MH

Name:......
Roll .l[o. : ... ... ....... ..

Inuigilator's Signature : ..

cs / M.TECH (BT) / SEM-2 I M'BT-?L5A / 2CI11

20ll
ANIMAL CELL CULTURE & ITS APPLICATION
Time AUotted : 3 Hours FuIl Marks : VO

figures in the margin indicate full marks.

The

Candidates are required" to giue their ansulers in their own tuords

as far as practicable.

GROUP -A
( Multiple Choice TYPe Questions I

1. Choose the correct alternatives for the following: 1O x 1 = 1O

i) Porogen which enhances macroporosity is

a) sugar and protein

b) sugar and salt
c) salt and carbohYdrate
d) salt and lipid.
ii) SAMs stands for
a) Self-Assembled Monolayers
b) Self-Assigned Membranes
c) Self-Adhered Monolayers
d) none ofthese.

3OOe5 (M.TECH) I Turn over

cs / M.TECH (BT) / SEM-2 IMBT-215A / 2011
iii) A Dendrimer based microbicide gel used for HIV
prevention is

a) VivaGel b) INGN 401

c) MRX 815 d) Abraxane.

iv) The enersr of green luminescent phosphors will be

approximately

a) 2'3 eV b) 1'9 eV

c) 3'1 eV d) 2'3 keV.

v) Direct band gap semiconductor are such materials

where

a) LE+O, Ak=O b) LE*O, Ak;iO

c) AE =0, Ak =0 d) AB =0, Ak *0

vi) One step for bioconjugation of quantum dots is

a) shell-TOP structure

b) core-shell structure

c) surface mo{ification of quantum dots

d) .HOMO-LUMOarrangernent.

3OO9s (M.TECH) 2
 cs / M.TECH (BT) / SEM-2 I MBT-215A / 2011

vii) Which of the following antibiotics is not related to

animal cell culture ?

a) G418 b) Hygromycin

c) Penicillin d) amp\lttin.

viii) Which of the following contaminations cannot be

detected by inverted microscoPe ?

a) Fungus b) Algae

c) Mycoplasma d) Bacteria.

ix) Which of the following media is being used in animal

cell culture ?

a) LB medium b) PDA medium

t SOC medium d) RPMI'

")
x) Which of the following cell lines can only grown in
suspension ?

a) HeLa b) McF-7

c) CoLo 125 d) CaCO-2.

a

3009s (M.TECH) 3 I Turn over

 cs / M.TECH (BT) / SEM_2 I MBT_2rsA I 2OrL

GROUP - B
{ Long Answer Type euestions }

Answer any four of the following. 4x15=60

2. a) What are autographts and allografts ? 2+2

b) Why are nanofibers regarded as popular synthetic

framework in present day tissue culture ? 2

c) Briefly explain what makes electrospun nanofibres well

accepted in tissue engineering. Draw a schematic

diagram of electrospinning process and give examples

of natural and synthetic polymers explored for the

fabrication of nanofibres. 2+3

d) what are the salient features involved in synthesis of

peptide amphiphile (pA) ? 4

3. a) write down the comparative grain size distribution of

water molecule, nanoparticle, blood cell, bacterial cells.

What do you mean by quantum confinement and

explain strong and weak quantum confinement ? How

are quantum dots different from nanoparticles ?

2+3+l
3009s (M.TECH) 4
 cs / M.TECH (BT) / SEM-2 IMBT_215A / 2011
b) Write down the relationship between the energr band
gap of quantum dots with its grain size and ener$/

band gap of the bulk materials.

c) How one can estimate optical band gap semiconducting

quantum dot ? Explain.

d) Explain the importance of nanostructured materials for

biological applications. 3

4. a) Write down the Shrordinger's equation of euantum

dots. Mention the dimensions of bulk, thin film,
nanowire and quantum dot. Write down the expression

for the density of state for quantum dot. 2+2+2

b) What do you mean by bi-functional quantum dot ?

Explain how it would be useful for biologicd

applications. l+2

c) Write short notes on the following : 2x3

i) Carbon nanotube

ii) Lithography.

3009s (M.TECH) 5 IT[rn over

cs / M.TECH (BTI / SEM-2 I MBT-215A / 2011
5. a) PS, normally located on the cytoplasmic surface of the

cell membrane, becomes exposed to the extracellular

environment.

Annexin V (human vascular anticoagulant with high

affinity for PS) allows the detection of PS.

Jrrtcl o canptothccin
PI
L- {rrcra ryrr,
lEtE.t-tb tllry
t
r<.1-..rr- &lL
a
'F-- j
-.
j:! ffi I
-t_!=^.
-
'{"}:'
'-.*4r. IC
raJrrf,
tIbo

Affl.xin-'',.

