Microbiology Exam 2 PDF

List the 6 essential macronutrients and name 1 of the essential micronutrients of a cell and summarize the overall use for them in the cell: Macronutrients: 1) Carbon - structure of proteins, nucleic acids, lipids 2) Nitrogen - structure of proteins, nucleic acids, ATP...

List the 6 essential macronutrients and name 1 of the essential micronutrients of a cell and summarize the overall use for them in the cell: Macronutrients: 1) Carbon - structure of proteins, nucleic acids, lipids 2) Nitrogen - structure of proteins, nucleic acids, ATP 3) Oxygen - structure of proteins, lipids, carbohydrates, nucleic acids 4) Hydrogen - hydrogen bonds: amino acids, lipids, nucleic acids, and sugars ( they maintain pH and respiration) 5) Phosphorus - structure of nucleic acids, lipids and ATP, found in coenzymes such as NAD+ 6) Sulfur - component of some vitamins (vitamin B1) and amino acids Met and Cys Micronutrients: 1) Iron and zinc 2) Potassium 3) Magnesium 4) Calcium Nutrients: acquired from environment to be used for cellular activities Macronutrients: required in relatively large quantities; play principal roles in cell structure and metabolism Micronutrients (trace elements): present in smaller amounts; involved in enzyme function and maintenance of protein structure. Briefly describe the process of binary fission: 1) A young cell 2) Chromosome is now replicated and new and old chromosomes move to different sides of cell 3) Protein band forms in center of cell 4) Septum formation begins 5) When septum is complete, cells are considered divided. Some species will separate completely while others remained attached, forming chains or doublets > 27 protein complex = division Define generation/doubling time, and explain how it leads to exponential growth: Generation time (doubling time): - Time required for complete fission cycle - Each cycle doubles population - Typically 20-60 minutes (shortest is 10 min, longest is days) - Influences incubation time Exponential growth: - Increasing bacterial population where the number of cells doubles at a constant rate with each generation Compare and contrast the four phases of growth in a bacterial growth curve, and draw a graph representing these phases of the growth curve: Growth curve = predictable pattern of growth in a population, typically measuring growth in a broth culture over time a) Lag phase - Flat line on graph when population appears not to be growing; Newly inoculated cells require a period of adjustment, enlargement, synthesis b) Exponential (log) phase - Period during which growth curve increases geometrically; continues as long as cells have adequate nutrients and favorable environment c) Stationary growth phase - Population enters survival mode due to limiting factors (nutrients/space/etc); Cells stop growing or grow slowly (some cells dead) d) Death phase - Limiting factors intensify and cells begin to die at an exponential rate Describe how we commonly quantify bacteria using key terms (2 ways): 1) Turbidimetry or OD600 (optical density at 600 nm) - measures turbidity (cloudiness) using 600 nm wavelength passing through the sample 2) Visible count technique - total number of cells counted over given time period -> count colonies of serial dilutions Explain the key terms used to express a microbe’s range of growth temperatures and oxygen requirements: 1) Temperature - [Cardinal temperatures] = range of temperatures for growth of given microbial species - Small chemical differences in bacterial membranes which affect their fluidity allow them to thrive at different temperatures - Temperature impacts if and how fast/slow microbe grows - Minimum temperature – lowest temperature they can survive - Maximum temperature – highest temperature they can survive - Optimum temperature – ideal temperature range to grow - -20 degrees C = freezer - 4 degrees celsius = refrigerator - 27 degrees C = room temperature - 37 degrees C = human body temperature - 100 degrees C = boiling point 2) Gases: - Oxygen requirements: Cellular reactions produces several toxic