What are critical functions of nucleotides
- storage and flow of genetic info: key structural comp on DNA and RNA
- storage and source of energy: energy rich phosphodiester bonds in ATP & GTP
- Component of key cofactors: NAD, FAD, coenzyme A, S- adensoylmethionine
- form activated intermediates: UDP glucose in glycogen synthesis, CDP= diacylglycerol in phospholipid synthesis
- Metabolic regulators: cAMP, cGMP are cellular second messengers.
What are three principal components nucleotides have
- nitrogenous base
- pentose sugar
- one/more phosphate groups
what are the two types of nitrogenous bases
- pyrimidine (little structure)
- purine (big structure)
(nitrogen and carbon in ring)
What include the pyrimidines
- Cytosine
- Thymine
- Uracil
“cut the pyramid”
what are the purines
- adenine
- guanine
“Pure As Gold”
what are the pentose sugars
- ribose (OH is on the bottom)
2. deoxyribose (just H on the bottom)
What are nucleosides formed by
attachment of nitrogenous base to sugar. Attachment is always to C-1 on sugar, N-9 of purine, ad N-1 of pyrimidine
How are nucleotides formed
by attachment of phosphate to sugar in nucleoside. Phosphates are never attached to base. Phosphates can be added to sugar.
adenine + sugar =
when it has all three component =
adenose; adenylate
What are two types of pathways of nucleotides
- De novo (from new): synthesis from metabolic precursors (aa, ribose - 5- phosphate, CO2, NH3) Energy expensive!
- salvage: recycle free bases and nucleosides released from nucleic acid breakdown. Energy economical! Do this a lot with purines!
which methyl group is primarily used
tetrahydrafolate
What
Build oratate first then attach it.
What are the precursors for purines and pyrimidines
inosine 5- monophosphate and orotidine 5’ monophosphate
Synthesis of common nucleotides DOES NOT proceed via their free bases: precursor is always coupled to:
ribose
5 phosphoribosyl-1 pyrophosphate (PRPP) is a key activated ____ intermediate which activates C1 on ribose. It is a key substrate in both purine and pyrimidine synthesis
sugar
The purine ring precursor ____ (a nitrogenous base) is synthesized stepwise directly on the ribose C-1
hypoxanthine
The pyrimidine ring precursor ____ is synthesized stepwise THEN attached to the ribose C-1.
orotate
where do you get ribose 5 - phosphate from
PPP; pentose phosphate pathway
How are purines synthesized
- assemble 5 member ring on C-1 of PRPP
2. complete 6 member ring
what aa are used to make purines
- 2 glutamine
- 1 glycine
- 1 aspartate
- 2 formate from tetrahydroflate
- 1 CO2- from bicarbonate
The nucleotide is called ____. The base is called ____
inosinate (IMP) -the base, phosphate and sugar; hypoxanthine.
You can convert inosinate to
Can convert it to AMP or GMP by adding nitrogen groups to two spots
How do you make the 5 membered ring
- Directly attach the N group of glutamine
- Add 2 glycine (C–C-N)
- Add 2 C via formate
- Add C02 from bicarbonate
- Add N from aspartate and then close the ring
what is the committed step
adding first N group on PRPP via glutamine PRPP amidotransferase
what is glutamine PRPP admidotransferase inhibited by
azaerine, acivian. This is a good target for chemotherapy
How many ATP are made from making inosinate
7 ATP
AMP uses ___as the N donor. GMP uses _____ as N donor.
aspartate; glutamine
Inosinate in ____
tRNA
How is purine regulated
almost exclusively via feed back inhibition of
- PRPP synthetase by end products
- committed step by end products
- branches by each end product
- reciprocal use of GTP and ATP in AMP, GMP pathways
How do you make pyrimidines
glutamine + bicarbonate to make carbamoyl phosphate
then add aspartate to make orotate and hook it up to PRPP. (making ring first and then adding it to the sugar) The first ring we’re making is UMP.
* this can happen in cytosol
How many ATPs does it take to make pyrimidine
2
what makes a pyrimidine
- glutamine
- 1 aspartate
- 1 CO2
- 2 ATP
where does pyramdine synthesis get N from
directly from glutamine
what is the committed step in making pyrymidines. what is it feedback inhibited by?
aspartate transcarbamoylase. Inhibited by CTP
Common nucleotides already have ____added. PRPP is key to both purine and pyrmidine synthesis.
sugar
What happens after you have UMP?
UTP –> animate it to CTP (by using glutamine as a N group donor)
Nucleoside monophosphate kinase uses ATP as source of phosphate and:
we can swap phosphate groups among all of our bases.
what enzyme gives you deoxyribonucleotides
ribonucleotide reductase; makes internal disulfide bond. Donates H and e- from enzyme to form disulfide bond.
Process of re reducing requires
glutathione (GSH) and NADPH
How can thymidine (dTMP) can be synthesized
From deoxy precursors:
- CDP –>deoxy CDP –>deaminated dUTP –> dUMP–>dTMP
- UDP–>dUDP–>dUTP –>dUMP–> dTMP
what enzyme is precursor for thymidine synthesis
dUMP
what enzyme converts dUMP to dTMP
thymidylate synthase
what is thymidylate synthase a good target for
chemotherapy; if you cant make T to go into DNA; DNA synthesis will slow down
what is a good agent for chemotherapy or what inhibits thymidylate synthase
flourouracil
what is difference bet dTMP and dUMP
methyl group; it
what donates a methyl group to make TMP
N10 tetrahydrofolate; it has to be regenerated.
what converts dihydrofolate to tetrahydrofolate
dihydrofolate reductase
what is dihydrofolate reducatase a good target for
chemotheraupetic agents and some classes of antibiotics.
what is dihydrofolate reductase inhibited by
methotrexate, aminopterin, & trimethoprim
what are breakdown products of pyrimidine
free ammonia (goes to urea) and succinate (goes to TCA cycle); so we mainly say breakdown product is UREA
what is breakdown product of purines
URATE; a lot recycled in salvage pathway
what enzyme is used to make purine, adenine via the salvage pathway
adenosine phosphoribosyltransferase (APRT)
what enzyme is used to make purine, guanine
HGPRT
What is the nucleotide catabolism for purines like
takes N group back off and forms inosine–> take sugar off and maky hypothanxine –> xanthine–> urate
What does SCID stand for
severe combined immuno deficient; complete lack of immune system; there is a deficiency in adenosine deaminada (ADA). T and B lymphocytes do not dev properly
what converts hypoxanthine to xanthine
xanthine oxidase; generating peroxide in our body.
what converts adenosine to inosine
adenosine deaminase
too much uric acid:
starts to precipitate and can cause gout. Therefore We inhibit enzymes: adenosime deaminase, & xanthine oxidase with inhibitor drugs
whats gout
heritable leading to elev uric acid in blood; can cause damage to kidneys
which mechanisms can lead to elevated serum urate:
- Hyperactive PRPP synthetase:excess PRPP accelerates purine biosynthesis
- Partial lack of HGPRT: reduced salvage pathway; leads to excess PRPP, and accelerated purine biosynthesis
how do you treat gout
allopurinol; enters salvage pathway and forms ribonucleotide; uses up PRPP which reduces purine biosynthesis. Other drugs include probenecid and febuxostat
what is Lesch-Nyhan Syndrome
complete genetic lack of HGPRT; X linked recessive (males) manifests early; mental retardation, poor coordination, self destructive, self mutilating, gout
