• Describe the alkaline vent theory
• Compare and contrast composition of cell wall in fungi, archaea and bacteria
• Describe endosymbiotic hypothesis for formation of Eukarya
• List major structures in bacteria and describe their function
• Describe gram staining and cell morphologies
Alkaline vent theory
Alkaline vent theory is how we believe the beginnings of bacteria and cellular life evolved, it includes
black smoker at the bottom of the sea, in a hydrothermal vent. This is the possible origins of cellular
life.
• Iron sulphur is within cavities in black smokers at the bottom of the ocean.
• Iron sulphur is able to undergo catalysis which includes taking small carbon compounds and
converting them into more complex versions.
• The top of the ocean is more acidic and the alkaline water will rise. This produces a proton
ion gradient in the water. This gradient is present in all cells.
• This proton motive force provides energy towards the catalysis by iron sulphur compounds
in cavities
• Polymers eventually emerge a result. In order for these RNA and proteins to escape from the
cavities, they need a 'capsule' in order to become free from them and this is how cell
membranes and walls emerged.
RNA, DNA and proteins
RNA was the original nucleic acid and it was able to undergo catalysis as it has catalytic properties. A
hammerhead ribozyme for example is a form of RNA that could replicate and therefore undergo
evolutionary pressure and have better catalytic features.
Proteins eventually took over as the main catalysis and DNA changed to RNA. RNA is now an
intermediate between the two.
Last Universal Common Ancestor
The last common universal ancestor (LUCA) was the last cell that eventually lead to the three main
domains of life: Bacteria, Archaea and Eukarya. Cyanobacteria around 3 billion years ago was able to
undergo photosynthesis which lead to the oxygen catastrophe (increase in atmospheric oxygen)
which killed off a lot of organisms but also lead to new organisms that utilized this oxygen.
Difference between Bacteria, Archaea and fungi
Archaea are similar to bacteria as they are prokaryotic, lack of nucleus and membrane bound
structures. They are able to survive in extreme environments for example Haloquadratum walsbyi is
able to survive in hydrothermal vents.
They do not cause harm to humans. RNA works as a messaging protein but also as a structural
element. 16s rRNA converts RNA to protein and is found in all forms of life. Archaea contain 16s
rRNA and bacteria contain 18s rRNA so its a good molecule to use to distinguish between bacteria
and archaea.
They also differ in cell walls. Archaea contain pseudopeptidoglycan which composes of a sugar
backbone with a cross linked amino acid chain.
Pseudopeptidoglycan Same composition as peptidoglycan
But instead of N-acetylmuramic acid, it's
N-acetyltalosaminuronic acid (NAT).
Chitin Similar to cellulose. Contains N-acetyl-
glucosamine. It's a polysaccharide
containing nitrogen.
Endosymbiotic hypothesis
This hypothesis explains how the domain Eukarya emerged.
• Believed to be bacteria and archaea that came together to form eukarya
• There are archaea that are able to phagocytose other bacteria and consume it
• The bacteria was not successfully digested and instead, the bacteria survived and provided
ATP to the archaea and underwent oxidative phosphorylation
• That bacteria in all of us today is the mitochondria. Therefore, the mitochondria is
hypothesised to be an ancestral bacteria.
• Evidence to support this is the mitochondria has an 16a rRNA ribosomal subunit and if
someone were to be injected with mitochondria, they would produce an immune response
towards that organelle
• This approach also occurred with the chloroplast- a photosynthetic organelle. An early
eukaryotic consumed a cyanobacteria
• The organism survived and provided energy and also fixed carbon to complex sugars and
also undergo photosynthesis.
, Difference between prokaryotes and eukaryotes:
Gemmate obscuriglobus is prokaryote with a membrane bound nucleus that defies the
classifications. It is said to be an intermediate between prokaryotes and eukaryotes.
Bacteria structure:
Structures in a typical bacterium:
Bacteria can undergo horizontal gene conjugation and this involves the nucleoid which includes the
chromosomal DNA. Antibiotic resistance works by a mechanism called efflux which is a process by
which bacteria transport compounds out of the cell which are potentially toxic.
• Inclusion bodies- a food source, bacteria store food
• Polysomes- a polymer of ribosomes. Bacteria can rapidly take one piece of mRNA and make
multiple mRNA's from one strand. mRNA can be fed through three ribosomes.
, • Capsule- secreted from the cell wall. Typically, a polysaccharide. It can cover certain bacteria
and the bacteria abilities to escape certain components in the immune system. The capsule
'covers' the antigens, and the immune system is unable to detect these to produce a
response and therefore inhibits phagocytosis. Streptococcus pneumoniae causes pneumonia
by getting to the alveoli and produces fluid production. The India ink stain is used to identify
these bacteria as the ink cannot penetrate the capsule so when stained, the bacteria is
visualised, the capsule is seen as a negative stained region.
• Flagellum- certain bacteria have it, they are capable of motility. Its chemotaxis, they can
detect a molecule and move towards it. E.g Staphylococcus aureus does not have a flagella
for example.
• Fimbriae- protein tubes originating from the membrane in all gram negative bacteria but not
in many gram positive bacteria. They are hair like structure on the surfaces. They are shorter
and stiffer than flagella and slightly smaller in diameter. They are often involved in the
adherence of bacteria to surfaces.
• Pilli- also hair like structure involved in specific attachment of prokaryotes to surfaces in
nature.
Peptidoglycan and Gram staining:
Bacteria can be divided into two groups due to differences in cell wall composition. It’s based on the
bacteria's ability to retain a crystal violet-iodine dye complex following acetone/alcohol treatment.
• Gram positive = retains the complex, blue/purple when visualised
• Gram negative = loss of complex, red/pink when visualised
Peptidoglycan is a polymer that contains:
1. N-acetylglucosamine
2. N-acetylmuramic acid
3. L-alanine
4. D-isoglutamic acid
5. L-lysine
6. D-alanine
7. Pentaglycine
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