Gene Expression Shred Fest I LO Flashcards
what determines the amount of protein within each cell? (4)
- amount of mRNA
- frequency of mRNA translation
- stability of the protein
- Rate of degradation of protein
what is the most important mechanism for determining gene expression and amount of protein synthesized?
transcription initiation
what are the 2 basic components important to eukaryotic gene expression?
- DNA control elements-part of DNA that acts locally (cis)
2. transcriptional activators/repressors that act on other genes to regulate their transcription (trans)
where do DNA control elements act?
locally, transcription factors bind to elements that control expression of that gene
what are the 3 DNA control elements?
- TATA box/initiator (promoter)
- promoter proximal element
- enhancer
what is the TATA box?
located 25-35 bp upstream of transcription start, determines site of transcription initiation and directs binding of RNA pol II
what is the promoter proximal element?
200 bps upstream of start site and about 20 bps long, helps regulate transcription
what is the enhancer?
200-tens of thousands bps upstream or downstream from promoter or within an intron
what binds at the TATA box?
general transcription factors like TATA binding protein
what are the 3 diseases associated with mutations in the DNA control elements?
- Thalassemias
- Hemophilia B-Leyden
- Fragile X-Syndrome
what does an enhancer do?
binding of proteins enhances transcription levels
what is a silencer?
Section of DNA that binds transcription regulating factors called repressors
how does a silencer work?
when repressors bind, RNA polymerase is prevented from initiating transcription, thus lowers or eliminates transcription
how is thalassemias inherited?
autosomal recessive
what is thalassemias?
blood disease that occurs due to different genetic mutations such as mutation or deletion
what mutation causes B-Thalessemias?
B-globin promoter mutation causing decreased transcription of this protein but not complete loss of this protein
what mutation causes yDB thalessemias?
deletion of locus control region (LCR) of B-globin gene cluster, very severe form because LCR directly regulate expression of all genes in that cluster
what chromosome is hemophilia B leyden linked to?
X
what does hemophilia B leyden affect?
blood clotting
how does hemophilia B leyden affect males?
have 1% of normal factor IX active until puberty, once androgen receptor becomes active, produce about 60% of normal factor IX
what is the presentation of fragile X syndrome?
mental retardation, dysmorphic facial features, postpubertal macroorchidism (abnormally large testes)
why does fragile-X syndrome develop?
expansion of CGG trinucleotide repeats in the 5’ region of FMR1 gene on X chromosome. normal humans have about 6-55 repeats but fragile X syndrome patient have between 230-4000 repeats
why does increasing the amount of CGG repeats cause fragile X syndrome?
there is an increase in the methylation of cytosine residues in CpG islands of FMR1 promoter, methylation then causes silencing of FMR1 gene
what is the severity of fragile X syndrome directly related to?
the number of CGG repeats
what does the mutation in hemophelia B leyden disease prevent?
binding of appropriate transcriptional activators to Factor IX gene
what are transcriptional factors?
proteins encoded by one gene that act on other genes to regulate their transcription (activators and repressors)
what are the 2 classes of activators and repressors?
- sequence-specific DNA binding proteins
2. Co-factors
what is a sequence-specific DNA binding protein?
protein that binds to the promoter or enhancer elements in their target genes to regulate transcription
how do sequence-specific DNA binding protein binds to the DNA?
insert alpha helices into the major groove of DNA
what are co-factors?
proteins that bind to sequence-specific DNA binding proteins rather than directly to DNA
what are the 4 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)
What is the difference between a DNA binding domain and an activation domain?
DNA binding domain protein binds directly to the DNA molecule. Activation domain has a protein to protein interaction that modifies transcription
what are the characteristics of a DNA binding domain?
- highly structured
- evolutionarily conserved
- structure allows them to bind directly to the DNA molecule
what are the characteristics of an activation/repressor domain?
- not highly conserved
- not very structured until they bind cofactors or general transcription factors
- recruits additional factors to upregulate or downregulate transcription
what are some examples of homeodomain proteins (helix-turn-helix)?
Hox family (embryologic development), Pit1 (pituitary development and hormone expression), msx (limb pattern formation)
what are some examples of zinc-finger proteins?
nuclear receptors such as estrogen, androgen receptors
what does a basic leucine zipper proteins and basic helix-loop-helix proteins require to bind to DNA?
homodimerization
what are some examples of basic leucine zipper proteins?
c-fos and c-jun (proto-oncogene)
what are some examples of helix-loop-helix (bHLH) proteins?
MyoD (muscle differentiation), myogenin (skeletal muscles development and repair), and MyF5 (muscle differentiation)
what is craniosynotosis and what mutation causes it?
- premature closing of one or more sutures in the skull.
- mutation in homeodomain of protein MSX2 (required in proper cranio-facial development)
- proline to histidine amino acid substitution
- one amino acid change in binding domain makes bind more strongly causing “gain of function” or “hypermorphic allele” leading to suture closure
what is the presentation of androgen insensitivity syndrome (AIS)?
feminization, undermasculinization of external genetalia at birth, abnormal secondary sexual development in puberty, and infertility
where is the mutation in androgen insensitivity syndrome?
DNA binding domain or ligand binding domain of androgen receptor (zinc finger binding domain), causes decreased sensitivity to androgen
what is Waardenburg syndrome type II?
mutation in MITF gene, renders gene nonfunctional, affects transcription of genes important in pigmentation and in hearing
what is combinatorial control?
when thousands of transcription factors can regulate tens of thousands of genes
what do activators and repressors regulate?
- assembly of initiation complexes
- rate of initiation of transcription
- changes in chromatin structure influencing binding to promoters
what is dimerization?
where multiple DNA binding factors (zinc finger etc) come together at binding sites and illicit different gene responses based on which factors are present in a cell at a certain time
what does heterodimerization allow for (2)?
- recognize different DNA sequences allows recognition of new DNA sites
- new combinations of activation domains to be brought together
