Chapter 4

Question 1

The conformations existing under a given set of
conditions are usually the ones that are

Answer 1

thermodynamically the
most stable — that is, having the lowest free energy (G).

Question 2

native protein

Answer 2

Proteins
in any of their functional, folded conformations are often called native proteins

Question 3

For the vast majority of proteins, a particular structure or small
set of structures is

Answer 3

critical to function. However, in many cases,
parts of proteins lack discernible structure. These protein
segments are intrinsically disordered. In some cases, entire
proteins are intrinsically disordered, yet are fully functional.

Question 4

stability

Answer 4

Stability is the tendency of a protein to maintain a native
conformation. Native proteins are only marginally stable; the ΔG
separating the folded and unfolded states in typical proteins
under physiological conditions is in the range of only 5 to 65
kJ/mol.

Question 5

Ionic interactions may b

Answer 5

either stabilizing or destabilizing. We must therefore look
elsewhere to understand why a particular native conformation is
favored

Question 6

On carefully examining the contribution of weak
interactions to protein stability, we find that

Answer 6

the hydrophobic
effect generally predominates. Pure water contains a network of
hydrogen-bonded H2O molecules. No other molecule has the
hydrogen-bonding potential of water, and the presence of other
molecules in an aqueous solution disrupts the hydrogen bonding
of water

Question 7

When water surrounds a hydrophobic molecule,

Answer 7

, the
optimal arrangement of hydrogen bonds results in a highly
structured shell, or solvation layer, of water around the molecule
(see Fig. 2-7). The increased order of the water molecules in the
solvation layer correlates with an unfavorable decrease in the
entropy of the water.

Question 8

Salt bridges, especially those that are partly or entirely
buried,

Answer 8

can thus provide significant stabilization to a protein
structure. This trend explains the increased occurrence of buried
salt bridges in the proteins of thermophilic organisms. Ionic
interactions also limit structural flexibility and confer a
uniqueness to a particular protein structure that the clustering of
nonpolar groups via the hydrophobic effect cannot provide.

Question 9

Peptide conformation is defined by three dihedral angles

Answer 9

(also
known as torsion angles) called ϕ (phi), ψ (psi), and ω (omega),
reflecting rotation about each of the three repeating bonds in the
peptide backbone.

Question 10

A dihedral angle is

Answer 10

the angle at the
intersection of two planes.

Question 11

In the case of peptides, the planes are
defined by bond vectors in the peptide backbone.

Answer 11

Two successive
bond vectors describe a plane. Three successive bond vectors
describe two planes (the central bond vector is common to both;
Fig. 4-2c), and the angle between these two planes is what we
measure to describe peptide conformation.

Question 12

good stuff on pg 491

Answer 12

kk

Question 13

A typical protein usually has

Answer 13

one or more stable threedimensional conformations that reflect its function. Some
proteins have segments that are intrinsically disordered but are
nonetheless essential for function

Question 14

Whereas nonpeptide covalent bonds, particularly disulfide
bonds, can play a role in stabilization of some structures, proteins
are stabilized largely by

Answer 14

multiple weak, noncovalent interactions
and forces

Question 15

The hydrophobic effect, derived from

Answer 15

the increase in entropy
of the surrounding water when nonpolar molecules or groups are
clustered together, makes the major contribution to stabilizing
the globular form of most soluble proteins.

Question 16

Hydrogen bonds and ionic interactions are optimized in the

Answer 16

thermodynamically most stable structures.

Question 17

Van der Waals interactions involve

Answer 17

attractive forces between
molecular dipoles that occur over short distances. Individually
these interactions are weak, but they combine in well-packed
protein structures to provide significant effects and stabilization.

