Nucleotide metabolism I

Question 1

What is the difference btw nucleosides and nucleotides.

Answer 1

• nucleoside: base (purine/pyrimidine) + sugar (ribose/deoxy-R)
• nucleotide: base + sugar + phosphate (MP, DP, TP)

_{<u>REMEMBER:</u> nucleo<u><strong>T</strong></u>ide = <u><strong>T</strong></u>hree diff. things}

Question 2

What does the -ate ending indicate?

ex: adenylate

Answer 2

nucleotide monophosphate

→ AMP

Question 3

How is DNA and RNA of ingested food metabolized?

Answer 3

1. intestine
   DNA/RNA → polynucleotides → nucleotides → bases
2. bases taken up into blood stream
3. then
   
   • enter extrahepatic tissues
   • enter liver, here degraded to urate
4. ​​urate enters blood stream again + excreted via urine

Question 4

How do extrahepatic tissues and liver differ in their nucleotide metabolism?

Answer 4

• liver:
  
  • able of de novo synthesis of nucleotides
  • able to break down purines + release urate into blood stream
• extrahepatic tissues: only salvage reactions

Question 5

Which enzyme catalyzes the common substrate for purine and pyrimidine synthesis?

Reaction.

Answer 5

PRPP synthetase

ATP + ribose-5-P → PRPP + AMP

→ phosphoribosyl pyrophosphate then used

Question 6

Where does the ribose-5-P used for the synthesis of PRPP originally come from?

Answer 6

• glc-6-P
• fru-6-P

⇒ enter PPP, ribose-5-P formed

Question 7

What are purine salvage reactions?

Which group of enzymes catalyzes these reactions?

Answer 7

purine bases formed during degradation of RNA/DNA can be used to synthesize nucleotides

done by phosphoribosyl transferases (PRT)

→ important in extrahepatic tissues since they are unable to undergo de novo synthesis of purines

Question 8

Which enzymes are responsible for salvage reactions of AMP, IMP and GMP?

Answer 8

base + PRPP → nucleotide + PP_i

• adenine phosphoribosyl transferase (APRT)
  adenine + PRPP → AMP + PP_i
• hypoxanthine-guanine PRT (HGPRT)
  guanine/hypoxant. + PRPP → GMP/IMP + PP_i

Question 9

Differentiate btw de novo synthesis and salvage reactions of purine nucleotides.

Answer 9

IMP = common intermediate

de novo synthesis:

• IMP formed in 10 steps
• then either AMP, or GMP formed via 2 further reactions

salvage reactions:

• directly IMP, AMP and GMP formed

Question 10

Which enzyme catalyzes the rate-limiting step of purine synthesis?

Reaction.

Answer 10

Gln PRPP amidotransferase
first step of purine synthesis

PRPP + Gln
→ 5’-phosphoribosyl-amine + PP_i + Glu

Question 11

Where do the C/N atoms of the purine ring originate from?

Answer 11

• N1 = Asp
• C2, 8 = N₁₀-formyl H₄F
• N3, 9 = Gln
• C4, 5, N7 = Gly

Question 12

AMP is synthesized in 2 steps from IMP.

Which enzyme catalyzes the first step?

Reaction.

Answer 12

adenylsuccinate synthetase

IMP + Asp + GTP → GDP + P_i + adenylosuccinate

→ N of AMP is originally from Asp

Question 13

AMP is synthesized in 2 steps from IMP.

Which enzyme catalyzes the final conversion of adenylosuccinate to AMP?

Reaction.

Answer 13

adenylosuccinase (ASA)

adenylosuccinate → AMP + fumarate

Question 14

GMP is synthesized in 2 steps from IMP.

Which enzyme catalyzes the first step?

Reaction.

Answer 14

IMP dehydrogenase

IMP + H₂O + NAD⁺ → NADH + XMP

XMP = xanthosine monophosphate

Question 15

GMP is synthesized in 2 steps from IMP.

Which enzyme catalyzes the final conversion of XMP to GMP?

Reaction.

Answer 15

GMP synthetase

XMP + Gln + ATP → AMP + PP_i + Glu + GMP

→ N of GMP is originally from Gln

Question 16

What is special about the function of the enzymes involved in the de novo synthesis of IMP?

