Cambridge Pre-U Biology
S24: The origins of life
Learning Outcomes
■
describe the evidence for a single origin of life in terms of conservation of key biochemical
mechanisms
■ describe and explain how eukaryotes are thought to have originated about 2.7 billion years
ago by endosymbiosis and the evidence that supports the theory of endosymbiosis
■ discuss the benefits and disadvantages of being multicellular
S24.1 What is life and what are its origins?
Life is difficult to define and eventually may prove not to be a useful concept.
There has always been a sense that there is something special about life, a unique ‘life
force’, described as an élan vitale by a French philosopher in 1907. This helps to explain why
scientists once believed it would be impossible to synthesise an organic molecule, although
the synthesis of urea by Wöhler in 1828 disproved this hypothesis and helped to dispel the
notion of a life force.
Another false notion about the nature of life, which was also abandoned in the 19th
century, was the ancient Greek idea of ‘spontaneous generation’. According to this theory,
life could arise within a short space of time from inanimate material. This was thought to
happen when maggots appear in dead flesh.
Nowadays, our studies of molecular biology and the distant origins of life blur the
distinction between what is living and what is not. Is a self-replicating molecule alive? Are
viruses, some of which can be crystallised, living? Deciding what life is may become even
more difficult in the future if we create intelligent (inorganic) machines, perhaps with
consciousness. Just as scientists used to debate whether fungi were plants or animals, it may
be decided by how we ‘classify’ life.
Even if we cannot easily define life, what is of interest is how matter spontaneously
organised itself over millions of years into complex systems that continued to evolve into
conscious beings. What basic rules govern how systems such as living organisms evolve?
Does it happen on other planets? If so, how common is it and what are the similarities and
differences compared with life on Earth? Discovering and being able to study life somewhere
else in the Universe – hopefully microbial life in our own solar system – would contribute
enormously to our understanding of life.
Some of the big questions are beginning to be answered. Darwin and Wallace’s theory
of evolution by natural selection (see ‘The Darwin–Wallace theory of evolution by natural
selection’ in Chapter 17) and the discovery of the structure of DNA (see ‘DNA replication’ in
Chapter 6) have radically advanced our understanding of life and underpin much of modern
research. The ability to sequence genomes is rapidly increasing our understanding of the
relatedness, and hence the evolution, of living organisms – particularly of microbial life,
where the huge variety is only just beginning to be appreciated.
One of the big questions, to be addressed in this chapter, is: what are the origins of life?
The scientific view is that living things have evolved from relatively simple chemicals. At the
same time, it should be acknowledged that other theories exist, including religious accounts.
Since all theories have their limitations and are subject to revision over time, scientists
should always be as open-minded as possible.
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Approximate time
(billions of years ago)
Event
4.6
Formation of planet Earth
3.9
Possible last universal common ancestor (LUCA) – the most
recent common ancestor of all living cells. First living cells
may have been heterotrophic prokaryotes feeding on organic
molecules in the ‘primeval soup’, or autotrophic prokaryotes
using carbon dioxide as a source of carbon
3.7
Sedimentary rocks in western Greenland contain graphite
formed by living organisms
3.5
Photosynthesis evolves (autotrophic organisms using light as a
source of energy); prokaryotes split into bacteria and archaea
3.48
Sandstone in Western Australia containing microbial mat fossils
(bacteria and archaea including stromatolites (thick biofilms))
3.2
First organisms (blue-green bacteria) to use water as a source
of hydrogen for photosynthesis; the splitting of water releases
oxygen into the atmosphere; oxygen begins to oxidise Fe2+ to
Fe3+ in the oceans and on land
2.7
Oxygen starts to accumulate rapidly in the atmosphere; aerobic
respiration becomes widespread, greatly increasing efficiency
of energy use; oxygen also results in an ozone layer in the
atmosphere which protects life from UV radiation – life can
therefore emerge from water, which filters UV light; reduced
greenhouse effects as gases like methane disappear, leading to
cooling of climate
2.7
First eukaryotic organisms (unicellular)
1.2
Oxygen concentration in atmosphere reaches current levels
0.8
First multicellular animals and plants
0.54
‘Cambrian explosion’ – first appearance of complex animals
0.5
First vertebrates
0.4 – 0.5
First plants on land
0.065
Extinction of the dinosaurs and about half of all animal species
0.002
First members of genus Homo
Table S24.1 Dates for the origin and evolution of life.
S24.2 The origin of complex organic molecules
The age of the Earth is generally agreed to be about 4.5–5 billion (thousand million) years.
The atmosphere of the early Earth was very different to that of today. It was a reducing
atmosphere, unlike the oxidising one of the present day, as evidenced by the presence of Fe2+
in the earliest rock formations, rather than Fe3+. With very little oxygen, the atmosphere
is thought to have contained hydrogen, ammonia, methane, carbon dioxide, hydrogen
sulphide, water, the inert gases and a few more gases. Also, with no ozone layer, due to the
lack of oxygen, radiation would have been far more intense. Electrical storms were more
violent and frequent.
