Gene Regulation

Question 1

What structural features do transcription factors share?

Answer 1

acidic and basic amino acids are confined within regions of the protein and have a specific sequence with a 3D sturcture

Question 2

What are 2 examples of transcription factors?

Answer 2

zinc finger and helix-turn-helix

Question 3

Regions (domains, motifs) may be one of several different sequences common to different classes of DNA _______ ________

Answer 3

binding proteins

Question 4

What type of bonds are important in DNA/protein interactions?

Answer 4

hydrogen bonds (H bonds)

Question 5

What is the helix-turn-helix?

Answer 5

homeodomain proteins (Hox, Msx-1, Barx-1)

Question 6

What is zinc finger?

Answer 6

steroid hormone receptor (ER, PR, AR, GCR)

Question 7

What are Leucine Zipeprs?

Answer 7

involved in protein/protein interactions (AP-1)

Question 8

What are activation domains?

Answer 8

interact with RNA polymerase

highly acidic OR glutamine - regions

Question 9

How can Leucine zippers from mammals and yeast be recognized?

Answer 9

by their sequence similarities

Question 10

What is a method to detect DNA/protein interactions?

Answer 10

gel mobility shift assays: AKA gel retardation assays or electrophoretic mobility shift assays

Question 11

How does the gel mobility shift assays work?

Answer 11

nuclear proteins are extracted and incubated with a specific tagged DNA sequence, the mixture is loaded onto a non-denaturing polyacrylamide gel, DNA migrates quickly and the DNA + protein complex migrates more slowly (band is “shifted”)

Question 12

What is a supershift?

Answer 12

DNA+ protein+ antibody

Question 13

What is a shift?

Answer 13

DNA+protein

Question 14

What are the first 4 steps for activation complexes and RNA polymerase (Pol II) bind?

Answer 14

activators
chromatin modifiers
coactivator complex (mediator)
TATA binding protein (TBP and TFIIB)

Question 15

What are the last 4 steps for activation complexes and RNA polymerase (Pol II) bind?

Answer 15

individual basal transcription factors
Pol II binds to Inr region
carboxy terminus of Pol II complexes with mediator
TFIIH phosphorylates Pol II (52 possible sites) and initiates transcription

Question 16

What do most transcription factors have?

Answer 16

both DNA binding domains and transactivation domains that interact with the transcriptional apparatus

Question 17

Transactivation domains are typically rich with what amino acids?

Answer 17

proline rich PPP glutamine rich QQQ or acidic

Question 18

Experimental production of a chimeric protein with the Sp1 DNA binding domain and the _______ transaction domain?

Answer 18

CTF1

Question 19

What helps to regulate mRNA stability or translation?

Answer 19

micro RNAs (miRNAs)
mRNA binding proteins

Question 20

What are other names for micro-RNAs?

Answer 20

small temporal RNAs (stRNAs)

small interfering RNAs (siRNAs)

Question 21

What do micro-RNAs do?

Answer 21

mediate the silencing of many genes

Question 22

Interaction of micro RNA and mRNA causes what to happen?

Answer 22

causes mRNA to degrade or causes inhibition of translation

Question 23

What are some miRNAs involved in forming?

Answer 23

heterochromatin

Question 24

What are the 3 stages of mouse tooth development?

Answer 24

initiation, bud stage , cap stage

Question 25

What happens during initiation of mouse tooth development?

Answer 25

oral epithelium induces formation of the dental lamina

Question 26

What happens during the bud stage of mouse tooth development?

Answer 26

epithelial tooth bud forms; surrounding mesenchyme condenses

Question 27

What happens during the cap stage of mouse tooth development?

Answer 27

dental papillae and enamel knot form. The cells of the enamel know will direct final tooth structures before dying via apoptosis

Question 28

What is molar vs incisor determined by?

Answer 28

growth factor signaling from overlying epithelium (FGF-8 vs BMP-4)
homeodomain proteins (transcription factors ) in mesial and distal mesenchyme (Msx-1 vs Barx-1)