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Flashcards in Eu TFs Deck (24):
1

What are transcription factors?

Any protein (other than RNA polymerase) required to initiate or regulate transcription

2

What are GTFs and STFs?

GTF = General (basal) TFs
- participate in the formation of the basal transcription complex near the start site (e.g. TFII etc.)
= start transcription with the help of RNA polymerase accurately

STF = Specific TFs
- stimulate (or repress) transcription of particular genes by binding to their regulatory sequences
= help with getting the right amount of product made at the right place and time

3

How do TFs bind to DNA?

By specific AA side chains: base-interactions

E.g. specific AA sequences on DNA alpha helix are able to interact with a series of base pairs

- A typical DNA-protein interface would have 10-20 contacts

4

How do AAs interact with base pairs of DNA + example?

Hydrogen bonding.

E.g. asparagine and arginine side chains can get involved with hydrogen bonding

Need series of AAs in right combination within protein that recognise base pairs to give right 3D arrangement (of those AAs) = specific binding to specific DNA sequence

5

How is specificity achieved through protein interactions with DNA?

When a particular protein interacts with a particular DNA sequence then just one AA interaction with one base pair is enough to give specificity needed.

6

Which DNA sequences regulate gene transcription?

1) Promoters
– close to transcription start site (usually a few hundred base pairs of start site)
 which include specific sequences.
Other reg sequences are much further away.

2) Enhancers/silencers
– distant from transcription start site


3) Insulators
– prevent interference between transcription units
 - stop enhancers from interfering with other genes

7

What and where is the promoter?

- DNA sequence that initiates and regulates transcription
- Mainly upstream (5’) of the transcribed sequence

8

How can STFs act with the TC?

Can act by interacting directly or indirectly with the transcription complex

9

What is the regulatory promoter?

Serves to increase transcription (or decides which cells are going to be transcribed in)

10

How do STFs act with the TC?

Can act by interacting directly or indirectly with the transcription complex.

11

What are 'housekeeping' genes?

- Genes expressed in all cells e.g. histone genes

12

What are 'housekeeping' genes?

- Genes expressed in all cells e.g. histone genes


13

What do the CAAT box, GC box and octamer all have in common?

They have a distinct pattern of nucleotides (consensus) found in the promoter region of some eukaryotic genes

14

What do the CAAT box, GC box and octamer all have in common?

They have a distinct pattern of nucleotides (consensus) found in the promoter region of some eukaryotic genes

15

What is the core promoter?

Sequences you need to get any appreciable transcription (e.g. took that piece of DNA and isolated it and put it in a test tube - core promoter is what you would need to get transcription)

16

What are enhancers and silencers?

Enhancers:
Help transcription - increase expression

Silencers:
Slows down transcription - decrease expression

17

What do promoter contain?

Binding sites for ‘ubiquitous’ TFs present in all tissues

Increase efficiency of transcription from promoters of housekeeping genes

18

Where are enhancers and silencers found?

Up to 50 kbp upstream or downstream of promoter

50 bp - 1.5 kbp

Contain multiple binding sites

19

What do tissues specific genes contain?

Many binding sites for ubiquitous and tissue-specific TFs


E.g. gloving genes contain bindings sites for the ubiquitous factors Sp1 and CP1 and also tissue-specific factors such as GATA-1

20

What are the structural motifs of TFs?

- proteins that bind DNA
- used to classify TFs into families

- usually have DNA binding domains; identify diff TFs, sometimes dimerisation domains
- 1 part of structure devoted to binding DNA, another to influencing transcription, additional bits of structures which interact with proteins

21

What are some examples of structural motifs of TFs?

1) helix-turn-helix
2) zinc finger
3) leucine zipper
4) helix-loop-helix

22

What are helix-then-helix motifs?

- DNA binding motif found in many pro and Eu TFs
- e.g. lack repressed binds DNA from 1 of 4 motifs
- 2 alpha helixes connected by AA “turn”
- C terminal “recognition” helix makes contact with major groove of DNA

23

What are are examples of helix-turn-helix examples?

1) Homeodomain proteins
2) POU proteins
3) Pax proteins

24

What are zinc finger motifs?

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