Bacterial Cell Structures: Morphology and Functions

Posted on Mar 18, 2025 in Biology

Living Preparations

Wet Mount

• Add a drop of the culture, and cover it with a glass slide.
• Benefits:
  • It’s fast.
  • Cells are alive, and you can see them in their natural shape.
  • Can examine their behavior.
• Disadvantages:
  • Hard to detect cells/characteristics.
  • Covering the glass can damage larger cells, contaminate the observer’s fingers, dry out, and also become anoxic.

Staining

• Increases contrast and sometimes size.
• Before staining, we must let it dry and fix it. That way, the sample does not get washed off.
• Positive staining:
  • Sticks to the specimen.
  • Gives them color.
• Negative staining:
  • Does not stick to the specimen.
  • Dark background – everything around is dark and stained, but not the cell.
• Simple stains:
  • One single dye.
  • Shows their size, shape, or arrangement.
  • Can only be positive or negative.
• Differential stains:
  • 2 different dyes: primary dye and counterstain.
  • Distinguishes between cell types or parts.
  • Both positive and negative can be seen at the same time.

Bacterial Shapes, Arrangements, and Sizes

General Shapes

• Coccus: roughly spherical.
• Bacillus: rod-shaped
  • Coccobacillus: short and plump.
  • Vibrio: gently curved, bent rods.
• Spiral: curviform or spiral-shaped. 2 types:
  • Spirillum
  • Spirochete
• Pleomorphism: cells of species vary in shape and size.

Arrangement or Grouping

• Cocci: greatest variety in arrangement, can make different organizations. Have different because they can divide.
  • Single
  • Pairs (diplococci)
  • Tetrads: grouping of 4
  • Irregular cluster (staphylococci or micrococci)
  • Chains (streptococci)
  • Cubical packet – sarcina
• Bacillus: split in the middle and grow outwards; that is why they don’t have that many. Less varied
  • Single
  • Pairs – diplobacilli
  • Chain – streptobacilli
  • Row of cells oriented side by side – palisades
• Spirilla
  • Occasionally found in short chains

Structural Biology: Bacteria and Archaea vs. Eukaryotes

Packaging of DNA

• Bacteria and archaea: packed out of genetic material – free in the cytoplasm. Has peptidoglycan holding it together.
• Eukaryotes – nucleus

Cell Wall Makeup

• Bacteria: peptidoglycan
• Archaea: distinct from bacteria and eukaryotes
• Eukaryotes: varies, if present at all

Internal Structures

• Bacteria and archaea: no membrane-bound organelles
• Eukaryotes: membrane-bound organelles

Structure Common to All Bacterial Cells

• Cell membrane: all bacterial cells and cells have this.
• Cytoplasm
• Ribosomes
• One or a few chromosomes.

Structure Found in *Some* Bacterial Cells

• Flagella
• Pili
• Fimbriae
• Capsules
• Slime layers
• Inclusions
• Actin cytoskeleton
• Endospores

External Structures

• Appendages: things sticking out of cells
  • Common but not present on all species
  • Can provide motility – move around and see different things
  • Attach to surfaces, attach to different things
  • Sensing

Flagella

• Can provide motility
• Difficult to visualize
• Do a wet mount, look for cells moving in multiple directions, moving in a controlled manner.
• Vary in both number and arrangement:
  • Polar arrangement: flagella attached at one or both ends of the cell.
    • Monotrichous: single flagellum
    • Lophotrichous: small bunches or tufts of flagella emerging from the same site.
    • Amphitrichous: flagella at both poles.
  • Peritrichous arrangement: dispersed randomly over the structure of the cell.
• Flagella structure:
  • Made of large numbers of proteins. Three parts:
    • Filament: they are really skinny. Major antibody target. Why? They are long and stick out a long way.
    • Hook (sheath): adaptor
    • Basal body: motor
  • Electric motor:
    • Driven by an ion gradient
    • More outside the cell than in
  • Rotates rapidly and moves either way. Go both ways:
    • Rotates 360 degrees
    • Reversible.
  • Propels cell through the environment:
    • Chemotaxis: toward/away from chemicals
    • Phototaxis: toward/away from light
    • Move by runs and tumbles.
    • The way it is moving determines whether it can do tumbles or runs. Depends:
      • Spin direction
        • Tumbles – clockwise
        • Runs – counterclockwise
        • Microbes do runs first, and then they stop and do tumbles
      • Spin duration:
        • Runs last longer when moving in a favorable direction.
        • Toward/away from something.
        • Would move towards food sources.
        • Move away from chemicals or bad things.

• Flagella of spirochetes
  • Axial filaments:
    • Most bacteria have an inner and outer membrane; flagella have its between them. This makes the entire cell spin.
    • Periplasmic
    • Bundles of many flagella.
  • They spin in a corkscrew motion.
  • As they rotate – cells twist.
  • Drill through viscous media.

