GENE REGULATION

The cell is the structural and functional unit of life. A single cell forms unicellular organisms like bacteria while a group of different cells forms multicellular organisms like animals, plants, humans, etc. A bacteria having a single cell is the complete life same as humans and plants which have billions of cells.

Life is life, it can be simple as seen in bacteria (unicellular bacteria) and it can be complex to understand like in humans. The functions and structure of cells are controlled by their nucleus. The nucleus has genes on which the information of life is present in the coded form. All types of life ( no matters it is a single cell-organism or multicellular organism) depend on the sum of these genes.

The genes can be divided into two categories:

Structural genes
Regulatory genes

Structural genes.

As the name shows, structural genes form the structure of cells. It encodes the amino acid sequences of proteins. These proteins can be enzymes and structural proteins but they never are regulatory proteins (i.e. controls the expression of a gene) because these proteins are formed by regulatory genes. Messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA) are encoded by structural genes. In short, it involves the formation of cellular structures.

Regulatory genes.

Regulatory genes control the expression of structural genes. It controls the amount of production of proteins by structural genes. It encodes miRNA (micro RNA) and siRNA (small interfering RNA or short interfering RNA or silencing RNA). It can be positive or negative in their actions and thus can be called positive regulators and negative regulators respectively. If it permits structural genes to form proteins then it is said to be a positive regulator while if it inhibits the production of proteins then it acts as a negative regulator.

Let’s understand the regulation of genes with a very simple example.

Gene regulation in prokaryotic cells.

Both structural and regulatory genes are involved in the process of regulation of genes. Let’s understand this with the help of E.coli cells. E.coli is a very simple prokaryotic cell. It is a heterotrophic organism so it can’t prepare its food. It usually depends on glucose for energy purposes but it can digest lactose as well (glucose + galactose = lactose).

in normal conditions, E.coli digests glucose because of its availability in the environment.
But when there is lactose in excess concentration in the environment then E.coli has to make some changes in its genes to digest lactose because the genes for the digestion of lactose is turn-off by E.coli cell for the sake to save cellular energy. This kind of gene regulation is commonly known as the Lac-operon of E.coli cells.
As we know that E.coli is a prokaryotic cell so it has a circular DNA. It has a polycistronic gene (a single mRNA can form multiple proteins).
In the case of E.coli, this polycistronic gene has three parts i.e. z-part, y-part, and a-part (these all are structural genes) which collectively form a mRNA.
An RNA polymerase binds with the promoter side and forms a mRNA.
After the translation of this mRNA, three types of proteins are formed:

z-part of gene forms B-galactosidase
y-part of gene forms permease
a-part of the gene forms trans-acetylase

B-galactosidase is involved in the breakdown of lactose.
Permease increased the permeability of lactose through the cell membrane.
The function of transacetylase is to acetylate nonmetabolizable galactosides and glucosides.
But in normal conditions, the gene that expresses this protein is inhibited by an inhibitor because there is no lactose in the environment for digestion and so no need of forming these proteins. However, the gene that is responsible for the digestion of glucose is working normally.
The expression of z-gene, y-gene, and a-genes is inhibited by i-gene (inhibitor gene).
This I-gene (with the help of RNA polymerase) produces an inhibitor that binds with the operator side of z,y, a- genes respectively.
In this way, negative gene regulation is occurred and inhibits structural gene expression.
But the expression of structural genes never be reduced or inhibited completely and a very small amount of B-galactosidase, permease, and transacetylase is continuously produced in the cell.
When there is a high concentration of lactose in the environment, a very small amount of lactose enters into the E.coli cell because of the presence of a small amount of permease in the cell.
The lactose that successfully enters into the cell changed into another form called alloo-lactose.
This allo-lactose removed the repressor or inhibitor that is bound on the operator side.
After the removal of the inhibitor, an excess amount of proteins like B-galactosidase, permease, and transacetylase started to produce in the cell because their structural genes are free now. In this way, a positive gene regulation takes place that helps in lactose digestion.

Gene regulation in eukaryotic cells.

Gene regulation in eukaryotic cells is a little bit more complicated and well-controlled than in prokaryotic cells. The formation of protein is divided into two processes which are transcription and translation. Transcription is the formation of mRNA from DNA molecules while translation is the formation of protein from the mRNA. The whole process is known as central dogma.

We can divide gene regulations in eukaryotes into different stages for easy understanding:

Genomic regulation
Transcription
RNA processing
Translation
Post-translational events

Genome regulation.

