Nucleotide Metabolism. Flashcards
What 3 components do nucleotides contain?
A nitrogenous base.
A ribose sugar or a de-oxyribose sugar.
At least 1 phosphate.
How many nucleotides are required for DNA synthesis?
4.
What consequences are there if the body cannot synthesise a DNA nucleotide?
It will have serious consequences as DNA cannot be synthesised.
Drugs that target nucleotide metabolism are often used to treat what illness’?
Cancer and bacterial infections.
What are nucleotides used for?
The building blocks for DNA and RNA.
Carriers for activated intermediates.
Structural components of coenzyme A, FAD, NAD+ and FAD+.
High energy molecules such as ATP, GTP and UTP.
The nitrogenous bases that make up nucleotides are derived from what 2 families?
Purines and pyrimidines.
What is the major difference between purines and pyrimidines?
Purines have 2 rings and pyrimidines only have 1.
What purines are found in DNA and RNA?
Adenine.
Guanine.
What are the pyrimidines that are common to DNA?
Cytosine.
Thymine.
What are the pyrimidines that are common to RNA?
Cytosine.
Uracil.
What are 2 other common bases that are found in cells and are involved in the metabolism of purines?
Hypoxanthine.
Xanthine.
Where is hypoxanthine found?
In inosine monophosphate (IMP).
What is the job of inosine monophosphate (IMP)?
It is an intermediate in purine synthesis and degradation.
Where is xanthine found?
In xanosine monophosphate.
What is the job of xanthine?
It is an intermediate in purine synthesis and degradation..
What is the location of some unusual bases?
In tRNA and in viral DNA.
Unusual bases account for what % of the bases in tRNA?
5%.
Unusual bases are often found as methyl derivatives of what bases?
As methyl derivatives of the major bases.
What 2 things need to be added together to make a nucleoside?
The addition of a pentose sugar to the base makes a nucleoside.
The addition of a ribose sugar to the bases A, G, C, T and U forms what?
Adenosine.
Guanidine.
Cytidine.
Thymidine.
Uridine.
If the pentose sugar is a deoxyribose then what is produced when a base is added?
A deoxyribonucleoside.
If A, G, C, T and U are added to a deoxyribose what is produced?
De-oxyadenosine.
De-oxyguanidine.
De-oxycytidine.
De-oxythymidine.
De-oxyuridine.
What kind of sugar does DNA have?
Deoxyribose sugars.
What kind of sugar does RNA have?
Ribose sugars.
What is the major difference between a ribose and a deoxyribose?
The number 2 hydroxyl group on a ribose is lost and replaced with hydrogen on a deoxyribose.
For a nucleotide to be made from a nucleoside what must be added?
At least 1 phosphate group.
What is associated with the negative charge in DNA and RNA?
The phosphate groups.
The addition of 1, 2 or 3 phosphate groups will form what?
Nucleoside monophosphate (NMP).
Nucleoside diphosphate (NDP).
Nucleoside triphosphate (NTP).
Nucleoside triphosphates are needed for what?
To make nucleotides and also for high energy molecules, e.g. ATP.
How is the type of pentose sugar donated in the nomenclature of nucleotides?
In the prefix e.g.
Ribonucleotide.
Deoxyribonucleotide.
How is the type of attached base donated in the nomenclature of nucleotides?
Adenosine triphosphate (ATP).
Deoxy-adenosine triphosphate (dATP).
De-novo purine synthesis is accomplished by what process?
By constructing the purine ring in a series of reactions that add the carbon and nitrogen to a preformed ribose 5-phosphate.
Ribose 5-phosphate is a product of what pathway?
The HMP pathway.
Where does purine synthesis take place?
In the cytoplasm of the cell.
What must occur before purine synthesis can take place?
The ribose 5-phosphate must be activated.
How is ribose 5-phosphate activated for purine synthesis?
By adding a pyrophosphate to it.
What does the activation of ribose 5-phosphate for purine synthesis form?
5-phosphoribosyl-1 pyrophosphate (PRPP).
What enzyme is used to activate ribose-5 phosphate in purine synthesis?
PRPP synthetase.
What is the foundation for the building of purine rings?
5-phosphoribosyl-1 pyrophosphate (PRPP).
What amino acids are used to form purine rings?
Glycine.
Glutamine.
Aspartate.
What molecule donates carbons to purine rings?
Tetrahydrofolate (THF).
What is the beginning of a purine base?
The activated ribose (5-PRPP) carbons, nitrogens and amino acids.
What is the rate limiting enzyme of purine synthesis?
Glutamine phosphoribosyl pyrophosphate amido transferase.
What is the job of glutamine phosphoribosyl pyrophosphate amido transferase?
To convert 5-PRPP to 5-phosphoribosylamine.
Where does the nitrogen for purine rings comes from?
From glutamine.
