Chapter 2 - Microbial Cell structure and function

The cell envelope

Consists of a series of layered structures that surround the cytoplasm and govern cellular interactions with the external environment. Consists of:

• Cytoplasmic membrane

• Cell wall

• Outer membrane

• S-layers

The cytoplasmic membrane

• Surrounds the cytoplasm

• Is selectively permeable

• In order for a cell to grow, nutrients must be transported inwards and waste products outwards.

Bacterial cytoplasmic membrane

• Is a phospholipid bilayer containing embedded proteins

• Is 8-10 nanometers wide

Phospholipids in bacteria cytoplasmic membrane.

• Contain a hydrophobic and hydrophilic part.

• Hydrophobic part consists of fatty acid chains

• The hydrophilic part consists of a glycerophosphate (glycerol molecule bound to a phosphate) and one of several other functional groups also bonded to the phosphate.

• Hydrophobic part and hydrophilic part are connected through an ester linkage.

Membrane proteins in bacteria cytoplasmic membrane

• Transmembrane proteins: Extend completely across the membrane

• Peripheral proteins: are more loosely attached.

  • Some peripheral membrane proteins are lipoproteins, proteins that contain a hydrophobic lipid tail that anchors the protein into the membrane.

Archaeal cytoplasmic membranes

• Similar to those of bacteria and Eukarya (phospholipid membrane)

• Chemistry is slightly different.

• Hydrophobic part is instead isoprenoid, which are bound to glycerol by ether bonds.

• Isoprenoid is formed from repeating units of the five-carbon hydrocarbon isoprene

Archaeal mono vs. bilayer

• When its a monolayer the hydrophobic part is two strands of phytanyl

• Some Archaea can also have lipid monolayers composed of diphosphoglycerol tetraether lipids or crenarchaeol.

Cytoplasmic membrane function

1. Permeability barrier: preventing the passive leakage of solutes into or out of the cell

2. The cytoplasmic membrane anchors several proteins that catalyze a suite of key cell functions

3. The cytoplasmic membrane of Bacteria and Archaea plays a major role in energy conservation and consumption.

Selective permeability in the cytoplasmic membrane

• Is a barrier to the diffusion of most substances, especially polar or charged molecules.

  • Charged molecules can’t go through because hydrophilic part is charged

• Most substances that enter or leave the cell must be carried in or out by transport proteins.

• Can go against concentration gradient

Three types of active transporters

1. Simple transport system

2. Group translocation

3. ABC transport systems

Are all energy driven

Simple transport system

• Are driven by the energy inherent in the proton motive force

• Can either have symport reactions (a solute and a proton are cotransported in the same direction)

• Or an antiport reaction (where a solute and a proton are transported in opposite directions)

• e.g. uptake of lactose by lac permease which is a symporter in E. coli.

How is group translocation different from simple transport?

1. The transported substance is chemically modified during the transport process

2. An energy-rich organic compound drives the transport event (rather than proton motive force)

   • e.g. uptake of glucose, mannose and fructose in E. coli.

   • These compounds are phosphorylated by the phosphotransferase system.

ABC transporter system

• Are modular systems that have three components:

  1. A binding protein

  2. a transmembrane protein channel and

  3. an ATP hydrolyzing protein.

• ABC stands for: ATP, binding, cassette. which is a structural feature of proteins that bind ATP

Peptidoglycan

• Is found in Bacteria cell walls.

• Unique to bacteria

• Is a polysaccharide

Structure peptidoglycan

• The sugar backbone of peptidoglycan is composed of alternating repeats of two modified glucose residues called N-acetylglucosamine and N-acetylmuramic acid.

• These are joined by a Beta-1,4 linkage.

• Attached to the latter residue is a short peptide side chain. The amino acid composition can vary considerably.

• Strands of peptidoglycan run parallel to each other around the circumference of the cell.

• The side chains of adjacent peptidoglycan strands are cross-linked together by covalent peptide bonds.

  • In this way, the peptidoglycan forms one single enormous molecule.

