Transcript Geomicrobiology

Membrane and metabolism
• As the membrane is the focus of gradients, this is where
electron transport reactions occur which serve to power the
cell in different ways
• Many enzymes important to metabolic activity are
membrane bound
H+ gradients across the membrane
• Proton Motive Force (PMF) is what drives
ATP production in the cell
(DpH=1.4 = 0.14 V = 23 KJ/mol)
Figure 5.21
Membrane functions (other)
• In addition to directing ion/molecule transport and
providing the locus for energy production,
membranes are also involved in:
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Phospholipid & protein synthesis for membrane
Nucleoid division in replication
Base for flagella
Waste removal
Endospore formation
• Though very small, the membrane is critical to
cell function  Lysis involves the rupture of this
membrane and spells certain death for the
organism
Cell Wall
• Cell wall structure is also chemically quite
different between bacteria and archaea
• Almost all microbes have a cell wall –
mycoplasma bacteria do not
• Bacteria have peptidoglycan, archaea use
proteins or pseudomurein
• The cell wall serves to provide additional
rigidity to the cell in order to help withstand
the turgor pressure developed through
osmosis and define the cell shape as well as
being part of the defense mechanisms
• Cell wall structure
• Two distinct groups of bacteria with very different
cell walls
– Gram negative has an outer lipid membrane (different
from the inner, or plasma membrane)
– Gram positive lacks the outer membrane but has a
thicker peptidogycan layer
Gram – cell wall
Peptidoglycan layer
• This layer is responsible for the rigidity of the cell wall,
composed of N-Acetylglucosamine (NAG) and Nacetylmuramic (NAM) acids and a small group of amino
acids.
• Glysine chains held together with peptide bonds between
amino acids to form a sheet
Outer membrane – Gram (-)
• Lipid bilayer ~7 nm thick made of phospholipids,
lipopolysaccharides, and proteins
• LPS (lipopolysaccharides) can get thick and is
generally a part that is specifically toxic (aka an
endotoxin)
• LPS layers are of potential enviornmental
importance as a locus of chelators and electron
shuttles
• Porins are proteins that are basically soluble to
ions and molecules, making the outer layer
effectively more porous than the inner
membrane, though they can act as a sort of
sieve
External features
• Glycocalyx (aka capsule – tightly bound
and adhering to cell wall, or slime layer –
more unorganized and loosely bound) –
helps bacteria adhere to surfaces as well
as provides defense against viruses
• Flagella – ‘tail’ that allows movement by
rotating and acting as a propeller
• Pili – thin protein tubes for adhesion
(colonization) and adhering to surfaces
Inside the cell
• Cytoplasm – everything inside the membrane
• Nucleoid/Chromosome – DNA of the organism – it
is not contained by a nuclear membrane (as
eukaryote cell)
• Ribosomes – made of ribosomal RNA and protein
 these are responsible for making proteins
• Vacuoles or vesicles – spaces in the cytoplasm that
can store solids or gases
• Mesosomes/Organelles –a membrane system
internal to the cell which facilitates protein function;
there are these structures specifically for
photosynthesis
Cell structure
Cytoplasmic
inclusions
Where found
Composition
Function
glycogen
many bacteria e.g. E. coli
polyglucose
reserve carbon and energy source
polybetahydroxy
utyric acid
(PHB)
many bacteria e.g. Pseudomonas
polymerized hydroxy
butyrate
reserve carbon and energy source
polyphosphate
(volutin
granules)
many bacteria e.g. Corynebacterium
linear or cyclical
polymers of PO4
reserve phosphate; possibly a reserve of high
energy phosphate
sulfur globules
phototrophic purple and green sulfur
bacteria and lithotrophic colorless
sulfur bacteria
elemental sulfur
reserve of electrons (reducing source) in
phototrophs; reserve energy source in
lithotrophs
gas vesicles
aquatic bacteria especially cyanobacteria
protein hulls or shells
inflated with gases
buoyancy (floatation) in the vertical water
column
parasporal
crystals
endospore-forming bacilli (genus
Bacillus)
protein
unknown but toxic to certain insects
magnetosomes
certain aquatic bacteria
magnetite (iron oxide)
Fe3O4
orienting and migrating along geo- magnetic
field lines
carboxysomes
many autotrophic bacteria
enzymes for autotrophic
CO2 fixation
site of CO2 fixation
phycobilisomes
cyanobacteria
phycobiliproteins
light-harvesting pigments
chlorosomes
Green bacteria
lipid and protein and
bacteriochlorophyll
light-harvesting pigments and antennae
Nucleoid
• Single strand of DNA, usually circular, usually
looks like a big ball of messed up twine…
• Size – smallest organism yet discovered
(Nanoarchaeum equitans) 490,889 base pairs; e.
coli 4.7 Mbp, most prokaryotes 1-6 million base
pairs (1-6 MBp); Humans 3300 MBp
• DNA is around 1000 mm long in bacteria, while the
organism is on the order of 1 mm long – special
enzymes called gyrases help coil it into a compact
form
Ribosomes
• Ribosomal RNA is single stranded
• RNA is a single stranded nucleic acid
– mRNA- messanger RNA – copies information from DNA
and carries it to the ribosomes
– tRNA – transfer RNA – transfers specific amino acids to
the ribosomes
– rRNA – ribosomal RNA – with proteins, assembles
ribosomal subunits
DNA is transcribed to produce mRNA
mRNA then translated into proteins.
RNA and protein construction
• The nucleotide base sequence of mRNA is encoded
from DNA and transmits sequences of bases used to
determine the amino acid sequence of the protein.
• mRNA (“Messenger RNA”) associates with the ribosome
(mRNA and protein portion).
• RNA (“Transfer RNA”) also required
• Codons are 3 base mRNA segments that specify a
certain amino acid.
• Most amino acids are coded for by more than one
codon.
• Translation ends when ribosome reached “stop codon”
on mRNA.
Transcription
RNA polymeraze takes the DNA and temporarily unwinds it, templates the
transfer RNA from that, using ribonucleoside triphosphates to assemble…
Translation
• mRNA is coded for one or more specific
amino acids and moves to the ribosome to
assemble amino acids into proteins
• On mRNA, codons are 3 bases, coded to
specific amino acids
• On tRNA, the anticodon
latches to the codon
on the mRNA
Protein Formation
•
The ‘code’ on
mRNA
determines the
sequence of
protein assembly
rRNA
• Ribosomes are made of proteins and rRNA, the
tRNA and mRNA come to it and assemble the
proteins
• rRNA plays a structural role, serving as a
support for protein construction, and a functional
role
• rRNA consists of two subunits, one 30S in size
(16S rRNA and 21 different proteins), one 50S in
size (5S and 23S rRNA and 34 different
proteins). The smaller subunit has a binding site
for the mRNA. The larger subunit has two
binding sites for tRNA.