In eukaryotes, DNA molecules are wrapped around histone proteins. For the formation of mRNA, it is important to unwrap the DNA so that RNA polymerase can work better.
Methyl groups are responsible for the wrapping of DNA on histone protein.
If methyl groups are permanently attached to any part of histone protein then this side of DNA is permanently locked and thus no mRNA is formed from that part of DNA and as we know no protein is formed.
It is the reason that our different cells of the tissues are very specific in their functions.
Acetyle-groups are responsible for the unwrapping of DNA molecules from histone proteins. These groups are attached with histone protein and unwrap them.
In this way, a genome is regulated by methyl and acetyl groups.

Transcription.

Transcription is the formation of mRNA from DNA molecules. As we discussed that DNA is always wrapped around histone protein and acetylation of DNA helps to unwrap it on histone protein.
Eukaryotes have a monocistronic gene (which means one mRNA can encode one polypeptide and thus only one type of protein is formed by one gene).
Let’s understand the regulation of genes at the transcriptional level with the help of a glucose-insulin example in humans.

Glucose is the major source of energy for humans. But its concentration is maintained by storing it in cells in its inactive form glycogen.
Insulin is responsible for converting glucose into glycogen.
RNA polymerase binds at the promotor side of the gene which is responsible for insulin formation but a repressor is also present at the operator side which inhibits the formation of mRNA which is responsible for insulin production.
When glucose concentration is going high in the human body, then a factor is produced which we called the transcription factor.
This transcription factor removes the repressor from the operator side and allows RNA polymerase to form mRNA for insulin production.
In this way, mRNA is regulated by transcription factors. Because of this regulation, a protein is formed only when it needs it.
Only genes can form mRNA whose transcription factor removes the repressor from the operator side and in this way, a specific group of cells forms specific products like insulin produced by the pancreas in humans.

RNA processing.

After the mRNA is formed, it remains unfunctional until it is processed. RNA processing has three stages:

Caping
Tailing
Slicing

Caping.

Modified guanine is added at the 5’ end of primary mRNA. This 5’ end has phosphate groups where the caping of guanosine takes place. Methyl groups are also involved in the cap region which indicates the formation of proteins. The capping process of mRNA helps to protect it from degradation.

Tailing.

A poly adenine tail (about 200 adenine groups) is attached with primary mRNA at the 3’ end. This tailing process increases the stability of primary mRNA.

Slicing.

The primary mRNA has coding regions which we called exons and non-coding regions which are called introns. In the process of slicing, the non-coding regions (i.e. introns) are removed or sliced and coding regions of exons are obtained which is a functional mRNA and ready to form a protein.

Translation.

The translation is the process of formation of protein from mRNA.
The functional mRNA is targeted towards ribosomes where it forms proteins.
Transfer RNA (tRNA) and ribosomal RNA (rRNA) are involved in the formation of protein.
Mostly mRNA is moved towards the rough endoplasmic reticulum (RER) where it forms proteins and then this protein is moved towards the Golgi apparatus and after this, it moved towards desired cellular organelles.
The mRNA is regulated by initiation factors.
A mRNA is a single-stranded long structure. Initiation factors decide where the formation of proteins starts. It can bind any point of mRNA (middle, beginning, etc) and forms proteins.
The mRNA is also regulated by microRNA (miRNA).
if an mRNA is harmful to the cell or not required, then micro RNA forms a single-stranded mRNA into double-stranded RNA.
As initiation factors can bind on single-stranded RNA, so a double-stranded RNA (formed by micro RNA) is not useable and no protein is formed from this.

Post-translational events.

The translation process forms primary structures of protein which is also inactive to use. This protein is continuously formed and binds with other molecules of proteins by peptide bonds and this peptide bond helps to form different structures of proteins.
So primary structure can convert into secondary structure of protein and then secondary to tertiary structure of protein and so on. It forms the quaternary structure of the protein which is the most complex structure of protein.
Different structures of proteins performed different functions.
As proteins form complex structures by folding themselves with the long chain of polypeptides, we can regulate them by breaking peptide bonds between protein molecules.
As proteins are a group of amino acids that binds together with peptide bonds. So it is also regulated by adding other molecules like phosphorous, OH group, carboxylic group, or any other group to amino acids by covalent bonds. It will ultimately change the function of the protein.
As a cell has many organelles (about 12 organelles are present in a general cell) and protein is the need of every organelle. So it is also regulated which type of protein is going to which organelle. As different organelle performs different functions, so same proteins in different organelles can perform different functions.