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Bioch3mistry Exam 3 > Nucleotide metabolism > Flashcards

Nucleotide metabolism Flashcards

1
Q

What is the difference between de novo synthesis and the salvage pathway?

A

De novo synthesis is the “from scratch” version of nucleotides, everything is combined

Salvage pathway is the recycling of the bases that are derived from the breakdown of DNA

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2
Q

Describe the amino acid derivatives that are involved in the synthesis of pyrimidines and describe what is derived from each

A

Glutamine is the main source of the ammonia in the rings and aspartate is also used for carbon access and carbonyls

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3
Q

Describe the de novo synthesis of pyrimidines

A

Form nitrogenous bases independent of PRPP (the ring is synthesized FIRST and then added to the ribose) in a unidirectional pathway in the CYTOPLASM

Uses Nh3 from Gln, Asp, and bicarbonate

Is allosterically regulated

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4
Q

Describe the de novo synthesis (very general) differences between purine and pyrimidine synthesis

A

pyrimidines are independent and are able to form their rings and then add to the ribose

Purines take more hand holding and have to be bound to the ribose and then they are formed piece by piece

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5
Q

Describe in your own words the allosteric regulation of the de novo synthesis of pyrimidines

A

Pyrimidines inhibits the de novo synthesis because if you have a lot of the end product, you do not want to waste energy for the reaction to keep happening

Purines will activate the synthesis of pyrimidines because you want to have something for the purines to bind to. Think about it, if you have too many purines, and they can’t bind to anything then they are useless

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6
Q

Describe carbamoyl phosphate synthetase II

A

Helps to take the bicarbonate to carbamoyl phosphate and hydrolyze NH3 from glutamine

Has 3 different active sites; one that binds glutamate, one that makes carbonic acid and holds it and then the last that holds carbamoyl phosphate

A channel is created between the active sites that helps protect the molecules from being lost to diffusion or hydrolysis by outside enzymes

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7
Q

Describe ATCases role in de novo synthesis

A

Takes carbamoyl phosphate to carbamoylaspartate

Inhibited by CTP and activated by ATP

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8
Q

Describe how carbamoylaspartate gets to orate in the de novo synthesis of pyrimidines

A

Dihydroorotase closes the ring of the molecule with the emission of water

And then dihydroorotate dehydrogenase, located in the mitochondria, takes DID to oroate

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9
Q

Describe the events that occur after Oroate is added to PRPP with the help of ornate phosphoribotransferase

A

UMP sythetase removes PPi when oroate is added to PPRP and decarboxylates the oroate to form uracil

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10
Q

Describe how UMP is converted to UTP

A

with the help of two kinases

Nucleoside monophosphate is turned into UDP with the help of nucleoside monophosphate kinases and ATP

Nucleoside diphosphate kinase then take the UDP to UTP

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11
Q

Describe how CTP is formed from UTP

A

CTP is the only nucleotide to be synthesized directly as a triphosphate with the help of CTP synthetase

(GTP activates and CTP inhibits)

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12
Q

Describe the synthesis of thymine

A

Via the salvage pathway. A thymine nucleotide is released from the DNA that is being degraded and then the thymine is converted into thymidine followed by the nucleotide form which are catalyzed by thymidine phosphorylase and thymidine kinase respectively

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13
Q

Describe the basics of the de novo synthesis of purines

A

Form bases on the PRPP via a branched pathway in the CYTOPLASM

Uses Nh3 from gln
Gly and Asp
N10-formyl-THF and HCO3-

the entire process requires a substantial amount of ATP

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14
Q

Describe the allosteric regulation of purine de novo synthesis

A

Inhibited by purines

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15
Q

List the steps involved in making IMP (the super basic ones)
ex: steps 1-3 form….

A

Steps 1-3 from the 5 membered ring

steps 4-10 form the 6 membered ring

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16
Q

What are steps 1-3 of forming the 5 membered ring

A
  1. swaps PPi on PRPP for the NH3 form Gln
  2. Glycine is added
  3. formyl group is added from N10THF
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17
Q

What are steps 4-10 of forming the 6 membered ring while making IMP

A
  1. adds an NH3 from Gln
  2. 5 membered ring is closed
  3. CO2 is added from HCO3 to Gln then to Gly
  4. Asp is added at the carboxyl
  5. second addition of formyl group from another N10THF to form a 6 membered ring
    10 6 membered ring is closed
18
Q

Describe where the reactions that take place in the formation of IMP take place (location)

A

1,4,8 take place on 3 individual

2,3,5
6,7
9,10
take place on 3 multifunctional proteins

proximity facilitates the flow

N10formylTHF reactions are provided by 2 additional enzymes

19
Q

Describe the branching of IMP (AMP and GMP)

A

AMP:

  • uses GTP for energy
  • replaces carbonyl with NH3 from Asp
  • releases fumarate
  • inhibited by AMP

GMP:

  • uses ATP for energy
  • redox with H2O to make 2nd carbonyl
  • replaces it with NH3 from Gln
  • inhibited by GMP
20
Q

Describe the differences between the nucleoside monophosphate and nucleoside diphosphate kinases

A

Nucleoside monophosphate are specific to each NMP

Nucleoside diphosphate kinase has broad specificity

21
Q

What kind of reaction is required to take deoxyribonucleotides?