oxygen products = Superoxide ion (𝑂2 −), hydrogen peroxide (𝐻2𝑂2), hydroxyl radicals (𝑂𝐻−), singlet oxygen (O or 1𝑂2) - Microbes fall into 1 of 3 categories: 1) Use oxygen and can detoxify it  2) Can neither use oxygen nor detoxify it 3) Do not use oxygen but can detoxify it 5 groups of organisms based on oxygen requirements: 1) Aerobe: - Use oxygen - Enzymes to process toxic oxygen products - Obligate aerobe: cannot grow without oxygen (most fungi and protozoa; some bacteria) 2) Facultative anaerobe: - Can use but does not require oxygen - Capable of growth in absence of oxygen - Many bacteria in this category (pathogens included) 3) Anaerobe: - Does not use oxygen - Strict/obligate anaerobes: die in presence of oxygen ( often live in deep muds, lakes, oceans and soil; human body this could be large intestine or oral cavity) 4) Microaerophile: - Does not grow at atmospheric concentrations of oxygen - Requires small amount of oxygen 5) Aerotolerant anaerobes: - Do not use oxygen - Can survive and grow to limited extent in its presence - Possess alternative mechanisms for breaking down toxic products Summarize each of the environmental factors impacting growth and if applicable, name the types extremophiles that live under those conditions: 1) Temperature: - Mesophiles = majority of medically significant organisms - 10 degrees C - 50 degrees C - Optimum 20 degrees C to 40 degrees C - Most human pathogens: 30 degrees C - 40 degrees C - Extremophiles: Psychrophiles and Thermophiles - Psychrophiles: “love” cold temperatures a) -15 to 15 degrees C; cannot grow > 20 degrees C b) Arctic locations - Thermophiles: “love” hot temperatures a) 45 - 80 degrees C  b) Hyperthermophiles: 80 - 113 degrees C, cannot grow < 50 degrees C c) Volcanic waters/soils and submarine vents 2) Gases 3) pH: - Most microbes prefer/require neutral pH - Alkalinophiles: prefer/require basic/alkaline environment - Hot pools and soils with high levels of basic minerals (Natronomonas- archaea) - Bacteria that decompose urine create alkaline conditions (Proteus, Klebsiella – both bacteria) - Acidophiles: prefer/require acidic environment - Thermoplasma (archaea) - Hot coal piles, pH 1-2 (1M HCl pH 0) - Molds and yeasts tolerate acid = common spoilage agents of pickled foods 4) Osmotic pressure: - Most microbes prefer/require isotonic environments - Osmophiles: high solute concentration; have cell envelope modifications to survive - Facultative halophiles: Resistant to salt (e.g. Staphylococcus aureus) MSA - Obligate halophiles: Require high concentrations of salt for growth (9-25% NaCl) - Extreme halophiles: Require salt, can grow in 36% NaCl such as in inland seas, salt mines, and in salted fish 5) Hydrostatic pressure: - Pressure exerted by water/fluid (at equilibrium at any point in time) due to the force of gravity - Most microbes prefer atmospheric pressure - Barophiles: strictly adapted to up to 1000x (deep sea) atmospheric pressure 6) Radiation: - Sunlight/UV - Photosynthesizers can use visible light rays as energy source, e.g. algae, cyanobacteria - Non-photosynthesizers damaged by light - Some radiation used as antimicrobial treatment 7) Fluid flow: - Many microbes live in fluid environment  - Fluid flow impacts population in attachment, nutrient access, motility, etc. 8) Other microbes: - Synergistic or antagonistic relationships between microbes can influence growth - Synergism: working together, e.g. biofilm, quorum sensing - Antagonism: toxin secretion/competition with other species 9) Chemicals: - Nutrient ability: Already discussed – is the right “food” available? - Antimicrobials: Agents that kill microbes First powerpoint^^ Name the four major contributions to the carbon cycle: The carbon cycle: carbon exists predominantly in mineral state and as organic reservoir in bodies of organisms (microbes play a key role in C recycling) 1) Respiration 2) Fermentation 3) Carbon fixation = photosynthesis 4) Methane production (methanogens) Define methanogen and explain the role of methanogens within the carbon cycle: - Methane gas plays secondary