The idea that such an atmosphere would favour the gradual accumulation of organic
compounds to form a ‘primeval soup’ in the oceans was first tested experimentally in 1953 by
Stanley Miller and Harold Urey. They attempted to simulate conditions on the primitive Earth
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using the apparatus shown in Figure S24.1. They subjected a mixture of gases (water, hydrogen,
ammonia and methane) to high voltage electrical discharges. They analysed the products and
discovered many molecules of biological importance, including amino acids, adenine and
simple sugars such as ribose. Subsequently, Leslie Orgel succeeded in synthesising nucleotides
in a similar experiment. We now believe that there was a relatively high concentration of
carbon dioxide in the primeval atmosphere, but Miller’s experiments have been repeated
using mixtures of carbon dioxide and water and only traces of other gases, and have produced
similar results. It seems that it is relatively easy to create the building blocks of life.
gases
electrical discharge
cooling jacket
3
boiling water
liquid containing products
Figure S24.1 The Miller–Urey experiment to study the origin of life. The apparatus contains a ‘sea’ of
sterile water under an ‘atmosphere’ of hydrogen, methane and ammonia. Electrodes give off a spark
to imitate lightning. After a week, amino acids, one of the basic building blocks of life, have formed.
S24.3 From molecules to cells
Self-replicating molecules and catalysts
The main sources of evidence used in tracing the history of cellular life are fossils and
biochemistry. Biochemistry is an increasingly important source of information. From simple
molecules, we have to speculate how more complex molecules such as proteins and nucleic
acids could evolve. Proteins and nucleic acids are polymers that can be made by a simple
chemical reaction (condensation) repeated many times. Amino acids can be joined to form
polypeptides, and nucleotides to form nucleic acids (see Chapter 2 in the Coursebook). Only
20 different amino acids (out of millions of possible ones) are used to make the proteins in all
living organisms, and only five nucleotides (of two types) are used to make RNA and DNA.
We learn from this that nature is ‘conservative’ and that complexity can arise from relatively
few simple building blocks and ‘rules’.
It has been demonstrated that these biological polymers could have been formed in
many different ways, for example by heating dry organic compounds. Some minerals have a
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catalytic effect. If a molecule evolves that can catalyse the production of more molecules like
itself, then we have the beginnings of self-replication, a key property of life.
Polynucleotides have the potential to self-replicate, because they can form complementary
pairs of bases: one molecule or polymer can act as a template for another. Of the two existing
polynucleotides, RNA and DNA, RNA is the simpler because it is single-stranded (DNA is
double-stranded). RNA has come to be seen as an ideal candidate for an early self-replicating
molecule that also has catalytic properties – a ribozyme or RNA enzyme.
A single RNA molecule can fold back on itself and base pair with itself, making any
number of shapes (Figure S24.2). A precise three-dimensional shape is a key feature of
enzymes. Experiments have shown that if a random mix of artificial RNA molecules is passed
through a column containing a chosen substrate, a few appropriate shapes will stick to the
substrate. If these molecules are allowed to act as templates for further RNA molecules,
and the experiment is repeated several times, a population of RNA molecules is created
that binds quite specifically to the substrate. This artificial selection could mimic a form of
natural selection of molecules if the RNA–substrate interaction favoured survival of the RNA
molecule. Such natural selection would apply to any favourable molecular interactions.
U
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Figure S24.2 An RNA molecule has the ability to fold over on itself by base pairing.
RNA can act as a catalyst, and the base sequence in RNA can also act as a store of
information. Informational molecules like RNA are an essential ingredient of life. Apart
from being able to make precise copies of themselves, they can act as codes which can
interact with other molecules to control the biochemistry of life.
Scientists continue to speculate and experiment to try to understand how RNA molecules
may have evolved to direct protein synthesis, perhaps forming the first primitive ribosomes.
However, it is still a matter of speculation whether RNA originally controlled production of
proteins or proteins controlled production of RNA.
Membranes
A final requirement for cellular life is the evolution of membrane-enclosed biochemistry. As
discussed in Chapter 2, given the evolution of molecules such as phospholipids – which have
both hydrophilic and hydrophobic components – micelles and bilayers forming vesicles will
occur spontaneously. It is not difficult, therefore, to imagine a membrane-enclosed structure
containing a self-replicating RNA molecule with a wide variety of catalysts. This would make
a self-contained system comparable to a living cell.
DNA
All cellular life now uses DNA as the permanent hereditary store of genetic information.
So why the switch from RNA? DNA is more stable than RNA and is easier to replicate
accurately. The presence of a duplicate complementary strand as a reference means that
copying errors and damage, for example by radiation, are more easily corrected.
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Three types of cell
As described in Chapter 1, in ‘Two fundamentally different types of cell’, the first cells were
prokaryotes. It was originally believed that prokaryotes eventually gave rise to eukaryotes,
and that these remained the two basic types of cell. In 1977, however, Carl Woese showed
that there were three basic types of cell. His discovery was a result of analysing the base
sequences of ribosomal RNA among prokaryotes. These revealed two very different groups
of prokaryote. Woese proposed that living organisms should therefore be classified into three
domains: bacteria, archaea and eukaryota.
The new group of prokaryotes, archaea, had originally been thought to be an ancient
group of bacteria and had been named Archaebacteria (‘archae’ means ancient). The
examples of Archaebacteria known at the time were specialised for living in extreme
conditions, such as at high temperatures or in high salt concentrations, but it was later
discovered that the archaea are widely distributed.
