10.V: Life

ribosome origins life prebiotic chemistry big history ribozyme enzyme

Life began with organic molecules such as this ribosome. 1

A. Pre-Biotic Chemistry:  The Ingredients of Life

B. Abiogenesis:  From Chemistry to Biology

C. The Earliest Life and the Universal Ancestor

D.  Two Billion Years of Bacteria

E.  Citations

A. Prebiotic Chemistry: The Ingredients of life

Life didn’t just suddenly happen one day. It resulted from a gradual series of small chemical steps over the first few hundred-million years of Earth’s existence. The period before life is sometimes called Earth’s pre-biotic past. The term Archaean eon is commonly used to refer to the period of time, about 3.8 – 2.5 billion years ago, when the oldest rocks solidified and the earliest signs of life appeared.

Earth’s early oceans teemed with many elements and compounds that had been present in the proto-planetary accretion disk.  In the oceans, they were free to move around and chemically react with each other at random.  The ocean was like one large chemistry experiment.  Over those first hundreds of millions of years, many of the key chemical ingredients of life achieved critical density in at least one part of the ocean.  Some of the chemicals have names that you are probably familiar with through a basic understanding of nutrition:  carbohydrates, lipids, nucleotides, and amino acids.  These are the basic macromolecules of organic chemistry.

glucose ring prebiotic chemistry big history

Glucose, one of the most important carbohydrates

A carbohydrate has the generic formula C_{m}(H_{2}O)_n, which explains why it is named as carbon hydrated (“with water added”).    A vital example of a carbohydrate is glucose or “blood sugar,” formed from six carbons.  The diagram illustrates a ring form of glucose.  The vertices of the hexagon that are unlabeled are understood to be carbon atoms. 2

An amino acid has the structure shown below.  It is derived from ammonia, NH3, by removing one hydrogen atom and replacing it with the more complicated part seen here.   Remember that ammonia was very common in the primordial atmosphere.  The letter R in the formula is the chemical equivalent of a variable.  It could represent any atom or molecule that could form a single bond with that particular carbon.  Thus, the variety of possible amino acids is endless.  As it turns out, only about 20 particular amino acids are found in life on Earth.  This suggests that life did not originate in very many separate incidents. 3

Amino acid prebiotic chemistry big history

Amino acid

Nucleotide nucleic acid DNA phosphate ribose nitrogenous base biochemistry big history

An example of a nucleotide. There are many varieties.

A nucleotide comes in three parts:  a sugar ring called a ribose, a base containing nitrogen, and at least one phosphate, containing phosphorus and oxygen atoms. 4

Lipids are the most loosely defined class of macromolecules.  They are defined by the property that they don’t dissolve in water.  Common examples of lipids are fats, oils, cholesterol, steroids, and vitamins.  They are made primarily of of carbon, hydrogen, and oxygen.  Some contain phosphorus or nitrogen as well.  Structurally, most lipid molecules have a “head” and at least one “tail.”  When placed in water, they line up in two rows like a double phalanx, with the hydrophilic heads facing away from each other toward the water, and the hydrophobic tails protected from the water between the heads.  This structure is called a lipid bilayer, and is the reason that these lipids don’t dissolve in water.

lipid bilayer biochemistry macromolecules big history

A lipid bilayer forms a water-tight membrane 5

It is indisputable that macromolecules appeared early in Earth’s history.  Working out the detailed steps of their evolution is a major challenge on the cutting edge of science today.  The lack of oxygen was a key factor.  If we tried synthesizing organic molecules in the open air today, the chemical constituents would be oxidized, changed or destroyed by the air itself, before we could finish our experiment.  It’s a well-known fact that life can only come from life in today’s world.  In one of the strangest twists of fate of all time, life required a lack of oxygen to get started, but now requires an oxygen-rich environment to survive.

