BIOL 303 Final Exam Study Guide PDF

BIOL 303 Final Exam Study Guide – Cumulative Section Chapter 1 – Introduction Robert Hooke - He described the common bread mold - Coined the term cell Antony van Leeuwenhoek - He ground lenses to view clothes, then used the same lens to investigate a drop of...

BIOL 303 Final Exam Study Guide – Cumulative Section Chapter 1 – Introduction Robert Hooke - He described the common bread mold - Coined the term cell Antony van Leeuwenhoek - He ground lenses to view clothes, then used the same lens to investigate a drop of lake water. - Described “wee animalcules” and “cavorting beasties” Louis Pasteur - Discovered that air has microorganisms Robert Koch - He established connection between bacteria and disease o Koch’s postulates ▪ Microorganisms must be present in every case of the disease, but they are absent from healthy organisms ▪ The suspected microbe must be isolated and grown in a pure culture ▪ The same disease results when the isolated microbe is put into a healthy host ▪ The same microbe must be isolated from the new host Members of the microbial work o Classification ▪ (comparing 16S RNA sequence) Bacteria, Archaea, and Eukarya ▪ Prokaryotes: no membrane-bound nucleus or organelles ▪ Eukaryotes: have organelles and nucleus o Characteristics o Similarities & differences ▪ Bacteria: Prokaryotes, unicellular, cell wall made of peptidoglycan ▪ Archaea: Prokaryotes, unicellular, cell wall without peptidoglycan ▪ Eukarya: Eukaryote, unicellular or multicellular, cell wall without peptidoglycan Chapter 2-3 – Microscopy and Cell Structure Principles of light microscopy - Bright-field microscopy, dark-field microscopy, phase-contrast microscopy, fluorescence microscopy, and confocal microscopy - So light passes through specimen → through a series of magnifying lenses  - Important factors = o Magnification – ocular x objective. Most light microscopes = parfocal o Resolution – the ability to make smth more clear or detailed. Measured as resolving power (the min distance between two objects that can be still viewed as 2 objects) o Resolution depends on the wavelength of light so the shorter the wavelength, the better. But the more light, the better o Contrast – determines how easily a cell can be seen. Transparent microbes lack contrast Electron microscopy - Electrons replace the light source - Wavelength of electron beam = shorter than light = higher resolution - Image capture on film → electron micrograph - Wavelength = ~100,000x shorter - 2 types of electron microscopes o Transmission (TEM) and Scanning (SEM) o Denser material = more scatter = less e- reach detector = darker o Can see internal structures Simple stains - Use one basic stain (positively charged chromophore) to target the cell on a clear background - Used for morphology – size, shape, arrangement of bacteria - Simple stains 1 color and there is no difference in the type of cell Differential stains o Differentiates cell types ▪ Gram – Gram + and – that differentiates cell wall structures and the thickness of the peptidoglycan layer ▪ Acid-fast – for Mycobacterium species for the cell wall containing mycolic acid Need high temp to stain cell Steps: 1. Bacterial smear with heat fixing 2. Carbol Fuchsin 3. Acid Alcohol 4. Methylene Blue Endospore stain o This is for the Bacillus and Clostridium that form dormant and resistant things called endospores. No dyes work for this but malachite green and safranin to counterstain the other cells  ▪ Steps: 1. Bacterial Smear 2. Malachite green 3. Water 4. Safranin Bacterial cell wall o Structure ▪ Cell envelope = plasma membrane + cell wall + outer membrane (for gram – only) (maybe cell capsule + slime layer) ▪ CELL WALL: Bacterial cell wall: rigid, surrounds the cytoplasmic membrane, determines shape, prevents lysis (hypotonic environment), has a unique chemical structure (so like can determine Gram + or -) Made of peptidoglycan (only found in bacteria) (peptid = protein and glycan = sugar); provides strength/stability The Glycan chain has NAG and NAM alternating subunits that are covalently joined together There’s a Direct-corss link which means the carboxyl groups and amino groups have a link between the amino acids There is also an indirect cross-link with the peptide interbrige, which is 4-6 amino acids attached to a NAM molecule Penicillin-binding proteins (PBP2) are enzymes that catalyze the making of peptide interridge between NAM’s chains