[28] Structural Biology and X-ray Crystallography

Question 1

What is Structural Biology?

Answer 1

The branch of molecular biology, biochemistry, and biophysics that deals with the molecular structure of biological macromolecules.

Question 2

What does Structural Biology study?

Answer 2

The structure and function of proteins, nucleic acids, and their complexes.

Question 3

What is the purpose of studying structures in Structural Biology?

Answer 3

Understanding the structure can often lead to insights on how the molecule functions.

Question 4

What is X-ray Crystallography?

Answer 4

A tool used for identifying the atomic and molecular structure of a crystal.

Question 5

How does X-ray Crystallography work?

Answer 5

It employs X-rays to create a diffraction pattern, which can be mathematically transformed to produce a 3D electron density map.

Question 6

What can be derived from the electron density map in X-ray Crystallography?

Answer 6

The mean positions of the atoms in the crystal can be determined, along with chemical bonds, their disorder, and other information.

Question 7

How has X-ray Crystallography contributed to Structural Biology?

Answer 7

It has determined the structure of many biological molecules, including vitamins, drugs, proteins and nucleic acids such as DNA.

Question 8

Why is it necessary to create a crystal for X-ray Crystallography?

Answer 8

Crystallization of the molecule is necessary to arrange it into a repeating pattern, which allows for the generation of a clear, interpretable diffraction pattern.

Question 9

What is the relationship between Structural Biology and drug design?

Answer 9

Structural knowledge of biological molecules is essential in understanding how drugs interact with these molecules, aiding in the design of more effective drugs.

Question 10

What are other methods used in Structural Biology besides X-ray Crystallography?

Answer 10

• Nuclear Magnetic Resonance (NMR) Spectroscopy
• Electron Microscopy

Question 11

What is the role of computer models in Structural Biology?

Answer 11

They can help predict molecular structures and to design new molecules for use as drugs.

Question 12

What are the challenges of X-ray Crystallography?

Answer 12

• Difficulty in obtaining good quality crystals
• The size of the molecules being studied
• Dynamic nature of biological molecules

Question 13

How are crystals prepared for X-ray Crystallography?

Answer 13

• Purification of the molecule
• Slow precipitation to encourage crystal growth

Question 14

How is data collected in X-ray Crystallography?

Answer 14

An X-ray beam is directed at a crystal, and the resulting diffraction pattern is captured on film or a detector.

Question 15

How does a protein’s structure impact its function?

Answer 15

The 3D shape of a protein determines its function, and alterations to the structure can change or inhibit this function.

Question 16

What is a “unit cell” in X-ray Crystallography?

Answer 16

The smallest repeated volume in the crystal lattice that shows the highest symmetry.

Question 17

What is “phase problem” in X-ray Crystallography?

Answer 17

The inability to directly measure the phase of the diffracted waves. Methods to solve the phase problem include multiple isomorphous replacement and molecular replacement.

Question 18

Why is Structural Biology important in the field of genetics?

Answer 18

It helps in understanding the physical basis for the effects of genetic mutations.

Question 19

How are the results of X-ray Crystallography validated?

Answer 19

By checking the quality of the crystallographic model against the diffraction data and other standards.

Question 20

What is a “Fourier transform” in the context of X-ray Crystallography?

Answer 20

A mathematical method used to transform the X-ray diffraction pattern into an electron density map.