Download BCHEM 254 – METABOLISM IN HEALTH AND DISEASES II Lecture

BCHEM 254 – METABOLISM IN HEALTH AND DISEASES II
Lecture 3
Nucleotide Catabolism
Christopher Larbie, PhD
Introduction
Nucleotides are the building blocks of nucleic acids, the information carrying
macromolecules of the cell. The two types of nucleic acids are ribonucleic acid, called
RNA, and deoxyribonucleic acid, called DNA. Nucleotides consist of three parts:
1. a sugar (either ribose (in RNA only) or 2-deoxyribose (in DNA only)).
2. a nitrogen base (a purine or pyrimidine ring) attached to the sugar 1' carbon.
3. a phosphate group or groups, usually attached to the sugar 5' carbon.
Nucleotides are important for reasons besides being precursors of nucleic acids.
Most of them provide energy used to drive biochemical reactions. ATP is the most
commonly used source, but GTP is used in protein synthesis as well as a few other
reactions. UTP is the source of energy for activating glucose (glycogen synthesis) and
galactose. CTP is an energy source in lipid metabolism (glycerolipid synthesis). AMP
is part of the structure of coenzymes like NAD and Coenzyme A. We can synthesize
nucleotides by both de novo (new synthesis from scratch) and salvage pathways and
reuse those we already have.
Nomenclature
Sugars: Nucleotides contain one of two kinds of sugar. Deoxyribonucleotides derive
their name from the fact that they contain deoxyribose whereas ribonucleotides
contain the sugar ribose. The sugar ribose is a product of the pentose phosphate
pathway. Deoxyribose is not synthesized, as such, in the cell but, as we shall see, is
produced by action of the enzyme ribonucleotide reductase on ribonucleotide
diphosphates.
1|Page
©2014 Dr. Christopher Larbie
Nitrogen Bases: There are two kinds of nitrogen-containing bases in nucleic acids:
purines and pyrimidines. Purines consist of two fused nitrogen-containing rings
with a total of nine ring atoms. Pyridmidines have only a six-membered nitrogencontaining ring. Purines and pyrimidines are "flat", hydrophobic, aromatic molecules
that absorb ultraviolet light (260 nm). There are two purines and three pyrimidines
that are of concern to us. Cytosine is found in both DNA and RNA. Uracil is usually
found only in RNA and thymine is normally only in DNA. There are exceptions,
however. Sometimes transfer RNA molecules will contain some thymine as well as
uracil (a few DNA molecules also have uracil instead of thymine).
Nucleosides (base and sugar): Covalently linking carbon 1 of a sugar (ribose or 2deoxyribose) with a nitrogen base (N 9 of a purine base or N 1 of a pyrimidine base)
creates a nucleoside. Purine nucleoside names end in -osine and pyrimidine
nucleoside names end in -idine. The convention is to number the ring atoms of the
base normally and to use l', etc. to distinguish the ring atoms of the sugar. Unless
otherwise specified, the sugar is assumed to be ribose. To indicate that the sugar is
2'-deoxyribose, a d- is placed before the name.
Nucleotides (base, sugar, and phosphate): Nucleosides with phosphate(s) linked on
the sugar portion of the molecule are called nucleotides. Nucleotides with one
phosphate are also called nucleoside monophosphates (NMP); those with two
phosphates are nucleoside diphosphates (NDP); and those with three phosphates are
nucleoside triphosphates (NTP). Thus, ATP is a nucleotide and it is also called a
nucleoside triphosphate. Generally, the phosphate is in ester linkage to carbon 5' of
the sugar. When more than one phosphate is present, they are generally in acid
anhydride linkages to each other. If the phosphate is on the 5' carbon, no position
designation in the name is required. If the phosphate is in any other position,
however, the position must be designated. For example, 3'-5' cAMP indicates that a
single phosphate is in ester linkage to both the 3' and 5' hydroxyl groups of an
adenosine molecule and forms a cyclic structure. 2'-GMP would indicate that a
phosphate is in ester linkage to the 2' hydroxyl group of a guanosine.
Salvage of Nucleotide Bases
Before considering de novo synthesis of nucleotides, it is important to remember that
the bases used in nucleotides can come both from new synthesis (de novo) or from
salvage of bases previously made. The figure below schematically depicts
breakdown/synthesis of nucleic acids along with breakdown/synthesis of
nucleotides.
