M4: Nucleotide metabolism L29

Question 1

What is the difference between the salvage pathway and the de novo pathway of nucleotides?

Answer 1

1. De novo pathway:
   - synthesis of nucleotides from starting materials: amino acids, ribose, CO2, etc.
   - highly conserved in eukaryotes (developed early in evolution)
2. salvage pathway:
   - recovery of “bases” for making new nucleotides
   - more divergent, varied (less conserved)

Question 2

What are the 2 de novo pathways?

Answer 2

1. Purine pathway
   - PRPP, glutamine, aspartate, CO2, glycine, formate => Inosine monophosphate (IMP)
2. Pyrimidine pathway
   - CO2, glutamine, aspartate, PRPP => Uridine monophosphate (UMP)

Question 3

What is the base of a nucleotide?

Answer 3

The “base” is the aromatic part (the purine or the pyrimidine) of the nucleotide.

Question 4

What is a nucleoside vs nucleotide?

Answer 4

Nucleoside: means no phosphate (ribose + base)
Nucleotide: means phosphosugar (ribose + base + phosphate on C5 of the ribose)

Question 5

Look at slide 10 and 11 to understand how the purine and pyrimidine cubes work. (provided on exam)

Answer 5

L29 S10&11

Question 6

What is a complication of the pyrimidine cube?

Answer 6

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.

Question 7

What’s the difference between purine and pyrimidine?

Draw their base (like what stays the same between all of the different bases) structures.

Answer 7

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).

Question 8

Where does the ribose link to purines? Pyrimidines?

Answer 8

Purines: links to N9
Pyrimidines: links to N1

Question 9

What are the 2 types of sugars? What’s the difference between them?

Answer 9

Deoxyribose (in DNA) and ribose (in RNA).
Ribose has a hydroxyl on the 2’C
Deoxyribose has a hydrogen on the 2’C

Question 10

What carbon of the sugar molecule does the base link to? what type of linkage is it?

Answer 10

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.

Question 11

What conformation (stereochemistry) are the sugars in?

Answer 11

D sugar, furanose conformation.

Question 12

Draw the 2 types of sugars, show where the base and phosphate link, and label the carbons.

Answer 12

L29 S13

Question 13

What is the numbering scheme of Pyrimidines? Purines? Sugar rings?

Answer 13

1. Primed numbers for sugar ring
2. 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

Question 14

Memorize slide 15 L29.

Answer 14

S15 L29

Question 15

Draw Adenine, what’s the base called, what’s the nucleoside called, what’s the nucleotide called?

Answer 15

S15 L29

Question 16

Draw Guanine, what’s the base called, what’s the nucleoside called, what’s the nucleotide called?

Answer 16

S15 L29

Question 17

Draw Cytosine, what’s the base called, what’s the nucleoside called, what’s the nucleotide called?

Answer 17

S15 L29

Question 18

Draw Uracil, what’s the base called, what’s the nucleoside called, what’s the nucleotide called?

Answer 18

S15 L29

Question 19

Draw Thymine, what’s the base called, what’s the nucleoside called, what’s the nucleotide called?

Answer 19

S15 L29

Question 20

Memorize metabolites on slide 18 L29 (structures and names).

Answer 20

Slide 18 L29

Question 21

Memorize the drugs and therapeutics on S18 L29.

Answer 21

S19 L29

Question 22

What are the steps of the de novo synthesis of purines?

Answer 22

The Purine ring is assembled on the ribose phosphate

1. 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.
2. 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
3. There are 11 steps to make IMP (inosine monophosphate)

Question 23

Describe how PRPP is synthesized.

Answer 23

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.

Question 24

Describe how Beta-5-phosphoribosilamine is synthesized.

Answer 24

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.

Question 25

What are the nitrogen donors for the biosynthetic pathways of purines and pyrimidines?

Answer 25

1. Glutamine: donates side chain N to generate glutamate

2. Aspartate (aspartic acid): Donates backbone N to generate fumarate

Question 26

What is the common reaction structure for changing a ketone group to an amine group?

Answer 26

1. Phosphate from ATP or GTP is added to the oxygen.
2. N from glutamine side chain or aspartic acid backbone is added to the C with the oxygen and phosphate on it.
3. Phosphate group released to generate amino group.

Question 27

“Nucleoside” means:
A. Base + Sugar + Phosphate(s)
B. Base only
C. Base + Ribose
D. Ribose + Phosphate(s)
E. Ribose only

Answer 27

C. Base + Ribose

Question 28

At which position is the sugar is attached?
A. Pyrimidine: N1, Purine: N1
B. Pyrimidine: N1, Purine: N9
C. Pyrimidine: N3, Purine: N1
D. Pyrimidine: N3, Purine: N7
E. Pyrimidine: N3, Purine: N9

Answer 28

B. Pyrimidine: N1, Purine: N9

Question 29

Do review Q 3

Answer 29

L29, Slide 32

Question 30

Do review Q 4

Answer 30

L29, Slide 33

Question 31

Which of the following are true?
A. Synthesis of nucleotides is one of most conserved aspects of life from bacteria to humans
B. Most dietary needs satisfied by de novo synthesis of new nucleotides
C. Nucleotides are the energy currency of life and part of many vitamins and co-factors
D. Oral drugs can be bases or nucleosides but rarely nucleotides

Answer 31

A. Synthesis of nucleotides is one of most conserved aspects of life from bacteria to humans
B. Most dietary needs satisfied by de novo synthesis of new nucleotides
C. Nucleotides are the energy currency of life and part of many vitamins and co-factors
D. Oral drugs can be bases or nucleosides but rarely nucleotides

Question 32

How are coffee (caffeine), chocolate (theobromine), and urine (uric acid) related? Select correct answer(s)
A. Two of the three are delicious
B. They are all contain purines
C. They are related to xanthine
D. They have extracyclic oxygens
E. You should not feed them to your dog

Answer 32

A. Two of the three are delicious
B. They are all contain purines
D. They have extracyclic oxygens
E. You should not feed them to your dog