VL 8 (Katja Arndt)

Question 1

Nucleotide Biosynthesis

Answer 1

Nucleotides can be synthesized de novo from amino acids, ribose-5-phosphate, CO2, and NH3.

• De novo pathway
  Activated Ribose (PRPP) + aa + ATP + CO2 + .. –> Nucleotide

Nucleotides can be salvaged from RNA,
DNA, and cofactor degradation.

• Salvage pathway
  Activated ribose (PRPP) + base –> nucleotide

Question 2

Nomenklatur of bases, nucleosides and nucleotides

Answer 2

Base:
* Adenine
* Guanine
* Thymine / Uracil
* Cytosine

Nucleoside
–> Ribonucleoside (2´OH) (RNA)
–>Desoxyribose (2´H) (DNA)
* Adenosine / Desoxyadenosine
* Guanosine / Desoxyguanosine
* Uridine / Thymidine
* Cytidine / Desoxycytidine

Nucleotide
–>Ribonucleotide
–>Desoxynucleotide
* Adenylate / Desoxyadenylate
* Guanylate / Desoxyguanylate
* Uridylate /Thymidylate
* Cytitidlate /Desoxycytidilate

Question 3

Explain de novo biosnthesis of nucleotides

Answer 3

• Nucleotide pools kept low -> cells must continually synthesize them
• This synthesis may limit rates of transcription and replication
• Biosynthesis approx. the same in all organisms studied
• Ribose-5-phosphate is activated to PRPP

Purine/Pyrimidine bases:
* Gln provides most amino groups
* Gly is precursor for purines
* Asp isprecurser for pyrimidines

Question 4

Explain de novo synthesis of purines

Answer 4

Purines are synthesized on a ribose molecule in the de novo pathway

Adenine and Guanine are synthesized as AMP and GMP via the common precursor IMP (inosinate)

• ATP is used to phosphorylate GMP precursor
• GTP is used to phosphorylate AMP precursor

Question 5

Explain de novo synthesis of Pyrimidine

Answer 5

• preassembled
• pyrimidine synthesis proceeds by FIRST making the pyrimidine ring (in the form of orotate) and THEN attaching it to ribose 5-phosphate.
• Aspartate and carbamoyl phosphate provide the atoms for the ring structure.

Steps:
1. NH3 (from Gln) and CO2 form Carbamoylphosphate
2. Reaction of Aspartate with Carbamoylphosphate
3. Ring closure
4. Formation of double bond = Orotate
5. Addition of ribose-5-phosphate via PRPP, to orotade yields the nucleotide (orotidylate)
6. Decarboxylation of orotidylate results in uridylate (UMP), the first possible pyrimidine

UMP –(phosphorylation)–> UTP –(amination converts)–> CTP

Question 6

Ribonucleotides are precursors to deoxyribonucleotides

Answer 6

• Deoxyribonucleotides are synthesized from ribonucleoside diphosphates.
• 2’-hydroxyl group of ribose is directly reduced to 2’-H bond… without activating the carbon!
• Mechanism: Two H atoms are donated by NADPH and carried by proteins thioredoxin or glutaredoxin

Question 7

How is dTMP build?

Answer 7

dTMP is made from dUTP

1. dUTP is made
2. dUTP -> dUMP by dUTPase
3. dUMP –> dTMP by thymidylate synthase (adds a methyl group from tetrahydrofolate)

• Folic Acid Deficiency Leads to Reduced Thymidylate Synthesis
• Thymidylate synthase and dihydrofolate reductase are targets of chemotherapy for cancer treatment.

Question 8

Explain slvage pathways of nucleotides

Answer 8

Nucleotides can be salvaged from RNA,DNA, and cofactor degradation.

Question 9

Anticancer drug 5-Fluoro-Uracil is activated by the salvage pathway

Answer 9

• 5-FU is converted into fluorodeoxy-uridylate (F-dUMP) by cancer cells.
• F-dUMP is a suicide inhibitor of thymidylate synthase (TS).

—> Inhibition of DNA and RNA synthesis
—> 5-FU acts on dividing and non dividing cells

Question 10

Catabolism of Purines

Answer 10

1. Dephosphorylation (via 5’-nucleotidase)
2. Deamination and hydrolysis of ribose lead to production of xanthine.
3. Hypoxanthine and xanthine are then oxidized into uric acid by xanthine oxidase. (Spiders and other arachnids lack xanthine oxidase.)

GMP –> Guanine –> Xanthine
AMP –> Adenosine –> Inosine –> Hypoxanthine –> Xathine

Xanthie –(Xamthine oxidas)–> Uric acid –> Urate

Question 11

What can you see in Gout?

Answer 11

• Excess Uric acid
• Painful joints (often in toes) due to deposits of sodium urate crystals -> Inflammation
• Primarily affects males
• May involve genetic under-excretion of urate and/or may involve overconsumption of fructose

Treatment: avoidance of purine-rich food
(seafood, liver)
Also treated with xanthine oxidase inhibitor
allopurinol (suicide inhibitor) =>(Hypo)Xanthine excreted

Question 12

Catabolism of Pyrimidins

Answer 12

• Leads to NH4+ -> urea
• Can produce intermediates of
  Citric Acid Cycle

e.g: Thymidine is degraded to succinyl-CoA
–> Transamination reaction (also found in amino acid degradation)