Microbiology Exam 1 Questions and Answers

Microbiology Exam 1 Questions and Answers What is microbiology about and why is it important? -Viruses, microogranisms, microbes (fungi) -Major key in digestion, oxygen production, carbon cycle, alcohol fermentation What two themes does microbiology revolve around? 1) Understanding basic life processes -microbes are excellent for understanding cellular processes in unicellular and multicellular organisms 2) Applying that knowledge to the benefit of humans -play an important role in medicine, agriculture and industry Why is a lab important for microbiology? - safely handle microorganisms- can cause disease -teaching labs contribute to salmonella infections- transmitted through phones- why its not permitted during lab -need microscope because we cant see with the naked eye ASEPTIC vs. STERILE: aseptic- to prevent contamination- washing hands sterile- no microbes, bacteria, fungi, viruses whatsoever cannot say aseptic technique is sterile technique Mixed vs. Pure Culture -Humans: mixed culture, skin (mixed culture), bladder (sterile, uterus, and brain) -Pure culture: only one species vs. Mixed culture: lots of different types Tools to study microorganisms •microscopy •culture: cells grown in/on nutrient medium •medium: liquid/solid mixture containing all required nutrients •growth to form a visible colony Historical Context of Microbiology -Microscopy was first because you couldn't really see much..could not see with the naked eye -A lot of gap (almost 200 years) because there needed to be scientists that wanted to go further than just looking in the microscope -Decide- "What do we do with these" People in Microbiology (Robert Hooke; Antoni van Leeuwenhoek; Louis Pasteur) Robert Hooke: -the first to describe the microbes -illustrated the fruiting structures of mold -lens maker Antoni van Leeuwenhoek: the first to describe bacteria Louis Pasteur: -discovered alcohol fermentation was a biologically mediated process -Drank wine- realized could not have wine without yeast- microbes are essential to the formation (fermentation) of wine and beer. -Also developed vaccines -disproved theory of spontaneous generation -developed vaccines for anthrax fowl cholera, and rabies Pasteur and Spontaneous Generation -Famous for disproving the concept of spontaneous generation -People believed that air was necessary to create life -Recognized heat killed microorganisms -Created sterile broth -Proved that is was sterile because it wouldnt go bad -Used swam neck flask- open to air, sterile broth- all dust and dirt was trapped in neck and broth stayed sterile -Proved that air did not create life- called biogenesis Koch, Infectious Disease, and the Rise of Pure Cultures -Robert Koch -discovered that using solid media proved a simple way to obtain pure cultures -observed that masses of cells (colonies) have different shapes, sizes, and colors -began with potato slices but eventually devises uniform and reproducible nutrient solutions solidified with gelatin and agar -developed techniques to obtaining pure cultures, still used today Koch's postulates -Still used today -Link between microbes and infection diseases -Flaw in this is that some diseases will only affect a certain type of species- some only human/some only animals- ex. HIV -Symptoms: multiple of different outcomes Joseph Lister SEMMELWEISZ -toward the early 1900s -advocated for aseptic techniques (handwashing)- people really didn't believe it -Ended up in psych ward He was a doctor- discovered antiseptic (listerine)- phenol (antiseptic) Ignaz Semmelweisz -Correlated frequent handwashing in the obstetrics ward with lower rates of infection (puerperal fever) -Women who had just given birth The Rise of Microbial Diversity -focuses on nonmedical aspects of microbiology Martinus Beijerinck -developed enrichment culture technique : microbes can be isolated from natural samples in a highly selective fashion by manipulating nutrient and incubation conditions -Put things into enrichment culture that you want to grow Sergei Winogradsky -Concept of chemolithotrophy -Demonstrated that specific bacteria are linked to specific biogeochemical transformations -Ex. S and N cycles -Winogradsky Collumn: have different colors- can usually visualize different microbes In the 20th Century, what two directions did Microbiology divide into 1) Applied 2) Basic -Molecular