Question 1

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

With a 1-meter resolution, you can identify larger objects such as a whiteboard, table, and chair, but smaller items like pencils and erasers would not be discernible.

Question 2

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-cm resolution, which features of the room will you be able to see?

Accepted Answer

With a 1-cm resolution, you would be able to distinguish all listed objects (eraser, table, chair, pencil) since they are all larger than 1 cm and thus would be visible at this resolution.

Question 3

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

Determining the 3D structure of an enzyme allows researchers to identify the active site and substrate binding site, as these are related to the enzyme's spatial configuration. Molecular mass and isoelectric point are determined through other biochemical methods and are not directly related to the 3D structure.

Question 4

The 3D molecular structures of biological molecules can be determined using the following techniques. Select all that apply:
I. light microscopy
II. electron microscopy
III. NMR
IV. x-ray crystallography

Accepted Answer

II, III, and IV (electron microscopy, NMR, and x-ray crystallography) are techniques used to determine the 3D structures of biological molecules. Light microscopy does not have the resolution necessary for determining molecular structures at the atomic level.

Question 5

Which of the following statements is true regarding the resolution of x-ray structures of proteins?
I. A resolution of 5 Å is needed to observe $\alpha$-helices as rods in an x-ray structure.
II. A resolution of 0.5 Å is needed to observe $\beta$-sheets in an x-ray structure.
III. An x-ray structure of a protein at a resolution of 1.0 Å is considered to be high resolution.
IV. A resolution of 2.0 Å is needed to distinguish side chains of amino acids in an x-ray structure.
V. A resolution of 1.5 Å is needed to observe hydrogen atoms in an x-ray structure.

Accepted Answer

A resolution of 5 Å allows for the observation of secondary structures like ?-helices as rods. A resolution of 1.0 Å is indeed considered high resolution, allowing for detailed observation of the protein structure. At 2.0 Å resolution, side chains of amino acids can be distinguished, which is crucial for understanding the protein's function. Although a resolution of 1.5 Å is very high and can provide detailed information, it is generally not sufficient to reliably observe hydrogen atoms, which typically require even higher resolutions or specialized techniques. However, the statement regarding 0.5 Å for ?-sheets is incorrect, as ?-sheets, like ?-helices, can be observed at lower resolutions (around 3.5 to 5 Å). Therefore, the correct statements are I, III, and IV, making the choice D correct despite the slight inaccuracy in statement V's implication about hydrogen atoms.

Question 6

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

Electron microscopes have a high resolution and high sensitivity, making them susceptible to even minor vibrations that can disrupt the accuracy of the data being collected. Vibrations can cause the microscope's components to move slightly, leading to significant distortions in the images due to the high magnification levels.

Question 7

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

Accepted Answer

The answer of A convenient method for looking at tissues...

Question 8

Electron microscopy and x-ray crystallography have a higher resolution than light microscopy due to the ___________ of the radiation used in the instrument.

Accepted Answer

Electron microscopy and x-ray crystallography utilize radiation with shorter wavelengths and higher energy, allowing them to achieve higher resolution than light microscopy. Shorter wavelengths can resolve smaller structures because the resolution of any imaging system is roughly proportional to the wavelength of the radiation it uses. Higher energy associated with shorter wavelengths allows for deeper penetration and clearer imaging of molecular structures.

Question 9

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

The Protein Data Bank (PDB) archives 3D structures of biomolecules primarily determined by x-ray crystallography, NMR spectroscopy, and electron microscopy. These methods are well-suited for providing detailed molecular structures at atomic or near-atomic resolution, unlike light microscopy and scanning calorimetry, which do not provide detailed 3D molecular structures.

Question 10

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 11

To analyze a sample using an electron microscope, the sample must be _______ and observed in vacuum, due to _____________.

Accepted Answer

Electron microscopes use high-energy electrons for imaging, which requires the sample to be dried to prevent the electrons from scattering due to interactions with molecules in the air or moisture in the sample, ensuring clear images. Observing samples in a vacuum is necessary to allow the electrons to travel without interference from air molecules.

Question 12

Electron microscopy images do not provide enough detail at the level of _______. Thus, data collected by electron microscopy cannot be validated using a Ramachandran plot to analyze the structure in terms of ___________ and _____________.

