Which one of the following statements about peptide bonds is FALSE. Peptide bonds are:
-charged.
-covalent.
-involved in forming the primary structure of proteins.
-amides.
-rigid and planar, with partial double-bond character.
charged.
Which of the following describes the entire three-dimensional structure of a single polypeptide?
Tertiary structure
Quaternary structure
Primary structure
Secondary structure
Tertiary structure
Which of the following amino acid residues form hydrogen bonds with Ala residues located in an alpha-helix?
-Polar residues involved in the stabilization of tertiary structure.
-Residues located within the same -helix.
-Residues in a neighbouring -helix.
Residues located within the same -helix.
A domain is:
-a folded segment of polypeptide with -a separate hydrophobic core.
-an -helix, ?-sheet or irregular secondary structure.
-the same as a protein's tertiary structure.
-always a motif.
a folded segment of polypeptide with -a separate hydrophobic core.
Which level of protein structure is defined as "the hydrogen bonded arrangement of the polypeptide backbone"?
Which level of protein structure is defined as "the hydrogen bonded arrangement of the polypeptide backbone"?
Secondary
Tertiary
Quaternary
Prima
Secondary
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.
-On the surface because they are less compact.
-In the core of the protein so that they can
On the surface so that they can interact with the solvent.
Which of the following statements about quaternary structure is TRUE?
-Quaternary structure is defined as the 3D structure of proteins with four subunits.
-Quaternary structure requires covalent interactions between polypeptide chains.
-Quaternary structu
Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
Which of the following series of amino acids is most likely to be buried in the center of a water-soluble globular protein?
Pro, Gln, His
Gly, Asn, Ser
Glu, Asp, Lys
Ala, Leu, Phe
Ala, Leu, Phe
Which of the following statements about peptide bonds is FALSE?
-Water is released when a peptide bond is formed.
-The peptide bond exhibits partial double bond character
-The peptide bond has restricted rotation around the bond between the carbonyl carbo
The peptide bond has restricted rotation around the bond between the carbonyl carbon and C.
Which one of the following sequences of five amino acids would most likely be located in the interior of a water soluble globular protein?
Tyr-Phe-Glu-Asn-Leu
Met-Phe-Pro-Ile-Leu
Glu-Asn-Ser-Thr-Gln
Val-Ala-Val-Glu-Val
Met-Phe-Pro-Ile-Leu
Compare the -helix with the structure of double-stranded DNA. Which statement is TRUE for both structures?
-The backbones are on the outside of the helix.
-The hydrogen bonds are perpendicular to the axis of the helix.
-Hydrogen bonds are the primary dete
The helices are right handed
Which one of the following statements about the ?-sheet is FALSE?
-The side chains in a ?-sheet alternate between the two sides of the sheet.
-The ?-sheet is a type of regular secondary structure.
-The ?-sheet is a type of secondary structure that fulfill
The ?-sheet is a type of secondary structure that fulfills the hydrogen bonding requirements of amino acid side chains.
What ultimately determines the unique three dimensional structure of soluble globular proteins?
-The number of subunits.
-The exact number of disulfide bonds.
-The exact number of H-bonds.
-The sequence of the amino acid residues.
-The prosthetic groups.
The sequence of the amino acid residues.
Which of the following sequences of amino acids is most likely to be at the surface of a water-soluble globular protein?
Pro-Phe-Thr
Ala-Leu-Phe
Gly-Tyr-Val
Glu-Asp-Lys
Ile-Ser-Met
Glu-Asp-Lys
Which of the following stabilizes the folding of a polypeptide backbone into regular secondary structure?
Disulphide bridges.
Hydrogen bonds.
Covalent bonds.
Electrostatic interactions.
Hydrophobic interactions.
Hydrogen bonds.
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 exists only in proteins containing more than one polyp
Quaternary structure is defined as the arrangement of polypeptide backbones in proteins with four subunits
Which one of the following statements about the -helix is FALSE?
-Side chains are located on the outside of an -helix.
-The -helix contains hydrogen bonds between the carbonyl oxygen of one residue and an amide hydrogen that is four residues closer to the
The -helix is a type of secondary structure that fulfills the hydrogen bonding requirements of amino acid side chains.
Which of the following is TRUE about prosthetic groups?
-Prosthetic groups are bound and released by the protein as needed.
-Prosthetic groups are an integral part of the three dimensional structure of the protein.
-Prosthetic groups are amino acids with
Prosthetic groups are an integral part of the three dimensional structure of the protein
Which of the following is FALSE with respect to ?-sheets?
