.
1, 2, 4, 17, 18, 19, 21, 25, 27, 29,
30, 32, 35, 49.
Protein Structure and Function
1. Match , 1 20 30 40 with statement:
o
a) 3-dimensional arrangement of atoms 30
b) Order of amino acid residues in peptide
chain 10
c) Interaction between subunits in proteins
that consist of more that 1 peptide chain
40
d) The hydrogen-bonded arrangement of
the polypeptide backbone 20
Protein Structure and Function
2. Define denaturation in terms of
secondary, tertiary, and quaternary
structure:
When a protein is denatured, the
interactions that determine secondary,
tertiary, and any quaternary structures
are overcome by the presence of the
denaturing agent. Only the primary
structure remains intact.
Primary Structure of Proteins
4. Suggest an explanation for the
observation that when proteins are
chemically modified so that specific
side chains have a different
chemical nature, these proteins
cannot be denatured reversibly.
When a protein is covalently
modified, its primary structure is
changed. The primary structure
determines the final three-
dimensional structure of the protein.
The modification disrupts the folding
process
Secondary Structure of Proteins
17. What is a β-bulge A β-bulge is a
common nonrepetitive irregularity found
in antiparallel β-sheets. A misalignment
occurs between strands of the β-sheet,
causing one side to bow outward
Secondary Structure of Proteins
18. What is a reverse turn? Draw
two types of reverse turns.
A reverse turn is a region of a
polypeptide where the direction
changes by about 180°. There are
two kinds—those that contain
proline and those that do not.
Type I turns
occur more
than twice as
frequently as
type II. Type I
turns contain
proline.
Type II turns usually
have Gly as the third
residue. Note the
hydrogen bond
between the peptide
groups of the first
and fourth residues
of the bends.
(Individual amino
acid residues are
framed by large blue
circles.)
Secondary Structure of Proteins
19. List differences between the
α-helix and β-pleated sheet
structure.
The α-helix is not fully extended,
and its hydrogen bonds are
parallel to the protein fiber.
The β-pleated sheet structure is
almost fully extended, and its
hydrogen bonds are perpendicular
to the protein fiber.
α-Helix (Cont’d)
Secondary Structure of Proteins
21. Why is proline frequently
encountered at the places in the
myoglobin and hemoglobin
molecules where the peptide chain
turns a corner. The geometry of
the proline residue is such that it
does not fit into the α-helix, but it
does fit exactly for a reverse turn.
Tertiary structure of Proteins:
25.Draw two types of hydrogen
bonds, primary structure and
tertiary structure:
See Figure 4.2 for a hydrogen bond
that is part of the α-helix (secondary
structure).
See Figure 4.13 for a hydrogen bond
that is part of tertiary structure
(side-chain hydrogen bonding).
H bonding in secondary
helix and tertiary
myoglobin
Tertiary Structure of Proteins
27. Draw a disulfide bond between
two cysteines in a polypeptide chain.
See Figure 4.13 for an example of a
disulfide bond.
Tertiary Structure of Proteins
29. What is the difference between
configuration and conformation?
Configuration refers to the position
of groups due to covalent bonding.
To change configuration you must
break a bond. Examples include cis
and trans isomers and optical
isomers.
Conformation refers to the
positioning of groups in space due to
rotation around single bonds. An
example is the difference between
the eclipsed and staggered
conformations of ethane.
CONFIGURATIONS
Carboxylic
acid group
Amino group
R group
CONFIGURATION
Resonance Structures of Peptide
Bond lIKE CONFIGURATION ?
