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Chapter 2

BIOLOGY 2EE3 Chapter Notes - Chapter 2: Glycosidic Bond, Atp-Binding Cassette Transporter, Magnetotactic Bacteria

Course Code
Turlough Finan

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Chapter 2 - Bacteria
- some bacteria are very rich in iron because of membrane enclosed magnetite particles
- these bacteria use the Earth's magnetic field in order to orient themselves and travel
- magnetotactic bacteria prefer environments with little or no oxygen
- bacteria use this ability to direct themselves towards areas which are anoxic
- this process is magnetic-aerotaxis by which they find the desired oxygen concentration by
moving a long a magnetic field
2.1 Morphology of bacterial cells
- shape of bacterial cell caused by organization of cell wall
- coccus is spherical; bacillus is rod, vibrio is curved rod, spirillum is spiral
- ecoli is rod shaped; vibrio cholerae is vibrio; staphylococcus aureus is spherical; treponema
pallidum is spirrilium
- morphology itself is not enough to classify bacteria
- ecoli are individual cells; other bacteria like bacillus anthracis or streptococcus pyogenes form
long chains and physically connected after division
- staphylococci usually produce irregular clumps rather than chains
- some bacteria do not create regular shapes but create variable shapes called pleiopmorphic
- mycoplasma genus are all pleiomorphic because they do not produce a cell wall
- some bacteria can form hyphae which are branching filaments and can also produce mycelia
which are 3-d networks penetrating out or into the soil surfaces; similar to fungi
- cyanobacteria form trichomes are smooth unbranched chains of cells; sometimes have
polysaccharide sheet coating
- between the cells in both trichomes and hyphae have intercellular connections for
nutrient/signalling molecules
- most bacteria are 0.5 to 5 micrometers in length
- some large bacteria have been found, largest is spherical thiomargarita namibiensis
- epulopiscium fiehelsoni have multiple genomes found in cytoplasm and replicate within
- all bacteria limited in shortest size by the rna genome as that is usually 0.5 micrometers itself
2.2 Cytoplasm
- cytoplasm is the aqueous environment inside bacteria and contains diverse components
- nucleoid is the largest entity and contains a mass of DNA (ususally single, circular
chromosome) coated with proteins and rna
- gas vesicles are also found in bacteria for buoyancy; inclusion bodies for storage of polymers
- no membrane surrounding the nucleoid

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- cations shield the negative charge of the sugar phosphate backbone which allows it to pack
more tightly
- topoisomerases are enzymes that allow the dna to coil upon itself (supercoiling)
- other proteins like dna/rna polymerases exist in the nucleoid and proteins that control gene
- most enzyme catalyzed metabolic reactions occur in the cytoplasm
- depending on conditions some bacteria have includion bodies which allow them to store extra
carbon, nitrogen and phosphorous
- no membrane surrounds this body, ex. PHB is a lipid polymer used to store carbons
- PHB can be 50% of dry weight (polyhydroxylalkanoates), used for plastic industry substitute
- sulfur globules are stores of sulfur to be used as energy when oxidizing sulfur compounds
- gas vesicles regulate buoyancy in a cell based on cell positions in water column in response to
- photosynthetic bacteria also have carboxysomes which help convert inorganic carbon to
organic carbon
- magnetosomes are a membrane enclosed organelle which have magnetite; these may provide
clues to bacterial evolution
2.3 The bacterial cytoskeleton
- cytoskeleton provides internal framework for cell and interact with plasma/cell wall
- the FtsZ protein forms the Z ring which is needed for bacterial division
- this protein is related to tubulin which is building block for microtubules in eukarya
- ftsz monomers polymerize to filaments that bundle to form z ring which form on the inner face
of plasma membrane
- z ring contracts by releasing subunits which ends up causing cell envelope to go inward until
cell division is done
- zring is missing but will reform from elements in the cytoplasm for the next division
- MreB protein is another important cytoskeleton element
- mreb is related to actin and form long helical bands underlying the plasma membrane
- mreb is universal in non spherical bacteria and help to guide cell wall formation/cell
-parM protein forms actin like filaments; found on certain plasmids
- role of parM is to ensure that during seperation there will be one copy of the plasmid on each
side of the cell
Perspective 2.1 - Marvelous Magnetosomes
- magnetoaxis is used to direct movement based on the earths magnetic field
- magnetosomes are used to achieve this and are filled with magnetite (Fe3O4)
- formed by the plasma membrane; and acts as a compass needle, organized in chains

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- they are organized into a chain through the mamk protein which creates actin like filaments
- discovered through using gfp to fluoresce the molecule
- mamj faciliates interaction between magnetosomes and the actin like filaments
2.4 The cell envelope
- all the layers as a membrane in total are called the cell envelope
The plasma membrane
- plasma membrane is bilayer composed of amphipathic phospholipids
- also called cytoplasmic membrane or cell membrane
- bacterial membranes lack sterol lipids like cholesterol, but form sterol like compounds like
- hopanoids are planar molecules and thought to stabilize the plasma membrane
- these molecules are abundant in soils and sediments
- membranes are not fluid depends on temperature, lipid type, other molecules
- membranes are not pure lipids, half composed of protein
- functions of membrane are transport. energy production, sensing
Permeability of the Plasma membrane to water
- has differential permeability, uncharged molecules like O2/CO2 flow through freely
- larger compounds that are polar or charged cross less easily
- water usually is small enough to pass through even though it is polar, might use aquaporins
- hypotonic if cytoplasm has higher solute concentration than external
- these changes can cause cell to swell/prune but cell wall helps prevent this
Nutirent transport
- there are facilitated diffusion systems which allow molecules (abundant in environment) to
cross without energy
- active transport systems require energy and drive against a gradient
- one way this is done is through symport; which occurs when one molecule travels down a
gradient and takes along a molecule not travelling along its gradient, energy is released which
allows the other molecule to move
- antiport involves the ejection of one molecule releasing energy to allow another one in
- ABC transporters (ATP binding cassette) have a nucleotide binding domain where ATP is
hydrolyzed to give energy for transport
- ABC transporters are made of 4 subunits, 2 hydrophobic in the membrane and 2 hydrophilic in
the cytoplasm
- also has a high-affinity solute binding protein which binds to substrates and brings them to the
complex which increases the affinity
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