Gene Expression

Question 1

List the key steps in eukaryotic gene regulation

Answer 1

Functional architecture of interphase nucleus
Chromatin remodeling
Assembly of the basal transcription complex
Control of chromatin and rate of transcription
DNA methylation and regulation of expression
Post-transcriptional regulation of expression

Question 2

What is the major on/off switch in gene regulation?

Answer 2

Structure of chromatin (functional architecture)

Question 3

Chromosomes structures continually re-arrange so that…. - how is this relevant to pre-mRNA?

Answer 3

Transcriptionaly active genes are cycle to the edge of chromosomes territories and channels. As a result pre-mRNA also does this to be ready for transport into the cytoplasm.

Question 4

Define heterochromatin and euchromatin

Answer 4

Hetero; some chromosome regions are highly condensed and cannot be transcribed
Euch; other regions are more open and can be transcribed

Question 5

Changes in chromatin organization is required for repair, replication, transcription etc.. nucleosome structure is vital here. Therefore, histone tails in nucleosides can be….?

Answer 5

Modified via phophorolaytion, methylation, etc… which allows acces to the underlying DNA.

Question 6

Define promoter and enhancers. How are they relative to gene regulation?

Answer 6

Promoter; sequence that serve to bind to RNA polymerase, initiates transcription.
Enhancer; a nucleotide sequence that enhance the transcription rate.
Both of these regulatory sequences control transcription and are key to gene regulation.

Question 7

Define/outline TATA box.

Answer 7

TATA Box is a promoter to which RNA polymerase will bind. It consists of an 8-BP consensus sequence, composed of AT base pairs. (Mutations affect transcription)

Question 8

Define/outline CAAT box.

Answer 8

CAAT box is similar to TATA but its a sequence consisting of CAAT or CCAAT. (Functions more like an enhancer)

Question 9

Define/outline GC box.

Answer 9

GC box has a consensus sequence of GGGCGG. (Functions more like an enhancer)

Question 10

Other than chromatin alterations, what other method regulates gene expression? Define/outline it, give example.

Answer 10

DNA methylation; adding/removing methyl groups form the DNA bases. Low amount of methylation = high levels of gene expression.
In mammals, the inactivated X chromosomes has a higher level of methylation that active X.

Question 11

Regulation of expression can occur at any point throughout the process, mostly in transcription but can occur post-transcription. Remember the modification process of pre-mRNA, outline the two opportunities here for regulation.

Answer 11

Alternative splicing to give multiple RNAs.
Regulation of mRNA stability.

Question 12

How are enhancers distinguished from promoters?

Answer 12

Unlike promoters, enhancers are not in a fixed position and can be downstream(in beta-globin gene), upstream(in yeasts), or within gene(regulates the immunoglobulin heavy chain gene). Orientation and experimental movement of enhancers minimally affects its action or transcription.

Question 13

Define cis and trans regulators.

Answer 13

Cis; found adjacent to the structural gene that they regulate.
Trans; such as binding proteins can regulate a gene on any chromosome.

Question 14

How is transcription stimulated at a distance, relative to enhancers?

Answer 14

First, transciptions factors bind to enhancers and alter chromatin configuration
Second, by looping the DNA, they bring enhancers and promoter into direct contact in order to form complexes with transcription factors.
Finally, in the last configuration, transcription is stimulated to a higher level increasing the rate.

Question 15

Looping of DNA for enhancers requires what type of protein?

Answer 15

Architectural proteins

Question 16

A second class of transcription factors that bind to enhancer sites can act as positive or negative factors(increase or decrease transcription). Positive class is split into two types. List & define them.

Answer 16

True activtors; function by contacting elements of transcription complex at the promoter and activating transcription.
Antirepressors; functions by altering chromatin structure to allow other factors to bind.

Question 17

True activators are proteins that have 2 domains. What are they?

Answer 17

DNA-binding domain; binds DNA sequences in the enhancer. Examples include, HTH and Zinc Finger.
Trans-activating domain; activates transcription via interactions binding RNA polymerase to other transcription factors at the promoter.

Question 18

Antirepressors remodel chromatin which is altered by 2 different processes. What are they?

Answer 18

First; is catalyses by an ATP hydrolysis dependent remodeling complex.
Second; is a histone modification catalyses by a histone acetyltransferase enzyme (HAT).

Question 19

Define alternative splicing, give an example.

Answer 19

Alternative splicing can generate different forms of a protein so that the expression of one can give rise to a family of related proteins.
PPT produces P and K. Alternative splicing of the PPT gene can exclude exons K it forms an alpha-PPT mRNA. The inclusion of P and K exons forms a beta-PPT mRNA.

Question 20

Briefly explain mRNA stability.

Answer 20

mRNA stability is intrinsic to the sequence of mRNA. mRNA molecules contain open reading frames that code or a protein but also have untranslated regulatory sequences that may comprise of stability sequences.