Molecular Biochemistry Exam 2

Which group of the 3rd residue is used to make its hydrogen bond in the alpha-helix?

C=O of the 3rd residue makes a hydrogen bond to N-H of the 7th (i.e n+4th) residue.

Which of the following is not a ligand to the porphyrin ring Fe(II) ion in oxymyoglobin?

CO

Examine the three sequences below for collagen-like proteins. If hydrogen bonding were the most important feature in determining strength in fibrous proteins, which of the following sequences likely has the highest melting temperature and why? (Note: Flp = fluoroproline; Hyp = hydroxyproline) 1. Pro-Hyp-Gly-Pro-Hyp-Gly-Pro-Hyp-Gly 2. Pro-Flp-Gly-Pro-Flp-Gly-Pro-Flp-Gly 3. Gly-Pro-Thr-Gly-Pro-Thr-Gly-Pro-Thr

"1" because Hyp has OH groups.

What is the fractional saturation of myoglobin at pO2 = 2.8 torr, if p50 = 2.8 torr?

0.50 Correct. Y = pO2 / (p50 + pO2) = 2.8 / (2.8 + 2.8) = 0.5

What is the fractional saturation of myoglobin at pO2 = 7.2 torr, if P50 = 2.8 torr?

0.72

Which of the curves does NOT show cooperative binding?

1. CORRECT. Curve 1 is hyperbolic, which is typically seen with non-cooperative binding.

The classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates that _______.

1° structure can determine 3° structure.

Hemoglobin is a heterotetramer. How many protomers are present in hemoglobin?

2

In a 12-residue alpha-helix, how many backbone hydrogen bonds will the 5th amino acid make and how many backbone hydrogen bonds will the 10th amino acid make?

2 and 1 Correct. The pattern for the 5th residue is 1 --> 5, and 5 --> 9. The 10th residue however, would make a hydrogen bond only with residue 6.

In an alpha-helix, which amino acid residue makes a hydrogen bond to the 3rd residue?

7th Correct. The pattern is n -> n+4.

Of the following, which amino acid is most likely to be found in position 1 or 4 on alpha keratin?

Ala

Which of the following series of amino acids is most likely to be buried in the center of a water-soluble globular protein?

Ala, Leu, Phe (non-polar side chains)

Which pairs of amino acid side chains could not interact in the interior of a protein by hydrogen bonding?

Ala, Lys The side chain of Ala is unable to make a hydrogen bond.

Proteins can denature due to a change in

All of the above (pH, Temperature, and ionic strength)

Which of the following is FALSE with respect to β-sheets?

Amino acid side chains protrude from one side of the β-sheet. CORRECT. This statement is false. The side chains in β-sheets protrude alternately from both sides of the sheet.

Which of the following statements is FALSE?

Both alpha-helices and β-sheets form only from adjacent (sequential) amino acid residues in the polypeptide. CORRECT. This statement is false. β-sheets form through interactions between portions of the polypeptide backbone which may be quite distant from one another.

Which of the following statements about -helices and β-sheets is FALSE?

Both have conformations that require specific angles of rotation around the peptide bond. There is no rotation around the peptide bond. The peptide bond is rigid and planar because of its partial double-bond character.

Which statement about the structure of collagen is FALSE?

Cross-linking of collagen by Pro and Lys residues explains its low solubility. Correct. Cross-linking of collagen by His and Lys residues explains its low solubility. An e.g. of such a cross-linking reaction is shown on page 139.

Which statement below does not describe fibrous proteins?

Domains have a globular fold.

Which of the following amino acids combinations have side chains with groups that have the greatest ability to stabilize the tertiary structure of a protein?

Glu and Lys

Which one of the following sequences of five amino acids would most likely be located on the surface of a soluble globular protein?

Glu-Asn-Ser-Thr-Gln (all polar)

Which of the following sequences of amino acids is most likely to be at the surface of a water-soluble globular protein?

