Background Information 4 – Molecules to Life

Water, the Elixir of Life

Ocean_park_wikiWater is truly a miraculous liquid that allows and facilitates life. Most other molecules in the same low molecular weight range are gases at atmospheric pressures and temperatures. Water remains in the liquid state over a wide range of temperatures and pressures due to hydrogen bonding. Hydrogen bonding is where the positively charged hydrogen atoms in one molecule are bonded to the electrons of atoms in other molecules. Water, with two positive hydrogen atoms bound to one negative oxygen atom, in a wide V shape, forms agglomerations of oriented molecules that are harder to break apart than most liquid arrangements. Physical properties that are affected include boiling point, freezing point, higher viscosity, higher surface tension and lower vapor pressure.

 Click on the link below for a Comparison of Liquid Properties of Water to Methanol

Water and Methanol Properties

Due to the hydrogen bonding, water also has a couple of other properties that make it more favorable to life. Once the boiling point of water is reached using 1 calorie/gram/degree, it takes an additional 540 calories/gram to produce steam, i.e. boil. Similarly, it takes an additional loss of 80 calories/gram to freeze water into ice at the freezing point. Note that these high heats of condensation and fusion can produce superheated or super cooled liquid water.

Tiny droplets of atmospheric water can remain liquid at extremely low temperatures until nucleated by a particle such as ash, dust, salt, meteoric debris or even a bacterium, at which time they instantly freeze and attract other water droplets, which is the first phase of forming rain or snow. The purity of evaporated water and the low pressure at the altitude of clouds contribute to this. The urban legend that a cup of water heated in the microwave oven can violently erupt spontaneously is based on superheating of extremely pure (distilled) water. Introduction of any nucleating substance such as tea or a spoon can cause instant boiling. This is rarely seen because most water contains enough nucleating minerals to prevent or reduce superheating.

Low vapor pressure and high surface tension inhibit evaporation, this means that large bodies of liquid water are possible. Unlike most other liquids that continue to shrink as they freeze, water expands by about 10%. This means that ice floats due to reduced density; otherwise the oceans would freeze solid from the bottom up. Water has a high heat capacity that makes it an excellent heat sink to regulate atmospheric temperatures, both as a liquid and as vapor in clouds. Clouds also reflect a significant amount of heat from the sun back into space. Water strongly absorbs infrared radiation (heat) from the sun, but it is transparent to UV and visible light. Attenuation of these wavelengths at depth in the oceans is due to salts and organics dissolved or suspended in it. Due to its polar nature and ability to split apart into H3O+ and OH ions, it has a high dielectric constant and readily dissolves most salts and many other molecules.

Click on the link below for comparison of some properties of water to typical low molecular weight molecules. Most are gases at ambient temperatures, but note Lithium Hydride and Boron Nitride which are solids.

Properties of Water and Other Molecules

Water is one of the most abundant molecules on the planet. Oceans and other bodies of water cover over 70% of earth’s surface; about 96% of earth’s water is salt water in oceans and over 3% is in glaciers or ground water. Less than 0.5% is in freshwater rivers, lakes and streams. Water is also contained in living things and as water of crystallization in many rocks and minerals. For example, the familiar blue Copper Sulfate crystal is composed of hydrates containing 5 water molecules in the crystal lattice called copper sulfate pentahydrate. Chemically it is written as CuSO4.5H20, or more precisely [Cu(H20)4]SO4.H2O reflecting the actual structure.

The water cycle consists of evaporation and plant transpiration into water vapor, clouds and fog (ground clouds) followed by condensation and precipitation. In most areas of the earth, dew or frost is deposited on most nights of the year when temperatures fall below the dew point – the temperature where the amount of water vapor in the air reaches the saturation point and coalesces on surfaces into droplets – even in very arid places. Plant life moderates temperature swings between night and day, but the relatively high humidity near plants results in formation of dew on most nights. In deserts, temperatures swing widely from scorching hot to freezing cold, so that even low humidity can reach saturation and become dew, frost or fog at night.

Although oxygen is optional or undesirable for some bacteria, water is required for all life. The interior of cells, including organelles, DNA and proteins, and cells of multicellular organisms are bathed in water solutions that facilitate life’s processes.

 

Of Molecules and Life

The size of molecules ranges from approximately 3 x 10-10 meters (30 billionths of a meter) for H2 to several meters for DNA, the inheritable genetic material that facilitates life processes inside each cell. Each molecule of human DNA is about 3 meters long, and contains approximately 6 billion base pairs[3] made up of about 400 billion atoms. Human DNA, contrary to what you may think, is not the longest or the most complex. It forms 46 chromosomes[4] composed of DNA tightly wound with proteins. Compare that to 48 for chimpanzee, gorilla, orangutan, beaver and deer mouse, 78 for dog, wolf, hare, chicken and dove, 8 for fruit fly, 6 for Mosquito, 20 for corn, and a whopping 1260 for adders-tongue fern (highest number known). As a matter of fact, many “lower” life forms have the higher numbers of chromosomes. Clearly, the number of chromosomes does not correlate to advanced species.

