Birla Institute of Technology (BIT Mesra) 2007 B.E BIOPHYSICS - Question Paper
BIRLA INSTITUTE OF TECHNOLOGY & SCIENCE, PILANI, RAJ.
BIOPHYSICS, BIOC331, first SEMESTER, 2007-08
COMPREHENSIVE EXAMINATION, Date: 6.12.2007, (OPEN BOOK)
(See the instructions before starting to answer)
1. For Part I, quiz answers should be written ONLY in the printed ans SHEET
given separately by indicating your option in the ans sheet as (A) or (B) etc.
Answers once written cannot be changed in any manner. Pencil should not be used
for answering.
2. Overwritten answers will be treated as unanswered. So, use ans sheet carefully.
3. Do rough work at the backside of the ques. paper.
4. every accurate ans will be awarded one marks. one mark will be deducted for every
two wrong answers. Maximum marks for Part I is 30
5. The maximum time allowed for Part I is 60 minutes. Part II may be collected as and when
Part I is submitted. Detach the ans sheet and submit only this.
6. Part II has total marks of 60.
PART I (Answer All; 1x30 = 30 Marks)
1. Which of the group of an amino acid without ionizable side chain, will be either protonated or
deprotonated, as the case may be, at pH 11.
(A) COOH (B) COO- (C) NH2 (D) NH3
+
2. presume that an amino acid without any ionizable groups in side chain, has isoelectric point at
pH 7. How is it charged at pH 3?
(A) positively (B) negatively (C) neutral overall (D) data insufficient
3. select which statements are/is accurate from subsequent about the peptide bond
1. is an amide linkage
2. has a partial double bond character.
3. is not ionized at physiological pH.
4. is ionized at physiological pH
(A) if 1, 2, and three are accurate (B) if one and three are accurate (C) if two and four are accurate
(D) if only four is accurate
4. Which 1 of the subsequent kinds of bonds or interactions is lowest important in determining
the three-dimensional folding of most proteins?
(A) Hydrogen bonds (B) Hydrophobic interactions (C) Disulfide bonds (D) pi bonds
5. Which sequence of atoms can be obtained in the backbone of polypeptides?
(A) C-N-N-C (B) C-C-C-N (C) C-C-N-C (D) N-C-C-C
6. A pair potential ranging from 2 identical spherical atoms has the form
A
2
U(r) = (4e /kBT)[(s/ r)12 - (s/
r)6 ] ; r is the separation ranging from the centers of the spherical atoms
and s is the diameter, e is the energy parameter and T is temperature, kB is the Boltzmann
constant. Which of the subsequent is true?
(A) r ¥; U(r) 0 and r 0 ; U(r) ¥
(B) r 0; U(r) 0 and r ¥ ; U(r) ¥
(C) r ¥; U(r) e and r 0 ; U(r) e/kB
(D) r 0; U(r) kBT and r ¥ ; U(r) ¥
7. The packing parameter of an amphiphilic aggregate is provided by the relation and dimension as
follows (where ‘v’ is quantity of hydrocarbon chain, ‘a0’ is optimum area per molecule and ‘lc’is
length of hydrocarbon chain):
(A) v/( a0lc ), dimensionless (B) v lc /a0
2
, dimensionless (C) a0 lc
2 /v, Å3 (D) None
8. List atoms commonly obtained in biological molecules that are often hydrogen bond acceptors.
(A) carbon (B) oxygen (C) nitrogen (D) Both B and C
9. Bilayers are observed to be twisted or buckled. This is due to
(A) Due to crystallization of molecules
(B) Due to elasticity of the bilayer and chirality of the molecules
(C) Due to extensive gauche bending of alkyl chains
(D) None
10. Most frequently observed Hydrogen bonds in the biological systems are
(A) Strong (B) Weak (C) Tandem (D) None
11. Interaction arising from the process of bringing 2 non-polar solutes from infinity to a
separation that corresponds to a final configuration within water at constant temperature and
pressure is:
(A) Hydrophobic effect (B) Hydrophobic interaction (C) Charge dipolar interaction (D)
Hydrophobic hydration
12. Disulfide bonds are formed by pairs of which amino acid?
(A) Glycine (B) Cysteine (C) Histidine (D) Proline
13. How do protein folding progresses towards the native state?
(A) by cooperative folding (B) by progressive stabilization of intermediates (C) by random
search through all possible conformational states (D) A and B
14. The subsequent double-stranded DNA molecules (only the "top" strand is shown) are current
in a dilute solution, which is heated sufficiently to denature all the DNA molecules. The solution
is then rapidly cooled to room temperature. DNA from which molecule will 1st show the
presence of double strands again after cooling?
