Materials for Biomedical Engineering. Mohamed N. Rahaman

Figure 2.16 Schematic comparison of (a) van der Waals bonding between nonpolar polyethylene macromolecules and (b) hydrogen bonding between polar nylon 6.6 macromolecules.

2.6 Atomic Bonding and Structure in Proteins

      Proteins are the most versatile macromolecules in living organisms and they serve crucial functions in essentially all biological processes (Alberts et al. 2014). They are not only long‐chain molecules but they can fold in a complex manner to give a variety of three‐dimensional shapes. The functionality of a protein depends critically on its conformation and, thus, an understanding of how atomic bonding controls the overall three‐dimensional shape of a protein is important. Because of its complexity, the conformation of proteins is often described at multiple levels, referred to as primary, secondary, tertiary, and quaternary structure, each emphasizing different features of the overall three‐dimensional structure.

      2.6.1 Primary Structure

The building blocks of simple proteins are approximately 20 naturally occurring α‐amino acids (Figure 2.17; Table 2.4). These amino acids have a characteristic composition that includes an amine (NH₂) group at one end of the molecule and a carboxyl (C=O)OH group at the other end. The molecules also have a side‐group, denoted generally as R, attached to the carbon atom between the NH₂ and (C=O)OH groups, which can be nonpolar, polar, positively charged or negatively charged. The simplest amino acid, glycine has R = H, the hydrogen atom. Proteins form by a condensation reaction involving the carboxyl group of one amino acid with the amine group of another amino acid, resulting in an amide bond between the two amino acids (Figure 2.18a). Conventionally, in drawing such structures, the NH₂ group of the amino acid or the N terminus of the protein is on the left whereas the (C=O)OH group of the amino acid or C terminus of the protein is on the right.

Figure 2.17 Side groups in 20 naturally occurring α‐amino acids which can be nonpolar, polar, negatively charged, or positively charged.

Table 2.4 The α‐amino acids of proteins.

Amino acid	Three‐letter symbol	One‐letter symbol	pKa value of side chain
Alanine	Ala	A
Valine	Val	V
Leucine	Leu	L
Isoleucine	Ile	I
Phenylalanine	Phe	F
Tryptophan	Trp	W
Methionine	Met	M
Proline	Pro	P
Glycine	Gly	G
Serine	Ser	S
Threonine	Thr	T
Cysteine	Cys	C
Tyrosine	Tyr	Y
Asparagine	Asn	N
Glutamine	Gln	Q
Aspartic acid	Asp	D	3.9
Glutamic acid	Glu	E	4.3
Lysine	Lys	K	10.5
Arginine	Arg	R	12.5
Histidine	His	H	6.0

Figure 2.18 Illustration of (a) condensation reaction between two amino acids resulting in the formation of an amide (peptide) bond, and (b) peptide composed of five amino acid residues, showing the atomic bonds in the chain backbone and side groups. The three‐letter symbol of each amino acid is given below its residue.

      A key feature of protein molecules is the presence of amide bonds in the chain backbone. These bonds are present in other macromolecules as well, such as in the synthetic polymer nylon 6.6 and other nylons, for example (Figure 2.16b). However, when it involves two natural amino acids, it is sometimes called a peptide bond. While there is no clear agreement on terminology, a protein molecule is often taken as composed of over 50–60 amino acid groups often called