Flashcards in Nucleotide Metabolism Deck (59):
What is illustrated by the Central Dogma of Molecular Biology?
The Central Dogma illustrates the major processes involved in the handling of genetic information.
What is DNA replication?
Process in which DNA molecules are replicated. Upon cell division, each daughter cell receives a copy of the original information found in the parental cell and uses this template to form a complementary strand.
What is transcription?
Process in which the transfer of information found in the dsDNA to the base sequence of an ssRNA.
(This is the first stage in the expression of genetic information.)
What is translation?
If the RNA is mRNA, then this process coverts the information in the RNA base sequences to the amino acid sequence of a protein.
What is reverse transcription?
In the life cycle of retroviruses, this process is used to synthesize DNA from the information in their RNA genomes.
What is repair?
Process in which damaged DNA is mended.
What is recombination?
Process in which rearrangements of genetic material are produced.
What are mutations?
Occasional mistakes in any of the processes.
What are the raw materials for evolution?
What is the purpose of the chemical properties of amino acids?
To direct the three-dimensional folding of the protein molecule and the assembly of subunits into active molecules.
What often undergo extensive processing?
Nucleic acids and proteins
What is under careful regulation?
The expression of genetic information
What are the three pathways associated with purines and pyrimidines?
1.) De Novo biosynthesis - made from new molecules
2.) Salvage synthesis - made from recycled parts
3) Degradation - breakdown when no longer needed
How does De Novo Purine Biosynthesis start?
De Novo Purine Biosynthesis starts with pentose sugar and then slowly builds the purine ring.
What is Step 1 of De Novo Purine Biosynthesis?
Step 1 is regulated, but not committed.
Alpha Ribose5P uses PRPP synthetase and ATP to for PRPP.
Negative Feedback - Purine nucleotides inhibit PRPP synthetase.
What is Step 2 of De Novo Purine Biosynthesis?
Step 2 is regulated and committed.
PRPP uses PRPP glutamyl amido transferase and glutamine to form 5-Phosphoribosylamine.
Negative feedback - Purine nucleotides inhibit PRPP glutamyl amido transferase.
Positive feedback - PRPP activates PRPP glutamy amido transferase.
What steps of De Novo Purine Biosynthesis involve glutamine?
(2) PRPP uses PRPP glutamyl amido transferase and glycine to for 5-Phosphoribosylamine.
(5) Formylglycinamide ribosyl5P uses ATP and glutamine to form Formylglycinamidine.
(15) Xanthosine monophosphate (UMP) uses ATP and glutamine to form Guanosine monophosphate (GMP)
What steps of De Novo Purine Biosynthesis involve folate derivatives?
(4) Glycinamide ribosyl5P uses formyl transferase and folate to form Formylglycinamide ribosyl5P.
(10) Aminoimidazolecarboxamide ribosyl5P uses transformylase and folate to form Amidoimidazolecarboxymide ribosyl phosphate.
What are the origins of residues of the purine ring?
1. Start at top N on big ring, N = Aspartate
2. Go counter clockwise around ring, C = Formate
3. N = Amide N of Glutamine
4. and 5. C = Glycine
6. C = CO2
7. Start at top N on little ring, N = Glycine
8. Go clockwise, C = Formate
9. N = Amide N of Glutamine
What are the inhibitors of De Novo Purine Biosynthesis?
Block steps 2, 5, 15:
Glutamine analogs like Azaserine are similar in structure to glutamine but not enough to continue the reaction. (Azaserine is too toxic to use in humans.)
What are the inhibitors of folate metabolism?
Block steps 4, 10:
Sulfonamides and Methotrexate are competitive antagonists in folate metabolism.
How do sulfonamides inhibit folate metabolism?
Bacteria synthesize folic acid from para amino benzoic acid (PARA). Sulfonamides are PABA analogs (competitive antagonists) and inhibit synthesis of folic acid in susceptible bacteria.
How does Methotrexate inhibit folate metabolism?
Bacteria and human use Dihydrofolate reductase to add 4 Hs to Folic Acid and form Tetrahydrofolate.
Methotrexate is a folate analog (competitive antagonist) that inhibits Dihydrofolate reductase and prevent the formation of Tetrahydrofolate. It is used in cancer chemotherapy.
In what does lack of folic acid result?
Neural Tube defects: Anencephaly and Spina Bifida
What is the function of Tetrahydrofolate (THF)?
It is a one carbon donor in steps 4 and 10 of Purine Biosynthesis pathway and in TMP synthesis of the Pyrimidine Biosynthesis pathway.
Where does THF get its carbon?
THF can get its carbon from serine side chains or from formate.
How do both sides of the De Novo Purine Biosynthesis pathway keep one another balanced?
An excess of ATP feeds back into GMP to generate formation of GTP. An excess of GMP feeds back into Adenylosuccinate to generate formation of ATP.
What two mechanisms are involved in the Purine Salvage pathways?
1.) Phosphorylation of Purine Nucleosides
2.) Phosphoribosylation of Free Bases
What is an example of phosphorylation of purine nucleosides?
Adenosine uses Adenosine kinase and ATP to form AMP.
What are two examples of phosphoribosylation of free bases?
1.) Adenine uses Adeninphosphoribosyl transferase (ARPT) and PRPP to form AMP.
2.) Hyoxanthine or Guanine use HGPRT and PRPP to form IMP or GMP.
What is significant about HGPRT?
HGPRT deficiency = X-linked Lesch-Nyhan Syndrome caused by purine overproduction and resulting in gout and kidney stones, neurological problems, mental retardation, bizarre self-mutilation.