Proteins are the work horses of life as structural units, molecular machines such as flagella and enzymes that perform specific metabolic functions. Proteins are composed of strings of hundreds or thousands of amino acids in very specific order to perform specialized functions. Each protein is internally linked and folded on more than one level to form molecular structures and machines, often in concert with other proteins. Among the molecular machines, enzymes act to cut, combine, hold and reorient other molecules that perform work such as metabolism. Each of the 20 amino acids[5] used to build proteins is encoded by a sequence of three specific base pairs of DNA. Genes contain sections of DNA made of a series of these triplets that encode for specific proteins and other non-coding DNA sections. RNA first copies the specific section of DNA, and then takes this information to special organelles called ribosomes that then read the RNA to build proteins, one amino acid at a time. This is a simplified picture of processes that are much more complex involving cutting, splicing and rearranging the mRNA (m for messenger).

DNA occurs as two copies, one from each parent in normal cells, and is packaged in very complex ways with proteins that can function as either structural supports or that facilitate gene regulation and expression. At the first level of organization, DNA is wound around roughly spherical complexes of eight special proteins called histones, often referred to as a “pearls on a string” arrangement, (more like “spools on a string”). Genes are most accessible in this form. As the DNA prepares for cell division, after making a copy of each strand, each copy is supercoiled into a condensed rope or “fiber” form. These supercoiled, tightly wound sections are then organized into stacks of loops around long scaffolding proteins, then into more condensed form with additional structural proteins to form chromosomes. The chromosomes are then pulled apart and the cell divides into two identical daughter cells.   Please keep in mind that this is a necessarily simplified picture of a much more complex process. Also note that each of these molecules is not “alive” themselves. All of these processes are chemical in nature and are facilitated by a host of other molecules.

Regardless of the size or complexity of the organism, these facts are true for all living things except viruses. Only the details of the process vary between prokaryotes and eukaryotes. Prokaryotes, consisting of bacteria and archaea, are without a separate nucleus and contain circular DNA, whereas eukaryotes, including everything above bacteria, from yeast and amoebae to humans, are composed of cells that have a nucleus which contains linear DNA. Both also have separate short sections of DNA in other structures such as ribosomes[6], mitochondria[7] and plastids[8].

Viruses consist of DNA or RNA enclosed in a protein shell and do not have the machinery for metabolism or to replicate by themselves. They inject their DNA into other cells and hijack their replicating machinery to make many copies of themselves that are then released through cell disruption. Most biologists believe that viruses are not alive, but they definitely use their own machinery to invade and inject their DNA into other cells. So, even though much of the viruses’ life cycle occurs inside other cells, they cannot be said to be dead either. They are more like parasitic spores. Conventional thinking about viruses has been put into question by recent discoveries of viruses as large as 1 micron (micrometers or millionths of a meter); which is 100 times as large as is typical, and is in the size range of some bacteria, with DNA large enough to rival both bacteria and some simple eukaryotes[9].

 

Living Things

Typical viruses range in size from 20 to 400 nm (nanometers or billionths of a meter). Bacteria range from 0.1 to 750 microns (micrometers or millionths of a meter) although most bacteria are in the 5 micron range. Organisms that contain a cell nucleus (Eukaryotes) contain one or more cells that range from about 10 microns to several feet long, for nerve cells, to multicellular organisms of several hundred tons for things like redwoods. The largest single cell is the ostrich egg.

Life on earth is practically ubiquitous[10]. Bacteria and Archaea[11] microbes are found in almost all known environments from the stratosphere to deep crust, from frozen arctic regions to hot deep-sea thermal vents, from deserts to oil wells to jet fuel tanks to radioactive nuclear wastes to very hot, very acid or very alkaline or very salty environments. Microorganisms have been found 25 miles (40 km) high in the atmosphere and down to 3 miles below the earth’s surface with no end in sight. The deeper you go into the earth’s crust, the hotter it becomes, and so there must be some depth where life ends. Microbes can survive at temperatures up to 250oF (122o C) in the high pressures of oceans, and are found in the ocean down to depths of 6 miles (10km) in the Marianas Trench, the deepest in the world.

They make up a significant portion of the biosphere and may exceed that of all other life forms in total mass. They even live on us, inhabiting places like our skin and gut, and are estimated to contribute significantly to our weight. They inhabit the guts of all animals to help them digest their food into a form that can be absorbed by cells, and can produce vitamins the animal itself cannot make on its own. For example, termites would not be able to digest the complex cellulosic fibers of wood without the symbiotic[12] archaea microbes in their gut which supply them with all the nutrients they need.

