Chapter One: Chemical Foundations of Life

This chapter introduces molecular biology by talking about the basics of biochemistry as it applies to life and living things. All of human life is based on water, which is a polar molecule that acts as a solvent for many biological molecules in living things. The bonds that make up biochemical molecules are also important in the discussion of molecular biology. The types of molecules that make up living organisms is also covered as are the different biochemical reactions that take place inside and outside the cell.

Water Biochemistry

Water is the common solvent found in all forms of life. Humans are about 70 percent water, while many marine organisms, such as jellyfish, are as much as 95 percent water. The oxygen that humans and animals breathe ultimately come from the water—turned into oxygen by the activities of photosynthetic plants. Plants and other organisms that are photosynthetic will take water and sunlight to make food, with oxygen as a waste product.

Water is extremely abundant with about 350 million cubic miles of water on earth. About 97 percent of this is in the oceans of the earth, covering two-thirds of the planet’s surface. About 90 percent of all of the fresh water on earth is frozen in the poles and in glaciers. Only 1 percent of the water on the planet is drinkable, mostly found in underground aquifers.

While water is a simple molecule, its characteristics are extremely important in molecular biology. Its chemical structure, H2O, means that it contains two atoms of hydrogen and one atom of oxygen, bonded in a V shape. Figure 1 shows what the molecular structure of water is:

Figure 1.

Water has a really small size but it has unique biochemical properties that make it easy to bond with other molecules through hydrogen bonding, which will be explained in a few minutes. Water is so important that it is involved in practically every chemical reaction and biological activity of the cell. It is the solvent that dissolves nearly every biological substance because it binds to other molecules and can exist on earth in every form: solid, liquid, and gaseous forms.

It takes a great deal of energy to change the inherent temperature of water because it has a high specific heat. The specific heat of something is the number of calories it takes to change a gram of a substance to a different temperature level. The specific heat of water is 1 calorie per gram or 4.18 joules per gram per degree Celsius, meaning that it takes 1 calorie to raise the temperature of a gram of water one degree Celsius. This is much higher that the specific heat of other common substances, meaning it plays a big role in temperature regulation in living things. Water also transmits light well. This means that it allows for photosynthesis to occur under the water.

Water is polar. This means that the positively negatively charged oxygen atom, having eight electrons around the molecule. The electrons orbit the eight protons in areas called orbitals. Two of the electrons fit within the first orbital and the six remaining electrons orbit the second orbital. Hydrogen has one proton and one electron. Because of the negatively charge pull of the oxygen electrons, the hydrogen atom donates and shares its atom with the oxygen in the second orbital of the oxygen molecule.

The term “polar” means that there is a net negative charge on the oxygen molecule and a net positive charge on the hydrogen molecules. This bond between the hydrogen and

oxygen atom is called a “covalent bond”, which will be discussed in a few minutes. Covalent bonds involve the sharing of electrons. The oxygen molecule is V shaped because of the way the orbitals around the oxygen molecule are shaped.

Because water is polar, it is able to dissolve other polar substances, including ions. Ions are atoms that have gained or lost an electron. One that has lost an electron is a cation and is positively charged. One that has gained an electron is an anion and is negatively charged. The polarity of water allows cations and anions to reside within the water solvent.

Cations and anions are ions that are known as “hydrophilic”, which means water-loving. Even molecules that are not officially charges and are neutral can be hydrophilic. Examples of hydrophilic substances include glucose and any type of salt or ion. On the other hand, fats and some proteins are hydrophilic, which means “water-hating”. They do not easily dissolve in water but will dissolve in nonpolar substances.

The terms “hydrophilic” and “hydrophobic” are important in the molecular biology of membranes or layers of hydrophobic and hydrophilic parts of molecules. Membranes can exist in water because they have atoms that are hydrophilic on the outside and atoms that are hydrophobic sandwiched between the hydrophilic parts. Water is so small that it can pass through most membranes without destroying the membrane itself. Figure 2 shows what a membrane looks like in water. Note that it is arranged in layers:

Figure 2.

Water has a high surface tension because the molecules stick together. This high surface tension means that it takes a great deal of force to separate the molecules and to break into the surface of the liquid. Think about insects that can walk on the surface of water in a lake, for example. Rain falling results in a droplet of liquid that stays on the surface of the earth, allowing more water to absorb into the soil for use by plants and other photosynthetic organisms.

Because the specific heat of water is so high, the temperature of oceans and lakes changes slowly, leaving a stable temperature on the earth’s surface. This stable environment is important for plants. It also helps maintain the temperature of an organism, which means that the organism’s biochemical reactions can happen in a stable environment.

The energy of vaporization of water is high. This means that it takes a great deal of heat to turn liquid water into water vapor. The water molecule vaporized takes the with it, leaving the remaining liquid water cooler. This is referred to as evaporative cooling. Evaporative cooling is used by animals to maintain their body temperature. This is the process that happens when humans sweat. It is a necessary process when exposed to the heat of the sun.

As mentioned, water is found in three states on this planet. Water is denser as a liquid, which is an unusual property of water. It means that the lattice of solid water floats on the surface of liquid water. Water is densest at 4 degrees Celsius and become solid at 0 degrees Celsius. Water also expands when it freezes into a lattice shape. These properties of water help animals survive in cold temperatures under the water.

As mentioned also is the ability of water to transmit light. What’s good about water is that it transmits certain wavelengths of light and scatters other wavelengths of light. Small wavelengths of light, such as UV light, can damage cells and are scattered by water vapor molecules surrounding the earth. On the other hand, blue and green wavelengths are transmitted easily through water; these are the wavelengths of light used most effectively by photosynthetic plants. What will absorb red light, which causes it to retain heat. This keeps the planet warm for the existence of light.