314
BIOLOGICAL MATERIALS
which we will use to estimate the sizes o f biological macromolecules. For example,
the protein haemoglobin, which has a molecular weight iWw = 68,000 Da, has the
length parameter d=4.8 nm, well within the nanoparticle range.
The twistings and turnings o f polypeptide nanowires to form a compact protein
structure held together by weak hydrogen and disulfide (-S-S-)
bonds can be
somewhat loose, with spaces present between the polypeptide nanowire sections, so
the density of the protein is less than that o f its constituent amino acids in the
crystalline state. This can cause Eq. (12.3) to underestimate the size parameter of a
protein. If the molecular weight o f a protein i s known and the volume is determined
from an electron micrograph such as those pictured in Figs. 12.1 and 12.2, then the
density p (in g/cm') can be calculated by an inversion of Eq. ( I 1.10)
where the molecular weight MW is in daltons, and the volume V is io cubic
nanometers.
Table 12. I lists the molecular weights Mw and various length parameters d for a
number of biological nanoparticles, Fig. 12.3 provides estimated molecular weights
and dimensions o f four proteins, and Table 12.2 lists sizcs for biological structures
and quantities that are larger than nanoparticles, in thc micrometer region. All the
amino acids have the common structure sketched in Fig. 12.4. with the acid or
carboxyl group -COOH at one end and an adjacent carbon atom that is bonded to a
hydrogen atom, an amino group NH2, and a group R that characterizes the particular
amino acid. Figure 12.5 presents the structures o f six o f the amino acids, including
the smallest acid, glycine, for which the R group is simply a hydrogen atom H, and
the largest tryptophan in which R is a conjugated double-ring system. The StruchIreS
o f the nucleotide building blocks of DNA and RNA are presented in Section 12.3. I .
12.2.2. Polypeptide Nanowire and Protein Nanoparticle
Figure 12.6 illustrates the manner in which amino acids combine together in chains
through the formation of a peptide bond. To form this bond the hydroxy (-OH) o f
the carboxyl group o f one amino acid combines with the hydrogen atom H o f the
amino group o f the next amino acid with the establishment o f a C-N peptide bond
accompanied by the release o f water (H20), as displayed in the figure. The figure
shows the formation o f a tripeptide molecule, and a typical protein is composed o f
one or more very long polypeptide molecules. Small peptides are called oligopeytides, and amino acids incorporated into polypeptide chains are often referred to as
anririo acid wsidiier to distinguish them from free or unbound amino acids. The
protein haemoglobin, for example, contains four polypeptides, each with about 300
amino acid residues.
The stretched-out polypeptide chain, o f the type shown at the top of Fig. 12.7, is
called the primary .struciure. To become more compact locally, the chains either coil
up in a what is called an uipha helix (a helix), or they combine in sheets called hetu
BIOLOGICAL MATERIALS
which we will use to estimate the sizes o f biological macromolecules. For example,
the protein haemoglobin, which has a molecular weight iWw = 68,000 Da, has the
length parameter d=4.8 nm, well within the nanoparticle range.
The twistings and turnings o f polypeptide nanowires to form a compact protein
structure held together by weak hydrogen and disulfide (-S-S-)
bonds can be
somewhat loose, with spaces present between the polypeptide nanowire sections, so
the density of the protein is less than that o f its constituent amino acids in the
crystalline state. This can cause Eq. (12.3) to underestimate the size parameter of a
protein. If the molecular weight o f a protein i s known and the volume is determined
from an electron micrograph such as those pictured in Figs. 12.1 and 12.2, then the
density p (in g/cm') can be calculated by an inversion of Eq. ( I 1.10)
where the molecular weight MW is in daltons, and the volume V is io cubic
nanometers.
Table 12. I lists the molecular weights Mw and various length parameters d for a
number of biological nanoparticles, Fig. 12.3 provides estimated molecular weights
and dimensions o f four proteins, and Table 12.2 lists sizcs for biological structures
and quantities that are larger than nanoparticles, in thc micrometer region. All the
amino acids have the common structure sketched in Fig. 12.4. with the acid or
carboxyl group -COOH at one end and an adjacent carbon atom that is bonded to a
hydrogen atom, an amino group NH2, and a group R that characterizes the particular
amino acid. Figure 12.5 presents the structures o f six o f the amino acids, including
the smallest acid, glycine, for which the R group is simply a hydrogen atom H, and
the largest tryptophan in which R is a conjugated double-ring system. The StruchIreS
o f the nucleotide building blocks of DNA and RNA are presented in Section 12.3. I .
12.2.2. Polypeptide Nanowire and Protein Nanoparticle
Figure 12.6 illustrates the manner in which amino acids combine together in chains
through the formation of a peptide bond. To form this bond the hydroxy (-OH) o f
the carboxyl group o f one amino acid combines with the hydrogen atom H o f the
amino group o f the next amino acid with the establishment o f a C-N peptide bond
accompanied by the release o f water (H20), as displayed in the figure. The figure
shows the formation o f a tripeptide molecule, and a typical protein is composed o f
one or more very long polypeptide molecules. Small peptides are called oligopeytides, and amino acids incorporated into polypeptide chains are often referred to as
anririo acid wsidiier to distinguish them from free or unbound amino acids. The
protein haemoglobin, for example, contains four polypeptides, each with about 300
amino acid residues.
The stretched-out polypeptide chain, o f the type shown at the top of Fig. 12.7, is
called the primary .struciure. To become more compact locally, the chains either coil
up in a what is called an uipha helix (a helix), or they combine in sheets called hetu