microbiology was fueled by the genomics revolution What are five examples of microbes? EXAMPLES OF MICROBES: 1) bacteria 2) protists 3) fungi 4) archaea (ORGANISMS- microorganisms) 5) viruses: (NOT AN ORGANISM- still a microbe) How would you define the term microbe? Definition: obligate acellular parasite- a microscopic unit that interacts with the environment Definition of a "Cell"- which three structures do Microbial cells have in common Cell: the basic unit of live, microorganisms and organism LUCA: every cell has a membrane for microbes to pass through 1) Plasma membrane: viruses can get a plasma membrane from the cell they are infecting 2) DNA genome- many viruses just have RNA genome, not DNA genome 3) Ribosomes- viruses do not have ribosomes- no gene to make ribosome- too small Which statement is false? A) Microbial cells can exist as single cells B) Microbial cells carry out their life processes of growth independently C) Microbial cells include both bacteria and viruses D) Microbial cells are surrounded by a plasma membrane C is False What don't viruses do? -Viruses do not have a metabolism -Can only get plasma membrane from cell they are infecting -RNA genome instead of DNA -No ribosomes- ribosome 20nm and virus 30nm -They do change and evolve, whereas the genetic material in another organism must undergo a mutation to change and evolve Properties of all cells vs. some cells Magnification vs. Resolution Magnification: to increase in magnification is to make something look larger Resolution: the ability to distinguish two adjacent objects as separate and distinct How to improve contrast in a light microscope? -Improving contrast results in a better final image -staining improves contrast- staining kills cells- GRAM STAIN Phase-contrast vs Dark-field microscopy Phase-contrast: -light bounces off the outline, creating better contrast -exploits difference in the refractive index of the cell Dark-field: -image appears light on dark background -good for motility Transmission electron microscope vs. Scanning electron microscope Transmission: -high magnification -enables visualization of structures at a molecular level Must be thin to be stained Scanning: -specimen coated with thin film of heavy metal -electron beam scans object -scattered electrons are collected and image is produced -15x-100,000x What is a cells morphology -cell shape -3 basic shapes for bacteria- great way to classify organisms a) Coccus- spherical (can form long chains or two chains stacked on each other b) Rod- bacillus- arranges in straight line (Chain=strep) c) Spirillum- spiral shape -Vibrio -Spirillum -Spirochete (unusual shape) Cell size and significance of being small? What is the advantage of being small? -Has to be a balance of surface to volume ration -High surface to volume ratio for single celled life What is the function of a cytoplasmic membrane and transport? -thin structure that surrounds cell -highly permeable - excretion of waste 1) Transport 2) Cell recognition and protein anchors 3) Energy to generate ATP- proton motive force Difference between Bacterial and Archaeal Membrane Bacterial/Eukaryotic: 1) Fatty acids 2) Ester linkages 3) Bilayer Archaeal: 1) Isoprenes 2) Ether linkages 3) Mono/Bi Layer Cell walls of bacteria vs archaea? -Cell wall is not the same as cell membrane -All cells have a membrane but not all cells have a wall -Bacterial cells have cell wall (Peptidoglycan= cell wall) How to differ in bacteria and their cell walls -Bacteria is separated into two groups based on their cell wall structure Identify via gram stain -Gram - Cell wall: two layers LPS and peptidoglycan -Gram + Cell wall: one layer- peptidoglycan NOT ALL PROKARYOTES HAVE A CELL WALL What is peptidoglycan -Rigid layer that provides strength to cell wall -Polysaccharide Peptidoglycan vs LPS Peptidoglycan= cell wall LPS= outer membrane -most of the cell wall is the outer membrane or the LPS -protects against antibiotics -replaces most of phospholipids -endotoxin: lipid A, toxic component of LPS Periplasmic Space: space between outer membrane and the cell wall Archaeal Cell Walls -No peptidoglycan -Typically no outer membrane -Contain pseudomurein: fake peptidoglycan -Only some contain pseudomurein What are S-Layers -most common Archaeal cell wall type -consist of protein or glycoprotein paracrystalline structure -in addition to other polysaccharides for cell