The Importance of Watson-Crick

Proposal
Storage of genetic information
Replication and inheritance
Expression of the genetic message

Chromosome Structure
The genetic material in cells is organized
intostructuralandfunctionaldomains.
To function, each chromosome need to have
An origin of replication
Centromere (for linear)
Telomere (for linear)

Prokaryotic Chromosomes
A single nucleic acid molecule (DNA or RNA;
linear or circular )
Largely devoid of associated proteins not true
Contain relatively little genetic information but
everything they need
Ability to package exceedingly long DNA
molecules into a relatively small volume

Chromosomes of Viruses
A nucleic acid molecule (DNA or RNA)
Either single- or double-stranded
Linear or circular
X174 bacteriophage single-stranded circular DNA
polyoma virus double-stranded circular DNA
bacteriophage lambda double-stranded linear but is
circular in host; 7 m long, packaged into 0.1 m side
protein head

Bacterial Chromosome
Structure
Prokaryotic cells (bacteria) contain their
chromosome as circular DNA
Usually the entire genome is a single circle,
but often there are extra circles called
plasmids
The DNA is packaged by DNA-binding
proteins.

Bacterial Chromosomes
Double-stranded DNA always
In a structure called nucleoid
Associated with DNA-binding proteins
containing (+) charged amino acids to bind
() charged phosphate groups
Is not functionally inert, can be readily
replicated and transcribed

Bacterial Chromosome
Structure
The bacterial DNA is packaged in loops
The bundled DNA is called the nucleoid.
It concentrates the DNA in part of the cell,
but it is not separated by a nuclear
membrane (as in eukaryotes)
The DNA does form loops to a protein core,
attached to the cell wall.

Supercoiled DNA
Both viruses and bacteria
High speed centrifugation results in three
bands of different density and compactness
Least dense linear
Two more dense
Circular
Circular supercoiled

Eukaryotic Chromosomes
Double-stranded DNA, linear
Binding with proteins
Several molecules of DNA may be present
in cell forming chromosomes
Number of chromosomes characteristic for
each species

Specialized Eukaryotic Chromosomes

Large chromosomes, structure seen under
light microscope
Polytene chromosomes
Lampbrush chromosomes

Polytene chromosomes
1881, Balbiani, Balbiani rings
Can be seen in the nuclei of interphase cell
Many rounds of replication without strand
separation or cytokinesis
The banding pattern is distinctive to each
chromosome

Polytene chromosomes
Bands and interbands
Puffs regions of gene activitty
A band can contain up to 107 base pairs of
DNA

Lampbrush Chromosomes
1892, in oocytes of sharks they are giant
chromosomes
Direct the metabolic activities of the
developing egg
Chromomeres, lateral loops
Active in synthesis of RNA

Differential Staining
Metaphase chromosomes differ from one another
in size and shape, and the absolute length of any
one chromosome varies depending on the stage of
mitosis in which it was fixed.
However, the relative position of the centromere is
constant, which means that that the ratio of the
lengths of the two arms is constant for each
chromosome.

Differential Staining
Centromere position and arm ratios can assist in
identifying specific pairs of chromosomes, but
some chromosomes still similar
Certain dyes would produce reproducible patterns
of bands when used to stain chromosomes.
Chromosome banding has since become a
standard and indispensible tool for cytogenetic
analysis.

Chromosome Banding
1970s chromosome-banding techniques
Giemsa banding
C-banding for centromeres

Uniform nomenclature

Chromosome Banding
G banding: produced by staining with
Giemsa after digesting the chromosomes
with trypsin
C banding: chromosomes are treated with
acid and base, then stained with Giemsa
stain
Q banding: chromosomes are stained with
a fluorescent dye such as quinacrine

Chromosome Banding
Each of these techniques produces a pattern of
dark and light (or fluorescent versus nonfluorescent) bands along the length of the
chromosomes.
Each chromosome displays a unique banding
pattern, analogous to a "bar code", which allows it
to be reliably differentiated from other
chromosomes of the same size and centromeric
position.

Chromatin
In eukaryotic cells the DNA in the nucleus
is not naked but is associated with protein
This nucleoprotein complex of DNA, RNA,
and protein is referred to as chromatin.

