What are microorganisms?
Mostly single-celled, inhabit all life-supporting environments, many beneficial and used to make products.
What is a culture in microbiology?
Growing microbes on nutrient media (liquid = broth, solid = agar).
What is a colony?
Visible growth of millions of cells from one original cell.
What is growth in microbial terms?
Increase in number through cell division.
What are the two main cell types?
What are plasmids?
Small, extra-chromosomal DNA used for horizontal gene transfer.
What is the cytoplasmic membrane?
Barrier separating cell interior and environment.
What is cytoplasm?
Water-based solution of macromolecules.
What are ribosomes?
Sites of protein synthesis.
What is the function of the cell wall?
Provides structural strength (not in all microbes).
What is metabolism?
Nutrient transformation via enzymes.
What is catabolism?
Break down to make energy.
What is anabolism?
Build macromolecules.
What processes are involved in gene expression?
Transcription, Translation, Replication.
What is motility in cells?
Self-movement.
What is differentiation in microbial cells?
Form specialized structures.
What is horizontal gene transfer?
Share genes via plasmids.
What is intercellular communication?
Chemical signaling between cells.
What is the size range for prokaryotes?
0.5–10 µm.
What is the size range for eukaryotes?
5–100 µm.
What is the significance of a higher surface-to-volume ratio?
Faster nutrient exchange → faster growth.
What are the common morphologies of microorganisms?
How many phyla of bacteria are there?
80+ phyla.
What are archaea often known for?
Often extremophiles (salt, acid), 5+ phyla.
What does Eukarya include?
Plants, animals, fungi; evolved from unicellular ancestors.
What are viruses?
Not alive; obligate intracellular parasites.
How do viruses replicate?
Take over host cells to replicate.
What is the size of the circovirus?
Smallest known virus (<0.2 µm).
What major elements do microorganisms contribute to the biosphere?
How do microorganisms impact agriculture?
Nitrogen fixation, gut health.
What are the positive impacts of microorganisms on food?
Yogurt, pickles, coffee, chocolate.
What are the negative impacts of microorganisms on food?
Spoilage, foodborne illness.
How do microorganisms contribute to industry?
Bioremediation, fermentation, pharmaceuticals, biofuels (methane, ethanol).
What environmental effects do microorganisms have?
Clean up pollutants, wastewater treatment.
Who was Leeuwenhoek?
First to see microbes.
Who was Robert Hooke?
Wrote first microbiology textbook.
What is magnification in microscopy?
Enlarging image.
What is resolution in microscopy?
Distinguishing two points.
What is contrast in microscopy?
Visibility against background.
What is simple staining?
Uses basic (positive) dyes (e.g., methylene blue, crystal violet).
What does a Gram stain reveal?
What is fluorescence microscopy?
Visualize natural/pigmented fluorescence.
What is DIC microscopy?
3D image with light beams.
What is confocal microscopy?
3D imaging by scanning z-plane with lasers.
What is Transmission EM (TEM)?
High resolution (0.2 nm), thin specimens.
What is Scanning EM (SEM)?
Surface imaging, specimens coated in heavy metals.
Who was Louis Pasteur?
Disproved spontaneous generation, developed germ theory, created vaccines.
What is germ theory?
Invisible microbes cause disease.
Who was Robert Koch?
Linked microbes to specific diseases (Koch’s Postulates).
What are Koch’s Postulates?
Developed methods linking microbes to specific diseases.
What did Koch study?
Anthrax, TB, cholera.
What award did Robert Koch receive in 1905?
Nobel Prize.
Who discovered bacterial transformation?
Griffith
What did Avery-MacLeod-McCarty prove about DNA?
DNA carries genetic information
Who are the scientists behind the DNA double helix model?
Watson, Crick, Franklin
What did Zuckerkandl & Pauling develop for evolution?
Molecular sequencing
What system did Carl Woese create using rRNA sequencing?
The three-domain system: Bacteria, Archaea, Eukarya
What method allows DNA extraction without culturing organisms?
PCR (Polymerase Chain Reaction)
What is the structure of the cytoplasmic membrane?
Phospholipid bilayer: hydrophilic heads outward, hydrophobic tails inward
What type of bonds are found in Bacteria and Eukarya membranes?
Ester bonds
What type of bonds are found in Archaea membranes?
Ether bonds
What are the two types of membrane proteins?
What is a function of the cytoplasmic membrane?
Selective permeability: nutrients in, waste out
What is the proton motive force (PMF) in membranes?
Energy conservation across the membrane
What is unique about archaeal membranes?
Isoprenoid chains with ether bonds, may be monolayer or bilayer
What is symport in membrane transport?
Solute + proton move in the same direction
What is antiport in membrane transport?
Solute and proton move in opposite directions
What does group translocation use during transport?
Phosphoenolpyruvate (PEP)
What does the phosphotransferase system transport?
Glucose, fructose, mannose
What is required for ABC transport?
Binding protein, transmembrane protein, ATPase
What is peptidoglycan made of?
Glycan + peptide
What characterizes Gram + bacteria?
Thick peptidoglycan, teichoic acids
What characterizes Gram - bacteria?
Thin peptidoglycan, periplasm, outer membrane (LPS)
What does lysozyme do?
Breaks glycosidic bonds
What does penicillin block?
Peptide cross-links
What do archaea have instead of peptidoglycan?
Pseudomurein
What is LPS composed of in Gram - bacteria?
Lipid A (endotoxin) + core + O-antigen
What is the role of Lipid A?
Toxic, causes immune response
What are porins?
Proteins that allow small molecules to pass
What connects the outer membrane to peptidoglycan?
Braun lipoproteins
What is the periplasm?
Space between outer membrane and cytoplasmic membrane
What is an S-layer?
Outermost protein layer in some bacteria and archaea
What are the functions of an S-layer?
Protection, adhesion, shape
What is unique about Mycoplasma?
No cell wall but may have waxy surface
What is Thermoplasma?
Archaeon with only an S-layer
What is a capsule in bacteria?
Tightly attached layer, visible with India ink
What is a slime layer?
Loose layer, easily removed
What are the functions of capsules and slime layers?
Adhesion, dehydration resistance, virulence
What are fimbriae?
Short, numerous structures for attachment
What are pili?
Longer, fewer structures with various functions
What is the function of Type IV pili?
Twitching motility, adherence, electron transfer
What do conjugative pili do?
Facilitate plasmid exchange
What are hami?
Archaeal hook-like structures for biofilms and adhesion
What are cell inclusions?
Storage of carbon or phosphate
What do gas vesicles provide for aquatic microbes?
Buoyancy
What are magnetosomes?
Structures that align cells with Earth's magnetic field
What is magnetotaxis?
Movement based on magnetic fields
Which groups produce endospores?
Bacillales, Clostridiales (Firmicutes)
What is the function of endospores?
Survival in harsh conditions
What is the structure of an endospore?
Core (DNA), inner membrane, cortex, coat, exosporium
What does dipicolinic acid + Ca²⁺ do in endospores?
Provides dehydration and heat resistance
What are the steps of sporulation?
What are the steps of germination?
What are the types of flagella in bacteria?
What is the process of endospore release?
What are the types of flagella in bacteria?
What powers bacterial flagella?
Proton motive force (PMF)
What are the two movements of flagella?
What are the components of bacterial flagella structure?
What are archaella?
Thinner than bacterial flagella, powered by ATP, built from proteins related to type IV pili
What is twitching motility?
Movement via type IV pili, uses ATP
What is gliding motility?
Smooth, helical motion; uses PMF and surface adhesion proteins
What is chemotaxis?
Movement in response to chemical signals (attractants/repellents)
What is the model organism for chemotaxis?
E. coli
What is phototaxis?
Movement in response to light
What is scotophobotaxis?
Movement away from darkness
What is osmotaxis?
Movement in response to ionic strength
What is hydrotaxis?
Movement in response to water
What is aerotaxis?
Movement in response to oxygen
What is the role of histones in eukaryotic cells?
Package DNA into nucleosomes
What is the process of mitosis?
Diploid → diploid
What is the process of meiosis?
Diploid → haploid
What is the function of mitochondria?
Site of ATP production via respiration
What are the inner membrane folds in mitochondria called?
Cristae
What occurs in the matrix of mitochondria?
Site of citric acid cycle
What is the function of chloroplasts?
Site of photosynthesis
What do chloroplasts contain?
Chlorophyll
What are thylakoids?
Membrane stacks in the stroma of chloroplasts
What are the components of the cytoskeleton?
What is the function of microtubules?
Shape and chromosome movement
What are microfilaments made of?
Actin-based
What is the function of intermediate filaments?
