Gene Expression I

Question 1

What macromolecule contained in a cell is responsible for the actions and properties of each cell type?

Answer 1

The proteins that the cell contains.

Question 2

What determines the amount of each protein in a particular cell?

Answer 2

1. The protein’s corresponding mRNA
2. The frequency at which the mRNA is translated into protein
3. The stability of the protein.

Question 3

What is gene expression a consequence of?

Answer 3

1. RNA synthesis
   2, RNA processing
2. Translation
3. Post-translational processing and protein stability

Question 4

What is the most important mechanism for determining whether or not most genes are expressed?

Answer 4

Transcription initiation (of RNA Synthesis)

Question 5

DNA Control Elements

Answer 5

DNA elements that act locally (cis). Binding of transcription factors to these elements controls expression of the gene that the element is associated with.

Question 6

Types of DNA control elements

Answer 6

1. TATA Box/Initiator sequence
2. Promotor Proximal elements
3. Enhancers

Question 7

TATA box/Initiator sequence

Answer 7

This element is generally 25-35 bps upstream of the transcription start site. It determines the site of transcription initiation and directs binding of RNA polymerase II. This is the site at which general transcription factors bind.

Question 8

Transcription Factors

Answer 8

In Eukaryotes, a protein that affects the regulation and transcription initiation of a gene by binding to a regulatory sequence near or within the gene.

Question 9

Promoter Proximal Elements

Answer 9

Generally located within 200 bps upstream of transcription start site and are ~ 20 bps long. They help to regulate transcription, and can be bound by factors in a cell type specific manner.

Question 10

Enhancers

Answer 10

Contain multiple control elements. An enhancer can be 200-tens of kilobases upstream or downstream from the promoter or the last exon of the gene, or within an intron. Similar to promoter proximal elements, enhancers may help to regulate transcription in a cell type specific manner.

Question 11

Name 3 disease that arise from mutations in DNA control elements

Answer 11

Thalassemias: (beta, and gamma-delta-beta)
Hemophilia B Leyden
Fragile X-Syndrome

Question 12

Beta Thalassemias

Answer 12

An inherited mild form of anemia due to deficient production of beta-globin protein. One way in which this disease can occur is a mutation in the beta-globin promoter- reducing the amount of beta-globin mRNA and thus protein produced (less promotion = less transcription) – associated with problems in the TATA box

Question 13

Gamma-delta-beta Thalassemia

Answer 13

Due to deletion of the locus control region (LCR) of the beta-globin gene cluster, resulting in the loss of globin transcription. (usually more severe)

Question 14

Hemophilia B Leyden

Answer 14

Due to inherited mutations in a DNA control element in the promoter of the Factor IX gene. X-linked disease that affects clotting. Tends to get partially better at puberty.(usually males)

Question 15

Fragile X-Syndrome

Answer 15

High number of CGG repeat in the 5’ region of the FMR1 gene (>200 vs ~6-50). This facilitates methylation of the cytosine residues in CpG islands and transcriptional inactivation of the FMR1 gene. (usually males)

Question 16

Describe the role of transcriptional activators and repressors

Answer 16

Proteins encoded by one gene that act on other genes to regulate their transcription. Can therefore diffuse around the nucleus and affect transcription of numerous genes. Can either activate or repress transcription.

Question 17

List the two classes of activators and repressors.

Answer 17

1. Sequence-specific DNA binding proteins

2. Co-factors

Question 18

Sequence-specific DNA binding proteins

Answer 18

Bind to promoter or enhancer elements (DNA control elements) in their target genes to regulate transcription.

Question 19

Co-factors

Answer 19

Do not bind directly to the DNA elements but rather bind to sequence-specific DNA binding proteins and affect transcription through this contact.

Question 20

Describe the domains of a sequence specific DNA binding protein.

Answer 20

Two major domains:

1. DNA binding domain (DBD): highly structured and evolutionarily conserved. They are folded so that they can “read” the DNA sequence and bind to their specific target DNA.
2. Activation (or repression) domain: not highly conserved and are very unstructured until they bind co-factors or general transcription factors.

Question 21

List the major families of sequence specific DNA binding proteins

Answer 21

1. Homeodomain Proteins (Helix-turn-helix)
2. Zinc-finger proteins
3. Basic leucine zipper proteins (bZIP)
4. Basic helix-loop-helix motif (bHLH)

Question 22

Describe the means for categorizing sequence specific DNA binding proteins into specific families.

Answer 22

More than 80% of sequence specific DNA binding proteins fall into 4 families. Each family is characterized by a conserved DNA binding domain. The domains of a particular family contain certain consensus amino acid sequences and are therefore similar in tertiary structure.

Question 23

Describe 3 particular human disorders that arises from a mutation in a sequence specific DNA binding protein

Answer 23

1. Craniosynostosis
2. Androgen insensitivity syndrome (AIS)
3. Waardenburg Syndrome type II

Question 24

Craniosynostosis

Answer 24

One particular variant of craniosynostosis (Boston-type) occurs as a result of a mutation in the homeodomain protein MSX2. MSX2 is normally required for proper craniofacial development by affecting the transcription of a number of genes important in this process. Craniosynostosis is characterized by the premature closure of one or more sutures in the skull.

Question 25

Androgen insensitivity syndrome (AIS)

Answer 25

It occurs in males who are a normal karyotype (46 X,Y), but have mutations in either the DNA binding domain or the ligand binding domain of the androgen receptor (a zinc finger DNA binding protein). AIS includes feminization or undermasculinization of the external genitalia at birth, abnormal secondary sexual development in puberty, and infertility.

Question 26

Waardenburg Syndrome type II

Answer 26

Mutations in the microphthalmia-associated transcription factor (MITF) gene. This gene encodes a transcription factor that plays a major role in the development of melanocytes. Is characterized by deafness, pigmentation anomalies of the eyes, and other pigmentation defects (hair, skin).

Question 27

“Combinatorial Control”

Answer 27

(The way that groups of regulatory proteins work together to determine the expression of a single gene) Many sequence specific DNA binding factors bind DNA as homo or heterodimers. If each monomer of the heterodimer has a different DNA binding specificity, the formation of heterodimers will increase the number of potential sequences to which that family of sequence specific transcription factors can bind.