micrb lec 2
What big idea does “bacterial cytoplasm” cover in this lecture?
What’s inside bacteria (DNA, ribosomes, cytoskeleton, storage bodies, microcompartments, endospores) and how those structures help survival/function.
What are the main cytoplasmic contents listed?
DNA (nucleoid + plasmids), ribosomes, cytoskeleton, inclusions/microcompartments, endospores.
Why do bacteria need “inclusions/microcompartments”?
Storage + specialized metabolic “zones” that make reactions more efficient or safer.
What is the nucleoid body?
The bacterial genome + proteins (DNA isn’t floating “naked”; it’s organized with proteins).
What is a common feature of bacterial genomes?
They tend to be circular, meaning replication doesn’t “lose the ends” like linear chromosomes can.
Why might circular DNA be useful during replication?
No chromosome ends to shorten each cycle → avoids “end-replication” problems.
What is a plasmid?
Small circular DNA (about 1,000–100,000 bp) separate from the main genome.
How do plasmids replicate?
They have their own origin of replication → replicate independently.
Can plasmids have multiple copies?
Yes, many cells carry multiple plasmid copies.
Name 3 functions plasmids can carry.
Antibiotic resistance, conjugation/transfer genes, virulence genes.
Why do plasmids matter clinically?
They can spread antibiotic resistance quickly between bacteria.
In EM images, how do plasmids compare to chromosomal DNA?
Plasmids appear as small circular structures compared to the large chromosome mass.
What do bacterial ribosomes do?
Protein synthesis (translate mRNA into protein).
What are the two main subunits shown?
50S (large) + 30S (small) subunits (together = bacterial 70S).
Why is “70S vs 80S” a big deal?
Many antibiotics target bacterial ribosomes because they differ from eukaryotic ribosomes.
What is FtsZ and what does it do?
A tubulin homolog for cell division (forms the division ring).
What is TubZ associated with?
Plasmid segregation (notably in Bacillus spp.).
What is MreB and its role?
An actin homolog important for cell shape, especially rod-shaped bacteria
What is MamK and where is it found?
Actin homolog that positions magnetosomes in magnetotactic bacteria.
What is CreS (crescentin) and what does it do?
Intermediate filament-like protein that makes rods curved (Caulobacter crescentus).
What is MinD’s key role?
Prevents FtsZ polymerization at cell poles, helping division occur mid-cell.
What does MinD prevent during E. coli division?
FtsZ forming rings at the poles (ends), so division happens in the right place.
If MinD fails, what’s the likely division problem?
Misplaced septa / division near poles → uneven daughter cells.
What’s the relationship between MreB and rod shape?
MreB is essential for maintaining rod morphology in many bacteria (like E. coli).
What might happen if MreB is knocked out?
Rod cells often become rounder or lose proper elongation.
What protein helps make Caulobacter curved?
Crescentin (CreS).
Shape advantage question: why might curvature help?
Can affect attachment, swimming behavior, or positioning in flow (conceptual
What happens to H. pylori shape when cytoskeletal proteins are missing?
It shifts from its normal shape toward a rod-like shape (loss of characteristic morphology)
What does this demonstrate about cytoskeletal proteins?
They strongly control bacterial shape, which can affect motility/colonization.
What topic begins next after cytoskeleton?
Inclusions and then microcompartments and endospores.
What are inclusions?
Intracellular bodies/granules of organic or inorganic material, often with enzymes, used for storage.
What can inclusions store (examples)?
Glycogen (glucose), poly-β-hydroxybutyrate (carbon), polyphosphate (volutin), cyanophycin (amino acids).
Why store nutrients internally?
Helps survive fluctuating environments—store during abundance, use during scarcity.
What is poly-β-hydroxybutyrate used for?
Carbon storage.
Do β-hydroxybutyrate inclusions have a membrane?
No membrane (precipitated/storage material).
What do polyphosphate inclusions store?
Phosphate reserves.
What do sulfur inclusions store?
Sulfur reserves (often from sulfur metabolism).
What’s emphasized about these inclusions physically? (sulfur inclusions)
They’re basically precipitated material (storage deposits).
What are bacterial microcompartments, and why do they exist?
Protein-based “mini-organelles” that concentrate enzymes/substrates and/or isolate reactions to improve efficiency and protect the cell. Protein-based “mini-organelles” that concentrate enzymes/substrates and/or isolate reactions to improve efficiency and protect the cell.
carboxysomes: what are they, whats inside and whats the advantage?