CONFORMATIONS
Secondary Structure
The atoms of the peptide bond lie
The6.3 Secondary
resonance a plane Structure
instabilization energy of
the planar
The structure
resonance is 88 kJ/mol
stabilization energy
of the planar
A twist structure
about the C-N bondis involves
88 kJ/mola
twist
A energy
twist aboutof the
88 kJ/mol
C-N bondtimes the
involves
square
a twist of the twist
energy angle.
of 88 kJ/mol times
the square
Twists of the
can occur twist
about angle.
either of the
bonds linking
Twists the alpha
can occur aboutcarbon
eitherto ofthe
the
bonds linking
other atoms of the alpha carbon
the peptide backboneto
the other atoms of the peptide
backbone
Consequences
Consequences of Amide
of the the Amide
Plane Plane
Two degrees of freedom per residue
for the peptide chain
Angle about the C(alpha)-N bond is
denoted phi
Angle about the C(alpha)-C bond is
denoted psi
The entire path of the peptide
backbone is known if all phi and psi
angles are specified
Some values of phi and psi are more
likely than others.
Steric Constraints on phi & psi
Unfavorable orbital overlap
precludes some combinations
of phi and psi
phi = 0, psi = 180 is
unfavorable
phi = 180, psi = 0 is
unfavorable
phi = 0, psi = 0 is unfavorable
Steric Constraints on phi & psi
G. N. Ramachandran was the
first to demonstrate the
convenience of plotting
phi,psi combinations from
known protein structures
The sterically favorable
combinations are the basis for
preferred secondary
structures
Tertiary Structure of Proteins
30.Proteins could have an infinite
number of conformations and
configurations. What limits them?
Tertiary Structure of Proteins
Five possible features limit possible protein
configurations and conformations.
(1) Although any one of 20 amino acids is
possible at each position, only one is used,
as dictated by the gene that codes for that
protein.
(2) Either a D- or an L-amino acid could be
used at each position (except for glycine),
but only L-amino acids are used.
(3) The peptide group is planar, so that only
cis and trans arrangements are observed.
The transform is more stable and is the one
usually found in proteins.
(4) The angles φ and ψ can theoretically
take on any value from 0° to 360°, but
some angles are not possible because
of steric hindrance; angles that are
sterically allowed may not have
stabilizing interactions, such as those
in the α-helix.
(5) The primary structure determines
an optimum tertiary structure.
Quaternary Structure:
32. Compare and contrast
Hemoglobin and myoglobin:
Similarities: both contain a heme
group; both are oxygen binding;
secondary structure is primarily α-
helix. Differences: hemoglobin is a
tetramer, while myoglobin is a
monomer; oxygen binding to
hemoglobin is cooperative, but
noncooperative to myoglobin.
Quaternary structure:
35. How are the differences between
the functions of hemoglobin and
myoglobin reflected in the shapes of
their oxygen binding curves? The
function of hemoglobin is oxygen
transport; its sigmoidal binding curve
reflects the fact that it can bind easily
to oxygen at comparatively high
pressures and release oxygen at lower
pressures. The function of myoglobin is
oxygen storage; as a result, it is easily
saturated with oxygen at low
pressures, as shown by its hyperbolic
binding curve
Myoglobin plots of %
saturation versus partial
pressure of oxygen are
hyberbolic. The bonding
curve for hemoglobin is
sigmoidal. The sigmoidal
curve indicates
cooperativity
49. Comment on the energetics of protein folding.
Protein folding is driven by many processes.
The intuitive ones are the direct interactions of
functional groups through covalent bonds,
electrostatic attractions, and hydrogen bonds.
These explain why parts of the protein are
attracted to each other and why a protein would
tend to adopt a shape making these interactions
possible.
However, much of the protein-folding process is
also driven by an entropy effect.
We refer to hydrophobic interactions as an
explanation of why nonpolar regions of the
protein tend to cluster together, usually in
the interior of the protein.
However, in reality, it is not the interaction
of nonpolar amino acids that drives this
process.
It is actually the increase in entropy of the
solvent, water.
When the hydrophobic regions of the
protein are isolated to the interior, the
water molecules surrounding the protein
are more free to rotate and move in less
restricted ways.
Thus, what drives much of protein folding
is not a ΔH change with the bonding of
specific amino acids, but rather a ΔS
increase of the solvent.
