Origin of Life

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Origin of Life
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• What is Life?
• Life resists a simple, one-sentence definition
  because it is associated with numerous emergent
  properties - properties that emerge as a result
  of interactions between components
• But, we can recognize life without defining it,
  by recognizing its properties
• Order
• Reproduction
• Growth and Development
• Energy Utilization
• Response to the Environment
• Homeostasis
• Evolutionary Adaptation

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• When did life arise on Earth?
• The Earth is thought to be approximately 4.6
  billion years old, but life is believed to have
  occurred approximately 4 billion years ago (bya)

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• What were the conditions like on Earth when life
  arose?
• Up to about 4 bya, asteroid impacts and volcanic
  eruptions resulted in the release of various
  gases that began to form an atmosphere
• It consisted mainly of CO2, with some nitrogen,
  water vapor and sulfur gases hydrogen quickly
  escaped into space
• CO2 in the atmosphere trapped solar radiation,
  making the Earths surface rather warm
• Earth was cool enough to form a crust, and water
  vapor condensed to form oceans
• Oceans in turn helped to dissolve CO2 from the
  atmosphere and deposit it into carbonate rocks on
  the seafloor

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• What were the conditions like on Earth when life
  arose? cont.
• Organic molecules were undoubtedly being formed
  on the Earths surface
• Lightening and ultraviolet radiation from the
  Sun acted on the atmosphere to forms small traces
  of many different gases, including ammonia (NH3),
  methane (CH4), carbon monoxide (CO) and ethane
• Also, cyanide (HCN) probably formed easily in
  the upper atmosphere, from solar radiation and
  then dissolved in raindrops

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What is the simplest living cell that one can
imagine?

• A universal minimal cell must contain the
  following
• Cell membrane
• Cytoplasm
• DNA and RNA
• Proteins
• Enzymes
• Ribozymes

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• Conditions that are necessary if life is to
  evolve from non-life
• Energy energy to form complex organic
  molecules
• Protection continued energy input will destroy
  complex organic molecules that form in reactions
  they must, therefore, be protected after they are
  formed
• Concentration Chemical reactions run better at
  high concentrations, but most reactions give
  rather low yields
• Catalysis All reactions inside our cells are
  aided by the necessary activity of enzymes

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Where did the basic building blocks come from?

• Miller-Urey Experiment
• A mixture of methane, ammonia, water vapor, and
  hydrogen was circulated through a liquid water
  solution and continuously sparked by a corona
  discharge elsewhere in the apparatus.
• After several days of exposure to sparking, the
  solution changed color.
• Subsequent analysis indicated that several amino
  and hydroxy acids had been produced by this
  simple procedure.

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• Additional experimental evidence
• Carl Sagan, and his colleagues made amino acids
  by long wavelength ultraviolet irradiation of a
  mixture of methane, ammonia, water, and H2S.
• It is quite remarkable that amino acids can be
  made so readily under simulated primitive
  conditions.
• However, when laboratory conditions become
  oxidizing, no amino acids are formed, suggesting
  that reducing conditions were necessary for
  prebiological organic synthesis.

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• Extraterrestrial delivery
• Comets and some meteorites are rich in amino
  acids, sugars, and fatty acids.
• However, the survival of organic matter during
  large impacts may be small.
• Interplanetary dust particles can have the same
  composition about 10,000 tons of dust falls to
  Earth every year.
• Hydrothermal Vents
• On the sea floor, where new ocean crust is
  forming, hot mineral-rich water is venting into
  the ocean many fresh mineral surfaces occur in
  these vents. 
• These surfaces catalyze the conversion of carbon
  dioxide and nitrogen gas to methane and ammonia,
  which are good ingredients from which to make the
  basic building blocks.

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Is it possible to simulate the production of
early organic polymers?

• The Dilemma Organic polymers such as proteins
  are synthesized by dehydration reactions
  (condensation) that remove hydrogen and hydroxyl
  (-OH) groups from the monomers, forming water as
  a by-product
• Also, enzymes within the cell are responsible
  for catalyzing these kinds of reactions

• Abiotic synthesis of polymers on the early Earth
  would have had to occur without the help of these
  enzymes
• Moreover, the monomers would have been present
  in dilute concentrations, making spontaneous
  condensation reactions rather unlikely

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• Potential Solutions
• Polymerization has been demonstrated in lab
  experiments when dilute solutions of organic
  monomers are dripped onto hot rocks
• The process appears to vaporize water and
  concentrate the monomers on the substrate
• On the early Earth, waves or rain may have
  splashed dilute solutions of organic monomers
  onto hot rocks and subsequently rinsed polymers
  back into the water
• Clay may have served as a substratum for the
  polymerization of monomers
• Various monomers bind to charged sites on clay
  particles clay may have concentrated various
  organic monomers present in dilute solutions
• At some of the binding sites, metal atoms, such
  as iron and zinc, function as catalysts
  facilitating the reactions that link monomers

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The formation of an early cell

• Review
• Cells exist in a watery world.
• A water molecule can behave as if charged
  because of its polar structure.
• This polar structure is the basis for an
  interesting relationship between water molecules
  and lipids

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• The lipids charged polar head (hydrophyllic)
  can form a weak bond with a water molecule, but
  the uncharged, nonpolar tail (hydrophobic)
  cannot.

• In a membrane, lipids are usually arranged in
  sheets made of two layers, with the lipids in
  each layer pointing in opposite directions.
• The water-loving heads contact water both inside
  and outside the cell, while the water- loathing
  tails stay tucked safely within the walls oily
  interior.
• Arranged this way, lipids make surprisingly good
  barriers.

