Purines and Pyrimidines

Question 1

Describe the function of the antiporter ORNT1

Answer 1

Ornithine is transported in

Citrulline is transported out

Question 2

What happens if you cannot run the urea cycle?

Answer 2

Cannot get nitrogen out, get a buildup of ammonia, which is toxic

Question 3

Which organ is the main site of the urea cycle? How do you get nitrogen there?

Answer 3

• The liver
• get nitrogen to the liver via Glutamine (extra nitrogen relative to glutamate)
• Also can get delivery through alanine via a transamination reaction (recall that alanine can be produced from pyruvate!)

Question 4

What are the control points for protein catabolism?

Answer 4

1. Transaminases
2. Carbamoyl phosphate synthetase I
   3 & 4) Glu dehydrogenase

Refer to the figure for where these number occur

Question 5

Creatine phosphate

Answer 5

Creatine phosphate - high energy phosphate form, reservoir in the muscle, used during exercise

Question 6

Branched Chain Amino Acids

Answer 6

They are:

• Val
• Ile
• Leu

Remove nitrogen through transamination. Get an alpha-ketoacid. You can then take this into Krebs for gluconeogenesis.

Question 7

Which enzyme is broken in MSUD?

Answer 7

branched-chain alpha-keto acid dehydrogenase complex

Question 8

What alpha-ketoacid do we see used in the TCA cycle regularly?

Answer 8

Pyruvate

If we used PDHC, then you would go from pyruvate –> acetyl-CoA; this is similar to what we are doing with the other branched chain AAs now. Just trying to get into the TCA cycle

Question 9

PURe As Gold; CUT the Py

Answer 9

Purines: Adenine and Guanosine
Pyrimidines: Cytosine, Uracil, Thymidine

Question 10

Which pyrimidines are in RNA vs. DNA

Answer 10

RNA:

1. UMP
2. CMP

DNA:

1. CMP
2. TMP

Question 11

What is the difference between nucleoside and nucleotide?

Answer 11

Nucleoside = Base + Sugar 
Nucleotide = Base + Sugar + Phosphate 

Can either build sugar and put a base on it or build a base and put a sugar on it

Question 12

Where does the Urea Cycle occur?

Answer 12

The mitochondria and cytosol

Question 13

Key differences in purine and pyrimidine nucleotide de novo synthesis:

Answer 13

Purine:

• Purine base made on the ribose
• initial nucleotide product is IMP
• I is converted to G and A as a monophosphate

Pyrimidine:

• Base ring is synthesized then attached to the ribose
• Initial nucleotide product is UMP
• U is converted to C as a triphosphate

Question 14

De novo synthesis of purines:

Answer 14

1. Get ribose sugar from HMP Shunt (key enzyme: G6PD)
2. Ribose 5-phosphate –(PRPP Synthetase)–> 5-Phosphoribosyl-1-pyrophosphate (PRPP); key step because this requires ATP
3. PRPP –(Glutamine phosphorphoribosyl pyrophosphate aminotransferase)–> 5’-Phosphoribsoylamine; key step because this is at the front end and is allosterically regulated
4. End at IMP

Question 15

What activates and inhibits PRPP synthase

Answer 15

1. Activation by Pi
2. Inhibition by purine ribonucleotides (end product inhibition)

First step is allosterically regulated

Question 16

What activates and inhibits glutamine phosphoribosyl pyrophosphate aminotransferase?

Answer 16

Activate:
1. PRPP

Inhibit:

1. AMP
2. GMP
3. IMP

Question 17

Sources of atoms for purine synthesis

Answer 17

1. Glutamine
2. Glycine
3. Aspartate
4. THF (methyl donor)
5. CO2

Question 18

Converting IMP to AMP and GMP

Answer 18

Need to get extra nitrogens hooked on

AMP and GMP come from IMP, and there is feedback inhibition from end-products

Source of energy:

1. For AMP production: uses GTP
2. For GMP production: uses ATP

If you have a lot of AMP, then you will shift to making more GMP and vice versa

Question 19

Generating Di and Tri-Phosphate forms

Answer 19

The following get us to the diphosphate form:

