Exam 1 Objectives - General Microbiology - Spring 2011 | BIOS 350, Study notes of Microbiology

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University of Illinois at Chicago BIOS 350--General Microbiology Exam 1 Objectives – Spring 2011 1) describe the importance of microbes for ourselves and the planet microbes contain an estimated 50% of the biological carbon and 90% of biological nitrogen on Earth Greatly exceed every other group of organisms on the planet Found everywhere from geothermal vents to ocean depths of the coldest Arctic ice Major contributors to the functioning of the biosphere Indispensible for the cycling f the elements essential for life Source of nutrients at the base of all ecological food webs Some microorganisms carry out photosynthesis Some microbes inhabit humans and is also important because they help the body digest food and produce vitamins B and K Modern biotechnology rests upon a microbiological foundation…microbes are necessary for production of bread, cheese, beer, antibiotics, vaccines, vitamins, enzymes and many other products Produce more oxygen than trees 2) describe the science of microbiology and how we define microorganisms. Microbiology: Generally defined as the study of organisms too small to be clearly seen by the unaided eye Microorganisms: these organisms are relatively simple in their construction and lack highly differentiated cells and distinct tissues o Less than 1mm in diameter and cannot be seen clearly by naked eye o Simple in construction and are characterized as either procaryotic or eukaryotic o Some are still visible without the help of a microscope 3) differentiate between prokaryotic and eukaryotic organisms. Procaryotic cells lack a true membrane-delimited nucleus o organisms with a primordial nucleus o have much simpler morphology than eukaryotic cells Eucaryotic cells have a membrane-enclosed nucleus, are more complex morphologically and are usually larger than procaryotic cells 4) differentiate between the old five kingdom classification system and the current three domain system. Old five kingdom scheme includes Monera, Protista, Fungi, Animalia and Plantae with microbes placed in the first three kingdoms Current three domain system: Bacteria (true bacteria), Archaea, Eukarya Carl Woese in 1970s demonstrated difference in Bacteria and Archaea which were previously both classified as Monera The five kingdom classification system was too simple 5) describe the general features of the members of the domain Bacteria, Archaea, and Eucarya. Bacteria (Termed bacterium) o Most prokaryotes that are usually single-celled organisms o Most have cell walls and contain peptidoglycan o Abundant in soil, water, and air o Major inhabitants of our skin, mouth, and intestines o Some live in extreme pH, extreme temperature, or salinity o Most play beneficial roles as cycling elements in biosphere, breaking down dead plant & animal material and producing vitamins o Cyanobacteria (blue-green algae) – produce significant amount of O2 via photosynthesis Archaea (Termed archaeon) o Unique rRNA sequence (ribosomal RNA) o Lack peptidoglycan in cell walls and have unique membrane lipids o Some have unusual metabolic characteristics o EXTREME temperatures o Thermophiles, halohiles; no pathogenic archaea yet identified o Produce methane gas Eucarya o Includes microorganisms classied as protists/fungi (as well as plants and animal  NOT microorganisms) o Protists: unicellular, but larger than prokaryotes; photosynthetic protists and cyanobacteria produce 75% of O2 in planet o Protozoa: unicellular, animal-like protists and motile usually…grazers & hunters…obtain nutrients by ingesting microbes and organic matter o Fungi: microorganisms ranging from unicellular form s(ueast) to molds and mushrooms  molds and mushrooms are multicellular and form thin, threadlike structures hyphae  absorbe nutrients from environment  make bread rise, produce antibiotics, decompose dead organisms  some cause plant diseases as well as in humans and other animals o also water mold and slime mold are in this domain o few cause disease in human and animals o algae and protozoa obtain energy and food in different ways, but still under the Protista kingdom o membrane-bound organelles o 6) describe a typical virus. Virus: acellular entitites that must invade a host cell to replicate Simplest is only composed of proteins and nucleic acid Smallest of all microbes (smallest is 10,000 times smaller than a typical bacterium) Cause a range of diseases including some cancers (oncogenes  chances of cancer are higher) (viroids and virusoid  composed of only RNA prion composed of only protein) Don’t obtain energy and material on their own Their genetic material can change over time  can evolve Smaller than procaryotes Don’t have a plasma membrane 7) differentiate between the fields of medical microbiology, immunology, microbial ecology, and microbial genetics and discuss the importance of each. Medical microbiology: diseases of humans and animals o Medical microbiologists identify the agent causing infectious diseases and plan measures for their control and elimination o Often involved in