Wk 1 Gene Expression INCOMPLETE Flashcards
What is a promoter?
Where do polymerases work?
Every polymerase works at a primer template junction
What is the bottom strand in transcription?
The coding strand
What is the top strand in transcription?
template strand
What is an enhancer in transcription?
What do interleukins do?
Influence fate decisions for cells
What are PU.1 and GATA-1?
transcription factors that act as target promoters for certain genes.
Act as promoters of their own genes and also bind and inhibit the same genes the other one activates.
Understand
*The myeloid progenitor cell makes some of each transcription factor, but one program must eventually dominate because they are mutually exclusive. The progeny remember the decision because they inherit a large amount of only one of the factors, so the myeloid and erythroid lineages are stable.
*The myeloid cells still have the genes for being erythroid, they just don’t express them. What makes this epigenetic decision stable?
What does cell fate depend on?
transcription factors. Forced expression of TFs can rewire the fate of a cell
How do DNA-binding proteins regulate transcription?
Scan the genome, find the sequence it likes (promoter) then recruit/activate RNA polymerase
Can access be restricted?
Yes, other proteins can get in the way so RNA polymerase won’t see the promoter
Make promoter, find RNA polymerase,
Example of polymerase blocking
Lac operon
What are recognition molecules?
change [DNA binding pro]
What is a role of chromatin?
Provides the “reversible accessibility barrier” function
What does methylation do to DNA?
Makes DNA Mute
What does histone acetylation do to DNA?
Histone Acetylation makes DNA Active
Correlates w/ increased transcription (drugs change acetylation state)
What is heterochromatin?
=Highly Condensed
What do the patterns of histone modifications do?
Give each nucleosome a personality….
What does the acetylation of lysine do?
It says, “increase transcription”
-This is KEY
What are writers in nucleosome modifications?
enzymes that add covalent modifications to histones (acetylation by histone acetyl transferases or
HATs, methylation, phosphorylation, ubiquitylation, sumoylation, etc.).
What are readers in nucleosome modifications?
protein domains that bind the modifications, either alone or in combination. The ‘reader’ motifs are
attached to proteins that then impact chromatin structure and/or transcription.
What are erasers in nucleosome modifications?
enzymes that remove covalent histone modifications (like histone deacetylases or HDACs).
What are remodelers in nucleosome modifications?
Enzymes that use energy (ATP) to move (translocate or evict) nucleosomes. This can either reveal DNA binding sites or hide them. Remodelers can also be readers (they remodel nucleosomes with specific modifications).
What factors alter the stability of chromatin barrier (AKA changing the accessibility of the DNA)?
co-activators and co-repressors of transcription
-they don’t recognize DNA sequences, the recognize DNA binding proteins (kind of get “trapped” by DNA binding PRO)
What is the difference b/w DNA binding proteins and co-factors?
DNA binding pro determine where something will happen
Co-factors determine what will happen there
INCOMPLETE
Skipped sections
What is splicing?
Process in translation that we can interfere with by blocking it, or masking splice sites to skip exons
What is a lariat?
How can splicing be manipulated?
Donor or acceptor blocking
make different mRNA by leaving out exons (can be forced by us but also occurs naturally - alternative splicing)
Steps of translation
- Ribosome binds mRNA
- assembly of ribosome-mRNA complex uses GTP, initiation factors (IFs or eIFs)
- peptide bond catalysis is part of enzyme (protein) and part ribozyme (RNA). Elongation and termination use specific factors. Translation factors are common targets of pathogens and antibiotics
Translations controls play major role in regulating iron metabolism
Ferric iron (3+)
transferrin receptors (on target cells to accept iron)
plasma transferrin (truck/bus carrying iron)
Fe3+ is dangerous, buried deep w/in transferrin for transport
Remember this
Have ways to sense environ to change behaviors
What is the role of aconitase?
-an RNA binding protein that also uses iron
can either bind iron or mRNA, and when it binds RNA it either stabilizes or destabilizes it, making a versatile translational switch
What is IRE?
Iron responsive element
How is globin translation, iron import and heme synthesis coordinated in developing RBCs?
If lots of heme around, heme kinase inactivates/ihibits (phosphorylates) eIF2, which turns off all protein translation (synthesis)
-If we don’t have iron, then don’t have heme, so heme kinase activated again to turn off protein translation
=> system keeps functioning only while heme inhibits heme kinase
-if heme is gone, system stops
How many base pairs of DNA?
46 chromosomes, 6B base pairs of DNA, 130M bps per chromosome
-we inherite one copy of each homologous chromosome from each parent
What are the stripes seen on chromosomes?
The cells were arrested in M phase w/ a microtubule poison, then stained, which reveals s/t about the density of protein-DNA (chromatin) complexes in condensed chromosomes
-karyotyping
What are common drivers of cancer?
- Rearrangements (translocations) of chromosomes
- aneuploidy (# chromosomes > or = 46 per cell) is common in tumor tissues
What translocations do we need to know?
t(8;21), t(15;17), inv(16), 11q23, FLT-3 mutation, t(9;22), t (11;14), t(14;18), t(8;14)
-know associated diseases
What defines a chromosome?
- A piece of DNA w/ ONE centromere/kinetochore w/ hundreds-thousands of head-to-tail repeats of the same 172 bp sequence, ~500,000 in total.
- –LOTS of replication origins (one origin can only support the copying of ~100,000 bp of DNA, we we need ~1000 origins per human chromosome)
- TWO telomeres (to stabilize the two ends of the linear chromosomes; sounds trivial but wait until you see what happens when they fail)
Do genes contribute to being a chromosome?
No. They’re the reason we have chromosomes, but they don’t do anything that contribute to the mechanical properties of a chromosome to make them functions as a hereditary information-transfer vehicle.
How much of DNA do known genes take up?
~2% of the DNA
What makes up the rest of our DNA?
Pseudogenes and transposons
-stuff we don’t understand (lots of long non-coding RNA is produced)
What is a gene?
What are pseudogenes?
nonfunctional segments of DNA that resemble functional genes.
What is a transposin?
-make up about half of human genome
2 kinds:
1. LINEs (long interspersed nucleotide elements) -a DNA element but it looks just like the transcribed RNA genome of a retrovirus
2. SINEs (short INEs) - don’t encode any genes
Retroposons (transposons that have RNA intermediates in the hopping
What happens to LINES?
LINEs are transcribed by RNA Pol II, the mRNA is copied into DNA by reverse transcriptase (which they encode), and the DNA is integrated into the genome at a new site, creating another copy of the LINE at a new location in the genome = transposition.
How do retroposons work?
Retroposons always make another copy of themselves when they transpose (start as one element, end up as two). DNA elements can either just move to another location (start as one, end as one) or increase in number (start as one, end as two) depending on how the DNA break is repaired.
What is the break apart strategy for FISH?
Finds a translocation
-looking for translocation, did it break them apart? FIX
