1. Chromosome Organization and Molecular Structure

2. Chromosomes are the structures that contain the genetic material
They are complexes of DNA and proteins
The genome comprises all the genetic material that an organism possesses
In bacteria, it is typically a single circular chromosome
In eukaryotes, it refers to one complete set of nuclear chromosomes
Note:
Eukaryotes possess a mitochondrial genome
Plants also have a chloroplast genome
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3. DNA sequences are necessary for
The main function of the genetic material is to store information required to produce an organism
The DNA molecule does that through its base sequence
DNA sequences are necessary for
1. Synthesis of RNA and cellular proteins
2. Replication of chromosomes
3. Proper segregation of chromosomes
4. Compaction of chromosomes
So they can fit within living cells
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4. VIRAL GENOMES
Viruses are small infectious particles containing nucleic acid surrounded by a capsid of proteins
For replication, viruses rely on their host cells
ie., the cells they infect
Most viruses exhibit a limited host range
They typically infect only specific types of cells of one host species
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5. Bacteriophages may also contain a sheath, base plate and tail fibers
General structure of viruses

6. Viruses with a simple structure may self-assemble
During an infection process, mature viral particles need to be assembled
Viruses with a simple structure may self-assemble
Genetic material and capsid proteins spontaneously bind to each other
Example: Tobacco mosaic virus
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7. A typical bacterial chromosome contains a few thousand different genes
Bacterial chromosomal DNA is usually a circular molecule that is a few million nucleotides in length
Escherichia coli  ~ 4.6 million base pairs
Haemophilus influenzae  ~ 1.8 million base pairs
A typical bacterial chromosome contains a few thousand different genes
Structural gene sequences (encoding proteins) account for the majority of bacterial DNA
The nontranscribed DNA between adjacent genes are termed intergenic regions
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8. A few hundred nucleotides in length
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9. The looped structure compacts the chromosome about 10-fold
To fit within the bacterial cell, the chromosomal DNA must be compacted about a 1000-fold
This involves the formation of loop domains
The looped structure compacts the chromosome about 10-fold
The number of loops varies according to the size of the bacterial chromosome and the species
E. coli has with 40,000 to 80,000 bp of DNA in each
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10. DNA supercoiling is a second important way to compact the bacterial chromosome
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11. EUKARYOTIC CHROMOSOMES
Eukaryotic species contain one or more sets of chromosomes
Each set is composed of several different linear chromosomes
The total amount of DNA in eukaryotic species is typically greater than that in bacterial cells
Chromosomes in eukaryotes are located in the nucleus
To fit in there, they must be highly compacted
This is accomplished by the binding of many proteins
The DNA-protein complex is termed chromatin
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12. Has a genome that is more than twice as large as that of
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13. Required for proper segregation during mitosis and meiosis
Eukaryotic chromosomes contain many origins of replication approximately 100,000 bp apart
Required for proper segregation during mitosis and meiosis
Kinetochore proteins link the centromere to the spindle apparatus
Prevent chromosome sticky ends which could lead to translocations and shortening

14. Repetitive Sequences
Sequence complexity refers to the number of times a particular base sequence appears in the genome
There are three main types of repetitive sequences
Unique or non-repetitive
Moderately repetitive
Highly repetitive
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15. Repetitive Sequences Unique or non-repetitive sequences
Found once or a few times in the genome
Includes structural genes as well as intergenic areas
In humans, make up roughly 41% of the genome
Moderately repetitive
Found a few hundred to a few thousand times
Includes
Genes for rRNA and histones
Origins of replication
Sequences that regulate gene expression and translation
Transposable elements
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16. Repetitive Sequences Highly repetitive
Found tens of thousands to millions of times
Each copy is relatively short (a few nucleotides to several hundred in length)
Some sequences are interspersed throughout the genome
Example: Alu family in humans
Represents 10% of human genome
Found every bp
Other sequences are clustered together in tandem arrays
Example: AATAT and AATATAT sequences in Drosophila
These are commonly found in the centromeric regions
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17. Introduction to chromatin structure
Chromatin is a complex made up of DNA and proteins.
The proteins consist of the basic histone proteins and some nonhistone proteins.

18. Histone proteins are basic
They contain many positively-charged amino acids
Lysine and arginine
These bind with the phosphates along the DNA backbone
Histone proteins have a globular domain and a flexible, charged amino terminus or ‘tail’
There are five types of histones
H2A, H2B, H3 and H4 are the core histones
Two of each make up the octamer
H1 is the linker histone
Binds to linker DNA
Also binds to nucleosomes
But not as tightly as are the core histones
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19. Diameter of the nucleosome
Vary in length between 20 to 100 bp, depending on species and cell type
Diameter of the nucleosome
Overall structure of connected nucleosomes resembles “beads on a string”
This structure shortens the DNA length about seven-fold
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20. Play a role in the organization and compaction of the chromosome
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21. Regular, spiral configuration containing six nucleosomes per turn
Irregular configuration where nucleosomes have little face-to-face contact
Regular, spiral configuration containing six nucleosomes per turn
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22. The nuclear matrix is hypothesized to be an intricate fine network of irregular protein fibers plus many other proteins bound to these fibers. This structure is very dynamic and complex.
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23. The third mechanism of DNA compaction involves the formation of radial loop domains
Matrix-attachment regions
Scaffold-attachment regions (SARs) or
25,000 to 200,000 bp
MARs are anchored to the nuclear matrix, thus creating radial loops
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24. Further Compaction of the Chromosome1 1 1 6 4 2 2 5 5 3 3 2 3 6 5 4 6 Z 2 1 4
2mm 3 Z 5 Z
(a) Metaphase chromosomes
(b) Chromosomes in the cell nucleus during interphase
Each of seven types of chicken chromosomes is labeled a
different color. Each occupies a specific territory during
interphase.
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25. There are two types of heterochromatin
Constitutive heterochromatin
Regions that are always heterochromatic
Permanently inactive with regard to transcription
Usually contain highly repetitive sequences
Facultative heterochromatin
Regions that can interconvert between euchromatin and heterochromatin
Example: Barr body formation during development in female
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26. The levels of compaction leading to a metaphase chromosome

27. Compaction level in euchromatin
During interphase most chromosomal regions are euchromatic
Compaction level in heterochromatin

28. Metaphase Chromosomes
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29. The condensation of a metaphase chromosome by condensin
The number of loops has not changed
However, the diameter of each loop is smaller
During interphase, condensin is in the cytoplasm
Condensin binds to chromosomes and compacts the radial loops
Condensin travels into the nucleus
The condensation of a metaphase chromosome by condensin
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30. Cohesins along chromosome arms are released
The alignment of sister chromatids via cohesin
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