Chapter 6: Proteins: Three-Dimensional Structure

Question 1

of a protein is its linear sequence of amino acids.

Answer 1

Primary structure

Question 2

is the local spatial arrangement of a polypeptide’s backbone atoms without regard to the conformations of its side chains.

Answer 2

Secondary structure

Question 3

refers to the three-dimensional structure of an entire polypeptide, including its side chains.

Answer 3

Tertiary structure

Question 4

refers to the spatial arrangement of protein’s subunits for those composed of two or more polypeptide chains.

Answer 4

Quaternary structure

Question 5

f a protein refers to the atoms that participate in peptide bonds, ignoring the side chains of the amino acid residues.

Answer 5

backbone
main chain

Question 6

The conformation of the backbone can therefore be described by the

Answer 6

torsion angles

Question 7

The sterically allowed values of ɸ and ψ
can be calculated. Sterically forbidden
conformations, have ɸ and ψ values that
would bring atoms closer than the
corresponding van der Waals distance.
Such information is summarized in a

Answer 7

Ramachandran diagram

Question 8

are forbidden conformations of a
polypeptide chain

Answer 8

Unmarked regions

Question 9

the only residue without a side chain

Answer 9

Gly

Question 10

is much less sterically
hindered than the other amino acid residues.

Answer 10

Gly

Question 11

what are α helix and the β sheet called

Answer 11

regular secondary structures

Question 12

α helix is what-handed

Answer 12

right

Question 13

the distance the helix rises along its axis per turn

Answer 13

pitch

Question 14

what is the backbone of both helixs

Answer 14

hydrogen bonds

Question 15

In β sheets, however, hydrogen
bonding occurs between

Answer 15

neighboring polypeptide chains

Question 16

α helices or the strands of β sheets, are often joined by stretches of polypeptide that
abruptly change direction called what?

Answer 16

reverse turns or β bends

Question 17

forms strong, insoluble fibers which are the major stress-bearing
components of connective tissues such as bone, teeth, cartilage, tendon, and the
fibrous matrices of skin and blood vessels

Answer 17

collagen

Question 18

is a mechanically durable and relatively unreactive protein used in various tissues such as hair (alpha) and feather (Beta)

Answer 18

keratin

Question 19

results from the dietary deficiency of vitamin C
common in sailors whose diets
were devoid of fresh foods on long voyages.

Answer 19

scurvy

Question 20

The protein’s three-dimensional structure is computed by interatomic distance
measurements, along with knowledge of the protein’s sequence and known geometric
constraints such as covalent bond distances and angles, group planarity, chirality, and
van der W aals radii.

Answer 20

NMR technique

Question 21

disadvantages of NMR technique

Answer 21

Present NMR methods are limited to determining the structures of proteins with
MW < 40 kD

Question 22

advantages of NMR technique

Answer 22

NMR can resolve the structures of proteins that fail to crystallize.
NMR can probe motions so it can also be used to study protein folding and dynamics.

Question 23

where are The charged polar residues Arg, His, Lys, Asp, and Glu usually located?

Answer 23

on the surface of a protein in contact with the aqueous solvent.

Question 24

where are the nonpolar residues Val, Leu, Ile, Met, and Phe

Answer 24

occur mostly in the interior of a protein, out of contact with the aqueous solvent

Question 25

where are the uncharged polar groups Ser, Thr, Asn, Gln, and T yr

Answer 25

are usually on the protein surface but also occur in the interior of the molecule.

Question 26

Large proteins usually fold into two or more globular clusters known as

Answer 26

domains

Question 27

why multisubunit proteins are so common.

Answer 27

1.Defects can be repaired by simply
replacing the flawed subunit

2.In the case of enzymes since each
subunit has an active site, substrate
channeling can occur where the
substrate of one subunit is readily
available as the product of a dif
subunit.

3. The subunit construction of many
   enzymes provides the structural basis
   for the regulation of their enzymatic
   activities.

Question 28

has the greatest influence on protein stability and is the major determinant of native protein structure.

Answer 28

hydrophobic effect

Question 29

make only minor contributions to protein stability.

Answer 29

hydrogen bonds

Question 30

which are motifs in nucleic acid–binding proteins.

Answer 30

Zinc fingers

Question 31

grow at temperatures near 100 oC.

Answer 31

hyperthermophiles

Question 32

what is more stable hyperthermophiles or mesophilic proteins

Answer 32

hyperthermophiles

Question 33

why are hyperthermophiles more stable

Answer 33

Networks of salt bridges

increased size of the protein’s hydrophobic core

increased size of the interface between its domains and/or subunits

more tightly packed core as evidenced by a reduced surface-to-volume ratio.

Question 34

how do Proteins Undergo Denaturation and Renaturation

Answer 34

1. heating
2. pH
3. Detergents
4. chaotropic agents

Question 35

tend to participate in signaling and regulation,

Answer 35

intrinsically disordered proteins

Question 36

involved largely in catalytic reactions,
transport processes, and structural functions

Answer 36

ordered proteins

Question 37

often adopt a specific secondary or tertiary structure when they bind to other molecules such as ions, organic molecules, proteins,
and nucleic acids

Answer 37

Intrinsically disordered proteins

Question 38

It is likely that the driving force in protein
folding is what has been termed a

Answer 38

hydrophobic collapse

Question 39

Folding, like denaturation, appears to
be a what process

Answer 39

cooperative process

Question 40

are essential proteins that bind to
unfolded and partially folded polypeptide chains to prevent the improper association of exposed hydrophobic segments that might lead to non-native folding as well as polypeptide aggregation and
precipitation

Answer 40

Molecular chaperones

Question 41

what is an example of a transmissible spongiform encephalopathies (TSEs) diseases

Answer 41

mad cow disease

Question 42

neurons develop large vacuoles that give brain tissue a spongelike microscopic appearance. These infectious diseases are caused by proteins called prions.

Answer 42

transmissible spongiform encephalopathies (TSEs)