Clas Blomberg - Physics of life-Elsevier Science (2007)

Chapter 12. The biological molecules 97
substances, for all kind of control purposes, for governing the genetic information by activation
and regulation, by standing for crucial steps in the transcription of information and
also for much of the structural properties of certain organisms.
Proteins are a main component of living cells. They constitute 15–20% of the weight of
a cell and since 70–75% is water, they provide most of the dry components. The most important
property of the proteins is that they make up the cell machinery: They are the active
components that catalyse various processes (as enzymes—all enzymes are proteins), and in
that way they control and direct chemical pathways behind all processes of a living cell.
Proteins, as haemoglobin, also transport various substances and control the transport of other
substances in and out of cells. They can act as receivers of various signals, for instance
light, trigger reactions and further signals if light is received.
They also have an important function in giving rise to various structural elements, particularly
in animals: Our hair and skin is composed of proteins (keratin) as our muscles
(myosin). Our bones are to a large extent build up by the protein collagen (the by far most
common substance in our bodies besides water). Leather, wool and silk are protein materials
which one tries to mimic by synthetic polymers.
In plants, structures are mainly formed by carbohydrates and not proteins. The most
important is cellulose that is built up by glucose. Cotton is a carbohydrate material as of
course paper and wood. The same general principles as we discuss here are valid for such
polymers, but here we will not consider these further.
Proteins are synthesized in living cells by a complicated process where amino acids are
selected (by other proteins) to be placed at a specific position in a protein chain according to a
specific pattern that is coded in the cell DNA, which will be further discussed in another section.
Normal protein chains may have about 100–290 amino acid units, and there is a large
variation. They are often built up as complexes with several chains, which together may
contain many thousand amino acid units. Proteins can also contain other groups and atoms
besides the amino acid chains. They can contain metal atoms or ions such as iron or copper,
which have important roles in catalysis or transport. A group with iron in haemoglobin helps
in transporting oxygen in blood and chlorophyll-bound magnesium plays a central role in
its light-absorbing unit. A relatively unusual element, molybdenum, is used in certain
enzymes particularly those that take up atmospheric nitrogen for the biological compounds.
Amino acids are the building blocks of proteins. The relevant molecules have a basic
form as shown in Figure 12.1.
R stands here for a side group, of which there are several possibilities with considerable
variation of what concerns their size and physical properties: from a hydrogen in glycine or
a methyl (CH 3 ) group in alanine to long acid or alkaline groups, and long, non-polar hydrocarbon
chains or aromatic groups. For building the proteins of the cells, twenty special choices
are used, which are considered as canonical amino acids (shown in Figure 12.4 below).
H
H
R
N
α
C C
H
O
O
H
Figure 12.1
The general form of an amino acid.