Lecture 5: Omics Approaches in Neuroscience Flashcards
What are the four major omics approaches?
- Genomics
- Transcriptomics
- Proteomics
- Metabolics
What is Genomics mostly about?
Understanding genes
What is Transcriptomics mostly about?
Understanding gene expression patterns (mRNA)
What does Proteomics and Metabolomics focus on?
The proteins and the various metabolites
What are Genes imprinted on?
DNA
What is the genetic material?
DNA
Through what process is DNA made usable?
Through a process known as transcription
What is Transcription?
A process where DNA becomes RNA and usable
Where does Translation occur?
In the ribosomes
What is the process of traslation?
mRNA becoming made into protein
What do the Omics approaches model?
The different products of the central dogma
What is the genome?
The measurement of DNA
What is the Transcriptome?
The expression of genes
What is the Proteome?
The totality of our proteins
What largely does things in our cells?
Proteins (enzymes, receptors)
What is the Central Dogma?
The process of DNA becoming RNA, RNA becoming proteins and then the proteins alter the biochemistry of a cell
What is captures in metabolomics?
The changing of the chemistry of cells due to proteins
With the compression of DNA what happens first?
The DNA is wrapped around histones
What is a nucleosome?
DNA being wrapped around histones
Why does DNA tightly compress?
To ensure that the genes won’t be expressed so things won’t bind for transcription
Why does the 3D structure of DNA matter a lot when getting things transcribed?
What is the promoter region of a gene?
Where the RNA polymerase sits and binds to the DNA
What do transcription factors do?
Associate with DNA to signal that a gene should be transcribed
What allows transcription to be controlled on a cell to cell basis?
The element of many transcription factors coming together
What is splicing?
Removing introns from RNA to produce mature messenger RNA that is required for a structure of a protein
What can be an important factor in the diversity of protein structures?
The use or non use of an exon in the production of a mature mRNA
What does the double helix wrap around?
The histones
What are beads on a string?
When the double helix wraps around a histone
What is the best example of Genomics?
The human genome project
What were a lot of the benefits in the human genome projects?
- Learned about the structure of genes
- Discovered new genes
- Characterization of genes
What caused the price of gene sequencing to go down?
The movement of gene sequencing to needing to map the whole genome to only mapping particular genes
What method was used to sequence the human genome?
Sanger sequencing
How does sanger sequencing work?
- Have a template
- Add a primer so you know where the start place is
- Add nucleotides and chain termination elements
- Measure the different lengths using gel electrophoresis or with fluorochromes using gel electrophoresis
Why does sanger sequencing have to run four samples?
Because of each of the different chain termination nucleotides
What is the relative length with gel electrophoresis?
The further it goes the shorter its length
What is the purpose of sanger sequencing?
To figure out the sequence of DNA
Why is sanger sequencing a bit slower?
Because there is a limited number of space on the gel electrophoresis
Why is next generation sequencing much more powerful than sanger sequencing?
Because it is parallel measured
What occurs in NGS?
- A sample is preprocessed into a library (shreds DNA into fragments)
- A library has genomic DNA with a certain number of BPs
- Then measure the reads
- This captures the whole genome
- Computers then piece all the fragments together through matching it to a baseline genome
What is NGS faster and cheaper?
Because it’s splices the genome into millions of pieces and measures the reads all at once
What are the applicable parts of sequencing?
To see a person’s DNA to see if there are mutations or heritability risks
What does the transcriptomics focus on?
The measurement of RNA and the expression of DNA
What end elements does mRNA have?
A guanine head and a polyA tail
What gives mature mRNA?
Introns being removed
What is RNA velocity based on the idea of?
Having more mature RNA that’s more stable, or more unspliced DNA indicates a gene that is more dynamically regulated
How does RNA sequencing work?
- A primer binds to the polyA tail of the mRNA
- It’s amplified to make cDNA from mRNA
- cDNA is then shattered into fragments
- Fragments are then the basis for library preparation
- Sequencing measures the different reads
- Bioinformatics maps the cDNA to a gene of interest
What is cDNA?
The amplification of mRNA
What does measuring the number of individual reads mapped to a given gene in RNA sequencing do?
Gives information on how much that given gene is expressed
What is the caveat to RNA sequencing?
A longer gene is gonna have more reads just because the gene is longer
Why is Proteomics a lot more complicated?
- Because the genome has different elements to regulate mRNA expression
- Each mRNA can make multiple different proteins
- Proteins are highly modified (ex. phosphorylation)
What are the two ways of measuring single proteins?
- Western blotting
* ELISA
How does western blot work?
Using gel electrophoresis to run a protein and using antibodies to label a certain protein
What is the benefit of western blot?
You get the size of a protein
What is the benefit of ELISA?
It is highly quantitative. Very sensitive for measuring the concentration of a protein
What is ELISA based on the idea of?
Antibodies at the bottom of the plate and different amplification that relate directly proportional to the amount of antibody
What occurs in 2D electrophoresis?
A gel is run in two directions with proteins go in two directions to spread apart the proteins of interest
What is one benefit to 2D gel electrophoresis?
Being able to see changes in proteins better
What does mass spectromics with proteins measure?
The size of a structure
How does mass spectrometry of proteins work?
- Breaking proteins into little pieces
- Coupled to electrospray ionization (turning a solid protein into a gas)
- Measurement of the peptide based on mass spectroscopy
- Identify and quantify proteins
- Conduct bioinformatics
What does mass spectroscopy of proteins tell you?
The amount of that protein in a sample
What are examples of Metabolomics?
- Hormones
- Signalling molecules
- Metabolic intermediates
What is the Human Metabolome Database?
Using different tools to study different metabolites
What are metabolites measured with?
Mass spectroscopy and NMR
What are the two types of mass spect tools?
Separation based tools and separation free tools
What do MS separation based tools do?
Separate based tools separate them into their chemical components
Why is NMR not used as widely as mass spec?
Because it is less sensitive
How does NMR work?
A nucleus is placed in a magnetic field and aligns then use radio waves of various frequencies. The spectrum that is released from this gives a lot a chemical information
What was the science breakthrough of 2018?
Single cell RNA sequencing
What is bulk sequencing used for?
Understanding things as a whole
What should be used if you want understand the different elements?
RNA sequencing
What do the dots on a scale represent?
How related each cell is to one another