(A) AGGTAATTTCGCCC (B) AGGTAAGCTTACCT (C) AGGTTGGGTGCTGA
(D)AAAAAAAAAAAAA
3
15. For alpha helix, provided pitch = p, residue per turn = n, rise per residue = h which can be used
to compute pitch
(A) p =n / h (B) p = n x h (C) p = h tan (n) (D) Sufficient parameters are not provided
16. provided the opted free energy contribution to the spontaneous aggregation of an amphiphilic
aggregate, identify the unfavorable free energy components:
(A) Hydrophobic, entropic (B) Hydrophobic, vander Walls interaction ranging from chains (C)
Translational-rotational, head group repulsion (D) Entropic, vander Walls interaction ranging from
chains
17. From the Brewster angle image in Fig. 1(attached), identify the region (shown as A,B,C, or
D) that has most probability with amphiphile in LE phase and write that option in the
corresponding box given in the ans sheet.
a
18. At high temperature and high water content what is the most likely phase of a lipid
(A) L- (B) Cubic (C) Crystalline (D) P-
19. Invariant or nonvariable region of a DNA structure is composed of
(A) Phosphodiester and sugar (B) base and phosphodiester (C) base and sugar (D) All regions
are variable.
20. A molecule has LJ energy parameter /kBT = 100. For a pair of such molecules the the pair
interaction potential energy at deepest is
(A) -100 kBT (B) -200 kBT (C) -100 kBT (D) -50 kBT
21. A protein molecule in a kinetically trapped conformational state has energy
(A) Higher than Native and lowered than completely denatured state
(B) Higher than completely denatured and lower than Native
(C) Equal to completely denatured state
(D) Equal to native
22. Bovine serum albumin (a protein) molecule has high dipole moment because
A
B
C
D
4
(A) Due to large size of it and its charge distribution anisotropy
(B) Due to the large dielectric constant of water compared to hemoglobin
(C) Due to attached water of hydration in the hydration shell
(D) Due to presence of metal ion in the structure
23. For which of the subsequent pair of basic unit and higher-level structure both are achiral
(not chiral)?
(A) Phospholipid and helical bilayer composed of it.
(B) Natural amino acid and protein composed of it.
(C) Natural sugars and DNA composed of it.
(D) None
24. Hydrophobic effect is due to
(A) Attraction ranging from nonpolar solute molecules in water
(B) Because it is entropically favorable to have nonpolar molecules together in water
(C) Because nonpolar molecules can be hydrogen bonded together
(D) Because the nonpolar molecules dissolved easily in water
25. Raman scattering is not possible with molecules having
(A) Isotropic polarizability
(B) Anisotropic polarizability
(C) Homonuclear diatomic structure
(D) None of the above
26. During osmosis process ranging from a pure solvent and a solute, the semipermeable membrane
allows to pass
(A) The solvent molecules
(B) The solute molecules
(C) Both
(D) None
27. In the scattering geometry with an angle of deflection (scattering angle) of , the related
scattering vector is provided by,
(A) Cos / 2 (B) 2Sin / (C) two Sin (/2) / (D) None
28. The enol and imino forms are current in physiological conditions in natural DNA at
subsequent % out of the total of A, T, G, C base pairs (as the case may be), respectively:
(A) 12.3%, 18.4%, 3.2%, 56% (B) 0.01% for all (C) 99.99% for all (D) 18.4%, 3.2%, 12.3%,
56%
29. Positively charge macromolecules are located in side two in an osmosis chamber (divided in
part one and two by a semipermeable membrane). A completely ionizable salt (X+ Y-) is added and
the corresponding Donnan ratio is obtained to be 10. How much excess concentration of X+ will be
after the equilibrium is established and in which side (1 or 2)?
