Microbiology Flashcards Test 2

What are the main stages of bacterial cell division?

Early: DNA replication, chromosome segregation, and FtsZ Z-ring formation.

Later: divisome assembly, septal peptidoglycan synthesis, membrane constriction, and daughter-cell separation.

FtsZ

Forms Z ring; GTPase; foundation for division machinery.

FtsA/ZipA

Anchor FtsZ to membrane.

FtsEX

Recruits/regulates amidases.

AmiA/B/C

Cleave peptidoglycan to separate cells.

FtsQ/L/B/K

• Stabilize and regulate the division site.

FtsI/FtsW/PBP1b

Synthesize peptidoglycan.

FtsN

Stabilizes division machinery.

Tol-Pal

• Location: Gram-negative bacterial cell envelope.

• Function: Maintains outer membrane integrity and helps coordinate cell division.

• Energy source: Proton motive force (PMF).

• Importance: Helps pull the outer membrane inward during cell division so daughter cells can separate properly.

What is the Z ring, and why is FtsZ GTPase activity important?

• A discontinuous ring of FtsZ at the midcell that organizes septum formation.

• GTP binding and hydrolysis support dynamic FtsZ filament assembly and remodeling.

How does the Min system position the Z ring?

• MinC: Inhibits FtsZ polymerization.

• MinD: Membrane anchor and activator of MinC.

• MinE: Promotes MinD release and Min-system oscillation.

What is polar inhibition?

The Min system prevents FtsZ from forming a Z ring near the cell poles, ensuring division occurs near the middle.

What is a division guillotine, and how is it prevented

• A division guillotine occurs when the septum forms across chromosomal DNA.

• SlmA binds SlmA binding sites (SBS) on the chromosome and inhibits nearby FtsZ assembly, creating a nucleoid occlusion zone.

How do bacilli and cocci differ in cell division?

• Bacilli are rod-shaped and generally form septa across their short axis.

• Cocci are spherical and can divide in different planes, producing different arrangements of cells.

Predict the effects of mutations in division proteins.

• No FtsZ → No Z ring or normal septation.

• No FtsA/ZipA → Defective Z-ring anchoring.

• No MinC → Incorrect division sites/minicells.

• No amidases → Daughter cells may remain attached.

• No SlmA → Increased risk of division over DNA. †

What environmental conditions limit bacterial growth, and how?

• Temperature: Cold reduces membrane fluidity and metabolism; heat denatures proteins and destabilizes nucleic acids.

• Salt: Causes osmotic stress and water loss.

• pH: Disrupts proteins and proton gradients.

• Pressure: Alters membrane and protein function.

• Oxygen: Can produce damaging reactive oxygen species.

How do extremophiles survive extreme environments?

• Cold: More fluid membranes and cold-adapted enzymes.

• Heat: Stable proteins, chaperones, and protective DNA-associated mechanisms.

• Salt: Compatible solutes or intracellular ions.

• Acid/alkaline conditions: Maintain internal pH.

• High pressure: Adapt membranes and proteins.

How can one adaptation protect against multiple environmental stresses?

Adaptations such as compatible solutes and protein-stabilizing systems can protect cellular structures against more than one stress.

What are the minimum, optimum, and maximum growth conditions?

• Minimum: Lowest condition supporting growth.

• Optimum: Condition producing the fastest growth.

• Maximum: Highest condition supporting growth.

Define the temperature-based microbial groups.

• Psychrophile: Grows optimally in cold environments.

• Psychrotroph: Can grow in the cold but prefers warmer conditions.

• Mesophile: Prefers moderate temperatures.

• Thermophile: Prefers high temperatures.

Define microbes adapted to salt, pressure, and pH.

• Halophile: High salt.

• Barophile: High pressure.

• Acidophile: Low pH.

• Alkaliphile: High pH.

Compare oxygen requirements.

• Obligate aerobe: Requires oxygen.

• Facultative anaerobe: Grows with or without oxygen.

• Aerotolerant anaerobe: Tolerates oxygen but does not use it for respiration.

• Strict anaerobe: Cannot tolerate oxygen.

• Microaerophile: Requires low oxygen concentration

Compare essential nutrients, growth factors, macronutrients, and micronutrients.

• Essential nutrients: Substances required for growth.

• Growth factors: Essential organic compounds a microbe cannot synthesize sufficiently.

• Macronutrients: Required in large amounts.

• Micronutrients: Required in trace amounts.

What are cofactors, and how do they add extra chemistry?

Nonprotein components, such as metal ions or organic coenzymes, that help enzymes carry out reactions their amino acids alone cannot perform.

Compare generalists and specialists.

• Generalists: Use many resources and tolerate varied conditions.

• Specialists: Adapted to particular resources or conditions.

Compare eutrophic and oligotrophic growth strategies.

