T22 - Nucleotide Metabolism

4 Example Roles of Nucleotides in Cell Metabolism

1. Building blocks of DNA and RNA

2. Co-substrates such as ATP

3. Supply components to other cofactors

4. Signalling molecules

3 Components of a Nucleotide

1. Nitrogenous base

2. Ribose/Deoxyribose sigar

3. 1-3 phosphoryl groups (ATP essentially)

Nitrogenous Base vs Nucleoside vs Nucleotide

• Nitrogenous base → Just the base by itself (adenine, guanine, thymine, cytosine)

• Nucleoside → Base + Sugar

• Nucleotide →> Base + Sugar + Phosphate

How many Rings do Purines have? Pyrimidines?

purines 2, pyrimidines 1

Which Bases are Purines

Adenine and Guanine → Silver (Ag) makes nice rings (plural for two rings)

Which Bases are Pyrimidines

Cytosine, Thymine(DNA), and Uracil (RNA)

List Where the Atoms in a Purine Structure comes from (1-9)

1. Asparte

2. N-formyl tetrahydrofolate

3. Glutamine

4. Glycine

5. Glycine

6. CO2

7. Glycine

8. N-formyl tetrahydrate

9. Glutamine

10. Ribose-P

How is PRPP used in Purine and Pyrimidine Synthesis

AKA Phosphoribosyl Pyrophosphate

both purines and pyrimidine nucleotides utilize an activated phosphorylated form of ribose 5-phosphate (PRPP) as part of their respective pathways

• purines → uses it as a scaffold upon which its nucleotides are built

• pyrimidines → its nucleotides uses PRPP at a later stage of its synthesis pathway

What Enzyme is Responsible for transforming Ribose 5-phosphate → PRPP

PRPP Synthetase

• Requires an ATP → AMP and the 2 terminal phosphoryl groups are attached onto the carbon 1 of Ribose 5-P to form Phosphoribosyl Pyrophasphate (see highlighted part in image)

1st Step of Purine Synthesis

PRPP → Phosphoribosyl Amine

Uses transfer of an amino group from glutamine to PRPP

• enzyme: Glutamine-PRPP Amidotransferase

• In: Glutamine de-aminase into Glutamate

  • NH2 attaches to carbon 9

• In: H2O Out: PPi → H2O → 2 Pi

How many Reactions to get from Phosphoribosyl Amine → Inosine Monophosphate (IMP)

(Apart of purine synthesis)

9 reactions (we don’t go into detail)

What must Happen to IMP to Create Adenine/Guanine-based Nucleotides (General)

The nitrogenous base of IMP must be altered

How to make Adenine-based Nucleotides from IMP (2)

IMP → AMP requires an amino group to be added on Carbon 6 of IMP

2 reactions required:

1. Aspartate in → donates amino group to another molecule

2. Fumarate out

How to make Guanine-based Nucleotides from IMP (2)

IMP → GMP requires an amino group to be added on carbon 2 of IMP

2 Steps required:

1. (not specified in course)

2. amino group comes from glutamine → glutamate

List Where the Atoms in a Pyrimidine Structure comes from (1-6)

1,4-6: Aspartate

2+3: Carbamoyl phosphate

T/F Carbamoyl phosphate used for pyrimidine synthesis is the same as the one found in urea cycle

False; the one used for pyrimidines is made in the cytosol, the one in urea cycle is made in the mitochondria

T/F Pyrimidine synthesis does not start with the PRPP scaffold

True; PRPP is added to orotate later in the pathway

1st Step of Pyrimidine Synthesis

Begins with a nitrogenous base called Orotate → formed after a series of 6 reactions that we don’t cover in this course

• PRPP is then added to Orotate and then COO (circled in red) is removed from the Orotidine ring to generate Uridine Monophosphate (UMP)

How to make Cytosine-based Nucleotides from UMP

UMP → UDP → UTP → CTP

• CTP cannot use UMP as stock, therefore we will have to change UMP into UTP by adding two phosphoryl groups

Requires 2 steps to add amino group to uracil to change into cytosine:

1. not covered in class

2. glutamine in, glutamate out

How to make Thymine-based Nucleotides from UMP

Thymine-based Nucleotides use a deoxyribose sugar (AKA will be in the form dTMP) so going from UMP to dTMP:

UMP → UDP → dUDP → dUMP → dTMP

• A phosphate goes in UMP → UDP

• UDP → dUDP modification to become deoxyribose (write out)

• A phosphate goes out dUDP → dUMP

• dUMP → dTMP requires an addition og a methyl group

Why are Purine Bases Recycled? What happens if they aren’t?

Purine synthesis if energetically costly and as a consequence, most of the purine bases are recycled to form new nucleotides

• purines that are not recovered are broken down into Uric Acid and Sodium Urate

T/F Uric acid and Sodium urate are relatively soluble

False; they are relatively insoluble → accumulation leads to gout

Explain Gout

excess concentrations of the waste products uric acid and sodium urate (stems from purine degradation) leads to the formation of crystal structures in the soft tissues of the kidneys, toes and joints.

• accumulation of the crystals in tissues mention leads to the painful symptoms associated with gout