General Transcription Factors in Eukaryotes

Question 1

Eukaryotic RNA polymerases, rely on proteins called ______________ to show them the way to their respective promoters.

Answer 1

transcription factors

Question 2

SUCH FACTORS ARE GROUPED INTO TWO CLASSES:

Answer 2

general transcription factors

gene-specific transcription factors (activators).

Question 3

General transcription factors and the three polymerases alone allow for only _____________, whereas Activators help cells exert exquisitely fine control over transcription.

Answer 3

minimal transcription control

Question 4

(11.1 Class II Factors)

The general transcription factors combine with RNA polymerase to form a ____________ that is competent to initiate transcription as soon as nucleotides are available.

This tight binding involves the formation of an ___________ in which the DNA at the transcription start site has melted to allow the polymerase to read it.

Answer 4

preinitiation complex ; open promoter complex

Question 5

(The Class II Preinitiation Complex)

Contains: _______ and six general transcription factors named ………

_____ general transcription factors and __________ bind in a specific order to the growing preinitiation complex, at least in vitro.

Answer 5

polymerase II ; TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH.

Class II ; RNA polymerase II

Question 6

(11.1 Class II Factors)

_________, as well as ________ and their colleagues:
performed DNA gel mobility shift and DNase and hydroxyl radical footprinting experiments

Figure 11.1a presents the results of a gel mobility shift assay performed by Danny Reinberg and Jack Greenblatt and their colleagues using TFIIA, TFIID, TFIIB, and TFIIF, as well as RNA polymerase II.

Answer 6

Danny Reinberg ; Phillip Sharp

Question 7

Four Distinct Preinitiation Complexes:

Transcription factors bind to class II promoters in the following order in vitro:

1. They added TFIID and TFIIA to the DNA containing the adenovirus major late promoter binds to the TATA box forming the DA complex
2. TFIIB in addition to D and A it forms a DAB complex
3. Next, TFIIF helps RNA polymerase bind to a region extending from at least position -34 to position +17, two new complexes appeared now it is DABPolF complex
4. Last, The remaining factors TFIIE and TFIIH bind to form the complete preinitiation complex = DABPolFEH

In vitro, the participation of TFIIA seems to be optional.

Answer 7

YES

Question 8

_______ and his coworkers extended this study in 1992 with TFIIE and H.

Answer 8

Reinberg

Question 9

Figure 11.1b demonstrates that they could start with the DBPolF complex and then add TFIIE and TFIIH in turn.

The final preinitiation complex formed in this experiment was ____________.

Answer 9

DBPolFEH.

Question 10

The order of addition of the general transcription factors (and RNA polymerase) to the preinitiation complex in vitro is as follows:

Answer 10

• TFIID (or TFIIA 1 TFIID)
  
  • TFIIB
  • TFIIF 1 polymerase II
  • TFIIE
  • TFIIH.

Question 11

Reinberg and colleagues used two different reagents to cut the protein–DNA complexes:

Answer 11

1.) 1,10-phenanthroline (OP)-copper ion complex, which creates hydroxyl radicals

2.) DNase I

Question 12

___________ is a very big protein, so we would expect it to cover a large stretch of DNA and leave a big footprint.

Answer 12

RNA polymerase II

Question 13

(Structure and Function of TFIID)

_______ is a complex protein containing a TATA-box binding protein (TBP) and 13 core TBP-associated factors (TAFs, or more specifically, TAFIIs).

Answer 13

TFIID

Question 14

(Structure and Function of TFIID)

The subscript “___” was traditionally used when the context was unclear, because TBP also participates in the transcription of class I and III genes and is associated with different TAFs (TAFIs and TAFIIIs) in class I and III preinitiation complexes, respectively.

Answer 14

II

Question 15

The _____________ binds to the minor groove of the TATA box and is highly evolutionarily conserved:

> Yeast, fruit flies, plants, and humans have TATA-box-binding domains that are more than 80% identical in amino acid sequence.

> These domains encompass the carboxyl-terminal 180 amino acids of each protein.

Answer 15

TATA-Box-Binding Protein (TBP)

Question 16

How does the TBP in TFIID bind to the TATA box?

________ and ________, showed convincingly that the TBP in TFIID binds to the minor groove of the TATA box.

Answer 16

Diane Hawley and Robert Roeder

Question 17

Tjian’s group demonstrated the importance of the carboxyl-terminal 180 amino acids of TBP when they showed by DNase I footprinting that a truncated form of human TBP.

Question 18

How does TFIID associate with the TATA box minor groove?

Nam-Hai Chua, Roeder, and Stephen Burley and colleagues began to answer this question when they solved the crystal structure of the TBP of a plant, ______________

The structure they obtained was shaped like a saddle, complete with two “________,”

Answer 18

Arabidopsis thalliana ; stirrups

Question 19

1993, ____________________ independently solved the crystal structure of TBP bound to a small synthetic piece of double-stranded DNA that contained a TATA box.

Answer 19

Paul Sigler and colleagues and Stephen Burley and colleagues