purine and pyridimine metabolism 1/2

What are the two purines? What are the three pyridimines in genetic material? what is the difference between ribose and deoxyribose?

for deoxyribose, the second carbon has an -H instead of an OH (de-oxy)

what is a nucleoside?

ribose sugar group attached to a nitrogenous base

what is GTP mainly used for?

protein synthesis

what are UDP-glucose and UDP-glucoronic acid used for

1. they are used for synthesis of polysaccharides and oligosaccharides chains of glyco proteins

2. glucoronidation reaction-detoxification (bilirubin conjugation)

what is adenosine a major component of?

cofactors for oxidation reactions: NAD+/NADH; FAD/FADH2; NADP+/NADPH

What does AMP do?

component of CoA which is involved in

1. synthesis of bile acids

2. activation of acetate and Fatty acids for biosynthesis and catabolic reactions

what medicine is caffeine a key element of? What is it an Antagonist of? What are its withdrawal symptoms?

key element of excedrin, Midol, migranal;

antagonist of adenosine receptors

withdrawal: headache, fatigue, and concentration problems

what three things can caffeine become and what are its functions?

List out the adenosine receptors and their functions

talk about the signal transduction properties of adenosine

can stimulate or inhibit adenyl cyclase

secondary messengers: AMP (AMPK), cAMP (PKA), cGMP (PKG)

what is the difference between nucleoside and nucleotide

nucleoside: nitrogenous base linked to a pentose sugar; lacks a phosphate group

Nucleotide: a nucleoside + a phosphate group.

where do most of purine biosynthesis occur? how is it transported? what is the energy requirement for synthesis of one purine?

Most de novo synthesis occur in the liver but the brain could do some nucleotide synthesis as well;

nucleoside/bases are transported via RBCs

6-high energy bond for one purine; therefore, salvage pathways are used by many cells to recycle purine bases (convert free bases and nucleoside to nucleotide)

Draw out where each atom came from for the purine bases? How many molecules? How many precursors? How does synthesis occur?

where are purines built from? What is the source of this? Describe this reaction? What is the limiting factor to this reaction?

built from activated form of ribose (5-phosphoribosyl 1- pyrophosphate (PRPP)

• catalyzed by PRPP synthetase

  • ATP→ AMP

Limiting factor: low [ribose-5-phosphate]

Ribose-5-phosphate came from the PPP pathway

what is the first purine nucleotide created? describe this molecule and the reaction that created it. In this reaction, what happens if there is folate deficiency?

IMP (inosine monophosphate);

• base = hypoxanthine

• can be converted to either AMP or GMP

Reaction:

• ten steps

• uses 4 ATP

• two N10- formyl-EH4 are used as donors of carbons

• requires folate (B9) and cobalamin (B12) as recyling of folate

  • deficiency in folate = impair cell division = megaloblastic anemia

what is the commited step of purine biosynthesis. Describe this reaction and how it is regulated

PRPP —> 5-phosphoribosylamine

• catalyzed by glutamine phosphoribosyl amidotransferase (GPA)

• Glutamine → glutamate; H2O → 2PPi

• regulated by: intracellular [PRPP] and [ GLN]; usual levels are far below GPA’s Km

  • increase in [] = increase in de novo synthesis

describe the synthesis of Adenosine Monophosphate

Aspartate + IMP → adenylosuccinate

• catalyzed by adenylosuccinate synthetase

• requires GTP

then, adenlosuccinate → AMP plus fumerate

• catalyzed by adenylosuccinase

describe the synthesis of Guanosine Monophospahte

IMP → XMP (xanthosine monophosphate)

• oxidized by IMP dehydrogenase

• NAD+ + H2O → NADH + H+

Then, XMP → GMP

• catalyzed by GMP synthetase

  • ATP + Gln → Glutamante + AMP

what is the amino group of AMP? GMP?

AMP: Asp

GMP: Gln

Describe how AMP and GMP become ATP and GTP?

nucleoside monophosphate Kinase: makes ADP and GDP

Nucleoside diphospahte kinase: makes ATP and GTP

describe the regulation of purine synthesis

what is the salvage pathway? why is it beneficial? what is the key enzyme? Why is this pathway important for some cell?

the salvage pathway interconnects free bases, nucleoside, and nucleotides

It is beneficial because it is energetically favorable and reduces levels of purine bases and nucleosides that could inhibit other metabolic reactions

key enzyme = hypoxanthine-guanine phosphoribosytransferase (HGPRT)

this is important because salvage of bases is a major form of nucleotide generation for lymphocytes!

Draw out the purine salvage pathways

relating to the purine salvage pathway, deficiency of what enzyme leads to immunodeficiency?

deficiency of PNP (purine nucleside phosphorylase)

• autosomal recessive

• leads to T-cells toxicity and death

• more sensitive to opportunistic infections

What is Lesch Nyhan Syndrome? explain the pathology, inheritance, symptoms and treatments

• caused by deficient in HGPRT

• since purine bases can’t be used → degradation → excessive uric acid

• X-linked recessive

• symptoms: mental retardation, self-mutilation (chew off fingers and lips), hyperuricemia (gout)

• treatment: allopurinol (xanthine oxidase inhibitor)

What is ADA1 deficiency? explain its pathology

• Adenosine deaminase deficiency

• causes severe combined immunodeficiency disease (SCID)

• deficiency = accumulation of deoxyadenosine → dATP → inhibits ribonucleotide diphosphate reductase

  • results in reduced generation of deoxyribonucleotides and impairs proliferation of lymphocytes

• loss of immune system, no T/B cells

what is myokinase? What does deficiency of AMP deaminase cause?

during excercise, muscles can use myokinase to turn 2ADP → ATP + AMP;

result in muscle fatique (during excercise) , weakness, cramping, pain

describe the synthesis of pyrimidines? What is CAD? what is carbamoyl phosphate derived from? How is CPSII different then CPSI?