Question 18

The nature of the covalent bonds in the polypeptide backbone
places constraints on s

Answer 18

n structure. The peptide bond has a partial
double-bond character that keeps the entire six-atom peptide
group in a rigid planar configuration. The N—Cα and Cα—C
bonds can rotate to define the dihedral angles ϕ and ψ,
respectively, although permitted values of ϕ and ψ are limited by
steric clashes and other constraints

Question 19

key convention on pg 490

Answer 19

kk

Question 20

can reread pgs 480-490m if u want, i feel like i missed them but am not sure

Answer 20

kk

Question 21

secondary structure

Answer 21

The term secondary structure refers to any chosen segment of a
polypeptide chain and describes the local spatial arrangement of
its main-chain atoms, without regard to the positioning of its side
chains or its relationship to other segments. A regular secondary
structure occurs when each dihedral angle, ϕ and ψ, remains the
same or nearly the same throughout the segment

Question 22

The α-helical segments in proteins o

Answer 22

these dihedral angles, and they even vary
somewhat within a single, continuous segment so as to produce
subtle bends or kinks in the helical axis

Question 23

In summary, five types of constraints affect the stability of an α
helix:

Answer 23

(1) the intrinsic propensity of an amino acid residue to form
an α helix; (2) the interactions between R groups, particularly
those spaced three (or four) residues apart; (3) the bulkiness of
adjacent R groups; (4) the occurrence of Pro and Gly residues; and
(5) interactions between amino acid residues at the ends of the
helical segment and the electric dipole inherent to the α helix.

Question 24

The tendency of a given segment of a polypeptide chain to
502
form an α helix therefore depends on

Answer 24

the identity and sequence
of amino acid residues within the segment.

Question 25

, the β conformation.

Answer 25

In 1951, Pauling and Corey predicted a second type of repetitive
structure, the β conformation. This is a more extended
conformation of polypeptide chains, and its structure is again
defined by backbone atoms arranged according to a characteristic
set of dihedral angles (Table 4-1

Question 26

In the β conformation,

Answer 26

the backbone of the polypeptide chain is extended into a zigzag
rather than helical structure

Question 27

a β sheet.

Answer 27

The
arrangement of several strands side by side, all in the β
conformation, is called a

Question 28

picture of a beta sheet on pg 504

Answer 28

kk

Question 29

The α helix and the β conformation are

Answer 29

the major repetitive
secondary structures in a wide variety of proteins, although other
repetitive structures exist in some specialized proteins (an
example is collagen; see Fig. 4-12).

Question 30

. Every type of secondary
structure can be completely described by the dihedral angles ϕ
and ψ associated with each residue. Ramachandran plots,

Answer 30

introduced by G. N. Ramachandran, are useful tools for
visualizing all of the ϕ and ψ angles observed in a particular
protein structure and are o

Question 31

In a Ramachandran plot,

Answer 31

the
dihedral angles that define the α helix and the β conformation
fall within a relatively restricted range of sterically allowed
structures

Question 32

Most values of ϕ and ψ taken from known
protein structures fall into

Answer 32

the expected regions, with high
concentrations near the α helix and β conformation values, as
predicted (Fig. 4-8b) The only amino acid residue often found in a conformation outside these regions is glycine.Because its side
chain is small, a Gly residue can take part in many conformations
that are sterically forbidden for other amino acids.

Question 33

tertiary structure

Answer 33

The overall three-dimensional arrangement of all atoms in
a protein is referred to as the protein’s tertiary structure.
Whereas the term “secondary structure” refers to the spatial
arrangement of amino acid residues that are adjacent in a
segment of a polypeptide, tertiary structure includes longer-range
aspects of amino acid sequence

Question 34

quaternary structure

Answer 34

The arrangement of these protein subunits
in three-dimensional complexes constitutes quaternary
structure.

Question 35

In considering these higher levels of structure, it is useful to
designate the major groups into which many proteins can be
classified:

Answer 35

: fibrous proteins, with polypeptide chains arranged in
long strands or sheets; globular proteins, with polypeptide
chains folded into a spherical or globular shape; membrane
proteins, with polypeptide chains embedded in hydrophobic lipid
membranes; and intrinsically disordered proteins, with
polypeptide chains lacking stable tertiary structures.

Question 36

The tight wrapping of the α chains in the collagen triple helix
provides

Answer 36

tensile strength greater than that of a steel wire of equal
cross section. Collagen fibrils (Fig. 4-12) are supramolecular
assemblies consisting of triple-helical collagen molecules
(sometimes referred to as tropocollagen molecules) associated in
a variety of ways to provide different degrees of tensile strength.

Question 37

The α chains of collagen molecules and the collagen molecules
of fibrils are cross-linked by unusual types of covalent bonds
involving Lys, HyLys (5-hydroxylysine), or His residues that are
present at a few of the X and Y positions. These links create

Answer 37

uncommon amino acid residues such as
525
dehydrohydroxylysinonorleucine. The increasingly rigid and
brittle character of aging connective tissue results from
accumulated covalent cross-links in collagen fibrils.