Cell wall in the gram-negative cell envelope

• Is 2-7 nm thick

• A single layer of peptidoglycan although it can be up to three layers thick in some places

• The peptidoglycan mesh so formed is flexible and porous but strong enough to resist turgor pressure and prevent rupture of the cytoplasmic membrane and cell lysis.

• Does not have a pentaglycine bridge

Cell wall in the gram-positive cell envelope

• Contains a thick peptidoglycan cell wall, (20-35 nm)

• Is much thicker than the wall of gram negative organisms

• As much as 90% of the gram-positive cell envelope can consist of peptidoglycan - which is 15 or more layers (the gram-negative cell wall typically contains only a single layer of peptidoglycan)

• Is stabilized by three dimensional peptide cross-links, which form between adjacent peptidoglycan strands both horizontally and vertically.

• With pentaglycine between chains

What gives strength and stability to the membrane in eukaryotes and prokaryotes?

• Eukaryotes: Sterols (Cholesterol)

• Prokaryotes: Hopanoids

Membrane bacteria vs. archaea

What is “Proton Motive Force”?

• A source of energy resulting from the transport of protons across the cytoplasmic membrane, generating a membrane electrochemical potential.

Teichoic acids

• Found in gram-positive bacteria embedded in the ell wall.

• Are composed of glycerol phosphate or ribitol phosphate with attached molecules of glucose or D-alanine.

• Individual alcohol molecules are then connected through their phosphate groups to form long strands, and these are then covalently linked to peptidoglycan

• Are responsible for the overall negative charge of the cell surface. They give flexibility to the cell wall.

Lysozyme

• Peptidoglycan can be destroyed by lysozyme

• An enzyme that cleaves the glycosidic bond between N-acetylglucosamine and N-acetylmuramic acid.

• This weakens the peptidoglycan and can cause cell lysis.

• Lysozyme is present in human secretions including tears, saliva and other bodily fluid, and functions as a major line of defense against bacterial infection.

• Many antibiotics target Ppeptidoglycan

Periplasm

• Found in gram negative cell wall

• Is the space between membranes

• Contains many extracellular proteins all synthesized in the cytoplasm:

  • Hydrolytic enzymes

  • Binding protein

  • Chemoreceptors.

Lipopolysaccharide (LPS)

• Found on top of cell wall

• Give negative charge

• Give rigidity to membrane structure

• Protect the cell against attacks from outside

• Lipid A is oftne poisonous (endotoxine)

Cell wall in Archaea

• Have no peptidoglycan and no outer membrane

• Some methanogenic Archaea have pseudomureine.

• Many Archaea have S-layers - a paracrystalline structure of proteins or glycoproteins.

Cell wall of some methanogenic Archaea

• Has pseudomureïne

• Pseudomureïne is a polysaccharide similar to peptidoglycan composed of acetylglucosamine and N-acetyltalosaminuronic acid

• Has beta 1-3 glycosidic bonds instead of beta 1-4

Slime layer

• A slime layer may be present on the outside of the cell wall

• Consists of polysaccharides

• There are 2 types:

  • Capsule: if tightly attached, tight matrix

  • Slime layer: loosely attached, easily deformed

Function of slime layer

• Protection dependent on environmental conditions

• Assists in attachment to surfaces

• Role in development of biofilms

• Prevent dehydration/desiccation

Pili

• Think (2-10 nm diameter) filamentous structures made of protein that extend from the surface of a cell and can have many functions.

• Play a role in DNA exchange between cells (conjugation)

• Play a role in transport of electrons

• Type IV pili needed for “twitching motility”

Fimbriae

• Short pili that mediate attachment

• Enable bacterial cells to stick to surfaces to form pellicles (thin sheets of cells on a liquid surface) or biofilms on solid surfaces.

Hami

• Certain archaea have a special type of pilus, called hamus

• Resemble type IV pili, but with a spiky end (hook)

• Used for attachment to surfaces and each other (making biofilms)

What are cell inclusions and what are their functions?

