Life and the Earth's Environment

While we can characterize living organisms by various chemical, physical, and biological parameters, the harmony that puts it all together and forms the spark we call life is far from understood. We see live organisms that may be stages toward more complete organisms. Viruses, for example, are essentially a piece of DNA or RNA coated with protein. It is by inserting this unit into cells of other animals that viruses reproduce and continue their lives. Infective viruses have been synthesized from elements. Several scientists have synthesized DNA and RNA molecules that replicate themselves in a test tube. But while we can concoct many of the molecules that must have been in the primeval soup in which life evolved, we cannot yet compose from elements a group of "cells that crawl out of a test-tube" on their own, to paraphrase Margulis and Sagan.

We do know a lot about the environmental conditions that sustain life. We have begun to understand that not only does the environment sustain life, but life in turn has made environmental conditions what they are today. We now discuss some peculiar features and compounds on Earth that make our environment particularly "fit" for our kind of life. Much of this discussion is based on three sources:

1. Microcosmsos: Four Billion Years of Microbial Evolution, by Lynn Margulis and Dorion Sagan, 1986.
2. Time's Arrow and Evolution, by Harold F. Blum, 1951.
3. Gaia, by James Lovelock, 1979

Blum discusses the "fitness of the environment," a concept originally proposed by Lawrence J. Henderson in 1913. <INSERT note on Henderson--write email to Beth> Certain aspects of the environment make the Earth particularly advantageous for living organisms to live, develop, and evolve. The Earth's size and its distance from the sun (a medium yellow star), and the nature of the sun itself, determine the gravitational force of the Earth and the amount and type of electromagnetic energy we receive. These factors provide the conditions under which life evolved, and that sustain life on Earth.

Materials for Life on Earth: Water, Carbon, Hydrogen, and Oxygen
<Might be good to put electron dot diagrams or something representative of these elements here for a visual effect? Needs some pictures to break the monotony...>

Hydrogen, oxygen, and carbon make up over 93% of the weight of the human body. Water is almost 80-90% by weight of all living organisms. Water has several physical and chemical properties that make it important in maintaining conditions fit for life on Earth.

Water
<student exercise on water?>
The large amount of water on the Earth's surface and the fact that at the average temperature over most of the Earth, water is in a liquid state, are both important to life. Water constitutes the largest fraction of most organisms.

If spread evenly over the Earth, the water present on Earth could form a layer about 2.5 km (1.6 miles) thick. Water has a high heat capacity. It can absorb quite a bit of heat (1 calorie for every gram for each degree rise in temperature) before its temperature rises significantly. This provides a moderating influence that prevents sudden rises in temperature, which could be damaging to live organisms. Water bodies on Earth work to moderate atmospheric temperature changes, and internal water helps organisms maintain temperature ranges.

Water also has a large latent heat of vaporization because a lot of energy is needed to break hydrogen bonds among water molecules. It takes a lot of heat to change liquid water to vapor--560 calories/gram. Thus organisms (plants and animals) can dissipate a lot of heat by having some of the water in them evaporate. For example, we are able to evaporate water from our body, as sweat, cooling the body because of the heat removed by the evaporating water.

Water has a high latent heat of fusion as well. Eighty calories are required to convert 1 gram of ice to water. In addition, because of the peculiarities of the hydrogen bond, ice is less dense than water. It rarely happens that a solid material is less dense than its liquid state. Ice also does not conduct heat well. The high latent heat, low heat conductivity, and low density of ice causes ice to float on water, keeping the warmer water sealed below the insulating ice layer on lakes and other bodies of water, and keeping the water habitable for aquatic life.

Water is a "universal" solvent. It is capable of dissolving a variety of materials. Salts dissolve in water to form ions <INSERT note on ions> and various ions play important roles especially in the conduction of nerve impulses. Balance of ionic flow across cell membranes (cell walls) are also an important mechanism of moving nutrients as well as in several other cell functions. <link to one of ornella's animations?>

Finally, water vapor is one of the greenhouse gases that keeps the Earth's atmosphere at the temperatures suited to life.

Hydrogen
Many of the special properties of water come from hydrogen. The small size of the hydrogen atom makes it possible to fit into many more molecular configurations than a bigger atom can. Thus hydrogen can form numerous compounds. Hydrogen is light and, due to its weight, all hydrogen gas could have escaped the Earth's gravitational pull when the Earth was still very hot. However, its high chemical reactivity with nitrogen, oxygen, and carbon, and the abundance of these elements on Earth made it possible for the Earth to retain a large amount of hydrogen in combination with these elements as ammonia, water, and methane during the primitive days of the Earth.

Carbon
The carbon compounds that make up essential molecules such as proteins are described in the notes on biological molecules. Carbon is second only to hydrogen in the number of compounds it can form, oxygen being the third in this capability. Carbon can form more than 2500 compounds with hydrogen. Then next elements that form most hydrides are boron and nitrogen; each of which can form only seven! The C-C bonds make possible a great variety of molecules with different chains and rings. C, H, and O combine together to from even a richer variety of compounds. The same number of atoms can yield completely different compound depending on the arraignment of atoms. For example, C can from butyl alcohol (the prefix butyl refers to 4 carbons) in two alternate forms with slightly different but similar properties.

