Genomes and Chromosomes: Part One
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What is a gene?
a segment of DNA containing a unit of biological information
a unit of inheritanace
What is a genome?
the entire genetic complement of an organism, made up of one or more lengthy DNA molecules, and comprising all that organism's genes and all of the intergenic DNA between those genes
all of the units of inheritance added together
I. Eukaryotic genomes are contained in __
Vary in size: __
Size coincides with __
Most of the genome is in the __, except the few DNA pieces in __ or __
- 10 b-50 Mb
- complexity of the organism
- mitochondria or chloroplasts
All eukaryotic nuclear genomes are made up of __, each contained in a different chromosome. The number of chromosomes varies between species and appears to be unrelated to the __
- linear DNA molecules
- biological features of the organism
The human nuclear genome: 3200 Mb of DNA divided into the __molecules, the shortest 48 Mb in length and the longest 250 Mb
Of the __, __are __ and __ are __. The majority of human cells are __ and have __, plus __ --> 46 in all.
These are called __, in contrast to __, which are __and have just __, comprising one of each __ and __
sex chromosomes, X and Y
two copies of each autosome
two sex chromosomes, XX (females) and XY (males)
sex cells, or gametes
autosome and one sex chromosome
II. Chromosomes contain __ and __
DNA and proteins
Chromosomes are most evident in cell division as __,which are ___.
What is the challenge with this? However, there is a __ that allows the__
- metaphase chromosomes
- much shorter than the DNA molecule
- fitting the DNA in is a challenge
- highly organized packaging system
- fit of lengthy DNA molecules into such small structures
Chromatin is __. It is __
a complex association between the DNA of the chromosomes and the proteins to which it binds, the latter including those responsible for packaging the DNA in a regular fashion within the chromosome
half protein and half DNA
Explain the protein portion of chromatin.
a portion is made up of a heterogeneous mixture of molecules involved in DNA replication and gene expression, including DNA and RNA polymerases and regulatory proteins. The remainder, associated most intimately with the DNA component of the chromosomes, consists of a group of proteins called histones
Histones contain a __and are remarkably similar in all species
The conservation indicates what?
This suggests that histones play a __
high proportion of basic amino acids
that histones were among the first proteins to evolve and that their structures have not changed for hundreds of millions of years
fundamental role within chromosomes
Histones are constituents of the __.
How were histones discovered?
biochemical work including nuclease protection experiments
In this procedure, a DNA-protein complex is treated with an endonuclease, an enzyme that cuts polynucleotides at internal phosphodiester bonds. The endonuclease has to gain access to the DNA in order to cut it, and hence can attack only the phosphodiester bonds that are not masked (“protected”) by attachment to a protein
These experiments were carried out on __that had been gently extracted from nuclei by methods designed to retain as much of the chromosome structure as possible.
The sizes of the resulting fragments were __ but rather had __ The conclusion was that what?
- not random
- lengths of approximately 200 bp and multiples.
- the protein in chromatin is associated with the DNA in a regular fashion, with individual proteins or protein complexes spread out at intervals 200 bp apart.
The biochemical results were complemented by electron microscopic observations of chromatin. The images showed __.These are believed to be __
- linear arrays of spherical structures referred to as beads on a string.
- the direct visualization of the protein complexes attached to a DNA molecule.
The spherical particles are __and contain equal amounts of each __except __.
What is the structure of the nucleosomes?
The histones form a barrel-shaped core octamer consisting of two molecules each of H2A, H2B, H3, and H4, with the DNA molecule wound twice around each nucleosome
In humans, exactly __ of DNA is associated with the __and hence protected from __. The only parts of the DNA molecule available to the endonuclease are the __
- 146 bp
- endonuclease digestion
- 50 to 70 bp stretches of linker DNA that join the individual nucleosomes to one another.
A single cleavage in each linker region therefore gives rise to __
fragments of DNA that are approximately 200 bp in length
The one histone not found in the core octamer of the nucleosome is __, which is ___.
not a single protein but a group of proteins, all closely related to one another and collectively called the linker histones.
In vertebrates, these include __. A single __ is attached to each __, to form the __, , but the precise positioning of this linker histone is not known
The most popular model places the linker histone where and for what reason?
histones H1a-e, H10, H1t, and H5.
on the outer surface of the nucleosome, possibly keeping the DNA in place
Nucleosomes associate to form the __
30 nm chromatin fiber
Despite the histone packing, there must be other higher levels of chromatin structure. The next level was discovered by electron microsocopic studies, which revealed a __, less dispersed than the beads-on-a-string form, about 30 nm in diameter. This fiber is formed by __
packing together individual nucleosomes.
Exactly how the nucleosomes are arranged is not understood, but the original “__” model is still favored. The __ reduces the length of the beads-on-a-string structure by about 7 times, so our original 6-cm piece of DNA is now about 1.4 mm in length
- 30-nm chromatin fiber
Between cell divisions, the __ is probably the most organized form of chromatin for those parts of a chromosome that __. The DNA in these regions cannot be too condensed. Why? __We refer to this as __.
- 30-nm fiber
- contain genes that are being expressed
- it must remain accessible to the proteins involved in the transcription process.
With the EM, we can see __ within the __, each loop between 40 and 100 kb in length and predominantly in the form of the 30-nm chromatin fiber. The loops are attached to the __, the complex network of protein and RNA fibrils that permeate the entire nucleus. The attachments to the matrix are made by __ or __
- loops of DNA
- euchromatin regions
- nuclear matrix
- AT-rich segments of DNA called matrix-associated regions (MARs) or scaffold attachment regions (SARs).
How DNA is packaged into more compact chromosome structures is poorly understood
__, __, and __ can be looked on as the first three levels of DNA packaging. Moving up the hierarchy, we eventually reach the __, the most compact form of chromatin in eukaryotes.
Nucleosomes, the 30-nm fiber, and euchromatin
It is thought that metaphase chromosomes are __, one possibility being that __
more condensed versions of the structure postulated for euchromatin
histones in different loops of the 30-nm fiber interact with one another to draw the euchromatin structure into more compact conformations
Why is it so hard to understand the higher levels of chromatin structure?
Chromosomes are visible only in dividing cells, when they are compact and distinguishable When non-dividing nuclei are examined, there are only light (euchromatin), and dark staining areas (heterochromatin)
Two types of heterochromatin are recognized
constitutive and facultative
a permanent feature of all cells and represents DNA that contains no genes and so can always be retained in a compact organization
Facultative heterochromatin: not a permanent feature but is seen in some cells some of the time; it is thought to contain genes that are inactive in some cells or at some periods of the cell’s life cycle; when these genes are inactive, their DNA regions are compacted into heterochromatin
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