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134 Cards in this Set
- Front
- Back
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Explain why DNA is more stable than RNA at alkaline pH?
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DNA lacks a hydroxyl group on the C2' carbon atom. This hydroxyl in RNA can catalyze the cleavage of the phosphodiester bond of the polynucleotide backbone.
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Describe the difference between 2'-endo and 3'-endo sugar puckers.
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C2'-endo: C2' carbon atom above the sugar ring plane and on the same side as the C5' carbon atom. Found in B-DNA and on the pyrimidines of Z-DNA.
C3'-endo: C3' carbon atom above the sugar ring plane and on the same side as the C5' carbon atom. Found in A-DNA and A-form RNA and on the purines of Z-DNA. |
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Helical sense of 3 forms of DNA
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A - right handed
B - right handed Z - left handed |
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Diameter of 3 forms of DNA
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A - 26 A
B - 20 A Z - 18 A |
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Base pairs per helical turn of 3 forms of DNA
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A - 11
B - 10.5 Z - 12 |
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Helix rise per base pair of 3 forms of DNA
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A - 2.6 A
B - 3.4 A Z - 3.7 A |
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Base tilt normal to the helix axis of 3 forms of DNA
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A - 20 degrees
B - 6 degrees Z - 7 degrees |
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Sugar pucker conformation of 3 forms of DNA
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A - C-3' endo
B - C-2' endo Z - C-2' endo for pyrimidines; C-3' endo for purines |
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Glycosyl bond conformation of 3 forms of DNA
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A - anti
B - anti Z - anti for pyrimidines; syn for purines |
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Explain why cytosine can form a Hoogsteen base pair with guanine in triple-stranded DNA when cytosine's N3 ring nitrogen is normally not protonated at neutral pH.
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Shift in pKa of cytosine N3 from 4.2 to > 7.5 in triple helix.
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Explain why DNA replication is called semi-conservative.
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Every daughter DNA was one strand from the parent molecule.
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Which surface of double-stranded DNA is flanked by the glycosidic bonds?
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minor groove
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Complete the table of abbreviations for deoxyribonucleotides.
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_________mono-__di-____tri-_
Adenine: dAMP dADP dATP Guanine: dGMP dGDP dGTP Cytosine: dCMP dCDP dCTP Uracil: dUMP dUDP dUTP |
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Complete the matrix of abbreviations for ribonucleotides.
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_________mono-__di-___tri-_
Adenine: AMP ADP ATP Guanine: GMP GDP GTP Cytosine: CMP CDP CTP Uracil: UMP UDP UTP |
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To which end of a growing polynucleotide strand are mononucleotides added?
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3'-end
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In which direction are the residues in a polynucleotide chain numbered?
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5'-to-3'
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What forces stabilize DNA double helices?
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Hydrogen bonding between bases and base stacking (hydrophobic effect and favorable van der Waals interactions).
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What chemical group is released upon the addition of a nucleotide to a growing polymer chain?
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pyrophosphate
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How does AZT block viral nucleic acid synthesis?
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The azide group replacing the O3' hydroxyl prevents addition of further nucleotides.
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How long is the DNA in one human cell? In one human?
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2 m, 2 x 10^14 m
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Human DNA in the nucleus is found in how many pieces?
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46: 22 pairs of chromosomes and X+Y for males and X+X for females.
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How many copies of mitochondrial DNA is found in human mitochondria?
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2-10
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How long is a human mitochondrial DNA in base pairs and in Angstroms?
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20,000 base pairs
20,000 x 3.4 A = 68,000 A or 6.8 microns |
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How many base pairs are in human genomes?
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3.2 billion
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Distinguish between monocistronic and polycistronic mRNA.
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monocistronic - one transcript: one gene
polycistronic - one transcript: several genes |
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Distinguish between introns and exons.
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intron - intervening sequence, non-coding, cleaved out
exon - expressed sequence, coding sequence |
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List common secondary structure elements found in RNA.
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internal loops
hairpin loops bulges double-helical domains three-way junctions single-stranded regions |
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Where are telomere located? What kinds of sequences do they have?
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At the ends of chromosomal DNA. They have G-rich sequences that repeat many times and form g-quartets.
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When designing a DNA insert in a molecular cloning experiment, how do you insure that the DNA insert goes into the vector in one direction?
