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Introduction to Metabolomics and Proteomics - Coggle Diagram
Introduction to Metabolomics and Proteomics
Metabolomics
Measurement of the
metabolome
, a collection of
small molecules
called
metabolites
that are present in a biological sample at a given time
We can distinguish between:
Endo-metabolome
Both represent a subgroup of the metabolome (
submetabolome
)
Exo-metabolome
Major approaches
Targeted analysis
Metabolic profiling
(= untargeted analysis to identify multiple metabolites, known and unknown)
Metabolic fingerprinting
(= analysis of intracellular profile of metabolites)
Metabolic footprinting
(=analysis of the extracellular profile of metabolites)
Metabolism
Primary
Essential for survival + growth
Few end products
Pathways are activated
Ex. of primary metabolites = proteins, lipids, DNA
Secondary
Multiple products, many of which are unknown
Pathways can be activated/inactivated depending on specific condition
Not fundamental for growth + survival, but provides a selective advantage in a certain environment
Ex. of secondary metabolites = alkaloids
Chemical
and
physical features
of metabolites
Acidity
Expressed by the
acid dissociation constant Ka
HA ⇄ A- + H+ ; Ka = [A-][H+] / [HA]
pKa
= log10 (Ka)
Henderson-Hasselback equation
:
pH = pKa + log10 ([A-] / [HA])
The equation is helpful to design experiments in
liquid-liquid extraction
: by changing pH, it's possible to change the form in which the molecule is present in a liquid (A- vs. HA)
Ex. if we choose a pH = pKa, the molecule will be 50% in the HA form and 50% in the A- form
Molecules with
multiple chemical groups
have
more than one Ka
(one for each ionizable group)
Chirality
Property of an object not to be the same as its mirror image
The mirror images of a molecule are called
enantiomers
Enantiomers have the same molecular formula and, therefore, the same physical properties. However, they have different optical activity and may interact differently with biological systems (like proteins)
Chiral carbons
C bound to 4 different functional groups
There could be multiple in the same molecule
Lipophilicity
Represents the tendency of a molecule to distribute differently between the lipophilic organic phase and the polar aqueous phase
Can be described through:
LogP
log10 (
Partition coefficient
)
P describes the propensity of a neutral compound to dissolve in a biphasic system composed of an organic + a water portion
P = [molecule in organic phase (n-octanol)]/[molecule in aqueous phase]
LogD
The parameter is analogous to LogP, but it's used when dealing with
ionizable solutes
It measures the different solubility in organic and aqueous phases for an ionizable compound
at a certain pH
A change in pH affects LogD because the functional groups will be differently ionized
This means that changes in pH will affect the molecule's solubility, and we can take advantage of this in liquid-liquid extraction
log10 (
Distribution coefficient
)
D = [HA] organic phase + [A-] organic phase / [HA] aqueous phase + [A-] aqueous phase
A molecule is composed by multiple functional groups, each with different polarity (polar, medium-polarity, non-polar groups)
By adding different functional groups to a chemical, we influence its polarity
Calculation of the total change in LogD =
sum of the individual changes in LogD associated with the addition of a certain group
, with respect to the original LogD
Rules of thumb for quick calculations:
If negative charge is gained (HA is deprotonated to A-), the LogD decreases of -3
The addition of a methyl group to the molecule increases the LogD of +0.88
The addition of a benzene ring to the molecule increases LogD of +2.13
Presence of
functional groups
Dictate which kind of
intermolecular forces
are established between neighboring molecules
Van der Waals forces
Dipole-dipole interactions
London dispersion forces
Hydrogen bonds
(F, O, N)
Ionic bonds
π - π stacking
(between aromatic rings)
Hydrophobic interactions