The term ‘Archaebacteria’ should no longer be used, because the archaea should not be
regarded as bacteria. In 1996, Woese published his analysis of the genome of the archaean
Methanococcus. This work led to the conclusion that archaea are more closely related to
eukaryotes than to bacteria, as the phylogenetic tree in Figure S24.3 shows. Phylogenetic
trees map the evolutionary relatedness of living organisms.
Bacteria
Archaea
Eukaryota
green
myxomycota
filamentous
animalia
bacteria
entamoebae
spirochetes
fungi
Gram
Methanosarcina
positives
Methanobacterium
halophiles
proteobacteria
plantae
Methanococcus
cyanobacteria
ciliates
Planctomyces
Thermoproteus
Pyrodicticum
Bacteroides
cytophaga
Thermotoga
Aquifex
flagellates
trichomonads
microsporidia
diplomonads
Figure S24.3 Phylogenetic tree based on small-subunit ribosomal RNA sequences showing three
domains of life. Carl Woese et al. 1990.
The term ‘prokaryote’ can still be used, but prokaryotes are no longer a recognised
taxonomic group.
S24.4 Evidence for a single origin of life
In 1859, Charles Darwin suggested that all living things may have evolved from a single
common ancestor. Since Darwin’s time, evidence has accumulated that tends to confirm his
view. We will now look at some of this evidence and mention Carl Woese’s view that it may
not be that simple!
The genetic code
Controlled production of proteins is important because proteins are much more efficient
and versatile catalysts than RNA. As part of this process, a code for amino acids evolved in
order to dictate the sequence of amino acids in proteins. The cracking of the genetic code
in the 20th century is one of the great landmarks in biology. As we see in Chapter 6, the
code is a three-base code for each amino acid. Only four bases are needed to code for the 20
amino acids used. In theory, a given organism could use any four bases from a vast number
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of possibilities. The fact that all living organisms use virtually the same codes for the same
amino acids strongly suggests that all cells have descended from a single line of original cells.
If life is discovered somewhere else in our solar system, one of the first things scientists
will want to study is its genetic code.
Conservation of key biochemical molecules and pathways
Proteins
The universal genetic code is the strongest piece of evidence for a single origin of life, but
there is further supporting evidence for this idea. One of the earliest proteins to be studied
was cytochrome c, which is found in all aerobic cells of bacteria, archaea and eukaryotes.
Cytochrome c is an example of a highly conserved molecule, meaning that it has undergone
only minor changes over the whole period of its evolution. A comparison of cytochrome c in
different eukaryotes shows that the molecule is strongly conserved. This is good evidence that all
eukaryotes share a common ancestor. The one-letter code for amino acids is used for showing
sequences of amino acids like those in Figures S24.4 and S24.5. This is a much easier way to show
the primary structure of proteins, which may have up to 500 or more amino acids, than the
