Chapter 4: The Three-Dimensional Structure of Proteins

Question 1

Protein structures follow 6 themes. Name them.

Answer 1

1. the three-dimensional structure or structures taken up by a protein are determined by its amino acid sequence.
2. the function of a typical protein depends on its structure
3. most isolated proteins exist in one or a small number of stable structural forms.
4. the most important forces stabilizing the specific structures maintained by a given protein are noncovalent interactions
5. amid the huge number of unique protein structures, we can recognize some common structural patterns that help to organize our understanding of protein architecture
6. protein structures are not static

Question 2

The conformations existing under a given set of conditions are usually the ones that are _____ the most stable—that is, having the lowest _____ _____ _____

Answer 2

• thermodynamically
• Gibbs free energy (G)

Question 3

native proteins

Answer 3

• Proteins in any of their functional, folded conformations
• marginally stable

Question 4

A given polypeptide chain can theoretically assume countless conformations, and as a result the unfolded state of a protein is characterized by a high degree of conformational ______. This ______, and the hydrogen-bonding interactions of many groups in the polypeptide chain with the solvent (water), tend to maintain the unfolded state. The chemical interactions that counteract these effects and stabilize the native conformation include ____ _____ and the ______ _____

Answer 4

• entropy
• entropy
• disulfide (covalent) bonds
• weak (noncovalent) interactions

Question 5

Many proteins do not have _____ _____. Outside the cell, the environment is often more oxidizing, and _____ formation is more likely to occur. In eukaryotes, disulfide bonds are found primarily in secreted, _____ proteins (for example, the hormone insulin). They are also uncommon in bacterial proteins

Answer 5

• disulfide bonds
• disulfide
• extracellular

Question 6

In general, the protein conformation with the lowest _____ _____ (that is, the most stable conformation) is the one with the maximum number of weak interactions.

Answer 6

free energy

Question 7

_____ _____ generally predominate. When water surrounds a hydrophobic molecule, the optimal arrangement of hydrogen bonds results in a highly structured shell, or _____ _____, of water around the molecule. The increased order of the water molecules in the solvation layer correlates with an unfavorable decrease in the _____ of the water. However, when _____ groups cluster together, the extent of the solvation layer decreases, because each group no longer presents its entire surface to the solution. The result is a favorable increase in _____ which is the major _____ driving force for the association of hydrophobic groups in aqueous solution

Answer 7

• hydrophobic interactions
• solvation layer
• entropy
• nonpolar
• entropy
• thermodynamic

Question 8

amino acid sequences of most proteins feature a significant content of _____ amino acid side chains (name five). These are positioned so that they are clustered when the protein is folded, forming a hydrophobic protein _____

Answer 8

• hydrophobic
• Leu, Ile, Val, Phe, and Trp
• core

Question 9

there are limits to the solubility of even the most _____ molecules as their presence causes a net decrease in _____ _____ per unit mass. Therefore, a solvation layer also forms to some extent around _____ molecules.

Answer 9

• polar
• hydrogen bonding
• polar

Question 10

important that any polar or charged groups in the protein interior have suitable _____ for hydrogen bonding or ionic interactions. One hydrogen bond seems to contribute little to the stability of a native structure, but the presence of hydrogen-bonding groups without partners in the _____ _____ of a protein can be so destabilizing that conformations containing these groups are often _____ _____.

Answer 10

• partners
• hydrophobic core
• thermodynamically untenable

Question 11

hydrogen bonds often have an important role in guiding the _____-_____ process.

