Module 13 - Nucleotide Metabolism Flashcards
What happens to all of the nucleic acid that we ingest?
The first thing that happens is that the nucleic acids are acted on by nucleases, which hydrolyze the phosphodiester bonds that connect the individual nucleotides together.
The products of this enzymatic activity are monophosphate nucleotides.
These are then acted on by phosphatases to remove the phosphate groups, which produces nucleosides, which are molecules that have a purine or pyrimidine molecule linked to a ribose or deoxyribose sugar.
While some of the nucleosides are acted on by nucleosidases which hydrolyze the linkage between the sugar and nitrogenous base, most of the nucleosides are absorbed into the enterocyte (cells lining the small intestine).
Where does nucleic acid digestion occur?
in the lumen of the small intestine
What do all nucleotides consist of?
a nitrogenous base (adenine, guanine, cytosine, uracil (RNA) and thymine (DNA)),
a ribose (RNA) or deoxyribose (DNA) sugar,
and one or more phosphate groups.
How are nucleosides similar to nucleotides?
nucleosides have no phosphate group
Nucleotides and Nucleosides Have Diverse Functions in the Cell
The nucleotide ATP is the major currency of energy in biological systems
Adenine-based nucleotides are components of three major coenzymes - NAD, FAD, Coenzyme A
Nucleotides are often linked to other biomolecules to form activated substrates
Some nucleotides and nucleosides are cellular and physiological regulators
Purine-based nucleotides can be synthesized in cells by one of two different pathways.
They can either be synthesized from “scratch”, using other molecules to donate the carbon and nitrogen atoms needed; this is referred to as the de novo Pathway.
Alternatively, they can be obtained from the Salvage Pathway, which salvages existing purine bases and converts them to nucleotides.
de novo Pathway precursor
In this pathway, the overall strategy is to start with ribose-5-P, a pentose sugar, and then to build the purine ring on this sugar to form both purine nucleotides
The overall de novo pathway
carbon 1 in ribose-5-P where the purine ring will be built is not very reactive. To make it reactive, ATP is used to add a pyrophosphate group onto carbon 1, to form phosphoribosylpyrophosphate (PRPP)
the first purine product of the pathway is inosine monophosphate (IMP)
The first committed and regulated step of the de novo pathway
catalyzed by glutamine-PRPP amidotransferase, which initiates the assembly of the purine ring on the ribose sugar by transferring an amino group from glutamine onto the ribose sugar.
What happens to the IMP?
It represents a branch-point, where it can either be used for AMP synthesis or for GMP synthesis
AMP Synthesis from IMP
To form AMP, a molecule of aspartate is used as a donor of an amino group.
GTP hydrolysis is used to provide energy to drive the reaction forward
This branch of the pathway is used to synthesize AMP, and is responding to signals in the cell that more adenine-based nucleotides, most likely ATP, is in short supply
GMP synthesis from IMP
glutamine donates an amino group to the ring rather than aspartate.
in this branch of the pathway, note that ATP rather than GTP is used as a provider of energy.
How is the de novo pathway regulated?
The regulation of this pathway is primarily through allosteric inhibition of glutamine-PRPP amidotransferase by end products of the pathway; IMP, AMP, and GMP
What is the salvage pathway?
involves the chemical joining of free purine bases that are generated in the cell during normal turnover and degradation of nucleic acids and nucleotides.
carbon 1 on ribose 5-P is not very reactive;
instead phosphoribosylpyrophosphate (PRPP) is used as the activated form to which purines are attached to the sugar
Which two enzymes drive the reaction forward?
Adenine phosphoribosyltransferase (APRT) catalyzes the attachment of adenine to PRPP, with the release of PPi which drives the reaction forward, to form AMP.
Hypoxanthine and guanine are linked to PPRP by the enzyme hypoxanthine-guanine phosphoribosyltransferase (HGPRT), to form IMP and GMP, respectively.
What is gout?
when concentrations of uric acid get too high in the blood, which can occur from overproduction or under-excretion of purines, uric acid crystallizes and deposits in joints and causes pain and inflammation
How are The pyrimidines that are required in the cell (uracil, cytosine and thymine) made?
They are all made de novo;
that is, there is very little salvaging of pyrimidines that are obtained through the diet or that are released as free pyrimidines when nucleotides are degraded.
How is the synthesis of pyrimidine-derived nucleotides different from the synthesis of purines?
While purines are synthesized onto a ribose sugar, pyrimidines are assembled separately and then added onto the ribose ring after the pyrimidine has been synthesized.
What is The first and rate-limiting step in pyrimidine synthesis?
it is catalyzed by carbamoyl phosphate synthetase II (CPS II)
This enzyme essentially fuses the amino group from glutamine to CO2 (in the form of HCO3-) and a phosphate from ATP to form carbamoyl phosphate.
The energy released from the hydrolysis of ATP drives this reaction forward.
How are CPS I and CPS II Similar/Different?
What is the first committed step in pyrimidine synthesis?
it is catalyzed by aspartate transcarbamoylase (ATCase).
this enzyme is allosterically inhibited by CTP, the final product of this pathway.
How are nucleoside monophosphates (NMPs) e.g. AMP and GMP converted to nucleoside diphosphates (NDPs)?
by enzymes called nucleoside monophosphate kinases, using ATP as the source of the phosphate group
There is actually a group of enzymes that carry out this process, since the enzyme is specific for which base is in the NMP
Nucleoside monophosphate kinases are specific for the base but not for the ribose sugar
How are NDPs converted to NTPs?
The nucleoside diphosphate produced by the nucleoside monophosphate kinases are next acted on by a single enzyme, nucleoside diphosphate kinase.
There is only one enzyme that acts on all nucleoside diphosphates because the enzyme has no specificity for either the base or the type of sugar.
This enzyme uses ATP to generate the other NTPs from NDPs that are required in the cell.
Where does the ATP required to convert NMPs to NTPs come from?
It is derived primarily from oxidative phosphorylation in the mitochondria, although recall that some ATP is produced in glycolysis via substrate-level phosphorylation.
What is required for DNA synthesis?
deoxyribonucleotides
How are deoxyribonucleotides synthesized from NDPs?
Deoxyribonucleotides are synthesized from nucleoside diphosphate molecules (NDPs) by a reduction reaction carried out by ribonucleotide reductase.
The substrates for this enzyme are ADP, GDP, CDP, and UDP. The 2’-OH position of the ribose ring becomes reduced to a hydrogen group to form deoxyribose
What is The ultimate source of reducing equivalents for the synthesis of deoxyribonucleotides?
comes from NADPH, which is produced in the pentose phosphate pathway.