Assign the boxes with right kind of cells-Live, dead or

-**-i!

apoptotic. 2

b) When the growth of a cell culture slows down at the end

of exponential growth phase, the probable reason is

either the cells have consumed essential factors or
nutrients, or the cells are producing toxic chemicals. If

the 2nd alternative is predominant, then how will you

remove the toxic metabolites from the medium ?
Discuss the procedures.

300es (M.TECH) 6
 cs / M.TECH (BT) / sEM_2 / MBT_}|;A / 2Ot1

c) What would be your stratery to test a new drug

for cell
toxicity ? Explain with at least three.
6

6. a) Why will you have to remove FBS by washing the pBS

before trypsinization ? How does the cell protect

itself
during freezing and thawing ? Write down 5 advantages
and 5 disadvantages of performing animal cell
culture us. bacterial culture. 1+2+5
b) one of the applicadons of animar cell curture is to study
cell cycle reguration. can you explain with a schematic

diagram the feedback control mechanism of cell cycle

?

7. aJ How will you use animal cell culture for protein

protein interaction ?
7

b) what would be your stratery to study siRNA in animal

cell culture ? Explain with a flow chart. g

============E

3OO9s (M.TECH)
 h-T-*A.
IrJame: .......
RolliVo. : .....
Inuigilntof s Stgnature
CS/M.Tech(BT) /SEM -2 lNrBT-zo4 / zOrL
2011
DOWNSTREAIU PROCESSING
TIme Atlotted: 3 Hours FuLl" Marks : 7O

Tte figttres in tlrc margin tndicate full marks.

Cardidates are reqwired to giue tteir answers in their own words
asfar as practicable,

GROT'P -A
( Multtple Choice TYPe guestions )

1. Choose the correct alternatives for any tenof the following :

1Ox1=10
i) The appropriate order of tJle following purification steps
that should be followed for the purification of a protein
from a complex mixture is
a) PreciPitation )

b) Ion exchange chrorpatograPhY

c) Affinity chromatograPhY
dl Hydrophobicinteractionchromatography
e) Gel ffltration.
ii) Proteins were separated in the 2D-PAGE according to
their
a) Overall charge b) Hydrophobicity
c) Mass d) Affinity towards gel.

3OO94 ( M.Tech ) ITurn over

CS/M.Tech(BT) /SEM-2/MBT -zO4 / 20 | r

iii) DNA-cellulose chromatography ls used for which

purpose ?
a) DNA-binding protein
b) Acidic or basic protein
c) Hydrophobic protein
d) Single as well as double stranded DNA.
iv) which protein of the following molecular weights will be
precipitated last during salt precipitation ?
a) 12 kDa b) 22O kDa
c) l2O kDa d) 97 kDa.
v) How.many band/bands will be obtained after
performing the SDS-PAGE of serum IgG under non-
reducing condition and in Native-PAGE ?
a) One b) Two
c) Three d) Four.
vi) Which one is corrept durr{rg chromatofocusing ?

a) The protein with the highest pI elutes first and the

protein with the lowest pI will elute last

b) The protein with the highest pI elutes last and the

protein with the lowest pI will elute first.
vii) After ammonium sulphate precipitation waht would be
the best chromatography method of separation of the
following ?

a) HIC b) RpC

c) IEXC d) cFC.

30094 ( M.Tech )
 CS/M.Tech(BT) /SE}/-2 / MBT -2O4 / 20 L I

vtu) whtch one of the following is the best for separating

protelns according toltreir sizes ?

a) Filtration
b) Membrane separation

c) Centrifugation

d) Gel filtration chromatography.

lx) iVtrietr one of the following is a gel filtration matrix ?

a) CM Sepharose b) phenyl agarose

c) Sephadec G-f OO d) protein A sepharose.

x) Which one of the followtng is an affinity column ?

a) Lentil lecttn sepharose

b) CM sepharose

c) Phenyl sepharose

d) Sepharose 48.

xi) Which one in the following is pseudoaffinity

chrorqatography matrix ?

a) Blue Sepherose

b) DEAE-Cellulose

c) Q-Sepharose

d) Sephacryl S-2OO.

3OO94(M.Tech) 3 [Turnover
CS/M.Tech(BT) /SEM-2 / MF.T -2o4 / 20 rl
)di) If you start with pH interval T - 4 on pBE g4, what will
be the fate of a protein whose pI is above T ?

' a) It will pass tlrrough ttre column

b) It will retain in the column.

>dii) The purity of an enzyme at various stages of

purification is best measured by

a) totai protein

b) total enzryrme activity

c) specific activity of the enzyme

' d) per cent recovery of protein

e) per cent recovery'of the enzyme.

xiv) In a mixture of the five proteins listed below, which

should elute second in size-exclr:sion ( gel filtration )
chromatography ?

a) Cytochrome c ( IV,= 13,OOO )

b) Immunoglobulin G { M r= I45,OOO )

Ribonuclease A ( M = 13,700 )
"l
d) RNA polymerase ( M r= 450,OOO )

e) Seirrm albumin ( M,:68,500 ).

