10.V: Life

ribosome origins life prebiotic chemistry big history ribozyme enzyme
The earliest living things were systems of organic molecules such as this ribosome.
Image by Harry Noller; click here for more information. 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

According to science, and contrary to virtually all creation mythology, life did not appear suddenly and fully formed.  It resulted from a gradual series of small chemical steps over the first few hundred-million years of Earth’s existence.  The Archean Eon is the geological term for the period of time, about 2.5 – 3.8 BYA, when the oldest rocks solidified and the earliest signs of life appeared.  Biologists use the term prebiotic, “before life”.       

Earth’s early oceans teemed with numerous elements and compounds that had been present in the proto-planetary accretion disk.  In the sea, they were free to move around and chemically react with each other at random.  During the Archean Eon, four special classes of macromolecules (large organic molecules) first formed.  These macromolecules are now the raw ingredients of life.  Each macromolecule is a polymer, a long chain of smaller units called monomers.  This table summarizes the four biological macromolecules and their monomer units.


Unit (monomer)

Macromolecule (long chain polymer)

Typical size (monomers per polymer)
Monosaccharide
1 to 3,000
Glycerol and fatty acid
1 to 4
Nucleotide
Nucleic acid
Millions
Amino acid
Protein
Hundreds
glucose ring prebiotic chemistry big history
The ring form of glucose 2

This diagram illustrates a ring form of glucose, the most important monosaccharide.  The unlabeled vertices of the hexagon represent carbon atoms, and there are some H’s not shown.  A carbohydrate has the generic formula C_{m}(H_{2}O)_n, which explains its name as carbon hydrated (with water added). 

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 complex structure seen here to the right of N.   The letter R in the formula is the chemical equivalent of a variable; it represents a large part of the molecule that has several variations. 

Amino acid prebiotic chemistry big history
Amino acid 3

Each amino acid is abbreviated by a single capital letter, so a protein can be “spelled” as a sequence of amino acids such as T-I-A-R-Q-F.   

A nucleotide has three parts:  a sugar ring called a ribose, at least one phosphate containing phosphorus and oxygen atoms, and a base containing nitrogen.  All of Earth’s life uses five bases, abbreviated as A, C, G, T, and U. 

Nucleotide nucleic acid DNA phosphate ribose nitrogenous base biochemistry big history
A nucleotide with base G. 4

The two forms of nucleic acid are Ribo-Nucleic Acid (RNA) and De-oxy-ribo-Nucleic Acid (DNA).  A nucleic acid is spelled as its sequence of bases, such as GGC-TAT-GAC- … .

The “double strand” of DNA.  Each strand is a long sequence of nucleotides.  This sequence reads “CAG-T” along the upper strand.  The two strands wrap around each other in a double helix shape as shown zoomed out at top. 5

Lipids are oily substances made primarily 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 heads facing away from each other toward the water and the tails protected from the water between the heads.  This structure is called a lipid bilayer, and it is the reason that fats and oils don’t mix with water.   

lipid bilayer biochemistry macromolecules big history
A lipid bilayer forms a water-tight membrane. 6

Some organic monomers are known to form in outer space 7 or in labs simulating early Earth conditions. 8 Only in living things, though, do they polymerize to create truly gigantic molecules capable of performing biological functions.  Working out the detailed steps of how macromolecules became abundant, large, and complex on Archean Earth is a major challenge on the cutting edge of science today. 

One known key factor was the absence of oxygen gas in the environment.  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.  How ironic that oxygen gas, our breath of life blanketing the planet today, would have been fatal to Earth’s first life.      

B. Abiogenesis:  From Chemistry to Biology

The term abiogenesis combines scientific fact with religious reverence to mean, “The creation of life from non-life.”  That life / non-life boundary is represented by the macromolecules we just introduced.

Every living thing performs a few functions that transcend ordinary chemistry.  First, it metabolizes.  That is, it takes matter and energy from the environment and organizes it into a specific form that we call “itself”.  The exchange of matter and energy with the environment must be performed in a controlled manner to keep the living thing in a steady state, technically called homeostasis.  A living thing can also reproduce.  The organism carries out all three of these life functions at the cellular level.  Within a cell, each macromolecule plays a specialty role.  These molecular roles may have started evolving independently of each other.  Like a band of superheroes, the macromolecules eventually joined forces to create the complete cell.

lipid bilayer cell membrane big history
A minimal lipid bilayer cell membrane 9

The lipids’ superpower is the protective vessel.  A 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, protecting the cell and maintaining homeostasis.   

