Exam 18: Determination of Macromolecular Structure

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

NMR structures in the PDB do not list the reliability factor, R, and the temperature factor, B, as is customary for x-ray structures. This is due to the fact that _____________________. I. NMR structures have a lower reliability II. temperature does not affect NMR structures III. NMR does not use diffraction data and electron density maps IV. NMR uses chemical shift correlations

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

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

The result of an NMR experiment is a __________. Often tetramethylsilane (TMS) is used as a ___________ peak in an H-NMR experiment.

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

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

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.

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

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.

Due to the complexity of biomolecules, multidimensional NMR techniques, such as _________ are needed to determine their 3D structure. Choose all that apply. I. correlation spectroscopy (COSY) II. electron energy loss spectroscopy (EELS) III. total correlation spectroscopy (TOCSY) IV. nuclear Overhauser effect spectroscopy (NOESY) V. total electron yield (TEY)

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

The chemical shift, $\delta$ , is independent of the NMR instrument used, since it is defined as a ratio of frequencies. Choose all statements that are true regarding the chemical shift, $\delta$ . I. The chemical shift, $\delta$ , is a characteristic of the electronic environment that the atoms are in. II. The chemical shift of the H in tetramethylsilane (TMS) is set 0 ppm as a reference. III. Compounds containing a single type of hydrogen atom will show only one peak in the H-NMR spectrum. IV. The chemical shift, $\delta$ is increasing left to right on an NMR spectrum.

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

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 ____________________.

Electron microscopy, x-ray crystallography and NMR spectroscopy are used to determine 3D structures of biomolecules. Using protein examples studied in chapter 3, which statements are true?

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.

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

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

_________________ generates the highest resolution 3D biomolecular structures.