Biosynthesis of Nucleotides

Question 1

What did John Buchanan contribute?

Answer 1

Understanding of how purines are synthesized

Question 2

What are nucleotides?

What do they carry?

Answer 2

Building blocks/precursors of nucleic acids.

Energy (ATP / GTP)

Question 3

How do nucleotides initiate glycogenesis?

Answer 3

Before glucose can be polymerized, UDP-glucose (a nucleotide) must be formed

Question 4

How can a nucleoside be made a nucleotide?

Answer 4

Add phosphate group on C5

Question 5

What are the 3 pentose sugars?

Answer 5

Ribose and deoxyribose

Question 6

On what end is a free sugar available for bonding on a nucleoside?

Answer 6

3’ end

Question 7

Purine vs Pyrimidine

Answer 7

Purine: 2 carbon-nitrogen rings – Adenine and guanine

Pyrimidine: 1 carbon-nitrogen ring – cytosine, thymine, uracil

Question 8

What bond connects nucleotides? Between what Carbons?

Answer 8

phosphodiester bond between C3 of one pentose sugar and C5 of another

Question 9

What is the difference between a nucleotide, nucleoside, and nitrogenous base?

Answer 9

Nitrogenous base: purine + pyrimidine
Nucleoside: pentose sugar + nitrogenous ring
Nucleotide: Phosphate group: pentose sugar + nitrogenous base

Question 10

What are the 2 pathways of nucleotide synthesis?

Answer 10

De-novo: synthesis of metabolic precursors (AA, ribose-5-phosphate, CO2, NH3/ammonia)

Salvage pathway: purine/pyrimidine bases released from the degradation of nucleotides are recycled to make new mRNA/nucleotides (doesn’t need precursors)

Question 11

Can purine/pyrimidine bases be synthesized as independent molecules?

Answer 11

No, they are ALWAYS part of a nucleotide.

Question 12

What are purine rings always built upon?

Answer 12

a Ribose phosphate

Question 13

What are pyrimidine rings first synthesized as? What are they attached to after?

Answer 13

Orotate, then attached to ribose phosphate

Question 14

What is the precursor for 5-phosphoribosyl 1-pyrophosphate (PRPP)?

Answer 14

Ribose-5-phosphate

Question 15

What AA is the precursor of purines?

Answer 15

Glycine

Question 16

What AA is the precursor of pyrimidines?

Answer 16

Aspartate

Question 17

What is the role of glutamine in nucleotide synthesis?

Answer 17

Amino group donor

Question 18

What is the 1st step in de novo synthesis of purines?

Answer 18

PRPP joins with glutamine which gives PRPP an amino group

Question 19

What does glycine provide in the de novo synthesis of purines?

Answer 19

Backbone

Question 20

What step in the de novo synthesis of purines only occur in higher eukaryotes?

Answer 20

AIR to CAIR

Question 21

What is the purine ring built on in de novo synthesis of purines?

Answer 21

PRPP

Question 22

What is the end product of the de novo synthesis of purines? Which is then converted to what?

Answer 22

IMP –> AMP/GMP

Question 23

In order to convert IMP to AMP, what AAs are used and how do they alter the molecule? de novo synthesis of purines

Answer 23

Aspartate gives an amino group (GTP dependent)

Fumarate backbone is then removed & amino group added to 6th carbon, forming AMP

Question 24

In order to convert IMP to GMP, what AAs are used and how do they alter the molecule? de novo synthesis of purines

Answer 24

IMP –> XMP

From XMP –> GMP:

• ATP dependent.
• amino group added from Glutamine onto 2nd C
• Glutamate backbone leaves

Question 25

Where does specific regulation start occurring in the de novo synthesis of purines?

Answer 25

IMP --> AMP/GMP

Question 26

What limits the synthesis of AMP? GMP? de novo synthesis of purines

Answer 26

GTP limits AMP ATP limits GTP Reciprocal inhibition.

Question 27

What inhibits the reaction from Ribose-5-phosphate --> PRPP in de novo synthesis of purines?

Answer 27

ADP

Question 28

What inhibits the reaction from PRPP --> 5-phosphoribosylamine in de novo synthesis of purines?

Answer 28

AMP, GMP, IMP

Question 29

What does the production of AMP from IMP inhibit in de novo synthesis of purines?

Answer 29

AMP inhibits 1st step of IMP-->AMP production

Question 30

What does the production of GMP from IMP inhibit in de novo synthesis of purines?

Answer 30

GMP inhibits 1st step of IMP-->GMP production

Question 31

What are the precursors of de novo synthesis of pyrimidines?

Answer 31

Aspartate, carbomoyl phosphate, PRPP

Question 32

Carbomoyl phosphate is required for de novo synthesis of pyrimidines in what part of the cell? Via what enzyme?

Answer 32

Cytosol via Carbamoyl phosphate synthetase 2

Question 33

What AA is used to produce orotate in de novo synthesis of pyrimidines? What is required for orotate to be converted to its end product?

Answer 33

Aspartate Orotate needs to be built on PRPP, if not it can't be converted to its end product

Question 34

What is the 1st nucleotide synthesized in de novo synthesis of pyrimidines? What is it ultimately converted to? Which AA helps? How?

Answer 34

UMP. CTP - Glutamine donates amino group on 4th Carbon

Question 35

What inhibits the de novo synthesis of pyrimidines?

Answer 35

CTP (product) inhibits 1st enzyme of the de novo synthesis of pyrimidines

Question 36

What is the main enzyme that participates in the conversion of riboneucleotides to deoxyriboneucleotides?

Answer 36

Ribonucleotide reductase

Question 37

What two enzymes transmit electrons from NADPH in the reduction of ribonucleotides to deoxyribonucleotides via ribonucleotide reductase?

Answer 37

Glutaredoxin and thioredoxin

Question 38

Discuss the electron path that involves glutaredoxin?

Answer 38

NADPH --> (GSSG-->2GSH) --> Glutaredoxin --> ribonucleotide reductase which converts (NDP-->dNDP + H2O)

Question 39

What does ribonucleotide reductase transfer to NDP to create dNDP + H2O

Answer 39

2 (-SH) groups

Question 40

What is the cofactor of Gultaredoxin?

Answer 40

2GSH

Question 41

What is the cofactor of Thioredoxin?

Answer 41

FADH2

Question 42

What is dTMP derived from?

Answer 42

CDP or UDP

Question 43

What differentiates Thiamine and Uracil?

Answer 43

Thiamine has a methyl group on C5

Question 44

Draw out the mechanism of CDP/UDP to dTMP.

Answer 44

Check

Question 45

What intermediate of the pentose phosphate pathway is PRPP made from?

Answer 45

Ribose-5-phosphate

Question 46

When high [NADPH] inhibits the pentose phosphate pathway, what doe G6P do?

Answer 46

It does glycolysis