Chapter 2 – Orientation for the Bio-Curious  31

size or direction) in some way. Molecular machines in the context of living organisms usually

take an input energy source from the controlled breaking of high-​energy chemical bonds,

which in turn is coupled to an increase in the local thermal energy of surrounding water

molecules in the vicinity of that chemical reaction, and it is these thermal energy fluctuations

of water molecules that ultimately power the molecular machines.

Many enzymes act in this way and so are also molecular machines; however, at the level

of the energy input being most typically due to thermal fluctuations from the water solvent,

one might argue that all enzymes are types of molecular machines. Other less common forms

of energy input are also exhibited in some molecular machines, for example, the absorption

of photons of light can induce mechanical changes in some molecules, such as the protein

complex called “rhodopsin,” which is found in the retina of eyes.

There are several online resources available to investigate protein structures. One of

these includes the Protein Data Bank (www.pdb.org); this is a data repository for the spatial

coordinates of atoms of measured structures of proteins (and also some biomolecule types

such as nucleic acids) acquired using a range of structural biology tools (see Chapter 5). There

are also various biomolecule structure software visualization and analysis packages available.

In addition, there are several bioinformatics tools that can be used to investigate protein

structures (see Chapter 8), for example, to probe for the appearance of the same sequence

repeated in different sets of proteins or to predict secondary structures from the primary

sequences.

2.3.4  SUGARS

Sugars are more technically called “carbohydrates” (for historical reasons, since they have a

general chemical formula that appears to consist of water molecules combined with carbon

atoms), with the simplest natural sugar subunits being called “monosaccharides” (including

sugars such as glucose and fructose) that mostly have between three and seven carbon atoms

per molecule (though there are some exceptions that can have up to nine carbon atoms) and

can in principle exist either as chains or in a conformation in which the ends of the chain link

to each other to form a cyclic molecule. In the water environment of living cells, by far the

majority of such monosaccharide molecules are in the cyclic form.

Two monosaccharide molecules can link to each other through a chemical reaction,

similar to the way in which a peptide bond is formed between amino acids by involving the

loss of a molecule of water, but here it is termed as glycosidic bond, to form a disaccharide

(Figure 2.6a). This includes sugars such as maltose (two molecules of glucose linked together)

and sucrose (also known as table sugar, the type you might put in your tea, formed from

linking one molecule of glucose and one of fructose).

All sugars contain at least one carbon atom which is chiral, and therefore can exist as two

optical isomers; however, the majority of natural sugars exist (confusingly, when compared

with amino acids) as the –​D form. Larger chains (Figure 2.6b) can form from more linkages to

multiple monosaccharides to form polymers such as cellulose (a key structural component of

plant cell walls), glycogen (an energy storage molecule found mainly in muscle and the liver),

and starch.

KEY POINT 2.8

Most sugar molecules are composed of D-​optical isomers, compared to most natural

amino acids that are composed of L-​optical isomers.

These three examples of polysaccharides happen all to be comprised of glucose monosac­

charide subunits; however, they are all structurally different from each other, again illus­

trating how subtle differences in small features of individual subunits can be manifest as big

differences as emergent properties of larger length scale structures. When glucose molecules