CH. 34 Nucleotide Syn 3

The pyrimidines are  ,  , and  

The first step of pyrimidine biosynthesis involves the formation of   de novo synthesis of a pyrimidine

The formation of the caramoyl phosphate requires  ,  , and  [derived from   hydrolysis].

CPS II is allosterically regulated in 2 ways:
• Activated by  ,  , and  
• Inhibited by  ,  

The second step of pyrimidine synthesis requires carbamoyl conversion to  

In the conversion of carbamoyl to orotate,   joins through   to make  
• After a couple of reactions  makes ->  , which has the basic pyrimidine ring shape.

In the third step of pyrimidine synthesis, orotate is combined with   to form  

After synthesis of orotate, the ring joins   via the enzyme orotate phosphoribosyl transferase to form  

The fourth step of pyrimidine biosynthesis involves the formation of a   base. Orotidylate (OMP) is decarboxylated via   to form  .

UMP is converted to UTP using  

What enzyme adds the P's to UMP?
The first - added by  
The second - added by  

*** TQ
UTP then gets converted to   by  , which uses   and  .

  is the only nucleotide synthesized de novo directly as a  , since it arises directly from UTP.

CTP is useful for RNA synthesis. In order to become  , it must first be dephosphorylated.
• An enzyme that does that is  .

***TQ
Order of synthesis of pyrimidines:  

dUTP is useless for   synthesis. It should not be incorporated into  . dUTP is a problem for the cell if DNA polymerase
recognizes dUTP just like   and it will put dUTP into
DNA if it finds it!

dUTP quickly gets converted into dUMP via  

  makes dTDP

  makes dTDP

  makes dTTP.

  is not regulated. If it finds a NDP or a dNDP, it will turn it into NTP or dNTP.

If   is not functional,you can’t replicate DNA! (  ->  

dUTP can also be directly made from deamination of  

C1 unit can be used directly as   in the conversion of   to   by Thymidylate Synthase

THF is   to dihydrofolate in
this reaction.

(Anti-metabolites rxn)

FH2
is reduced to FH4 by
 . This is
called   recycling.

TEST QUESTION

-When THF recovery is blocked (  is not happening) with  , the DHF reductase binds to   with . It causes the indirect blockage of  

 , a pro-drug, gets converted to  . It Covalently binds and permanently Inhibits   This process specificially blocks   synthesis and   synthesis.

 dysfunction, as well as   and/or   deficiencies result in
decreased DNA synthesis
• causes megaloblastic anemia

If vitamin B12, which accepts methyl groups from 5-methylTHF, is deficient,   accumulates.

Remember that 5-Me-THF is needed for synthesis of
  from  .

Since 5-methyl-THF cannot be reconverted to otherfolate
derivatives, a  deficiency is secondarily produced (the
methyl trap theory).

Pyrimidine rings can be degraded to  
and  , which can then be excreted
via the lungs and kidneys.

UTP and CTP can get hydrolyzed via  , yielding   and  

The 1st step in pyrimidine nucleotide degradation from   and   is   to the nucleosides by pyrimidine-specific 5’-nucleotidases, yielding   and .

A   is a hydrolytic enzyme that catalyzes the hydrolysis of nucleoside monophosphate into
nucleoside and phosphate.

Cytidine and uridine are broken-down by   into sugar-P + pyrimidine.
•   use Pi (instead of water) to phosphorylase the pyrimidine from the (deoxy)ribose, yielding  .

The final break-down molecule of both cytosine and uracil is  

The break-down to thymine yields
  which can go into TCA cycle.

  -> converts a monophosphate into a diphosphate.

ONE ENZYME converts ALL of the diphosphates into triphosphates:  , which is an important enzyme to balance the stoichiometry of triphosphates.

Carbamoyl phosphate synthetase is activated by   and
  and is inhibited by  ,  , and  .

The second reaction is catalyzed by Aspartate
Transcarbamoylase, ATCase, which has allosteric regulation
and feedback inhibition
. • ATCase is allosterically regulated by 3 effectors:
•   (activates), and   (activates) •  (feedback inhibitor)

Regulation of the first two enzymes of the pathway is
important for balance:
• a high concentration of  
stimulates synthesis of  
• high concentration of   turns off the
pathway.

Test Question!
AZT resembles  

The azido-group of AZT blocks  
• There’s no  (mechanism of chain termination)

Viral RNA-dependent DNA polymerase (reverse transcriptase) is
100X more sensitive to   than host cell  .

Ribonucleotide Reductase (RNR), catalyzes all the conversions from  

Ribonucleotide Reductase (RNR): After the  is formed (reduced), the enzyme reverses to the   state
and is ready for another cycle.

RNR regulation: R2 subunit
• The small subunit, R2, forms a   that is
needed for the mechanism.
• Cells must control proper balance of  ,
otherwise mutations can occur.

RNR regulation: R1 subunit
1) Specificity site: tells the enzyme which  to
transform into  
2) Activity site: on/off switch.   turns the enzyme on.   turns the enzyme off (feedback inhibition).

TEST QUESTION
R1 subunit  site -> tells the enzyme which   can bind to the active site and transform into  .

dATP and ATP are both purines which favor the binding of   (UDP
and CDP).

dATP inhibits the other  ! But it also promotes   activity towards
pyrimidines. These are 2 apparently opposite effects and the outcome depends on  .

At very high concentration, dATP   inhibits

At moderately high concs, dATP   of pyrimidines in order
to balance purines vs. pyrimidines without totally shutting down the enzyme.

Test Question: Diphosphates bind to the  

Test Question: Triphosphates bind to the   site