Protein-shell compartments with carbonic anhydrase + RuBisCo; they trap CO₂ near RuBisCo, boosting carbon fixation efficiency.
Gas vesicles: what are they + why do they matter for cyanobacteria?
Gas-filled structures that provide buoyancy control, letting cells position for optimal light/nutrients in water.
magnetosomes: what are they and what behaviour do they enable
Membrane-enclosed magnetic iron particles that allow alignment with Earth’s magnetic field (magnetotaxis) to find favorable environments (often oxygen gradients).
endospores: when are they made, what are they for and are they reproductive?
Made under stress (nutrient lack, heat, chemicals, radiation, drying). They’re dormant survival structures, non-reproductive, extremely resistant.
Sporulation vs germination (what’s the difference)?
Sporulation = vegetative cell → endospore. Germination = endospore → active vegetative cell when conditions improve.
Why are endospores clinically important?
They survive harsh cleaning/antibiotics → persist and cause recurring contamination/infection risk.
What do “terminal/subterminal/central endospores” describe?
The position of the spore inside the cell—useful for identification.
What is the bacterial plasma membrane and its 3 big jobs?
Phospholipid bilayer + proteins. Jobs: selective barrier, transport/protein platform, energy conservation (maintains gradients like PMF).
What determines membrane fluidity (high yield)?
Fatty acid length + saturation: more unsaturated/shorter → more fluid; more saturated/longer → less fluid (cold adaptation often increases fluidity).
Why do phospholipid head groups matter?
They change membrane charge and interactions, affecting protein binding and transport.
What is undecaprenyl pyrophosphate used for (conceptually)?
A lipid carrier that shuttles cell-envelope building blocks across the membrane for assembly outside.
Integral vs peripheral membrane proteins (1-card distinction)?
Integral = embedded/spanning (α-helices or β-barrels). Peripheral = surface-associated (ionic/lipid anchors/loops), can detach more easily.
Diffusion vs facilitated diffusion vs active transport (one comparison card).
diffusion: passive, no protein, small non polar + some small molecules (O2/co2, water)
facilitated diffusion: passive but needs protein (channels/carriers), selective
active transport: moves agaisnt gradient, requires energy (ATP or PMF)
What typically can cross the membrane without a transporter vs what usually cannot?
can: small hydrophobic, O₂/CO₂, some water.
Cannot: ions, large polar molecules (sugars, amino acids) without transport proteins.
osmosis: what is it, and why don’t bacteria usually burst?
Water movement down its gradient; bacteria avoid bursting mainly due to cell wall peptidoglycan (and sometimes S-layers) resisting internal pressure.
Uniport vs symport vs antiport (and what powers sym/anti commonly)?
Uniport moves one solute. Symport moves two in same direction; antiport opposite directions. Sym/anti commonly use PMF (one downhill drives another uphill).
PMF (proton motive force): what is it and what does it power?
An H⁺ electrochemical gradient across the membrane. Powers transport (sym/antiport), motility in some bacteria, and supports ATP generation concepts.
Why is the potassium channel example used in membranes?
To show channels are highly selective—structure can prefer K⁺ over similar ions (like Na⁺).
Glucose uptake trick: how do cells keep glucose moving inward?
They phosphorylate glucose immediately → traps it inside and maintains a gradient for continued uptake.
ABC transporters: what are they and when are they useful?
ATP-powered pumps that move substances (often nutrients) against gradients, especially when resources are scarce.
What is the bacterial “cell envelope”?
Everything outside cytoplasm: plasma membrane + cell wall (peptidoglycan); Gram− also has an outer membrane with periplasm.
peptidoglycan: what is it made of and what’s the main purpose?
Alternating sugars MurNAc + GlcNAc with peptide cross-links → strong mesh that prevents osmotic lysis and maintains shape.
Why is peptidoglycan a major antibiotic target?
Humans don’t have it; disrupting synthesis weakens the wall → bacteria can lyse.
Gram-positive vs Gram-negative peptidoglycan differences (one card).
gram+: thick PG (many layers, ~20–35 nm).
Gram−: thin PG (~2–7 nm) located between inner and outer membranes.
What is the periplasm (especially in Gram−) and why does it matter?
Space between membranes containing enzymes/transport proteins; important for nutrient processing and defense.