Answer 11

protein-folding

Question 12

strength of a salt bridge increases as it moves to an environment of _____ _____ _____, ´ (p. 50): from the polar aqueous solvent (´ near 80) to the nonpolar protein interior (´ near 4). Salt bridges, especially those that are partly or entirely _____, can thus provide significant _____ to a protein structure

Answer 12

• lower dielectric constant
• buried
• stabilization

Question 13

The Peptide Bond Is _____ and _____

Answer 13

• Rigid
• planar

Question 14

The planar peptide group

• Each peptide bond has some _____-_____ character due to resonance and cannot _____
• Although the N atom is represented with a partial positive charge, bond orbitals and quantum mechanics show that N has a net charge that is

Answer 14

• double-bond
• rotate
• neutral or slightly negative

Question 15

The planar peptide group

• _____ bonds separate sequential α carbons in a polypeptide chain
• _____ and _____ bonds can rotate, described by dihedral angles designated φ and ψ, respectively. _____ bond can’t rotate
• Other single bonds in the backbone may also be rotationally hindered, depending on

Answer 15

• Three
• N—C_α
• C_α—C
• C—N
• the size and charge of the R groups.

Question 16

The planar peptide group

• φ and ψ are _____ or _____ when the first and fourth atoms are farthest apart and the peptide is fully extended
• looking along the bond undergoing rotation, the φ and ψ angles _____ as the fourth atom rotates clockwise relative to the first

Answer 16

• 180º
• -180º
• increase

Question 17

secondary structure

Answer 17

• a segment of a polypeptide chain and describes the local spatial arrangement of its main-chain atoms
• ignores side chains or its relationship to other segments

Question 18

• A regular secondary structure occurs when
• Examples of secondary structures are

Answer 18

• each dihedral angle, φ and ψ, remains the same or nearly the same throughout the segment
• the α helix and β conformations; another common type is the β turn

Question 19

undefined or random coil

Answer 19

Where a regular pattern is not found in the secondary structure

Question 20

α helix

Answer 20

• polypeptide backbone is tightly wound around
• R groups protrude outward from the helical backbone
• a single turn of the helix extends about 5.4 Å
• each helical turn includes 3.6 amino acid residues often deviate slightly
• right-handed α helix is the common form
• left-handed α helices are less stable; not observed in proteins

Question 21

Why does the α helix form more readily than many other possible conformations?

Answer 21

• optimal use of internal hydrogen bonds
• stabilized by a hydrogen bond between the hydrogen atom attached to the nitrogen and the carbonyl oxygen atom of the fourth amino acid on the amino-terminal side
• every peptide bond (except those close to each end of the helix) participates in such hydrogen bonding
• At the ends there are always three or four amide carbonyl or amino groups that cannot participate in this helical pattern of hydrogen bonding
  
  • exposed to the surrounding solvent
  • they hydrogen-bond with water
  • or other parts of the protein may cap the helix to provide needed hydrogen-bonding partners

Question 22

What is the length of a polypeptide with 80 amino acid residues in a single contiguous α helix?

Answer 22

• α helix has 3.6 residues per turn
• rises 5.4 Å
• Thus rise for each amino acid residue is 1.5 Å (5.4 / 3.6)
• The length of the polypeptide is therefore

80 residues × 1.5 Å/residue = 120 Å.

Question 23

Hellix dipole

Answer 23

• transmitted through the intrachain hydrogen bonds, resulting in an overall helix dipole
• In pic, the amino and carbonyl of each peptide bond are indicated by “+” and “-“ symbols
• Non–hydrogen-bonded amino and carbonyl near each end of the helical region are circled and shown in color

Question 24

Proline occurs infrequently in α helices because

Answer 24

• have the least proclivity to form helices
• nitrogen atom is part of a rigid ring making rotation about the N—C_α bond is not possible which introduces a destabilizing kink
• nitrogen atom of a Pro residue in a peptide linkage has no substituent hydrogen to participate in hydrogen bonds with other residues

Question 25

Glycine occurs infrequently in α helices because

Answer 25

• it has more conformational flexibility than the other amino acid residues.
• Polymers of glycine tend to take up coiled structures quite different from an α helix

Question 26

negatively charged amino acids are often found near the _____ terminus of the helical segment, where they have a stabilizing interaction with the _____ charge of the helix dipole; a positively charged amino acid at the amino-terminal end is destabilizing. The opposite is true at the carboxyl-terminal end of the helical segment.

