1.4Biological Materials

Among the materials that constitute a cell, water is the most abundant - normally representing approximately 70-80% of the total volume - and has many substances dissolved in it. After water, proteins and lipids are the most common cell materials (Table 1-2).

Table 1-2. Cellular components

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Biological Materials

Proteins are long molecules built from 20 different amino acids linked by peptide bonds. Figures 1-3A and B show the structures of amino acids. Those that constitute most of the proteins found in organisms on earth are L-amino acids, while D-amino acids are found only in the cell walls of bacteria and some other organisms. The sequential order of amino acids (i.e., primary structures) is determined by DNA, and the higher-order structure (i.e., the 3-D structure) is determined from this order. For example, main-chain structures include alpha helices and beta sheets, and main chains with no fixed structure are called random coils (i.e., secondary structures). A three-dimensional structure consisting of a protein chain is called a tertiary structure. Sometimes, multiple protein chains together form a complex that performs functions; this is known as a quaternary structure (Fig. 1-3C).
Proteins with certain shapes have specific functions. They work as enzymes to control biological reactions in the living body, as structural and cytoskeletal proteins to support cellular structures, and as receptors to receive external stimuli inside the cell membrane. Most hereditary diseases in humans are caused by functional changes in proteins due to DNA mutation.

Fig. 1-3A. Amino acids and proteins

A) Differences between D- and L-amino acids. Most amino acids on earth, except those that constitute the cell walls of bacteria and some other exceptions, are L-amino acids.

Fig. 1-3B. Amino acids and proteins

B) The 20 amino acids and their abbreviations. Among amino acids that make up proteins in humans, leucine (L) is the most abundant, and tryptophan (W) is the least abundant.

Fig. 1-3C. Amino acids and proteins

C) An example of a peptide. This peptide is abbreviated as AYDG (the N-terminus is always drawn on the left-hand side). The amino acid sequence at the top is the primary structure, followed in descending order by the second structure (the main chain), the tertiary structure (a three-dimensional structure) and the quaternary structure (intersubunit interaction).

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Lipids are important components of biological membranes, which consist of a phospholipid bilayer intertwined with mobile proteins. A phospholipid is a molecule in which two hydrophobic fatty acid chains and a hydrophilic chain with phosphorus are linked to a glycerol backbone and form a bilayer with its hydrophobic parts facing inward and its hydrophilic parts in contact with the water surface (see Chapter 5). Ions and polar substances can barely penetrate this structure. The ratio of proteins to lipids changes depending on the biological membrane, and the proportion of proteins increases progressively in the order of myelin, red cells, hepatocytes and inner mitochondrial membrane. In triglycerides, all hydroxyl groups form ester bonds with fatty acids, and play an energy-storage role. The body fat percentage in humans is normally 21% in men and 26% in women; the higher ratio for females explains their better survival rate during famines. Various steroid hormones are synthesized from cholesterol.
Let’s look at the structure of fatty acids. A fatty acid is a carbon chain with a carboxyl group located at its end (Fig. 1-4). Those that do not contain double bonds are saturated fatty acids, and those with double bonds are unsaturated. For example, ω-3 fatty acids have a double bond on the third carbon counting from the terminal carbon, and C20:5 means that the fatty acid has 20 carbon atoms and 5 double bonds. ω-6 fatty acids, which are abundant in the fat found in the flesh of terrestrial animals, have a double bond on the sixth carbon from the end; arachidonic acid, an important component of the cell membrane in humans, can therefore be termed a ω-6 fatty acid and C20:4. ω-3 and ω-6 are also expressed as n-3 and n-6, respectively.

Fig. 1-4. Fatty acids

ω-3 fatty acids have a double bond located on the third carbon from the left. ω-6 amino acids have a double bond located on the sixth carbon. C22:6 means that the amino acid has 22 carbons and 6 double bonds. In organic chemistry terms, linoleic acid is known as 9, 12-octadecadienoic acid because the double-bond location is counted from the carboxyl-group side. EPA is eicosapentaenoic acid, and DHA is docosahexaenoic acid.

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Carbohydrates are an important energy source. Glucose is derived from glycogen and starch - both energy reserves - in animals and plants, respectively. ATP is synthesized, while glucose is broken down into water and carbon dioxide through the glycolytic pathway, the citric acid cycle and the electron transport system. Carbohydrates are also constituents of materials such as nucleic acid (deoxyribose and ribose), glycoprotein (mannose, glucosamine, etc.) and cell walls (cellulose).
Figure 1-5 shows the structure of glucose. Maltose is a disaccharide formed from two units of α-D-glucose joined with an α (1→4) glycosidic linkage because water is removed from -OH groups at C-1 and C-4. Looking at the location of the -OH group at C-1, the difference between α-D-glycosidic linkage and β-D- glycosidic linkage can be seen. Starch (amylose) is a long molecule consisting of a large number of glucose units joined together mainly by α-D-glycosidic bonds, and cellulose is a long molecule consisting of a large number of glucose units linked by β-D-glycosidic bonds. Lactose is sometimes abbreviated as Galβ (1→4) Glc.

Fig. 1-5. Examples of carbohydrate structures

A) Glucose is commonly drawn using Haworth’s cyclized structural formula.
B) Structure of maltose
C) Structural differences between starch (amylose) and cellulose
D) Structure of lactose


More on Amino Acids

In the main text, we learned that amino acids have amino and carboxyl groups, and that there are 20 amino acid types. Here are some other important aspects of amino acids.
Looking at the structure of lysine, we see it has a carbon linked with the amino and carboxyl groups (α-carbon), followed by β-, γ-, δ- and ε-carbons, in that order. Since amino group is linked to ε-carbon, this group is known as a ε-amino group. You might remember the ornithine cycle for urea synthesis from high school biology class. Did you know that ornithine has an amino group linked to δ-carbon?
Let’s look at the structure of glutamic acid. The carboxyl group is linked to γ-carbon. γ-aminobutyric acid (GABA) is synthesized when an α-carboxyl group is decarboxylated by the decarboxylase. In other words, an excitatory transmitter is quickly transformed into an inhibitory transmitter in the brain. Now, let’s look at the structure of histidine. How will decarboxylase change it?

Column Fig. 1-3. Examples of amino acids

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Living bodies utilize other minerals in addition to elements such as C, H, O, N, P and S that are found in proteins, lipids, nucleic acids, carbohydrates and other materials. Na, K and Cl are necessary for homeostasis (i.e., the maintenance of osmotic pressure and generation of potential difference), Zn is a constituent of enzymes, Fe is a constituent of hemoglobin, Mn is involved in oxygen generation during photosynthesis, and Mg is a constituent of chlorophyll and involved in the ATP hydrolysis reaction. Additionally, Ca is important for Ca-dependent enzymatic reactions and coagulation as well as being a constituent of bone, and Co and I (iodine) are essential elements of vitamin B12 and thyroid hormones, respectively. Se, a trace component, is sometimes incorporated into an amino acid called selenocysteine, and plays a role in enzymatic activities.

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