-?-sheets may be parallel or anti-parallel.
-Strands in a ?-sheet are connected by irregular loops.
-?-sheets are stabilized by non-covalent forces.
-Amino acid side chains protrude from one side o
Amino acid side chains protrude from one side of the ?-sheet.
Which of the following statements about prosthetic groups is INCORRECT?
-Heme is an example of a prosthetic group.
-Prosthetic groups increase the inherent chemical reactivity of proteins.
-Prosthetic groups are not amino acids.
-Prosthetic groups form an
Prosthetic groups form an integral part of the secondary structure of proteins.
Which of the following statements about the -helix and ?-sheet are TRUE?
1. They are both types of secondary structure.
2. They are both stabilized by hydrogen bonds between amino acid side chains.
3. The polypeptide backbone is fully extended in both str
1 and 4
Which of the following statements about the peptide bond is FALSE?
-It is a bond that displays resonance.
-It is a phosphodiester bond.
-It exhibits partial double bond character.
-Atoms of the peptide bond are located in a single plane.
-It is formed whe
It is a phosphodiester bond.
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.
-They alternate between the outside and the inside of the helix.
-They form the hydrogen bonds that produce
They are found on the exterior of the helix.
Which of the following statements is FALSE?
-Both -helices and ?-sheets have conformations that minimize steric strain in the polypeptide backbone.
-Both -helices and ?-sheets have R groups that are oriented away from the core of the structure.
-Both -hel
Both -helices and ?-sheets form only from adjacent amino acid residues in the polypeptide.
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 yo
It is likely to be an integral membrane protein.
Why do Tyr and/or Trp residues tend to destabilize an -helix when they occur next to each other in a protein?
-The R group of neither amino acid can form a hydrogen bond.
-There is steric hindrance between the bulky Tyr and/or Trp side chains.
-There are
There is steric hindrance between the bulky Tyr and/or Trp side chains.
Which of the following is TRUE for a ?-pleated sheet?
A. There are hydrogen bonds perpendicular to the direction of the polypeptide chain.
B. The polypeptide chain is almost fully extended
C. The polypeptide chains may be hydrogen bonded together in paral
A, B, and C are correct
What is the major role played by prosthetic groups in proteins?
-They provide reactive groups not found in amino acid side chains.
-They bind to the enzyme, participate in the catalytic reaction, and then leave the active site.
-They are required to promo
They provide reactive groups not found in amino acid side chains.
Why does a decrease in pH alter/disrupt the tertiary structure of an enzyme?
-It reduces disulphide bonds.
-It promotes proteolytic cleavage of peptide bonds.
-It disrupts ion pairs/salt bridges.
-It reduces hydrophobic interactions.
-It deprotonates pros
It disrupts ion pairs/salt bridges
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
Val-Thr-Val-Glu-Val
Tyr-Phe-Glu-Asn-Leu
Met-Phe-Pro-Ile-Leu
Glu-Asn-Ser-Thr-Gln
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...............
Hydrogen bonds with other residues in the same -helix.
In an -helix, which amino acid makes a hydrogen bond to the 2nd residue?
6th.
1st.
3rd.
5th.
6th.
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?
0 and 0.
1 and 1.
3 and 2.
2 and 1
2 and 1
Who is credited with the discovery of the -helix secondary structure of proteins?
Watson and Crick.
Linus Pauling.
Robert Corey.
Chou and Fasman.
Linus Pauling.
Which statement about disulfide bonds is false?
-Disulfide bonds can occur between two different polypeptide chains.
-Disulfide bonds help stabilize extracellular proteins.
-Disulfide bonds are rare in intracellular proteins because the cytoplasm is a red
Disulfide bonds can occur between either Cys or Met residues.
Which treatment is least likely to cause a protein to denature?
-Temperatures approaching 100oC.
-High concentrations of salts
-Extremes of pH.
-High concentrations of chaotropic agents like urea or the guanidinium ion
-High concentrations of detergents l
High concentrations of salts
Which statement about the structure of collagen is FALSE?
Cross-linking of collagen by Pro and Lys residues explains its low solubility.
Lysyl oxidase, the enzyme that converts Lys residues to those of the aldehyde allysine, is the only enzyme implicated
Cross-linking of collagen by Pro and Lys residues explains its low solubility.
In an -helix, which amino acid residue makes a hydrogen bond to the 3rd residue?
1st
7th
6th
4th
7th
Which group of the 3rd residue is used to make its hydrogen bond in the -helix?
-side chain
-C-H
-C=O
-N-H
C=O
Which of the following is NOT a feature of the -keratin coiled-coil?