How is Adenosine degraded?
1.) Adenosine uses Adenosine deaminase to form Inosine.
2.) Inosine uses Purine nucleoside phosphorylase to form Hypoxanthine.
3.) Hypoxanthine uses Xanthine oxidase to form Xanthine.
4.) Xanthine uses Xanthine oxidase to form Uric Acid.
How is Guanosine degraded?
1.) Guasosine uses Purine nucleoside phosphorylase to form Guanine.
2.) Guanine uses Guanase to form Xanthine.
3.) Xanthine uses Xanthine oxidase to form Uric Acid.
What is significant about Adenosine deaminase?
SCID = Adenosine deaminase deficiency resulting in severe combined immune deficiency from lack of T cells and B cells.
What is significant about Purine nucleoside phosphorylase?
Immune deficiency = Purine nucleoside phosphorylase deficiency resulting is less severe immune deficiency from last of T cells.
How is Allopurinol used in the prevention of gout?
Uric acid is water insoluble and precipitates in joints (gout) and kidneys (stones). Allopurinol prevents gout because is a Xanthine analog and will inhibit Xanthine oxidase from from forming Uric acid. The resulting build of Hypoxanthine is water soluble.
How does De Novo Pyrimidine Biosynthesis start?
De Novo Pyrimidine Biosynthesis starts by making the ring then attaches the sugar.
What is Step 1 of De Novo Pyrimidine Biosynthesis?
Step 1 is regulated, but not committed.
Building blocks CO2, Glutamine, ATP use Carbamoyl phosphate synthetase II (CPS II) to form Carbamoyl Phosphate (CAP).
Negative feedback: UTP end products inhibit CPS II.
Positive feedback: ATP activates CPS II because need number of pyrimidines to equal number of purines.
What is significant about Orotic Acid?
Orotic Acid is the first step with the complete pyrimidine ring then uses Orotate phosphoribosyl transferase and PRPP to add the sugar and form OMP.
What step uses Orotidylic acid decarboxylase?
OMP uses Orotidylic acid decarboxylase to form UMP.
What is significant about Orotate phosphoribosyl transferase and Orotidylic acid decarboxylase?
Deficiency in Orotate phosphoribosyl transferase and/or Orotidylic acid decarboxylase results in Orotic Aciduria.
What do inhibitors of folate metabolism like Methotrexate also shut down the De Novo Pyrimidine Biosynthesis pathway?
Methotrexate also shuts down this pathway because dUMP uses Thymidylate synthetase to form TMP.
How is Thymidylate synthetase also inhibited by 5-Flourouracil?
1.) 5-Flourouracil is converted to F-dump, an analog that interferes with the addition of a methyl group.
2.) F-dUMP binds an S-Enzyme.
3.) Thymidylate synthetase interacts through thiol group to covalently attach Methylene THF.
4.) Enzyme and Methylene THF become permanently attached, initiating suicide inhibition.
What are the origins of residues of the pyrimidine ring?
1. Start at bottom N = Aspartate
2. 3. 4. Go counter clockwise, C = Aspartate
5. N = Carbamoyl phosphate
6. C = Carbamoyl phosphate
What is HAT?
HAT is a laboratory growth medium containing Hypoxanthine, Aminopterin, and Thymidine
What happens to cells in HAT?
Normal cells live and grow but Lesch-Nyhan cells die.
Why do normal cells live and Lesch-Nyhan cells die in HAT?
Aminopterin is similar in structure to Methotrexate so it interferes with Dihydrofolate reductase in folate metabolism. Normal cells live because Purines can use Hypoxanthine in the Salvage pathway and Pyrimidines can use Thymidine in the Salvage pathway. Lesch-Nyhan cells die because they lack HGRPT and cannot use the Salvage pathway.
What is HAT used to detect?
HAT is used to test for HGRPT and/or Dihydrofolate reductase deficiency.
What are two examples of Salvage of Pyrimidine Nucleosides?
1.) Uridine or Cytodine can use Uridine-Cytidine kinase and ATP to form UMP or CMP.
2.) Thymidine can use Thymidine kinase (TK) and ATP to form TMP.
Why is Thymidine kinase (TK) a target for herpes treatment?
Viral TK has a different function. Acyclovir is a guanosine analog but has an open ring structure that viral TK will convert to Acyclovir-triphosphate which will inhibit herpes DNA polymerases from further DNA synthesis without affecting normal cellular processes.
Are Pyrimidines degraded?
How are Deoxynucleosides formed?
In DNA, NDP (AGCU) Ribonucleotide reductase in conjunction with Thioredoxin reductase to form dNDP.
(T is not included because it is made by adding a methyl group in De Novo Purine Biosynthesis.)
What happens if PRPP synthetase is superactive?
Purine overproduction, Gout
What happens if HGPRT is partially deficient?
Purine overproduction, Gout
What happens if HGPRT is completely deficient?
Lesch-Nyhan Sydrome: Purine overproduction, Gout, Cerebral Palsy, Mental Retardation, Self-Mutiliation
What happens if Adenosine deaminase is deficient?
Severe Combined Immune Deficiency (SCID) due to a lack of T Cells and B Cells
What happens if Purine nucleoside phosphorylase is deficient?
Immune deficiency due to a lack of T Cells
What happens if Orotate phosphoribosyltransferase and Orotidylate decarboxylase are deficient?
More severe Type I Orotic Aciduria that can be treated with Pyrimidine nucleosides