Nucleotide Metabolism (Week 4--Kurdistani)

Question 1

Nucleotide vs. nucleoside

Answer 1

Nucleotide: base + pentose/ribose sugar + phosphate (ex: AMP, GMP, CMP, UMP, dTMP)

Nucleoside: base + pentose/ribose sugar (ex: adenosine, guanosine, cytidine, uridine, deoxythimidine)

Question 2

What are the 2 types of pentose sugars?

Answer 2

Ribose (in RNA) has 2’ OH

Deoxyribose (in DNA) has 2’ H

Question 3

What are the 2 types of bases?

Answer 3

Purines: adenine (A), guanine (G)–have 2 rings

Pyrimidines: cytosine (C), uracil (U), thymine (T)–have 1 ring

Note: T only in DNA and U only in RNA

Question 4

Where does the base attach to the pentose sugar?

Answer 4

Base attaches to 1’ carbon of pentose sugar, on same side of base as 5’ carbon (which eventually picks up phosphate)

Attachment is by beta-glycosidic linkage (enzyme that cleaves linkage is called phosphorylase)

Question 5

Cellular roles of nucleotides

Answer 5

1) Monomeric units of nucleic acids
2) Energy metabolism: ATP, activated intermediates (UDP-glucose)
3) Regulation of physiological processes: adenosine and coronary blood flow, cAMP/cGMP as signaling molecules, allosteric regulators
4) Coenzyme components: FAD, NAD+, CoA

Question 6

How do you synthesize nucleotides (purines and pyrimidines)?

Answer 6

1) De novo biosynthesis: from scratch; from AAs, ribose-5-P, CO2, NH3
2) Salvage pathway: recycling from pre-existing nucleotides (cells die and you can use their old nucleotides)

Note: purines do de novo more; pyrimidines do salvage more

Question 7

Why do we do de novo synthesis?

Answer 7

Don’t get enough nucleotides in diet

Question 8

How does de novo synthesis of nucleotides occur?

Answer 8

Occurs in most cells, but liver is major site of de novo synthesis

Purines: the purine rings are built onto ribose-5-phosphate

Pyrimidines: the pyrimidine ring is synthesized then attached onto the ribose-5-phosphate

Phosphoribosylpyrophosphate (PRPP) is intermediate in both purine and pyrimidine synthesis

Question 9

What is PRPP?

Answer 9

Phosphoribosyl-pyrophosphate (PRPP) is an activated ribose sugar that is used to synthesize nucelotides de novo

Ribose 5-phosphate + ATP –> PRPP + AMP

(PRPP synthetase catalyzes reaction; ribose 5-phosphate comes from pentose phosphate pathway, which is a shunt off of glycolysis)

Takes energy to synthesize PRPP (and thus nucleotides)

Question 10

Steps in de novo biosynthesis of PURINEs

Answer 10

1) Regulated step: Ribose-5-phosphate + ATP –> PRPP + glutamine (via PRPP synthetase); at this step, control enzyme activity via feedback/feedforward to slow/speed process
2) Committed step: PRPP + glutamine –> 5-phosphoribosyl amine + glutamate +PPi (via amidophosphoribosyl transferase); this is point of no return (and often is regulated by final product)
3) 9 more steps then get IMP (inosine monophosphate)
4) IMP converted to GMP (by ATP) or AMP (by GTP)
5) GMP and AMP are phosphorylated, then phosphorylated again or acted on by ribonucleotide reductase (RNR) to make dGDP and dADP
6) Get GTP, ATP, dGTP, or dATP

Question 11

What are purines degraded to?

