Section D - Prokaryotic and
Eukaryotic Chromosome
Structure
Contents
D1 Prokaryotic chromosome structure
The Escherichia. coli chromosome, DNA domains, Supercoling of the
genome, DNA-binding proteins
D2 Chromatin Structure
Chromatin, Histones, Nucleosomes, The role of H1, Linker DNA, The
30 nm fiber, Highter order structure
D3 Eukaryotic Chromosomal Structure
The mitotic chromosome, The centromere, Telomeres, Interphase
chromosome, Heterochromatin, Euchromatin, DNase Ⅰ
hypersensitivity, CpG methylation, Histone variants and modification
D4 Genome complexity
Noncoding DNA, Reasociation Kinetics, Unique sequence DNA,
Tandem gene clusters, Dispersed repetitive DNA, Satellite DNA,
Genetic polymorphism
D5 The flow of genetic information
The central dogma, Prokaryotic gene expression, Eukaryotic gene
expression
D1 Prokaryotic chromosome structure —
The Escherichia. coli chromosome
•
•
•
A single closed-circular DNA, 4.6Mp
The DNA packaged into a region known
as Nucleoid that contains high
concentration of DNA (up to 30-50 mg/ml)
as well as all proteins associated with
DNA.
Continuous replication (no cell cycle)
D1 Prokaryotic chromosome structure —
DNA domains
•
Observed under electron microscope
•
50-100 domains or loops per E. coli chromosome, with
50-100 kb/loop
•The ends of loops are
constrained by binding to
a structure which
probably consists of
proteins attach to part of
the cell membrane.
D1 Prokaryotic chromosome structure —
Supercoling of the genome
• E. coli chromosome as a whole is negatively
supercoiled.
• Individual domains may be supercoiled
independently (topological independent).
• Direct biochemical evidence is lacking for
different level of supercoiling in different
domains.
D1 Prokaryotic chromosome structure —
DNA-binding proteins
• Histone-like proteins essential for DNA
packaging to stabilize and constrain the
supercoiling.
• HU: a small basic dimeric (碱性双体) protein,
non-specific binding to DNA, most abundant.
• H-NS (protein H1): neutral monomeric (中性单
体), partially non-specific binding
• Site-specific DNA binding proteins important
for organization of DNA domains (RNA
polymerases, IHF etc).
D2 Chromatin Structure —
DNA
DNA
compaction
Chromatin
10nm "beads-ona-string" fibre
nucleosome
metaphase
chromosome
30nm fibre
• Fig. 1: The major structures in DNA compaction; DNA,
the nucleosome, the 10nm "beads-on-a-string" fibre, the
30nm fibre and the metaphase chromosome.
Mitosis 有丝分裂
Interphase间期
Chromatin
(diffused)
Chromosome
(condensed)
D2 Chromatin Structure —
•
•
Histones
The major protein components of chromatin.
Four families of core histone: H2A, H2B, H3 and H4, An
additional non-core histone H1.
• Small, 10 kDa for core histones and 23 kDa for H1.
• Basic (rich in lysine and arginine) and tightly binds to
DNA.
Top view
Histone
octamer
Side view
D2 Chromatin Structure —
Nucleosomes
• The nucleosome core is the
basic unit of chromosome
structure, consisting of a protein
octamer containing two each of
core histones.
• With 146 bp of DNA wrapped
1.8 times in a left-handed fashin
around it.
• The wrapped of DNA into
nucleosomes accounts for
virually all of the negative
supercoiling in eukaryotic DNA.
D2 Chromatin Structure —
The role of H1
• Stabilizes the point at which DNA enters
and leaves the nucleosome core.
•C- tail of H1: stabilizes
the DNA between the
nucleosome cores.
linker histone H1 and H5 family
D2 Chromatin Structure —
Linker DNA
• The additional DNA required to make up
the 200 bp nucleosomal repeat, ~55 bp
D2 Chromatin Structure —
The 30 nm fiber
•Higher ordered
•Left-handed helix
•Six nucloesomes per turn
D2 Chromatin Structure —
Highter order structure
• On the largest scale, chromosomal DNA is organized
into loops of up to 100 kb in the foem of the 30nm fiber
D3 Eukaryotic Chromosomal Structure —
The mitotic chromosome
Telomere
Sister chromatid
Centromere
Mitotic
chromosome
at metaphase
Nuclear matrix
Chromatid
Loops of
30nm fiber
Mitotic chromosome
D3 Eukaryotic Chromosomal Structure —
The centromere
•
•
•
The region where two chromatids are joined.
