Basically, email replies usually follow the normal pattern of writing professional emails . You may have to begin with an acknowledgement of the last email before replying the questions in the email. Each question should be answered on a separate paragraph. This will help you cover all questions and also help your recipient easily grasp your answers. Very importantly, learn to always acknowledge the emails you receive if you cannot reply within 24 hours of receiving them. You can store templates for acknowledging emails professionally in your “canned responses” if you are using Gmail.