Answer 11

Purines (AMP, GMP) degraded to xanthine then to uric acid which is excreted in urine

If uric acids loses H+, turns into urate, which is insoluble and can cause gout if it accumulates enough

Note: food purines are degraded to uric acid by gut epithelium

Question 12

Gout

Answer 12

Caused by too much uric acid in the blood (hyperuricemia)

Primary gout: inherited; more in males, overactivity of PRPP synthetase; Lesch-Nyhan syndrome is X-linked recessive (get gout AND neurological symptoms)

Secondary gout: medications, too much cell death (chemo), chronic kidney failure

Clinical characteristics: hyperuricemia, arthritis (usually in big toe), kidney malfunction

Pathology: precipitation of sodium urate crystals in joints or other tissues, or in urinary tract (or kidneys); tophi are large visible crystals in joints/soft tissue

Question 13

Treatment of gout

Answer 13

NSAIDs, corticosteroids, colchicine, allopurinol, avoid alcohol and foods with purines

Colchicine interferes with function of microtubules so inflammatory cells (neutrophils) can’t get to site where crystals formed so can’t cause inflammation

Allopurinol is similar to hypoxanthine (which is a substrate for xanthine oxidase in the process of degrading purines) so it essentially inhibits xanthine oxidase so that xanthine can no longer be turned to uric acid (“suicide inhibitor” because enzyme converts it to oxipurinol (alloxanthine) which does not dissociate and inhibits the enzyme)

Probenecid inhibits uric acid reabsorption at PCT (tx chronic gout)

Sulfinpyrazone Inhibits uric acid reabsorption (tx chronic gout or gouty arthritis)

Question 14

Pseudogout

Answer 14

Arthritis caused by deposition of calcium pyrophosphate crystals, in knee or wrist

Caused by excessive Ca2+ in blood (overactive parathyroid gland, hemochromatosis, hypothyroidism); incidence increases with age

Question 15

Adenosine deaminase (ADA)

Answer 15

Enzyme that degrades d-adenosine –> d-inosine that then goes to hypoxanthine (via purine nucleoside phosphorylase) then uric acid

This is how dAMP is degraded; note that AMP is degraded to uric acid differently–using AMP deaminase for AMP –> IMP –> inosine –> hypoxanthine –> uric acid

Question 16

Severe Combined Immunodeficiency Disorder (SCID)

Answer 16

Severe defects in level and activity of B and T cells causes recurrent infections and failure to thrive

Caused by deficiency in adenosine deaminase (ADA) that causes elevated levels of ATP and thus dATP

dATP is highly toxic because inhibits RNR, so inhibits synthesis of other deoxynucleotides and DNA so cells can’t divide/signal. Lymphoid cells most susceptible to ADA deficiency

Treatment: bone marrow transplant or gene therapy

Question 17

What hapens when you have deficiency in purine nucleoside phosphorylase (PNP)?

Answer 17

Get increased levels of GTP and dGTP, which also inhibit RNR (like ATP and dATP) and cause toxicity to immune system

Get less severe form of immunodeficiency

Question 18

Purine salvage pathways to synthesize nucleotides

Answer 18

Adenine and Guanine use different enzymes for the purine salvage pathway:

1) Adenine + PRPP –> AMP + PPi (via adenine phosphoribosyl transferase (APRT))
2) Guanine (or hypoxanthine) + PRPP –> GMP (or IMP) + PPi (via hypoxanthine (guanine) phosphoribosyl transferase (HGPRT))

Question 19

What exactly is “salvaged” in the purine salvage pathways?

Answer 19

The base–adenine or guanine (so the rings with the nitrogen in them!)

(note that this is different from pyrimidine salvage, which uses nucleosides!)

Question 20

Lesch-Nyhan Syndrome

Answer 20

Defective HGPRT causes increased uric acid (orange crystals in diaper!)

X-linked so primarily in males

Get neurological defects (dystonia, choreoathetosis, ballismus), behavior problems (aggressive, compulsive self-mutilation)

Mechanism of hyperuricemia: decreased salvage leads to (1) more purine degradation and (2) buildup of PRPP which stimulates committed step in de novo purine synthesis so get more uric acid generation

Treatment: allopurinol to reduce uric acid production, hydration to prevent urate crystal deposition (esp in kidney)

Question 21

Pyrimidine de novo biosynthesis

Answer 21

Pyrimidine ring synthesized first then attached to ribose (unlike purine, which is built ON ribose)

However, note that it’s not exactly the final pyrimidine ring that is synthesized–it still has a CO2 on there that shouldn’t be, and this ring is called orotate

