The preceding section reviewed the major metabolic reactions by which the cell obtains and stores energy in the form of ATP. This metabolic energy is then used to accomplish various tasks, including the synthesis of macromolecules and other cell constituents. Thus, energy derived from the breakdown of organic molecules (catabolism) is used to drive the synthesis of other required components of the cell. Most catabolic pathways involve the oxidation of organic molecules coupled to the generation of both energy (ATP) and reducing power (NADH). In contrast, biosynthetic (anabolic) pathways generally involve the use of both ATP and reducing power (usually in the form of NADPH) for the production of new organic compounds. One major biosynthetic pathway, the synthesis of carbohydrates from CO2 and H2O during the dark reactions of photosynthesis, was discussed in the preceding section. Additional pathways leading to the biosynthesis of major cellular constituents (carbohydrates, lipids, proteins, and nucleic acids) are reviewed in the sections that follow.
Carbohydrates
In addition to being obtained directly from food or generated by photosynthesis, glucose can be synthesized from other organic molecules. In animal cells, glucose synthesis (gluconeogenesis) usually starts with lactate (produced by anaerobic glycolysis), amino acids (derived from the breakdown of proteins), or glycerol (produced by the breakdown of lipids). Plants (but not animals) are also able to synthesize glucose from fatty acids—a process that is particularly important during the germination of seeds, when energy stored as fats must be converted to carbohydrates to support growth of the plant. In both animal and plant cells, simple sugars are polymerized and stored as polysaccharides.
Gluconeogenesis involves the conversion of pyruvate to glucose—essentially the reverse of glycolysis. However, as discussed earlier, the glycolytic conversion of glucose to pyruvate is an energy-yielding pathway, generating two molecules each of ATP and NADH. Although some reactions of glycolysis are readily reversible, others will proceed only in the direction of glucose breakdown, because they are associated with a large decrease in free energy. These energetically favorable reactions of glycolysis are bypassed during gluconeogenesis by other reactions (catalyzed by different enzymes) that are coupled to the expenditure of ATP and NADH in order to drive them in the direction of glucose synthesis. Overall, the generation of glucose from two molecules of pyruvate requires four molecules of ATP, two of GTP, and two of NADH. This process is considerably more costly than the simple reversal of glycolysis (which would require two molecules of ATP and two of NADH), illustrating the additional energy required to drive the pathway in the direction of biosynthesis.
In both plant and animal cells, glucose is stored in the form of polysaccharides (starch and glycogen, respectively). The synthesis of polysaccharides, like that of all other macromolecules, is an energy-requiring reaction. As noted earlier, the linkage of two sugars by a glycosidic bond can be written as a dehydration reaction, in which H2O is removed (see Figure 2.3). Such a reaction, however, is energetically unfavorable and therefore unable to proceed in the forward direction. Consequently, the formation of a glycosidic bond must be coupled to an energy-yielding reaction, which is accomplished by the use of nucleotide sugars as intermediates in polysaccharide synthesis (Figure 2.40). Glucose is first phosphorylated in an ATP-driven reaction to glucose-6-phosphate, which is then converted to glucose-1-phosphate. Glucose-1-phosphate reacts with UTP (uridine triphosphate), yielding UDP-glucose plus pyrophosphate, which is hydrolyzed to phosphate with the release of additional free energy. UDP-glucose is an activated intermediate that then donates its glucose residue to a growing polysaccharide chain in an energetically favorable reaction. Thus, chemical energy in the form of ATP and UTP drives the synthesis of polysaccharides from simple sugars.
Figure 2.40
Synthesis of polysaccharides. Glucose is first converted to an activated form, UDP-glucose, at the cost of one molecule each of ATP and UTP. The glucose residue can then be transferred from UDP-glucose to a growing polysaccharide chain in an energetically (more...)
Lipids
Lipids are important energy storage molecules and the major constituent of cell membranes. They are synthesized from acetyl CoA, which is formed from the breakdown of carbohydrates, in a series of reactions that resemble the reverse of fatty acid oxidation. As with carbohydrate biosynthesis, however, the reactions leading to the synthesis of fatty acids differ from those involved in their degradation and are driven in the biosynthetic direction by being coupled to the expenditure of both energy in the form of ATP and reducing power in the form of NADPH. Fatty acids are synthesized by the stepwise addition of two-carbon units derived from acetyl CoA to a growing chain. The addition of each of these two-carbon units requires the expenditure of one molecule of ATP and two molecules of NADPH.
The major product of fatty acid biosynthesis, which occurs in the cytosol of eukaryotic cells, is the 16-carbon fatty acid palmitate. The principal constituents of cell membranes (phospholipids, sphingomyelin, and glycolipids) are then synthesized from free fatty acids in the endoplasmic reticulum and Golgi apparatus (see Chapter 9).