The earth is believed to be 4.5 billion years old, and possible signs of microbes are found in rock strata as far back as 3.8 billion years ago.  The first fossils of multicellular soft-bodied life occur at 580 million year ago[13]. The earliest fossils of hard-bodied or shelled life occur at 5.4 million years ago in the so-called Cambrian Explosion, which contained all existing body types. Single celled eukaryotes consist of a variety of protozoans, diatoms, algae, yeasts and fungi. The simplest multicellular organisms are colonies with little or no differentiation or specialized cells. Beyond that, are true multicellular organisms with specialized cells performing specific functions to benefit the entire organism.   Plankton, on which all of ocean life is based, consists mostly of microscopic single celled and multicellular organisms.

Almost all of life on earth ultimately depends on photosynthesis, which uses the energy of sunlight to turn water and carbon dioxide into sugars or starches, releasing oxygen. The only exceptions are those few that derive energy from other sources deep in the crust or oceans. There is an elaborate balancing act whereby plants produce food and oxygen from sunlight, carbon dioxide and water, while animals eat the food to build other molecules and derive energy while releasing carbon dioxide and organic wastes that feed the plants.

The most primitive photosynthetic organisms are specialized cyanobacteria, also called “blue-green algae,” that were present very early in earth’s history. Although they use a primitive form of photosynthesis, it is similar, and indeed most of it is a part of the photosynthetic mechanism used by higher plants today. Cyanobacteria use a pigment called phycocyanine instead of chlorophyll used by green bacteria and higher plants to collect energy from sunlight for photosynthesis, but use the energy in the same way. Some scientists believe the chloroplasts in plants originated as captured cyanobacteria or similar microbes forming endosymbionts[14]. Both have the same double stacked internal membrane layers (lamella), circular DNA and ribosomes that perform similar functions. Cyanobacteria can also be symbionts of other organisms such as coral.

It is thought that much of the oxygen in the atmosphere was first produced by early cyanobacteria under anaerobic (excluding oxygen) conditions[15] releasing oxygen as a waste material that was toxic to them. Aerobic (using oxygen) microbes are thought to have developed later to use this waste product. An atmosphere with low or no oxygen would have lacked an ozone layer so that the surface would have been bathed in deadly UV light. Any life forms at that time would have needed shielding such as deep water or soil. Additionally, before photosynthesis, all life would have had to depend on energy sources other than Oxygen such as Hydrogen Sulfide. Life may have begun either deep inside the earth or at the bottom of deep oceans in locations such as hydrothermal vents that supplied these other energy sources. After there was sufficient oxygen to form a suitable ozone layer, photosynthetic bacteria could then utilize sunlight and carbon dioxide directly from the atmosphere to produce more oxygen and reduce initial carbon dioxide levels.

At each stage, from anaerobic to aerobic to photosynthetic prokaryotes to single celled eukaryotes to colonies to multicellular organisms, required great leaps in complexity and functions. Then more adaptation was required to go from individuals to interdependent colonies such as ants, from aquatic to amphibian to land-based forms until every niche is thoroughly filled with vast communities of interacting organisms called ecosystems. These changes are thought to be the result of evolution.

 

[1] Sublime means the solid transitions directly into a gas without first becoming a liquid.

[2] The familiar hydrochloric acid, (aka muriatic acid), liquid is actually a gas dissolved in water.

[3] Base pair refers to the paired molecules AT or GC as rungs of a twisted ladder shaped molecule with sugar phosphates as the sides. A = Adenine; T=Thymine; G=Guanine; C=Cytosine.

[4] Chromosome is a large section of DNA carrying many genes.

[5] Amino acids occur in two forms, the D and L isomers. D means Dextro or right-handed and L means Levo or left-handed, referring to the way they bend polarized light. Only the L isomers of the 20 amino acids are used by living things. Similarly, sugars occur as D and L, but only the D form is used by living things.

[6] Ribosomes are organelles that build proteins from amino acids following instructions from mRNA.

[7] Mitochondria are organelles that produce energy for the cell. Each cell contains many mitochondria which have their own DNA and replicate independently of cell division.

[8] Plastids are small membrane enclosed structures with specific functions such a chloroplasts which use energy from the sun, water and carbon dioxide to build sugars.

[9] “Ever-Bigger Viruses Shake the Tree of Life,” Science, Vol. 341, 19 July 2013, p. 226.

[10] Ubiquitous – present everywhere

[11] Archaea is a recent change in nomenclature separating bacteria into two domains. Many archaea are extremophiles with internal structures or systems that are different from bacteria.

[12] Symbiotic is a relationship between organisms that benefits both organisms, which are called symbionts.

[13] Ediacaran formation in Western Australia

[14] Endo means internal so an endosymbiont is one that lives inside its host.

[15] Cyanobacteria can exist in either aerobic or anaerobic conditions. Under anaerobic conditions, only the most primitive part of photosynthetic mechanism is used.

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