Orotate attached to PRPP to form UMP

From UMP –> UTP –> CTP

Last pyrimidine we need to synthesize is thymidine: dUTP –>dUMP –> dTMP

Question 22

6 steps to synthesize UMP

Answer 22

1) NH3 (from AA glutamine) + HCO3- + 2 ATP –> carbamoyl phosphate
2) Carbamoyl phosphate + aspartate –> carbamoyl aspartate
3) Carbamoyl aspartate –> dihydroorotate
4) Dihydroorotate –> orotate
5) Orotate + PRPP –> orotidine monophosphate (OMP)
6) Orotidine monophosphate –> uridine monophosphate (UMP)

Question 23

In the pyrimidine ring that is formed de novo, where do the N’s and C’s come from?

Answer 23

N1, C4,5,6 come from aspartate

C2, N3 come from carbamoyl phosphate (and furthermore, N3 usually comes from glutamine)

Question 24

Enzymes that catalyze the 6 steps of de novo synthesis of UMP

Answer 24

CAD catalyzes steps 1, 2, 3: multifunctional polypeptide (CPSII, ATCase, DHOase)

UMPS catalyzes steps 5, 6: multifunctional polypeptide (OPRT, ODC)

Reactions 1, 5, 6 are regulated

Question 25

Where do the 6 steps of pyrimidine de novo biosynthesis occur, and what is the significance of this?

Answer 25

All steps occur in cytoplasm, except step 4 which is in the mitochondria

Step 4 is dihydroorotate –> orotate (via dihydroorotate dehydrogenase, enzyme that is in the intermembrane space of the mitochondria)

Significance is that this links synthesis of nucleotides to availability of energy! If limited O2 (decreased ATP), decrease activity of DHODH and get decreased synthesis of nucleotides, which is good because don’t want to be making nucleotides when you don’t have enough energy)

Question 26

What does UMPS do, and how does it interact with the chemotherapeutic 5FU?

Answer 26

Multifunctional, but adds orotate to PRPP then converts that to UMP

UMPS is also what targets and activates 5FU (chemotherapeutic drug): give cells 5FU, and UMPS places 5FU onto PRPP (as if 5FU was a base like orotate) to make active form of 5FU drug which is like a nucleotide

Note: cancer cells can be resistant to 5FU if they don’t have UMPS since UMPS is needed to get active form of 5FU

Question 27

How does 5FU target cancer cells?

Answer 27

Since cancer cells upregulate the pyrimidine synthesis pathway compared to normal cells (which still do have some of this pathway), 5FU acts mostly to inhibit UMP synthesis in cancer cells

Question 28

What is the link between the urea cycle and pyrimidine synthesis and what is the significance of that?

Answer 28

Carbamoyl phosphate is the product of step 1 of pyrimidine synthesis and is necessary for urea cycle to proceed (ornithine –> citrulline)

Significance is that if problem with urea cycle, will get backup of carbamoyl phosphate in the mitochondria –> carbamoyl phosphate will leak out into cytoplasm and cause increase in pyrimidine biosynthesis pathway –> causes more uracil production, and get uracil in blood

Question 29

Regulation of pyrimidine synthesis (what activates/inhibits pathway)?

Answer 29

Inhibition occurs by end products UTP and CTP on initial step, and UMP inhibits its own formation

Activation by ATP and PRPP on first step

Question 30

Hereditary Oroticaciduria

Answer 30

Can’t make UMP because deficiency of OPRT (orotate-phosphoribosyl transferase; step 5) and/or ODC (orotidine monophosphate decarboxylase; step 6) (both part of UMPS)

Causes accumulation of orotic acid (orotate), which is excreted in urine, also causes anemia, retarded growth, immunodeficiency

Treatment: include uridine (nucleoside) in diet to increase UMP levels, which allows you to make pyrimidines again AND gives negative feedback on system so don’t get buildup of orotic acid

Very rare, only 17 cases worldwide

Question 31

We give uridine (nucleoside) to increase UMP in people with hereditary oroticaciduria, not uracil (base). Why wouldn’t giving uracil help?

Answer 31

Remember, we use nucleosides for salvage pathway of pyrimidines, NOT bases!

If we gave uracil, we’d have to attach it to PRPP, and that’s the step that is defective!

