Prokaryotic transcription factors

Question 1

What is a transcription factor?

Answer 1

Protein that plays a critical role in the regulation of transcription. Typically at the initiation stage

Question 2

What are the 2 functions of transcription factors?

Answer 2

1. Direct sequence specific binding to DNA, often close to core promoter
2. Regulate transcription

Question 3

What is the typical mechanism for how transcriptional activators increase the rate of transcription?

Answer 3

Stabilize the interactions between RNAP and the promoter by forming direct physical contact

Question 4

Why are transcription factors modular?

Answer 4

They have distinct domains with distinct functions, and they all function relatively independently. We can mix and match domains in the lab

Question 5

What are the 2 main domains of transcription factors?

Answer 5

1. DNA binding domain

2. Activation domain that makes the physical contact with the basal transcription machinery

Question 6

What are two other domains that transcription factors may have?

Answer 6

Ligand/protein binding domains that can sense environmental changes, and dimerization domains

Question 7

How conserved are the DNA binding domains of transcription factors?

Answer 7

Highly conserved between transcription factors

Question 8

What is one common protein motif found in the DNA binding domains of transcription factors?

Answer 8

Helix-turn-helix

Question 9

What is the helix-turn-helix motif?

Answer 9

Two alpha helices connected by a short amino acid turn

Question 10

How do transcription factors acting as dimers help with increasing the strength of the protein’s interaction with the target DNA?

Answer 10

Each subunit has a DNA binding domain, so they’ll use them to interact with adjacent major grooves in the DNA. The interaction is stronger when two cooperating proteins are binding to DNA

Question 11

How do helix-turn-helix motifs bind to DNA?

Answer 11

The second helix will recognize and bind to the major groove in the target DNA. That helix will lie inside the major groove

Question 12

What sequences in the DNA are recognized by the DNA binding domains of transcription factors?

Answer 12

Palindromic sequences, even imperfect ones

Question 13

How are transcription factors sequence specific when the overall structure of the DNA binding domains are conserved?

Answer 13

Hydrogen bonds between the DNA and a small number of amino acids just outside the recognition helix

Question 14

What are hydrogen bonds formed between the DNA backbone and amino acids from outside the recognition helix doing?

Answer 14

Stabilizing the interaction. Not sequence specificity

Question 15

What are two ways to control the expression of transcription factors at the level of transcription?

Answer 15

1. Control if they’re expressed at all

2. Control how much they’re expressed

Question 16

What are 5 ways to control the expression of transcription factors at the post-translation level?

Answer 16

1. Concentration of the protein (targeting for degradation when there’s too much)
2. Phosphorylation and other modifications that cause reversible conformation changes
3. Small ligand binding
4. Interactions with other proteins
5. Localizing a transcription factor away from the DNA

Question 17

What are 5 mechanisms of transcription activation through transcription factors?

Answer 17

1. Form direct physical contact with RNAP and DNA to stabilize their interaction
2. Alter the conformation of promoter DNA
3. Anti-repression
4. Pre-recruitment activation
5. DNA looping with enhancers

Question 18

How can transcription factors activate transcription by forming direct physical contact with RNAP?

Answer 18

Stabilize the interactions between RNAP and the promoter, which makes transcription more likely to proceed

Question 19

How can transcription factors activate transcription by altering the conformation of promoter DNA?

Answer 19

Changes the spacing of the core promoter elements, so the consensus sequences make better contact with the sigma subunit

Question 20

How can transcription factors activate transcription by anti-repression?

Answer 20

Blocks the activity of a repressor so that RNAP can do its thing

Question 21

How can transcription factors activate transcription by pre-recruitment activation?

Answer 21

Enhances the assembly of the RNAP holoenzyme

Question 22

How can transcription factors activate transcription by DNA looping through enhancers?

Answer 22

Only happens with the sigma 54 subunit. Activators bind to enhancers and loop the DNA, then the sigma can form the open complex

Question 23

What are 3 mechanisms by which transcription factors can repress transcription?

Answer 23

1. Steric hindrance and blocking RNAP from binding
2. Altering promoter conformation
3. Interfering with activators

Question 24

What is a complex promoter? How common are they?

Answer 24

A promoter regulated by more than one transcription factor. Most promoters are complex