NUIP 2080 Exam 1 Study Guide PDF

NUIP 2080 Exam 1 (Chapters 1-5, 7) Chapter 1 - Microbes are both cellular (living) and acellular (nonliving) - Acellular infectious agents: viruses, prions - Cellular Microorganisms - Eukaryotes (have nucleus): algae, fungus, protozoa - Prokaryotes (no true nu...

NUIP 2080 Exam 1 (Chapters 1-5, 7) Chapter 1 - Microbes are both cellular (living) and acellular (nonliving) - Acellular infectious agents: viruses, prions - Cellular Microorganisms - Eukaryotes (have nucleus): algae, fungus, protozoa - Prokaryotes (no true nucleus: bacteria, archaea - Microbes vs. Pathogens - Most microbes do not cause disease (they are nonpathogens) - Human Microbiome (Indigenous Microbiota) is composed of all the microbes that live on and in us, have colonized us - Microbes that do cause disease = pathogens - Opportunistic pathogens are microbes that are awaiting the opportunity to spread disease, the only cause disease under certain conditions, when they are in the right spot in the body it is fine, it turns bad when they move to a system they are not normally in - Infectious Disease vs. Microbial Intoxication - Infectious Disease: - Pathogen colonizes person\'s body, and this pathogen causes disease - Microbial Infection: - Pathogen creates a toxin in vitro, person ingests a toxin, this toxin causes disease - Pioneers in Microbiology - Anton van Leeuwenhoek - Considered the "father of microbiology" - Created single lens microscope - Louis Pasteur - Developed pasteurization - Discovered (in the field of wine) that yeast on grapes fermented sugars into alcohol, but bacteria on grapes fermented sugars into vinegar - Heated up grapes to kill the bacteria, and make wine taste better - Robert Koch - Developed Koch's postulates - an experimental procedure to prove a specific microbe is the cause of a specific infectious disease 1. If a microbe causes a disease, everyone who has that disease will be infected with that microbe; the microbe should not be found in healthy organisms 2. That pathogen can be isolate through microbiology and cultured in a lab 3. If culture grown in lab is given to healthy organism, then that individual will become infected with specified disease 4. Once individual is disease you should be able to isolate pathogen again, and this pathogen should be identical to the specific causative agent - If organism fulfills Koch's postulates it is proven to be the cause of that infectious disease Chapter 2 - Limitations of naked eye - Resolving power of unaided human eye is 0.2mm - Microscopes allow us to see things that are too small for our eyes alone to see - Light Microscopy vs. Electron Microscopy - Light Microscopy - uses visible light to magnify a specimen - Resolution is limited by the wavelength of visible light (approx. 0.45µm) - Humans cannot see anything less than half the wavelength of visible light - Electron Microscopy - uses an electron beam and magnets to magnify a specimen - Electron beam illuminates and magnets focus the beam - Allows for visualization of tiny microbes, higher magnification than light microscopes - Cannot view live organisms because it kills them - Resolution is not limited by the wavelength of visible light - Light Microscopes - Simple vs. Compound - Simple Microscope - contains only one lens (basically a magnifying glass) - limited in ability to magnify (4-100x) - Compound Microscope - Contains more than one magnifying lens - Total magnification is product of magnifying power of ocular lens and magnifying power of objective (power of ocular lens x power of objective) - Brightfield vs. Darkfield - Brightfield - See sample against bright background - Visualize natural color of bacteria - Darkfield - See sample against dark background - Visualize light reflected off the bacteria - Phase contrast microscopy - Allows for the observation of living unstained organisms - You can visualize movement of organisms - Electron Microscopes - Transmission vs. Scanning - Transmission Electron Microscope - Uses electron beam to penetrate extremely thin surface - More of a 2d image - Magnification is 1000x greater than that of compound light microscope - Scanning Electron Microscope - Electrons bounce off surface of specimen to produce image of outer surfaces - More of a 3d image - Worse resolution than transmission microscope, but a lot better than light microscope Chapter 3 - Taxonomy - Defined as the process of identifying, classifying, and naming living things - Origin of Taxonomy - Carolus Linneas created hierarchical classification system (2 kingdoms- plants and animals) and binomial nomenclature (refer to organism by Genus & species - Viruses are excluded from taxonomy because they are not living- they don\'t have cells - Cells - Fundamental unit of a living organism - Exhibit basic characteristics