30 BIOCHEMISTRY FUNDAMENTALS
biochemical reactions, or structural materials in muscles and tendons, or small
molecule carriers such as the dioxygen - carrying metalloproteins myoglobin
and hemoglobin. At least one - third of all proteins and enzymes contain metals
and are known as metalloproteins and metalloenzymes. Some of these will be
the bioinorganic chemistry topics treated in Chapters 5 , 6 , and 7 of this text.
The recently coined term, proteomics, refers to the study of a large collection
of proteins that occur and function together in a particular biochemical entity
such as a cell or other organelle. Important interactions among proteins in a
proteome distinguish the proteome ’ s behavior as being more complex than
that of a single protein studied individually.
A second major area of biochemical importance concerns study of nucleo-
tide polymerization to produce ribonucleic acids (RNA) and deoxyribonucleic
acids (DNA). Genes, the basis for inherited characteristics, are contained in
DNA double - helical sections incorporated into coiled and supercoiled DNA
structures. Genomics, the study of the total genetic assemblage of any species,
is now a well - known topic to all, especially with the announcement of the
sequencing of the human genome in 2001. More information on this topic is
given in Section 2.3.6.
The goal of this chapter is to provide a basic understanding of the structure
of, and biochemical processes undertaken by, proteins and nucleic acids. This
knowledge will be needed by students, teachers, and researchers wishing to
understand and replicate the catalytic activity of metalloenzymes or to design
compounds (many of them containing inorganic atoms) that will be able to
detect, diagnose, and treat disease.
2.2 Proteins,
2.2.1 Amino Acid Building Blocks,
Polypeptides are formed through the polymerization of any combination of
the 20 naturally occurring amino acids (aa). In humans, 10 of these amino acids
are essential (cannot be synthesized by the body and must be ingested in the
diet). The 10 essential amino acids (see Figure 2.1 for full names and structure)
are: arg, his, ile, leu, lys, met, phe, thr, trp, and val. Relatively short amino acid
chains, called polypeptides, have important hormonal (control) functions in
biological species. Proteins are classifi ed as polypeptide chains exceeding 50
amino acids in length, whereas enzyme molecules usually contain more than
100 amino acid residues. Amino acids contain a central carbon, called the α
carbon, to which four substituent groups are attached: (1) the amine group
( – NH 2 ); (2) a carboxylic acid group ( – COOH), a hydrogen atom ( – H), and a
side chain ( – R) group unique to each amino acid. The structure of these
basic building blocks are grouped in Figures 2.1 – 2.4 to indicate the neutral,
polar, acidic, or basic characteristics of their R groups. The three - and one -
letter common abbreviations for amino acids are shown in the fi gures. The