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Add restriction sites to each end that have different overhanging bases after cleavage by the two restriction enzyme.
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Which enzyme reseals the DNA backbone after cleavage?
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DNA ligase
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List the features of large RNA molecules.
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1) single-stranded
2) half of length involved in double helical domains 3) helical domains evolve in concerted fashion; this allows their prediction by sequence comparison 4) single-stranded regions stabilize the tertiary interactions by non-Watson-Crick base pairs 5) planar in shape |
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List the functions of nucleotides other than serving as residues of DNA and RNA.
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1) second messenger, e.g. cyclic AMP
2) chemical energy storage, e.g. ATP 3) activation of carbohydrates, e.g. glucose-6-phosphate: UDP, GDP, and CMP 4) activation of acetyl groups, e.g. Coenzyme A 5) transfer of electrons, e.g. FAD 6) allosteric effector, e.g. AMP, ADP, ATP, GTP |
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List five features in common between purine and pyrimidine de novo pathways.
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1) phosphoribosyl pyrophosphate (PRPP) important in both pathways (the ribose ring is retained)
2) an amino acid is an important precursor in both pathways glycine for purines (contributes 3 ring atoms) aspartate for pyrimidines (contributes 4 ring atoms) 3) glutamine is an important source of amino groups (aspartate is also a source of amino groups in the purine synthesis) 4) multienzyme complexes are involved 5) cellular pools of nucleotides are often less than 1% of the amount required to synthesize the cell's DNA. DNA synthesis can be limited by nucleotide biosynthesis-->good drug target |
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List five differences between purine and pyrimidine de novo pathways.
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1) In the pyrimidine de novo pathway, a free base is assembled before a ribose ring is added.
2) In the pyrimidine de novo pathway, the different end products are made in a serial fashion rather than in parallel 3) In the pyrimidine de novo pathway, the end-products are nucleoside triphosphates rather than monophosphates in the purine pathway. 4) In the pyrimidine de novo pathway, there is only one site of feedback inhibition rather than 3 in the purine de novo pathway. 5) In the pyrimidine de novo pathway, ATP is an allosteric effector while no pyrimidine ribonucleotide is an allosteric effector of the purine de novo pathway. In other words, levels of purine ribonucleotides control the levels of pyrimidines but not vice versa. |
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How is human PRPP synthetase allosterically regulated?
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It is inhibited by rising levels of ADP.
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What is the first committed step of the purine biosynthesis pathway?
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PRPP + L-glutamine + H2O --> 5-phosphoribosyl-1-amine + L-glutamate + PPi
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Glutamine PRPP amidotransferase inverts the configuration of what?
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C1' carbon atom of PRPP
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Where does the nitrogen in 5-phosphoribosyl-1-amine come from?
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the amido group of glutamine
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What is the half-life of 5-phosphoribosyl-1-amine?
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30 seconds
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What three intermediates or end-products of purine biosynthesis slow down glutamine PRPP amidotransferase when their concentrations rise? What conformational change do they induce which causes a change in activity? How do rising levels of PRPP regulate glutamine PRPP amidotransferase?
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IMP and the end-products AMP and GMP are negative effectors of glutamine PRPP amidotransferase. High levels of these three nucleotides promote the dimerization of this enzyme. The dimer is inactive.
High levels of PRPP disrupt the dimeric form and favor the monomeric form which is active. |
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Name the nucleotide that is at the branch-point in the purine biosynthesis pathway.
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inosine 5' monophosphate
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Describe the conversion of IMP to Adenylosuccinate.
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Aspartate is added to the C6 carbon atom of IMP to produce adenylosuccinate. This reaction is catalyzed by adenylosuccinate synthetase, it requires GTP, and it leads to the replacement of the O6 oxygen atom of inosine with the backbone nitrogen of aspartate - the nitrogen that will become the N6 nitrogen of adenylate.
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Describe the conversion of Adenylosuccinate to Adenylate.
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Adenylosuccinate lyase catalyzes an alpha-beta elimination reaction that converts adenylosuccinate to adenylate via the release of the aspartate carbon backbone as fumarate.
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Describe te conversion of IMP to XMP.
