Molecules of Living Systems

Key Points 

      1.    What are the types of chemical bonds and molecular interactions that occur in cells?

      2.    Why is liquid water important for the evolution of cell metabolism?

      3.   Why is the chemistry of life based on the chemistry of carbon?

4.    What are the building blocks of large organic macromolecules? 


Chemical Bonds

    In the final analysis, cells derive their energy and main constituents through their ability to manipulate the chemical bonds of certain types of molecules. Rearrangement of chemical bonds can release energy that can be used to drive cell processes or synthesize molecules essential for cell function. Certain types of chemical bonds play an important role in these processes.

Covalent bonds result from the equal (nonpolar) or unequal (polar) sharing of pairs of electrons to fill the outer electron shells of pairs of atoms. Noncovalent bonds consist of the following interactions: 1) ionic bonds result from transfer of electron(s) from one atom to another leading atoms with positive charges and negative charges to attract each other; 2) hydrogen bonds are weak electrostatic interactions with a single hydrogen atom shared between two electronegative atoms; 3) hydrophobic interactions occur between groups insoluble in water which tend to clump together minimizing exposure to H 2O; and 4) van der Waals (dispersive) interactions are very weak interactions occurring between electrically neutral molecules that are very close together, due primarily to slight perturbations of electron distributions between the atoms. 



Manipulation of chemical bonds essential for life could not occur were it not for the presence of liquid water on Earth. The life-supporting properties of water flow from the unique structure of the
H 2O molecule. The H 2O molecule is asymmetric, the electronegative oxygen atom forming polar, covalent bonds with two hydrogen atoms. The two bonds are highly polar because the O is strongly attractive for the pair of shared electrons, whereas, the H is only weakly attractive. Although, overall the H 2O molecule is neutral, the unequal distribution of electrons leads to the formation of a partial dipole, with a positive charge around the two H atoms and a negative charge around the O atom. The electrical attraction between the positively charged H region of one H 2O molecule and the negatively charged O region of another molecule can result in formation of a hydrogen bond between them. It is the cumulative effect of many weak hydrogen bonds continually forming and breaking between water molecules that give water its unique properties. It is only because of the hydrogen bonds, which links water molecules together, that water is a liquid at room temperature, with a high heat capacity and a high heat of vaporization. Hydrogen bonding also makes water a good solvent by surrounding hydrophilic ions or polar molecules on their surface and carrying them into solution.  Molecules that contain mostly nonpolar bonds are usually insoluble in water, and are called hydrophobic. (fig

            One of the simplest kinds of chemical reactions occurring in cells, and one that has profound significance in cell metabolism, is the dissociation of H+ ions (protons) from polar molecules as they dissolve in water. When a polar molecule is surrounded by water molecules, the H+ is attracted to the water molecule, generating H3O+, a hydronium ion.  A molecule capable of releasing (donating) a hydrogen ion when it dissolves is called an acid. By convention, the H 3O+ is referred to as the H+ concentration and is expressed using the pH scale.  pH is a measure of H+ concentration (pH = - log [H+]).  Because the concentration of H+ ions in cells (the acidity) may affect the structure and function of other molecules, cellular pH must be closely regulated.  On the other hand, a base is a proton acceptor, capable of  raising the pH by binding H+ ions from H 2O molecules, forming OH -.  Because OH - combines with H 3O + to form two molecules of H 2O, an increase in the OH - concentration forces a decrease in the H 3O + concentration and vice versa.  Water is an example of an amphoteric molecule, a molecule that can serve as both an acid and a base. A pure solution of water contains an equally low (10 -7 M) concentration of both ions; it is considered neutral, having a pH of 7. Cell pH is kept close to neutrality by the presence of certain molecules that act as buffers to resist changes in pH by taking up or releasing H+ ions depending on conditions, and thus, minimizing fluctuation in cell pH. 



The chemistry of life is based on the chemistry of the carbon atom. Aside from water, most of the molecules in a cell contain carbon. Because it is small (atomic weight: 12 daltons) and because it has four electrons (and four electron vacancies) in its outer shell, carbon can form up to four covalent bonds with other atoms. Most important, one carbon atom can bind to another carbon atom forming carbon-carbon containing backbones, which may be linear, branched or cyclic, generating large and complex molecules. Carbons can be connected by single (C-C), double (C=C, C=O and C=N) or triple bonds (C=C, C=N). Carbon compounds are very stable. 

The small organic molecules of the cell range in molecular weight from 100 1000 daltons and contain up to 30 or so carbon atoms. They have several different functions. Some act as energy sources and are broken down and converted to other small organic molecules by cell metabolism. Others serve as monomers for the synthesis of larger, polymeric macromolecules.  Included in this class are: metabolic intermediates (metabolites), compounds formed along chemical pathways leading to end products that may or may not have another function; vitamins, cofactors in certain enzymatic reactions; steroid or amino acid hormones; molecules involved in energy storage (ATP, creatine phosphate); regulatory molecules (cyclic AMP); and, metabolic waste products (urea). This class of small organic molecules represents only about 10% of the total organic carbon pool in cells. However, within this group are the building blocks of the major components of the cell, the macromolecules. 

As we will see, a recurrent theme in cell function is the recycling of organic compounds. Monomers, used to synthesize macromolecules, are eventually regenerated as these large polymers are broken down and recycled.  These monomers can be grouped into four broad families: sugars, fatty acids, amino acids, and nucleotides. These four families of organic molecules, along with the macromolecules made by linking them into long chains, account for a large fraction of the cell mass.