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B. Abiogenesis:  From Chemistry to Biology

The four macromolecules, like a team of superheroes, eventually banded together their unique powers in order to create life.  The term abiogenesis is a great word combining scientific fact with religious reverence to say, “The creation of life from non-life.”

lipid bilayer cell membrane big historyThe lipids provided the most obvious superpower – a protective vessel.  The lipid bilayer can curve and form a closed surface.  That creates an enclosed cell structure sheltered from the outside environment.  The lipid bilayer becomes the cell membrane, helping to keep the cell protected and regulated inside. 6

The carbohydrate’s superpower is the ability to provide energy.  Remember that chemical bonds store energy.  The bonds in a carbohydrate, or sugar, are especially effective at storing energy and giving it up again on demand.  The most universally important carbohydrate is glucose, or what we now call blood sugar.  It is the primary source of energy for almost all life except plants.  A macromolecule called adenosine triphosphate, ATP, is made by all living things to store biological energy.  ATP is formed from a nucleotide, a sugar, and phosphates.

Amino acids and nucleotides can form long chains called polymers.  When amino acids are polymerized, they form a protein.  Long chains of nucleotides form nucleic acids called RiboNucleic Acid (RNA) and DeoxyriboNucleic Acid (DNA).  Proteins and nucleic acids have the most amazing superpowers of them all.  Together, they perform the two basic functions of life:  reproduction (often called replication at the cellular level) and metabolism.  Metabolism is essentially “eating” – keeping the cell or body alive with food and energy from the environment.  In today’s world, to manage cell reproduction and metabolism, nucleic acids and proteins polymerize each other in a cycle.  DNA makes RNA, which makes proteins, which help make more DNA and RNA.  Nobody knows exactly how that cycle got started.  This question is in fact the great unanswered chicken-and-egg problem lying at the heart of abiogenesis science.

The RNA World Hypothesis proposes that small RNA molecules appeared first and were able to perform a mediocre job of both replication and metabolism.  In modern life, polymerization requires catalysts, molecules that help ignite a chemical reaction.  Some RNA’s, called ribozymes, are effective catalysts.  This has led to the idea that early ribozymes could catalyze their own replication!  These early RNA’s got a gradual start on catalyzing the synthesis of proteins, which eventually became better catalysts than the RNA themselves.  The proteins, in turn, helped create DNA, which became better at storing self-replicating information than RNA.  Proteins and DNA gradually took over their specialty roles from RNA, which then became relegated to its go-between in the modern cycle of life.  It is difficult to form or replicate ribozymes in laboratories.  However, it is not impossible.  The RNA World Hypothesis holds a lot of promise and is being actively studied at this time.

A minority hypothesis, metabolism-first, proposes that organic compounds such as amino acids were first synthesized with non-organic catalysts, such as metals and clay.  In this world system, nucleotides would have come later, with the assistance of amino acids.  The metabolism-first hypothesis is older and predates the discovery of ribozymes.  Obviously, the question of exactly how life began is far from resolved, shrouded in complex chemistry and long-lost environmental conditions.  Along with the big bang, it is another one of the great frontier questions of science.  Since it is such an important and unresolved question, it is also the subject of endless religious speculation.

C. The Earliest Life and the Universal Ancestor

What we do know is that within half a billion years of Earth’s formation, roughly 4 billion years ago, “life as we know it” existed on Earth, formed from the macromolecules described above.  Each unit of life was a microscopic cell, a microbe, drifting in the ocean.  Before cells, life was too amorphous to define.  In a primordial soup type of environment, different types of molecules would depend on each other for energy, parts, and help with reproduction.  By itself, each molecule was not “alive.”  It would be impossible to trace lineage in such an environment.  Most biologists, then, define the beginning of life with the first self-sustaining, self-reproducing cells.

prokaryote bacteria cell evolution big history

Structure of the earliest cells: Your ancestors 4 billion years ago resembled this prototypical prokaryote, about 0.001 millimeter long. 7