Gram positive = peptidoglycan and THICC. Still permeable to things tho. Made with teichoic acid. Negatively charged. Gram negative – more complex than gram+ because it has a thin inner layer of peptidoglycan + outer membrane (made of lipoproteins and lipopolysaccharides (LPS). NO TEICHOIC ACIDs. o Variation ▪ Mycloplasma species = cause pneumonia or “walking pneumonia” Have NO CELL wall and variable shape. Antimicrobials are directed towards cell walls ineffective Membrane has sterols that help with stability ▪ Archaea = have a bunch of different cell wall types No peptidoglycan but smth similar called pseudomurein NAG, NAT Some have s-layers (sheets of self-assembling protein or glycoproteins) Archaeal cell envelopes: theyre different than bacterial cell envelopes bc they lack cell walls, have maybe S-layer, but little known is known  o Antimicrobials ▪ Antibicrobials target peptiglycan like penicillin & lysozyme. Cell wall damage = lysis. ▪ Penicillin = prevents cross-linking of glycan chains. So, it stops the enzyme penicillin binding proteins that cause cross linking with peptide chains More effective against G+ because it can’t pass outer membrane of G- bacteria. ▪ Lysozyme: The enzyme found in tears and saliva that breaks NAG-NAM bands/destroys cell wall structure. More effective against G+ because it can’t pass outer membrane of G- bacteria. Cell wall differences affect staining so G+ = purple, G- = pink Capsules and Slime Layer o Capsules = well-organized layers made of polysaccharides (covalently bonded) and hard to wash away. ▪ The function of both slime and capsule layer is to protect from phagocytes, help in attaching to surface, and exclude viruses. o Slime layer = polysaccharide layers that are not organized and easily washed away Flagella and Pili o Flagella – used to move but too thin to see with light microscope ▪ They swim with rotary flagella and spin it like a helicopter to move thru liquids. Can be used to cause disease. Like Helicobacter pylori can break thru mucus in stomach ▪ 1 flagellum = monotrichous; 2 flagella = amphitrichous; A few = Iophotirchous; Multiple = peritrichous ▪ Flagella has: 1. Filament – made of flagellin (helical shape) 2. Hook – flexible and connects to basal body 3. Basal Body – anchors flagellum into cell wall + cytoplasmic membrane ▪ To make flagella, new flagellin molecules transported through the hollow filament, and the subunits self-assemble with the help of filament cap at the tip not base ▪ To move: atp needed. Use 2 parts: rotor (moving like “motor”) and stator (stationary parts) → to move forward, counterclockwise. Called running. Stopping = clockwise/tumble. o Pilli – thinner than flagella but similar structure. Protein arranged helically.  ▪ Function: 1. So, it allows attachment to surfaces (fimbriae) and other bacteria 2. Twitches/moves on solid surface; or can glide 3. F pilus is ling and used for conjugation (transfer of DNA between 2 bacteria). ▪ Made of pilin proteins ▪ The 2 archaeal pili: Cannulae – tubelike thing on thermophilic archaea. Hami – resemble grappling hooks and can attach to cell surfaces in biofilms Chemotaxis o Movement based on chemicals. o Nutrients = attract; toxins = repel o Runs + tumbles = movement o Random walk but movement away from repellents = “biased random walk” o Done thru chemoreceptors and depends on chemical concentration Endospores o Dormant and form when nutrients go down. Endospores resist heat, UV, gamma, chemical disinfectants, and desiccation. o Endospores are in vegetative/mother cell, which is produced through germination (activation, germination, outgrowth). Commonly produced by Clostridium and Bacillus o Endospore made of: ▪ Core wall – G+ cell wall; has nucleoid and ribosomes ▪ Cortex – many layers of peptidoglycan. Maintains the core’s dehydrated state ▪ Spore coat – several protein layers and calcium ▪ Exosporium – think outermost structure. Not in all species Comparisons between bacteria, archaea, eukaryotes  Morphology and arrangement of prokaryotic cells o Cocci = Spherical o Bacilli = Rods o Vibrio = curved rods o Coccobacillus = short rod o Spirillum = spiral shaped o Spirochete = “helical” shaped and unique form of motility o Pleomorphic = alter their shape based on environment o Pairs = diplococci; chains = streptococci; grape-like structures = staphylococcus Chapter 4 – Microbial Growth Principles of Bacterial Growth o Prokaryote cells divide through binary fission (equally into 2) o Exponential growth = population doubles each cell division o Generation time: time required for population to double (dependent on species and environmental conditions ▪ The power of exponential growth happens during optimal conditions Nt = N0 x 2^n o Nt = final # of cells o N0 = initial number of cells o n = number of generations Formation and characteristics of biofilms o Biofilms = multicellular associations; very common; ubiquitous in nature o Cause slipperiness of rocks, slimy gunk in sink drain, scum in the toilet bowl, dental plaque o Most microbes attach to surface (so theyre sessile) vs. free floating (plantonic) o They adhere to using Extracellular Polymeric Substances (EPS) ▪ Enzymes ▪ Glycoproteins ▪ Nucleic acids ▪ Globular proteins ▪ Polysaccharides o FORMATION: 1. Planktonic bacteria attach to the surface. 2. Density increases (as in they reproduce) and form microcolonies 3. They communicate through autoinducers using quorum sensing 4. More cells = more chemical signals 5. When a limit Is reached, there is a trigger in gene expression 6. Cells produce fimbriae to attach to each other and maybe substrates 7. Cells produce slimy extracellular matrix of proteins, polysaccharides, and nucleic acids (EPS) 8. After a lil while, nutrients and O2 decrease  9. Cells grow flagella and become planktonic a. QUORUM sensing: a. AHL is an autoinducer and moves into the cell when cell population is high. i. Pseudomonas aeruginosa uses this to express virulence factors b. Biofilm characteristics a. Have multiple species b. Channels present when waste and food flow through c. Cells within a biofilm are phenotypically different than planktonic cells d. Different genes are turned on/off so they produce different proteins This causes chronic infections Bacterial growth in laboratory settings o Culture medium is solid or liquid to grow or store microorganisms in lab. o There are 2 requirements for cultivation. 1. Chemically defined and complex. ▪ Chemically defined (used for research experiments): 1. have exact amounts of pure chemicals 2. Quantity of nutrients has to be controlled so that people can see the exact amount of nutrients a microbe uses ▪ Complex/undefined media 1. Exacts amounts of chemical composition is UNKNOWN (like blood agar just has blood) 2. Its practical for routine culture maintenance bc its easy to make o Prokaryotes grow on agar plates or in tubes or broths ▪ Termed batch culture which is a closed system ▪ Nutrients are not renewed so they die ▪ Continuous culture though Is the opposite o Cells on the edge of the agar plate have more oxygen. Cells in the middle have more competition. Nutritional Growth Requirements Streak for isolation o Goal is to obtain pure culture and each streak has less colonies, finally isolating Factors Affecting Growth o Temperature = (although microbes can live in harsh environments) ▪ Microbes cannot regulate their internal temp so enzymes have optimum temps. Below the optimum temps, enzymes are not catalytic and high temp can be lethal Psychrophiles = -20 to 15 C; found in cold and have antifreeze proteins Psychrotrophs = 0 to 30 C; like food spoilage in the fridge. Its still cold but its rotting. Mesophiles = 25 to 45; the ones with humans and animals  Thermophiles = 45 to 70 C; hot springs Hyperthermophiles = 70 to 110 C; most are archaea; these resist denaturing FREEZING CAN PRESERVE FOOD BUT NOT KILL MICROBES Serratia marcesens less than 27 C? = red. More? White o Oxygen 1. Obligate aerobes = cannot grow with O2; final electron acceptor in ETC 2. Obligate anaerobes = needs to NOT have O2; uses alternate electron acceptors for ETC 3. Facultative anaerobes = Prefer oxygen but uses fermentation when O2 nor present 4. Aerotolerant anaerobes = indifference but use fermentation for energy. Aka obligate fermenters 5. Microaerophiles = low O2 for aerobic respiration Laboratory Cultivation o Selective and differential media ▪ Selective: stops some organisms from growing and helps the desired organisms to grow Example: MacConkey agar stops G+ but helps G- to grow ▪ Differential: Some kind of college change helps identify bacteria based on metabolic or phenotypic differences Example: MacConkey agar for lactose fermenters vs. non- fermenters Blood agar: Hemolytic vs. non hemolytic. o Beta = clear zone, everything around it is clear o Alpha = small zone of inhibition  o Gamma = no hemolysis Chapter 5 – Control of microbial