Biochem Lecture 5

Question 1

Purine

De novo synthesis usually in

Answer 1

Purine

De novo synthesis usually in liver, cytoplasm

Question 2

Pyrimidine De novo synthesis

Primarily occur in?

Answer 2

Pyrimidine

Primarily in extrahepatic tissue, tissue outside the liver, cytoplasm and mitochondria

Question 3

Purine Synthesis De Novo

Steps

Answer 3

Begin with Ribose 5 phosphate which you get from the pentose 5- phosphate pathway
Step 1) Need ATP, along with catalyzation by PRPP synthetase
This adds two phosphate groups to the ribose 5 phosphate and it becomes
PRPP, this molecule is SUPER important for pyrimidine and purine metabolism
Step 2) Commitment step (no going back!) PRPP catalyzed by Glutamine PRPP-amidotransferase
Gln-PRPP takes amide nitrogen from gln and gives it to PRPP
Gln-> Glu
Glutamate is released
Phosphates released
PRA is made
Nitrogen of Glu becomes N-9 of purine

Question 4

ATP

Answer 4

Adenosine triphosphate (ATP): most common source of energy in cells

Question 5

cAMP

Answer 5

second messenger, important signaling molecule

Question 6

Guanosine triphosphate: GTP

Answer 6

source of energy in protein metabolism, important signaling molecule

Question 7

Guanosine diphosphate (GDP):

Answer 7

important signaling molecule

Question 8

2nd commitment step, what enzyme used in purine synthesis and what does it do?

Answer 8

Gln-PRPP amidotransferase takes the amide Nitrogen from Glutamine and gives it to PRPP and Glutamine gets converted into Glutamate

Question 9

1st step of purine synthesis, what enzyme used and what does it do?

Answer 9

PRPP Synthetase (PRS) used to creat PRPP with the use of ribose phosphate with ATP and this adds 2 phosphate groups

Question 10

After first two steps of purine synthesis.. multiple steps take place to create what?

Answer 10

the first nucleotide, IMP.

Question 11

GMP needs what energy source to be created?

Answer 11

ATP

Question 12

AMP needs what energy source to be created?

Answer 12

GTP

Question 13

How to get IMP to GMP

Answer 13

● IMP dehydrogenase: IMP → Xanthosine 5’ monophosphate (XMP)
● GMP Synthetase: XMP → GMP

Question 14

Enzymes for IMP to AMP:

Answer 14

● Adenylosuccinate synthetase: IMP → Adenylosuccinate (sAMP)
● Adenylosuccinase: sAMP → AMP

Question 15

What happens when PRPP is produced in excess? what takes place.

Answer 15

Feed-forward inhibition:
● Excess PRPP
○ PRPP amidotransferase is positively activated by high concentrations of PRPP

Question 16

Feedback inhibition in purine synthesis

Answer 16

Feedback Inhibition:
● PRPP is inhibited by IMP, AMP or GMP
● GMP inhibits IMP dehydrogenase
● AMP inhibits Adenylosuccinate synthetase

Question 17

Amino Acids used in purine synthesis de novo pathway

Answer 17

Amino Acids used: Entire Glycine molecule, amino nitrogen of Aspartate, amide nitrogen of Glutamine

Question 18

All purine nitrogen atoms come from:

Answer 18

All purine nitrogen atoms come from: GLY, ASP GLU

Question 19

What is % of daily purine biosynthesis by the salvage pathway

Answer 19

90% of daily purine biosynthesis

Question 20

Purine Salvage pathway main idea

Answer 20

Purine bases attach to 5-phosphoribosyl 1-pyrophosphate (PRPP) to form nucleoside monophosphates (AMP, IMP or GMP)

Question 21

Adenine → AMP in salavage purine pathway. what enzyme is used

Answer 21

Catalyzed by APRT

Question 22

Hypoxanthine → IMP

Guanine → GMP

Answer 22

Both catalyzed by: HGPRT

Question 23

Purine Catabolism

Answer 23

Purine bases are first converted into Xanothine and then into uric acid for secretion by Xanthaine Oxidase

Question 24

Diseases associated with Purine metabolism : Gout and treatments

Answer 24

1. Gout
   ○ Caused by hyperuricemia
   ○ Excess uric acid in blood is not processed through the kidney leading lower excretion in urine