Teichoic acids: where are they found and what’s their general role?
In Gram+ walls, contribute to structure and surface properties (often negatively charged polymers).
What is special about the Gram-negative outer membrane?
It’s asymmetric: inner leaflet phospholipids, outer leaflet LPS → strong barrier.
lps: what are the key takeaways you must remember?
LPS contributes negative charge, barrier strength, attachment/biofilms; lipid A = endotoxin; O-antigen helps with immune interactions.
Why do Gram-negative bacteria need porins?
Outer membrane is very impermeable; porins (often trimeric β-barrels) allow passive entry of certain small molecules.
Why are some antibiotics harder to use against Gram− bacteria?
The outer membrane + LPS barrier limits entry; access may depend on porins and transport.
If a molecule is charged, what’s your default assumption about crossing the membrane?
It won’t cross without a transporter (channel/carrier/active system).
If the question says “against the concentration gradient,” what transport category should you think of first?
Active transport (ATP or coupled transport like PMF-driven symport/antiport).
If a question mentions “survival under heat/chemicals/desiccation,” what structure is most likely involved?
Endospores.
If a question mentions “Gram− endotoxin,” what molecule and subcomponent should pop into your mind?
LPS, specifically lipid A.
Gram stain steps in order (memorize).
Crystal violet → iodine → alcohol (decolorizer) → safranin (counterstain).
If CreS is expressed in E. coli and you Gram-stain it, what do you expect to see?
Pink curved cells (because E. coli is Gram-negative = pink; CreS makes it curved).
Inclusions vs microcompartments (one-liner difference).
Inclusions = precipitated storage materials; microcompartments = protein shell “organelle-like” structures with enzymes inside.
What image clues were given for carboxysomes vs gas vesicles vs endospores?
Carboxysome = large, hexagonal; gas vesicle = smaller-looking (endospore would fill the cell more); note: some granules are darker than gas vesicles/endospores.
Which structure is produced under nutrient-limiting conditions?
Endospores
Which protein is most important for orienting to Earth’s magnetic field?
MamK.
A protein that forms a pore in the inner membrane is best described as what?
Polytopic integral membrane protein (multiple transmembrane segments can form a channel/pore).
Porin vs “inner membrane pore protein”
Porins are classically associated with the Gram-negative outer membrane; an inner membrane pore is an integral membrane transporter/channel.
Transport examples you MUST know, diffusion, facilitated diffusion,
diffusion: O₂/CO₂ + water; Facilitated diffusion: K⁺; Active transport: lactose via sym/antiport, glucose via group translocation, maltose via ABC transporter.
Halophile in a hypotonic solution — what happens?
It would burst if it weren’t for peptidoglycan holding the cell together.
If sucrose enters via a protein carrier and requires PMF, what is it using?
A symporter (PMF-driven coupled transport).
Gram+ vs Gram− quick memory hook
Gram+ = purple = thick peptidoglycan; Gram− = pink = thin peptidoglycan + outer membrane + periplasm.
What is pyrophosphate?
Two phosphates linked together (phosphoanhydride).
Which set of molecules all contain pyrophosphate?
NDP, undecaprenyl pyrophosphate, and ATP.
Which is NOT found in the Gram-negative outer membrane?
Undecaprenyl pyrophosphate (it’s a carrier lipid used in biosynthesis, not a structural OM component).
What does “O-antigen” mean in LPS, and why does it matter?
It’s the outer polysaccharide part of LPS that’s highly variable between strains, which affects immune recognition/strain differences.
What does it mean that alanine can be in both D and L stereochemistries in peptidoglycan?
Bacteria use both forms (D-Ala and L-Ala) in the tetrapeptide; D-amino acids are uncommon in human proteins, which helps make peptidoglycan distinct.
One of the most common lipids in E. coli” — what should you know?
The major membrane phospholipid is usually phosphatidylethanolamine (PE) (high-yield to remember for Gram-negative inner membranes).
If a cell swells in a solution, what kind of solution is it?
Hypotonic (water moves into the cell).
What is “peptidoglycan remodeling by cleaving the polysaccharide backbone” describing (enzyme + action)?
Lysozyme cleaves the glycan backbone (the sugar-sugar linkages), weakening the wall.
Where are genes encoding antibiotic resistance likely found
Plasmids (common site for transferable resistance genes).