tracking down new, unidentified pathogens such as the agent that causes variant Creutzfeldt-Jakob disease (human version of ‘mad cow disease’), hantavirus, West Nile virus, and virus responsible or SARS o Microbiologists also study ways in which microorganisms cause disease Immunology: concerned with how the immune system protects the body from pathogens and the response of infectious agents Origin of nucleus is still unresolved Other thery: endosynmbiosis hypothesis Procaryotes to protoeucaryotes (have nucleus but not organelles, no membrane) to eucaryotes procaryotes do cleavage and eucaryotes have spindle fibers the nucleus developed mechanisms 15) describe the current views on the evolution of mitochondria and chloroplast along with the evidence supporting these views. Endosymbiotic hypothesis: generally accepted as origin of mitochondria and chloroplasts o both organelles have bacteria-like ribosomes o most have a circular chromosome o both are double membrane o both can replicate independently of the cell mitochondria are believed to have descended from α-proteobacteria ancestor that became engulfed in a precursor cell…provided function essential to host (possibly for oxygen toxicity elimination since intracellular bacterium was aerobic) also accounts for evolution of chloroplasts from endosymbiotic caynobacterium…the cyanobacterium gave rise to green algae and plant cholorplasts mitochondria and hydrogenosomes are aerobic and anaerobic versions of same ancestral organelle Endosymbiotic events needed for evolution of mitochondria happened later and gave rise to early fungi and animal cells, eventually endosymbiotic events  development of chloroplasts and plants o Believe that chloroplast came after mitochondria 16) explain how heritable genetic changes take place in prokaryotes. Genetic heritable changes in Archaea and Bacteria are introduced by o Mutation o Lateral gene transfer (importance of transduction)  3 types:  transformation – procaryotes take in naked DNA from the environment and there’s naked DNA because it’s released from broken down organisms and dying organisms  conjugation – bacteria share plasmids through their sex pili  transduction – viruses (more specifically bacteriophages) deliver genetic material into the cell and make new ones Procaryotic evolution is rapid o Haploid genome o Rapid rate of cell division prockaryotic evolution results in generation of microbial diversity upon selective processes ( new species) When selection is applied, very small genetic differences can result in one population taking over Haploid genome – having one copy of each gene, there is no backup copy, thus you see changes quicker 17) describe the field of taxonomy and the differences between classification, nomenclature, and identification. Taxonomy: the science of biological classification. Consists of classification, nomenclature, and identification Classification: scheme by which to organize (taxa) Nomenclature: branch of taxonomy concerned with assigning name to taxonomic groups Identification: process of determining if a particular isolate belongs to recognized taxon 18) list the taxonomic ranks for the prokaryotes. Rank: domain (either bacteria or archaea for prokaryotes), phylum, class, order, family, genus, and species o King Philip Came Over From Great Spain (eucaryotes) o Domain, phylum, class, order, family, genus, species, and strain (for bacteria)  Strain: different ‘strains’ of the same thing, for example: different types of flu 19) explain how the prokaryotic definition of species differs from the typical biological definition of species. Cannot use definition based on interbreeding because procaryotes are asexual collection of strains that share many stable properties and differ significantly from other groups of strains Also suggested as a definition of species collection of organisms that share the same sequences in their core housekeeping genes o housekeeping genes: create proteins that are enzymes that regulate metabolism 20) explain the meaning of strain, biovar, morphovar, and serovar. Strain - Descended from a single, pure microbial culture o Eukaryotic subspecies is a correlation biovars – differ biochemically and physiologically o ex: one type can digest sugar and one can’t o ex: one can produce toxin and one can’t morphovars – differ morphologically o have same general shape, but some strain have capsules and one doesn’t  capsulated bacteria are more likely to cause disease serovars – differ in antigenic properties o antibody generator that produces other 21) describe the importance of scientific names and how to properly write out a scientific name. each species is assigned to a genus; the genus is a well-defined group of one or more species that is clearly separate from other genera binomial system (Linnaues): first part is capitalized and the generic name – second part is the uncapitalized species name/specific epithet species name is stable, in contrast, generic name can change if organism is assigned to another genus 22) differentiate between the various classical and molecular characteristics which are used to help determine a microbe’s taxonomy and