Question 32

What happens when you degrade pyrimidines?

Answer 32

Pyrimidine rings fully degraded to soluble structures!

(unlike purines that make uric acid)

Question 33

Pyrimidine salvage

Answer 33

Salvage pathway dominates over de novo synthesis for pyrimidines

Food pyrimidines are absorbed as their nucleosides –> pyrimidine nucleoside + PRPP (via pyrimidine phosphoribosyl transferase) –> UMP??

Note: since pyrimidines are recycled at the level of the nucleotide you shouldn’t have to react with PRPP…looks like Uridine has to react with PRPP (wikipedia) but Cytidine and deoxyThymidine probably don’t and are just used as they are…

Question 34

Purines vs. pyrimidines (de novo synthesis, salvage, degradation)

Answer 34

Purines: de novo synthesized onto PRPP; first nucleotide made is IMP; salvaged through base; degraded to uric acid

Pyrimidines: de novo synthesize rings first then add to PRPP; first nucleotide made is UMP; salvaged through nucleoside; degraded to AA, CO2, NH3

Question 35

Ribonucleotide reductase (RNR)

Answer 35

Fe-containing multifunctional enzyme with redox-active thiol groups that can transfer electrons during reduction reactions

RNR reduces NDP (ribonucleotide) –> dNDP (deoxyribonucleotide)

After catalyzing reaction, RNR needs to be re-oxidized by thioredoxin (note ultimate source of electrons is NADPH)

Note that at this stage, have 2 phosphates attached (XX DI phosphate)

Also, dATP inhibits RNR just because of feedback inhibition

Question 36

How are dNTPs produced?

Answer 36

Phosphorylation of dNDPs (duh…di to tri-phosphate) catalyzed by nucleoside diphosphate kinase

Question 37

What is thymine?

Answer 37

Thymine is a pyrimidine that is only in DNA, and is different from uracil just by 1 methyl group (thymine = 5-methyluracil)

Question 38

How do we make dTMP?

Answer 38

dUMP + THF –> dTMP + dihydrofolate (DHF) (via thymidylate synthase)

Question 39

Why do we use dUMP and not dUTP to make dTTP for DNA synthesis?

Answer 39

Because DNA polymerase isn’t good at distinguishing between dUTP and dTTP but we don’t want dUTP incorporated into DNA!

Don’t want lots of dUTP around!

Question 40

How do we regenerate THF from DHF (after THF has helped to make dTMP from dUMP)?

Answer 40

DHF + NADPH + H+ –> THF + NADP+ (via dihydrofolate reductase)

The enzyme dihydrofolate reductase is very important because this whole cycle is required for DNA synthesis to occur!

Question 41

What drugs inhibit dihydrofolate reductase and what is the significance of this?

Answer 41

Chemotherapeutic drugs and antibiotics target and inhibit dihydrofolate reductase so you can’t regenerate THF from DHF

This means you can’t continue doing DNA synthesis (because don’t have thymidine nucleotide)!

These drugs can be used to kill ectopic pregnancy embryo

Question 42

What compounds are “carriers” of methyl groups, and what is actually the source of the methyl group?

Answer 42

THF and SAM are carriers of methyl groups, but serine is the original source of the methyl group

Question 43

FdUMP

Answer 43

5-fluorodeoxyuridylate

When 5FU is given as a drug, remember UMPS adds a ribose sugar onto it to make it like a nucleotide, and FdUMP is the “nucleotide” it is converted to

FdUMP is a suicide inhibitor of thymidylate synthase, so prevents thymidine synthesis and thus DNA synthesis

Enzyme thymidylate synthase tries to react with FdUMP, but FdUMP has a F where UMP just has an H, and thymidylate synthase trying to react with that C-F bond inactivates the thymidylate synthase

Question 44

5FU is called a DNA synthesis inhibitor but why is this technically not true?

Answer 44

Because 5FU inhibits nucleotide synthesis, specifically it inhibits thymidine synthesis.

