BIO CHEM Practice set

Which of the following residues most likely occupy the positions d on heptad repeats (abcdefg) that form coiled-coil structure? Which of the following residues most likely occupy the positions d on heptad repeats (abcdefg) that form coiled-coil structure? Ala Ile or Leu Ser Glu or Lys

Ile or Leu

What type of interaction would you expect between the following groups in a tertiary structure? glutamic acid and lysine

salt bridge

Indicate whether the following statements describe the primary, secondary, tertiary, or quaternary protein structure. Hydrogen bonding between amino acids in the same polypeptide gives a coiled shape to the protein.

secondary protein structure

Indicate whether the following statements describe the primary, secondary, tertiary, or quaternary protein structure. Several polypeptide chains in a β-pleated sheet are held together by hydrogen bonds between adjacent chains.

secondary protein structure

Indicate whether the following statements describe the primary, secondary, tertiary, or quaternary protein structure. R groups interact to form disulfide bonds or ionic bonds.

tertiary protein structure quaternary protein structure

Because an alpha helix is a dipole, the ends of alpha helices are typically located where?

the surface of a protein

It is a common observation that antiparallel strands in a β sheet are connected by short loops, but that parallel strands are connected by α helices. Why do you think this is?

Antiparallel strands of beta sheet can produce a polypeptide chain that is capable of folding back on itself. Small number of amino acids are required to accomplish polypeptide folding and make a turn. But, in parallel beta strands the polypeptide must be of equal length as that of the beta strands. Therefore, for a long peptide stability can be provided by a backbone formed by hydrogen bonding with an alpha helix. Thus, antiparallel strands in a β sheet are connected by short loops, but that parallel strands are connected by α helices.

The tertiary structure is one level of protein structure. The tertiary structure occurs due to which of the following interactions or bonds with the protein? A. Peptide bonds occur between amino acids. B. Hydrogen bonds occur between peptide bonds to form a beta-pleated sheet. C. Attractions and repulsions occur between the R groups of the amino acids. D. Hydrogen bonds occur between peptide bonds to form an alpha helix.

Attractions and repulsions occur between the R groups of the amino acids.

Melittin is a 25-residue polypeptide found in bee venom. In its monomeric form, melittin is thought to insert into lipid-rich membrane structure. Considering this information, decide which of the following is likely to be the amino acid sequence for melittin. Melittin is a 25-residue polypeptide found in bee venom. In its monomeric form, melittin is thought to insert into lipid-rich membrane structure. Considering this information, decide which of the following is likely to be the amino acid sequence for melittin. A. GSTSQTESHTDTDSCQSWIKRKRNN B. GEDASLRVSTGNPSLDSYIKRKRNN C. GLGAVLRVLTGLPALISWIKRKRNN D. GKEAENDEQSTTNEDYSKIKRKRNN

C. GLGAVLRVLTGLPALISWIKRKRNN

Many beta-sheets are amphipathic, meaning one side of the sheet contains mainly hydrophobic residues while the other side has mostly hydrophilic residues. Which of the following amino acid sequence is compatible with such structure? Many beta-sheets are amphipathic, meaning one side of the sheet contains mainly hydrophobic residues while the other side has mostly hydrophilic residues. Which of the following amino acid sequence is compatible with such structure? A. MGLNQSDMFLLV B. CALIFNGMDEQN C. DLSFNVEMQLTV D. SGVLDSTEMVHK

DLSFNVEMQLTV

What would you expect about the formation of a α-helix for a segment of a protein chain that contains glutamate approximately every fourth residue with all other residues being mostly hydrophobic?

Helix formation would be favored at low pH.

Which of the following statements is true about backbone of polypeptide chain? A. It contains too many carbon atoms, thus it is highly hydrophobic. B. It consists of repeating units of "Cα-N-C". C. It is very polar and has great potential to form hydrogen-bonds. D. All of the above

It is very polar and has great potential to form hydrogen-bonds.

Which of the following peptides contains heptad repeats and can potentially form coiled-coil structure with each other in an aqueous environment? Which of the following peptides contains heptad repeats and can potentially form coiled-coil structure with each other in an aqueous environment? MKQLEDKVEELLSKVYHLENE VKQSEKDSEEVSLKNYQSEDN LSFAAAMNGLALSFAAMNDEN None of these peptides contains heptad repeats.

MKQLEDKVEELLSKVYHLENE

The Anfinsen experiment elegantly demonstrated that the three dimensional structure of ribonuclease is determined by its amino acid sequence. In this experiment, Anfinsen used 8 M urea and large excess of β-mercaptoethanol to denature the protein and to reduce the disulfide bonds, respectively. He removed both chemicals simultaneously to allow the proper refolding of the protein. What will happen if one removes β-mercaptoethanol first and then slowly remove urea to allow the protein to refold?