Provide structural support
What does the rER do?
Protein synthesis (has ribosomes)
What does the sER do?
Lipid and carbohydrate metabolism
What is the function of the Golgi apparatus?
Modifies and packages proteins
What do lysosomes contain?
Digestive enzymes
What is the difference between cilia and flagella?
What is the structure of eukaryotic cilia and flagella?
9+2 microtubule arrangement (tubulin-based)
What is stored in ATP?
Energy in phosphate bonds
What is oxidation?
Loss of electrons (e⁻)
What is reduction?
Gain of electrons (e⁻)
What are the microbial metabolic types?
What do chemoorganotrophs use?
Organic compounds (e.g., glucose)
What do chemolithotrophs use?
Inorganic molecules (e.g., H₂, NH₄⁺)
What do phototrophs use for energy?
Light
What is the redox tower?
Shows electron donors (top) and acceptors (bottom)
What is the formula for energy released in redox reactions?
ΔG° = –nFΔE₀
What are electron carriers?
What is substrate-level phosphorylation?
Direct transfer of phosphate, used in fermentation
What is oxidative phosphorylation?
PMF drives ATP synthesis via ATP synthase, used in respiration
What is photophosphorylation?
Light energy creates PMF
What are energy-rich compounds?
What is the role of enzymes?
Lower activation energy
What is the active site of an enzyme?
Enzyme binding region
What are prosthetic groups?
Permanently bound to enzymes (e.g., heme)
What are coenzymes?
Loosely bound to enzymes (e.g., NAD⁺)
What is fermentation?
Anaerobic process; no external e⁻ acceptor.
How is ATP generated in fermentation?
Via substrate-level phosphorylation.
What occurs during respiration?
Uses O₂ or other acceptors for ATP production.
What is the ATP yield in aerobic respiration?
Via oxidative phosphorylation.
What is the role of electron transport in respiration?
Creates proton motive force (PMF).
What is the outcome of glycolysis?
Glucose → 2 pyruvate, 2 NADH, net 2 ATP.
What are the stages of glycolysis?
Stage I: preparatory; Stage II: payoff.
What does the citric acid cycle produce per glucose?
6 CO₂, 4 NADH, 2 FADH₂, 2 ATP.
What is the purpose of the glyoxylate cycle?
Conserves carbon when using C₂ compounds.
What can be fermented in fermentative diversity?
Amino acids, sugars.
What is the function of NADH dehydrogenase?
Oxidizes NADH in the electron transport chain.
What are the components of the ETC?
NADH dehydrogenase, flavoproteins, cytochromes.
What is PMF?
Proton motive force; drives ATP synthesis.
How does ATP synthase function?
Uses PMF to synthesize ATP; reversible action.
What is anaerobic respiration?
Uses non-O₂ electron acceptors (e.g., NO₃⁻).
What is chemolithotrophy?
Uses inorganic e⁻ donors (e.g., H₂, NH₄⁺).
What is the role of light in phototrophy?
Generates proton motive force (PMF).
What is the Calvin cycle used for?
Carbon fixation by autotrophs.
What is gluconeogenesis?
Synthesis of glucose from non-carbohydrate sources.
How are amino acids synthesized?
From glycolysis/TCA intermediates.
What are purines derived from?
Inosinic acid.
What is the function of lipids and fatty acids synthesis?
Fatty acid synthesis via acyl carrier protein (ACP).
What are macronutrients?
Needed in large amounts: C, N, O, H, P, S, K⁺, Mg²⁺, Ca²⁺, Fe²⁺.
What distinguishes complex media?
Made of extracts; exact composition unknown.
What is the purpose of selective media?
Inhibits the growth of some microbes.
What does the viable count measure?
Only living cells.
What distinguishes types of media?
Using indicators (e.g., pH dye).
What does solid media contain?
Agar.
What is a microscopic count?
Total cell number (includes live/dead).
What is a viable count?
Living cells only (CFU; 30–300 rule).
What is the spread plate method?
Cells on surface.
What is the pour plate method?
Cells in and on agar.
What is turbidity/optical density (OD)?
Estimate of cell number via spectrophotometer.
What is binary fission?
Cell doubles DNA and divides → 2 daughter cells.
What is generation time?
Time to double.
What are the growth phases in batch culture?
What happens during the lag phase?
Metabolism adjusts, no division yet.
What occurs in the exponential phase?
Active division.
What characterizes the stationary phase?
Nutrients limited, waste accumulates.
What happens in the death phase?
Cell death exceeds growth.
What is the formula for microbial growth?
( N_t = N_0 \times 2^n )
What is the formula for specific growth rate?
( k = \frac{0.693}{g} )
What is generation time in growth dynamics?
Time taken for a population to double.
What is a continuous culture (chemostat)?
Fresh media added, waste removed.
What does the dilution rate control?
Growth rate and density.
What are biofilms?
Sessile cells bound in extracellular polysaccharide matrix.
Why are biofilms more resistant?
More resistant and pathogenic than planktonic cells.
Where are biofilms commonly found?
On medical devices, teeth, pipes, hot springs.
What are the cardinal temperatures?
Minimum, Optimum, Maximum growth temperatures.
What is the optimal temperature?
All enzymes function best.
What are psychrophiles?
Cold-loving organisms (<15°C).
What are psychrotolerant organisms?
Grow in cold, prefer 20–40°C.
What are mesophiles?
Grow at 20–45°C (includes pathogens like E. coli).
What are thermophiles?
Heat-loving organisms (45–80°C).
What are hyperthermophiles?
Organisms that thrive at >80°C (e.g. Pyrolobus).
How do cold-adapted organisms survive?
More α-helices, unsaturated fatty acids, cryoprotectants.
How do heat-adapted organisms survive?
Heat-stable proteins, saturated lipids, ether-linked monolayers.
What are pH preferences in microbes?
What are halophiles?
Require salt for growth.
What are halotolerant organisms?
Tolerate salt, but do not require it.
What are extreme halophiles?
Require 15–30% NaCl.
What are compatible solutes?
Keep internal water balance in cells.
What are the oxygen requirements for microbes?
What are toxic oxygen species?
Superoxide (O₂⁻), H₂O₂, OH⁻.
What is the role of superoxide dismutase?
Converts O₂⁻ to H₂O₂.
What does catalase/peroxidase do?
Converts H₂O₂ to H₂O + O₂.
What is moist heat sterilization?
More effective than dry heat (autoclave).
What is D value in heat sterilization?
Time to reduce population by 90%.
What is thermal death time?
Time to kill all cells.
What is pasteurization?
Kills pathogens, reduces microbial load.
What is the purpose of UV radiation?
Surface sterilization.
What is ionizing radiation used for?
Deep penetration for sterilization.
What do filters do in sterilization?
Sterilize heat-sensitive liquids (e.g., membrane filters).
What are cidal agents?
Kill microbes (bactericidal).
What are static agents?
Inhibit growth (bacteriostatic).
What are lytic agents?
Cause lysis of cells (bacteriolytic).
What does MIC stand for?
Minimum inhibitory concentration.
What is the disk diffusion method?
Zone of inhibition test for antimicrobial activity.
What are sterilants?
Kill all microbes, including spores; used on surfaces.
What are disinfectants?
Kill most microbes; used on surfaces.
What are sanitizers?
Reduce microbial numbers; used on surfaces.
What are antiseptics?
Reduce/kill microbes; used on skin.
What is a virus?
Obligate intracellular parasite; requires host cell to reproduce.
What is a virion?
Complete infectious virus particle (genome + protein coat).
Are viruses considered living?
No metabolism, no independent reproduction.
What are the components of a virus?
What is a capsid?
Protein shell made of capsomeres.
What is an envelope in viruses?
Lipid bilayer from host membrane (only in enveloped viruses).
What are naked viruses?
Viruses that lack an envelope.
What is the genome of viruses made of?
What is a nucleocapsid?
The combination of the capsid and the genome.
What are bacteriophages?
Viruses that infect bacteria (e.g., T4, Lambda).
What are animal viruses?
Viruses that often have an envelope.
What are plant viruses mainly composed of?
Mostly RNA, naked, spread by wounding or vectors.
What is the symmetry type of helical viruses?
Rod-shaped (e.g., Tobacco Mosaic Virus).
What is the symmetry type of icosahedral viruses?
Spherical (e.g., HPV).
What is the symmetry type of complex viruses?
Bacteriophages with head + tail (e.g., T4).
What is the function of lysozyme in viruses?
Breaks peptidoglycan to inject genome or release.
What does neuraminidase do?
Breaks down host glycoproteins (e.g., flu virus).
