Microbio - Module 2: Bacterial Cell Structure

How was the term "prokaryote" originally defined in 1962?

• By the features organisms lack compared to eukaryotes (specifically lacking a membrane-bound nucleus, a cytoskeleton, membrane-bound organelles, and internal membranous structures).

Why is defining "prokaryotes" based on absent features scientifically inaccurate?

Modern biochemical, genetic, and genomic analyses show that Bacteria and Archaea are fundamentally distinct domains of life, not just two forms of a single structural group.

Who proposed abandoning the term "prokaryote" in 2006, and why?

Microbiologist Norman Pace, because the term fails to reflect the evolutionary differences and unique traits of Bacteria and Archaea.

Which two domains of life were historically grouped together under the term "prokaryote"? (originally no longer now)

Bacteria and Archaea.

Since the microbial world has a variety of morphologies, what are the three groups? explain for ea

• shape

  • cocci—spherical cells

  • rods—oblong cells

• arrangement

  • determined by plane of division

  • determined by separation or not

• size—varies

whats the general shape of cocci (s., coccus)?

• spherical

match ea cocci arrangment to its description:

1. Diplococci

2. Streptococci

3. Staphylococci

4. Tetrads

5. Sarcina

6. bacilli

7. vibrios

8. how do spirilla and spirochetes differ in their structure?

9. mycelium

10. pleomorphic

1. Diplococci: Divide and remain in pairs.

2. Streptococci: Divide on 1 plane to form chains.

3. Staphylococci: Divide in random planes to form grape-like clusters.

4. tetrads: Divide in 2 planes to form a square of 4.

5. Sarcina: Divide in 3 planes to form a cubic packet of 8.

6. rod shaped

7. comma shaped

8. spirilla—rigid, spiral-shaped. spirochetes—flexible, spiral-shaped

9. network of long filaments

10. bacteria that r variable in shape

bacterial cell size

whats considered small, avg, very large?

• small = 0.3 um (mycoplasma)

• avg = 1.1-1.5 x 2-6 um long (e. coli)

• very large = 600 × 80 um

size-shape relationship

do cells want a low or high surface area-to-volume ratio (S/V ratio)? And why?

• high surface area to vol ratio

• inc efficiency of nutrient uptake and diffusion of

  molecules within a cell.

what are good protective mechansism from predation for cells?

Large size and odd shape

what are the common bacterial structures?

whats a cell envelope and what does it consist of?

what are the external structures?

—layers that surround the cell

• plasma membrane

• cell wall

cytoplasm

nucleoid

external structures

• pili

• flagella

Bacterial Cell Envelope

Besides the plasma membrane and cell wall, the cell envelope includes AT LEAST ONE additional layer, what could they be?

• capsule

• slime layer

whats the most important membrane that required for all living organisms?

plasma membrane

plasma membrane functions

Innermost membrane that encompasses the cytoplasm.

Selectively permeable barrier that acquires nutrients and

eliminates waste.

Interacts with external environment.

• Detects and responds to surrounding chemicals.

• Transport systems used for nutrient uptake.

• Metabolic processes (that is, respiration &

photosynthesis

Plasma Membrane Structure is Dynamic

explain the structure

what is it composed of? which part is hydrophilic, hydrophobic?

Plasma membrane is a thin structure (7 to 8 nm) composed

of 2 lipid sheets.

Amphipathic lipids

• Hydrophilic—Polar ends that interact with water.

• Hydrophobic—Non-polar tails that are insoluble in water

and interact with each other.

Bilayer forms spontaneously

in aqueous environment.

• Hydrophilic on surface.

• Hydrophobic ends buried.

what proteins are on the plasma membrane? What is the function of the second type of protein?

peripheral membrane proteins—Loosely connected to

the membrane and easily removed.

• 20 to 30% of the total membrane proteins.

Integral membrane proteins—Amphipathic proteins that

are embedded within membrane and not easily removed.

• Hydrophobic region buried in membrane lipids.

• Hydrophilic regions project from the surface.

