Solutions Manual For First Course in Systems Biology 2nd Edition By Eberhard Voit 9780815345688 ALL Chapters .

j1




Systemsq Biology:q Aq Textbookq Answersq toq Problems




Contents


1 Introduction .......................................................................................................... 3

2 Modelingq ofq Biochemicalq Systems .................................................................... 3
Answersq toq Problems .......................................................................................... 3

3 Specificq Biochemicalq Systems.......................................................................... 10

Answersq toq Problems ........................................................................................ 10
4 Modelq Fitting ..................................................................................................... 13
Answersq toq Problems ........................................................................................ 13

5 Analysisq ofq High-Throughputq Data ................................................................. 18
Answersq toq Problems ........................................................................................ 18
6 Geneq Expressionq Models .................................................................................. 20

Answersq toq Problems ........................................................................................ 20
7 Stochasticq Systemsq andq Variability .................................................................. 24
8 Networkq Structures,q Dynamics,q andq Function ................................................ 31

9 Optimalityq andq Evolution ................................................................................. 34

Answersq toq Problems ........................................................................................ 34
10 Cellq Biology ........................................................................................................ 38
Answersq toq Problems ........................................................................................ 38



SystemsqBiology:qAqTextbook.qEddaqKlipp,qWolframqLiebermeister,qChristophqWierling,qAxelqKow
ald,qHansq Lehrach,q andq Ralfq Herwig
Copyrightq ©q2009qWILEY-
VCHq Verlagq GmbHq &q Co.q KGaA,q WeinheimqISBN:q 978-3-527-31874-
2

, j
2 qSystemsqBiology:qAqTextbookqAnswersqtoqProblems

11 ExperimentalqTechniquesq inq MolecularqBiology ............................................ 40
Answersq toq Problems........................................................................................ 40

12 Mathematics ...................................................................................................... 44
13 Statistics ............................................................................................................. 44

14 Stochasticq Processes ......................................................................................... 44
15 Controlq ofq Linearq Systems ............................................................................... 44
16 Databases ........................................................................................................... 44

Answersq toq Problems........................................................................................ 44
17 ModelingqTools ................................................................................................. 46

Answersq toq Problems........................................................................................ 46

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1 Introduction




2 Modelingq ofq Biochemicalq Systems



Answersq toq Problems

Problemq1q
Problemq 1a


Pi

HK PGI FBP
Gluc G6P F6P F1,6P
PFK

ATPqqq ADP

ATPqqq ADP



v1 v2 v4
S1 S2 S3 S4
v3

S5 S6
S5 S6


Forqdrawingqtheqnetworkqyouqmayqeitherquseqtheqbiologicalqnamesqorqnumberedqab
breviations.qTheqsecondqversionqsimplifiesqtheqmathematicalqanalysis.qTheqODEqsys
temq reads:

, j
4 q2qqModelingqofqBiochemicalqSystems


S_q1qq¼qq—qv1
S_q2qq¼qv1q—qv2
S_q3qq¼qv2q—qv3q þqv4
S_q4qq¼qv3q—qv4
S_q5qq¼qq—qv1q—qv3
S_q6qq¼qv1q þqv3


Problemq1b
Theq stoichiometricq matrixq reads
0 1
—q1 0 0 0q
Bq 1 — 1 0 0C
0 1 —1 1C
Nq ¼ q :
B 0 0 1 — 1CC
@ —1 0 —1 0 A
1 0 1 0

Theq rankq ofq Nq isq 4.q Itq hasq 6q rowsq andq 4q columns.

Problemq1c
Sinceqtheqnumberqofqcolumnsq(4)qisqequalqtoqtheqrankqofqN,qweqfindqnoqsolutionqKqf
orqtheqequationqNq·qKq¼q0.qHence,qthisqsystemqhasqnoqsteadyqstate,qexceptqofqtheqtriv
ialqsteadyq stateq whereqflallq uxesq vanishes.
TwoqlinearqindependentqsolutionsqGqforqtheqequationqGq·qNq¼q0qareqð0;q0;q0;q0;q1;q1
Þqandqð1;q1;q1;q1;q0;q0Þ.qThisqmeansqthatqweqfindqtwoqconservationqrelationsqforqtheqgi
venqreactionq system:q ATPqþqADPq ¼q const:q andq S1q þqS2qþqS3q þqS4q ¼qconst:
Pleaseqkeepqinqmindqthatqinqrealityqtheqmetabolitesqofqglycolysisqareqinvolvedqinqf
urtherq reactions,q whichq mayq violateq theseq conservationq relations.

Problemq1d
TheqreactionqsystemqinqExampleq2.6qhasqonlyqthreeqreactionsqsinceqreactionqFBPqwa
sqneglected,qbutqalsoqsixqsubstrates.qThisqimpliesqthatqExampleq2.6qshowsqaqnontrivi
alqsteady-
stateqfluxqandqanqadditionalqconservationqrelation.qNote:qdifferentqmodelqformulatio
nsq canq implyq differentq analysisq results.

Problemq2q

Problemq2a
N1:
d
q q q dq q dq dq dq
Sq1 ¼ Sqq2 ¼ S3qq ¼ q—q S4qq ¼q —q2q S5qq ¼q1v
dt dt dt dt dt