Lesk: Introduction to Genomics, third edition Chapter 13, Answers for Exercises

Exercise 13.1. (a) Surface plasmon resonance, co-immunoprecipitation. (b) X-ray and NMR structure determi-
nation, Cryo-electron microscopy, Two-hybrid screening systems, Chemical cross-linking

Exercise 13.2. (a) V4 –V3 . (b) V6 –V3 . (c) V6 –V5 . (d) V1 –V4 . (e) V6 –V3 .

Exercise 13.3. (a) Directed graphs: phylogenetic trees, metabolic pathways, citation patterns in the scientific
literature. (b) Labelled graphs: Metabolic networks (the enzymes that catalyze the steps label the edges),
Chemical bonding patterns in molecules (the type of bond – e.g., single, double, . . . – labels the edge).
(c,d)
Graph nodes edges

Sets of people who people acquaintance

have met each other

Electricity distribu- sources, distributors, and loads transmission lines

tion systems

Phylogenetic trees species ancestry relationships

Metabolic path- metabolites reactions

ways

Chemical bond- atoms chemical bonds

ing patterns in
molecules

Citation patterns in articles + books references

scientific literature

The World-Wide Web sites references

Web
Exercise 13.4. (a) 6 stops; change at Bank
(b) King’s Cross → Russell Square → Holborn → Tottenham Court Road → Oxford Circus → Warren Street
→ Euston → King’s Cross
(c) 2/30

Exercise 13.5. (a) Heathrow Terminal 4 → Upminster

(b) Kensington (Olympia), all stops from West Brompton through Wimbledon, and all stops from Upney to
Upminster.
(c) All stops between Stanmore and Kingsbury, all stops between Neasden and Kilburn, Swiss Cottage, St
John’s Wood, Southwark, Bermondsey, North Greenwich.

Exercise 13.6. (a) the two downstream nodes of the fork, and the intermediate node of the ‘one-two punch’.
(b) the intermediate node of the ‘one-two punch’.

c Arthur M. Lesk 2017 1

Lesk: Introduction to Genomics, third edition Chapter 13, Answers for Exercises

Exercise 13.7.

Transcriptional regulators
... 50 outgoing connections ...
... ...
1-2 punch
Scatter

Fork

5 intermediate nodes

Target genes

Ultimate receptor of signal

Exercise 13.8. From Figure 13.21(b), lowest graph, there would be two intervals of output, corresponding to
first the red and then the green curve exceeding the threshold.

Exercise 13.9. e−0.8×4 /e−0.8×2 = e−0.8×2 = 0.202

Exercise 13.10.
(a)
C T A T C A C C G C A A G G G A T A A
G A T A G T G G C G T T C C C T A T T
(b) 11 base pairs (c) corresponds approximately to 1 turn of the double helix This is consistent with the
interactions of the protein with adjacent major grooves in the DNA (Figure 13.8).

Exercise 13.11.

lactose glucose
absent absent

AND

transcription?

Exercise 13.12. 1–d, 2–d, 3–c, 4–b, 5–a.

c Arthur M. Lesk 2017 2

Lesk: Introduction to Genomics, third edition Chapter 13, Answers for Exercises

Exercise 13.13.

Exercise 13.14.
glucose

gluconeogenesis glycolysis

fermentation
pyruvate ethanol
oxaloacetate
❉ Pyruvate
decarboxylase

acetyl-CoA
❉ Citrate synthase
glyoxalate Krebs
cycle cycle

succinate

oxidative
phosphorylation

c Arthur M. Lesk 2017 3