Origin of Life

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

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)

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 Earth’s 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

What were the conditions like on Earth when life arose? cont.

• Organic molecules were undoubtedly being formed on the Earth’s 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

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

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

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.

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.

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.

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

•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

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

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

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

• The lipid’s 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 wall’s oily interior. • Arranged this way, lipids make surprisingly good barriers.

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 life’s first shelter

• 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.

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.

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.

QuestionHow did the early organic molecules and other biological molecules become self-replicating and self-regulating?

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?

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?

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.

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)

• 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.

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.

RNA Speed Rate of Reaction cont.

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

• 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

Conclusions