A chemistry review

Theres a very good reason that chemistry is a prerequisite for Bio 201 a lot of biology
doesnt make much sense if you dont understand chemistry. Heres a brief review of
the chemistry that will be most relevant to our study of molecular biology. Specifically,
this review will cover hydrogen bonds, bond strengths in an aqueous system, and how
to tell whether a molecule is hydrophobic or hydrophilic.
Hydrogen bonds
When an electronegative atom is covalently bonded to a hydrogen, the bond will be
polar, with the electronegative atom pulling slightly more on the electrons than the
hydrogen does. (In a biological system, your main electronegative atoms are going to
be oxygen and nitrogen.) This will give the electronegative atom a partial negative
charge and the hydrogen a partial positive charge. This hydrogen is termed a hydrogen
bond donor. Another electronegative atom (usually in a different molecule) can be a
hydrogen bond acceptor.
Hydrogen bonds (H-bonds) are actually just weak electromagnetic attractive
interactions. Individual H-bonds have very little strength, especially at typical biological
temperatures (since heat increases kinetic energy and kinetic energy can break bonds).
Several H-bonds can create a stronger interaction. The two strands of DNA in even the
smallest human chromosome are held together by about 100 million H-bonds, which is
why DNA has to be heated far above the 37 C of a healthy human being for the strands
to separate spontaneously.
Hydrogen bonds are incredibly important in molecular biology. This is because
molecular biology involves a lot of temporary interactions for example, an enzyme will
bind to its substrate, do whatever enzymatic reaction it does, and then release the
altered substrate and bind a new, unaltered molecule and repeat the process. If
enzymes bound their substrates covalently, this would be a very big problem, because
covalent bonds are much less easy to make and break. Similarly, there are many
proteins whose functions involve binding to DNA. Generally speaking, things that bind
covalently to DNA cause cancer, because they stay bound. DNA-binding proteins can
bind and release easily, because they use a lot of hydrogen bonds.

Shown below are guanine and cytosine. The R in the diagrams indicates where the
sugar attaches to the base. Identify the potential hydrogen bond donors and acceptors
on the nucleotide bases.

Guanine

Cytosine

Bond strengths in an aqueous system

Since living organisms are aqueous systems, bond strengths in aqueous systems are
important to understanding biology. Ionic bonds, which are strong in solids, are much
weaker in water. (Its much easier to dissolve table salt in water than to melt it with
heat!) The reason for this is that water molecules, which are polar, compete with the
ions interactions. A positively charged sodium ion will interact much more strongly with
a negatively charged chloride ion than with the partial negative charge of the oxygen
atom in a molecule of water, but when the water molecules vastly outnumber the
chloride ions, the ions will interact with water instead of each other.
The strongest bonds present in aqueous systems are covalent bonds. Ionic bonds are
next. Hydrogen bonds are like fractional ionic bonds, interactions between atoms with
partial charges, and are therefore weaker than ionic bonds. The van der Waals force is
the weakest of all.

How to tell hydrophobic molecules from hydrophilic ones

Generally speaking, hydrophilic molecules are either polar or charged. (There are some
exceptions, like O2 or CO2, which are hydrophilic without being polar, but theyre
generally both small and inorganic.) Hydrophobic molecules are generally nonpolar.
Charged molecules are easy to identify, so well focus on how to tell polar from
nonpolar.
Biological molecules are largely made up of carbon, hydrogen, oxygen, and nitrogen.
Phosphorus and sulfur are involved, too, but theyre not as abundant as the other four.
Fortunately, since weve only got four elements to be concerned with, identifying polar
versus nonpolar molecules is pretty straightforward. Oxygen and nitrogen are the most
electronegative atoms that are generally found in living organisms. So, molecules with
oxygen and/or nitrogen in them are going to tend to be polar. Carbon, on the other
hand, is fairly neutral as far as electronegativity goes, so the presence of lots of carbon
generally makes for a nonpolar molecule.
The general formula of an amino acid is as follows:
H
|
H2NCCOOH
|
R
The R group is what makes each amino acid unique. When we refer to the chemical
characteristics of an amino acid, we generally mean the properties of the R group.
Below are some amino acids with the R groups in blue; identify which are polar and
which are nonpolar.

There are also some side chains that are amphipathic (having both polar and nonpolar
characteristics). We wont be emphasizing those very heavily, because it can be tricky
to recognize when the polar element predominates and when the nonpolar element is
more important. Below are a few amphipathic amino acids; identify which portions of
them are polar or nonpolar.