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analytical exam 2 > metabolics > Flashcards

metabolics Flashcards

1
Q

what is metabolics?

A

what is happening now, it allows the study and characterisation phenotype within living organism

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2
Q

what elements are metabolites made from?

A

H, C, N, O and S

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3
Q

what is MS2

A

if know elements and their weights and atomic mass it is a direct refection of make up

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4
Q

which AA are associated with detoxification reactions

A

cysteine and methionine- sulphur containing AA

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5
Q

what are metabolites

A

anything that can be metabolised

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6
Q

what is the citric acid cycle

A

where you make ATP, ADP and AMP implication in cancer and aging

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7
Q

what does it mean if see genomic expression but no metabolimics?

A

the event isn’t stable enough

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8
Q

what is primary metabolites

A

biomolecules that are synthesised by the cell because they are essential for growth and maianataince of a biological system

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9
Q

what are secondary metabolites

A

organic compounds produced by bacteria, fungi, or plants which aren’t directly involved in normal growth and mainatance of a biological system

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10
Q

what are examples of primary metabolism

A

amino acids, carbohydrate and alchohols and vitamins B2 and B12

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11
Q

what are examples of secondary metabolites

A

Phenolic, steroids, essential oils and alkaloid metabolites

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12
Q

what is 2HG

A

muatations in IDG result in the conversion of isocitrate to 2-HG instead of alpha ketoglutarate. This leads to altered methylation in cell and promotes tumour growth

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13
Q

how is tyoe 2 diabetes caused

A

icreased level of TAG which leads to saturation of acetyl-coA leading to desythestization

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14
Q

what is the Warburg effect?

A

cancer and tumourgenesis are due to tumour cells generating energy through the non oxidative breakdown of pyruvate.

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15
Q

why do plants have largest metabolome

A

because they can’t. move

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15
Q

why do plants have largest metabolome

A

because they can’t. move

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16
Q

what are all lipids made from

A

C, O, H double bond

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17
Q

what is metabolite target analysis s

A

quailitive and quantitive anaylsis of one, or several metabolites related to a specific matabolic reaction

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18
Q

what is metabolic foot printing

A

analysis of the metabolites screted or excreted by an organism; if the organism is growing in culture it would include its envioemnt

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19
Q

what is metabolic profiling

A

Identification and quantification of a selective number of predefined metabolites, which are related to a specific pathway

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20
Q

metabolic finger printing

A

global, high throughput, rapid analysis to provide sample classification. Also utilised as a screening tool to discriminate between samples from different biological status or orgin.

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21
Q

what are the main steps of untergetting metabolomics work flow

A
  • experimental design
    -sample prep
    -sample anaylis by MS and NMR
    -pre processing data analysis
    -metabolite identification
    -hypothesis
    -ecperimental validation
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22
Q

what should you do in discovery work

A

identify a panel of biomarkers taht can refine disovery to validation

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23
Q

what is a spectroscopic technique

A

a non destructive technique taht uses radiowae laser so can profile samples at a decent enough reoliutio

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24
Q

what are the main spectroscopic techniques that are used?

A

NMR and FTIR

25
Q

what is FTIR

A

it gives out a vibartional signature but is sensitive to water so needs to be processed properly

26
Q

what is the gold standard in metabolic?

A

LC/MS

27
Q

Which mass analyses are good for discovery work

A

QTOF and orbi trap

28
Q

what is the advantages if quadrouple mass analyser

A

Robust, simple, low maintaince, relatively inexpensive

29
Q

what are the disadvantages of the quadruple mass analysers

A

low mass resolution, low sensitivity, slow scan speed

30
Q

what is the disadvantage of having a too long. TOF

A

the ions can diffuse

31
Q

how does orbital work

A

the heavier the ion the longer it takes to orbit, ms2 analyses the results

32
Q

what is the simplist mass spec analyser

A

quadropole

33
Q

how does quadropole Give you the mass

A

the ratio of voltage is directly proptional to the mass

34
Q

what is MS3 used for

A

when you know the fragments after further smashing up fragments after using low res mass spec

35
Q

how do we know that the sample is fragmenting in MS2?

A

precursor intensity decreases with higher eV as more % is converted into fragments

36
Q

what does MS1 do

A

quick ID based on hi res ion mass measurement

37
Q

what does MS2 do

A

structural fragments for confirmation

38
Q

what does electro spray ionisation do

A

converts liquid samples to gas phase ions

39
Q

what is the mobile phase in GC

A

a coil

40
Q

what is the mobile phase in LC

A

pac column

41
Q

how does chromotogrpahy work

A

through plate theory and van deemter

42
Q

what does the van deemter equation state

A

the plates height can be decreased or enlarged by temp flow

43
Q

what is the most basic type of LC

A

TLC

44
Q

When would you use GC

A

if you sample was a gas, anything with a smell

45
Q

how does gas chormotgrpahy work

A

uses volatility go the gases. The most volatile are eluted quicker. It is then fragmented by election impact

46
Q

what is the major cost of gas chromoatgrpahy

A

electricity and gas

47
Q

what would not be detected in NMR

A

low abundance metabolites

48
Q

which chromatography is the gold standard

A

LC

49
Q

which types of chromatography would you use to separate complex liquid mixtures

A

PR, HILIC and lipidomics

50
Q

what analysis is required after LC

A

DDA or DIA

51
Q

What are the disadvantages of LC

A
  • easily broken
    -long downtime
    -high operational skill needed
    -sophisticated downstream analysis needed
52
Q

what makes the high pressure in LC

A

solvent, column, flow rate and gradient composition

53
Q

what would you use GC for

A

sweat analysis, breath analysis, pesticides

54
Q

what disadvantage of GC

A

low coverage can only look at low molecular weigh metabolites

55
Q

what are the 3 different phases of LC metabolimics

A

reverse pahse- non polar. helix phase- polar and ion chomrotgarphy- sugar

56
Q

what are the advantages and disadvantages of polarity switching

A

reduced the time but reduces quality of data as one mode will be surpassed and other will be over expressed

57
Q

why is plastic a contimanation an issue and how is it over come

A

use plastic tools, have to use low bais to stop plastic leaching from the solvent. Would show as a bleed across the results. At proeitn would see much less as would be absorbed

58
Q

what are QCs

A

10% of samples go into a master pool. It is themes reproducible data point. Inject aliquots of QC at regular intervals to demonstrate stability and quality of aquisition

59
Q

what is unsupervised anaylisis

A

clustering algortm which doesn’t now you labelling or class structures. Allows you to see outliers

60
Q

what is the most commonly used data analysis in unsupervised

A

pca, which removes noise from data set. Anything after PC1,2, and 3 is noise

analytical exam 2 (6 decks)

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