Chromatin
Euchromatin and heterochromatin
Visible chromosomes in mitosis tightly
coiled chromatin fibers
Interphase chromatin is uncoiled
A contraction in length of 10,000 times

Heterochromatin and Euchromatin

Heterochromatin
Tightly packed, dark staining
Transciptionally inactive, late replication
Facultative or constitutive

Euchromatin
Light staining, less tightly packed
Transciptionally active

Heterochromatin
Some parts of chromosome remain condensed
through cell cycle, stain deeply during interphase.
Heterochromatin genetically inactive, replicates
later during S phase
Areas of centromeres, telomeres
Whole chromosome inactivation Barr body
Position effect inactivity in adjacent regions

Chromatin
DNA in E.coli 1200 m long
DNA in human chromosomes range from
19,000 to 73,000 m
All 46 chromosomes almost 2 meters
Diameter of a nucleus is 5-10 m

How much chromatin or more precisely

DNA, does a cell have?
Determination of the amount of DNA per nucleus
can be determined by carrying out cytochemical
tests, e.g., Feulgen reaction, or Schiff's reagent.
Following the specific staining of DNA in the
nucleus, the slide with stained cells can be viewed
with a special cytophotometric microscope and the
amount of DNA per cell determined.

C value
The amount of DNA per haploid genome is called
the C value.
In eukaryotes the DNA content per haploid
genome is generally expressed in picograms (pg).
1 pg = 109 bp of DNA
1 pg of DNA = about 31 cm of DNA

DNA Packaging
Humans have 3.65 pg/haploid genome
Thus, the human diploid nucleus has
greater than _______________________ of
DNA.
Yet the nucleus has an average diameter of
only 6 m.
How does all this DNA get packaged into
such a tiny space?

Beads on a String
An average sized human chromosome possesses DNA that
is about 5 cm in length when stretched out. However, at
metaphase of mitosis, it is 5 um, a 10,000-fold reduction.
Folding of the DNA is made possible because the DNA is
___________________ -- to form chromatin.
Experimental methods have been developed to spread
chromatin on an EM grid and visualize its structure.
If nuclei are lysed in dilute salt and the chromatin spread,
one sees what is referred to as the "beads-on-a-string"
structure, with beads evenly spaced out.

Nucleosome
How much DNA is associated with one repeating unit or
bead?
Nucleases cleave exposed DNA between beads. Isolate
beads and electrophorese DNA on a gel. Fragments are
about 140bp
That much DNA is wrapped around the bead.
The linker DNA varies from species to species (for sea
urchins, it is about 100 bp; in humans, it is about 60 bp).
The protein bead is the basic packing unit of chromatin
and is called a nucleosome

Chromatin proteins
Proteins associated with DNA are histones
and nonhistones
Positively charged histones bond
electrostatically to the negatively charged
phosphates; five types H1, H2A, H2B,
H3, H4
Less positively charged - nonhistones

Nucleosome
The bead proteins are histone proteins.
The histones are about 100 - 150 amino acids in length and
are all highly basic. This gives them a net (+) charge,
allowing them to bind to DNA.
The bead histones:

H2A
H2B
H3
H4

These range in MW from 11000 14000 Da

H1, the fifth histone, is larger (about 21,000 Da MW) and
is not part of the bead.

Histones
For H2A, H2B, H3, and H4, one half of the amino
acids making the protein is highly basic
(+charged) while the other half is hydrophobic
The basic end is for interacting with DNA, while
the hydrophobic end is more important for
protein-protein interactions.
H1 has basic residues at the two ends and is more
hydrophobic and acidic in the middle.

Nucleosome Core
The nucleosome core, the "bead" structure consists
of two each of H2A, H2B, H3, and H4, to form an
octamer (8) protein core.
Wrapped around each octamer is about 140bp
DNA.
H1 is associated with the DNA linker and serves
to link adjacent nucleosomes. Thus, there is only
one H1 histone per nucleosome.
When treating chromatin with diltule salt. H1 is
removed, so that explains why the beads on a

30 nm chromatin fiber -- the native

chromatin structure
In the absence of salt and with careful lysis on an
EM grid, most of the chromatin is seen as a fiber
with a diameter of between 20-30 nm, commonly
known as the 30nm chromatin fiber
The nucleosomes in the 30 nm chromatin fiber are
packed in a spiral manner, with 6-7 cucleosomes
per turn.
H1 allows for the interaction between nucleosomes
and is responsible for the formation of the helical
shape

Looped domains
Packing of the DNA in 30 nm chromatin fibers only
reduces the 5 cm of DNA down to just over
_________________________________.
The probable next level of folding was originally
suggested by lampbrush chromosomes and polytene
chromosomes, which appear to be organized
_____________________________________________
A looped domain is simply a 30 nm chromatin fiber that is
bent to ________________________.
A single looped domain may have between 20,000 100,000 bp of DNA.
A chromosome would be organized in a series of looped
domains.