(A) 10 fold, in side 1
5
(B) 10 fold, in side 2
(C) 20 fold, in side 1
(D) 20 fold, in side 2
30. Factors favorably affecting the cooperativity of helix – coil transition are
(A) The hydrogen bonding of residues, The dipole moment alignment
(B) The van der Waals interactions among residues, The dipole moment alignment
(C) A,B
(D) None
6
BIRLA INSTITUTE OF TECHNOLOGY & SCIENCE, PILANI, RAJ.
BIOPHYSICS, BIOC331, first SEMESTER, 2007-08
COMPREHENSIVE EXAMINATION, Date: 6.12.2007
(See the instructions before starting to answer)
PART I
ans SHEET
ID No. NAME
No. of accurate
answer
No. of wrong
answer
No. of
unanswered
question
Total marks
Recheck request (if any):
1. eight 15 22 29
2. nine 16 23 30
3. 10 17 24
4. 11 18 25
5. 12 19 26
6. 13 20 27
7 14 21 28
A
7
BIRLA INSTITUTE OF TECHNOLOGY & SCIENCE, PILANI, RAJ.
BIOPHYSICS, BIOC331, first SEMESTER, 2007-08
COMPREHENSIVE EXAMINATION, Date: 6.12.2007, (CLOSED BOOK)
INSTRUCTION: There are 6 (6) ques. with sub-parts. Attempt all the ques.. begin
answering every ques. on a fresh page and ans all parts of the ques. together. Write brief
answers to the point with proper justification. Pencil should not be used.
PART II (60M)
Q.1.
(a) subsequent amino acid (only neutral form is shown) is titrated and pKa values are found as
2.18, 8.9 and 10.28, respectively. provided that n-butyl amine has pka = 10.59. Write the ionization
scheme (successive ionizations) of the amino acid from low pH (=1) to high pH (=14). give
justification supporting the scheme.
(b) A 88 kilo Dalton protein has a two-stranded alpha-helical structure (ignore any turn in the
structure i.e. consider the whole structure as composed of helical form). If the mean residue mass
is 110 Daltons and rise per residue of an alpha helix is 1.5 Å, then compute the length of the
molecule
(c) A 50 residue segment of a protein folds into a 2 stranded antiparallel beta sheet structure
with a 4-residue hairpin turn, rise per residue of an beta sheet is 3.5 Å then compute the longest
dimension of this motif.
3+3+4 = 10M
Q.2.
(a) The shape of hair is determined in part by the trend of disulfide bonds in its major protein,
keratin. How curls are induced?
(b) Considering only the 2 major factors leading to the formation of an alpha helical structure,
where it is more probable to form helix: in water or in hexane? Justify your ans.
(c) Write the relation describing the supercoiling of nucleic acid and discuss every parameter.
3+3+4 = 10M
Q.3.
Time scale of orientational motion of pure water molecules is w = eight ps. When the aqueous
solution of whale myoglobin is studied, at lowest 3 various time scales are observed
experimentally. They are of the order of 1 = 80 ns, 2 = 10 ns and 3 = 40 ps.
(a) discuss the origin of 1
8
(b) discuss the origin of 2 and 3.
(c) Which experiment can investigate the rotational motions indicated by 1, 2 and 3 and
define the basic principle of the experimental technique (you can discuss for a single
component system, for example).
3+3+4 = 10M
Q.4.
After drawing the scattering geometry of X-ray, discuss what is structure factor and derive a
relation for atomic scattering factor (atom placed at origin).
3+3+4 = 10M
Q.5.
Write principles of 2 experimental methods for determining the molecular weight of
biological molecules in solution without destroying the molecular structure.
5+5 = 10M
Q.6.
A lipid molecule has head group immersed in aqueous medium (which has dielectric constant as
e(w)) as shown beneath. The avg. direction of the head group and alkyl chain is indicated by
the arrow () in the diagram. The head group has opposite charges of magnitude ± QL separated
by y. Suppose the solution is made acidic by HCl and a Chloride ion of charge QCl is situated at a
distance [(yCosf)/2] vertically from air/water interface and t distance away from the center O.
Consider that ion is in the grey quadrant (region). Derive an expression for the interaction
ranging from the head group and chloride ion. The final expression should contain the provided symbol
like e(w), QL , QCl , y, f etc and no various symbol.
