Midterm 2- Notes 2 Flashcards
What are amplified tremendously in eukaryotes?
Transposons
- 45% of human genome DNA
- 77% of frog genome DNA
- > 85% of conifer genome DNA
What can be a downside to amplification of transposons?
Can be a huge metabolic cost
What is the benefit of junk DNA?
It can act as a buffer against mutagens
- important in long lived organisms that have a huge generation time
What are transposons? (2)
- Mutagens
2. Toys of evolution
What can too much movement of a transposons cause?
Loss of function
Junk
Stuff you put in your attic with the idea of possibly reusing it
- could be a good thing
Garbage
Stuff you throw away as it has no use you can think of
TE
Transposable elements
What can TE lead to?
Evolutionary events
- inactivation of target genes
Whats the only way a gene can be fixed?
If the original function is being maintained
What 3 things can TE lead to?
- Inactivation of target genes
- Gene duplication
- Miss and match of genes
What happens if transposons get domesticated?
They change and fulfill a cellular function and perform enzymatic functions
- eg) TF binding sites
RAG1
Recombination Activating Gene 1
What is RAG1?
It is a protein that in humans is encoded by the RAG1 gene and is involved with the activation of immunoglobin VDJ recombination
What are TE toys of?
Biotech
What can TEs be used as? (3)
- Tagged mutagens
- Tools to make transgenic organisms
- Gene therapy
What can you use transposons as?
A shuffle to bring foreign DNA into the cell
What does gene inactivation normally cause?
Trouble
- detrimental phenotypes
How are transposons integrated?
By random and can happen in a functional gene
What can the integration of transposons in a functional gene do?
Knock out its function
- LOF
What do transposons cause?
50-80% of spontaneous mutations in drosophila but only 0.1-1% in humans
What are transposons likely responsible for? What are 3 examples?
- 5-1% of human illnesses
- Hemophila
- Duchenne muscular dystrophy
- Certain cancers
Can losing a gene have an adaptive advantage?
Yes
What is an example of losing a gene and having it be an adaptive advantage?
Green grapes
- promotes survival in humans
What are green grapes a mutant of?
Red grapes
What creates green grapes?
A lack of TF that switch on the genes during development
What makes red grapes red?
Primarily anthocyanin
- complex biosynthetic pathways
What does biosynthesis involve?
Large number of enzymes
- intermediates are involved from the same pathway that can be precursors for something else
Genes encoding biosynthetic enzymes are what?
Transcriptionally regulated
What increases during berry development?
Transcription
When is berry colour determined?
In early development
What are the 2 redundant transcriptional activators?
- MYBA1
- MYBA2
- need a LOF
What are both MYBA1 and MYBA 2 able to do?
Up-regulate pigment biosynthetic genes during berry development
What was discovered base on controlled crosses and micro-satellite mapping?
Green berry phenotype segregates as single recessive locus
- need both mutations in order to had the green phenotype
What type of sequencing did they use in the grape mapping?
Sanger
What type of gene was red and green grapes?
Red = heterozygous Green = homozygous
What caused the green grape?
1 locus
- but contains 4 MYBA genes that are highly similar to each other
What did they find between the MYBA3 and the MYBA4 genes?
That there was no difference
- only a difference in the MYBA1 and the MYBA2 genes
What did they find out about the MYBA1 gene? (2)
- Located just upstream of the coding region
- LTR transposon with high abundance in grape - Likely disrupts MYBA1 expression
- not allowing expression of the gene and creating LOF
Why does the MYBA1 gene not allow expression?
Because it sits between the promoter and the coding region which inhibits the expression
What did they find out about MYBA2?
That it had 2 mutations
What 2 mutations did they find in MYBA2?
- One point mutation
- causing Arg to change to Lys in the DNA binding domain - Di-nucleotide deletion (2 point deletions)
What kind of change did the single point mutation make in the MYBA2 gene?
A non-synonomous change
What did the di-nucleotide deletion cause? (2)
- A frame shift
2. Stop codon
What is common in all white grapes?
All produce homogenous for both mutations
- come from the same origin
What 2 things were discovered by the green grape experiment?
- 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 - 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