• Carry out important functions (that is, transport).

whats the plasma membrane mainly composed of what kind of lipids? what are the other smaller lipids?

• mainly phospholipids

SMALLER LIPIDS:

hopanoids—Hydrophobic molecule similar to cholesterol.

• Distort the bilayer, which impacts the fluidity and shape in membrane region.

• Form functional membrane microdomains that are platforms for protein complex assembly.

what do bacterial cells take for nutrients? where are they found?

Macronutrients—required in large amounts.

• Found in organic molecules (that is, proteins, lipids,

nucleic acids, and carbohydrates).

• Cations contribute to activity and stability of molecules and

cell structures.

• Important in cellular processes (that is, protein synthesis).

Micronutrients—required in small amounts.

• Ubiquitous in nature and usually present in adequate

amounts to support microbial growth.

• Work to assist enzyme catalysis and maintain protein

structure.

what are growth factors? can u name four of them?

Organic compounds required for survival.

• Essential cell components (or their precursors) that the

cell cannot synthesize and must be supplied by

environment.

microbes can only take in nutrients in what way? What mechanisms do they use?

Microbes can only take in dissolved particles across a

selectively permeable membrane.

• microorganisms use transport mechanisms

  • Passive diffusion

  • Facilitated diffusion

  • Primary and secondary active transport

  • Group translocation

Passive diffusion

• mlcls move fr region of highr concentration to one of lowr concentration

• Requires a large concentration gradient for adequate nutrient uptake.

• The rate of diffusion decreases as more nutrients accumulate in the cell.

• H2O, O2, and CO2 easily cross the plasma membrane via passive diffusion.

facilitated diffusion

what is it? done with the help of what and name them? is it energy dependent? what is direction of movement? what impacts the rate of uptake? when would transport stop?

Movement across the plasma membrane with the help of

transport proteins.

• Channels—proteins that form pores for substances to

pass through.

• Carriers—proteins that have high substrate specificity in

transport.

Truly diffusion because it is not energy dependent.

• Direction of movement is from high to low concentration.

• Size of concentration gradient impacts rate of uptake.

• Rate increases with the concentration gradient.

• If the gradient is lost, transport stops.

active transport

Transport of molecules against the concentration gradient.

Energy-dependent process.

• ATP or proton motive force used.

Involves carrier proteins that control the rate of transport.

• When the solute concentration is high, carrier saturation

effect is observed

Primary Active Transport

does it use energy?

Use energy from ATP hydrolysis to move substances against concentration gradient without modifying them.

Uniporters—single molecule transported across membrane.

ATP-binding cassette (ABC) transporters

Consist of:

• 2 hydrophobic membrane

spanning domains.

• 2 cytoplasmic associated ATP-

binding domains

Secondary Active Transport

Use potential energy of ion gradients to cotransport

substances without modifying them.

• Move both the ion and the substance across the membrane.

• Symport—2 substances both move in the same direction.

• Antiport—2 substances move in opposite directions.

Group Translocation

Energy dependent transport that chemically modifies the molecule as it is brought into cell.

Best known translocation system is phosphoenolpyruvate:

sugar phosphotransferase system (PTS).

• Imports sugars while

phosphorylating them

wht do microorganisms require when building molecules? why is it important?

Microorganisms require iron for building molecules important in

energy-conserving processes.

• Ferric iron is very insoluble so uptake is difficult.

Siderophores—secreted by bacteria and complex with ferric ion

for transport into cell

bacterial cell wall

functions?

Cell wall functions:

• Maintains shape of the bacterium.

• Helps protect cell from osmotic lysis and toxic materials.

• May contribute to pathogenicity.

Peptidoglycan (murein)—Rigid structure lying outside the plasma membrane.

Two types of bacteria based on Gram stain.

• Gram-positive: stain purple; thick peptidoglycan

• Monoderm—single membrane

• Gram-negative: stain pink or red; thin peptidoglycan and outer membrane.

• Diderm—plasma membrane and an outer membrane

Peptidoglycan Structure

Meshlike polymer of identical subunits forming long strands.

Two alternating sugars:

• N-acetylglucosamine (NAG).