Answer 26

• amino
• positive

Question 27

five types of constraints affect the stability of an α helix

Answer 27

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

Question 28

β sheet

Answer 28

• backbone extends into a zigzag structure gives rise to a pleated appearance
• arrangement of several segments side by side
• Hydrogen bonds form between adjacent segments of polypeptide chain within the sheet
• segments are usually nearby but can also be distant from each other, even in different polypeptide chains
• R groups of adjacent amino acids protrude from the zigzag structure in opposite directions

Question 29

β sheet

two types

Answer 29

• parallel or antiparallel
• repeat period is shorter for the parallel conformation, 6.5 Å, vs. 7 Å for antiparallel
• interstrand hydrogen bonds are in-line in the antiparallel and not in-line for the parallel variant

Question 30

β Turn

Answer 30

• In globular proteins
• have a compact folded structure
• turns or loops where the polypeptide chain reverses direction
• connect the ends of two adjacent segments of an antiparallel β sheet
• 180” turn involving four amino acid residues, with the carbonyl oxygen of the first residue forming a hydrogen bond with the amino-group hydrogen of the fourth.
• central two residues do not participate in any inter-residue hydrogen bonding
• Glycine often occur in β turns because they are small and flexible
• Proline often occur in β turns because the amino nitrogen assumes the cis configuration a form that is particularly amenable to a tight turn

Question 31

γ Turn

Answer 31

• Considerably less common
• a three-residue turn with a hydrogen bond between the first and third residues

Question 32

• Every type of secondary structure can be completely described by
• As shown by a _____ _____ the dihedral angles that define the α helix and β conformation fall within a relatively restricted range of sterically allowed structures

Answer 32

• the dihedral angles φ and ψ associated with each residue
• Ramachandran plot

Question 33

Circular dichroism spectroscopy

Answer 33

• method for assessing common secondary structure and monitoring folding in proteins

Question 34

tertiary structure

Answer 34

• The overall three-dimensional arrangement of all atoms in a protein is referred to as the protein’s
• includes longer-range aspects of amino acid sequence
• held in their positions by several kinds of weak interactions (and sometimes by covalent bonds such as disulfide cross-links) between the segments

Question 35

quaternary structure

Answer 35

• contain two or more separate polypeptide chains, or subunits, which may be identical or different

Question 36

fibrous proteins

Answer 36

• polypeptide chains arranged in long strands or sheets
• consist largely of a single type of secondary structure, and their tertiary structure is relatively simple
• structures that provide support, shape, and external protection to vertebrates
• insoluble in water, conferred by a high concentration of hydrophobic amino acid residues both in the interior of the protein and on its surface

Question 37

globular proteins

Answer 37

• polypeptide chains folded into a spherical or globular shape
• often contain several types of secondary structure
• most enzymes and regulatory proteins are globular proteins

Question 38

motif, fold or

(more rarely) supersecondary structure

Answer 38

• a recognizable folding pattern involving two or more elements of secondary structure and the connection(s) between them
• simply a folding pattern, any advantageous folding pattern
• a single large motif may comprise the entire protein
• “fold” is applied more commonly to somewhat more complex folding patterns.
• example: β-α-β, β barrel, α-keratin: distinctive arrangement of eight α helices in myoglobin, replicated in all globins and is called the globin fold

Question 39

domain

Answer 39

• part of a polypeptide chain that is independently stable or could undergo movements as a single entity with respect to the entire protein

Question 40

In a protein with multiple domains, each domain may appear as a distinct _____ _____. extensive contacts between domains make individual domains hard to _____. Different domains often have _____ _____

Answer 40

• globular lobe
• discern
• distinct functions

Question 41

• Hydrophobic interactions make a large contribution to the stability of protein structures. Burial of hydrophobic amino acid R groups to exclude water requires at least
• Simple motifs, such as the _____ loop create two such layers

Answer 41

• two layers of secondary structure
• β-α-β

Question 42

• Where they occur together in a protein, α helices and β sheets generally are found in
• This is because the backbone of a polypeptide segment in the βconformation cannot readily __________ to an α helix that is adjacent to it.

