1. CHAPTER 24 Genes and Chromosomes
Key topics:
Organization of information in chromosomes
DNA supercoiling
Structure of the chromosome

2. Management and Expression of Genetic Information
Previous chapters dealt with
metabolic pathways, in which the chemical structures of small molecules were modified by enzymes
signal transduction pathways, in which interactions of ligands with receptor proteins caused physiological responses
The following chapters deal with
information pathways, in which genetic information stored as the nucleotide sequence is maintained and expressed

3. The Central Dogma of Molecular Biology
The discovery of double-helical structure of DNA in 1953 laid a foundation to thinking of biomolecules as carriers of information
It was well understood by 1950 that proteins play roles of catalysts but their role in information transfer was unclear
Francis Crick proposed in 1956 that “Once information has got into a protein it can’t get out again”
The Central Dogma was proposed by Francis Crick at the time when there was little evidence to support it, hence the “dogma”

4. How does genes function? Central Dogma: DNA to RNA to Protein.

5. Genes and Chromosomes What is gene? What is chromosome?
One gene-one enzyme.
One gene-one protein (polypeptide).
Genes are segments of DNA that code for polypeptides and RNAs.
What is chromosome?
Chromosome consists of one covalently connected DNA molecule and associated proteins
Viral genomic DNA may be associated with capsid proteins
Prokaryotic DNA is associated with proteins in the nucleoid
Eukaryotic DNA is organized with proteins into a complex called the chromatin

6. DNA is a Very Large Macromolecule
The linear dimensions of DNA are much bigger than the virions or cells that contain them
Bacteriophages T2 and T4 are about 0.2 m long and 0.1 m wide
Fully extended T4 DNA double helix is about 60 m long
DNA in the virion or cell is organized into compact forms, typically via coiling and association with proteins

7. The Size and Sequence of DNA Molecules in Bacteria and their viruses
Bacteria(E. coli) 4,639, mm mm

8. T2 phage

9. The sizes of E. coli cell and its DNA

10. DNA from a lysed E. coli cell

11. TABLE 24-2 DNA, Gene, and Chromosome Content in Some Genomes11

12. DNA, Chromosomes, Genes, and Complexity
Note that despite the trends in the previous table, neither the total length of DNA, nor the number of chromosomes correlates strongly with the perceived complexity of the organisms
Amphibians have much more DNA than humans
Dogs and coyotes have 78 chromosomes in the diploid cell
Plants have more genes than humans
The correlation between complexity and genome size is poor because most of eukaryotic DNA is non-coding
Recent experimental work by Craig Venter suggests that a minimal living organisms could get by with less than 400 genes

13. DNA content and C-value paradox

14. Eukaryotic genomes have several sequence components
Nonrepetitive DNA: the complexity of the slow component corresponds with its physical size, i.e., unique sequences.
Moderately repetitive DNA:.component with a Cot1/2 of 10-2 and that of nonrepetitive DNA. Contains families of sequences that are not exactly the same, but are related. The complexity is made up of a variety of individual sequences, each much shorter, whose total length together comes to the putative complexity. Usually dispersed throughout the genome.
Highly repetitive DNA: component which reassociates before a Cot1/2 of Usually forms discrete clusters.

15. Types of sequences in the human genome

16. Composition of the Human Genome
Notice that only a small fraction (1.5 %) of the total genome encodes for proteins
The biological significance of non-coding sequences is not all clear
Some DNA regions directly participate in the regulation of gene expression (promoters, termination signals, etc)
Some DNA encodes for small regulatory RNA with poorly understood functions
Some DNA may be junk (pieces of unwanted genes, remnants of viral infections

17. Many eukaryotic genes contain intervening sequences (introns)

18. Some Bacterial Genomes Also Contain Introns
It was thought until 1993 that introns are exclusive feature of eukaryotic genes
About 25% of sequenced bacterial genomes show presence of introns
Introns in bacterial chromosome do not interrupt protein-coding sequences; they interrupt mainly tRNA sequences
Introns in phage genomes within bacteria interrupt protein-coding sequences
Many bacterial introns encode for catalytic RNA molecules that have ability to insert and reverse transcribe themselves into the genomic DNA

19. Transposons DNA sequence is not completely static
Some sequences, called transposons, can move around within the genome of a single cell
The ends of transposons contain terminal repeats that hybridize with the complementary regions of the target DNA during insertion
To be covered in Ch. 25.

