Week 4: Nucleotide Metabolism II Flashcards
What does ribonucleotide reductase do?
Converts NDP (nucleotide diphosphate) to dNDP (deoxynucleotide diphosphate)
What are the kinetic requirements for nucleotides to enter the synthesis pathway?
Low Km, high Vmax
Why is it critical to keep nucleotide levels (C, G, A and T) at low and relatively equal levels?
To ensure accuracy in nucleotide selection for metabolism
How can “the wrong” nucleotide be synthesized?
Though the Km is very high and Vmax is very low for these situations, if there is an imbalanced amount of one nucleotide, it can oversaturate and begin to enter the synthesis pathway
What is the overall function of the conversion of NDP to dNDP?
To create dNDPs for DNA synthesis
Which NDP to dNDP conversion is unusual, and how does it occur?
dTDP is unusual because you start with dUDP, and have to add an H group to it to convert it to dTDP (requires the removal of -OH group, and then the reduction by hydrogen to make it a 2’ deoxynucleotide)
Where do the electrons come from to deoxygenate and reduce an unusual dNDP?
The electron pair comes from reduced cysteine
Where do the hydrogens used to reduce ribonuclease reductase derive from?
NADH or NADPH
How many sites does ribonucleotide reductase have, and what are their functions?
There are two main regulatory sites–a secondary site for determining substrate specificity, and a primary site to turn the enzyme on/off–and an active site
What substrates bind to the on/off regulatory site of ribonucleotide reductase and how do they function?
ATP turns on the enzyme (positive feedback when there is not enough dATP) and dATP turns off the enzyme when enough has been made
What is the function of dUTPase in the process of forming dTMP?
It is a “sanitizing” enzyme that removes a pyrophosphate (beta and gamma phosphates), converting dUTP to dUMP
What other dNTP can be converted to dTMP and how does that occur?
dCTP can be deaminated to dUTP by deaminase, which can then be dephosphorylated by dUTPase, forming dUMP
What kind of group is added to dUMP to convert it to dTMP? What enzyme catalyzes it?
A methyl group at the 5C position on the 6-membered ring above the ribose molecule. Thymidylate synthase catalyzes it.
How is 7,8-Dihydrofolate converted back to N5N10-Methylene-tetrahydrofolate?
Reduction by NADPH/H+ (by dihydrofolate reductase, involved in chemotherapy) and the addition of a methyl group by the demethylation of serine to glycine
Generally speaking, how is AMP converted to uric acid, and why is this done?
AMP is converted to hypoxanthine (removal of Pi, NH3, and ribose), then xanthine (oxidation), then uric acid (another oxidation) for disposal. This is done to ensure proper balance of purines in the body, as AMP acts as an indicator of overall [NTP]
What is the result of the dysfunction of ADA?
The dysfunction of Adenosine DeAminase means 2’-deoxyadenosine cannot be shunted through the disposal pathway (uric acid), and instead is converted to dATP via the deoxynucleoside kinase enzyme. ADA deficiency causes SCID, improper B- and T-lymphocyte development in ADA-deficient patients.
