Transcriptional circuits in prokaryotes and eukaryotes

Question 1

what is the trasncriptome?

Answer 1

Only about 50% of the prokaryotic genome is transcribed

Segment which is transcribed is known as the transcriptome 

Only a fraction of the transcriptome is transcribed at any one time

Question 2

what are the three types of genes?

Answer 2

One type of gene gives rise to many copies of RNA and this is referred to as abundant transcript

If abundant transcripts is found in every cell type we then refer ot them as housekeeping genes 

Another type is where not as many RNA copies are produced and these are known as rare transcript 

Finally the last type of gene has no transcript in some type of cells like beta globin genes which are only expressed in red blood cells

Question 3

what are inducible genes?

Answer 3

Transcription is induced by a stimuli

This results in a gene which is a rare or no transcript to become an abundant transcript

Question 4

regulation of genes (promoter regions)

Answer 4

Recruit RNA polymerase to a DNA template

Question 5

regulation of genes (enhancers)

Answer 5

DNA sequences which increase transcription

Can reside 5’ to 3’ to a transcription unit and also found in introns 

Contain DNA sequences which contain very strong binding sites for transcription factors 

Not immediately adjacent to the site of transcription

Question 6

recruitment of RNA polymerase to promoter

Answer 6

RNA polymerase slides along the duplex without being able to efficiently recognize promoters

Recognition of promoter by initiation factors: 

In prokaryotes – sigma factor 

In eukaryotes – TFII basal transcriptional machinery 

Once RNA polymerase binds to DNA, converted from a closed to an open compound

Question 7

Prokaryotic promoters

Answer 7

Sigma factors recognizes the -35 and -10 motifs common to prokaryotes and enables RNA polymerase to make a stable contact with DNA

Question 8

Consensus sequence and how its determined

Answer 8

DNA having similar structure and function in different organisms

Determined by aligning many nucleotide sequences that share a common function then determining the most commonly expressed nucleotide at each position

Question 9

eukaryotic promoters

Answer 9

TATA box is needed to recruit general transcription factors and then RNA polymerase

Question 10

Transcriptional switches (prokaryotic cells)

Answer 10

CAP protein binds to the promoter region under low glucose level and RNA polymerase binds to the promoter region

Lactose will bind to the lac repressor and RNA polymerase binds to the promoter region 

Lactose will bind to the LAC repressor and RNA polymerase will transcribe the LAC ZYA gene 

RNA formed translate into proteins which utilize energy from lactose 

Lac repressor binds to promoter region where there’s sufficient amount of glucose 

This prevents transcription

Question 11

Transcriptional switches (eukaryotic cells) (oestrogen responsive transcription)

Answer 11

Oestrogen binds to oestrogen receptor complex

This changes the shape of the receptor protein allowing the hormone-receptor complex to enter the nucleus and bind to the oestrogen responsive element and induce the expression of the genes

Question 12

Transcriptional switches (eukaryotic cells) (tissue specific transcription)

Answer 12

Promoter sequence contains different DNA sequences to which transcription factors bind to

Tissue specific factors like GATA-1 (red blood cells) recruit transcription factors and ensure transcription occurs in specific tissue

Question 13

Transcriptional switches (eukaryotic cells) (A complex regulatory circuit like the cell cycle)

Answer 13

Cdks are enzymes which phosphorylate transcription factors

These Cdks are cyclin dependent  

Promoters for G1/S transition genes are activated by a factor called E2F

Question 14

Regulatory element

Answer 14

Needed to regulate the recruitment of RNA polymerase

Regulatory factors bind to the promoter region and help recruit general transcription factors 

Tamoxifen

Used to treat breast cancer by competing with oestrogen receptor complex to bind to oestrogen receptor complex and preventing transcription as RNA polymerase is unable to bind