mslsc2001c04 course instructor dr. gautam kumar · 2020-04-10 · biosynthesis and degradation of...

Metabolism MSLSC2001C04

Course Instructor Dr. Gautam Kumar

Dr.Gautam Kr. Dept. of Life Sc. 1

Dr.Gautam Kr. Dept. of Life Sc. 2

Nucleotides

Biosynthesis and Degradation of Nucleotides

Precursors of DNA and RNA:

Two types of pathways lead to nucleotides: • The de novo pathways: Synthesis of nucleotides begins with their metabolic precursors:

amino acids, ribose 5-phosphate, CO2, and NH3

• de novo pathways for purine and pyrimidine biosynthesis appear to be nearly identical in all living organisms.

Purine Base

• The free bases Guanine, Adenine, Thymine, Cytosine, and Uracil are not intermediates in these pathways

Pyrimidine Base

Origin of the carbon and nitrogen atoms of the purine ring

Dr.Gautam Kr. Dept. of Life Sc. 3

• Several important precursors are shared by the de-novo pathways for synthesis of Pyrimidines and Purines

• Phosphoribosyl pyrophosphate (PRPP) is important in both, and in these pathways

• 5-phosphoribosyl-1- pyrophosphate (PRPP)

• Amino acid is an important precursor in each type of pathway: Glycine for Purines and Aspartate for Pyrimidines

• Aspartate and Glutamine is also used as the source of an amino group in the purine pathways

Dr.Gautam Kr. Dept. of Life Sc. 4

De novo synthesis of purine nucleotides: Construction of the purine ring of inosinate

(IMP)

De Novo Purine Nucleotide Synthesis Begins with PRPP

Dr.Gautam Kr. Dept. of Life Sc. 5

• The first intermediate with a complete purine ring is inosinate

(IMP).

Purine ring

Dr.Gautam Kr. Dept. of Life Sc. 6

• The first intermediate with a complete purine ring is inosinate (IMP)

Dr.Gautam Kr. Dept. of Life Sc. 7

• Pyrimidine Nucleotides Are Made from Aspartate, PRPP, and Carbamoyl Phosphate

The six-membered pyrimidine ring is made first and then attached to Ribose 5-phosphate

Required in this process is carbamoyl phosphate, also an intermediate in the urea cycle

Carbamoyl phosphate required in pyrimidine biosynthesis is made in the cytosol by a different form of the enzyme, Carbamoyl phosphate synthetase - II

Pyrimidine ring is synthesized as Orotate, attached to ribose phosphate, and then converted to the common pyrimidine nucleotides

Once Orotate is formed, the ribose 5-phosphate side chain, provided once again by PRPP, is attached to yield orotidylate

Dr.Gautam Kr. Dept. of Life Sc. 8

v

• Once orotate is formed, the ribose 5- hosphate side chain, provided once again by PRPP, is attached to yield orotidylate v

Dr.Gautam Kr. Dept. of Life Sc. 9

• Orotidylate is then decarboxylated to uridylate, which is phosphorylated to UTP.

• CTP is formed from UTP by the action of cytidylate synthetase

• The nitrogen donor is normally Glutamine, although the cytidylate synthetases in many species can use NH+

4 directly.

Dr.Gautam Kr. Dept. of Life Sc. 10

Thymidylate Is Derived from dCDP and dUMP

DNA contains thymine rather than uracil

De novo pathway to thymine involves only deoxyribonucleotides

The immediate precursor of thymidylate (dTMP) is dUMP

A one-carbon unit at the hydroxymethyl (-CH2OH) oxidation level is transferred from N5,N10-methylenetetrahydrofolate to dUMP, then reduced to a methyl group

Dr.Gautam Kr. Dept. of Life Sc. 11

Ribonucleotides Are the Precursors of Deoxyribonucleotides

Reduction of Ribonucleotides to Deoxyribonucleotides by Ribonucleotide reductase

• Electrons are transmitted to the enzyme from NADPH by (a) Glutaredoxin or (b) Thioredoxin

Ribonucleotide reductase

Dr.Gautam Kr. Dept. of Life Sc.

12

ADP dADP dATP GDP dGDP dGTP CDP dCDP dCTP UDP dUDP dUTP dUMP dTMP R

ibo

nu

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de

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Deoxyribonucleoside triphosphate biosynthesis

DTTP

Dr.Gautam Kr. Dept. of Life Sc. 13

• Degradation of Purines Produces: Uric Acid

Primates excrete much more nitrogen as urea via the urea cycle than as uric acid from purine degradation.

Similarly, fish excrete much more nitrogen as NH+

4 than as urea produced by the pathway shown here.

T lymphocytes and B lymphocytes do not develop properly

Gout is a disease of the joints caused by an elevated concentration of uric acid in the blood and tissues.

Dr.Gautam Kr. Dept. of Life Sc. 14

• Degradation of Pyrimidines Produces: Urea

Thymine, for example, is degraded to methylmalonylsemialdehydean intermediate of valine catabolism.

It is further degraded through propionyl-CoA and methylmalonyl-CoA to succinyl- CoA

The pathways for degradation of pyrimidines generally lead to NH+

4 production and thus to urea synthesis.

Dr.Gautam Kr. Dept. of Life Sc. 15

• The salvage pathways: Recycle the free bases and nucleosides released from nucleic acid breakdown

The bases are synthesized and then attached to ribose Adenosine phosphoribosyltransferase

Purine and Pyrimidine Bases Are Recycled by Salvage Pathways

• Free purine and pyrimidine bases are constantly released in cells during the metabolic degradation of nucleotides.

Free Adinine AMP + PPi

Dr.Gautam Kr. Dept. of Life Sc. 16

Lesch-Nyhan syndrome

• Children with this genetic disorder, which becomes manifest by the age of 2 years, are sometimes poorly coordinated and mentally retarded.

lack of hypoxanthine-guanine phosphoribosyltransferase

Many Chemotherapeutic Agents Target Enzymes in the Nucleotide Biosynthetic Pathways

• Analogs of glutamine interfere in a number of amino acid and nucleotide biosynthetic pathways

• Acivicin shows promise as a cancer chemotherapeutic agent.

Dr.Gautam Kr. Dept. of Life Sc. 17

• One inhibitor that acts on thymidylate synthase, fluorouracil, is an important chemotherapeutic agent.

• Fluorouracil and methotrexate are important chemotherapeutic agents. In cells, fluorouracil is converted to FdUMP, which inhibits thymidylate synthase.

• Methotrexate, a structural analog of tetrahydrofolate, inhibits dihydrofolate reductase; the shaded amino and methyl groups replace a carbonyl oxygen and a proton, respectively, in folate

Dr.Gautam Kr. Dept. of Life Sc. 18