Gene expression I Flashcards
how many base pairs does a human cell contain?
6X10^9
3 things that determine amount of protein in a particular cell
- protein’s corresponding mRNA
- frequency of mRNA translation into protein
- stability of protein
What is most important mechanism for determining if genes are expressed?
transcription initiation
location of tata box/ initiator sequence
25-35 bps upstream of transcription start sight
3 roles of tata box
- determines site of transcription initiation
- directs binding of RNA polymerase II
- Site of binding of transcription factors
location of promoter or proximal elements
200bps upstream of transcription start site
20bps long
role of promoter proximal elements
- help regulate transcription
2. bound by factors in cell specific manner
location of enhancers
200- tens of kilobases upstream or downstream from promoter, or last exon of gene, or within an intron
length of enhancers
control element 8-20bps in length, with multiple control elements contained in each enhancer
function of enhancers
regulate transcription in cell type specific manner
beta thalassema pathology
deficient production of beta globin by erythroid cells
beta thalassemia cause
mutation in beta globin promoter- reducing amount of beta globin mRNA and thereby protein produced
hemophilia b Leyden cause
x- linked disorder
mutations in DNA control element of promoter of factor IX gene (thereby inhibiting binding of transcriptional activators)
hemophilia b leyden and puberty
prior to puberty: males have 1% of normal factor 9 that is active
after puberty: androgen receptor becomes active and can bind at promoter site and increase transcription to 60% normal around factor 9
gamma alpha beta thalassemia
deletion of locus control region of beta globin gene cluster
-lcr is essential for transcription of all genes within the cluster
fragile x syndrome rate and symptoms
1/1500 males
Symptoms: mental regardation, dysmorphic facial features, postpubertal macroorchidism
What are CGG repeats?
CGG repeats in 5’ region of FMR1 gene
facilitates methylation of cytosine residues in CpG islands and transcriptional inactivation of FMR1 Gene
Fragile x syndrome pathology
expansion of repeat sequence CGG in 5’ region of FMR1 gene to >200 vs normal 6-50 repeats in the region
leads to increased methylation of FMR1 gene and thereby increase transcriptional silencing of FMR1 gene
what are transcriptional activators and repressors?
proteins encoded by one gene that act on another gene to regulate their transcription
can diffuse around nucleus and activate or repress transcription
what are two classes of activators and repressors?
- sequence specific dna binding proteins
2. co- factors
where do sequence specific DNA binding proteins bind?
promoter or enhancer elements (dna control elements) in target genes to regulate transcription
usually bind to elements 6-8 base pairs long
how do sequence specific DNA binding proteins bind?
inserting alpha helices into major groove of DNA
contacts between amino acid side chains of protein and the bases of the dna
where do co-factors bind?
bind to sequence specific DNA binding proteins to modify transcription before this contact
Two components of modular sequence specific dna binding proteins
- dna binding domain: highly structured and evolutionary conservation, folded so they can read DNA sequence and bind to specific target dna
- Activation or repression domain: not highly conserved and are unstructured until they bind to co-factors
What are families of sequence specific DNA binding proteins?
characterized by conserved DNA binding domain; domains of a particular family contain certain consensus amino acid sequences and are similar in tertiary structure
more than 80% fall into one of four categories
homeodomain proteins (helix turn helix)
Hox
Pit1
Msx
zinc finger proteins
nuclear receptors:
estrogen
androgen
retinoic acid
basic leucine zipper proteins (bZIP)
c-fos
c-jun
basic helix loop helix motif (bHLH)
MyoD
myogenin
Myf5
craniosynostosis rate
1/3000 infants
craniosynostosis mutation
mutation in homeodomain of MSX2 (helix turn helix)
required for proper craniofacial development
what is the quality of mutation that occurs in craniosynostosis?
gain of function/ hypermorphic allele: one amino acid substitution that allows protein to bind more strongly
affects transcription of other genes critical for suture closure leading to premature closure of one or more sutures in the skull
androgen insensitivity syndrome phenotype
feminization/ undermasculation of external genetalia at birth, abnormal secondary sexual development in puberty, and infertility
androgen insensitivity syndrome karyotype and mutation
males with normal karyotype 46 X,Y
mutations in either DNA binding domain or ligand binding domain of androgen receptor (zinc finger)
what is the quality of mutation that occurs in androgen sensitivity syndrome?
mutation makes individual less responsive to androgens to varying levels (complete, partial, or mild)
phenotype of waarden burg syndrome type II
deafness, pigmentation anomalies of eyes, hair and skin
mutation in waardenburg syndrome type II
15-20% of patients: mutations in microphthalmia associated transcription factor (bHLH)
gene encodes transcription factor that plays important role in development of melanocytes
What is combinatorial control?
dna binding factors can bind as heterodimers thus increasing the number of potential sequences to which that family of specific transcription factors can bind though combination of different monomers
zinc finger, bZIP, and bHLH all form heterodimers
After transcriptional activators are bound to DNA control elements, how do they stimulate transcription?
- regulate assemby of initiation complexes and rate of initiation of transcription
- regulate changes in chromatin structure influencing the ability of general transcription factors to bind promoters
