Session I ( August, 19th, 2009).

Levels of Organization

Organization of matter into higher and higher levels of complexity is found within all organisms. Simple chemicals are combined into huge molecules, molecules are combined into cells, and group of cells work together to form multicellular organisms. Each level of organization is part of the next higher one, and at each level, new properties not present in the previous one emerge.

Atoms

The atomic level is the lowest level of organization of matter in Biology. Atoms are the smallest units of matter that can exist independently, but they are not however, the smallest units of matter. Subatomic particles which construct atoms, determine the many different types of atoms and their properties. Each atom type is called and element, the building materials of all physical parts of the universe. The same atoms found in Mars, are found in living organisms on Earth. No life signs are found at the atomic level of organization.

Molecules and Compounds

At the next level of organization are combinations of elements called molecules and compounds. Held together in predictable combinations by forces called bonds, molecules are the smallest neutral particles of a substance that can exist inedpendently, whereas compounds are chemical combinations of two or more elements in definite ratios. Compounds have very different properties from those of the atoms that formed them. Associations of molecules and compounds represent an increase in complexity, but they are not necessarily a sign of life. It is only among a certain sublclass of molecules, involving the element carbon extensively, that first signs of life emerge.

Monomers

Monomers are small molecules that have the ability to join together to form long strings or polymers. Among the types of monomers found in living organisms are amino acids, saccharides and nucleotides, all composed mainly of the elements C,H,O,N,P and S.

Polymers and Macromolecules

These are very large molecules synthesized by linking together smaller molecules (monomers). Polymers characteristic of life fall into four major categories: Proteins, Lipids, Carbohydrates and Nucleic Acids. Each is composed of its own special class of monomers. Proteins for example are long strings of amino acid monomers joined together in precise sequences.

It is at this macomolecular level of organization that properties emerge in which we can clearly recognize signs of life. The presence of this macromolecules on Mars for example, would be a confirmation of presence of life. For example, some proteins have the ability to speed up or accelerate the rate of chemical reactions. Amino acids alone do not have this ability but the ability to influence these reactions emerges at the macromolecular level of organization.

The Cell

It is the lowest level of organization at which we can say that life truly exists. Suddenly, at this level, we see a whole array of properties emerge that belong to life. These properties are not those of any individual macromolecule, but instead they appear only after macromolecules are correctly assembled. For example, the components of a cell have little or no capacity to grow, reproduce, respond to stimuli, and so on. Yet, the cell, can carry various of these functions.

As a result, there are many important unifying themes of Biology to be found in the study of cells. Many basic discoveries have been made in the areas of cell and molecular biology by breaking open cells and analyzing which class of macromolecule was responsible for a particular property. The DNA for example, is now known to carry the coded genetic and hereditary instructions for building and maintaining the cell and the organism. There are, however, levels of organization beyond that of the cell. Just as the properties of cellular life are more than the sum of the various constituents, so the properties of multicellular life are more than the sum of the individual properties of all their cells.

The Macromolecules

Water

Water is the most abundant molecule in living organisms (50-90% of the fresh weight) so is not a surprise that life on the planet started in it. But, why is water so important for life? This liquid, which covers 3/4 of the earth's surface its a quite unique molecule with very unique properties that made life possible on the planet.

Molecular structure of Water

Each water molecule is formed by the covalent union between an atom of Oxygen (O-2) and two atoms of Hydrogen (H+). This is, Hydrogen contributes to the bond by sharing its only electron, and Oxygen shares its two electrons with the same number of Hydrogen atoms.

Even though water as a whole, has a neutral net charge, it is a polar molecule. Due to the electronegativity of O, electrons shared in the bond, are strongly attracted toward the O. In this way, a bipolar momentum forms, where electrons in a particular moment are closer to O giving that side of the molecule a slightly negative charge, wheareas the H+ in the opposite side of the molecule, acquiere a slightly positive charge.

When this charged regions interact with another molecule of water. The bipolar momentum on both molecules will form what is called a hydrogen bond. A charge on the oxygen atom of one water molecule attracts the oppositely charged hydrogens on another water molecule, and the two molecules are momentarily held together. This interactions are very weak and only last a small part of a second but millions of them form and break every instant. Although each individual hydrogen bond is weak, all the hydrogen bonds added together create a total force that is quite strong. The property of hydrogen bonding in water molecules, explain why water is a liquid at room temperature and why is not a solid. If water molecules were not able to form hydrogen bonds between themselves, they would be jostling around as gas molecules at room temperature. The consecuence of the hydrogen bond is the unique set of physical and chemical properties of water.

Surface tension

If you put gently a razor blade on water surface, it will float as if water was a solid. This is the result of cohesion or mutual attraction between water molecules. (cohesion is by definition the union between molecules of the same substance, adhesion is the union of molecules of different substances).

Capillarity

If you hold two glass slides together and dip the corner of them in water, the combination of cohesion and adhesion will result in water climbing up between the slides. This property is relevant to plants. Capillarity allows water molecules to fill up the small spaces between soil, being available for roots to use it.

Absorption

It is the permeation of a molecule into another material, such as water permeates through wood and it swells. Absorption pressure this is, the force that water molecules apply to the other substance can be very high. Thanks to absorption, seeds can break open their teccas while sprouting.

