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Exam 3 microbiology seyler, Study notes of Microbiology

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Microbiology Test 3 Review
Lecture Objectives
Lecture 8
• Contrast the location of the proton gradient
in prokaryotes and eukaryotes.
• Contrast substrate-level phosphorylation
with aerobic and anaerobic respiratory
mechanisms for generating ATP.
• Trace the flow of energy from a glucose
molecule, through glycolysis, the citric acid
cycle, electron transport, to the synthesis of
ATP.
• Differentiate inhibitors and uncouplers of
ATP synthesis.
Lecture 9
Differentiate catabolic and anabolic
reactions.
Identify the primary macromolecule
polymers, their building blocks, and
construction to the extent discussed in
lecture
Describe the pentoses and hexoses used in
polysaccharide and nucleic acid synthesis.
Describe how glucose can be produced in
the cell and the role of activated forms of the
sugar in its polymerization.
List the catabolic pathways that can
provide intermediates for the production of
amino acids.
Identify the precursors of purine and
pyrimidine ring structures for the synthesis
of nucleotides.
Binary Division
Outline the steps in simple cell division.
Define the divisome and identify
components and their functions.
Describe FtsZ, its role in cell division, and
proteins that affect its localization.
Identify other proteins discussed in class
that affect cell shape.
Discuss peptidoglycan breakdown and
synthesis during cell division including the
roles of autolysin, bactoprenol, and
peptidoglycan transpeptidase
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Microbiology Test 3 Review Lecture Objectives Lecture 8

  • Contrast the location of the proton gradient in prokaryotes and eukaryotes.
  • Contrast substrate-level phosphorylation with aerobic and anaerobic respiratory mechanisms for generating ATP.
  • Trace the flow of energy from a glucose molecule, through glycolysis, the citric acid cycle, electron transport, to the synthesis of ATP.
  • Differentiate inhibitors and uncouplers of ATP synthesis. Lecture 9
  • Differentiate catabolic and anabolic reactions.
    • Identify the primary macromolecule polymers, their building blocks, and construction to the extent discussed in lecture
  • Describe the pentoses and hexoses used in polysaccharide and nucleic acid synthesis.
    • Describe how glucose can be produced in the cell and the role of activated forms of the sugar in its polymerization.
    • List the catabolic pathways that can provide intermediates for the production of amino acids.
    • Identify the precursors of purine and pyrimidine ring structures for the synthesis of nucleotides. Binary Division
    • Outline the steps in simple cell division.
    • Define the divisome and identify components and their functions.
    • Describe FtsZ, its role in cell division, and proteins that affect its localization.
    • Identify other proteins discussed in class that affect cell shape.
    • Discuss peptidoglycan breakdown and synthesis during cell division including the roles of autolysin, bactoprenol, and peptidoglycan transpeptidase