30094 ( M.Tech )
 CS/M.TechtBT) /SEM-? / MF^T -2O4 / 20 | L

xv) which one of the following is the best organrc modifier

used in RpC ?

a) Isopropanol b) Acetonitrile

c) ,Dthanol d) Methanol.

GROTIP -B
( Short Answer Tyrye gfuestions )
Answer arrf three of the following. 3 x b = lE
2. How are the inner volume and the void volume of a gel
filtration column determined ? How are the proteins of
unknown molecular weights determined by get liltration ?

S+2
3. outline the mechanism of action of detergent on the cell
wall. what is cell permeabilization and what is lts use ? 2 + S

4. why is ammonium sulphate a popular choice for salting

out ? Describe the effects of the following :

a) Concentration of protein

b) Molecular weight of protein on the salting out of a

protein. what are the mechanisms involved during pEG
mediated precipitation ? I+2+2
5. Discuss tJre principles involved for tJre separation of mixture
proteins by high resolution chromatofocusiqg technique.

3OO94 { M.Tech ) ITtrrn over

CS/ M.Tech(BT) /SE}l{-2 / lyIBT -2O4 / 20 1L

6. What is concentration polarization ? What is membrane

fouling?Whatisflocculation? I + 2 +2
7. Briefly comment on aqueous two-phase extraction process
used for the separation of biomolecules.

GROUP - C'
( Long Answer TYPe $uestions )
Answer any three of the following. 3 x l5 = 45

8. What ale the faqtors that affect the hydrophobic interacUon

between proteins and the ligands ? Discuss the principle of
affinity chromatography and distinguish between specific
and non-specific interaction in affinity chromatography.
Ammonium sulphate in being used to precipitate a
humanized monoclonal antibody from 1O liters of cell culture
media, the initial concentration of the antibody in this liquid
being O.5 mg/ml. Solid ammonium sulphate is added to the
liquid such that the concentration of lhe salt is

1.5 kg-moles/m3. This results in the precipitation of 9oo/o of

the antibody. When the arrtmonium sulphate concentration of
the mixture is raised to 1.75 kg-mole/m3. a further 76.50/o

of the remaining'antibody is precipitated' Predict the

unur-onium sulphate concentration needed for total antibody

precipitation. What is the solubility of the antibody in

ammonium sulphate free aqueous medium ? 2+5+8

30094 ( M.Tech ) 6
 CS /M.Tech(B1 75By _2
/ MrBT _2O4 / 20 t L

9. Explain the following ftrrns and their significances in column

chromatography: tox lit
a) Partition coefficient
b) Retention time
c) Retention volume

d) Capacity factor
e) 'Relative
retention
0 Resolution

d column efficiency in terms of plate height and number

of theoretical plates

h) Symmetry factor
i) Separation factor or selectivity factor

, Capacity of an IEX column.

10. Explain constant pressure filtration in batch mode with
incompressible cake. Discuss ttre principle of separation of
biomolecules by centrifugal filtration. what are the strong
and weak ion-exchangers in protein separation ? what are
the advantages of weak ion exchangers ( DEAE_ & CM_ )
over strong exchangers ( g- & S_ ) ? What are the
advantages of chromatofocusing over IEX chromatography
technique ? 5+5+l+2+2
I 1. write a note on the different ligand immobilization
techniques to the chosen matrices of affinity
chromatography. Discuss principle and practice of
immobilized metal a{fininity chrornatography ( IMAC
). lo + E

30094 ( M.Tech ) 7 IT\rrn over

CS/ M.Tech(BT) /SEM-2 / IIIBT -2O4 / 20 I I
12. Explain the principle involved in reverse phase ( RPC ) and
hydrophobic interaction chromatography ( HIC ) techniques.
Distinguish between the mechanisms of reverse phase and
hydrophobic interaction chromatographic techniques. What
are the factors that affect the ttren hydrophobic interaction
between proteins and the ligands ? 5+5+5
13. Discuss the common theoretical principles involved in the
different electrophoretic methods of separation. Discuss the
mechanism involved during the polymerization of acrylamide.
Discuss the principle of Native-PAGE and SDS-PAGE during
the separatidn of mixture of proteins and explain how
unkown molecular weight of proteins can be determined by
the PAGE. Discuss the basic principle of isoelectric
focusing. 3+2+5+5
14. Write short notes on anylfiue of the following : 5x3
a) Isopycnic.ultracentrifugailon
b) Affinity ultrafiltration
c) Retention coefffcient or reJection coefficient

d) Microffltration
e) Hyperfittration
0 Dialysis
g) Pervaporation

h) Membrane modules.

