Welcome to Scribd, the world's digital library. Read, publish, and share books and documents. See more
Download
Standard view
Full view
of .
Look up keyword
Like this
29Activity
0 of .
Results for:
No results containing your search query
P. 1
Ch 6 - Problems

Ch 6 - Problems

Ratings: (0)|Views: 4,855 |Likes:
Published by Khris Griffis

More info:

Published by: Khris Griffis on Apr 17, 2010
Copyright:Attribution Non-commercial

Availability:

Read on Scribd mobile: iPhone, iPad and Android.
download as PDF, TXT or read online from Scribd
See more
See less

03/31/2013

pdf

text

original

 
1.
Draw a cis peptide bond and identify the groups that experience steric interference.
Answer:2.
Helices can be described by the notation
n
m
, where
n
is the number of residues per helical turn and
m
isthe number of atoms, including H, in the ring that is closed by the hydrogen bond. (a) What is thisnotation for the
α
helix? (b) Is the 3
10
helix steeper or shallower than the
α
helix?
Answer:(a)
3.6
13
;
(b)
steeper.
3.
Calculate the length in angstroms of a 100-residue segment of the
α
keratin coiled coil.
Answer:
(100 residues)(1
α
-helical turn/3.6 residues) (5.1 Å/keratin turn) = 142 Å
4.
Hydrophobic residues usually appear at the first and fourth positions in the seven-residue repeats of  polypeptides that form coiled coils. (a) Why do polar or charged residues usually appear in the remainingfive positions? (b) Why is the sequence Ile–Gln–Glu–Val–Glu–Arg–Asp more likely than the sequenceTrp–Gln–Glu–Tyr–Glu–Arg–Asp to appear in a coiled coil?
Answer:(a)
The first and fourth side chains of the two helices of a coiled coil form buried hydrophobicinteracting surfaces, but the remaining side chains are exposed to the solvent and therefore tend to be polar or charged.
(b)
Although the residues at positions 1 and 4 in both sequences are hydrophobic, Trp and Tyr aremuch larger than Ile and Val and would therefore not fit as well in the area of contact between thetwo polypeptides in a coiled coil.
5.
Globular proteins are typically constructed from several layers of secondary structure, with a hydrophobiccore and a hydrophilic surface. Is this true for a fibrous protein such as
α
keratin?
Answer:
A fibrous protein such as
α
keratin does not have a discrete globular core. Most of the residues in itscoiled coil structure are exposed to the solvent. The exception is the strip of nonpolar side chains at theinterface of the two coils.
Problemshttp://edugen.wiley.com/edugen/courses/crs1900/rc/voet9301c06/dm9ld...1 of 44/17/2010 9:12 AM
 
6.
The digestive tract of the larvae of clothes moths is a strongly reducing environment. Why is this beneficial to the larvae?
Answer:
The reducing conditions promote cleavage of the disulfide bonds that cross-link 
α
keratin molecules. Thishelps the larvae digest the wool clothing that they eat.
7.
Describe the primary, secondary, tertiary, and quaternary structures of collagen.
Answer:
Collagen's primary structure is its amino acid sequence, which is a repeating triplet of mostlyGly–Pro–Hyp. Its secondary structure is the left-handed helical conformation characteristic of itsrepeating sequence. Its tertiary structure is essentially the same as its secondary structure, since most of the protein consists of one type of secondary structure. Collagen's quaternary structure is the arrangementof its three chains in a right-handed triple helix.
8.
Explain why gelatin, which is mostly collagen, is nutritionally inferior to other types of protein.
Answer:
Because collagen has such an unusual amino acid composition (almost two-thirds consists of Gly and Proor Pro derivatives), it contains relatively fewer of the other amino acids and is therefore not as good asource of amino acids as proteins containing a greater variety of amino acids.
9.
Is it possible for a native protein to be entirely irregular, that is, without
α
helices,
β
sheets, or other repetitive secondary structure?
Answer:
Yes, although such irregularity should not be construed as random.
10.
(a) Is Trp or Gln more likely to be on a protein's surface? (b) Is Ser or Val less likely to be in the protein'sinterior? (c) Is Leu or Ile less likely to be found in the middle of an
α
helix? (d) Is Cys or Ser more likelyto be in a
β
sheet?
Answer:
(a) Gln; (b) Ser; (c) Ile; (d) Cys. See Table 6-1.
11.
What types of rotational symmetry are possible for a protein with (a) four or (b) six identical subunits?
Answer:
(a)
4
and
 D
2
; (b)
6
and
 D
3
.
12.
You are performing site-directed mutagenesis to test predictions about which residues are essential for a protein's function. Which of each pair of amino acid substitutions listed below would you expect todisrupt protein structure the most? Explain.
(a)
Val replaced by Ala or Phe.
(b)
Lys replaced by Asp or Arg.
(c)
Gln replaced by Glu or Asn.
(d)
Pro replaced by His or Gly.
Problemshttp://edugen.wiley.com/edugen/courses/crs1900/rc/voet9301c06/dm9ld...2 of 44/17/2010 9:12 AM
 
