Chapter 6 Post-lecture-1 (protein structure)

Where in a globular protein is the amino acid alanine likely to be located?

the hydrophobic interior

Which of the following statements characterize an α helix (A) or antiparallel β strand (B)? 1 The rise per residue is 1.5 Å. 2 The side chains are located on opposite faces of the secondary structure element. 3 There are 2 residues per turn. 4. The pitch is 5.4 Å.

A-1,4; B-2,3

In most cases, mutations in the core of a protein that replace a smaller nonpolar side chain in the wild-type (e.g., Ala, Val) with a larger nonpolar side chain (e.g., Leu, Ile, Phe, Trp) in the mutant, result in significant destabilization and misfolding of the mutant. What feature of the protein core explains this observation? Why would such a mutation prevent a protein from folding properly? Match the items in the left column to the appropriate blanks in the sentences on the right.

Interactions of NONPOLAR side chains in the protein sequence lead to the formation of a tightly packed HYDROPHOBIC core. Thhis core is stabilized be a LARGE number of VAN DER WAALS CONTACTS. When a mutatuin occurs, it destabilizes the protein core and weakens VAN DER WAALS CONTACTS leading to misfoldings.

Are the helices bound to the DNA likely to be amphiphilic? Explain. Match the words in the left column to the appropriate blanks in the sentence on the right.

No. DNA is charged and therefore polar, so most of the DNA-binding helix is likely to be composed of polar residues that interact with either the DNA or the solvent.

Where do you predict the N- and C-termini are located for Max? Match the words in the left column to the appropriate blanks in the sentences on the right.

The N -terminus is interacting with the DNA. The first reason for this is because the α amino group of the N-terminus is positively charged and will interact favorably with the negative charge on the phosphodiester backbone of the DNA. The second reason is that this orientation also situates the partial positive end of the helical macrodipole for favorable electrostatic interactions with the negatively charged phosphodiester backbone of the DNA.

What would be the effect of a mutation that placed a proline residue at point A in the structure?

This would break the helix near the binding sites and Fe2 could not be bound, and the mutant protein would be nonfunctional.

https://session.masteringchemistry.com/problemAsset/1943542/1/T-1027351b.jpg What type of protein secondary structure does the structure shown here (Figure 2) represent?

α-helix

https://session.masteringchemistry.com/problemAsset/1943542/1/T-1027351a.jpg What type of protein secondary structure does the structure shown here (Figure 1) represent?

β-sheet

Which statements about the "energy landscape" model of protein folding are true? 1 The depth of the funnel corresponds to free energy, and the width of the funnel corresponds to the number of conformational states at a given value of free energy. 2 This model averts Levinthal's paradox. 3 The classical pathway model and the folding funnel are not compatible. 4 The trajectory of protein folding is "downhill". It proceeds with a decrease in free energy.

1, 2, and 4

The stability of the folded structure of a globular protein depends on the interplay of which of these factors: 1 ΔH generally favors the folded state and is associated with changes in noncovalent bonding interactions. 2 ΔH of the surrounding medium, which generally favors the folded state of the protein. 3 ΔSconformation of the protein favors the unfolded state. 4 ΔSsolvent is favorable due to the release of water from clathrates. This occurs when solvent exposed hydrophobic groups become buried within the molecule.

1, 3, and 4

Complete the following vocabulary exercise relating to the level of structure in proteins. Match the words in the left-hand column with the appropriate blank in the sentences in the right-hand column.

1. Tertiary structure is achieved when a protein folds into a compact, three-dimensional shape stabilized by interactions between side-chain R groups of amino acids 2. Primary structure is the sequence of amino acids in a protein. 3. Quaternary structure is the result of two or more protein subunits assembling to form a larger, biologically active protein complex. 4. Secondary structure describes the alpha-helices and beta-sheets that are formed by hydrogen bonding between backbone atoms located near each other in the polypeptide chain.

Which of the following statements about protein folding and structure are true?

Chaperones, like the GroEL-ES complex, work by providing a sequestered environment in which proteins can safely explore the conformational space towards productive folding. Misfolded proteins often aggregate in large structures in the cell. Misfolded proteins are thermodynamically stable versions of a protein. The native structure of a protein is entirely encoded in its amino acid sequence.

https://session.masteringchemistry.com/problemAsset/2708019/7/6.1.png Part A Polyglycine, a simple polypeptide, can form a helix with ϕ=−80∘ , ψ=+150∘. From the Ramachandran plot (see the figure on the left), describe this helix with respect to handedness.

It could have a left-handed polypeptide II helix structure.

Which of the following statements regarding Anfinsen's denaturing experiments with ribonuclease A (RNAse A) are valid? 1 Exposing the denatured protein to air oxidation and then dialysis to remove urea restored the protein to its original functionality. 2 Removing urea by dialysis and then allowing air oxidation of the denatured protein restored the protein to its original functionality. 3 Denaturing the protein with both urea and β-mercaptoethanol yielded an inactive protein. 4 Anfinsen concluded that protein folding is determined by its primary sequence.