30094 ( M.Tech ) 8
 r)F'
s';(

Inuigilator's Signature : "

CS/M.Tech (BT) /SDM-2/MBT-20B / zoLL
2U^rl
BIOPROCESS ENGINEDRING & TECHNOLOGY
Full Marks : 70
Tirne Allotted : 3 Ilours

Theftgures in the margin indicateJull marks'

Cand.id.ates are required' Lo giue their
ansuers in their ou;n words
asJar as Practicable'

GROUP - A
( MultiPle Choiee TYPe $uestions )

1. Choose the correct alternatives for any ten of the foliowin$ :

10x1-1O
oxidation of
i) Which of the following is not true about the
glucose ?

a) Glycolysis produces 3o/o of the energy ultimately

obtained from $lucose
b) The first stage of $lycolysis involves
phosphorylation of glucose to 1' 6-fructose
biPhosPhate
c) Gycolysis occurs within the mitochondria
d) Glucose enters the' Krebs cycle as pyruvate'
e) The Krebs cycle generates 36 ATP molecules'
by the
ii) Lactic acid is produced from pyruvic at industrial
helP of
a) StrePtococcus b) Lactococcus
c) StaPhglooccus d) all of these'

I Turn over
3OO93 (M.Tech.)
 CS /M.Tech (BT) /SEM-2 / MBT _2Og / 2Ot I

iii) which of the following processes can be used to bring

two genetically different parents ( cells ) together for
common desirable characters ?

a) Hybridization b) protoplasm fusion'

c) pCR d) Sexual reproduction.
. iv)' The sequential events du.5rg the process protoplasmic
fusion are
(i) membrane contact
(ii) nuclear fusion
(iii) heterokaryon formation
(iv) membrane fusion at contact area
(v) hybrid formation.
a) (i), (ii), (iii), (iv), (v) b) (i), (iii), (ii), (v), (iv)
c) (i), (iv), (iii), (ii), (v) d) (i), (v), (iv), (iii), (ii).
v) If Damkohler number is less then I
a) Mass transfer is limiting
b) Reaction rate is limiting
c) Oxygen concentration is limiting
d) Shear rate is limiting.
-
vi) ksc value is ielated to
a) O, transfer rate
b) Mass transfer unit
c) Enz5rme immobilization constant rate
d) Rate of diffusion.

30093 (M.Tech.) 2
 CS /M.Tech (BT)/SBM-2/MBT -zjs / 2OL I
vii) For enz5rmatic reaction, at low substrate concentration,
rate is

a) lst order with respect to substrate concentration

b) Zero order with respect to substrate concentration

c) Fractional order with respect to substrate

concentration

d) None of these.

viii) Air-lift fermenter is used for the production of

a) Alcohol b) Penicillin

c) Enzymes d) Mabs.

ix) Which of the following best explains why fructose is

often used as a carbohydrate substitute in special food
for patients with diabetes mellitus ?

a) Fructose is a better substrate for hexokinase

b) Fructose stimulates residual insulin release

c) Fructose has a specific kinase in liver that allows

bypass of phosphofructokinase

d) is phosphorylated and cleaved to triose

Fructose..
phosphates, which cannot be used for
gluconeogenesis

e) Hexokinase phosphorylates fructose in

extrahepatic tissues, and its activity will not' ,pe
affected by high glucose concentrations in diabetes.

3OO93 (M.Tech.) I Turn over

CS / M.Tech (BT)/SEM-? / MBT-2O3 / 2O I I

x) which of the following two compounds are the primary

products of the pentose phosphate pathway ?
a) NAD+ and ribose
b) NADH and ribose
c) NADP+ and ribose
d) NADPH and ribose
e) NAD+ and glucose
0 NADI{ and glucose
g) NADP+ and glucose
h) NADPH and glucose.
)d) The media for large scale industrial fermentation
processes usually
a) use highly purified carbon sources
b) do not require a nitrogen source because the
atmosphere provides nitrogen
c) all of these
d) more than one of these, but not all
e) consist of waste products from other processes,
such as grain milling.
, xii) The term'primary metabolite'refers to
a) a product that is produced during the primary
state of growth
b) thb major waste product produced during growth
of a culture
c) a product that is produced during the end of the
growth phase, frequently at or near stationary
phase
d) all of these
e) more than one of these, but not all.

30093 (M.Tech.) 4
 CS / M.Tech (BT) /SEM-2 / MBT -2oB / 2Or I

GROUP -B
2 state whether the following statements are True or Folse:
Give a reasoning of not more than 3O words in support of
your elnswer. (anyJiue ) 5x5
a) Animal cell culture is best carried out in a perfusion
system.

b) Micro-array technologr has been suggested to provide

the equivalent of the chemist's pertodic table.

c) The term'antibiotic' refers to microbial products or their

derivatives that effect micro-organisms, but is

sometimes used to encompass some synthetic agents.

d) Vectors typically code for a phenotlpic trait that can be

used to detect their presence.

e) Plasmids are always present as a single copy per host

cell.

