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Chapter 3: The Molecules of Life - Proteins and Nucleic Acids

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Organic Molecules II: Proteins and Nucleic Acids

Web Lecture

Functional Groups

Amino Acids: C, H, O and N

Amino acids are molecules with a carbon on one end that attaches to an amine group (NH2, a carboxyl group (O=C-OH), and a neutral hydrogen atom. Because of the difference in charge, however, most amino acids undergo a shift in structure, relocating the hydrogen ion of the carboxyl on the amine group, and creating a polarized "head" to the molecule.

Amino acid formation

Polypeptide organization

Amino acids undergo dehydration synthesis to form peptide bonds between the end carbon of one amino group and the amine nitrogen of another. The chains that result are very stable, and when they are folded into secondary and tertiary structures, can be thousands of amino acid groups long, creating proteins. Proteins are the builders of cells: they are to regulate growth, repair damage. With yet another fold on top of the tertiary structures, they become the basic components of those essential enzymes mentioned earlier.

The proteins found in humans are built from twenty amino acids that can be divided into three groups by the way they combine: polar, non-polar, and ionic (electrically charged). Polar amino acids are hydrophilic, which means they are attracted to water molecules, which you will recall, are also polar. Some of the amino acids should be old friends. Tryptophan is the stuff in turkey that makes you want to take a nap after a large Thanksgiving dinner.

Essential amino acids are the ones you can't make, and have to get from the environment. There isn't a list in the text, because the ability to make amino acids differs between species. In Jurassic Park, the assumption was that the dinosaurs couldn't make lysine. If it wasn't available for them to eat (and the builders of the park had left it out of the food chain on purpose), the dinos would die. For the record, humans cannot synthesize phenylalanine, valine, leucine, isoleucine, threonine, tryptophan, or lysine. Inadequate amounts of these in the diet lead to retarded growth, mental apathy, and various physical deformities. All essential amino acids are readily available from animal products; so if you eat meat, you probably don't have to worry much about amino-deficiency problems. Vegetarians who will eat cheese and eggs are usually able to compensate for the lack of amino acids in plants, but strict vegans can run serious health risks unless they eat specific vegetables in sufficient quantity on a regular basis. Beans and corn together will contain all of the amino acids that you can't make from other foods, so these two crops have become very important food staples in most parts of the world.

The folded structures of proteins are held in place by those H-bonds we discussed before. When a hydrogen is attached to an oxygen or nitrogen atom, the hydrogen's electron is so strongly attracted to the oxygen or nitrogen that it stays mostly between the two atoms, leaving the external side of the hydrogen's positive proton nucleus exposed. The positive area can attract local negative areas elsewhere in the molecule with enough force to hold the molecule shape. These H-bonds are not nearly as strong as ionic or covalent bonds, and they can be broken if the chain is heated, dried out, or exposed to acids.

When multiple polypeptide chains are combined together (quaternary structure), the result is an enzyme with a specific function, dictated by a unique sequence of amino acids. Change any amino acid, the position of the hydrogens change and the shape of the protein changes.

The creation and denaturing of protein structure has some very practical results. If you heat milk enough, the protein casein in the milk, which are partly held in place by hydrophilic attractions to nearby water molecules, dry out. The individual casein protein chains unkink and link together, forming a "skin" on the surface of the milk. Most of us consider this a defect in our enjoyment of our bedtime cup of cocoa, although the casein is actually very nutritious. As with most chemical reactions, what is a problem in one situation can be an advantage in another situation. If you control the formation of casein chains by adding rennet to milk, though, you get cheese.

Take a look at John Kyrk's site on amino acid and polypeptide formation. His animations will help you visualize the difference between left and right forms of the amino acid, and how peptide bonds form.

Nucleic Acids

Nucleotides consist of a phosphate ion (PO4), a 5-carbon sugar called a ribose, and a base, which is one of five amino acids. Two nucleotides link together through their phosphate ions in a phosphodiester bond (a special kind of ester bond). The DNA/RNA strands which govern the way cells operate and reproduce are long sequences of nucleotides. We are definitely going to discuss this in more depth, so don't worry about all the details right now.

Do remember that all four of the major types of organic molecules form strands of multiple units made out of variations of very simple molecules, just as we write many words from 26 letters and a few punctuation marks, and create poems, novels, and textbooks. These chains form by the process of dehydration synthesis, and can be dissolved by hydrolysis, both of which depend on the availability of liquid water.