-The two coils are held together by hydrogen bonds.
-A seven-residue pseudo-repeat occurs, with contact between coils mediated by residues at positions a and d.
-The two coils have a sli
The two coils are held together by hydrogen bonds.
Which of the following is NOT a feature of the peptide bond?
-As a result of the peptide bond, only two dihedral angles per residue in a polypeptide chain can vary freely.
-Six atoms, including two alpha-carbons are in the plane of each peptide bond.
-The
The peptide bond has 10% double bond character.
Which statement about the structure of collagen is FALSE?
-Collagen has the general repeating sequence (Gly-X-Y)n, where X is often Pro and Y is often 4-hydroxyproline (Hyp).
-Collagen is formed by three left-handed helices.
-Glycine is essential at every
The three helices of collagen form a left-handed superhelix.
Which of the following statements is true because of the hydrophobic effect?
-Charged polar residues R, H, K, E, and D are usually found on the surfaces of proteins.
-Uncharged polar residues S, T, N, Q, and Y are usually found on the surface of proteins,
Nonpolar residues V, L, I, M, and F are found in the interior of proteins
Which statement is not a consequence of the hydrophobic effect?
-The entropy of water increases when proteins fold.
-Metal ions can function to stabilize folded proteins.
-The folding of proteins is generally a favorable process.
-Nonpolar side chains are
Metal ions can function to stabilize folded proteins.
Which pairs of amino acid side chains could not interact in the interior of a protein by hydrogen bonding?
Asp, Asn
Ala, Lys
Gln, Thr
Ser, His
Ala, Lys
Which pair of amino acid side chains could form an ion pair?
Glu, Gly
Lys, Arg
Asp, Gln
His, Asp
His, Asp
Irregular loops of secondary structure tend to be located on the outside of folded proteins because:
-The side chains in loop structures are free to form H bonds with water.
-These regions of a peptide tend to contain mostly polar side chains.
-The peptid
The peptide bonds in loop structures are free to form H bonds with water.
What is the primary driving force in the formation of protein tertiary structure?
-The formation of van der Waals interactions between neighbouring groups.
-The exclusion of non-polar substances from aqueous solution.
-Energy released when additional hydr
The exclusion of non-polar substances from aqueous solution.
Which of the following statements about quaternary structure is TRUE?
-Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
-Quaternary structure is defined as the 3D structure of proteins with four subun
Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
What BEST distinguishes irregular secondary structure from regular secondary structure?
-Irregular secondary structure is disordered (random) whereas regular secondary structure is ordered.
-In a given protein the conformation of irregular secondary struc
Unlike regular secondary structure, successive residues in irregular secondary structure do not have the same backbone configuration.
Which of the following statements about quaternary structure is FALSE?
-Quaternary structure is fine-tuned by ion pairs, disulfide bonds, and hydrogen bonds.
-Quaternary structure is defined as the arrangement of polypeptide backbones in proteins with fou
Quaternary structure is defined as the arrangement of polypeptide backbones in proteins with four
What is the major factor that "drives" the folding of proteins into their tertiary structure?
-Formation of the maximum number of ionic interactions.
-Formation of the maximum number of hydrophilic interactions.
-Placement of polar amino acid residues on
Placement of hydrophobic amino acid residues within the interior of the protein.
Which of the following statements about quaternary structure is TRUE?
-Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
-Quaternary structure is defined as the precise, 3-D arrangement of polypeptide
Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
In a Ramachandran diagram, ______ of the area represents allowed conformations of a polypeptide chain.
more than 90%
more than 50%
about 50%
less than 25%
none of the above
less than 25%
Conformation(s) that has (have) both a favorable hydrogen bonding pattern and and values that fall within the allowed Ramachandran conformational regions is (are)
helix.
collagen helix.
sheet.
All of the above.
None of the above
All of the above.
Which one of these characteristics is not true for the helix?
-Proline is typically not found in the helix.
-There is a requirement for glycine every third amino acid residue.
-It is right-handed.
-There are 3.6 amino acids per turn.
-A hydrogen bond form
There is a requirement for glycine every third amino acid residue.
Which statement below does not describe fibrous proteins?
-The proteins are usually water soluble.
-Domains are compact and globular.
-These proteins usually perform a protective, connective, or supportive role in the organism.
-These proteins are usually
Domains are compact and globular
Crystalline proteins assume nearly the same structures as the proteins in solution. Several lines of evidence support this statement; which is the most compelling?
-Different crystal forms of the same protein have virtually identical conformations.