Growth in controlled environments is e>rpensive and is

used primarily for products employed in maintaining
animal human health.

g) The "New Biotechnologi" is making it increasingly

possible to use recombinant DNA techniques to produce

memy kinds of physiologically active suhstances.

30093 (M.Tech.) I Turn over

 CS / M.Tech (BT) / SEM-2 / l/rBT,2OB / 2Ot t

3. Match the following :

a) Monod Equation i) Recombinant strain of

E.coli

b) Citric Aeid ii) Unstructured model

c) Penicillin Recovery iii) Aspergillus niger

d) Adsorption iv) Solvent Extraction

( Podbieb:iak Sotvent
Extractor)
e) Used in Humulin

production v) Surfacelmrnobilization.

cRottP - c
( Long Answer Type euestions )
Answer any three of the following. 3 x lO = BO

4. Ethanol is to be used as a substrate for single-cell protein

production in a chemostat. The available equipment can
achieve an oxygen transfer rateof ro g o2ll of liquid per
hour. Assume the kinetics of cell growth on ethanol
is of Monod type, with Fm = O.bh-1, K" = 30 111glL,
Yx/s =0,5 cells/g ethanol arrd yO2/S:2 g Orlg ethanol.
we rvish to operate chemostat with an ethanol concentration
in the feed of 22 g/L. we also wish to maximize biomass
productivity and minimize the loss of unused ethanol in the
effluent. Determine the required dilution rate and whether
sufficient oxygen can be provided.

30093 (M.Tech.) 6
 CS/.M.rech (BT)/S EM-z / MBT -2OS / ZOt I
5. a) The manufacture of paper includes th,e
usr: of bleach
and formaldehyde based glue. The microbial
enzyrne
rgrlanase whitens paper by digesting dark lignins.
oxidase causes tre fibres to stick together
and celiulase
will remove ink. List b advantages of using these
microbial enzJames over traditional chemicar methods for
making paper.

b) Write a short note on Microbial Steroid

Bioconversion.
b+5
6. a) Descrlbe Lactic acid production with
flow sheet.

b) The growth of S. cereuisae otrr glucose under anaerobic

conditions can be described by the following
overall
reaction:

Co Hrz Oe + F NH3 -. O .59 CHr.zq No.z Oo.+s(Uiomass)

+ O.43 CaHsOs +1.54 CO2 +l.B C2H5OH + 0.36 H2O

i) Determine the biomass yield coefficient yxzs.

ii) Determine the product yield coefficients

YEtoH/s,Ycor/s

iii) Determine the coefficient

B. 5+b
30093 (M.Tech.)
I Turn over
CS /M.Tech (BT) / SEl{-2 / i|i/.BT -2O3 / 2Or I
7. 'Culture techniques can be classified into batch, fed-batch,

"and continuous operation.' hplain each of the process in

brief and elucidate any one example.

8. a) Elaborate on the strategies to be devised to desi$n a

b) Describe the strategies for sterilization of industrial

fermentation media. 5+5

30093 (M.Tech.) 8
 ,^.^s

cs/na.rech (BT) / sFjvr_2 / MIBT-2O2 / zlt I

20t].
IMMUNOLOGY
Time Allotted" : B Flours
Full Marks : 70

TheJigures in the margin indicafeJull

marks.
Candidales are required to giue their ansuters jn
their own uord.s
asJar as practicable,

GROUP _ A
Multiple Choice Type euestions
(
)
l' choose the correct alternativ." ,o, arry tenof
the folrowingi :

1Ox1=10
i) A patient

antihistamincs. The s5rmptoms are most

likely to be
caused by

a) interleukin-2

b) slow-r:eacting substance A ( leukotrienes

)

c) serotonin

d) bradykinin.

3OC92 (M.Tech.)
I Turn over
CS / M.Teeh (BT) /SEM-? / MBT -2O2 / 2Ol I

ii) Penicillin is a hapten in both humans and mice. To

explore the hapten-carrier relationship. a mouse was
injectecl with penicillin covalently bound to bovine
serum albumin and, at the same time, with egg albumin
to which non-penicillin was bound. Of the following,
which one will induce a secondary response to penlcillin
when injected into the mouse I month later ?
a) Penicillin

b) Penicillin bound to egg albumin

c) Egg albumin

d) Bovine scrum albumin.

iii) C3 is cleaved to form C3a and C3b by C3 convertase.

C3b is involved in all of the following except

a) altering vascular permcability

b) promoting phagocytosis

c) forming alternative pathway C3 convertase

d). forming C5 convcrtase.

iv) An Rh-negative woman rnarried to a heterozygous

Rh-positive man has three children. The probability that
all three of their children are Rh-positive is

- a\ I:2 b) l:4
c) l:8 d) I :6.

