Nucleotide Metabolism Flashcards
distinguish between the heterocyclic nitrogenous bases (purine and pyrimidine), nucleosides, nucleotides, and nucleic acids
give the names of the purine bases, pyrimidine bases, and their corresponding nucleosides
if given the chemical structure of a nucleotide, recognize it as a nucleotide, be able to say whether it is a purine or pyrimidine nucleotide, and be able to say whether or not it is the deoxy version
purine bases -- nucleoside : hypoxanthine (gets made first) -- inosine adenine -- adenosine guanine -- guanosine *purines have two rings
pyrimidine bases -- nucleoside : uracil -- uridine cytosine -- cytidine thymine -- thymidine *pyrimidine has one ring
nucleoside = nitrogenous base + pentose sugar by glycosidic bond
nucleotide = nucleoside + phosphate(s)
(the activated precursors of DNA and RNA)
nucleic acid = chain of nucleotides linked by phosphodiester bonds
on the pentose’s anomeric carbon is a spot for an OH group. if that OH group isn’t present, the nucleotide is. deoxy version
describe numerous functions served by nucleotides, and the importance of de novo synthesis of nucleotides (include starting materials)
functions:
- dATP, dGTP, dCTP, and dTTP donate building blocks for making DNA
- ATP, GTP, CTP, and UTP donate building blocks for making RNA
- NAD+, FAD, and CoASH all have nucleotide part(s)
- ATP and GTP are important energy molecules in cells by breaking their high energy bonds
- high energy donors of building blocks for biosynthetic pathways (i.e. - UDP-glucose)
- cAMP, second messenger in many signal transduction events
- many enzymes in cells are allosterically controlled by the cell’s level of adenosine nucleosides (AMP, ADP, and/or ATP)
nucleotides aren’t absorbed well from the diet so the body has to be able to make them from scratch. the starting material are CO2, glucose, amino acids, and tetrahydrofolate derivatives
name the precursors that donate components for the de novo synthesis of purine nucleotides
what organ is good at de novo synthesis
amino acids: glutamine (2), aspartate, and glycine
ribose & phosphate
carbons from formyl-FH4 (2)
CO2
the liver is good at de novo synthesis
describe the formation and function of phosphoribosyl pyrophosphate (PRPP). give the reaction catalyzed by PRPP synthetase.
what does PRPP leave after making its donation?
where does its donation come from?
phosphoribosyl pyrophosphate = good donor of ribose-5-phosphate for purine and pyrimidine nucleotide synthesis
PRPP synthetase rxn
ribose-5-phosphate + ATP –> PRPP + AMP
when PRPP donates ribose-5-P, a PPi is leftover
ribose-5-P comes from PPP (an isomerase converts ribulose-5-P –> ribose-5-P)
say what is donated in a biosynthetic pathway when PRPP goes in and PPi comes out.
Say what kind of atom is donated in a biosynthetic pathway when formyl tetrahydrofolate goes in and tetrahydrofolate comes out.
say what kind of atom is donated in a biosynthetic pathway when aspartate goes in and fumarate comes out
ribose-5-P is donated when PRPP goes in and PPi comes out
a N is added when glutamine comes in and N comes out
a C is added when formyl-FH4 goes in and FH4 comes out
a N is added when an aspartate goes in and a fumarate comes out
describe the conversion of hypoxanthine nucleotides into adenine nucleotides.
describe the conversion of hypoxanthine nucleotides into guanine nucleotides.
inosine = hypoxanthine’s nucleotide/nitrogenous base
all the needed adenine nucleotides come from IMP –> AMP
- for the hypoxanthine of IMP to become an adenine of AMP, a gain of a N has to happen. source: aspartate (becomes fumarate)
all the needed guanine nucleotides come from IMP –> GMP
- for the hypoxanthine of IMP to become a guanine of GMP, a gain of a N at a different place gets added. source: glutamine (becomes glutamate
name the precursors that donate components for the de novo synthesis of pyrimidine nucleotides
describe the rxn catalyzed by carbamoyl phosphate synthetase 2 (CPS-2).
glutamine (amide N), aspartate (3 carbons + N), CO2
carbamoyl phosphate reacts with aspartate and donates a carbamoyl group. The CN is added at the same time.
compare the two carbamoyl phosphate synthetases (CPS-2 and CPS-1)
similarities:
- in both rxns, the carbon part comes from CO2 and phosphate part comes from one of the 2 ATPs in the rxn. the carbomyl phosphate will always donate its carbamoyl
differences:
- the N in the CPS1 rxn comes from NH4+, the N in the CPS2 rxn comes from glutamine (becomes glutamate)
- cellular compartment for CPS1 is mitochondria; for CPS2 it’s the cytosol
- pathway for CPS1 is urea cycle; pathway for CPS2 is pyrimidine biosynthesis
describe orotate as a pyrimidine and name the precursors for its synthesis.
say what orotate must react with in order to form a pyrimidine nucleotide.
what’s required to turn uracil to a cytosine?