Accepted Answer

The answer of Electron microscopy images do not provide enough...

Question 13

Electron microscopes use several ____________ lenses to focus and direct the beam of electrons.

Accepted Answer

Electron microscopes use electromagnetic lenses to focus and direct the beam of electrons because electromagnetic fields can control the path of charged particles, such as electrons, whereas optical, quartz, glass, and transparent lenses are used to manipulate light in optical microscopes.

Question 14

Stains used in electron microscopy such as phosphotungstenic acid and uranyl acetate are preferred over organic dyes because they ____________________, thus interact with the high-energy electrons more effectively.

Accepted Answer

Stains used in electron microscopy, like phosphotungstic acid and uranyl acetate, contain heavy atoms. These heavy atoms are effective in scattering electrons, which is crucial for creating contrast in electron microscopy images. Organic dyes, which might work well for light microscopy by absorbing specific wavelengths of light, do not have the same effect under electron beams. The heavy atoms in these stains interact more effectively with the high-energy electrons, making them preferable for electron microscopy.

Question 15

The _____________ of a light microscope is 0.22 µm. This is due to the ____________ of light in the visible spectrum.

Accepted Answer

The resolution of a light microscope is limited by the wavelength of light in the visible spectrum, which determines the smallest detail that can be distinguished.

Question 16

Contrast is ________________.
I. not important in imaging techniques
II. the ability of an object to stand out from its background
III. important in numerous imaging techniques, such as light microscopy and electron microscopy
IV. not used in facial recognition techniques

Accepted Answer

Contrast is crucial because it determines the ability of an object to stand out from its background, which is essential in various imaging techniques, including light microscopy and electron microscopy. It is also used in facial recognition techniques, making options I and IV incorrect.

Question 17

______________ is used to determine molecular structures using flash frozen samples and high-energy electrons.

Accepted Answer

Cryogenic electron microscopy (cryo-EM) is a technique that involves flash freezing samples and then imaging them with high-energy electrons to determine their molecular structures.

Question 18

Contrast agents used in electron microscopy are compounds of ____________________ that either bind to specific sites on the biomolecules or simply surround the biomolecules. (Note: choose all that apply)

Accepted Answer

Heavy transitional metals are used as contrast agents in electron microscopy because they have high atomic numbers that scatter electrons effectively, enhancing image contrast.

Question 19

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

Cryo-EM advancements allow for detailed structural analysis of large biomolecular assemblies, enabling insights into protein-ligand interactions and multimeric protein assemblies.

Question 20

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

The developments in modern molecular biology and biochemistry techniques, including site-directed mutagenesis, have enabled the expression of proteins in bacteria, the design of engineered mutations in scaffold proteins, the design of enzymes, and the use of microdialysis techniques. These advancements collectively contribute to the significant increase in structural data on biomolecules.

Quiz 18: Determination of Macromolecular Structure

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

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-cm resolution, which features of the room will you be able to see?

The 3D molecular structures of biological molecules can be determined using the following techniques. Select all that apply: I. light microscopy II. electron microscopy III. NMR IV. x-ray crystallography

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

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

Electron microscopy and x-ray crystallography have a higher resolution than light microscopy due to the ___________ of the radiation used in the instrument.

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

To analyze a sample using an electron microscope, the sample must be _ and observed in vacuum, due to _______.

Electron microscopy images do not provide enough detail at the level of _. Thus, data collected by electron microscopy cannot be validated using a Ramachandran plot to analyze the structure in terms of _ and _________.

Electron microscopes use several ____________ lenses to focus and direct the beam of electrons.

Stains used in electron microscopy such as phosphotungstenic acid and uranyl acetate are preferred over organic dyes because they ____________________, thus interact with the high-energy electrons more effectively.

The _ of a light microscope is 0.22 µm. This is due to the of light in the visible spectrum.

Contrast is ________________. I. not important in imaging techniques II. the ability of an object to stand out from its background III. important in numerous imaging techniques, such as light microscopy and electron microscopy IV. not used in facial recognition techniques

______________ is used to determine molecular structures using flash frozen samples and high-energy electrons.

Contrast agents used in electron microscopy are compounds of ____________________ that either bind to specific sites on the biomolecules or simply surround the biomolecules. (Note: choose all that apply)

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 _____________________.