• Eutrophic: Nutrient-rich environments; often favor rapid growth.

• Oligotrophic: Nutrient-poor environments; favor efficient nutrient uptake and slower growth.

Compare prototrophic, fastidious, and non-culturable bacteria.

• Prototrophic: Can synthesize required growth factors from basic nutrients.

• Fastidious: Require specific nutrients or growth factors.

• Non-culturable: Cannot readily be grown under standard laboratory conditions

What is the great plate anomaly, and how can it be addressed?

Many microbes observed in nature do not grow on standard laboratory plates. Researchers can use modified media, co-cultures, environmental growth conditions, and cultivation devices

What four chemical classes restrict microbial growth?

• Protein denaturants: Alcohols.

• Poisons: Cyanide.

• Membrane disruptors: Detergents.

• Antibiotics: Penicillin

Compare passive and facilitated diffusion

Both move substances down their concentration/electrochemical gradients without direct energy input.

• Passive diffusion occurs through the membrane

• Facilitated diffusion uses transport proteins.

Why does facilitated diffusion reach a maximum rate?

• Transport proteins become saturated.

• Transport rate depends on substrate concentration and the number of available transport proteins.

What is an ABC transporter?

• An ATP-binding cassette transporter that uses ATP hydrolysis for active transport.

• It generally contains membrane-spanning components and ATP-binding domains; some importers also use substrate-binding proteins

Compare primary and secondary active transport.

• Primary active: Directly uses energy such as ATP.

• Secondary active: Uses energy stored in an ion gradient.

• Both can concentrate substrates against their gradients

What is a TRAP transporter?

A tripartite ATP-independent periplasmic transporter that uses an ion gradient, often sodium, to import substrates through an elevator-like conformational mechanism.

What is the PTS transport system?

A phosphotransferase system that uses phosphoenolpyruvate (PEP) to phosphorylate sugars during import

Which PTS components are shared, and which are substrate-specific?

• Shared: Enzyme I (EI) and HPr.

• Usually substrate-specific: Enzyme II components.

Why does PTS phosphorylate sugars during transport?

Phosphorylation helps trap sugars inside the cell and prepares them for metabolism.

Compare Sec and TAT secretion.

Feature	Sec	TAT
Protein state	Unfolded	Folded
Signal sequence	Sec signal peptide	Twin-arginine signal
Energy	ATP and/or PMF	PMF
Chaperones	Help prevent premature folding	Help folding/quality control

What is transertion?

Coupling of transcription, translation, and membrane insertion of proteins.

What is a pseudopilus?

A pilus-like structure in the Type II secretion system that helps push substrates through the outer membrane.

Compare Type I, II, and III secretion systems.

System	Protein state	Mechanism
Type I	Unfolded	Direct export across both Gram-negative membranes; ATP-driven
Type II	Folded	Sec/TAT first, then outer membrane secretion using a pseudopilus
Type III	Unfolded	ATP/PMF-assisted injection into host cells

Which secretion systems use signal sequences?

• Sec: N-terminal signal peptide.

• TAT: Twin-arginine signal peptide.

• Type I: Typically a C-terminal secretion signal.

• Type II: Uses Sec/TAT signals for the first transport step.

• Type III: Uses secretion targeting information, often near the N-terminus, without a typical cleavable signal peptide. †

Which secretion systems are associated with Gram-negative bacteria?

• Types I, II, and III are characteristic Gram-negative secretion systems.

• Sec and TAT are found more broadly.

Which secretion systems transport across which membranes?

• Sec/TAT: Cytoplasmic membrane.

• Type I: Cytoplasmic and outer membranes.

• Type II: Outer membrane after Sec/TAT transport.

• Type III: Both bacterial membranes and often the host membrane.

What are the biological functions of Type I, II, and III secretion?

• 
  

  Type	Biological function
  Type I	Specialized secretion of one specific protein directly outside the bacterium.
  Type II	Secretes folded extracellular proteins, including enzymes and toxins.
  Type III	Injects toxins and effector proteins directly into host cells using a needle complex.

What do efflux pumps transport, and why are they important?

They export antibiotics, toxins, metabolites, and other compounds, helping bacteria resist harmful substances and maintain cellular homeostasis.

Name the six major efflux pump families.

ABC, MFS, RND, SMR, MATE, and PACE.

What are bacterial extracellular vesicles (bEVs)?

Membrane-derived particles released by bacteria that can transport proteins, lipids, nucleic acids, toxins, and other molecules.

What are two benefits of producing bEVs?

• Improved infection outcomes through delivery of virulence-associated cargo.

• Rapid membrane remodeling to remove or redistribute membrane components.

What are two costs of producing bEVs?

• Metabolic costs of producing and losing cellular materials.

• Potential competition with bacteria for host-cell binding sites.

How do Gram-positive bacteria release bEVs through their cell wall?