Glu-Asp-Lys (all polar, charged side chains)

Which of the following supersecondary structures (motifs) is a Greek key motif:

Greek Key motif

Which treatment is least likely to cause a protein to denature?

High concentrations of salts. High salt concentrations will effect a protein's solubility, but probably will not denature it.

Which pair of amino acid side chains could form an ion pair?

His, Asp His can become positive, while Asp can become negative.

Which of the following stabilizes the folding of a polypeptide backbone into regular secondary structure?

Hydrogen bonds. CORRECT. Folding of a polypeptide backbone into regular secondary structure is stabilized by hydrogen bonds

Which of the following statements does not apply to the K value in the equation for the oxygen binding curve of myoglobin?

If Y > K, then myoglobin is less than 50% saturated with oxygen.

Fetal hemoglobin has a higher affinity for oxygen than maternal hemoglobin. Which of the following statements correctly outlines the mechanism behind this observation?

In fetal hemoglobin, the residue His143 is mutated to Ser143, and so the protein binds BPG with lower affinity. CORRECT. The mutation of His143 to Ser143 reduces the number of positively charged groups available to form salt bridges with BPG. This reduces the affinity of hemoglobin for BPG and thus the T (low-affinity) state of hemoglobin is less stable.

Which of the following best describes the tertiary structure of myoglobin?

It contains heme, which is slotted into a hydrophobic pocket between alpha-helix E and alpha-helix F. CORRECT. Tertiary structure describes the precise atomic positioning of all atoms in a protein, including those in prosthetic groups.

Why does a decrease in pH alter/disrupt the tertiary structure of an enzyme?

It disrupts ion pairs/salt bridges. Ion pairs/salt bridges are relatively weak, non-covalent interactions between charged R groups.

Which of the following statements about the peptide bond is FALSE?

It is a phosphodiester bond. CORRECT. This statement is false. Peptide bonds are amides, not phosphodiesters. Phosphodiester bonds link adjacent nucleotides in a nucleic acid.

Who is credited with the discovery of the alpha-helix secondary structure of proteins?

Linus Pauling.

Which one of the following sequences of five amino acids would most likely be located in the interior of a water soluble globular protein?

Met-Phe-Pro-Ile-Leu (all non-polar)

Which statement is not a consequence of the hydrophobic effect?

Metal ions can function to stabilize folded proteins. The binding of metal ions by proteins is largely unrelated to the hydrophobic effect.

Which of the following statements about the structure of myoglobin is FALSE?

Myoglobin contains all three types of secondary structure. CORRECT. Myoglobin contains only two types of secondary structure, -helices and loops. It contains no β-sheet.

When considering fibrous proteins, which of the following statements is TRUE?

Noncovalent interactions contribute to the strength of all of these proteins.

Which of the following statements is true because of the hydrophobic effect?

Nonpolar residues V, L, I, M, and F are found in the interior of proteins. The hydrophobic effect causes nonpolar side chains to be buried inside proteins.

Where are irregular secondary structures (loops) generally found in soluble globular proteins and why?

On the surface so that they can interact with the solvent. The peptide groups of the polypeptide backbone in irregular secondary structure do not form hydrogen bonds with one another. Therefore, they are available to form hydrogen bonds with the solvent (water) at the surface of the protein.

Which of these characteristics does not describe the β sheet?

Parallel β sheets containing fewer than five chains are the most common.

What is the major factor that "drives" the folding of proteins into their tertiary structure?

Placement of hydrophobic amino acid residues within the interior of the protein. This placement occurs through the hydrophobic effect which is the primary "driving force" in protein folding.

In a protein, the most conformationally restricted amino acid is ______; the least conformationally restricted is ______.

Pro, Gly

Which is NOT a conclusion drawn from the experiments of Christian Anfinsen about renaturation of Ribonuclease A?

Proteins are marginally stable in solution. This experiment did not address the magnitude of the protein's stability.

Which statement about the families of protein folding patterns is false?

Proteins of similar tertiary structure tend to have a very similar primary structure. Proteins of similar tertiary structure tend to have a very similar primary structure is the False statement: Some families of similar tertiary structure have many members of unrelated primary structure.