What did the first living thing look like?  The earliest cells are believed to have been very similar to modern bacteria.  Biologists call small, simple cells prokaryotes.  Each prokaryotic cell can contain DNA in three forms.  It has a large, single, crumpled up ring of DNA called a nucleoid, many smaller rings called plasmids, and a random assortment of viruses.  The nucleoid is considered the cell’s true DNA, or its genes / genome, because it synthesizes the proteins that make up the cell.  Plasmids and viruses are free-riders.  They can only survive inside the cell, but they reproduce on their own cycle and do not contribute proteins to the cell structure.  Some plasmids and viruses are helpful to a host, some are neutral, and some are harmful.  Cells have had a love / hate relationship with viruses since life began.  Some viruses are effective at splicing themselves into a host cell’s nucleoid.  In that way, they actually become part of the genome of the host and its descendants, permanently into the future.  A large portion of your genome was seeded by viruses in your ancestors’ genes billions of years ago

Some fundamental biological characteristics are shared by every living cell in the world today.  For instance, all living things have the same DNA / RNA chemistry and utilize the same 20 amino acids.  These specific universal similarities strongly suggest that life all descends from one abiogenetic event, not several independent ones.  That is, all life on Earth today – you, your cat, the vegetables you ate for dinner, the cotton you’re wearing, and your germs – is one gigantic family tree!  We all share common ancestors.  The most recent one, before life diversified into separate lines of descent, was the Last Universal Common Ancestor, LUCA.

The traditional viewpoint was that one special bacterium played the role of LUCA.  That is, if we had omniscient knowledge of all living things’ family trees and traced them back three or four billion years, we would find that they all converge at one special greatest-grandfather cell.  Current research indicates that LUCA was probably more like a bacteria colony. 8 Before cell membranes were well-developed, genes were more readily mobile.  Cells swapped DNA with each other “horizontally,” as distinguished from “vertical” gene transfer down the family tree from parent to child.  In the Archaean Eon, the whole community of life was constantly inter-mixing and evolving as a whole.  As cellular reproduction became faster and more reliable, vertical lineage gradually overtook horizontal gene transfer and defined the “descent” of life as understood by evolutionary theory.

Most certainly, the LUCA community was localized.  Organic material was too dilute to turn the whole ocean into a living sea.  A current leading hypothesis suggests that cells first formed near hydrothermal vents on the ocean floor. 9 They were a unique environment on early Earth, fissures in the Earth’s crust where hot gases came up from below.  The vents provided geothermal energy, microscopic pores for physical structure, rich chemistry, and a chemical “proton gradient” similar to what cells use to create ATP.  In other ways, the environment was extreme, with temperatures and water chemistry that most forms of modern life could not survive.  However, several varieties of extremophile microbes can be found thriving near hydrothermal vents today, even in boiling water and super salty, acidic, or alkaline conditions without oxygen.  Extremophiles display an incredible amount of chemical diversity, suggesting that they have been evolving for an exceptionally long time.  Ironically, the harsh physical conditions of ocean vents may have been necessary for microbes to establish themselves, as it was the only environment harsh enough to kill antibiotics! 10 This combination of factors makes extremophile microbes leading candidates for the living cells most resembling LUCA.

D. Two Billion Years of Bacteria

For biology’s first two billion years, half of its history, life was no more than humble microbes. In many ways, Earth is a bacteria’s world. They were the first true life forms on the planet and are likely to be the last. By far, most of the planet’s biomass is bacteria and similar microbes. 11 Within your body, bacteria outnumber your own cells. If you could trace all of your ancestors, you would find that the vast majority of them were germs. Think about that the next time you sneeze!

Bacteria are not the only major form of microbe.  A very recent discovery is the entire biological domain of archaea.  These microbes are structurally similar to bacteria, with important chemical differences.  We now understand that archaea not only are an essential part of the biosphere, but played a vital role in our evolution, maybe even as our direct ancestors.