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Conversion of IMP to guanylate starts with a NAD+ dependent hydroxylation of the purine ring at the C2 carbon atom by IMP dehydrogenase to yield xanthylate or xanthosine 5' monophosphate or XMP. This has a carbonyl oxygen atom at the C2 position.
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Describe the conversion of XMP to GMP.
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XMP glutamine amidotransferase transfers an amido nitrogen from the side chain of glutamine to the C2 carbon atom of XMP to give guanylate or guanosine 5' monophosphate or GMP for short. A glutamate is released. Like the second amidotransferase reaction, this reaction also requires ATP.
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Describe the conversion of AMP to ATP.
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Adenylate or AMP is then converted into ADP by adenylate kinase. ADP is usually converted to ATP by nucleoside diphosphokinase.
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Describe the conversion of GMP to GTP.
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GMP is converted to GDP by a guanylate kinase and GDP is converted to GTP by nucleoside diphosphokinase which is not base specific.
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High levels of what inhibit adenylosuccinate synthetase?
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AMP
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High levels of what inhibit IMP dehydrogenase?
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GMP
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How many moles of ATP are consumed in the synthesis of 1 IMP?
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6
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What is the source of the formyl group on formyl tetrahydrofolate?
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glycine, serine, histidine, or tryptophan
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Describe how the precursors of purine biosynthesis were identified.
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Birds excrete most of their excess nitrogen as purine uric acid. Uric acid is insoluble and easily isolated by crystallization. Isoptically labeled compounds were fed to pigeons, their uric acid was crystallized to purify it, and the uric acid was chemically degraded to isolate the radioactively labeled fragments to identify the low molecular weight precursors to purine.
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List the purine ring atoms in the order that they are added to the purine ring; note the compound from which they originate.
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N9 - glutamine
C4, C5, N7 - glycine C8, N10 - formyltetrahydrofolate N3 - glutamine C6 - CO2 in higher, HCO3 in lower eukaryotes and bacteria N1 - aspartate C2, N10 - formyltetrahydrofolate |
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Which steps of the purine biosynthesis pathway are irreversible?
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The ten steps from PRPP to IMP.
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Which intermediate in the purine biosynthesis pathway is the first stable intermediate?
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IMP
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High levels of ______ drive promote the first step of purine biosynthesis.
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PRPP
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What is the source of C2 and N3 of the pyrimidine ring?
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carbomyl phosphate
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What is the source of the N1, C6, C5, and C4 in the pyrimidine ring?
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L-dihydroorotate
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What is the first aromatic ring structure in the pyrimidine biosynthetic pathway?
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orotate
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List the three activities in the human enzyme CAD.
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C: carbamoyl phosphate synthetase
A: aspartate transcarbamoylase D: dihydroorotase |
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What is the first nucleotide in the pyrimidine biosynthetic pathway?
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orotidylate
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How many ATPs are consumed in the synthesis of CTP in the pyrimidine biosynthetic pathway?
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3
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How is the pyrimidine biosynthetic pathway regulated by feedback inhibition?
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Rising concentrations of cytidine triphosphate inhibit aspartate transcarbamoylase. This is the major regulatory mechanism operating on this pathway.
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Explain the allosteric regulation of ATCase by CTP in the absence and presence of ATP.
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The bacterial ATCase has six catalytic subunits and six regulatory subunits. The catalytic subunits bind the substrate molecules and the regulatory subunits bind the allosteric inhibitor, CTP. The entire ATCase has two conformational states: active and inactive. Each subunit, likewise, has two conformational states: active and inactive. The enzyme is maximally active when no CTP is bound to the regulatory subunits. As CTP binds to the regulatory subunits, they change conformation and these conformational changes are transmitted to the catalytic subunits. These in turn shift to the inactive conformation. When ATP levels are high, the presence of ATP prevents the conformational changes induced by CTP binding and the enzyme activity is essentially normal.
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Outline the steps of pyrimidine biosynthesis. List the names of the intermediates.
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Step 1: condensation of aspartate and carbamoyl phosphate to give N-carbamoylaspartate
Step 2: ring closure with loss of a water molecule to give L-dihydroorotate Step 3: oxidation with NAD+ to orotate Step 4: transfer of ribosylphosphate to give the first nucleoside in the pathway - orotidylate or orotidine 5'-monophosphate or OMP Step 5: decarboxylation removes carboxyate group on C6 to give uridylate or uridine 5'-monophosphate or UMP Step 6: phosphorylation gives uridine 5'-triphosphate or UTP Step 7: transfer of a glutamine amido group to the C4 position gives cytidine 5'-triphosphate or CTP |
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Describe the tunneling that occurs in carbamoyl phosphate synthetase.
