1. Chromosomes, Chromatin, and the Nucleosome
Chromosomes: DNA associated with proteins
The chromosome is a compact form of the DNA that readily fits inside
the cell.
Packaging the DNA into chromosomes serves to protect the DNA from
damage.
Only DNA packaged into a chromosome can be transmitted efficient to
daughter cells.

2. Table I: variation in chromosome makeup in different organisms
The traditional view is that prokaryotic cells have a single, circular chromosome,
and eukaryotic cells have multiple, linear chromosomes.

4. Table 2. Comparison of the gene density in different organisms’ genomes

5. Comparison of the chromosomal gene density for different organisms
65kb region

6. The organization and content of the human genome

7. Pseudogenes arise from the action of an enzyme called reverse transcriptase

8. The majority of human intergenic sequences are
Composed of repetitive DNA
(dinucleotide repeats)
( greater 100bp, mostly transposable
element)

9. Contribution of introns and repeated sequences to
Table 7-3
Contribution of introns and repeated sequences to
different genomes
introns (p. 135)

10. Chromosome duplication and segregation
Eukaryotic chromosomes require Centromeres, Telomeres, and Original of Replication to be maintained during cell division

11. More or less than one centromere leads to chromosome loss or breakage

12. Centromere size and composition varies dramatically

13. Telomeres
1. Telomeres are bound by a number of proteins. These proteins distinguish the natural ends of the chromosome form sites of chromosome breakage and other DNA breaks in the cell.
DNA ends are the sites of frequent recombination and DNA degradation. The
Proteins at telomeres form a structure that is resistant to both events.
2. Telomeres act as a specialized origin of replication that allows the cell to replicate the ends of the chromosomes.

14. The eukaryotic mitotic cell cycle

15. Each chromosome of the duplicated pair is called a chromatid, the two chromatids of a given pair are called sister chromatids.

16. The events of mitosis

17. Changes in chromatin structure-DNA condensation and
decondensation
Chromosomes are maximally condensed in M phase

18. Sister Chromatid cohension and Chromosome condensation are mediated by SMC ((structural maintenance of
chromosome) proteins

19. Models for the structure of cohesins and condensins
The structural of cohesin is a large ring composed of two SMC proteins and a third non-SMC protein. SMC (structural maintenance of
chromosome) proteins

20. Mitosis maintains the parental chromosome Number

21. Meiosis reduces the parental chromosome number
cohesion is lost
Formation of chiasma
Homologous recombination

22. Formation of chromatin structure

23. nucleosome- building blocks of chromosomes
Histones are small, positively-charged proteins
H2A: red
H2B: yellow
H3: purple
H4: green

25. The assembly of a nucleosome

26. The N-terminal tails are
accessible to protease trypsin (specifically cleaves protein positively-charged amino acids)

27. The nucleosome has an approximate twofold axis of symmetry

28. Interactions of the histones with nucleosomal DNA
H2A.H2B dimer
H3.H4 tertramer
Each associate with about 30 bp of DNA on either side of the central 60 bp
central 60bp region and two ends

29. Histones contact the minor groove of the DNA by forming
a large number of hydrogen bonds
The large number of the hydrogen bonds provide the driving force to bend the DNA

30. Higher-order chromatin structure
H binds to linker DNA at one end of
The nucleosome and the central DNA helix

31. The addition of H1 leads to more compact nucleosomal DNA
Without H1

32. Histone H1 induces tighter DNA wrapping around the nucleosome

33. 30-nm fiber
Superhelix, 6 nucleosome per turn, supported by EM and X-ray studies
Based on zigzag pattern upon H1 addition, requires linker DNA to pass through
central axis,

34. The core Histone N-terminal tails are required for the
formation of the 30-nm fiber
The tail of H2A, H3 and H4 interact with adjacent nucleosome

35. Higher compaction of DNA involves large loops of
nucleosomal DNA
Nuclear scaffold (Topo II, SMC)

36. Histone variants alter nucleosome function
1. H2A.z histone inhibits nucleosome from forming repressive chromatin structures, creating regions of easily accessible chromatin that are more compatible with transcription
2. CENP-A replace H3, is associated with nucleosomes that include centromeric DNA

37. Regulation of chromatin structure
The interaction of DNA with histone octamer is dynamic
Unwrapping of the DNA from nucleosome is responsible for the accessibility of the DNA

38. Nucleosome movement by nucleosome remodeling complexes
restructure

39. ATP-dependent chromatin remodeling complex
SWI/SNF subunits Bromodomain
ISWI subunits No
Mi2/NuRD subunits chromodomain

40. Nucleosome Positioning by DNA-binding proteins
exclusion

41. Nucleosome Positioning by DNA-binding proteins
Inducing assembly

42. Modifications of the histone N-terminal tails alters
the function of chromatin
Acetylation: transcription activation

43. Effects of histone tail modification

44. Nucleosome modifying enzymes

45. Chromatin remodeling complex and histone modifying enzymes
work together to alter chromatin structure

46. Nucleosome Assembly The inheritance of histones after DNA replication
The old histones are present on both of the daughter chromosome
H3.H4 tetramers remain bound to one of the two daughter duplexe at random but H2A.H2B dimers are released and enter the local pool for new nucleosome assembly.

47. Inheritance of parental H3.H4 tetramers
facilitate the inheritance of chromatin
state

48. Nucleosome Assembly
The assembly of nucleosomes is not a spontaneous process,
it requires high salt condition in-vitro.
Proteins required to direct the assembly of histones to
DNA are histone chaperones.
Name histones bound
CAF H3. H4
RCAF H3. H4
NAP H2A.H2B
(negatively-charged protein)

49. How histones chaperones facilitate the assembly of nucleosome
during DNA replication
(sliding clamp)