Protein 3D Model

1. Which level of protein structure is described by the 3-dimensional folding of a polypeptide chain into a stable shape (for example, α-helices and β-sheets arranged and folded)?

A. Primary B. Secondary C. Tertiary D. Quaternary

2. In a ribbon model representation of a protein, what does the “ribbon” typically show?

A. The side-chain atoms only B. The backbone path of the polypeptide and major folding features C. Only the surface of the protein accessible to solvent D. The DNA or RNA bound to the protein

3. A “surface” model of a protein structure aims to show:

A. Just the amino acid sequence B. The internal voids and cavities only C. The external contour and how the protein might interact with other molecules D. Only the α-helix and β-sheet regions

4. Which of the following is not a method typically used to determine a protein’s 3-D structure experimentally?

A. X-ray crystallography B. Nuclear Magnetic Resonance (NMR) spectroscopy C. Cryo-electron microscopy D. Gel electrophoresis

5. The number of amino acids and the sequence of amino acids in a protein refers to its:

A. Secondary structure B. Tertiary structure C. Primary structure D. Quaternary structure

6. When two or more polypeptide chains (subunits) come together to make a functional protein complex, this describes:

A. Primary structure B. Secondary structure C. Tertiary structure D. Quaternary structure

7. Why is 3-D modelling of proteins (via computational or printing methods) valuable in biology or teaching?

A. It makes proteins heavier so they are easier to work with in the lab B. It helps visualise how the protein folds and might interact with other molecules C. It changes the amino acid sequence to a more stable one D. It removes the need to understand chemical bonds

8. Which representation would best highlight pockets or grooves on a protein’s surface (potential binding sites)?

A. Wire-frame only showing backbone B. Ribbon model showing only helices and sheets C. Surface / space-filling model showing external contour D. Sequence list of amino acids

9. If a protein’s tertiary structure is mis-folded, what is a possible consequence for a cell?

A. Nothing happens—the function remains unchanged B. The amino acid sequence becomes mutated automatically C. The protein may become non-functional or even harmful D. The protein will always fold correctly eventually

10. In 3-D models of proteins printed for teaching, designers often choose between “ribbon” and “surface” models. What is one advantage of the ribbon model for students?

A. It shows every single atom making the protein B. It shows the backbone folding path clearly (helices, sheets, turns) C. It shows the external texture of the protein exactly D. It shows solvent molecules and ions bound

11. Which of the following is a good reason to use computational modelling (in silico) of a protein’s 3-D structure rather than only relying on experimental methods?

A. Experimental methods always give wrong results B. Computation is faster and can predict folding for proteins not yet resolved experimentally C. Computational models never need validation D. Experimental methods are illegal in many countries

12. When viewing a 3-D protein structure in a software viewer, the “PDB code” refers to:

A. The code segment that binds DNA B. The identifier for a protein structure in the Protein Data Bank C. The name of the software used D. The temperature at which the protein was solved

13. Which amino acid property is most directly responsible for driving hydrophobic collapse in protein folding (one of the key drivers for 3-D shape)?

A. Positive charge B. Negative charge C. Lack of charge and non-polarity (hydrophobic) D. Presence of sulfur

14. A student prints a 3-D model that shows different colours for each subunit of a tetrameric protein. Why might this be pedagogically useful?

A. To make the model prettier with more colours B. To help visualise how the subunits fit together and where interfaces are C. To hide the fact that it has four subunits D. To show only the amino acid sequence

15. Which statement is true about the relationship between structure and function for proteins?

A. The function of a protein depends only on its amino acid sequence, not its shape B. The 3-D shape of a protein has no bearing on its ability to bind other molecules C. The specific fold and surface features of a protein enable its function (e.g., binding, catalysis) D. Proteins always work the same way regardless of their shape

Protein 3D Structure Viewer & Quiz

1. Explore the Protein 3D Model

2. Protein 3D Structure – Multiple Choice Questions