What is the role of RNA replicase?
Replicates viral RNA genomes.
What does reverse transcriptase do?
Makes DNA from RNA (e.g., HIV).
What are the 5 key steps of the viral replication cycle?
What is the eclipse phase in viral growth?
No complete virions inside or outside.
What is the maturation phase in viral growth?
Virions assemble inside the cell.
What is burst size?
The number of virions released per cell.
How does bacteriophage T4 infect E. coli?
Via LPS receptor.
How does T4 inject its DNA?
Tail fibers attach, sheath contracts, DNA injected (capsid stays out).
What does T4's lysozyme do?
Breaks the bacterial cell wall.
What are the early proteins in T4?
Replication enzymes.
What are the late proteins in T4?
Structural parts.
What happens during lysis in T4?
Mature virions are released.
What is the CRISPR-Cas system?
Cuts viral DNA as a prokaryotic defense.
What do restriction enzymes do?
Cleaves foreign DNA.
What are toxin-antitoxin systems?
Inactivate virus parts as a defense.
What is a temperate virus?
Can enter lysogeny (dormant state).
What is a prophage?
Viral DNA integrated into the host genome.
What does a repressor protein do?
Maintains lysogeny in temperate viruses.
What triggers induction in lysogenic cycles?
Switch to lytic cycle.
What is a lysogen?
A host cell containing a prophage.
How does a whole animal virus enter a host cell?
Via endocytosis.
Where do DNA viruses replicate?
In the nucleus.
Where do RNA viruses replicate?
In the cytoplasm.
What do retroviruses do?
Convert RNA to cDNA and integrate into host genome.
What are the outcomes of animal virus infections?
What are plant viruses primarily?
Mostly ssRNA, naked, enter via wounds or insect vectors.
What is a plaque assay?
Clear zones where virus lysed cells.
What is titer in virology?
PFU/mL (plaque-forming units).
What is plating efficiency?
Less than 100% due to unsuccessful infections.
What is the Central Dogma of molecular biology?
DNA → RNA → Protein.
What is a gene?
A functional DNA unit.
What is a genome?
Total genetic information.
What is replication?
DNA copied.
What is transcription?
DNA to RNA.
What is translation?
RNA to protein.
What sugar does DNA contain?
Deoxyribose.
What sugar does RNA contain?
Ribose.
What are the base pairs in DNA?
A-T, G-C.
What are the base pairs in RNA?
A-U, G-C.
What are phosphodiester bonds?
Links nucleotides (3’ → 5’).
What is the structure of DNA?
Antiparallel strands, complementary, double helix.
What is the major groove in DNA?
A protein binding site.
What is supercoiling in DNA?
Packs long DNA into cells.
What is negative supercoiling?
Left-hand supercoiling (most cells).
What is positive supercoiling?
Right-hand supercoiling (extreme thermophiles).
What does DNA gyrase do?
Introduces negative supercoils.
What are chromosomes?
Main genome; circular in prokaryotes.
What can plasmids carry?
What are transposable elements?
Moveable DNA segments.
What are operons?
Gene clusters transcribed together.
What is the overview of DNA replication?
Semiconservative process.
What are resistance genes?
Genes that provide resistance to antibiotics or environmental stressors.
What are virulence factors?
Molecules produced by pathogens that contribute to their ability to cause disease.
What are bacteriocins?
Antimicrobial peptides produced by bacteria to inhibit the growth of similar or closely related bacterial strains.
What is the direction of DNA replication?
Semiconservative, occurs in the 5’→3’ direction.
What is the main replication polymerase?
DNA Polymerase III (Pol III).
What does primase do?
Makes RNA primers for DNA replication.
What is the function of DNA ligase?
Seals nicks in the DNA by forming phosphodiester bonds.
What does helicase (DnaB) do?
Unwinds the DNA helix during replication.
What is the role of SSBP?
Stabilizes single-stranded DNA (ssDNA).
What does DnaA recognize?
The origin of replication in DNA.
What is the function of DnaC?
Acts as a loader protein for helicase.
What is a replisome?
The complete replication complex involved in DNA replication.
What is the role of the Tau subunit?
Holds DNA polymerases together during replication.
What are the characteristics of the leading strand?
Undergoes continuous synthesis during DNA replication.
What are Okazaki fragments?
Segments of DNA synthesized discontinuously on the lagging strand.
What is theta replication?
A bidirectional method of DNA replication observed in prokaryotes.
What is the proofreading function in DNA replication?
Exonuclease activity of Pol I and III corrects errors.
What is the role of Tus protein?
Terminates DNA replication at the terminus.
What helps in partitioning chromosomes?
FtsZ protein aids in dividing chromosomes during cell division.
What is the function of RNA polymerase in bacteria?
Synthesizes RNA without the need for a primer.
What does the sigma factor do?
Finds the promoter region for RNA polymerase binding.
What are the -10 and -35 regions?
Promoter regions recognized by the sigma factor in bacterial transcription.
What are the two types of termination in bacterial transcription?
Intrinsic (stem-loop + poly-U) and Rho-dependent (Rho protein).
What is a monocistronic transcription unit?
Contains one gene coding for one mRNA.
What is a polycistronic transcription unit?
Operon containing multiple genes coding for one mRNA.
What are the rRNA genes in bacteria?
16S, 23S, and 5S rRNA genes with spacers.
What is the RNA polymerase in archaea similar to?
Similar to eukaryotic RNA polymerase II.
What do promoters in archaea contain?
TATA box and BRE elements.
What are the termination methods in eukaryotes?
Inverted repeats or Eta protein involvement.
What processing occurs to eukaryotic RNA?
5’ cap addition, splicing, and poly-A tail addition.
What is a codon?
A sequence of 3 bases that codes for one amino acid.
What is the start codon?
AUG, which codes for methionine.
What is the start codon for bacteria?
fMet (formylmethionine).
What are the stop codons?
UAA, UAG, UGA.
What is wobble in translation?
Loose base pairing in the third position of a codon.
What is codon bias?
Preference for certain codons over others in protein synthesis.
What is the anticodon?
Three-base region on tRNA that matches a codon.
What does aminoacyl-tRNA synthetase do?
Charges tRNA with the appropriate amino acid.
What is added post-transcriptionally at the 3’ end of tRNA?
CCA sequence.
What is the prokaryotic ribosome composition?
70S ribosome made of 30S and 50S subunits.
What rRNA is part of the 30S subunit?
16S rRNA.
What rRNA is part of the 50S subunit?
23S and 5S rRNA.
What is the A site in the ribosome?
Site where new tRNA enters during translation.
What is the P site in the ribosome?
Site where the growing peptide chain is held.
What is the E site in the ribosome?
Exit site for tRNA after it has delivered its amino acid.
What is the Shine-Dalgarno sequence?
Ribosome binding site located before the start codon AUG.
What are the steps of translation initiation?
30S + mRNA + fMet-tRNA + initiation factors → 50S joins.
What occurs during elongation in translation?
Peptide bonds form; GTP is used for energy.
What is translocation in translation?
Movement of the ribosome forward along the mRNA.
What happens during termination of translation?
Stop codon is reached, release factor is activated, and the polypeptide is released.
What are polysomes?
Multiple ribosomes translating a single mRNA simultaneously.
What is trans-translation?
tmRNA rescues stalled ribosomes by providing a template.
What are chaperones?
Proteins that assist in the folding or refolding of other proteins.
What do DnaK and DnaJ do?
Bind to new proteins to assist in their folding.
What is the role of GroEL/GroES?
Help fold partially folded proteins.
What is the function of CspA?
Acts as a cold shock RNA chaperone.
What is the signal sequence in protein secretion?
N-terminal sequence that directs the protein for export or integration.
What does the Sec system do?
Exports unfolded proteins across the membrane.
What is the role of SecA?
Facilitates the secretion of proteins in the Sec system.
What does SRP stand for?
Signal Recognition Particle, involved in membrane insertion of proteins.
What is the Tat system?
Exports folded proteins across the membrane.
What does the Type I secretion system do?
One-step ABC transporter for toxins and biofilm components.
What is the Type II secretion system?
Two-step system that transports proteins from the periplasm to the environment.
What does the Type III secretion system do?
Injects toxins directly into host cells (injectisome).
What is the Type IV secretion system?
Delivers proteins or DNA to other cells in one step.
What does the Type V secretion system do?
Two-step autotransporters that use the Sec system and fold themselves.
What is the Type VI secretion system?
One-step system that injects proteins into other bacteria using a needle-like structure.
What is constitutive expression?
Genes that are always expressed regardless of conditions.
What is regulated expression?
Genes that can be turned on or off depending on environmental conditions.