-Enzym
Enzymes are often catalytically active in the crystalline state
Of the following, which amino acid is least likely to be found on the surface of a single-subunit protein?
Trp
Ser
Gly
Asp
Lys
Trp
Lysine can form a salt bridge by associating with a nearby _____ residue.
Pro
Ser
Glu
Gln
Gly
Glu
The low pH found in the gut can enhance the digestibility of dietary protein by causing _____.
-prion formation
-protein denaturation
-amide hydrolysis
-cysteine oxidation
-disulfide reduction
protein denaturation
For -sheets, the terms 'parallel' and 'anti-paralllel' refer to ___________.
-the quaternary structure of the protein
-the orientation of the hydrogen bonding
-the orientation of the amide crosslinks
-the topology of the reverse turns
-the 'direction' of
the 'direction' of the associated peptide strands
In protein X-ray crystallography, X-ray radiation is utilized because _______.
-X-ray lenses are very precise
-X-ray diffraction patterns are most readily interpreted
-the colors of protein crystals block visible light
-the wavelength of X-ray radiation i
the wavelength of X-ray radiation is close to the observed covalent bond lengths
The classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates that _______.
-1� structure can determine 3� structure
-denaturation does not disrupt protein 2� structure
-disulfide bonds do not stabi
1� structure can determine 3� structure
Evolutionary processes have resulted in proteins having ________.
-core ion-pairing
-efficient folding pathways
-extremely stable 3� structures
-single subunits
-similar 1� structures
efficient folding pathways
Molecular chaperones assist proteins in the formation of ________.
-aggregates
-3� structure
-amide bonds
-1� structure
-none of the above
3� structure
Chaperonins such as the GroEL/ES system function ____.
-with thermophilic proteins only
-at low pH
-in an ATP-dependent fashion
-in a non-aqueous environment
-in vitro only
in an ATP-dependent fashion
Protein diseases are caused by _____.
-mutations affecting the 1� structure
-mutations affecting the 3� structure
-changes in the post-synthetic -processing of proteins
-All of the above.
-None of the above.
All of the above.
Which of the following pairings of a supersecondary structure / motif and a statement describing it is INCORRECT:
-immunoglobulin fold: two beta-alpha-beta-alpha-beta units that combine to form a dinucleotide-binding site.
-beta-hairpin motif: two anti-pa
immunoglobulin fold: two beta-alpha-beta-alpha-beta units that combine to form a dinucleotide-binding site.
Which of the following statements about domains found in multi-domain proteins is false?
-They contain 20-50 amino acids.
-They are often structurally independent.
-They resemble small, globular proteins.
-They often have specialized functions
They contain 20-50 amino acids
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.
-Known geometric constraints such as covalent bond
The ability of the protein to crystallize.
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:
-Hydrophobic effect: In proteins, the tendency of nonpolar side chains to minimize their co
Cosmotropic agent: Denatures proteins by increasing the solubility of nonpolar groups in water (e.g.'s include urea and the guanidinium ion)
Which pairs of amino acid side chains could interact in the interior of a protein only via van der Waals interactions?
Arg, Thr.
Gln, His.
Val, Leu.
Ser, Ser.
Val, Leu
Which of the following pairings of an item related to protein folding and a descriptive statement about it is INCORRECT:
-Molecular chaperones : Essential proteins that bind to unfolded and partially folded polypeptide chains to prevent the improper assoc
Heat shock proteins (Hsp) : Catalyze the formation of native disulfide bonds.
Which of the following is not a disease that is caused by protein misfolding?
Down's syndrome.
Bovine spongiform encephalopathy.
Alzheimer's disease.
Creutzfeldt-Jakob disease.
Down's syndrome.
Which statement about the structure of collagen is FALSE?
The introduction of vitamin C containing limes to the diet of the British navy alleviated scurvy and led to the nickname "limey" for the British sailor.
The modified prolines found in collagen are
Collagen include the nonstandard residue 3-hydroxylysine (Hyl)
In the experiment of Christian Anfinsen, which condition permitted Ribonuclease A to renature?
-The presence of O2 at pH 8.0 during renaturation.
-The use of 8 M urea to denature the protein.
-The presence of 2-mercaptoethanol during denaturation.
-Exposu
The presence of O2 at pH 8.0 during renaturation.
Which is NOT a conclusion drawn from the experiments of Christian Anfinsen about renaturation of Ribonuclease A?
-A protein's primary structure can determine its tertiary structure.
