The Building Blocks of Biochemistry

Submitted by ChemPRIME Staff on Thu, 12/16/2010 - 16:17

It has been estimated that even a unicellular organism may contain as many as 5000 different substances, and the human body probably has well over 5 000 000. Only a few of these are exactly the same in both species, and so the total number of different compounds in the living portion of the earth (the biosphere) is approximately (105 compounds/species) × 106 species = 1011 compounds. If it were possible for chemists to synthesize one of these every second, 24 hours a day, 7 days a week, about 3000 years would be required to make all of them—obviously a hopeless task, even if we knew the composition and structure of each one.

How then can we make sense out of the chemistry of living systems? Fortunately nearly all the substances found in living cells are polymeric—they are built up by different combinations of a limited number of relatively small molecules. For example, the basic structures of all proteins in all organisms consist of covalently linked chains containing 100 or more amino acidA carboxylic acid containing an amino group (-NH2). In an alpha amino acid, the amino group is attached to the carbon atom adjacent to the carboxyl group. residues. Only 20 different amino acids are commonly incorporated in proteins, but the number of ways of arranging 100 of these in a chain taking any of the amino acids at random for each place in the chain is 20100 \cong 10130, allowing an almost infinite variety of structures. Just as an understanding of the properties of atomsThe smallest particle of an element that can be involved in chemical combination with another element; an atom consists of protons and neutrons in a tiny, very dense nucleus, surrounded by electrons, which occupy most of its volume. and their bonding characteristics was a significant aid in predicting the chemistry of molecules, a knowledge of the properties of simple molecular building blocks gives us a starting point for the study of biochemistry. Each of the building blocks and their polymeric forms has at least one major role to play in the chemistry of life. Most are quite versatile, serving several functions. Let us take a look at the building blocks of biochemistry:

Sugars, or carbohydrates are molecules that follow the form Cx(H2O)y. A simple sugar can serve as an energyA system's capacity to do work. source for an organism. Simple sugars can dimerize into disaccharides or polymerize into Polysaccharides. Uses for polysacharides range from energy storage, such as glycogen stored in your liver and muscles, to structural support, such as cellulose that makes up cell walls for plants.

glucose, a monosaccharide sucrose, a disaccharide glycogen a polysaccharide

Amino Acids as mentioned earlier are a class of 20 molecules that polymerize to form proteins. Proteins take on a large variety of roles, from catalyzing important reactions as enzymes, to providing structural support, such as collagen, to serving as hormone or neurotransmitter signals.

L-alanine, an amino acid A protein, a blue GPF varient, shown in stick form. Ribbon view of the same protein.

Nucleotides are a slightly more complexA central metal and the ligands surrounding it; also called coordination complex. class of biological molecule, consisting of a phosphate groupThose elements that comprise a single column of the periodic table. Also called family., a ribose or deoxyribiose sugar, and a nitrogenous baseIn Arrhenius theory, a substance that increases the concentration of hydroxide ions in an aqueous solution. In Bronsted-Lowry theory, a hydrogen-ion (proton) acceptor. In Lewis theory, a species that donates a pair of electrons to form a covalent bond.. Nucleotides, such as ATP serve as carriers of energy in a cell and provide energy to run processes that would otherwise be non-spontaneousCapable of proceeding without an outside source of energy; refers to a reaction in which the products are thermodynamically favored (product-favored reaction).. Nucleotides are able to polymerize into nucleic acids by forming a phosphodiester bond between the phosphate group of one nucleotide and a hydroxyl groupThe functional group of an oxygen atom bonded to an hydrogen atom, -OH; found in alcohols. on the ribose or deoxyribose of another nucleotide. The polymeric nucleic acids are able to store information for building proteins.

dATP, a nucleotide B-DNA the polymer and a nucleic acid.

Fatty Acids can already be considered somewhat polymeric, as they consist of a end carboxylic acidAn organic compound containing the functional group -C(=O)OH. followed by a hydrocarbonA compound containing only the elements carbon and hydrogen. chain of varying lengths. Three fatty acids can be attached to glycerol to form triglycerides. Other chemical groups can be added to the three hydroxyl groups of glycerol, thus yielding many chemical variations, which along with other non-polarDescribes a molecule that has separated, equal positive and negative charges that consitute a positive and a negative pole; such a molecule tends to assume certain orientations more than others in an electric field. chemicals are all included in the umbrella category of fats and lipids. Functions of these polymers again range from energy storage, to forming membranes necessary to structure, to signaling.

palmitic acid, a fatty acid. A triacylglycerol.

Salts can be thought of as a polymers when considering the ionic crystal lattice. This can be applied to extracellular structures such as shells, teeth and bones. In cells, salts serve roles as ions in solution. Effects in this "monomeric" form include Ca2+ signaling, setting up electrochemical gradients to do work, or influencing osmotic properties.

Water polymerizes in ice formation. Much of this structure still remains in liquidA state of matter in which the atomic-scale particles remain close together but are able to change their positions so that the matter takes the shape of its container form, and hydrogen bonding networks still remain. So not only does water provide the solventThe substance to which a solute is added to make a solution. medium for all chemical reactions in cells, its structure dictates the way proteins fold, and how membranes form. It also maintains rigidity of cell walls, and serves as a thermoregulator. By virtue of its large polarity water is a good solvent for ionic substances and therefore provides a means of transporting inorganicPertaining to the chemistry of elements other than carbon and compounds containing at most a small amount of carbon. nutrients such as NH4+, NO3, CO32–, PO43–, and monatomic ions throughout higher organisms. Its ability to dissolve a wide variety of substances also makes it useful for disposing of wastes. Many of the human body’s defense mechanisms against external toxic substances involve conversion into water-solubleAble to dissolve in a solvent to a significant extent. forms and elimination via urine.

A water molecule. Ability to hydrogen bond allows for proton transfer, and confers structural elements to liquid water.

Vitamins and trace elements, while not as prevalent as the chemical compounds discussed above, trace elements, such as zinc, copper, and iron are highly important to biological function, often serving key structural and chemical purposes in protein function. Vitamins are organic compounds that often augment proteins to help with biological functions.

Vitamin B1, also known as thiamine. This organic molecule helps with the enzymatic activity of the protein pyruvate dehydrogenase complex.

It is clear from this overview that both monomeric and polymeric forms of the chemical components of chemicals in living systems serve important functions. Also, those functions change depending on which building blocks are used for polymerizationThe process of forming a polymer from monomers.. However, the properties of these polymers can be understood in terms of the monomers and how they combine.