What is an operon?
A cluster of 2 or more genes under a single promoter.
What is a promoter?
DNA sequence where RNA polymerase binds to initiate transcription.
What is an operator?
Site where repressor proteins bind to regulate gene expression.
What are inverted repeats?
Sequences where proteins often bind in DNA.
What is a homodimer?
A protein composed of two identical subunits that bind to both strands of DNA.
What is a helix-turn-helix?
A common DNA-binding motif consisting of a recognition helix and a stabilizing helix.
What is the helix-turn-helix motif?
Common DNA-binding motif with: - Recognition helix: binds DNA - Stabilizing helix: supports recognition helix
What does a zinc finger do?
Binds zinc in eukaryotes
What is a leucine zipper?
Positions helices for binding
What is an activator in transcription factors?
Turns transcription on
What is a repressor in transcription factors?
Turns transcription off
What are effectors?
Small molecules that bind TFs: - Inducer: turns on transcription - Co-repressor: turns off transcription
What are allosteric proteins?
Change shape/function when bound by effector
What is the mechanism of repression in the arginine operon?
Anabolic mechanism with arginine as co-repressor
What is the induction mechanism in the lac operon?
Catabolic mechanism with lactose as inducer
What does LacI do in the absence of lactose?
Binds operator, turning transcription off
What happens when lactose is present?
Binds LacI, preventing DNA binding → transcription on
What is negative control in transcription?
Uses repressors to inhibit transcription
What is positive control in transcription?
Uses activators to promote transcription (e.g., maltose activator)
What is a regulon?
Multiple operons controlled by the same TF
What is an example of a regulon?
Maltose regulon = several operons, one activator
What is a two-component system?
Involves: - Sensor kinase: autophosphorylates after sensing signal - Response regulator: gets phosphate, binds DNA
What does the phosphatase do in a two-component system?
Resets system by removing phosphate
What are MCPs?
Methyl-accepting chemotaxis proteins (chemoreceptors)
What does CheA do in chemotaxis?
Sensor kinase that regulates movement based on attractants and repellents
What is quorum sensing?
Detects cell density via autoinducers, activating group behavior genes
What is an example of a behavior regulated by quorum sensing?
Bioluminescence, biofilm, virulence (e.g., Shiga toxin)
What is catabolite repression?
Prefers glucose over other sugars, causing diauxic growth
What is the role of cAMP in catabolite repression?
Low when glucose is high; activates CRP to bind DNA
What is required for lac operon regulation?
What is feedback inhibition?
End product of a pathway inhibits first enzyme via allosteric site
What is post-translational regulation?
Covalent modification (e.g., phosphorylation) alters enzyme activity
What is super-resolution microscopy?
Light microscopy using fluorophores to visualize cell structures in real time
What is GFP?
Green fluorescent protein; a reporter gene product
What initiates chromosome replication?
DnaA-ATP binds OriC, unwinding by gyrase, tau → replisome forms
What is hemimethylation?
Only parent strand is methylated post-replication
What does SeqA do?
Binds hemimethylated sites to block reinitiation
What is the Par System?
Ensures one copy of chromosome per daughter cell
What are the components of the Par System?
What does the Structural Maintenance Complex do?
Separates interlinked chromosomes
What proteins are involved in cell division?
Fts proteins
What are the components involved in chromosome segregation?
What is the Structural Maintenance Complex?
What is the function of the MinCDE system?
Ensures Z-ring forms at mid-cell:
- MinD = inhibitor
- MinC = blocks FtsZ
- MinE = removes MinCD from center.
What is the role of MreB in bacterial shape?
Bacterial actin that positions elongation enzymes (RodA); loss → cocci shape.
What proteins determine bacterial shape?
What are the steps in peptidoglycan biosynthesis?
What is the function of transpeptidation?
Crosslinks muramic acids; catalyzed by FtsI (PBP); blocked by penicillin.
What are the types of PBP?
What are the stages of biofilm formation?
What is the role of c-di-GMP in biofilm formation?
Inhibits motility, activates EPS production, regulates surface proteins.
What is the significance of Pseudomonas aeruginosa biofilm?
Thick biofilm = antibiotic resistance; quorum sensing (AHLs) activates biofilm genes.
What happens during explosive death in biofilms?
Prophage-encoded lysis releases DNA → biofilm scaffold.
What are the targets of antibiotics?
What are the mechanisms of antibiotic resistance?
What are spontaneous mutations?
Mutations caused by DNA pol errors (no external cause).
What are the types of mutants?
What are the types of point mutations?
What are the effects of insertions/deletions?
What are the types of reversions?
What are the mutation rates in bacteria?
10⁻⁶ – 10⁻⁷ per kb per replication; eukaryotes: 10× lower; viruses: much higher.
What are some examples of mutagens?
What do alkylating agents do?
Modify bases, causing mismatches.
What do intercalating agents induce?
Frameshifts.
What do nonionizing radiation cause?
Pyrimidine dimers.
What is the effect of ionizing radiation?
Radicals that damage DNA.
What does RecA do in the SOS system?
Senses damage and activates SOS.
What is the role of LexA in the SOS system?
SOS repressor cleaved by activated RecA.
What is translesion synthesis?
Bypasses lesions with error-prone polymerase.
What is transformation in bacteria?
Uptake of free DNA.
What is transduction?
Virus-mediated DNA transfer.
What is conjugation in bacteria?
Plasmid-mediated, cell-to-cell contact.
What are the fates of incoming DNA?
What does RecA mediate in homologous recombination?
Strand invasion and heteroduplex formation.
What is the mechanism of transformation?
Pili bind and pull DNA → degraded to ssDNA → RecA mediates recombination.
What regulates competence in bacteria?
Quorum sensing, chitin sensing, and catabolite repression.
What is electroporation?
Artificial transformation via electric shock.
What is generalized transduction?
Any gene transferred via random packaging of host DNA.
What is specialized transduction?
Only specific chromosomal genes transferred during incorrect excision of prophage.
What is phage conversion?
Phenotype of host altered by lysogeny (e.g., toxin production).
What is required for conjugation?
Direct contact and a conjugative plasmid (e.g., F plasmid).
What is the donor and recipient in conjugation?
Donor = F⁺; Recipient = F⁻.
What is rolling circle replication?
Nick, transfer, and synthesize copy.
What is the role of TraI in conjugation?
Helicase + nicking enzyme.
What are Hfr strains?
F plasmid integrates into chromosome, transfers part during conjugation.
What are F' plasmids?
F plasmid excised with host genes, creating partial diploid (merodiploid).
What are the types of viral genomes?
DNA or RNA, ss or ds; RNA genomes usually smaller.
What is the smallest DNA virus?
Circovirus: <2 kb, ssDNA.
What is the largest virus?
Pandoravirus: >2.5 Mb.
What are viroids?
Smallest plant pathogens, no capsid, RNA only.
What is the Baltimore classification based on?
How viruses produce +mRNA.
What is an example of Class I virus?
T4, Lambda (dsDNA).
What is an example of Class II virus?
PhiX174, M13 (ssDNA).
What is an example of Class III virus?
Reovirus (dsRNA).
What is an example of Class IV virus?
Poliovirus, MS2, Coronavirus (ssRNA+).
What is an example of Class V virus?
Rabies, Influenza (ssRNA-).
What is an example of Class VI virus?
HIV (ssRNA+ retrovirus).
What is an example of Class VII virus?
Hepatitis B (dsDNA through RNA).
What are early proteins in viruses?
Regulatory enzymes.
What are late proteins in viruses?
Structural proteins for virion assembly.
What is taxonomy based on for viruses?
Polyphasic: phenotype, genotype, phylogeny.
What is the smallest ssDNA phage?
PhiX174: circular ssDNA, overlapping genes.
What does Gene A in PhiX174 do?
Shuts down host DNA synthesis.
What is the dsDNA phage T4 known for?
Large, uses modified cytosine (5-hmC), virulent.
What is the lambda phage?
Temperate, integrates via integrase.
What type of genes does T7 transcribe?
Linear, early genes transcribed by host RNA pol.
What does T7 bring for replication?
Brings own DNA polymerase; concatemer cutting.
What type of virus is Lambda?
Temperate, has cohesive ends, integrates via integrase.
What dominates during Lambda lysis?
Cro dominates during lysis.
What dominates during Lambda lysogeny?
cI (lambda repressor) dominates during lysogeny.
What is possible during Lambda excision?
Transduction is possible during excision.
Where does Poxvirus replicate?
Replicates entirely in cytoplasm.
What type of DNA does Adenovirus have?
Linear dsDNA; terminal protein primes replication.