part in the carbon cycle - More potent greenhouse gas than CO2: a) Can trap nearly 20x more heat in the atmosphere b) Methane released from GI tracts of ruminant animals accounts for 20% of global methane production c) “Swamp gas” Methanogen - Convert CO2 and H2 into methane (CH4) - Live in anaerobic ecosystems - Archaea (Methanopyrus kandleri, Methanobacterium petrolearium, Methanococcus jannaschii) Name and summarize the four reactions involved in the nitrogen cycle including the starting and ending products (e.g. nitrogen gas and ammonia): The Nitrogen Cycle: - Nitrogen gas N2 accounts for nearly 80% of air volume - Nitrogen cycle more intricate than other cycles a) Multiple reactions must occur b) Higher plants utilize 𝑵𝑶𝟑 − and 𝐍𝑯𝟒 + c) Microorganisms use all forms of nitrogen Four types of reactions: - Nitrogen fixation: a) Atmospheric nitrogen (N2) to ammonia b) Performed by bacteria c) Enzyme complex nitrogenase d) Mostly in soil, aerobic and anaerobic e) Some free-living, some symbiotic with plants - Ammonification: a) Decomposition of organic matter by Clostridium and Proteus bacteria, produces ammonia (NH4 +) b) Organic nitrogen (proteins, nucleic acid) -> bacteria -> NH4+ - Nitrification: a) Ammonia to nitrate b) Nitrate = most oxidized form of nitrogen used by plants (and fungi and bacteria) c) Carried out by obligate aerobe bacteria in two steps: 1) Bacteria (such as Nitrosomonas) oxidize ammonia (NH3)to nitrite (𝑁𝑂2 − ) 2) Bacteria (such as Nitrobacter) oxidize nitrite (NO2 −) to nitrate (NO3 − ) - Denitrification: a) Conversion of NO3 − or NO2 − through intermediate steps to atmospheric nitrogen (N2 ) b) Carried out by hundreds of different species (genera: Bacillus, Pseudomonas, Spirillum, Thiobacillus) c) Contributes to nitrogen loss in soils Describe the relationship between rhizobia and legumes: Symbiotic relationship between rhizobia and legumes ( peas, beans, clover, alfalfa, etc…) - Rhizobia: Gram-negative, motile, bacillus, bacteria - Colonize legume roots and produce root nodules - Supplies reduced nitrogen (ammonia) to the plant - Example: Sinorrhizobium meliloti colonizing alfalfa roots Define microbial ecosystem and discuss one example: Microbial ecology = study of microbes in natural habitats Ecosystem = collection of organisms together with surrounding physical and chemical factors; biotic and abiotic factors Aquatic and Soil Environments: - Plankton: floating community that drifts with waves and currents - Phytoplankton: photosynthetic algae and cyanobacteria - Zooplankton: microscopic consumers such as protozoa and invertebrates Explain eutrophication and specifically how microbes are responsible for its impact on aquatic life: Eutrophication: addition of excess nutrients to aquatic ecosystems 1) Heavy surface growth of cyanobacteria and algae shuts off oxygen supply to lake 2) Aerobic heterotrophs deplete oxygen further by decomposing organic matter 3) Causes massive die-offs of strict aerobes (fish, invertebrates) 4) Only anaerobic or facultative microbes survive Define metagenomic sampling and briefly explain how it has changed our view of microbiology: Metagenomic sampling: 1) DNA is obtained, fragmented, and fitted with adaptors 2) Sequences are added to a PCR machine, where they are immobilized using the adaptor sequences and copied via PCR  3) The millions of amplified sequences are sequenced inside the machine using various methods 4) The sequences are aligned using software, and entire genomes are revealed How it changed our view of microbiology: - Microbial abundance and diversity - Identification of microbes in new places - Novel genes/traits in microbes Define “One Health” and how it impacts human disease: - Microbes circulate among human hosts, animal hosts, and environmental reservoirs - Changes in environment can lead to transmission to pathogens to animals and humans that previously were not exposed to them 1) Pathogen evolution - better adapted to different hosts 2) Increase in disease incidence 3) Changes in disease location Second powerpoint^^ Summarize glycolysis, the