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Bio 361 - Molecular Genome and Genomics > Midterm 2 - Notes 1 (Part 1) > Flashcards

Midterm 2 - Notes 1 (Part 1) Flashcards

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1
Q

Where can transposons be found? (2)

A
  1. Prokaryotes

2. Eukaryotes

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2
Q

What are 3 examples of transposons?

A
  1. Ac/Ds in maize
  2. P-element in drosophila
  3. IS element in E.coli
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3
Q

What does the protein coding region encode for?

A

Transposase

- site specific endonuclease DNA ligase

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4
Q

What 2 features do transposons have?

A
  1. Transposase

2. Two inverted repeated sections on either side of the transposase

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5
Q

What is an important hallmark for the inverted repeat sections?

A

That the repeats are short

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6
Q

What does length of the transposons depend on?

A

The target site

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7
Q

What do the protein coding regions contain?

A

Promoter

- drives the expression of the transposons

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8
Q

What does the transposase machinery do?

A

Cut out DNA/transposons and re-intergrate is somewhere else

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9
Q

What can you find inbewteen the two inverted regions?

A

Transposase

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10
Q

Transposase

A

Is an enzyme required for transposition of the IS element to a new site
- it catalyzes the process

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11
Q

IS

A

Insertion sequence

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12
Q

What does transposase do?

A

Ligates transposon into target site

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13
Q

What does cellular DNA polymerase and ligase do?

A
  1. Fills in overhangs

2. Joins ends

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14
Q

What does DNA polymerase and ligase create?

A

Short direct repeats specific for target sites

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15
Q

What happens when DNA polymerase and ligase are in the coding region?

A

It can be duplicated

- not shifted over

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16
Q

What does jumping (copy and paste) not lead to?

A

Increase in transposons copies

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17
Q

When can amplification only occur? If what 2 things happens?

A

During replication of host DNA

  1. Transposons jump from already replicated DNA to a region not yet replicated
  2. Transposons jumps in a germ line cell
18
Q

Why do transposons need to be in a germ line? (2)

A
  1. So they can get passed onto generations

2. So they can increase in numbers

19
Q

What happens if movement happens in the S phase?

A

Can have a chance of increase in numbers

20
Q

What were the first transposons discovered?

A

Ac/Ds system affecting colour development in maize

21
Q

What mechanisms do transposons act through?

A

Cut and paste mechanism

22
Q

What does the 5’ end of a transposon do?

A

It is the recognition site which cuts them and creates a blunt end

23
Q

What defines the frequency of a transposon

A

The expression level of a transposon gene

24
Q

What creates sticky ends?

A

Transposase cuts randomly in the genomic DNA

25
Q

What are 2 major classes of transposons?

A
  1. Transpose as DNA (DNA transposons)

2. Transpose vie RNA intermediate (retro-transposons)

26
Q

What does transpose as DNA (DNA transposons) involve?

A

Tranposase

27
Q

What mechanisms does transpose as DNA (DNA transposons) use?

A

Cut and paste mechanism

28
Q

What does retro-transposons involve? (2)

A
  1. Reverse transcriptase

2. Integrase (similar to transposase)

29
Q

What mechanism does retro-transposons use?

A

Copy and paste mechanism

30
Q

How does the copy and paste mechanism work?

A

Make a copy of RNA and insert it somewhere else in the genome while also remaining in its original location
- just creates a copy of the original

31
Q

What will transposons always do?

A

Amplify

32
Q

What will the original transposon always do?

A

Stay where it was but duplicate

33
Q

What are 2 major classes of retro-transposons?

A
  1. Retroviral-like retrotransposons

2. Non-retroviral-like retrotransposons

34
Q

What do retroviral-like retrotransposons contain? (3)

A
  1. Long direct terminal repeats (LTR)
    - at each end
  2. Reverse transcriptase
  3. Integrase
35
Q

LTR

A

Long Terminal Repeats

36
Q

How do retroviral-like retrotransposons move?

A

Via an RNA intermediate whose production is driven by a promoter in the LTR

37
Q

What are 4 examples of retroviral-like retrotransposons?

A
  1. Copia = drosophila
  2. Ty1 = yeast
  3. THE1 = human
  4. Bs1 = maize
38
Q

What does non-retroviral-like retrotransposons contain? (4)

A
  1. AT-rich regions at flanking sites
  2. Non LTRs
  3. Reverse transcriptase
  4. Endonuclease
39
Q

What is at the 3’ end of non-retroviral-like retrotransposon RNA transcript?

A

Poly A tail

40
Q

What is at the 5’ end of non-retroviral-like retrotransposons?

A

Often truncated (shortened by cutting it)

41
Q

How does non-retroviral-like retrotransposons move?

A

Via an RNA intermediate that is often synthesized from a neighbouring promoter

42
Q

What are 3 examples of non-retroviral-like retrotransposons?

A
  1. F-element = drosophila
  2. L1 = human
  3. Cin4 = maize

Bio 361 - Molecular Genome and Genomics (35 decks)

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