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• How did scientists show that differentiated cells of both plants and animals did, in principle, not loose large blocks of DNA (genomic information)? How many protein coding genes do humans have? Do you expect that Arabidopsis has a similar number of protein coding genes?

  They initially showed this with an experiment in which they placed the nucleus of a skin cell of a frog in the egg of a (different) frog from which the nucleus was removed. The egg grew to a normal tadpole. Further experiments include the growing of an entire plant from a single (differentiated) cell and the removing and replacing of the nucleus of a differentiated cow’s cell in a cow’s egg.
  
  Humans have approximately 25.000 protein coding genes.
  
  I expect that Arabidopsis has a smaller amount of protein coding genes because their morphology is less complicated.

• Which two molecular components interact together to regulate the level of transcription of specific genes? 

  Transcription factors and DNA.

• We have seen that control of gene transcription by transcription factors (step 1) plays an important role in specification of different cell types. Which other two steps are of importance?

  4 Translation control
  6 Protein expression control.

• What is the present day advantage of having introns in genes?

  They can form the bends that are necessary to line up parts of the DNA that need to be next to each other for transcription.

• Which two components are important to switch genes on or off (genetic switches)? 

  Short stretches of DNA with a defined sequence and regulatory proteins that recognize and bind to this DNA.

• How does a transcription factor (gene regulatory protein) recognize a DNA sequence?

  By specific structures like a helix-turn-helix structure or a homeodomain.

• Describe the function of the two major domains present in gene activator proteins.

  The first domain (DNA binding domain) of a transcription factor ensures that the transcription factor recognises and binds the DNA sequence.
  
  The second domain (activation domain) recognises and binds other transcription factors (in the TATA box) and thereby accelerates transcription initiation.

• What is the size of the DNA sequences that are recognized by transcription factors?

  The size of the DNA sequences that are recognized by transcription factors are small. Usually around
  6-20 nucleotides long.

• What is the difference between promoter and enhancer/gene regulatory sequences and what is the role of DNA looping in the control of gene expression?

  The promotor region is the meeting place for general transcription factors.
  
  The enhancer ensures faster initiation of transcription.
  
  The enhancer region is usually far away from the promotor region but because of DNA looping, the regions are next to each other.

• Briefly describe how you would demonstrate that genes encoding proteins that are only found in hepatocytes (liver cells) are transcribed in liver cells but not in the cells of other tissues. 

  By using reporter constructs. So place a reporter protein gene in front of the gene we want to inspect.