Midterm 2 - Notes 1 (Part 1)

Question 1

Where can transposons be found? (2)

Answer 1

1. Prokaryotes

2. Eukaryotes

Question 2

What are 3 examples of transposons?

Answer 2

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

Question 3

What does the protein coding region encode for?

Answer 3

Transposase

- site specific endonuclease DNA ligase

Question 4

What 2 features do transposons have?

Answer 4

1. Transposase

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

Question 5

What is an important hallmark for the inverted repeat sections?

Answer 5

That the repeats are short

Question 6

What does length of the transposons depend on?

Answer 6

The target site

Question 7

What do the protein coding regions contain?

Answer 7

Promoter

- drives the expression of the transposons

Question 8

What does the transposase machinery do?

Answer 8

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

Question 9

What can you find inbewteen the two inverted regions?

Answer 9

Transposase

Question 10

Transposase

Answer 10

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

Question 11

IS

Answer 11

Insertion sequence

Question 12

What does transposase do?

Answer 12

Ligates transposon into target site

Question 13

What does cellular DNA polymerase and ligase do?

Answer 13

1. Fills in overhangs

2. Joins ends

Question 14

What does DNA polymerase and ligase create?

Answer 14

Short direct repeats specific for target sites

Question 15

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

Answer 15

It can be duplicated

- not shifted over

Question 16

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

Answer 16

Increase in transposons copies

Question 17

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

Answer 17

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

Question 18

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

Answer 18

1. So they can get passed onto generations

2. So they can increase in numbers

Question 19

What happens if movement happens in the S phase?

Answer 19

Can have a chance of increase in numbers

Question 20

What were the first transposons discovered?

Answer 20

Ac/Ds system affecting colour development in maize

Question 21

What mechanisms do transposons act through?

Answer 21

Cut and paste mechanism

Question 22

What does the 5’ end of a transposon do?

Answer 22

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

Question 23

What defines the frequency of a transposon

Answer 23

The expression level of a transposon gene

Question 24

What creates sticky ends?

Answer 24

Transposase cuts randomly in the genomic DNA

Question 25

What are 2 major classes of transposons?

Answer 25

1. Transpose as DNA (DNA transposons) | 2. Transpose vie RNA intermediate (retro-transposons)

Question 26

What does transpose as DNA (DNA transposons) involve?

Answer 26

Tranposase

Question 27

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

Answer 27

Cut and paste mechanism

Question 28

What does retro-transposons involve? (2)

Answer 28

1. Reverse transcriptase | 2. Integrase (similar to transposase)

Question 29

What mechanism does retro-transposons use?

Answer 29

Copy and paste mechanism

Question 30

How does the copy and paste mechanism work?

Answer 30

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

Question 31

What will transposons always do?

Answer 31

Amplify

Question 32

What will the original transposon always do?

Answer 32

Stay where it was but duplicate

Question 33

What are 2 major classes of retro-transposons?

Answer 33

1. Retroviral-like retrotransposons | 2. Non-retroviral-like retrotransposons

Question 34

What do retroviral-like retrotransposons contain? (3)

Answer 34

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

Question 35

LTR

Answer 35

Long Terminal Repeats

Question 36

How do retroviral-like retrotransposons move?

Answer 36

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

Question 37

What are 4 examples of retroviral-like retrotransposons?

Answer 37

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

Question 38

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

Answer 38

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

Question 39

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

Answer 39

Poly A tail

Question 40

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

Answer 40

Often truncated (shortened by cutting it)

Question 41

How does non-retroviral-like retrotransposons move?

Answer 41

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

Question 42

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

Answer 42

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