• N- acetylmuramic acid (NAM).

Alternating D- and L- amino acids.

peptidoglycan chains are crosslinked by ____ for strength. Between ea amino acid theres a direct cross-link of what? Theres also an indirect link of what?

1. peptides for strength

2. carboxyl group and amino groups

3. peptide interbridge (may form)

gram-positive cell walls

whats it mainly composed of?

what kind of acid may it contain?

Composed primarily of peptidoglycan.

May also contain teichoic acids (negatively charged).

• Polymers of glycerol.

• Help maintain cell envelope.

• Protect from environmental substances.

• May bind to host cells to initiate infection.

Periplasmic Space of Gram-Positive Bacteria

which is more complex, gram neg or pos?

it contains few what?

why is it clinically important? what does it contain?

• less complex than Gram-neg

• btwn plasma membrane and cell wall

• periplasm has relatively few proteins

• the periplasmic space is of particular clinical importance in that it is the site, in some

species, that contains beta-lactamase, an enzyme responsible for degrading the

penicillin group of antibiotic drugs, leading to penicillin resistance.

Gram-Negative Cell Wall Basic Structure

which is more complex, gram neg or pos?

describe structure of peptidogylcan and locaation?

whats outer membrane composed of?

What does it NOT have that gram positive does have?

• More complex than Gram-positive.

• Consist of a thin layer of peptidoglycan surrounded by an outer membrane.

• Outer membrane composed of lipids, lipoproteins, and lipopolysaccharides.

• No teichoic acids.

Gram-Negative Cell Walls

Outer membrane (OM) outside thin peptidoglycan layer. Braun’s lipoproteins connect OM to peptidoglycan. Peptidoglycan is approximately 5 to 10% of cell wall weight.

Periplasmic space differs from that in Gram-positive cells.

• May constitute 20 to 40% of cell volume.

• Many enzymes present in periplasm.

• Hydrolytic enzymes, transport proteins and other proteins.

LPS—Lipopolysaccharide

wht are the three parts

Consists of three parts:

• Lipid A—buried in outer membrane.

• Core polysaccharide—10 sugar structure joined to Lipid A.

• O side chain (O antigen)—polysaccharide that extends outward from the core

Importance of LPS

• Contributes to negative charge on cell surface.

• Helps stabilize outer membrane structure.

• Creates a permeability barrier.

• Host defense protection.

• Acts as an endotoxin.

Gram-Negative Membrane Transport

Two-step process:

• First the solute crosses the outer membrane

into the periplasm.

• Then crosses the plasma membrane.

Facilitated transport by porins.

Channels to let small molecules (600 daltons) pass

comparison gram +ve vs -ve

explain this diagram

The diagram of the gram-positive cell wall shows alternative

NAG(N-acetylglucosamine) and NAM (N-acetylmuramic acid) in a chain; these are shown as alternative orange and blue spheres. The chains or orange and blue spheres are connected to other chains with smaller yellow spheres in a chain labeled pentapeptide and smaller green spheres labeled tetrapeptide. Each NAG in the chain is connected to the NAG in the chains next to it by both a tetrapeptide (green) connected to a pentapeptide (yellow circles). The diagram of the gram-negative cell wall has the same NAG and NAM chains. But this time they are linked with a direct line to the chains next to them

cell walls and osmotic protection

1. hypotonic environments

2. hypertonic environments

1. • Solute concentration outside cell less than inside cell.

   • Water moves into cell and cell swells.

   • Cell wall protects from lysis.

2. • Solute concentration outside cell is greater than inside.

   • Water leaves cell and cytoplasm shrivels up.

