The Japanese are a very high context culture. When they speak their words are paid careful attention to because they are important. They use many nonverbal signs to communicate with each other. To an outsider these nonverbal cues might seem confusing or even go unnoticed, but to a member of Japanese society they hold a deeper meaning.
In Japan, people bow as a sign of respect. One should bow to their elders, people of status, and anyone else they regard highly. When one bows to another the other person always bows in return as a sign of their gratitude and to return their respect.
When a Japanese student has a question it is expected that they raise their hand in class. In the classroom a student may raise their hand to ask a clarifying question, but not to give their own opinion. Classes are held in a lecture format and never include class discussion.