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Neuro > Lecture 5: Omics Approaches in Neuroscience > Flashcards

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
Q

What is splicing?

A

Removing introns from RNA to produce mature messenger RNA that is required for a structure of a protein

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26
Q

What can be an important factor in the diversity of protein structures?

A

The use or non use of an exon in the production of a mature mRNA

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27
Q

What does the double helix wrap around?

A

The histones

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28
Q

What are beads on a string?

A

When the double helix wraps around a histone

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29
Q

What is the best example of Genomics?

A

The human genome project

30
Q

What were a lot of the benefits in the human genome projects?

A
  • Learned about the structure of genes
  • Discovered new genes
  • Characterization of genes
31
Q

What caused the price of gene sequencing to go down?

A

The movement of gene sequencing to needing to map the whole genome to only mapping particular genes

32
Q

What method was used to sequence the human genome?

A

Sanger sequencing

33
Q

How does sanger sequencing work?

A
  • 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
Q

Why does sanger sequencing have to run four samples?

A

Because of each of the different chain termination nucleotides

35
Q

What is the relative length with gel electrophoresis?

A

The further it goes the shorter its length

36
Q

What is the purpose of sanger sequencing?

A

To figure out the sequence of DNA

37
Q

Why is sanger sequencing a bit slower?

A

Because there is a limited number of space on the gel electrophoresis

38
Q

Why is next generation sequencing much more powerful than sanger sequencing?

A

Because it is parallel measured

39
Q

What occurs in NGS?

A
  • 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
Q

What is NGS faster and cheaper?

A

Because it’s splices the genome into millions of pieces and measures the reads all at once

41
Q

What are the applicable parts of sequencing?

A

To see a person’s DNA to see if there are mutations or heritability risks

42
Q

What does the transcriptomics focus on?

A

The measurement of RNA and the expression of DNA

43
Q

What end elements does mRNA have?

A

A guanine head and a polyA tail

44
Q

What gives mature mRNA?

A

Introns being removed

45
Q

What is RNA velocity based on the idea of?

A

Having more mature RNA that’s more stable, or more unspliced DNA indicates a gene that is more dynamically regulated

46
Q

How does RNA sequencing work?

A
  • 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
Q

What is cDNA?

A

The amplification of mRNA

48
Q

What does measuring the number of individual reads mapped to a given gene in RNA sequencing do?

A

Gives information on how much that given gene is expressed

49
Q

What is the caveat to RNA sequencing?

A

A longer gene is gonna have more reads just because the gene is longer

50
Q

Why is Proteomics a lot more complicated?

A
  • Because the genome has different elements to regulate mRNA expression
  • Each mRNA can make multiple different proteins
  • Proteins are highly modified (ex. phosphorylation)
51
Q

What are the two ways of measuring single proteins?

A
  • Western blotting

* ELISA

52
Q

How does western blot work?

A

Using gel electrophoresis to run a protein and using antibodies to label a certain protein

53
Q

What is the benefit of western blot?

A

You get the size of a protein

54
Q

What is the benefit of ELISA?

A

It is highly quantitative. Very sensitive for measuring the concentration of a protein

55
Q

What is ELISA based on the idea of?

A

Antibodies at the bottom of the plate and different amplification that relate directly proportional to the amount of antibody

56
Q

What occurs in 2D electrophoresis?

A

A gel is run in two directions with proteins go in two directions to spread apart the proteins of interest

57
Q

What is one benefit to 2D gel electrophoresis?

A

Being able to see changes in proteins better

58
Q

What does mass spectromics with proteins measure?

A

The size of a structure

59
Q

How does mass spectrometry of proteins work?

A
  • 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
Q

What does mass spectroscopy of proteins tell you?

A

The amount of that protein in a sample

61
Q

What are examples of Metabolomics?

A
  • Hormones
  • Signalling molecules
  • Metabolic intermediates
62
Q

What is the Human Metabolome Database?

A

Using different tools to study different metabolites

63
Q

What are metabolites measured with?

A

Mass spectroscopy and NMR

64
Q

What are the two types of mass spect tools?

A

Separation based tools and separation free tools

65
Q

What do MS separation based tools do?

A

Separate based tools separate them into their chemical components

66
Q

Why is NMR not used as widely as mass spec?

A

Because it is less sensitive

67
Q

How does NMR work?

A

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
Q

What was the science breakthrough of 2018?

A

Single cell RNA sequencing

69
Q

What is bulk sequencing used for?

A

Understanding things as a whole

70
Q

What should be used if you want understand the different elements?

A

RNA sequencing

71
Q

What do the dots on a scale represent?

A

How related each cell is to one another

Neuro (6 decks)

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