The rate of the rate limiting step of purine synthesis is controlled by?
The intracellular amounts of glutamine and PRPP.
What inhibits glutamine phosphoribosyl pyrophosphate amido transferase when in purine synthesis?
The purine nucleotides AMP, GMP and IMP.
What is the product of phosphoribosyl pyrophosphate amido transferase when in purine synthesis?
IMP.
GMP.
AMP.
How can di and triphosphates be formed from the monophosphates in purine synthesis?
Phosphate groups can be added by specific kinases to form the di and triphosphates.
What is the first purine that is always made by glutamine phosphoribosyl pyrophosphate amido transferase?
IMP (inosine monophosphate).
How can AMP and GMP be synthesised from IMP?
IMP can synthesise AMP and then AMP can synthesise GMP.
The synthesis of AMP from IMP requires what molecule to be present?
GTP.
The synthesis of GMP from AMP requires what molecule to be present?
ATP.
How many ATP molecules are required for purine synthesis?
4 ATP molecules.
What coenzyme does glutamine phosphoribosyl pyrophosphate amido transferase require?
Tetrahydrofolate (THF) and purines cannot be synthesised without it.
What part of the purine synthesis an important target site for drugs in microorganisms?
THF.
Why is THF in microorganisms a target sequence for drugs?
Because they require THF for purine synthesis.
What are the family of drugs that will competitively inhibit the synthesis of THF?
Sulphonamides.
How do sulphonamides inhibit the synthesis of THF in microorganisms?
Via competitive inhibition.
How do sulphonamides inhibit microorganisms from growing?
They inhibit purine synthesis so DNA synthesis cannot take place.
What drug will competitively inhibit THF synthesis in humans?
Methodextrate.
What kind of disease is methodextrate used to fight in humans?
Cancer.
How does methodextrate work?
By inhibiting dihydrofolate reductase which is responsible for activating folate, this stops purine synthesis in the body and prevents the cancer cells from dividing.
How can cancer cells become resistant to methodextrate?
By up-regulating the gene for dihydrofolate reductase.
What drug will inhibit THF synthesis in prokaryotes.
Trimethoprim.
How do bacteria obtain folic acid?
They synthesise their own folic acid.
How do mammals obtain folic acid?
Via the diet.
What is the most common vitamin deficiency in the world?
A folate deficiency.
What are the symptoms of folate deficiencies?
Megaloblastic anaemias.
Low haemoglobin levels.
High levels of megaloblastic cells in the bone marrow.
Large immature erythrocytes.
What kind of cells are particularly affected by a folate deficiency?
Rapidly growing cells.
What is a common symptom of a folate deficiency that is caused in babies due to the pregnant mother not taking enough folate?
Neural tube defects such as spina bifada.
Homocysteine-anemia is also a common symptom.
What happens to purines that come from the normal turnover of cellular nucleic acids or are obtained from the diet?
They can either be degraded or salvaged.
When IMP purines and guanine nucleotides are degraded, what intermediates do they produce?
Hypoxanthine and guanine.
What intermediates do adenosine nucleotides produce when they are degraded?
Adenosine.
Will hypoxanthine, guanine and adenosine be fully degraded in purine degradation?
No.
They can be recycled.
The recycling of hypoxanthine and guanine in purine degradation requires what enzyme?
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT).
The recycling of adenosine in purine degradation requires what enzyme?
Adenosine phosphoribosyltransferase (APRT).
How are the hypoxanthine, guanine and adenine intermediates recycled?
They still have their ring structures and HGPRT or APRT can take PRPP and attach it to the ring to recreate XMP.
The re-attachment of PRPP to hypoxanthine creates what?
IMP.
The reattachment of the PRPP to guanine creates what?
GMP.
The re-attachment of PRPP to adenosine by APRT creates what?
AMP.
The process of adding PRPP to a recycled purine can be thought of as adding what to what?
Adding of a sugar to a base.
HGPRT + hypoxanthine = what?
IMP.
HGPRT + guanine = what?
GMP.
APRT + adenosine = what?
AMP.
A deficiency in HGPRT will affect what?
The salvage of guanine and hypoxanthine from nucleotide degradation.
What causes a deficiency in HGPRT?
An X linked recessive disorder called in Lesch-Nyhan syndrome.
What is Lesch Nyhan syndrome is characterised by?
Increased levels of PRPP.
Decreased levels of IMP and GMP.
Increased de-novo synthesis of IMP and GMP.
What are the symptoms of Lesch Nyhan syndrome?
Excessive production of uric acid.
Self mutilation.
Involuntary movements.
What is the final product of purine degradation?
Uric acid.
What is hyperuriceamia also known as?
Gout
When guanine and hypoxanthine are being broken down, what will degrade them?
Xanthine oxidase.
What does xanthine oxidase degrade guanine and hypoxanthine to?
