Molecular Biology

Proteins Amino Acids Polypeptides Dehydration Synthesis Chains Methylamine Life Bonding



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Of all the chemical manifestations in the universe, amino acids are without question the most incredible stuff ever to have chemically evolved. But quite amazingly, amino acids are a totally natural occurrence and just about anywhere you find liquid water, you are almost sure to find amino acids too. More awesomely still, given stable environmental conditions and enough time, where you find amino acids you will likely find another natural occurrence, the essence we call life.

The building blocks of life and agents of its processes are substances called proteins, and proteins are nothing more than polymer chains of amino acids joined by peptide bonds. More than 50,000 different types of proteins have been catalogued, most consisting of the twenty standard amino acids. There are actually many other non-standard amino acids, but these are only rarely found in proteins.

Understanding how amino acids form proteins, also referred to as polypeptide chains, is as simple as understanding the bonds or electrical protocol which join atoms of elements to form molecules. There are basically three different types of bonding which occur between elements and molecules, they are Ionic, Covalent, and hydrogen bonds. The peptide bonds which join amino acids to form proteins are of the covalent variety. If science and chemistry are not your forte, the next two paragraphs provide a brief primer on covalent bonding which may be helpful in understanding protein synthesis. Other readers more well versed in chemical bonding may want to skip ahead.

Elements, of course, are made up of Protons, Neutrons and Electrons. The protons and neutrons are found in the nucleus of the atom and exhibit a slightly positive electrical charge. Compared to the nucleus, electrons are infinitesimally small particles which carry a negative charge. Electrical charges are exactly like the poles of a magnet in that like charges repel and opposing charges attract each other. Protons, being positively charged, attract negatively charged electrons pulling them in towards the nucleus of the atom. If a proton and electron could actually get together their charges would cancel out an a neutrally charged particle appropriately referred to as a neutron is formed. But electrons are also high energy particles and are moving through space at slightly less than the speed of light. This high velocity and subsequent centrifugal force causes the electrons to orbit the nucleus of the atom at a great distance, and prevent it from crashing into the nucleus of the atom.

The number of electrons which can obit any given atom is determined by the number of protons in the atoms nucleus. In addition, only so many electrons can orbit the nucleus at any given distance. Scientists in the field of Quantum Mechanics perceive electron orbits to be representative of shells and have designated these shells or levels as K,L,M,N,O and P. The first shell(K) can hold only two electrons and the next further out (L) eight. Subsequent shells can hold more electrons, but to achieve a status of electrical equilibrium(balance) the outermost shell can never have more than 2 electrons in the case of the K shell, or 8 electrons in the case of the other shells. An element with less than 2 or 8 electrons in its outermost shell will share (in the case of covalent bonding) the electrons in its outermost shell with another atom or atoms to achieve its balanced state. For instance, hydrogen is an atom consisting of one proton and one electron in its K shell, and it needs a second electron to achieve equilibrium. Nitrogen is an atom with 7 protons, 2 electrons in its K shell and 5 electrons in its L shell, and it needs to share 3 electrons to essentially achieve its L shell octet. The number of electrons an atom will share in a covalent bond is called its valence and the valence number is expressed as a + or - electrical charge condition. If you mix some hydrogen gas H-1 with some nitrogen N+3 gas, compress them to put their atoms in close proximity and apply a little heat, you will end up with a nitrogen atom covalently bonded to three hydrogen atoms and chemically represented as NH3; more commonly known as the molecule Ammonia. Carbon is an atom with 6 protons and 6 electrons, 2 in the K shell and 4 in the L shell. Just like nitrogen, carbon will share its 4 valance electrons with 4 separate hydrogen atoms to form a molecule of methane CH4.