phylogeny. Classical characteristics o Morphological –shape, capsule, size o Physiological – directly related to nature and activity of microbial enzymes and transport proteins  What happens in the cell o Metabolic – same as physiological o Ecological – ability of microorganism to colonize in a specific environment  Where the organism might grow, habitat o Genetic – study of chromosomal gene exchange via transduction, transformation, conjugation  Question to ask:does conjugation occur? Molecular characteristics o nucleic acid base composition – microbial genomes may be directly compared, and taxonomic similarity estimated (Greater G-C connection  stronger bonds due to H bonds) if organisms differ in G+C content by more than 10% their genomes are quite different  ratio of G & C o nucleic acid hybridization – similarity between genomes can be compared more directly by use of nucleic acid hybridization studies. Two strains whose DNAs show at least 70% releatedness under optimal hybridization conditions and less than 5% in Tm = often considered members of same species  separating DNA strain between organisms and then allowing them to mix  make the DNA single stranded, mix them together to see how much hydrogen binding occurs  more hydrogen bonds means they are more related o nucleic acid sequencing – actual analysis of the sequences of nucleic acid, more bases in common means the organisms are more in common o genomic fingerprinting – similar to DNA fingerprinting  cut with restriction enzymes and determine banding patterns o amino acid sequencing – directly reflect mRNA sequences…sequences of proteins with dissimilar functions often change at different rates…determine amino acid sequence of proteins with same function  most direct approach. If sequences are similar, may be related  not as specific as DNA sequencing  isolate similar proteins and analyze the amino acid sequence 23) describe the various types of phylogenetic trees and how to interpret them. Universal phylogenetic tree - (proposed by Norman Pace) analysis based on SSU rRNA sequence analysis of organisms from all three domains, doesn’t measure time but evolutionary distance between organisms Nodes: taxonomic unit (ex: species, genes) Terminal notes: living organisms Eosites – sulfur dependent procaryotes that form a separate through that is more related to eukaryotes than Archaea Evolutionary distance – measures difference between sequences of species Parsimony analysis – relationships are determined by estimating the minimum number of sequence changes required to give the final sequences being compared Some can be rooted or unrooted o Rooted: gives a node that serves as the common ancestor o Unrooted: phylogenetic relationships without providing evolutionary path 24) discuss the impact horizontal gene transfer has had on the development of phylogenetic trees. Extensive horizontal gene transfer has occurred within and between domains Pattern of microbial evolution is not as linear and treelike as once thought One of the biggest problems of constructing a satisfactory tree is how frequent horizontal gene transfer occurs 25) explain the importance of proper preparation and staining of microbial specimens. Increases visibility of specimen (when using a light microscope) Accentuates specific morphological features Preserves specimens 26) define fixation and differentiate between heat and chemical fixation with examples. Fixation (def.) – preserves internal and external structures and fixes them in position o Inactivates enzymes that might disrupt cell morphology and toughens cell structures so that they do not change during staining and observation o Microorganism is usually killed Heat fixation – usually used with procaryotes o Preserves overall morphology but not internal structures o Ex: smear staining o To observe the flagella, their thickness is increased by coating them without mordant such as tannic acid and potassium alum, and then staining with pararosaniline or basic fuchsin 31) describe the size, shape, arrangement and any variation on these for prokaryotic organisms. Prokaryotes lack internal membrane systems Prokaryotes are divided into bacteria and archaea Bacteria and archaea differ in many physiological and biochemical traits Shapes:  Two most common shapes are cocci and rods  Cocci o roughly spherical cells o exist singly or can be associated in characteristic arrangements that are frequently useful in their identification o diplococci arise when cocci divide and remain together to form pairs. o Long chains of cocci result when cells adhere after repeated divisions in one plane— Streptococcus, Enterococcus, & Lactococcus o Divisions in three planes can produce symmetrical clusters of cocci o Staphlococci – sheet of cocci cluster o Tetrad – 4 cocci cluster o Sarcinae – 8 cocci cube  Rods o Bacillus megaterium is an example of rod-shaped bacteria. o Streptobaccili – long chain of rods o Rods, sometimes called Bacilli differ considerably in their length-to-width ratio (cocobacilli = short and white) o Shape of the rod’s end varies between species and may be flat, rounded, cigar-shaped or bifurcated. o Many rods occur singly, but some remain together after division to form pair or chains  Vibros o most-closely resemble rods, are “comma” shaped  Spirilla o Rigid, spiral-shaped prokaryotes that usually have tufts of flagella at one or both ends of the cell  Spirochetes o Flexible, spiral-shaped bacteria that have a unique, internal flagellar arrangement. o Actinomycetes typically form long filaments called hyphae and may branch to form a network called mycelium (they are similar to filamentous fungi in this sense)  Hyphomicrobium is oval- to pear-shaped and produces bud at the end of long hypha.  