structure -outermost later Cell Surface Structure Capsules and slime layers -assist in attachment to surfaces -protect against phagocytosis -prevent desiccation Fimbriae and pili -enable organisms to stick to surfaces -protein structure -Pili longer than fimbriae -Conjugative/sex pili facilitate genetic exchange between cells Cell inclusions -Inclusions act as energy reserves -enclosed thin membrane -reduces osmotic stress -Carbon storage polymers (glucose) Flagella and Swimming Motility Flagella: assists in swimming -helical in shape -Prokaryotes have flagella on cell wall -Eukaryotes have them as an extension of the cell membrane Peritrichous: all the way around Polar iophotrichous: just one What are endospores and how are they formed? -formed during endosporulation or sporulation -resistant to heat, harsh chemicals, radiation -structures to endure unfavorable growth conditions -dormant stage of bacterial life cycle -Three types 1) Terminal 2) Subterminal 3) Central Why does fermentation not happen in an aerobic environment? Fermentation does not happen in an aerobic environment, because if there was oxygen readily available, the cell would go into respiration as it is more energetically favorable. (fermentation is only used to generate oxidative cofactors-- not as energetically favorable) You and your friend are studying for the first microbiology exam. Your friend says that "Fermentation and anaerobic respiration are the same since they both happen in the absence oxygen." Is your friend correct or incorrect? Explain. Incorrect, they are two different processes. In fermentation you do not need an energized membrane, while in anaerobic respiration you do. In fermentation the oxidative cofactors are replenished and the only ATP are generated through substrate level phosphorylation, while anaerobic respiration goes through Krebs cycle and ETC and generates ATP and its electron acceptor is something other than oxygen. (everything else is the same between aerobic and anaerobic) Different types of nutrients for cell microbes Nutrients: supply of monomers required for cell growth -Water is used to help dissolve nutrients and maintain osmotic pressure 1) Macronutrients: -C, H, O, N, P, S, Se -required by all cells -Carbon most abundant Heterotrophs use organic carbon Autotrophs use CO2 Fastidious: need additional nutrients 2) Micronutrients -all other elements -iron (Fe)- cellular respiration -trace metals- enzyme cofactors Transporters, three classes and their function in the cell -transport nutrients in the cell 1) Simple transport: use energy from proton motive force 2) Group translocation: chemical modification of the transported substance 3) ABC transporter: periplasmic binding proteins are involved in energy coming from ATP Classification of organisms based on their metabolism Classifying each organisms lifestyle: 1) Thiobacillus denitrificans oxidizes ammonia (NH3) for energy to conserve ATP and fixes CO2 2) A group of marine organisms, the "thiosulfate (S2O3-) oxidizing bacteria", as their name implies, obtain energy via the oxidation of thiosulfate. Many of these organisms require pyruvate for growth. 3) Organisms in the genus Roseobacter can obtain energy via aerobic anoxygenic photosynthesis and they require glucose for growth 4) What are humans? 1) Chemolithoautotroph 2) Chemolithoheterotroph 3) Photoorganoheterotroph/Photoheterotroph 4) Chemoorganoheterotroph Electron tower -In the electron tower- the donor is always above the receptor -The further they are apart- the more energy -The acceptor is always on the left- the donor is always on the right -Reduction potential E0, expressed in volts: tendency to donate electrons -Anything on the same plane could never be a redox couple -More negative donates to more positive For questions 1-3, consider the following electron acceptors: • S0- (Elemental Sulfur) • NO3- (Nitrate) 1. Reduction of which of the above compounds by H2 would yield the most ATP? 2. Which of the two compounds could accept electrons from NADH? 3. Which of the two compounds could accept electrons from FADH2? • Organisms in the genus Acidianus can use S0 (elemental sulfur) as either an electron donor OR an electron acceptor. Under anoxic conditions So acts as electron acceptor. Under oxic conditions, it is the electron donor. a) What is the electron acceptor under oxic conditions? b) Propose an inorganic electron