Final: Pyrimidines + Deoxynucleotides (Ben) Flashcards
What are the 3 important pyrimidines in RNA/DNA?
Their structure?
- Cytosine - 2-oxo-4-amino
- Uracil - 2,4-oxo
- Thymine - 2,4-oxo-5-methyl
For the basic ring structure of a pyrimidine…
What molecules contribute the C and N atoms?
- Aspartate (contributes 1 N and adjacent 3 Cs)
- Glutamine (other N)
- CO2 (last C)
What activated ribose molecule (also used in purine synth) contributes the ribose-5-P to pyrimidine synth?
PRPP
De novo pyrimidine synthesis is awful…
describe its 5 steps (up to the “parent pyrimidine”) with their enzymes and co-factors.
(Again, just a review card. Will go into more detail on the main steps later.)
-
Carbamoyl Phosphate Synthetase II
- CO2 + 2 ATP + Gln –> Carbamoyl-P + Glu + 2 ADP/Pi
-
Aspartate Transcarbamoylase
- Carbamoyl-P + Asp –> Carbamoyl aspartate + Pi
-
Dihydro-orotase
- Carbamoyl aspartate –> Dihydro-orotate + H2O
-
Dihydro-orotate Dehydrogenase
- Dihydro-orotate + NAD+ –> Orotate + NADH + H+
-
Orotate Phosphoribosyl Transferase** **(OPT)
- Orotate + PRPP** –> **Orotidylate (parent pyrimidine)
After formation of the “parent pyrimidine”, several (4) steps can be taken to form UMP and eventually CTP.
What are they?
(probably not super important)
-
Orotidylate (OMP) Decarboxylase
- OMP –> UMP + CO2
-
Pyrimidine Mono-P Kinase
- UMP + ATP –> UDP + ADP
-
Pyr Di-P Kinase
- UDP + ATP –> UTP + ADP
-
CTP Synthetase
- UTP + Gln + ATP–> CTP + Glu + ADP + Pi
In pyrimidine synthesis, there are two multi-action polypeptides that together perform 5 of the 9 enzymatic reactions which eventually result in CTP.
What are these two peptides called and which enzymatic actions does each of them have?
-
CAD
- has Carbamoyl-P Synthetase II, Aspartate Transcarbamoylase and Dihydro-orotase actions (rxns 1-3)
-
UMP synthase
- has Orotate Phosphoribosyl Transferase and OMP decarboxylase actions (rxns 5 + 6)
At what two steps is pyrimidine synthesis regulated and how?
-
CAD
- inhibited by UMP
- activated by PRPP and ATP
-
UMP synthase
- inhibited by UMP
What is the order in which the molecules contributing C and N to the core pyrimidine ring are added?
Via what enzymes?
Which step(s) use ATP?
All are added by the CAD multifunctional enzyme…
-
CO2 and Glutamine (C + N) added by CPS-II using 2 ATP
- yielding 2 ADP but only one Pi because one is kept on carbamoyl-P
-
Aspartate (C, C, C, N) added by Aspartate Transcarbamoylase
- and the Pi is now lost
How many ATP equivalents are used to make the parent pyrimidine orotidylate (OMP)?
And to complete a molecule of CTP?
- For one OMP
-
4 ATP equivalents
- 1 ATP –> AMP for PRPP synth ( = 2 equiv. )
- 2 ATP for CPS-II action
-
4 ATP equivalents
- For one CTP
- 8 ATP equivalents
- same 4 as in OMP
- plus 4 for UMP > UDP > UTP > CTP
How are pyrimidines salvaged?
Via kinases that add P grps to their nucleoside forms…
-
Cytidine/Uridine Kinase
- nucleoside + ATP –> nucleoside-MP + ADP
- CMP can be converted to UMP via cytidylate deaminase (using H2O, losing NH3)
How are pyrimidine nucleotides broken down?
Sort of similar to purine catabolism…
- 5’ Nucleotidase removes Pi from UMP/CMP/TMP to make nucleoside
- Further breakdown results in release of CO2, NH3, and β-Alanine
In the de novo synthesis of purines vs. pyrimidines, what are the similarities/differences in…
- … when PRPP is added (+ its allosteric effect) ?
- … H4F’s contribution ?
- … Aspartate’s contribution?
- … origin of amino grps?
- … contributors of ring atoms?
-
PRPP (allosterically activates both)
- purines: added 1st step ; pyrimidines: added at end
-
H4F
- purines: two C ; pyrimidine: only -CH3 in Thy
-
Asp
- purines: one N ; pyrimidine: C, C, C, N
-
Amino Grps
- purines: Asp/Gln ; pyrimidine: Gln only
-
Ring Atoms
- purines: Gln, Gly, Asp, H4F, CO2 ; pyrimidines: Gln, Asp, CO2
In salvage of pyrimidines vs. purines …
- … what are the starting molecules, in general?
- … is PRPP used?
- … is ATP used?
-
Starting Molecules
- Purines: bases ; Pyrimidines: nucleosides (base + ribose)
-
PRPP use
- only in purines b/c bases must be phosphoribosylated (R-5-P)
-
ATP use
- only in pyrimidines b/c ribose is there, just need P
In catabolism of purines vs. pyrimidines, what are the differences in…
- … excretion of ring nitrogens?
- … fate of amino groups?
- …diseases?
-
Ring nitrogens:
- purines: excreted as urate ; pyrimidines: not excreted
-
Amino groups:
- aminos are saved in both catabolic processes
-
Diseases:
- purines: hyperuricemia ; pyrimidines: orotic aciduria
What is the enzyme responsible for formation of deoxynucleotides from nucleotides?
How does it do this?
Ribonucleotide Reductase
- heterodimeric (R1/R2 subunits)
- reduces nucleotide diphosphates (UDP, GDP, ADP, CDP)
- reduces the 2’ OH of ribose using its -SH groups
- -SH groups oxidize to become S-S which is then reduced back to -SH via Thioredoxin Reductase (also has -SH grps which ox. to S-S)
- TRase is then reduced by FADH2 and FADH2 is reduced by NADPH
How is ribonucleotide reductase regulated?
2 ways
- Induction - is an S phase enzyme only induced in dividing cells
-
Allosteric
- the different deoxynucleoside triphosphates (not the direct diphosphate products of the enzyme) inhibit the synthesis of some dNTPs while enhancing the synthesis of others
- the specific way this inhibition works regulates the ratio of dNDPs made by RReductase
- remember the CUGA order of the nucleoside diphosphates substrates… starting with dTTP (2nd product), each product inhibits its own synthesis plus that of all products above it, while stimulating synthesis of the product just below it + ATP enhances synthesis of all products
How is thymidylate synthesized?
And how can this be targeted with a drug?
Thymidylate Synthase
- dUMP + CH2-H4F –> dTMP + H2F
- inhibited by 5-fluorouracil, an anti-cancer agent and “suicide inhibitor”
