Lecture 25: Nucleotide Metabolism Flashcards
purine bases
adenine
guanine
attachment for sugar is at N9 position (9 atoms in ring)
pyramidine bases
cytosine
uracil
thymine
sugar attached at N1 position (6 atoms in ring)
bases can be salvaged or resued (T or F)
TRUE
nucleotide structure
base
ribose sugar
1, 2, or 3 phosphate groups
nucleotide functions
building blocks of DNA and RNA
energy currency
components of coenzymes
signal transduction
where do the nitrogens for the bases come from
amino acids
glycine, aspartate, glutamate
where do ribose sugars come from?
PPP!
what happens when bases are degraded?
uric acid (purine degredation) pyramidine catabolism= lots of metabolites, like NH4+
phosphates named…
alpha beta gamma in order carbons in sugar get primes as well as number
nucleoside
just sugar and base
Whats at the 2’ carbon in a deoxyribose sugar (DNA)?
no hydroxyl group
Whats at the 2’ carbon in a ribose sugar (RNA)?
hydroxyl group
what does having/not having a hydroxyl group mean
stability difference
having a hydroxyl group makes it more unstable: can undergo cleavage reaction :O
so RNA is less stable than DNA
thats why we dont store genetic material in RNA
Nucleotide 4 major functions”
nrg currency: ATP
second messengers: cAMP
coenzymes: NAD+
build RNA and DNA
What base is in all: ATP, cAMP, NAD+, DNA, RNA
ADENINE!!!!
How do the two strands of DNA interact?
non covalent interactions between bases
Direction of DNA strand:
5’ to 3’
How are nucleotides in a SINGLE strand linked?
covalently linked
phosphodiester bonds
connect C3’ to C5’
What bases pair?
TA
GC
UA
Coenzyme A
has an adenine base!!!
thats what the A stands for
examples of coenzymes with adenine
NADP, NAD, FAD, coA
Salvage pathway for nucleotide components: used for RNA synth
put in triphosphate form to get triphosphate (use kinases)
synth RNA
enzymes used are polymerases
RNA degredation
endonucleases break it down
left w/ oligonucleotides: short pieces of RNA
phosphodiesterases break phosphodiesterase bonds: release single nucleotide
Changing attachment: attach a different base
remove phosphate group: just sugar and base
then remove base: left w/ ribose 1 phosphate
move the ribose so now its ribose 5 phosphate
PRPP puts pyrophophate group at 1’
attach a base
bam! New nucleotide
How does most nucleic acid degredation take place in cells?
nucleic acid degredation: normal process of nucleic acid turn over INSTEAD OF using nucleotides from diet
review slide 10
review slide 10
all nitrogens in the bases come from…
amino acids
pyramides nitrogens: largely come from aspartate
Why are pyrimidine and pure biosynth different?
purine bases are built directly onto ribose sugars
pyramidine bases built first then put on ribose sugar
significant things about purine biosynth
start with the sugar
use lots of enzymes:
PRPP synthtase uses ATP to make PRPP at 1’ position
base building has begun (with attaching a nitrogen)
lots of energy invested: directly takes 5 ATP
SEE SLIDE 12
base shown in slide 12 is IMP: what is it a precursor to?
AMP and GMP
How to get IMP AMP and GMP
3 paths
- use nitrogen from aspartate, use GTP hydrolysis, lose fumerate, adenine is attached: form AMP
- put an oxygen on I. using NADH. Use ATP to take nitrogen from glutamine. Get GMP
why use ATP to make GMP and use GTP to make AMP?
You don’t want to use the nucleotide you’re trying to make!
You can’t have a step that would be dependent on what you’re trying to make! that would be dumb.
regulation of purine biosynth
regulated at multiple steps
product feedback regulates the enzymes
ATP is used as a substrate in GMP biosynth. GTP is used as a substrate in AMP biosynth. What does this achieve
balance of ATP and GTP production
Purine degredation
convert to uric acid and excrete
AMP degredation
deaminated by AMP deaminase… makes IMP
IMP dephosphorylated= isosine (I)
purine nucleoside phosphorylase=free base (hypoxanthine)
base (hypoxanthine) oxidized to make uric acid
uric acid excretion
break down of purines by primates, some insects etc
NOT A WAY TO GET RID OF EXTRA NITROGEN
because nitrogen excretion through urea needs more water
JUST AS A BREAKDOWN OF PURINES!!!!!!!!
Gout
defect in purine metabolism
uric acid build-up in joints
treat by allopurinol to inhibit xanthine oxidase
What causes Lesch-Nyhan disease and SCID?
defects in enzyme HGPRT and ADA respectively
also result in gout
Lesch-Nyhan disease
severe nuerological disorders and gout
due to uric acid build up on body
pyrimidine biosynth
first make base (orotate), then link it to ribose-5P to make UMP
UMP
common uncleotide.
convert it to UTP, then CTP
Regulation of pyrimidine biosynth: bacteria
1 enzyme (ATCase)
inhibited by CTP
stimulated by ATP (cells ready to divide)
Regulation of pyrimidine biosynth: animal cells
inhibition from products of inidividual steps
reactions stimulated by PRPP and ATP (cells are ready to divide, so we need to make more ATP and DNA)
Ribonucleotide reductase
converts ribonucleotides to deoxyribonucleotides
reduce C-2’, remove the hydroxyl group! (now enzyme is oxidized)
reduce enzyme sulfide bond
so basically (after next two slides) the electrons come from NADPH
to regenerate Ribonucleotide reductase after reducing its sulfied bond
reduce it with thioredoxin
How does thioredoxin get re reduced?
picks up hydrogen atoms from enzyme thioredoxin reductase (contains FAD and oxidizes NADPH)
Regulation of Ribonucleotide reductase
2 regulatory sites:
regulatory site
substrate specificity site
Ribonucleotide reductase: REGULATORY SITE
ATP or dATP binds here
controls overall enzyme activity
Ribonucleotide reductase: SUBSTRATE SPECIFICITY SITE
choose which substrates to bind and do reactions on
ATP, dATP, dTTP, dGTP bind here
synthesis of thymine containing nucleotides (so only DNA)
3 ways:
1: dephosphorylate dUTP–>dUMP
2. deaminate dCTP to make dUTP, then to dUMP
3. phosphorylate deoxyuridien to get dUMP
Why go to dUMP?
this leads down a pathway to make dTTP, which we can use in DNA synth
why don’t we want much dUTP???
its not incorporated into DNA, it has URIADINE!!! (U is just for RNA)
RNA World Hypothesis
it can both carry genetic stuff and do enzyme stuff
it had its own thing to catalyze: RIBOZYMES
then Ribonucleotide reductase (an enzyme made of PROTEINS) emerged, and DNA made more sense
