Exam 3: Protein Structure and Function

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

You have isolated a previously unstudied protein, identified its complete structure in detail, and determined that it catalyzes the breakdown of a large substrate. You notice it has two binding sites. One of these is large, apparently the bonding site for the large substrate; the other is small, possibly a binding site for a regulatory molecule. What do these findings tell you about the mechanism of this protein?

An amino acid has an R- group that is positively charged at cellular pH. Which of the following categories would best describe it?

You are studying a protein that is shaped like a doughnut. The shape is a function of which levels) of protein structure?

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 structu proteins in order to understand what they do and how they do it. One of the most powerful techniques in existence today is X 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 a- 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.] -If you were reading off the sequence of amino acids in Figure 3.1 to a biologist friend, what should the first three letters be?

Which of the following is not a major functional class of proteins?

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 structu proteins in order to understand what they do and how they do it. One of the most powerful techniques in existence today is X 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 a- 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.] -Refer to Figure 3.1. Which level of structure is being maintained by the disulfide bond?

Which of the following statements about the peptide- bonded backbone is correct?

If the primary structure of a protein is incorrect

Consider the HIV enzyme called protease. The amino acid residues at the active site are highly hydrophobic. In designing a drug that would bind to the active site and jam it, researchers should use which type of molecule?

Which is not a role proteins play in organisms?

A peptide bond is

An amino acid has an R- group that is negatively charged at cellular pH. Which of the following categories would best describe it?

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?

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?

Which of the following statements about peptides is correct?

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?

The aquaporin family of proteins plays a major role in the transport of water all over the body. During the folding process of these proteins, a- helices start forming as

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