Chapter 9: Bioinformatics Exercise 9.

Introduction to Lipidomics

Exercise Objectives
 Retrieve data about lipid structures and biological properties.
 Use the LipidBank and LIPID MAPS databases.
 Name lipids using the (n-x) nomenclature.

Difficulty
 10 questions
 Computer-Related: Easy
 Subject-Related: Easy

Resources & Websites

 Figure 9-9, Chapter 9
 Review of Gangliosides:
o http://www.lipidhome.co.uk/lipids/sphingo/gang/index.htm
 LipidBank:
o http://www.lipidbank.jp
 About LipidBank:
o http://www.lipidbank.jp/help/about.html
 LIPID MAPS:
o http://www.lipidmaps.org
 About LIPID MAPS:
o http://www.lipidmaps.org/about/about_consortium.html
 PubChem:
o https://pubchem.ncbi.nlm.nih.gov

Exercise
In this exercise, the structures of different classes of lipids will be studied using the LIPID
MAPS and LipidBank databases, which both serve as a compendium of chemical data for
lipids.

Instructions
4. Go to:
a. http://www.lipidmaps.org
b. http://www.lipidbank.jp.
5. For LIPID MAPS:
a. Click on the “Resources” tab.
b. Click on the “Databases” sub-tab.
c. Select the “Structure Database (LMSD).”
d. Choose the “Text/Ontology-based search” option.
6. Use the following “Ontology search parameters” for LIPID MAPS:
Chapter 9: Bioinformatics Exercise 9.2

a. Group: #Carbon (number of carbons)

b. Group: #Double bonds (number of double bonds)
c. Group: #Rings (number of rings)
7. For LipidBank, use the following search options:
a. Choose the class of lipid either on the home page or at the top of the
search page.
b. Select a source (under “Properties”).
c. Select SUGAR CHAIN SERIES.
Chapter 9: Bioinformatics Exercise 9.2

Assessment Questions

1. As listed in the LIPID MAPS Structure database, a synonym for 18:2-3 using the (n-
x) nomenclature system is ____________, where x represents _________________.

A. 18:2n-3; the position of the first double bond counting from the methyl end
of the fatty acid.
B. 18:2n-3,6; the positions of the double bonds counting from the methyl end
of the fatty acid.
C. 18:2n-3; the position of the last double bond counting from the methyl end
of the fatty acid.
D. 18:2n-3,6; the positions of the double bonds counting from the carboxyl end
of the fatty acid, respectively.

2. According to the LIPID MAPS Structure database, lipids containing 22 carbons and 2
rings are NOT found in which of the following main classes of lipids?

A. phospholipids
B. eicosanoids
C. glycolipids
D. isoprenoids

3. As observed in the LipidBank database, the lipopolysaccharide referred to as Lipid A

from Helicobacter pylori strain 206-1 is composed of:

I. two 3-hydroxyfatty acids

II. three 3-hydroxyfatty acids
III. a 1,4 glycosidic linkage between the monosaccharides
IV. a 1,6 glycosidic linkage between the monosaccharides
V. a 1,4 glycosidic linkage between the monosaccharides
VI. a 1,6 glycosidic linkage between the monosaccharides

A. II and VI
B. I and V
C. I and IV
D. I and VI

4. As observed and listed in the LipidBank database, the c-series gangliosides at a

minimum contain:

I. at least 2 sialic acids

Chapter 9: Bioinformatics Exercise 9.2

II. at least 3 sialic acids

III. contain a 2,8 glycosidic linkage between two sialic acids
IV. contain a 2,3 glycosidic linkage between a sialic acid and galactose
V. contain a 2,3 glycosidic linkage between a sialic acid and glucose
VI. a glycosidic bond between galactose and cerebroside
VII. a glycosidic bond between glucose and cerebroside
VIII. a branched galactose

A. II-IV, VII, VIII

B. II, III, V, VII
C. I, III, IV, VII
D. II-IV, VII

5. Using the SugarBind database, which of the following classes of lipids serves as the
ligand for the leptin HpaA (See Bioinformatics Exercise 6.2)?

A. sphingophospholipid
B. glycosphingolipid
C. lipopolysaccharide
D. glycerophospholipid

6. According to the LipidBank database, what is the common name for the ligand of
HpaA (Hint, use the class and lipid name gained from the SugarBind database as
navigation and search terms in LipidBank)?

A. cytolipin H
B. SM4
C. KDN-GM4
D. cytolipin

7. Using the SugarBind database, (a) search for the ganglioside abbreviation of G M1
(“GM1”), which is a ‘ligand’, (b) click and browse through the relevant links provided
for each of the search results (e.g., structure, lectins, etc.); the information provided
in these links indicate that the GM1 lipids containing branched oligosaccharide
prosthetic groups bind to ______ lectins, while the GM1 lipids containing linear
oligosaccharide prosthetic groups bind to ______ lectin/s.

A. multiple; 1
B. 2; multiple
C. multiple; multiple
D. multiple; 2
Chapter 9: Bioinformatics Exercise 9.2

8. Which of the following statements are consistent with the structure and
nomenclature of GM1 lipids (to answer this question, use the search results from
question 7, and use the provided link for the ‘Review of Gangliosides’ as a guide)?

I. The sialic acid is always linked to D-Gal.

II. The sialic acid can be linked to different sugars.
III. The tetrasaccharide of Gal-GalNAc-Gal-Glc is always conserved.
IV. The tetrasaccharide of Gal-GalNAc-Gal-Glc can be organized in any
order.
V. Multiple sialic acids are linked to the lipid.
VI. D-Glc is bound to ceramide.
VII. D-Glc is bound to glycerol.
VIII. Sialic acid is represented by a purple triangle.
IX. Sialic acid is represented by a purple diamond.

A. I, IV, VII, VIII

B. II, III, VI, IX
C. II, III, VI, VIII
D. III, V, IX

9. According to the search results from question 7, which of the following lipids is
(currently) only associated with influenza?

A. GM1 with a linear oligosaccharide prosthetic group

B. GM1 with a branched oligosaccharide prosthetic group

10. According to the LipidBank database, this GM1 lipid with a linear oligosaccharide
prosthetic group (as obtained from the search results of question 7) is also referred
to as _______, and has been isolated from the human brain and ________.

A. de-N-acetylated GM1; bovine brain

B. de-N-acetylated GM1; bovine brain
C. GM1b positional isomer; chemical syntheses
D. GM1b; human erythrocytes