Answer:(a)
Phe. Ala and Phe are both hydrophobic, but Phe is much larger and might not fit as well in Val's place.
(b)
Asp. Replacing a positively charged Lys residue with an oppositely charged Asp residue would bemore disruptive.
(c)
Glu. The amide-containing Asn would be a better substitute for Gln than the acidic Glu.
(d)
His. Pro's constrained geometry is best approximated by Gly, which lacks a side chain, rather than a residue with a bulkier side chain such as His.
13.
Laboratory techniques for randomly linking together amino acids typically generate an insoluble polypeptide, yet a naturally occurring polypeptide of the same length is usually soluble. Explain.
Answer:
A polypeptide synthesized in a living cell has a sequence that has been optimized by natural selection sothat it folds properly (with hydrophobic residues on the inside and polar residues on the outside). Therandom sequence of the synthetic peptide cannot direct a coherent folding process, so hydrophobic sidechains on different molecules aggregate, causing the polypeptide to precipitate from solution.
14.
Given enough time, can all denatured proteins spontaneously renature?
Answer:
 No.
15.
Describe the intra- and intermolecular bonds or interactions that are broken or retained when collagen isheated to produce gelatin.
Answer:
Hydrophobic effects, van der Waals interactions, and hydrogen bonds are destroyed during denaturation.Covalent cross-links are retained.
16.
Under physiological conditions, polylysine assumes a random coil conformation. Under what conditionsmight it form an
α
helix?
Answer:
At physiological pH, the positively charged Lys side chains repel each other. Increasing the pH abovethe p
(>10.5) would neutralize the side chains and allow an
α
helix to form.
17.
It is often stated that proteins are quite large compared to the molecules they bind. However, whatconstitutes a large number depends on your point of view. Calculate the ratio of the volume of ahemoglobin molecule (65 kD) to that of the four O
2
molecules that it binds and the ratio of the volume of a typical office (4 × 4 × 3 m) to that of the typical (70-kg) office worker that occupies it. Assume thatthe molecular volumes of hemoglobin and O
2
are in equal proportions to their molecular masses and thatthe office worker has a density of 1.0 g/cm
3
. Compare these ratios. Is this the result you expected?
Answer:
The molecular mass of O
2
is 32 D. Hence the ratio of the masses of hemoglobin and 4 O
2
, which is equalto the ratio of their volumes, is 65,000/(4 × 32) = 508. The 70-kg office worker has a volume of 70 kg ×
Problemshttp://edugen.wiley.com/edugen/courses/crs1900/rc/voet9301c06/dm9ld...3 of 44/17/2010 9:12 AM

Activity (29)

You've already reviewed this. Edit your review.
1 hundred reads
1 thousand reads
Celia Foster liked this
Celia Foster liked this
Celia Foster liked this
Celia Foster liked this
Celia Foster liked this
Erica Leigh liked this
Morgan Weir liked this

You're Reading a Free Preview

Download
/*********** DO NOT ALTER ANYTHING BELOW THIS LINE ! ************/ var s_code=s.t();if(s_code)document.write(s_code)//-->