Chp 4 Problems

The least restricted ϕ and ψ angles are found in polypeptides in which class of secondary structure? a. right-handed α helix b. β sheet c. left-handed α helix d. loop

d

A group of scientists isolate a novel strain of bacteria. Although the bacteria have normal nucleic acids and proteins, the strain has an abnormal membrane. In this strain, the lipid bilayer is twice as thick (70 Å) a that of a normal strain of bacteria. This extra thickness is entirely due to longer hydrophobic tails and not due to changes in the charged head groups of the phospholipids that comprise the membrane. If you isolated a single transmembrane helix from a protein from this strain, how long would you expect it to be?

Answer: 70 Å membrane/1.5 Å per residue of alpha helix = at least 47 residues.

In contrast to globular proteins and regions exposed to the cytoplasm, the integral membrane portions of membrane proteins contain very few residues not ordered into secondary structure elements such as β sheets and α helices. Why is satisfying backbone hydrogen bonds by forming secondary structure elements more important for protein folding in the membrane than in solution?

Answer: In solution, residues in loop segments can form backbone-water hydrogen bonds and thus do not pay a large energetic penalty for failing to satisfy these interactions with other backbone atoms. In contrast, in the membrane the lipid tails do not provide hydrogen bond donor or acceptors. Additionally, there is no energetic gain from burying a hydrophobic core in the membrane since the hydrophobic environment negates the importance of the hydrophobic effect. Secondary structure formation is an efficient mechanism for completely satisfying the hydrogen bonding requirements of the peptide backbone. These hydrogen bonds provide the major energetic force driving folding in the membrane.

Why are binding sites in proteins often located at interdomain boundaries?

Answer: Mutations that confer novel binding are more likely to be tolerated by the protein if they do not interfere with proper folding, making surface residues at interdomain boundaries better candidates for binding sites. Also, interdomain regions possess deep invaginations within which small molecules can bind.

Draw an alanine-alanine dipeptide. Indicate the peptide bond. What factors restrict the rotation about the peptide bond?

Answer: Rotations are strongly hindered because the peptide bond has partial double bond character. Evidence for this double bond character includes the observation from high resolution crystal structures that the peptide bond length is shorter than normal single N-C bond lengths.

Why are isolated secondary structural elements not usually stable in isolation, even though all backbone hydrogen bonds are satisfied?

Answer: The hydrophobic effect is the major force driving protein folding and governing the stability of globular proteins. Isolated secondary structural elements cannot bury hydrophobic residues away from water and thus do not gain stability from the hydrophobic effect. While backbone hydrogen bonds could contribute stabilizing energy to the folded state, the backbone -NH and -C=O groups of the unfolded polypeptide hydrogen bond to water. Upon folding, formation of secondary structure elements replaces hydrogen bonds to water with hydrogen bonds to other parts of the protein backbone. Thus the summed energy of hydrogen bonding does not change upon folding.

The simplest form of the Ramachandran diagram (shown in Figure 4.20) is calculated by ignoring hydrogen bonding, interactions with water, and the hydrophobic effect. Why is this simple form of the diagram still an effective predictor of protein backbone conformation?

Answer: The simplest Ramachandran diagram shows which conformations are prevented due to interatomic collisions. The repulsive energy of such collisions is so high that it dominates the forbidden regions of the diagram. Taking the other forces into account modulates the favorability of some regions of the Ramachandran diagram, but the overall forbidden and allowed zones are not changed.

A scientist isolates a membrane protein that transports sodium ions from inside the bacterium (where it is at low concentration) into solution (where the sodium ion concentration is high). a. Does this protein use active or passive transport? b. What are two energy sources for accomplishing this transport?

Answer: a. This protein uses active transport since it is moving an ion to a region of higher concentration from inside the cell where the ion is at a lower concentration. b. Two mechanisms for coupling energy to transport against a concentration gradient are to convert light energy to a conformational or chemical change (as in rhodopsin) and to use ATP hydrolysis to drive a conformational in the protein (as in the maltose transporter).

_______ residues form cis peptide bonds in proteins with significant frequency.

Answer: Proline

Match the following proteins with their quaternary structure: a. hemoglobin b. RNA polymerase c. myoglobin i. one subunit ii. many structurally similar subunits iii. many subunits of varied structure

Answer: a-ii, b-iii, c-i

α helices that have one hydrophobic face and one hydrophilic face are known as _________ helices.

Answer: amphipathic

Soluble proteins have mostly _________ sidechains on the inside and mostly ________ sidechains on the outside.

Answer: hydrophobic, hydrophilic

SH2 domains bind to _________ and SH3 domains bind to _________.

Answer: phosphorylated tyrosine residues, proline containing peptides

The organization of the protein subunits in multimeric proteins is known as the ___________ structure.

Answer: quaternary

Globular proteins are generally embedded in the interior of a lipid bilayer. True/False

False

Most protein conformational changes involve breaking and reforming several covalent bonds along the polypeptide chain. True/False

False

The secondary structure of a protein refers to the extent and order of its α helices and β sheets. True/False

True

Draw a helical wheel for the following sequences: a. Leu-Asp-Lys-Ile-Val-Arg-Phe-Leu-Gln-Ser-Tyr b. Leu-Asp-Leu-Lys-Arg-Ser-Glu-Leu-Asn-Tyr-Asn For each, highlight the hydrophobic residues by marking them with an asterix (*). Do these sequences form amphipathic helices?

a. Yes, this forms an amphipathic helix. b. No, this does not form an amphipathic helix

The only genetically encoded amino acid without a stereoisomer is: a. alanine b. tryptophan c. glycine d. proline e. lysine

c

Which of the following statements regarding protein domains is NOT true? a. Secondary structural elements of a domain generally pack so that a hydrophobic core is formed. b. A protein domain normally contains 50-200 residues. c. Protein domains are units of tertiary protein structure. d. Proteins are only comprised of one protein domain.

d