20. Eukaryotic Chromosomes

21. Important Structural Elements of the Eukaryotic Chromosome
Telomeres cap the ends of linear chromosomes and are needed for successful cell division
Centromere functions in cell division; that’s where the two daughter chromosomes are held together during mitosis (i.e. after DNA replication but before cell division)

22. Centromere: Mitotic segregation of chromosomes
Centromere: Mitotic segregation of chromosomes. Simple-sequence DNA is located at centromere in higher eukaryotes.
Telomere: At ends of chromosomes. (TTAGGG)n in human.

23. Telomeres and Cellular Aging
In many tissues, telomeres are shortened after each round of replication (end-replication problem of linear DNA); the cellular DNA ages
Normal human cells divide about 52 times before losing ability to divide again (Hayflick limit)

24. How is DNA packed in the chromosomes
DNA Supercoiling.
Proteins assisted packaging (nucleosomes)

25. DNA Supercoiling DNA in the cell must be organized to allow:
Packing of large DNA molecules within the cells
Access of proteins to read the information in DNA sequence
There are several levels of organization, one of which is the supercoiling of the double-stranded DNA helix

26. Supercoils

27. Supercoiling of DNA can only occur in closed-circular DNA or linear DNA where the ends are fixed.
Underwinding produces negative supercoils, wheres overwinding produces positive supercoils.

28. Negative and positive supercoils .
Topoisomerases catalyze changes in the linking number of DNA.

29. Supercoiling induced by separating the strands of duplex DNA (eg
Supercoiling induced by separating the strands of duplex DNA (eg., during DNA replication)

30. Relaxed and supercoiled plasmid DNAs

31. Negative supercoils facilitate separation of DNA strands (may facilitate transcription)

32. Topology of cccDNA is defined by: Lk = Tw + Wr, where Lk is the linking number, Tw is twist and Wr is writhe.

33. Intertwining of the two strands
Nodes = ss crossing on 2D projection.
Right-handed crossing = +1/2
Left-handed crossing = -1/2
Lk = number of times one strand winds around the
other on 2D projection.
One linking number = 2 nodes.

36. Promotion of cruciform structures by DNA underwinding

38. Mechanism of Type I topoisomerase action

41. Proposed mechanism of Type II topoisomerase action

42. Topoisomerases are Targets for Antibiotics and Anti-cancer Drugs
Bacterial topoisomerase
inhibitors
Type I topoisomerase
inhibitors 42

43. Human Type II topoisomerase inhibitors43

44. DNA damages are produced by topoisomerase inhibitors
Most topoisomerase inhibitors act by blocking the last step of the topoisomerase reaction, the resealing of the DNA strand breaks. Therefore, these inhibitors will produce single-strand or double-strand DNA breaks in the DNA.

45. Plectonemic supercoiling

46. DNA Compaction Requires Solenoidal Supercoiling, not plectonemic supercoiling.

47. Changes in chromosome structure during the cell cycle

48. Protein-assisted Packaging of DNA
Nucleosomes are the fundamental organizational units of eukaryotic chromatin

49. Each nucleosome has a histone core wrapped by DNA (146 bps) in a left-handed solenoidal supercoil about 1.8 times. The linker DNA is about 54 bps in length.

50. DNA wrapped around a nucleosome core

51. Histones are small, basic protein
Histones are small, basic protein. The histone core in nucleosomes contains two copies each of H2A, H2B, H3 and H4. Histone H1 binds to linker DNA.

52. Chromatin assembly

53. Nucleosomes are packed into successively higher-order structures
The 30 nm fiber, a higher-order organization of nucleosomes.

54. A partially unraveled human chromosome, revealing numerous loops of DNA attached to scaffold.

55. Higher order of folding is not yet understood
Higher order of folding is not yet understood. Certain regions of DNA are associated with a nuclear scaffold. The scaffold associated regions are separated by loops of DNA with 20 to 100 kb long.

56. Model of DNA compaction in eukaryotic chromosomes

57. Condensed chromosome are maintained by SMC proteins

59. Model for the effect of condensins on DNA supercoiling