Answer 16

8 steps are catalyzed by 3 multifunctional enzymes

only 2 steps have their own enzymes

• step 1: Gln PRPP amidotransferase
• step 8: adenylosuccinase (ASA)

Question 17

How much energy is needed for de novo synthesis of

• IMP
• AMP
• GMP

Answer 17

• IMP: 6 ATP equ.
• AMP: + 1 GTP
• GMP: + 2 ATP equ.

Question 18

What is the importance of AMP kinase during exercise?

Reaction.

Answer 18

exercise leads to a decrease in cellular ATP which activates AMP kinase (AMPK)

2 ADP ⇔ ATP + AMP

also phosphorylates multiple downstream targets involved in other E metabolism pathways, leading to:

• acceleration of all ATP-producing pathways
• deceleration of all ATP-consuming pathways

⇒ preserves the cellular ATP concentration
by incr. the cellular AMP concentration

Question 19

What is the function of the purine nucleotide cycle?

Where does it happen?

Answer 19

in cytosol of skeletal myocytes
uses the excess AMP generated in muscle during exercise to fuel TCA cycle

→ incr. rates of oxidative phosphorylation in muscle

Question 20

The purine nucleotide cycle is composed of 3 enzyme-catalyzed reactions.

Which reaction is unique to this cyle and not involved in normal purine metabolism?

Answer 20

AMP deaminase

AMP + H₂O → NH₃ + IMP

→ now IMP can be used for new AMP synthesis to generate fumarate to fuel TCA cycle
_{(first by action of adenylosuccinate snythetase, then adenylossucinase)}

Question 21

Which products are formed in the purine nucleotide cycle?

What is their physiological role?

Answer 21

• fumarate fuels TCA cycle
• NH₃ released into blood stream, later converted in kidney used to buffer lactate/ketone bodies produced during exercise in muscle
• excess IMP converted to inosine, released into blood stream, degraded to urate for excretion in liver

⇒ ↑NH₃, ↑urate during exercise

Question 22

What is the consequence of a myoadenylate deaminase deficiency?

Answer 22

AMP cannot enter purine nucleotide cycle
most common inherited metabolic dysfunction in skeletal muscle

• fatigue
  due to excess adenosine in brain/muscle after exercise
• muscle pain, cramping, weakness
  probably due to incr. lactate levels/adenosine

​NOTE: NH₃, urate are NOT elevated during exercise

Question 23

What causes Lesch-Nyhan syndrome?

Consequence + symptomes?

Answer 23

hypoxanthine-guanine PRT deficiency
purine bases cannot be recycled in salvage reactions, converted to urate in liver

⇒ hyperuricemia + ↓GTP level in basal ganglia

symptomes:

• only in males (X-chromosomal recessive)
• mental retardation
• self-mutilation, aggression

Question 24

How is PRPP synthetase inhibited?

Answer 24

• AMP
• GMP

​→ are purine nucleotides (sort of product inhibition)

Question 25

Gln PRPP amidotransferase catalyzes the rate-limiting step of purine synthesis. How is it regulated?

Answer 25

_allosterically_ * activated by: **PRPP** (substrate) * inhibited by: **IMP, GMP, AMP** (product inhibition)

Question 26

How do AMP and GMP regulate the synthesis of purines?

Answer 26

sort of product inhibition, inhibit their formation on 3 levels: 1. _both_ inhibit formation of common precursor IMP **(PRPP synthetase, Gln PRPP amidotransferase)** 2. inhibit their own synthesis * _​​AMP:_ **adenylosuccinate synthetase** * _GMP:_ **IMP dehydrogenase** **​**⇒ signalling, there's already enough of us, we don't need to produce more

Question 27

How do ATP and GTP regulate the synthesis of purines?

Answer 27

* _**ATP**:_ activates **GMP synthetase** (_second_ step of GMP synthesis) * _**GTP**:_ activates **adenylsuccinate synthetase​** (_first_ step of AMP synthesis) _{don't understand the physiological concept behind this, just remember it}

Question 28

What are the basic steps of purine catabolism? Where does it mainly happen?

Answer 28

**mainly in liver** 1. purine nucleotide → purine nucleoside 2. ... → purine base 3. ... → xanthine 4. ... → urate → urate eventually released into bloodstream, excreted via urine

Question 29

Which enzymes catalyze the catabolism of purine nucleotides? Reaction scheme. Name the individual products.

