Question 1

During multidimensional NMR the sample is pulsed with a radio-frequency at different angles, which leads to _________. Choose all that apply.
I. different relaxation times
II. heating of the sample
III. identification of nuclei which are within three bonds of each other in the molecule
IV. identification of nuclei which are spatially in close-proximity in the folded protein
V. identification of side chains

Accepted Answer

A)  I, II and III 
B)  II, III and V 
C)  II, III and IV 
D)  I, III and IV 
E)  II and V

Question 2

Developments of modern molecular biology and biochemistry techniques such as site-directed mutagenesis have led to an explosion of new structural data collected on a large variety of biomolecules, due to _____________________.

Accepted Answer

A)  expression of proteins in bacteria 
B)  design of engineered mutations in scaffold proteins 
C)  design of enzymes 
D)  microdialysis techniques 
E)  all of the above

Question 3

Neutrons interact stronger with _____________ atoms than x-rays.

Accepted Answer

The answer of Neutrons interact stronger with _____________ atoms than...

Question 4

The 3D structures of biomolecules are available in the Protein Data Bank, PDB. They were determined by using ______.

Accepted Answer

A)  x-ray crystallography 
B)  electron microscopy 
C)  NMR 
D)  neutron scattering 
E)  all of the above

Question 5

Which statement is true about nuclear magnetic resonance, NMR?

Accepted Answer

A)  NMR is used in organic chemistry to determine the structure of organic molecules. 
B)  NMR is used in biochemistry to determine the structure of biomolecules in solution. 
C)  NMR is used in a clinical setting as a diagnostic tool, called MRI. 
D)  NMR is a non-destructive analytical technique 
E)  all of the above

Question 6

Determining the 3D molecular structure of an enzyme allows researchers to predict several structural features of the enzyme. Select all features that can be investigated, once the 3D structure of an enzyme is available:
I. active site
II. substrate binding site
III. molecular mass
IV. isoelectric point

Accepted Answer

A)  I 
B)  II 
C)  I and II 
D)  III and IV 
E)  All of the above

Question 7

Advances in electron microscopy and computer technology make it possible to improve the resolution of cryo-EM, such that large biomolecular assemblies can be structurally analyzed, providing information about ______.
I. protein - ligand interactions
II. multimeric protein assemblies
III. degradation mechanisms
IV. excessive interactions
V. weak associations

Accepted Answer

A)  I and II 
B)  II and III 
C)  I and IV 
D)  III, IV and V 
E)  II and V

Question 8

One-dimensional NMR spectra are analyzed based on the _____________.

Accepted Answer

A)  number of peaks 
B)  position of the peaks relative to a standard 
C)  splitting of the peaks 
D)  number of equivalent nuclei in each peak, calculated by integrating the area under the peak 
E)  all of the above

Question 9

To achieve a high-quality single crystal of a protein, the solvent needs to be removed by _________.
I. boiling it off
II. slowly evaporating it
III. slowly diffusing it through a microdialysis membrane
IV. centrifuging it

Accepted Answer

A)  I and II 
B)  II and III 
C)  I, III, and IV 
D)  II and IV 
E)  none of the above

Question 10

The resolution of an imaging technique must be matched to the size of the objects that are to be observed. If you were to map your classroom with a 1-meter (roughly 3.3 feet) resolution, which features of the room will you be able to see?
I. white board
II. table
III. chair
IV. pencil
V. eraser

Accepted Answer

A)  I 
B)  II 
C)  III 
D)  I, II, and III 
E)  IV and V

Question 11

A major difference between light microscopy and electron microscopy lies in the ______of light used and ________ of the two methods.

Accepted Answer

The answer of A major difference between light microscopy and...

Question 12

The following nuclei are all spin active and are used in NMR experiments. The ones that have a ___________ abundance are ___(list all)_______ and they are more useful in biochemical experiments.

Accepted Answer

The answer of The following nuclei are all spin active...

Question 13

High-quality protein crystals used in x-ray crystallography ____________.
I. can be as small as 0.1 mm
II. should have few impurities
III. cannot have cracks
IV. can be needle-shaped
V. can be oil-like

Accepted Answer

A)  I and II 
B)  I, II and III 
C)  I, III, and IV 
D)  II, III and V 
E)  III, IV, and V

Question 14

Order the steps that are needed to determine the 3D structure of a protein by x-ray crystallography.
I. diffraction pattern recorded using a diffractometer
II. data analysis
III. protein crystallization
IV. protein expression and purification

Accepted Answer

A)  I, II, III, IV 
B)  IV, III, I, II 
C)  II, I, IV, III 
D)  III, I, II, IV 
E)  IV, I, II, III

Question 15

The phi and psi bond angles in solved x-ray structures of proteins are mapped on a _______________ plot to verify that the secondary structure elements fall in the predicted areas.