-A protein can fold spontaneously to its native structure without the -pr
Proteins are marginally stable in solution
Which one of the following statements about peptide bonds is FALSE. Peptide bonds are:
-charged.
-covalent.
-involved in forming the primary structure of proteins.
-amides.
-rigid and planar, with partial double-bond character.
charged.
Which of the following describes the entire three-dimensional structure of a single polypeptide?
Tertiary structure
Quaternary structure
Primary structure
Secondary structure
Tertiary structure
Which of the following amino acid residues form hydrogen bonds with Ala residues located in an alpha-helix?
-Polar residues involved in the stabilization of tertiary structure.
-Residues located within the same -helix.
-Residues in a neighbouring -helix.
Residues located within the same -helix.
A domain is:
-a folded segment of polypeptide with -a separate hydrophobic core.
-an -helix, ?-sheet or irregular secondary structure.
-the same as a protein's tertiary structure.
-always a motif.
a folded segment of polypeptide with -a separate hydrophobic core.
Which level of protein structure is defined as "the hydrogen bonded arrangement of the polypeptide backbone"?
Which level of protein structure is defined as "the hydrogen bonded arrangement of the polypeptide backbone"?
Secondary
Tertiary
Quaternary
Prima
Secondary
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.
-On the surface because they are less compact.
-In the core of the protein so that they can
On the surface so that they can interact with the solvent.
Which of the following statements about quaternary structure is TRUE?
-Quaternary structure is defined as the 3D structure of proteins with four subunits.
-Quaternary structure requires covalent interactions between polypeptide chains.
-Quaternary structu
Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
Which of the following series of amino acids is most likely to be buried in the center of a water-soluble globular protein?
Pro, Gln, His
Gly, Asn, Ser
Glu, Asp, Lys
Ala, Leu, Phe
Ala, Leu, Phe
Which of the following statements about peptide bonds is FALSE?
-Water is released when a peptide bond is formed.
-The peptide bond exhibits partial double bond character
-The peptide bond has restricted rotation around the bond between the carbonyl carbo
The peptide bond has restricted rotation around the bond between the carbonyl carbon and C.
Which one of the following sequences of five amino acids would most likely be located in the interior of a water soluble globular protein?
Tyr-Phe-Glu-Asn-Leu
Met-Phe-Pro-Ile-Leu
Glu-Asn-Ser-Thr-Gln
Val-Ala-Val-Glu-Val
Met-Phe-Pro-Ile-Leu
Compare the -helix with the structure of double-stranded DNA. Which statement is TRUE for both structures?
-The backbones are on the outside of the helix.
-The hydrogen bonds are perpendicular to the axis of the helix.
-Hydrogen bonds are the primary dete
The helices are right handed
Which one of the following statements about the ?-sheet is FALSE?
-The side chains in a ?-sheet alternate between the two sides of the sheet.
-The ?-sheet is a type of regular secondary structure.
-The ?-sheet is a type of secondary structure that fulfill
The ?-sheet is a type of secondary structure that fulfills the hydrogen bonding requirements of amino acid side chains.
What ultimately determines the unique three dimensional structure of soluble globular proteins?
-The number of subunits.
-The exact number of disulfide bonds.
-The exact number of H-bonds.
-The sequence of the amino acid residues.
-The prosthetic groups.
The sequence of the amino acid residues.
Which of the following sequences of amino acids is most likely to be at the surface of a water-soluble globular protein?
Pro-Phe-Thr
Ala-Leu-Phe
Gly-Tyr-Val
Glu-Asp-Lys
Ile-Ser-Met
Glu-Asp-Lys
Which of the following stabilizes the folding of a polypeptide backbone into regular secondary structure?
Disulphide bridges.
Hydrogen bonds.
Covalent bonds.
Electrostatic interactions.
Hydrophobic interactions.
Hydrogen bonds.
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 exists only in proteins containing more than one polyp
Quaternary structure is defined as the arrangement of polypeptide backbones in proteins with four subunits
Which one of the following statements about the -helix is FALSE?
-Side chains are located on the outside of an -helix.
-The -helix contains hydrogen bonds between the carbonyl oxygen of one residue and an amide hydrogen that is four residues closer to the
The -helix is a type of secondary structure that fulfills the hydrogen bonding requirements of amino acid side chains.
Which of the following is TRUE about prosthetic groups?
-Prosthetic groups are bound and released by the protein as needed.
-Prosthetic groups are an integral part of the three dimensional structure of the protein.
-Prosthetic groups are amino acids with
Prosthetic groups are an integral part of the three dimensional structure of the protein
Which of the following is FALSE with respect to ?-sheets?
