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 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

3. 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 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

4. 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 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display VIRAL GENOMES

5. General structure of viruses Bacteriophages may also contain a sheath, base plate and tail fibers

6. During an infection process, mature viral particles need to be assembled Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Viruses with a simple structure may self-assemble Genetic material and capsid proteins spontaneously bind to each other Example: Tobacco mosaic virus

7. 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 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

8. A few hundred nucleotides in length These play roles in DNA folding, DNA replication, gene regulation, and genetic recombination

9. To fit within the bacterial cell, the chromosomal DNA must be compacted about a 1000-fold –This involves the formation of loop domains Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display The number of loops varies according to the size of the bacterial chromosome and the species E. coli has 50-100 with 40,000 to 80,000 bp of DNA in each The looped structure compacts the chromosome about 10-fold

10. DNA supercoiling is a second important way to compact the bacterial chromosome Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

11. 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 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display EUKARYOTIC CHROMOSOMES

12. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Has a genome that is more than twice as large as that of

13. Prevent chromosome sticky ends which could lead to translocations and shortening Required for proper segregation during mitosis and meiosis Eukaryotic chromosomes contain many origins of replication approximately 100,000 bp apart Kinetochore proteins link the centromere to the spindle apparatus

14. 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 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Repetitive Sequences

15. 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 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Repetitive Sequences

16. 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 5-6000 bp –Other sequences are clustered together in tandem arrays Example: AATAT and AATATAT sequences in Drosophila These are commonly found in the centromeric regions Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Repetitive Sequences

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. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 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

19. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Overall structure of connected nucleosomes resembles “beads on a string” This structure shortens the DNA length about seven-fold Vary in length between 20 to 100 bp, depending on species and cell type Diameter of the nucleosome

20. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Play a role in the organization and compaction of the chromosome

21. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Regular, spiral configuration containing six nucleosomes per turn Irregular configuration where nucleosomes have little face-to-face contact

22. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 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.

23. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display The third mechanism of DNA compaction involves the formation of radial loop domains Matrix-attachment regions Scaffold-attachment regions (SARs) or MARs are anchored to the nuclear matrix, thus creating radial loops 25,000 to 200,000 bp

24. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Further Compaction of the Chromosome Each of seven types of chicken chromosomes is labeled a different color. Each occupies a specific territory during interphase. (b) Chromosomes in the cell nucleus during interphase (a) Metaphase chromosomes Z 1 1 2 2 3 3 4 4 5 5 6 6 Z 5 1 6 4 2 3 1 5 Z 3 2 2mm2mm

25. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 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

26. The levels of compaction leading to a metaphase chromosome

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

28. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Metaphase Chromosomes

29. The condensation of a metaphase chromosome by condensin Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display The number of loops has not changed However, the diameter of each loop is smaller Condensin travels into the nucleus Condensin binds to chromosomes and compacts the radial loops During interphase, condensin is in the cytoplasm

30. The alignment of sister chromatids via cohesin Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Cohesins along chromosome arms are released