Krebs cycle and the electron transport chain (ETS), and estimated ATP, NADH/FADH2 , carbon/CO2 yield for each: Glycolysis: - Glucose is enzymatically converted to pyruvic acid/pyruvate - Occurs in cytoplasm (for bacteria and eukaryotes) - 9 step process - once per glucose molecule - Uses 2 ATp but produces 4 ATP - Overall yields ATP and NADH - Two steps utilize 1) Yields 2 ATP (substrate-level phosphorylation) Use 2, produce 4 = +2 2) Yields 2 NADH 3) Yields 2 pyruvates (per 1 glucose) The Krebs cycle: - Occurs in cytoplasm (bacteria) or mitochondrial matrix (eukaryotes)  - Cycle of 8 steps ( plus precursor step) (precursor step = oxidation and decarboxylation of pyruvic acid produces acetyl CoA) - Starts with pyruvate in precursor step which is converted into acetyl - Coa - Substrate level phosphorylation - Yields ATP, NADH, and CO2 - Cycle happens twice for each glucose 1) Yields 2 ATP - substrate-level phosphorylation 2) Yields 8 NADH and 2 FADH2 3) Starts with 2 pyruvates→acetyl-CoA No C yielded, except: Yields 6 CO2 Electron Transport System (Respiratory chain): Two part process: 1. Chemiosmosis- use NADH/FADH2 create PMF 2. ATP synthesis- use PMF to make ATP - Coupled together = oxidative phosphorylation - Requires oxygen - Occurs at membranes - Electrons passed from NADH/FADH2 down redox molecules (proton pumps) - Flow of electrons allows the active transport of H+ outside membrane - Creates proton motive (PMF) force= electrochemical gradient, potential energy - Transferred finally to terminal electron acceptor = oxygen - Catalyzed by cytochrome oxidase - Receive electrons from cytochrome, pick up hydrogens from solution, and react with oxygen to form water - ATP synthesis- use PMF to make ATP - ATP synthase is enzyme complex that transports H+ into cell and catalyzes ATP production from ADP - 1 NADH = 3 ATP molecules - 1 FADH2 = 2 ATP molecules - anaerobic respiration: - Same steps for glycolysis and Krebs Cycle in aerobic respiration - Can involve a different set of cytochromes/electron transporters than in aerobic respiration  1) Yields variable ATP, ~34 – oxidative phosphorylation 2) Yields NAD+ and FAD+ 3) N/A for carbon 4) 10 NADH x 3 ATP/NADH= 30 plus 2 FADH2 x 2 ATP/FADH2= 34 total ATP from ETS For glycolysis, the Krebs cycle, and the ETS, compare and contrast the processes between bacteria and eukaryotes: Glycolysis: Bacteria: - Occurs in the cytoplasm - Similar pathway to eukaryotes, involving the conversion of glucose to pyruvate Eukaryotes: - Occurs in the cytoplasm - Follows the same basic steps as in bacteria, producing pyruvate, ATP, and NADH The Krebs cycle: Bacteria: - Takes place in the cytoplasm Eukaryotes: - Occurs in the mitochondria - More compartmentalized with distinct regulation and enzyme localization. Electron transport system: Bacteria: - Occurs in the plasma membrane (lacks mitochondria) - Uses a variety of electron donors and acceptors, and the chain can vary widely between species. - Some bacteria have simpler or branched chains, and can use alternative pathways for respiration (e.g., anaerobic respiration) Eukaryotes: - Occurs in the inner mitochondrial membrane - Involves chemiosmosis to produce ATP via ATP synthase, using the proton gradient created by electron transport Compare and contrast anaerobic respiration and aerobic respiration: Anaerobic respiration: - No oxygen required - Use of non-oxygen terminal electron acceptor (typically uses oxygen-containing ion instead of O2 ); like nitrate, sulfate, carbonate - Example: Nitrate Reduction- Nitrate reductase catalyzes removal of oxygen from nitrate (NO3 −) reducing it to nitrite (NO2 −) and water - Still accepts electron from cytochrome and uses hydrogen atom - Not as much ATP produced Aerobic respiration in eukaryotes vs bacteria - Differences in aerobic respiration: 1) Locations of ETS and Kreb’s Cycle - ETS: Bacteria = cell membrane, eukaryotes = mitochondrial membrane - Krebs: Bacteria = cytoplasm, Eukaryotes = mitochondrial matrix 2) Electron carriers in membrane are different redox molecules with same function 