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Exam 1
How to start the processes of life
Chemistry to biology transition
The origin of life – two approaches
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Define life here:
Molecular assembly that is alive if it continually regenerates itself, replicates
itself, and is capable of evolving
◦  Top-down strategy:
"  Look at present biology, extrapolate backwards
◦  Bottom-up strategy:
"  Collection of inanimate elements, molecules and minerals, figure out how
they came together to create living organisms
"  Assemble artificial cells from scratch using non-living organic and inorganic
materials
Miller-Urey experiments
Several variations this experiment have been performed:
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Used different types of energy source
◦  UV light to mimic the sun, as opposed to discharges to mimic lightning
! 
Used different types of original molecules available
◦  Different types of atmospheric chemistry
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Between all of these experiments:
◦  All of the amino acids used by life produced
"  including all five bases used in DNA and RNA
◦  Several complex sugar molecules and lipids also produced
How to transition from chemistry => biology?
! 
Life needs a self-replicating molecule
◦  Initially wasn’t DNA
"  too complex, also require RNA for
replication
◦  Discovered that RNA can catalyze
biochemical reactions (similar to
enzymes) and that they can at least
partially catalyze their own replication
◦  RNA is now thought to be the initial selfreplicating molecule
Spontaneous chemical reactions produce
short RNA strains
Free floating RNA bases
U
G
U
A
G
C
G
U
C
A
A
G
G
C
U
A
G
G
U
C
A
A
G
U
C
C
Base pairing rules build a “complementary”
strand of RNA
A
C
A
G
U
C
A
A
G
U
C
C
A
C
Base pairing rules build a “complementary”
strand of RNA
C
G
A
G
U
C
U
A
The complimentary strand
serves as a template for
copying the original RNA
“gene”
•  This process explains how RNA can self-replicate.
•  The self-replicating molecules may then have competed with each
other, evolved through some kind of ‘molecular’ natural selection.
Question: WHY?
•  Even though perhaps RNA naturally replicated itself - why would
the success of this process matter to nature???
•  All this eventually led to complex organisms and intelligence?
•  Why would it not just continue on at the low level of “curiosity
chemistry”?
! 
The first step in the evolution of
cellular life was RNA-based
catalysis and information
storage.
! 
RNA is able to store information
(similar to DNA) and catalyze
reactions (similar to enzymes)
◦  Enzyme is a substance produced
by living organism acting as
catalyst to bring about specific
biochemical reactions.
! 
May have supported cellular or
pre-cellular life.
Competitive RNA survival:
! 
Those RNA/protein molecules that may be concentrated in some form
of “bubble”, or “pre-cell” would benefit over others not in isolation.
! 
Molecular evolution would have been
much faster if confined in a closed
environment (similar to living cells)
◦  keep the molecules concentrated to
increase the rate of reactions
! 
Isolation from outside would have
facilitated natural selection among
RNA molecules
◦  Ex: RNA assembles a protein that is able to
speed up its replication.
◦  If the enzyme floats freely in the ocean it
can speed up the replication of a
competitor RNA, but if it is enclosed within
a cell it gives the cell RNA an advantage
over other cells.
Advances in the development of
artificial cells. Short RNA (red) is
adsorbed to a particle of clay and
encapsulated within a fatty acid
vesicle (green). The assembly of
RNA within the vesicle is
coordinated by the clay particle.
Rasmussen et al, Science 303 (2004)
963.
! 
Later on, the RNA world evolved into the DNA and protein
world of today.
◦  DNA (due to its greater chemical stability) took over the
role of data storage.
◦  Proteins (more flexible in catalysis) became the specialized
catalytic molecules.
! 
How did the RNA world got started?
Bottom-up hypothesis
! 
Experiments show that several types of
inorganic minerals can facilitate the selfassembly of complex organic molecules.
! 
The first molecules of RNA were
probably made on the surfaces of clays or
other minerals.
! 
Clays contain layers of molecules to
which organic molecules can adhere,
◦  The proximity makes them interact,
forming longer chains.
◦  Experiments – produced RNA chains
more than 100 bases in length.
! 
Lipid pre-cells can form on the surface of clay minerals that help assembly
RNA molecules, sometimes with RNA inside them.
! 
RNA world might have been born on early Earth with the catalytic
assistance of clay minerals.
Membrane formation
“Pre-cells” may have been common, can be easily seen in lab experiments:
1. 
2. 
Amino acids in cooling water form enclosed spherical structures
Lipids in water form closed “membranes”
Membrane formation
! 
If we cool a warm-water solution of amino acids, they can form bonds
among themselves to make an enclosed spherical structure.
Not alive, but with lifelike properties:
◦ 
◦ 
◦ 
◦ 
! 
Grow/shrink in size by absorbing/removing short chains of amino
acids
When they reach an unstable size they split into two daughter shells
They allow some molecules to cross in or out, block others
Store electrical energy on surface: could help chemical reactions
inside
The second type of membrane forms when we mix lipids with water.
Summary chemistry to biology transition scenario
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Life on Earth formed spontaneously from increasingly complex chemical
reactions.
! 
A combination of atmospheric chemistry, chemistry near deep sea vents,
and molecules from space made areas with abundant complex organic
molecules
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More complex molecules (short strands RNA) grew with the aid of clay
minerals. Some RNA molecules became capable of self-replication
! 
Membranes formed spontaneously and enclosed some of the complex
molecules, facilitating their interactions
! 
Natural selection changed the pre-cells increasing their complexity becoming living organisms
! 
DNA became the favoured hereditary molecule