Chapter 2 – Orientation for the Bio-Curious  35

It is also worth noting here that there are nonbiological applications of DNA. For example,

in Chapter 9, we will discuss the use of DNA origami. This is an engineering nanotechnology

that uses the stiff properties of DNA over short (ca. nanometer distances) (see Section 8.3)

combined with the smart design principles offered by Watson–​Crick base pairing to generate

artificial DNA-​based nanostructures that have several potential applications.

RNA consists of several different forms. Unlike DNA, it is not constrained solely as a

double-​helical structure but can adopt more complex and varied structural forms. Messenger

RNA (mRNA) is normally present as a single-​stranded polymer chain of typical length of a

few thousand nucleotides but potentially may be as high as 100,000. Base pairing can also

occur in RNA, rarely involving two complementary strands in the so-​called RNA duplex

double helices, but more commonly involving base pairing between different regions of

the same RNA strand, resulting in complex structures. These are often manifested as a

short motif section of an RNA hairpin, also known as a stem loop, consisting of base pair

interactions between regions of the same RNA strand, resulting in a short double-​stranded

stem terminated by a single-​stranded RNA loop of typically 4–​8 nucleotides. This motif is

found in several RNA secondary structures, for example, in transfer RNA (tRNA), there are

three such stem loops and a central double-​stranded stem that result in a complex charac­

teristic clover leaf 3D conformation. Similarly, another complex and essential 3D structure

includes rRNA. Both tRNA and rRNA are used in the process of reading and converting the

DNA genetic code into protein molecules.

One of the subunits of rRNA (the light subunit) has catalytic properties and is an example

of an RNA-​based enzyme or ribozyme. This particular ribozyme is called “peptidyl trans­

ferase” that is utilized in linking together amino acids during protein synthesis. Some

ribozymes have also been demonstrated to have self-​replicating capability, supporting the

RNA world hypothesis, which proposes that RNA molecules that could self-​replicate were

in fact the precursors to life forms known today, which ultimately rely on nucleic acid-​based

replication.

2.3.6  WATER AND IONS

The most important chemical to life as we know is, undeniably, water. Water is essential in

acting as the universal biological solvent, but, as discussed at the start of this chapter, it is

also required for its thermal properties, since the thermal fluctuations of the water molecules

surrounding molecular machines fundamentally drive essential molecular conformational

changes required as part of their biological role. A variety of electrically charged inorganic

ions are also essential for living cells in relative abundance, for purposes of electrical and

pH regulation, and also as being utilized as in cellular signaling and for structural stability,

including sodium (Na^+​), potassium (K^+​), hydrogen carbonate (HCO3

−), calcium (Ca2+​), mag­

nesium (Mg^2+​), chloride (Cl⁻), and water-​solvated protons (H^+​) present as hydronium (or

hydroxonium) ions (H3O^+​).

KEY POINT 2.11

To maintain the pH of a solution requires a chemical called a “pH buffer.” The cell

contains many natural pH buffers, but in test tube experiments, we can use a range

of artificial buffers at low millimolar concentrations that can constrain the pH of a

solution to within a specific narrow range. For example, a simple pH buffer used is

“phosphate-​buffered saline,” which contains phosphate ions, plus additional sodium

ions, which can maintain the pH over a range of 6–​8.

Other transition metals are also utilized in a variety of protein structures, such as zinc (Zn,

e.g., present in a common structural motif involving in protein binding called a “zinc finger

motif”) as well as iron (Fe, e.g., located at the center of hemoglobin protein molecules used to