Question 38

Fibroin is rich in

Answer 38

Ala and Gly residues, permitting
a close packing of β sheets and an interlocking arrangement of R
groups (Fig. 4-13). The overall structure is stabilized by extensive
hydrogen bonding between all peptide linkages in the
polypeptides of each β sheet and by the optimization of van der
Waals interactions between sheets.

Question 39

To understand a complete three-dimensional structure, we need
to analyze its folding patterns. We begin by defining two
important terms that describe protein structural patterns or
elements in a polypeptide chain; then we turn to the folding rules.
The first term is motif, also called a fold.

Answer 39

A motif or fold is
a recognizable folding pattern involving two or more elements of
secondary structure and the connection(s) between them ex- loops, barrels , pg 536
good ex is the coiled coil of a keratin, which is also found in some other proteins.
also a domain is the second thing

Question 40

Note that a motif is not a
hierarchical structural element falling between secondary and
tertiary structure. It is simply a

Answer 40

a folding pattern.

Question 41

domain

Answer 41

The second term for describing structural patterns is domain. A
domain, as defined by Jane Richardson in 1981, is a part of a
polypeptide chain that is independently stable or could undergo
movements as a single entity with respect to the entire protein. Polypeptides with more than a few hundred amino acid residues
537
o

Question 42

stable folding patterns in proteins pg 540

Answer 42

kk

Question 43

p27

Answer 43

. The flexible structure of p27 allows it to accommodate
itself to its different target proteins. Human tumor cells, which
are cells that have lost the capacity to control cell division
normally, generally have reduced levels of p27; the lower the
levels of p27, the poorer the prognosis for the cancer patient.

Question 44

A multisubunit protein can also be referred to as an

Answer 44

n oligomer or
multimer. If an oligomer has nonidentical subunits, the overall
structure of the protein can be asymmetric and quite
complicated. However, many oligomers have identical subunits or
repeating groups of nonidentical subunits, usually in symmetric
arrangements. As noted in Chapter 3, the repeating structural
unit in such an oligomeric protein, whether a single subunit or a
group of subunits, is called a protomer.

Question 45

Tertiary structure is the complete

Answer 45

three-dimensional structure
of a polypeptide chain. Many proteins fall into one of four general
classes based on tertiary structure: fibrous, globular, membrane,
or disordered.

Question 46

Insoluble fibrous proteins, such as those that make up keratin,
collagen, and silk, have

Answer 46

simple repeating elements of secondary
structure. In some fibrous proteins, the individual polypeptide
chains interact to form complex quaternary structures like coiled
coils for strength and flexibility.

Question 47

Globular proteins have more

Answer 47

complicated tertiary structures,
often containing ontaining several types of secondary structure in the same
polypeptide chain, and fulfill many different functional roles in
the cell

Question 48

The first globular protein structure to be determined, by x-ray
diffraction methods, was that of

Answer 48

the O2-binding protein
myoglobin. The myoglobin structure revealed for the first time
how protein structure and function are connected.

Question 49

The complex structures of globular proteins can be analyzed by
examination of folding patterns, called motifs or folds. The many
thousands of known protein structures are

Answer 49

are generally assembled
from a repertoire of only a few hundred motifs. Domains are
regions of a polypeptide chain that can fold stably and
independently.

Question 50

Some proteins or protein segments are intrinsically
disordered, lacking

Answer 50

definable three-dimensional structure. These
proteins o

Question 51

Based on structural similarities, proteins can be organized into

Answer 51

families and superfamilies, which are informative about protein
function and evolution

Question 52

Quaternary structure results from

Answer 52

m interactions between the
subunits of multisubunit (multimeric) proteins or large
supramolecular assemblies. Some multimeric proteins are
composed of repeated subunits called protomers.

Question 53

Most proteins can be denatured by heat, which has complex
effects on

Answer 53

many weak interactions in a protein (primarily on the
hydrogen bonds). If the temperature is increased slowly, a
protein’s conformation generally remains intact until an abrupt
loss of structure (and function) occurs over a narrow temperature
556
range (Fig. 4-24). The abruptness of the change suggests that
unfolding is a cooperative process: loss of structure in one part of
the protein destabilizes other parts.