-?-sheets may be parallel or anti-parallel.
-Strands in a ?-sheet are connected by irregular loops.
-?-sheets are stabilized by non-covalent forces.
-Amino acid side chains protrude from one side o
Amino acid side chains protrude from one side of the ?-sheet.
Which of the following statements about prosthetic groups is INCORRECT?
-Heme is an example of a prosthetic group.
-Prosthetic groups increase the inherent chemical reactivity of proteins.
-Prosthetic groups are not amino acids.
-Prosthetic groups form an
Prosthetic groups form an integral part of the secondary structure of proteins.
Which of the following statements about the -helix and ?-sheet are TRUE?
1. They are both types of secondary structure.
2. They are both stabilized by hydrogen bonds between amino acid side chains.
3. The polypeptide backbone is fully extended in both str
1 and 4
Which of the following statements about the peptide bond is FALSE?
-It is a bond that displays resonance.
-It is a phosphodiester bond.
-It exhibits partial double bond character.
-Atoms of the peptide bond are located in a single plane.
-It is formed whe
It is a phosphodiester bond.
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.
-They alternate between the outside and the inside of the helix.
-They form the hydrogen bonds that produce
They are found on the exterior of the helix.
Which of the following statements is FALSE?
-Both -helices and ?-sheets have conformations that minimize steric strain in the polypeptide backbone.
-Both -helices and ?-sheets have R groups that are oriented away from the core of the structure.
-Both -hel
Both -helices and ?-sheets form only from adjacent amino acid residues in the polypeptide.
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 yo
It is likely to be an integral membrane protein.
Why do Tyr and/or Trp residues tend to destabilize an -helix when they occur next to each other in a protein?
-The R group of neither amino acid can form a hydrogen bond.
-There is steric hindrance between the bulky Tyr and/or Trp side chains.
-There are
There is steric hindrance between the bulky Tyr and/or Trp side chains.
Which of the following is TRUE for a ?-pleated sheet?
A. There are hydrogen bonds perpendicular to the direction of the polypeptide chain.
B. The polypeptide chain is almost fully extended
C. The polypeptide chains may be hydrogen bonded together in paral
A, B, and C are correct
What is the major role played by prosthetic groups in proteins?
-They provide reactive groups not found in amino acid side chains.
-They bind to the enzyme, participate in the catalytic reaction, and then leave the active site.
-They are required to promo
They provide reactive groups not found in amino acid side chains.
Why does a decrease in pH alter/disrupt the tertiary structure of an enzyme?
-It reduces disulphide bonds.
-It promotes proteolytic cleavage of peptide bonds.
-It disrupts ion pairs/salt bridges.
-It reduces hydrophobic interactions.
-It deprotonates pros
It disrupts ion pairs/salt bridges
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
Val-Thr-Val-Glu-Val
Tyr-Phe-Glu-Asn-Leu
Met-Phe-Pro-Ile-Leu
Glu-Asn-Ser-Thr-Gln
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...............
Hydrogen bonds with other residues in the same -helix.
In an -helix, which amino acid makes a hydrogen bond to the 2nd residue?
6th.
1st.
3rd.
5th.
6th.
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?
0 and 0.
1 and 1.
3 and 2.
2 and 1
2 and 1
Who is credited with the discovery of the -helix secondary structure of proteins?
Watson and Crick.
Linus Pauling.
Robert Corey.
Chou and Fasman.
Linus Pauling.
Which statement about disulfide bonds is false?
-Disulfide bonds can occur between two different polypeptide chains.
-Disulfide bonds help stabilize extracellular proteins.
-Disulfide bonds are rare in intracellular proteins because the cytoplasm is a red
Disulfide bonds can occur between either Cys or Met residues.
Which treatment is least likely to cause a protein to denature?
-Temperatures approaching 100oC.
-High concentrations of salts
-Extremes of pH.
-High concentrations of chaotropic agents like urea or the guanidinium ion
-High concentrations of detergents l
High concentrations of salts
Which statement about the structure of collagen is FALSE?
Cross-linking of collagen by Pro and Lys residues explains its low solubility.
Lysyl oxidase, the enzyme that converts Lys residues to those of the aldehyde allysine, is the only enzyme implicated
Cross-linking of collagen by Pro and Lys residues explains its low solubility.
In an -helix, which amino acid residue makes a hydrogen bond to the 3rd residue?
1st
7th
6th
4th
7th
Which group of the 3rd residue is used to make its hydrogen bond in the -helix?
-side chain
-C-H
-C=O
-N-H
C=O
Which of the following is NOT a feature of the -keratin coiled-coil?
