chapter 19

Question 1

What is epigenetic regulation?

Answer 1

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

Question 2

What is post transcriptional control?

Answer 2

events that take place at the end of transcription and the beginning of translation

Question 3

what is a chromatin

Answer 3

( DNA and Proteins it is complexed with)

Question 4

t/f epigenetic regulation is passed down progenies via gametes?

Answer 4

T

1. ) HAT / HDAC
2. ) Methylation
3. ) Chromatin remodeling complex

Question 5

What is a histone?

Answer 5

• 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”

Question 6

What is a nucleosome?

Answer 6

DNA wrapped around that octamer structure that the histone is in.

Question 7

Describe the affinity and or association that attracts DNA and histones?

Answer 7

• 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.

Question 8

What is Linker DNA?

Answer 8

regions that bind nucleosomes together with one anther.

Question 9

What is a 30 nm fiber?

Answer 9

• if the answer has anything to do with nucleosomes associating linker regions and this is the condensed product, then go with it.

Question 10

How can you scan through the genome and asses the condensation level of the chromosome?

Answer 10

• 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.

Question 11

What is an interesting point on the condensed patterns of the chromosomal condensed maps

Answer 11

• 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.

Question 12

What are the differences in their respective abilities to be transcribed: condensed vs. decondensed?

Answer 12

• 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.

Question 13

What are the effects of the chemical modifications to histones?

Answer 13

• make the histones more or less likely to participate in higher order chromatin structure.

Question 14

What is histone deacetylation?

Answer 14

• 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.
  —————————————————————————
  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.

Question 15

Where does DNA methylation take place?

what does it look for prior to methylation?

Answer 15

• cytosine’s.

- C & G right next to each other in the right context.

Question 16

Where is the area of heavy methylation?

- Is this area more likely to be transcribed?

Answer 16

near the promoter.

- less likely, methylated DNA tends to attract enzymes like HDAC which promote DNA condensation.

Question 17

What is the chromatin remodeling complex?

Answer 17

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.

Question 18

T/F Epigenetic modifications can be inherited?

Answer 18

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.

Question 19

What are the promoters in eukaryotic cells?

- What is a TATA box and Tata binding protein?

Answer 19

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.

Question 20

What are regulatory sequences?

- what is important to know about regulatory sequences and how they associate.

Answer 20

• involved in controlling how and when that gene is transcribed.
• these are bound by proteins called transcription factors.

Question 21

What are transcription factors and how are they involved with regulatory sequences?

Answer 21

• 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.

Question 22

What are the other proteins that have to help play a role in RNA polymerase binding to the TATA box?

Answer 22

• Transcription factors and regulatory sequences:

Question 23

Describe the promotor region of eukaryotic cells?

Answer 23

• 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.

Question 24

What are proximal promotor elements?

Answer 24

• 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.

Question 25

What is role of enhancers? | - what is true of the transcription factors that bind to enhancers?

Answer 25

- position-independent: you can place it in a ton of different locations and it would work just fine. - usually more than one type of enhancer per gene. 2. ) these transcription factors usually tend to increase the likelihood of transcription. - positive role in gene transcription

Question 26

What is the role of silencers?

Answer 26

- regulatory sequences that are independent and are found before, after, and in the middle of the gene. - But they bind to transcription factors that are negative regulators of transcription.

Question 27

What are the two very broad categories of transcription factors?

Answer 27

Basal transcription factors: they bind directly at the promotor region (example TBP) - they are required apparently. - ------------------------------------------------------------------------------ - Regulatory transcription factors: they interact with PPEs, enhancers, and silencers. - Each gene can be regulated in a unique way if the right regulatory transcription factors are present.

Question 28

t/f each transcription factor binds to a unique piece of DNA?

Answer 28

True, they do this because the major grove of the DNA where the complementary bases are exposed.

Question 29

What is the idea of differential gene expression?

Answer 29

How do different cells transcribe different sets of genes ?

Question 30

What must happen in order to transcribe a gene?

Answer 30

1.) decondense the chromatin in that area. 2.) express the necessary regulatory transcription factors to bind to the PPEs and enhancers of that gene. ALSO IMPORTANT TO BE MINDFUL OF: - different cell types have different patterns of chromatin condensation, and express different sets of regulatory transcription factors, so they transcribe unique sets of genes - Some genes will have similar enhancers and PPEs so that if the right regulatory transcription factor is present all of those genes can be transcribed at the same time essentially allowing genes to function like a fucking unit.

Question 31

What is post-transcriptional control?

Answer 31

- regulating the events between the end of transcription and the end of translation. - impacts the functionality of the protein - -------------------------------------------------------------------------- - all the steps necessary to go from pre- mRNA to translation itself: RNA splicing, processing, RNA export, stability of the RNA in the cytoplasm, assembly of the ribosomal subunits on the RNA. - All of these steps can be regulated in post-transcriptional control.

Question 32

Describe post transcriptional regulation in RNA splicing?

Answer 32

-reminder that eukaryotic genes have introns, which must be spliced out of the primary RNA to make the mRNA. - This process is heavily regulated. ------------------------------------------------------------------------------ -

Question 33

Describe the post-translation regulation in RNA interference?

Answer 33

- increased turn-over or degradation of of specific mRNA. - involves a special kind of gene known as a micro-RNA (miRNA). They encode little short RNAs that have a high degree of internal self complementarity. - The miRNA then binds to the risc complex, which uses the little miRNA that was ripped in half as a probe to look for any complementary mRNAs. IF FOUND: They bind to one anther and the risc complex typically cleaves the mRNA and then it gets degraded. --------------------------------------------------------------------------- CONCLUSION: great way for the cell to be cleared of certain mRNA via transcription of the miRNA.

Question 34

Describe the post-translational regulation in regulation of the translation process itself

Answer 34

- This process isn't specific to shit, regulating translation tends to happen on more of a global scale( globally increase of decrease levels of translation within the cell) - i.e: phosphorylation of a particular ribosomal subunit protein in response to a fever. - - activating proteins that bind to ribosomes and either increasing or decreasing the rate in which they assemble to an mRNA. - or they can bind to mRNA and prevent them from binding to ribosomes and assembling.

Question 35

Name some examples of post-translational regulation? | What is it?

Answer 35

- covalent modifications to proteins that increase or decrease their activity. - chaperones assisting in protein folding - phosphorylation, glycosylation, or other enzymatic modifications of proteins that alter the activity of that protein. - targeted protein destruction by ubiquitination. - cyclin levels dropping in the cell cycle.