Pili and Fimbriae

• Fimbria:
  • Fibers of proteins
  • Sticking out of the cells, fuzzy barrier outside.
  • Cells use them to attach to stuff.
    • Attaches cell to surface
      • Maybe host
    • Attaches to other cells
      • Biofilms
  • Sometimes provide motility
    • Pulls cell across a solid surface.
• Pilus
  • Tube made from pilin
  • Attach two cells together
  • Genetic material – tube
    • Conjugation

The S-Layer and Glycocalyx

• The cells usually have a coating of repeating protein (S-Layer) or polysaccharide (Glycocalyx) units or both.
• Protects cell
• Help adhere to the environment
• Differ in:
  • Thickness
  • Organization
  • Chemical composition

S-layer

• Protein shield
• May also aid in attachment to surfaces

Slime Layer

• Loose shield
• Promotes surface attachment/community formation
• Protects some bacteria from loss of water and nutrients
• Slimy and gross looking.
• Starts with just carbs, and then protein gets added, and others.

Capsule

• Glycocalyx bound more tightly to the cell.

Functions of the Glycocalyx

1. Slime layer
   1. Formation of biofilms
   2. Allows attachment to many surfaces
   3. Mainly protects groups.
2. Capsule
   1. Important for pathogenesis
   2. Prevents phagocytosis
   3. Blocks access by drugs
   4. Mainly protects individuals

The Cell Envelope: The Boundary Layer of Bacteria

• Outside of the cytoplasm
  • Separates self from everything else
• Composed of two or three basic layers
  • Cell wall
    • Not all bacteria have one
  • Cell membrane
  • In some bacteria, the outer membrane
    • Gram (-)

Differences in Cell Envelope Structure

• One major way of classifying bacteria is whether Gram-positive or Gram-negative
• Differences lie in the cell envelope:
• Gram-positive
  • Two layers
    • Cell wall and cytoplasmic membrane
• Gram-negative
  • Three layers
    • Cell wall (thinner/more flexible), and cytoplasmic membrane
    • Extra layer – the outer membrane

The Gram-Negative Outer Membrane

• Mixture of lipids, proteins (similar to cell membrane), but with specialized polysaccharides and proteins unique to OM
  • Outer leaflet (outside face of membrane): contains lipopolysaccharide
  • Inner leaflet (inside face of membrane): phospholipid layer anchored by lipoproteins to cell wall
• Outer membrane acts like a sieve
  • Only relatively small molecules can penetrate
  • Access provided by special membrane channels formed by porin proteins
    • Generally non-selective

Can alter size when stressed – keep out antibiotics

Lipopolysaccharide

• Major component of the outer leaflet of an outer membrane
  • Provides:
    • Structural integrity
    • Protection from some chemicals
    • Negative charge

• Three domains
  • Lipid A (endotoxin)
  • Core polysaccharide
  • O Antigen
• Dominant antigen of Gram-negative cells
  • Endotoxin (lipid A) especially
    • Recognized by the immune system → fever and toxic shock
  • Some species constantly shed/change O antigen
    • Avoid immune detection
      • Immune system is always looking for the wrong thing
    • Or, if you think you’re hardcore and competitors aren’t, make the immune system always active

The Bacterial Cell Wall

• Helps determine the shape of a bacterium
• Provides strong structural support
  • Keeps cell from bursting or collapsing
    • Tire to membrane’s inner tube
    • Osmotic pressure differences
  • Rigidity due to peptidoglycan (PG) content
    • PG structure:
      • Long chains of repeats of disaccharide (a.k.a. glycan)
        • NAG: N-acetyl glucosamine
        • NAM: N-acetyl muramic acid
      • Peptide chains connect chains of glycan repeats
        • Cell held in place by a chain-link fence instead of a pile of ropes
          • Many layers of chain link
• Target of many antibiotics

Gram Staining

• Most universal diagnostic staining technique for bacteria
  • Primary stain: Crystal Violet
  • Counterstain: Safranin
• Differentiation of microbes as Gram-positive or Gram-negative
  • Main differences based on cell wall thickness/characteristics

The Structure of the Bacterial Cell Wall

• Gram-positive cell wall
  • Thick (20 to 80 nm), homogeneous sheath of peptidoglycan
  • Contains tightly bound acidic polysaccharides
    • Teichoic acid and lipoteichoic acid
    • Make cell wall more acidic
      • Negatively charged
    • Important for cell division
    • Target of antimicrobial peptides
• Gram-negative cell wall
  • Single, thin (1 to 3 nm) sheet of peptidoglycan
    • More flexible
    • Not as strong
    • Need strength from LPS in outer membrane to replace strength from the rigidity of Gram +’s thicker cell wall
  • Periplasmic space surrounds the peptidoglycan
• Atypical cell walls
  • Mycobacteria and Nocardia
    • Modified Gram-positive
      • Cell wall has special lipids embedded on the outer surface
        • Peptidoglycan but also mycolic acid
        • Neither crystal violet nor safranin binds great to it
          • Can look Gram +, Gram -, or unstained
        • Why use acid-fast stain on them
• Archaea
  • No peptidoglycan
  • Some have walls of polysaccharide or protein
  • Others → no cell wall