Endolysins/autolysins remodel or degrade local peptidoglycan, helping vesicles pass through the thick cell wall.

How are microbes classified by energy, electron, and carbon sources?

Source	Classification
Light energy	Photo-
Chemical energy	Chemo-
Organic electrons	Organo-
Inorganic electrons	Litho-
Organic carbon	Heterotroph
CO₂ carbon	Autotroph

What three energy intermediates must cells generate?

ATP, reducing power (such as NADH/NADPH), and a proton motive force or equivalent electrochemical ion gradient.

How do different metabolic classes generate energy intermediates?

• Chemotrophs: Oxidize chemicals to obtain energy and reducing power.

• Phototrophs: Use light-driven electron transport.

• Fermenters: Use substrate-level phosphorylation and regenerate electron carriers.

What is glycolysis?

Conversion of glucose to pyruvate, producing ATP and NADH.

What is the Entner-Doudoroff (ED) pathway?

An alternative glucose catabolism pathway that produces pyruvate, ATP, NADH, and NADPH.

What is the pentose phosphate pathway (PPP)?

• Input: Glucose (through glucose-6-phosphate).

• Main function: Rearranges sugars to produce different sugars needed by the cell.

• Products: Five-carbon sugars, such as ribose-5-phosphate, and NADPH.

• ATP production: Does not directly produce ATP.

• Importance: Provides sugars for making nucleotides (DNA and RNA) and NADPH for biosynthesis.

What is beta-oxidation?

Breakdown of fatty acids into acetyl-CoA, producing reduced electron carriers such as NADH and FADH₂.

What is the role of the TCA cycle?

• Input: Acetyl-CoA (derived from pyruvate or fatty acids).

• Main product: NADH.

• Other products: FADH₂, CO₂, and a small amount of ATP (or GTP).

• Purpose: NADH carries electrons to the electron transport chain (ETS), which helps generate a proton motive force (PMF) used to make ATP

What is an electron donor versus electron acceptor?

• Donor: Gives electrons and is oxidized.

• Acceptor: Receives electrons and is reduced.

How do you calculate the standard reduction potential difference?

\(\Delta E^{\circ\prime}=E^{\circ\prime}_{acceptor}-E^{\circ\prime}_{donor}\)

What does a positive ΔE°′ indicate?

The overall electron transfer is thermodynamically favorable under standard biochemical conditions.

What is the electron donor in NAD⁺/NADH and Fe³⁺/Fe²⁺?

NADH, which is oxidized to NAD⁺.

What is the electron acceptor in FAD/FADH₂ and NO₃⁻/NO₂⁻?

NO₃⁻, which is reduced to NO₂⁻.

How does an electron transport chain generate ATP?

Electron transfer releases energy used to generate a proton motive force (PMF), which can power ATP synthase.

Why do bacteria have flexible electron transport chains?

They can use different electron donors, carriers, and terminal acceptors depending on environmental conditions.

Why do electron transport chains have different P/O ratios?

Different electron entry points and transport components move different numbers of protons, producing different ATP yields per oxygen reduced.

Compare aerobic and anaerobic respiration.

• Aerobic: Oxygen is the terminal electron acceptor.

• Anaerobic: Uses a terminal acceptor other than oxygen, such as nitrate.

What is lithotrophic respiration?

Respiration using reduced inorganic compounds as electron donors; the terminal acceptor depends on the organism

What enzyme is used to oxidize hydrogen?

Hydrogenase, which oxidizes H₂ and transfers electrons to carriers that can support NADH formation.

How can hydrogen sulfide oxidation support NADH production?

Electrons from H₂S oxidation enter an electron transport system and may be driven uphill through reverse electron transport to reduce NAD⁺.

How do fermenting bacteria generate NADH?

During oxidation of organic substrates, such as glycolytic intermediates

How do fermenting bacteria regenerate NAD⁺?

They transfer electrons from NADH to an organic electron acceptor, often pyruvate or a derivative.

What is the terminal electron acceptor in fermentation?

An internally derived organic molecule, rather than an external respiratory electron acceptor.

How do fermenters without an ETC produce ATP?

Primarily through substrate-level phosphorylation, glycolysis.

Fermentation regenerates NAD⁺ so glycolysis can continue.

How can fermenters without an ETC generate a PMF?

By using ATP-driven proton pumps or ion-translocating metabolic reactions.

What is unique about Corynebacterium matruchotii?

It undergoes non-binary fission, elongating at one pole and forming multiple septa to produce several daughter cells.

What is unique about Halomonas titanicae?

A steel-associated, aerobic halophile described in the guide as using iron oxidation for energy.

What is unique about Deinococcus radiodurans?

Extremely radiation-tolerant bacterium with multiple chromosome copies organized in a toroidal nucleoid

What is unique about Prochlorococcus marinus?

