Lecture 15a Flashcards
When is transcription above basal level?
When an enhancer is used.
When is transcription below basal level?
When a silencer is used.
T/F: When a silencer is used, RNA polymerase is not present.
False! RNA polymerase is present, however, initiation nor elongation cannot start.
What are 2 ways we can tell transcription is taking place in bacteria as opposed to in eukaryotes?
1) The mRNA is translated at the same time it is being transcribed.
2) The DNA that is being transcribed is stretched out and naked.
Where do transcription and translation occur in eukaryotes?
Transcription occurs in the nucleus.
Translation occurs in the cytoplasm.
What kind of proteins get transported into the nucleus?
Proteins with Nuclear Localization Sequences (NLSs) are transported into the nucleus.
What does importin do?
It is a protein that transports other proteins into the nuclear pores.
T/F: There is only one type of Nuclear Localization Sequence (NLSs).
False! There is a lot of diversity in NLSs.
What are steroid hormones?
They are produced by glands and secreted into the bloodstream, then taken up by cells.
What do steroid hormones bind?
Steroid receptors, which are transcription factors.
Generally speaking, what happens when a steroid receptor binds a steroid hormone?
This activates gene transcription/expression.
What type of hormone is glucocorticoid?
It is a steroid hormone.
What does glucocorticoid bind?
glucocorticoid binds a glucocortoid receptor.
When HSP90 is bound to the glucocorticoid receptor, is it active or inactive?
It is inactive.
When glucocorticoid binds the glucocorticoid receptor, what happens?
HSP90 is released.
When HSP90 is released, what is now exposed?
This exposes a nuclear localization sequence and a dimerization surface.
After the dimerization surface has been exposed on the glucocorticoid receptor, what occurs?
Two identical glucocorticoid receptors are able to dimerize to each other.
After the homodimer has formed, what occurs?
Importin will then bring it into the nucleus through the nuclear pores.
Generally speaking, what are Glucocorticoid Response Elements (GREs)?
They are enhancers.
Where are GREs located? What is the purpose of this location?
They are located near dozens of different genes.
The purpose of this is so that the hormone can activate many genes.
When the glucocorticoid dimer binds to the GRE, what happens?
Transcription of the target gene is activated.
T/F: Glucocorticoids are limited in what they do.
False! Glucocorticoids do a LOT of things depending on the cell type.
What are examples of what glucocorticoids do?
Fat breakdown, stimulate glucose synthesis, anti-inflammatory response, etc.
What is Chromatin?
This is the complex formed by the chromosomal DNA and the proteins that associate with the DNA across regions/domains of the chromosome.
T/F: Chromatin is only in prokaryotes.
False! Chromatin is only in eukaryotes.
T/F: Transcription factors are considered Chromatin.
False! While many transcription factors bind chromosomal DNA, they are not considered Chromatin, because they occupy sites rather than regions/domains.
How did scientists discover nucleosomes?
Eukaryotic cells were broken open and things that looked like pearl necklaces spilled out. The round things were named ‘nucleosomes’ which translates to nuclear bodies.
How many histone molecules make up a nucleosome?
8 histone molecules make up a nucleosome.
What makes up a nucleosome?
Double-stranded DNA wrapped around the octamer of histone proteins.
How many types of histones are there? How many of each type is present in a nucleosome?
There are 5 types of histones. However, H2A, H2B, H3, and H4 are the core histones. Two of each of these make up the octamer.
Which histone is the linker histone? What does this mean?
H1 is the linker histone, meaning that it binds to linker DNA and also binds to nucleosomes.
T/F: H1 binds to nucleosomes just as tightly as the core histones.
False! H1 binds to nucleosomes, but it does not do so as tightly as the core histones.
What bp of DNA and what degree of turns makes up the octamer?
146 base-pairs of DNA make 1.65 negative superhelical turns around the octamer.
Is the histone octamer positively or negatively charged? Why is this beneficial?
The histone octamer is postively charged, which is good, because the negatively charged DNA will be attracted to it.
What is the benefit of the nucleosomes (beads on a strong)?
The structure of the nucleosomes shortens the DNA length about seven-fold.
What is the size relation between DNA and histones?
In real life, the DNA is larger in relation to the histones.
What causes the nucleosomes/beads on a string appearance?
Low salt concentration (0.001 - 0.05 M NaCl).
When we are at a physiological salt concentration, what happens? What size are the fibers?
A 5th histone, called H1, becomes attached and causes the nucleosomes to be in 30-nm fibers.
T/F: At low salt concentrations, H1 is present.
False! At low salt concentrations, H1 falls off and is not attached.
What diameter is DNA normally at and what does it look like? What about at a low salt concentration?
DNA is naturally at 30 nm in a zig-zag configuration.
At low salt concentration, DNA is at 11 nm.
How are the 30-nm fibers organized?
They are organized into loops.
What two proteins are important in the formation of loops in 30-nm fibers?
CTCF proteins and SMC proteins.
What does the SMC protein do in loop formation?
The loop will form in the chromatin and be passed through the SMC protein.
When does the chromatin stop being pulled through the SMC protein?
Once the CTCFs on each side of the chromatin make contact with each other, stabilizing and forming the loop.
T/F: In metaphase/mitosis, the chromosomal DNA is even more highly compacted.
True!
What salt concentration are we at?
Low
What salt concentration are we at?
Physiological level
What salt concentration are we at?
Low
What salt concentration are we at?
Physiological level
