Molecules Found in Living Systems | Biochemistry

In this article, we present some of the types of molecules that are found in living things. The molecular drama is a grand spectacular with, literally, a cast of thousands; a single bacterial cell contains some 5,000 different kinds of molecules, and a eukaryotic cell-the sort of cell that makes up the tissues of animals and plants-has about twice that many.

Thousands of molecules, however, are composed of relatively few elements. Similarly, relatively few kinds of molecules play the major roles in living systems. If you bear with us, you will find that you readily learn to recognise the players and their roles and to distinguish the stars from the members of the chorus.

The Central Role of Carbon:

Water makes up about 60 to 70 percent, on the average, of a living system, and ions such as K⁺, Na⁺, and Ca²⁺ account for no more than 1 percent. Almost all the rest, chemically speaking, is composed of organic molecules-molecules containing carbon.

In general, an organic molecule derives its overall shape from the arrangement of the carbon atoms that form the backbone, or skeleton, of the molecule. A carbon atom has six protons and six electrons, two electrons in its innermost orbital and four in its outer orbitals. Thus carbon can form four covalent bonds with as many as four different atoms. Methane (CH₄), which is natural gas, is an example.

Even more important, in terms of carbon’s biological role, carbon atoms can form bonds with each other. Ethane contains two carbons; propane, three; butane, four; and so on, forming long chains. In these compounds, every carbon bond that is not occupied by another carbon atom is taken up by a hydrogen atom. Compounds consisting of only carbon and hydrogen are known as hydrocarbons.

Chains containing oxygen atoms in addition to carbon and hydrogen are common in living systems. When these atoms occur in the ratio of one carbon to two hydrogens to one oxygen (CH₂O) the compounds they form are known as carbohydrates. Sugars are carbohydrates. The sugar glucose is a carbohydrate whose skeleton contains six carbon atoms. In solution, glucose forms a ring. Rings of carbon atoms are common types of biological molecules, so common, in fact, that the C’s are usually omitted in representations of the ring form.

Functional Groups:

The specific chemical properties of a molecule derive principally from groups of atoms, known as functional groups that are attached to the carbon skeleton. An OH (hydroxyl) group is an example. When one hydrogen and one oxygen are bonded covalently, one electron is left over for sharing.

A compound with a hydroxyl group in place of one or more of the hydrogens in a hydrocarbon is known as an alcohol. Thus methane (CH₄), with the replacement of one hydrogen atom by a hydroxyl group, becomes methanol, or wood alcohol (CH₃OH), a pleasant-smelling, poisonous compound noted for its ability to cause blindness and death. Ethane similarly becomes ethanol, or grain alcohol (C₂H₅OH), which is present in all alcoholic beverages. Glycerol, C₃H₅(OH)₃, contains, as its formula indicates, three carbon atoms, five hydrogen atoms, and three hydroxyl groups.

The carboxyl group (COOH), is a functional group that gives a compound the properties of an acid.

Many functional groups are polar and so have a partial positive or negative charge in aqueous solution. Some of these tend to become fully ionised, depending on the pH of the solution.

Thus these groups confer water-solubility and local electric charge to the molecules that contain them. Many functional groups participate directly in chemical reactions. Functional groups are essential for recognising a particular molecule and helping predict its properties.

Alcohols, with polar hydroxyl groups, tend to be soluble in water, for instance, whereas hydrocarbons such as butane, with only nonpolar functional groups (such as methyl groups), are highly insoluble in water. Sugars contain hydroxyl groups plus an aldehyde group or a ketone group.

Aldehyde groups are often associated with pungent odours and tastes. Smaller molecules with aldehyde groups, such as formaldehyde, have unpleasant odours, whereas larger ones, such as the chemicals that give vanilla, apples, cherries, and almonds their distinctive flavors, tend to be pleasing to the human sensory apparatus.

Four Representative Molecules:

Figure 3-3 shows four kinds of molecules found frequently in living systems. The first (a), as you will recognise, has a long hydrocarbon chain; this chain, being nonpolar, is hydrophobic. Because of the COOH, you know that it is an acid. It is a fatty acid, a major component of fats, lipids, and waxes.

The second molecule (b) is a sugar. It is recognisable as a sugar because it consists of a carbon skeleton with hydrogen and oxygen atoms in the ratio of CH₂O, and it has a ketone group characteristic of a sugar. In aqueous solution, it forms a ring, as shown here.