three-letter code used in the Coursebook (see Appendix 1 and Figure 2.18). The one-letter code
is easy to find by searching the internet. It is the code used to store information about proteins
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I A
L H
I S
I S
V A
V P
I A
V A
110
V
V
V
V
V
V
V
W
V
W
W
R
R
R
R
R
R
R
R
R
R
R
H
M
M
N
M
D
D
T
A
M
T
L
L
L
L
F
L
L
M
L
L
L
V
V
V
V
V
V
V
V
V
V
V
G
G
G
G
D
G
G
G
G
G
G
V
V
V
V
T
V
V
V
T
V
V
C
C
C
T
I
A
A
S
I
T
S
V T
V T
Y T
M T
M T
Y T
Y T
M T
L T
M T
M T
120
E
E
E
E
E
E
E
N
V
A
N
D
E
D
A
E
E
E
A
D
D
E
E
E
E
E
E
E
E
E
E
E
E
A
A
A
A
A
I
A
V
A
A
V
K
K
K
K
K
K
K
R
K
K
R
E
A
A
A
A
A
A
A
A
Q
N
L
L
L
S
E
M
M
M
L
M
M
A
A
A
A
A
A
A
A
A
A
A
A E
E E
E E
K Q
A D
A E
A E
E E
E E
S E
E E
130
V
V
V
I
A
I
I
F
N
V
F
E
E
E
T
L
E
E
E
E
E
E
V
V
V
V
I
V
V
Y
Y
V
Y
Q
Q
Q
K
N
V
V
D
D
E
D
D
D
D
D
D
D
D
D
T
D
D
G
G
G
G
V
G
G
E
E
G
E
P
P
P
P
D
P
P
P
P
P
P
N
N
N
D
•
N
N
D
N
D
D
E D
D D
L D
D T
D K
D E
D E
D Q
D Q
D E
E Q
140
G
G
G
G
G
G
G
G
G
G
G
E
E
E
N
A
E
E
N
E
N
N
M
M
M
V
S
M
M
P
I
N
P
F
F
F
V
I
F
F
K
E
F
K
M
M
M
T
Q
T
T
K
K
K
K
R
R
R
R
R
R
R
R
R
S
R
P
P
P
P
P
P
P
P
P
P
P
G
G
G
G
G
G
G
G
G
G
G
K L
K L
K L
K L
W L
K L
K L
K L
K L
K L
K L
150
F
S
S
S
I
S
S
A
S
S
S
D
D
D
D
D
D
D
D
D
D
D
Y
F
V
V
K
R
K
Y
V
F
V
F
P
F
F
L
P
L
V
L
L
I
P
M
P
P
P
P
P
P
P
P
P
M
V
M
S
N
Q
E
G
D
F
G
P
P
P
P
P
P
P
P
P
P
P
human
mouse
cow
fruit fly
thread worm
potato
thale cress
yeast
yeast
bread mould
yeast
V
V
V
V
V
V
V
V
V
V
V
F N
P N
P N
P N
P N
A N
S N
P N
K N
P N
P N
160
S
P
P
E
K
E
E
E
D
V
C
E
E
E
E
K
A
S
Q
E
E
Q
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
R
R
R
R
A
R
R
R
R
R
R
A
A
A
A
A
F
F
A
F
A
A
A
A
A
A
A
A
A
A
A
S
A
N
N
N
N
N
N
N
N
N
N
N
N G
N G
N G
N G
N G
G G
G G
Q G
N G
N G
Q G
170
A
A
A
A
A
A
A
A
A
A
A
L
L
L
V
A
Y
V
L
L
A
L
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
D
D
D
D
D
D
D
D
D
D
D
L
L
L
L
L
L
L
L
L
L
L
S
S
S
S
S
S
S
S
S
S
S
Y
Y
Y
Y
L
L
L
L
L
C
L
I V
I V
I V
I V
N A
I T
V T
I V
I V
V V
I V
180
R
R
R
S
L
K
K
K
K
R
K
A
A
A
A
A
A
A
A
A
G
A
R
R
R
R
R
R
R
R
R
R
R
M
M
M
K
R
M
N
M
M
M
M
G
G
G
G
G
N
N
Q
G
G
G
G
G
G
G
G
G
G
G
G
G
G
E
E
E
E
D
Q
Q
P
C
Q
C
D
D
D
D
D
N
N
D
D
D
D
V V
V V
V V
V I
V V
V V
V V
V I
V I
V I
V I
190
F
F
E
F
F
T
F
F
F
V
T
S
S
S
S
S
A
A
A
S
S
S
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
T
T
T
T
T
T
T
T
T
T
T
G
G
G
G
G
G
G
G
G
G
G
V
V
V
V
V
V
V
V
V
V
V
C
C
C
H
L
N
N
P
P
T
P
• E
• E
• E
• D
• E
• D
• D
E F
D E
• E
D E
200
F
P
P
A
A
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
T
T
T
A
A
A
A
A
A
A
A
G
G
G
G
G
G
G
G
G
G
G
V
V
V
V
V
V
I
V
A
V
V
S
S
S
V
K
S
S
V
S
E
A
L
L
L
L
V
L
I
L
V
V
L
A
A
A
A
D
A
A
P
G
P
P
E G L
E G L
E G L
E G Q
D G K
E G L
E G L
P G A
A G L
D G M
P G S
210
V
V
V
V
A
M
M
N
N
N
N
F
F
F
F
V
V
V
V
F
F
V
N
N
N
N
N
N
N
N
N
N
N
P
P
P
P
P
P
P
P
P
P
P
V
V
V
V
V
V
V
V
V
F
V
F
F
F
F
F
F
F
F
F
F
F
human
mouse
cow
fruit fly
thread worm
potato
thale cress
yeast
yeast
bread mould
yeast
P
P
P
P
P
P
P
P
P
P
P
G Q
G Q
G Q
G G
G G
G G
G G
G G
G T
G T
G G
220
A
A
A
A
I
A
A
S
G
G
S
L
L
L
L
I
L
L
L
L
L
L
A
G
G
G
S
A
A
A
A
A
A
M
M
M
M
M
M
M
M
M
M
M
A
A
A
A
P
P
P
G
A
A
A
P
P
P
Q
Q
K
K
R
R
R
M
P
P
P
V
Q
M
M
V
V
P
V
I
I
I
L
L
L
L
L
L
L
L
Y T
Y T
Y N
Y N
F D
N D
N D
F D
V D
F D
F D
230
D
E
E
E
E
G
E
D
G
D
D
V
V
V
V
G
A
A
L
L
A
M
L
