M4: Nucleotide metabolism L29 Flashcards
What is the difference between the salvage pathway and the de novo pathway of nucleotides?
- De novo pathway:
- synthesis of nucleotides from starting materials: amino acids, ribose, CO2, etc.
- highly conserved in eukaryotes (developed early in evolution) - salvage pathway:
- recovery of “bases” for making new nucleotides
- more divergent, varied (less conserved)
What are the 2 de novo pathways?
- Purine pathway
- PRPP, glutamine, aspartate, CO2, glycine, formate => Inosine monophosphate (IMP) - Pyrimidine pathway
- CO2, glutamine, aspartate, PRPP => Uridine monophosphate (UMP)
What is the base of a nucleotide?
The “base” is the aromatic part (the purine or the pyrimidine) of the nucleotide.
What is a nucleoside vs nucleotide?
Nucleoside: means no phosphate (ribose + base)
Nucleotide: means phosphosugar (ribose + base + phosphate on C5 of the ribose)
Look at slide 10 and 11 to understand how the purine and pyrimidine cubes work. (provided on exam)
L29 S10&11
What is a complication of the pyrimidine cube?
Complication: uracil is only in RNA and thymine is only in DNA. This makes a difference in the ribose that’s put on (deoxyribose or a ribose with a hydroxyl) thats why we have 2 forms of uridine nucleosides: Uridine and deoxy-uridine.
What’s the difference between purine and pyrimidine?
Draw their base (like what stays the same between all of the different bases) structures.
Purine: 2 rings
Pyrimidine: 1 ring
L29 S12 (need to know the numbering of the atoms, where each atom comes from, and where the ribose links).
Where does the ribose link to purines? Pyrimidines?
Purines: links to N9
Pyrimidines: links to N1
What are the 2 types of sugars? What’s the difference between them?
Deoxyribose (in DNA) and ribose (in RNA).
Ribose has a hydroxyl on the 2’C
Deoxyribose has a hydrogen on the 2’C
What carbon of the sugar molecule does the base link to? what type of linkage is it?
The base links to the sugar on 1’C.
The bond formed is beta-glycosidic where the base is facing up (towards O) and hydrogen is facing down.
If it was the opposite way, it would be an alpha-glycosidic bond.
What conformation (stereochemistry) are the sugars in?
D sugar, furanose conformation.
Draw the 2 types of sugars, show where the base and phosphate link, and label the carbons.
L29 S13
What is the numbering scheme of Pyrimidines? Purines? Sugar rings?
- Primed numbers for sugar ring
- Unprimed for bases
- Pyrimidines: Nitrogens at 1, 3 (not 5). Attached to sugar at N1
- Purines: Nitrogens at 1, 3, 7&9 (not5). Attached to sugar at N9
Memorize slide 15 L29.
S15 L29
Draw Adenine, what’s the base called, what’s the nucleoside called, what’s the nucleotide called?
S15 L29
Draw Guanine, what’s the base called, what’s the nucleoside called, what’s the nucleotide called?
S15 L29
Draw Cytosine, what’s the base called, what’s the nucleoside called, what’s the nucleotide called?
S15 L29
Draw Uracil, what’s the base called, what’s the nucleoside called, what’s the nucleotide called?
S15 L29
Draw Thymine, what’s the base called, what’s the nucleoside called, what’s the nucleotide called?
S15 L29
Memorize metabolites on slide 18 L29 (structures and names).
Slide 18 L29
Memorize the drugs and therapeutics on S18 L29.
S19 L29
What are the steps of the de novo synthesis of purines?
The Purine ring is assembled on the ribose phosphate
- 5-phosphoribose => PRPP
- Ribose ring with phosphate on 5C of the sugar, from this we make PRPP which is used as a scaffold to build the purine. - PRPP => 5-phosphoribosylamine
- This is a 5-phosphoribose with a nitrogen that will become N9 in the purine ring.
- regulation at steps 1&2
- pathway committed at step #2 because 5-phosphoribosylamine is only used to make purines - There are 11 steps to make IMP (inosine monophosphate)
Describe how PRPP is synthesized.
Ribose-5-phosphate + ATP to PRPP + AMP
The ATP is added because you have to activate C1 of the ribose by adding 2 phosphates onto it. The phosphates are put on in the alpha conformation (alpha sugar anomer) because when you add Nitrogen, it will invert it to a beta conformation.
Describe how Beta-5-phosphoribosilamine is synthesized.
This is a committing step therefore it is the site of purine specific regulation.
PRPP + Glutamine + H2O to Beta-5-phosphoribosilamine + Glutamate + PPi
- This causes the anomeric inversion to form beta anomer
- Release of PPi makes it an irreversible reaction: There’s another enzyme that hydrolyzes pyrophosphate to 2 separate phosphate molecules. That is very energetically favoured. At equilibrium the cell has very little or no pyrophosphate in the cell (due to the PPi being hydrolyzed) so the rxn can’t run backwards.
- Glutamine is the N donor for this reaction.
