Nucleic Acids (Lecture 31)

Question 1

Why is DNA the genetic material?

Answer 1

removing the 2’OH makes the DNA phosphodiester backbone more stable

Thymine allows spontaneous deamination of cytosine to be detected (not in RNA uracil is present)

Question 2

why is thymine used in DNA?

Answer 2

a sponeowus deamination event occurs within cells, which causes cytosine to change to uracil. since, Uracil is not a base incorporated into DNA, it can be recognized as a mutation and essentially replaced to its proper base pair

Question 3

DNA is ____ reduced (more/less)

Answer 3

more

Question 4

which molecule is used for reductions and why?

Answer 4

NADPH because enzymatic reactions are reversible, thus to drive the reaction forward, the concentration of the subtracters drives reactions. the ratio of NADPH/NADP+ is very high in the cell, thus it’ll make reactions run forward.

Question 5

which molecule is used for oxidations and why?

Answer 5

NAD+ because enzymatic reactions are reversible, thus to drive the reaction forward, the concentration of the subtracters drives reactions. the ratio of NAD+/NADH is very high in the cell, thus it’ll make reactions run forward.

Question 6

how is ribonucleotide reductase activity regulated?

Answer 6

ATP(+)/dATP(-) levels

Question 7

how is ribonucleotide reductase selectivity regulated?

Answer 7

dATP/dGTP/dTTP

balance different bases of nucleotides

Question 8

which element of RR helps with oxidation?

Answer 8

free tryrosine radical

Question 9

what is the target for inhibition, what in habits this target and why?

Answer 9

the free radical tyrosine is inhibited by hydroxyurea. this will block DNA synthesis by blocking there production of dNTPs

Question 10

why is RR inhibition therapeutically important?

Answer 10

if DNA cant be synthesized viruses, bacteria, cancer cells cannot replicate

Question 11

what is the function of uracil-DNA glycosyalse?

Answer 11

removes uracil base from DNA to allow for an excision repair to follow

Question 12

what is the complication with the pyrimidine pathway?

Answer 12

need to keep uracil on only ribose and thymine on only deoxy ribose

this is because incorporation of uracil in DNA mimics a deamination of cytosine, which would trigger a DNA repair mechanism and in turn substitute the wrong base

Question 13

how is the pyrimidine pathway complication resolved?

Answer 13

a specific enzyme UTPase will hydrolyze dUTP (to dUMP) to decrease its concentration and prevent its incorporation into DNA

Question 14

how is are the nascent pyrimidine rings prevented from diffusing through the plasma membrane?

Answer 14

a charged carboxylic acids is added to the 6th position to keep the molecule charged and sequestered within the cytosol. The charged carboxylic acid gives the molecule a low membrane permeability.

Question 15

step 1 of pyrimidine de novo pathway:

Answer 15

carbonyl phosphate synthetase II will add 2ATP + HCO3- and glutamine to make carbuaamoul phosphate

glutamate is released

Question 16

why is pyrimidine synthesis regulated at the second steno in bacteria and the first step in animals?

Answer 16

bacteria only have 1 carbonyl phosphate (responsible for both the urea cycle and the synthesis of pyrimidines). these reactions re not separated

bacteria dint have mitochondria

in animals, there are 2 enzymes (cytosol and mitochondria), therefore the synthesis of pyrimidines can be regulates at the first step.

Question 17

how do bacteria regulate the synthesis of pyrimidines ?

Answer 17

during the second step:

allosterically activated ATP under low aspartate conditions

allosterically inhibited by CTP under low aspartate conditions

Question 18

what occurs during the allosteric activation/inhibition of bacteria?

Answer 18

ATC undergoes a conformational change which affects the Km of the bound substrates (better or not as well binding of aspartate)

Question 19

step 2 of pyrimidine den novo synthesis:

Answer 19

carbonyl phosphate is cpoonverted into carbonyl aspartate with the assiteion of aspartate via ATCase

Question 20

what occurs in steps 1, 2 and 3?

Answer 20

channeling of the intermediates carbonyl phosphate-carbomoyl aspartate and dihydroorotate

Question 21

step 4 of pyrimidine de novo synthesis

Answer 21

oxidation of dihydroorotate to orotate via hihydroorotate dehydrogenase

quinone is added this occurs in the mitochondria

Question 22

what occurs in steps 5 and 6?

Answer 22

channeling

5. add phsophoribeose via PRPP to generate OMP
6. OMP decarboxylase converts OMP to UMP

Question 23

loss of step 5 or 6 of pyrimidine de novo synthesis would cause

Answer 23

orotic aciduria

genetic disease

symptom: cannot decarboxylate or attache orotate to phosphoribose, the there will be an accumulation of orotate in the blood, which will be secreted into the urine.

Question 24

how is CTP synthesized?

Answer 24

made at the triphosphate level

UTP is combined with glutamine (a nitrogen donor) via CTP synthase to form UTP

Question 25

how is pyrimidine synthesis inhibited?

Answer 25

pyrimidine nucleoside triphsopahtes

Question 26

how is pyrimidine synthesis activated?

Answer 26

ATP and PRPP (increased concentration)