You can also tell that it is soluble because of the OH (alcohol) groups that confer solubility. This particular sugar is fructose. The third molecule (c) is an amino acid. An amino acid consists of a carbon atom bonded to one hydrogen atom and to three functional groups. One of these groups is always a carboxyl group, which gives the molecule its acidic properties. Because of the amino group, an amino acid is also a weak base. The third functional group varies from amino acid to amino acid; in this case it is a methyl (CH₃) group, and the amino acid is alanine.

The fourth molecule (d) is a nitrogenous base. It is called nitrogenous because the rings of the molecule contain not only carbon but also nitrogen. It is a base because of the amino group. This nitrogenous base is called adenine and it is definitely one of the stars in the biological drama.

It has been said that it is necessary only to be able to recognize about 30 molecules for a working knowledge of the biochemistry of cells. One of these is a fatty acid; two others are the sugars glucose and ribose; five are nitrogenous bases such as adenine; and 20 are the biologically important amino acids. So, as you can see, the cast of characters is nearly complete.

The Energy Factor:

Covalent bonds-the bonds commonly found in organic molecules-are strong, stable bonds consisting of electrons moving in orbitals about two or more different atomic nuclei. These bonds have different characteristic strengths, depending on the configuration of these orbitals. Bond strengths are conventionally measured in terms of kilocalories per mole. Chemical reactions always involve a change in electron configurations and therefore in bond strengths.

Consider, for example, the burning of methane, represented by the following equation:

CH₄ + 2O₂ → CO₂ + 2H₂O

This reaction can be set in motion by a spark, which is what causes explosions in coal mines, and it releases energy in the form of heat. The amount of energy released can be measured quite precisely. It turns out to be 213 kilocalories per mole of methane.

This can be expressed by a simple equation:

ΔH°= -213 kcal

The Greek letter delta (0) stands for change, H for heat, and the superscript ° indicates that the reaction occurs under certain standard conditions of temperature and pressure. The minus sign indicates that energy has been released.

Similarly, changes in energy occur in the chemical reactions that take place in living systems. However, living systems have evolved strategies for minimising the energy required to set a reaction in motion and also the proportion of energy released as heat. (The word “strategy” in its ordinary meaning is a deliberate plan to achieve a specified goal. Biologists use it to mean a group of related traits evolved by natural selection to solve particular problems encountered by living systems.)

Carbohydrates: Sugars and Polymers of Sugars:

Carbohydrates are the principal chemical energy sources of most living things. In addition, they form a variety of structural components of living cells; plant cell walls, for example, are mostly made of cellulose, which is the most common organic compound in the biosphere.

Large molecules that are made up of similar or identical subunits are known as polymers (“many parts”) and the subunits are called monomers (“single parts”). In the case of carbohydrates, the monomers are mono-saccharides, single sugars, and the polymers are polysaccharides.

Mono-Saccharides: Ready Energy for Living Systems:

Mono-saccharides (sugars) can be described as (CH₂O)_n; n may be as small as 3, as in C₃H₆O₃, or as large as 8, C₈H₁₆O₈. As shown in Figure 3.6 , they are characterised by hydroxyl groups and an aldehyde or a ketone group.

Like hydrocarbons, carbohydrates can be oxidised to yield carbon dioxide and water:

(CH₂O)_n + nO₂ → (CO₂)n + (H₂O)n

This reaction is also energy-yielding, and the amount of energy released as heat can be calculated by burning sugar molecules in a calorimeter. The same amount of energy is released when the equivalent amount of carbohydrate is oxidised in a living cell as when it is burned in a calorimeter.

This statement comparing the oxidation of food molecules with that of fuel molecules is not a metaphor; it is a fact. Look for instance at Table 3.2 in which energy costs for running different kinds of machinery-biological and manmade are compared, and note the remarkable similarities. (There are at least two other interesting generalisations that can be formulated from these data. Can you find them?)

A principal energy source for vertebrates is the monosaccharide glucose. It is in this form that sugar is generally transported in the animal body. A patient receiving an intravenous feeding in a hospital is getting glucose dissolved in water. This glucose is carried through the bloodstream to the cells of the body where the energy-yielding reactions are carried out.

