Our respiratory system consists of trachea, bronchial tubes, etc. Which are covered with mucus and hair-like projections called cilia.

When we breathe, mucus helps us trap harmful substances like germs, dust, etc. Whereas cilia help us to expel these harmful substances out of our respiratory system.

However, when we smoke, we inhale thousands of chemicals. These chemicals damage or even paralyze the cilia. Causing them to lose their ability to expel harmful substances. So, these substances remain in our respiratory system. Hence, in order to remove these harmful substances, our body makes us cough.

Also note that, sometimes this cough gets worse in the morning. Why? Because during sleep. The cilia begin to repair themselves and start expelling the harmful substances.
Now, to remove all the harmful substances, our body starts coughing more in the morning.

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