Nucleotide Metabolism

1. Nucleotides consist of a) sugar, b) nitrogenous base, and c) phosphate

2. Nucleosides consist of a a) sugar and b) nitrogenous base

3. The sugars of nucleosides and nucleotides are either ribose (found in ribonucleotides of RNA) or deoxyribose (found in deoxyribonucleotides of DNA).

4. Unless otherwise specified, the term "nucleotide" will be used in this class to indicate either ribonucleotides (contain ribose) or deoxyribonucleotides (contain deoxyribose).

5. Unless otherwise specified, the term "nucleoside" will be used in this class to indicate either ribonucleosides (contain ribose) or deoxyribonucleosides (contain deoxyribose).

6. The term nucleoside phosphate is equivalent to a nucleotide (nucleoside + phosphate + base = nucleotide). This is true whether it is a monophosphate, diphosphate, or triphosphate.

7. The nitrogenous bases found in nucleotides include adenine (purine), guanine (purine), thymine (pyrimidine), cytosine (pyrimidine), and uracil (pyrimidine).

8. The bases adenine, guanine, and cytosine are found in both ribonucleotides and deoxyribonucleotides. Thymine is almost always found in deoxyribonucleotides. Uracil is found primarily in ribonucleotides and rarely in DNA, but does appear as a deoxyribonucleotide intermediate in thymidine metabolism.

9. Nucleosides are named according to the base they contain. Nucleosides containing purines are named by adding "os" before the "ine." Thus, nucleosides containing guanine are called guanosine. Nucleosides containing pyrmidines are named with the suffix "idine" at the end of the name of the base they contain. Thus, the pyrimidine nucleosides are cytidine, uridine, and thymidine.

10. Ribonucleotides are the building blocks of RNA and deoxyribonucleotides are the building blocks of DNA.

11. Nucleotides and nucleosides are made in cells by two general mechanisms - salvage pathways (use breakdown products of other nucleotides/nucleosides) or de novo pathways (synthesize nucleotides/nucleosides from scratch).

12. In salvage pathways, nucleic acids can be broken down to nucleoside monophosphates or individual bases. Monophosphates be rephosphorylated to triphosphates by kinases in order to reincorporate them into nucleic acids. Alternatively, nucleoside monophosphates can lose a phosphate (becoming nucleosides) or can lose the phosphate and the sugar to become a base. Bases can either be broken down or reconverted back to nucleoside monophosphate by addition of appropriate sugars and/or phosphates.

13. De novo synthesis of nucleotides utilizes very simply precursors - amino acids, carbamoyl phosphate, and sugars. Activated carbon moieties are donated by folate derivatives.

14. De novo synthesis of pyrimidines is fundamentally different from that of purines. In purine biosynthesis, the base is assembled on the sugar. In pyrimidine biosynthesis, the base is made apart from the sugar and later attached to it.

15. In de novo synthesis of nucleotides, ribonucleotides are synthesized first. Deoxyribonucleotides are made from ribonucleoside diphosphates. Atoms in the ring of pyrimidines come from aspartate and carbamoyl phosphate.

16. The enzyme carbamoyl phosphate synthetase has an interesting catalytic strategy involving channeling (I called it tunneling) of the substrates through the enzyme as catalysis occurs. This is important because some of the intermediates (such as carboxyphosphate and carbamic acid) are very unstable in aqueous solution.

17. The most important regulatory enzyme for the entire pathway of pyrimidine biosynthesis is aspartate transcarbamoylase (ATCase), which plays an important role in balancing the amounts of purines and pyrimidines and also measuring the amount of energy available (via the amount of ATP present). The enzyme catalyzes the linkage of aspartate to carbamoyl phosphate and is allosterically activated by ATP and allosterically inactivated by CTP.

18. The first pyrimidine nucleotide made in the de novo pyrimidine pathway is UMP.

19. UMP is phosphorylated to UDP (by uridine monophosphate kinase) and then to UTP (by nucleoside diphosphokinase = NDPK) before conversion to CTP. Each nucleoside monophosphate has a specific kinase to convert it to the diphosphate, but all diphosphates (purines, pyrimidines, and all deoxyribonucleoside diphosphates) are converted to triphosphates by NDPK.

20. Conversion of UTP to CTP is catalyzed by the enzyme CTP synthase and it is inhibited by CTP, thus providing a balance between the amount of CTP and UTP.

21. De novo synthesis of purines uses atoms from aspartate, glycine, glutamine, carbon dioxide, and tetrahyrdofolate derivatives to make the purine ring.

22. The most important regulatory enzyme for the first part of purine biosynthesis is PRPP amidotransferase. It is inhibited fully by AMP and GMP, but is only partly inhibited (is still partly active) when only one of these molecules is present. This enzyme helps to control purine production and also slows purine production when one nucleotide gets to be in too high of a concentration.

23. In the process of making IMP, fumarate is released, thereby connecting purine biosynthesis to the citric acid cycle.

24. The first purine-like intermediate in de novo purine biosynthesis is inosinic acid (or IMP), which has the purine-like base hypoxanthine linked to ribose (and ribose is linked to phosphate).

25. IMP can be converted to AMP or GMP. The pathway by which IMP leads to GMP is inhibited by GMP and uses energy from ATP, whereas the pathway where IMP is converted to AMP is inhibited by AMP and uses energy from GTP. Thus, the critical balance of these two nucleotides is maintained using this scheme.

26. The pathway to GMP involves oxidation, whereas the pathway that leads to AMP uses aspartic acid to donate an amine and fumarate is again released.

27. Nucleoside monophosphates from de novo synthesis can be converted by kinases to nucleoside diphosphates and nucleoside triphosphates. These enzymes include AMP kinase (also called adenylate kinase) and GMP kinase (also called guanylate kinase), which convert nucleoside monophosphates to nucleoside diphosphates, and nucleoside diphosphate kinase (NDP kinase or NDPK), which converts all nucleoside diphosphates to nucleoside triphosphates.