growth & antibiotics Keywords o Sterilization – process of removing and destroying all microbes except prions. ▪ Achieved through filtration, heat, chemicals, irradiation o Disinfection – killing, inhibition or removal of disease-causing microorganisms. ▪ Some endospores might still exist. Done through heat or disinfectants ▪ Disinfectants = inanimate (nonliving) objects; aka germicides, bactericides, fungicides ▪ Antisepsis = destruction of microbes on living tissue Antiseptic like listerine, etc. o Decontamination = reduce pathogens so its safe to handle o Sanitation – reduce total microbial population to meet health standards o Pasteurization – briefly heating to reduce spoilage that eliminates pathogens without altering the food o Preservation – delaying spoilage ▪ Bacteriostatic – stops growth but does not kill Highly resistant microbes Biosafety levels for LABS 1. Bio Safety 1: Non-pathogens – no special precautions. Just wash your hands 2. Bio Safety 2: Causes mild disease or difficulty to get through aerosols. Biological safety cabinets and sterilize waste. Most university labs. 3. Bio Safety 3: Aerosol transmitted and potentially lethal WITH TREATMENT 4. Bio Safety 4: Aerosol transmitted and lethal pathogens with NO TREATMENT Medical instruments classification (critical, noncritical, etc.) o Sterilant: heat-sensitive critical instruments like the arthroscope o High-level disinfectants: semi-critical instruments (endoscopes) o Intermediate-level disinfectants: non-critical instruments (stethoscopes) Chemicals classification (sterilant, high-level, etc.) o Sterilant (sporicide) → destroys everything microbial (not prions), but endospores too after 6–10-hour treatment. Example: Bleach o High-level disinfectants (virucide) → destroys all viruses, fungi, and vegetative cells but not endospores. Example: iodine. o Intermediate-level disinfectants (disinfectant) → Destroys most viruses, fungi, vegetative cells but not endospores. Example: lysol o Low-level disinfectants → destroys some viruses, fungi, and vegetative cells. But not endospores, mycobacteria, naked viruses, or endospores. Used on furniture, walls, etc. Chapter 27 – Antibiotics  Selective Toxicity o Selectively kill or inhibit the pathogen while damaging host as little as possible. Causes greater harm to the microbes than the human host bc it causes issues to microbes’ internal structure. o Therapeutic index = toxic dose50/effective dose50 Antimicrobial Action (Bacteriostatic vs -cidal) o Bacteriostatic chemicals inhibit bacterial growth. This action is reversible. o Bactericidal chemicals kill bacteria and this action is irreversible. Antibiotic Spectrum of Activity o Broad-spectrum antimicrobials = wide range ▪ PRO: important for treating acute life-threatening diseases ▪ CON: Disrupts normal microbiota that help protect against pathogens (Dysbiosis) o Narrow spectrum antimicrobials affect = limited range ▪ PRO: less disruptive to microbiota ▪ CON: Requires the identification of pathogen, testing for sensitivity Effect of combinations (additive, synergistic, etc.) o Antagonistic = medications that interfere with each other o Synergistic = when medications enhance each other o Additive = neither Penicillin and derivatives mode of action o Mode of action: blocks enzymes (penicillin-binding protein/transpeptidase). Prevents the making of full cell walls which kills the cells. Mechanisms of Acquired Resistance  o When a microorganism has to the ability to resist the activity of an antimicrobial agent to which it used to get affected by. 1. Spontaneous Mutations a. Occur naturally during replication when just a single bp mutation encoding 30S ribosomal protein yields to resistance to streptomycin. Combination therapy of multiple antibiotics can be used bc theres no freaking way bacteria will gain resistance to both antibiotics. b. Horizontal Gene transfer i. Genes encoding resistance can spread to different strains, species, etc. Most commonly through conjugative transfer with R plasmids. Kirby-Bauer disc diffusion test o It’s the one where you put antibiotics on a streaked agar plate. You see whether a strain is susceptible, intermediate, or resistant. Limitations are that the molecular weight, stability, amount, etc. must be considered. Minimum Inhibitory Concentration vs Minimum Bactericidal Concentration o MIC is the lowest concentration of the drug that stops growth. Tested by serial dilution of antibiotic (broth