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Exam 3: Protein Structure and Function

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Question 1

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What type of interaction is directly responsible for the formation of secondary structure?

A) peptide bonds between adjacent amino acids
B) peptide bonds between nonadjacent amino acids
C) hydrogen bonds between sections of the polypeptide backbone
D) hydrogen bonds between side chains of amino acids

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Question 2

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In cells,the activity of enzymes is often regulated by other molecules.Why is this necessary?

A) because all enzymes require some help from another molecule to function correctly
B) because other molecules are necessary to prevent enzymes from denaturing
C) because each enzyme has multiple functions
D) because it is unlikely that all reaction products are required all of the time

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Question 3

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You disrupt all hydrogen bonds in a protein.What level of structure will be preserved?

Which of the following would be an example of a cofactor?

Suppose you discovered a new amino acid.Its R-group contains only hydrogen and carbon atoms.Predict the behavior of this amino acid.

Refer to the following paragraph and Figure 3.1 to answer the following questions. Figure 3.1 Since structure correlates so well with function,biochemists are constantly looking for new ways to probe the complex structure of proteins in order to understand what they do and how they do it.One of the most powerful techniques in existence today is X-ray crystallography.The main difficulty with this technique is getting the protein to crystallize.Once crystallized,the protein is bombarded with X-rays to create a pattern that can be analyzed mathematically to determine the three-dimensional structure of the protein.This analysis has been performed by Krzysztof Palczewski on the protein rhodopsin,which is a light-sensitive protein found in species ranging from ancient bacteria (archaea) to humans.The structure (schematically shown above,where each letter represents an amino acid) is characterized by a single polypeptide chain with several α-helical segments that loop back and forth across the cell membrane.Another notable feature is the disulfide bond (-S-S-) that can be seen at the bottom of the third transmembrane segment.[Figure adapted from K.Palczewski et al. ,Science 289 (2000) : 739.] -How many times does the protein in Figure 3.1 cross the cell membrane?

A series of hydrophobic side chains will congregate together as a protein folds in an aqueous solution and be stabilized by _____.

An enzyme has a total of four active sites.When you denature the molecule and study its composition,you find that each active site occurs on a different polypeptide.Which of the following hypotheses does this observation support?

At the pH found in cells (about 7.0) ,what happens to the carboxyl group on an amino acid?

Which one of the following is not a component of each monomer used to make proteins?

Aquaporins are proteins that control the passage of water molecules across the cell membrane.The protein forms a pore,or opening,in the membrane.You isolate what you think are two different molecules of aquaporin,and determine that one of the proteins has a larger pore diameter than the second.Which of the following do you conclude?

Which of the following observations is the strongest argument in favor of the hypothesis that protein structure and function are correlated?

What is the pattern component of the theory of chemical evolution?

You collect data on the effect of pH on the function of the enzyme catalase in human cells.Which of the following graphs would you expect?

The functional groups of amino acids _____.

The lock-and-key analogy for enzymes applies to the _____.

At the pH found in cells (about 7.0) ,what happens to the amino group on an amino acid?

Refer to the following paragraph and Figure 3.1 to answer the following questions. Figure 3.1 Since structure correlates so well with function,biochemists are constantly looking for new ways to probe the complex structure of proteins in order to understand what they do and how they do it.One of the most powerful techniques in existence today is X-ray crystallography.The main difficulty with this technique is getting the protein to crystallize.Once crystallized,the protein is bombarded with X-rays to create a pattern that can be analyzed mathematically to determine the three-dimensional structure of the protein.This analysis has been performed by Krzysztof Palczewski on the protein rhodopsin,which is a light-sensitive protein found in species ranging from ancient bacteria (archaea) to humans.The structure (schematically shown above,where each letter represents an amino acid) is characterized by a single polypeptide chain with several α-helical segments that loop back and forth across the cell membrane.Another notable feature is the disulfide bond (-S-S-) that can be seen at the bottom of the third transmembrane segment.[Figure adapted from K.Palczewski et al. ,Science 289 (2000) : 739.] -What is the location of the C-terminus of the protein in Figure 3.1?

You've just sequenced a new protein found in mice and observe that sulfur-containing cysteine residues occur at regular intervals.What is the significance of this finding?

HIV is the virus that causes AIDS.In the mid-1990s,researchers discovered an enzyme in HIV called protease.Once the enzyme's structure was known,researchers began looking for drugs that would fit into the active site and block it.If this strategy for stopping HIV infections were successful,it would be an example of what phenomenon?