BB451 exam 2 - Nucleotide Metabolism Flashcards
nucleoside
sugar + nitrogenous base
nucleotide
sugar + nitrogenous base + phosphate
purines
adenine, guanine
double ring
pyrimidine
thymine, cytosine, uracil
single ring
adenine pairs with..
thymine (DNA)
uracil (RNA)
guanine pairs with…
cytosine
deamination of cytosine
–> uracil
2 general pathways of synthesis
de novo - from scratch
salvage - use breakdown products of others
___ synthesized first
ribonucleotides
deoxyribonucleotides made from…
ribonucleoside diphosphates
de novo synthesis precursors for pyrimidine synthesis
amino acids, carbamoyl phosphate, sugars
pyrimidine ring + PRPP –>
UTP
pyrimidine synthesis: base if made…
base made apart from sugar and later attached to it
carbamoyl phosphate synthetase
enzyme that uses tunneling/channeling of substrates though it to protect intermediates from water
bicarbonate + NH3 + 2 ATP –> carbomyl phosphate + aspartate –> ring
most important regulatory enzyme in pyrimidine synthesis
ATCase
balance amounts of purines and pyrimidines
measures amount of energy available via amount of ATP present
ATCase catalyzes
aspartate + carbomoyl phosphate –> pyrimidine ring
ATCase allosterically activated by
ATP and inactivated by CTP (end product)
RPRR
source of NADPH and ribose
ribose -5 phosphate via pentose phosphate pathway
first pyrimidine nucleotide made
UMP
UMP is …
phosphorylated to UDP by uridine monophosphate kinase (UMP kinase) uses ATP (can run backwards to get ATP)
UDP converted to UTP by..
NADPK (for all diphosphates)
can go back and forth to balance triphosphates
UTP to…
CTP via CTP synthase by amination
CTP synthase
last regulated enzyme
UTP –> CTP
inhibited by CTP (balance between CTP and UTP)
*completed synthesis of ribo-pyrimidines (UTP and CTP)
purine synthesis: base is assembled…
on the sugar (PRPP ring)
purine synthesis uses atoms from….
aspartate, glycine, glutamine, CO2, tetrahydrofolate derivate (single C donor)
most important regulatory enzyme in purine synthesis
PRPP amidotransferase
controls purine production - slows when one nucleotide is too high in concentration
balance between AMP and GMP
PRPP amidotransferase inhibited by
fully by AMP and GMP (end products)
partly when only one is present
purine synthesis begins with
PRPP - ribose ring
single carbon donor in purine synthesis
folate
shortage of folate in pregnancy..
–> neural tube defects (70% reduction by supplementation)
first purine like intermediate
IMP (I in some transfer RNAs)
branch on synthesis of GMP and AMP
purine link base hypoxanthine linked to ribose
process of making IMP
fumarate released (connecting to CAS)
IMP oxidation –>
GMP
inhibited by GMP, energy from ATP
IMP –> AMP
aspartic acid donates amine
fumarate released
inhibited by AMP, energy from GTP
balance between AMP and GTP
- PRPP amidotransferase
- GMP production inhibited by GMP, energy from ATP
- AMP production inhibited by AMP, energy from GTP
AMP and GMP –> ADP and GDP by
AMP kinase and GMP kinase
ADP and GDP –> ATP and GTP by
NDPK
deoxyribonucleotides made starting with..
RNR (ribonucleotide reductase)
catalyzes ribonucleoside diposphates –> deoxyribonucleoside diphosphates
ex: ADP —> dADP
RNR works on…
all ribonucleoside diphosphates
dADP –> dATP via
NDPK (all nucleoside diphosphates)
making thymine nucleotides (first 2 steps)
UDP–> dUDP via RNR
dUDP –> dUTP via NDPK
making thymine nucleotides…dUTP –> dUMP by
dUTPase
making thymine nucleotides dUMP –> dTMP by
thymidylate synthase - requires folate to put methyl group onto U to make T
dTMP–>
dTDP –> dTTP via NDPK
why T in DNA not U
u will form stable base pairs with G (instead of A)
favor Gs where there should be As
regulation of RNR responsible for…
balancing how much of any deoxyribonucleotide
uses tyrosine radical to pull oxygen off ribose at position 2 –> deoxyribose
RNR is made of…
2 pairs of identical subunits (dimer of dimers)
R1 = large w/ 2 allosteric sites and active site
R2 = small, forms tyrosine radical
2 allosteric sites of RNR
specificity site and activity site
specificity site
fine tuning
controls which substrate binds and which deoxyribonucleotides are made
binding of deoxypyrimidine triphosphates to specificity site of RNR –>
inhibit binding and reduction of pyrimidine diphosphates at active site, stimulate binding/reduction of purine diphosphates at active site
activity site
controls whether or not RNR is active
on/off switch
ATP activates, dATP inactivates
during thymidylate synthase activity (dUMP–>dTMP) ____ is produced
dihydrofolate (from tetrahydrofolate derivative)
must be converted back to tetrahydrofolate to keep synthesis occurring
dihydrofolate –> tetrahydrofolate by
DHFR (dihydrofolate reductase)
DHFR is target of ….
anticancer drugs that inhibit it
ex: methotrexate (resembles dihydrofolate, competitive inhibitor) and aminopterin
DHFR inhibitors as a cancer treatment
cant make AMP, GMP,TMP
nucleotides critical for cancer cells –> stop cell division
- will also harm regular cell division
- high dose for cancer treatment then flushed out
use compound that look like ___ as ___
look like folates as antibiotics
bacteria make own folate –> inhibit synthesis of folate
breakdown of purine –>
xanthine –> uric acid via oxidation
uric acid
from breakdown of purines
excretory role in birds and dalmations
not very water soluble –> gout
antioxidant, protective role against disease (ex: multiple sclerosis)
treatment for gout
allopurinol, suicide inhibitor or xanthine oxidase enzyme
HGPRT
direct salvage of guanine nucleotides and indirectly involved in salvage of adenine nucleotides through IMP and hypoxanthine
Les-Nyhan syndrome
deficiency of HGPRT (for catabolism of guanine and adenine)
PRPP accumulates –> neurological problems
deficiency in adenosine deaminase –>
severe combine immune deficiency
dATP accumulates in immune cells –> shutting off RNR and stopping division
