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
Amino acid sequence is:
primary structure.
Secondary and higher orders of structure are determined by all EXCEPT:
peptide bonds.
The resonance structure which forms the "amide plane" contains which atoms?
C?-NH-CO-C?
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 ?-carbon.
?-carbon, nitrogen of the peptide bond
A Ramachandran plot shows:
the sterically allowed rotational angles between C? and the amide nitrogen (C?-N) as well as between C? and the amide carbonyl carbon (C?-CO).
Alpha helices are stabilized primarily by:
hydrogen bonds between the main chain peptide bond component atoms.
In the majority of ?-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 C?-N-C bond angle.
Proline, hydroxyproline
If the following section of a polypeptide is folded into an ?-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 ?-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)
Antiparallel ?-sheets have:
usually all of their hydrophobic residues on one side of the sheet.
?-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 ?-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.
The amino acid residue most likely to be found in a beta turn is:
glycine
____________ ?-sheets characteristically distribute hydrophobic side chains on both sides of the sheet, and _____________ ?-sheets are usually arranged with all their hydrophobic residues on one side of the sheet.
Parallel, antiparallel
_____________ form between two normal ?-structure hydrogen bonds and are comprised of two residues on one strand and one residue on the opposite strand.
?-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. ?-helices and ?-sheets often associate and pack close together.
c. secondary structures form whenever possible.
d. proteins are stable as a single-
D
The "Greek Key" topology is composed of ___________.
Discreet regions of ?-sheet oriented in an antiparallel fashion
Fibrous proteins contain polypeptide chains___________ producing long fibers or large sheets.
organized approximately parallel along a single axis
?-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 st
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 pr
D
The unique composition of collagen is accommodated in a structure called a(n):
triple helix.
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 ?-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 ?-helix and ?-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 ?-barrel would most likely be composed of ____________.
parallel ?-sheets connected by regions of ?-helix AND parallel ?-sheets connected by regions of random coil.
Flexible, disordered segments of proteins are commonly high in the amino acid:
lys
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 flexib
E
Which statement is correct about the ????? motif?
The cross-over connection itself contains an ?-helical segment.
All are true about the tertiary structure of the enzyme triose phosphate isomerase EXCEPT:
a. Its ?-strands are parallel.
b. Its ?-helices are in the interior of the molecular structure.
c. It contains a ?-barrel in the center of its structure.
d. It is c
b. Its ?-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 ?-sheet.
c. antiparallel ?-sheet.
d. antiparallel ?-helix.
e. all are true.
E. all are true
______________ are examples of antiparallel ?-helix proteins.
Hemoglobin
______________ is an example of a disulfide-rich protein.
Insulin
________________ are proteins that help other proteins to fold.
Molecular chaperones
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 ?-strands are parallel.
b. Its ?-helices are in the interior core of the molecular structure.
c. It contains a ?-barrel in the center of
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, B, A, C, E