A marine photosynthetic cyanobacterium that can depend on a heterotrophic helper such as Alteromonas to detoxify hydrogen peroxide.

What is unique about Salmonella enterica serotype Typhi?

Causes typhoid fever and produces enterobactin and salmochelin, siderophores involved in iron acquisition and immune evasion.

What is unique about Bdellovibrio bacteriovorus?

Predates Gram-negative bacteria, uses type IV pili and hydrolytic enzymes, and can divide by non-binary fission.

What is unique about Yersinia pestis?

Causes bubonic and pneumonic plague, is associated with rodents and fleas, and injects effectors using Type III secretion.

What is unique about Bacillus cereus?

Causes foodborne illness and produces extracellular vesicles described as nutrient-storage “lunch boxes.”

What is unique about Halobacterium salinarum?

An archaeon that uses retinal-containing bacteriorhodopsin to generate a light-driven proton gradient without a conventional photosynthetic ETC.

What is unique about Sinorhizobium meliloti?

Fixes nitrogen in plant root nodules, receives sugars and controlled oxygen supply from its host, and produces rhizopines.

Compare cyclic and acyclic phototrophy.

• Cyclic: Electrons return to bacteriochlorophyll, generating PMF and ATP.

• Acyclic: Electrons are used to reduce NAD⁺ to NADH, while also generating PMF and ATP.

What serves as the electron donor and terminal electron acceptor in cyclic phototrophy?

Bacteriochlorophyll serves as both the original electron donor and terminal electron acceptor.

How are electrons replenished during acyclic phototrophy?

An external electron donor, such as H₂S, replaces electrons used to reduce NAD⁺ to NADH.

How do antennae and accessory pigments increase the amount of light energy bacteria can harness?

They increase the surface area for light absorption and allow bacteria to absorb more wavelengths of light, funneling energy to reaction centers.

How does oxygenic acyclic phototrophy produce ATP, PMF, and NADH?

• Two photosystems use light to excite electrons.

• H₂O serves as the electron donor, releasing O₂.

• The electron transport chain generates PMF.

• PMF drives ATP synthesis.

• NAD⁺ is the final electron acceptor and is reduced to NADH.

What is carbon fixation, and what does the Calvin cycle require?

Carbon fixation converts CO₂ into sugars using RuBiSCO, ATP, and NADPH. Producing one glucose from 6 CO₂ requires 18 ATP and 12 NADPH

What is photorespiration, and how do carboxysomes prevent it?

Photorespiration occurs when the enzyme RuBisCO binds O₂ instead of CO₂ during carbon fixation.

• RuBisCO reacts with oxygen rather than fixing carbon dioxide.

• This produces a wasteful reaction that reduces the efficiency of carbon fixation.

• The cell must use energy to recover useful carbon compounds.

Carboxysomes are protein-based compartments found in certain bacteria that help prevent photorespiration.

• They contain RuBisCO.

• They concentrate CO₂ around RuBisCO.

• This makes RuBisCO more likely to bind CO₂ instead of O₂, improving carbon fixation.

Why do bacteria maintain separate NADH and NADPH pools?

• NADH: Primarily supplies electrons for catabolism.

• NADPH: Supplies electrons for anabolism and biomass synthesis.

How does nitrogen enter biological systems?

• Directly through premade amino acids.

• Through ammonia incorporated into glutamate.

• Atmospheric N₂ can first be converted into ammonia through biological nitrogen fixation

What is the structure and function of nitrogenase, and how do bacteria protect it from oxygen?

• an oxygen-sensitive enzyme complex that converts atmospheric nitrogen (N₂) into ammonia (NH₃) during nitrogen fixation.

• has two main protein components:

1. Fe protein (iron protein): Transfers electrons to the other component using ATP.

2. MoFe protein (iron-molybdenum protein): Uses those electrons to reduce N₂ into NH₃.

3. Because O₂ inactivates nitrogenase, bacteria use several strategies:

   • Anaerobic conditions: Fix nitrogen where oxygen is absent.

   • Rapid respiration: Consume oxygen quickly to maintain low intracellular O₂.

   • Heterocysts: Specialized cyanobacterial cells that provide a low-oxygen environment.

   • Root nodules: Symbiotic bacteria use leghemoglobin to help maintain low free-oxygen levels.

Purple sulfur vs. purple non-sulfur bacteria

Sulfur bacteria can directly reduce NAD⁺; non-sulfur bacteria use reverse electron transport.

Reverse electron transport

Uses energy to drive electrons toward NAD⁺ reduction when the reaction center is not strong enough.

Bacteriorhodopsin

Uses light to pump H⁺ directly, creating PMF without an ETC.

RuBiSCO reaction

Combines a 5-carbon RuBP with CO₂ to produce two 3-carbon molecules.