3) Amount of ATP produced - more in bacteria Aerobic and anaerobic respiration: net yield ATP - 2 ATP from glycolysis - 2 ATP from Krebs cycle - 34 ATP from ETS - Total = 38 ATP Describe microbial fermentation using key terms and name the two major useful products (categories) it can make: Fermentation: - Prokaryotes and Eukaryotes (Advantage- quick energy (fast) - No oxygen required - Incomplete oxidation of glucose - Glycolysis + 2 ATP - Organic compounds as terminal electron acceptors - Produces NADH, regenerates NAD+ - Alcoholic or Acidic – but varied pathways Explain the term amphibolism and define precursor molecule: Amphibolism: - Catabolic and anabolic pathways integrated to improve cell efficiency - Strategic molecular intermediates (precursor molecules) that can be diverted into other pathways - “amphi”= “two” or “both” Precursor molecule = compound that is source of another compound Discuss the relationship between light-dependent and light independent reactions of photosynthesis: Photosynthesis: Light-dependent reactions: - Photophosphorylation: uses light to make ATP (phosphorylation event from ADP to ATP) - Only in presence of sunlight - Hydrolysis – break apart water, yields oxygen - Photosystems I & II - Catabolic, energy-producing reactions - Produces ATP and NADPH Light-independent reactions: - Also called The Calvin Cycle - Sunlight not required - Anabolic, synthetic reactions – produces glucose - Uses ATP, NADPH, and CO2 ^^These are from the Third powerpoint - microbial metabolism Compare and contrast key features of eukaryotic and bacterial chromosomes: Microbial chromosomes: Chromosome: A discrete cellular structure composed of a neatly packaged DNA molecule Eukaryotic chromosomes: - Located in the nucleus - Vary in number - a few to 100s - Linear - Can occur in pairs (diploid) or singles (haploid) – think mitosis/meiosis - Larger Bacterial (and Archeal) chromosomes: - Located in cytoplasm (nucleoid) - Usually one - Typically circular - Single copies - Smaller Escherichia coli: ~4.3 Mbp, ~4300 genes, single chromosome Tapeworms: ~115-141 Mbp, ~10-12,000 genes, multiple chromosomes (usually 8 to 9) Summarize the steps of bacterial DNA replication and the enzymes used in this process: 4 Major Processes: 1) DNA replication 2) Gene expression: DNA transcription to mRNA 3) Gene expression: mRNA translation into protein 4) Operons Bacterial cell division = Binary fission  - When a bacterial cell is dividing/reproducing (binary fission), it needs to make a copy of its chromosome = DNA replication Bacterial DNA replication: - Semiconservative replication: Each daughter molecule is identical to the parent in composition, neither is completely new (half parental, half newly-synthesized) - The template strand = original parental DNA strand - 1 parental molecule → 2 daughter molecules - 1 origin of replication = sequence where bidirectional replication starts - Replication fork = Can only add nucleotides in the 5 to 3 direction, add to free 3’ OH of the preceding nucleotide Summarize the steps of bacterial transcription and define the key factors used: Transcription: DNA -> mRNA - 3 step process: 1) Initiation (promoter region): - Promoter = DNA sequence on template strand that is recognized by the RNA polymerase - These promoter sequences provide the signal for RNA polymerase to bind to DNA 2) Elongation: - Proceeds in the 5’ to 3’ direction - The mRNA is assembled by the addition of nucleotides that are complementary to the DNA template 3) Termination: - Terminator = DNA sequence on template strand that signals to the RNA polymerase to stop - RNA polymerase synthesizes mRNA from DNA Summarize the steps of bacterial translation and define the key factors used: Translation: mRNA -> protein - 3 step process: 1) Initiation:  2) Elongation: 3) Termination: Translation: - Entrance of tRNA’s 1 and 2 - Formation of peptide bond - Discharge of tRNA at E site - First translocation - Formation at peptide bond - Discharge of tRNA 2: second translocation; enter tRNA 4 - Formation of peptide bond - Ribosome and tRNAs used