Question 1

______________ uses crystallized biomolecules in order to improve the signal of the diffraction pattern.

Accepted Answer

X-ray crystallography uses crystallized biomolecules to enhance the signal of the diffraction pattern, allowing for the determination of the atomic structure of the molecules.

Question 2

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

The correct sequence for determining the 3D structure of a protein by x-ray crystallography starts with protein expression and purification (IV), followed by protein crystallization (III), then recording the diffraction pattern using a diffractometer (I), and finally data analysis (II).

Question 3

In order to achieve high purity and molecular uniformity a purified protein sample has to be treated with ______and ______. Then, this protein can be used to grow single crystals for x-ray crystallography.

Accepted Answer

The answer of In order to achieve high purity and...

Question 4

Membrane proteins are usually difficult to crystallize and require the addition of _________ during purification and crystallization.

Accepted Answer

Octyl glucoside is a detergent that helps solubilize membrane proteins, making them easier to purify and crystallize.

Question 5

Growing perfect single crystals of biological molecules is difficult and requires varying of the following parameters during crystallization:

Accepted Answer

Growing perfect single crystals of biological molecules is indeed challenging and requires the careful adjustment of various parameters, including temperature, pH, and the concentration of additives such as polyethylene glycol and glycerol. These factors influence the solubility and stability of the molecules, thereby affecting the crystallization process.

Question 6

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

The correct methods for achieving a high-quality single crystal of a protein involve slowly evaporating the solvent or slowly diffusing it through a microdialysis membrane. These techniques allow for a controlled environment where the protein can orderly aggregate and form crystals without denaturation or damage. Boiling would denature the protein, and centrifuging does not remove solvent in a way that is conducive to crystal formation.

Question 7

Choose all the methods that can be used to crystallize proteins and nucleic acids:
I. transformation
II. hanging drop crystallization
III. sitting drop crystallization
IV. diffraction
V. microdialysis

Accepted Answer

The answer of Choose all the methods that can be...

Question 8

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

High-quality protein crystals used in x-ray crystallography should indeed be as small as 0.1 mm, should have few impurities, and cannot have cracks to ensure the accuracy and quality of the diffraction data obtained. Needle-shaped crystals can also be used, but the statement about being oil-like is not accurate for crystals used in x-ray crystallography.

Question 9

Some x-ray diffractometers use x-rays of various wavelengths that can be generated by ____________.

Accepted Answer

The answer of Some x-ray diffractometers use x-rays of various...

Question 10

Monochromatic x-rays used in x-ray diffractometers are generated by ________________.

Accepted Answer

Monochromatic x-rays in x-ray diffractometers are generated by bombarding a metal surface with high-energy electrons, which causes the metal to emit x-rays of specific wavelengths.

Question 11

The advantages of using a synchrotron for x-ray crystallography are _____________________.

Accepted Answer

Synchrotrons produce very bright, high-intensity x-rays that are polychromatic. This allows for fast data collection and high-resolution data, making all of the options correct advantages of using a synchrotron for x-ray crystallography.

Question 12

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

X-ray diffraction data is primarily used to generate the electron density map of a protein or nucleic acid, which is then used to determine the 3D structure by locating the positions of atoms within the molecule.

Question 13

The ________________________ method is used to solve the _______________ in x-ray crystallography by comparing diffraction data before and after soaking the protein crystal in solutions made with heavy atoms, such as mercury, gold, or iodine.

Accepted Answer

The correct method is multiple isomorphous replacement (MIR), and it is used to solve the phase problem in x-ray crystallography. This technique involves soaking the protein crystal in heavy atom solutions to create differences in diffraction patterns, which can then be used to determine phase information.

Question 14

X-ray crystallography uses wavelengths of x-rays in the range of 0.1 - 1 Å which are similar to the ____.
I. resolution
II. size of atoms in the structure
III. structure
IV. lengths of covalent bonds
V. all of the above

Accepted Answer

X-ray crystallography utilizes wavelengths in the range of 0.1 - 1 Å, which are similar to the size of atoms and the lengths of covalent bonds in the structure, allowing for the detailed analysis of atomic arrangements.

Question 15

The root-mean-square deviation (RMSD) of bond lengths and bond angles of molecular structures are reported in PDB files to help researchers distinguish between higher and lower quality structures. Well defined structures have ____________________.

Accepted Answer

Well-defined structures typically have very small RMSD values for bond lengths (less than 0.01 Å) and bond angles around 1.0°, indicating minimal deviation from ideal geometry.

Question 16

High quality x-ray structures of proteins have ________________ I. a reliability factor, R, between 0.2 and 0.6. A lower value indicates a more reliable structure. II. a reliability factor, R, between 2 and 6. A higher value indicates a more reliable structure. III. a temperature factor B between 30 Å² and 60 Å². A lower value indicates greater confidence in the data. IV. a temperature factor B between 3 Å² and 6 Å². A higher value indicates greater confidence in the data

Accepted Answer

The reliability factor, R, for high-quality x-ray structures is typically between 0.2 and 0.6, with lower values indicating more reliable structures. The temperature factor B is usually between 30 Å² and 60 Å², with lower values indicating greater confidence in the data.

Question 17

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

The Ramachandran plot is used to visualize dihedral angles phi (φ) and psi (ψ) of amino acid residues in protein structure, helping to verify secondary structure elements.

Question 18

The files of x-ray structures available in the Protein Data Bank, PDB, list a B factor, known as a temperature factor. This factor describes ___________________.
I. how large a biomolecule is
II. how strong the interactions between the chains are
III. how much flexibility various loops have in the structure
IV. how much thermal motion there was in the crystal in various regions
V. linearity of the molecule

Accepted Answer

The B factor, or temperature factor, in x-ray structures indicates the flexibility and thermal motion in different regions of the crystal structure, corresponding to options III and IV.

Question 19

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

Accepted Answer

The Protein Data Bank (PDB) contains 3D structures of biomolecules determined by various methods, including X-ray crystallography, electron microscopy, NMR, and neutron scattering.

Question 20

X-rays interact with the electron clouds in the structures of proteins, while neutrons used in neutron scattering interact with the ___________________.

Accepted Answer

Neutrons interact with the nuclei of the atoms, which makes neutron scattering a complementary technique to X-ray scattering that interacts with electron clouds.

Quiz 18: Determination of Macromolecular Structure

______________ uses crystallized biomolecules in order to improve the signal of the diffraction pattern.

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

In order to achieve high purity and molecular uniformity a purified protein sample has to be treated with and . Then, this protein can be used to grow single crystals for x-ray crystallography.

Membrane proteins are usually difficult to crystallize and require the addition of _________ during purification and crystallization.

Growing perfect single crystals of biological molecules is difficult and requires varying of the following parameters during crystallization:

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

Choose all the methods that can be used to crystallize proteins and nucleic acids: I. transformation II. hanging drop crystallization III. sitting drop crystallization IV. diffraction V. microdialysis

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