Question 1

A high-field NMR instrument uses a _______________.

Accepted Answer

A)  superconducting cryomagnet cooled with liquid helium or nitrogen 
B)  radiofrequency pulse generator 
C)  probe 
D)  detector 
E)  all of the above 
A)  superconducting cryomagnet cooled with liquid helium or nitrogen 
B)  radiofrequency pulse generator 
C)  probe 
D)  detector 
E)  all of the above

Question 2

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

A)  heavy transitional metals 
B)  non-metals 
C)  metalloids 
D)  alkali metals 
A)  heavy transitional metals 
B)  non-metals 
C)  metalloids 
D)  alkali metals

Question 3

Look at the data presented in the image and choose which statements are true:
I. The data show a well-resolved x-ray structure, due to the low RMDS values and acceptable B and Rwork values.
II. The data show a poorly-solved x-ray structure due to the high RMDS values and out of range B and Rwork values.
III. The data were recorded at a good resolution, in the range 2.7 - 3.1 Å.
IV. The data show that the x-ray structure does not contain any solvent molecules.
V. The data show a poorly-solved x-ray structure due to the high number of atoms.

Accepted Answer

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

Question 4

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

A)  are cheaper 
B)  have a brighter color 
C)  contain heavy atoms 
D)  bind better 
E)  are soluble 
A)  are cheaper 
B)  have a brighter color 
C)  contain heavy atoms 
D)  bind better 
E)  are soluble

Question 5

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

Accepted Answer

A)  Crystallization 
B)  X-ray crystallography 
C)  NMR 
D)  light microscopy 
E)  Calorimetry 
A)  Crystallization 
B)  X-ray crystallography 
C)  NMR 
D)  light microscopy 
E)  Calorimetry

Question 6

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

Accepted Answer

A)  optical 
B)  electromagnetic 
C)  quartz 
D)  glass 
E)  transparent 
A)  optical 
B)  electromagnetic 
C)  quartz 
D)  glass 
E)  transparent

Question 7

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

secondary

Question 8

Biochemical research is usually done by large research groups. The members have a variety of responsibilities and contributions to the project. Read the section Giving credit where is due in this chapter. Choose the sentences which best describe a fair way of listing authors on the research paper published by a particular research group at a university.
I. The first author on the paper is the one who has done most of the work on the study and the principal investigator (lab director or professor) is the last author.
II. Group members who contributed to some sections of the paper are listed.
III. The animal technician will be added as an author to some of the papers published by the group.
IV. Students will be listed as authors even if they have not contributed to this particular research.
V. The order of listing the names of the authors is not important.

Accepted Answer

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

Question 9

NMR can be used for determining the 3D structure of proteins in solution. This allows for getting insight into how the protein structure ________________.

Accepted Answer

A)  changes when temperature changes 
B)  looks like in its biologically active form 
C)  changes when the ionic strength of the solution changes 
D)  accommodates the binding of ligands 
E)  all of the above 
A)  changes when temperature changes 
B)  looks like in its biologically active form 
C)  changes when the ionic strength of the solution changes 
D)  accommodates the binding of ligands 
E)  all of the above

Question 10

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

A)  I, II, and III 
B)  II, III, and IV 
C)  II and IV 
D)  III, IV and V 
E)  all of the above 
A)  I, II, and III 
B)  II, III, and IV 
C)  II and IV 
D)  III, IV and V 
E)  all of the above

Question 11

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

Accepted Answer

A)  using a cyclotron or particle accelerator 
B)  a xenon lamp 
C)  a radioactive source 
D)  all of the above 
E)  none of the above 
A)  using a cyclotron or particle accelerator 
B)  a xenon lamp 
C)  a radioactive source 
D)  all of the above 
E)  none of the above

Question 12

The ______________ equation is used in interpreting protein NMR data.