Lecture 10

  • Identify the variables that influence cell populations (current population, generation time, growth time) and how to predict future or past populations using the formulae: g = t/g, N = No2n, and its rearranged form: n = 3.3(logN – logNo).
  • Outline the steps of batch culture growth, identifying the various phases and what is happening during each.
  • Contrast batch culture growth with chemostat growth in terms of the condition of the cell population.
  • Outline experimental uses of chemostat growth. Lecture 11
  • Describe differences between the three mechanisms of determining cell populations, whether direct or indirect, what units are used to describe the count, and whether all cells or only viable cells are enumerated.
  • Describe the cardinal temperatures of growth and the categories of cells based on their growth abilities at various temperatures. Name adaptations that enable growth under these temperatures.
  • Give examples of microbes with growth abilities under various pH conditions. List qualities related to pH that affect growth.
    • Describe relationships that various microbes have with respect to osmotic pressures. List an important adaptation that enables growth at high osmolarity.
    • List five classes of relationships that microbes have with oxygen, and why these relationships exist. Discuss oxygen’s toxicity methods used to control oxygen concentrations during laboratory growth. Lecture 12
    • Differentiate the processes of heat sterilization and pasteurization. Identify typical use cases for each.
    • Define the decimal reduction time and how it is affected by temperature.
    • Differentiate the antimicrobial activities of ionizing radiation vs UV radiation.
    • Describe what a decimal reduction dose is and how it relates to a lethal dose of radiation.
    • Differentiate the three classes of filters described in class and how HEPA filters fit into this classification.
    • Differentiate bactericidal, bacteriostatic, and bacteriolytic chemicals.
    • Compare and contrast MIC and disc diffusion assays for assessment of chemical antimicrobial activity.
  • Gluconeogenesis: glucose from non-carbohydrates
  • Amino acids from protein
  • Lactate from anaerobic glycolysis in muscles
  • Glycerol from breakdown of triglycerides in fat stores
  1. Purines are made from Amino Acids and pyrimidines are made from Pyrimidines
  2. In fatty acid biosynthesis, Acyl Carrier Protein holds the elongating fatty acids. In bacteria, what does “growth” refer to? What process do most bacteria use for growth? Describe this process.
  • Growth refers to an increase in the number of cells
  • Most bacteria uses Binary Fission:
  1. Cell replicates DNA
  2. Cell elongates and two DNA molecules move to opposite poles
  3. Septum forms in the middle
  4. Septum is completed resulting in two identical daughter cells
  5. The doubling of a population is called a Generation
  6. How are the different Fts proteins involved in cell division? What is the divisome?
  • Fts Proteins:
  • FtsZ: Forms a ring (Z-ring) at the cell’s midline to mark the division site.
  • FtsA: Anchors the FtsZ ring to the membrane and recruits other proteins.
  • FtsI: Aids in peptidoglycan synthesis during septum formation.
  • FtsK: Involved in chromosome segregation and separation.
  • Divisome: The divisome is a protein complex formed during bacterial cell division. It is responsible for synthesizing new cell wall material, enabling septum formation, and ensuring the two daughter cells separate properly.
  1. What are the MinB, MinC and MinD proteins and their functions?
  • MinB: Refers to the system as a whole, which includes MinC, MinD, and MinE proteins.
  • MinC: Acts as a cell division inhibitor by preventing FtsZ ring assembly in incorrect locations.
  • MinD: Recruits MinC to the membrane and assists in its movement.
  • MinE: Oscillates from pole to pole, ensuring the MinC-MinD complex concentrates at the poles, leaving the cell's center free for Z-ring formation.
  1. How do autolysins and bactoprenol aid in peptidoglycan synthesis?
    • Autolysins: enzyme that creates small cuts in the peptidoglycan layer allowing for insertion of new building blocks during cell wall growth
    • Bactoprenol: lipid carrier that transports peptidoglycan precursors across the cytoplasmic membrane to the growing cell wall
  2. What is peptidoglycan transpeptidase? What does it do and what is it the target of?
    • Catalyzes the cross linking of peptidoglycan chains which provides strength and rigidity to the bacterial cell wall
    • Targer of beta-lactam antibioticas (penicillin) which inhibits its activity leading to weakened cell walls and bacterial lysis
  3. Know the stages of growth in batch culture and what is happening in each. That is, why is there a lag phase, what is happening in the exponential phase, what brings on the stationary phase, and the death phase. Be able to draw a graph of a typical batch culture and label the different phases.
    • Why is there a lag phase: new environment, the bacteria uses up their initial energy stores and begin to replicate
    • Exponential phase: cells divide at their maximum rate
    • Stationary and death phase: depletion of nutrients, high levels of toxic waste, loss of cell integrity, energy starvation
  4. Know the formulae related to the dynamics of population growth, and be able to describe what each of the variables represents. Be able to calculate aspects of growth using different formulae. - Exponential Growth: N=N0eμtN = N_0 e^{ \mu t} o NN: Final cell number o N0N_0: Initial cell number o μ \mu: Specific growth rate o tt: Time - Generation Time (g): g=ln(2)μ