The sites of attachment to the mitotic spindle
via kinetochore.
Centromere DNA.
Chromosomal components:
① Chromatid
② Centromere/Primary Constriction
③ Short arm
④ Long arm
D3 Eukaryotic Chromosomal Structure —
Telomeres
• Specialized DNA sequences which form the ends of the
linear DNA of the eukaryotic chromosome.
• Contains up to hundreds copies of a short repeated
sequence (5’-TTAGGG-3’ in human).
• Synthesized by the enzyme
telomerase (a
ribonucleoprotein)
independent of normal DNA
replication.
• The telomeric DNA forms a
special secondary structure
to protect the chromosomal
ends from degradation.
Human chromosomes (grey) capped by telomeres (white).
D3 Eukaryotic Chromosomal Structure —
Interphase chromosome
• In interphase, the chromosomes
adopt a much more diffuse
structure, although the
chromosomal loops remain
attached to the nuclear matrix.
• Cannot be visualized individually.
D3 Eukaryotic Chromosomal Structure —
Heterochromatin 异染色质
•
•
•
Highly condensed
Transcriptionally inactive
Can be the repeated satellite DNA close
to the centromeres, and sometimes a
whole chromosome (e.g. one X
chromosome in mammals)
D3 Eukaryotic Chromosomal Structure —
Euchromatin
• Euchromatin: chromatin other than
heterochromatin.
• More diffused and not visible
• The region where transcription takes place
• Not homogenous, only a portion (~10%)
euchromatin is transcriptionally active where the
30nm fiber has been dissociated to “beads on a
string” structure and parts of these regions may
be depleted of nucleosome.
Animal cells
Plant cells
•The nucleus of a human cell showing the location of
heterochromatin.
D3 Eukaryotic Chromosomal Structure —
DNase Ⅰ hypersensitivity
• Active regions of
chromatin, or regions
where the 30nm fiber is
interrupted by the
binding of a specific
protein to the DNA, or
by ongoing transcription,
are characterized by
hypersensitivity to
deoxyribonuclease
Ⅰ(DNase Ⅰ ).
D3 Eukaryotic Chromosomal Structure —
CpG methylation
• Methylation of C-5 in the cytosine （胞嘧啶）base of 5’CG-3’
• Occurs in mammalian cells
• Signaling the appropriate level of chromosomal packing
at the sites of expressed genes
• CpG methylation is associated with transcriptionally
inactive regions of chromatin
• Islands of unmethylated CpG are coincident with
regions of DNase I hypersensitivity
• “Islands”: surround the promoters of housekeeping
genes.
• Responsible for epigenetic （渐成说） and may also to
RNA silencing.
D3 Eukaryotic Chromosomal Structure —
Histone variants and modification
• The major mechanisms for the condensing and decondensing
of chromatin operate directly through the histone proteins
which carry out the packaging.
• Histones undergo posttranslational modifications which alter
their interaction with DNA and nuclear proteins.
• The H3 and H4 histones have long tails can be covalently
modified. Modifications of the tail include methylation,
acetylation, phosphorylation, etc.
• The core of the histones (H2A and H3) can also be modified.
• Histone modifications act in diverse biological processes such
as gene regulation, DNA repair and chromosome condensation
(mitosis).
D4 Genome complexity —
Noncoding DNA
• DNA sequence that does not code for
protein or RNA, including
• Introns (unique sequence) in genes
• DNA consisting of multiple repeats, can be
tandemly repeated sequences (e.g.
satellite DNA) or interspersed repeats (e.g.
Alu element) etc.
