Module 13 - Nucleotide Metabolism

Question 1

What happens to all of the nucleic acid that we ingest?

Answer 1

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).

Question 2

Where does nucleic acid digestion occur?

Answer 2

in the lumen of the small intestine

Question 3

What do all nucleotides consist of?

Answer 3

a nitrogenous base (adenine, guanine, cytosine, uracil (RNA) and thymine (DNA)),

a ribose (RNA) or deoxyribose (DNA) sugar,

and one or more phosphate groups.

Question 4

How are nucleosides similar to nucleotides?

Answer 4

nucleosides have no phosphate group

Question 5

Nucleotides and Nucleosides Have Diverse Functions in the Cell

Answer 5

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

Question 6

Purine-based nucleotides can be synthesized in cells by one of two different pathways.

Answer 6

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.

Question 7

de novo Pathway precursor

Answer 7

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

Question 8

The overall de novo pathway

Answer 8

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)

Question 9

The first committed and regulated step of the de novo pathway

Answer 9

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.

Question 10

What happens to the IMP?

Answer 10

It represents a branch-point, where it can either be used for AMP synthesis or for GMP synthesis

Question 11

AMP Synthesis from IMP

Answer 11

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

Question 12

GMP synthesis from IMP

Answer 12

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.

Question 13

How is the de novo pathway regulated?

Answer 13

The regulation of this pathway is primarily through allosteric inhibition of glutamine-PRPP amidotransferase by end products of the pathway; IMP, AMP, and GMP

Question 14

What is the salvage pathway?

Answer 14

involves the chemical joining of free purine bases that are generated in the cell during normal turnover and degradation of nucleic acids and nucleotides.

Question 15

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?

Answer 15

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.

Question 16

What is gout?

Answer 16

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

Question 17

How are The pyrimidines that are required in the cell (uracil, cytosine and thymine) made?

Answer 17

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.

Question 18

How is the synthesis of pyrimidine-derived nucleotides different from the synthesis of purines?

Answer 18

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.

Question 19

What is The first and rate-limiting step in pyrimidine synthesis?

Answer 19

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.

Question 20

How are CPS I and CPS II Similar/Different?

Answer 20

Question 21

What is the first committed step in pyrimidine synthesis?

Answer 21

it is catalyzed by aspartate transcarbamoylase (ATCase).

this enzyme is allosterically inhibited by CTP, the final product of this pathway.

Question 22

How are nucleoside monophosphates (NMPs) e.g. AMP and GMP converted to nucleoside diphosphates (NDPs)?

Answer 22

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

Question 23

How are NDPs converted to NTPs?

Answer 23

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.

Question 24

Where does the ATP required to convert NMPs to NTPs come from?

Answer 24

It is derived primarily from oxidative phosphorylation in the mitochondria, although recall that some ATP is produced in glycolysis via substrate-level phosphorylation.

Question 25

What is required for DNA synthesis?

Answer 25

deoxyribonucleotides

Question 26

How are deoxyribonucleotides synthesized from NDPs?

Answer 26

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

Question 27

What is The ultimate source of reducing equivalents for the synthesis of deoxyribonucleotides?

Answer 27

comes from NADPH, which is produced in the pentose phosphate pathway.