To begin our journey, it is essential to clearly define and distinguish between nucleotides and nucleosides, understand their basic chemical structure, and appreciate their diverse and vital roles in biological systems.
A molecule composed of two main parts:
The Bond: The nitrogenous base is attached to the C1' carbon of the pentose sugar via a β-N-glycosidic bond.
A Nucleotide is simply a Nucleoside with one or more Phosphate groups attached.
The type of pentose sugar determines whether the nucleotide is for RNA or DNA.
These are cyclic, planar, relatively water-insoluble compounds that absorb UV light. They are categorized into two classes based on ring structure.
Characterized by a double-ring structure (a six-membered pyrimidine ring fused to a five-membered imidazole ring).
The two major purine bases are:
Characterized by a single-ring structure (a six-membered heterocyclic ring).
The three major pyrimidine bases are:
| Base | Nucleoside (Ribose) | Nucleotide (Ribose-MP) | Nucleoside (Deoxyribose) | Nucleotide (Deoxyribose-MP) |
|---|---|---|---|---|
| Adenine (A) | Adenosine | Adenylate (AMP) | Deoxyadenosine | Deoxyadenylate (dAMP) |
| Guanine (G) | Guanosine | Guanylate (GMP) | Deoxyguanosine | Deoxyguanylate (dGMP) |
| Cytosine (C) | Cytidine | Cytidylate (CMP) | Deoxycytidine | Deoxycytidylate (dCMP) |
| Uracil (U) | Uridine | Uridylate (UMP) | - (rarely found in DNA) | - |
| Thymine (T) | Ribothymidine (rare) | Ribothymidylate (rTMP) | Deoxythymidine | Deoxythymidylate (dTMP) |
Note: For deoxyribonucleotides, the 'd' prefix is used (e.g., dATP, dGMP).
Note: Thymine is predominantly found in DNA. While "ribothymidine" exists, uracil is the primary pyrimidine in RNA.
Nucleotides are far more than just building blocks for nucleic acids; they play incredibly diverse and crucial roles in almost every aspect of cellular life.
Many essential coenzymes, critical for enzymatic reactions, are derivatives of nucleotides:
"De novo" means "from scratch," and indeed, the purine ring is constructed from small, simpler precursors in this pathway. This process primarily occurs in the liver, but also in other rapidly dividing cells.
Unlike pyrimidine synthesis where the base is formed first and then attached to the sugar, purine synthesis begins with the sugar and builds the ring directly upon it.
α-D-Ribose-5-Phosphate (a product of the Pentose Phosphate Pathway).
The purine ring (specifically the imidazole ring, followed by the pyrimidine ring) is built in a series of ten steps, consuming energy (ATP) and incorporating atoms from various small molecules.
Note: The intermediate after 5-phosphoribosyl-1-amine is called Glycinamide Ribonucleotide (GAR), as glycine is incorporated early on.
The atoms that make up the purine ring come from surprisingly diverse and simple sources. It is helpful to visualize the purine ring and where each atom originates:
The series of reactions from 5-Phosphoribosyl-1-amine to IMP involves:
Once IMP is formed, it serves as a branch point for the synthesis of the two major purine ribonucleotides: Adenosine Monophosphate (AMP) and Guanosine Monophosphate (GMP). These two pathways are reciprocally regulated to ensure balanced production.
The synthesis of purine nucleotides is tightly regulated to match the cell's needs and to maintain a balanced pool of ATP and GTP.
Inhibited by both purine nucleotides (AMP, GMP) and pyrimidine nucleotides.
We just learned how to make Purines (the double ring). Now, we look at Pyrimidines (the single ring: C, T, and U).
Location: Like Purines, this happens in the Cytoplasm (fluid) of the cell. It is very active in the liver.
This is the opposite of Purine synthesis.
The Pyrimidine ring is simpler. It comes from just 3 sources:
This amino acid provides the bulk of the ring: N1, C4, C5, and C6.
The goal is to make UMP (Uridine Monophosphate). Once we have UMP, we can make all the others.
Glutamine + CO₂ + 2 ATP → Carbamoyl Phosphate
Carbamoyl Phosphate + Aspartate → Carbamoyl Aspartate
Enzyme: Aspartate Transcarbamoylase (ATCase).
This step fuses the pieces together to start the ring.
Loss of water closes the ring to form Dihydroorotate.
Enzyme: Dihydroorotase.
Note: In humans, enzymes 1, 2, and 3 are combined in one big protein called "CAD".
Dihydroorotate → Orotate.
Enzyme: Dihydroorotate Dehydrogenase.
⚠️ Important Location Exception:
This is the ONLY enzyme in the pathway located on the Inner Mitochondrial Membrane. All others are in the cytosol. It uses FAD to pass electrons to the electron transport chain.
Orotate + PRPP → Orotidine Monophosphate (OMP).
Enzyme: Orotate Phosphoribosyltransferase (OPRT).
This is the moment the Ring meets the Sugar (PRPP).
OMP loses CO₂ → Uridine Monophosphate (UMP).
Enzyme: OMP Decarboxylase.
Goal Achieved! We have the first Pyrimidine Nucleotide.
We have UMP, but we need C, T, and the DNA versions ("d").
We take UTP and add an amino group.
