Structure
Gram-Positive Cell Walls
Composition:
Primarily made up of peptidoglycan.
May contain large amounts of teichoic acids.
Functions of Teichoic Acids:
Help maintain cell envelope.
Protect against environmental substances.
May bind specifically to host cells.
Certain gram-positive bacteria have an additional protein layer on the surface of the peptidoglycan.
Periplasmic Space of Gram + Bacteria
Definition:
Located between the plasma membrane and the cell wall, smaller than in gram-negative bacteria.
Characteristics:
Contains relatively few proteins.
Enzymes secreted by gram-positive bacteria are referred to as exoenzymes.
Function:
Aid in degradation of large nutrients.
Gram-Negative Cell Walls
Complexity:
More complex than gram-positive cell walls.
Structure:
Composed of a thin layer of peptidoglycan, surrounded by an outer membrane.
Outer Membrane Composition:
Made up of lipids, lipoproteins, and lipopolysaccharides (LPS).
Absence of teichoic acids.
Peptidoglycan Layer:
Generally thinner than that found in gram-positive bacteria.
Periplasmic Space:
Differences in volume compared to gram-positive cells, may constitute 20–40% of the cell volume.
Enriched with hydrolytic enzymes, transport proteins, and other proteins.
Function:
Facilitates compartmentalization leading to specialized functions.
Lipopolysaccharides (LPS)
Composition:
Made up of three main parts:
Lipid A
Core polysaccharide
O side chain (O antigen)
Lipid A is embedded in the outer membrane, while the core polysaccharide and O side chain extend out from the cell.
Importance of LPS
Functions:
Contributes to the negative charge on the cell surface.
Stabilizes the outer membrane structure.
May facilitate attachment to surfaces and biofilm formation.
Serves as a permeability barrier.
Provides protection from host defenses (specifically via O antigen).
Can act as an endotoxin, particularly lipid A.
Endotoxin Assay
Historical Context:
First documented by Fred Bang in 1956 using the Limulus Amebocyte Lysate (LAL) assay.
Components:
Granules containing a clotting factor known as coagulogen, associated with hemocyanin.
Mechanism:
Factors involved include Factor C, Factor B, and F, which play roles in detecting endotoxins through clotting responses.
Gram-Negative Outer Membrane Permeability
Permeability:
The outer membrane is more permeable than the plasma membrane due to porin proteins and transporter proteins.
Porin proteins form channels allowing small molecules (600–700 daltons) to pass through.
Mechanism of Gram Stain Reaction
Process:
The Gram stain reaction is influenced by the structure of the cell wall.
Ingram-positive cells, the shrinking of pores in the peptidoglycan layer constricts and prevents loss of crystal violet during the decolorization step.
The thinner peptidoglycan layer and larger pores of gram-negative bacteria prevent retention of crystal violet.
Osmotic Protection
In Hypotonic Environments:
Solute concentration outside the cell is lower than inside, leading to water influx and cell swelling.
The cell wall provides protection from lysis.
In Hypertonic Environments:
Solute concentration outside the cell is higher than inside, causing water to leave the cell and leading to plasmolysis.
Evidence of Protective Nature of the Cell Wall
Mechanisms:
Lysozyme can break the bond between N-acetyl glucosamine and N-acetylmuramic acid.
Penicillin inhibits peptidoglycan synthesis.
When treated with either of the above substances in a hypotonic solution, bacterial cells will lyse.
Loss of Cell Wall Survival in Isotonic Environments
Definitions:
Protoplasts: Refers to cells from gram-positive organisms following cell wall loss.
Spheroplasts: Refers to cells from gram-negative organisms following cell wall loss.
Mycoplasma: A genus of bacteria that do not produce a cell wall, possessing a plasma membrane that is more resistant to osmotic pressure.
Components Outside of the Cell Wall
Definition:
Outermost layer in the cell envelope consisting of the glycocalyx.
