MODULE 4: Chapter 5.3

Question 1

Who first modeled the structure of DNA using X-ray diffraction data?

Answer 1

James Watson and Francis Crick

They used data from Rosalind Franklin.

Question 2

In what year was the first protein molecular structure solved by X-ray crystallography?

Answer 2

1957

Question 3

Which protein’s low-resolution structure was reported by John Kendrew?

Answer 3

Myoglobin

Question 4

Who shared the 1962 Nobel Prize in Chemistry with John Kendrew?

Answer 4

Max Perutz

Question 5

What are the three primary methods for determining the molecular structure of proteins?

Answer 5

• X-ray crystallography
• Nuclear magnetic resonance (NMR) spectroscopy
• Cryo-electron microscopy

Question 6

What can insights from a protein’s structure help us understand?

Answer 6

• Normal cellular function
• Contribution of mutant proteins to disease
• Drug design to disrupt protein function

Question 7

What principle does X-ray crystallography rely on?

Answer 7

Diffraction of X-rays by a protein crystal

Question 8

What is formed from the measurements of scattered X-rays in X-ray crystallography?

Answer 8

An electron density map

Question 9

What is the significance of the electron density map in protein modeling?

Answer 9

It helps to build a model of the protein that matches the regions of electron density.

Question 10

What are the two most difficult steps in X-ray crystallography?

Answer 10

• Growing diffraction-quality crystals
• Determining the phases of the diffracted X-rays

Question 11

What is required for protein crystallization?

Answer 11

High concentrations of proteins

Question 12

What is a heavy atom derivative used for in X-ray crystallography?

Answer 12

To determine the phases of the diffracted X-rays

Question 13

What does the resolution of a protein structure indicate?

Answer 13

The level of detail in the electron density maps

Question 14

What style of protein modeling was developed by Jane Richardson?

Answer 14

Ribbon style

Question 15

What does NMR spectroscopy utilize to determine the structure of proteins?

Answer 15

Intrinsic magnetic properties of certain atoms

Question 16

What isotopes are most commonly used in NMR spectroscopy?

Answer 16

• 1H
• 15N
• 13C

Question 17

What is the limitation of protein size for NMR structure determination?

Answer 17

Proteins must be less than ∼100 kDa

Question 18

What type of data does NMR spectroscopy provide?

Answer 18

Relative locations of atoms

Question 19

What type of structures can NMR data result in?

Answer 19

A family of structures

Question 20

What was a significant advancement in cryo-electron microscopy recognized by the Nobel Prize?

Answer 20

Development of cryo-EM as a tool for biomolecular structure determination

Question 21

What is the advantage of cryo-electron microscopy over X-ray crystallography?

Answer 21

No need for crystals or high sample concentrations

Question 22

What is commonly done to biological samples before imaging in cryo-EM?

Answer 22

Rapidly frozen to produce vitreous ice

Question 23

What is a key feature of the images obtained from cryo-electron microscopy?

Answer 23

They are two-dimensional projections of three-dimensional particles

Question 24

What is the purpose of computational algorithms in cryo-EM?

Answer 24

To create three-dimensional images from two-dimensional projections

Question 25

What technique uses an electron beam focused by electromagnetic lenses to produce two-dimensional projections of three-dimensional objects?

Answer 25

Cryo-electron microscopy (cryo-EM) ## Footnote Cryo-EM is used to analyze large assemblies and multiple conformations.

Question 26

What is required to create high-resolution two-dimensional projections in cryo-electron microscopy?

Answer 26

Computational algorithms to identify similarly oriented objects ## Footnote These algorithms help in generating high-resolution images from randomly oriented samples.

Question 27

What are the primary types of protein samples used in X-ray crystallography and NMR spectroscopy?

Answer 27

X-ray crystallography uses ordered arrays of protein molecules in a crystal; NMR spectroscopy uses concentrated protein solutions ## Footnote Each method has its own limitations based on the type of sample used.

Question 28

What is a significant limitation of X-ray crystallography?

Answer 28

Difficulties in obtaining protein crystals for new proteins ## Footnote Conditions for crystallization are often unknown and challenging.

Question 29

What type of protein regions are especially difficult to analyze using X-ray crystallography?

Answer 29

Disordered regions or proteins in multiple conformations ## Footnote These cannot pack in an ordered, regular pattern needed for crystal formation.

Question 30

What is the theoretical size limitation of proteins studied by X-ray crystallography?

Answer 30

There is no theoretical size limitation ## Footnote This allows for the study of very large proteins.

Question 31

What concentration range is typically required for NMR spectroscopy?

Answer 31

Approximately 0.1 to 0.5 mM ## Footnote This concentration may not be achievable for all proteins.

Question 32

What is a major challenge in determining structures of large proteins using NMR spectroscopy?

Answer 32

Signal loss from larger proteins due to slower reorientation ## Footnote This limits full structure determinations to relatively small proteins and complexes.

Question 33

What advantage does NMR spectroscopy have over X-ray crystallography?

Answer 33

Ability to observe conformational changes or dynamic fluctuations ## Footnote This is particularly useful for studying proteins that undergo structural changes.

Question 34

Fill in the blank: A structure determination technique where the diffraction of X-rays from crystals of biomolecules is used to determine the locations of atoms in the structure is called _______.

Answer 34

X-ray crystallography

Question 35

Fill in the blank: A method of structure determination that detects nuclear spin properties of certain atoms (1H, 13C, 15N) to deduce their relative locations is known as _______.

Answer 35

NMR spectroscopy

Question 36

What is molecular replacement in the context of X-ray crystallography?

Answer 36

A procedure comparing the phases of diffracted X-rays with those from a similar protein of known structure ## Footnote This technique helps in solving the phase problem in crystallography.

Question 37

True or False: Cryo-electron microscopy can visualize biomolecular structures using focused beams of electrons.

Answer 37

True