   • Plasmolysis

evidence for protection of cell wall

• remember that bacterial cell wall is largely made of peptidoglycan, mesh net that surrounds cell thats made fr repeating sugars—NAG and NAM

• lysozyme breaks bond btwn NAG and NAM

• penicilin inhibits (prevents) bacteria fr making strong peptidoglycan → since cell wall is weak → cell undergoes lysis(bursts cuz cell wall prevents cell fr bursting) if in hypotonic solution (less solute outside than inside)

what type of environment can cells tht lose a cell wall is survival possible in?

isotonic environments

• protoplast—gram positive bacterial cell tht has lost its cell wall

• spheroplast—gram negative cell that lose cell wall ONLY PART OF CELL WALL IS REMOVED (outer membrane remains) in isotonic environments

• mycoplasma—bacteria that naturally dont have cell wall, BUT plasma membrane more resistant to osmotic pressure

gram-positive organisms appear what color? gram neg are what color?

pos = purple/blue

neg = pink/red

Extracellular Vesicles (EVs)

• Small membrane-bound particles (20 to 400 nm in size).

• Develop when a membrane buds out, pinches off, and is released from the cell.

• Gram-Positive EV—Made of the plasma membrane surrounding a small amount of cytoplasm.

• Gram-Negative EV—Made of LPS- containing OM surrounding a sample of periplasm

are extracellular vesicles cells? explain

NOOOOO

• they do not reproduce

Can carry some ATP but do not have the ability to conserve

energy.

They play role in cell-cell interactions.

• Transfer genetic information between cells.

• Transfer toxin molecules.

Components Outside of the Cell Wall

Outermost layer in the cell envelope.

• Capsules—well-organized layers made of polysaccharides

that are covalently bonded and difficult to wash away.

• Slime layers—polysaccharide layers that are unorganized

and easily washed away.

• Glycocalyx—polysaccharide extension that aids in

attachment to solid surfaces.

• S-layers—geometric pattern made of protein that aid in

protecting from ion and pH fluctuations.

Components Outside of Cell Wall—Capsules

Well organized and not easily removed from cell.

Usually composed of polysaccharides.

Visible in light microscope.

Protective advantages.

• Resistant to phagocytosis.

• Protect from desiccation.

• Exclude viruses and detergents.

components Outside of Cell Wall—Slime Layers

• Similar to capsules except diffuse, unorganized, and

easily removed.

• Slime may facilitate motility

Components Outside of Cell Wall—S Layers

Regularly structured self-assembling layers of protein or glycoprotein.

• In Gram-negative bacteria, S layer adheres to outer membrane.

• In Gram-positive bacteria, associated with peptidoglycan.

S Layer functions:

• Protect from ion and pH fluctuations, osmotic stress, enzymes, and predation.

• Maintains shape and rigidity.

• Promotes adhesion to surfaces.

• Protects from host defenses.

• Potential use in nanotechnology.

name 6 Bacterial Cytoplasmic Structures

• Cytoskeleton

• Intracytoplasmic membranes

• Inclusions

• Ribosomes

• Nucleoid

• Plasmids

define Protoplast and Cytoplasm

• Protoplast—plasma membrane and everything within.

• Cytoplasm—material bounded by the plasma membrane

Bacterial Cytoskeleton

Cytoskeleton—Protein filaments that polymerize to form

functional filaments that extend to full inner dimensions of the

cell.

Homologs(similar) of eukaryotic cytoskeletal elements have been identified in bacteria.

• Actin filaments, microtubules, and intermediate filaments.

Functions are similar as in eukaryotes:

• Participate in cell division.

• Localize proteins.

• Maintain cell shape.

Best Studied Examples of Bacterial Cytoskeleton

Molecules

FtsZ—many bacteria

• Forms ring at center of a dividing cell that constricts

as daughter separates.

MreB—many rods

• Maintains shape by positioning peptidoglycan synthesis machinery.

CreS—maintains curve shape

Intracytoplasmic Membranes

(folds or bumps in bacterial plasma membrane)

Plasma membrane infoldings.

• Observed in many photosynthetic bacteria.

• Observed in many bacteria with high respiratory

activity.

• May be aggregates of spherical vesicles.

Inclusions

Formed by aggregation of organic or inorganic substances.

Primary function of inclusions is to segregate cellular

components so they do not diffuse freely in the cytoplasm.

Granules, crystals, or globules of organic or inorganic

material that are stockpiled by the cell for future use.

Some are enclosed by a single-layered protein or lipid shell.