<INSERT picture of methane to show the bonding orbitals>

The -OH group is the hallmark group of an alcohol. These same number of atoms could also form an ether characterized by the -O- bond between carbon groups. Thus these atoms can form diethyl ether, two ethyl (C₂H₅) groups bridged by O, as in:

<INSERT FIGURES>

For much larger molecules with many C atoms, the possible arrangements become very large. Recall that carbon is the middle element in the first period of the Periodic Table. It has four electrons (1s²2s²2p²) in the outer shell, needing four more to complete the outer shell. This capacity to form four covalent bonds makes for the capability of carbon to form compounds. The four bonding electrons and various spatial arrangements give carbon its enormous versatility.

This versatility and the fact that carbon dioxide is a gas at ordinary temperatures are two important aspects in carbon being the chemical basis of life. Photosynthesis occurs because CO₂ is a gas and is soluble in H₂O, so that this mixture, with energy from the violet part of sunlight, can form sugars.

The versatility of carbon comes from its central position in the periodic table. People have conjectured why silicon in an analogous position and, being one of the most plentiful elements in the Earth's crust, did not become that centerpiece. SiO₂ is **** form in plenty--as sand. But it becomes a gas at only 3000°, and it is not soluble in water. The chemical versatility of silicon is indeed the property we value for its use for computers.

Oxygen
With carbon and hydrogen, oxygen forms the third principal element in living systems. As we see later in this unit, our atmosphere was not always oxygen-rich. About 2000 million years ago, there was only about 0.0001% oxygen in the atmosphere. During the Archean and Proterozoic ages (when plants started to use photosynthesis), there was a radical increase of the O₂ concentration to the almost 20% that it is today. This resulted in a major extinction of some bacteria as discussed in a later section.

As silicon is to carbon, so is sulfur to oxygen. So we could imagine a material and life configuration where H₂S instead of H₂O was the basic "liquid" of life. (H₂S is actually a gas at Earth's average temperatures.) However the H-O bond is stronger than the H-S, and oxygen is 50 times more plentiful on Earth than sulfur.

Other Elements
The other elements that play a vital role in living systems are N, Ca, P, Na, Fe, K, Cl, S, Zn, and Mg. Together these form about 1.72 atomic percent of the human body. Along with H, O, and C, these elements account for 99.96% of the human body. Lighter elements dominate this list and these elements have more specific roles in the function of biological molecules than the more general C, O, and H trio.

Nitrogen and sulfur are components of all proteins. Phosphorus is an essential component for the storage and use of energy in all cells. Cellular energy resides in phosphate bonds. Mg is a central component of chlorophyll, and iron is a component of hemoglobin and other respiratory enzymes. These elements serve very specialized but important functions.

Metals such as Fe and Na are rare in the body but play important roles either in very specific molecules as Fe in hemoglobin, Zn in gene transcription proteins, or Mg in chlorophyll; or with a specific function such as Na or K ions providing the flow of ions for conduction of information along nerves. Most metals, however, are toxic to most organisms. Examples of metal toxicity that have become significant environmental problems in the last half-century are cases of lead poisoning, mercury poisoning (Minamata disease), and poisoning by metals such as chromium (Cr), aluminum (Al), and cadmium (Cd). The amounts of chromium and cadmium in the environment have increased due to numerous technological uses ranging from steel production to household batteries.

The Cell: Basic Parts & Functions

The basic parts of the cell and the function of each are described in the notes on cells for those who require such a review.

Evolution

Evolution is defined as the gradual change of any object, in our case, the biological system, through time. We discussed briefly in the previous section some of the aspects of the complex intricate system of the chemistry of biomolecules. We now shift to the level of the organism--cells organized into tissues, organs, and organism--which have persisted and changed through time. Broadly speaking, the first single-celled organism did not have a nucleus. These prokaryotes persist today as microbes, such as bacteria and viruses.

Protein synthesis was an early step in the evolution of organisms who were then capable of reproducing themselves using their RNA. It is not clear when the first cells in the form we know now were formed. Somewhere, in the primordial soups, some molecules got enclosed inside a membrane to form a cell. RNA molecules within this cell could then facilitate reproduction of the cell. All we can surmise is that this aggregation of molecules started about 3.5 billion years ago. It is believed that RNA came after proteins and enzymes evolved. Once a cell was established, RNA evolved into DNA, making a subcellular structure we now call the nucleus. The DNA, which is a coil of two strands of RNA (with the bases A, C, G, and T, whereas RNA has A, C, G, U), is the molecule that enables protein synthesis.

Some of the prokaryotic bacteria we know like mycoplasms, different varieties of **** e-coli, and staphylococcus still abound on Earth. Bacteria live in an enormous variety of environments, often symbiotic with other organisms. Thus benign forms of e-coli live in our guts and numerous bacteria live in soil and in plants. Species of bacteria can use a variety of organic molecules such as sugars and polypeptides as their food. Bacteria are the most abundant type of cell on earth. The early bacteria seemed to have used ATP to store the energy of sunlight. Blue-green algae is a type of bacteria that converts CO₂ and N₂ into its food.

As plants developed the capability of photosynthesis, the composition of the early atmosphere (mostly CO2) began to change over billions of years to this current composition of 20% oxygen and only traces of CO₂ as the plants "fixed" the carbon. Many of the early bacteria were used to an oxygen-poor environment and several of them then became extinct. Others formed a symbiotic association with oxygen--using (aerobic) types of cells to form the present day cells with nuclei (eucaryotes). The different organelles in the cell such as the chloroplasts and mitochondria are now believed to have been separate organisms that associate with each other to form mutually beneficial colonies we now call cells.

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