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7: Metabolism II

In the last chapter, we focused on metabolic pathways that played important oxidative/reductive roles relative to cellular energy. In this chapter, the pathways that we cover have lesser roles from an energy perspective, but important roles, nonetheless, in catabolism and anabolism of building blocks of proteins and nucleic acids, nitrogen balance, and sugar balance. In a sense, these might be thought of as the “kitchen sink" pathways, but it should be noted that all cellular pathways are important. In this second section of metabolism, we cover metabolic pathways that do not have a strong emphasis on oxidation/reduction.

  • 7.1: Carbohydrate Storage and Breakdown
    Carbohydrates are important cellular energy sources. They provide energy quickly through glycolysis and passing of intermediates to pathways, such as the citric acid cycle, amino acid metabolism (indirectly), and the pentose phosphate pathway. It is important, therefore, to understand how these important molecules are made.
  • 7.2: Pentose Phospate Pathway
    Portions of the PPP are similar to the Calvin Cycle of plants, also known as the dark reactions of photosynthesis. We discuss these reactions separately in the next section. The primary functions of the PPP are to produce NADPH (for use in anabolic reductions), ribose-5-phosphate (for making nucleotides), and erythrose-4-phosphate (for making aromatic amino acids). Three molecular intermediates of glycolysis can funnel into PPP (or be used as usual in glycolysis).
  • 7.3: Calvin Cycle
    The Calvin Cycle occurs exclusively in photosynthetic organisms and is the part of photosynthesis referred to as the “Dark Cycle." It is in this part of the process that carbon dioxide is taken from the atmosphere and ultimately built into glucose (or other sugars). Though reduction of carbon dioxide to glucose ultimately requires electrons from twelve molecules of NADPH (and 18 ATPs). One reduction occurs 12 times (1,3 BPG to G3P) to achieve the reduction necessary to make one glucose.
  • 7.4: C4 Plants
    The Calvin Cycle is the means by which plants assimilate carbon dioxide from the atmosphere, ultimately into glucose. Plants use two general strategies for doing so. The first is employed by plants called C3 plants (most plants) and it simply involves the pathway described above. Another class of plants, called C4 plants employ a novel strategy for concentrating the CO2 prior to assimilation.
  • 7.5: Urea Cycle
    Yet another cyclic pathway important in cells is the urea cycle (Figure 7.5.1). With reactions spanning the cytoplasm and the mitochondria, the urea cycle occurs mostly in the liver and kidney. The cycle plays an important role in nitrogen balance in cells and is found in organisms that produce urea as a way to excrete excess amines.
  • 7.6: Nitrogen Fixation
    The process of nitrogen fixation is important for life on earth, because atmospheric nitrogen is ultimately the source of amines in proteins and DNA. The enzyme playing an important role in this process is called nitrogenase and it is found in certain types of anaerobic bacteria called diazotrophs. Symbiotic relationships between some plants (legumes, for example) and the nitrogen-fixing bacteria provide the plants with access to reduced nitrogen.
  • 7.7: Amino Acid Metabolism
    The pathways for the synthesis and degradation of amino acids used in proteins are the most varied among the reactions synthesizing biological building blocks. We start with some terms. First, not all organisms can synthesize all the amino acids they need. Amino acids that an organism cannot synthesize (and therefore must have in their diets) are called essential amino acids. The remaining amino acids that the body can synthesize are called non-essential.
  • 7.8: Amino Acid Catabolism
    Breakdown of glutamine by glutaminase is a source of ammonium ion in the cell. The other product is glutamate. Glutamate, of course, can be converted by a transamination reaction to alpha-ketoglutarate, which can be oxidized in the citric acid cycle.
  • 7.9: Nucleotide Metabolism
    Synthesis of ribonucleotides by the de novo method occurs in two pathways – one for purines and one for pyrimidines. What is notable about both of these pathways is that nucleotides are built from very simple building blocks.
  • 7.10: Pyrimidine de novo Biosynthesis
    Starting materials for pyrimidine biosynthesis include bicarbonate, amine from glutamine, and phosphate from ATP to make carbamoyl-phosphate (similar to the reaction of the urea cycle). Joining of carbamoyl phosphate to aspartic acid (forming carbamoyl aspartate) is catalyzed by the most important regulatory enzyme of the cycle, aspartate transcarbamoylase (also called aspartate carbamoyltransferase or ATCase).
  • 7.11: Purine de novo Biosynthesis
    Synthesis of purine nucleotides differs fundamentally from that of pyrimidine nucleotides in that the bases are built on the ribose ring. The starting material is ribose 5-phosphate, which is phosphorylated by PRPP synthetase to PRPP using two phosphates from ATP. PRPP amidotransferase catalyzes the transfer of an amine group to PRPP, replacing the pyrophosphate on carbon 1. Thus begins the synthesis of the purine ring.
  • 7.12: Deoxyribonucleotide de novo Biosynthesis
    Synthesis of deoxyribonucleotides de novo requires an interesting enzyme called ribonucleotide reductase (RNR). RNR catalyzes the formation of deoxyribonucleotides from ribonucleotides. The most common form of RNR is the Type I enzyme, whose substrates are ribonucleoside diphosphates (ADP, GDP, CDP, or UDP) and the products are deoxyribonucleoside diphosphates (dADP, dGDP, dCDP, or dUDP). Thymidine nucleotides are synthesized from dUDP.

Thumbnail: Metabolic Metro Map. Image used with permission (CC BY-SA 4.0; Chakazul).​​​​​​

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