chapter 19 Flashcards
What is epigenetic regulation?
Getting the chromatin ( DNA and Proteins it is complexed with) into a physical state that allows the transcriptional proteins to assemble correctly on the DNA
What is post transcriptional control?
events that take place at the end of transcription and the beginning of translation
what is a chromatin
( DNA and Proteins it is complexed with)
t/f epigenetic regulation is passed down progenies via gametes?
T
- ) HAT / HDAC
- ) Methylation
- ) Chromatin remodeling complex
What is a histone?
- covalent modifications of either DNA or the proteins that are primarily involved in the packaging of DNA.
- he also said: “proteins that bind to DNA”
What is a nucleosome?
DNA wrapped around that octamer structure that the histone is in.
Describe the affinity and or association that attracts DNA and histones?
- Electrostatic: histones tend to be positivity charged via there amino acids, and DNA obv has a negative charge. These differences in their polarity attract one anther.
What is Linker DNA?
regions that bind nucleosomes together with one anther.
What is a 30 nm fiber?
- if the answer has anything to do with nucleosomes associating linker regions and this is the condensed product, then go with it.
How can you scan through the genome and asses the condensation level of the chromosome?
- DNase 1: nuclease that degrades DNA. It is used as a proxy for telling us condensation level of the chromosome.
- the condensed state of the chromosome is usually too tightly packed for outside proteins to enter and interact with it.
- the Decondensed version there is lots of opportunities for DNA to interact with outside proteins in these linker regions.
- therefor DNA in the decondensed state, when treated with DNase 1 is degraded and the condensed form stays intact.
What is an interesting point on the condensed patterns of the chromosomal condensed maps
- there are static meaning that they are not permanent therefore, the same cell grown under two different conditions will exhibit different patterns of chromosomal condensation and de-condensation.
What are the differences in their respective abilities to be transcribed: condensed vs. decondensed?
- condensed is unable to be transcribed, because the transcriptional machinery cannot access the DNA.
- decondensed is able to be transcribed because the transcriptional machinery has access to the DNA.
What are the effects of the chemical modifications to histones?
- make the histones more or less likely to participate in higher order chromatin structure.
What is histone deacetylation?
- histones can be acetylated on lysine’s, via the enzyme HAT.
- HAT will take an acetyl group and stick it on a lysine, which reduces the overall net positive charge of histones. Which causes them to have much weaker interactions with the DNA.
- ## so the chromosomes are in a more relaxed and almost decondensed state.or the reverse process can occur.
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The enzyme, HDAC takes the acetyl groups off of the histones and then allows the histones to interact more strongly with the DNA. - Thus, ultimately producing higher levels of chromosomal condensation.
Where does DNA methylation take place?
what does it look for prior to methylation?
- cytosine’s.
- C & G right next to each other in the right context.
Where is the area of heavy methylation?
- Is this area more likely to be transcribed?
near the promoter.
- less likely, methylated DNA tends to attract enzymes like HDAC which promote DNA condensation.
What is the chromatin remodeling complex?
makes slight repositioning of nucleosomes, which brings an area of DNA that is associated with the histones into a linker region so it can be more easily assessable or vice versa:
- it can move DNA from the linker region from the linker region into the nucleosome making it tougher to transcribe.
T/F Epigenetic modifications can be inherited?
T, via the proof of the rat experiment.
- tested if diet played a role in gene expression of her offspring.
- focused on a gene that is encoded for cellular metabolism.
- low levels of this gene expression is linked to rat diabetes.
- One mom was feed a sufficient amount of nutrients, and the other mom was feed the same amount of calories but primarily in carbs and lipids.
- Dad’s were given controlled from a set environment and everything regarding treatment post birth was the same.
CONCLUSION: The rats whos mom ate like shit had low expression of the gene related to mouse metabolism, and therefore proved that it is a heritable thing.
What are the promoters in eukaryotic cells?
- What is a TATA box and Tata binding protein?
TATA , they are found just in front of the transcriptional start site.
- This is what allows RNA polymerase to bind and begin transcription.
2. ) in eukaryotic cells it is analogous to -35 and -10 boxes in prokaryotic promoters; Tata Binding protein is analogous to Sigma ( kind of), TBP binds to a specific part of the TATA box and helps facilitate RNA polymerase, binding to that area.
What are regulatory sequences?
- what is important to know about regulatory sequences and how they associate.
- involved in controlling how and when that gene is transcribed.
- these are bound by proteins called transcription factors.
What are transcription factors and how are they involved with regulatory sequences?
- Transcription factors are proteins that bind regulatory sequences to the TATA and they alter how RNA Polymerase interacts with the promoter.
- ## Can be positive or negative promoter.
What are the other proteins that have to help play a role in RNA polymerase binding to the TATA box?
- Transcription factors and regulatory sequences:
Describe the promotor region of eukaryotic cells?
- It is in front of the start site for coding, and doesn’t contain any information necessary for protein encoding, but it is vital for RNA polymerase to bind to it and carry out transcription.
What are proximal promotor elements?
- regions found just in front of the promotor and like the promotor is position dependent.
- the transcription factors that bind to PPEs tend to increase the likelihood of transcription.