Looped Domains
This formation of looped domains reduces
our "average" chromosome to about
___________________ (a _____________
further reduction than the 30 nm fiber).
This looped domain structure for
chromosomes is probably how a typical
interphase chromosome is organized.

Nucleosome
Chromatin consists of repeating units (~ 200bp)
____________________________
Chromatin fibers are composed of linear arrays of
spherical particles _______________________
Each nucleosome consists of (H2A)2(H2B)2 and
(H3)2(H4)2 tetramers in association with about 200 bp of
DNA
Nucleosome core particle consists of 147 bp, the rest is
linker DNA associated ______________________

http://www.johnkyrk.com/chromosomestructure.html - animation
http://www.biostudio.com/demo_freeman_dna_coiling.htm

DNA packaging
2 nm DNA molecule is coiled into a 11 nm in diameter
nucleosome first level, 1/3 reduction
Further packaged into a 30 nm structure solenoid
second level, spiral with 6-7 nucleosomes per turn; H1
clamp holds the helical shape 50-fold reduction
Forms a series of loops and further condense into 300 nm
in diameter chromatin fiber 10-fold from previous level
Form chromosome arms that constitute a chromatid 700
nm in diameter H1 phosphorylation

Mitotic chromosome structure

The further reduction, or coiling, is accompanied
by ____________________________ of all the
histone H1 molecules in the cell nucleus at 5
different specific serine residues.
Because of the part that histone H1 plays in
packing nucleosomes together, its phosphorylation
by phosphokinase seems likely to have a causal
role in chromosome ______________________

Scaffold
Digestion of DNA away from metaphase
chromosomes reveals a protein network, or
scaffold, shaped like the chromosome, that may be
responsible for maintaining
____________________________________.
DNA folding is precise and always occurs the
same way for a chromosome, as can be
demonstrated by __________________________

Nuclear Scaffold
Nuclear scaffold system, termed the nuclear matrix,
determines the shape of the nucleus
Provides a 3-dimensional lattice for organizing the DNA
into specific functional units.
The nuclear matrix is a riboprotein structure that organizes
50,000 loop domains of DNA of approximately 60
kilobase lengths each
During replication the loops are reeled through fixed
replicating sites attached to the nuclear matrix

Histone Modifications
Phosphorylation of histones may be important in
__________________________________.
Acetylation of histones may _________________
histones' affinity for DNA (lysine most commonly
is acetylated, resulting in decreased charge).
Acetylation of histones may be important in
___________________________ (allowing
greater accessibility of DNA by RNA
polymerase).

Chromatin Structure of Active

Genes
Interphase chromatin can be divided into
two classes:
______________________ - packaged
similarly as mitotic chromatin (tightly), very
little transcription of DNA
______________________- packaged as
looped domains, this is "active chromatin",
containing genes that are transcribed.

How do genes that are in the process

of transcription look?
Active genes are still associated with
______________________________
As a rule, active genes are hypomethylated at
Cytosine residues.
Active genes, as a rule, have more
_________________________________
The promoter region of active genes is
hypersensitive to DNAse I (suggesting fewer
histones here to allow for RNA polymerase to
initiate transcription more easily).

Nuclear Architecture
In the eukaryotic nucleus, chromosomes occupy
individual, nonoverlapping territories and reactions of
DNA and RNA metabolism are confined to discrete
structuresinthenuclearinterior
The highest order packing may result from attachment of
chromosomestoanuclearmatrixornuclearscaffold
The loop organization of DNA in interphase seems to be
maintained by anchoring of specific DNA sequences
(MAR/SAR)toaproteinnetworkofthenucleoskeleton.
MARmatrixattachmentregion
SAR scaffold attachment region

Conclusions
Nucleus has a very high level of structural and functional
organization
In the interphase, DNA is
___________________________ then during cell
division but each chromosome has a specific location
within nucleus and is anchored by specific sequences
Mitotic chromosome is __________________________
with several levels of organization
The basic level of condensation is
__________________________________ DNA
wrapped around histone proteins