This discussion reviews three topics for science students: water, pH, and the chemical bonds within protein chains.
To begin, though, consider the periodic table, which is a compact and very basic aid for discussing chemistry. It may be viewed on a single sheet of paper. This discussion begins with hydrogen, carbon, nitrogen, and oxygen from the first two rows, which are especially pertinent in biochemistry. Elements in the third row will be included later.
Periodic Table of Elements – PubChem
The periodic table is arranged by increasing nuclear charge from left to right across each row with each successive element gaining one proton. Hydrogen, the simplest element, has one proton, and helium has two, completing the first row. In the second row, carbon is element number six, with four more protons than helium. Nitrogen has five more than helium, and oxygen has six more. These four elements are enough for an introduction to biological chemistry. Neutrons and the remaining elements can be set aside for now.
We have not yet mentioned electrons, which form bonds between elements. Hydrogen, carbon, nitrogen, and oxygen can also exist on their own. Unbonded hydrogen is a gas. Carbon can bond to itself to form solids, including diamond in its pure, compressed form. Two nitrogen atoms can share electrons to form diatomic nitrogen gas, and oxygen can do the same.
The variety of compounds found on Earth depends on elements binding to one another in heterologous combinations. Without this, our world would be quite different.
This essay focuses on two topics: (1) water and its acidity and (2) the backbone structure of proteins. Many biochemistry and molecular biology textbooks including Molecular Cell Biology by Darnell, Lodish, and Baltimore, cover these subjects in much greater detail.
Oxygen and hydrogen. If oxygen and hydrogen are placed together with a small spark, they combine explosively to form water, releasing a large amount of heat. Please do not try this at home. Water is a highly stable compound, and without it, life would be impossible.
Water is represented chemically as the symbol H2O. Free hydrogen and oxygen molecules would not normally exist independently within water, but small amounts of hydrogen ions, H+, and hydroxide ions, OH–, will be present at concentrations of ~10-7 M. Pure water has a pH of 7; that is, the concentrations of both OH– and H+ are 10-7 M. All science students should know that pH of any aqueous solution is defined as the negative log of the hydrogen ion concentration. Example: The log10 of 10-7 is “-7”, and the negative of this is “7” … The lower this number, the more acidic the solution.
Water has several unique properties to consider. One is that it is an excellent solvent for many biologically important ions, including Na+, K+, Ca++, and Mg++. Amino acids and many proteins, those which also have strong ionic properties, are often soluble in water. Water is a good solvent because it is a polar molecule. Molecular polarity arises within the molecule from a separation of charge.
Although water has no net charge per se, electrons are drawn more strongly toward oxygen than toward hydrogen. As a result, the region around oxygen is slightly negative, while the regions around the two hydrogen atoms are slightly positive. This creates a dipole. Because this molecule is bent, with an H-O-H bond angle of 104.5°, water has the shape of an isosceles triangle. In short, its polarity makes water an excellent biological solvent.
Water acidity. As previously stated, a pH of 7 of pure water is a statement that pure water contains 10-7 M hydrogen ions, H+. For electrical neutrality in pure water, it would also contain the same concentration of hydroxide ions, OH–. In any aqueous solution, the product of the concentrations of OH– and H+ must remain the same. This product of 10-14 M2 is set by the energetics and thermodynamics of the water association/disassociation reaction. This you may learn when you study physical chemistry in college.
An important reaction in water occurs between the solvent, water, and a solute, carbon dioxide, which is a gas at room temperature. Carbon dioxide is present in small amounts in the atmosphere, oceans, and Earth’s crust. It is produced by fossil fuel combustion and by animal respiration. When carbon dioxide combines with water, a weak acid forms.
H2O + CO2 ↔ HCO3– + H+
This reaction produces two ions, including a free hydrogen ion, that is a proton. As a result, the hydrogen ion concentration increases, the pH decreases, and the solution becomes more acidic. The reaction involves bonds between carbon and oxygen, carbon and hydrogen, and between oxygen and hydrogen. Like all chemical bonds, these depend on electrons surrounding atomic nuclei.
Oxygen has eight protons and therefore eight electrons. Only six of these are valence electrons, as the first two electrons complete the innermost core and don’t participate in bonding activity. Electron orbitals fill according to quantum mechanical rules, and a stable, complete, outer arrangement of electrons would include eight. Because oxygen contributes only six valence electrons, it needs two more for this eight-electron configuration to be completed. In water, those electrons are supplied by two hydrogen atoms, giving H2O.