30092 (M.Tech.)
 CS / M.Tech (BT)/SEM'2 / .ly/BT -2A2 / 2i)1 |

v) A primary immune resporlse in an adult hurnan

requires approximately holv rnuch tirnc to prodr:cc:
cletectable antibody levels in the blood ?

a) 12 hours b) '3 days

c) I week ^ d) 3 weeks.

vi) A recipient of a 2-haplo type MIlC-matched kidney from

a relative still needs immunosuppression to prevent
graft rejection because

a) graft-versus-host disease is a problem

b) minor histocompatibility anti$ens will not be

matched

c) minor histocompatibitity anti$ens will be matched

d) complement components will not be matched'

what is the role of class II MHC proteins on donor cells

in graft rejection ?

a) They are the receptors for interleukin-2' which is

produced by macrophase when thery attack the
donor cells

b) They are recognized by helper T cells, which then

activate cytotoxic T cells to kill the donor cells

c) They induce the production of blocking antibodies

that Protect the $raft

d) They induce IgE which mediatcs graft rcjection'

30092 (M.Tech.) I Turn over

CS /M.Tech (IlT) /SEM-2 /MBT -2O2 I 2OI I

viii) chemically induced tumors have tumor-associated

transPlantation anti$ens that
a) are aiways the same for a given carcinogen
b) are different for two tumors of different histologic
types even if induced by the same carcinogen
c) are very strong anti$ens
d) do not induce an immune response'
ix) Poliomavirus ( a DNA virus ) cause tumours in nude
' mice ( nude mice do not have a thymus' because of a
genetic defect ) but not in normal mice' The best
interPretation is that
a) macrophages are required to reject poliomavirus-
I ittOuced tumours
b)naturalkillercellscanrejectpoliomavirus-induced
tumours without help from T-lymphocytes
c) T-tymphocytes play an important role in the
rejection of polimavirus-induced tumours
d) B-lymphocytes play no role in rejection of
Poliomavirus- induced tumours'
x)Yourpatientbecameitllodaysagowithaviraldisease.
Laboratory examination reveals that the patient's
antibodiesagainstthisvirushaveahighratiooflgMto
IgG. What is Your conclusion
a)Itisunlikelythatthepatienthasencounteredthis
organism PreviouslY
b) The patient is predisposed to IgE-mediated
h5rPersen sitivitY re action
.

c) The information given is irrelevant to previous

anti$en exposure
d) It is likely that the patient has an autoimmune
disease.

30092 (M.Tech.)
 CS / M.Tech (BT) /SEl/r-z / l/rFT -292+ZOt t
xi) The main aclvantage of passive immunization over active
immunization is that
a) it can be administered orally
b) it provides antibody more rapidly
c) antibody persists for a longer period
d) it contains primarily IgM.
xii) which one of the following is the best method of
reducing the effect of graft-versus:-host disease in a
bone marrow recipient ?
a) Matching the complement components of donor
and recipient
b) Administering alpha interferon
c) Removing mature T-cells from the graft
' d) Removing pre-B-celis from the graft.

GROUP - B
( Short Answer Type Questions )

Answer any three of the following. 3x5=15

2. After infection with HIV- I it takes a long time before AIDS
develops in most patients. Answer the following :
a) what happens immediately after infection and during
the long clinically silent period with respect to virus
load, cD4 T cells and the immune response against the
virus, and
b) what is the reason that clinical immunosuppression
finally sets
in ? Name two bacterial
components/substances that bind to Tolt-like receptors
on monocytes and macrophages and stimulate
production of pro-inflammatory cytokines ( e.g. II_I,
TNF-a ) 2+2+l
30092 (M.Tech.) 5 I Turn over
 CS /M.Tech (BT) / SEM-2 / I/rFT -2o2 / 2Ot I

3' state two genetic and two environmental risk factors for
the
development of autoimmune disease. Severar bacteria
that
cause meningitis produce a capsular polysaccharide.
Name
3 such bacteria, and describe the role of the capsule in
development of meningitis. What is GALT ? 2+2+l
4. There are at least 3 different mechanisms by which bacteria
can survive in macrophages. Mention those mechanisms and
give exarnple of bacteria able to use these respective
mechanisms. Antigen presenting celrs have been shown
to
present lysozyme peptide 46-61 together with the class
II LAk
rnolecule. when CD4_TH cells are incubated with Apcs
and
natrve lysoz-v'me or the synthetic lysozyme peptide 46-6r,
TH-cell activation occurs.
a) If chloroquine is added to the incubation mixture,
presentation of the native protein is inhibited, but the
peptide continues to induce TH-cell activatlon. Explatn
why this occurs.
b) If chloroquine addition is delayed for 3 h, presentation
of the native protein is not inhibited. E>rplain why this
occurs. 3+2
5. In an immunolog5r laboratory exercise, you are studying the
response of mice injected intraderma[y with complete
antibodies to the IgE Fc receptor ( Fc_Rl ) or with Fab
fragments of such antibodies
a) Predict the response expected with each type of
antibody.
b) would the responses observed depend on whether the
mice were alrergic ? Explain. How do you explain better
a^ntigen presentation of an Apc if grown in cholesterol
rich medium ? 2+2+l
30092 (M.Tech.) 6
 CS / M.Tech (BT) /SEM-2 / MBT -2O2 / 2Ol I

