Diversity Through Regulation

Question 1

trans-acting regulatory proteins

Answer 1

• regulatory protein acts at a great distance from where it is transcribed (eg. on a different chromosome)

Question 2

cis-acting regulatory proteins (2)

Answer 2

• regulatory element is on same DNA molecule as gene being regulated
• may be near the gene (eg. promoter sequences) or at some distance (eg. enhancer sequence)

Question 3

activator proteins (3)

Answer 3

• bind to enhancers, promoting activity of transcription complex
• some are more powerful than others
• some work synergistically

Question 4

trans-acting repressor proteins

Answer 4

• bind to cis-acting regulatory sequences and block activators to prevent transcription

Question 5

how can activator proteins work synergistically

Answer 5

• can promote greater levels of transcription in combination than either activator can promote on their own

Question 6

how can genes expression be regulated in time and space? (3)

Answer 6

• WHERE the gene is expressed
• WHEN is the gene being expressed
• HOW MUCH is this gene expressed/transcript made

Question 7

WHERE can a gene be expressed (3)

Answer 7

• cell
• tissue
• organ

Question 8

WHEN can be gene be expressed (2)

Answer 8

• at specific stage or multiple stage in life history

- during development

Question 9

correlation between mRNA levels to protein levels (2)

Answer 9

• poor correlation

- there are further downstream regulatory levels that can disrupt the correlation

Question 10

how can upstream regulatory regions be classified (2)

Answer 10

• constitutive

- regulative

Question 11

constitutive upstream regulatory regions

Answer 11

• this is when a gene is turned on and actively transcribed all the time

Question 12

regulative upstream regulatory regions

Answer 12

• this is a case where the transcription from a gene is tightly regulated as to where and when it is expressed

Question 13

transcription factor characteristics (4)

Answer 13

• can act on many genes
• can have dozens of enhancers
• may also have positive feedback loops regulating their own activities
• can be activators or repressors with varying affinities

Question 14

Pax6 gene (3)

Answer 14

• protein encoded from this gene is a TF that controls expression of genes that are involved in eye development in humans (eyeless for mice)
• gene evolved once and were used as a control gene for eye development in descendant species
• role is conserved across a wide phylogeny

Question 15

what happens when the Pax6 gene is present in the proper cell

Answer 15

• the eye develops normally

Question 16

what happens when the Pax6 gene is non-functional or altered

Answer 16

• partial absence of eye

Question 17

what happens when Pax6 is present in structure other than the eye

Answer 17

• eyes will grow on those structures

Question 18

regulatory elements in regulatory genes vs structural/housekeeping genes

Answer 18

• regulatory genes (genes for TFs) often have more complex cis-regulatory elements than structure/housekeeping genes

Question 19

what is an example of how cis-regulatory elements can modulate gene expression

Answer 19

• some genes may only be activated when specific relative concentrations of different TFs lead to activation of the enhancer for the gene

Question 20

what does a gene regulatory network allow for

Answer 20

• precise control of where and when a gene is expressed, and how much is expressed

Question 21

how do gene regulatory networks achieve their control (3)

Answer 21

• each regulatory protein can act on many genes
• cis-regulatory regions can be modular, with dozens of enhancers to allow for complex control of gene expression
• regulatory proteins may have feedback loops regulating their own activities

Question 22

gene evolution (3)

• modes (2)
• result

Answer 22

• evolution of genes
• evolution of regulatory elements
• results in increase in gene function diversity

Question 23

Sonic Hedgehog (Shh) (2)

Answer 23

• signally molecule that regulated limb development

- critical for development of vital organs

Question 24

where would you find sequence changes in Shh gene (2)

Answer 24

• in regulatory regions or TF binding site

- would not see changes in protein coding sequences because it is still needed for development of other vital organs

Question 25

Shh is critical for development of CNN, brain, and other organs, but the ZRS element that regulates its expression is defective in snakes: why do other systems still develop normally?

Answer 25

- there must be other enhancer elements that direct expression of SHH in CNS, brain and other organs

Question 26

how do combinatorial possibilities of TFs maximize diversity of organisms from a limited number of genes (4)

Answer 26

- more TFs can create more unique combinations of control, allowing for more complex control of gene expression - expansion of regulatory regions allow for more TF binding sites, and even more combinations - concentrations and rations of activators and repressors determine whether particular region is activated or repressed - regulatory regions allow for modular control of gene expression (multiple enhancers, each regulating expression in a different tissue)