Since all molecules occupy space and have specific shapes, it is important for students to understand the shapes. One rule in biology is that form meets function. To understand function, students need to understand the structure. Students can view small molecules and compare their structures. Students can look at one protein in different ways.
Many text books have very good content, both in text and in graphics.
However, some concepts are so difficult that students have a difficult time constructing mental models which put all the information into one integrated picture. To help students with difficult concepts, I have begun to create Molecular Movies which summarize well written text. These animations cannot replace the text but they help students who have read the material. This example shows how B cells discover the body has a bacterial infection and they must repsond by making antibodies. There are some methods that are easier to understand if students can see what is supposed to happen, rather than just reading about them.