Biochem: Nucleotides

Nitrogenous base

A purine (2 rings) or pyrimidine (1 ring).

Purine

A nitrogenous base with 2 rings; adenine and guanine.

Pyrimidine

A nitrogenous base with 1 ring; cytosine, uracil, and thymine.

Nucleoside

Nitrogenous base + sugar.

Nucleotide

Nucleoside + 1–3 phosphate groups.

Base vs nucleoside vs nucleotide

Base = nitrogenous base; nucleoside = base + sugar; nucleotide = base + sugar + phosphate(s).

DNA base pairing

A-T and G-C.

RNA base pairing

A-U and G-C.

3'-5' bond

The bond linking nucleotides in DNA and RNA.

Purines + ribose

-osine.

Pyrimidines + ribose

-idine.

Nucleotides

Building blocks of DNA and RNA.

ATP

Cellular energy currency.

GTP

Cellular energy currency.

cAMP

Signal transduction.

cGMP

Regulation of physiological processes such as vascular tone and cardiac function.

SAMe

Methyl donor.

FAD+

Coenzyme and prosthetic group.

NAD+

Coenzyme and prosthetic group.

Coenzyme A

Coenzyme involved in metabolism.

UDP-glucose

Carrier of an activated intermediate.

CDP-choline

Carrier of an activated intermediate.

Pyrimidine precursors

Aspartate, glutamine, CO2, and PRPP.

First enzyme of pyrimidine synthesis

CPS-2.

CPS-2 reaction

ATP + glutamine + CO2 → carbamoyl phosphate + glutamate.

CPS-2 location

Cytosol of many cells.

CPS-2 function

Pyrimidine biosynthesis.

CPS-2 nitrogen source

Glutamine.

ATCase

Aspartate transcarbamoylase.

ATCase reaction

Carbamoyl phosphate + aspartate → carbamoyl aspartic acid.

Dihydroorotase

Converts carbamoyl aspartic acid to dihydroorotic acid by loss of H2O.

First 3 pyrimidine enzymes

CPS-2, ATCase, and dihydroorotase; they form a complex.

Dihydroorotic acid dehydrogenase

Oxidizes dihydroorotic acid to orotic acid.

Location of dihydroorotic acid dehydrogenase

Mitochondria.

PRPP role in pyrimidine synthesis

Donates ribose-5-phosphate to form OMP.

OMP decarboxylase

Converts OMP to UMP.

First nucleotide produced in pyrimidine synthesis

UMP.

Pyrimidine synthesis steps

CPS-2 → ATCase → dihydroorotase → dihydroorotic acid dehydrogenase → OMP → UMP.

Pyrimidine products

UTP, CTP, and TMP.

CPS-2 inhibitor

UTP.

CPS-2 stimulators

PRPP and ATP.

Pyrimidine regulation

UTP provides negative feedback; PRPP and ATP stimulate CPS-2.

CPS-1 location

Liver mitochondria.

CPS-1 function

Urea cycle.

CPS-1 nitrogen source

NH4+.

CPS-1 regulation

Negatively regulated by lower pH.

CPS-1 vs CPS-2

CPS-1 is mitochondrial and functions in the urea cycle using NH4+; CPS-2 is cytosolic and functions in pyrimidine synthesis using glutamine.

Purine synthesis starting material

Ribose-5-phosphate.

Purine ring synthesis

The ring is synthesized on the sugar.

PRPP

Links purine and pyrimidine synthesis.

PRPP synthase

Enzyme that synthesizes PRPP from ribose-5-phosphate.

First step of purine synthesis

Synthesis of PRPP by PRPP synthase.

Purine precursors

Aspartate, glycine, glutamine, folate derivatives, and CO2.

PRPP glutamyl amidotransferase

Combines glutamine and PRPP to form PRA.

PRA

Phosphoribosylamine; product of the PRPP glutamyl amidotransferase reaction.

PRPP glutamyl amidotransferase significance

Irreversible and rate-limiting step of purine synthesis.

First purine nucleotide produced

IMP.

IMP

Inosine monophosphate; first nucleotide produced in de novo purine synthesis.

First purine ring formation

Requires glycine, methyleneTHF, glutamine, and ATP.

Second purine ring formation

Involves aspartate and folate followed by ring closure to form IMP.

IMP branches

IMP branches into AMP and GMP.

A branch

IMP → AMP.

G branch

IMP → GMP.

Purine synthesis regulatory enzymes

PRPP synthase, PRPP glutamyl amidotransferase, adenylosuccinate synthase, and IMP dehydrogenase.

Purine regulation

Regulatory enzymes control the pathway according to cellular nucleotide needs.

Direct salvage

Base + PRPP → NMP via phosphoribosyl transferase.

Phosphoribosyl transferase (PRT)

Enzyme involved in direct base salvage.

Indirect salvage

Base + ribose-1-phosphate → ribonucleoside → NMP.

Indirect salvage enzymes

Ribonucleoside phosphorylase followed by ribonucleoside kinase.

Direct vs indirect salvage

Direct salvage converts a base directly to an NMP; indirect salvage first forms a ribonucleoside.

Salvage

Recycling bases to conserve energy.

Why salvage is important

It is important in rapidly dividing cells and requires less energy than de novo synthesis.

Liver and salvage

The liver provides bases for other organs.

Pyrimidine degradation

Excess pyrimidines are degraded into compounds that can enter the TCA cycle.

Thymine degradation

Thymine → succinyl-CoA → TCA cycle.

Cytosine and uracil degradation

Cytosine/uracil → β-alanine → acetyl-CoA → TCA cycle.

Purine degradation

Excess purines → xanthine → uric acid.

Xanthine oxidase

Converts xanthine to uric acid.

Urate oxidase

Also called uricase; converts uric acid to allantoin.

Allantoin

A more water-soluble product of uric acid degradation.

Most mammals and uric acid

Most mammals convert uric acid to allantoin using urate oxidase.

Humans and great apes

Humans and great apes do not have functional urate oxidase because of accumulated mutations.

Humans, great apes, and Dalmatians

Excrete uric acid.

Birds, insects, and most reptiles

Excrete uric acid.

Gout

Crystals can form in soft tissues and joints when serum urate exceeds its solubility limit.

Dalmatians and uric acid

Dalmatians can have problems associated with uric acid excretion.

Dietary goals for Dalmatians with uric acid problems

Reduce purines, increase moisture, and alkalinize urine.

Lower pH

According to the lecture, lower pH = urate.

Higher pH

According to the lecture, higher pH converts uric acid to urate.

Folate

Water-soluble B vitamin.

Folate sources

Yeast, liver, and leafy plants.

Can animals make folate?

Animals cannot make folate themselves.

Folate functions

Purine biosynthesis, amino acid metabolism, one-carbon metabolism, and DNA replication.

One-carbon metabolism

A network of reactions that transfers single-carbon units through folate, vitamin B12, and methionine cycles.