Treatments :inhibition of enzyme that catalyzes uric acid (xanthine oxidase)
Drug: Allopurinol: an analog of hypoxanthine, potent inhibitor of xanthine oxidase (floods the enzyme)
ents:
● Probenecid: increases excretion of uric acid in urine; decreases renal tubular reabsorption of urate (removes it from blood)

Question 25

Lesch-Nyhan Syndrome (LNS) : Purine Diseases

Answer 25

Rare inherited disorder caused by deficiency in HGPRT
Results in increase of Hypoxanthine and guanine since it’s not being converted into IMP an GMP.
Early symptoms: sand-like uric acid crystals
Treatment: Inhibition of Xanthine Oxidase

Question 26

Pyrimidine Synthesis: De Novo

Answer 26

Steps:
Synthesis of Carbamoyl phosphate from glutamine and carbon dioxide, ATP
Carbamoyl phosphate synthetase (CPS or CPSll)
Committed step:
Carbonyl phosphate plus aspartate uses ACTASE to generate N-Carbamoyl Aspartate
3. Dihydroorotase is used with product to create dihydroorotate then dihydroorotate dehydrogenase is used to make orotic acid
Final two steps:
● First reaction carried out by: N terminal enzyme orotate phosphoribosyltransferase
○ Converts Orotic Acid to Orotidine-5’-monophosphate

● Terminal reaction carried out by: C-terminal enzyme OMP decarboxylase
○ Converts orotidine-5’-monophosphate to uridine monophosphate

Catalyzed by: Uridine 5’-monophosphate synthase which is a bifunctional enzyme (N-terminal and C-terminal function as separate enzymes)

Question 27

Amino acids needed in Pyrimidine De Novo Synthesis:

Answer 27

Glutamine and Aspartate because they are smaller

Question 28

Key difference in Pyrimidine and Purine De novo Synthesis:

Answer 28

Purine: ring built on PRPP which supplies sugar group, so starting point is PRPP.
● Pyrimidine: ring is made first and then PRPP is added

Question 29

UTP can be converted to CTP

○ using:

Answer 29

ATP, Glutamine CTP synthetase

Question 30

dUMP to dTMP

Answer 30

dUMP to dTMP (RNA to DNA)

Enzyme: Thymidylate Synthase

Question 31

Ribonucleotides to 2’deoxyribonucleotides

Answer 31

Uses nucleotide diphosphate, NTP, Mg2+

Enzyme: Ribonucleotide reductase

Question 32

Regulation of De novo Synthesis in Pyrimidines:

Answer 32

Feedback Inhibition: Carbomyl phosphate synthetase (CPS- first step) is inhibited by CTP (product) due to excess CTP
● CTP also inhibits its own enzymes

Question 33

Pyrimidine Synthesis: Salvage Pathway

Answer 33

Pyrimidine bases turned into nucleotides
Uracil or Cyotsine bases
Ribose 1 phosphate is catalyzed by pyrimidine nucleoside phosphorylases
Which makes uridine or cytidine resulting in a nucleoside
Next uridine kinase is used on the nucleosides to create a nucleotide
Enzymes for Uridine and Cytidine: Uridine kinase/Uridine-cytidine kinase (SAME THING)

Question 34

dine Catabolism:

When pyrimdines breakdown remember that they break down from

Answer 34

RNA, DNA to Nucleotides to Nucleosides, and ultimately only break down into Thymine and Uracil.

Question 35

Pyrimidine bases are converted into ? during pyrimidine catabolism

Answer 35

Pyrimidine bases are converted into β-amino acids,β-alanine, β-aminoisobutyrate, CO2 and NH4.
Uracil→ β-Alanine
○ Thymine → β-Aminoisobutyrate

Question 36

Pyrimidine Metabolism Disorders:

● Uridine monophosphate synthase deficiency (hereditary orotic aciduria)
treatment

Answer 36

○ Uridine monophosphate (bifunctional enzyme) catalyzes orotate phosphoribosyltransferase and orotidine-5’-monophosphate decarboxylase reactions.
○ Deficiency of enzyme, orotic acid accumulates causing megaloblastic anemia, orotic crystalluria and nephropathy, cardiac malformation, strabismus and recurrent infections
Orotate + PRPP
OMP
UMP
Treatment:
● Oral Uridine
● Supplementation: Xuriden (uridine triacetate)