Marks – Reading Quizzes and Assignments
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New marking scheme; grades in between
NCR/CR, CR/CR+
Reading Quizes will be multiple choice, solely to
make sure material is read
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Reading Quiz:
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Free points if you've done the reading
0 NCR, 3 NCR+, 2 CR, 6 CR+, 1 CR++
Assignments:
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0 NCR, 0 NCR+, 4 CR, 9 CR+, 1 CR++
Summary of last class: Stellar cycle
Summary of Last Class
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Stars form in turbulent gas clouds
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Dense regions begin to collapse, heat up, spin up
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Disks form
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Planet formation
If massive enough, nuclear burning begins in core
Very massive stars burn very fast; more modest stars
(the Sun) burn over billions of years; smaller stars
slower still
Smaller stars eject some of their mass leaving behind
a white dwarf
Larger stars blow up completely, ejecting almost all
heavy elements into gas clouds for next stage of star
formation
Feedback:
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Most unclear item from last week's readings?
What we're going to cover today
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Earths Biochemistry
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Building blocks for complex chemistry
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Amino acids -> proteins, nucleotides -> DNA
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Evolution
Early life on Earth
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Life <-> Atmosphere
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Chemical origin of life
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Protocells
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Miller-Urey
Earth's Biochemistry
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Abundance of Elements
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Building blocks of biochemistry
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Polymers
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Proteins
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Amino Acids
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DNA/RNA
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Nucleic Acids
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Reproduction
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Genes
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Expression of Genes
Abundance of Elements
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Hydrogen and Helium most
abundant in Universe (from
Big Bang)
Not most abundant on rocky
planets – evaporation
Heavy elements produced in
stars, and will follow similar
overall pattern
Systems that have material
processed by more stars will
have overall more heavy
elements compared to H, He.
Carbon
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Of the commonly occurring heavy
elements, Carbon can form the basis
for very complex molecules
Complex molecules can interact with
each other in more varied ways
More complex interactions -> more
pathways for life to begin
Silicon
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Plentiful
Similar to Carbon (can form
4 bonds)
Tends to react with oxygen
to form simple crystalline
structures - `silicates'
Rocks, Sand
Silicon good for making
computers; not so good for
making entire living
organisms.
Oxygen
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Plentiful
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Can only form two bonds
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VERY REACTIVE
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Makes stuff burn,
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rust...
Good for extracting energy in
organisms if controlled
Very little free oxygen on early
earth
For early organisms, Oxygen was
a poisonous pollutant
Water
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`Polar': + and – charges
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Molecules attracted to each other
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Water expands when freezes
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Very high boiling point
Very active:
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Other polar molecules attracted
to water/dissolve in it easily
(hydrophilic/water-soluble)
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Non-polar molecules repelled,
don't dissolve (hydrophobic)
Building Blocks of Life
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These machinery of life is made of polymers
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Built out of chains of simpler molecules
(monomers)
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`modular'
Three important polymers in Earth's biology:
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Proteins
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DNA
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Building blocks for everything
Repository of genetic information
RNA
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Takes information from DNA, builds proteins
Scale: Needle, Salt Grain (~5x mag)
Scale: Cells (~ 100x mag)
Paramecium
Human Egg
Grain of Salt
Amoeba
Human Hair
Scale: Cells (~ 1000x mag)
Human Egg
E. Coli
Bakers Yeast
Red Blood Cells
Scale: Cells + Viruses (~ 100,000x mag)
HIV
Tobacco Mosaic virus
E. Coli
Bacteriophage
DNA strand
Molecules (~ 1,000,000x mag)
Strand of Bacterial DNA
Glucose
Hemoglobin
Things are Very Different when
you're a Molecule
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Gravity is not so important
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Electrical, molecular forces are
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WATER
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Constantly jostled by water molecules
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Some parts of molecules attracted to water
(hydrophilic)
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Some parts repelled (hydrophobic)
Molecules behave like little machines that are
pushed around by electrical forces
Proteins
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Proteins are long strings of
amino acids
The strings fold into
complex shapes as they form
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Buffeted by water
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Bonds linking one part
of chain to the other
Proteins
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A protein's function is
determined by it's shape or
structure.
