Molecular Biochem Test 2 Chp 6-8

In an -helix, which amino acid makes a hydrogen bond to the 2nd residue?

6th

Which statement about the structure of collagen is FALSE?

Cross-linking of collagen by Pro and Lys residues explains its low solubility.

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? Residue Numberφ Ψ31-61-4432-72-2933-66-6534-67-2335-81-51BreakBreakBreak42-3014243-14215044-15412145-9113646-110174

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

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

Hydrogen bonds.

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

The presence of O2 at pH 8.0 during renaturation.

Which statement about the structure of collagen is FALSE?

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

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

The two coils are held together by hydrogen bonds.

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

There is steric hindrance between the bulky Tyr and/or Trp side chains.

these are all correct

-Helix: a regular secondary structure discovered by Linus Pauling in 1951, in which the C=O oxygen of the nth residue makes a hydrogen bond to the N-H hydrogen of the (n+4)th residue of a polypeptide chain. Coiled-coil: two -helices that twist around each other to form a left-handed coil. Collagen helix: a triple helix composed of three left-handed helices that are wound around each other with a right-hand twist. -Sheet: a regular secondary structure, proposed by Pauling and Corey, in which extended polypeptide chains form interstrand hydrogen bonds. , Angles: The torsion angles describing rotation about the C -N and C -C bonds in a polypeptide chain. ω Loops: common, highly compact, peptide segments that typically occur on the protein surface and may have important roles in biological recognition processes. Peptide Bond: this bond lacks rotational freedom because of its 40% double-bond character. Ramachandran Diagram: a plot of , values that indicates the sterically allowed conformations of a polypeptide.

What is the probability of refolding a denatured protein to its native conformation, in which three disulfide bonds can form randomly from 6 Cys residues?

1/5 x 1/3 = 1/15

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

1° structure can determine 3° structure.

In a 12-residue -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

The first step in the folding of disordered polypeptides into ordered functional protein is the formation of ______.

2ndary

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

7th

Which of the following lines in the figure at right indicates a hairpin structure?

A B and D

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

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

Amino acid side chains protrude from one side of the β-sheet.

Which of the following statements is FALSE?

Both -helices and -sheets form only from adjacent (sequential) amino acid residues in the polypeptide.

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.

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

C=O

The computational tools described below facilitate the classification and comparison of protein structures. Which of the following pairings of a computational tool and a descriptive statement about it is INCORRECT:

CE: Finds proteins in the Protein Data Bank that can be structurally aligned with the query structure. The CE system uses the Molecular Modeling Database (MMDB), an NCBI-generated database that is derived from PDB coordinates but in which molecules are represented by connectivity graphs rather than sets of atomic coordinates.

Which statement about the structure of collagen is FALSE?

Collagen include the nonstandard residue 3-hydroxylysine (Hyl).

Which of statements in the following list pairing a term / structure / chemical with its definition or an effect it has on protein tertiary structure is INCORRECT:

Cosmotropic agent: Denatures proteins by increasing the solubility of nonpolar groups in water (e.g.'s include urea and the guanidinium ion).

Which of the following is not classified as a Molecular Graphics Program for viewing macromolecular structures in three dimensions?

Dali.

Which statement about disulfide bonds is false?

Disulfide bonds can occur between either Cys or Met residues.

Which statement below does not describe fibrous proteins?

Domains have a globular fold.

Which of the following labelings of symmetries of oligomeric proteins is incorrect:

E = D6

Molecular chaperones bind to unfolded or partially folded polypeptide chains in order to accomplish which of the following?

Ensure that improper aggregation of hydrophobic segments does not occur.

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

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

these are correct

GroEL and GroES: Highly symmetrical multi-subunit chaperonin complex that is essential for the survival of E. coli; GroEL resembles a hollow cylinder/barrel that is capped by GroES. (Chaperonins are a large multisubunit class of chaperones.) Molecular chaperones : Essential proteins that bind to unfolded and partially folded polypeptide chains to prevent the improper association of exposed hydrophobic segments that might lead to non-native folding as well as polypeptide aggregation and precipitation. Molecular chaperone: Binds to unfolded and partially folded proteins to prevent improper association of exposed hydrophobic segments. Molten globule: A collapsed state of a protein in which nonpolar groups are largely buried, but they are not well packed.

Which is NOT a result of the existence of Cys residues in -keratin?

Hair has the property of "springiness" when stretched slightly.

Which of the following pairings of an item related to protein folding and a descriptive statement about it is INCORRECT:

Heat shock proteins (Hsp) : Catalyze the formation of native disulfide bonds.