Prokaryotes reproduce asexually.  A bacteria or archaea reproduces by making a genetic copy of itself.  In a world of finite resources, then, it should be obvious that the microbes that survive and reproduce most readily will quickly outnumber the less blessed.  This is one of the oldest characterizations of evolution:  “survival of the fittest.” 12 If a cell is more durable in the water, better able to detect food or heat, more resistant to viruses, or able to reproduce more rapidly than its neighbors, it will become more predominant in the colony.  Again, this comes back to the theme of complexity and stability.  Stable cells survive in the long run; unstable cells do not.  As generations go by, each successive improvement in survival or reproduction skills makes the cell progressively more complex.  After millions and billions of generations, they become mean, lean survival machines.

If prokaryotes make copies of themselves, then why are they not all identical?  Even in an asexual species, there are two sources of diversity.  The first one is genetic mixing, in the form of horizontal gene transfer.  The second source of diversity is mutations:  errors in reproduction.  A DNA sequence might be replicated with a simple “typo” so the copy is not exactly like the original.  Most mutations are harmful or neutral.  A lucky few mutations are positive.

During the first one or two billion years of evolution, microbes perfected their basic structure and chemistry.  A crucial outcome of this period was the standardization of pathways, the multi-step chemical processes that cells use for life functions.  The earliest microbes metabolized by anaerobic respiration, which burns sugar in the absence of oxygen.  The first step in anaerobic respiration is glycolysis, the breakdown of glucose to form ATP.  Glycolysis is still the first chemical step of aerobic respiration, which the cells of your body use to get energy from food.  Another fundamental pathway, photosynthesis, evolved at least 3.5 billion years ago in a microbe like cyanobacteria (“blue-green algae”). 13 Photosynthesis uses sunlight to create glucose.  This is how plants metabolize.

Another key development of life’s first billion years was the development of the cell membrane.  From its origins as a mere lipid coating, the membrane evolved into a highly active part of the cell’s anatomy.  The membrane was embedded with complex proteins that regulated the flow of specific particles in and out of the cell.  As time went on, the lipid bilayer became increasingly impermeable and energy efficient. 14 Some membrane proteins bonded to carbohydrate chains.  These were something like feelers, allowing the cell to communicate with its environment.

cell membrane protein channel big history

A highly evolved cell membrane with embedded proteins and carbohydrate chains. The protein channel is shown in an “open” position that would allow particles to pass through. The carbohydrate chains are sensors, granting the cell the means to sense its immediate environment. 15

Bacteriologists describe prokaryotes as “slowly evolving generalists.” 16 A common core of genes across bacterial species suggests that they evolved vital life functions billions of years ago, and are still substantially similar to their archaean ancestors. 17 Each bacterium is self-contained.  It performs all of its own vital functions – growth, mobility, metabolism, repair, reproduction.  Under moderate environmental stress, a bacteria population survives by sheer numbers:  a milliliter of water can contain more bacteria than there are people on Earth.  They can also reproduce in minutes or hours.  For these reasons, bacteria do not require much teamwork to survive most challenges.

In large numbers, bacteria do form colonies.  Sometimes colonies can grow to macroscopic size.  Stromatolites are formed by mounds of cyanobacteria that secrete a biofilm (similar to dental plaque).  Particles of mineral get trapped in the film and eventually form sedimentary mounds.  The oldest fossils in the world are stromatolites formed by bacteria 3.5 billion years ago.

In rare instances, bacteria can exhibit an amazing form of multi-cellular, almost “social” cooperation.  A myxobacteria colony organizes itself into a radial star-shaped formation that spreads out in search of food.  When food is scarce, the myxobacteria return to the center of the colony and form themselves into a structure called a fruiting body, resembling a miniature tree!  The fruiting body often forms on the external surface of a log or rock, where the spores may be picked up by the wind and carried to more favorable locations.  This kind of life cycle is so well organized that it appears intelligent, yet it occurs naturally in organisms as simple as bacteria.  It is a striking example of an emergent property, a property of many cells that could not be predicted by studying one cell. 18

myxobacteria swarm cell colony emergent property

Myxobacteria swarming in a “socially organized” manner when food is plentiful …

 

myxobacteria swarm cell colony emergent property

… and resting in “fruiting body” formation when food is scarce.

