This discussion reviews two key concepts for college and advanced high school science students.
The periodic table is a compact reference for discussing chemistry. For biochemistry, the first two rows are especially pertinent. This discussion begins with hydrogen, carbon, nitrogen, and oxygen. Elements in the third row will be included later.
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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 very 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 cover these subjects in much greater depth, including Molecular Cell Biology by Darnell, Lodish, and Baltimore.
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 not be possible.
Water is represented chemically as 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 in small amounts at concentrations of ~10-7 M each. In other words, pure water has a pH of 7. All science students should know that pH is defined as the negative log of the hydrogen ion concentration. The log 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 that need to be considered. One is that it is an excellent solvent for many biologically important ions, including Na+, K+, Ca++, and Mg++. Amino acids and proteins, which also have ionic properties, are often highly soluble in water. Water is such a good solvent because it is a polar molecule. Molecular polarity arises from a separation of charge within the molecule. Although water has no net charge, 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 the 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 means 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–.
An important reaction in water occurs between the solvent, water, and a solute, carbon dioxide gas. 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, or 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. Electron orbitals fill according to quantum mechanical rules, and a stable outer arrangement of electrons would have eight electrons. Because oxygen contributes only six valence electrons, it needs two more to complete this eight-electron configuration. For 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 needs four more to complete its outer shell. Oxygen, by contrast, has six valence electrons and needs two more. In CO2, one carbon shares electrons with two oxygen atoms, forming two strong double bonds that satisfy the electron requirements of all three atoms.
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 the reaction.
In this reaction, CO2 combines with an OH– group present at low concentration in pure water to form a bicarbonate ion, HCO3–. Carbon sits at the center of this structure. One oxygen forms a strong double bond with carbon, while the remaining two oxygens have single bonds that are arranged to produce the bicarbonate ion.
For these remaining oxygen-containing groups, one of these bonds to both hydrogen and carbon, creating an attached -OH group. The other oxygen bonds to carbon without a proton and thus carries the negative charge, giving 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. These four elements from the first two rows of the periodic table, H, C, N, and O, are also essential for amino acids. Amino acids share a common core structure but differ in their “side groups”. As amino acids link together to form proteins, these side groups give proteins their structural and functional variety.
At the center of the common amino acid chain structure is a carbon atom with four bonding positions.
Two of these bonds connect as carboxyl binding to amino groups. Such bonds join adjacent amino acids through a “peptide link”. Because the peptide bond has a resonance bonding behavior, its electrons are distributed in a way that gives both a polar and a nonpolar character.
A third bond on the central carbon holds a hydrogen atom, and the fourth attaches the side chain giving the protein chains their variety.
Protein structures. Proline is unusual among amino acids in these protein chains because it introduces a kink into the chain. Its distinctive linkage to the amino acid core disrupts regular patterns in a protein’s structure.
This discussion also will 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 can lose electrons to form the ions Na+ and Mg++.
The element chlorine, which forms a diatomic gas, has 17 protons and electrons for each chloring atom and each atom is one electron short of a full outer shell. If it gains an electron in solution, it becomes the anion Cl–. Sulfur and phosphorus can also gain or share electrons in this way, and this allow them to form important biological bonds or anions.
All these atoms can acquire or share electrons to form chemical bonds. Sulfur, for example, can bond with hydrogen or carbon. A sulfur atom is an important feature of the amino acid cysteine, which, like proline, helps determine protein structure. Instead of bonding with hydrogen, the sulfur atom in the amino acid cysteine can form a covalent bond with the sulfur of another cysteine. These covalent links help stabilize a protein’s shape.
Phosphorus can combine with four oxygen atoms to form the phosphate anion, PO4-3, or, with an added proton as HPO4-2. Phosphate can also modify proteins by forming covalent links to carbon-containing groups.
The covalent addition of phosphate to proteins, called phosphorylation, is a key biochemical mechanism. This can alter protein binding and activity, store and transfer energy, and contribute to the structure of phospholipids in cell membranes, which form the essential barrier between the cell and its surroundings.
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.
In summary, phosphorylation is an essential and versatile biochemical mechanism.
Chemistry can be beautiful too.
Science Essays for College Students 
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