dilution test). Limitations is we cannot tell if it Is bacteriostatic or cidal. o MBC is the minimal lethal/bactericidal concentration Chapters 7,8,10 – Bacterial Genetics Genotype Phenotype DNA Replication o Enzymes involved o Origin of replication o Differences Between Eukaryotes and Prokaryotes Transcription o Sigma factor o Differences Between Eukaryotes and Prokaryotes Terminology (genome, pangenome, etc.) Bacterial gene regulations o Operon o Enzyme categories (constitutive, inducible, repressible) o Sigma factors o DNA-binding proteins and mechanisms (induction and repression) Eukaryotic gene regulation - RNA interference (RNAi) Chapter 9 – Genetic Change Genetic Change in Bacteria  Spontaneous mutations o Base/point substitution o Deletion/addition o Transposons Induced mutations -> Radiation (UV, Xrays) Repair of thymine dimers Horizontal gene transfer (all types) o Mechanisms Mobile gene pool o Plasmids o Agrobacterium tumefaciens Genetic engineering o CRISPR Chapters 12 & 28 – Identifying and Classifying Bacteria Principles of taxonomy o Identification: process of characterization through morphology, physiology, and genotype o Classification: arrangement of organisms into groups based on identified characteristics o Nomenclature – System of assigning names Microscopic morphology – first step; uses to shape, size, staining, etc. to determine the broad characteristics. Helps with the decision for appropriate therapy. Biochemical tests – o Ph indicators o Sugar fermentation which has phenol red. If positive, then bacteria ferment sugar = red o Urease production – Ammonia and CO2; phenol red o Breath test – used to detect helicobacter pylori – patient drinks solution with carbon-labeled urea and produces CO2 and this is captured and tested Sequencing Ribosomal RNA Genes – 16s rRNA is used bc its stable, has conserved regions (identical regions) and variable regions (different regions). o Process: DNA isolated from pure culture o 16s rDNA is PCR-ed using primers that attach the conserved/identical regions o Goes through Sanger sequence o The variable/different region is compared to known databases Characterizing Strain Differences (all typing methods) o Biochemical typing → a group with “metabolic pattern” is called biovar or biotype o Serological typing → a group with "antigens” called serovar or serotype o Phage typing → relies on differences in susceptibility to bacteriophages  o Antibiograms → Antibiotic susceptibility with zones of inhibition o Molecular Typing → uses subtle differences in DNA; Restriction fragment length polymorphisms (RFLP) cut DNA, separate fragments with gel electrophoresis. Different RFLP = different strain. For this, the 16S gene is NOT unique enough so the whole genome is used Chapter 6 – Phages Infectious agents, not organisms General Characteristics of Viruses o Anatomy o Informal grouping Lytic phage infections Temperate phage infections Filamentous phage infections Specialized Transduction Bacterial Defenses Against Phages Chapter 11 – Animal Viruses Replication of RNA viruses Steps (5): 1. Attachment → viral spikes (made of glycoproteins) bind to receptors on host cell surface. Specific range. Narrow host range – influenza; broad host range – rabies virus. 2. Entry – only enveloped viruses enter thru endocytosis and fusion with cytoplasmic membrane, leaving free nucleocapsid. a. If enveloped = viral envelope fuses with endosome membrane b. If not enveloped = nucleic acid is released in cytoplasm 3. Uncoating – separation of nucleic acid from protein coat (triggered by virus-host interactions) 4. Synthesis → making new viral particles a. Expression of viral genes to make the structure b. The actual making and duplicating copies of the genome 5. Replication of DNA viruses a. It happens in the host cell nucleus and uses host dna poly. dsDNA replication straight forward. Antigenic Drift vs. Shift o Drift → Minor change in virus genetic code which slowly causes mutations. o Shift → if 2 different strains of a virus infect the host at the same time, the make a novel hybrid strain. Sudden, major shift in the virus genetic makeup. Chapter 25 – Pathogenesis Principles of Infectious Disease o Resident vs transient microbiota. o Disease o Pathogen o Host o Colonization o Symptoms vs. Signs o Primary vs. Secondary Infection o Opportunistic Pathogen o Virulence o LD50 o Toxicity o Infectious dose o Disease triangle o Acute vs Chronic vs Latent Infections