It's structure is determined by the
amino acids its made up of
Enzymes are proteins which
speed up certain reactions
Maltase breaks maltose down
into two glucose molecules
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Maltose fits into `active site'
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Lock-and-key
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E. Coli has ~1000 different
proteins
Amino Acids
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tyrosine
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alanine
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Building blocks of proteins
Twenty of them occur in Earth's
biology
Simple molecules: 13 – 27 atoms
Carbon, Hydrogen, Oxygen,
Nitrogen; two also have Sulfur
Chemically identical mirror images
of these compounds (right-handed
versions) do not occur in Earth's
biology
Typical protein might be built of
~100 amino acids
Amino Acids
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Amino acid consists of:
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NH3 group (amine)
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COOH group (acid)
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Connected by a Carbon which also
connects to a side chain
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It's the properties of the side chain
which differentiate the amino acids
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5 are hydrophobic, 7 hydrophilic, 8
are water-neutral
Amino Acids
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The COOH end of one amino acid links
up with the NH3 group of the next
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Bond called `peptide bond'
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Water released
``polypeptides''
Side chains are on alternate sides of the
chain
In principle, uncountably vast numbers of
proteins are possible
In practice, most organisms make/use
fewer than 10,000
Nucleic Acids
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(RNA only) (DNA only)
Proteins are encoded in a cell's
DNA, and built on a `scaffold' of
RNA.
RNA and DNA are both polymers
of nucleotides – molecules with
bases as shown here
Both DNA and RNA have an
`alphabet' of 4 bases
Nucleotides
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These bases attach to a sugar and
phosphate to form nucleotides
These nucleotides are the
monomers that make up DNA,
RNA
Sugar, phosphate makes up the
backbone of the structure, with the
base sticking out
DNA
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A strand of DNA contains a long
series of nucleotides, in a series
of genes (AAGCTC...)
Each gene is separated by a stop
signal
Contains all the information for
making all the proteins in the cell
DNA
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Proteins are made when an
enzyme walks long the DNA
strand, transcribing it into an
RNA strand
The RNA strand then gets
translated into a protein.
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Each 3 `letter' sequence gets
translated into a single
amino acid
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64 possible 3-letter
sequences; 20 amino acids
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Some acids have several
translations
DNA
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DNA strands come in
interwoven pairs.
Each pair is linked up at every
base
Each base with link up with
only one other base;
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(U/T) with A
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C with G
Both strands have
complementary information
Reproduction
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This `interwoven complementary
pair' makes replication fairly
straightforward
Enzymes can march along the
strand, separating it in two
Each strand can then be matched up
with the corresponding nucleotides,
and rebuild its second half
One twisted pair becomes two,
containing same information
Mutation and Evolution
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``The capacity to blunder slightly is
the real marvel of DNA. Without
this special attribute, we would still
be anaerobic bacteria, and there
would be no music.'' -- Lewis
Thomas, The Medusa and the Snail
Replication does not always occur
perfectly
DNA can be damaged, or `typos' can
occur during copying
Mutation of single cell usually has
no effect. But mutation in a sex cell
will cause mutation in offspring
Mutation and Evolution
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Some of these mutations have no
effect at all
Of those that do, the vast majority
are extremely damaging and kill
offspring - doesn't propagate
Some are fairly neutral (or have
good+bad consequences) and will
persist in future generations
Some are so positive that greatly
helps survivability/reproduction, and
soon propagates through much of
species
Diversity and Adaptability
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Having a wide range of neutral mutations is greatly
advantageous for species survivability
If new danger occurs (predator, disease), better
chance that some in the population will have chance
of survival
Danger of mono cultures
Origin of Life On Earth
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Earth's Formation
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Atmosphere
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Evolution of Atmosphere
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Life and the Atmosphere
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Chemical model
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Primordial Soup
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Miller-Urey
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Other Alternatives
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Polymerization
