Chemistry of Cells - Biomolecules and Their Properties

         Cells may be described as chemical reaction vessels in miniature.  Cells are made up of chemically reactive biomolecules, themselves built up from elements and atoms, which are the material substance of the universe. Living things have been highly selective in the combinations of the elements of which they are made.  The elemental composition of cells does not reflect the abundance of the natural elements in the Earth's crust upon which they live.  Does the selection of these elements, and the molecules they construct, make the chemistry of life unique, and if so how?

The tenet of Self-Organization (Origin of Cells section), which suggests that the natural order may lead to greater organizational complexity in living systems, can be seen to be at work in the chemical makeup of cells, especially when two or more atoms combine reactively to form a molecule. A molecule is the smallest part of a substance, which keeps all the properties of that substance and is composed of one or more atoms.  The self-assembly of atoms into molecules, and molecules into compounds, and compounds or macromolecules into organelles, and organelles or cells into tissue has resulted in a complexity of chemical properties, which has been favored by cells over eons of evolutionary time.   This natural selection of molecules, these biomolecules with unique chemical properties, has give rise to cells exhibiting the properties we define as living.

        Even the most complex and complicated biological molecules, such as muscle glycogen, nor-adrenaline, or the multi-subunit enzyme complex, pyruvate dehydrogenase, can be divided into smaller and smaller basic molecules.  It is the structure of such complex biological molecules and how their 3-D shape and conformation determines the biological role they play in the complex chemical processes we define as life.

Small Biomolecules - Simple Sugars and The Orientation of Atoms in Space

Key Points
   1. What are the common biomolecules, found in living systems, which are universal to all cells?
   2.  How is chemical structure related to biological function?
   3. What is biological activity and how is it related to molecular structure?
   4.  What role do the simple sugars plat in biological structure and function?

            The large organic molecules, which are most abundant in all cells, are the carbohydrates, lipids, proteins, and nucleic acids. A remarkable uniformity exists in the molecular components of organisms--in the nature of the structural makeup, as well as in the ways in which they are assembled and used. The assembly of these complex workhorse macromolecules is from smaller organic building blocks, which I will refer to as small biomolecular precursors (monomers). They are the simple sugars, the fatty acids, the amino acids, and the nucleotides. These small biomolecules have been found in all known cells and living systems. The essential feature of these monomer precursors is their capacity to form chemical bonds to at least two other monomer precursors forming linear, chainlike polymers, as well as cross-linked, network polymeric products.

            The simple sugars, monosaccharides, are monomeric molecules containing C, H, and O in the often consistent ratio of CH ₂O.  Molecular structure, which relates to the orientation of covalent bonds and/or functional groups in 3-D space is critically important to biological function.  The simple sugars may to used to easily demonstrate the importance of molecular structure, spatial orientations, and shape to biological activity.

The simple sugars found in all living cells and are classified by the number of C's they contain and/or the number of individual monomers present (see Table 1).

                Structural formulas help identify the orientation and location of chemical bonds between the atoms of a molecule. An isomer is a molecule with the same empirical formula (such as glucose and galactose - C ₆H ₁₂O ₆), but which has a different structural formula. Structural formulas are particularly useful for showing how compounds with the identical kind and number of atoms differ architecturally.  Figure 1, below, shows the difference between the spatial arrangement of the hydroxyls on three common, but different hexose sugars. These small spatial differences in the orientation of the functional group -OH are readily recognizable by enzymes and other receptor proteins and therefore can result in molecules with uniquely different biological properties and vastly different biological effects.

Figure 1.  Isomers of hexose sugars - glucose, galactose, and mannose.
	Glucose, galactose and mannose all have the same empirical formula (C 6H 12O 6), but as figure 1 reveals, in glucose the hydroxyl on carbon number 4 is oriented below the plane of the hexose ring structure, while in galactose that hydroxyl points above the plane of the ring. Mannose differs from glucose via the hydroxyl orientations at carbon number 2.

        Glucose is found in fruits and honey and is the major free sugar circulating in the blood of higher animals.  Galactose is often found in nature combined with other sugars, as, for example, with glucose, making the sugar lactose (milk sugar). Galactose is also found in carbohydrate-containing lipids called glyco-lipids, which occur in the brain and other nervous tissues of most animals. Mannose is a stereo-isomer of glucose, as its hydroxyl group on C2 is the mirror image of glucose. Reduction of the aldehyde group in the sugar mannose by a reducing agent forms mannitol, which is a slightly sweet crystalline alcohol found in many plants and commonly used as a diuretic and in testing kidney function. Thus the orientation of atoms is space is key to biological properties.               

Figure 2.    alpha/beta hydroxyl orientation in glucose.

Another key example of how spatial orientation of atoms is important to biological activity can been seen in the disaccharides and polysaccharides formed from glucose monomers.  The orientation of the hydroxyl group on carbon 1 in glucose can be seen in the figure to the left. The hydroxyl at this asymmetric or center carbon can rapidly change its orientation between two positions called alpha, where the hydroxyl is below the plane of the ring and  beta, where the hydroxyl is above the plane of the ring.

             A disaccharide is formed by linking together two hexoses, usually via the hydroxyl group on an asymmetric carbon,  with any other hydroxyl group on another hexose. As soon as one sugar is linked to another, the alpha or beta form is frozen.  The reaction that links two sugars together is called a condensation reaction and water is eliminated, while forming a covalent link, called a glycosidic bond between the two carbons atoms on each hexose monomer. The glycosidic bond (-C-O-C-) can form either with the oxygen link oriented below the ring's plane (alpha) or above (beta).  Table 4 reveals some common disaccharides found in cells with their respective glycosidic bond orientations.

                 The differences in biological activity among these disaccharides seems obvious and stresses the concept that spatial orientation of functional groups is most important to chemical reactivity.  Large linear and branched molecules can be made from the repeating monomeric units of simple sugars. Short chains of carbohydrate monomers are called oligosaccharides, while longer chains are called polysaccharides.  Table 3. Shows some common polysaccharides found in cells. 

             The spatial and structural differences between amylose, plant starch, and cellulose are minor.  In starch, a common easily digestible human food source, the glycosidic linkage is alpha, while in cellulose, an indigestible structural plant polymer the glycosidic links are beta.  Cellulose digestion in lower termite families depends upon symbiotic flagellate protozoa, which live anaerobically (without oxygen) in the termite hindgut and secrete the enzymes cellulase and cellobiase that can break down beta-1,4 linkage of the cellulose polymer into glucose and acetic acid.  Humans lacks the enzyme cellulase or the symbiotic protozoa to make it and thus the cellulose man ingests in vegetables and fruits is indigestible. It cannot be absorbed from the digestive tract, and the residue that is not broken down by bacteria must be expelled from the body. Ruminant organisms, such as cows, sheep, and deer contain cellulose digesting bacteria and protozoa in their four stomachs, and survive on the glucose which is made available to them by these symbiotic cells.  What appears to be a minor spatial orientation difference between two molecules, starch and cellulose, turns out to be of great significance biologically.  

            The spatial arrangement of atoms in a molecule is referred to as its configuration and configuration is critically important to biological function. The orientation of atoms seems then to be able to do biological work.  

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