-The two coils are held together by hydrogen bonds.
-A seven-residue pseudo-repeat occurs, with contact between coils mediated by residues at positions a and d.
-The two coils have a sli
The two coils are held together by hydrogen bonds.
Which of the following is NOT a feature of the peptide bond?
-As a result of the peptide bond, only two dihedral angles per residue in a polypeptide chain can vary freely.
-Six atoms, including two alpha-carbons are in the plane of each peptide bond.
-The
The peptide bond has 10% double bond character.
Which statement about the structure of collagen is FALSE?
-Collagen has the general repeating sequence (Gly-X-Y)n, where X is often Pro and Y is often 4-hydroxyproline (Hyp).
-Collagen is formed by three left-handed helices.
-Glycine is essential at every
The three helices of collagen form a left-handed superhelix.
Which of the following statements is true because of the hydrophobic effect?
-Charged polar residues R, H, K, E, and D are usually found on the surfaces of proteins.
-Uncharged polar residues S, T, N, Q, and Y are usually found on the surface of proteins,
Nonpolar residues V, L, I, M, and F are found in the interior of proteins
Which statement is not a consequence of the hydrophobic effect?
-The entropy of water increases when proteins fold.
-Metal ions can function to stabilize folded proteins.
-The folding of proteins is generally a favorable process.
-Nonpolar side chains are
Metal ions can function to stabilize folded proteins.
Which pairs of amino acid side chains could not interact in the interior of a protein by hydrogen bonding?
Asp, Asn
Ala, Lys
Gln, Thr
Ser, His
Ala, Lys
Which pair of amino acid side chains could form an ion pair?
Glu, Gly
Lys, Arg
Asp, Gln
His, Asp
His, Asp
Irregular loops of secondary structure tend to be located on the outside of folded proteins because:
-The side chains in loop structures are free to form H bonds with water.
-These regions of a peptide tend to contain mostly polar side chains.
-The peptid
The peptide bonds in loop structures are free to form H bonds with water.
What is the primary driving force in the formation of protein tertiary structure?
-The formation of van der Waals interactions between neighbouring groups.
-The exclusion of non-polar substances from aqueous solution.
-Energy released when additional hydr
The exclusion of non-polar substances from aqueous solution.
Which of the following statements about quaternary structure is TRUE?
-Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
-Quaternary structure is defined as the 3D structure of proteins with four subun
Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
What BEST distinguishes irregular secondary structure from regular secondary structure?
-Irregular secondary structure is disordered (random) whereas regular secondary structure is ordered.
-In a given protein the conformation of irregular secondary struc
Unlike regular secondary structure, successive residues in irregular secondary structure do not have the same backbone configuration.
Which of the following statements about quaternary structure is FALSE?
-Quaternary structure is fine-tuned by ion pairs, disulfide bonds, and hydrogen bonds.
-Quaternary structure is defined as the arrangement of polypeptide backbones in proteins with fou
Quaternary structure is defined as the arrangement of polypeptide backbones in proteins with four
What is the major factor that "drives" the folding of proteins into their tertiary structure?
-Formation of the maximum number of ionic interactions.
-Formation of the maximum number of hydrophilic interactions.
-Placement of polar amino acid residues on
Placement of hydrophobic amino acid residues within the interior of the protein.
Which of the following statements about quaternary structure is TRUE?
-Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
-Quaternary structure is defined as the precise, 3-D arrangement of polypeptide
Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
In a Ramachandran diagram, ______ of the area represents allowed conformations of a polypeptide chain.
more than 90%
more than 50%
about 50%
less than 25%
none of the above
less than 25%
Conformation(s) that has (have) both a favorable hydrogen bonding pattern and and values that fall within the allowed Ramachandran conformational regions is (are)
helix.
collagen helix.
sheet.
All of the above.
None of the above
All of the above.
Which one of these characteristics is not true for the helix?
-Proline is typically not found in the helix.
-There is a requirement for glycine every third amino acid residue.
-It is right-handed.
-There are 3.6 amino acids per turn.
-A hydrogen bond form
There is a requirement for glycine every third amino acid residue.
Which statement below does not describe fibrous proteins?
-The proteins are usually water soluble.
-Domains are compact and globular.
-These proteins usually perform a protective, connective, or supportive role in the organism.
-These proteins are usually
Domains are compact and globular
Crystalline proteins assume nearly the same structures as the proteins in solution. Several lines of evidence support this statement; which is the most compelling?
-Different crystal forms of the same protein have virtually identical conformations.