L
L
L
I
V
V
V
V
V
V
E
E
E
E
E
E
E
E
D
E
E
F
V
F
V
V
V
V
V
V
F
V
D
D
D
E
K
E
E
E
E
E
E
D
D
D
D
D
D
D
D
D
D
D
G
G
G
G
G
G
G
G
G
G
G
F P
T P
T P
T P
T P
I P
T P
T P
T P
T P
T P
240
A
A
A
P
A
A
A
A
A
A
A
T
T
T
T
T
T
T
T
S
T
T
M
M
M
Q
M
E
E
T
T
T
T
S
S
S
S
S
A
A
S
S
A
S
Q
Q
Q
Q
Q
Q
Q
Q
Q
Q
Q
I
V
V
L
Q
M
M
M
M
A
M
A
A
A
A
A
G
G
A
A
A
A
K
K
K
K
K
K
K
K
K
K
K
D V
D V
D V
D V
D V
D V
D V
D V
D V
D V
D V
250
C
A
C
A
S
V
V
T
V
V
T
T
T
T
T
A
S
S
T
E
N
T
F
F
F
F
F
F
F
F
F
F
F
E
L
L
L
M
L
L
L
L
L
L
R
R
R
K
H
S
S
H
N
H
N
W
W
W
W
W
W
W
W
W
W
W
A
A
A
T
A
A
A
C
A
A
C
S
S
A
S
A
A
A
S
A
S
A
E P
E P
E P
E P
F P
E P
E P
E P
E P
E P
E P
260
E
E
E
E
F
E
E
E
E
K
E
M
H
H
H
M
M
M
M
M
L
M
D
D
D
D
D
E
E
D
D
D
D
H
H
H
D
T
E
E
E
D
I
E
R
R
R
R
R
R
R
R
R
R
R
K
K
K
K
K
K
K
K
K
K
K
A
R
R
Q
K
L
L
A
R
K
M
M
M
M
L
W
M
M
L
M
M
L
G L
G L
G L
L I
A L
G F
G F
G L
G M
G F
G L
270
M
M
M
V
I
W
W
A
V
V
T
L
L
L
I
A
I
I
M
L
I
V
M
L
L
G
A
F
F
I
V
T
I
M
M
M
I
L
V
L
V
V
V
I
M
M
M
L
I
L
L
L
T
L
L
A
G
G
G
P
S
S
S
S
T
S
human
mouse
cow
fruit fly
thread worm
potato
thale cress
yeast
yeast
bread mould
yeast
L
L
L
F
F
L
L
S
V
I
S
L V
L L
L L
L T
V A
A L
A L
L Y
L F
L T
L Y
280
P
P
P
V
V
L
L
L
A
A
L
L
L
L
I
V
Q
Q
L
L
L
L
V
T
V
S
L
A
A
S
S
S
S
V
V
V
V
I
A
A
V
V
M
I
T
A
A
V
V
V
V
W
Y
W
W
I
M
M
I
G
V
V
V
V
Y
V
K
K
K
K
K
R
R
K
K
K
K
R
R
R
R
R
R
R
K
R
R
K
H K
H K
H K
H K
M I
L R
L R
F K
Y K
F K
F K
290
W
W
W
W
W
W
W
W
W
W
W
S
S
S
S
S
S
S
A
A
T
A
V
V
V
S
F
V
V
S
W
P
G
L
L
L
L
T
L
L
I
L
I
I
K
K
K
K
K
K
K
K
K
K
K
S
S
S
S
S
S
S
S
S
N
T
R
R
R
R
Q
R
R
R
A
R
R
K
K
K
K
K
K
K
K
K
K
K
F A
F A
F A
F V
F L
F V
F V
F V
F V
F F
F V
300
V
V
V
F
F
L
L
F
Y
Y
F
R
R
R
V
K
D
D
N
D
Q
N
P
P
P
P
T
V
V
P
P
R
P
P
P
P
K
V
V
V
P
P
P
P
K
K
K
E
K
N
N
K
K
I
K
•
•
•
K
G
•
•
•
S
K
P
•
•
•
•
R
•
•
•
P
•
R
•
•
•
•
E
•
•
•
P
•
K
•
•
•
•
P
•
•
•
P
•
•
•
•
•
•
K
•
•
•
T
•
•
•
•
•
•
A
•
•
•
N
•
•
•
•
•
•
Q
•
•
•
L
•
•
•
•
•
•
•
•
•
•
A
•
•
•
•
•
•
•
•
•
•
L
•
•
•
•
•
•
•
•
•
•
P
•
•
•
•
•
•
•
•
•
•
Q
•
•
•
•
•
•
•
•
•
•
Q
•
•
•
•
•
•
•
•
•
•
R
•
•
•
•
•
•
•
•
•
•
K
•
•
•
•
•
•
•
•
•
•
S
•
•
•
•
•
•
P
•
•
•
A
•
•
•
•
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•
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•
A
•
•
K
K
K
K
K
K
K
K
K
Q
K
Figure S24.4 The conservative composition of cytochrome c in, from top: human, mouse, cow,
fruit fly, thread worm, potato, thale cress, yeast, bread mould and three species yeasts. The
numbers indicated are related to the sequence of the yeast Saccharomyces cerevisiae which
is the yeast species beneath bread mould. Identical residues are marked in blue; similar (or
‘conservative’) replacements in turquoise.
6
Cambridge Pre-U Biology
in databases. Chimpanzee cytochrome c is identical to that of humans. Yeast, Saccharomyces
cerevisiae, differs from humans in 44 of the 104 amino acids. This is still too many similarities
for the difference to be due to chance. Proteins that have a common ancestor, like the different
forms of cytochrome c, are called homologues and are described as homologous.
The structure of the protein ubiquitin, from the Latin ubique meaning ‘everywhere’, is
highly conserved, showing little variation in the sequence of amino acids throughout the
four eukaryote kingdoms (Figure S24.5).
