Genome Structure II

Chromosomes aligning in the middle of the cell between the two micro-tubule organizing centers

Chromosome segregation starts only after all sister chromatid pairs have achieved _______ _______

Chromosome segregation is triggered by ________ destruction of the ______ molecules, resulting in the loss of sister crhomatid _______. This loss occurs as cells enter _________, during which the sister chromatids separate and move to _________ sides of the cell.

During anphase, after the two sister chromatids are no longer held together, they cannot resist the outward pull of the _______ ________. _______ _______ ensures that the two members of a sister chromatid pair are pulled toward opposite poles and each daughter cell receives one copy of each ______ chromosome

The final step of mitosis is ________, during which the ______ ______ reforms around each set of segregated daughter chromosomes. At this point, cell division can be completed by physically separating the shared _______ of the two presumptive cells in a process called ________

During the mitotic cell cycle, gap 1 occurs before ____ ________, and gap 2 occurs between ___ phase and ___ phase. The gap phases of the cell cycle provide time for the cell to accomplish which two goals:

If there is a problem with a previous step in the cell cycle, _____ ______ ________ stop the cell cycle to providetime for the cell to complete that step.

Meiosis ______ the parental chromosome number. These cells go on to form _____ and _____ cells involved in mating. This is accomplished by following DNA replication with two rounds of ________ ________

Like the mitotic cell cycle, the meiotic cell cycle includes: (3)

Cells that enter meiosis must be _______ and thus contain two copies of each _______ before DNA replication, one from each ______. After DNA rep. these related sister chromatid pairs are called ______. They then pair with each other and ______.

The most significant difference between the mitotic and meiotic cell cycles occurs during ______ _______. Unlike mitosis, during which a single round of ______ ______ follows DNA replication, chromosomes participating in meiosis undergo two rounds of _______ _______ known as?

Like mitosis, each of the segregation events includes a _______,  ________, and ________ stage.

During the metaphase of meiosis I, also called _______, the homolgs attach to opposite poles of the ______ _______. This attachment is mediated by _______

During metaphase I, because both kinetochores of each sister-chromatid pair are attached to the same pole of the microtubule spindle, this interaction is referred to as _______ _______ as opposed to the _______ ______ seen in mitosis

As in mitosis, the paired homologs initially resist the tension of the spindle pulling them apart. In the case of meiosis I, this resistance is mediated through the physcial connections between the homologs, called _______ or ________, that are the result of _________ between homologs.

The chiasma also requires ______-_______ _______ along the arms of the sister chromatids. When cohesion along the arms is eliminated during _________, the recombined homologs are released from each other and segregated to _______ poles of the cell.

The second round of segregation during meisosis, ________, is very similar to mitosis. The major difference is that a round of ____ _______ does not precede this segregation event.

Before meiosis II, a ______ is formed in association with each of the two newly separated sister-chromatid pairs. As in mitosis, during ________, these spindles attach in a _______ manner to the kinetochores of each sister chromatid pair

The second round of chromosome segregation occurs in _______ and is initiated by the elimination of centromeric _______. At this point, there are ____ sets of chromosomes in the cell, each of which contains _____ copy of each chromosome.

At the end of meiosis II, a ______ forms around each set of chromosomes, and then the cytoplasm is divided to form _____ _____ cells. These cells are now ready to mate to form new _____ cells

_______ are the building blocks of chromosome, in fact, the majority of the DNA in eukaryotic cells is packaged into _______.

Each nucleosome is composed of a core of _____ ______ proteins and the ____ wrapped around them. The DNA between each nucleosome (the string in the beads on a string) is called _____ ____

By assembling into nucleosomes, the DNA is compacted approximately _______ which is far short of the 1000-10,000 fold DNA compaction observed in euk. cells. This is just the first step of DNA compaction however, and it is very important.

The DNA most tightly associated with the nucleosome, called _____ _____, is wound about 1.65 times around the outside of the ______ ________ like thread around a spool.

The length of DNA associated with each nucleosome can be determinded using ______ treatment, and _____ DNA (147bp) is longer than _____ DNA (20-60bp)

In any cell, there are stretches of DNA that are not packaged into _______. Typically, these are regions of DNA engaged in what activities?

These sites are typically associated with _______ proteins that are either regulating or participating in these events.

Histones are small ______ charged proteins, and are by far the most abundant proteins associated with _______ _____.