Types:
Glycoprotein/polysaccharide structures.
Capsules and slime layers are included.
S-layers:
Aid in attachment to solid surfaces, e.g., biofilms in plants and animals.
Capsules
Composition:
Usually made of polysaccharides, well-organized, and not easily removed from the cell.
Microscopic Visibility:
Visible under light microscopes.
Protective Benefits:
Protects against phagocytosis.
Prevents desiccation.
Excludes viruses and detergents.
Slime Layers
Definition:
Similar to capsules but are diffuse, unorganized, and easily removed.
Function:
May aid in bacterial motility.
Endospore
Characteristics:
Non-reproductive structure, occurring in a dormant state.
Generally initiated due to a lack of nutrients.
Contains DNA packaged into a cortex.
Highly resistant to heat and radiation with a potential to remain viable for over 100,000 years.
Half-life of DNA is approximately 521 years.
Key Component:
Dipicolinic acid (DPA).
S Layers
Structure:
Regularly structured layers of protein or glycoprotein that self-assemble.
In gram-negative bacteria, the S layer adheres to the outer membrane; In gram-positive bacteria, it associates with the peptidoglycan surface.
S Layer Functions
General Functions:
Found in all bacteria and archaea.
Provides protection from ion and pH fluctuations, osmotic stress, enzymes, and predation.
Maintains cell shape and rigidity.
Promotes adhesion to surfaces.
Protects from host defenses.
Nanotechnology Applications:
Potential use mentioned due to the spontaneous association of S layers.
Archaeal Cell Envelopes
Differences from Bacterial Envelopes:
Vary in molecular makeup and organization.
S layers may be only component outside the plasma membrane.
Capsules and slime layers are rare.
Archaeal Membranes
Composition:
Unique lipids characterized by isoprene units (five carbon, branched).
Ether linkages rather than ester linkages to glycerol.
Some have a monolayer instead of a bilayer structure.
Archaeal Cell Walls vs. Bacterial Cell Walls
Differences:
Archaeal cell walls lack peptidoglycan.
Most common structure is the S layer.
Possibility of a protein sheath external to the S layer.
S layer may be separated from the membrane by pseudomurein, which may act as the outermost layer, similar to gram-positive microorganisms.
Peptidoglycan and Pseudomurein Differences
Key Differences:
Peptidoglycan:
Contains 1→4 glycosidic bonds.
Utilizes D-amino acids.
Contains N-acetylmuramic acid.
Pseudomurein:
Contains 1→3 glycosidic bonds.
Utilizes L-amino acids.
Contains N-acetyltalosaminuronic acid.
Bacterial and Archaeal Cytoplasmic Structures
Components:
Cytoskeleton.
Intracytoplasmic membranes.
Inclusions.
Ribosomes.
Nucleoid and plasmids.
Protoplast and Cytoplasm
Definitions:
Protoplast: Refers to the plasma membrane and everything within it.
Cytoplasm: Material bounded by the plasma membrane.
The Cytoskeleton
Homologs:
Identified for all three eukaryotic cytoskeletal elements in bacteria and two in archaea.
Functions:
Role in cell division, protein localization, and determination of cell shape.
Bacterial Cytoskeletal Proteins
Types:
Tubulin homologs:
FtsZ: Involved in cell division.
BtubA/BtubB: Function unknown.
TubZ: Potentially involved in plasmid segregation.
Actin homologs:
MamK: Involved in positioning magnetosomes.
MreB/Mbl: Responsible for maintaining shape and possibly involved in chromosome segregation.
ParM: Believed to be involved in plasmid segregation.
Intermediate filament homologs:
Cres (crescentin): Induces curvature in curved rods.
Best Studied Examples of Cytoskeletal Proteins
FtsZ:
Identified in many bacteria and archaea; forms a ring during septum formation in cell division.
MreB:
Observed in many rod-shaped bacteria and some archaea; maintains cell shape by positioning the peptidoglycan synthesis machinery.