of life - Obtain nutrients from environment - Produce energy for metabolism - Grow and reproduce - Respond to environmental stimuli - Can mutate/evolve - Eukaryotes vs. Prokaryotes - Eukaryotes - Have a true nucleus - Have membrane bound organelles - Larger - Prokaryotes - No true nucleus - Fewer organelles - Smaller - Much simpler than eukaryotes but have everything they need to live and reproduce - Cellular Structures of both Eukaryotes & Prokaryotes - Cellular Membrane - Outside structure of cell, controls what moves in/out of cell - Cytoplasm - Semifluid, gelatinous matrix that contains organelles - Important Eukaryotic Cellular Structures - Nucleus - Command center of cell - Contains chromosomes comprised of genes (DNA) that code for all components of the cell (genome) - Ribosomes - Site of protein synthesis, allows cells to make proteins - Also, in prokaryotic cells - Cell Wall -- plants only - External structure that provides rigidity, shape, and protection of cell - Of greater importance in prokaryotes - Motility Structures - Flagella - Long thing protrusions - Propels cell with whip like motions - Cilia - Multiple short hairlike extensions - Beat in coordinated movements to move things past it - Prokaryote Characteristics - No true nucleus, still has DNA - DNA is not bound in nucleus, it is a singular, long, supercoiled strand within cytoplasm - Cytoplasm contains mostly chromosomes and ribosomes - Sometimes includes plasmids which are small circular fragments of DNA - No other organelles - Prokaryotic Bacterial Cell Wall - Very important structure in bacteria - Provides strength and shape - Holds cells together - Primary component is peptidoglycan - 2 polysaccharides w/ a short peptide chain - Prokaryotes need a substantial cell wall to contain everything - Peptidoglycan configuration is very important in characteristic of bacteria, composition classifies bacteria - Gram negative - Peptidoglycan layer is smaller - This layer is sandwiched between plasma membrane (below) and lipopolysaccharide rich outer envelope (above) - Gram positive - Thick robust peptidoglycan layer - Cell membrane is beneath - Prokaryotic Glycocalyx - a slimy gelatinous material produced by the cell membrane - Secreted to coat cell wall - Protects bacteria from phagocytosis - Contains slime layer and capsule - Capsule- well organized and firmly attached - Slime layer- not firmly attached or organized - Prokaryotic Bonus Attachments - Flagella - Long hairs, Allow motility, different in structure than eukaryotic flagella - Fimbriae - Shorter and rigid, cover entire cell or at poles, few to 100 per cell, help cell adhere to surfaces - Pili - Only 1 or 2, longer and thicker, involved in motility- not as much as flagella, sex pilus does conjugation - Prokaryotic Spores (endospore) - Spores are thick walled packets that can survive extreme conditions - Spores contain a copy of chromosome, minimal cytoplasm, and several thick protein coats - Prokaryotic Reproduction - Binary Fission - One cell splits in half to become 2 cells - Chromosome is duplicated one goes to each daughter cell Chapter 4 - Acellular microbes include viruses, viroids, and prions - Viruses - 5 properties that distinguish virus from living cell - Possess RNA or DNA, not both - Unable to replicate on their own, require host cell - Do not divide by binary fission or mitosis - Lack ability to produce energy - Depend on ribosomes and enzymes of host cell to make nucleic acids and proteins so they can replicate - Anatomy (Structure) - Nucleic acid, holds either DNA or RNA - Capsid (coat protein) - Made of capsomeres - Protects viral genome from host endonucleases - Contains binding site - "Nucleocapsid" is nucleic acid and capsid - Some viruses only have nucleocapsid - Envelope (not all viruses) - Derived from host cells - Made of cell wall of host cell, lipids, proteins, carbs - Have binding sites - Classification - By type of genetic material - Is nucleic acid double or single stranded - Is nucleic acid + or - - Presence or absence of capsule - Type of host virus it infects - Theories of evolution - Escaped Gene theory - Viruses are pieces of host cell RNA or DNA that escaped from living cell - Viral Life Cycle 1. Attachment- virus attaches to protein receptor on cell 2. Penetration- virus enters host cell 3. Uncoating -- viral capsid release viral nucleic acid (goes to nucleus and ribosomes) 4. Biosynthesis -- viral RNA/DNA replicated in nucleus, nucleic acid reaches ribosome to make their own proteins 5. Assembly -- new virions are created and packaged 6. Release -- new complete virions are released to go infect other cells - Ways virus can leave the cell - Budding- nucleic acid comes up to surface, forms pouch in cell membrane, and breaks off from cell in vesicle - Leaves damaged cell - Exocytosis -- nucleic acid comes up to surface and virus is spat out, not vesicle - Cell left unharmed - Apoptosis -- virus particles get assembled then burst out of cell - Leads to cell death - Timeframe of Infection - Bacterial Infection - Slow build, binary fission causes doubling of bacteria to occur at steady rate - Can tell when you\'re getting sick, symptoms progress over days - Viral Infection - Replicate by assembly of preformed components into many particles - Make the parts, assemble final product, then release - All synthesis occurs during the eclipse period - No slow build, infection suddenly hits you, go from having 1 virus to 100+ - Latent viral infections - Some viruses remain in infected cells indefinitely - When conditions are right virus can become active - Ex: herpes virus and reemergence of cold sores & varicella (chicken pox) and emergence of shingles - No immune response when not active in cell - Retroviruses - RNA viruses, their genome codes for 2 special enzymes: reverse transcriptase and integrase - Insert viral DNA into host cell DNA and leave it there, host cell will always be infected - Cell not only replicates its own dna but also viral dna - This is an example of a proviruse- viral genome becomes part of host genome - Steps of Retrovirus Infection 1. Virus binds to receptor 2. Fusion -- virus released into cell 3. Reverse Transcription -- reverse transcriptase enzyme translates viral genome (RNA) into DNA 4. Integration -- DNA is chaperoned by integrase enzyme to nucleus, there viral DNA is inserted into host DNA 5. Replication 6. Assembly 7. Budding - Bacteriophages (phages) - Viruses that infect bacteria - They way bacteriophage attacks bacteria is equivalent to how virus attack human cells - Viroids - Short naked fragments of single stranded RNA floating around the world - Can kill plant, no known animal disease caused by viroids - Prions - Small infectious proteins - Can cause fatal neurologic disease (Mad Cow Disease) - Cellular microbes (prokaryotes) include bacteria and archae - Bacteria- single celled organisms - Can be characterized by cell wall - Gram Positive (purple)- thick peptidoglycan layer on top of plasma membrane - Gram Negative (pink)- thin peptidoglycan layer sandwiched between envelope and plasma membrane - Atypical. - no cell wall - Can also be characterized by - shape & arrangement - Cocci- small and round - Diplococci- hang out in pairs - Streptococci -- hang out in long strands - Staphylococci- hang out in clusters - Bacilli- rod shaped (lots of gram -- rods) - Coccobacilli- rounded rods - Vibrio -- bean shaped cells - Coryneform bacilli -- club shaped - Diplobacilli -- pairs - Streptobacillus- strands - Spirilla -- curved - Borrelia - Treponema - Leptospira - Staining - Simple stain -- gives info on shape, size, morphology - Gram stain (gram + or -) - Structural stain -- shows us capsule, flagella, endospores - motility (if and how they move) - colony morphology (what colony looks like in lab), - atmospheric requirements (aerobic or anaerobic) - Obligate aerobes, require oxygen comparable to room air (21%) - Obligate anaerobes- require no oxygen present - Others are in between - There are unique/atypical bacteria - Obligate intracellular organisms- must live inside of host cell - Mycoplasma -- smallest microbe, no cell wall, changes shapes - Archaea - Prokaryotes that live in extreme conditions - Different than bacteria - have cell walls but no peptidoglycan - More like eukaryotes than bacteria Chapter 5 - Eukaryotic Microbes include algae, protozoa, fungi, lichens, slime molds - Pathogenic to humans: protozoa, fungi (algae rarely) - Algae - Photosynthetic protists, more plantlike, but not plants - Rarely cause human infections - Protozoa - Non photosynthetic protists, more animal like - Most are single celled, free-living microorganisms found in soil and water - Characterized by locomotion -- way they move - Can cause disease or be symbiotic with humans - Symbiosis -- living together for mutual benefit - Fungi - Found virtually everywhere - Most diverse group of organisms - Include yeasts, molds, and mushrooms (fleshy fungi) - Can be unicellular (yeats or microsporidia) or multicellular (fleshy fungi) - Cell walls of fungi contain chitin - Saprophytes (saprophytic fungi) live on organic matter in water and soil and absorb nutrients from dead/decaying matter - Considered "garbage disposals" of natural world - Can be classified on sexual reproduction - Budding - Hyphal extension - Spore formation - Anatomy - Hyphae- fungal filaments - Mycelium- mass of intertwined hyphae - Yeast - Eukaryotic, single celled - Usually produce by budding - Found in soil, water, and on surfaces of fruits and vegetables - Can be human pathogens - Candida (Candida Albicans) - Lives on skin and mucous membranes - Opportunistic infections, most likely to infect immunocompromised patients - Cryptococcus - Causes lung infections and meningitis - Again, most likely to infect immunocompromised patients - How they spread\... 