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62 Cards in this Set
- Front
- Back
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What compounds are nucleic acids found in? |
CoA, NTs, nucleosides, FAD, NADH, ATP, GTP, RNA |
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What type of bond links pentose and the nucleic acid? |
a B-N-Glycosidic Bond |
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What way does a Beta bond "point" |
Up |
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What is tautomerization? Give an example? |
The movement of a Hydrogen around a molecule. example, Keto <-->Enol form. |
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What is the sugar in RNA? |
D-Ribose |
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What is the sugar in DNA? |
2-Deoxy -D-Ribose |
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What does is produced when an Aldehyde reacts intramolecularly with a Hydroxyl group? If there are 5 carbons in the structure, how many molecules make up the ring? |
A hemi Acetal? 5 member ring (one molecule is oxygen) |
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What two forms can glucose be in? |
Chair conformation, and boat conformation |
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In DNA, what "Sugar pucker" is favoured? Why is this significant? |
2' endo. This is important as it promotes a very regular structure as the Oxygen bound to the this carbon is far away from the plane of the ring. |
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In RNA, what "Sugar pucker" is favoured? |
3' endo. This pucker allows for much more variability in shapes. |
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which bases are the Purines? What do they look like? |
Guanine, Adenine. one 6 member ring bound to a 5 member ring. 4 Nitrogens total. SP2 hybridized, planar, and aromatic |
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Which bases are the pyramidines? What do they look like? |
Cytosine, Thymine and uracil. One 6 membered ring with two Nitrogens total. SP2 hybridized, planar, and aromatic |
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what is a nucleoside? |
a N base + a ribose, no phosphate |
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If NTs don't go through the salvage pathway, what do purines get broken down into? Pyrimidines? |
Purines= Uric Acid Pyrimidines= carbon skeletons and ammonia. |
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Which enzymes catalyzes the formation of 5- phosphoribosyl 1-pyrophosphate?
how many ATP equivalents are used? |
PRPP Synthetase, or PRPP Kinase
2 ATP equivs are used. |
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How is ribose-5- phosphate made in the cell? |
Glucose --> Pentose Phosphate pathway --> ribose 5- Phosphate |
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Which ring is made first in purine synth? |
the 5 member ring. |
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How many ATP equivalents are used to make Inositate (IMP) from Ribose - 5- phosphate |
7 |
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How many ATP Equivalents are used to make Inositate (IMP) from PRPP (5-Phoshoribosyl 1-pyrophosphate |
5 |
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Which Enzyme catalyzes first reaction of Purine synthesis from PRPP? |
Glutamine PRPP amidotransferase |
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WHat stereochemical effect does Glutamine PRPP amidotransferase have on PRPP? |
It changes the C1 anomeric Carbon from Alpha --> Beta |
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What energy source do we use to make adenylate from IMP? |
GTP (1 equiv) |
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What energy source do we use to make guanylate from IMP? |
ATP (2 equivs) |
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What type of regulation is primarily seen in purine synthesis? |
Feedback Inhibition |
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What molecule inhibits PRPP Synthetase? |
ADP (comes from ATP) |
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Which molecules inhibit Glutamine - PRPP Amidotransferase? |
AMP, GMP, IMP |
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What molecule inhibits GMP Synthesis? |
GMP |
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What molecule inhibits AMP Synthesis? |
AMP |
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How can Feedback inhibition be overcome? |
If the molecule that is the substrate for the enzyme that is being inhibited is increased. |
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What molecule does Purine degradation lead to? |
Uric Acid |
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What does a Nucleotidase do? |
It cleaves off a Phosphate using H20 It turns Nucleotides into Nucleosides |
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Nucleoside Phosphorylase |
Uses a PO4 to split up the Base and the Ribose. THe resulting product is 1-Phospho - D- Ribose |
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Nucleosidase |
Splits apart a base and the Ribose use an H20 molecule |
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Xanthine Oxidase |
Can take several substrates, and oxidizes them to make them more soluble. Makes Uric Acid. |
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What is Gout? |
It is the build up of Uric Acid in the extremities of the limbs. It is general caused by a defect in an enzyme purine metabolism, or by a reduce in secretion of uric acid into the urinary tract. |
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What drug can be used to "Cure" Gout? How does it work. |