Specific heat

The ability of water to stabilize temperature depends on its relatively high specific heat. The specific heat of a substance is defined as the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1º C. The specific heat of water is 1.00 cal/g ºC. Compared to other substances, water has an unusually high specific heat. For example, ethyl alcohol, the type in alcoholic beverages, has a specific heat of 0.6 cal/g ºC. Because of the high specific heat of water relative to other materials, water will change its temperature less when it absorbs or loses a given amount of heat. The reason you can burn your finger by touching the metal handle of a pot on the stove when the water in the pot is still lukewarm is that the specific heat of water is ten times greater than that of iron. In other words, it will take only 0.1 cal to raise the temperature of 1 g of iron 1ºC. Specific heat can be thought of as a measure of how well a substance resists changing its temperature when it absorbs or releases heat. Water resists changing its temperature; when it does change its temperature, it absorbs or loses a relatively large quantity of heat for each degree of change. Given that a big amount of energy its needed or lost to raise water temperature, animals that live in oceans of big lakes enjoy of a relative constant temperature. In the same way, given that there is a high water content in living organisms they maintain a constant inner body temperature. This water property is crucial because all of the relevant biochemical reactions take place only in a narrow interval of temperatures.

Vaporization heat

It is the physical change from a liquid to a gas. For a water molecule to separate of its neighbor molecules, hydrogen bonds must break. This requires an input of energy (540 cal/g). As a consequence, when water turns into vapor on a leaf or on the skin surface, the escaping molecules carry large amounts of heat with them. In this way, evaporation has a cooling effect. This is a way for organisms to unload heat excess and stabilize their temperature.

Freezing Point

It is the physical change from liquid to solid. In most liquids density raises when temperature drops. This raise in density is a product of individual molecules moving slowly so space between them become smaller. Water density, behaves in the exact same way until it reaches 4C., at this temperature water molecules get so close to each other that they can form 4 hydrogen bonds, making the strutcture very stable in the form of crystals. The space needed to form these 4 hydrogens bonds is bigger than when there are only 3 (liquid phase). The result of this is a drop of ice density which allows it to float. This is of relevance because, without this property lakes would freeze from the bottom to the top and no life could take place. Also, the solubility properties of water are affected by this property. The presence of solutes in water drops water's freezing point. Some polar fish that are cold resistant, have in their blood a protein called antifreeze protein which prevents the formation of ice crystals in the blood.

Water is a Solvent

Other molecules and ions will dissolve in water. Any liquid capable of dissolving or dispersing other substances is a solvent. Water is a very good solvent because of the two opposite charges it carries on the same molecule. Almost every substance will dissolve in water in some extent. Because of it polarized nature, however, water is a better solvent for ionized or polarized substances than it is for nonionized or polarized substances.

Sodium chloride dissolves readily in water because the positively charged sodium ion attracts the partially negative oxygen atoms of water molecules. Water molecules surround the ion, forming a shell with the negative oxygen atoms facing inward and the positive hydrogens facing outward. A similar shell forms around chloride ion, but in this case the positively charged hydrogen atoms are attracted to the negatively charged chloride ion and form a shell with the hydrogen atoms facing inward. Strong interactions between water molecules and other polar substances cause the dissolving substance, the solute, to break up and disperse through the water. The result is called a solution. Any substance capable of dissolving in water is said to be hydrophilic, meaning water loving.

Some substances, however, do not form solutions when placed in water (oil, gasoline). These molecules do not ionize (like sodium chloride) or polarize (like water), so there are no charges to attract the water molecules. Such substances are called hydrophobic, meaning water fearing.

Almost all vital chemical reactions necessary to keep cells alive take place in water. Water is the universal solvent for all life's molecules, big and small. From the moment they first formed on the primitive earth, the simple precursor molecules of life dissolved in water. From this solution the higher orders of complexity arose and the first cells were created. Without the special solvents properties of water, life would not be possible.

Water can Ionize

As we have seen before, electrons in water molecules are not equally shared between the oxygen and hydrogen atoms, giving the molecule a slightly ionic character. Occasionally, however water molecules break into two unequal pieces to give an hydronium ion (H3O+) and a hydroxyl ion (OH-). A process such as this is called ionization.

Water can ionize quite readily. In the billions and billions of water molecules in a cup of pure drinking water, there will be about 1, 000,000,000,000,000 hydronium ions and exactly the same number of hydroxyl ions. Although this seems a lot, it is only a small fraction of the total water molecules in the cup. It is important to note that for each hydronium ion there is a corresponding hydroxyl ion.

This is not always the case however. Certain substances when added to water, can change the number of hydronium ions in the water, turning the solution acidic. For example HCL ----> H+ + Cl- Solutions with higher hydronium ion concentrations than that of pure water are called acids.

Other substances dissolve in water to give hydroxyl ions. For example sodium hydroxide (NaOH), when in solution with water, gives sodium ions (Na+) and hydroxyl ions (OH-). NaOH ----> Na+ + OH-

Hydroxyl ions react with the naturally ocurring hydronium ions to give water molecules again, depleting the concentration of hydronium ions in the solution. OH- + H3O+ ------> H2O

A solution with a hydronium concentration lower than that of pure water (and consequently with a higher hydroxyl ion concentration) is said to be alkaline or basic.

Hydronium ion concentration is conveniently represented by a scale of values that goes from 1 to 14. This is the pH scale. Pure water is right in the middle of the scale with a pH value of 7 (1x10-7). As the concentration of hydronium increases, the numbers decrease, so a strong acid with a very high hydronium ion concentration has a value on this scale of 1 to 2, whereas a strong alkaline solution with a very low hydrogen ion concentration has a value of 11 to 14.

Water is more than just a solvent into which life's molecules dissolve and react. Water molecules also participate in many critical synthetic and breakdown reactions that build and destroy cells and cellular structures.

Take a look at this video on water properties.