To xanthine and then uric acid.
What will cause hyperuricaemia?
Excess degradation of purine nucleotides or under excretion of uric acid.
What drug can inhibit xanthine oxidase so that uric acid isn’t formed, relieving the symptoms of gout?
Allopurinol.
How does allopurinol relieve the symptoms of gout?
It inhibits xanthine oxidase and leads to the accumulation of xanthine which is more soluble than uric acid and can be excreted through the kidney.
How does pyrimidine synthesis differ from purine synthesis?
Pyrimidines are synthesised before attachment to ribose 5-phosphate.
What is the rate limiting step of pyrimidine synthesis?
The synthesis of carbamoyl phosphate from glutamine and CO2.
What enzyme in pyrimidine synthesis will synthesise carbamoyl phosphate from glutamine and CO2?
Carbamoyl phosphate synthetase II (CPSII).
Is folic acid is required for pyrimidine synthesis?
No.
What amino acids are used in pyrimidine synthesis?
Glutamine.
Aspartic acid.
What is the source of the amino group in pyrimidine synthesis?
Glutamine.
What is the source of the amino group in purine synthesis?
Ammonia.
What substrates does CPS II require to form carbamoyl phosphate in pyrimidine synthesis?
2 ATP molecules.
A CO2.
A glutamine.
Where is CPS II located?
In the cytoplasm.
What will activate CPS II in pyrimidine synthesis?
ATP.
What is the final product of CPS II in pyrimidine synthesis?
UTP.
What will inhibit CPS II in pyrimidine synthesis?
UTP.
After carbamoyl phosphate has been formed, a few more steps occur until what ring structure is formed?
Orotate.
What 2 steps are required to form UTP from orotate?
Orotate + Orotate phosphoribosyl transferase + PRPP gives oritidine 5-monophosphate (OMP).
This is when the sugar group is added in pyrimidine synthesis.
Oritidine 5-monophosphate + OMP decarboxylase gives uridine monophosphate (UMP).
What is always synthesised 1st in pyrimidine synthesis?
UMP.
How is UMP converted to UDP?
By nucleoside monophosphate kinase.
How is UDP converted to UTP?
By UTP nucleoside diphosphate kinase.
How is UTP converted to CTP?
By CTP synthase where glutamine is the nitrogen donor.
What is the product of CPS II?
Carbamoyl phosphate.
What is the substrate of CPS II?
CO2, glutamine and ATP.
What process is CPS 1 involved in?
Urea synthesis.
What process is CPS II involved in?
Pyrimidine synthesis.
What is the source of nitrogen for CPS I?
Free ammonia.
What is the source of nitrogen for CPS II?
Glutamine.
What is the cellular location of CPS-1?
Mitochondria.
What is the cellular location of CPS-II?
Cytoplasm.
What is CPS-I activated by?
N-acetylgluatamate.
What is CPS-II inhibited by?
UTP or UDP.
A deficiency in OMP decarboxylase or in orotate phosphoribosyl transferase results in what?
Orotic adicuria and UMP cannot be synthesised.
What are the symptoms of orotic adicuria?
Slow growth.
Megaloblastic anaemia.
The secretion of a lot of orotate (orotic acid) in the urine.
What nucleotides are used in DNA synthesis?
Deoxyribonucleotides.
What catalyses the formation of deoxyribonucleotides from ribonucleotides?
Ribonucleotide diphosphate reductase.
Ribonucleotide diphosphate reductase catalyses the formation of what from ADP, CDP, GDP and UDP?
ADP - dADP.
CDP - dCDP.
GDP - dGDP.
UDP - dUDP.
What are 2 important inhibitors of ribonucleotide diphosphate reductase?
dATP and hydroxyurea.
What anticancer drug will target ribonucleotide diphosphate reductase?
Hydroxyurea.
Why is hydroxyurea used as an anti cancer drug?
To prevent the synthesis of DNA which stops cellular growth, inhibiting tumour growth.
dThymidine MP is synthesised from what molecule?
dUMP.
What enzyme is responsible for synthesising dThymidine MP from dUMP?
Thymidilate synthase.
What coenzymes does thymidilate synthase use when it synthesises dthymidine MP from dUMP?
THF.
What inhibits thymidilate synthase when it synthesises dthymidine MP from dUMP?
MTX.
How is 5-fluouracil an inhibitor of thymidate synthase?
5-fluorouracil is converted to 5-FdUMP which is a very strong inhibitor of thymidate synthase and is often used as an anticancer drug.
Why is 5-fluouracil a good anticancer drug?
Because it prevents the synthesis of a single nucleotide (d thymidine) meaning that cancer tumours are inhibited from growing.
How does methotrexate inhibit the synthesis of dthymidine?
By inhibiting thymidate synthase by blocking the availability of THF.
What kind of disease is methotextrate used to fight?
Cancer.
