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eubacteria
Prokaryotes are older, about 4000
Million years old
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• DNA lacks histones
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• Can do horizontal transfer

Eukaryotes
About 2000 million years old
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This is double
membrane bound
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• every 200 bp (base-pairs) of
DNA is bound by a big lump of
proteins called a nucleosome
(composed of two copies each
of 4 different kinds of histone
protein – so 8 histones total per
200 bp)
...


Bacterial RNA polymerase uses a
protein called ‘σ factor’ to find
where to bind to DNA and begin
transcription
...
Curiously, the TFIIB
protein which binds to the TBP is
homologous to the σ-factor
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• Can do horizontal
transfer - up to
40% of their
DNA comes from
archaea via
horizontal
transfer with
eubacteria
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transcription

DNA

age

CBG
...
Colin D
McClure
Lecture notes

mRNA not post-transcriptionally
modified

It is thought that the MRCA of
eukaryotes, archaea and eubacteria
used both TBP and the σ factor, but
that these were respectively later
lost
mRNA is post-transcriptionally
modified

lipid

organelles

translation

CBG
...
Colin D
McClure
Translation starts off with
Translation starts off with
Translation starts off
formylated methionine, aka
methionine (AUG codon)
...

like eukaryotes
• Uses methylated cap to help
ribosome bind, and sometimes a
Kozac fragment

• Involves SDS sequences to
help ribosome bind
• Simple organelles – typically
not membrane bound
...

• No endosymbiotic organelles
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• Characteristic lipid is
hopanoids
• membranes contain mostly
acyl ester lipids
...
(complex
endo-membrane system)
...

• All are membrane bound, and
nucleus has two membranes
around it
...

(though some eukaryotes have
lost them, such as
microsporidia
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• Characteristic lipid is
cholesterol
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• 70S ribosomes,
however;
Archaeal
ribosomes are
more homologous
to eukaryotic
ribosomes
...


• membranes
contain mostly
terpenoid ether
lipids
...
01 - Replication, transcription and translation - Prokaryotes and Eukaryotes - 8/2/2019 - Dr
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This is
Flagella is a membranous tube
• Archaeal flagella
powered directly by a PMF and
containing a ‘9+2’ ring of tubulin
are not
may be homologous to the F-Type microtubules which move against
homologous to
ATP-Synthase
...
the flagellum whip side to side to
but are
propel movement
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• Powered by
ATPases, not
PMF
...

• Cell division by fission
...

spindle divide the condensed
binary fission
...

myosin is responsible for
resembles that of
pinching off the daughter cells
• Chromosomes do not
Eukaryotic DNA
during
cytokinesis
...

Replication
...

• Unlike eubacteria
but somewhat
similar to
eukaryotes, some
archaea such as
Haloferax volcanii
are thought to be
able to undergo
recombination of
Nuclear DNA
...
This
is hypothesized by
some to be a
precursor to sex
...
01 - Replication, transcription and translation - Prokaryotes and Eukaryotes - 8/2/2019 - Dr
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They’re so small in
cytoskeleton
cytoskeleton, just
fact that they don’t really have • cytoplasm contains many fibrillike bacteria
...
Motor
around, they rely mostly on
proteins (kinesin, dynein,
internal diffusion
...
) move along these
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• For example, a cilia has 9 pairs
of tubulin filaments in a circle,
with another pair at the center
...

• They rely on their cytoplasmic • Energy production occurs all
• They rely on their
membranes to get energy;
over cytoplasm wherever
cytoplasmic
Larger size means more
mitochondria/plastids are,
membranes to get
Demand for Energy/ATP, but
therefore S
...
A:V ratio, so
source and therefore reduced
size means more
proportionally reduced energy
S
...
This restricts size
not limit cell energy supply
...
A:V
• About 1 µm size on average – • Eukaryotic cells can therefore
ratio, so
E
...
Namibiensis (~ 750 µm) are
prokaryotes
reduced energy
exceptions
...
This
• Some mitigate this using
larger than the average
restricts size
membranal folds that increase
prokaryote
...
A
...
01 - Replication, transcription and translation - Prokaryotes and Eukaryotes - 8/2/2019 - Dr
...

He came up with the clade (see right) that
proposed that eukaryotes and archaea were more
closely related to each other than either was to
bacteria
...

• However, his tree is affected by LBA
...
This
explains the position of microsporidia on the
diagram to the right
...
This error also undermines his tree as a whole
because it is very possible that it also occurred elsewhere but has not been identified
...
This is uncertain though, just like the
idea that they are sister groups to each other
...
It is fairly certain now though that archaea are more
closely related to eukaryotes than prokaryotes, because they share several biochemical features:
o Use of TBP
o START codon coding for methionine instead of formylmethionine, just like eularyote
o Use of histones
• however, up to 40% of archaea DNA comes from archaea via horizontal transfer with eubacteria
...