Question 54

The Anfinsen experiment provided the first evidence that

Answer 54

he
amino acid sequence of a polypeptide chain contains all the
information required to fold the chain into its native, threedimensional structure. Subsequent work has shown that only a
minority of proteins, many of them small and inherently stable,
will fold spontaneously into their native form. Even though all
proteins have the potential to fold into their native structure,
many require some assistance.

Question 55

chaperonins

Answer 55

are elaborate protein complexes required for the
folding of some cellular proteins that do not fold spontaneously.
In E. coli, an estimated 10% to 15% of cellular proteins require the
resident chaperonin system, called GroEL/GroES, for folding
under normal conditions (up to 30% require this assistance when
the cells are heat stressed). T

Question 56

The maintenance of the steady-state collection of active
cellular proteins required under a particular set of conditions —
called proteostasis — involves a

Answer 56

an elaborate set of pathways and
processes that fold, refold, and degrade polypeptide chains.

Question 57

The three-dimensional structure and the function of most
proteins can be destroyed by

Answer 57

denaturation, demonstrating a
relationship between structure and function. Heat, extremes of
pH, organic solvents, solutes, and detergents can all be used to
denature proteins.

Question 58

Some denatured proteins can renature spontaneously to form

Answer 58

biologically active protein, showing that tertiary structure is
determined by amino acid sequence

Question 59

Protein folding occurs too fast for it to be a completely random
process. Instead, protein folding is generally

Answer 59

hierarchical.
Initially, regions of secondary structure may form, followed by
folding into motifs and domains. Large ensembles of folding
intermediates are rapidly brought to a single native
conformation

Question 60

For many proteins, folding is facilitated by

Answer 60

Hsp70 chaperones
and by chaperonins. Disulfide-bond formation and the cis-trans
isomerization of Pro peptide bonds can also be catalyzed by
specific enzymes during folding.

Question 61

Protein misfolding is the molecular basis for

Answer 61

many human
diseases, including cystic fibrosis and amyloidoses such as
Alzheimer disease.

Question 62

An advantage of nuclear magnetic resonance (NMR) studies is

Answer 62

that they are carried out on macromolecules in solution, whereas
x-ray crystallography is limited to molecules that can be
crystallized. NMR can also illuminate the dynamic side of protein
structure, including conformational changes, protein folding, and
interactions with other molecules.

Question 63

NMR is a manifestation of

Answer 63

nuclear spin angular momentum, a
quantum mechanical property of atomic nuclei. Only certain
atoms, including 1H,
13C,
15N,
19F, and 31P, have the kind of
nuclear spin that gives rise to an NMR signal.

Question 64

Nuclear spin
generates

Answer 64

a magnetic dipole. When a strong, static magnetic field
is applied to a solution containing a single type of
macromolecule, the magnetic dipoles are aligned in the field in
one of two orientations: parallel (low energy) or antiparallel (high
energy). A short (∼10 μs) pulse of electromagnetic energy of
suitable frequency (the resonant frequency, which is in the radio
frequency range) is applied at right angles to the nuclei aligned in
589
the magnetic field.

Question 65

In cryo-electron
microscopy (cryo-EM),

Answer 65

a sample containing many individual
copies of the structure of interest is quick-frozen in vitreous (or
noncrystalline) ice and kept frozen while being observed in two
dimensions with the electron microscope, greatly reducing
damage to the specimen by the electron beam.

Question 66

In x-ray crystallography,

Answer 66

protein molecules are crystallized in
well-ordered orientations that diffract x-rays. The patterns and
intensities of the diffracted x-rays depend on the structure of the
protein and its crystalline properties. Mathematical methods can
then reconstruct the protein structure that produces a particular
diffraction pattern.

Question 67

NMR is often carried out on molecules in solution and yields
information about

Answer 67

atomic nuclei and their chemical
environment. Protein structures can be computed from NMR data
using hundreds of distance and geometric constraints obtained
from multi-dimensional NMR experiments.

Question 68

Biomolecules are frozen in vitreous ice for imaging by

Answer 68

cryoEM. The individual molecules are then identified and
computationally sorted. The sorted two-dimensional images are
then combined using computers to produce a three-dimensional
structure.