Lecture 9

Question 1

what is the dogma of biology ?

Answer 1

DNA -> RNA -> proteins

Question 2

name some protein modifications

Answer 2

• phosphorylation
• acetylation
• glycolisation
• proteolytic cleavage
• hydroxylation

Question 3

describe what proteomics consists of, main difference with genomics ?

Answer 3

Study of proteomes and their function ; sequence mapping, 3D structure, protein interactions

Directly specifies physiological states (compared to genomics)

Question 4

main technique used to measure proteomics (2 methods)

Answer 4

mass spectrometry

• top down : measure intact proteins
• bottom up : cleave protein in short peptides

Question 5

difference between untargeted and targeted proteomics

Answer 5

1) targeted : presence and quantity of a specific protein -> sensitive

2) untargeted : quantitative + qualitative study of present proteins -> less sensitive

Question 6

how much does the environment influence the genome VS metabolome ?

Answer 6

genome : almost no influence

metabolome : big influence

Question 7

what are small molecules ? (metabolites)

Answer 7

• low molecular weight organic compound
• 50-1500 daltons
• include human and microbial compounds
• concetration detectable by modern instrumentation

Question 8

what is metabolimics ? what is the metabolome ?

Answer 8

• study of metabolites within cells, biofluids, tissues or organisms.
• complete collection of small molecules (endogenous and exogenous, transient or ven theoretical)
  Its size is not clear.

Question 9

why do plants have a higher chemical diversity ?

Answer 9

more chemicals because they need them to defend themselves (can’t run away like us)

Question 10

what is the general concentration range for all metabolites ?

Answer 10

mM to fM

Question 11

why are metabolites so relevant ?

Answer 11

• biomarkers (signals of diseases)
• most drugs are metabolites
• cofactors to many proteins

Question 12

how are the time fluctuations between metabolites, proteins, genes different ?

Answer 12

metabolites : huge variability, time fluctuation
Proteins : a little bit
Genes: no variation

Question 13

NMR (nuclear magnetic resonance) : advantages and drawbacks

Answer 13

+) quantitative, high reproducibility, structure elucidation -> population based studies

-) low sensitivity, signal overlap

Question 14

how does LC-MS work ?

Answer 14

mobile phase - stationary phase (column) - detector (MS).

Liquid sample introduced before column ; speed of traveling through column will depend on the level of affinity with stationary phase

Question 15

how does mass spectrometry work ?

Answer 15

Sample is ionized -> we measure the mass-to-charge ratio of ionized analytes -> detect the nb of ions at each m/z value -> spectra

Sample can be gas, liquid or solid

Question 16

how does the time-of-flight mass spectrometer work ?

Answer 16

the elements with a lower mass will fly quicker and hit the detector first

Question 17

3 approaches in metabolomics for profiling

Answer 17

(un)targeted profiling
Isotopic profiling (labeled elements)
MS imagins : visualize tissues for example

Question 18

what needs to be optimized in targeted and untargeted approaches ?

Answer 18

targeted -> front end method (like spectrometer)

untargeted -> bacl end processing (bioinformatics)