D58 patch
7 - 12
20
42 - 49
51 54-55 57-60
69-73
Animalia
Homo sapiens
Caenorhabditis
Geodia
Nematoatostelia
M
M
M
M
Fungi
Saccharomyces
Neurospora
Encephalitozocn
M O I F V K T LT G K T I T L E V E S S D T I D N V K S K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L E V E S S D T I D N V K Q K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L E V E P S D S I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
Plantae
Arabidopsis
Chlamydomonas
Pyropia
M O I F V K T LT G K T I T L E V E S S D T I D N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L A D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L E V E S S D T I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L A D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L E V E S S D T I D N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
Entamoeba
Polysphondylium
Dictyostelium
Physarum
Monosigs
Trichomonas
Giardia
Monocercomonoides
Naegieria
Trypanosona
Leishnania
Bigelowielia
Phytophthora
Thalassicsira
Phaeodactyium
Paramecium
Plasmodium
Theileria
Cryptosporidium
M O I F V K T LT G K T I T L E V E P N D S I E A I K A K I Q E K E G I P P D Q Q R L I FA G K Q L E D E R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L E V E G S D T I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L E V E G S D N I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L E V E S S D T I E S V K T K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G H T I T L E V E P S D S I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K V I T L E V E P T D R I E D V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G N T L Q D Y S I Q K D S T L H LV L R L R G G
M O I F V K T LT G K T I T L E V E P T D T I N N I K A K I Q D K E G I P P D Q Q R L I F S G K Q L E D G R T L Q D Y S I Q K D AT L H LV L R L R G G
M O I F V K T LT G K T I T L E V E N A D T I E S V K Q K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L Q D Y N I Q K E AT L H LV L R L R G G
M O I F V K T LT G K T I T L E A E S N D T I E N V K S K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L E A E P S D T I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L A D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L E V D S S D T I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D E R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L D V E P S D T N T V K Q K I Q D K E G I P P D Q Q R L I FA G K Q L E D E R T L A D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L D V E P S D S I D N V K Q K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L D V E P S D T I D N V K T K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L D V E P S D T I D N V K T K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L D V E P S D T I D AV K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L D V E S S D T I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L E V E P S D T I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
M O I F V K T LT G K T I T L E V E P S D T I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
Protista
O
O
O
O
I
I
I
I
F
F
F
F
V
V
V
V
K
K
K
K
T
T
T
T
LT G K T I T L E V E P S D T I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
LT G K T I T L E V E A S D T I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
LT G K T I T L E V E A S D T I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
LT G K T I T L E V E P S D T I E N V K A K I Q D K E G I P P D Q Q R L I FA G K Q L E D G R T L S D Y N I Q K E S T L H LV L R L R G G
Figure S24.5 Conservation of the protein ubiquitin throughout the four eukaryote kingdoms.
Amino acid variations are highlighted in colour.
Protein synthesis
Like the genetic code, the machinery for protein synthesis is common to all cells, namely
ribosomes, transfer RNA and messenger RNA. Like cytochrome c and ubiquitin, ribosomal RNA
is highly conserved. Furthermore, the amino acids used by living cells are always L-amino acids.
Any given amino acid can exist in an L-form or a D-form (Figure S24.6). The L-form rotates
polarised light to the left (anticlockwise), and the D-form rotates it to the right. (L = laevorotatory,
D = dextrorotatory; laevo and dextro are Latin for left and right, respectively.) In any natural
mixture, such as in the ‘primeval soup’, there would have been equal numbers of the L- and
D-forms of each amino acid. In theory, either form could be used to make proteins. Presumably
by chance, the L-form was chosen. Alternatively, some selective advantage was gained early in
evolution for all species to contain only one form, again which one depending on chance.
Figure S24.6 L- and D-isomers of an amino acid, alanine (left and right, respectively).
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ATP
All cells require energy. Another ‘molecular fossil’ is ATP (see ‘The structure of DNA
and RNA’, in Chapter 6). All living cells use ATP as an energy carrier and therefore have
mechanisms for making ATP. NADP is another molecule found in all living cells that is
concerned with energy metabolism.
The oldest metabolic pathways concerned with energy metabolism are anaerobic, since they
evolved before the presence of oxygen in the Earth’s atmosphere. One of the oldest, which is found
in virtually all cells, is glycolysis, which drives the production of ATP using energy from sugars.
Protein degradation: the ubiquitin/proteasome mechanism
One of the oldest organelles, present in all eukaryotes, archaea and some bacteria, is the
proteasome (see Chapter S1). The core of the eukaryote proteasome, which contains the
proteases, is a 20S particle. Many archaea and some bacteria share homologues of the 20S
proteasome. The 20S proteasome also shares some features of the protein in bacteria that has
a similar protease function.
The mechanism by which the protein ubiquitin (Figure S24.5) targets proteins for
destruction is highly conserved. Multiple copies of ubiquitin are added to target proteins such
as key signalling proteins or those that may become harmful to the cell, for example damaged,
mutant or misfolded proteins. Recognition by the proteasome of these ‘ubiquinated’ proteins
results in breakdown to their constituent amino acids. The ubiquitin/proteasome mechanism
gives a high level of specificity and control in all cellular metabolic processes.
There are numerous other examples of highly conserved molecules and structures which
offer useful clues as to the relatedness of living organisms and point to common ancestry.
Examples mentioned in other chapters of the Coursebook include histones (see Chapter 4)
and basal bodies/centrioles (see Chapter 1).
New from old
The examples above show that, as mentioned before, nature is conservative and, where possible,
tends to use what is already available rather than reinvent. This gives us clues about the
relatedness of different organisms, because ancient bits of cell machinery and molecules are seen
in a wide variety of organisms. Sometimes molecules or structures are modified for different
functions, like making a new house from the bricks of an old house. Protein structure is a good
example. New proteins can evolve by recombining useful bits (domains) of pre-existing proteins.