orotate = first pyrimidine formed in the pyrimidine nucleotide biosynthesis pathway
precursors:
- aspartate donates most of its structure to orotate minus the carboxyl group
- PRPP
orotate reacts with PRPP for the donation of ribose-5-P.
orotate + PRPP –> orotadine (orotate with a ribose-5-P attached)
eventually the aspartate loses its carboxyl group and oratate becomes uracil. this is how we get to uracil monophosphate in de novo pyrimidine nucleotide synthesis (uracil nucleotides form first)
glutamine (becomes glutamate) is needed to turn uracil –> cytosine
describe the conversion of uracil nucleotides into thymine nucleotides, and the regeneration of the methylene tetrahydrofolate for this reaction.
give the rxns catalyzed by thymidylate synthase, dihydrofolate reductase, and serine hydroxymethyltransferase
in order to convert uracil nucleotides to thymine nucleotides, a carbon needs to be donated through the thymadylate synthase rxn:
dUMP + methylene-FH4 –> dTMP
- methylene-FH4 = methyl donor; gets oxidized to dihydrofolate
the deoxynucleotides are needed to make thymine nucleotides (thymine is nitrogenous base in DNA, not RNA)
dihydrofolate reductase rxn
- turns dihydrofolate –> FH4 using NADPH as reducing agent
serine hydroxymethyl transferase rxn
- FH4 + serine –> methylene FH4 + glycine
- this is the body’s main way of synthesizing glycine
- serine’s carbons can come from glucose
describe the conversion of nucleotides into their deoxy versions. explain the need for deoxy versions of nucleotides
give the rxns catalyzed by ribonucleotide reductase and thioredoxin reductase.
describe the oxidized and reduced forms of thioredoxin, and the role of NADPH in the production of deoxy(ribo)nucleotides
when a nucleotide is a nucleoside diphosphate (ADP, GDP), it can be reduced to its deoxy version. ribonucleotide reductase changes a ribose to a deoxyribose for both purine AND pyrimidine nucleotides
- ribose loses an O from the 2’ position
- reducing agent: thioredoxin
thioredoxin = couple of cysteine groups with their SH side chains reacting to form a disulfide
for the ribonucleotide reductase rxn to work, we need a reduced thioredoxin (with the SH groups rather than disulfide from the start). We get here using the thioredoxin reductase rxn
oxidized thioredoxin gets reduced using NADPH as reducing agent
thioredoxin reductase = selenoprotein – has selenocysteine with sidechain (CH2SEH)
describe the rxns catalyzed by AMP deaminase, 5’-nucleotidase, purine nucleoside phosphorylase, and phosphoribomutase
give the reactions catalyzed by, and the cofactors required by xanthine oxidase
AMP deaminase rxn:
- AMP loses an amino group as NH4+
- product = inosine monophosphate (IMP)
5’-nucleotidase rxn:
- turns nucleotide –> nucleoside by breaking the phosphoester bond from the ribose
- hydrolysis rxn
- phosphatase
examples: turns IMP –> inosine & GMP –> guanine
purine nucleoside phosphorylase rxn
- phosphorylysis of glycosidic bond from ribose’s anomeric C1
- products: ribose-1-P and hypoxanthine (if inosine was purine or guanine if pyrimidine)
phosphoribomutase rxn
ribose-1-P –> ribose-5-P
xanthine oxidase rxn
hypoxathine –> xanthine AND xanthine –> uric acid
- oxidizing agent: O2 (gets reduced to H2O2)
- catalytic cofactors:
1. molybdenum (Mo) can change from charge of +6 to +4 and back
2. irons (going from Fe3+ <–> Fe2+ and FAD (changing from FAD <–> FAD2H)
uric acid/urate is associated with what pathologies and how?
gout – caused by crystallization or urate in joint spaces
kidney stones– caused by crystallization in kidneys
describe the formation of uric acid/urate
uric acid is product of purine nucleotide degradation. it’s an important endogenous antioxidant ending in free radical damage. it’s mostly put off as a waste product in urine.
describe the reactions and enzymes of the purine salvage pathways.
describe the reactions catalyzed by adenine phsohoribosyltransferase (APRT) and hypoxanthine-guanine phoosphoribosyltransferase (HGPRT)
explain effects of mutations for the gene coding for HGPRT
purine salvage pathways:
a purine base can react with PRPP to become a nucleotide rather than being degraded to uric acid
phosphoribosyltransferase rxns include a transfer of a ribose-50P from PRPP to a purine base, turning it into a purine nucleotide. there are two:
1. adenine phosphoribosyltransferase (APRT)
adenine –> AMP with donation of ribose-5-P by PRPP
2. hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
PRPP donates ribose-5-P to turn hypoxanthine –> inosine and guanine –> guanosine
mutations for HGPRT make the gene work less well than it should. effects:
- degradation happens more than needed, person more prone to gout
- total HGPRT deficiency is called lesch-nyhan syndrome where patient self-mutilate, suffer from severe mental retardation, and have a short life expectancy. It’s an x-linked recessive disorder so most likely to manifest in XY rather than XX
