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Where is DNA found?

The nucleus of eukaryotic cells


The levels of ___ organization vary throughout the cell cycle.



Describe the organization of chromosomes during interphase.

During interphase, chromosomes are found in the nucleus, surrounded by a nuclear membrane, and they are somewhat less organized. In other words, the chromatin is in a relatively extended form.


Describe the organization of chromosomes during mitosis.

During mitosis, chromosomes are beginning to condense.


Chromosomes are most condensed during what phase of mitosis?



During interphase, ___ and ___ occur.

DNA replication and gene expression


Three types of DNA sequences are required to produce a eukaryotic chromosome that can be replicated and then segregated in mitosis. What are they?

1. Centromere: used to help pull the daughter chromatids to different daughter cells
2. Origins of replication: start of replication in the S phase
3. Telomere: found at the ends of linear chromosomes, protect DNA from being recognized as broken.


Do bacterial cells have telomeres? If not, why not?

No - they are circular.


Describe the chromosome at metaphase.

The sister chromatids are attached and each contains one of two identical sister DNA molecules generated by DNA replication. It is in its most highly condensed form.


Both centromeres and telomeres are packaged into ___, a very highly compacted form of DNA. Other regions can be in ___ or ___.

Heterochromatin; heterochromatin; euchromatin


Visualizing chromosomes helps achieve two primary goals. What are they?

1. Determine chromosomal abnormalities associated with particular diseases.
2. Determine chromosomal biology - for example, determine that chromosomes localize to subnuclear domains, even in interphase cells.


Giemsa-stained early mitotic chromosomes exhibit what phenomenon?

Characteristic banding pattern that helps distinguish the various chromosomes.


What is a karyotype?

The arrangement of the full chromosome set in numerical order


More recently, each chromosome can be visualized as a different color in ___.

Chromosome painting (spectral karyotyping)


In interphase cells, each of the chromosomes is localized to a different ___.

Subnuclear region


What is chromatin?

DNA bound to histone proteins and DNA bound to non-histone proteins.


In total, a chromosome is about ___% DNA and ___% protein by mass.

33; 66


Compare the arrangement of genes in the genome of humans and the genome of yeast S. cerevisiae.

Yeast DNA is primarily made up of genes that code for proteins; there are a few repetitive sequences. Human DNA has a more repeat sequences that do not code for proteins than genes that do code for protein.


One gene may be composed of ___, ___, and ___.

Exons (code for proteins), Introns (do not code for proteins, are spliced out), Regulatory sequences (promoter elements)


A small amount of human DNA actually codes for proteins or functional RNA. Over ___ consist of repetitive sequences. The remainder are introns or regulatory sequences.



About half of human DNA involve ___ sequences. The other half involve ___ sequences.

Repeated; unique


The unique sequences of the human genome include ___ (introns, protein-coding regions) and non-repetitive DNA that is neither in introns nor codons.



The repeated sequences of the human genome include simple sequence repeats, segmental duplications, and ___. Describe these.

Transposons; remnants of jumping genes, which can move from one location to another within a chromosome via different mechanisms.


____ proteins have a fundamental role in packaging DNA into highly condensed chromosomes.



DNA is more active in its ___ form.



Describe the levels of condensation from naked DNA to the mitotic chromosome.

First level: Beads-on-a-string chromatin (DNA wrapped around core histone proteins)
Second level: Compacted beads-on-a-string into a 30 nm fiber
Third level: 30 nm fibers are looped with proteins attached to the base
Fourth level: Further condensed
Fifth level: Entire mitotic chormosome


Each DNA molecule has been packaged into a mitotic chromosome that is ___-fold shorter than its extended length.



What is a nucleosome?

DNA wrapped around a core of histone proteins.


Nucleosomes are on average ___ nucleotide pairs apart.



What connects the "beads" together?

Linker DNA


If you utilize a nuclease at a low concentration, it will digest the linker DNA, and the nucleosome dissociates into...

...the octameric histone core of proteins and ~147-nucleotide-pair DNA double helix.


Dissociating the octameric histone core gives...

...2 of each of 4 proteins: H2A, H2B, H3, and H4


Each of the four core histone proteins have 3 ___, as well as additional amino acids forming ___.

Alpha helices; N- and C-termini tails


Describe the folding of histone proteins.