to synthesize polypeptides (proteins) from mRNA Identify differences in bacteria versus eukaryotes for DNA replication, transcription, and translation: Eukaryotic vs Prokaryotic DNA Replication: - Eukaryotic DNA replication: similar to bacterial and archaeal DNA, but… 1) Nucleus, not cytoplasm like bacteria 2) Replication proceeds from multiple origins 3) “End replication problem”- 3’ ends = telomeres (chromosome ends) cannot be completely copied 4) Different nomenclature (Example: Polymerase III vs Polymerase δ/ε) Eukaryotic vs Prokaryotic DNA transcription and translation: - Difference in location - Co-transcriptional translation only in prokaryotes (Transcription and translation can happen at the same time (because all processes occur in cytoplasm) - Processed mRNA in eukaryotes only (transcription yields pre-mRNA) 1) 5’ cap + 3’ poly A tail 2) Introns and exons; splicing - Introns: intervening sequences that do not code for protein - Exons: coding regions - Spliceosomes: enzymes that carry out splicing Define operon and differentiate between repressible and inducible operons and how they work: Operon = Coordinated set of genes regulated (and transcribed) as a single unit in bacteria and archaea (not in eukaryotes) - Regulator: encodes for repressor protein - Repressor: binds to operator and blocks RNA polymerase - Operator: location where repressor protein sits to block RNA polymerase Inducible operon: - Operon turned on by the substrate(s) for which structural genes encode; typically catabolic - Enzymes needed to metabolize nutrient only produced when that nutrient present Repressible operon: - Several genes in a series turned off (repressed) by the product synthesized by the enzyme; typically anabolic Inducer: substrate that binds to repressor, resulting in conformational change and removal from operator Corepressor: substrate that binds to repressor, resulting in conformational change and binding to operator Define phase variation: Phase variation: Result of bacteria turning on/off a group of genes (genetic changes) leading to reversible phenotypic changes. - Mediated by regulatory proteins, such as operon repressors - Heritable—passed down to subsequent generations in a clonal population (same colony) - (Streptococcus pneumoniae) (Vibrio vulnificus) ^^ This is 4th power point - microbial genetics part 1 List traits of a plasmid and what types of genes they encode: Plasmid: - Found in prokaryotes and eukaryotes BUT very common in prokaryotes - Small, circular DNA  - Replicate independently of chromosome - Contain up to few dozen genes - Up to several copies per cell - Non-essential for survival, but often carry useful traits - Transferred mainly through conjugation or transformation Resistance (R) Plasmid: - Plasmid with antibiotic resistance gene(s) - Other factors can be encoded on R plasmids as well - Some include genes for conjugation - Pilus-synthesis genes - One of the major underlying contributors to drug resistance is horizontal gene transfer mechanisms between bacteria Name and define the two main mechanisms of gene transfer in bacteria: Mechanisms of gene transfer: - Horizontal gene transfer: a) Transfer of DNA that results in organisms acquiring new genes that did not come directly from parent organisms b) All results in genetic changes via recombination = event in which one cell donates DNA to another cell, which becomes incorporated in the recipient bacterium - Vertical gene transfer: a) Passed down from parent to daughter cell (binary fission); includes chromosome, plasmids and any mutations acquired b) Spontaneous mutation: A random change in the DNA arising from errors in DNA replication that occur randomly c) Induced mutation: Result from exposure to known mutagens (ultraviolet = Causes cross-links between adjacent pyrimidines) Describe the process of transformation using key terms: Transformation: - Recipient Cell = Competent cell (Competent Cells: cells that can take up free DNA via transformation) - Natural competence- natural ability (use nucleases, ~80 species) - Artificial competence- induced