2|Page
©2014 Dr. Christopher Larbie
Note that, starting at the bottom, nucleobases (such as thymine, guanine, etc.) and
nucleoside monophosphates can be interconverted by action of the enzyme
phosphoribosyl transferase on them in the presence of 5-phospho-α-D-ribosyl-1pyrophosphate (PRPP). Notice also the central role that mononucleotides have in the
process. They can be converted to nucleoside triphosphates and DNA, or can be
converted to either nucleosides (by action of nucleotidases) or broken down to
nucleobases (reversal of phosphoribosyl transferase reaction).
Ribonucleotide reductase produces dADP, dGDP, dCDP and dUDP. These
diphosphodeoxyribonucleosides are phosphorylated by ATP to generate the dNTPs.
The enzyme is the same nucleoside diphosphate kinase that phosphorylates the
ribonucleotides.
dNDP + ATP → dNTP + ADP Nucleoside diphosphate kinase
NDP + ATP → NTP + ADP Nucleoside diphosphate kinase
Dietary Nucleic Acids
Nucleic acids are ubiquitous biomolecules. A significant amount of nucleic acids are
ingested in our diets. Nucleic acids are digested in our intestinal tract to nucleotides
by various nucleases and phosphodiesterases. Nucleotides are then
dephosphorylated by nonspecific phosphatases.
NMP + H2O → Nucleoside + Pi
5’-nucleotidase
The nucleosides are hydrolyzed by nucleosidases to release the bases.
Nucleoside + H2O → base + ribose
3|Page
©2014 Dr. Christopher Larbie
The ribose liberated in this reaction can be catabolized for energy. And is the only
portion of the nucleotide that can be used as a source of metabolic energy. Very little
of the nucleic acids ingested in our diets become incorporated into the nucleic acids
in our cells. Most of the ingested bases are excreted. The salvage pathways are to
continuously recycle cellular constituents not incorporated dietary bases.
Purine Nucleotide Catabolism
The purine nucleotides are catabolized by the following pathways. GMP is
converted into guanosine by 5’-nucleotidase. Next guanosine is converted into
guanine and ribose-1-phosphate by purine nucleoside phosphorylase. Guanine is
then converted into xanthine by guanine deaminase.
AMP has two degradation pathways. One pathway converts AMP into IMP by AMP
deaminase. IMP is dephosphorylated by 5’-nucleotidase to form inosine. Inosine is
4|Page
©2014 Dr. Christopher Larbie
broken down into ribose-1-phosphate and hypoxanthine by purine nucleoside
phosphorylase. The major pathway begins with dephosphorylating AMP by 5’nucleotidase to form adenosine which is then deaminated by adenosine deaminase
to form inosine. Inosine is converted into ribose-1-phosphate and hypoxanthine as
previously described. Hypoxanthine is converted into xanthine by xanthine oxidase.
Xanthine oxidase then oxidizes xanthine to produce uric acid. Animals excrete uric
acid.
5|Page
©2014 Dr. Christopher Larbie
Adenosine Deaminase
A genetic deficiency of adenosine deaminase causes severe combined
immunodeficiency syndrome (SCID). Lack of adenosine deaminase activity causes
an inability of B and T lymphocytes to proliferate and produce antibodies.
Adenosine deaminase activity is also impaired in other diseases such as AIDS,
anaemia, lymphomas and leukemias. Adenosine deaminase deficiency is another
target for gene therapy. Gene therapy is the attempt to repair a genetic deficiency by
the introduction of a function gene. So far Gene therapy has experienced lots of
setbacks. A loss or lack of adenosine deaminase activity causes deoxyadenosine to be
converted into dAMP. dAMP is then converted in to dATP. The result is high
concentrations of dATP. dATP is a potent inhibitor of deoxynucleotide biosynthesis.
Remember that dATP binds to the activity site of ribonucleotide reductase and turns
the enzyme off.
Pyrimidine Nucleoside Catabolism
Pyrimidines are also catabolized as shown. β-Alanine is then deaminated by a
transaminase to form Malonic semialdehyde which is then oxidized and converted
into malonyl-CoA. Malonyl-CoA as a precursor for fatty acid biosynthesis. βAminoisobutryate is also deaminated by a transaminase to form Methylmalonic
semialdehyde which is then oxidized and converted into methylmalonyl-CoA which
is converted into succinyl-CoA by methylmalonyl mutase.
6|Page
©2014 Dr. Christopher Larbie