Few prokaryotes are flat, square-to-rectangular boxes like myxobacteria.  Some prokaryotes are variable in shape and lack a single, characteristic form called pleomorphic. 32) identify and label the structures associated with a prokaryotic cell. Plasma membrane Selectively permeable barrier, mechanical boundary of cell, nutrient and waste transport, location of many metabolic processes (respiration, photosynthesis), detection of environmental cues for chemotaxis (with special receptor molecules), electron transport chain, lipid bilayer in which proteins float Gas vacuole Buoyancy for floating in aquatic environments Ribosomes Protein synthesis Inclusion bodies Storage of carbon, phosphate, and other substances Nucleoid Localization of genetic material (DNA) Periplasmic space Contains hydrolytic enzymes and binding proteins for nutrient processing and uptake Cell walls Provides shape and protection from osmotic stress Capsules and slime layers Resistance to phagocytosis, adherence to surfaces Fimbriae and pili Attachment to surfaces, bacterial mating Flagella Swimming motility Endospore Survival under harsh environmental conditions Cytoplasm Location of glycolysis *no single prokaryote possesses all of these structures at all times. Some are found only in certain cells in certain conditions or in certain phases of the life cycle. Membranes are an absolute requirement for all living organisms Plasma membrane encompasses the cytoplasm Some prokaryotes also have internal membrane systems o Photosynthetic cyanobacteria = have chloroplasts; thylakoids have membranes 33) describe the chemical nature and discuss the function of the plasma membrane in a prokaryotic cell. Separate the cells from its environment Selectively permeable barrier o it allows particular ion and molecules to pass, either into or out of the cell, while preventing the movement of others. Special receptor molecules = detect and respond to chemicals in surroundings o Ex: cells with flagella swim towards nutrients Membranes are an absolute requirement for all living organisms (thus viruses, who don’t have the membrane, is one point where it is considered non-living) o Quorum sensing – sending out chemicals to similar bacteria to read population numbers. Once the population is high enough, the cells start producing toxins  The toxins kill tissue = more nutrients for bacteria Plasma membrane encompasses the cytoplasm o Surrounds the cytoplasm and its contents o Glycolysis occurs in cytoplasm o Electron transport chain (in eukaryotes, in the mitochondria) in plasma membrane Some prokaryotes also have internal membrane systems o Plasma membrane vary depending on the lipids they carry Functions of the plasma membrane o Separation of cell from its environment o Location of crucial metabolic processes o Detection of and response to chemicals in surroundings with the aid of special receptor molecules in the membrane o Selectively permeable barrier (some molecules are allowed to pass into or out of the cell. Transport systems aid in movement of molecules) Transport systems are used for tasks such as nutrient uptake, waste excretion and protein secretion. Prokaryotic plasma membrane is also the location of a variety of crucial metabolic processes: respiration, photosynthesis, and the synthesis of lipids and cell wall constituents. Membrane contains special receptor molecules that help prokaryotes detect and respond to chemicals in their surroundings. The plasma membrane is in lipid bilayer structure with proteins afloat in them o Membrane is amphipathic – asymmetric, with polar head outside (hydrophilic) and nonpolar tails inside (hydrophobic) o Saturated – all single C-C bonds. Makes membrane more stiff and rigid because of more hydrophobic interactions o Unsaturated – has some double C-C bonds. Makes membrane less stiff and more fluid because the tails are shorter and thus less hydrophobic interactions. Also, the double bonds create kinks in the tail, spreading the phospholipids out a little bit. Peripheral protein– loosely associated with the edge of the membrane and easily removed Integral – embedded within the membrane and not easily removed (amphipathic) o Polyphosphate Granules – Made up of volutin granules and metachromatic granules  Turn reddish pink when stained with methylene blue  Linear polymers of phosphates o Sulfur Granules – store sulfur for extra energy  Sulfur used in proteins, energy from hydrogen sulfide o Magnetosomes – contain iron in the form of magnetite = orient cells in magnetic fields (point away from north). Kind of rare.  