What is the structure of Polyomavirus (SV40)?
Circular dsDNA; can be lytic or transforming.
What is the replication method of Herpesvirus?
Replicates in nucleus via rolling circle; 3-stage gene expression.
What is the genome type of positive-strand RNA viruses?
Genome = mRNA.
What does MS2 encode?
Encodes 4 proteins; overlapping genes.
What is unique about Poliovirus's genome?
Has VPg at 5’; translated into polyprotein → cleaved.
Where does Coronavirus replicate?
Replication occurs in cytoplasm via - strand intermediate.
How does Rabies virus replicate?
Replicates in cytoplasm; released by budding.
What is unique about Influenza's genome?
Has a segmented genome → antigenic shift.
What does Hemagglutinin do in Influenza?
Binds host cells.
What is the structure of Reovirus?
Has a double capsid; mRNA translated into two proteins.
What disease does Rotavirus cause?
Causes dehydration and diarrhea in infants.
What is the lifecycle of Retroviruses?
+RNA → reverse transcription → dsDNA → integration (provirus).
What enzymes do Retroviruses bring?
Brings reverse transcriptase, integrase, protease.
How do Hepadnaviruses replicate?
Replication in nucleus; DNA → RNA intermediate → reverse transcribed to DNA.
What are Viroids?
ssRNA, no capsid; infect plants.
How do Viroids spread?
Spread via plasmodesmata.
What do Viroids replicate as?
Replicate as dsRNA → trigger RNA silencing.
What are Prions?
Infectious proteins; no nucleic acid.
What diseases are caused by Prions?
Cause spongiform encephalopathies (e.g., CJD, mad cow).
What do Prions cause in the brain?
Amyloid buildup in brain; change normal proteins → plaques.
What is Omics?
Broad field analyzing large pools of biomolecules.
What is a Genome?
Entire genetic content (genes, regulatory/noncoding DNA).
What is Genomics?
Mapping, sequencing, analyzing, and comparing genes.
What is Genome Sequencing?
Determining DNA/RNA nucleotide order.
What is Genome Annotation?
Identifying genes and functional elements.
What is Genome Assembly?
Aligning fragments into full sequence.
What are ORFs?
Open reading frames; functional ORFs encode proteins.
What is the accuracy of annotation for ORFs?
≤70% of ORFs have known function.
What are hypothetical proteins?
ORFs with unknown function.
What are Noncoding RNAs?
No start codon, may have many stop codons (e.g., tRNA, rRNA).
What is the genome size range for bacteria/archaea?
Range from ~121 genes to thousands.
What does comparative genomics do?
Uses databases to compare species and infer gene function.
What is the minimum genome size for free-living microbes?
Unknown minimum genome size for free-living microbes.
What is the genome structure of Yeast (S. cerevisiae)?
16 chromosomes, 13.4 Mbp, ~6000 ORFs.
How many ORFs are essential in Yeast?
~900 ORFs are essential according to knockout studies.
What does Functional Genomics study?
Studies gene expression, protein function, metabolite activity.
What is the goal of Functional Genomics?
Understand transcriptome, proteome, and metabolome.
What is the DISARM system?
Antiphage system in Bacillus paralicheniformis; resistance to 8 phages.
What does the DISARM system encode?
Encodes a methylase; acts like a restriction-modification system.
What does Metagenomics study?
Studies total DNA/RNA from environmental samples.
What is a Metagenome?
All genes in a microbial community.
What do Metatranscriptomics and Metaproteomics study?
Gene expression patterns in nature.
What is the Microbiome?
10x more prokaryotic cells than human cells; most live in large intestine.
What is the effect of Firmicutes on health?
↑ Firmicutes → obesity.
What is the Mycobiome?
>60 fungi on skin, mouth, moist surfaces.
What can microbiome studies reveal?
May reveal disease connections.
What is Transcriptomics?
Study of total RNA produced under a condition.
What are Microarrays (gene chips)?
Solid supports with attached DNA for gene expression analysis.
What is transcriptomics?
Study of total RNA produced under a condition.
What are microarrays (gene chips)?
Solid supports with attached oligonucleotides.
What is detected by fluorescent cDNA in microarrays?
Gene expression.
What does proteomics study?
Protein structure, function, and activity.
What is the proteome?
All proteins expressed by a genome or at one time (translatome).
What methods are used in proteomics?
What does systems biology integrate?
Data from genomics, transcriptomics, proteomics, metabolomics, and pharmacogenomics.
What is an iPOP?
Integrative personal omics profile.
How is omics used in medicine?
Personalized medicine, diagnostics, immune tracking.
What has omics helped develop?
New immunotherapies.
What must be addressed for routine clinical use of omics?
Ethical considerations.
What is PCR?
In vitro DNA replication; amplifies DNA up to a billionfold.
What machine automates the PCR process?
Thermocycler.
What does qPCR measure?
Initial DNA amount.
What does RT-PCR convert?
RNA to DNA using reverse transcriptase.
What are the components of PCR?
What are the steps of PCR?
What are applications of PCR?
What does gel electrophoresis separate?
Nucleic acids by size and charge.
How does DNA migrate in gel electrophoresis?
To positive electrode due to negative phosphate backbone.
What visualizes DNA in gel electrophoresis?
Ethidium bromide (fluorescent dye).
What is nucleic acid hybridization?
Base pairing of complementary DNA or RNA sequences.
What is the purpose of molecular cloning?
Transfer of gene from original source into a vector for manipulation and expression.
What forms during molecular cloning?
Recombinant DNA (DNA from multiple sources).
What is the foundation for genetic engineering?
Molecular cloning.
What do all microbes conserve via catabolism?
Energy and obtain reducing power.
How is ATP generated?
What is respiration?
Needs external electron acceptor; includes aerobic and anaerobic.
What is the Calvin Cycle?
Most widespread CO₂ fixation pathway.
What is the key enzyme in the Calvin Cycle?
RubisCO; converts CO₂ to G3P.
What is photosynthesis?
Light energy → chemical energy → biomass.
What are the two types of photosystems in phototrophic bacteria?
Photosystem I (FeS type) & Photosystem II (Q-type).
What are the two groups of cyanobacteria?
Morphological Groups: Chroococcales, P.
What are the two types of photosystems in totrophic bacteria?
Which bacteria have both photosystems?
Cyanobacteria (oxygenic)
What are the morphological groups of Cyanobacteria?
What is the function of thylakoids in Cyanobacteria?
Sites of light reactions
What do Cyanobacteria fix?
What are heterocysts in Cyanobacteria?
O₂-free cells for N₂ fixation; thick walls, no PSII.
What role do Cyanobacteria play in ecology?
What do purple sulfur bacteria use as an electron donor?
H₂S
What characterizes purple nonsulfur bacteria?
They are photoheterotrophs and colored by carotenoids.
What are the characteristics of green sulfur bacteria?
What cycle do green nonsulfur bacteria use?
3-hydroxypropionate cycle
What are the two main reservoirs in the carbon cycle?
What is the process of photosynthesis in the carbon cycle?
CO₂ → (CH₂O)
What is the process of respiration in the carbon cycle?
(CH₂O) → CO₂
What are the end-products of decomposition?
Methane (CH₄) and CO₂
Why is CH₄ considered a potent greenhouse gas?
It is produced from anoxic environments.
How are the carbon and nitrogen cycles related?
Fertilizers ↑ growth, linking both cycles.
What is methanogenesis?
CO₂ reduced to CH₄ (mainly using H₂).
What do syntrophs provide to methanogens?
Substrates
What is the major process of denitrification?
NO₃⁻ → N₂
What is the major reservoir of sulfur?
Rocks and oceans (as SO₄²⁻).
How is H₂S produced?
By microbes or geochemically; toxic.
What do sulfur-oxidizing chemolithotrophs use for energy?
Sulfide at oxic/anoxic boundaries.
What is the human microbiome?
All microbes in a specific human environment.
What is the difference between microbiome and microbiota?
Microbiome: All microbes; Microbiota: Microbes in a specific microhabitat.
What is used to identify bacteria at body sites?
16S rRNA sequencing
What is a common bacteria found in the skin?
Propionibacterium
What is a common bacteria found in saliva?
Streptococcus
What is a common bacteria found in the urogenital tract?
Lactobacillus, Bifidobacterium
What is a common bacteria found in the GI tract?
Bacteroidetes
What questions are under study regarding the microbiome?
What type of digestive system do humans have?
Monogastric, omnivorous
When does colonization of the GI tract begin?
At birth; affected by delivery method and diet.
What is the surface area of the GI tract?
400 m²
What is common in the stomach/duodenum?