Allopurinol. it is a suicide inhibitor of xanthine oxidase. Allopurinol is very structurally similar to Xanthine. Since to Uric acid can't be produced, all upstream products build up (such as AMP, GMP, IMP) causing negative feedback on purine synth. |
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What is the first step of Pyrimidine synthesis? (what enzyme, what is used, and what is formed?) |
Carbamoyl Phosphate synthetase II. Uses 2 ATP equivs, makes Carbamoyl Phosphate. |
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What is the difference wrt to PRPP when comparing purine and pyrimidine synthesis? |
In Purine synthesis, We start with PRPP and then add a base. in pyrimidine synthesis we make the base first and then add PRPP |
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How is CPSII regulated? |
it is inhibited by UTP, and positively regulated by PRPP |
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What reaction is the second reaction in pyrimidine synthesis? What type of rxn is this? |
The ATCase (Aspartate transcarbamolylase) reaction. a condensation reaction, in which Pi and an H2O leave. |
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How is ATCase (aspartate transcarbamoylase) regulatedH |
It is inhibited by CTP, and positively regulated by PRPP. |
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How many ATP equivs are needed to make UTP from PRPP? Where are they invested |
2. Are used during the first rxn catalyzed by CPSII |
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How many condensation reactions are in pyrimidine synthesis? |
2 (ATCase, and dihydroorate dehydrogenase (don't need to know I don't think) |
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How is CTP Made From UTP? |
CTP Synthetase is used, requires 1 ATP, and Glutamine. Glutamate and ADP + Pi are the products
UTP + ATP + Gln --> CTP + Glu + ADP + Pi |
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how many ATP does it take to make UTP from Ribose- 5- Phosphate? |
6 (2 for R5P--> PRPP, 2 for PRPP --> UMP, 2 for UMP--> UTP |
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What is Orotic aciduria? How is it treated? |
Deficiency in UMP synthetase. It is treated by feeding the pyrimidines (like UMP). Orotic acid can be safely excreted through the kidneys. Pyridine synthesis is decreased. I think risk of anemia though? |
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What are pyrimidines degraded into? |
Carbon skeletons and NH4+ |
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Which N. Base can end up as succinyl-CoA, which can feed into the TCA cycle? |
Thymine |
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What is the first molecule Cytosine is degraded into during pyrimidine degradation? |
Uridine. |
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What do Phosphoribosyltransferases (PRTs) do? |
They are the enzyme responsible for the salvage of Nitrogenous bases, they add a base to a PRPP to form a Base-ribose-phosphate (a BMP) |
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What is Lesch-Nyhan syndrome? |
Caused by a deficiency in Hypoxanthine Guanine phosphoribosyltransferase deficiency (HGPRT). up to 20x the normal amount of uric acid in the urine. This can be treated with Allopurinol (a suicide inhibitor of xanthine oxidase. this will prevent the production of uric Acid) Uric acid builds up because GMP and IMP salvage has decreased, THis will cause PRPP levels to increase, thereby Increasing Purine synthesis, and thereby purine degradation, making Uric acid. This also causes an imbalance in NTs (which is very dangerous). AMP will build up. |
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What type of enzyme converts a nucleotide monophoshate to a nucleotide di phosphate? |
Nucleoside monophosphate kinase |
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What type of enzyme converts a nucleotide diphoshate to a nucleotide triphosphate? |
Nucleoside diphosphate kinase |
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What enzyme catalyzes the change of RNA--> DNA (removes a hydroxyl group from the 2' carbon) |
Ribonucleotide reductase |
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What type of chemistry does ribonucleotide reductase use? |
radical chemistry |
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What form must the substrate be in for ribonucleotide reducatase to work? |
The diphosphate form. |
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Where do the electrons come from the reduce the 2' carbon/ |
From cysteine resides within ribonucleotide reductase |
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What replenishes the disulphide bonds among the cysteine residues within ribonucleotide reductase to replenish the enzymes activity? and what reduces this molecule? |
Thioredoxin. NADPH |
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What's the point of adding a radical electron onto the molecule? |
to make it more labile (more reactive) |
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How would we make dTTP (deoxythymidine triphosphate from pyrimidine synthesis? |
We first get UMP, then from UMP, we make UTP. From UTP, we use thymidylate syntheses, producing dTMP. From dTMP we can use nucleoside monophopshate kinase and nucleoside diphosphate kinase to make dTTP |
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How much ATP does it take to make ATP from Ribose-5 Phophosphate, Gly, Asp, Gln, Formyl-THF, and Co2? |
10 ATP. 2 ATP to take Ribose- 5 -PO4 to PRPP. 5 ATP to take PRPP to IMP. 1 ATP from IMP to AMP and 2 ATP to take AMP--> ATP
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what happens If you hydrolyze the N-glycosyl bond b/w the deoxyribose and the purine DNA? |
the ribose will linearize and expose a reactive aldehyde group. |
