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PHAR211 > Metabolomics 1 > Flashcards

Metabolomics 1 Flashcards

1
Q

What is metabolomics?

A

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

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2
Q

What is a metabolome?

A

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

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3
Q

What is a primary metabolite?

A

performs normal physiological functions such as cell growth

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4
Q

What is an intermediary metabolite?

A

maintains homeostasis such as energy intermediates

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5
Q

What is the human metabolome?

A

an analog of human genome

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6
Q

What does a metabolome provide information on?

A

important information on biological, physiological and pathophysiological processes

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7
Q

What is excluded from a metabolome?

A

enzymes
genetic materials
structural molecules

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8
Q

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

A

false

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9
Q

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

A

true

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10
Q

What are metabolites?

A

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

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11
Q

What are the techniques used in metabolomics?

A

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

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12
Q

What is liquid chromatography?

A

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

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13
Q

What is the mobile phase in LC?

A

liquid

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14
Q

What are examples of liquid chromatography?

A

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

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15
Q

What is the equation for resolution?

A

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

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16
Q

What does Rs of 1 mean?

A

the molecules are not yet separated
-not pure

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17
Q

What does Rs of 1.5 mean?

A

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

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18
Q

Describe the effect of resin particle size on resolution.

A

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

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19
Q

Describe HPLC.

A

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

20
Q

How is retention decided for normal-phase HPLC?

A

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

21
Q

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

A

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

22
Q

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

A

silica
CN
NH2

23
Q

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

A

nonpolar solvents or solvent mixtures such as hexane

24
Q

How is retention decided for reverse-phase HPLC?

A

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

25
Q

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

A

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

26
Q

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

A

bonded hydrocarbons such as C18 and C8

27
Q

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

A

polar solvents or solvent mixtures such as methanol and acetonitrile

28
Q

What is the particle size for UPLC?

A

1.7-1.8 um

29
Q

What is the column pressure for UPLC?

A

up to 1030 bar

30
Q

What are the advantages of UPLC?

A

increased resolution, sensitivity, and speed

31
Q

What is the mobile phase in gas chromatography?

A

gas

32
Q

What is the stationary phase in gas chromatography?

A

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

33
Q

Which gases are used in gas chromatography?

A

helium (most common)
hydrogen
nitrogen

34
Q

Which field is gas chromatography widely used in?

A

analytical chemistry

35
Q

What is the purpose of gas chromatography?

A

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

36
Q

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

A

polyethylene glycol
polysiloxanes
hydrocarbons
esters
amides

37
Q

What are the carrier gases?

A

helium
hydrogen
nitrogen

38
Q

Differentiate the carrier gases.

A

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

39
Q

How are molecules characterized in metabolomics?

A

mass spectrometry
NMR

40
Q

What is the HMDB?

A

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

41
Q

How many metabolite entries are in the HMDB?

A

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

42
Q

What are the different metabolomics studies?

A

metabolite target analysis
metabolite profiling
metabolic fingerprinting
metabolic profiling

43
Q

What is metabolite target analysis?

A

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

44
Q

What is metabolite profiling?

A

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

45
Q

What is metabolic fingerprinting?

A

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

46
Q

What is metabolic profiling?

A

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

PHAR211 (16 decks)

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