Most likely, the protein will not refold to its native state, because wrong disulfide bonds may form under this condition.

Which level of protein structure corresponds to the particular sequence of amino acids in the polymer, which are held together by peptide bonds?

Primary

Give two reasons to explain why a proline residue in the middle of an α-helix is predicted to be destabilizing to the helical structure.

Pro does not have the α−NH group that acts as a stabilizing H-bond donor in the middle of the helix. E. Pro is not able to adopt the ideal ϕ and ψ angles for an α -helix. This is so because proline does not have an NH group and thus cannot adopt the ideal ϕ and ψ angles.

In a protein, the most conformationally restricted amino acid is ________, and the least conformationally restricted is ________________. In a protein, the most conformationally restricted amino acid is ________, and the least conformationally restricted is ________________. Trp, Gly Met, Cys Pro, Gly Ala, Pro

Pro, Gly

Which of the following describes the correct sequence of events in determining the crystal structure of a protein? Which of the following describes the correct sequence of events in determining the crystal structure of a protein? A. Grow crystal of purified protein; compute electron density map; diffract the X-ray with the crystal; refine the structure model. B. Purify the protein; grow the crystal; diffract the X-ray with the crystal; compute electron density map; build atomic model; refine the structure. C. Purify the protein; diffract the X-ray; compute electron density map; refine the structure; build atomic model. D. None of the above.

Purify the protein; grow the crystal; diffract the X-ray with the crystal; compute electron density map; build atomic model; refine the structure.

Because an alpha-helix is a highly restricted structure, not every residue is compatible with its formation. Which of the following groups of amino acid residues is NOT compatible with the formation of alpha-helix? Because an alpha-helix is a highly restricted structure, not every residue is compatible with its formation. Which of the following groups of amino acid residues is NOT compatible with the formation of alpha-helix? A. Phe, His, and Tyr B. Ser, Thr, and Asp C. Ala, Leu, and Phe D. Gln, Met, and Ala

Ser, Thr, and Asp

The disulfide bond between two cysteine molecules is a _________________ bond formed by __________________________.

The disulfide bond between two cysteine molecules is a covalent bond formed by reduction.

What determines a protein's native structure?

The protein's linear amino acid sequence

In Anfinsen experiment, ribonuclease is first treated with urea and β-mercaptoethanol. What are the functions of urea and β-mercaptoethanol?

Urea is used to denature the protein and β-mercaptoethanol is used to reduce the disulfide bonds.

It is a common observation that antiparallel strands in a beta sheet are connected by short loops, while parallel strands are often connected by short strands alpha helices disulfide bonds extensive ionic interactions

alpha helices

What functional groups are found in all α-amino acids?

ammonium group carboxylate group

One important property of ionizable functional groups is that their pKA values can be heavily influenced by the local chemical environment. For example, the carboxyl group on the aspartate side chain could have different pKa values, depending on where it is located in a protein. In which of the following environments, the carboxyl group on the aspartate side chain has the highest pKa value? A. an aspartate side chain on the surface of a protein with no other ionizable groups nearby B. an aspartate side chain buried in a hydrophobic pocket on the surface of a protein C. an aspartate side chain in a hydrophobic pocket adjacent to a glutamate side chain D. an aspartate side chain in a hydrophobic pocket adjacent to a lysine side chain

an aspartate side chain in a hydrophobic pocket adjacent to a glutamate side chain

What type of interaction would you expect between the following groups in a tertiary structure? two cysteines

disulfide

What type of interaction would you expect between the following groups in a tertiary structure? serine and aspartic acid

hydrogen

What type of interaction would you expect between the following groups in a tertiary structure? two leucines

hydrophobic interaction

Indicate whether the following statements describe the primary, secondary, tertiary, or quaternary protein structure. Peptide bonds join the amino acids in a polypeptide chain.

primary protein structure

The portion of a protein that has a tertiary structure of its own is called a ______________________________________.

protein domain

Which of the following terms best describes three-dimensional relationship of the different polypeptide chains in a multi-subunit protein or protein complex? coiled-coil protein domain tertiary structure quaternary structure

quaternary structure

Which of the following statements is true about βαβ motif? Which of the following statements is true about βαβ motif? βαβ motif is composed of two antiparallel beta strands and one alpha helix. Proteins with beta structure are built from multiple βαβ motifs. βαβ motif is built from two parallel beta strands connected with an alpha helix. βαβ motif was first identified from the structure of green fluorescence protein.

βαβ motif is built from two parallel beta strands connected with an alpha helix.