilizes mRNA and is required for translation Protein Synthesis Translation - Amino acids ❖ Building blocks of proteins (polymers) Translation and the Genetic Code - Translation ❖ Synthesis of proteins from RNA - Genetic Code ❖ Triplet of nucleic acid bases (codon) encodes a single amino acid - Degenerate code ❖ Multiple codons encode a single amino acid - Anticodon ❖ tRNA recognizes codon - Stop codons ❖ Terminate translation (UAA, UAG, UGA) - Start codon ❖ Translation begins with AUG - Reading frame ❖ Triplet code requires translation to begin at the correct nucleotide - Shine-Dalgarno sequence ❖ Ensure proper reading frame - Open reading frame (ORF) ❖ AUG followed by a number of codons and a stop codon in the same reading frame Transfer RNA - At least on tRNA per amino acid - tRNA is cloverleaf in shape - In order for tRNA and amino acid to be brought together it needs certain enzymes (aminoacyl- tRNA) Protein Synthesis - Ribosomes ❖ Sites of protein synthesis - S = Svedberg units ❖ Combination of rRNA and protein Protein Structures - A polypeptide folds to form a more stable structure - Secondary structure ❖ Interaction of the R groups force the molecule to twist and fold in a certain way - Tertiary structure ❖ Three-dimensional shape of polypeptide - Quaternary structure ❖ Number and types of polypeptides that make a protein Protein Folding and Secretion - Denaturation - Occurs when proteins are exposed to extremes of heat  - Causes the polypeptide chain to unfold - Destroys secondary, tertiary, and/or quaternary structure of the protein - Biological properties of protein is lost in denaturation - Tat system ❖ Proteins fold in the cytoplasm are exported by a transport system distinct from Sec, called the Tat protein export system - Cannot unfold in cytoplasm because transport will be hard to do When transcribing for amino acid always put N terminus and C terminus