Which of the following statements about quaternary structure is FALSE?

Quaternary structure is defined as the arrangement of polypeptide backbones in proteins with four subunits. Quaternary structure does not require four subunits.

Which of the following statements about quaternary structure is TRUE?

Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.

Structurally, myoglobin and hemoglobin are very similar proteins. In which of the following levels of structure do they differ most?

Quaternary structure. CORRECT. Myoglobin does not have quaternary structure whereas hemoglobin does.

Which of the following amino acid residues form hydrogen bonds with Ala residues located in an alpha-helix?

Residues located within the same alpha-helix. CORRECT. Groups in the peptide bonds that link Ala with neighbouring residues form H bonds with other peptide groups in the same alpha-helix.

Which level of protein structure is defined as "the hydrogen bonded arrangement of the polypeptide backbone"?

Secondary

Which of the following describes the entire three-dimensional structure of a single polypeptide?

Tertiary structure

Which of the following is not a requirement for the structural determination of a protein using two-dimensional (2D) NMR spectroscopic techniques such as NOESY?

The ability of the protein to crystallize.

Which one of the following statements about the alpha-helix is FALSE?

The alpha-helix is a type of secondary structure that fulfills the hydrogen bonding requirements of amino acid side chains. CORRECT. This statement is false. Amino acid side chains play no role in the formation of secondary structure.

What is the primary driving force in the formation of protein tertiary structure?

The exclusion of non-polar substances from aqueous solution. The hydrophobic effect is the major factor determining the stability and structure of native proteins.

Compare the alpha-helix with the structure of double-stranded DNA. Which statement is TRUE for both structures?

The helices are right handed.

Which of the following is NOT a feature of the peptide bond?

The peptide bond has 10% double bond character. Correct. The peptide bond has 40% double bond character.

Which of the following statements about peptide bonds is FALSE?

The peptide bond has restricted rotation around the bond between the carbonyl carbon and Calpha CORRECT. Peptide bonds do not have restricted rotation about the bond between a carbonyl-carbon atom and a Calpha atom. Instead, restricted rotation occurs about the carbonyl-carbon atom of one residue and the N atom of the adjoining residue.

Irregular loops of secondary structure tend to be located on the outside of folded proteins because:

The peptide bonds in loop structures are free to form H bonds with water. CORRECT. The polypeptide backbone in loop structures does not have the extensive pattern of hydrogen bonding seen in -helices and β-sheets and so the peptide groups in loop structures are free to form hydrogen bonds with water molecules.

In the experiment of Christian Anfinsen, which condition permitted Ribonuclease A to renature?

The presence of O2 at pH 8.0 during renaturation. These conditions allowed the simultaneous and reversible re-oxidation and refolding of the polypeptide chain that is necessary to refold to the native state.

Which of the following statements is true regarding collagen?

The requirement for glycine every 3rd amino acid is essential for the triplet helix formation.

What ultimately determines the unique three dimensional structure of soluble globular proteins?

The sequence of the amino acid residues. CORRECT. The sequence of amino acids in a polypeptide determines the structure of that polypeptide.

Which statement about the structure of collagen is FALSE?

The three helices of collagen form a left-handed superhelix. Correct. The three helices of collagen form a right-handed superhelix.

Which of the following is NOT a feature of the alpha-keratin coiled-coil?

The two coils are held together by hydrogen bonds. Correct. They are held together primarily by hydrophobic contacts involving nonpolar side chains.

Which one of the following statements about the β-sheet is FALSE?

The β-sheet is a type of secondary structure that fulfills the hydrogen bonding requirements of amino acid side chains. CORRECT. This statement is FALSE. Hydrogen bonds in a β-sheet occur between groups in the polypeptide backbone not between amino acid side chains.

Which one of these characteristics is not true for the alpha helix?

There is a requirement for glycine every third amino acid residue.

Why do Tyr and/or Trp residues tend to destabilize an alpha-helix when they occur next to each other in a protein?