• May be referred to as microcompartments.

• Often used to sequester enzymes that produce toxic

intermediates.

1. 📦 Store materials for later

2. 🚧 Keep substances separated

3. 🧪 Can contain enzymes that make toxic substances

Easy memory:
Inclusions = "inside storage containers." 🦠📦

Microcompartments

Not bound by membranes but compartments for specific

functions.

Carboxysomes—CO2 fixing bacteria.

• Contain the enzyme carbonic anhydrase that

release CO2 into a shell so it accumulates to high

concentration.

• Then RuBisCO makes sugar.

Gas Vacuoles

• Involved in bacterial movement.

• Provide buoyancy to aquatic bacteria.

• tiny air-filled floatation devices in bactereia (bacterial floaties) help them float/move in water

• Made of aggregates of hollow, cylindrical gas vesicles.

Magnetosomes

• Found in aquatic bacteria.

• Magnetite particles for orientation in Earth’s magnetic field.

• like tiny compass inside water bacteria, helps direct bacteria where to move

• Cytoskeletal protein MamK helps form magnetosome chain

Ribosomes

Complex protein/RNA structures

• Sites of protein synthesis.

• Bacterial and archaea ribosome = 70S (← what they’re called)

Bacterial ribosomal RNA (rRNA) has TWO parts:

• small subunit = 30s

16S rRNA in small subunit

• large subunit = 50s

23S and 5S rRNA in large subunit

The Nucleoid

• Usually not membrane bound (few exceptions).

• Location of chromosome and associated proteins.

• Usually 1 closed circular, double-stranded DNA molecule.

• Supercoiling and nucleoid proteins aid in folding and structure

Plasmids

Extrachromosomal DNA that is usually small, closed circular

DNA molecules.

Exist and replicate independently of chromosome.

• Episomes—are plasmids that able to integrate into bacterial chromosome.

• Inherited during cell division.

Benefit the survival of the organism by

1) providing antibiotic resistance to naturally occurring antibiotics in a

competitive environmental niche

2) producing toxins under similar circumstances, or

3) allowing the organism to utilize particular organic compounds that

would be advantageous when nutrients are scarce

Plasmid Classification

plasmids can be classified based on:

• WHAT THEY DO

• HOW THEY MOVE BTWN BACTERIA

1. Functional Classification = WHAT THEY DO

Plasmids are classified into five primary functional classes:

• Fertility (F) Plasmids: Contain tra genes used for conjugation, allowing them to transfer DNA between bacteria via a sex pilus (←tiny connection/bridge)

• Resistance (R) Plasmids: Carry genes that provide protection against antibiotics or poisons, such as the widely studied pBR322.

• Col Plasmids: Encode bacteriocins (like colicin), which are proteins that kill other competing bacteria.

• Degradative Plasmids: Enable the host to digest unusual substances like toluene, camphor, or salicylic acid.

• Virulence Plasmids: Turn a bacterium into a pathogen by carrying toxin or infection-related genes (e.g., the Ti plasmid in Agrobacterium).

Transferability & Mobility (MOB)

Plasmids are classified by how they move between host cells:

•Conjugative: Self-transmissible plasmids that carry all necessary genes for conjugation.

•Mobilizable: Lack the full machinery but can "hitchhike" if a conjugative plasmid is present.

•MOB Typing: A sequence-based system that groups plasmids based on the amino acid

sequence of their relaxase proteins (e.g., MOBP, MOBQ)

External Structures

Extend beyond the cell envelope in bacteria.

Function in protection, attachment to surfaces, horizontal

gene transfer, cell movement.

• Pili and fimbriae

• Flagella

Pili and Fimbriae

Fimbriae (s., fimbria); pili (s., pilus).

• Short, thin, hairlike, protein appendages (1,000/cell).

• Can mediate attachment to surfaces, motility, and DNA uptake.

Sex pili (s., pilus).

• Longer, thicker, less numerous (10/cell).

• Genetically encoded on plasmids.

• Required for conjugation.

Flagella

Threadlike, locomotor appendages extending outward from plasma

membrane and cell wall.