• Adenylate kinase
• Guanylate kinase

This gets us to the triphosphate form:

• Nucleoside diphosphate kinase
• ATP acts as energy donor to get the other ribonucleotides to the triphosphate form

Question 20

Carbamoyl phosphate synthetases

Answer 20

1. 2ATP + CO2 + glutamine –(Carbamoyl phosphate synthetase II) –> Carbamoyl phosphate

Note:

• Carbamoyl phosphate synthetase I is in the mitochondria and is part of urea. Uses Ammonia as source of nitrogen and is activated by N-acetyl-glutamate.
• Carbamoyl phosphate synthetase II is in the cytosol and is part of pyrimidine biosynthesis. Uses gamma-amide group of glutamine and is inhibited by UTP (end product inhibition) and activated by ATP

Question 21

Pyrimidine synthesis (Cytosol)

Answer 21

1. 2 ATP + CO2 + Glutamine – (Carbamoyl phosphate synthetase II)–> Carbamoyl phosphate; key step because energy invested as 2 ADP
2. Get finished base (orotate) + add PRPP –> OMP –> UMP
3. Ends at UMP

Question 22

Sources of atoms for pyrimidine synthesis

Answer 22

1. CO2 and glutamine
2. Aspartate
3. Ribose sugar is added last

Question 23

Synthesizing CTP from UTP

Answer 23

UTP – (CTP synthetase)–> CTP

1. Uses Glutamine -> Glutamate
2. Requires ATP

Question 24

Conversion or ribonucleotides to deoxyribonucleotides

Answer 24

1. Ribonucleoside diphosphate –(Ribonucleotide reductase)–> deoxyribonucleoside diphosphate

Question 25

On/Off sites and regulation of ribonucleotide reductase

Answer 25

1. Activity sites (on/off switch) - ATP activates the enzyme - dATP inhibits the enzyme so based off of the ratio of dATP:ATP 2. Substrate specificity sites (determine which one is made) - ATP, dATP, dTTP, or dGTP regulate the reduction of specific deoxyribonucleotides

Question 26

Without U there's no T... what am I referring to?

Answer 26

You can't make dTMP or dTTP without first going through dUMP. UMP->UDP->dUDP->dUMP->dTMP->dTDP->dTTP

Question 27

Things to remember about mono and di...

Answer 27

1. Ribonucleotide reductase uses dNDP or NDP (diphosphate) | 2. UTP -> CTP

Question 28

THF's role in U-->T

Answer 28

THF is a methyl donor 1. dUMP --(THF)--> dTMP 2. N5, N10 THF --> Dihydrofolate --> THF to recycle it. Note: methotrexate inhibits THF recycling to N5,N10 THF, which is why it is used against cancer cells.

Question 29

Degradation of purine and pyrimidines

Answer 29

Channel the base into uric acid 1. PRPP --> IMP --> inosine OR you can do step 2 2. AMP --> adenosine --(adenosine deaminase)--> inosine 3. Inosine -- (purine nucleoside phosphorylase) --> hypoxanthine 4. Hypoxanthine --(xanthine oxidase)--> xanthine 5. Xanthine -- (xanthine oxidase)--> uric acid

Question 30

Deficiency of adenosine deaminase results in what?

Answer 30

Accumulation of dADP or dAMP and poisons ribonucleotide reductase. Results in SCID!

Question 31

Allopurinol is used to treat what disease process, and which enzyme specifically?

Answer 31

Tx for gout via xanthine oxidase

Question 32

2 key enzymes in purine and pyrimidine degradation?

Answer 32

1. ADA (adenosine deaminase) | 2. Xanthine oxidase

Question 33

HGPRT deficiency results in what?

Answer 33

Inability to salvage hypoxanthine or guanine Need to do a bunch of de novo synthesis, this results in excessive production of uric acid --> Lesch-Nyhan

Question 34

Salvage pathways

Answer 34

Adenine phosphoribosyl transferase: - Adenine + PRPP --> AMP + PPi HGPRTase: - Hypoxanthine + PRPP --> IMP + PPi - Guanine + PRPP --> GMP + PPi Note: we can also salvage U, C, and T