Carbohydrates brought the superpower of, well, super power.  The bonds in a carbohydrate are effective at storing energy and giving it up again on demand.  Glucose is the primary source of energy for almost all life today except plants.  All living things make a macromolecule called ATP to store energy as well. 1 ATP is formed from a nucleotide, a sugar, and phosphates.

Proteins are the metabolic heavy lifters.  They break down molecules from the environment, harness their energy, and reassemble them into the cellular structure of the living thing.  Each cell is composed mostly of water and protein. 

Nucleic acids are the masters of reproduction, which is often called replication at the cellular level.  The base sequence of a DNA molecule, like ACG-TAC-TTA, may look like a code, and in fact that’s exactly what it is.  The code contains the information necessary to replicate a copy of itself.  The “miracle of life” is that some sequences of DNA code – genes – are also used to synthesize proteins! Take a deep breath; here’s how it works:

When a gene opens up and exposes itself to its surroundings, each exposed base chemically attracts a corresponding RNA base.  The sequence in our example would attract or “transcribe” the sequence ACG-UAC-UUA, because RNA uses U instead of T. 2 Next, each triplet of bases in the RNA attracts or “translates” into a certain amino acid (T-Y-L in this example).  Hundreds of amino acids formed this way will join end-to-end to create a protein.

To complete the life cycle, proteins catalyze (facilitate) nucleic acid functions – including the transcription-translation processes that create new proteins!  Catalysis is represented by the dashed arrows in the diagram below.

The cycle of life that occurs in every living cell on Earth today.   10

A quick glance at this diagram makes it clear that today’s life cycle has no beginning or end.  Earth’s first life must have done something a bit differently. Which came first, nucleic acids or proteins?  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. 11 Biochemistry requires catalysts, molecules that help ignite a chemical reaction.  Some RNAs, called ribozymes, are effective catalysts. This has led to the idea that early ribozymes could catalyze their own replication! 12 Theoretically, ribozymes then gradually started catalyzing the synthesis of proteins, which eventually became better catalysts than the RNA themselves.  The proteins, in turn, helped replicate DNA, which is better at storing self-replicating information than RNA.  Proteins and DNA gradually took over their specialty roles from RNA, which was ultimately relegated to its role as the go-between in the modern cycle of life.  Every cell today contains ribosomes, tiny structures containing little more than ribozymes and proteins.  They may offer us the closest possible glimpse to abiogenesis.   

The RNA World is a favored hypothesis today, but it is by no means proven.  Alternative explanations for the beginning of life involve proto viruses, 13 reproducing bubbles, 14 or catalytic clay! 15

C. The Earliest Life and the Universal Ancestor

Within half a billion years of Earth’s formation, roughly 4 billion years ago, 16 “life as we know it” existed on Earth.  Each unit of life was a microscopic cell, a microbe, drifting in the ocean. 

The earliest cells were smaller and simpler than the cells of your body.  Biologists call such primitive cells prokaryotes.  Today’s prokaryotes are divided into two kingdoms called bacteria and archaea. These two types look alike but have significant chemical differences. 3

prokaryote bacteria cell evolution big history
The prototypical prokaryote, about 0.001 millimeter long. 17

Each prokaryotic cell contains 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 constitutes the cell’s true DNA, or its 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 almost 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 small percentage of your genome was seeded by viruses in your ancestors’ DNA billions of years ago. 18

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 21 amino acids.  These specific universal similarities strongly suggest that life all descends from one abiogenetic episode, 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 planetary family tree!  We all share common ancestors.  The most recent one, before life diversified into bacteria and archaea, was the Last Universal Common Ancestor, LUCA.

LUCA was probably not a single cell but a colony in a state of horizontal gene transfer. 19 For prokaryotes, sex and reproduction are unrelated modes of genetic exchange.  We visualize genes passing vertically “down” a family tree.  Prokaryotes can also transfer DNA “horizontally” between sisters.  Horizontal gene transfer was common before cells had well-developed membranes.  It helped the community of LUCA life to inter-mix and evolve as a whole.  As cell structure and function improved, vertical lineage gradually overtook horizontal gene transfer and led to more isolated and diverse cells.

