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Basic evolutionary genomics > Basic genomis > Flashcards

Basic genomis Flashcards

1
Q

Mention two methods developed in mid /1970’s that you can use to sequence DNA

A
  1. Chemical Method rarely used devoloped by Maxam - Gilbert.
  2. Sanger method or also known as a dideoxy or enzymatic developed by Frederick Sanger. This method is still used today with a little change to the basic method although great improvement have been made in efficiency and automation. Sanger Method is considerate a gold standard and the best method to estimate the new generation of DNA.
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2
Q

To carry out the Sanger method, it is necessary to implement the following requirements:

A

Requirement:

  1. Template DNA (to be sequenced) which is typically purified with plasmid and insert DNA.
  2. Specific primer DNA (~20 nucleotides long)
  3. DNA polymerase
  4. Deoxy-nucleotides =dNTPs (dATP, dGTP, dCTP, dTTP)
  5. Dideoxy nucleotides =ddNTPs (ddATP, ddGTP, ddCTP, ddTTP) low concentration called terminators.
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3
Q

Describe in steps the procedure carried out by Singer Method

A

Steps:

  1. DNA and primers heated to denature then cooled to anneal.
  2. Polymerase adds nucleotides specific to the template on end of primer.
  3. Occasionally a ddNTP is incorporated and the enzyme stops.
  4. Fragments of different lenghts are separated and then sequence is read.
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4
Q

What are the difference between the original and modern method?

A

Original method:
1. 4 reactions run, 1 with each ddNTP
2. Fragments separated on polyacrylamide slab gel , 1 line per ddNTP.
3. Entire gel dried and exposed to X-ray film.
4. Sequence interpreted from band order by human inspection.
Modern method:
1. All 4 fluorescently - labeled ddNTP used in 1 reaction each a different color.

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5
Q

What is the biggest problem in genomics?

A

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6
Q

There are two kind of methods for sequencing larger pieces of DNA. Mention the main of each method and the pro and con.

A

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7
Q

How big is a bacterial genomes, vertebrate genomes and in a scale of individual genes?

A

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8
Q

Define C-value and the C-value paradox.

A

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9
Q

Describe the two methods that could be used to sequence a genome. Mention the pro and con each one.

A

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10
Q

Mention briefly the three methods to be used to identify the location of genes.

A

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11
Q

What else we can find when we are sequencing genomes?

A

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12
Q

What and why was the first complete geneome sequence of a free living organism? When was it published and genome size?

A

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13
Q

What and why was the first complete geneome sequence of a free living organism using WSF before human genome? When was it published and genome size?

A

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14
Q

When was it published the human genome? What is the genome size? Which are the two independent groups that worked on the human genome? How they worked?

A

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15
Q

What is transcriptomics? Describe the EST sequencing, pro and con.

A

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16
Q

What is the Microarrays method? How you can measure gene expression? Mention the two main approaches that are used to determine relative expression differences.

A

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17
Q

What is the Affymetrix affy gene chips? Describe the procedure, Pro and con.

A

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18
Q

What is the SAGE? Describe the procedure, Pro and con.

A

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19
Q

What is the RNAq? Describe the procedure, Pro and con.

A

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20
Q

Which fields can investigate the function of a particular gene?

A

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21
Q

Define the main of Forward genetics and its procedure.

A

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22
Q

Define the main of Reverse genetics. Describe the different kind of methods that could be implemented to carry out it.

A

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23
Q

Define the main of Site directed mutagenesis and transgenics method and its procedure.

A

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24
Q

What is interactomics, complementation groups, modifier screens?

A

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25
Q

Define the following terms:

  1. Back mutations
  2. Enhancers
  3. Epistasis
A

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26
Q

Mention and describe the procedure of the two methods used for detection protein - protein interactions.

A

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27
Q

Define the characteristics of two best used organism to implement in the detection of protein-protein interaction.

A

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28
Q

Define the main of protein microarray method.

A

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29
Q

Define the main of 2D PAGE method.

A

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30
Q

What means next generation sequencing?

A

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31
Q

Mention how was the pre next generation? Pro and con.

A

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32
Q

Mention the three new generation technologies?

A

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33
Q

Describe the main of 454 and its procedure.

A

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34
Q

Describe the main of Solexa or Illumina and its procedure.

A

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35
Q

Describe the main of Solid (ABI) and its procedure.

A

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36
Q

The applications used in the next generation sequencing.

A

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37
Q

Mention the two newer generation sequencing methods These offer some advantage over the previous methods in terms of speed, size, cost, read length.

A

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38
Q

Describe the main of the PacBio and its procedure. Pro and con.

A

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39
Q

Describe the main of the Ion torrent and its procedure. Pro and con.

A

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40
Q

Mention the new technology which is coming soon.

A

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41
Q

What is heat shuck protein and chaperones?

A

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42
Q

Mention a data base used for bacteria genomes.

A

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43
Q

What the FlyBase date base do?

A

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44
Q

In which statistical software you can use to do shotgun sequencing?

A

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45
Q

Mention a data base used for human genome.

A

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46
Q

Which data base is used to screen for comparison between normal and cancer tissues?

A

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47
Q

Which data base is used to look for protein and genetic interactions?

A

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48
Q

Dideoxy nucleotides are called in Sanger sequencing

A

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49
Q

In WGS what is used for cloning

A

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50
Q

HSP83 for what the number stands: molecular weight (kilo dalton)

A

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51
Q

SAGE stands for:

A

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52
Q

Genome size of a typical bacteria such as H. influ

A

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53
Q

In Proteomics mostly used

A

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54
Q

What is used for knowk down?

A

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55
Q

The fraction of heterochromatin in Drosophila

A

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56
Q

Which sequence platform uses single molecule sequencing?

A

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57
Q

Which sequence platform don’t sequence by synthesis?

A

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58
Q

What the difference between modern and original Sanger seq, why modern Sanger only one
reaction?

A

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59
Q

What is Synthetic lethal?

A

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60
Q

Compare Ion torrent and 454

A

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61
Q

What is N50 contig length?

A

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Basic evolutionary genomics (1 decks)

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