Accepted Answer

A)  protein 
B)  Southern 
C)  Scatchard 
D)  Ramachandran 
E)  Hill

Question 16

The Protein Data Bank, PDB, is an international database of 3D molecular structures of biomolecules obtained by using _______________.
I. x-ray crystallography
II. light microscopy
III. scanning calorimetry
IV. NMR
V. electron microscopy

Accepted Answer

A)  I, II, and III 
B)  I, III, and V 
C)  III, IV and V 
D)  II, III, and V 
E)  I, IV and V

Question 17

A convenient method for looking at tissues and cells to observe the organelles is _________.

Accepted Answer

A)  x-ray crystallography 
B)  chromatography 
C)  light microscopy 
D)  electron microscopy 
E)  none of the above

Question 18

X-ray diffraction data is used to generate the ___________ of the protein that can be used to build the 3D structure of the protein or nucleic acid.

Accepted Answer

A)  map of the atoms 
B)  distribution of atoms 
C)  electron density map 
D)  grid of the bonds 
E)  none of the above

Question 19

The difficulty in using x-ray crystallography to determine the 3D structure of a protein relies in __________.
I. solving the diffraction data
II. transferring data
III. growing single crystals
IV. solving the phase problem by multiple isomorphous replacement
V. stabilizing the crystal

Accepted Answer

A)  I and II 
B)  I and III 
C)  II, III, and V 
D)  III and IV 
E)  I, III and V

Question 20

Electron microscopes are usually installed in a vibration-proof room. Even small vibrations such as a truck passing outside can make acquiring data difficult. This is due to ____________.
I. interference
II. high resolution of the instrument
III. high sensitivity of the instrument
IV. temperature

Accepted Answer

A)  I and II 
B)  II and III 
C)  III and IV 
D)  I and IV 
E)  All of the above

Exam 18: Determination of Macromolecular Structure

Developments of modern molecular biology and biochemistry techniques such as site-directed mutagenesis have led to an explosion of new structural data collected on a large variety of biomolecules, due to _____________________.

Neutrons interact stronger with _____________ atoms than x-rays.

The 3D structures of biomolecules are available in the Protein Data Bank, PDB. They were determined by using ______.

Which statement is true about nuclear magnetic resonance, NMR?

One-dimensional NMR spectra are analyzed based on the _____________.

To achieve a high-quality single crystal of a protein, the solvent needs to be removed by _________. I. boiling it off II. slowly evaporating it III. slowly diffusing it through a microdialysis membrane IV. centrifuging it

The resolution of an imaging technique must be matched to the size of the objects that are to be observed. If you were to map your classroom with a 1-meter (roughly 3.3 feet) resolution, which features of the room will you be able to see? I. white board II. table III. chair IV. pencil V. eraser

A major difference between light microscopy and electron microscopy lies in the of light used and __ of the two methods.

The following nuclei are all spin active and are used in NMR experiments. The ones that have a _________ abundance are _(list all)_______ and they are more useful in biochemical experiments.

High-quality protein crystals used in x-ray crystallography ____________. I. can be as small as 0.1 mm II. should have few impurities III. cannot have cracks IV. can be needle-shaped V. can be oil-like

Order the steps that are needed to determine the 3D structure of a protein by x-ray crystallography. I. diffraction pattern recorded using a diffractometer II. data analysis III. protein crystallization IV. protein expression and purification

The phi and psi bond angles in solved x-ray structures of proteins are mapped on a _______________ plot to verify that the secondary structure elements fall in the predicted areas.

The Protein Data Bank, PDB, is an international database of 3D molecular structures of biomolecules obtained by using _______________. I. x-ray crystallography II. light microscopy III. scanning calorimetry IV. NMR V. electron microscopy

A convenient method for looking at tissues and cells to observe the organelles is _________.

X-ray diffraction data is used to generate the ___________ of the protein that can be used to build the 3D structure of the protein or nucleic acid.

The difficulty in using x-ray crystallography to determine the 3D structure of a protein relies in __________. I. solving the diffraction data II. transferring data III. growing single crystals IV. solving the phase problem by multiple isomorphous replacement V. stabilizing the crystal

Electron microscopes are usually installed in a vibration-proof room. Even small vibrations such as a truck passing outside can make acquiring data difficult. This is due to ____________. I. interference II. high resolution of the instrument III. high sensitivity of the instrument IV. temperature