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Lecture 5: Omics Approaches in Neuroscience Flashcards

1
Q

What are the four major omics approaches?

A
  • Genomics
  • Transcriptomics
  • Proteomics
  • Metabolics
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2
Q

What is Genomics mostly about?

A

Understanding genes

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3
Q

What is Transcriptomics mostly about?

A

Understanding gene expression patterns (mRNA)

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4
Q

What does Proteomics and Metabolomics focus on?

A

The proteins and the various metabolites

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5
Q

What are Genes imprinted on?

A

DNA

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6
Q

What is the genetic material?

A

DNA

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7
Q

Through what process is DNA made usable?

A

Through a process known as transcription

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8
Q

What is Transcription?

A

A process where DNA becomes RNA and usable

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9
Q

Where does Translation occur?

A

In the ribosomes

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10
Q

What is the process of traslation?

A

mRNA becoming made into protein

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11
Q

What do the Omics approaches model?

A

The different products of the central dogma

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12
Q

What is the genome?

A

The measurement of DNA

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13
Q

What is the Transcriptome?

A

The expression of genes

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14
Q

What is the Proteome?

A

The totality of our proteins

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15
Q

What largely does things in our cells?

A

Proteins (enzymes, receptors)

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16
Q

What is the Central Dogma?

A

The process of DNA becoming RNA, RNA becoming proteins and then the proteins alter the biochemistry of a cell

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17
Q

What is captures in metabolomics?

A

The changing of the chemistry of cells due to proteins

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18
Q

With the compression of DNA what happens first?

A

The DNA is wrapped around histones

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19
Q

What is a nucleosome?

A

DNA being wrapped around histones

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20
Q

Why does DNA tightly compress?

A

To ensure that the genes won’t be expressed so things won’t bind for transcription

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21
Q

Why does the 3D structure of DNA matter a lot when getting things transcribed?

A
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22
Q

What is the promoter region of a gene?

A

Where the RNA polymerase sits and binds to the DNA

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23
Q

What do transcription factors do?

A

Associate with DNA to signal that a gene should be transcribed

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24
Q

What allows transcription to be controlled on a cell to cell basis?

A

The element of many transcription factors coming together

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25
What is splicing?
Removing introns from RNA to produce mature messenger RNA that is required for a structure of a protein
26
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
27
What does the double helix wrap around?
The histones
28
What are beads on a string?
When the double helix wraps around a histone
29
What is the best example of Genomics?
The human genome project
30
What were a lot of the benefits in the human genome projects?
* Learned about the structure of genes * Discovered new genes * Characterization of genes
31
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
32
What method was used to sequence the human genome?
Sanger sequencing
33
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
34
Why does sanger sequencing have to run four samples?
Because of each of the different chain termination nucleotides
35
What is the relative length with gel electrophoresis?
The further it goes the shorter its length
36
What is the purpose of sanger sequencing?
To figure out the sequence of DNA
37
Why is sanger sequencing a bit slower?
Because there is a limited number of space on the gel electrophoresis
38
Why is next generation sequencing much more powerful than sanger sequencing?
Because it is parallel measured
39
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
40
What is NGS faster and cheaper?
Because it's splices the genome into millions of pieces and measures the reads all at once
41
What are the applicable parts of sequencing?
To see a person's DNA to see if there are mutations or heritability risks
42
What does the transcriptomics focus on?
The measurement of RNA and the expression of DNA
43
What end elements does mRNA have?
A guanine head and a polyA tail
44
What gives mature mRNA?
Introns being removed
45
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
46
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
47
What is cDNA?
The amplification of mRNA
48
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
49
What is the caveat to RNA sequencing?
A longer gene is gonna have more reads just because the gene is longer
50
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)
51
What are the two ways of measuring single proteins?
* Western blotting | * ELISA
52
How does western blot work?
Using gel electrophoresis to run a protein and using antibodies to label a certain protein
53
What is the benefit of western blot?
You get the size of a protein
54
What is the benefit of ELISA?
It is highly quantitative. Very sensitive for measuring the concentration of a protein
55
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
56
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
57
What is one benefit to 2D gel electrophoresis?
Being able to see changes in proteins better
58
What does mass spectromics with proteins measure?
The size of a structure
59
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
60
What does mass spectroscopy of proteins tell you?
The amount of that protein in a sample
61
What are examples of Metabolomics?
* Hormones * Signalling molecules * Metabolic intermediates
62
What is the Human Metabolome Database?
Using different tools to study different metabolites
63
What are metabolites measured with?
Mass spectroscopy and NMR
64
What are the two types of mass spect tools?
Separation based tools and separation free tools
65
What do MS separation based tools do?
Separate based tools separate them into their chemical components
66
Why is NMR not used as widely as mass spec?
Because it is less sensitive
67
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
68
What was the science breakthrough of 2018?
Single cell RNA sequencing
69
What is bulk sequencing used for?
Understanding things as a whole
70
What should be used if you want understand the different elements?
RNA sequencing
71
What do the dots on a scale represent?
How related each cell is to one another

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