Z
f AIR
O
WATER
10M
END
BIRLA INSTITUTE OF TECHNOLOGY & SCIENCE, PILANI, RAJ. BIOPHYSICS, BIOC331, 1st SEMESTER, 2007-08 COMPREHENSIVE EXAMINATION, Date: 6.12.2007, (OPEN BOOK)
(See the instructions before starting to answer)
1. For Part I, quiz answers should be written ONLY in the printed ANSWER SHEET provided separately by indicating your choice in the answer sheet as (A) or (B) etc. Answers once written cannot be changed in any manner. Pencil should not be used for answering.
2. Overwritten answers will be treated as unanswered. So, use answer sheet carefully.
3. Do rough work at the backside of the question paper.
4. Each correct answer will be awarded 1 marks. 1 mark will be deducted for every two wrong answers. Maximum marks for Part I is 30
5. The maximum time allowed for Part I is 60 minutes. Part II may be collected as and when Part I is submitted. Detach the answer sheet and submit only this.
6. Part II has total marks of 60.
PART I (Answer All; 1x30 = 30 Marks)
1. Which of the group of an amino acid without ionizable side chain, will be either protonated or deprotonated, as the case may be, at pH 11.
(A) COOH (B) COO- (C) NH2 (D) NH3+
2. Assume that an amino acid without any ionizable groups in side chain, has isoelectric point at pH 7. How is it charged at pH 3?
(A) positively (B) negatively (C) neutral overall (D) data insufficient
3. Choose which statements are/is correct from following about the peptide bond
1. is an amide linkage
2. has a partial double bond character.
3. is not ionized at physiological pH.
4. is ionized at physiological pH
(A) if 1, 2, and 3 are correct (B) if 1 and 3 are correct (C) if 2 and 4 are correct (D) if only 4 is correct
4. Which one of the following types of bonds or interactions is LEAST important in determining the three-dimensional folding of most proteins?
(A) Hydrogen bonds (B) Hydrophobic interactions (C) Disulfide bonds (D) pi bonds
5. Which sequence of atoms can be found in the backbone of polypeptides?
(A) C-N-N-C (B) C-C-C-N (C) C-C-N-C (D) N-C-C-C
6. A pair potential between two identical spherical atoms has the form
U(r) = (4e /kBT)[(o/ r)12 - (o/ r)6 ] ; r is the separation between the centers of the spherical atoms and o is the diameter, is the energy parameter and T is temperature, kB is the Boltzmann constant. Which of the following is true?
(A) r <x; U(r) 0 and r 0 ; U(r)
(B) r 0; U(r) 0 and r ; U(r)
(C) r <; U(r) and r 0 ; U(r) /kB
(D) r 0; U(r) -> kBT and r -> ; U(r) ->
7. The packing parameter of an amphiphilic aggregate is given by the relation and dimension as follows (where v is volume of hydrocarbon chain, ao is optimum area per molecule and /cis length of hydrocarbon chain):
7 7 2 7 2 3
(A) v/( a0ic ), dimensionless (B) v lc/a0 , dimensionless (C) a0 lc /v, A (D) None
8. List atoms commonly found in biological molecules that are often hydrogen bond acceptors. (A) carbon (B) oxygen (C) nitrogen (D) Both B and C
9. Bilayers are observed to be twisted or buckled. This is due to
(A) Due to crystallization of molecules
(B) Due to elasticity of the bilayer and chirality of the molecules
(C) Due to extensive gauche bending of alkyl chains
(D) None
10. Most frequently observed Hydrogen bonds in the biological systems are (A) Strong (B) Weak (C) Tandem (D) None
11. Interaction arising from the process of bringing two non-polar solutes from infinity to a separation that corresponds to a final configuration within water at constant temperature and pressure is:
(A) Hydrophobic effect (B) Hydrophobic interaction (C) Charge dipolar interaction (D) Hydrophobic hydration
12. Disulfide bonds are formed by pairs of which amino acid?
(A) Glycine (B) Cysteine (C) Histidine (D) Proline
13. How do protein folding progresses towards the native state?
(A) by cooperative folding (B) by progressive stabilization of intermediates (C) by random search through all possible conformational states (D) A and B
14. The following double-stranded DNA molecules (only the "top" strand is shown) are present in a dilute solution, which is heated sufficiently to denature all the DNA molecules. The solution is then rapidly cooled to room temperature. DNA from which molecule will first show the presence of double strands again after cooling?
