Penguins have lungs as respiratory organs like us. They are able to live on land and at sea. Consequently, this means that penguins have to breach while they are swimming. For example, fish do not need to breach because they have gills, so they are not dependent on air. They take in water in their mouth and oxygen is filtered out of the water by their gills. Penguins breath in air through their mouth and nostrils, then the air gets through the air tube to the lungs. There the gas exchange takes place.
In the lung, oxygen is given from the inhaled air to the blood. The red blood cells transport this oxygen to the heart firstly and then it is pumped through the whole body. The oxygen is given to cells in organs so that they can use it for energy production. Carbon dioxide is produced by this reactions and is transported back to the heart by the blood. From there the blood with high carbon dioxide content flows back to the lungs where the carbon dioxide can get outside the body with exhaled air.
Tierphysiologie by Roger Eckert, 4th Edition (German book)