1. DNA and Chromosomes

2. Genes are carried by Chromosomes
Two plant cells visualized by light microscope, DNA stained with DAPI
Chromosome in Cells
DNA (deoxyribonucleic acid)
AGTC
Human 46 chromosomes
22 homologs, x, or x/y

3. Experimental procedures demonstrating that DNA is the genetic material

4. The Structure and Function of DNA
Genetic information is carried in the linear sequence of nucleotides in DNA
Genetic information contains instructions to synthesize proteins
DNA forms double helix with two complimentary strands holding together by hydrogen bonds between A-T (2 bonds) and G-C (3 bonds)
DNA duplication occurs using one strand of parental DNA as template to form complimentary pairs with a new DNA strand.
DNA is in nucleus in eucaryotes

5. 1953 Watson and Crick determined the structure of DNA
DNA and its Building
Nucleotides: Guanine (G), Adenine (A), Cytosine (C), Thymine (T).
Polarized strand, 5’->3’
Base inside, sugar outside

6. DNA and its Building
Antiparallel strands

7. A always pairs with T, and G with C,
DNA Pairs
A always pairs with T, and G with C,
A-T two hydrogen bonds, G-C three hydrogen bonds

8. 10.4 nucleutides/turn; 3.4 nm between nucleutides
DNA Double Helix
10.4 nucleutides/turn; 3.4 nm between nucleutides

9. Genome: the complete set of information in an organism’s DNA
DNA to Protein
Genome: the complete set of information in an organism’s DNA
Total length of DNA about 2 meters long in a human cell, encoding about proteins

10. To carry the genomic information to daughter cells DNA Duplication
Using itself as template

11. Cell Nucleus, compartmentalized DNA activity
Nuclear pores allow communication
Nuclear lamina and cytoskeleton mechanically support the nucleus

12. Chromosomal DNA and its Packaging
A gene is a nucleotide sequene in a DNA molecule that act as a functional unit for protein production, RNA synthesis.
Introns and Exons
Chromosome: single long DNA contains a linear array of many genes.
Human genome contains 2.3x109 DNA nucleotide pairs, with 22 different autosomes and 2 sex chromosomes.
Chromosomal DNA: replication origins, telomeres, centromeres
Histones form the protein core for DNA wrapping
Nucleosome: repeating array of DNA-protein particles
Modification of Chromatin and nucleosomes: histone H1, ATP-driven chromatin remodeling complexes, and enzymatically catalyzed covalent modification of the N-terminal tails of Histones

13. Complex of DNA and protein is called chromatin
Human Chromosome
Complex of DNA and protein is called chromatin
44 homologous chromosomes and 2 sex chromosomes
Complementary DNA with different Dyes
The arrangement of the full chromosome set is called karyotype

14. Banding Pattern of human chromosomes Giemsa Staining
Green line regions: centromeres
Encoding ribosome

15. The organization of genes of a human chromosome

17. Conservation between human and mouse genomes
Usually important genes are encoded by conserved regions
Note: Human chromosome 1 and mouse chromosome 4
mouse
human
centromere

18. Chromosomes exist through the cycle Mitotic and interphase chromosome
Cell Cycle
DNA molecule not only carries genetic information, but also undergoes conformational change
Chromosomes exist through the cycle
Mitotic and interphase chromosome
Single chromosome can only be visible during mitosis

19. Chromosomes at interphase and M phase

20. Three important DNA sequences Telomere, replication origin, centromere

21. DNA Molecules are highly condensed in chromosomes
Nucleosomes of interphase under electron microscope
Nucleosome: basic level of chromosome/chromatin organization
Chromatin: protein-DNA complex
Histone: DNA binding protein
A: diameter 30 nm; B: further unfolding, beads on a string conformation