Low colonization due to pH ~2; common bacteria: Firmicutes, Bacteroidetes, Actinobacteria.
What bacteria is known to be acid-resistant and may cause ulcers?
Helicobacter pylori
What is the function of the large intestine?
Fermentation chamber.
What are the phyla found in the large intestine?
What are the enterotypes found in the large intestine?
What are some microbial benefits in the GI tract?
Why does the immune system need microbial stimulation?
To develop properly post-birth.
What does saliva contain that helps in oral health?
What are the stages of dental issues related to biofilms?
Plaque → caries → endocarditis, systemic effects.
What is the state of the lower respiratory tract in healthy adults?
Sterile
What pathogens can reach the lungs?
Pathogens reaching lungs are <10 µm.
What bacteria are commonly associated with UTIs?
What causes the slightly acidic environment of the vagina?
Lactobacillus acidophilus fermentation of glycogen → lactic acid.
What happens when antibiotics are used in the vagina?
↓ lactobacilli, ↑ pH → Candida albicans overgrowth.
What are the three environments of the skin?
What factors influence skin microbiota?
Weather, hygiene, age.
How is microbial distribution on skin visualized?
Using heat maps.
What dominates the human virome?
Bacteriophages at mucosal surfaces.
What protective role do bacteriophages serve?
They act as the first line of defense.
What factors influence microbial distribution?
What visual method is used to show microbial distribution?
Heat maps
What dominates the human virome at mucosal surfaces?
Bacteriophages
What is the protective role of bacteriophages?
First line of defense
What type of immunity do bacteriophages provide?
Host-independent immunity
What are some diseases caused by viruses?
What is the Human Microbiome Project (HMP)?
Baseline from medical students
What is a limitation of the Human Microbiome Project?
Lacks global diversity
What is a key characteristic of mouse models in microbiome studies?
Larger cecum than humans
What can mouse models be raised as for microbiome studies?
Germ-free
What is one use of mouse models in microbiome research?
Study diet, antibiotics, fecal transplants
What type of microbes are present in the first year of life?
How does vaginal birth affect microbiome?
Similar to mother (includes Bacteroides)
What is the microbiome composition after a C-section?
More Proteobacteria
What type of bacteria increases with breastfeeding?
Bifidobacterium
What promotes Bifidobacterium in breastfed infants?
Milk oligosaccharides
What changes occur in gut microbiota maturation?
How does diversity in gut microbiota change with age?
Diversity ↓; early experiences shape adult microbiota
What disorder is linked to chronic gut inflammation?
IBD (Inflammatory Bowel Disease)
What is dysbiosis?
Imbalance in gut microbiota
What is linked to IBD?
What is the link between obesity and gut microbiota?
No clear Bacteroidetes-Firmicutes link in humans
What types of bacteria increase in obese individuals?
What effect do oral antibiotics have on gut microbes?
Reduce both harmful and beneficial microbes
What risk increases due to antibiotics?
What is C. difficile?
Antibiotic-resistant spore-former
What is the purpose of a fecal transplant?
Reintroduces normal microbiota
What is a benefit of fecal transplants?
Highly effective for treating C. difficile infections
What are probiotics?
Live organisms (e.g., Lactobacillus, Bifidobacterium) that provide health benefits
What are prebiotics?
Indigestible carbs that nourish beneficial bacteria
What are synbiotics?
Contain both prebiotics and probiotics
What success have synbiotics shown in treatment?
Dramatic success in sepsis treatment in children
What is microbial adherence?
Growth on/in host; essential for infection
What is the difference between infection and disease?
Infection = growth; Disease = damage to host tissue
What are adhesins?
Structures (capsules, fimbriae, pili, flagella) that bind to host receptors
How does N. gonorrhoeae adhere to hosts?
Uses pili
How does S. pneumoniae adhere to hosts?
Uses capsules
Where does colonization start?
At mucous membranes
What is biofilm?
A structure formed by colonization, e.g., dental plaque
What is bacteremia?
Bacteria in blood
What is septicemia?
Bacteria grow in blood, leading to sepsis/death
What is viremia?
Viruses in blood
What is pathogenicity?
Ability to cause disease
What does virulence measure?
Severity of disease (measured by LD₅₀)
What is attenuation?
Loss of virulence, often used in vaccines
Where are virulence genes found?
On plasmids/pathogenicity islands (e.g., SPI1, SPI2 in Salmonella)
Who are compromised hosts?
Hospital patients, AIDS patients
What are nosocomial infections?
Hospital-acquired infections
What are opportunistic pathogens?
Cause disease in weakened hosts only
What role do enzymes play in virulence?
Break down tissues to invade
What does hyaluronidase do?
Breaks polysaccharides
What does collagenase do?
Breaks collagen
What does streptokinase do?
Dissolves clots
What does coagulase do?
Promotes clotting (protects bacteria)
What do IgAases do?
Cleave IgA to evade immune system
What are AB-type exotoxins?
A = active part; B = binding
What does diphtheria toxin do?
Blocks protein synthesis via EF-2
What does botulinum toxin do?
Blocks acetylcholine → flaccid paralysis
What does tetanus toxin do?
Blocks inhibition → spastic paralysis
What does cholera toxin do?
Increases cAMP → ion/water secretion → diarrhea
What are cytolytic toxins?
Destroy membranes (e.g., hemolysins, leukocidins)
What do superantigens do?
Overactivate immune system (e.g., TSS from S. aureus)
What are endotoxins?
Found in Gram-negative LPS, released upon lysis
What do xins do?
Destroy membranes (e.g., hemolysins, leukocidins).
What are superantigens?
Overactivate the immune system (e.g., TSS from S. aureus).
Where are endotoxins found?
In Gram-negative LPS, released upon lysis.
What is the toxic portion of endotoxins?
Lipid A → fever, inflammation, shock.
How are endotoxins measured?
By Limulus Amebocyte Lysate (LAL) Assay.
What is innate immunity?
Nonspecific, rapid, present from birth; involves phagocytes.
What is adaptive immunity?
Specific, slower; involves lymphocytes (B and T cells).
What are the main types of phagocytes?
Neutrophils, macrophages, dendritic cells, eosinophils.
What do mast cells & basophils do?
Trigger inflammation.
What do NK cells do?
Kill compromised host cells (no MHC I).
What are epitopes?
Antigen fragments presented on MHC to lymphocytes → activation, memory.
What are plasma cells?
B cells that produce antibodies.
What is immune memory?
Faster response to previously encountered antigens.
What do normal microbiota do?
Compete with pathogens.
What are examples of mechanical barriers?
Cilia, mucus, flushing of urinary tract.
What are examples of chemical barriers?
Stomach acid (pH 2), lysozyme in tears/saliva, defensins, amyloid proteins.
What do tight junctions do?
Prevent invasion between epithelial cells.
Where do all immune cells originate?
From hematopoietic stem cells in bone marrow.
What are the primary lymphoid organs?
Bone marrow (B cell development) and thymus (T cell maturation).
What are the secondary lymphoid organs?
Spleen, lymph nodes, MALT – sites of antigen recognition.
What does MALT stand for?
Mucosa-associated lymphoid tissue – gut, respiratory, etc.
What is lymph?
Drains into blood via thoracic duct → left subclavian vein.
What is diapedesis?
Movement of cells from blood into tissues.
What directs hematopoiesis?
Cytokines and chemokines.
What is plasma?
Blood without cells.
What is serum?
Plasma without clotting proteins.
What is the myeloid lineage?
Monocytes → Macrophages & dendritic cells (APCs, MHC II).
What are the types of granulocytes?
Neutrophils, eosinophils, basophils, mast cells.
What do neutrophils do?
Rapid responders.
What do eosinophils fight?
Parasites.
What do basophils & mast cells release?
Histamine; trigger inflammation.
What do B cells do?
Produce antibodies; act as APCs.
What do T cells recognize?
Antigen-MHC complexes.
What do NK cells kill?
Virus-infected/tumor cells.
What is the role of phagocytes?
Key in innate immunity and activating adaptive response.
What happens during invasion?
Pathogen attaches, enters, and multiplies in host tissues.
What do chemokines do?
Recruit neutrophils to infection site.
What is margination?
Neutrophils stick to blood vessel walls.
What is phagolysosome?
Formed from fusion of phagosome + lysosome.
What are reactive oxygen species used for?
To kill ingested pathogens.
What are some evasion strategies of pathogens?
Carotenoids, leukocidins, capsules.
What is inflammation?
Redness, swelling, heat, pain.
What triggers inflammation?
PRRs binding PAMPs → cytokine release (IL-1, IL-6, TNF-α).
