Deck 4: Protein Three-Dimensional Structure

Question 1

Due to the side group steric clash, almost all peptide bonds are _______________ in their configuration.

Answer 1

trans

Question 2

The peptide bond is also known as a(n) _______________.

Answer 2

amide bond

Question 3

Use the following to answer questions
Choose the correct answer from the list below. Not all of the answers will be used.
a) amino
b) water
c) protons
d) DNA
e) secondary structure
f) tertiary structure
g) Ramachandran
h) RNA
i) domain
j) cystine
k) proline
l) Sanger
m) D amino acids
n) cysteine
According to convention, ____________ is the terminus drawn on the left side of a peptide.

Answer 3

a

Question 4

Use the following to answer questions
Choose the correct answer from the list below. Not all of the answers will be used.
a) amino
b) water
c) protons
d) DNA
e) secondary structure
f) tertiary structure
g) Ramachandran
h) RNA
i) domain
j) cystine
k) proline
l) Sanger
m) D amino acids
n) cysteine
____________: Compact regions that may be connected by a flexible segment of polypeptide chain.

Question 5

Every third residue in the protein collagen is _______________.

Question 6

The _______________ indicates the left- or right-handedness of an alpha helix.

Question 7

Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such as _______________.

Question 8

Use the following to answer questions
Choose the correct answer from the list below. Not all of the answers will be used.
a) amino
b) water
c) protons
d) DNA
e) secondary structure
f) tertiary structure
g) Ramachandran
h) RNA
i) domain
j) cystine
k) proline
l) Sanger
m) D amino acids
n) cysteine
____________: The type of structure to which α helices, β sheets, and turns are referred.

Question 9

_______________ is a fibrous protein and is the primary component of wool and hair.

Question 10

Use the following to answer questions
Choose the correct answer from the list below. Not all of the answers will be used.
a) amino
b) water
c) protons
d) DNA
e) secondary structure
f) tertiary structure
g) Ramachandran
h) RNA
i) domain
j) cystine
k) proline
l) Sanger
m) D amino acids
n) cysteine
Two amino acids undergo oxidation to form a dimer called ____________.

Question 11

The secondary structure that is stabilized by CO and NH hydrogen bonding within the peptide chain is the _______________.

Question 12

Peptides differ from proteins in _______________.

Question 13

The _______________ of a disulfide bridge results in a separation of two protein chains.

Question 14

Use the following to answer questions
Choose the correct answer from the list below. Not all of the answers will be used.
a) amino
b) water
c) protons
d) DNA
e) secondary structure
f) tertiary structure
g) Ramachandran
h) RNA
i) domain
j) cystine
k) proline
l) Sanger
m) D amino acids
n) cysteine
The overall structure of a protein is referred to as ____________.

Question 15

Use the following to answer questions
Choose the correct answer from the list below. Not all of the answers will be used.
a) amino
b) water
c) protons
d) DNA
e) secondary structure
f) tertiary structure
g) Ramachandran
h) RNA
i) domain
j) cystine
k) proline
l) Sanger
m) D amino acids
n) cysteine
When a peptide bond is formed, a(n) ____________molecule is also made.

Question 16

Use the following to answer questions
Choose the correct answer from the list below. Not all of the answers will be used.
a) amino
b) water
c) protons
d) DNA
e) secondary structure
f) tertiary structure
g) Ramachandran
h) RNA
i) domain
j) cystine
k) proline
l) Sanger
m) D amino acids
n) cysteine
Changes in ____________ create amyloid fibers which are insoluble and are the source of mad cow disease, and Alzheimer's, and Parkinson's diseases.

Question 17

Use the following to answer questions
Choose the correct answer from the list below. Not all of the answers will be used.
a) amino
b) water
c) protons
d) DNA
e) secondary structure
f) tertiary structure
g) Ramachandran
h) RNA
i) domain
j) cystine
k) proline
l) Sanger
m) D amino acids
n) cysteine
The plot that allows one to investigate the likely orientation of certain amino acid pairs is called the ____________.

Question 18

Use the following to answer questions
Choose the correct answer from the list below. Not all of the answers will be used.
a) amino
b) water
c) protons
d) DNA
e) secondary structure
f) tertiary structure
g) Ramachandran
h) RNA
i) domain
j) cystine
k) proline
l) Sanger
m) D amino acids
n) cysteine
____________: This amino acid residue disrupts the α helix because its side chain contains a unique ring structure that restricts bond rotations.