donor that might reduce S0 under anoxic conditions. Energy-Rich compounds -biosynthesis of insoluble polymers that can be oxidized to generate ATP 1) Prokaryotes: -glycogen -elemental sulfur 2) Eukaryotes: -starch -lipids What is glycolysis? What are the two reaction series that differ in mechanism of ATP synthesis 1) Fermentation: substrate-level phosphorylation- ATP is directly synthesized from an energy-rich intermediate 2) Respiration: oxidative phosphorylation- ATP is produced from proton motive force formed by the transport of electrons MANY PROKARYOTES (MICROBES) DO NOT HAVE KREBS CYCLE Substrate-level phosphorylation vs. Oxidative phosphorylation Both are redox reactions -A lot more energy from oxidative phosphorylation -(occurs in membrane) -generates more ATP -uses ETC -Substrate-level phosphorylation -no energized membrane -not a lot of energy -donor on similar plane as acceptor Energetic Process- Steps 1) GLYCOLYSIS —> net 2ATP, NAD+ in and NADH out to produce—> 2) PYRUVATE NAD+ has limited supply— (not enough ATP to make more— need molecules to make it— recycles back to NAD+ after making pyruvate through)— 3) FERMENTATION or RESPIRATION When does fermentation vs. respiration occur? Fermentation: -ONLY happens in the absence of oxygen -only used to regenerate NAD+ (side products: lactic acid, alcohol) *—regenerates oxidized cofactors -NO ATP generated* Once oxygen is available... -It is used as electron acceptor in Respiration -more energetically favorable -generates more ATP If a cell is fermenting and we are adding Nitrate (NO3) it will still respire because the difference on the electron tower will be much greater (more energy than fermentation) What are common microbial fermentations 1) yeasts 2) lactic acid bacteria 3) propanoic acid 4) enterobacteriaceae Electron transport chain and the proton motive force -ETC in cytoplasmic membrane- electrons separated from protons -Final carrier donates the electrons and protons to the terminal electron acceptor (O2) Respiration and its two parts RESPIRATION: -broken down into two parts 1) KREBS CYCLE: -moves to the ETC -NAD+ > NADH 2) ETC: -NADH > NAD+ -O2 is electron acceptor -In prokaryotes (something other than oxygen (something lower on electron chart)) -generates ATP through oxidative phosphorylation Growth and Binary fission -Growth: don't increase in size, just numbers -Binary fission: cell division in prokaryotes- fission is to split into two -Increase by a factor of 2 with each generation time -(Original cells) x (2^n) -generation time- time for microbial cells to double in number (nutritional, genetic factors, and temperature)- 20 minutes Generation Time- Calculations N= number of cells present (N0= original number of cells) X (2^n)- n= number of generations Generation time (g)= t/n t= duration of exponential growth n= number of generations during that period of growth The Microbial Growth Cycle -Batch culture: closed-system microbial culture of fixed volume -Four phases in a closed system growth curve -Growth curve: (will run out of) nutrients, space, water, oxygen, too many toxins produced -Lag phase will not occur in culture-culture transfer What is a continuous culture? -Continuous culture: open system of microbial culture in a fixed volume -Chemostat: most common type of continuous culture device -Steady state: cell density and substrate concentration do not change over time *-LAG PHASE: cells wont grow in the beginning because they have to get acclimated to the environment -Once they have acclimated, they will grow in an exponential phase: LOG PHASE* What are some environmental effects of growth? -pH, temperature, light -Once go past optimum peak, cells will die- optimum is where the cells work most efficiently- can function below optimum Temperature limits for growth of living organisms: five distinctions Animals < Plants < Microorganisms- Eukaryotic < Bacteria and Archaea How do proteins and membrane stabilize at high temperatures? -modifications in cytoplasmic membranes ensure heat stability *-Archaeal membranes- ether linkages and monolayer -Monolayer- stabilizers internal environment (bilayer would melt)* -Bacteria- long-chain saturated fatty acids -Archaea- isoprene units form monolayer Intracellular pH levels -Intracellular pH must stay relatively close to neutral (5-9) even if external pH is highly acidic or basic -Buffers maintain pH -Stomach- near