Biomolecules and the Chemistry of Life - Common Mistakes

Common Mistakes

Chemistry

1. Don’t confuse ions and isotopes. Remember, ions are charged particles. They form when electrons are gained or lost, which creates an imbalance in the number of protons relative to electrons. Isotopes are electrically neutral but have different numbers of neutrons. A way to remember this is that iso– means "same or equal," so an isotope is an atom of the same type but containing a different number of neutrons.

2. We’ve talked a lot about electrical charges—so much so that you may feel like your brain has been electrocuted in the process.

To put it all in a nutshell:

• Protons are positive (+1).
• Electrons are negative (-1).
• Neutrons are neutral.
• Ions can be positive or negative, depending on how many electrons they have gained or lost.
• Molecules are electrically neutral, but can have positive and negative regions if their component atoms aren’t sharing nicely.

3. The pH scale is a measure of acidity.

Here it is in a nutshell:

• Something that is more acidic has a lower pH. On a scale of 0 to 14, acids have a pH of less than 7. We realize this is counterintuitive, but that’s how it is. Higher acidity = lower pH. Take it or leave it.
• Something that is less acidic is called basic and has a higher pH. On a scale of 0 to 14, bases have a pH of greater than 7.
• Something that has a pH of exactly 7 is neutral. Pure water is one such solution.

Biological Molecules

1. How do you remember which base pairs are complementary? The easiest way is to realize that cytosine (C) and guanine (G) are both curvy letters. Adenine (A) and thymine (T) are straight letters. If you’re thinking about RNA, this doesn’t quite work, because U takes the place of T but is another curvy letter. If it helps, remember that U comes right after T in the alphabet!

2. You have probably noticed that throughout this section, we have been talking about different groups. These functional groups often occur in organic compounds, and they all they have special names. Don’t be intimidated; learning them will make your life easier. Functional groups are friends. FFs for life!

Functional Group	Chemical Structure
Hydroxyl
Carbonyl
Carboxyl
Amino
Phosphate

Hydroxyl (OH) – Oxygen is bound to carbon on one side and singly bound to a hydrogen on the other side. Hydroxyl groups are polar since the oxygen hogs the electrons it is supposed to be sharing with hydrogen. This hogging means that any organic compound with a hydroxyl group will have polar areas. Do not get this functional group confused with the hydroxide ion (OH^-), which is a negatively charged unit.

Carbonyl (ACHOB) – Oxygen is doubly bound to carbon (C=O). Depending on where the doubly bound oxygen occurs along the carbon backbone, you can get totally different classes of sugars. If the doubly bound oxygen is at the end of the carbon chain, it forms an aldehyde (RCHO). If the doubly bound oxygen attached to any other carbon, the sugar is a ketone (RCOR').

Carboxyl (RCOOH) – A carbon is bound to two oxygens. One oxygen forms a double bond with the carbon (C=O), and the other forms a single bond (C–O). The oxygen with a single bond is also bound to a hydrogen (O–H or OH). Carboxyl groups are characteristic of fatty acids and are what allow three fatty acids to bind to a molecule of glycerol, which produces a triglyceride. Carboxyl is also one of the functional groups comprising an amino acid.

Amino (CNH2) – A nitrogen is singly bound to two hydrogens (N–H) and singly bound to a carbon (N–C). This functional group is found in amino acids, hence the name.

Phosphate (H₂PO₄R) – A phosphorous atom is singly bound to three oxygens (P–O) and doubly bound to one more oxygen (P=O). Two of the singly bound oxygens have a hydrogen attached, making –OH depending on pH conditions. The last singly bound oxygen is bound to a carbon (C–O). Phosphates form the polar "head" of the phospholipids and form part of the "backbone" of nucleic acids.