Flashcards in Biochemistry Lecture 5 - Control of Gene Expression Deck (30):
What is a "housekeeping protein?"
A protein that is common to many different cell types.
What ultimately determines different cell types?
Their protein population.
What are the four global transcription control mechanisms?
1. Configuration of genes in chromatin
2. Locus control regions
3. Histone acetylation
4. DNA methylation
How many DNA base pairs are wrapped in the core of a nucleosome?
What is the transcription activity of heterochromatin?
It is transcriptionally inactive (too tightly bound up)
What is the transcription activity of euchromatin?
It is transcriptionally active
What regions of DNA are especially sensitive to DNase I?
Control regions such as enhancers.
What is the LCR and what does it do?
The Locus Control Region regulate chromatin organization - they "open up" a chromatin domain to increase transcriptional activity.
What is SWI-SNF?
It is an example of a nucleosome remodeling enzyme that can alter nucleosome structure for transcription activity.
On which amino acid residue does acetylation of histones occur?
Lysine residues. At physiological pH, lysine is protonated and carries a positive charge on the amino group (NH3+), owing to its electrochemical attraction to negatively charged DNA. Acecylation of the amino group neutralizes the positive charge, therefore weakening the attraction to DNA.
What is the overall effect of acetylation of histones?
Acetylation increases transcriptional activity.
What is histone acetyltransferase activity and what has it?
HAT, activators and co-activators possess HATs.
What does a histone deacetylase do?
It deacetylates the lysine residues of histones to decrease transcriptional activity.
How does methylation affect transcriptional activity?
Methylation decreases transcriptional activity.
In mammals, to what sequence of DNA does DNA methyltransferase methylate, and exactly where does this methylation occur?
The fifth carbon atom of cytosine residues are methylated at CpG dinucleotide sequences.
Why are CpG sequences hotspots for mutation?
CpG sequences are often methylated, and deamination of a methylated cytosine residue results in a thymine residue, which is not detected by repair machinery.
What is a CpG island and for what genes will you find them near? Are they methylated?
CpG islands are long stretches of C-G that are often found near the promoter regions for the genes that code for housekeeping proteins. They almost always lack methylation.
Do proteins have different domains that can serve different functions and/or bind to different structures? Name one example.
Yes! Example is the activators that make up part of the transcription machinery apparatus. p53 is a specific activator.
What binds to the TATA box?
TATA binding protein (TBP)
What binds to TBP?
TBP binds to the TATA box and coactivators in the transcription apparatus.
How do heat-shock genes illustrate the concept of inducible gene expression?
Heat-shock transcription illustrates that the transcriptional apparatus may be missing one component that shows up when the appropriate environmental condition presents itself.
How is the insulin gene an example of inducible gene expression?
Glucose must first bind to the PDX1 complex as an activator for transcription to begin.
What does a DNA microarray test for?
It is a technique used to determine differences in the mRNA population between two cell types. It can pick up deletions or insertions.
What is one notable gene that is often overexpressed in breast tumor cells? How could this overexpression be analyzed?
ErbB2/HER-2/neu gene. Could be analyzed via DNA microarray.
In what ways are RNA-seq superior to DNA Microarray?
RNA-seq is highly qualitative and will tell you the sequences of mRNA so that therapies such as siRNA can be targeted exactly where its needed.
What is antisense therapy supposed to accomplish?
It is supposed to bind to mRNA before it can be translated (doesn't work very well in vivo)
In short, how does siRNA work?
The dsRNA is introduced into the cell and is recognized by the RISC complex (the complex normally attacks viral RNA which is often ds), the RISC complex cleaves and denatures the siRNA, then finds the complimentary endogenous mRNA target and degrades it.
What is Oct-2 and what cells and genes does it affect?
It is a transcription factor for B cells in the genes involved in Ig heavy and light chains.
What is Isl-1 and what cells and genes does it affect?
It is a transcription factor for pancreatic islet cells in the insulin gene.