Cell Wall-deficient Bacteria

• Mycoplasmas
  • Smallest bacteria
    • Pleomorphic
    • Lots of fun shapes (cocci, filaments, toroids, etc.)
  • No cell walls
    • Special sterols to strengthen the wall
    • Very resistant to lysis
• Other bacteria may lose the wall at a certain stage of lifestyle

• Wall-less Archaea often use special fatty acids
  • Ether linkage
  • Branching for better packing

The Structure of the Cell Membrane

• AKA cytoplasmic membrane
• Very thin (5-10 nm)
• Contains
  • Phospholipids (30-40%)
  • Proteins (60-70%)
• Exceptions: mycoplasmas and archaea
  • Other additional lipids for stability
• Functions
  • Provides a site for:
    • Energy reactions
    • Nutrient processing
    • Nutrient synthesis
  • Regulates transport
    • Selectively permeable
  • Secretion

Differences in Cell Envelope have Consequences

• Outer membrane – extra barrier in Gram (-)
  • Less sensitive to some antimicrobial chemicals
    • Can’t get through porins to block cell wall synthesis
  • Generally more difficult to inhibit or kill than gram-positive bacteria
    • Unless treated with alcohol to permeabilize/dissolve
    • Need different drugs than Gram (+)
• Cell envelope can interact with human tissues and cause disease
  • Toxins attached to Gram (+) cell walls
    • Corynebacterium diphtheriae
    • Streptococcus pyogenes
  • Toxic cell membrane lipids
    • Mycobacterium sp.
  • Stimulate the immune system
    • Toxic shock
    • Autoimmune disorders
    • Obesity and Type II diabetes related to endotoxins in some patients?

Bacterial Internal Structure

• Contents of cell’s cytoplasm
  • Gelatinous solution
    • 70%-80% water
    • So packed with other stuff + so many H-bonds between things that it’s not fluid though
    • Organized, not a random sack of stuff
  • Site for many metabolic activities
    • Catabolic (breaking down food for energy)
    • Anabolic (building macromolecules)
  • Contains larger, discrete cell areas/structures:
    • Nucleoid (chromatin)
    • Ribosomes
    • Granules
    • Actin strands
    • Separate structures or regions (some surrounded by membranes) but NONE of them are organelles

Bacterial Chromosome

• Single circular strand of DNA
  • Some have more than one chromosome
  • Others can be linear
• Aggregated in a dense nucleoid
  • Tightly supercoiled
  • Sometimes wrapped around histones into chromatin
• Genetic material also present on plasmids
  • What do we know about them?
  • Why do we care?

Ribosomes

• Protein-making machinery
• 1000’s/cell
  • How many depends on what the cell is doing
  • More active cells have more
• Made of RNA and protein
  • 3 Ribosomal RNA (rRNA)
    • Catalytically active RNA
    • Does the actual work of gluing together amino acids
  • ~80 proteins between 2 subunits
    • Provide structure, shape, regulation
• Characterized by S units
  • Bacterial ribosome is 70S
    • 50S subunit: 23S and 5S rRNA
    • 30S subunit: 16S rRNA

Inclusion Bodies

• May or may not be bound by a single membrane
  • Even if they have a membrane, not organelles
• Membrane-bound inclusions:
  • Storage of supplies for a rainy day
    • Glycogen, poly β-hydroxybutyrate (PHB)
      • Provide energy
  • Gas Vesicles
    • Allow bacteria to float in water
    • Get to the right level of light exposure
• Granules
  • Type of inclusion body
    • Not enclosed by membranes
  • Crystals of inorganic compounds
• Magnetosomes
  • Magnetic iron crystals
  • Allow orientation in a magnetic field → magnetotaxis
  • Usually allows them to swim down → away from O2

The Cytoskeleton

• Long polymers of actin-like proteins
• Arranged in helical ribbons around the cell just under the cell membrane
  • Important for cell division
  • Machinery travels along it to find the middle
• Contribute to cell shape

Bacterial Endospores: An Extremely Resistant Stage

• Dormant bodies produced by Bacillus, Clostridium, and Sporosarcina
  • All Gram (+)
  • A few Gram (-) make them too
• Two-phase life cycle

1. Vegetative cell
   • Metabolically active and growing
   • Can be induced by the environment to undergo spore formation (sporulation)
2. Endospore Formation
   • Wait out the bad times
   • Can wait a very long time