6. In patients with infectious mononucleosis a disease cause by

the so called EBV - lymphocyte counts in patients increase
mainfold over those in healthy individuals. Does this mean
that the immune system reacts against the virus ? Due to
genetic defects a person X has no antibodies and a person
Y has no T-lymphocyts. Which person is more likety to
succumb to

a) influenza

b) diphtheria

c) malignant myeloma ? 2+l+l+l

GROUP -C
( Long Answer Type $uestions )

Answer any three of the following. 3x l5 = 45

7. What is the advantage of secondary antibody over primary

antibody in diagnosis ? What is the mechanism of action of
immunosuppressive drug ? What are their side effects ? How
do you explain that graft rejection is attributed to antibody
diversity ? What are the difficulti-es to produce any antidote
against AIDS ? What are anti$enic drift and anti$enic
shift ? 2+3-v2+3+3+2
8. Dcplain the role of HLA-DM/DO interaction in the loading of
peptides to MHC ? What is MLR ? What do you mean by
humanized antibody, diabodies and sin$le chain antibody ?
Describe one method of humanized antibody production.
How does antidiotype vaccine work ? How do you use
dendriticcellfor antitumour therapy ? 2 + 2 + 3 + 3 +2 + 3

30092 (M.Tech.) 7 I Turn over

h-
 CS / M.Tech (BT)/SEl|i.{-2 / MBT -2Oz / ZOI1

9. which property of RBC helps it in easier blood transfusion?

what is clonal deletion and clonal selection ? Explain
immunoglobulin super 'family. How are bacterial non-
peptides presented as antigen ? How is ELISpOT assay done

? What is the significance of conjugate vaccine ? Horv is

reverse vaccinologr performed ? l+2+2+3+3+2+2
10. How does tumour evade our immune system ? How do
NSAID and DIMARD help in rheumatoid arthritis ? write
down the molecular pathogenesis of multiple sclerosis.
Describe the mechanism of joining of two genes of an
immunoglobulin. 3+2+2+4+4
I l. How do you. tackle when you are allergic to a necessary
drug .? How does yoga therapy help in asthma patients ?

Complement is both a component of innate and adaptive

immunity. E>rplain how are our own cells resistant to
complement mediated lysis ? What is clonal energ/ ? What is

the cause of SCID and its therapy ? 3+3+2+2+2+3

30092 (M.Tech.) 8

il
 h.Ae)^'
bT
NQme :

Roll No. ;

Inuigilator's Signature : '....'

CS/M.Tech (B"r) I S,DM-2 IMBT-zol I 2OiL
201 1
ADVANCED BIOINFORMATICS
Time Atlotted :3 Hours
Full Marks :7O

Thefigures in the margtn indicateJull marks'

candid,ates are required- to giue their anstuers
ln their own urords
asJar as Practicable'

OUP. A
( Multiple Choice TYPe $uestions )

1. Choose the correct alternatives for any ten of the

following:
lOxl=1O
wtrich is
'i) Most micro-arrays consist of a solid support on
immobilized

a) DNA b) RNA

c) Genes d) TranscriPts.

ii) The PAM25O matrix is defined as having an evolutionary

divergence in which what percenta$e of amino
acids
over
between two homologous sequences have changed
time ?

a) lo/o b) 2O"/"

c) 8O"/" d) 25O"/".

I Turn over
3OOgt {M,Tech)
CS /M.Tech (BT)/SEM-2/MBT -2Ol / 2Ol I

iii) According to molecular clock hypothesis

a) all proteins evolve at the same, constant rate
b) all proteins evolve at a rate that matches the fossil
record
c) for every given protein, the rate of molecular
evolution gradually slows down like a clock that
runs down
d) for every given protein, the rate of molecular
evolution is approximately constant in all
evolutionary lineages.
iv) You have a protein sequence, and you want to quickly
predict its structure. After performing BLAST and PSI-
BLAST searches, you identify the most closely related
proteins with a known structure as several }rraving l7o/o
amino acid identity to your protein. Which of these
options is best ?

a) X-ray crystallography
b) NMR
c) Submitting your sequence to a protein structure
prediction server that performs homologz
modelling
d) Submitting your sequence to a protein structure
prediction server that performs ab inifio modelling.
v) An advantage of X-ray crystallography relative to NMR
for structure determination is that using X-ray
crystallography
a) it is easier to solve the structure of transmembrane
domain- containing proteins
b) it is easier to grow crystals than to prepare
samples for NMR
c) it is easier to interpret diffraction data
d) it is easier to determine the structures of large
proteins.