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A tunnel about 100 A long through the center of the protein links three active sites. Glutamine binds to the first active site at one end of the tunnel. The glutamine donates it amido nitrogen as NH4+. The NH4+ travels down the tunnel to the second active site where it is combined with bicarbonate in a reaction that requires ATP to give carbamate. The carbamate re-enters the tunnel to reach the third active site where it is phosphorylated to carbamoyl phosphate.
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Which two common pyrimidines are made by the pyrimidine biosynthetic pathway?
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uracil and cytosine
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What is the source of the nitrogen in the N4 atom?
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glutamine
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What is the order of the synthesis of CTP and UTP?
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UTP --> CTP
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List 5 ways in which the pyrimidine biosynthesis differs from purine biosynthesis.
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1) 4 of 6 ring atoms come from aspartate
2) Orotate is the last closed ring intermediate that is free from a ribose ring. 3) The steps leading to UTP and CTP are sequential; not parallel like the last steps leading to GMP and AMP 4) The end products are triphosphates; they are monophosphates at the end of purine biosynthesis 5) Either UTP or CTP can serve as an intermediate leading to dTTP. |
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How are the purine and pyrimidine biosynthetic pathways linked?
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ATP is an allosteric regulator of ATCase.
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List 5 features shared by purine and pyrimidine de novo synthesis.
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1) Phosphoribosyl pyrophosphate (PRPP) provides the ribose ring in both pathways.
2) An amino acid is an important precursor in both pathways: glycine contributes 3 ring atoms in purines and aspartate contributes 4 ring atoms in pyrimidines. 3) Glutamine is an important source of nitrogen atoms (5). Aspartate is also a source of nitrogen atoms (2) in the purine synthesis. 4) Multi-enzyme complexes are involved. 5) Cellular pools of nucleotides are often less that 1% of the amount required to synthesize the cell's DNA, so DNA synthesis can be limited by nucleotide biosynthesis. This makes nucleotide metabolism a good drug target. |
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Outline the electron transfer pathway from NADPH in the reduction of ribonucleotide reductase (RNR) via glutathione and glutathione reductase.
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NADPH + H+ + oxidized glutathione --> reduced glutathione + glutaredoxin reductase --> reduced glutaredoxin + oxidized RNR --> reduced RNR
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Outline the electron transfer pathway from NADPH in the reduction of ribonucleotide reductase (RNR) via FAD and thioredoxin reductase.
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NADPH + H+ + oxidized FAD in thioredoxin reductase --> reduced FAD + oxidized thioredoxin --> reduced thioredoxin + oxidized RNR --> reduced RNR
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How does one active site cysteine in the R2 subunit of aerobic bacterial RNR become a thiyl radical?
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A binuclear iron center in the R2 subunit uses molecular oxygen to create a radical on the hydroxyl oxygen of tyrosine. This tyrosyl radical is thought to make one active site cysteine in the R2 subunit into a thiyl radical.
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What converts the C3' carbon of the ribonucleotide in the RNR active site into a radical?
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The thiyl radical on the R2 side of the active site converts the C3' carbon atom of the substrate ribonucleotide into a radical.
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What protonates the O2' hydroxyl on the ribonucleotide substrate in the RNR active site? What stabilizes the resulting positive charge on the O2' oxygen atom?
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The nearby O2' hydroxyl accepts a proton during a two electron transfer from the hydroxyl oxygen to a thiol sulfur on the R1 subunit side of the active site. The resulting cation on the O2' oxygen atom is stabilized by the radical at the C3' position.
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What is the source of the two electrons that are transferred to the C2' carbocation? What structural change in RNR active site occurs as a result of this transfer?
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Another two-electron transfer from a cysteine on the R1 subunit to the C2' carbon atom leads to the formation of the 2' deoxy product and the formation of a disulfide bond between the two cysteines in the R1 subunit.
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How is the thiyl radical on the R2 side of RNR regenerated after the reduction of the ribose ring?
