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Bio 361 - Molecular Genome and Genomics > Midterm 2- Notes 2 > Flashcards

Midterm 2- Notes 2 Flashcards

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1
Q

What are amplified tremendously in eukaryotes?

A

Transposons

  • 45% of human genome DNA
  • 77% of frog genome DNA
  • > 85% of conifer genome DNA
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2
Q

What can be a downside to amplification of transposons?

A

Can be a huge metabolic cost

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3
Q

What is the benefit of junk DNA?

A

It can act as a buffer against mutagens

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

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4
Q

What are transposons? (2)

A
  1. Mutagens

2. Toys of evolution

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5
Q

What can too much movement of a transposons cause?

A

Loss of function

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6
Q

Junk

A

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

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7
Q

Garbage

A

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

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8
Q

TE

A

Transposable elements

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9
Q

What can TE lead to?

A

Evolutionary events

- inactivation of target genes

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10
Q

Whats the only way a gene can be fixed?

A

If the original function is being maintained

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11
Q

What 3 things can TE lead to?

A
  1. Inactivation of target genes
  2. Gene duplication
  3. Miss and match of genes
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12
Q

What happens if transposons get domesticated?

A

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

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13
Q

RAG1

A

Recombination Activating Gene 1

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14
Q

What is RAG1?

A

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

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15
Q

What are TE toys of?

A

Biotech

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16
Q

What can TEs be used as? (3)

A
  1. Tagged mutagens
  2. Tools to make transgenic organisms
  3. Gene therapy
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17
Q

What can you use transposons as?

A

A shuffle to bring foreign DNA into the cell

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18
Q

What does gene inactivation normally cause?

A

Trouble

- detrimental phenotypes

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19
Q

How are transposons integrated?

A

By random and can happen in a functional gene

20
Q

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

A

Knock out its function

- LOF

21
Q

What do transposons cause?

A

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

22
Q

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

A
  1. 5-1% of human illnesses
  2. Hemophila
  3. Duchenne muscular dystrophy
  4. Certain cancers
23
Q

Can losing a gene have an adaptive advantage?

A

Yes

24
Q

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

A

Green grapes

- promotes survival in humans

25
Q

What are green grapes a mutant of?

A

Red grapes

26
Q

What creates green grapes?

A

A lack of TF that switch on the genes during development

27
Q

What makes red grapes red?

A

Primarily anthocyanin

- complex biosynthetic pathways

28
Q

What does biosynthesis involve?

A

Large number of enzymes

- intermediates are involved from the same pathway that can be precursors for something else

29
Q

Genes encoding biosynthetic enzymes are what?

A

Transcriptionally regulated

30
Q

What increases during berry development?

A

Transcription

31
Q

When is berry colour determined?

A

In early development

32
Q

What are the 2 redundant transcriptional activators?

A
  1. MYBA1
  2. MYBA2
  • need a LOF
33
Q

What are both MYBA1 and MYBA 2 able to do?

A

Up-regulate pigment biosynthetic genes during berry development

34
Q

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

A

Green berry phenotype segregates as single recessive locus

- need both mutations in order to had the green phenotype

35
Q

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

A

Sanger

36
Q

What type of gene was red and green grapes?

A 
Red = heterozygous 
Green = homozygous
37
Q

What caused the green grape?

A

1 locus

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

38
Q

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

A

That there was no difference

- only a difference in the MYBA1 and the MYBA2 genes

39
Q

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

A
  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
40
Q

Why does the MYBA1 gene not allow expression?

A

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

41
Q

What did they find out about MYBA2?

A

That it had 2 mutations

42
Q

What 2 mutations did they find in MYBA2?

A
  1. One point mutation
    - causing Arg to change to Lys in the DNA binding domain
  2. Di-nucleotide deletion (2 point deletions)
43
Q

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

A

A non-synonomous change

44
Q

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

A
  1. A frame shift

2. Stop codon

45
Q

What is common in all white grapes?

A

All produce homogenous for both mutations

- come from the same origin

46
Q

What 2 things were discovered by the green grape experiment?

A
  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

Bio 361 - Molecular Genome and Genomics (35 decks)

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