CreS:
Rarely observed; maintains curved shape.
Intracytoplasmic Membranes
Presence:
Infoldings of the plasma membrane observed in many photosynthetic bacteria.
Functionally analogous to thylakoids of chloroplasts; associated with ATP formation.
Notable mention of anammoxosome in Planctomycetes, which plays a role in global nitrogen cycles/anaerobic ammonium oxidation.
Reaction: ext{NH}4^+ + ext{NO}2^-
ightarrow ext{N}2 + 2 ext{H}2 ext{O}.
Inclusions
Description:
Granules of organic or inorganic materials stockpiled by the cell for future use.
Some inclusions enclosed by single-layer membranes, with variable compositions, including proteins and lipids.
Often referred to as microcompartments.
Storage Inclusions
Functions:
Storage of nutrients, metabolic end products, energy, and building blocks.
Examples:
Glycogen: Storage form of glucose.
Carbon storage: Poly-β-hydroxybutyrate (PHB).
Phosphate storage: Polyphosphate (Volutin).
Amino acid storage: Cyanophycin granules (R/D).
Microcompartments
Definition:
Not bound by membranes, but compartmentalized for specific functions.
Example:
Carboxysomes: Found in CO2-fixing bacteria; contain the enzyme ribulose-1,5-bisphosphate carboxylase (Rubisco) used for CO2 fixation.
Other Inclusions
Examples:
Gas Vacuoles: Found in aquatic, photosynthetic bacteria and archaea, providing buoyancy in gas vesicles.
Magnetosomes: Found in aquatic bacteria, containing magnetite particles for orientation along Earth’s magnetic field; composed of mineralized iron oxide.
Associated Protein: MamK helps form magnetosome chains.
Ribosomes
Structure:
Complex structures composed of protein and RNA, serving as sites of protein synthesis.
Ribosome Size:
Bacterial and archaeal ribosome = 70S.
Eukaryotic ribosome = 80S (S = Svedburg unit).
Ribosomal RNA:
16S in the small subunit, 23S and 5S in the large subunit.
Archaea have an additional 5.8S present in the eukaryotic large subunit.
Protein Variability:
Archaeal ribosomes are more similar to eukaryotic ribosomes than to bacterial ones.
The Nucleoid
Description:
Irregularly shaped region found in bacteria and archaea, typically not membrane-bound.
Houses the chromosome and associated proteins.
Generally consists of a single closed circular, double-stranded DNA molecule.
Supercoiling and nucleoid proteins (like HU) likely assist in DNA folding and differ from histones.
Plasmids
Definition:
Extrachromosomal DNA found in bacteria, archaea, and some fungi, typically composed of small, closed circular DNA molecules.
Can replicate independently of chromosomes, with some evolving into episomes that may integrate into chromosomes.
Gene Content:
Usually contain few, non-essential genes that can confer selective advantages to the host organism, such as drug resistance.
Modern Microbiology and Genomics
Fields:
Molecular microbiology incorporates genomics, transcriptomics, proteomics, and metabolomics.
Genomics: The study of all genetic material (DNA) within living cells.
Transcriptomics: The study of RNA expression patterns.
Proteomics: The study of all proteins produced by cells.
Metabolomics: The study of metabolic expressions in cells.
Insight on Gene Function
Statistics:
Of 473 studied genes, 324 (around 68%) are for housekeeping functions (protein synthesis, DNA repair, cell membrane protection).
Approximately 32% (or 149 genes) have undefined roles.
Biologist Perspectives:
J. Craig Venter emphasizes importance of studying the interplay of genes, rather than solely focusing on isolated gene functions, suggesting the roles of many unknown genes involve composing cellular functions.
Panspermia Hypothesis in Microbiology
Concept:
Proposes transfer of life via interplanetary mechanisms; experiments conducted to test extremophilic organisms' survivability in outer space.
Results indicate protective aggregations of cells essential for harsh conditions survival.