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The Formation and Significance of Liposomes

• When Alex Bangham (circa 1960) extracted lipids
  from egg yolks and threw them into water, he
  found that the lipids would naturally organize
  themselves into double-layered bubbles roughly
  the size of a cell these bubbles became known as
  liposomes.
• This discovery led Bangham and Deamer to
  speculate that liposomes may have predated
  life.and may have provided lifes first shelter

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• Deamer took mixtures of fatty acids, glycerol,
  and phosphates and found that in the right
  concentrations they formed into lipids, and in
  turn, the lipids spontaneously assembled into
  liposomes.
• Question How could macromolecules have gotten
  inside them?
• Deamer extracted lipids from egg yolk, and mixed
  some of it into a small test tube of water
• He then extracted a few drops from the mixture
  and put them on a glass slide.
• To this he added a some fluorescently stained
  DNA
• The slide on a hot plate to simulate primordial
  tide pool after a few minutes, the lipids and
  DNA on the slide dried into a thin film.
• Deamer later added a few drops of water and put
  it under a fluorescent microscope
• He noticed the lipids swelled into bubbles some
  containing fluorescent DNA
• Provided proof that as the planes of lipids
  curled up into vesicles, the DNA that had been
  sandwiched in between them got trapped inside.

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• An Extraterrestrial Solution?
• Deamer also wondered whether outerspace could
  have supplied early membranes
• He examined a 200-pound meteorite that had
  fallen in Murchison, Australia, with the interest
  in determining whether there were any things in
  the meteor that form bilayers?
• Deamer ground a piece of the Murchison meteorite
  and extracted the organic carbon, made it into a
  slurry, dried it, and then added water again.
• He took the extract and put it on a slide and
  noticed that the whole slide began to fill with
  little vesicles.

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• Early Sources of Cellular Energy
• Meteorites are comprised of a group of chemicals
  named polycyclic aromatic hydrocarbons (PAHs)
  that are made of hexagons of carbon and hydrogen
  atoms linked in various arrangements.

• PAHs may have made life possible on early Earth
  because the give off electrons when exposed to
  light
• These electrons could have supplied energy to
  early cells.

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Question How did the early organic molecules and
other biological molecules become
self-replicating and self-regulating?
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The Central Dogma A Brief Review

• DNA is replicated when cells divide and when sex
  cells are formed.
• Genes are transcribed to produce single strands
  of RNA
• RNA (messenger RNA) provides the template from
  which protein synthesis is carried out.
• Strands of messenger RNA are translated to
  produce a sequence of amino acids (protein).

• Which came first, DNA, RNA or protein?

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The First Genetic Material The RNA World
Hypothesis

• The Idea Primitive RNA molecules may have
  assembled themselves randomly from building
  blocks in the primordial ooze and performed
  simple chemical chores.
• The Evidence In the early 1980's, Sidney Altman
  and Thomas Cech, discovered a kind of RNA - a
  ribozyme - that could edit out unnecessary parts
  of the message it carried before delivering it to
  the ribosome.
• Long before there were enzymes or DNA, RNA
  molecules may have been capable of
  self-replication
• But skeptics argued that an RNA's being able to
  cleave itself was all well and good, but what
  about all the other chemical reactions that But
  could RNA serve as the sole information molecule
  and enzyme of early cells?

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• RNA and Translation
• Harry Noller attempted to map ribosomes and
  figure out which of its proteins were responsible
  for translation of mRNA.
• He treated the ribosomes with protein-digesting
  enzymes to show that the rest of the ribosome
  couldn't translate mRNA.
• Despite these efforts, translation persisted it
  suggested that RNA was doing the translating.
• Noller's et al. Later identified a few crucial
  locations in ribosomal RNA that allow
  translation.

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RNA Speed Rate of Reaction

• RNA was also hypothesized to help catalyze the
  synthesis of new RNA (e.g., it was acting like a
  type of enzyme)

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RNA Speed Rate of Reaction cont.

• Interestingly, Charles Wilson was successful in
  getting RNA to speed a reaction that doesn't
  involve DNA or RNA
• Wilson found and cultivated ribozymes that could
  carry out alkylation a hundred times faster than
  the protein that's normally responsible for it in
  a series of experiments designed to mimic
  evolution.
• He began with billions of messenger RNAs, random
  sheets torn from volumes of DNA , and presented
  them with carbon and nitrogen atoms.
• Some were able to stick one of each atom
  together.

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RNA Speed Rate of Reaction cont.

• Although RNAs can't reproduce like animals or
  plants, given the right materials, they can make
  copies of themselves that are more or less
  identical.
• Surprisingly, it's the less-identical ones -
  those that have errors in them - that win over
  time.
• Subtle differences that may make an RNA better
  able to put carbon and nitrogen together - or
  render it completely useless, which is usually
  what happens.
• By selecting the RNAs that could speed
  alkylation and then letting them reproduce,
  generation after generation, Wilson eventually
  wound up with a group of RNAs that were really
  good at sticking the atoms together.

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Conclusions

• The rudiments of RNA-directed protein synthesis
  may have been the weak binding of specific amino
  acids to bases along RNA molecules, which
  functioned as templates holding a few amino acids
  together long enough for them to be linked.

• If RNA happened to synthesize a short
  polypeptide chain that in turn behaved as an
  enzyme helping the RNA molecule to replicate,
  then the early chemical dynamics included
  molecular cooperation and competition

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Conclusions

• The first steps toward replication and
  translation of genetic information may have been
  taken by molecular evolution even before RNA and
  polypeptides became packaged within membranes
• Once primitive genes and their products became
  confined to membrane enclosed compartments the
  units could have evolved collectively