Metabolomics 1

Question 1

What is metabolomics?

Answer 1

quantitative study of a whole set of small molecules (metabolome)

Question 2

What is a metabolome?

Answer 2

complete set of small molecules, such as carbohydrates and lipids, in a biological sample

Question 3

What is a primary metabolite?

Answer 3

performs normal physiological functions such as cell growth

Question 4

What is an intermediary metabolite?

Answer 4

maintains homeostasis such as energy intermediates

Question 5

What is the human metabolome?

Answer 5

an analog of human genome

Question 6

What does a metabolome provide information on?

Answer 6

important information on biological, physiological and pathophysiological processes

Question 7

What is excluded from a metabolome?

Answer 7

enzymes
genetic materials
structural molecules

Question 8

True or false: all changes in genome or transcriptome cause abnormality or disease

Answer 8

false

Question 9

True or false: not all enzymes and protein products detected by proteomics are functional

Answer 9

true

Question 10

What are metabolites?

Answer 10

final result of cellular functions
quantifiable molecules with the closest link to phenotype

Question 11

What are the techniques used in metabolomics?

Answer 11

LC-MS, especially HPLC-MS
GC-MS
NMR
capillary electrophoresis
-CD-MECC

Question 12

What is liquid chromatography?

Answer 12

an analytical technique used to separate or purify molecules dissolved in a solvent
for separation or purification of small molecules

Question 13

What is the mobile phase in LC?

Answer 13

liquid

Question 14

What are examples of liquid chromatography?

Answer 14

partition chromatography
HPLC
UPLC
HPLC and UPLC are commonly used in metabolomics

Question 15

What is the equation for resolution?

Answer 15

Rs = V2-V1/(W1+W2)/2

Question 16

What does Rs of 1 mean?

Answer 16

the molecules are not yet separated
-not pure

Question 17

What does Rs of 1.5 mean?

Answer 17

peaks are separated
- > 1.5 is the cut off for good separation

Question 18

Describe the effect of resin particle size on resolution.

Answer 18

smaller particle size –> higher pressure
smaller particle size –> better resolution
small size + low flow rate = good resolution

Question 19

Describe HPLC.

Answer 19

separation of small molecule compounds dissolved in a solution
mixture of compounds is injected onto the column
compounds are separated based on difference in partition coefficients between the mobile phase and stationary phase
-mobile phase: solvent
-stationary phase: column
mobile phase should be degassed to avoid air bubbles

Question 20

How is retention decided for normal-phase HPLC?

Answer 20

retention is decided by the interaction of the polar parts of the stationary phase and solute

Question 21

What is the difference between the stationary phase and mobile phase in normal-phase HPLC?

Answer 21

packing material (stationary phase) must be more polar than mobile phase with respect to the sample

Question 22

What are the common column ligands in normal-phase HPLC?

Answer 22

silica
CN
NH2

Question 23

What are the mobile phase solvents for normal-phase HPLC?

Answer 23

nonpolar solvents or solvent mixtures such as hexane

Question 24

How is retention decided for reverse-phase HPLC?

Answer 24

retention is decided by the interaction of the nonpolar parts between the stationary phase and the solute

Question 25

What is the difference between the stationary phase and mobile phase in reverse-phase HPLC?

Answer 25

packing material (stationary phase) must be relatively nonpolar than the mobile phase with respect to the sample

Question 26

What are the common column ligands used in reverse-phase HPLC?

Answer 26

bonded hydrocarbons such as C18 and C8

Question 27

What are the common mobile phase solvents used in reverse phase HPLC?

Answer 27

polar solvents or solvent mixtures such as methanol and acetonitrile

Question 28

What is the particle size for UPLC?

Answer 28

1.7-1.8 um

Question 29

What is the column pressure for UPLC?

Answer 29

up to 1030 bar

Question 30

What are the advantages of UPLC?

Answer 30

increased resolution, sensitivity, and speed

Question 31

What is the mobile phase in gas chromatography?

Answer 31

gas

Question 32

What is the stationary phase in gas chromatography?

Answer 32

liquid (GLC, liquid coated on a solid) and solid (GSC, not widely used due to limited number of stationary phase)

Question 33

Which gases are used in gas chromatography?

Answer 33

helium (most common) hydrogen nitrogen

Question 34

Which field is gas chromatography widely used in?

Answer 34

analytical chemistry

Question 35

What is the purpose of gas chromatography?

Answer 35

separation of gaseous and volatile substances GLC principle - separation by partition coefficient

Question 36

What can be used as a stationary phase for GC capillary columns?

Answer 36

polyethylene glycol polysiloxanes hydrocarbons esters amides

Question 37

What are the carrier gases?

Answer 37

helium hydrogen nitrogen

Question 38

Differentiate the carrier gases.

Answer 38

helium: -excellent thermal conductivity -expensive hydrogen: -better thermal conductivity -reacts with unsaturated compounds and inflammable nitrogen: -reduced sensitivity -inexpensive

Question 39

How are molecules characterized in metabolomics?

Answer 39

mass spectrometry NMR

Question 40

What is the HMDB?

Answer 40

detailed information of small molecule metabolites found in human body -chemical data -clinical data -molecular biology/biochemistry data

Question 41

How many metabolite entries are in the HMDB?

Answer 41

220,945 -water soluble and lipid soluble metabolites -metabolites that would be regarded as either abundant or relatively rare

Question 42

What are the different metabolomics studies?

Answer 42

metabolite target analysis metabolite profiling metabolic fingerprinting metabolic profiling

Question 43

What is metabolite target analysis?

Answer 43

quantitative or semi-quantitative clinical and pharmaceutical analysis of a specific group of metabolites

Question 44

What is metabolite profiling?

Answer 44

analysis of a large group of metabolites that is either related to a specific metabolic pathway or a class of compounds more targeted than metabolite fingerprinting

Question 45

What is metabolic fingerprinting?

Answer 45

providing information from spectra of total composition of metabolites H NMR metabolic fingerprinting powerful method for discriminating between biological samples on the basis of differences in metabolism disease diagnosis

Question 46

What is metabolic profiling?

Answer 46

how metabolites are organized into pathways understand mechanism of diseases or drugs