Chapter 7 Notes A
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What experiments were done to prove that different cells possess the same DNA?
1) An adult frog's skin cells were cultured. They removed the nucleus of the frog cell and injected it into a denucleated egg. The egg still developed into a normal embryo and, eventually, a tadpole.
2) Carrots: they took single cells and they were fully grown into carrots.
3) Cows that produced a lot of milk--> epithelial cells were taken and placed into an unfertilized egg--> calf developed
What did these experiments suggest?
They suggest cells contain entire spoke of genetic information necessary to make the whole animal
What is a microarray?
It is an experiment in which a small chip is spotted with single stranded DNA fragments; rows and columns, each section with a different DNA (ss)
Take mRNA from tissues--> cDNA--> Wash cDNA with the ssDNA--> hybridization will occur between complementary strands
What does a microarray show?
It shows patterns of different colors in different tissues. The patterns are very similar, revealing that different genes are activated in different tissues in a tissue specific manner.
- Some genes are on/ others are off.
- Green means the gene is upregulated; red means the gene is downregulated
What other way of demonstrating the expression of genes was performed?
- Separating a tissue on the basis of size and isoelectric point.
- The pattern of spots were very different for each sample
Despite the various gene regulation controls, what is the easiest control?
The easiest control is at the transcription level; the rest are controls when the cell changes its mind.
What are characteristic features of DNA? What is the importance?
They have major and minor grooves. Proteins interact best at the major groove because it is capable of distinguish between the base pairs, whether it is CG, GC, AT, or TA. This is because the major groove reveals four atoms as opposed to three
What interactions allow the protein to bind to DNA?
Any protein that interacts with DNA is __
- H bonds
- hydrophobic interactions
- ionic bonds
a transcription factor
What are DNA elements?
specific sequences in the promoter region of genes that specific proteins bind to in order to turn on or off the genes
How do proteins bind?
They have side chains protruding out from the proteins that can bind tightly to the base pair.
There are families of __ with __.
Explain the helix turn helix motif.
two alpha helices separated by a short turn= DNA binding portion of TF
There is a recognition helix that slides into the major groove and has amino acid side chains that bind to DNA
To get enough hydrogen bonds to bind between the protein and DNA, what must happen?
They must form dimers
What are homeodomains?
protiens associated with developmental genes
Explain the zinc finger motif.
There's an alpha helical section; two strands of beta sheets
What can happen with the alpha helical portions?
changing the AA sequence changes the sequence of DNA it binds to
A(n) __ is not always the motif that interacts with DNA. __ also interact. Name an example.
Met repressor: turn off genes associated with methionine production
Explain the leucine zipper.
Alpha helical in nature
several leucines that wind around each other
What can make TFs complicated?
If they form a heterodimer, they bind a certain way. Changing the orientation of the heterodimer causes different binding.
But, it does lead to diversity.
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