Lecture 7: Introduction to Nucleic Acids, Nucleotide biosynthesis and catabolism

Question 1

Deoxyribonucleic acids (DNA)

Answer 1

NUCLEOTIDE = Phosphate + Sugar + Base
NUCLEOSIDE = Sugar + Base
Deoxyribose exists as the beta anomer in DNA

The nucleic acid bases are grouped into purines (two rings) ( adenine and guanine) and pyrimidines (one ring) (cytosine and thymine) .
These groupings are made on the basis of their biosynthesis and catabolism

Question 2

Primary structure of DNA

Answer 2

The sequence of the bases, held together by the sugar phosphate backbone

Question 3

secondary structure of DNA

Answer 3

Directionality
- one strand 5’ to 3’
- one strand 3’ to 5’
- for this reason they are described as ‘anti parallel’

Message in code is complementary

Right handed helix

Major groove and minor groove

Dimensions (idealised or mean structure )
- base pairs 0.34 nm apart
- one helical turn 3.4 nm therefore 10 base pairs (bp’s) per turn
- diameter of helix 2 nm

Base Pairing:
2 H-bonds between A and T
3 H-bonds between C and G

Question 4

tertiary structure DNA

Answer 4

Chromosomal packing of DNA onto chromatin.

Chromatin is a complex made up mainly of histone proteins with DNA and RNA

This is a form of solenoidal supercoiling

Question 5

RNA primary structure

Answer 5

Is a complementary code to DNA (transcription)
Is similar to DNA with the following exceptions:
Ribose is used instead of deoxyribose
Uracil is used rather than thymine

Question 6

secondary RNA

Answer 6

Single stranded

Some regions of helical secondary structure exist due to base pairing within the same strand (see t-RNA)

Adenine pairs to uracil; guanine pairs to cytosine

Question 7

TERTIARY structure RNA

Answer 7

Three types of RNA are involved in protein synthesis

Messenger RNA (mRNA) Relays the code for a protein from DNA to the protein production site
Transfer RNA (tRNA) The adapter unit linking the triplet code on mRNA to specific amino acids
Ribosomal RNA (rRNA)
Present in ribosomes (the production site for protein synthesis). Important both structurally and catalytically

Question 8

Biosynthesis of nucleic acids

Answer 8

The two biosynthetic pathways are the SALVAGE and DE NOVO pathways

Question 9

De novo synthesis of purine
nucleotides

Answer 9

Starting point is sugar phosphate which is phosphorylated and then the purine ring is assembled on the ribose ring

Committed step is conversion of PRPP to 5-phosphoribosylamine

Note : The configuration at C-1 is inverted at this stage from a to b.
The resulting glycosidic bond has the b configuration that
is seen in naturally occurring nucleotides

First ring is then built of the ribose

energy is provided by accompanying dephosphorylation of ATP to ADP
additional atoms or groups are added with accompanying loss from other molecules
Where a “single carbon addition” is required, the C is often provided from a tetrahydrofolate compound and this provides a useful approach to inhibition of synthesis.

then the second ring is then built

Common precursor inosine 5’-phosphate can then create both AMP and GMP
By using a common precursor, the synthesis is very efficient (energy, enzymes)

Question 10

De novo synthesis of pyrimidine
nucleotides

Answer 10

In contrast to the de novo synthesis of purines, where the nucleic acid ring is assembled on the ribose ring, in the de novo synthesis of pyrimidines, the nucleic acid ring is assembled first and then attached to the ribose ring

The de novo synthesis of pyrimidine nucleotides is a biochemical pathway by which cells synthesize pyrimidine bases (cytosine, thymine, and uracil) from simple organic molecules. Here is a simplified overview of the process:

1. Formation of Carbamoyl Phosphate:
   
   • The enzyme carbamoyl phosphate synthetase II (CPS II) catalyzes the reaction that combines glutamine, CO2, and ATP to form carbamoyl phosphate.
   • Glutamine + CO2 + 2 ATP → Carbamoyl phosphate + Glutamate + 2 ADP + Pi
2. Formation of Carbamoyl Aspartate:
   
   • Aspartate transcarbamoylase (ATCase) catalyzes the reaction between carbamoyl phosphate and aspartate to form carbamoyl aspartate.
   • Carbamoyl phosphate + Aspartate → Carbamoyl aspartate + Pi
3. Cyclization to Dihydroorotate:
   
   • Dihydroorotase catalyzes the cyclization of carbamoyl aspartate to form dihydroorotate.
   • Carbamoyl aspartate → Dihydroorotate + H2O
4. Oxidation to Orotate:
   
   • Dihydroorotate dehydrogenase catalyzes the oxidation of dihydroorotate to form orotate.
   • Dihydroorotate + NAD+ → Orotate + NADH + H+
5. Formation of Orotidine Monophosphate (OMP):
   
   • Orotate phosphoribosyltransferase (OPRTase) catalyzes the reaction that combines orotate with phosphoribosyl pyrophosphate (PRPP) to form orotidine monophosphate (OMP).
   • Orotate + PRPP → Orotidine monophosphate (OMP) + PPi
6. Decarboxylation to Uridine Monophosphate (UMP):
   
   • OMP decarboxylase catalyzes the decarboxylation of OMP to form uridine monophosphate (UMP).
   • OMP → UMP + CO2
7. Conversion to Other Pyrimidine Nucleotides:
   
   • UMP can be phosphorylated to form UDP (uridine diphosphate) and then further to UTP (uridine triphosphate).
   • UMP + ATP → UDP + ADP
   • UDP + ATP → UTP + ADP
   • UTP can be converted to CTP (cytidine triphosphate) by the enzyme CTP synthetase, using glutamine as a nitrogen donor.
   • UTP + Glutamine + ATP → CTP + Glutamate + ADP + Pi

Key Points:

• Carbamoyl phosphate is synthesized in the cytoplasm (distinct from the urea cycle which occurs in mitochondria).
• The pathway involves both cytosolic and mitochondrial enzymes.
• Pyrimidine synthesis is regulated primarily at the first step (CPS II), which is feedback-inhibited by UTP and activated by PRPP and ATP.

This pathway ensures that cells have a sufficient supply of pyrimidine nucleotides for DNA and RNA synthesis, especially during cell division and growth.

Question 11

Reductive Catabolism Pyrimidine bases

Answer 11

Reductive breakdown of pyrimidine bases results in small soluble molecules that are easily excreted.

Question 12

Oxidative Catabolism Pyrimidine bases

Answer 12

Key Points for catabolism of pyrimidines:
Can occur through oxidative or reductive pathways
Products of catabolism are small, water soluble compounds
Degradation products are readily excreted

Question 13

Catabolism of Purine nucleotides

Answer 13

Catabolism of the purine nucleotides leads ultimately to the production of uric acid which has low solubility and is excreted in the urine as sodium urate crystals.

Question 14

Clinical problems of nucleotide catabolism

Answer 14

Clinical problems associated with nucleotide metabolism in humans are predominantly the result of abnormal catabolism of the purines.

The clinical consequences of abnormal purine metabolism range from mild to severe and even fatal disorders.

Clinical manifestations of abnormal purine catabolism arise from the insolubility of the degradation byproduct, uric acid.

Excess accumulation of uric acid leads to hyperuricemia, more commonly known as gout.