Gene Expression I Flashcards
What macromolecule contained in a cell is responsible for the actions and properties of each cell type?
The proteins that the cell contains.
What determines the amount of each protein in a particular cell?
- The protein’s corresponding mRNA
- The frequency at which the mRNA is translated into protein
- The stability of the protein.
What is gene expression a consequence of?
- RNA synthesis
2, RNA processing - Translation
- Post-translational processing and protein stability
What is the most important mechanism for determining whether or not most genes are expressed?
Transcription initiation (of RNA Synthesis)
DNA Control Elements
DNA elements that act locally (cis). Binding of transcription factors to these elements controls expression of the gene that the element is associated with.
Types of DNA control elements
- TATA Box/Initiator sequence
- Promotor Proximal elements
- Enhancers
TATA box/Initiator sequence
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.
Transcription Factors
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.
Promoter Proximal Elements
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.
Enhancers
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.
Name 3 disease that arise from mutations in DNA control elements
Thalassemias: (beta, and gamma-delta-beta)
Hemophilia B Leyden
Fragile X-Syndrome
Beta Thalassemias
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
Gamma-delta-beta Thalassemia
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)
Hemophilia B Leyden
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)
Fragile X-Syndrome
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)
Describe the role of transcriptional activators and repressors
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.
List the two classes of activators and repressors.
- Sequence-specific DNA binding proteins
2. Co-factors
Sequence-specific DNA binding proteins
Bind to promoter or enhancer elements (DNA control elements) in their target genes to regulate transcription.
Co-factors
Do not bind directly to the DNA elements but rather bind to sequence-specific DNA binding proteins and affect transcription through this contact.
Describe the domains of a sequence specific DNA binding protein.
Two major domains:
- 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.
- Activation (or repression) domain: not highly conserved and are very unstructured until they bind co-factors or general transcription factors.
List the major families of sequence specific DNA binding proteins
- Homeodomain Proteins (Helix-turn-helix)
- Zinc-finger proteins
- Basic leucine zipper proteins (bZIP)
- Basic helix-loop-helix motif (bHLH)
Describe the means for categorizing sequence specific DNA binding proteins into specific families.
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.
Describe 3 particular human disorders that arises from a mutation in a sequence specific DNA binding protein
- Craniosynostosis
- Androgen insensitivity syndrome (AIS)
- Waardenburg Syndrome type II
Craniosynostosis
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.
Androgen insensitivity syndrome (AIS)
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.
Waardenburg Syndrome type II
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).
“Combinatorial Control”
(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.