D4 Genome complexity —
Reasociation Kinetics（复性动力学）
D4 Genome complexity —
Unique sequence DNA
• The slowest to reassociate （复性最慢）
• Corresponds to coding regions of genes
occurring in one or a few copies/haploid
genome
• All the DNA in E. coli genome has a
unique sequence.
D4 Genome complexity —
Tandem gene clusters
• Tandem gene clusters:
(1) moderately repetitive DNA consists of a
number of types of repeated sequence.
(2) genes whose products are required in
unusually large quantities, e.g. there are
10-10000 copies of rDNA encoding 45S
precursor and X100 copies of histone
genes.
D4 Genome complexity —
Dispersed repetitive DNA
• Moderately repetitive (x100- x1000 copies)
• Scattered throughout the genome
• Human Alu elements: 300bp, 300 000 –
500 000 copies of 80-90% identity
• Human L1 element
• Alu + L1= ~ 10% of human genome.
• Functions of these repetitive DNA：largely
unknown
D4 Genome complexity —
•
•
•
•
•
Satellite DNA
Highly repetitive DNA (>106), very short (2 to 20-30bp,
mini- or micro-), in tandem arrays
concentrated near the centromeres and forms a large
part of heterochromatin.
as separate band in buoyant density gradient
no function found, except a possible role in kinetochore
binding
Minisatellite repeats are the basis of the DNA
fingerprinting techniques.
D4 Genome complexity —
Genetic polymorphism
1. Single-nucleotide polymorphism
2. Simple sequence length polymorphism
3. Restriction fragment length polymorphism
4. Single strand conformation polymorphism
D5 The flow of genetic information —
The central dogma
D5 The flow of genetic information —
Prokaryotic gene expression
DNA
Promoter
5‘
3‘
mRNA
Transcribed region
Transcription
AUG
Terminator
RNA polymerase
stop RBS AUG
5‘
stop
5‘ pop
OH 3‘
RBS
Translation
Proteins
3‘
Ribosomes,
aminoacyl-tRNAs
D5 The flow of genetic information —
Eukaryotic gene expression
DNA
Promoter
5‘
3‘
Transcribed region
Transcription
Pre-mRNA
AUG
5‘
RNA polymerase Ⅱ
EXONS
stop
INTRON
5‘ pop
RNA processing
mRNA
AUG
Poly( A) site
Splicing, capping,
polyadenylation
stop
AAA…3‘
Poly( A) tail
5‘ MeGppp
CAP
Translation
Proteins
3‘
Ribosomes,
aminoacyl-tRNAs
Cellular organelles you should further understand
Cytoplasm－－－cellular organelles
类囊体
Mitochondrion
池
Golgi Apparatus。The Golgi
is principally responsible
for directing molecular
traffic in the cell
Chloroplast
The endoplasmic reticulum
(ER) is responsible for the
production of the protein
and lipid components of
most of the cell's
organelles.
Cellular organelles（continue）
肌动蛋白
Lysomoes（溶酶体），which
contains hydrolytic enzymes
The ribosome plays a key role in
the synthesis of proteins.
Cytoskeleton(细胞骨架)
The vacuole is used only in plant cells.
It is responsible for maintaining the
shape and structure of the cell.
Multiple choice questions
1．Which of the following is common to both E. coli
and eukaryotic chromosomes?
A the DNA is circular.
B the DNA is packaged into nucleosomes.
C the DNA is contained in the nucleus.
D the DNA is negatively supercoiled.
2．A complex of 166 bp of DNA with the histone
octamer plus histone HI is known as a . . .
A nucleosome core.
B solenoid.
C 30 nm fiber.
D chromatosome.
3．In what region of the interphase chromosome does
transcription take place?
A the telomere.
B the centromere.
C euchromatin.
D heterochromatin.
4． Which statement about CpG islands and methylation is not
true?
A CpG islands are particularly resistant to DNase I.
B CpG methylation is responsible for the mutation of CpG to TpG in
eukaryotes.
C CpG islands occur around the promoters of active genes.
D CpG methylation is associated with inactive chromatin.
5．Which of the following is an example
of highly-repetitive DNA?
A Alu element.
B
histone gene cluster.
C
DNA minisatellites.
D dispersed repetitive DNA.
THANK YOU !