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Beginnings of life
Earth's Formation
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Condensed out of solar disk
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Small pieces (planetesimals) merging together
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Very hot – radioactive materials, collisions
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Ultraviolet radiation from sun (no protecting
ozone)
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Photodissociation
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Crust takes a long time to form
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Very geothermally active
Atmosphere
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Probably never had an atmosphere that formed
with the planet; planetsimals too small to capture
atmosphere
As Earth becomes massive enough to trap gases,
atmosphere forms as colliding objects (lateaccreting material) are vaporized
Volatile elements (lightest and easiest to
vaporize) can most easily diffuse away
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Hydrogen, carbon, nitrogen, oxygen
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Free hydrogen most easily evaporated
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Photodissociation breaks up molecules
Evolution of Atmosphere
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As hydrogen leaves, ozone can form
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Less hydrogen to suck up free oxygen into
water
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Cuts down ultraviolet light, photodissociation
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Atmosphere begins to stabilize
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Water vapor
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Carbon Dioxide
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Nitrogen
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Carbon Monoxide
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Very little Oxygen
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Even less Ozone
Evolution of Atmosphere: CO2
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Most atmospheric gases easily dissolved in water
Gases easily exchanged between oceans and
atmosphere
CO2 in water can form calcium carbonate (limestone,
chalk)
CO2 tends to get sucked out of the atmosphere
Can be released by volcanoes, eroding rocks, decay
of more complex chemicals, and life
Evolution of Atmosphere
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Nitrogen:
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Released from subsurface rock into
atmosphere through vents -- `outgassing'
Argon:
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Inert gas; does not willingly interact with
other elements
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Mostly comes from decay of radioactive
potassium on Earth's crust and from below
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`Outgassed'
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Of limited importance because of its inert
nature
Evolution of Atmosphere: Argon
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Inert gas; does not willingly interact with other
elements
Mostly comes from decay of radioactive
potassium on Earth's crust and from below
`Outgassed' through volcanic vents, etc.
Significant trace quantities in modern
atmosphere (~1%)
Of limited importance because of its inert nature
Origin of Life: Chemical model
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Very difficult for compounds essential for life
(amino or nucleic acids) to form in the presence
of free Oxygen
Oxygen is so reactive it immediately reduces any
forming organic compounds to carbon dioxide,
etc.
Earliest rocks (2.5 billion years or longer ago)
appear to have formed in low-Oxygen
environments.
If life had to form on Earth today, very difficult
to see how it would happen.
Origin of Life: Chemical model
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Absent Oxygen, possible for building blocks to
form spontaneously via chemical reactions
Energy is available:
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Geothermal (underwater volcanic vents)
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Solar (light, ultraviolet)
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Electrical (lightning)
All the elements are available in atmosphere, on
surface, in oceans
Primordial Soup
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Refers to the early mix of chemicals in the
atmosphere and oceans
Lots of dissolved raw ingredients in oceans,
atmosphere
Oceans more plausible:
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Higher density, easier for reactions to
occur
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Most creatures have abundances of
elements similar to oceans
Something needs to occur for reactions to occur
Miller-Urey Experiment
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1953 here in Chicago
Simulates oceans and
atmosphere of a young
Earth
Ammonia, methane,
hydrogen in atmosphere
After only a few days,
two amino acids and the
nucleotide bases have
formed!
Miller-Urey Experiment
Miller-Urey Experiment
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Atmosphere is not realistic
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Far too much hydrogen
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In 1950s, simpler theories of planet
formation; planet formed all at once, with
atmosphere from solar nebula
Almost certainly didn't happen that way
Far less Hydrogen in atmosphere than MillerUrey Experiment suggested
Miller-Urey Experiment
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Useless? No!