neutral- mesophillicneutrophile would grow in intestines Oxygen relationships of microorganisms- five different types Thioglycollate- pink layer- oxygenated layer- rest contains no oxygen -Obligate aerobe (A): nothing is growing in the anoxic zone— cells are located purely in aerobic environment— has aerobic respiration metabolism -Facultative aerobes (C): higher ratio in the oxic zone than anoxic zone— can do aerobic respiration, anaerobic respiration (grows in anaerobic zone), and can also do fermentation (ex. E. Coli) -Microaerophiles (D) : requires a small amount of oxygen— uses aerobic respiration -Aerotolerant anaerobes (E): does not use oxygen, but can grow in oxic zone— has enzymes that break down toxic byproducts— only uses fermentation -Obligate anaerobe (B): because nothing is growing in the oxic zone— all growing in the anoxic zone— uses anaerobic respiration and fermentation to metabolize Why is oxygen toxic? -Molecular oxygen is not toxic (O2) -Exposure to O2 yields toxic byproducts: a) superoxide anion (O2-) b) hydrogen peroxide (H2O2) c) hydroxyl radical (OH-) How does pressure affect microbes? -Microbes that live on land and water surface live at 1 atmosphere (atm) -Some bacteria and archaea live in deep sea with very high hydrostatic pressures 1) barotolerant: adversely affected by increased pressure but not as severely as non-tolerant organisms 2) barophilic (peziophilic) organisms: require or grow more rapidly in the presence of increased pressure- change membrane fatty acids to adapt to high pressures Definition of a gene -A segment of DNA specifying a protein (via mRNA), a rRNA, or tRNA -Information in the gene is present as the sequence of bases in the DNA -Purines: A and G -Pyrimidines: C and U and T T for DNA U for RNA The steps in genetic information flow 1) replication 2) DNA 3) transcription 4) RNA 5) translation 6) PROTEIN DNA structure -double stranded molecule forming a helical configuration -measured in number of base pairs -Complementary and antiparallel: one chains in a 5'-phosphate end and the other group a free 3' hydroxyl -Supercoiling: a solution to pack a large amount of DNA into small cells or viral particles- nick: break in phosphodiester bond in one strand -In prokaryotes: supercoiling is produced by enzymes caled topoisomerases -Jim Watson and Max Delbruck wrote a letter explaining the double helix Supercoiling in Prokaryotes -In prokaryotes, supercoiling is done by topoisomerases -Topoisomerase II- a DNA gyrase- makes double-strand breaks -Enzyme reverse gyrase introduces positive supercoiled -Supercoiling affects gene expression Synthesis of three types of macromolecules -Three bases on a mRNA molecule encode for a single amino acid -Messenger RNA is template for protein synthesis Different genetic elements in cells -Chromosome -Plasmids: DNA molecules that exist separately from the chromosome fo the cell -Transposable elements: molecules of DNA that can move from one site on a chromosome to another -Mitochondria and chloroplasts contain their own DNA chromosomes -Viruses contain a genome, either DNA or RNA, that controls their own replication DNA Replication -Semiconservative replication: (prokaryotes and eukaryotes) both new and old strands serve as templates for the synthesis of two new strands- new strands are elongated by addition to 3' end -Growth proceeds from the 5'-phosphate to the 3'-hydroxyl end -5'-P of the incoming nucleotide is attached to the previously added nucleotide -DNA polymerase catalyzes each reaction Modes of replication (3 types) -Semiconservative- one and one strand -Conservative- exact copy, strands stay intact -Dispersive- pieces integrated DNA polymerase -requires a primer, composed of RNA -short segment synthesized by the enzyme primase -all enzymes add a nucleotide to preexisting 3' -OH group -extension is continuous on leading and discontinuous on the lagging strand -Primase: ribonucleotide triphosphates -DNA polymerase: deoxyribonucleotide triphosphates DNA gyrase replaces supercoils ahead of replisome Helicase unwinds double helix at the replication fork Single strand binding proteins prevents single strands from annealing DNA polymerase III -sealing two fragments on the lagging strand -synthesizes DNA in the 5' to 3' direction toward the primer of a previously synthesized fragment of lagging strand -DNA polymerase I then replaces polymerase III