27. Omics cascade Flashcards
1
Q
what is the omics cascade?
A
- genomics
– DNA - transcriptomics
– RNA - proteomics
– proteins - metabolomics
– metabolites
2
Q
what are transcriptomics?
A
- study of transcriptome
– set of all RNA transcripts produces by genomes at point in time
– including non-coding in individual or population of cells
3
Q
what are the two main techniques of transcriptomics?
A
- microarray assay
- RNA sequencing
– both extract and convert mRNA to complementary DNA or cDNA
4
Q
what are the applications of transriptomics?
A
- medical biosciences
- agriculture
- bioprocesses
- marine biology
- reduce complexity seen on metagenomicswh
5
Q
what are the challenges of transcriptomics?
A
- low recovery of high quality RNA
– from environmental samples - short half life of mRNA
- difficulties enriching mRNA
6
Q
what are proteomics?
A
- study of composition, structure, function, interactions of proteins
– directing cell activity - proteome
– entire set of proteins produces/modified by organism or system - proteome differes from cell to cell
– constantly changes through biochemical interactions with genome and environment - transcription of gene gives only rough estimate of level of expression of protein
- proteins experience post translational modification
– profoundly affect activities
7
Q
what are proteins?
A
- large complex molecules
– composed of sequence amino acids - made of long chains of amino acids
– peptides
8
Q
what is 2D sodium dodecyl sulfate polyacrylamide gel electrophoresis?
A
- 1st dimension
– pH gradient, proteins separated based on isoelectric point (PI)
– PI is pH with no net charge in protein - 2nd dimension
– separate proteins based on molecular weights - when comparing protein expression across different experimental samples
– gells typically stained with silver/coomassie blue for total protein - various image analysis platforms used to scan and compare
9
Q
what is the proteomics workflow?
A
- protein mixture
– proteolytic digestion using trypsin - intact protein
- peptide mixture
- LC-MS/MS
- thousands of MS/MS spectra
- protein database search
- computational analysis with various search algorithm
- protein identification
10
Q
proteomics
A
- 3D structure prediction of protein
- determine time of protein synthesis
- rates of production, degradation, steady-state abundance of protein
- protein modifications
– post-translational modifications - protein transport between subcellular compartments
- involvement of proteins in metabollic pathways
- interactio of proteins with one another
11
Q
what are the applications of proteomics?
A
- bioprocesses
- medical microbiology
- discovery of new drugs
- study of diease mechanisms
- agriculture
- study complex microbial communities in biofil
– or symbiotic interactions of microorganisms in environment
12
Q
what are metabolomics?
A
- qualitative and quantitative measures of low molecular-weight molecules
– involved in metabolic reactions required for maintenance, growth, normal fxn of microbial community - metabolite
– organic molecule with M<1500 Da
– sugars, AAs, ketones, organic acids, amines, lipids, steroids, alkaloids, pollutants, drugs
13
Q
what is the metabolomics workflow?
A
- sample preparation
- sample analysis
– by HPLC
– MS
– NMR - pre processing data analysis
- metabolite identification
- pathway analysis
14
Q
why are metabolomics important?
A
- diagnostic clinical assays
– test small moleculess - medical drugs are small molecules
– derived from pre-existing metabolites - several genetic disorders
– involve disease of metabolising small molecules - metabolites serve as cofactors
– and signaling of molecules and proteins
15
Q
how is the omics cascade compared?
A
- coverage
– 1: chemicals
– 2: protein
– 3: genes - chemistry diversity
– 1: 2x10^5 chemicals
– 2: 20 AAs
– 3: 4 bases