A

Reduction from ribose

22
Q

Describe ribonucleotide reductase

A

1 enzyme acts on all NDPs and can act on NTPs to make dNDPs with the help of NADPH

electrons are passed through free radicals

catalytic Tyr radical is stabilized by 2 Fe ions

23
Q

Describe important aspects of the structure of the ribonucleotide reductase

A

has two allosteric sites: one active site controls the overall activity and the other controls the substrate specificity

the active sites are the catalytic sites

24
Q

Describe the allosteric regulation of ribonucleotide reductase

A

allosteric binding dictates ACTIVITY site preferences; activity is an on/off switch (ATP promotes function
dATP turns it off)

SPECIFICITY site is a volume dial (dATP specifically pyrimidines are preferred, dTTP-GDP is preferred and pyrimidines are inhibited, dGTP-ADP is preferred and pyrimidines are inhibited)

25
Q

Describe the formation of dATP (use picture on slide 30.32)

A

ADP is reduced with rNDP reductase to dADP which is then converted to dATP with nucleoside diphosphate kinase

26
Q

Describe the formation of dGTP(use picture on slide 30.32)

A

GDP is reduced with rNDP reductase to form dGDP that is converted to dGTP with nucleoside diphosphate kinase

27
Q

Describe the formation of dCTP (use picture on slide 30.32)

A

CDP is reduced with rNDP reductase to form dCDP which is converted into dCTP with nucleoside diphosphate kinase

Note: dCMP can beamed from dCDP which can be used in the pathway to create dTTP

28
Q

Describe the formation of DTTP (use picture on slide 30.32)

A

First half part 1:
UDP is reduced by rNDP to form dUDP that is made into dUTP with nucleoside diphosphate kinase to form dUMP
OR
First half part 2:
CDP is reduced by rNDP reductase to form dCDP which is made into dCMP which can be hydrolyzed and an amine removed (deamination) to form dUMP

Second half:

  • thymidylate synthase adds a methyl to dUMP to create dTMP
  • ATP is used to make dTDP
  • ATP is used again to make dTTP
29
Q

Describe the two steps of salvage in the pyrimidines

A

Phosphorylases and kinases

phosphorylates make nucleosides and kinases make nucleotides

30
Q

Describe the two kinases that are present in the cytoplasm. (involved salvage and catabolism)

A

Thymidine kinase 1 (takes thymidine to dTMP) with the help of ATP

deoxycytidine kinase (takes deoxy (C,G,A) to d(c,G,A)MP with the help of ATP

31
Q

Describe the two kinases that are involved in salvage and catabolism that are found in the mitochondria

A

Thymidine kinase 2 takes thymidine and deoxycytidine to dTMP and dCMP with the help of ATP

Deoxyguanosine kinase takes deoxy(G, A) to d(g,A)MP with the help of ATP

32
Q

Describe how antivirals are able to work

A

Viruses also has thymidine kinase but it is not as discriminating as the human kinases and they will accept purines and Thymines

acyclovir can be used as a viral treatment as it binds to the viral thymidine kinase but not the human version; this can then be incorporated into the viral DNA where it will terminate synthesis and kill the virus

33
Q

Describe salvage and catabolism that is used by purines

A

Uses phosphoribosyltransferases for one step process of salvage and catabolism

-adenine phosphoribzosyltransferase makes AMP and HGPRT makes IMP/GMP

34
Q

Describe what nitrogenous bases can be broken down into

A

Uric acid is the final product of purine catabolism

B-ureidoproponic acid can be converted into alanine and CO2 and NH3 by ureidopropionic to complete pyrimidine catabolism

35
Q

Describe uric acid

A

antioxidant

insoluble

36
Q

Describe Gout

A

high concentrations of irate can cause crystallization in the joints which leads to inflammation, arthritis, and joint degeneration

37
Q

Describe Lesch-Nyhan syndrome

A

HPRT deficiency, which leads to an increased level of urate and gout symptoms

38
Q

Describe SCID

A

Severe combined Immunodeficiency Disease (SCID)

deficiency of adenosine deaminase; dAMP accumulates which can be converted to dATP which inhibits ribonucleotide reductase which means that dNTPs are not produced and neither can DNA

39
Q

Who is vitamin B9?

A

N10-formylTHF; used in the de novo synthesis of purines and pyrimidines

40
Q

What are two ways to create dUMP?

A
  1. removal of PPi from dUTP

2. deamination from dCMP

41
Q

Why are enzymes such as thymidylate synthase targeted by cancer medications?

A

Targeting the enzymes is halting the deoxyribose version of our pyrimidines which halts DNA synthesis and division, stopping the cancer in its tracks

42
Q

Describe endonuclease versus exonuclease

A

Endonuclease cut in the middle of things

Exonuclease cut from the end and keep going

BOTH are very non-specific enzymes

Bioch3mistry Exam 3 (9 decks)

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