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The atmosphere has a partial pressure of oxygen of 160mm Hg, but in the alveoli it is 105mm Hg. The partial pressure of carbon dioxide in the atmosphere is 0.3mm Hg, but 40mm Hg in the alveoli. How are these difference maintained, and what is the mechanism behind it?

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Many different factors contribute to this difference being maintained. These include long, thin airways, big lungs, and homeostatic mechanisms.

The alveolar air in the lungs is connected to the outside air by long, thin tubes (the trachea is about 11 cm long). Because of this, there is almost no diffusion between the outside air and the alveolar air. To fill our lungs with fresh atmospheric air and get rid of stale, alveolar air, we need to breathe.

Breathing creates pressure gradients between the alveoli and the atmosphere. During inhalation, fresh air from the atmosphere is "pulled" into the lungs. During exhalation, stale air from the alveoli is pushed out of the lungs. If we are not active, each breath pumps only a small amount of air in and out of the lungs. The average volume of a breath (inhalation or exhalation) is about 500 milliliters. 150 milliliters of air get "stuck" in the airways during inhalation and are exhaled into the atmosphere during the next exhalation. Likewise, 150 milliliters of air get "stuck" in the airways during exhalation and are inhaled into the alveoli during the next inhalation. Only 350 milliliters of fresh air are inhaled into the alveoli in each breath, and only 350 milliliters of stale air are exhaled into the atmosphere. Since the lungs are big (about 2.5 liters), pumping 350 milliliters of fresh air in and 350 milliliters of stale air out doesn't make much of a difference to the overall composition of the alveolar air.*

Homeostatic mechanisms in the body try to keep the partial pressure of carbon dioxide in the blood at about 5% of atmospheric pressure. If our carbon dioxide levels change and chemoreceptors detect the change, the respiratory center in the brain alters our breathing rate and depth to bring carbon dioxide levels back to normal. For example, we usually generate about 250 ml of carbon dioxide every minute, which corresponds to 17 ml every four seconds (the duration of a breath.) The homeostatic mechanisms make us breathe about 500 ml of air in every breath so that every exhalation contains 17 ml of carbon dioxide from 350 ml of alveolar air. This keeps the ratio at 5%. Homeostatic mechanisms also increase respiratory rate and volume during exercise.

*During exercise, however, the alveolar air composition changes rapidly due to large and fast breaths.

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There are two main reasons for the pO2 in the alveolar air being lower than the atmospheric pO2. First, the diffusion of CO2 from the blood lowers the alveolar pO2. Secondly, there is a lot of water vapor inside the lungs, and all this vapor lowers the alveolar pO2 as well.

This is the equation:

PaO2 = FiO2(Patm - PH2O) - PaCO2[FiO2 + (1-FiO2) / R] 

Source: https://en.wikipedia.org/wiki/Alveolar_gas_equation

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