Functions:

• Motility

• Attachment to surfaces

• Virulence factors

Patterns of flagella distribution:

• Monotrichous—one flagellum.

• Polar flagellum—flagellum at end of cell.

• Amphitrichous—one flagellum at each end of cell.

• Lophotrichous—cluster of flagella at one or both ends.

• Peritrichous—spread over entire surface of cell

Bacterial Flagella

Thin, rigid protein structures that cannot be observed with bright-field

microscope unless specially stained.

Ultrastructure composed of 3 parts:

• Filament—extends from cell surface to the tip.

• Basal body—embedded in cell envelope.

• Hook—short curved segment

Motility

Flagellar movement

• Swimming

• Swarming

• Spirochete motility

Twitching and gliding motility

Chemotaxis

Swimming

Flagellum rotates like a propeller.

• Very rapid rotation up to 1100 revolutions/sec.

• In general, counterclockwise (CCW) rotation causes forward motion (run).

• In general, clockwise rotation (CW) disrupts run causing cell to stop and tumble.

Mechanism of Flagellar Movement

Flagellum is a two-part motor producing torque:

Rotor—moving parts

• C (FliG protein) ring turn and

interact with stator.

Stator—stationary parts

• Form channel through plasma membrane.

• Protons move through Mot A and Mot B channels using

energy of proton motive force.

• Torque powers rotation of the basal body and filament

Swarming

Occurs on when cells move in unison across a moist surfaces.

• Most swarmers have peritrichous flagella.

• Commonly, the cell produces a molecule that lowers surface tension.

1. Twitching and Gliding Motility

2. Twitching motility

3. Gliding

1. - Occurs on solid surface.

• Does not involve flagella.

• May involve Type IV pili and slime.

2. • Pili at ends of cell.

   • Short, intermittent, jerky motions.

   • Cells are in contact with each other and surface

3. Smooth movements that do not require appendages.

Chemotaxis

• Movement toward a chemical attractant or away from a chemical repellent.

• Chemical attractants and repellents bind chemoreceptors that transmit signals throughout the chemosensing system.

• In presence of attractant/repellant, tumbling frequency is reduced; runs toward/away from compound are longer.

• Behavior of bacterium altered by temporal concentration of chemical

The Bacterial Endospore

Complex, dormant structure formed by some bacteria.

Form in response to nutrient depletion.

Resistant to numerous environmental conditions:

• Heat, UV radiation, gamma radiation, chemical disinfectants, and desiccation.

Endospore Structure

• Spore surrounded by thin covering called exosporium.

• Thick layers of protein form the spore coat.

• Cortex, beneath the coat, thick peptidoglycan.

• Core has nucleoid and ribosomes

Sporulation

Process of endospore formation.

Organized process that occurs over several hours.

Normally starts when growth slows due to lack of nutrients.

• Produces a dormant cell that can persist until nutrients are

available and growth resumes.

Endospore Formation

Steps of Endospore Formation

DNA Replication (Axial Filament Formation):

The bacterium copies its DNA and stretches the genetic material into a long, thread-like structure across the cell.

Asymmetric Cell Division (Septum Formation):

A membrane wall (septum) divides the cell unequally into a small forespore (the future

spore) and a larger mother cell.

Engulfment:

The mother cell membrane grows around and completely engulfs the forespore, placing a double membrane around it.

Cortex Formation:

A thick layer of peptidoglycan called the cortex, builds up betweentthe wo membranes.

Spore Coat Formation: A tough, protein-based outer coat forms around the cortex, giving the spore high resistance to chemicals and heat.

Maturation and Dehydration:

Dipicolinic acid and calcium are added to the core while water is pumped out, making the spore metabolically dormant and heat-resistant.

Release:

The mother cell lyses and releases the mature endospore into the environment.

Formation of Vegetative Cell

Three Stages:

• Activation

• Prepares endospores for germination.

• Germination

• Starts when germinant receptors detect small molecules (that is,

sugars and amino acids).

• Outgrowth

• Emergence of vegetative cell