Prokaryotic chromosome structure and organization

2. Inheriting Traits
• We inherit many of our physical characteristics or traits from our
parents.
• This is known as heredity – the passing of traits from one generation to
the next.
• In scientific terminology, a trait is a particular characteristic or feature
of an organism.

3. Why are traits inherited?
• Chromosomes contain the hereditary (genetic) information in living cells.
• All living cells and viruses contain genetic information in chromosomes.
• Each unique sequence of DNA (gene) carries a particular instruction for a
cell.
• Genes vary in size from about 100 to 2.5million base pairs. The length of
the sequence of DNA and the precise order of the base pairs in a gene are the
critical factors that determine what the gene product (usually a protein) will
be like and what it will do in a cell.

4. Prokaryotes

5. INTRODUCTION
• The term “prokaryote” means “primitive nucleus”. Cell in prokaryotes have no
nucleus. The prokaryotic chromosome is dispersed within the cell and is not
enclosed by a separate membrane.
• Much of the information about the structure of DNA has come from studies of
prokaryotes, because they are less complex (genetically and biochemically)
than eukaryotes.
• Prokaryotes are monoploid = they have only one set of genes (one copy of the
genome).
• In most viruses and prokaryotes, the single set of genes is stored in a single
chromosome (single molecule either RNA or DNA).
• Prokaryotic genomes are exemplified by the E. coli chromosome.
• The bulk of the DNA in E. coli cells consists of a single closed-circular DNA
molecule of length 4.6 million base pairs.
• The DNA is packaged into a region of the cell known as the nucleoid.

6. DNA domains
• Experiments in which DNA from E.
coli is carefully isolated free of most
of the attached proteins and observed
under the electron microscope reveal
one level of organization of the
nucleoid.
• The DNA consists of 50–100 domains
or loops, the ends of which are
constrained by binding to a structure
which probably consists of proteins
attached to part of the cell membrane.
The loops are about 50–100 kb in size.

7. Supercoiling of the genome
• The E. coli chromosome as a whole is negatively supercoiled,
although there is some evidence that individual domains may be
supercoiled independently.
• Electron micrographs indicate that some domains may not be
supercoiled, perhaps because the DNA has become broken in one
strand, where other domains clearly do contain supercoils.
• The attachment of the DNA to the protein–membrane scaffold may
act as a barrier to rotation of the DNA, such that the domains may be
topologically independent.

8. DNA-binding proteins
• The most abundant of these are protein HU, a small basic (positively charged) protein.
• It’s binds DNA nonspecifically by the wrapping of the DNA around the protein, and H-NS
(formerly known as protein H1), a monomeric neutral protein, which also binds DNA
nonspecifically in terms of sequence. These proteins are sometimes known as histone-like
proteins, and have the effect of compacting the DNA, which is essential for the packaging
of the DNA into the nucleoid, and of stabilizing and constraining the supercoiling of the
chromosome.
• Half of this is constrained as permanent wrapping of DNA around proteins such as HU.
Only about half the supercoiling is unconstrained.
• RNA polymerase and mRNA molecules, site-specific DNA-binding proteins such as
integration host factor (IHF), a homolog of HU, which binds to specific DNA sequences
and bends DNA through 140 .

10. Eukaryotes

11. INTRODUCTION
• In humans the average DNA molecule is about 6.5x107 base pairs in length.
• The nucleus of a human cells is just 6mm in diameter, yet it contains 1.8m of DNA.
• This can only be achieved because DNA in eukaryotes is tightly packaged into
chromosomes.
• DNA is coiled around small proteins (histones).
• Where the DNA is wrapped around a core of histone proteins it forms a particle about
10nm in diameter called a nucleosome.
• The nucleosomes give the DNA strand the appearance of a string of beads, and this
arrangement of DNA wrapped around histones serves to package the DNA efficiently and
protected from enzymatic degradation.
• When a eukaryotic cell is preparing to divide, chromosomes become very condensed and
are visible under a light microscope.