There is steric hindrance between the bulky Tyr and/or Trp side chains. CORRECT. The R groups of Trp and Tyr are extremely bulky and so when they occur next to each other in a polypeptide, steric hindrance may affect the formation and stability of an alpha-helix.

Which of the following statements is TRUE regarding the R-groups of amino acid residues in an alpha-helix?

They are found on the exterior of the helix. CORRECT. This statement is true. The core of an alpha-helix is a solid, rod-like structure and the amino acid R groups project away from this structure.

Which of the following statements about domains found in multi-domain proteins is false?

They contain 20-50 amino acids. Domains usually contain 100-200 amino acids.

What BEST distinguishes irregular secondary structure from regular secondary structure?

Unlike regular secondary structure, successive residues in irregular secondary structure do not have the same backbone configuration. CORRECT. This is the best description of the difference between regular and irregular secondary structure, because it specifically compares conformations of the polypeptide backbones.

Which pairs of amino acid side chains could interact in the interior of a protein only via van der Waals interactions?

Val, Leu. Val, Leu are both aliphatic side chains whereas the other pairs shown can hydrogen bond.

A domain is:

a folded segment of polypeptide with a separate hydrophobic core.

Which of the following has (have) both a favorable hydrogen bonding pattern and Φ and Ψ values that fall within the allowed Ramachandran conformational regions?

all of the above -β sheet -collagen -alpha helix

The structure of hen egg white protein has been solved and the torsion angles φ and Ψ are shown for each residue in the table below. What structure motif most likely forms as a result of this protein sequence?

alpha Helix connected to a β strand with a break (or loop/turn) in between.

Based on what you know about fibrous protein structure and sequence, what type of fibrous protein is this sequence most likely to from (You can assume that the protein is longer than what is shown and is repeating as shown, also note the polarity of each amino acid.)? Val - Cys - Lys - Val - Cys - Ala - Cys - Val - Cys - Lys - Val - Cys - Ala - Cys

alpha Keratin.

Which of the following represents the true protomer of hemoglobin?

alpha beta

Hydrogen bonds and maximum separation of amino acid side chains make the _____very stable and energetically ______________.

alpha helix and β sheet, favorable

If the gene for myoglobin is "knocked out" in mice, the mice:

appear normal, with lighter colored muscle tissue.

Which one of the following statements about peptide bonds is FALSE. Peptide bonds are:

charged. CORRECT. Peptide bonds are not charged.

In most peptide groups the ______ conformation is not sterically favored.

cis

Myoglobin's primary physiological role is to facilitate oxygen ________.

diffusion

Noncovalent forces that stabilize protein structure include all of the following except __________.

disulfide bridges

Which of the following amino acids has the most significant role in the molecular mechanisms of hemoglobin's function?

histidine CORRECT. Histidine residues play several critical roles in hemoglobin function. For example, think of the proximal histidine, the distal histidine, and the histidine residues involved in the binding of 2,3-bisphosphoglycerate (BPG)

Which of the following triggers the transition from T state to R state (low to high affinity) in hemoglobin?

oxygen binding CORRECT. When oxygen binds to the Fe(II) ion in the heme ring, at its 6th coordination position, the Fe(II) ion is pulled into the plane of the heme ring. It is this binding interaction that initiates the transition from T to R state.

The low pH found in the gut can enhance the digestibility of dietary protein by causing ___.

protein denaturation

In the absence of ascorbic acid, prolyl oxidase is unable to oxidize proline residues in collagen to hydroxyproline, resulting in:

scurvy

Myoglobin and a single chain of hemoglobin have similar ______ structures.

tertiary

For β-sheets, the terms 'parallel' and 'antiparallel' refer to ___________.

the 'direction' of the associated peptide strands

In a Ramachandran diagram, a larger area represents sterically allowed torsion angles of Φ and Ψ that are allowed in _____ rather than in ______ because there is greater opportunity for separation of amino acid side chains.

β sheet... alpha helix