Molecular Text 4.3

·         The proteins that bind to the DNA to form eukaryotic chromosomes are traditionally divided into two general classes: the __ and the __. The complex of both classes of proteins with the nuclear DNA of eukaryotic cells is __
o   The total mass of histones in chromatin is about equal to that of __

·        Histones are responsible for the __
o   When __ are broken open very gently and their contents examined under the EM, most __is in the form of a fiber with a diameter of about 30 nm
§  If partially unfolded, it looks like __, with the string being __and the beads being a __ that consists of DNA wound around a protein core formed from histones

·         Structural organization of __ was determined after first __ from __ by __ with particular enzymes (called __) that break down __ by __.
o   After digestion for a short period, the exposed DNA between the nucleosome core particles, the __, is degraded.

§  Each individual __ particle consists of a complex of __—two molecules each of histone, __(4)__—and __ that is 147 nucleotide pairs long.
·         The histone octamer forms a __ around which the double-stranded DNA is wound

·         Each nucleosome core particle is separated from the next by a region of __, which can vary in length from a few nucleotide pairs up to about 80
o   Nucleosome technically refers to a __, but it is often used synonymously with __

·         Nucleosome repeat at interval of about __
o   The formation of nucleosome converts a DNA molecule into a __ 

·         A nucleosome has a __ around which DNA is tightly wrapped in a __
o   All four of the histones that make up the core of the __are relatively small proteins (102-135 amino acids), and they have a __, known as the __, formed from __ connected by __

§  In assembling a nucleosome, what happens?

·         The interface between __ and __ is extensive: __ are formed between __ and the __ in the __
o   Nearly half of these bonds form between the __ and the __
Numerous __ and __ also hold DNA and protein together in the __. These numerous interactions explain in part why DNA of virtually any sequence can be what?. 

·         The path of the DNA around the histone core is __; rather, __ are seen in the DNA; and the bending requires a __
o   Certain __in the __ are especially easy to compress, and some nucleotide sequences bind the __more tightly than others
§  For most of the DNA sequence found in chromosomes, the sequence preference of nucleosome must be __ to allow __, inasmuch as nucleosomes can occupy any one of a number of positions relative to the DNA sequence in most chromosomal regions

·         In addition to its histone fold, each of the core histones has an __, which extends out from the __.
o   These histone tails are subject to __ that in turn control critical aspects of __ and __ 

·         The __are among the most highly conserved eukaryotic proteins, suggesting that the functions of __involve nearly all of their amino acids, so that a change in any position is deleterious to the cell
o   Most changes in __ are lethal; the few that aren’t lethal cause changes in the normal pattern of __

·         Despite the high conservation of the core histone, eukaryotic organisms also produce smaller amounts of __that differ in amino acid sequence from the main one. These variants, combined with a surprisingly large variety of __ that can be added to the __ in __, make possible the many different __ that are required for DNA function in higher eucaryotes. 

·         It was believed that nucleosomes do what because of the __. This would be bad since what?

o   In actuality, DNA __from each end at rate of about 4 times per second, remaining exposed for 10 to 50 milliseconds before the__ __.
§  Thus, most of the DNA in an isolated nucleosome is in principle __ 

·         For the chromatin in a cell, a further __ is clearly required, because eukaryotic cells contain a large variety of__
o   The subunits in these complexes that __ is evolutionarily related to the __, and it binds both to the __ and to the __

§  By using the __ to move this DNA relative to the __, this subunit changes the structure of a __temporarily, making the DNA __. 
·         Through repeated cycles of ATP hydrolysis, the __ can catalyze __, and by pulling the __ along the DNA double helix in this way, they make the nucleosomal DNA available to other proteins in the cell 

o   In addition, by cooperating with __that serve as __, some remodeling complexes are able to do what—catalyzing either an __, or the complete __

·      Cells contain dozens of different __ that are specialized for different role. Most are large protein complexes that can contain 10 or more subunits.
o   The activity of these complexes is controlled by __
§  As gene are turned on and off, __ are brought to __ where they act __to __

·         A __can occupy any one of a number of positions relative
o   The most important influence on nucleosome positioning appears to be the __. Some bound proteins favor the formation of a __adjacent to them

§  Others create obstacles that force the nucleosome to __
·         The exact position of nucleosome along a stretch of DNA depends mainly on the __
o   Due to the presence of __, the arrangement of nucleosome on DNA can be highly __, changing rapidly according to the needs of the cell