13. Chromatin
Chromatin is isolated from interphase nuclei, the individual
chromosomes are not recognizable. Instead one observes an irregular
aggregate of nucleoprotein. Chemical analysis of isolated chromatin
shows that it consists primarily of DNA and proteins and lesser amounts
of RNA.
This proteins are two major classes:
Basic proteins-positively charged at neutral pH called histones.
A heterogeneous largely acidic (negatively charged at neutral pH) group
of proteins collectively referred to as non-histone chromosomal
proteins.

14. Histones
• The major protein components of chromatin are the histones. Most of the
protein in eukaryotic chromatin consists of histones.
• Five families, or classes of histones:
• H2A, H2B, H3 and H4: core histones. The core histones are small
proteins, with masses between 10 and 20 kDa.
• H1: little larger at around 23 kDa.
• All histone proteins have a large positive charge; between 20 and 30%
of their sequences consist of the basic amino acids, lysine and arginine.
• This means that histones will bind very strongly to the negatively
charged DNA in forming chromatin.

15. 10 nm filament; nucleosomes
protein
purification
histones
(= 1g per g DNA)
H1 •Basic (arg, lys);
•+ charges bind
H3 to - phosphates
H2A on DNA
H2B
H4
DNA

16. • Members of the same histone class are very highly conserved between
relatively unrelated species, ex: between plants and animals, which
testifies to their crucial role in chromatin.
• H1 histones are somewhat distinct from the other histone classes in a
number of ways; in addition to their larger size, there is more variation
in H1 sequences both between and within species than in the other
classes.

17. 1. DNA compacting ratio
2. Nucleosomes
I) Ultrastructure of nucleosome core protein
II) Bonding between histone core and DNA
III) Bending of DNA in a nucleosome
IV) Packing of nucleosomes into compact chromatin fiber.

18. DNA compaction ratio
• Human chromosome 22 contains about 48 million nucleotide pairs.
Stretched out end to end, its DNA extend about 1.5 cm.
• Chromosome 22 measures only about 2µm in length, giving end-toend compaction ration of nearly 10,000 fold.
• Compression is performed by proteins.

19. Nucleosomes
• The basic unit of chromatin is the nucleosome. The nucleosome is
composed of approximately 146 base pairs of DNA wrapped in 1.8
helical turns around an eight-unit structure called histone protein
octamer.
• This histone octamer consists of two copies each of the histones H2a,
H2b, H3, and H4.
• The space in between individual nucleosomes is referred to as linker
DNA, and can range in length from 8 to 114 base pairs, with 55 base
pairs being the average.
• Linker DNA interacts with the linker histone, called H1.

22. Bonding between histone core and DNA
• About 142 hydrogen bonds are formed between DNA and the histone
core in each nucleosome. Nearly half of these bonds form between the
aminoacid backbone of the histones and phosphodiester bonds of
DNA.
• For example: all core histones are rich in lysine and arginine.
• positive charge of these aminoacids can effectively neutralized the
negatively charged DNA backbone.

23. Bending of DNA in a nucleosome
• Two main influences determine where nucleosomes form in the DNA:
• Difficulty of bending: bending of the DNA double helix into two tight
turns around the outside of the histone octamer, a process that required
firm compression of the minor groove of the DNA helix.
• A-T rich sequences in the minor groove are easier to compress than GC rich sequences.
• The presence of certain other tightly bound proteins on the DNA also
influences the position of nucleosomes on DNA molecule.

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

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

27. Structural Organization of the Core Histones

28. 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

29. Zigzag model of the 30-nm chromatin fiber

30. 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

31. The function of Histone H1

32. The function of Histone
tails

33. Chromatin Remodeling

34. Cyclic Diagram for nucleosome
formation and disruption

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

38. Eukaryotes
Prokaryotes
Location of Chromosomes
In the nucleus
In the cytoplasm
Structure of Chromosomes
Double stranded molecules of
DNA, with attached protein
molecules.
Single, circular chromosome
composed of DNA, with very few
or no attached proteins.
Number of Chromosomes
Varies from species to species.
Humans have 46.
One.
Reproduction
Nuclear DNA is replicated prior
to cell division and the
chromosomes distributed evenly
to daughter cells.
Single circular chromosome is
replicated prior to cell division.
Each daughter cell receives one
copy of this chromosome.
Extra-chromosomal DNA
Mitochondria contain DNA.
Small circular DNA molecules
known as plasmids.

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