Detect magnetic fields and allow them to swim to down in their environment  Help detect the magnetic field line  Microaerophiles = use low concentrations of O2 for metabolism  Swim to find the layer of H2O where O2 levels are the most beneficial 38) compare and contrast the structure and function of prokaryotic and eukaryotic ribosomes. Complex structures consisting of protein and RNA Sites of protein synthesis Smaller than eucaryotic ribosomes o procaryotic ribosomes Þ 70S o eucaryotic ribosomes Þ 80S (slightly bigger. Sediment out faster) S = Svedburg unit, a measure of sedimentation velocity in a centrifuge Prokaryotic: Site of protein synthesis and smaller than Eukaryotic ribosomes 39) describe the nature of the nucleoid region in the prokaryotic cell. Irregularly shaped region. Just the location where the prokaryote makes chromosomes. Location of chromosome usually 1/cell Not membrane-bound 40) compare and contrast the bacterial main chromosome and a plasmid. Chromosome o Usually a closed circular, double-stranded DNA molecule o Looped and coiled extensively o Nucleoid proteins probably aid in folding o nucleoid proteins differ from histones Plasmid o Usually small, closed circular DNA molecules o Exist and replicate independently of chromosome o Have relatively few genes present o Genes on plasmids are not essential to host but may confer selective advantage (e.g., drug resistance) o Not in all prokaryotes o Conjugation – prokaryotes sharing plasmids 41) discuss the role of the cell wall for the prokaryotic cell paying close attention to cellular changes when cells are placed in an isotonic, hypotonic, or hypertonic solution. Cell Wall o Rigid structure that lies outside of the plasma membrane = determines the shape  Protects the cell from osmotic lysis  May also contribute to pathogenicity (def: protect from harmful material) Very few prokaryotes lack cell walls (ex: Mycoplasma) Isotonic – just right Hypotonic – more water outside of the cell; water goes into cell o No cell wall eukaryote -takes in too much water and explodes from pressure = osmotic lysis o Prokaryote with cell wall – cell wall prevents cell from bursting Hypertonic – More solutes inside = everything shrivels up o No cell wall eukaryote – shriveled. o Prokaryote with cell wall – cell wall remains, but plasma membrane still shrivels = plasmolysis 42) describe the chemical structure of bacterial peptidoglycan and not how the peptidoglycan subunits are arranged in a Gram positive and Gram negative cell. Bacteria are divided into two major groups based on the response to gram-stain procedure o Gram-positive bacteria stain purple  Thick peptidoglycan o Gram-negative bacteria stain pink  Thin peptidoglycan Staining reaction due to cell wall structure Meshlike polymers composed of identical subunits Contain N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) (has lactic acid) Chains of peptidoglycan subunits are cross-linked by peptides Pentaglycine interbridge – only found in Gram positive Peptide bonds – found in both Gram positive and negative Murein – similar to peptidoglycan 43) diagram and label a Gram positive cell wall discussing the function of all structures in detail. Gram-Positive cell walls o Composed primarily of peptidoglycan o May also contain large amounts of teichoic acids  Teichoic acids – polymers of glycerol or ribitol joined by phosphate groups. Covalently connected to the peptidoglycan itself (if attached to plasma membrane lipids = lipoteichoic acids). Give Gram-positive cell wall negative charge. May help in maintaining the structure of the wall. o Some gram-positive bacteria have layer of proteins (wall surface proteins) on surface of peptidoglycan Periplasmic space of gram-positive bacteria o Lies between plasma membrane and cell wall and is smaller than that of gram-negative bacteria o periplasm (fluid in periplasmic space) has relatively few proteins o enzymes secreted by gram-positive bacteria are called exoenzymes The periplasmic space of the gram-positive bacteria: lies between the plasma membrane and the cell wall and is smaller that that of the gram-negative bacteria because the peptidoglycan layer in the gram-positive is much thicker. 44) explain the role of an exoenzyme produced by a prokaryotic cell. Exoenzymes perform many of the same functions that periplasmic enzymes do for gram-positive bacteria Aid in breaking down the area around the cell or protect the surrounding o Proteins can pass through plasma membrane Stay in periplasmic space Attached to plasma membrane Only present in gram-positive 45) diagram and label a Gram negative cell wall discussing the function of all structures in detail. Consist of a thin layer of peptidoglycan surrounded by an outer membrane Outer membrane composed of lipids, lipoproteins, and lipopolysaccharide (LPS) No teichoic acids More complex than gram-positive walls Peptidoglycan is ~2-5% of wall weight Periplasmic space (very large) differs from that in gram-positive cells o may constitute 20-40% of cell volume o many enzymes present in periplasm Outer membrane lies outside the thin peptidoglycan layer Braun’s lipoproteins connect outer membrane to peptidoglycan