omics

Question 1

discuss the different omics approaches

Answer 1

genomics
transcriptomics
proteomics
metabollomics

over 20 omics approaches exist

Question 2

why do omics exist

Answer 2

you cant engineer something until you understand it

Question 3

discuss omics in general

Answer 3

’‘-omics’’ suffix means the study of something in biology.
as you travel down the central dogma, the omes become more dynamic. the genome is the same over time and in all cells. the proteome changes
omics experiments give a lot of data which has to be analysed by computer
its important to check for p hacks and ensuring the data hasnt been made to support the hypothesis is a dishonest way
a single omics approach shouldnt be used to sopport a hypothesis, multiple omics approaches should show the same thing

Question 4

discuss genomics

Answer 4

what: study of the genome

how:
a) sanger sequencing
b) next generation sequencing such as nanopore sequencing; when DNA goes though a bacterial membrane channel the current changes depending on the base in the channel.
technology placed in a mini-iON device and allows for an entire genome to be sequenced in a few hours; can be done in the field, is cheap, not limited to 1kb bases
c) gene knock out

because of next generations sequencing and because of how cheap is to sequence a genome (£30 for a bacteria), an exponentional number of genomes are being sequenced at the minute; more data than scientists are able to study

types;

a) comparative genomics; using differerences to explain biological function
b) metagenomics; studying genomes of samples taken from the environment rather than from cultured microorganisms
c) synthetic genomics; DNA assembly for example codon optimisation; only one codon is needed for a AA; the others could be used to select for other molecules
d) fucntional genomics; studying genomics to understand biological fucntion

Question 5

discuss the 5 ways a transcriptome can be studied

Answer 5

what; the study of the mRNA in a cell; tells you which cellular processes are active and which genes are being expressed.

how:

1) northern blot; electrophoresis then nitrocellulose filter, probes, estimate size of band
2) RT-qPCR; amplify RNA and roughly estimate the amount of RNA present
3) digital droplet PCR:the PCR sample is seperated in thousands of parts, each droplet is tested for flroescence whcih indicates the RNA of interest is present; starting amount of RNA can be worked very precisely; absolute quantification
4) DNA microorrays; a glass slide with many wells each containing different probes exist. cDNA is made from mRNA and when the florescent labelled cDNA is added to the plate, it can be checked which wells floresce and therefore which genes mRNA sequences were present
5) next generation RNA sequencing (RNAseq); sequences entire transcriptome

Question 6

describe why the proteome is more complex than the genome

discuss how structural proteomics is studied

Answer 6

25,000 genes exist but 400,000 proteins due to splicing of introns
differential spatial and temporal expression
post translation modification modification;
a)phosphoproteomics; reversable addition of phosphates. needs to be studied to understand the cell cycle and cancer
b)glycosylation; addition of sugar; key to recognition. O/N linked. very hard to study as many sugars exist
c)nitrosylation;
d)ubuiquitination

VDJ recombination; cant study genome to understand antibody production, have to study proteins

how to study:
1)protein isolation; lyse cells
2)protein purification;perform centrifugation
3)protein seperation based on physcial properties
i)2D gel electrophoresis
a)iso electric focusing; based on charge and weight
b)SDS-PAGE; based on size
limitations; cant use hydrophobic proteins, small concentration proteins, small proteins, large proteins, limited pH scale on isoelectric gel
c)Difference gel electrophoresis; different protein o
different gels
ii) 2D chromatography; cation/anion exchange
4) analysis of seperation methods; look at gel or chromatographybtrace
5) protein isolation from seperation methods; spot picking machine to take a band, or taking a specific fraction from chromatography apparatus
6) protein analysis; mass spectrometry; mass/charge of ions in protein can be figured out due to how their path is deflected by a magnet.
vacuum needed so air doesnt deflect particles
data analaysis of results
alternatively to mass spec, X-ray crstallography can be done to understand protein characteristics
ELISA

Question 7

discuss metallomics

Answer 7

what: the study of free metal and metal proteins (20% of proteins)

Question 8

discuss metabolomics

Answer 8

what: the study of metabolites (non protein, DNA and RNA molecules)
it is used to check a strain is producing the metbaolite its sopposed to and not getting stuck on an intermediate; artemisinin
the cell metabolism is stopped via rapid cooling; must be done more than once because metabolites are constantly being converted to different metabolites

how
gel filtration chromatography; small particles enter holes in gel agarose beads and take longer to travel down the tbe compared to larger molecules