1 H2A and 1 H2B interact to form a heterodimer. This occurs twice. H3 and H4 form a heterodimer. 2 H3-H4 heterodimers form a tetramer. The H3-H4 tetramer and 2 H2A-H2B heterodimers come together to form the octameric protein. The tetramer is in the middle, sandwiched between the H2A-H2B heterodimers.


Where are the amino termini of the core particles found and what is their role?

Outside of the structure; allow for epigenetic modifications


Nucleosomes are dynamic; what allows for changes?

ATP-dependent chromatin remodeling complexes.


ATP-dependent chromatin remodeling complexes function in different ways. Describe TWO.

1. Cause nucleosome sliding (nucleosome is moved relative to the DNA, making various regions more or less accessible)
2. Exchange of histone proteins (H2A-H2B can be removed and exchanged by chaperones)
3. Removal of histone proteins (entire octamer can be removed)


How are nucleosomes packed together into the 30 nm fiber?

1. Interactions between the tails of the histone protein in one nucleosome core particle with the adjacent nucleosome core particle
2. Histone H1 (linker histone) binds where the DNA enter and exit the nucleosome core particle, bringing the DNA closer together and helping compact the fiber.


Describe the fractal globule model for interphase chromatin.

This model involves a knot-free conformation that permits dense packing and retains the ability to easily fold and unfold any genomic locus. Each 30 nm fiber folds about 5 megabases of DNA into a subregion of space. This allows for accessibility and avoids tangling.


Where are highly active genes in euchromatin located in the nucleus?

Interior of the nucleus


Where are genes in silenced heterochromatin localized?

Periphery of the nucleus


What is the basic structural unit of the chromosome?



Describe the difference between genetic and epigenetic inheritance.

If a gene is turned off in genetic inheritance, it will be inherited as such. If a gene is turned off in epigenetic inheritance, it can be turned back on in the production of germ cells.


Why is heterochromatin resistant to gene expression?

It contains such highly compacted chromatin.


Genes relocated to ___ are silenced.



Describe the epigenetic discovery made in fruit flies.

In fruit flies, the expression of the White gene gives the fly its red eye color. If this gene is turned off, the eye is white. There is normally a barrier separating the White gene from heterochromatin. If an inversion occurs, the White gene is located near heterochromatin without a barrier.


Describe three models for barrier proteins.

1. Physical barrier
2. Shield - binds to DNA, protects adjacent nucleosomes from the heterochromatin
3. Enzymatic activity


Post-translational covalent modifications or combinations of modifications of amino acids in ___ affect chromosome structure in different ways.

Histone protein tails


What are some examples of post-translational modifications of amino acids in histone protein tails?

1. Methylation of lysine
2. Phosphorylation of serine
3. Acetylation of lysine
4. Ubiquitylation


What happens to lysine if it is acetylated? What happens to lysine if it is methylated?

It loses its charge; the 3D structure changes (no change in charge, can be mono-, di-, or tri-methylated).


What happens to serine if it is phosphorylated?

It becomes negatively charged.


How is epigenetic information translated into meaning?

1. Histone protein tails are post-translationally modified
2. Reader proteins translate this information into meaning


What does H3 K9 methylation lead to?

Heterochromatin formation, gene silencing


What does H3 K4 and H3 K9 methylation lead to?

Gene expression


Covalent modifications of histone tails attract ___ complexes.



Describe the reader and writer complexes.

A reader complex involves multiple protein modules attached to a scaffold protein. These modules bind to specific histone modifications on the nucleosome. The reader complex binds and attracts other components that have catalytic activities and additional binding sites.


Describe the process of recruitment of reader-writer complexes and how it can spread chromatin changes along a chromosome.

1. A regulatory protein binds a writer protein.
2. This modifies a histone protein.
3. This binds a reader protein.
4. The process repeats until a barrier is reached.


___ variants also affect chromosome structure.



Are epigenetic modifications maintained after DNA replication?

Yes, more often than not


Describe the clinical use of Vorinostat, a histone deactylase inhibitor.

Lysine and DNA interact well due to the respective positive and negative charges. If lysine is acetyled, it loses its charge, weaking its association with DNA. Vorinsotat is a histone deactylase inhibitor, which means it inhibits decatylation, increasing histone acetylation.