The study of biology requires an understanding of simple organic chemistry and simple biological chemistry. Carbohydrates, lipids, proteins and nucleic acids, the players in molecular biology, are themselves composed of smaller building blocks. This chapter contains a review of important chemical interactions and concepts you will encounter in this course.
There are single, double, and triple covalent bonds:
Bond Number Example Energy (kcal/mol) H | single H--C--H ~80 | H H H | | double H--C==C--H ~150 | | H H H | C triple ||| ~200 C | HNote that carbon-carbon bonds are unusually strong and stable covalent bonds.
The major organic elements have standard bonding capabilities:
ELEMENT NUMBER OF COVALENT BONDS Hydrogen (H) 1 Carbon (C) 4 Nitrogen (N) 3 Oxygen (O) 2 Phosphorus (P) 5 Sulfur (S) 2Several also have other possible bond numbers that occur in biological systems:
ELEMENT # of Covalent Bonds EXAMPLE Nitrogen (N) 4 Ammonia H (positive charge |+ on nitrogen) H--N--H | H Oxygen (O) 1 ionized ethanol H H | | _ (negative charge H--C--C--O on oxygen) | | H H Sulfur (S) 1 ionized mercaptoethanol H H | | _ (negative charge H--C--C--S on the sulfur) | | H HCovalent bonds can also have partial charges when the atoms involved have different electronegativities. Water is perhaps the most obvious example of a molecule with partial charges. The symbols delta+ and delta- are used to indicate partial charges.
Oxygen, because of its high electronegativity, attracts the electrons away from the hydrogen atoms, resulting in a partial negative charge on the oxygen and a partial positive charge on each of the hydrogens.
The possibility of hydrogen bonds (H-bonds) is a consequence of partial charges.
Hydrogen bonds have polarity. A hydrogen atom covalently attached to a very electronegative atom (N, O, or P) shares its partial positive charge with a second electronegative atom (N, O, or P). One example, shown above, involves the hydrogen bonding between water molecules.
More examples: H | R--O--H ||| N--R R==N--H ||| O==R | Note that R stands for H any side group.Hydrogen bonds are ~5 kcal/mol in strength. These bonds are frequently found in proteins and nucleic acids, and by reinforcing each other serve to keep the protein (or nucleic acid) structure secure. But, since the hydrogen atoms in the protein could also H-bond to the surrounding water, the relative strength of protein-protein H-bonds vs. protein-H2O bonds is smaller than 5 kcal/mol.
H H | ~~~~ | CH3 CH3
pH = -log10[H+]The [H+] in pure water is 10^-7; therefore the pH of pure water is:
pH = -log10(10^-7) pH = - (-7) pH = 7pH 7 is often referred to as "neutral pH". Everything below pH 7 has a higher concentration of H+ and is considered acidic. Everything above pH 7 has a lower concentration of H+ and is considered basic; you can also think of this as a higher concentration of OH-.
A lower pH always means a higher concentration of H+. The biochemically useful ends of the scale are 1 M HCl, which is pH 0, and 1 M NaOH, which is pH 14. In general, cellular pH is approximately 7.2-7.4. It is very closely controlled in the cytoplasm of a healthy cell.
Last modified on: 31 January, 2000 by Dave Ussery