Carbon has six protons and six electrons. Beyond the first two inner electrons, it has four valence electrons and, therefore, needs four more to complete its outer shell. Oxygen, by contrast, has six valence electrons and needs only two more. In the molecule CO2, one carbon shares electrons with two oxygen atoms, forming two strong double bonds that satisfy the electron requirements of all three atoms. These two strong double bonds form a linear molecule and is a gas at room temperature.
In summary, water and carbon dioxide are chemically stable compounds, as shown on the left side of the reaction above. What, then, happens on the right side, where hydrogen ions, H+, and bicarbonate ions, HCO3–, appear? The answer is that some of the original bonding is rearranged during a reaction between carbon dioxide and water.
In this reaction, CO2 combines with an OH– group, which is present at low but sufficient concentrations in water, to form a bicarbonate ion, HCO3–. Carbon sits at the center of this structure. One oxygen of the HCO3– ionic molecule forms a strong double bond with carbon. The remaining two oxygens have single bonds with the central carbon in an arrangement producing the bicarbonate ion.
Of the two remaining oxygen-containing groups just mentioned, one of these binds to both a hydrogen atom and the central carbon, creating an attached -OH. The other oxygen binds to carbon without a proton and thus carries the negative charge. This gives bicarbonate its anionic character. The remaining proton enters the water solution, associating with a water molecule to form hydronium, H3O+.
That concludes the brief discussion of dissolved CO2 in water.
Proteins. The four elements from the first two rows of the periodic table, H, C, N, and O, are also essential for the amino-acid molecules that form proteins. Amino acids share a common core structure but differ in their “side groups”. As they link together forming proteins, these “side groups” give proteins their structural and functional variety.
At the center of the common, repeating portion of the amino acid chain structure is a carbon atom with four bonding positions.
A bond connects two amino acids: a carboxyl group of one amino acid (-COOH) binding to an amino group (-NH2) of another. Such bonds release a water molecule and join the two adjacent amino acids via a “peptide link”. This peptide bond has a “resonance” behavior, meaning that its electrons are distributed giving both polar and nonpolar characteristics to the bond.
A third bond on the central carbon is to a hydrogen atom, and a fourth bond attaches the side chain, giving the protein chains their variety.
Tertiary structure of proteins. Proline is unusual among the amino acids in protein chains because it introduces a kink into the amino acid chain-link formation. This distinctive linkage disrupts the regular pattern. In introducing a kink, this allows the amino acid chain to fold back on itself in forming globular structures, of which there are many.
An elementary discussion such as this would also require several elements from the third row of the periodic table: sodium (Na), magnesium (Mg), phosphorus (P), sulfur (S), and chlorine (Cl). Beyond the 10 protons and electrons of neon which completes the second row, sodium has one additional proton and electron for a total of 11, and magnesium has 12. In solution, Na and Mg may lose electrons to other constituents, forming the ions Na+ and Mg++.
The element chlorine, which forms a diatomic gas, has 17 protons and electrons for each chlorine atom, and a chlorine atom is one electron short of the full outer shell configuration. If a chlorine atom gains an electron in solution, it becomes anionic chloride, Cl–. Sulfur and phosphorus can also gain or share electrons in this way. This allows them to form biological anions in solution or to make bonds within biological molecules.
Like other atoms, sulfur can acquire or share electrons to form chemical bonds. It can bind with hydrogen or carbon. The sulfur atom is a defining feature of the amino acid cysteine, which, like proline, helps determine protein structure. Rather than bonding with hydrogen, the sulfur atom in the amino acid cysteine may form a covalent bond with the sulfur atom of another cysteine within an amino acid chain. These covalent links help stabilize the shape of a protein chain, hence help shape the protein that is formed from it.
Phosphorus, also in the third row of the periodic table, may combine with four oxygen atoms to form the phosphate anion, PO4-3, or, with an additional proton to form HPO4-2. The attachment of a phosphate ion may modify proteins with covalent links to carbon-containing side groups.
The covalent addition of phosphate to proteins, called phosphorylation, is a key biochemical mechanism in altering protein binding and activity, storing and transferring energy, or in contributing to the structure of phospholipids. Phospholipids, phosphorylated lipid molecules, form naturally into cell membranes. They are essential in forming the barrier between the cell and its surroundings.
Summary of the functions of phosphorylation. Phosphorylation may regulate protein function by altering protein structure, act as a molecular switch for cell signaling, support energy production and storage, contribute to sugar metabolism, and help in formation of phospholipids.
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