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The radical is transferred from the C3' carbon atom back to the thiol group in the R2 subunit. This regenerates the thiyl radical.
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When does the deoxyribonucleotide leave the active site of RNR?
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After the reduction of the ribose ring and the transfer of the radical from the C3' carbon atom to the active site thiol.
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How is the disulfide bond on the R1 subunit side of the active site of RNR reduced?
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Reduced thioredoxin or reduced glutaredoxin then reduces the disulfide bond on the R1 subunit to complete the regeneration of the active site.
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What is the ultimate source of electrons for ribonucleotide reduction?
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NADPH
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Is dTTP a substrate for ribonucleotide reductase?
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No, UDP is reduced to dUDP
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List the substrates of E. coli RNR.
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ADP, GDP, UDP, CDP
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Which allosteric effectors bind to the primary regulation sites on E. coli RNR?
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ATP, dATP
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Which allosteric effectors bind to the substrate specificity sites on E. coli RNR?
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ATP, dATP, dGTP, dTTP
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How is the specificity of RNR controlled so that there are balanced pools of deoxyribonucleotides available for DNA synthesis?
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The identity of the effector bound to the specificity sites controls which ribonucleoside diphosphates are reduced.
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How does RNR respond to the presence of ATP bound to its primary regulatory site?
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ATP activates the reduction of all four substrates.
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How does RNR respond to the presence of dATP bound to its primary regulatory site?
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dATP inhibits the reduction of all four substrates.
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How does the binding of ATP or dATP to the substrate specificity site change of the substrate specificity of RNR?
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The binding of ATP or dATP to the substrate specificity site promotes the reduction of the pyrimidine ribonucleotide diphosphates CDP and UDP by inducing conformational change in the active site that favors the binding of CDP and UDP.
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How does the binding by dTTP (dUDP is eventually converted to dTTP) to the substrate specificity change the substrate specificity of RNR and lead to a balanced pool of pyrimidine and purine dexoyribonucleotides?
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It inhibits the reduction of the pyrimidine ribonucleoside diphosphates dUDP and dCDP. However, dTTP binding to the substrate specificity site changes the conformation of the active site to favor the binding of GDP. This raises the concentration of purine deoxyribonucleotides as the pyrimidine deoxyribonucleotides rise in concentration.
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What happens to the substrate specificity of RNR when the concentration of dGDP
rises? |
As the concentration of dGDP rises, it binds to the substrate specificity site and this further inhibits the reduction of UDP and CDP and while also inhibiting the reduction of GDP. Meanwhile, dGTP binding stimulates the reduction of ADP.
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In what major way do the substrate binding sites and regulatory binding sites differ in their substrate speicificity?
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The substrate binding sites bind only nucleoside 5’-diphosphates. The regulatory binding sites bind only nucleosides 5’-triphophates.
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Which single deoxyribonucleoside triphosphate shutdown RNR by feedback inhibition?
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dATP
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Why is the reduction of ribonucleotides by RNR such a remarkable reaction in biology?
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RNR catalyzes the reduction of an unactivited C2’ carbon atom.
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How are the deoxyribonucleoside 5’–diphosphates converted to deoxyribonucleoside 5’–triphosphates?
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Nucleoside diphosphate kinase generally uses ATP to convert the nucleoside diphosphates to the nucleoside triphosphates.
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How can dCTP also serve as a source of dTMP?
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dCTP can be deaminated by cytidine deaminase to give dUTP, so CDP can also ultimately be converted to dTMP
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What reaction is catalyze by dUTPase? Why must this reaction be efficient?
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dUTP has two phosphates removed by dUTPase to give dUMP. This reaction must be very efficient to keep dUTP pools low. Larger pools of dUTP increase the probability of the base uracil appearing in DNA.
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Which enzyme converts dUMP to dTMP?
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Thymidylate synthase
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What is the source of the methyl group on the C5 carbon atom of thymine?
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N5,N10-methylenetetrahydrofolate
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Outline the regeneration of N5,N10-methylenetetrahydrofolate.
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The reduction of uracil to thymine occurs with the oxidation of the methylene tetrahydrofolate to dihydrofolate. Dihydrofolate is reduced to tetrahydrofolate by dihydrofolate reductase.