• based synthesized first

  • from Asp and carbamoyl phosphate

  • CAD = the first three enzyme of pathway rolled up into one peptide

    • Carbamoyl phosphate synthetase II, Asp transcarbamoylase, and dihydro-orotase

Carbamoyl phosphate derived from CO2 and Gln; II is different because uses Gln as source of nitrogen and occurs in cytosol.

how is pyrimidine synthesis regulated? how does folate deficiency relate to this?

regulation at CPSII

• activated by PRPP, inhibited by UTP

• phosphorylation by MAP kinase = more sensitive to PRPP, less sensitive by UTP

  • occurs as cell approach S-phase

• folate deficiency result in anemia (macrocytic or macroblastic) bc of limited dTMP synthesis

draw out the general pathway for pyrmidine synthesis

draw out the step where orotate → UMP. Where are the two enzymes located? What are the consequences to deficiency of this and how do we treat this?

UMP synthase = polypeptide that contains both enzymes mentioned

Deficiency:

• hereditary orotic acidura

• accumulation of Orotic Acid

• blocks pyrmidine synthesis = growth retardation, megaloblastic anemia

Treatment:

• oral administration of Uridine

  • converts to UMP by bypassing metablic block

what is the second cause of orotic acidura?

deficiency in ornathine transcarbamoylase = accumulation of carbamoyl phosphate in mitochondria = leakage to cytosol; there pyrimidine production = orotic acidura

HOW is CTP produced? What are precursor to RNA Synthesis? How do we synthesize deoxyribonucleotides? how is dTTP produced?

1. CTP produced by addition of amino group from Gln to C4 of UTP

2. UTP and CTP = precursor to RNA

3. deoxyribonucleotides occur at the diphosphate level via Ribonucleotide reductase (RR)

   1. CDP → dCDP; UDP → dUDP

4. dTTP is produced via methylation of dUMP

   1. catalyzed by thy-midy-late synthase from N5,N10, methylene-THF

describe two cancer drugs

5-fluorouracil inhibits thymidylate synthase (no dTMP synthesis)

Metho- trexate inhibits dihydrofolate reductase (FH2 → 5,10, methylene-FH4

describe further the mechanism of methotrexate action. What is this drug used to treat?

1. inhibition of purine/pyrimidine synthesis

2. reduces antigen-dependent T-cell proliferation

3. suppress inflammation via adenosine release

used to treat;

1. cancer

2. psoriasis

3. rheumatoid arthiritis

4. systemic lupus erythematosus

5. Skin/muslce inflammation

Draw out how ribonucleotide reductase transform NDP to dNDP. Describe the two sites of RR

one site is for the alosteric regulator

• ATP = activate

• dATP = deactivate

second site = substrate specificity

describe further how RR is regulated

draw out degradation of purine bases to uric acid; what does xanthine oxidase/dehydrogenase contain? What is the oxidase responsible for?

contains 2 molybdenum atoms

oxidase is responsible for oxidative damage to tissues during reperfusion

what is the final product of purine degradation? What is special at this? For this molecule, what happens at physiological pH?

uric acid; special becasue half of anti-oxidant capacity of blood plasma comes from this

at physiological pH, creates urate

Is urate soluble? what is hyperuricemia? What is the consequence of hyperuricemia?

no, normal urate [] very close to solubility constant

hyperuricemia: increased [urate] = formation and deposition of urate crystal in tissues and joint

describe factors contributing to hyperuricemia

1. gender (plasma uric acid is higher in males)

2. obesity

3. diet (high protein diet → rich nucleic acid and high alcohol consumption = higher levels of urate)

   1. oxidation of alcohol = consumes ATP = increase Adenine nucleotide turnover

4. lactic acidosis

   1. URAT1 exchanges lactic acid with reabsorption of uric acid

5. genetic factors (involved with renal urate transport system

What is gout? what are some disorder that causes overproduction of purines? treatments and prevention of gout?

metabolic arthritis; due to disorder of uric acid metabolism

• associated with deposition of monosodium urate crystal

  • either underexcretion or too much production (primary gout) of uric acid

disorders that causes too much purines

1. PRPP synthetase overactivity

2. Glucose 6 phosphatase deficiency (vongierke)

Treatment

1. NSAIDS or injection of glucocorticoids

Prevention

1. allopurinol

2. limited consumption of alcohol (lactate production) and purine rich foods (meat, fish, spinach, and dry beans)

3. uricosuric drugs = increased excretion of uric acid from urine

what is xanthinuria?

disease where mutation in xanthine dehydrogenase gene or the molybdenum cofactor gene

causes catabolism of purine to stop at xanthine and hypoxanthine compounds

blood uric acid = low, high level of excretion of xanthine

can lead to formation of renal xanthine stones

list out the diseases associated with elevated uric acid levels and ones with decreased levels

describe the mechanism of allopurinol. What is a complication of this

strucural analogue of hypoxanthine; means substrate for xanthine oxidase

converts to oxypurinol (inhibitor of xanthine oxidase)

decreased uric acid creation bc reduced purines can now be spread over three products: hypoxanthine, xanthine, and uric acid

Complication: rapid decrease in uric acid level = quick dissolution of urate crystal = trigger proinflammatory cytokine production and development of inflammation