QUESTION: 609 Topic Exam C: Section 3 (science)

All proteins consist of a string of amino acids linked together by peptide bonds. Because of its unique sequence of amino acids, every protein is distinct. Each protein folds into a specific conformation when manufactured by

cells. All proteins must attain three-dimensional structures to properly function in the cell. While the peptide bonds between the amino acids are relatively rigid, all the other chemical bonds within a protein are flexible and can contort within certain limits. The ability of a protein to fold depends on the flexibility of these chemical bonds. A small protein of about 100 amino acids could undergo an astronomical number of trials and errors before assuming its final structure. This sampling of many conformations before attaining the right one would take far too long and so scientists hypothesize that there must be pathways which guide individual proteins to the right conformations, thereby eliminating total randomness in sampling. Three pathway models of protein folding have been proposed.

Diffusion-collision model
This model suggests that an amino acid within a protein can diffuse within its environment until it collides with its specific partner amino acid, to which it adheres. When all the amino acids, are involved in favorable interactions, the protein ceases to diffuse and the proper conformation is attained.

Nucleation model
This model postulates that the acquisition of the proper fold within several amino acids would trigger the folding process. These amino acids act as nucleation centers and cause a domino effect in promoting protein folding. The protein can be imagined to sequentially acquire its proper conformation beginning from the nucleation centers.

Hydrophobic-collapse model
Out of the 20 different amino acids, some are hydrophobic. A hydrophobic amino acid is one that does not like to be associated with water but does like to be associated with others like itself. In the hydrophobic-collapse model, hydrophobic amino acids in the protein collapse into the center of the protein leaving the hydrophilic (water-loving) amino acids to surround them and interact with water.

A fourth, all-inclusive view of protein folding is that similar proteins can fold via any of the three models. What cannot be said of proteins that conform to this all-inclusive model?

The structure of a protein can be attained by any model.
The length of the protein does not influence the choice of a model.
The sequence of the protein determines the folding pathway.
A folding pathway that is hindered by a mutation can be compensated by another.

Answer(s): C

Explanation:

Choices A and D demonstrate that a protein fold can be achieved by any of the three suggested pathways.
While sequence is the only element important in the folding process, hence negating choice B, the fact that similar proteins can attain proper conformations via any of the proposed pathways, in this particular case, suggests that sequence does not determine the folding pathway.

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QUESTION: 610 Topic Exam C: Section 3 (science)

SDS-PAGE is a technique used by scientists to separate proteins according to their size. The compound SDS confers a uniform negative charge to individual proteins, causing these negatively charged proteins to travel toward the anode (positive end) when placed in an electric field. The migrating proteins are further placed in a uniform matrix (PAGE) in order to separate the different sizes. A bigger, heavier protein meets more resistance than a smaller, lighter one while traveling through the matrix, and hence migrates more slowly. The size of a protein is measured in Daltons (Da). The relationship between the logarithm values of the weights of seven proteins and the distances they travel in the matrix in a given period of time is illustrated in the graph. A list of the discrete data point values for each protein, as well as the corresponding weight, is presented under the graph on the next page.

Which statement characterizes the migration of SDS-associated proteins?

Diffusion moves the proteins from a region of higher concentration to one of lower concentration.
An electric field causes negatively charged objects to migrate toward the anode (positive end).
The electrical resistance of negatively charged objects determines the speed of migration.
Osmosis of water indirectly causes the migration of the proteins.

Answer(s): B

Explanation:

SDS-associated proteins, which are negatively charged, will travel toward the positive end of an electric field. All the other options are true statements, but do not describe the SDS-PAGE context.

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QUESTION: 611 Topic Exam C: Section 3 (science)

SDS-PAGE is a technique used by scientists to separate proteins according to their size. The compound SDS confers a uniform negative charge to individual proteins, causing these negatively charged proteins to travel toward the anode (positive end) when placed in an electric field. The migrating proteins are further placed in a uniform matrix (PAGE) in order to separate the different sizes. A bigger, heavier protein meets more resistance than a smaller, lighter one while traveling through the matrix, and hence migrates more slowly. The size of a protein is measured in Daltons (Da). The relationship between the logarithm values of the weights of seven proteins and the distances they travel in the matrix in a given period of time is illustrated in the graph. A list of the discrete data point values for each protein, as well as the corresponding weight, is presented under the graph on the next page.

A protein of weight 45,000 Da would be expected to migrate to the region on the graph marked:

Answer(s): A

Explanation:

From the table, the weight 45,000 falls between the first two data points. This would correspond to region W on the graph.

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QUESTION: 612 Topic Exam C: Section 3 (science)

SDS-PAGE is a technique used by scientists to separate proteins according to their size. The compound SDS confers a uniform negative charge to individual proteins, causing these negatively charged proteins to travel toward the anode (positive end) when placed in an electric field. The migrating proteins are further placed in a uniform matrix (PAGE) in order to separate the different sizes. A bigger, heavier protein meets more resistance than a smaller, lighter one while traveling through the matrix, and hence migrates more slowly. The size of a protein is measured in Daltons (Da). The relationship between the logarithm values of the weights of seven proteins and the distances they travel in the matrix in a given period of time is illustrated in the graph. A list of the discrete data point values for each protein, as well as the corresponding weight, is presented under the graph on the next page.

A protein essential for metabolism has just been discovered. SDS-PAGE reveals that this protein migrates a distance of 1.7 cm. Which statement best characterizes the new protein?

The weight of the protein is somewhere between 6,000 Da and 11,000 Da.
The weight of the protein is somewhere between 11,000 Da and 17,000 Da.
The weight of the protein is somewhere between 14,000 Da and 17,000 Da.
The weight of the protein is somewhere between 17,000 Da and 35,000 Da.

Answer(s): D

Explanation:

Since a protein weighing 17,000 Da travels 1.8 cm, and since the new protein traveled only 1.7 cm, we can confidently conclude that the new protein is heavier and thus rule out choices A, B, and C. Choice D is the only answer allowing for heavier weights.

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