However, that in turn inhibits DNA synthesis since you need thymidine to synthesize DNA

Question 45

Antifolates

Answer 45

DHF analogs that competitively bind to and inhibit DHF reductase (can’t re-form THF)

Ex: aminopterin, methotrexate (amethopterin)

Question 46

Trimethoprim

Answer 46

Antibiotic

Antifolate that binds better to bacterial DHF reductase (can’t re-form THF) so is used as antibiotic

Question 47

Folate and folic acid

Answer 47

Folate is natural form

Folic acid is synthetic form

Does 1 carbon transfers

Metabolic roles: synthesis of thymidine (using methylene-THF) and purines (which we didn’t talk about), synthesis of methyl donor S-adenosylmethionine (SAM), conversion of homocysteine to methionine (N5-methyl-THF)

Question 48

Can humans synthesize folic acid?

Answer 48

No, only bacteria can so we have to eat folate in our diet to get it

Question 49

How do sulfa drugs work?

Answer 49

Since bacteria use para-amino benzoid acid (PABA) as a precursor for folic acid synthesis, we can give sulfonamide, an analog of PABA to inhibit folic acid synthesis in bacteria

Inhibiting folic acid synthesis in bacteria eventually causes bacteria to not be able to make thymidine, so get DNA synthesis inhibition in bacteria

Question 50

What are vitamin B12 and folic acid important for?

Answer 50

Need vitamin B12 and folic acid in the reaction where you take methyl group from THF, transfer it to methionine to make SAM and turn homocysteine –> methionine

Homocysteine –> methionine (this rxn is very important because need SAM and THF to do make purines and dTMP (DNA synthesis!!!))

Question 51

Deficiency in vitamin B12 and folic acid

Answer 51

Caused by inadequate intake or for B12 also could be due to poor absorption due to lack of intrinsic factor

Low folic acid can cause neural tube defects

Low vitamin B12 can cause megaloblastic anemia, pernicious anemia, paresthesias, peripheral neuropathy, irritability, dementia, depression, psychosis

Question 52

Anti-metabolites

Answer 52

Inhibit nucleotide synthesis or inhibit DNA synthesis directly

Used as cancer drugs

Antifolates (deplete cells of thymidine), 5FU, 6-MP, araC, 5-azacytidine, AZT, acyclovir, other pyrimidine or purine analogs

Like 5FU, are activated in specific cell type (cells growing rapidly)

Question 53

6-mercaptopurine (6-MP)

Answer 53

Is an antimetabolite (purine analog) that inhibits amido-phosphoribosyl-transferase (enzyme that catalyzes committed step in purine de novo synthesis, NOT APRT!)

Converted to nucleotide analog by HGPRT in salvage pathway: 6-MP + PRPP –> 6-MP-ribose-phosphate + PPi

Used for childhood leukemia

Note: relies on salvage pathway to be activated but inhibits de novo pathway

Other derivatives exist with similar effects: Imuran (Azathioprine) used as immunosuppressant

Question 54

Cytosine arabinose (araC)

Answer 54

Another nucleotide analog (anti-metabolite) that has same base but slightly different ribose sugar

Gets incorporated into DNA but because of slightly different structure, inhibits DNA chain synthesis

Question 55

5-Azacytidine

Answer 55

Another anti-metabolite (similar to cytidine) thats base has nitrogen group instead of carbon

When you try to make thymidine from cytidine (I thought you made T from U…) by methylating that carbon, realize it’s nitrogen instead so can’t methylate!

Used to treat myelodysplastic syndrome (inhibits DNA synthesis)

Used in basic science to decrease DNA methylation in cultured cells

Question 56

Azido-3’-deoxythymidine (AZT)

Answer 56

Nucleotide (pyrimidine) analog that was one of the first HIV anti-retroviral drugs

Instead of OH group, has N3 (azide) group

Inhibits viral polymerase, inhibits reverse-transcription

Question 57

Acyclovir

Answer 57

Acycloguanisine (purine analog) is like guanine but ribose sugar ring is actually open!

Must be phosphorylated by viral thymidine kinase to be activated (our kinases can’t)

Activated acyclovir is a DNA polymerase inhibitor

Question 58

What happens to that hypoxanthine that builds up if you use a xanthine oxidase inhibitor for treating gout?

Answer 58

Hypoxanthine is more soluble, so is just excreted!