General characteristics and components
The term originates from the Latin word nucleus, which translates to "core" or "nucleus". This is no coincidence, as these macromolecules were first discovered specifically within cell nuclei. Polynucleotides are huge linear biopolymers consisting of repeating units—mononucleotides.
Each nucleotide has a strictly defined chemical structure and always consists of three key components:
- Nitrogenous base — a cyclic structure (a purine or pyrimidine derivative).
- Sugar (pentose) — a carbohydrate with five carbon atoms.
- Phosphate group — a phosphoric acid residue.
In biochemistry, it is important to distinguish between two similar terms. If you combine only the cyclic nitrogenous base and the pentose, you get a molecule called a nucleoside. As soon as a phosphate group is attached to this structure, the molecule turns into a full-fledged nucleotide.
Nitrogenous bases
Nitrogenous bases are heterocyclic compounds that are divided into two chemical groups depending on their structure:
- Purine bases (purines). Their molecular skeleton consists of two fused rings: a six-membered and a five-membered one. These include adenine (contains an $NH_2$ group) and guanine (contains $=O$ and $NH_2$ groups).
- Pyrimidinic bases (pyrimidines). Their structure is more compact and formed by just a single six-membered ring. This group includes cytosine, uracil, and thymine.
Important distinction: uracil is found exclusively in RNA. In DNA molecules, it is replaced by thymine, which chemically is a methylated uracil (having an additional $-CH_3$ methyl group).
Nomenclature of main components:
| Nitrogenous base | Nucleoside | Nucleotide | Code |
|---|---|---|---|
| Adenine | Adenosine | Adenosine monophosphate (AMP) | A |
| Guanine | Guanosine | Guanosine monophosphate (GMP) | G |
| Cytosine | Cytidine | Cytidine monophosphate (CMP) | C |
| Uracil | Uridine | Uridine monophosphate (UMP) | U |
| Thymine | Thymidine | Thymidine monophosphate (TMP) | T |
Pentoses and phosphate group
The sugar (pentose) acts as a linking element and forms the solid backbone of the nucleic acid. There are two variants of this carbohydrate:
- Ribose — found in RNA. Its distinguishing feature is the presence of a hydroxyl group ($-OH$) at the second carbon atom ($2'$) of the sugar ring.
- Deoxyribose — found in DNA. As the prefix "deoxy-" implies, the second carbon atom ($2'$) lacks an oxygen atom.
The phosphoric acid residue is necessary to unite individual monomers into a long polymer chain. Depending on the number of attached phosphate groups, nucleotides can be classified as monophosphates, diphosphates, and triphosphates.
Structure of the polynucleotide chain
Linear polynucleotides form a chain whose backbone consists of strictly alternating sugar and phosphate residues. The units are stitched together via phosphodiester bonds.
The chemical mechanism of this connection is as follows: the phosphate group attached to the $5'$ carbon atom of one pentose ring binds to the $3'$ carbon atom of the next pentose molecule.
Due to this type of bonding, the polynucleotide chain has a pronounced directionality (polarity):
- At the $5'$ end of the macromolecule, there is a free phosphate group.
- At the $3'$ end, a free $3'$ hydroxyl group remains.
In molecular biology, there is a strict rule: any nucleic acid sequence is conventionally read and written exclusively in the $5'$ to $3'$ direction ($5' \rightarrow 3'$).
Briefly: answers to topical questions
What biological functions do free mononucleotides perform in the cell?
Free nucleotides are associated with the following cellular roles by source:
- Deoxyribonucleoside triphosphates (dATP, dGTP, dTTP, dCTP) are substrates for DNA polymerase; DNA polymerase links nucleotides together and elongates the polynucleotide chain in the 5' → 3' direction.
- ATP is used by DNA ligase to seal Okazaki fragments into a single strand with the formation of a phosphodiester bond.
- Free nucleotides are part of the nucleoplasm; the nucleoplasm serves as the medium for nuclear metabolism and ensures the normal functioning of genetic material.
- Nucleotides are transported in the hyaloplasm as part of its transport function.
Which enzymes catalyze the formation and cleavage of phosphodiester bonds between nucleotides?
The processes of formation and cleavage of phosphodiester bonds are catalyzed by ligases, topoisomerases, and various nucleases.
- DNA ligase — catalyzes the formation of a phosphodiester bond when joining DNA fragments.
- DNA topoisomerase — temporarily introduces single-strand breaks in phosphodiester bonds to relieve DNA torsional stress, and then reseals them.
- UV endonuclease — makes incisions in the DNA strand to remove pyrimidine dimers during repair.
- Endonuclease ($Ca^{2+}, Mg^{2+}$-dependent) — cleaves DNA at linker sites during apoptosis.
- RNase — degrades the initial viral RNA strand.
How not to confuse purines and pyrimidines? The lengths of their names are inversely proportional to the sizes of their molecules. «Purine» is a short word, but the molecule is large (two rings at once). «Pyrimidine» is a long word, but the molecule is small (only one ring). And thymine is easily remembered as «methylated uracil».
Class and exam questions
How does a nucleoside differ from a nucleotide?
A nucleoside is a two-component molecule consisting solely of a nitrogenous base and a sugar. If a phosphoric acid residue is covalently attached to it, it becomes a nucleotide.
What is the main structural difference between pentoses in DNA and RNA?
The difference lies in the second carbon atom ($2'$) of the sugar ring. Ribose (in RNA) has a hydroxyl group ($-OH$) there, whereas deoxyribose (in DNA) lacks an oxygen atom.
How to determine the direction of a polynucleotide chain?
The direction is determined by the free chemical groups at the ends of the polymer. The $5'$ end always features a free phosphate group, and the $3'$ end features a hydroxyl group. The chain is written from the $5'$ to the $3'$ end.
What else to study on this topic
- Nomenclature and letter codes of mononucleotides (AMP, GMP, etc.)
- Chemical differences in the structure of adenine and guanine
- Detailed mechanism of phosphodiester bond formation
- Classification of nucleotides by the number of phosphate groups (mono-, di-, and triphosphates)
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