We must remove the oxygen from the Ribose sugar.
DNA needs Thymine (T), not Uracil (U). We must convert dUMP to dTMP.
The Reaction:
dUMP + Methylene-Tetrahydrofolate → dTMP.
The Enzyme:
Thymidylate Synthase
Cancer cells divide fast and need lots of DNA (lots of Thymine). We can kill cancer by stopping this enzyme.
| Enzyme | Activators (Go!) | Inhibitors (Stop!) |
|---|---|---|
| CPS-II (Step 1) | PRPP, ATP | UTP, CTP (The Products) |
| Ribonucleotide Reductase | Complex regulation to ensure a perfect balance of all 4 DNA blocks (dATP, dGTP, dCTP, dTTP). | |
Concept: "De Novo" synthesis is like cooking a meal from scratch (expensive). "Salvage" is like eating leftovers (cheap and efficient).
We take a free Base (Adenine, Guanine, etc.) and re-attach it to a sugar (PRPP).
Adenine + PRPP → AMP.
Deficiency: Causes kidney stones (2,8-Dihydroxyadenine stones).
This enzyme does double duty:
Cause: Total deficiency of HGPRT.
If HGPRT is missing, the body cannot recycle Purines.
This is less critical clinically, but still important.
What happens to old DNA and RNA? The body must break them down safely.
For Purines (A and G), this process is critical because the final waste product is Uric Acid, which can cause disease if it builds up.
The degradation involves three main phases:
AMP needs to be stripped down to Hypoxanthine.
AMP + H₂O → Adenosine + Pi
Enzyme: 5'-Nucleotidase.
(Alternate path in muscle: AMP Deaminase can turn AMP directly into IMP).
Adenosine + H₂O → Inosine + NH₃
Enzyme: Adenosine Deaminase (ADA)
Inosine + Pi → Hypoxanthine + Ribose-1-P
Enzyme: Purine Nucleoside Phosphorylase (PNP).
GMP is stripped down to Xanthine.
Both Hypoxanthine (from AMP) and Xanthine (from GMP) meet here. The goal is Oxidation.
The drug Allopurinol (used for Gout) works by inhibiting Xanthine Oxidase. This stops the production of Uric Acid.
Unlike Purines, Pyrimidine degradation is "clean." The products are water-soluble.
The final products are simple molecules that dissolve easily:
They share a pathway. Cytosine is converted to Uracil first.
Thymine (DNA only) has a methyl group, so its product is slightly different.
Dihydropyrimidine Dehydrogenase (DPD) is the rate-limiting enzyme for breaking down pyrimidines.
Patients with cancer are often given the drug 5-Fluorouracil (5-FU). This drug mimics Uracil.
The Danger: If a patient has a genetic DPD Deficiency, they cannot break down the drug. The drug builds up to toxic levels, causing death or severe side effects (neurotoxicity, bone marrow failure).
Note: Unlike Purines (Gout), there are no "accumulation diseases" for natural pyrimidines because they are water-soluble.
The body must balance these pools perfectly. Too little DNA means cells can't divide. Too much wastes energy.
This section explains the "Traffic Lights" (Regulation) and what happens when the traffic lights break (Disease).
We control the flow at 3 main checkpoints.
Enzyme: Glutamine:PRPP Amidotransferase
This enzyme makes ALL DNA building blocks (dATP, dGTP, dCTP, dTTP). Its regulation is complex.
What is it? High Uric Acid leads to sharp crystals depositing in joints (painful arthritis) and kidneys (stones).
X-Linked Recessive
Defect: Near total absence of HGPRT (Salvage Enzyme).
Adenosine Deaminase (ADA) Deficiency
Defect: Failure of UMP Synthase (OPRT + OMP Decarboxylase).
Cancer cells need nucleotides to grow. We use drugs to starve them.
Inhibits Dihydrofolate Reductase (DHFR). Prevents regeneration of THF (Folate). Stops Thymine and Purine synthesis.
"Suicide Inhibitor" of Thymidylate Synthase. Directly stops DNA from getting Thymine.
Inhibits Ribonucleotide Reductase. Stops conversion of RNA → DNA.
Inhibits De Novo Purine Synthesis (PRPP Amidotransferase).
To complete our study of nucleotides, we must look at a few specific drugs and environmental factors that affect these pathways.
This is a powerful immunosuppressant drug used to prevent **Graft Rejection** (e.g., after a kidney transplant).
These are antibiotics. They target bacteria by starving them of Nucleotides.
Bacteria must make their own Folic Acid (Folate) from scratch using a molecule called PABA (Para-aminobenzoic acid).
Sulfonamides look exactly like PABA (Structural Analogs). The bacteria try to use the drug instead of PABA, and their Folic Acid synthesis fails.
Humans cannot make Folic Acid. We must eat it in our diet. Therefore, Sulfa drugs kill bacteria but leave human purine synthesis alone.
Historically, Gout was often associated with "High Living" and alcohol. However, there is an environmental link.
We learned that Orotic Aciduria causes Anemia because the body cannot make Pyrimidines (DNA).
Feeding a diet rich in Uridine results in:
Test your knowledge with these 40 questions.
Question 1/40
Here are your results, .
Your Score
38/40
95%