With that much hydrogen in atmosphere,
within only a few days formed a bunch of
important compounds
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With much less hydrogen its much harder
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Early Earth had millions of years
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Very suggestive that this is the right track, but
need to experimentally verify that still
feasible in lower-hydrogen atmosphere
Amino acids are also found in meteorites...
Other Alternatives
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Amino acids from space?
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Meteor impact w/ amino acids
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Causes crater
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Pools with water
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Breakdown of other organics provides
hydrogen
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Back to Miller-Urey
Or
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Whatever process produces amino acids in
molecular clouds/meteors also at play on
early Earth
Polymerization
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One way or another, can seem to form amino or
nucleic acids
Even if it requires a fairly rare event, over
hundreds of millions of years and an entire
planet, a lot of rare things can happen
How to form the polymers --- protein or
DNA/RNA?
In our biology, enzymes build proteins out of
amino acids or DNA/RNA out of nucleotides
But these enzymes are themselves proteins.
Polymerization
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No good answer to this question yet
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Best lead so far:
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Can also build `RNA-enzymes'
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If can get a bit of RNA to form from
nucleotides, can self-catalyze, building
more
Have to get the RNA to form in first place
Clay grain may allow polymerization the same
way dust grains in molecular clouds allow for
molecule formation
Polymerization
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May be `missing link'; some previous life form
that was based on something simpler and helped
form polymers
But if it existed, where did it go? Successful life
forms tend to stay
Blue-green algae has existed for 3 billion years
essentially unchanged
Perhaps couldn't survive oxygen in atmosphere
Beginnings of life
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Once polymers form, process speeds up
Proteins can act on other proteins, and on
RNA/DNA.
RNA can act on Proteins, RNA, DNA
New proteins, RNA, DNA constantly being
created, acted on, edited
As soon as some combination of molecules is
created that can self-replicate, there's an
explosion
`Chemical evolution' takes over
Chemical systems can get more and more
complicated
Beginnings of life
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Once polymers form, process speeds up
Proteins can act on other proteins, and on
RNA/DNA.
RNA can act on Proteins, RNA, DNA
New proteins, RNA, DNA constantly being
created, acted on, edited
As soon as some combination of molecules is
created that can self-replicate, there's an
explosion
`Chemical evolution' takes over
Chemical systems can get more and more
complicated
Life and the Atmosphere
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Rocks that formed 2.5 billion years ago did so in
very oxygen-poor conditions
Microscopic fossils -> life was certainly present
~3 billion years ago
For at least 500 million years, life existed
without significant oxygen in atmosphere
`blue-green algae' (cyanobacteria)
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Single-celled prokaroyotes
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Anaerobic bacteria
Single-handedly modified atmosphere by
`exhaling' enough Oxygen to allow Oxygenbreathers to begin to evolve
Life and the Atmosphere
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Life begins processing Nitrogen
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Some bacteria `fix' Nitrogen into soil
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Some plants release Nitrogen into
atmosphere
Newly formed Oxygen reacts with all Carbon
Monoxide in atmosphere to form CO2
Large amount of Oxygen, absence of Carbon
Monoxide in atmospheres of extra-solar planets
could be a sign of life.
Summary
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``Big Picture'' fairly clear; details murky
4.5 Gyr ago, Earth forms. Atmosphere contains
Carbon, Nitrogen, some small hydrogen, no
Oxygen; comes from impacts, outgassing
Primordial soup of organic compounds and
phosphates form over few hundred million years
from raw ingredients and abundant energy
sources
Continuing chemical reactions give amino acids,
nucleotides
Polymers of these form on surfaces of clays (?)
Polymers act on each other, creating complex
interacting systems; complexity grows.
Reading for Next Week
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Chapter 9 – evolution of intelligent life on earth
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Going from simple biochemistry to simple
life, then complex life
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Eukariotic life and cell functioning
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Reproduction and genes
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Multicellular life
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Development of intelligent life
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Future evolution and co-evolution