What stimulates fever?
IL-1, IL-6, TNF-α stimulate hypothalamus → prostaglandins → ↑temp.
What are the benefits of fever?
Slower pathogen growth, ↑transferrins (bind iron).
What is systemic inflammation?
Risk of septic shock (↓BP, cytokine storm).
What is the key event in the complement system?
C3 cleavage → C3a + C3b.
What are the three pathways of the complement system?
Classical, MBL, Alternative.
What is the end result of the complement system?
MAC formation (C5b–C9) → lysis (mostly Gram-).
What is opsonization?
C3b enhances phagocytosis.
What are anaphylatoxins?
C3a, C5a: attract WBCs, inflammation.
What does mannose binding lead to?
What are the roles of NK cells?
What do interferons do?
What defines adaptive immunity?
What is the role of B cells?
What is the role of T cells?
What happens during the primary response?
What happens during the secondary response?
What is specificity in immunity?
What is tolerance in immunity?
What is positive selection in T cell development?
What is negative selection in T cell development?
What is clonal deletion in T cell selection?
What happens to B cells during negative selection?
What do non-self-reactive B cells do?
What are T-independent antigens?
What are T-dependent antigens?
What is an antigen?
What is an immunogen?
What is an epitope?
What is a hapten?
What is natural active immunity?
What is natural passive immunity?
What is artificial active immunity?
What is artificial passive immunity?
What are the functions of antibodies?
What is the Fc region of an antibody?
What is the Fab region of an antibody?
What is the function of IgG?
What is the function of IgM?
What is the function of IgA?
What is the function of IgE?
What is the function of IgD?
What is the primary response characterized by?
What is the secondary response characterized by?
What is class switching?
What is VDJ recombination?
What does the light chain consist of?
What are CDRs in antibodies?
What is somatic hypermutation?
What is allelic exclusion?
What is MHC class I expressed on?
What does MHC class I present to?
What is the source of antigen for MHC class I?
What is MHC class II expressed on?
What does MHC class II present to?
What is the source of antigen for MHC class II?
What are the HLA genes for class I?
What are the HLA genes for class II?
What is the structure of MHC class I?
What is the structure of MHC class II?
What does MHC class I present?
What happens when MHC class I presents peptides?
What does MHC class II present?
What is the result of MHC class II presentation?
What is polymorphism in MHC?
What is polygeny in MHC?
What is a peptide motif?
What are anchor residues?
What does polygeny refer to?
Multiple MHC genes = broader antigen presentation.
What is a peptide motif?
Specific structure that fits MHC groove.
What are anchor residues?
Hold peptide in groove.
What is the structure of T Cell Receptors (TCR)?
α and β chains, each with V and C domains.
How does TCR diversity occur?
From VDJ recombination (like BCR).
What does TCR recognize?
Peptides presented by MHC.
What are the two signals required for T Cell activation?
What happens without signal 2 in T Cell activation?
Anergy (nonresponsive).
What does Tc subset recognize?
CD8+ MHC I
What is the function of Tc cells?
Kills infected cells.
What does Th1 subset recognize?
CD4+ MHC II
What is the function of Th1 cells?
IL-2, IFN-γ → activate macrophages, cell-mediated immunity.
What does Th2 subset recognize?
CD4+ MHC II
What is the function of Th2 cells?
IL-4, IL-5 → activate B cells → antibody production.
What does Th17 subset recognize?
CD4+ MHC II
What is the function of Th17 cells?
IL-17 → recruit neutrophils, inflammation.
What does Treg subset recognize?
CD4+ MHC II
What is the function of Treg cells?
IL-10, TGF-β → suppress immune response.
What is Type I Hypersensitivity?
IgE binds mast cells → allergen triggers degranulation → histamine release → allergy symptoms.
How is Type I Hypersensitivity treated?
Epinephrine (anaphylaxis), antihistamines, or desensitization.
What is Type IV Hypersensitivity?
Th1 cell-mediated, occurs 24–48 hrs after exposure.
What is an example of Type IV Hypersensitivity?
Poison ivy, Tuberculin test.
What are some autoimmune diseases?
Type I Diabetes (Th1 attacks β-cells), SLE (Type III, immune complexes), Hashimoto’s (autoantibodies).
How are autoimmune diseases treated?
With steroids or monoclonal antibodies (e.g., Humira).
What are examples of superantigens?
From S. aureus (TSS) and S. pyogenes (scarlet fever).
What is Primary Immunodeficiency?
SCID → no functional B/T cells.
What is Secondary Immunodeficiency?
AIDS; HIV kills CD4+ T cells → opportunistic infections.
What are live attenuated vaccines?
Strongest, may revert.
What are inactivated vaccines?
Safer, less effective.
What are toxoid vaccines?
Inactivated toxins (e.g., tetanus).
What are conjugate vaccines?
Poor antigens (polysaccharides) linked to proteins for memory (e.g., Hib, pneumococcal).
What are DNA/mRNA vaccines?
Host cells make antigen → no infection risk (e.g., COVID mRNA vaccine).
What are checkpoint inhibitors in immunotherapy?
Block immune suppression (e.g., PD-1 blockade by pembrolizumab).
What is Adoptive T Cell Therapy?
CAR-T cells: engineered to recognize tumors.
What are tumor-infiltrating lymphocytes?
Harvested, expanded, reinfused.
How does gut microbiota influence immunotherapy?
Especially Bifidobacterium influences success.
What are cell wall inhibitors in antibacterial drugs?
Penicillin, cephalosporins (β-lactam ring) inhibit transpeptidation.
What do cell wall inhibitors target?
Effective mostly against Gram+.
What are protein synthesis inhibitors?
30S: Tetracycline, streptomycin.
50S: Erythromycin, chloramphenicol.
What are nucleic acid inhibitors?
Quinolones: inhibit DNA gyrase.
Rifampin: blocks RNA polymerase (orange-pink urine).
What do sulfa drugs target?
Folate metabolism (PABA analogs).
What are membrane disruptors in antibacterial drugs?
Daptomycin, polymyxins.
What are some antiviral drugs?
Acyclovir (nucleoside analog), Tamiflu (neuraminidase inhibitor), interferons.
What mechanisms do antiviral drugs target?
Reverse transcriptase, fusion, or release mechanisms.
What are some antifungal drugs?
Polyenes, azoles, polyoxins: target ergosterol or chitin synthesis.
What is the issue with drug resistance?
Resistance to antibiotics is widespread; new strategies are essential.
What is the treatment for TB (Mycobacterium)?
Isoniazid (targets mycolic acid).
What is the treatment for S. pyogenes (strep throat)?
Penicillin.
What are treatments for Lyme disease and RMSF?
Doxycycline.
What is the treatment for Cholera?
Fluid/electrolyte therapy, not antibiotics.
What is the treatment for Pertussis (whooping cough)?
Macrolides (e.g., azithromycin).
What is the treatment for H. pylori?
Neutralizes HCl; linked to ulcers.
What are microorganisms?
Mostly single-celled, inhabit all life-supporting environments, many beneficial and used to make products.
What is a culture in microbiology?
Growing microbes on nutrient media (liquid = broth, solid = agar).
What are the two main cell types?
What is the significance of a higher surface-to-volume ratio?
Faster nutrient exchange → faster growth.
What are the common morphologies of microorganisms?
What major elements do microorganisms contribute to the biosphere?
How do microorganisms contribute to industry?
Bioremediation, fermentation, pharmaceuticals, biofuels (methane, ethanol).
What does a Gram stain reveal?
What system did Carl Woese create using rRNA sequencing?
The three-domain system: Bacteria, Archaea, Eukarya
What is the structure of the cytoplasmic membrane?
Phospholipid bilayer: hydrophilic heads outward, hydrophobic tails inward
What is unique about archaeal membranes?
Isoprenoid chains with ether bonds, may be monolayer or bilayer
What are the steps of sporulation?
What are the types of flagella in bacteria?
What are the types of flagella in bacteria?
What are archaella?
Thinner than bacterial flagella, powered by ATP, built from proteins related to type IV pili
What is the difference between cilia and flagella?
What are the microbial metabolic types?
What is the function of lipids and fatty acids synthesis?
Fatty acid synthesis via acyl carrier protein (ACP).
What are the growth phases in batch culture?
How do heat-adapted organisms survive?
Heat-stable proteins, saturated lipids, ether-linked monolayers.
What are pH preferences in microbes?
What are the oxygen requirements for microbes?
What are the components of a virus?
What are the 5 key steps of the viral replication cycle?
What are the outcomes of animal virus infections?
What are virulence factors?
Molecules produced by pathogens that contribute to their ability to cause disease.