Only statements 2, 3, and 4 are valid.

Biochemists talk about protein structure at four distinct levels: primary, secondary, tertiary and quaternary structure. Below are depictions of each of these levels of protein structure. For each image, match the term and the written description of the level of protein structure that the image depicts. Drag the appropriate items to their respective bins.

Primary structure: The amino acid sequence that makes up a protein monomer. Secondary structure:Local regions of polypeptide backbone structure with regular folding. Tertiary structure: The three-dimensional positions of all the atoms in the protein, including side chains Quaternary structure: The organization of multiple monomers, called subunits, in the functional protein.

Determine whether each term describes the primary, secondary, or tertiary structure of proteins (or forces relating to the primary, secondary, or tertiary structure of proteins). Drag each item to the appropriate bin.

Primary structure: amide bond Secondary structure: alpha helix, beta-pleated sheet Tertiary structure: disulfide bond, salt bridge

Sort the images according to the level of structure in the proteins shown. Sort the items into the appropriate bin.

Primary structure: https://session.masteringchemistry.com/problemAsset/1943240/1/T-1027346a.jpg secondary structure: https://session.masteringchemistry.com/problemAsset/1943240/1/T-1027346e.jpg tertiary structure: https://session.masteringchemistry.com/problemAsset/1943240/1/T-1027346c.jpg quaternary structure: https://session.masteringchemistry.com/problemAsset/1943240/1/T-1027346d.jpg

Disulfide bonds have been shown to stabilize proteins (i.e., make them less likely to unfold). Consider the cases shown schematically below for two variants of the same protein. In case #1 the disulfide forms between Cys residues that have been introduced near the protein N- and C-termini, and in case #2 the disulfide forms between Cys residues that have been introduced in the middle of the protein sequence. https://session.masteringchemistry.com/problemAsset/2738835/5/6_23.png Which protein is likely to be more stable? (Note: Assume the disulfide bond is intact in both the unfolded and folded states). Explain your reasoning. Match the items in the left column to the appropriate blanks in the sentences on the right.

Protein #1 will be more stable because its disulfide bond will constraint the UNFOLDED form greatly comparing to the disulfide bond in protein #2. This means that the unfolded protein form of protein #1 will be less stable than the protein #2 leading to a greater stability when folded.

It has been found that in some of the α-helical regions of hemerythrin, about every third or fourth amino acid residue is a hydrophobic one. Suggest a structural reason for this finding.

The four helices could be arranged so that the hydrophobic side chains would point toward the center of the bundle to stabilize hydrophobic core.

The Foundation Figure began by discussing the importance and relevance of protein structure. Fill in the blanks in the paragraph below with a word or phrase from the word bank that best completes the sentence. Match the words in the left column to the appropriate blanks in the sentences on the right

The structure of a protein dictates the partners with which it can interact. Therefore, the structure of a protein is directly related to its function. The contours of a protein determine the shape that its interaction partner must have, whereas the surface chemistry of a protein determines the kinds of chemical interactions that the protein will make with its interaction partner (e.g. Coulombic interactions or hydrogen bonding). Therefore, a protein will only bind to molecules that have the appropriate shape and chemistry (i.e. only those that are complementary to the protein).

Armed with a growing library of protein structures and decreasing costs of ever-more-powerful computers, biochemists can now attempt to solve protein structures computationally. This software takes the amino acid sequence and runs folding simulations. Each simulation calculates the free energy for that conformation. The process is repeated until the software fails to identify a conformation of a lower free energy. This final conformation is deemed the lowest free conformational energy for the given polypeptide. Using computational biochemistry software, you find a predicted structure for your protein of interest. Using this prediction, you identify a potential binding site for a drug that is known to bind your protein of interest. However, when you mutate the putative binding site in the protein, you find no effect on the binding of drug, indicating that the software has failed to find the native structure for your protein of interest. Identify whether each of the following statements is a likely or an unlikely reason for the failure of the software to determine the native structure. Drag the appropriate items to their respective bins.

Yes, Likely reason for the failure: The protein represents a new fold that was previously unidentified. The software was trapped in a local minimum, e.g. a folding intermediate. The software identified an alternate biological conformation of the protein, e.g. a misfolded aggregate. The protein has many different conformations of similar low free energy, only one of which binds the drug. No, Unlikely reason for the failure: The amino acid sequence alone is not sufficient to specify its native structure.

Draw the dipeptide Gly-Gly. Draw the molecule on the canvas by choosing buttons from the Tools (for bonds), Atoms, and Advanced Template toolbars. The single bond is active by default.

https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=11163&t=l Add a hydrogen to the N terminus nitrogen so it has a positive charge. Remove the hydrogen on the C terminus oxygen so it has a negative charge