1. Adhesion and Colonization a. Penetrate between and within cells 2. Hyphal Penetration and Invasion 3. Vascular dissemination b. Hypae reach blood vessel 4. Endothelial colonization and penetration - Molds - Grow in soil, water, and on foods - Grow as cytoplasmic filaments (hyphae)- hyphae create mycelium - Above surface -- aerial hyphae - Below surface -- vegetative hyphae - Can produce toxins - Dimorphic Fungi - Dimorphic = two forms - Exist at yeast at body temp and mold at room temp - Microsporidia - Obligate intracellular parasitic fungi - Can cause infection in immunocompromised hosts - Ex: Pneumocystis jirovecii - Fleshy Fungi - Not microorganisms we can see them - Ex: mushrooms, toadstools - Medical significance of fungi - Disease caused by fungi- mycoses - Superficial (epidermis) - Cutaneous (dermis) - Subcutaneous (hypodermis) - Systemic (into bloodstream and organs) - Can extend from skin or mucous membranes - Spores can be inhaled - Most commonly opportunistic - Dermatophytes are molds that infect the skin, cause athletes foot, ringworm Chapter 6 - Physiology- vital life process (functions) of organisms - Microbial physiology -- functions of microbes - Essential nutrients -- material that is required for life than an organism cannot synthesize (can\'t make on their own, must obtain from environment) - Metabolism -- chemical reactions that occur within cell - Biologic catalyst -- specialized proteins that start or accelerate a biochemical reaction - Metabolic Enzymes- specialized proteins coded for by microbial genome, to start of accelerate reaction - All metabolic enzymes are biologic catalysts - Metabolic Enzymes - Very specific, a particular enzyme catalyzes one specific reaction, acts on one substrate - Substrate- substance on which metabolic enzyme acts - Unique shape allows enzyme to interact with one substrate - Some require co enzyme or co factor - When an enzyme isn't the right shape, it isn't active - Cofactor attaches to protein, activating it, and making it right shape for substrate to bind - Metabolite is the end product of substrate (broken apart or put together) - When there is interaction between enzyme and substrate - Substrate is changed - Enzyme stays the same - Catabolism v Anabolism - Catabolism (Catabolic Enzymes) - Enzyme breaks down something - Creates cellular energy (ATP) - Anabolism (Anabolic Enzymes) - Enzyme builds something - Uses cellular energy (ATP) - Inhibition of Enzymes - Heavy metals can prevent some enzymes from working - Inhibitors - Are compounds that are similar in shape to substrate - Can be used to prevent enzyme from binding to substrate - If vital enzyme is prohibited, it could lead to death of organism - Bacterial Genetics - Genetics: study of heredity - Genotype: collection of genes possessed by organism - Genotype determines everything about organism - Phenotype: physical traits of organism - Phenotype is determined by genotype - Bacterial Chromosome - Chromosomes (double stranded DNA) code for multiple genes - Genes (found on chromosomes) - Direct function of cell - Provide cell with particular traits - Produce products (usually proteins) important for function, growth, and replication of cell - Genetic Mutations - Are accidental alterations of DNA - Mutations can be - Beneficial- increase the ability of bacteria to survive - Harmful- weaken or kill bacteria - Silent -- no obvious change to cell function - Products of mutation = mutants - Relatively infrequent (1 per million rounds of DNA replication) - Mutagens are physical or chemical agents that increase rate of mutations - Ways Bacteria gather new information - Mutation - Lysogenic Conversion - Process that occurs when - Phage (virus that infects bacteria) transfers genetic info to bacteria - Genetic material integrates into bacterial DNA - Results in bacteria expressing new traits - Transduction - Also mediated by phage - Transfer of genetic material from one bacteria to another - Transformation - Bacterial cell takes up "naked" DNA fragments from environments - Conjugation - Bacteria sex - Movement of genetic material from one bacterium to another - Transmission of plasmid through conjugative pore - Genetic Engineering - Transfer of eukaryotic genes into easily cultured cells - Allows the manufacturing of important gene products (proteins) - Important in synthesis of antibodies, and creation of vaccines - Gene Therapy - Many diseases are a result of a single gene mutation - Gene therapy involves the transfer of a normal gene into the host with disease - This allows host to begin to make normal gene products