22. Nucleosome Structures
Histone octamer
2 H2A
2 H2B
2 H3
2 H4

23. X-ray diffraction analyses of crystals
Structure of a nucleosome core particle

24. Structural Organization of the Core Histones

25. The Assembly of the Core Histones

26. Notice the long tails of the octamer

27. The bending of DNA in a nucleosome
1. Flexibility of DNAs: A-T riched minor groove inside and G-C riched groove outside
2. DNA bound protein can also help

28. Zigzag model of the 30-nm chromatin fiber

29. Irregularities in the 30-nm fiber
Flexible linker, DNA binding proteins
Structural modulators: H1 histone, ATP-driven Chromatin remodeling machine, covalent modification of histone tails

30. The function of Histone H1

31. The function of Histone tails

32. Chromatin Remodeling

33. Cyclic Diagram for nucleosome formation and disruption

34. Covalent Modification of core histone tails Acetylation of lysines
Mythylation of lysines
Phosphorylation of serines
Histone acetyl transferase (HAT)
Histone deacetylase (HDAC)

36. Summary DNA, Chromosome Centromere, telomere, replication origin
Nucleosome, Chromatin,
Histone: H1, H2A, H2B, H3, H4
Histone octamer, DNA packaging
DNA binding proteins, Histone modifications

37. The Global Structure of Chromosomes
Some rare cases of interphase chromosomes, certain features maybe universal
Representative forms forming typical interphase chromosome
Chromosome at mitosis

38. Lampbrush chromosomes (amphibian oocyte, immature eggs)

39. A model for the structure of a lampbrush chromosome
Chromomeres: highly condensed and in general not expressed until unfolding

40. A polytene chromosome from Drosophila salivary gland
Dark bands and interbands

41. Electron Microscope image of Drosophila polytene chromosome

42. Folding and refolding at a time course of 22 hours
Chromosome puffs
Folding and refolding at a time course of 22 hours

43. RNA synthesis in Chromosome puffs
Red: newly synthesized BrUTP; Blue: old ones diffused

44. RNA synthesis in Chromosome puffs

45. RNA synthesis in Chromosome puffs

46. Model of RNA synthesis in Chromosome puffs

47. A model for the structure of an interphase chromosome

48. Position Effects on Gene Expression Heterochromatin: condensed
Euchromatin: loose

49. Speculative Model for the heterochromatin at the ends of yeast chromosomes
Sir: Silent information regulator binding to unacetylated histone tails

50. Speculative Model for the heterochromatin at the ends of yeast chromosomes
DNA-binding proteins recognize DNA sequence close to telomere, recruit Sir proteins and cause histone tail modification, forming heterochromatin

51. Two speculative models for how the tight packaging of DNA in heterochromatin can be inherited during chromosome replication

53. The specialized nucleosome formed on centromeres
Also belongs to heterochromatin

54. The structure of a human centromere Alpha satellite DNA sequence
Kinetochore inner plate
Kinetochore outer plate
Spindle microtubules

55. The plasticity of human centromere formation

57. A typical mitotic chromosome at metaphase

58. SEM of a region near one end of a typical mitotic chromosome

59. EM of a mitotic chromosome

60. Condensin plays important roles
Chromatin Packing
Condensin plays important roles

61. The SMC (Structural Maintenance of Chromosomes) proteins in condensins

62. Selective localization of two interphase chromosomes
Chromosome 18 (red) and 19 (turquoise)

63. Specific regions of interphase chromosomes in close proximity to the nuclear envelope
Two different regions of chromosome 2 (yellow and magenta) close to the nuclear envelop (green)

64. Summary
Chromosomes are decondensed during interphase and hard to visualize
Lampbrush chromosomes of vertebrate oocytes and polytene chromosomes in the giant secretory cells of insects are exceptions, revealing the global organization of chromosome
Gene expression needs the decondensation of chromosome loops
Euchromatin and heterochromatin
Telomere and centromere are general heterochromatin
Chromosomes are spatially organized and deposited in nucleus
Mitotic chromosomes are condensed and organized.