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. 20 These vents 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.  The environment was extreme, with temperatures and water chemistry that most forms of modern life could not survive.  However, several varieties of extremophile microbes (mostly archaea) thrive 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.  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 prokaryotes.  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 archaea. 21 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!    

A prokaryote reproduces asexually 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.” 22 If a cell is more durable in water, better able to detect food or heat, more resistant to viruses, or able to reproduce more rapidly than its neighbors, it will come to dominate the colony. 

If prokaryotes make copies of themselves, then why are they not all identical?  Even in an asexually reproductive species, there are two sources of diversity.  The first one is horizontal gene transfer, “unreproductive sex”.  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.  After millions and billions of generations, prokaryotes became mean, lean survival machines.      

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”). 23 Photosynthesis uses sunlight to create glucose. 

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. 24 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 protein channels and carbohydrate feelers. 25

Bacteriologists describe prokaryotes as “generalists.” 26 Each cell is self-contained.  It performs all of its own vital functions – growth, mobility, metabolism, repair, and reproduction.  Under moderate environmental stress, a bacteria population survives by sheer numbers:  a small bucket of seawater contains more bacteria than there are people on Earth. 27 They can reproduce in minutes or hours.  For these reasons, bacteria do not require much teamwork to survive most challenges.  When populations are dense, bacteria form colonies.  Sometimes colonies can grow to macroscopic size.  The oldest visible fossils in the world are mounds of mineralized biofilm (similar to dental plaque) formed by bacteria colonies 3.5 billion years ago.

An undeniable difference between chemistry and biology is the sense of “awareness” exhibited by living things.  It is most profound in animals, but we can already begin leading into that discussion with bacteria behavior.  Although nobody would argue that a bacterium is conscious, it is capable of sensing environmental conditions and moving toward nourishment and away from harm.  This process is regulated by special proteins. 28 In rare instances, bacteria can exhibit an astonishing form of multi-cellular, seemingly 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 compact structure called a fruiting body, resembling a miniature tree!  The fruiting body often forms on the external surface of a log or rock, where its spores may be picked up by the wind and carried to more favorable locations.  This is a perfect example of an emergent property, exhibited not by a bacterium (singular) but only by bacteria (plural). 

Even at the outset of life, then, we see that living things automatically behave in ways that favor their own survival.  Or, if they don’t, they die out and their suicidal behavior disappears with them.  Survivors always behave like they are fulfilling a “purpose” to survive.