Question 19

Use the following to answer questions
Choose the correct answer from the list below. Not all of the answers will be used.
a) amino
b) water
c) protons
d) DNA
e) secondary structure
f) tertiary structure
g) Ramachandran
h) RNA
i) domain
j) cystine
k) proline
l) Sanger
m) D amino acids
n) cysteine
____________: Codes for the sequence of amino acids.

Question 20

The _______________ β-sheet structure occurs when the two strands are oriented in opposite directions (N →
C).

Question 21

What is the approximate mass of a protein containing 200 amino acids? (Assume there are no other protein modifications.)

A) 20,000
B) 11,000
C) 22,000
D) 222,000
E) None of the above.

Question 22

What determines a protein's function?

A) its structure
B) its gene sequence
C) N-terminal amino acids
D) None of the above.
E) All of the above.

Question 23

_______________ refers to the spatial arrangement of subunits and the nature of their interactions.

Question 24

Which of the following amino acid residues would most likely be buried in the interior of a water-soluble, globular protein?

A) Aspartate
B) Serine
C) Phenylalanine
D) Lysine
E) Glutamine

Question 25

How does the protein backbone add to structural stability?

Question 26

Collagen contains _______________, a modified amino acid.

Question 27

A protein whose peptide backbone is mostly extended and hydrogen bonded to different strands of the protein is composed mostly of the _______________ secondary structure.

Question 28

The folding of a protein into its native shape can best be described as:

A) a random event.
B) a random event catalyzed by ribosome proteins to maintain a low energy structure.
C) a series of controlled folds with a few random-shaped structures.
D) a series of repeatable random events where the lowest energy structure is maintained.
E) an event where the highest possible energy state is stabilized with discrete folding intermediates.

Question 29

Which of the following protein(s) contain examples of α-helical character?

A) keratin
B) ferritin
C) myosin
D) tropomyosin
E) All of the above.

Question 30

Where are Ω and β turns and loops often found?

A) in a hydrophobic pocket
B) on the interior cleft
C) at the protein interface with ligand
D) on the surface of proteins
E) None of the above.

Question 31

What structure(s) did Pauling and Corey predict in 1951?

A) α helix
B) β sheet
C) β turn
D) A, B, and C
E) A and B

Question 32

Compact, globular proteins are typically water _______________ and consist mostly of _______________ secondary structure.

Question 33

What is the advantage of protein interaction and assembly with other proteins?

Question 34

How does a protein's amino acid sequence influence the tertiary structure?

Question 35

A protein is considered to be _______________ when it is converted into a randomly coiled structure without its normal activity.

Question 36

Why is the peptide bond planar?

A) Bulky side chains prevent free rotation around the bond.
B) It exhibits partial double-bond character, preventing rotation.
C) Hydrogen bonding between the NH and C=O groups limits movement.
D) None of the above.
E) All of the above.

Question 37

Key properties of proteins include:

A) a wide range of functional groups.
B) an ability to possess either rigid or flexible structures as dictated by functional requirements.
C) the ability to interact with other proteins.
D) A and B.
E) All of the above.

Question 38

_______________ is the major fibrous protein present in skin, bone, tendon, cartilage, and teeth.

Question 39

Why are all the theoretical combinations of phi and psi not possible?

Question 40

The configuration of most α-carbon atoms of amino acids linked in a peptide bond is:

A) cis.
B) circular.
C) parallel.
D) trans.
E) perpendicular.

Question 41

What can you deduce from this information?

Question 42

What is the advantage of having certain regions of partially correct folded regions?

Question 43

What causes this latency?

Question 44

What are prions?

Question 45

In the ribonuclease experiments performed by Anfinsen, what was the significance of the presence of the reducing agent β-mercaptoethanol?

Question 46

What is the "hydrophobic effect" as it relates to protein structure?

Question 47

Describe some of the features of an α helix.

Question 48

What are the key characterisics that make the peptide bond important to protein folding/structure?

Question 49

What is the advantage of having certain regions of partially correct folded regions?

Question 50

What is the sequence of amino acids found in collagen? What is the significance of the sequence and what is the complication of scurvy?