-Enzym
Enzymes are often catalytically active in the crystalline state
Of the following, which amino acid is least likely to be found on the surface of a single-subunit protein?
Trp
Ser
Gly
Asp
Lys
Trp
Lysine can form a salt bridge by associating with a nearby _____ residue.
Pro
Ser
Glu
Gln
Gly
Glu
The low pH found in the gut can enhance the digestibility of dietary protein by causing _____.
-prion formation
-protein denaturation
-amide hydrolysis
-cysteine oxidation
-disulfide reduction
protein denaturation
For -sheets, the terms 'parallel' and 'anti-paralllel' refer to ___________.
-the quaternary structure of the protein
-the orientation of the hydrogen bonding
-the orientation of the amide crosslinks
-the topology of the reverse turns
-the 'direction' of
the 'direction' of the associated peptide strands
In protein X-ray crystallography, X-ray radiation is utilized because _______.
-X-ray lenses are very precise
-X-ray diffraction patterns are most readily interpreted
-the colors of protein crystals block visible light
-the wavelength of X-ray radiation i
the wavelength of X-ray radiation is close to the observed covalent bond lengths
The classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates that _______.
-1� structure can determine 3� structure
-denaturation does not disrupt protein 2� structure
-disulfide bonds do not stabi
1� structure can determine 3� structure
Evolutionary processes have resulted in proteins having ________.
-core ion-pairing
-efficient folding pathways
-extremely stable 3� structures
-single subunits
-similar 1� structures
efficient folding pathways
Molecular chaperones assist proteins in the formation of ________.
-aggregates
-3� structure
-amide bonds
-1� structure
-none of the above
3� structure
Chaperonins such as the GroEL/ES system function ____.
-with thermophilic proteins only
-at low pH
-in an ATP-dependent fashion
-in a non-aqueous environment
-in vitro only
in an ATP-dependent fashion
Protein diseases are caused by _____.
-mutations affecting the 1� structure
-mutations affecting the 3� structure
-changes in the post-synthetic -processing of proteins
-All of the above.
-None of the above.
All of the above.
Which of the following pairings of a supersecondary structure / motif and a statement describing it is INCORRECT:
-immunoglobulin fold: two beta-alpha-beta-alpha-beta units that combine to form a dinucleotide-binding site.
-beta-hairpin motif: two anti-pa
immunoglobulin fold: two beta-alpha-beta-alpha-beta units that combine to form a dinucleotide-binding site.
Which of the following statements about domains found in multi-domain proteins is false?
-They contain 20-50 amino acids.
-They are often structurally independent.
-They resemble small, globular proteins.
-They often have specialized functions
They contain 20-50 amino acids
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.
-Known geometric constraints such as covalent bond
The ability of the protein to crystallize.
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:
-Hydrophobic effect: In proteins, the tendency of nonpolar side chains to minimize their co
Cosmotropic agent: Denatures proteins by increasing the solubility of nonpolar groups in water (e.g.'s include urea and the guanidinium ion)
Which pairs of amino acid side chains could interact in the interior of a protein only via van der Waals interactions?
Arg, Thr.
Gln, His.
Val, Leu.
Ser, Ser.
Val, Leu
Which of the following pairings of an item related to protein folding and a descriptive statement about it is INCORRECT:
-Molecular chaperones : Essential proteins that bind to unfolded and partially folded polypeptide chains to prevent the improper assoc
Heat shock proteins (Hsp) : Catalyze the formation of native disulfide bonds.
Which of the following is not a disease that is caused by protein misfolding?
Down's syndrome.
Bovine spongiform encephalopathy.
Alzheimer's disease.
Creutzfeldt-Jakob disease.
Down's syndrome.
Which statement about the structure of collagen is FALSE?
The introduction of vitamin C containing limes to the diet of the British navy alleviated scurvy and led to the nickname "limey" for the British sailor.
The modified prolines found in collagen are
Collagen include the nonstandard residue 3-hydroxylysine (Hyl)
In the experiment of Christian Anfinsen, which condition permitted Ribonuclease A to renature?
-The presence of O2 at pH 8.0 during renaturation.
-The use of 8 M urea to denature the protein.
-The presence of 2-mercaptoethanol during denaturation.
-Exposu
The presence of O2 at pH 8.0 during renaturation.
Which is NOT a conclusion drawn from the experiments of Christian Anfinsen about renaturation of Ribonuclease A?
-A protein's primary structure can determine its tertiary structure.
-A protein can fold spontaneously to its native structure without the -pr
Proteins are marginally stable in solution