Euk. cells have 5 abundant histones: H1, H2A, H2B, H3, and H4, the last four of which are ______ histones. They are present in _____ amounts in the cell

Two copies of ______ ______ form the protein core around which nucleosomal DNA is wrapped. H1 binds to _______ ______ and is refferred to as a ______ _____

T or F: Linker histones are twice as abundant as other histones
True False

The core histones each have an amino terminal extension, called a ______ because it lacks a defined structure and is accessible within the intact _______

The histone tails are not required for the association of DNA with the histone octamer, because, DNA is still tightly associated with the _______ after protease (_____) treatment.

The histone tails are sites of extensive ____-_________  modifications that alter the function of individual nuleosomes. Name the modifications and the residues they are likely to occur on.

Wrapping of the DNA around the histone protein core stores _______ _______

Each nucleosome added to a covalently closed circular template changes the ______ _____ of the associated DNA by approximately 1.2 because the remainder of the DNA is kept relaxed by _________. The DNA that is packaged into nucleosomes would become ______ ______ if the nucleosomes were removed from the DNA. Thus nucleosomes can be viewed as storing or saving ______ ______

When is useful to use negative superhelicity to drive unwinding of DNA in the cell? Negatively supercoiled DNA favors DNA _______, so removal of a nucleosome not only allows increased ______ to the DNA, but also facilitates DNA _______ of nearby DNA sequences

If nucleosomes store negative superhelicity in Euk cells, what does this in prok. cells?

Gyrase requires _____ to introduce negative supercoils, without it, it can only _____ DNA

Bacteria that don't maintain their DNA in a negatively supercoiled state prefer to grow at ______ _______ and must expend energy to prevent DNA unwinding due to ________. Their topoisomerase is called ______ _______.

Reverse gyrase increases _____ _____ by using ATP, this keeps the genome _______ supercoiled which prevents ________

The two types of chromatin are heterochromatin and euchromatin. Heterochromatin is characterized by ______ _______ with a variety of dyes and a more _______ appearance. Euchromatin had the _______ characteristics, staining poorly and having a more open structure

Heterochromatic regions of chromosomes have ______ _______ _______, while euchromatic regions showed ______ _____ ______. Heterochromatic regions are composed ______ DNA assembled into higher order structures that result in a barrier to ______ _____. Euchromatic ______ are found in much less organized assemblies

Binding of H1 to linker DNA stabilizes ______ _______ chromatin structures in heterchromatic regions. In the test tube, as salt concentration are _______, the addition of histone H1 results in the nucleosomal DNA forming a ______ _____.

In the 30nm fiber, DNA becomes less accessible to many _____ ______ ______. State an example

There are two models of the 30nm fiber, the _______ model and the ______ model.

In the solenoid model, the nucleosomal DNA forms a _______ containing approximately ___ nucleosomes per turn. In this model, the flat surfaces on either face of the histone octameter disc are _______ to each other, and the DNA surface of the nucleosomes forms the ______ surface of the superhelix.

In the solenoid model, the linker DNA (within the ________) circles around the central axis as DNA moves from one _______ to the next

The zigzag model of the 30nm fiber is formed when H1 is added. Here, the 30nm fiber is a ______ form of the zigzag nucleosome arrays. Unlike the solenoid model, the zigzag conformation requires the _____ ___ to pass through the _____ axis. As a result, _____ linker DNA is favored in this form.

Core histones lacking their _____-______ _____ are incapable of forming 30nm fibers. The most likely role of the tail is to ______ the 30nm fiber by interacting with _______ _______.

Further compactin of DNA involves _____ ____ of nucleosomal DNA. Together, the packaging of DNA into nucleosomes and the ____ _____ results in the compaction of the linear length of DNA by ~____ fold (still not enough to fit 1-2meters of DNA into a nucleus ~10^-5m across)

Additional folding of the 30nm fiber is required to _____ the DNA further. Although the exact nature of this folded structure remains unclear, on popular model proposes the ______ ______ forms loops of 40-90kb that are held together at their _____ by a proteinaceous structure called the _____ ______.

Two classes of proteins that contribute to the nuclear scaffold are ________ & the _____ proteins

When histones are isolated from cells, a subset of their _____ ____ _____ is typically modified with a variety of small molecules. Lysines in tails are frequently modified with a single _____ or _____ group, and arginines are modified with ___ to ____ _____groups

Serines and threonines (and one tyrosine) are subject to modification with ________. Although less common, other modification with larger moieties including ____-______ and the small protein _____ and _____ are also found attached to the histones.

_______ & ________ each acts to reduce the overall positive charge of the histone tails

Acetylation of lysine _______ its positive charge, in turn ______ the affinity of the tails for the ________ charged backbone of the DNA.

Modification of the histone tails affects the ability of nucleosome arrays to form more repressive _____ ______ structures.