Accepted Answer

A)  Wetterhahn 
B)  Sanger 
C)  Djerassi 
D)  Karplus 
E)  Wüthrich 
A)  Wetterhahn 
B)  Sanger 
C)  Djerassi 
D)  Karplus 
E)  Wüthrich

Question 13

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

A)  eraser 
B)  table 
C)  chair 
D)  pencil 
E)  all of the above 
A)  eraser 
B)  table 
C)  chair 
D)  pencil 
E)  all of the above

Question 14

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

Accepted Answer

A)  cleaned; safety 
B)  bleached; contamination 
C)  dried; the use of high-energy electrons 
D)  soaked; impurities 
E)  sonicated; safety 
A)  cleaned; safety 
B)  bleached; contamination 
C)  dried; the use of high-energy electrons 
D)  soaked; impurities 
E)  sonicated; safety

Question 15

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

Accepted Answer

A)  power; color 
B)  intensity; brightness 
C)  resolution; wavelength 
D)  contrast; speed 
E)  intensity; power 
A)  power; color 
B)  intensity; brightness 
C)  resolution; wavelength 
D)  contrast; speed 
E)  intensity; power

Question 16

Due to the complexity of biological molecules, NMR spectrometers that are used for analysis of biological molecules require a static field of _______.

Accepted Answer

A)  60 MHz 
B)  100 MHz 
C)  at least 300 MHz 
D)  500 MHz 
E)  900 MHz 
A)  60 MHz 
B)  100 MHz 
C)  at least 300 MHz 
D)  500 MHz 
E)  900 MHz

Question 17

Statistical data on the experimental setup of an x-ray diffraction structure includes _________________.
I. total number of reflections recorded
II. number of atoms
III. types of heavy atoms used in phasing the crystal
IV. number of residues
V. shape and dimension of the unit cell

Accepted Answer

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

Question 18

The pharmaceutical industry uses F19-NMR to characterize novel drug compounds. This is possible only if those drugs ______.
I. are soluble
II. contain fluorine in their molecule
III. are easy to synthesize
IV. can ionize

Accepted Answer

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

Question 19

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

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

Question 20

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

Accepted Answer

A)  temperature 
B)  pH 
C)  concentration of polyethylene glycol 
D)  concentration of glycerol 
E)  all of the above 
A)  temperature 
B)  pH 
C)  concentration of polyethylene glycol 
D)  concentration of glycerol 
E)  all of the above

Exam 18: Determination of Macromolecular Structure

A high-field NMR instrument uses a _______________.

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)

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.

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

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

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 _____________.

NMR can be used for determining the 3D structure of proteins in solution. This allows for getting insight into how the protein structure ________________.

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

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

The ______________ equation is used in interpreting protein NMR data.

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?

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

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

Due to the complexity of biological molecules, NMR spectrometers that are used for analysis of biological molecules require a static field of _______.

Statistical data on the experimental setup of an x-ray diffraction structure includes _________________. I. total number of reflections recorded II. number of atoms III. types of heavy atoms used in phasing the crystal IV. number of residues V. shape and dimension of the unit cell

The pharmaceutical industry uses F19-NMR to characterize novel drug compounds. This is possible only if those drugs ______. I. are soluble II. contain fluorine in their molecule III. are easy to synthesize IV. can ionize

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

The Chemical Foundations of Biochemistry

Nucleic Acids

Proteins I

Proteins Iienzymes

Membranes and an Introduction to Signal Transduction

Carbohydrates I

The Common Catabolic Pathway

Carbohydrates II

Lipids I

Lipids II

Amine Metabolism

Metabolism Integration

Nucleotide Deoxynucleotide Metabolism

Dna Replication, Damage and Repair

Rna Synthesis

Protein

Control of Gene

Allosterism and Receptor-Ligand

Designer Proteins and Protein Folding

Biomolecule Purification

Bioinformatics and Omics

Signal

Protein Trafficking

Photosynthesis Nitrogen

Filters

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 _________.

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

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

The pharmaceutical industry uses F¹⁹-NMR to characterize novel drug compounds. This is possible only if those drugs ______. I. are soluble II. contain fluorine in their molecule III. are easy to synthesize IV. can ionize