Answer 42

• different structural layers
• hydrogen-bond

Question 43

Segments adjacent to each other in the amino acid sequence are usually _____ adjacent to each other in the folded structure. _____ segments of a polypeptide may come together in the tertiary structure, but this is not the norm

Answer 43

• stacked
• Distant

Question 44

• The _____ conformation is most stable when the individual segments are twisted slightly in a righthanded sense.
• This influences both …
• Two parallel β strands, for example, must be connected by a ____ _____
• Right-handed connections tend to be _____ than left-handed connections and tend to bend through _____ angles, making them easier to form
• The twisting of β sheets also leads to a characteristic twisting of the structure formed by many such segments together, as seen in the ____ _____ and _____ ____ _____, which form the core of many larger structures

Answer 44

• β
• the arrangement of β sheets derived from the twisted segments and the path of the polypeptide connections between them
• crossover strand
• shorter
• smaller
• β barrel
• twisted β sheet

Question 45

α / β barrel

Answer 45

• a series of β-α-β loops arranged so that the strands form a barrel creates a particularly stable and common motif
• each parallel β segment is attached to its neighbor by an α-helical segment
• right handed
• found in many enzymes, often with a binding site in the form of a pocket near one end of the barrel

Question 46

typical connections

Answer 46

Question 47

crossover connections

Answer 47

Question 48

right-handed connection

Answer 48

Question 49

left-handed connection

Answer 49

Question 50

twisted β sheet

Answer 50

Question 51

proteins can be organized based on the presence of the various motifs. The top two levels of organization, _____ and _____, are purely structural. Below the fold level categorization is based on _____ ______

Answer 51

• class
• fold
• volutionary relationships.

Question 52

protein family

Answer 52

• Proteins with significant similarity in primary structure and/or with similar tertiary structure and function
• protein tertiary structure is more reliably conserved than amino acid sequence.
• The comparison of protein structures can thus provide much information about evolution

Question 53

superfamilies

Answer 53

Two or more families with little similarity in amino acid sequence sometimes make use of the same major structural motif and have functional similarities

Question 54

Other families may be present in only a small group of organisms, indicating that the structure arose _____ _____

Answer 54

more recently

Question 55

multimer

Answer 55

• multisubunit protein
• A multimer with just a few subunits is often called an oligomer
• If a multimer has nonidentical subunits, the overall structure of the protein can be asymmetric and quite complicated
• most multimers have identical subunits or repeating groups of nonidentical subunits, usually in symmetric arrangements
• repeating structural unit in such a multimeric protein, whether a single subunit or a group of subunits, is called a protomer

Question 56

Intrinsically disordered proteins

Answer 56

• some proteins or protein segments lack an ordered structure in solution
• As many as a third of all human proteins
• have properties that are distinct from classical structured proteins
• lack a hydrophobic core
• characterized by high densities of charged amino acid residues such as Lys, Arg, and Glu
• Pro residues are also prominent, as they tend to disrupt ordered structures

Question 57

• Structural disorder and high charge density can facilitate the function of some proteins as
• The lack of an ordered structure can facilitate a kind of functional promiscuity, allowing one protein to …

Answer 57

• spacers, insulators, linkers in larger structures, or scavengers
• interact with multiple partners

Question 58

proteostasis.

Answer 58

• The continual maintenance of the active set of cellular proteins required under a given set of conditions
• requires the coordinated function of pathways for protein synthesis and folding, the refolding of proteins that are partially unfolded, and the sequestration and degradation of proteins that have been irreversibly unfolded

Question 59

Proteins that are not properly folded often have exposed _____ surfaces that render them _____ leading to the formation of inactive aggregates. These aggregates may lack their normal function but are not _____; their _____ in cells lies at the heart of diseases ranging from diabetes to Parkinson and Alzheimer diseases

Answer 59

• hydrophobic
• sticky
• inert
• accumulation

Question 60

Pathways that contribute to proteostasis.

