In the format of the IUPAC name of the organic compound, the term ‘Root’ is used to represent:

the number of carbon atoms in the parent chain

The correct answer is option 3. the number of carbon atoms in the parent chain.

In the International Union of Pure and Applied Chemistry (IUPAC) nomenclature system for naming organic compounds, the term "root" refers to the main carbon chain or backbone of the molecule. This main chain is also known as the parent chain.

Here's an explanation of each option provided:

1. Functional groups that may be present in the compound:  Functional groups are specific arrangements of atoms within a molecule that confer particular chemical properties and reactivity. In IUPAC nomenclature, functional groups are indicated by suffixes or prefixes in the compound's name, not by the term "root."

2. The cyclic or acyclic nature of the given compound:  The cyclic or acyclic nature of a compound is typically indicated by prefixes such as "cyclo-" for cyclic compounds or by simply describing it as acyclic. The term "root" is not specifically used to indicate this aspect of the compound's structure.

3. The number of carbon atoms in the parent chain:  This is correct. The "root" in the IUPAC name represents the main carbon chain of the molecule, which contains the maximum number of carbon atoms. The parent chain is the longest continuous chain of carbon atoms in the molecule, and its length determines the base name of the compound.

4. The presence of side chains or substituent groups:  Substituent groups or side chains are additional groups attached to the main carbon chain. In IUPAC nomenclature, these substituents are indicated by prefixes or suffixes in the compound's name, such as alkyl groups (methyl, ethyl, etc.) or functional groups. The term "root" specifically refers to the main carbon chain itself, not to the substituent groups.

So, in summary, the term "root" in the IUPAC name of an organic compound represents the number of carbon atoms in the parent chain, determining the base name of the compound.