ability a) Chemical: Treat with CaCl2 and heat-shock b) Electrical Current: Electroporation Process: 1) Double stranded DNA binds to the surface of a competent cell  2) Single strand enters the cell; the other strand is degraded 3) The strand integrates into the recipients cell’s genome by homologous recombination (the strand it replaced will be degraded) Briefly summarize Griffith’s experiment and what he demonstrated: Describe in detail the process and steps in generalized and specialized transduction using key terms: Transduction: - Transfer of DNA via bacteriophage: 1) Generalized transduction - Random fragments (any gene) of disintegrating host DNA taken up by a phage during assembly - Cell A: - a phage infects cell A (the donor cell) by normal means - during replication and assembly, a phage particle incorporates a segment of bacterial DNA by mistake - a cell then lyses and releases the mature phages, including the genetically altered one - Cell B: - the altered phage absorbs and penetrates another host cell (cell B), injecting the DNA from cell A rather than viral nucleic acid - Cell B receives this donated DNA, which recombines with its own DNA. Because the virus is defective, it is unable to complete lytic cycle 2) Specialized transduction - Temperate/lysogenic phages only, Highly specific part of host genome is incorporated into phage - Prophage within the bacterial chromosome - Excised phage DNA contains some bacterial DNA - New viral particles are synthesized. Some contain bacterial DNA in addition to phage DNA - Cell A lyses and releases all new bacteriophages - Then goes to Cell B - In cell B, infection of recipient cell transfers bacterial DNA to a new cell - Recombination results in two possible outcomes: either bacterial DNA or a combination of viral and bacterial DNA Describe in detail the process and steps in conjugation (F factor transfer and Hfr) using key terms: Conjugation: - Direct contact between donor and recipient cell - Origin of transfer = DNA sequence that initiates transfer of F factor F factor transfer involves a donor cell with an F plasmid (F+ cell) directly transferring the plasmid to a recipient cell (F- cell) via a pilus, while Hfr conjugation occurs when the F factor is integrated into the donor's chromosome, leading to the transfer of a portion of the chromosomal DNA alongside the F factor to the recipient cell Hfr = high frequency of recombination ^^ this is the 5th powerpoint - genetics part 2 Define natural, semi-synthetic and synthetic antimicrobial drugs: Antibiotics: drugs that target bacteria - Competition between microbes - Alexander Fleming Natural antibiotics – produced by bacteria and fungi Semi-synthetic: created by chemically altering structure of natural antibiotics Synthetic: created in the lab; mimic action of natural compounds Define selective toxicity: Selective toxicity = Antimicrobial drugs should kill or inhibit microbial cells without simultaneously damaging host tissues (the perfect drug does not exist) Define therapeutic index, and identify whether a high or low index is preferable in a drug: Therapeutic index (TI): ratio measuring toxicity of a drug - dose of the drug that is toxic to humans its minimum effective (therapeutic) dose - The smaller the ratio, the greater potential for toxicity - TI of 1.1 is a riskier choice than TI of 15 - A higher index is preferable in a drug State and define the three categories of drug side effects: 1) Direct damage to tissues through toxicity = Drug toxicity can cause a wide variety of side effects in liver, kidneys, GI tract, cardiovascular system, respiratory tract, nervous system, skin, bones and teeth - Diarrhea = Most common complaint with oral antimicrobial therapy - Can progress to severe intestinal irritation or colitis - Some drugs directly irritate intestinal lining; also disruption of gut microbiota 2) Allergic reactions = - Drug stimulates allergic response - Response to intact drug molecule or substances from body’s metabolic alteration of drug - Often rash/hives; can include shortness of