30091 (M.Tech)
 CS / M.Tech tBT) / SEM-2 / MBT'2Al / 2Ol I

vi)Youhavetwodistantlyrelatedproteins.WhichBLOSUM
or PAM matrix is best to use to compare then ?

a) BLOSUM4S or PAM250

b) BLOSUM4S or PAMI

c) BLOSUMSO or PAM250

d) BLOSUMSO or PAM1

vii) If you want literature information' what is the best

website to visit ?

a) OMIM b) Entrez

c) Pubmed d) PROSITE'

viii) Which-of the following BLAST programs is best used for

the analYsis of immuno$lobulins ?

a) RPS-BLAST

b) PHI-BLAST

c) IgBLAST

d) ProDom'
or cRNA
ix) RNA samples are commonly converted to cDNA
for rnicro-array studies and visualized by labelling
with

a) radioactivity or phosphorescence

b) radioactivitY or fluorescence

c) radioactMtY or RNA Probes

d) radioactivitY or DNA Probes'

30091 (M.Tech) 3 I Turn over

CS / M.Tech (BT) /SEM-2 / MBT'2OI / 2Ol

x) A major advantage of two-dimensional protein gels as a

high throughput technolog5r for protein analysis is that
a) sample preparation and the process or running two
dimensional gels is straight forward and can be
automated
b) the result of two-dimensional gels includes data on
both the size and the charge of thousands of
proteins
c) the technique is well suited to the detection of low-
abundance Proteins
d) the technique is well suited to the detection of
hydroPhobic Proteins.
xi) which of the following statements best illustrates the
theory behind the hidden Markov model ( HMM ) ?
a) It relies on first creatin$ a phylogenetic tree
, b) It calculates the probability of an amino acid
'occurrence at each Position

c) lt calculates a multiple sequence alignment based

on scores from randomly generated sequences
d) .It only aligns sequences that belong to an already
described Protein familY.
xii) You have 200 viral DNA sequences of 5OO residues
eaqh, and you want to know if there are any pairs that
are identical ( or nearly identical ). Which of the
following is the most efficient method to use ?
a) BLAST
b) Maximum-likelihood phylogenetic analysis
c) Neighbour-joiningphylogeneticanalysis
d) Popset.

30091 (M.Tech)
 CS /M.Tech (BT)/SEM-2/MBT-2OI I 2Ol I

GROUP - B
( Short Answer Type $uestions )
Answer any three of the following. 3x5=15

2. Write down the different technologies that are used in lead

identification ? In what manner quantitative structure-

activity relationship ( QSAR ) is helpful in screening

prospective drug molecules ? 2+3

3. What is the full form of SNP ? SNPs can help in explainin$

why different people respond differently to the same drug.

Explain how it can be accomplished. L+4

4. What is pair-wise sequence alignment ? Calculate the Log

Odds score for changes between Phe and Tyr at an

evolutionary distance of 250 Pams. | +4

t

5. What is MSA ? Write down the flowchart of Global Multiple

SequenceAlignment. 2+3

6. What is the' importance of Data Bank ? What are the

applications of RNA structure modelling ? 2+3

3OO9r (M.Tech) I Turn over

 CS / M.Tech (BT) /SEM-2 / I/rF.T -2O I / 2OI t

GROIJP -C
(Long Answer Type euestions
)
Answer any three of the following. 3 x l5 = 4b
7. Let Sl = 64uq11CAGTTA and 52 = GGATCGA.

a) Build the advanced D5mamic programming table (

Using
Needleman/Wunsch Algorithm ) for the strings.

b) List alr optimal globar alignments betwben sl and s2.

c) What is gap ? What are the different tlpes of gaps
that
can be assigned to sequence analysis algorithm
?

d) Mention the difference between local arignment and

globalalignrnent. S +2+2+6
8' what is homolog5r modelling ? wrile down the steps to be
used for homolog)r modeling. what are the difficulties
of
hornology modelling ? How can you solve or minimize
these
difficuities ? 3+6+3+3
L Write short notes on anylftue of the following : bx3
a) Dot matrix
b) Identity and similarity
c) BACs

d) Motif
e) PSSM

0 Sequence database
g) Bootstrap analysis.

30Ogl (M.Tech) 6
 -2OL / 2OI
/M.Tech (BT) /SEM-2 / MBT 1
CS

networks
ro. what are neural networks ? why do you use neural
rotein structures ? What do you know about
structure and tertiary structure of a protein
?
secondary

WritetwopubliclyavailableHMMimplementationsoftwares'
Howarethep,oc.ssesofenergyminimizationandmolecular
protein structures ?
dynamics useful in the prediction of
2+2+4+2+5

of microarraY
11. What are ttre advanta$es and . disadvantages
stePs of this
exPeriment ? Write down the different
6+9
exPeriment.

3OO91 (M.Tech)