  • Dilution Errors: Mistakes in preparing dilutions can skew results.
  • Incubation Conditions: Temperature or time inconsistencies affect colony growth.
  • Selective Media: Can exclude certain viable cells.
  1. What are some advantages/disadvantages of indirect measurement?
  • Advantages:
  • Less time-consuming.
  • Can track cell growth dynamically.
  • Disadvantages:
  • Does not provide exact cell counts.
  • Cannot distinguish between live and dead cells.
  1. What assumption is made in relating the viable count results to cell number?
  • each viable cell gives rise to a single colony. This may not hold true in cases of cell clumping or if some cells require specific conditions to grow.
  1. How can you use the indirect measurement technique to determine how many colonies may be present at a particular OD?
  2. Define minimum, maximum and optimum temperatures.
  3. Know the different temperature classes of organisms.
  • • Psychrophiles: Thrive at cold temperatures (below 15°C, with an optimum near 5°C).
  • • Psychrotolerant: Prefer moderate temperatures but can survive in cold environments.
  • • Mesophiles: Grow best between 20–45°C, common in humans and animals.
  • • Thermophiles: Thrive at 50–80°C.
  • • Hyperthermophiles: Prefer extreme heat (above 80°C, some near boiling water).
  1. Distinguish between psychrophilic and psychrotolerant organisms.
  • Psychrophilic Organisms: Grow optimally at temperatures below 15°C and often live in permanently cold environments (e.g., polar regions).
  • Psychrotolerant Organisms: Can survive in cold environments but have a growth optimum closer to mesophilic conditions (20–30°C). Found in temperate regions and capable of cold storage survival.
  1. What are some molecular adaptations to psychrophily? To thermophily?
  • Psychrophily:
  • Increased proportion of unsaturated fatty acids in membranes for fluidity at low temperatures.
  • Cold-adapted enzymes with flexible structures for functionality in freezing conditions.
  • Production of antifreeze proteins to prevent ice crystal formation.
  • Thermophily:
  • Heat-stable proteins with highly hydrophobic cores and increased ionic bonding.
  • Saturated fatty acids in membranes for rigidity at high temperatures.
  • Specialized DNA-binding proteins to stabilize genetic material at elevated temperatures.
  1. What three generalizations can be made about thermophilic growth?
  • Thermophiles require specialized enzymes and membrane structures to survive high temperatures.
  • They are often found in extreme environments like hot springs or hydrothermal vents.
  • Protein and DNA structures in thermophiles are highly resistant to denaturation.
  1. Distinguish between acidophiles and alkaliphiles.
  2. What do compatible solutes do? Why are they important for organisms such as halophiles?
  • Function: Compatible solutes help cells balance osmotic pressure by maintaining internal water content without interfering with cellular processes. They are small organic molecules like proline, betaine, or glycerol that accumulate in the cytoplasm.
  • Importance for Halophiles: Halophiles live in high-salt environments where osmotic pressure threatens to dehydrate them. Compatible solutes allow these organisms to retain water and survive extreme salinity.
  1. What are the different types of bacterial relationships with oxygen? How are these different types of organisms distributed in a soft agar tube?
  • Aerobes: Require oxygen and grow at the top of the tube where oxygen is most available.
  • Obligate Anaerobes: Cannot tolerate oxygen and grow at the bottom of the tube.
  • Facultative Anaerobes: Prefer oxygen but can grow anaerobically; distributed throughout the tube, with denser growth at the top.
  • Microaerophiles: Require low oxygen levels and grow just below the surface.
  • As temperature increases, decimal reduction time decreases
  1. Differentiate between quinones and quinolones.
  • Quinones: organic coumpounds involved in redox reactions, electron transport chain carriers, coenzyme Q
  • Quinolones: antibiotics that interfere with bacterial DNA replication
  1. Ultraviolet radiation causes damage to DNA
  2. Ionizing radiation causes damage through what?
  • DNA breakage and reactice oxygen species
  1. Why is ionizing radiation more effective than UV radiation for sterilization of food products?
  • Ionizing Radiation: o Penetrates deeper into materials, ensuring sterilization throughout food products. o Damages DNA and other cellular structures via double-strand breaks and generates reactive oxygen species (ROS), killing microorganisms effectively.
  • UV Radiation: o Has limited penetration; it primarily sterilizes surface microorganisms by inducing thymine dimers in DNA.
  1. What is the definition of lethal dose? What is the lethal dose for humans?
  • Lethal Dose (LD) refers to the amount of a substance or exposure that results in death for a specified percentage of the population, often expressed as LD50 (the dose lethal to 50% of the population).
  • Lethal Dose for Humans:For radiation, the LD50 for humans is approximately 4 - 5 Gy (gray) without medical intervention.
  1. Name three types of filters used in sterilization and distinguish between them. Which type is commonly used for sterilization of heat-sensitive liquids and why? Which type is used to isolate specimens for electron microscopy?
  2. Distinguish between bactericidal, bacteriostatic, and bacteriolytic agents. (Know differences between graphs.)
  • Bactericidal: Kill bacteria directly without lysing them (e.g., penicillin).
  • Bacteriostatic: Inhibit bacterial growth but do not kill bacteria (e.g., tetracycline).
  • Bacteriolytic: Cause bacterial lysis, breaking cells apart (e.g., lysozyme).