Cell inclusions are considered various nutrients or pigments that can be found within the cell, but do not have activity like other organelles

Their functions include:

• Energy reserves

• Carbon resevoirs

• And/or have special functions

• Enclosed by thin membrane

• Reduce osmotic stress

Carbon storage polymers

• A type of inclusion body in a prokaryotic organism

• An example: poly-B-hydroxybutyric acid (PHB)

• Another example: glycogen: polymer of glucose

Polyphosphate granules

• Many prokaryotic and eukaryotic microbes accumulate inorganic phosphate in the form of polyphosphate granules.

• These granules are formed when phosphate is in excess and can be drawn upon as a source of phosphate for nucleic acid and phospholipid biosynthesis when phosphate is limiting

• In some organisms, polyphosphate can be broken down to synthesize ATP from ADP

Sulfur globules

• Many gram-negative bacteria and several archaea oxidize reduced sulfur compounds, such as hydrogen sulfide (H₂S)

• These organisms are sulfur bacteria → discovered by Winogradsky

• Oxidation of the sulfide generates electrons for use in energy metabolism (chemolithotrophy) or CO₂ fixation (autotrophy)

• Found in the periplasm

Magnetosomes

• Magnetic iron oxides

• Allow cell to orient using the magnetic field of the earth

• Magnetotactic bacteria are all motile (they have flagella)

• Respond to O₂ concentration

• Mostly micro-aerophilic (Survive best in environments with little oxygen)

• These structures are biomineralized particles of the magnetic iron oxides magnetite [Fe(II)Fe(III)2O4] or greigite [Fe(II)Fe(III)2S4]

gas vesicles

• Some bacteria and archaea can float because they contain gas vesicles.

• Allows cells to position themselves in regions of the water column that best suit their metabolisms.

• Example: Cyanobacteria that form massive accumulations called blooms in lakes.

  • These are usually near the lake surface where sunlight is most intense and photosynthesis can occur at maximal rates.

• They take up gas from surrounding water phase

• The gas is in structures made of protein, which is impermeable to water and solutes

• Gas vesicles are composed of two proteins GvpA and GvpC

Endospores

• Certain species of Bacteria produce specialized spores called endospores

• Endospores are highly differentiated dormant cells that function as survival structures and can tolerate harsh environmental conditions

• Are a dormant stage of a bacterial life cycle: vegetative cell → endospore → vegetative cell.

Sporulation

• The process of cellular differentiation in endospores.

• Is triggered when some nutrient becomes limiting

• It happens in three steps:

  1. Activation: heated for several minutes at elevated but sublethal temperature

  2. Germination: rapid loss of refractility and loss of resistance to heat and chemicals

  3. Swelling from water uptake and synthesis of RNA, proteins and DNA

Flagella

• Long, thin appendages (15-20 nm wide); helical shape; composed of flagellin

• Different arrangements: polar, lophotrichous, amphitrichous, peritrichous

• Tiny rotating machines (reversible)

• Increase or decrease rotational speed relative to strength of proton motive force

Flagellar synthesis

• More than 50 genes

• Filament grows from tip

• Build from cytoplasmic membrane

• Flagelline produced in cytoplasm.

Archaella

• Archaea version of flagellum

• Half the diameter of bacterial flagella

• Moves by rotation

• Composed of several different filament proteins with little homologous bacterial flagellin

• Speeds vary from 0.1 - 10x

• Similar structure to type IV pili

• Drive by ATP (not the PMF)

Surface motility

• bacteria only

• requires surface contact

• slower and smoother than swimming

• different mechanisms

  • excretion of polysaccharide slime

  • type IV pili/twitching motility

  • gliding-specific proteins
    

Chemotaxis

Taxis: directed movement in response to chemical or physical gradients

• chemotaxis: response to chemicals

• phototaxis: response to light

• aerotaxis: response to oxygen

• osmotaxis: response to ionic strength

• hydrotaxis: response to water

How is a gradient sensed in chemotaxis?

• By specific receptor proteins (MCP)

  • The signal is transmitted to the flagellum

Measuring chemotaxis

• Measured by inserting a capillary tube containing an attractant or a repellent in a medium of motile bacteria

• Can also be seen under a microscope

Phototaxis

• Green algae were not sensitive to red light

• They were sensitive to blue-green light as they orientated towards it.