What are bacteriocins?
Antimicrobial peptides produced by bacteria to inhibit the growth of similar or closely related bacterial strains.
What are the characteristics of the leading strand?
Undergoes continuous synthesis during DNA replication.
What is the proofreading function in DNA replication?
Exonuclease activity of Pol I and III corrects errors.
What helps in partitioning chromosomes?
FtsZ protein aids in dividing chromosomes during cell division.
What are the -10 and -35 regions?
Promoter regions recognized by the sigma factor in bacterial transcription.
What are the two types of termination in bacterial transcription?
Intrinsic (stem-loop + poly-U) and Rho-dependent (Rho protein).
What are the steps of translation initiation?
30S + mRNA + fMet-tRNA + initiation factors → 50S joins.
What happens during termination of translation?
Stop codon is reached, release factor is activated, and the polypeptide is released.
What is the signal sequence in protein secretion?
N-terminal sequence that directs the protein for export or integration.
What does the Type I secretion system do?
One-step ABC transporter for toxins and biofilm components.
What is the Type II secretion system?
Two-step system that transports proteins from the periplasm to the environment.
What does the Type V secretion system do?
Two-step autotransporters that use the Sec system and fold themselves.
What is the Type VI secretion system?
One-step system that injects proteins into other bacteria using a needle-like structure.
What is regulated expression?
Genes that can be turned on or off depending on environmental conditions.
What is a helix-turn-helix?
A common DNA-binding motif consisting of a recognition helix and a stabilizing helix.
What is the helix-turn-helix motif?
Common DNA-binding motif with: - Recognition helix: binds DNA - Stabilizing helix: supports recognition helix
What are effectors?
Small molecules that bind TFs: - Inducer: turns on transcription - Co-repressor: turns off transcription
What is the mechanism of repression in the arginine operon?
Anabolic mechanism with arginine as co-repressor
What is positive control in transcription?
Uses activators to promote transcription (e.g., maltose activator)
What is a two-component system?
Involves: - Sensor kinase: autophosphorylates after sensing signal - Response regulator: gets phosphate, binds DNA
What does CheA do in chemotaxis?
Sensor kinase that regulates movement based on attractants and repellents
What is an example of a behavior regulated by quorum sensing?
Bioluminescence, biofilm, virulence (e.g., Shiga toxin)
What is the role of cAMP in catabolite repression?
Low when glucose is high; activates CRP to bind DNA
What is required for lac operon regulation?
What is post-translational regulation?
Covalent modification (e.g., phosphorylation) alters enzyme activity
What is super-resolution microscopy?
Light microscopy using fluorophores to visualize cell structures in real time
What initiates chromosome replication?
DnaA-ATP binds OriC, unwinding by gyrase, tau → replisome forms
What are the components involved in chromosome segregation?
What is the function of the MinCDE system?
Ensures Z-ring forms at mid-cell:
- MinD = inhibitor
- MinC = blocks FtsZ
- MinE = removes MinCD from center.
What is the role of MreB in bacterial shape?
Bacterial actin that positions elongation enzymes (RodA); loss → cocci shape.
What proteins determine bacterial shape?
What are the steps in peptidoglycan biosynthesis?
What is the function of transpeptidation?
Crosslinks muramic acids; catalyzed by FtsI (PBP); blocked by penicillin.
What are the types of PBP?
What are the stages of biofilm formation?
What is the role of c-di-GMP in biofilm formation?
Inhibits motility, activates EPS production, regulates surface proteins.
What is the significance of Pseudomonas aeruginosa biofilm?
Thick biofilm = antibiotic resistance; quorum sensing (AHLs) activates biofilm genes.
What happens during explosive death in biofilms?
Prophage-encoded lysis releases DNA → biofilm scaffold.
What are the targets of antibiotics?
What are the mechanisms of antibiotic resistance?
What are the types of mutants?
What are the types of point mutations?
What are the effects of insertions/deletions?
What are the types of reversions?
What are the mutation rates in bacteria?
10⁻⁶ – 10⁻⁷ per kb per replication; eukaryotes: 10× lower; viruses: much higher.
What are some examples of mutagens?
What are the fates of incoming DNA?
What is the mechanism of transformation?
Pili bind and pull DNA → degraded to ssDNA → RecA mediates recombination.
What is specialized transduction?
Only specific chromosomal genes transferred during incorrect excision of prophage.
What is the replication method of Herpesvirus?
Replicates in nucleus via rolling circle; 3-stage gene expression.
What is the lifecycle of Retroviruses?
+RNA → reverse transcription → dsDNA → integration (provirus).
How do Hepadnaviruses replicate?
Replication in nucleus; DNA → RNA intermediate → reverse transcribed to DNA.
What is the minimum genome size for free-living microbes?
Unknown minimum genome size for free-living microbes.
What does Functional Genomics study?
Studies gene expression, protein function, metabolite activity.
What does the DISARM system encode?
Encodes a methylase; acts like a restriction-modification system.
What does systems biology integrate?
Data from genomics, transcriptomics, proteomics, metabolomics, and pharmacogenomics.
What are applications of PCR?
How does DNA migrate in gel electrophoresis?
To positive electrode due to negative phosphate backbone.
What is the purpose of molecular cloning?
Transfer of gene from original source into a vector for manipulation and expression.
How is ATP generated?
What are the two types of photosystems in phototrophic bacteria?
Photosystem I (FeS type) & Photosystem II (Q-type).
What are the two types of photosystems in totrophic bacteria?
What are the morphological groups of Cyanobacteria?
What role do Cyanobacteria play in ecology?
What characterizes purple nonsulfur bacteria?
They are photoheterotrophs and colored by carotenoids.
What are the characteristics of green sulfur bacteria?
What are the two main reservoirs in the carbon cycle?
What is the difference between microbiome and microbiota?
Microbiome: All microbes; Microbiota: Microbes in a specific microhabitat.
What questions are under study regarding the microbiome?
What is common in the stomach/duodenum?
Low colonization due to pH ~2; common bacteria: Firmicutes, Bacteroidetes, Actinobacteria.
What are some microbial benefits in the GI tract?
What does saliva contain that helps in oral health?
What are the stages of dental issues related to biofilms?
Plaque → caries → endocarditis, systemic effects.
What causes the slightly acidic environment of the vagina?
Lactobacillus acidophilus fermentation of glycogen → lactic acid.
What happens when antibiotics are used in the vagina?
↓ lactobacilli, ↑ pH → Candida albicans overgrowth.
What type of microbes are present in the first year of life?
What changes occur in gut microbiota maturation?
How does diversity in gut microbiota change with age?
Diversity ↓; early experiences shape adult microbiota
What is the link between obesity and gut microbiota?
No clear Bacteroidetes-Firmicutes link in humans
What are probiotics?
Live organisms (e.g., Lactobacillus, Bifidobacterium) that provide health benefits
What is the difference between infection and disease?
Infection = growth; Disease = damage to host tissue
What are examples of chemical barriers?
Stomach acid (pH 2), lysozyme in tears/saliva, defensins, amyloid proteins.
What are the primary lymphoid organs?
Bone marrow (B cell development) and thymus (T cell maturation).
What does mannose binding lead to?
What do interferons do?
What is negative selection in T cell development?
What is the secondary response characterized by?
What is the result of MHC class II presentation?
What are the two signals required for T Cell activation?
What is Type I Hypersensitivity?
IgE binds mast cells → allergen triggers degranulation → histamine release → allergy symptoms.
How is Type I Hypersensitivity treated?
Epinephrine (anaphylaxis), antihistamines, or desensitization.
What are some autoimmune diseases?
Type I Diabetes (Th1 attacks β-cells), SLE (Type III, immune complexes), Hashimoto’s (autoantibodies).
What are conjugate vaccines?
Poor antigens (polysaccharides) linked to proteins for memory (e.g., Hib, pneumococcal).
What are checkpoint inhibitors in immunotherapy?
Block immune suppression (e.g., PD-1 blockade by pembrolizumab).
What are cell wall inhibitors in antibacterial drugs?
Penicillin, cephalosporins (β-lactam ring) inhibit transpeptidation.
What are protein synthesis inhibitors?
30S: Tetracycline, streptomycin.
50S: Erythromycin, chloramphenicol.
What are nucleic acid inhibitors?
Quinolones: inhibit DNA gyrase.
Rifampin: blocks RNA polymerase (orange-pink urine).
What are some antiviral drugs?
Acyclovir (nucleoside analog), Tamiflu (neuraminidase inhibitor), interferons.
What is the issue with drug resistance?
Resistance to antibiotics is widespread; new strategies are essential.
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