Then the methylene group is regenerated on tetrahydrofolate by serine hydroxymethyl transferase to give methylene tetrahydrofolate. |
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Why are thymidylate synthase, dihydrofolate reductase, and serine hydroxymethyl transferase good drug targets?
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These enzymes are the only pathway to thymine. Thymine is essential for the synthesis of DNA. Inhibition of this pathway will stop DNA synthesis by infectious agents.
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What is the source of the reducing equivalents in the reduction of dihydrofolate by dihydrofolate reductase?
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NADPH
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Outline the path from dCDP to dTMP?
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dCDP -1-> dCTP -2-> dUTP -3-> dUMP -4-> dTMP
1: nucleoside diphosphate kinase 2: deaminase 3: dUTPase 4: thymidylate synthase |
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Outline the path from dUDP to dTMP?
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dUDP -1-> dUTP -2-> dUMP -3-> dTMP
1: nucleoside diphosphate kinase 2: dUTPase 3: thymidylate synthase Then thymidylate synthetase converts it to dTTP. |
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Describe how azaserine can interrupt both the purine and pyrimdine de novo biosynthetic pathways.
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In both pathways, an ammonia group is extracted from the side-chain of glutamine several times to provide nucleotide nitrogen atoms. In the purine de novo pathway, this happens twice leading to IMP and a third time to GMP. In the pyrimidine de novo pathway, this happens in the formation of carbamoyl phosphate and the conversion of UTP to CTP. Azaserine is an analog of glutamine that inhibits the amido transferase activity.
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List the steps of AMP catabolism in humans.
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1) Alpha-phosphate removed by 5’-nucleotidase leaving adensoine
2) N6 of adenine is replaced with O6 by adenosine deaminase leaving inosine 3) Ribose ring removed by nucleosidase leaving the free base hypoxanthine 4) O2 add to C2 ring atom of hypothanine by xanthine oxidase to give xanthine 5) O8 add to C8 ring atom of xanthine by xanthine oxidase to give uric acid |
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List the four steps of GMP catabolism in humans.
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1) Alpha-phosphate removed by 5’-nucleotidase leaving guanine
2) Ribose ring removed by nucleosidase leaving the free base guanine 3) N2 amino group of guanine is removed from C2 ring atom by guanine deaminase to give xanthine 4) O8 add to C8 ring atom of xanthine by xanthine oxidase to give uric acid |
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How much uric acid is excreted per day by humans?
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600 mg
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What is the largest source of nitrogen excretion by humans?
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The urea cycle
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Adenosine Deaminase deficiency leads the build up of what compound? What is the consequence for RNR of the build-up of this compound?
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dATP
High concentrations of dATP bind the primary regulatory sites and inhibits the reduction of all four ribonucletides. This leads to a decline in the pools of dNTP for DNA synthesis. |
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What kind of cells in humans are very sensitive to low levels of dNTP?
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T lymphocytes and B lymphocytes do not develop properly.
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What is the principle symptom of individuals with Adeosine deaminase deficiency?
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Individuals with ADA deficiency lack an effective immune system and must live in a sterile “bubble” environment to survive.
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Describe how the lack of adenosine deaminase activity leads to a 100-fold increase in dATP.
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Adenosine deaminase is in the purine catabolic pathway. The lack of this activity leads to the build-up of dATP by 100-fold. The high concentration of dATP inhibits ribonucleotide reductase and leads to a decline in the pools of dNTPs.
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Describe how allopurinol is effective in treating the symptoms of gout.
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Allopurinol is converted to oxypurinol by xanthine oxidase of the purine degradation pathway. Oxypurinol inactivates xanthine oxidase. This prevents the conversion of xanthine to uric acid. Xanthine and hypoxanthine are much more water soluble than uric acid so they do not readily crystallize in joints and are easily excreted. After the administration of allopurinol, the concentration of uric acid declines.
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Describe how the lack of hypoxanthine-guanine phosphoribosyl transferase leads the Lesch-Nyhan syndrome.
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This purine salvage pathway enzyme transfers ribose 5’-phosphate from PRPP to the free bases guanine and hypoxanthine.
The absence of this purine salvage pathway enzyme leads to the rise of PRPP levels. PRPP is a substrate in the first committed stop of the purine de novo pathway. As a result, purines are overproduced by the de novo purine pathway. The overproduction of purines leads to high levels of uric acid production. |
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How is CMP catabolized to uracil?