Answer 29

**_5' nucleotidases_** specific for each purine nucleotide **monophosphate nucleotide + H₂O → nucleoside + P_i**​ * AMP → adenosine * IMP → inosine * XMP → xanthosine * GMP → guanosine

Question 30

Which enzymes catalyze the catabolism of purine nucleosides? Reaction scheme. Name the individual products.

Answer 30

**_purine nucleoside phosphorylases (PNPs)_** again, specific for each nucleoside **nucleoside + P_i → purine base + ribose-1-P** * inosine → hypoxanthine * xanthosine → xanthine * guanosine → guanine

Question 31

One purine nucleoside is not directly converted to its purine base. Which nucleoside is it, how is catabolized instead? Enzyme + reaction.

Answer 31

**_adenosine deaminase (ADA)_** adenosine not directly converted to adenine **adenosine + H₂O → NH₃ + inosine** → inosine then converted by its PNP to hypoxanthine __NOTE:_ _{don't mix it up w/ AMP deaminase (purine nucleotide cycle)}

Question 32

How are the purine bases catabolized? Enzymes + reactions.

Answer 32

_hypoxanthine and guanine_ are converted individually to **common product xanthine** * **_xanthine oxidase_** hypoxanthine + H₂O + O₂ → H₂O₂ + xanthine * **_guanase_** guanine + H₂O → NH₃ + xanthine ​_{according to lectures H2O2 is formed instead of NADH​}

Question 33

How is xanthine catabolized? Enyzme + reaction.

Answer 33

_by **xanthine oxidase**_ **xanthine + H₂O + O₂ → H₂O₂ + urate** _NOTE:_ same enzyme also catalyzes hypoxanthine to xanthine ​_{according to lectures H2O2 is formed instead of NADH}

Question 34

What is primary hyperuricemia? List reasons.

Answer 34

deficiencies in purine metabolism * **PRPP overproduction** * **absence of purine salvage reactions** * **low ATP level, disturbed ATP metabolism**

Question 35

Explain how PRPP overproduction can cause hyperuricemia. 2 examples for conditions that lead to PRPP overproduction.

Answer 35

↑PRPP → ↑purine synthesis → ↑urate * **_mutation in PRPP synthetase_** prevents allosteric inhibition → ↑ PRPP * _**Von Gierke disease** = glucose-6Pase deficiency_ more G6P available for PPP, overproduction of ribose-5P → ↑ PRPP

Question 36

Which pathology would cause absence of purine salvage reactions? How would this cause hyperuricemia?

Answer 36

_e.g. **HGRPT deficiency** (**Lesch-Nyhan syndrome)**_ hypoxanthine and guanine cannot be used to recover IMP and GMP, no synthesis of AMP possible ⇒ purine bases are transported to liver and degraded to urate for excretion

Question 37

How can a disturbed ATP metabolism cause hyperuricemia? In which disease could such phenomenon be seen?

Answer 37

* **_heavy exercise_** high energy consumption → ↓ATP → ↑AMP → ↑NH₃, urate * **_hereditary fructose intolerance_** deficiency of aldolase B → accumulation of F1P + trapping of P_i (fructokinase requires ATP) → inhibition of glucose production and reduced regeneration of ATP → ↑AMP → urate _{heavy exercise leading to hyperuricemia is prbly rather a thing in theory than in real life o.O}

Question 38

What is secondary hyperuricemia? List reasons.

Answer 38

_incr. amount of degradable purines due to breakdown of DNA_, can be caused by * **tissue damage** * **cancer​​, chemotherapy** (= tumor lysis syndrome)

Question 39

- don't have to know, but I think a doctor should know - What are symptoms of hyperuricemia? What is the biochemical reason for it?

Answer 39

**urate** has _low solubility_ in blood (especially in acidic pH range) ⇒ **accumulates** and forms * **urate crystals:** as can be seen in diapers (indicating Lesch-Nyhan syndyrome) * **Na-urate crystals** → causing lithiasis in hollow organs * **tophi** = urate accumulation in soft tissues/joints → inflammation reaction, pain (**_gout_**)

Question 40

- don't have to know, but I think a doctor should know - Which medication can be administered to treat gout? Mechanism.

Answer 40

**_allopurinol_** = competitive inhibitor of hypoxanthine converted by xanthine oxidase to _oxopurinol_ ⇒ **now hypoxanthine/xanthine in urine instead of urate** (have higher solubility, don't form crystals)