Ionic bonds are generally stronger than covalent bonds because in ionic bonding one atom donates one or more electrons to the other atom, it doesn't just share them. As a result, molecules and compounds formed with ionic bonds do not readily react with other molecules or compounds. Sodium Chloride NaCl (common table salt) is an example of a strong ionic bond between atoms of Sodium and Chlorine. In most cases, covalent bonds tend to be metastable, meaning that the bond can be broken or modified under certain circumstances to change the chemical nature of the molecule or molecules. For instance, if you were to take some methane and ammonia, combine them in a glass container and then shine ultraviolet light on them as a source of energy, after a while you would notice some yellowish brownish stuff forming on the wall of the glass container. This stuff would be representative of a number of new molecules including a group known as amines. There would probably be several flavors of amine in the mixture, the simplest and most abundant being methyamine with traces of other amine compounds including propylamine, monoethanolamine, diethanolamine, triethanolamine, and so on.

Methylamine (NH2CH3) results when a methane and ammonia molecule each give up one of their bonds with a hydrogen atom and become covalently bonded together. The CH3 molecule actually replaces one of the hydrogen atoms on the ammonia molecule. Incidentally, the resulting covalent bond will not be quite as metastable as the original bond between the respective carbon and nitrogen atoms.

Now, if we were to repeat our glass container experiment again, but this time include some additional gasses such as oxygen and carbon dioxide, both of which are naturally occurring, we would notice a whole lot of modified compounds including combinations of elemental oxygen, (O) hydrogen/oxygen (OH) (called a hydroxyl group) attached to the methylamine compounds that form. In this case, the methane is not really methane any more because in place of one of its hydrogen atoms there may be another carboxyl group (COOH) which kind of looks like a methane molecule with oxygen atoms where the hydrogen atoms ought to be. The resulting molecule would have the formula NH2CH2COOH. Interestingly, this formula also represents the simplest amino acid found in proteins called glycine. Interestingly, 18 of the remaining 19 amino acids we are concerned with here are all based on the methylamine based glycine model. The exception is the amino acid proline which has a modified amide configuration.

Basically you can build the other amino acids from glycine by replacing another of the methyl molecules hydrogen atoms with a variety of other compounds, the simplest being another methane (CH3) molecule. In this case you would have the amino acid Alanine. This adaptation is referred to as an R group and by changing the R factor all of the other amino acids can be formed, again with the exception of proline. So we can think of the basic amino acid formula as NH2CH(R)COOH.

As you can see, this profusion of naturally occurring chemical reactions is becoming fraught with complexities, but amino acids represent only the first level of this complexity as the fundamental constituents of proteins. Theoretically speaking, there is a seemingly infinite number of possible combinations of R groups in combination with amide and carboxyl groups to form an equally immense number of different amino acids, given the right environmental factors. Fortunately, there are just 20 amino acids that are involved in proteins and life, at least here on Earth. It is chemically conceivable that some bizarrely different amino acids have formed some equally freakish proteins resulting in some anachronously divergent life forms elsewhere in the universe. But what ever the resulting form, it is totally predictable that it has come about through the very same processes of chemical bonding that glue amino acids together into proteins here on Earth.

If we were to do another experiment by dissolving small quantities of all 20 amino acids in a glass of water, and then leave it stand for a day, we would find that what began as a somewhat acidic mixture (tangy to the taste) had jelled or congealed into a slimy sticky mess. So what happened? Well, it turns out that all of these amino acids exhibit a degree of polarization, one end of the molecule the, carboxyl group, carrying a net negative charge and the amide group carrying a net positive charge. In a reaction called dehydration synthesis the amine end of one amino acid attaches itself to the carboxyl group of another amino acid by exchanging the bond between the carboxyl groups OH radical with one of the hydrogen bonds of the amide on the other amino acid. In the process, the replaced OH radical and sacrificed H atom of the amide combine to form a molecule of water (H2O), hence the classification as dehydration synthesis. The resulting bond is referred to as an amide or peptide bond. In this way, amino acids string themselves together in immensely long sequences referred to as polypeptide's or proteins. But as mentioned, peptide bonds are metastable and the process can be reversed by hydrolyzing (adding water) to the protein.

Certainly this chemistry involves some complexities, but nothing to the degree that any element of intelligent design is required to manifest its happening. Its a natural chemical process that conforms to the electrical protocol which defines the bonds that old all of the matter in the universe together. Interestingly, there is another structure made of amino acids called nucleotides. In fact, we could think of nucleotides as a kind of macro proteins, but we will leave that bit of complexity for another article.

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