Graphs:

  • Bactericidal: Declining viable cell count while total cell count remains steady.
  • Bacteriostatic: No change in cell count but stops growth.
  • Bacteriolytic: Both total and viable cell counts decrease.
  1. Define minimum inhibitory concentration. Lowest concentration of an antimicrobial agent that prevents visible growth of an organism
  2. Describe the disc-diffusion technique.
  • A microorganism is spread across an agar plate.
  • Discs impregnated with antimicrobial agents are placed on the plate.
  • After incubation, clear zones (zones of inhibition) around the discs indicate effectiveness.
  1. What is a zone of inhibition? What method can you use to determine if an organism is resistant to a certain antibiotic?
  • A clear area around an antibiotic-impregnated disc where bacterial growth is inhibited in the disc-diffusion technique (e.g., Kirby-Bauer method).
  • The size of the zone is measured to determine the effectiveness of the antibiotic.
  1. What are chemical antimicrobial agents that kill everything except endospores?
  • Disinfectants
  1. Antiseptics are chemical antimicrobial agents that are safe for application to living tissue.
  2. What are chemical antimicrobial agents that kill ALL living cells? Sterilants
  3. Sanitizers are chemical antimicrobial agents that reduce microbial populations to “safe” levels.
  4. What are two types of synthetic agents? Know examples of each.
  5. Growth Factor Analogs: Mimic growth factors to disrupt vital cellular processes. Examples: o Sulfa drugs interfere with folic acid synthesis. o Isoniazid targets mycolic acid synthesis in tuberculosis bacteria.
  6. Nucleic Acid Base Analogs: Mimic nucleotides to disrupt DNA and RNA synthesis. Examples:
  1. What are some reasons why antibiotics harm bacteria but not humans? a. Bacteria have unique structures or enzymes (e.g., peptidoglycan cell wall, bacterial ribosomes) that antibiotics target. b. Human cells lack processes like folic acid synthesis that are vital in bacteria. c. Antibiotics are designed to exploit differences in molecular machinery between prokaryotic and eukaryotic cells.
  1. Define Antibiotic Spectrum, Antibiotic Synergism, and Antibiotic Antagonism
  • Antibiotic Spectrum: o The range of bacterial species an antibiotic is effective against. o Broad-Spectrum Antibiotics: Target a wide variety of bacteria (e.g., tetracyclines). o Narrow-Spectrum Antibiotics: Effective against specific types of bacteria (e.g., penicillin).
  • Antibiotic Synergism: o When two antibiotics work together to enhance their effectiveness. o Example: Penicillin (targets cell wall) + aminoglycosides (inhibit protein synthesis).
  • Antibiotic Antagonism: o When one antibiotic interferes with the action of another. o Example: Combining bacteriostatic and bactericidal agents may hinder effectiveness (e.g., tetracycline + penicillin).
  1. Five Mechanisms of Resistance and Examples
  2. Enzyme Inactivation: o Example: Bacteria produce beta-lactamase, which destroys beta-lactam antibiotics (e.g., penicillin). o Horizontally Transferred: Yes.
  3. Altered Target Sites: o Example: Modification of ribosomal binding sites to resist tetracycline or erythromycin. o Horizontally Transferred: Yes.
  4. Efflux Pumps: o Example: Pumping out antibiotics (e.g., tetracycline) via efflux proteins. o Horizontally Transferred: Yes.
  5. Reduced Permeability: o Example: Altered porin proteins reduce drug entry (e.g., resistance to aminoglycosides). o Horizontally Transferred: No.
  6. Metabolic Pathway Bypassing: o Example: Bacteria circumvent blocked pathways, such as sulfonamide- resistant bacteria synthesizing folic acid differently.

o Horizontally Transferred: Yes.

  1. Difference Between Viruses and Virions
    • Viruses: Intracellular entities that actively replicate and express genes within host cells.
    • Virions: Complete, infectious virus particles outside the host cell, consisting of nucleic acid and a protective protein coat.
    • Key Difference: Viruses are active inside cells, while virions are typically outside cells.
  2. Baltimore Classification Scheme The Baltimore Classification System categorizes viruses based on their type of nucleic acid and replication strategy:
    1. Class I: dsDNA viruses (e.g., Herpesvirus).
    2. Class II: ssDNA viruses (e.g., Parvovirus).
    3. Class III: dsRNA viruses (e.g., Reovirus).
    4. Class IV: (+)ssRNA viruses (e.g., Poliovirus).
    5. Class V: (−)ssRNA viruses (e.g., Influenza virus).
    6. Class VI: ssRNA-RT (reverse transcribing) viruses (e.g., HIV).
    7. Class VII: dsDNA-RT viruses (e.g., Hepatitis B virus).
  3. What Macromolecule Surrounds the Capsid? What Is the Subunit of Capsids?
    • Macromolecule: Protein.
    • Subunit of Capsids: Capsomeres, which self-assemble into the protective capsid structure.
  4. Difference Between a Naked Virus and an Enveloped Virus
    • Naked Virus: o Lacks a lipid envelope. o Typically more resistant to environmental stresses (e.g., poliovirus).
    • Enveloped Virus: o Has a lipid envelope derived from the host cell membrane. o Generally more sensitive to desiccation or detergents (e.g., influenza virus).
  5. Identifying Features of a Complex Virus
    • Features: o Contains intricate structures, such as tails or fibers, in addition to the capsid. o Often has a combination of helical and icosahedral symmetry.
    • Example: o Bacteriophage T4, which infects bacteria.
  6. Where Is the Membrane from an Enveloped Virus Derived?
    • Source: Derived from the host cell membrane during viral budding.
    • Primary Macromolecule in the Envelope: o Lipids, with embedded viral glycoproteins that aid in host cell attachment.