As measured in a calorimeter, the oxidation of a mole of glucose yields 673 kilocalories:

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O

ΔH° = -673 kcal

Disaccharides: Transport Forms:

Disaccharides consist of two single sugars (mono-saccharides) covalently bonded together. Although glucose is the common transport sugar for vertebrates, sugars are often transported in other organisms as disaccharides.

Sucrose, commonly called cane sugar, is the form in which sugar is transported in plants from the photosynthetic cells (mostly in the leaf), where it is produced, to other parts of the plant body. Sucrose is composed of the mono-saccharides glucose and fructose.

As is the case with all disaccharides and, indeed with most organic polymers, a molecule of water is removed in the course of bond formation, a reaction known as condensation. Thus, only the monomers of carbohydrates actually have a CH₂O ratio because of the removal of two atoms of hydrogen and one of oxygen every time such a bond is formed.

When the sucrose molecule is split into glucose and fructose, as it is when it is used as an energy source, the molecule of water is added again. This splitting requires the addition of a water molecule and so is known as hydrolysis, from hydra, meaning “water,” and lysis, meaning “breaking apart.”

Another common disaccharide is lactose, a sugar that occurs only in milk. Lactose is made up of glucose combined with another mono-saccharide, galactose. Sugar is transported through the blood of many insects in the form of another disaccharide, trehalose, which consists of two glucose units linked together.

Polysaccharides: Sugars in Storage:

Polysaccharides are made up of mono-saccharides linked together in long chains. Some of them are storage forms of sugar. Starch, for instance, is the principal food storage form in most plants. A potato, for example, contains starch produced from the sugar formed in the green leaves of the plant; the sugar is transported underground and accumulated there in a form suitable for winter storage, after which it will provide for new growth in the spring.

Starch occurs in two forms, amylose and amylopectin. Both consist of glucose units linked together. Glycogen is the principal storage form for sugar in higher animals. Glycogen has a structure much like that of amylopectin except that it is more highly branched, with branches occurring every eight to ten glucose units. In vertebrates, glycogen is stored principally in the liver and in muscle tissue.

When there is an excess of glucose in the bloodstream, the liver forms glycogen. When the concentration of glucose in the blood drops, the hormone glucagon, produced by the pancreas, is released into the bloodstream; glucagon stimulates the liver to hydrolyse glycogen to glucose, which then enters the bloodstream.

Formation of polysaccharides from monosaccharide’s requires energy. However, when the cell needs energy and these polysaccharides are hydrolysed, the energy released is available for cellular work.

Structural Polysaccharides:

A major function of molecules in living systems is to form the structural components of cells and tissues. The principal structural molecule in plants is cellulose. In fact, half of all of the organic carbon in the biosphere is incorporated into cellulose. Wood is about 50 percent cellulose, and cotton is nearly pure cellulose.

Cellulose molecules form the fibrous part of the plant cell wall. The cellulose fibers, cemented together by other kinds of polysaccharides, surround the plant cells, which, in effect, live in little cellulose boxes. When the cells are young, these are flexible and stretch as the cell grows, but they become thicker and more rigid as the cell matures. In some plant tissues, such as the tissues that form wood and bark, the cells eventually die, leaving only their tough outer cellulose-containing walls.

Cellulose is a polymer composed of monomers of glucose, just as starch and glycogen are. Starch and glycogen can be readily utilised as fuel by almost all kinds of living systems, but only a few microorganisms- certain bacteria, protozoa, and fungi can hydrolyse cellulose. Cows and other ruminants, termites, and cockroaches can use cellulose for energy only because of microorganisms that inhabit their digestive tracts.

To understand the differences between structural polysaccharides, such as cellulose, and energy-storage polysaccharides such as starch or glycogen, we have to look briefly once again at the glucose molecule. You will remember that the molecule is basically a chain of carbon atoms and that when it is in solution, as it is in the cell, it assumes a ring form. The ring may close in either of two ways.

One ring form is known as alpha, and the other as beta. The alpha and beta forms are in equilibrium, with a certain number of the molecules changing from one to the other all of the time, going through the open- chain structure to reach the other form. Starch and glycogen are both made up entirely of alpha units. Cellulose consists entirely of beta units. Because of this slight difference in structure, cellulose is impervious to the enzymes that so successfully break down the storage polysaccharides.

Chitin, which is a major component of the exoskeletons of insects and also of the cell walls of many fungi, is a tough, resistant, modified polysaccharide.