• Note that bacteria/prokaryotes have lost and gained a lot of genes since LUCA, therefore it is wrong
to think of them as most closely representing LUCA
...
01 - Replication, transcription and translation - Prokaryotes and Eukaryotes - 8/2/2019 - Dr
...
33, there are 2 main hypotheses for endosymbiotic origin of mitochondria
...

o The hydrogen hypothesis proposes that a gradual relationship evolved between hydrogen
bacteria which produced Hydrogen and CO2, and a different cell which used these waste
products to make methane
...
A contact which eventually
led to complete engulfment
...
This comes from
the fact that mitochondria are related to Rickettsia, an endo-parasite which frequently infects cells and
lives inside them (it causes typhus), proposing a mechanism for how mitochondria came to be inside
eukaryotic cells
...
This is more plausible
when you consider that Mitochondria diverged from bacteria billions of years ago, so it should not
look similar to lineages which look like they evolved more recently than this
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There is no
evidence for this claim
...
01 - Replication, transcription and translation - Prokaryotes and Eukaryotes - 8/2/2019 - Dr
...
Specifically, this mitochondrial
RNA Polymerase (RNAP) resembles that of a T7 Bacteriophage virus
...

• Be aware that Eukaryotic nuclear DNA has been tainted and mixed with the DNA of their Prokaryotic
endosymbionts, (such as in plants whose nuclear genome now codes for part of RubisCO)
...

• Lynn also proposed that flagella and cytoskeletons could be the product of endosymbiosis, however,
this has since been proven false, as these structures lack their own DNA and other distinctive features
found in endosymbionts
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• Crick was right, Watson was wrong
...
2 examples of this are:
Creutzfeldt Jakob disease – spread by cannibalism
BSA – Bovine Spongiform Encephalopathy aka ‘mad cow’ disease
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01 - Replication, transcription and translation - Prokaryotes and Eukaryotes - 8/2/2019 - Dr
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The Lamarckist model suggests that behavioural activities can cause inheritable changes,
(Phenotype
DNA) though this has been since disproven
...
This is not equivalent to the AUG start
codon
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• The template strand is indicated as – and the coding strand as +
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• Transcription produces RNA, which is spliced (in eukaryotes) and then translated
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• The start codon is downstream of the 3’ UTR, and is always ‘AUG’
...
STOP codons can be as follows:
o UAA
o UGA
o UAG
• It also has a 3’ UTR region which comes after the STOP codon
...

• Additionally, note that proteins are described having a ‘C-terminus’ and an ‘N-terminus’
...

NB; Italicise and don’t capitalise gene names, because proteins and their genes share a name and are
distinguished only by this italicisation and capitalisation (or lack thereof)
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g
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Summary
Feature
Eubacteria
Transcription σ factor

Translation

• Formyl-met
• 70S
Ribosomes

Eukarya
TATA (TBP)

Archaea
TATA (TBP)

• Methionine
• 80S
ribosomes

• Methionine
• 70S
Ribosomes

endosymbionts
Mitochondrial RNAP
similar to T7
Bacteriophage
• Formyl-met
• 70S ribosomes

CBG
...
Colin D
McClure
DNA
• No junk
• linear
• No nucleus
• No nucleus
chromosom • histones &
• No nucleus
• Circular DNA
es
nucleosomes
• No histones
• DNAP looks both
•
histones
&
bacterial and viral
•
Circular
&
• Circular &
nucleosome
plastids
plastids
s
...

• This twirls
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• Homologous to
Type IV pilli
• Binary fission

Archaea
• Archaea look like eubacteria superficially, but they are more closely related to eukaryotes
...

• These could have been endosymbiosed according to multiple different hypotheses, as either a
fortuitous predator-prey interaction, as a gradual developing relationship, or the result of a parasitic
relationship
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The rest all can be done in reverse and there are example of RNA, DNA and
Proteins that can replicate themselves
...
01 - Replication, transcription and translation - Prokaryotes and Eukaryotes - 8/2/2019 - Dr
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• Produces RNA
Translation
• Starts off with RNA that has START (AUG) & STOP codons
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arenicola is a bizarre eukaryote;
o They are predators when young
o They then endosymbiose an alga of the Nephroselmis genus, lose their predatory lifestyle and
become photosynthetic
...
arenicola then undergoes division, one daughter cell ‘inherits’ the Nephroselmis
alga and continues living an autotrophic lifestyle, while the other cell becomes a predator
...
arenicola is thought by some to be in the process of becoming fully endosymbiotic

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