Chromatin/Histone structure
Practice Problems
Modifying chromatin state
Gal3/Gal4/Gal80 Enzymes
100
What is a nucleosome?
One Nucleosome is approximately 146 base pairs wrapped 1.7 times around a histone octamer (8 histone proteins)
The 8 histone proteins include two of each: H2A, H2B, H3, and H4
100
What is the result of a mutation that leads to deletion of the gal 80 gene?
The gal enzyme genes would be expressed higher than a non mutant
This is because gal80 binds to the activation domain of the gal4, which blocks the ability of the gal 4 to interact with transcription machinery to have transcription occur, however without gal 80, gal4 allows for transcription to go on resulting in higher expression.
100
What is chromatin remodeling?
Changes in histone-DNA interactions, allowing for DNA to become more or less accessible to regulatory proteins such as GTFs or TFs
100
What are Gal Enzyme genes?
Gal enzyme genes are genes that encode enzymes involved in the galactose metabolism pathway. These Gal4/Gal3/Gal 80 are TFs that help with the gene regulation of this process by helping enhance/inhibit transcription
200
when multiple DNA-wrapped nucleosomes coil and condense together, creating a 30-nanometer-thick fiber called ____
Chromatin fiber
200
1. Which of the following best describes the role of a “writer” protein in genetics?
A) It removes genetic marks
B) It binds to specific DNA sequences to enhance transcription
C) It adds chemical modifications to histones or DNA
D) It reads histone modifications and recruits transcriptional machinery
C
200
Describe the four ways chromatin can be remodeled
200
The _____ TF protein is required to activate the GAL enzyme genes.
Gal 4
It binds to an upstream activation sequence (UAS), this is a sequence located upstream of the GAL enzyme genes
300
highly condensed, visible structure of tightly packed chromatin fibers that appears during cell division
Chromosomes
300
You generate a yeast strain with a mutation that inactivates a histone acetyltransferase (HAT) enzyme. This enzyme normally acetylates lysines on histone tails. What effect would this mutation likely have on gene expression, and why?
Gene expression would be lower, because acetylation normally loosens chromatin structure and promotes transcription. Without the HAT, chromatin remains more compact, reducing access to transcription machinery.
300
Histone tails interact with ____ of the DNA helix
sugar-phosphate backbone
300
How does Gal4 protein turn gene expression off or on?
***** Keep in mind this is only to transcribe the genes that code for the enzymes for the metabolism of galactose, every gene differs in it's own way in how their own TFs act, this is just a general example.
Gal4 requires its activation domain to initiate transcription so
Without that activation domain, you cannot express the gene
400
describe the differences between euchromatin vs heterochromatin
Euchromatin is less compacted whereas heterochromatin is more compacted and is usually found in regions consisting of inactive gene.
**Some regions of the genome are always heterochromatic, often near telomeres and centromeres, while some heterochromatic regions can unpack and become euchromatin
400
What would result if a mutation caused gal3 to no longer bind to galactose?
Galactose needs to be bound to gal 3 in order for gal 3 to have a conformation that can bind to gal 80 as well. So not being able to being take off the gal 80 off of gal 4, would cause expression to be off
400
How can we use the histone tail to open up chromatin to enhance transcription?
Acetylation
Addition of acetyl groups to the tail reduce interactions between the tails and the negatively charged backbone of the DNA, also helping loosen interactions among adjacent nucleosome, all helping DNA that is tightly bound to the histone become open and availible for transcription
These acetyl groups also create a binding site for proteins
400
What does Gal80 do?
binds to Gal4 activation domain, prevents other proteins from binding to Gal4 such as transcription machinery to initiate transcription. . So Gal80 acts as a repressor of GAL enzyme gene expression
500
What is the difference between H1 Histone and the Histone Octamer?
Histone Octamer forms the core of the nucleosome which DNA coil around, and it is made of 8 histone proteins: 2 H2A, 2 H2B, 2 H3, 2 H4.
The H1 histone protein is a single distinct protein that is not a part of the core, but rather binds to linker DNA between nucleosomes and helps compact chromatin structure further by locking DNA onto the nucleosome.
500
What results when the H1 histone phosphorylated?
the H1 histone helps keep the DNA bound to the nucleosome, so adding a phosphate group changes the charge of the H1 histone, causing a looser interaction with the DNA, causing DNA to be less wound to the nucleosome and having an open structure now for transcription factors to come to to start transcription
500
Histone tails are made up of amino acids as well, which specific amino acid gets acylated, which ones are they and why?
Lysine
This amino acid is positively charged, which causes less transcription overall, so adding an acetyl group gets rid of that positive charge, changing the chromatin structure
500
What does gal3 in presence of galactose do?
What does gal3 in absence of galactose do?
***The general role of Gal3 is to release gal80 from gal4, allowing transcriptional activation
When galactose is present it binds to gal3, WHICH causes gal3 to have a shape that can bind to gal80, taking gal80 away from gal4, so gal4 can do its job of activating transcription
When galactose is absent, gal 3 has a specific shape that doesn't bind to gal80, causing gal80 to remain stuck to gal4, inhibiting transcription activation of the genes.