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1. The enzyme nucleotidase removed the phosphate of CMP to give the nucleoside cytidine.
2. Cytidine deaminase replaces N4 with O4 on cytidine to give uridine. 3. Uridine phosphorlyase adds a phosphate to the C1’ position and frees the base uracil |
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What is the source of the electrons for the reduction of thymine and uracil?
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NADPH
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Describe why trimethoprim is effective as an antibiotic.
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The folate analog trimethoprim binds bacterial dihydrofolate reductase 100,000 times more tightly than to mammalian dihydrofolate reductase thereby shutting down the synthesis of purines and thymidylate in bacteria without severe side effects in humans.
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How is the nucleoside thymidine salvaged?
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Thymidine kinase adds a phosphate group to the nucleoside thymidine.
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Humans have two thymidine kinases: I and II. Which is cell cycle independent?
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II
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Describe how viral thymidine kinase activates the prodrugs aciclovir and ganciclovir and how this inhibits viral DNA replication.
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The viral thymidine kinases are 3000 times more effective at phosphorylating the guanosine analogs aciclovir and ganciclovir than the cellular thymidine kinase. The monophosphate forms are converted to triphosphate forms that are then added to the growing viral DNA chain by the viral DNA polymerase. The incomplete ring structure of aciclovir and ganciclovir inhibits further extension of the DNA chain (i.e., the rings lack at O3’ for the creation of the next phosphodiester bond.
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How is the free base adenine salvaged?
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Adenosine phosphoriboysltransferase adds PRPP to adenine to give AMP.
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How is the free base guanine salvaged?
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Hypoxathine-guanine phsophoribosyltransferase adds PRPP to guanine to give GMP
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How is the free base hypoxanthine salvaged?
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Hypoxathine-guanine phsophoribosyltransferase adds PRPP to hypoxanthine to give IMP which is the branchpoint intermediate in the purine biosynthetic pathway.
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The genetic lack of Hypoxathine-guanine phsophoribosyltransferase (HGPT) leads to which disease in males? Why only males?
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Lesch-Nyhan syndrome.
The defective gene for HGPRT is on one of the mother’s two X chromosomes. |
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How does the absence of the salvage enzyme Hypoxathine-guanine phsophoribosyltransferase promote purine biosynthesis?
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The absence of this activity prevents the transfer of PRPP to free purines in the purine salvage pathway. This leads to the build up of PRPP which then accelerates the de novo biosynthesis of the purines and thereby increases the production of uric acid.
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What are the symptoms of the Lesc-Nyhan syndrome?
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The build up of uric acid leads to the symptoms of gout plus mild mental retardation, anti- social behavior and compulsive self-destructive behavior. The brain is especially
dependent on the purine salvage pathways and this may account for the damage to the central nervous system. People with this syndrome generally died in their first or second decade from kidney failure. |
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How do the high levels of uric acid cause the symptoms of gout?
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Uric acid has low solubility and is can from crystals in the joints. This makes the joints inflamed, painful and arthritic. Walking and the weight of bedsheets becomes unbearable. Uric acid also forms deposits in kidney tubules. This can cause kidney failure eventually.
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How does the drug allopurinol alleviate the symptoms of gout?
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Xanthine oxidase converts allopurinol to oxypurinol. Oxypurinol is a strong competitive inhibitor of xanthine oxidase. The inhibition of xanthine oxidase stops the production of uric acid and leads to the build –up of hypoxanthine and xanthine—both of which are more soluble than uric acid. Both hypoxanthine and xanthine are excreted.
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List three drugs that inhibit dihydrofolate reductase of infectious agents. Which pyrimidine’s biosynthesis is blocked by these three drugs?
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1. methotrexate
2. aminopterin 3. trimethoprin thymine |
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What is the active form of fluorouracil?
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The salvage pathway converts it to the deoxyribonucleoside 5’-monophosphate FdUMP which binds and inactivates thymidylate synthase.
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Why is FdUMP called a suicide inhibitor?
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It binds thymidylate synthase irreversibly by forming two covalent bonds.
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History of a patient with pleural disease
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- Pain
- Weight loss - Hemoptysis (suggest malignancy) - Fever/chills (suggests infection) - Arthritis - Collagen Vascular Dz |
