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The atria fill with blood while the ventricles are pumping blood out. The atrioventricular valves slam closed when the ventricles begin contracting (this is the first heart sound) and the pulmonary and aortic valves open to allow blood flow.
When the atria are filled with blood, they contract while the ventricles relax and receive the blood from the atria. The pulmonary and aortic valves slam closed when the ventricles complete their contractions (this is the second heart sound) and the atrioventricular valves open to allow blood flow.