(A) AGGTAATTTCGCCC (B) AGGT AAGCTT ACCT (C) AGGTT GGGT GCT GA (D)AAAAAAAAAAAAA
15. For alpha helix, given pitch = p, residue per turn = n, rise per residue = h which can be used to calculate pitch
(A) p =n / h (B) p = n x h (C) p = h tan (n) (D) Sufficient parameters are not given
16. Given the selected free energy contribution to the spontaneous aggregation of an amphiphilic aggregate, identify the unfavorable free energy components:
(A) Hydrophobic, entropic (B) Hydrophobic, vander Walls interaction between chains (C) Translational-rotational, head group repulsion (D) Entropic, vander Walls interaction between chains
17. From the Brewster angle image in Fig. 1(attached), identify the region (shown as A,B,C, or D) that has most probability with amphiphile in LE phase and write that choice in the corresponding box provided in the answer sheet.
18. At high temperature and high water content what is the most likely phase of a lipid
(A) L-a (B) Cubic (C) Crystalline (D) P-P
19. Invariant or nonvariable region of a DNA structure is composed of
(A) Phosphodiester and sugar (B) base and phosphodiester (C) base and sugar (D) All regions are variable.
20. A molecule has LJ energy parameter s/kT = 100. For a pair of such molecules the the pair interaction potential energy at deepest is
(A) -100 keT (B) -200 keT (C) -V100 keT (D) -50 keT
21. A protein molecule in a kinetically trapped conformational state has energy
(A) Higher than Native and lowered than completely denatured state
(B) Higher than completely denatured and lower than Native
(C) Equal to completely denatured state
(D) Equal to native
22. Bovine serum albumin (a protein) molecule has high dipole moment because
(A) Due to large size of it and its charge distribution anisotropy
(B) Due to the large dielectric constant of water compared to hemoglobin
(C) Due to attached water of hydration in the hydration shell
(D) Due to presence of metal ion in the structure
23. For which of the following pair of basic unit and higher-level structure both are achiral (not chiral)?
(A) Phospholipid and helical bilayer composed of it.
(B) Natural amino acid and protein composed of it.
(C) Natural sugars and DNA composed of it.
(D) None
24. Hydrophobic effect is due to
(A) Attraction between nonpolar solute molecules in water
(B) Because it is entropically favorable to have nonpolar molecules together in water
(C) Because nonpolar molecules can be hydrogen bonded together
(D) Because the nonpolar molecules dissolved easily in water
25. Raman scattering is not possible with molecules having
(A) Isotropic polarizability
(B) Anisotropic polarizability
(C) Homonuclear diatomic structure
(D) None of the above
26. During osmosis process between a pure solvent and a solute, the semipermeable membrane allows to pass
(A) The solvent molecules
(B) The solute molecules
(C) Both
(D) None
27. In the scattering geometry with an angle of deflection (scattering angle) of 9, the related scattering vector is given by,
(A) Cos 9 / 2X (B) 2Sin 9 / X (C) 2 Sin (9/2) / X (D) None
28. The enol and imino forms are present in physiological conditions in natural DNA at following % out of the total of A, T, G, C base pairs (as the case may be), respectively:
(A) 12.3%, 18.4%, 3.2%, 56% (B) 0.01% for all (C) 99.99% for all (D) 18.4%, 3.2%, 12.3%,
56%
29. Positively charge macromolecules are located in side 2 in an osmosis chamber (divided in part 1 and 2 by a semipermeable membrane). A completely ionizable salt (X+ Y-) is added and the corresponding Donnan ratio is found to be 10. How much excess concentration of X+ will be after the equilibrium is established and in which side (1 or 2)?
