Biochemistry: A Short Course: Biochemistry chap4 test Flashcards


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1

1. 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.

Answer: b

2

2. 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.

Answer: d

3

3. 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: a

4

4. 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 ____________.

Answer: j

5

5. 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.

Answer: e

6

6. 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.

Answer: i

7

7. 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.

Answer: k

8

8. 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
____________.

Answer: g

9

9. 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.

Answer: e

10

10. 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 ____________.

Answer: f

11

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

oxidation

12

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

amide bond

13

13. Peptides differ from proteins in _______ .

the number of amino acid residues

14

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

trans

15

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

alpha helix

16

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

screw sense

17

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

α-keratin

18

18. Every third residue in the protein collagen is _______ .

glycine

19

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

β-mecaptoethanol

20

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

antiparallel

21

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

β-sheet

22

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

denatured

23

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

Collagen

24

24. Collagen contains _______ , a modified amino acid.

hydroxyproline

25

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

soluble; an alpha helical

26

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

Quaternary structure

27

27. 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.

Answer: A

28

28. 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.

Answer: C

29

29. 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.

Answer: E

30

30. 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.

Answer: B

31

31. 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.

Answer: D

32

32. 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

Answer: E

33

33. 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.

Answer: E

34

34. Which of the following amino acid residues would most likely be buried in the interior of a watersoluble,
globular protein?
A. Aspartate
B. Serine
C. Phenylalanine
D. Lysine
E. Glutamine

Answer: C

35

35. 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.

Answer: D

36

36. 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.

Answer: D

37

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

A protein will spontaneously fold into a three-dimensional structure determined by the amino
acid sequence.

38

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

When proteins interact or assemble, new functions and specificity become available. Protein
interactions allow new binding sites at the assembly interface, and provide multifunctional activity and
specificity, such as found in polymerases and signal transduction.

39

39. How does the protein backbone add to structural stability?

The protein backbone contains the peptide bond, which has NH molecules and C=O (ketone)
groups. Hydrogen-bond formation between the hydrogen on the nitrogen and the oxygen support the
protein conformation.

40

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

Steric hindrances of the side chains make certain combinations and angles impossible.

41

41. Describe some of the features of an α helix.

The α helix is a coil stabilized by intrachain hydrogen bonds between the carbonyl oxygen of
a residue and the amide hydrogen of the fourth residue away. There are 3.6 amino acids per turn. The
hydrogen bonds are between amino acid residues that have two intervening residues. Thus, these
amino acid residues are found on the same side of the coil. The helix is almost always right-handed,
although left-handed helices are, in theory, possible.

42

42. What is the “hydrophobic effect” as it relates to protein structure?

The three-dimensional structure of a water-soluble protein is stabilized by the tendency of
hydrophobic groups to assemble in the interior of the molecule.

43

43. What are the key characteristics that make the peptide bond important to protein
folding/structure?

The resonance of the amide bond create a planar, rigid region of the peptide backbone with
the R groups on opposite sides of the peptide bond. This results in a limit to the types and angles of
conformation, allowing a predictable folding pattern.

44

44. What are prions?

Prions are proteins that can assume (after infection or by other causes) a new protein
structure that is self-propagating. Prion diseases have several variants, at least one of which is fatal to
humans.

45

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

The reducing agent reduced incorrectly paired disulfide bonds, allowing them to reform with
the correct pairing until the most stable conformation of the protein had been obtained.

46

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

If some regions interact preferentially, lending stability to certain conformations as the
protein folds, they can impact the overall structure of the protein.

47

47. A primary sequence of a protein contains a run of reasonably small amino acids, containing few
branched amino acids or serines. This sequence ends in a proline. What can you deduce from this
information?

The sequence is likely an alpha helix. The smaller amino acids do not sterically hinder the
side groups on the outside of the helix and the absence of amino acids that would interfere with the
helix are all evidence for this secondary structure. The proline is likely to be the end of the sequence.

48

The sequence is likely an alpha helix. The smaller amino acids do not sterically hinder the
side groups on the outside of the helix and the absence of amino acids that would interfere with the
helix are all evidence for this secondary structure. The proline is likely to be the end of the sequence.

If some regions interact preferentially, lending stability to certain conformations as the
protein folds, they can impact the overall structure of the protein.

49

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

Gly-Pro-Pro. The small side group of the glycine allows for a tight screw turn for this atypical
helix. The prolines are important to stabilize tight three-amino-acid helices. In addition, the prolines are
also hydroxylated by an enzyme which requires ascorbic acid to maintain activity. Without the
hydroxylation of collagen by prolyl hydroxylase, the collagen superstructure is less stable and results in
adverse flexibility of the connective tissues (scurvy).

50

50. Prion diseases are often latent; that is, those with prion diseases are asymptomatic for many
years after their initial infection. What causes this latency?

Prion diseases are protein based; more specifically, protein-structure based.Because it takes
time to converted the prion protein from the soluble, mostly helical form to the beta-strand, insoluble
form,there is a lag time befor enough proteins are converted to the polymer which causes cell injury
This characteristic ofprion diseases makes it difficult to diagnose before it is too late.