Sometimes the genes for two or more proteins are joined to code for a larger protein complex. If,
say, a vertebrate protein shares domains with a prokaryote protein, this is evidence for an ancient
common ancestor. Figure S24.7 shows some examples of different proteins with shared domains.
Figure S24.7 Examples of different proteins with shared domains. The control of the cell cycle is
described in Chapter S5.
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Lateral gene transfer
Some caution must be exercised in making judgements about species relatedness on the basis
of common molecules and structures. It is believed that early in evolution, gene swapping
between different species (lateral gene transfer) was much more common than it is now. A
molecule or molecules shared between two very different species could be a result of lateral
gene transfer rather than indicating a close evolutionary relationship. Bacteria may have
gained proteasomes by such gene swapping, and on this basis do not necessarily share a
common ancestor with archaea and eukaryotes.
LUCA
To summarise, there is a great deal of evidence that points to life having evolved from
a single ancestor. This ancestor has been called the ‘last universal common ancestor’ or
LUCA for short. It may have lived in the deep oceans in hot alkaline hydrothermal vents.
Caution has to be shown when interpreting evidence because lateral gene transfers can
obscure relationships and much of what we believe is based on speculation. Some scientists,
including Woese, believe that LUCA was not a single organism, but a whole mix of different
evolutionary lines with high mutation rates and gene swapping, which eventually led to the
three current domains.
Question
24.1 I f an extraterrestrial life form had the same genetic code as life on Earth, what possible
explanations could be given?
S24.5 The origin of eukaryotes and the theory
of endosymbiosis
The origin of the eukaryotic cell is one of the most interesting and hotly debated current
issues in biology. It is believed that eukaryotes arose as a result of fusion between archaeans
and bacteria.
As Table S24.1 shows, when life began 3.8 billion years ago, there was no atmospheric
oxygen, so only anaerobic bacteria were able to exist. Then, 3.2 billion years ago,
photosynthetic bacteria began to produce oxygen as a by-product of photosynthesis.
Geological evidence indicates that oxygen was present at high enough levels 2.7 billion years
ago to support aerobic respiration. Eukaryotes are thought to have originated at this time by
a process known as endosymbiosis. ‘Endo’ means ‘inside’, and a ‘symbiont’ is an organism
that lives in a mutually beneficial relationship with another organism.
The theory of endosymbiosis proposes that an ancestral prokaryote engulfed a
bacterium capable of aerobic respiration. This engulfed bacterium eventually became the
mitochondrion inside the ancestral heterotrophic eukaryote (Figure S24.8). One lineage
of these ancestral eukaryotes in turn engulfed a photosynthetic prokaryote (a free-living
blue-green bacterium), which became the chloroplast of the now ancestral photosynthetic
eukaryote. Acquiring mitochondria greatly increased the energy available to the new cells,
and this may have been responsible for their greatly increased volume (eukaryotic cells can
be up to 15 000 times larger than prokaryotes).
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nuclear envelope
endoplasmic
reticulum
nucleus
infolding
of plasma
membrane
mitochondrion
cell with
nucleus and
endomembrane
system
cytoplasm
e
plastid
engulfing of
photosynthetic
prokaryote
DNA
Tim
Ancestral
photosynthetic
eukaryote
Ancestral
prokaryote
engulfing
of aerobic
heterotrophic
prokaryote
plasma
membrane
mitochondrion
Ancestral
heterotrophic
eukaryote
Figure S24.8 The theory of endosymbiosis. This diagram shows the origin of the eukaryotic cell,
mitochondria and chloroplasts.
Question
24.2 Suggest the evolutionary benefits of endosymbiosis for:
a the engulfed bacterium
b the host cell.
Evidence for the theory of endosymbiosis
Support for the theory of the origin of eukaryotes by endosymbiosis comes from many
ultrastructural and biochemical similarities of mitochondria and chloroplasts with living
bacteria. Both organelles are separated from the cell contents by two phospholipid bilayer
membranes (see Figures 1.22 and 1.29 in the Coursebook). The outer membrane of the
organelle is derived from infolding of the ancestral prokaryote cell surface membrane to
form a vesicle which surrounds the engulfed bacterium and the inner membrane is derived
from the bacterial cell surface membrane.
Strong evidence for the bacterial origin of mitochondria and chloroplasts comes from the
presence of their own circular loop of DNA, which actively codes for certain vital proteins.
However, some of their genes have moved to the nucleus of the cell, so that division of these
organelles cannot take place without input from the nucleus.
The endosymbiont theory is discussed under ‘Ultrastructure of an animal cell’ in Chapter
1 of the Coursebook.
Question
24.3 S
uggest how the eukaryotic cell may benefit from controlling the division of its
mitochondria and chloroplasts.
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When the eukaryote cell divides, its mitochondria and chloroplasts divide by binary fission,
identical to that of bacterial cells (Figure S24.9). This presents further evidence for the theory
of endosymbiosis because these organelles cannot be newly synthesised by the eukaryotic cell.
DNA replication
cell elongation
septum formation
cell separation
each daughter cell
receives one copy
of the chromosome
Figure S24.9 Binaryfissioninbacteria.
Mitochondria, chloroplasts and bacteria are all of a similar size, between 1 and 10 µm. They
are generally much smaller than eukaryotic cells, which are 10–100 µm, providing further
support for the origin of these eukaryotic organelles by endosymbiosis.
