Download Part II Control of Cellular Function from Nucleus

Gene and
Chromosome
DNA is the genetic material
Genes and Chromosome
• Molecular Definition of Gene
• the structure and function of DNA
• The global structure of
chromosomes
• Organelle DNA
Molecular Definition of Gene
• The entire nucleic acid sequence that is
necessary for the synthesis of a
functional protein and RNA
• Coding region (exon and intron) +
Regulatory sequences (e.g. promotor,
enhancer, polyadenylation site, splicing
sites)
• There are also tRNA and rRNA genes
Gene & Protein
Baterial Operon and Simple
Eukaryotic Transcription Unit
Complex Eukaryotic Transcription
Complex
The Structure and Function
of DNA
• A DNA molecule consists of two
complementary chains of
nucleotides
• The structure of DNA provides a
mechanism for heredity
Structure and Composition of DNA & RNA
Structure and Composition of DNA & RNA
Structure and Composition of DNA & RNA
Structure and Composition of DNA & RNA
The DNA double helix
DNA is a template for its
own duplication
The Global Structure of
Chromosome
• Nucleotides --> DNA --> Gene -->
Chromosome --> Genome
• Human DNA is ~ 2 meters long. The
nucleus of DNA is about 6 µM in diameter.
• Specialized proteins bind to and fold DNA
into coils and loops, providing higher level
of organization.
• Although DNA is tightly packed, it can be
easily accessed by many enzymes that
replicate, repair or express its genes.
Nucleus
A Karyotype of Human
Chromosomes
Normal & Aberrant
Chromosome
Organization of Genes on Human
Chromosome
Content of the Human
Genome
Interface / Mitotic
Chromosome
Chromatin Packing
Nucleosomes
Structural Organization of the
Nucleosome
Structural Organization of the
Nucleosome
Structural Organization of the
Nucleosome
Organization of the Core
Histones
Organization of the Core
Histones
Organization of the Core
Histones
Chromosome Remodeling
• ATP-driven chromatin remodeling
machines change nucleosome
structure
• Covalent modification of the histone
tails can profoundly affect chromatin
Irregularities in Chromatin
Structure
A role Histone H1 in remodeling
Chromosome structure
Histone Tails
Mechanism of Chromatin
Remodeling Complex
Cycle of Chromosome
Remodeling
Covalent Modifications of Histone Tails
Covalent Modifications of Histone Tails
Heterochromatin/Euchromatin
• There are two types of chromatin in
interface, heterochromatin and
euchromatin
• Heterochromatin is a highly condensed,
and organized
• 10% of the genome is packed into
heterochromatin
• Heterochromatin is resistant to gene
expression
• Heterochromatin is concentrated in
specific regions e.g. centromeres and
telomeres
Organelle DNA
• Mitochondria and Chloroplast DNA
• Exhibit cytoplasmic inheritance
• Encode rRNA, tRNA, and some
mitochondrial proteins
• Product of mitochondrial genes are
not exported
• Mitochondrial gene codes differ
from the standard nuclear code
DNA Replication,
Repair, and
Recombination
Eukaryotic Cell Cycle
Eukaryotic Cell Cycle
DNA Replication
• DNA Polymerase
• Replication Fork
– DNA polymerase
– DNA primase
protein
– DNA helicase
- Sliding Ring
- Single-strand binding
• DNA polymerization in 5’-3’ direction
– Leading strand
– Lagging strand
• Proofreading mechanisms
• DNA Topoisomerase
DNA Double Helix is the
Template
Mg2+ is required for
polymerization
DNA Polymerase
DNA replication is
semiconservative
DNA Replication of a
Circular Chromosome
Replication Fork
Why only 5’--> 3’ Direction ?
Why only 5’--> 3’ Direction?
For High Fidelity DNA
Synthesis
Why only 5’--> 3’ Direction?
For High Fidelity DNA
Synthesis
• 5’- 3’ Polymerization
• 3’- 5’ Exonucleolytic Proofreading
• Strand-directed mismatch repair
Editing by DNA Polymerase
Exonucleolytic Proofreading by DNA Polymerase
Exonucleolytic Proofreading by DNA
Polymerase
5’- 3’ Direction is Energy
Efficient
DNA Synthesis of the Lagging
Strand
RNA Primer Synthesis
Other Enzymes & Proteins
in DNA Replication
DNA Ligase
Bacterial Replication Fork
Mammalian Replication Fork
DNA Helicase
SSB
Single-Strand DNA-Binding
Protein (SSB)
Sliding Clamp for DNA
polymerase
Sliding Clamp for DNA
polymerase
Sliding Clamp
Moving Replication Fork
Moving Replication Fork
Mismatch Proofreading
Proteins
DNA Topoisomerase
Winding Problem
DNA Topoisomerase I
DNA Topoisomerase I
DNA Topoisomerase II = DNA
Gyrase
DNA Topoisomerase II
The Initiation and
Completion of DNA
Replication in Chromosome
DNA
Replication
in Bacteria
Refractory period for DNA
initiation
Eukaryotic Chromosome
Contains Multiple Origin of
Replication
Identification of yeast origin of
replication
Eukaryotic Origin of
Replication
• Last multisubunit complex(ORC;
origin recognition complex) binds to
eukaryotic origin of replication
• All yeast Origin of replication has
been identified (about 150
nucleotide pairs)
• The mammalian origin of replication
sequence is difficult to identify
Yeast Origin of Replication
Telomere
DNA Repair
Spontaneous Alterations
Depurination and
Deammination
Thymine Dimer
Deamintation
Depurination
Double-Strand Break
Repair
DNA Recombination
Junction
ssDNA Hybridization
Rec A in Homologous
Recombinaton at DNA
Synapsis
Holiday Junction
Resolving Holiday Junction
General Recombination in
Mitotic and Meiotic Cells
Site Specific
Recombination
• Moving of mobile genetic elements
between non-homologous DNA
• Transpositional site-specific
recombination
– DNA only transposition
• Cut and Pase transposition
• Replicative transposition
– Retroviral-like retrotransposition
– Nonretroviral retrotransposition
• Conservative site-specific recombination
Bacterial Transposons
Cut-and-Paste
Transposition
Replicative Transposon
Replicative Transposon
Retrovirus
Site-specific recombintaion by a
retro virus or a retrovirus-like
retrotransposon
Nonretroviral
Retrotransposon
Conservative site specific
recombination