Proteins: Secondary, Tertiary, and Quaternary Structure
Amino acid side chains capable of forming hydrogen bonds are usually located on the protein ___________ and form hydrogen bonds primarily with the ___________________.
surface, water solvent
__________ amino acids are almost never found in the interior of a protein, but the protein surface may consist of ____________________ amino acids.
Polar, both polar and nonpolar
Electrostatic interactions among amino acid residues on proteins may be damped out by high concentrations of:
salts
An electrostatic interaction might occur within a protein between which of the following amino acid pairs at typical physiological pH?
Lys/Asp
__________________ between tightly packed amino acid side chains in the interior of the protein are a major contribution to protein structure.
Van der Waals interactions
A hydrophobic interaction might occur within a protein between which of the following amino acid pairs?
Val/Leu
All of the information necessary for folding the peptide chain into its "native" structure is contained in the __________________of the peptide.
amino acid sequence
Planarity of the peptide bond means that rotation is allowed about the bond linking the _____________ and the carbon of the peptide bond, and also about the bond linking the ________________ to the adjacent α-carbon.
α-carbon, nitrogen of the peptide bond
A Ramachandran plot shows:
the sterically allowed rotational angles between Cα and the amide nitrogen (Cα-N) as well as between Cα and the amide carbonyl carbon (Cα-CO).
Alpha helices are stabilized primarily by:
hydrogen bonds between the main chain peptide bond component atoms.
In the majority of α-helixes, each peptide carbonyl is hydrogen bonded to the peptide N-H group ______ residues farther _____ the chain.
4, up
__________ and ___________ act as helix breakers due to their unique structure, which fixes the value of the Cα-N-C bond angle.
Proline, hydroxyproline
If the following section of a polypeptide is folded into an α-helix, to which amino acid is the carbonyl group of alanine hydrogen bonded?
ala-ser-val-asp-glu-leu-gly
glutamic acid
When the peptide (AEFFLAMEP) forms an α-helix, which amino acid residue would be closest to being in the same position on the same face of the helix as is the initial alanine residue?
E(8)
β-Turns in a peptide chain form a tight loop with hydrogen bonding of the carbonyl oxygen with:
amide proton of the residue three positions down the chain.
Polylysine is a random coil when the pH is less than 11, while it forms an α-helix if the pH is raised to greater than 12. This is because at pH 12:
the lysine residues are neutral which eliminates electrostatic repulsion between the R groups.
____________ β-sheets characteristically distribute hydrophobic side chains on both sides of the sheet, and _____________ β-sheets are usually arranged with all their hydrophobic residues on one side of the sheet.
Parallel, antiparallel
_____________ form between two normal β-structure hydrogen bonds and are comprised of two residues on one strand and one residue on the opposite strand.
α-Turn
Tertiary structure is defined as:
the folding of a single polypeptide chain in three-dimensional space.
Tertiary structure of proteins depends on all EXCEPT:
a. protein structure depends on primary structure.
b. α-helices and β-sheets often associate and pack close together.
c. secondary structures form whenever possible.
d. proteins are stable as a single-layer structure.
e. peptide segments between secondary structures are short.
D
The "Greek Key" topology is composed of ___________.
Discreet regions of β-sheet oriented in an antiparallel fashion
Fibrous proteins contain polypeptide chains___________ producing long fibers or large sheets.
organized approximately parallel along a single axis
α-Keratin has all of the following characteristics EXCEPT:
a. primary component in hair, claws, fingernails, and horns of animals.
b. consists of four helical strands arranged as twisted pairs of two-stranded coiled coils.
c. has associated hydrophobic strips on the two coiled coils.
d. principal constituent of connective tissues in animals.
e. has covalent disulfide bonds to stabilize the structure.
d. principal constituent of connective tissues in animals.
The "permanent" part of adding wave in hair is primarily due to:
reduction and re-oxidation of disulfide bonds in hair fibers.
Silk fibers consist of _________ proteins consisting of alternating ______ and _____ or ________ residues.
fibroin; glycine; alanine; serine
Collagen has the following characteristics EXCEPT:
a. Tropocollagen is the basic structural unit.
b. There is about 33% glycine in collagen.
c. Both intermolecular and intramolecular crosslinks help to stabilize the collagen fibrils.
d. Modification of prolines occurs prior to collagen synthesis.
e. Inextendable fibrous protein are components of connective tissues.
D
Prolyl hydroxylase has all of the following characteristics EXCEPT:
a. requires citric acid.
b. is activated by Fe2+.
c. hydroxylates proline residues in proteins.
d. requires molecular oxygen.
e. requires α-ketoglutarate.
A
A major stabilizing factor in the triple helix is a ___________ structure such that ______ residues from the three strands stack along the center of the triple helix.
staggered, gly
In hemoglobin, a __________ protein, the space between the helices is filled efficiently and tightly with mostly ____________ amino acid chains and with _____________ side chains facing the outside of the protein structure.
globular, hydrophobic, polar
Why should the core of most globular and membrane proteins consist almost entirely of α-helix and β-sheets?
Highly polar N-H and C=O moieties of the peptide backbone must be neutralized in the hydrophobic core of the protein.
The outward face of a(n) ______________________ consists mainly of polar and charged residues, whereas the inner face contains mostly nonpolar, hydrophobic residues.
amphiphilic helix
A β-barrel would most likely be composed of ____________.
parallel β-sheets connected by regions of α-helix AND parallel β-sheets connected by regions of random coil.
All are true for collective motions of proteins EXCEPT:
a. are movements of groups of atoms covalently linked in such a way that the group moves as a unit.
b. include trypsin ring flips
c. include cis-trans isomerization of prolines.
d. involve the flexible antigen-binding domains of immunoglobulins.
e. all are true.
E
Which statement is correct about the β−α−β motif?
The cross-over connection itself contains an α-helical segment.
All are true about the tertiary structure of the enzyme triose phosphate isomerase EXCEPT:
a. Its β-strands are parallel.
b. Its α-helices are in the interior of the molecular structure.
c. It contains a β-barrel in the center of its structure.
d. It is composed entirely of alternating α-helices and β-strands.
e. All are true.
b. Its α-helices are in the interior of the molecular structure.
All are classes of globular proteins according to type and arrangement of secondary structure EXCEPT:
a. small metal- and disulfide-rich proteins.
b. parallel or mixed β-sheet.
c. antiparallel β-sheet.
d. antiparallel α-helix.
e. all are true.
E. all are true
All are structural and functional advantages to quaternary structure EXCEPT:
a. cooperativity.
b. stability.
c. bringing catalytic sites together.
d. genetic economy and efficiency.
e. all are true.
E
All of the statements about the tertiary structure of the enzyme triose phosphate isomerase are correct EXCEPT:
a. Its β-strands are parallel.
b. Its α-helices are in the interior core of the molecular structure.
c. It contains a β-barrel in the center of its structure.
d. It is composed entirely of alternating α-helices and β-strands.
e. Hydrophobic residues are buried between concentric layers.
B
Arrange the steps involved in folding of globular proteins into a proper sequence.
A. "Molten globule" formation of assembled domains.
B. Formation of domains through cooperative aggregation of folding nuclei.
C. Adjustment in the conformation of domains.
D. Rapid and reversible formation of local secondary structure.
E. Final protein monomer formation.
D, B, A, C, E