There is a close similarity between the biochemical processes taking place in mitochondria
and chloroplasts (aerobic respiration and photosynthesis) and those same processes taking
place in free-living bacteria. This points to the conservation of the original processes and
provides strong evidence for the theory of endosymbiosis.
QUesTion
QUesTion
24.4
akeatabletosummarisetheevidencefortheevolutionofmitochondriaand
M
chloroplastsbythetheoryofendosymbiosis.
S24.6 From single-celled to multicellular
organisms
The first multicellular organisms are thought to have evolved only about 1 billion years ago
(Table S24.1). It is a common assumption that evolution results in continuous improvement
over time. It is true that it tends to result in increasing complexity, but success and
complexity are not necessarily related. What we have to try to understand are the rules that
govern the evolution of systems. Complexity may be an inevitable product of these rules, in
which case multicellular organisms are not necessarily ‘superior’ to unicellular organisms.
There may even be a downside to complexity (compare human management structures,
which can evolve to become too complex). In fact, given that unicellular organisms are
capable of occupying more extreme habitats than multicellular organisms (with the possible
exception of humans) and are estimated to make up more than half the Earth’s biomass,
it is easy to argue that they are better adapted for long-term survival than multicellular
organisms. Arguments are complicated by the fact that we naturally think of ourselves as
superior to all other forms of life, and we are multicellular.
It has been argued that multicellular organisms gain by showing division of labour between
cells. The cells are specialised for particular functions. Thus multicellular organisms can exploit
resources more successfully. For example, a tree can acquire water and mineral nutrients from
roots in the soil, and energy from leaves well above ground level. Note that this involves the
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necessity for a long-distance transport system, but this in itself is not an advantage of being
multicellular, even though it involves division of labour and specialised cells such as those
found in xylem and phloem. Water and mineral ions are transported from roots to shoots
within the dead, lignified xylem tissue, and soluble organic substances made by photosynthesis
are transported from the leaves to the rest of the plant in the phloem tissue, made up of sieve
elements, companion cells, parenchyma and fibres (see Chapter 7).
Another example of division of labour is the digestive system of humans, which is made
up of four different regions: the mucosa, inner submucosa, muscularis externa and serosa
(see Chapter S22). The different tissues in these regions all play an important role in both
mechanical and chemical digestion. The epithelium of the mucosa in turn contains many
different types of specialised cell, such as the mucous, parietal and chief cells, all involved
in specific digestive functions (see Chapter S22). Does this division of labour, involving
specialised cells, enable humans to exploit a wider range of foods than, say, bacterial cells?
The ability to produce specialised cells also means that greater independence from the
environment can be achieved. In order to maintain stable conditions for cells to operate
in, multicellular organisms have complex homeostatic mechanisms. Increasing complexity
and cooperation of specialised cells has meant that the development of coordination
systems, such as hormones in plants and the endocrine and nervous systems in animals
(see Chapter 15), has become a necessity. This cooperation between specialised cells gives
the organism more capabilities than any single cell can have.
As the size of an organism increases, the surface area to volume ratio decreases –
reducing the effectiveness of diffusion in, for example, allowing gas exchange and uptake of
nutrients (see Figure S24.10). For single-celled organisms this imposes an upper limit on the
size of the cell, and therefore organism. For larger multicellular organisms, this relationship
has resulted in the need for transport systems to supply cells with essentials such as nutrients
and oxygen for respiration, as well as the removal of waste products such as carbon dioxide
and nitrogenous waste.
8
6
4
2
Surface area
(square cm)
24
96
216
384
volume
(cubic cm)
8
64
216
512
3.0
1.5
1.0
0.75
Surface area/
volume
Figure S24.10 Surface area to volume ratio decreases as the size of a single-celled or multicellular
organism increases.
Although discussing the relative benefits and disadvantages of being multicellular is thoughtprovoking, it may be another sterile exercise, like trying to define life. It is possible to argue
that since both single-celled and multicellular organisms survive and reproduce (the purpose
of life), both adequately fulfil their purpose. Natural selection has ensured that they do not
occupy the same ecological niches, so there is no competition.
Here are some points to consider when making judgements.
•
•
•
•
Who is the judge?
How do we measure success?
Total biomass
Range of habitats
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•
•
•
•
•
Speed of reproductive cycle
Ability to survive globally catastrophic events like meteorite impacts
Complexity
Intelligence/size of brain
Capabilities/versatility (note that some bacteria can live without oxygen)
Summary
■
■
■
■
■
■
■
Life is thought to have evolved from complex organic molecules that were created by
natural processes in the ‘primeval soup’ of the oceans.
There is strong evidence for a single origin of life. The universal genetic code is the
strongest single piece of evidence. The earliest common ancestor of all living things is
known as the last universal common ancestor (LUCA).
RNA may have been the first self-replicating molecule and enzyme.
There are three basic types of cell, giving rise to the three domains of life: bacteria,
archaea and eukaryota.
Archaeans are more closely related to eukaryotes than to bacteria.
Eukaryotes are thought to have evolved from archaeans about 2.7 billion years ago by a
process of endosymbiosis. Mitochondria and chloroplasts are descendants of bacteria
that were engulfed by a heterotrophic archaean.
Multicellular organisms are larger and more complex than unicellular organisms, but
this does not necessarily mean they are more fit for survival. Both have advantages and
disadvantages compared with each other.
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