Metabolic Pathways

Metabolic Pathways

• Cellular Pathways

Gene Transcription Networks

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Metabolic Networks

  

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Cell Cycle Regulation Networks

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Signaling Networks 

All these networks are independent and interconvertible. The molecules formation from transcription will involve in metabolic processes that control cell cycle regulation through signaling networks.

Signaling Networks:
Mechanism of the signal. All organisms initiate functional processes through the signal. Just through an initiation signal, the whole process starts. For example:
Tumor necrosis factor (TNF) is a receptor protein present on the cell surface. Certain peripheral proteins transduce its signal and a cascade of reactions form.

Tumor Necrosis Factor:
It plays an important role in the initiation of tumors or cancer. An outside-in cascade generates ultimately an enzyme or transcription factor forms which on entering the nucleus starts generating such gene which was switched off. On switching on it in turn activates other genes by signaling thus a whole network forms.

Many receptors are involved in signaling.
For Example:
Epidermal Growth Factor Receptor (EGFR). When EGF binds then outside in a signal generates. Certain peripheral proteins are present. A kinase domain is present in the cytoplasmic region. It catalyzes the phosphorylation of other proteins and self as well. It modifies the protein.

Thus biochemical changes transfer from one molecule to other. When phosphorylation occurs then the conformational change that occurs is a signal for other protein.
In both cases either autophosphorylation or phosphorylation of other, protein will go from a non-conformational state to a conformational state i.e. from an inactive to an active state.
For example:
Opening of cleft ➡️ available for binding
Closing of cleft ➡️ no binding

Ultimately another kinase i.e.MAPK (mitogen-activated protein kinases) activates.
After activation, it can go inside the nucleus & phosphorylates various transcription factors in the nucleus. Modification induces diversity among them. Transcription factors will bind with promotor & the whole process will start. Molecules other than EGF can also bind with EGFR activation occur then accordingly initiation of the signal cascade will be different when different proteins will be phosphorylated.

Two aspects are important in signaling network:

1. Feedback:
Regulatory paints of signaling reaction. For Example, Insulin & Glucagon regulate each other, insulin is not allowed to be more, and glucagon is not allowed to be less.
Sometimes, the product itself can act as a regulatory event.
For example:
The follicle-stimulating hormone secreted by the pituitary is regulated by own amount. When the amount is more then it is repressed by the hypothalamus till the normal level is reached.
Similarly, the amount of O2 & CO2 in the blood is sensed & regulated. These are kept in balance, not allowed to be more. Even if oxygen is in more amount than required then it will be toxic. Likewise, if the water is n more amount then there will be hydro toxicity.
Feedback is of two types:
Positive feedback ➡️ upregulation ( To increase oxygen)
Negative feedback ➡️ downregulation (To decrease CO2)

2. Alternative Pathway
To switch over on the alternative pathway is another option i.e change from one mechanism to others. Example, to shift from anaerobic to the anaerobic pathway. If extra energy is required then the environment generates process through signals.

Cell Cycle Regulation Network:
Many metabolic processes are in the form of cycle e.g cell cycle etc. Many reactants come from different processes. Cyclic regulations are involved in defined points. there are a number of cell cycle regulations which are involved.
Go phase may remain for months & years when environment changes then it may change.

Simulation Of Cellular Metabolism:
E-cell simulation environment. (E cell-SE)
An object-oriented software suite for modeling, simulation, and analysis of biological cells.

• Regulatory networks can be simulated through it.

• Multiple algorithms are used process can be regulated by mincing on invivo process by simulating it.

By conversation of parameters (pH, temperature etc) for a single time interval, various processes can be viewed.

Outside In ➡️ When the stimulus is outside the cell and the response is within the cell.
Inside Out ➡️ Stimulating agent is within the cell and response is outside the cell.

In some receptors, the binding site is in an inactive state for binding with a ligand. In inside out from inside a molecule will bind with it for example, the selection is a receptor. Forcol ( a carboxylic acid) binds with it and the extracellular part goes through a specific change.

Intracellular signaling cascade ➡️ Initiation and process within the cell.

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