2.2. The molecular parts list[[Student version, December 8, 2002]] 41
2.2 The molecular parts list
Proceeding with our program (Roadmap, page 32), we now take a brief tour of the chemical world,
from which all the beautiful biological structures shown earlier arise. In this book we will not
beparticularly concerned with the details of the chemical structures shown here. Nevertheless, a
certain minimum of terminology is needed to make the ideas we will study concrete.
2.2.1 Small molecules
Of the hundred or so distinct kinds of atoms, our bodies consist mostly of just six: carbon, hydrogen,
nitrogen, oxygen, phosphorus, and sulfur. Other atoms (such as sodium and chlorine) are present
in smaller amounts. A subtle change in spelling communicates a key property of many of these
single-atom chemicals: In water, neutral chlorineatoms (abbreviated Cl) take on an extra electron
from their surroundings, becoming “chlorideions” (Cl−). Other neutral atomsloseone or more
electrons in water, such as sodium atoms (abbreviated Na), which become “sodium ions” (Na+).
Of the small molecules made by joining these atoms, the most important one in cells is water,
which constitutes 70% of our body mass. We will explore some of the remarkable properties of water
in Chapter 7. Another important inorganic (that is, non-carbon-containing) molecule is phosphoric
acid (H 3 PO 4 ); in water this molecule separates into the negatively chargedinorganic phosphate
(HPO^24 −,also called Pi)and two positively charged hydrogen ions (also called “protons”). (You’ll
look more carefully at the dissociation of phosphate in Problem 8.6.)
An important group of organic (carbon containing) molecules have atoms bonded into rings:
- Simple sugars include glucose and ribose, with one ring, and sucrose (cane sugar), with two.
- The four “bases” of DNA (see Section 2.2.3) also have a ring structure. One class (the
pyrimidines: cytosine, thymine) has one ring; the other (the purines: guanine and adenine)
has two. See Figure 2.13. - Aslightly different set of four bases is used to construct RNA: here thymine is replaced by
the similar one-ring molecule uracil.
The ring structures of these molecules give them a fixed, rigid shape. In particular, the bases
areflat(or “planar”) rings (in contrast, the sugars are “puckered”). Joining a base to a simple
sugar (ribose or deoxyribose) and one or more phosphates yields anucleotide.Thusfor example,
the nucleotide formed from the base adenine, the sugar ribose, and a single phosphate is called
“adenosine monophosphate,” orAMP.The corresponding molecules with two or three phosphate
groups in a row are called “adenosine diphosphate” (ADP)or“adenosine triphosphate” (ATP)
respectively (Figure 2.14). The nucleotide triphosphates are sometimes referred to generically as
“NTPs.”
Nucleotide triphosphates such as ATP carry a lot of stored energy, due in part to the self-
repulsion of a large electric charge (equivalent to four electrons), held in close proximity by the
chemical bonds of the molecule. (We will begin to study the idea of stored chemical energy, and its
utilization, in Chapter 8.) In fact, cells use ATP as a nearly universal internal energy currency; they
maintain high interior concentrations of ATP for use by all their molecular machines as needed.^4
(^4) Toalesser extent cells also use guanosine triphosphate (GTP), and a handful of other small molecules, for similar
purposes. Nucleotides also serve as internal signaling molecules in the cell. A modified form of AMP, called “cyclic
AMP” or cAMP, is particularly important in this regard.