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

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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 - Sliding Ring– DNA primase - Single-strand

binding protein– DNA helicase

• 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

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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