What life is

 


The chemistry of life

To understand the mechanism of life, or how living organisms manage to reproduce, grow, move, think, eat and do whatever it is that they are doing, biologists can apply chemistry and physics to the study of life. The important foundation for any biologist who wants to understand mechanisms are based on the answers to the following questions:

What is an element?

What is a molecule?

What is a macromolecule?

Why is carbon important?

Understanding the physics and chemistry of biologically important molecules allows insight into the structure and function of cells. The 20th century has made great progress in molecular biology and biochemistry. The 21st century will make great progress in putting the molecular pieces together and reconnect classical biology with molecular biology and the whole with its parts, a science called systems biology.

Biological macromolecules are defining the properties of cells. These molecules include proteins, nucleic acids, carbohydrates and lipids. The properties they convey are enzymatic activity (metabolism), genetic inheritance, reproduction, and cell growth, and energy storage and conversion and interaction with the environment.

All living organisms use the same four types of macromolecules for cellular metabolism and reproduction. Together, they illustrate the commonalties of life on earth. The way they are used in different forms and combinations explains today's variety or biodiversity. Both aspects, sameness and variety, are the result of biological evolution.

An interesting link between hierarchical organization and chemistry is the combinatorial nature of living things. With this I mean that cells are made of macromolecules, macromolecules of molecules and molecules of elements. In living things we find a 'language' or information system that is used to make the next higher level of organization. Six select elements make the majority of biological molecules, select molecules are the building blocks of macromolecules, select macromolecules are the building blocks of cells. We can see them as letters, words and sentences - an alphabet to create information used to make structures with function.

For instance, biological molecules are made of carbon (C), hydrogen (H), oxygen (O), nitrogen (N), sulfur (S) and phosphor (P) plus many ionic species (e.g. sodium, potassium, chloride, calcium, magnesium, iron, copper, cobalt, manganese, selenium). So how does the molecular alphabet of life work? The table shows the basic elements found in the four classes of macromolecules.

Macromolecules Elements* KEGG structures of building blocks
Lipids C, H, O Fatty acids
Carbohydrates C, H, O Monosaccharides
Proteins C, H, O, N, S Amino acids
Nucleic acids C, H, O, N, P Nucleotides

*These combinations show the most common types and there are of course lipids and carbohydrates that have N, P and S. Examples are phospho-, sulfo- and sphingolipids, and glucosamines. Hydrocarbons, however, are very rare and are either waste products or energy sources (e.g. methane) or secondary metabolites (e.g. carotenes).

The origin of structural variability

Looking at this table, how then can lipids and carbohydrates be different? This, of course, comes from the way the elements are put together. Lipids have higher proportions of hydrogen bound to carbons (they are hydrocarbons), while carbohydrates have one equivalent of water (H2O) for every carbon (C), i.e., they are carbohydrates. Variability comes also in form of carbon backbone structures. With this we mean the modes of connection between neighboring carbon atoms via chemical bonds. What is found in nature is that carbon backbones vary in the following four modes:

linear
branched
cyclic
double bonds

In addition, the number of carbon atoms that can be built into these backbone structures seem unlimited, creating the foundation of an incredibly diverse three dimensional diversity. All bonds not used for carbon-carbon linkage is used to add either hydrogen, oxygen, nitrogen, sulfur or phosphorus atoms. Now we get a good impression of the ability to create very large numbers of different molecular structures using only six different elements.

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 Copyright © 1999-2011 Lukas K. Buehler