Exam 18: Determination of Macromolecular Structure

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

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?

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

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

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