 

E.  Citations

  1. This incredible imagery was accomplished in Harry Noller’s lab at UCSC. Prof. Noller was kind enough to grant me permission for use, along with this description:  “It is a representation of a functional complex of the 70S ribosome from Thermus thermophilus” (appropriately enough, one of the most primitive life-forms) “that we published in 2001 (Yusupov et al., Science) containing an mRNA and three tRNAs.  The 16S rRNA is cyan, 23S rRNA gray, 5S rRNA gray-blue, small subunit proteins dark blue, large subunit proteins magenta, tRNAs orange and red, and mRNA (barely visible center left) green.” 
  2. Image By NEUROtiker (Public domain) via Wikimedia Commons, http://commons.wikimedia.org/wiki/File%3AAlpha-D-Glucopyranose.svg
  3. Amino acid image By Benjah-bmm27 (Public domain) via Wikimedia Commons, http://commons.wikimedia.org/wiki/File%3AAlpha-amino-acid-2D-flat.png (accessed 5/16/15)
  4. Nucleotide image described here as public domain.
  5. By Masur (public domain), via Wikimedia Commons, http://commons.wikimedia.org/wiki/File%3ABilayer_scheme.svg
  6. Image By Philcha (Public domain), via Wikimedia Commons
  7. Image by Mariana Ruiz Villarreal, placed into the public domain via Wikimedia Commons
  8. Woese, Carl, “The Universal Ancestor,” Proceedings of the National Academy of Science, PNAS June 9, 1998 vol. 95 no. 12 6854-6859, http://www.pnas.org/content/95/12/6854.long, accessed 9/02/13
  9. Lane, Allen, and Martin, “How did LUCA make a living?  Chemiosmosis in the beginning of life,” BioEssays 32:271-280 (2010), http://www.molevol.de/publications/188.pdf, accessed 8/25/13
  10. Gupta R.S. (2000). “The natural evolutionary relationships among prokaryotes”. Crit. Rev. Microbiol 26 (2): 111–131. doi:10.1080/10408410091154219PMID 10890353.
  11. Whitman et al, “Prokaryotes: The unseen majority,” Proc. Natl. Acad. Sci. USA Vol. 95, pp. 6578–6583, June 1998, http://www.pnas.org/content/95/12/6578.full.pdf, accessed 9/03/13
  12. Spencer, Herbert, Principles of Biology, 1864, Vol. 1, p. 444.
  13. Awramik, Stanley, “The oldest records of photosynthesis,” Photosynthesis Research 33: 75 – 89, 1992,  http://www.geol.ucsb.edu/faculty/awramik/pubs/AWRA9275.pdf, accessed 9/03/13
  14. Mulkidjanian et al, “Co-evolution of primordial membranes and membrane proteins,” Trends in Biochemical Sciences, April, 2009, 34(4): 206 – 215, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752816/, accessed 9/03/13
  15. Image by Mariana Ruiz Villarreal, placed into public domain via Wikimedia Commons
  16. Gerhart & Kirschner, Cells, Embryos, and Evolution (1997), Blackwell Science, p. 8
  17. Koonin et al, “Sequence similarity analysis of Escherichia coli proteins:  functional and evolutionary implications,” Proceedings of the National Academy of Sciences of the USA, 1995, 92(25): 11921-5, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC40515/pdf/pnas01503-0609.pdf, accessed 9/05/13
  18. Myxobacteria sketches: Thaxter, Roland, “On the Myxobacteriaceae, a New Order of Schizomycetes”, Bot. Gaz. 17(12):389-406 (1892) (public domain), http://www.jstor.org/stable/2464109?seq=13#page_scan_tab_contents (accessed 6/27/15)
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