Midterm 2- Notes 2

Question 1

What are amplified tremendously in eukaryotes?

Answer 1

Transposons

• 45% of human genome DNA
• 77% of frog genome DNA
• > 85% of conifer genome DNA

Question 2

What can be a downside to amplification of transposons?

Answer 2

Can be a huge metabolic cost

Question 3

What is the benefit of junk DNA?

Answer 3

It can act as a buffer against mutagens

- important in long lived organisms that have a huge generation time

Question 4

What are transposons? (2)

Answer 4

1. Mutagens

2. Toys of evolution

Question 5

What can too much movement of a transposons cause?

Answer 5

Loss of function

Question 6

Junk

Answer 6

Stuff you put in your attic with the idea of possibly reusing it
- could be a good thing

Question 7

Garbage

Answer 7

Stuff you throw away as it has no use you can think of

Question 8

TE

Answer 8

Transposable elements

Question 9

What can TE lead to?

Answer 9

Evolutionary events

- inactivation of target genes

Question 10

Whats the only way a gene can be fixed?

Answer 10

If the original function is being maintained

Question 11

What 3 things can TE lead to?

Answer 11

1. Inactivation of target genes
2. Gene duplication
3. Miss and match of genes

Question 12

What happens if transposons get domesticated?

Answer 12

They change and fulfill a cellular function and perform enzymatic functions
- eg) TF binding sites

Question 13

RAG1

Answer 13

Recombination Activating Gene 1

Question 14

What is RAG1?

Answer 14

It is a protein that in humans is encoded by the RAG1 gene and is involved with the activation of immunoglobin VDJ recombination

Question 15

What are TE toys of?

Answer 15

Biotech

Question 16

What can TEs be used as? (3)

Answer 16

1. Tagged mutagens
2. Tools to make transgenic organisms
3. Gene therapy

Question 17

What can you use transposons as?

Answer 17

A shuffle to bring foreign DNA into the cell

Question 18

What does gene inactivation normally cause?

Answer 18

Trouble

- detrimental phenotypes

Question 19

How are transposons integrated?

Answer 19

By random and can happen in a functional gene

Question 20

What can the integration of transposons in a functional gene do?

Answer 20

Knock out its function

- LOF

Question 21

What do transposons cause?

Answer 21

50-80% of spontaneous mutations in drosophila but only 0.1-1% in humans

Question 22

What are transposons likely responsible for? What are 3 examples?

Answer 22

0. 5-1% of human illnesses
1. Hemophila
2. Duchenne muscular dystrophy
3. Certain cancers

Question 23

Can losing a gene have an adaptive advantage?

Answer 23

Yes

Question 24

What is an example of losing a gene and having it be an adaptive advantage?

Answer 24

Green grapes

- promotes survival in humans

Question 25

What are green grapes a mutant of?

Answer 25

Red grapes

Question 26

What creates green grapes?

Answer 26

A lack of TF that switch on the genes during development

Question 27

What makes red grapes red?

Answer 27

Primarily anthocyanin | - complex biosynthetic pathways

Question 28

What does biosynthesis involve?

Answer 28

Large number of enzymes | - intermediates are involved from the same pathway that can be precursors for something else

Question 29

Genes encoding biosynthetic enzymes are what?

Answer 29

Transcriptionally regulated

Question 30

What increases during berry development?

Answer 30

Transcription

Question 31

When is berry colour determined?

Answer 31

In early development

Question 32

What are the 2 redundant transcriptional activators?

Answer 32

1. MYBA1 2. MYBA2 - need a LOF

Question 33

What are both MYBA1 and MYBA 2 able to do?

Answer 33

Up-regulate pigment biosynthetic genes during berry development

Question 34

What was discovered base on controlled crosses and micro-satellite mapping?

Answer 34

Green berry phenotype segregates as single recessive locus | - need both mutations in order to had the green phenotype

Question 35

What type of sequencing did they use in the grape mapping?

Answer 35

Sanger

Question 36

What type of gene was red and green grapes?

Answer 36

``` Red = heterozygous Green = homozygous ```

Question 37

What caused the green grape?

Answer 37

1 locus | - but contains 4 MYBA genes that are highly similar to each other

Question 38

What did they find between the MYBA3 and the MYBA4 genes?

Answer 38

That there was no difference | - only a difference in the MYBA1 and the MYBA2 genes

Question 39

What did they find out about the MYBA1 gene? (2)

Answer 39

1. Located just upstream of the coding region - LTR transposon with high abundance in grape 2. Likely disrupts MYBA1 expression - not allowing expression of the gene and creating LOF

Question 40

Why does the MYBA1 gene not allow expression?

Answer 40

Because it sits between the promoter and the coding region which inhibits the expression

Question 41

What did they find out about MYBA2?

Answer 41

That it had 2 mutations

Question 42

What 2 mutations did they find in MYBA2?

Answer 42

1. One point mutation - causing Arg to change to Lys in the DNA binding domain 2. Di-nucleotide deletion (2 point deletions)

Question 43

What kind of change did the single point mutation make in the MYBA2 gene?

Answer 43

A non-synonomous change

Question 44

What did the di-nucleotide deletion cause? (2)

Answer 44

1. A frame shift | 2. Stop codon

Question 45

What is common in all white grapes?

Answer 45

All produce homogenous for both mutations | - come from the same origin

Question 46

What 2 things were discovered by the green grape experiment?

Answer 46

1. That you need both mutations for the green grape - they are redundant genes because they are right beside each other and segregate as a single locus 2. Only this mutation happened once in early grape domestication and we selected the green variety and after that we breed them this way - this is why there are so many varieties