breath, swelling of lips, face, or tongue, and fainting 3) Disruption in the balance of normal microbial biota = - Broad-spectrum antimicrobial treats infection, but destroys normal biota - Superinfection Define superinfection, and summarize how it develops in a patient: Superinfection: Microbes once small in number overgrow and cause disease Define broad-spectrum and narrow-spectrum antimicrobials: Broad spectrum = - Effective against more than one group of bacteria Narrow spectrum = - Only target a specific group Name the five major cellular targets of antibiotics, the mechanism(s) of action of the antibiotic on that target, and list the major subtypes of antibiotics associated with each target: 1) Cell wall: beta-lactams - Beta-lactams: Penicillins, Cephalosporins, Carbapenems - Penicillins target: cell wall peptidoglycan synthesis and repair (Natural or semi-synthetic derivatives) - Cephalosporins target: cell wall peptidoglycan synthesis and repair (semi-synthetic) - Carbapenems target: Target: cell wall peptidoglycan synthesis and repair (Natural, semi-synthetic, & synthetic) - Non beta lactams: still target the cell wall synthesis/repair by different mechanisms - Bacitracin: narrow-spectrum for superficial skin infections by streptococci and staphylococci (in Neosporin); natural antibiotic - Isoniazid: Mycobacterium tuberculosis (TB infections) in combo with other drugs - Vancomycin: narrow-spectrum used for drug-resistant staphylococcal infections or with penicillin allergy; natural antibiotic 2) Cell membrane: - Polymyxins: target = Disrupts membranes (cytoplasmic and/or outer membrane) and membrane permeability (Acts as cationic detergent (fatty acid)  - Daptomycin: target = Disrupts membranes (cytoplasmic and/or outer membrane) and membrane permeability 3) DNA/RNA: - Fluoroquinolones: target DNA replication (Inhibit DNA unwinding/separation→ inhibit DNA replication) - Rifamycin: target Transcription (mRNA synthesis) (Inhibits RNA polymerase → inhibits transcription) 4) Folic acid synthesis in cytoplasm: - Sulfonamides (sulfa drugs): target folic acid metabolism (Inhibits enzymes in tetrahydrofolate synthesis, precursor to nucleotides) 5) Proteins synthesis inhibitors acting on ribosomes: - Aminoglycosides: target ribosome/protein synthesis (Bind to the 30S subunit → misreading of mRNA, leading to abnormal proteins) - Tetracyclines: target ribosome/protein synthesis - Oxazolidinones: target ribosome/protein synthesis - Pleuromutilins: target ribosome/protein synthesis (Block peptidyl transferase (adds amino acids to tRNAs before use in translation) - Macrolides: target ribosome/protein synthesis (Block protein synthesis by blocking translocation) State the major modes of action of anti-viral drugs: 3 modes: 1) Attachment/ 2. Penetration = Prevent attachment or penetration into the host cell 4) Nucleic acid synthesis = Prevent replication, transcription or translation of viral molecules 5) Assembly/ 6. Release = Prevent virion assembly or release from the host cell List the major challenges in eukaryotic antimicrobial therapy: State the ways that microbes acquire antimicrobial resistance genetically: Identify the five cellular mechanisms that microbes use to resist antimicrobials: Name and summarize each method for testing antimicrobial susceptibility: State the ways humans have contributed to antibiotic resistance: ^^ these are from the slides - Control of Microbial Growth: Therapeutics Distinguish among the microbial control mechanisms: sterilization, disinfection, antisepsis, and decontamination: Compare the action of microbicidal and microbistatic agents and identify factors that impact the microbial death rate: Name four types of cellular targets for physical and chemical agents and the modes of action: Identify methods/agents of physical, mechanical, and chemical control of microorganisms and: a) Under what mechanism does it fit? sterilization, disinfection, antisepsis, and decontamination b) What is/are the cellular target(s)? Cell Wall, Cytoplasmic Membrane, Protein/Nucleic Acid Synthesis, Protein Function