Week 3: Chromatin Architecture, DNA Replication - DNA polymerases, Paper 1 Flashcards
What do chromatin modifications do and why is this important?
Bonus: What energy source do these reactions depend on?
Some affect how tight/loose nucleosomes are wrapped (nucleosome association with DNA) (most true for acetylation). This is important because nucleosomes need to be “moved” - chromatin remodeling complexes
They also “mark” or “tag” nucleosomes
These are ATP-dependent processes
Describe the roles of “readers” and “writers” in modifications
A
some proteins are readers - bind to a particular modified histone
some proteins are writers - put on modification
some proteins readers/writers - bind to 1 modification, put on another
What are chromatin boundaries/what do they do?
Chromatin boundaries define where you find particular modifications
They stop modifications from spreading over a particular area
Some of these boundaries are created by chromatin loops
What experiment led to the idea of chromatin loops?
Chromatin loops were first suggested based on microscopy of fruit fly cells with polytene chromosomes
- particular genes were found in particular places in the nucleus
What are potential reasons for chromatin loops?
- localize different regions of chromatin compaction - more compact
- could allow enhancers and promoters to “get closer” to one another
- could also get genes expressed together closer to each other
How are chromatin loops or “interaction domains” detected?
Chromatin Conformation capture: asks whether a particular sequence is near another in the nucleus
Chromatin 3C, 4C, 5C(dont need to know) and Hi-C
Where does DNA replication start?
What does it need to start at?
At an origin
It needs to start at a primer
How does DNA replication progress (where does it move)?
Bidirectional from origin
- 2 replication forks
What direction is synthesis in DNA rep and how does this affect synthesis of the two new strands?
5’ to 3’ (adds to 3’ OH)
Because of this, the 2 new strands are synthesized differently
1. Leading strand - highly procressive (keeps going, going, going in same direction) synthesis
2. Lagging - not processive
Explain the story of how scientists found that the first DNA pol isolated (from E. coli) that got the Nobel prize was not in fact chromosomal DNA replication polymerase
- discovered this by doing reverse genetics - found gene that encoded this protein (took 3,478 assays) - found one that seemed to be the one: named Pol-A = DNA Pol I
- Next they could isolate and look for others: found 3 DNA pols (Pol III is the one that does chromosomal DNA rep) (Pol I, Pol II, Pol III)
Why did only Pol I “show up” at first? - lots more Pol I than Pol II and Pol III in cell (Pol I = 400 enzymes. E. coli cell, Pol II = very few, Pol III = about 10 enzymes/cell)
Does it make sense that there are multiple types of DNA Pol?
Yes, DNA pol need different characteristics (processivity, fidelity (accuracy), diff needs by the cell, diff origins, etc)
There are families of them, all have similar structure (also to RNA)
What is the general structure of DNA pol
A right hand with a thumb, palm, and fingers
How is the location of a chromosome correlated with its transcriptional activity?
Nuclear location of the chromosome is correlated with its transcriptional activity
- central location of gene rich chromosomes
- heterochromatic regions in which genes are silenced, are often associated with the nuclear envelope
Does the degree of heterochromatic spreading vary cell to cell?
yes
Are new heterochromatic states heritable?
Yes