Proteins
In contrast to carbohydrates and lipids, proteins (as well as nucleic acids) contain nitrogen in addition to carbon, hydrogen, and oxygen. Nitrogen is incorporated into organic compounds from different sources in different organisms (Figure 2.41). Some bacteria can use atmospheric N2 by a process called nitrogen fixation, in which N2 is reduced to NH3 at the expense of energy in the form of ATP. Although relatively few species of bacteria are capable of nitrogen fixation, most bacteria, fungi, and plants can use nitrate (NO3-), which is a common constituent of soil, by reducing it to NH3 via electrons derived from NADH or NADPH. Finally, all organisms are able to incorporate ammonia (NH3) into organic compounds.
Figure 2.41
Assimilation of nitrogen into organic compounds. Ammonia is incorporated into organic compounds by all organisms. Some bacteria are capable of converting atmospheric nitrogen to ammonia, and most bacteria, fungi, and plants can utilize nitrate from soil. (more...)
NH3 is incorporated into organic molecules primarily during the synthesis of the amino acids glutamate and glutamine, which are derived from the citric acid cycle intermediate α-ketoglutarate. These amino acids then serve as donors of amino groups during the synthesis of the other amino acids, which are also derived from central metabolic pathways, such as glycolysis and the citric acid cycle (Figure 2.42). The raw material for amino acid synthesis is thus obtained from glucose, and the amino acids are synthesized at the cost of both energy (ATP) and reducing power (NADPH). Many bacteria and plants can synthesize all 20 amino acids. Humans and other mammals, however, can synthesize only about half of the required amino acids; the remainder must be obtained from dietary sources (Table 2.2).
Figure 2.42
Biosynthesis of amino acids. The carbon skeletons of the amino acids are derived from intermediates in glycolysis and in the citric acid cycle.
Table 2.2
Dietary Requirements for Amino Acids in Humans.
The polymerization of amino acids to form proteins also requires energy. Like the synthesis of polysaccharides, the formation of the peptide bond can be considered a dehydration reaction, which must be driven in the direction of protein synthesis by being coupled to another source of metabolic energy. In the biosynthesis of polysaccharides, this coupling is accomplished through the conversion of sugars to activated intermediates, such as UDP-glucose. Amino acids are similarly activated before being used for protein synthesis.
A critical difference between the synthesis of proteins and that of polysaccharides is that the amino acids are incorporated into proteins in a unique order, specified by a gene. The order of nucleotides in a gene specifies the amino acid sequence of a protein via translation, in which messenger RNA (mRNA) acts as a template for protein synthesis (see Chapter 3). Each amino acid is first attached to a specific transfer RNA (tRNA) molecule in a reaction coupled to ATP hydrolysis (Figure 2.43). The aminoacyl tRNAs then align on the mRNA template bound to ribosomes, and each amino acid is added to the C terminus of a growing peptide chain through a series of reactions that will be discussed in detail in Chapter 7. During the process, two additional molecules of GTP are hydrolyzed, so the incorporation of each amino acid into a protein is coupled to the hydrolysis of one ATP and two GTP molecules.
Figure 2.43
Formation of the peptide bond. An amino acid is first activated by attachment to its tRNA in a two-step reaction involving the hydrolysis of ATP to AMP. The tRNAs serve as adaptors to align the amino acids on an mRNA template bound to ribosomes. Each (more...)
Nucleic Acids
The precursors of nucleic acids, the nucleotides, are composed of phosphorylated five-carbon sugars joined to nucleic acid bases. Nucleotides can be synthesized from carbohydrates and amino acids; they can also be obtained from dietary sources or reused following nucleic acid breakdown. The starting point for nucleotide biosynthesis is the phosphorylated sugar ribose-5-phosphate, which is derived from glucose-6-phosphate. Divergent pathways then lead to the synthesis of purine and pyrimidine ribonucleotides, which are the immediate precursors for RNA synthesis. These ribonucleotides are converted to deoxyribonucleotides, which serve as the monomeric building blocks of DNA.
RNA and DNA are polymers of nucleoside monophosphates. As for other macromolecules, however, direct polymerization of nucleoside monophosphates is energetically unfavorable, and the synthesis of polynucleotides instead uses nucleoside triphosphates as activated precursors (Figure 2.44). A nucleoside 5′-triphosphate is added to the 3′ hydroxyl group of a growing polynucleotide chain, with the release and subsequent hydrolysis of pyrophosphate serving to drive the reaction in the direction of polynucleotide synthesis.
Figure 2.44
Synthesis of polynucleotides. Nucleoside triphosphates are joined to the 3′ end of a growing polynucleotide chain with the release of pyrophosphate.
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Molecular Medicine: Phenylketonuria.