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

High concentrations of salts.

The short amino acid sequence shown below occurs within the longer amino acid sequence of a large protein. This specific portion of the amino acid sequence adopts an -helical conformation.............Ala-Val-Ala-Val-Ala-Val-Ala-Val-Ala-Val...............When the protein has adopted its tertiary conformation, which of the following hydrogen bonds are most likely to be formed by groups on the amino acid residues in this short segment?

Hydrogen bonds with other residues in the same -helix.

these are correct

Hydropathy value: A measure of the combined hydrophobicity and hydrophilicity of an amino acid residue. Hydrophobic effect: In proteins, the tendency of nonpolar side chains to minimize their contacts with water. Ion pairs: Electrostatic interactions that usually occur on the surfaces of proteins. Metal ion: Can stabilize folded proteins, e.g. by the tetrahedral coordination of Zn2+. Detergent: Interferes with the hydrophobic interactions responsible for a protein's native structure. Ribonuclease A: A protein that can rapidly renature spontaneously. Hydrogen bonds: They fine-tune tertiary structure by selecting a unique conformation among many hydrophobically-stabilized ones.

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

It disrupts ion pairs/salt bridges.

You have been shown the detailed 3-D structure of an unknown protein. The information indicates that the protein's non-polar amino acid side chains are all exposed on the surface, whereas its polar side chains are all "buried" in the interior. What can you conclude about this protein?

It is likely to be an integral membrane protein.

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

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.

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.

Which of the following contribute to the minimization of energy that occurs with protein folding?

Orientating amino acid groups to maximize hydrogen bonding.

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.

Which of the following is TRUE about prosthetic groups?

Prosthetic groups are an integral part of the three dimensional structure of the protein.

Which of the following statements about prosthetic groups is INCORRECT?

Prosthetic groups form an integral part of the secondary structure of proteins.

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

Proteins are marginally stable in solution.

Which of the following does NOT support the existence of protein folding pathways?

Proteins lose entropy when they fold into a compact conformation.

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

Proteins of similar tertiary structure tend to have a very similar 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.

Which of the following statements about quaternary structure is TRUE?

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

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

Residues located within the same -helix.

Which of statements in the following list pairing a biochemical term related to protein structure with its definition or a statement concerning it is INCORRECT:

Reverse turns: usually composed of 3 successive residues that cause an abrupt change in the direction of the polypeptide.

Why would you be unlikely to see an helix containing only the following amino acids: Arg, Lys, Met, Phe, Trp, Tyr, Val?

Steric hindrance between the side chains projected from the side of the helix.

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

The -helix is a type of secondary structure that fulfills the hydrogen bonding requirements of amino acid side chains.

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.

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

The exclusion of non-polar substances from aqueous solution.

Compare the -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.

Which of the following statements about peptide bonds is FALSE?

The peptide bond has restricted rotation around the bond between the carbonyl carbon and C.

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.

Which of the following statements is NOT correct with respect to the ribbon diagrams shown?

The secondary structure of protein 3 is composed entirely of -helices

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

The sequence of the amino acid residues.

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.

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

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

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

They are found on the exterior of the helix.

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

They contain 20-50 amino acids.

What is the major role played by prosthetic groups in proteins?

They provide reactive groups not found in amino acid side chains.

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.

A domain is:

a folded segment of polypeptide with a separate hydrophobic core.

Which of the following occurs first when folding a disordered polypeptide chain into a stable protein formation?

aggregation of hydrophobic regions in the protein

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

ala

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

charged

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

cis

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

disulfide bridges

Which of the following is not a disease that is caused by protein misfolding?

down's syndrome

Evolutionary processes have

enhanced efficient folding pathways.

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

fold inside a fold

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?

helix collagen helix β sheet all of the above

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

helix and sheet, favorable

A chaperonin

helps fold some proteins in their lowest energy state.

Which of the following pairings of a supersecondary structure / motif and a statement describing it is INCORRECT:

immunoglobulin fold: two - - - - units that combine to form a dinucleotide-binding site.

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

it is a phosphodiester bond

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

linus pauling

Proteins can denature due to a change in

pH. temperature. ionic strength. all of the above.

In general molecular chaperone proteins function by

preventing premature folding by binding hydrophobic regions of the protein.

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

pro, gly

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

protein denaturation

Chaperonins such as the GroEL/ES system

require ATP hydrolysis.

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

scurvy

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

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

the 'direction' of the associated peptide strands

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

val, leu