Up to Chapter 10

Back to Section 10.IV: Sun, Earth, and Moon

Continue to Section 10.VI: Ch. 10 Summary

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. NEUROtiker (Public domain) via Wikimedia Commons
  3. Image by Benjah-bmm27 (Public domain) via Wikimedia Commons
  4. The nucleotide image is described as in the public domain at https://hubpages.com/health/Nucleotide-Supplements-is-There-any-Evidence-to-Support-Their-Use# (accessed 7/31/19). 
  5. Image by Thomas Shafee (CC BY 4.0) https://commons.wikimedia.org/wiki/File:DNA_chemical_structure_2.svg (accessed and saved 7/27/19).
  6. By Masur (public domain), via Wikimedia Commons, http://commons.wikimedia.org/wiki/File%3ABilayer_scheme.svg
  7. Max Bernstein, “Prebiotic materials from on and off the early Earth”, Philos Trans R Soc Lond B Biol Sci. 361(1474):1689-1702 (10/29/2006), https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664678/ (accessed and saved 7/07/19).
  8. This field of chemistry dates to the classic Miller-Urey experiment.  Stanley Miller, “A Production of Amino Acids under Possible Primitive Earth Conditions”, Science 117:3046, 528-529 (5/15/1953), https://science.sciencemag.org/content/117/3046/528 (accessed and saved 7/07/19).
  9. Image By Philcha (Public domain), via Wikimedia Commons (accessed 8/01/19)
  10. Diagram by Philippe Hupé (CC BY-SA 3.0, https://creativecommons.org/licenses/by-sa/3.0), https://commons.wikimedia.org/wiki/File:Central_dogma_of_molecular_biology.svg (accessed and saved 7/08/19), revised by Scot Fagerland.
  11. Alex Rich, “On the Problems of Evolution and Biochemical Information Transfer”, Horizons in Biochemistry, Michael Kasha and Bernard Pullman, eds., Academic Press (1962), 103-126, https://archive.org/stream/in.ernet.dli.2015.141670/2015.141670.Horizons-In-Biochemistry_djvu.txt (OCR copy with several errors, accessed and saved 7/07/19).
  12. Kelly Kruger et al., “Self-splicing RNA:  Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena”, Cell 31(1):147-157 (11/01/1982), https://doi.org/10.1016/0092-8674(82)90414-7 (accessed 7/07/19).
  13. See e.g. Anatoly D. Altstein, “The progene hypothesis:  the nucleoprotein world and how life began”, Biology Direct 10:67 (11/26/2015), https://www.ncbi.nlm.nih.gov/pubmed/26612610 (accessed and saved 7/10/19).
  14. David Segré et al., “The lipid world”, Orig Life Evol Biosph 31(1-2):119-45 (Feb – Apr 2001), https://www.ncbi.nlm.nih.gov/pubmed/11296516 (accessed and saved 7/27/19).
  15. Alexander G. Cairns-Smith, “The clay-making machine”, Seven Clues to the Origin of Life, Cambridge University Press (Cambridge, 1985), pp. 80 – 86, https://www.krusch.com/books/evolution/Seven_Clues_Origin_Life.pdf  (accessed and saved 7/27/19).
  16. M.S. Dodd et al., “Evidence for early life in Earth’s oldest hydrothermal vent precipitates”, Nature 543(7643):60-64, http://eprints.whiterose.ac.uk/112179/
  17. Image by Mariana Ruiz Villarreal aka LadyOfHats, placed into the public domain via Wikimedia Commons, https://commons.wikimedia.org/wiki/File:Average_prokaryote_cell-_en.svg (accessed and saved 8/01/19).
  18. Robert Belshaw et al., “Long-term reinfection of the human genome by endogenous retroviruses”, PNAS 101(14):4894-9 (4/06/2004), https://www.ncbi.nlm.nih.gov/pmc/articles/PMC387345/ (accessed and saved 7/14/19).
  19. Carl Woese, “The Universal Ancestor,” PNAS 95(12):6854-9 (6/09/1998), http://www.pnas.org/content/95/12/6854.long, accessed and saved 7/14/19.
  20. Nick Lane, John F. Allen, and William 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 and saved 7/14/19.
  21. William Whitman et al, “Prokaryotes:  The unseen majority,” Proc. Natl. Acad. Sci. USA Vol. 95, pp. 6578–6583, June 1998, https://www.pnas.org/content/95/12/6578 , accessed and saved 7/14/19.
  22. Herbert Spencer, Principles of Biology, 1864, Vol. 1, p. 444.
  23. Stanley Awramik, “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
  24. Armen Y. Mulkidjanian et al, “Co-evolution of primordial membranes and membrane proteins,” Trends in Biochemical Sciences, 34(4): 206 – 215 (3/18/2009), http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752816/ , accessed and saved 7/14/19.
  25. Image by Mariana Ruiz Villarreal, placed into public domain via Wikimedia Commons , https://commons.wikimedia.org/wiki/File:Cell_membrane_detailed_diagram_en.svg (accessed and saved 5/23/15).
  26. Gerhart & Kirschner, Cells, Embryos, and Evolution , Blackwell Science (1997), p. 8.
  27. J.E. Hobbie, R.J. Daley, and S. Jasper, “Use of nuclepore filters for counting bacteria by fluorescence microscopy”, Appl Environ Microbiol. 33(5):1225-1228 (May, 1977), https://www.ncbi.nlm.nih.gov/pmc/articles/PMC170856 (accessed and saved 7/14/19).
  28. Pamela Christine Lyon, “The cognitive cell:  Bacterial behavior reconsidered”, Frontiers in Microbiology 6(264):1-18 (4/14/2015), https://www.ncbi.nlm.nih.gov/pubmed/25926819 (accessed and saved 7/14/19).
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