(A) 10 fold, in side 1
(B) 10 fold, in side 2
(C) 20 fold, in side 1
(D) 20 fold, in side 2
30. Factors favorably affecting the cooperativity of helix - coil transition are
(A) The hydrogen bonding of residues, The dipole moment alignment
(B) The van der Waals interactions among residues, The dipole moment alignment
(C) A,B
(D) None
BIRLA INSTITUTE OF TECHNOLOGY & SCIENCE, PILANI, RAJ. BIOPHYSICS, BIOC331, 1st SEMESTER, 2007-08 COMPREHENSIVE EXAMINATION, Date: 6.12.2007 (See the instructions before starting to answer)
PART I
ANSWER SHEET
ID No. NAME
|
No. of correct answer |
No. of wrong answer |
No. of unanswered question |
Total marks |
Recheck request (if any):
|
1. |
8 |
15 |
22 |
29 | |||||
|
2. |
9 |
16 |
23 |
30 | |||||
|
3. |
10 |
17 |
24 | ||||||
|
4. |
11 |
18 |
25 | ||||||
|
5. |
12 |
19 |
26 | ||||||
|
6. |
13 |
20 |
27 | ||||||
|
7 |
14 |
21 |
28 | ||||||
BIRLA INSTITUTE OF TECHNOLOGY & SCIENCE, PILANI, RAJ. BIOPHYSICS, BIOC331, 1st SEMESTER, 2007-08 COMPREHENSIVE EXAMINATION, Date: 6.12.2007, (CLOSED BOOK)
INSTRUCTION: There are six (6) questions with sub-parts. Attempt all the questions. Start answering each question on a fresh page and answer all parts of the question together. Write brief answers to the point with proper justification. Pencil should not be used.
PART II (60M)
Q.1.
(a) Following amino acid (only neutral form is shown) is titrated and pKa values are obtained as 2.18, 8.9 and 10.28, respectively. Given that rc-butyl amine has pka = 10.59. Write the ionization scheme (successive ionizations) of the amino acid from low pH (=1) to high pH (=14). Provide justification supporting the scheme.
i
0
O=o
1 C'J C'J CM C'J CM
I I X I I I
fjoooo-z
CM
X
(b) A 88 kilo Dalton protein has a two-stranded alpha-helical structure (ignore any turn in the structure i.e. consider the whole structure as composed of helical form). If the mean residue mass is 110 Daltons and rise per residue of an alpha helix is 1.5 A, then calculate the length of the molecule
(c) A 50 residue segment of a protein folds into a two stranded antiparallel beta sheet structure with a 4-residue hairpin turn, rise per residue of an beta sheet is 3.5 A then calculate the longest dimension of this motif.
3+3+4 = 10M
Q.2.
(a) The shape of hair is determined in part by the pattern of disulfide bonds in its major protein, keratin. How curls are induced?
(b) Considering only the two major factors leading to the formation of an alpha helical structure, where it is more probable to form helix: in water or in hexane? Justify your answer.
(c) Write the relation describing the supercoiling of nucleic acid and explain each parameter.
3+3+4 = 10M
Q.3.
Time scale of orientational motion of pure water molecules is Tw = 8 ps. When the aqueous solution of whale myoglobin is studied, at least three different time scales are observed experimentally. They are of the order of T1 = 80 ns, T2 = 10 ns and T3 = 40 ps.
(a) Explain the origin of T1
(c) Which experiment can investigate the rotational motions indicated by T1, T2 and T3 and describe the basic principle of the experimental technique (you can explain for a single component system, for example).
3+3+4 = 10M
After drawing the scattering geometry of X-ray, explain what is structure factor and derive a relation for atomic scattering factor (atom placed at origin).
3+3+4 = 10M
Write principles of two experimental methods for determining the molecular weight of biological molecules in solution without destroying the molecular structure.
5+5 = 10M
A lipid molecule has head group immersed in aqueous medium (which has dielectric constant as (w)) as shown below. The average direction of the head group and alkyl chain is indicated by the arrow () in the diagram. The head group has opposite charges of magnitude Ql separated by y. Suppose the solution is made acidic by HCl and a Chloride ion of charge QCl is situated at a distance [(yCos)/2] vertically from air/water interface and t distance away from the center O. Consider that ion is in the grey quadrant (region). Derive an expression for the interaction between the head group and chloride ion. The final expression should contain the given symbol like (w), Ql , Qci , y, etc and no different symbol.
END
10M
8
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Attachment: |
| Earning: Approval pending. |
