Foundation of Life

CHEMICAL FOUNDATION OF LIFE

LEARNING OBJECTIVES

1. Define the term matter, and distinguish between an atom, a molecule, an element, and a compound.

2. Describe how protons, electrons, and neutrons are arranged into atoms.

3. Define the terms atomic symbol, atomic number and mass number (or "atomic weight"), and use these concepts to describe the structure of selected elements that are significant to living things.

4. Define isotope, and identify possible uses for isotopes in scientific study.

5. Explain how electrons are distributed in atoms, and how this affects the number and types of chemical bonds that can be formed.

6. Describe the various types of chemical bonds, the circumstances under which each of them forms, and their relative strengths.

7. Identify the properties of water that make it vital for life.

8. Define the terms organic compound and inorganic compound, and give examples of each.

9. Understand how small organic molecules can be assembled into large macromolecules by condensation and how large macromolecules can be broken apart into their basic subunits by hydrolysis.

10. List the four large "molecules of life," identify their composition and structure, and describe some of the functions they perform in the cell.

A Brief Look at Biochemistry

Many of the compounds found in living systems are large - they're often referred to as macromolecules. In this brief summary, I want to concentrate on some of the most important macromolecules: proteins, carbohydrates, lipids and nucleic acids.

Proteins

Proteins are large molecules composed of smaller subunits called amino acids. There are about twenty common amino acids found in living systems. Each amino acid contains a central carbon atom bonded to a hydrogen atom (-H), an amino group (-NH2), a carboxyl group (-COOH) and a variable group that's often symbolized with the letter -R.

Proteins are formed by a dehydration synthesis in which the hydrogen atom of the amino group of one amino acid joins with another amino acid's carboxyl group, specifically the -OH of that carboxyl group, to form water. The resulting covalent bond between amino acids is called a peptide bond. Thus, peptide bonds couple amino acids together to form proteins. The linear arrangement of amino acids is called the primary structure of the protein. A very short chain of amino acids, perhaps nine amino acids in a row, is most often called a peptide. A very long chain of amino acids is called a protein. Chains of amino acids of intermediate lengths may be referred to as polypeptides.
Proteins are made of amino acid subunits. Since the carboxyl group has an electrically negative region near its double bonded oxygen and the amino group has an electrically positive region around its hydrogen, there will be regular and repeating interactions among subunits. Those regular interactions create two types of folding: pleated sheet and alpha helix. Those regular and repeating shapes are called the secondary structure of the protein.

I want to say again that proteins are made of subunits called amino acids. Some amino acids ionize in aqueous solution and living things, as you may recall, are comprised of aqueous solutions. Due to the ionization of amino acids, some parts of the protein will have negative charges and other parts will have positive charges. Because of ionization, the molecule we call protein will not be in a linear form when it's in an aqueous solution - it will have a unique shape beyond the alpha helix and pleated sheet. Since the molecule is flexible, the protein will "curl-up" into a unique shape that depends in part on the nature of the solution in which that the protein is dissolved. Furthermore, if the pH of the solution were to change, the shape and function of the protein would be expected to change too. The unique overall shape of the protein is called the tertiary structure of the protein.

A few large proteins are comprised of two or more polypeptide chains. That association of separate polypeptide chains is referred to as quaternary structure. Hemoglobin is made-up of four subunits of two distinct types of polypeptide chains. Hemoglobin is therefore said to have quaternary structure.

Carbohydrates

Like proteins, carbohydrates are large molecules made of repeating subunits. The subunits of carbohydrates are called simple sugars (monosaccharides). Two subunits can be coupled together by a dehydration synthesis to form a disaccharide or several hundred monosaccharides may be coupled to form a polysaccharide. One common disaccharide is sucrose, which we often call table sugar (or just sugar - as in "please pass the sugar"). Sucrose is made of a glucose monomer bonded to a fructose monomer. Starch is used by plants to store energy, and it is a polymer of glucose. Animals store excess carbohydrate as a polymer called glycogen, also made entirely of glucose subunits.

Lipids

When I think of lipids, I think of anything that's not soluble in water. I know my ideas aren't definitions, but they're not bad ways of thinking of things as long as you're reasonable. The lipids most important in biology are fats, phospholipids, steroids, and waxes. Lipids are said to be hydrophobic (water hating) because they do not dissolve in water.

Oils are a type of fat - a molecule made of glycerol and three fatty acids. Fats are energy storage molecules. In fact, fat has about twice the calories of carbohydrate or protein on a weight basis (a pound of fat has twice the energy of a pound of either protein or carbohydrate). Fat is also used as insulation and padding by animals. If the fat contains double bonds in it's fatty acid, we say the fat is unsaturated (a saturated fat has no double bonds between the carbons). If there are many double bonds, the fat is called "polyunsaturated". Polyunsaturated fats are liquid at room temperature, while saturated fats are fairly solid at room temperature. Most folks believe polyunsaturated fats are better in the human diet than saturated fats since high levels of saturated fats in the diet are associated with cardiovascular disease.

Phospholipids are similar to fats since both are made of glycerol and fatty acids. But phospholipids have only two fatty acids bonded to each molecule of glycerol rather than three as fats do. Unlike fats, phospholipids contain phosphorus.

Steroids are made of four fused rings. Cholesterol is a very common animal steroid (and it's never found in plants). Cholesterol is found in animal cell membranes (it makes them less flexible) and it's the starting molecule for the synthesis of sex hormones such as testosterone and estrogen.