Chapter 2 – Orientation for the Bio-Curious  51

three translational, three rotational, and three intrinsic vibrational energy modes (note each

vibrational mode has two degrees of freedom of potential and kinetic energy) plus up to three

additional extrinsic vibrational modes since each atom can, in principle, independently form

a hydrogen bond with another nearby water molecule, indicating a mean energy of ~9 kBT

per molecule.

Following collision with a biological molecule, some of this kinetic energy is transferred,

resulting in kBT scale energy fluctuations; kBT itself is often used by biologists as a standard

unit of energy, equivalent to 4.1 pN nm at room temperature. This is roughly the same energy

scale as molecular machines undergoing typical displacement transitions of a few nanometers

through forces of a few piconewtons. This is because molecular machines have evolved to

siphon-​off energy from the thermal fluctuations of surrounding water to fuel their activity.

The hydrolysis of one molecule of ATP in effect releases 18 kBT of chemical potential energy

from high-​energy phosphate bonds to generate thermal energy.

Note that some senior biologists still refer to an energy unit of the calorie (cal). This

is defined as the energy needed to raise the temperature of 1 g of water through 1°C at a

pressure of one atmosphere. Intuitively, from the discussion earlier, this amount of energy, at

room temperature, is equivalent to 4.1 J. Many bond energies, particularly in older, but still

useful, biochemistry textbooks are often quoted in units of kcal.

The temperature units used by most biologists are degrees Celsius (°C), that is, 273.15 K

higher than absolute temperature. Warm-​blooded animals have stable body temperatures

around 35°C–​40°C due to complex thermoregulation mechanisms, but some may enter

hibernation states of more like 20°C–​30°C. Many cold-​blooded animals thrive at a room tem­

perature of 20°C, and some plants can accommodate close to the full temperature range of

liquid water. Microbes have a broad range of optimal temperatures; many lie in the range of

20°C–​40°C, often optimized for living in the presence of, or symbiotically with, other multi­

cellular organisms. However, some, including the so-​called extremophiles, many from the

archaea domain of organisms, thrive at glacial water temperatures in the range 0°C–​5°C, and

at the high end some can thrive at temperatures of 80°C–​110°C either in underwater thermal

vents or in atmospheric volcanic extrusions. The full temperature range when considered

across all organisms broadly reflects the essential requirement of liquid water for all known

forms of life. Many proteins begin to denature above 50°C, which means that their tertiary

and quaternary structures are disrupted through the breaking of van der Waals interactions,

with the result of the irreversible change of their 3D structure and thus, in general, destruc­

tion of their biological function.

There are some well-​known protein exceptions that occur in types of extremophile cells

that experience exceptionally high temperatures, known as thermophiles. One such is a

thermophilic bacterium called Thermus aquaticus that can survive in hot water pools, for

example, in the vicinity of lava flow, to mean temperatures of 80°C. An enzyme called “Taq

polymerase,” which is naturally used by these bacteria in processing of DNA replication,

is now routinely used in polymerase chain reactions (PCR) to amplify a small sample of

DNA, utilized in biomedical screening and forensic sciences, as well as being routinely used

in abundance for biological research (see Chapter 7). A key step in PCR involves cycles of

heating up replicated (i.e., amplified) DNA to 90°C to denature the two helical strands from

each DNA molecule, which each then acts as a template for the subsequent round of amp­

lification, and Taq polymerase facilitates this replication at a rate >100 nucleotide base pairs

per second. The advantage of the Taq polymerase is that, unlike DNA polymerases from

non-​thermophilic organisms, it can withstand such high heating without significant impair­

ment, and in fact even at near boiling water temperatures of 98°C, it has a stability half-​life

of 10 min.

2.5.4  TIME

Time scales in biology are broad. Ultimately, the fastest events are quantum mechanical

concerning electronic molecular orbitals, for example, a covalent bond vibrates with a time