Three kinds of processes contribute to proteostasis.

1. proteins are synthesized on a _____
2. multiple pathways contribute to protein folding, many nvolve the activity of _____ (including _____) which contribute to the refolding of proteins that are ,,,
3. proteins that are irreversibly unfolded are subject to _____ and _____ by several additional pathways. Partially unfolded proteins and protein-folding intermediates that escape the quality-control activities of the chaperones and degradative pathways may _____, forming both disordered aggregates and ordered amyloidlike aggregates that contribute to

Answer 60

1. ribosome
2. • chaperones
   • chaperonins
   • partially and transiently unfolded
3. • sequestration
   • degradation
   • aggregate
   • disease and aging processes.

Question 61

denaturation

Answer 61

• A loss of three-dimensional structure sufficient to cause loss of function
• does not necessarily equate with complete unfolding
• under most conditions denatured proteins exist in a set of partially folded states

Question 62

Most proteins can be denatured by heat, which has complex effects on many _____ _____ in a protein (primarily on the _____ _____)

Answer 62

• weak interactions
• hydrogen bonds

Question 63

the transition from the folded to the unfolded state is abrupt suggesting unfolding is a cooperative process: loss of structure in one part of the protein _____ other parts

Answer 63

destabilizes

Question 64

• Proteins can also be denatured by extremes of
• Each of these denaturing agents represents a relatively mild treatment in the sense that no _____ _____ in the polypeptide chain are broken
• Organic solvents, urea, and detergents act primarily by
• extremes of pH alter the _____ _____ on the protein, causing

Answer 64

• pH, by certain miscible organic solvents such as alcohol or acetone, by certain solutes such as urea and guanidine hydrochloride, or by detergents
• covalent bonds
• disrupting the hydrophobic interactions
• net charge
• electrostatic repulsion and the disruption of some hydrogen bonding

Question 65

The midpoint of the temperature range over which denaturation occurs is called the melting temperature, or _____.

Answer 65

Tm

Question 66

renaturation

Answer 66

Certain globular proteins denatured by heat, extremes of pH, or denaturing reagents will regain their native structure and their biological activity if returned to conditions in which the native conformation is stable.

Question 67

• the amino acid sequence of a polypeptide chain contains all the information required to _____ the chain into its native, three-dimensional structure
• only a _____ 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 _____

Answer 67

• fold
• minority
• assistance

Question 68

Thermodynamically, the folding process can be viewed as a kind of _____-_____ ______. The unfolded states are characterized by a high degree of conformational _____ and relatively high _____ _____. As folding proceeds, the narrowing of the funnel reflects the ______ in the conformational space that must be searched as the protein approaches its native state. Small depressions along the sides of the free-energy funnel represent _____ _____ that can briefly slow the folding process. At the bottom of the funnel, an ensemble of folding intermediates has been reduced to a single _____ _____

Answer 68

• free-energy funnel
• entropy
• free energy
• decrease
• semistable intermediates
• native conformation

Question 69

• Thermodynamic stability is not evenly distributed over the structure of a protein—the molecule has
• variations in the stability of regions within a protein are often essential to _____ _____
• Intrinsically disordered proteins or protein segments do not …

Answer 69

• regions of relatively high stability and others of low or negligible stability
• protein function
• fold at all

Question 70

chaperones

Answer 70

• proteins that interact with partially folded or improperly folded polypeptides, facilitating correct folding pathways or providing microenvironments in which folding can occur
• Two major families of chaperones, both well studied, are the Hsp70 family and the chaperonins

Question 71

_____ _____ is a substantial problem in all cells, and a quarter or more of all polypeptides synthesized may be destroyed because they do not fold correctly. In some cases, the misfolding causes or contributes to the development of _____ _____

Answer 71

• protein misfolding
• serious disease

Question 72

misfolded proteins can be degraded by a system of proteases called the _____-_____ _____

Answer 72

• ubiquitin-proteasome system