• DNA and Chromosomes

Chromosome in CellsDNA (deoxyribonucleic acid)

AGTCHuman 46 chromosomes22 homologs, x, or x/y

Genes are carried by Chromosomes

Two plant cells visualized by light microscope, DNA stained

with DAPI

Experimental procedures demonstrating that DNA is the genetic material1940s

• Genetic information is carried in the linear sequence of nucleotides in DNA

• Genetic information contains instructions to synthesize proteins

• DNA forms double helix with two complimentary strands holding together by hydrogen bonds between A-T (2 bonds) and G-C (3 bonds)

• DNA duplication occurs using one strand of parental DNA as template to form complimentary pairs with a new DNA strand.

• DNA is in nucleus in eucaryotes

The Structure and Function of DNA

1953 Watson and Crick determined the structure of DNA

DNA and its BuildingNucleotides: Guanine (G), Adenine (A), Cytosine (C),

Thymine (T).Polarized strand, 5’->3’

Base inside, sugar outside

DNA and its BuildingAntiparallel strands

DNA PairsA always pairs with T,

and G with C,A-T two hydrogen bonds, G-C three hydrogen bonds

DNA Double Helix10.4 nucleutides/turn; 3.4 nm between nucleutides

DNA to ProteinGenome: the complete set of information in an organism’s DNA

Total length of DNA about 2 meters long in a human cell, encoding about 30000 proteins

To carry the genomic information to daughter cellsDNA Duplication

Using itself as template

Cell Nucleus, compartmentalized DNA activity

Nuclear pores allow communicationNuclear lamina and cytoskeleton mechanically support the nucleus

• A gene is a nucleotide sequene in a DNA molecule that act as a functional unit for protein production, RNA synthesis.

• Introns and Exons• Chromosome: single long DNA contains a linear array of

many genes. • Human genome contains 2.3x109 DNA nucleotide pairs, with

22 different autosomes and 2 sex chromosomes.• Chromosomal DNA: replication origins, telomeres,

centromeres• Histones form the protein core for DNA wrapping• Nucleosome: repeating array of DNA-protein particles• Modification of Chromatin and nucleosomes: histone H1,

ATP-driven chromatin remodeling complexes, and enzymatically catalyzed covalent modification of the N-terminal tails of Histones

Chromosomal DNA and its Packaging

Human ChromosomeComplex of DNA and protein is called chromatin

44 homologous chromosomes and 2 sex chromosomesComplementary DNA with different Dyes

The arrangement of the full chromosome set is called karyotype

Banding Pattern of human chromosomes

Giemsa StainingGreen line regions:

centromeres

Encoding ribosome

The organization of genes of a human chromosome

Conservation between human and mouse genomesUsually important genes are encoded by conserved regions

Note: Human chromosome 1 and mouse chromosome 4

human mousecentromere

Cell CycleDNA molecule not only carries genetic information, but also undergoes

conformational changeChromosomes exist through the cycleMitotic and interphase chromosome

Single chromosome can only be visible during mitosis

Chromosomes at interphase and M

phase

Three important DNA sequencesTelomere, replication origin, centromere

DNA Molecules are highly condensed in chromosomesNucleosomes of interphase under electron microscope

Nucleosome: basic level of chromosome/chromatin organization Chromatin: protein-DNA complex

Histone: DNA binding proteinA: diameter 30 nm; B: further unfolding, beads on a string conformation

Nucleosome StructuresHistone octamer

2 H2A2 H2B2 H32 H4

X-ray diffraction analyses of crystalsStructure of a nucleosome core particle

Structural Organization of the Core Histones

The Assembly of the Core Histones

Notice the long tails of the octamer

The bending of DNA in a nucleosome1. Flexibility of DNAs: A-T riched minor groove inside and G-C

riched groove outside2. DNA bound protein can also help

Zigzag model of the 30-nm chromatin fiber

Irregularities in the 30-nm fiberFlexible linker, DNA binding proteins

Structural modulators: H1 histone, ATP-driven Chromatin remodeling machine, covalent modification of histone tails

The function of Histone H1

The function of Histone tails

Chromatin Remodeling

Cyclic Diagram for nucleosome formation and

disruption

Covalent Modification of core histone tails

Acetylation of lysinesMythylation of lysines

Phosphorylation of serines

Histone acetyl transferase (HAT)

Histone deacetylase (HDAC)

• DNA, Chromosome

• Centromere, telomere, replication origin

• Nucleosome, Chromatin,

• Histone: H1, H2A, H2B, H3, H4

• Histone octamer, DNA packaging

• DNA binding proteins, Histone modifications

Summary

• Some rare cases of interphase chromosomes, certain features maybe universal

• Representative forms forming typical interphase chromosome

• Chromosome at mitosis

The Global Structure of Chromosomes

Lampbrush chromosomes (amphibian oocyte, immature eggs)

A model for the structure of a lampbrush chromosome

Chromomeres: highly condensed and in general not expressed until

unfolding

A polytene chromosome from Drosophila salivary glandDark bands and interbands

Electron Microscope image of Drosophila polytene chromosome

Chromosome puffsFolding and refolding at a time

course of 22 hours

RNA synthesis in Chromosome puffsRed: newly synthesized BrUTP; Blue: old ones diffused

RNA synthesis in Chromosome puffs

RNA synthesis in Chromosome puffs

Model of RNA synthesis in Chromosome puffs

A model for the structure of an interphase chromosome

Position Effects on Gene Expression

Heterochromatin: condensedEuchromatin: loose

Speculative Model for the heterochromatin at the ends of yeast chromosomes

Sir: Silent information regulator binding to unacetylated histone tails

Speculative Model for the heterochromatin at the ends of yeast chromosomes

DNA-binding proteins recognize DNA sequence close to telomere, recruit Sir proteins and cause histone tail modification, forming heterochromatin

Two speculative models for how the tight packaging of DNA in heterochromatin can be inherited during chromosome replication

The specialized nucleosome formed on centromeresAlso belongs to heterochromatin

The structure of a human centromere

1. Alpha satellite DNA sequence

2. Kinetochore inner plate3. Kinetochore outer plate4. Spindle microtubules

The plasticity of human centromere formation

A typical mitotic chromosome at metaphase

SEM of a region near one end of a typical mitotic

chromosome

EM of a mitotic chromosome

Chromatin PackingCondensin plays important roles

The SMC (Structural Maintenance of Chromosomes) proteins in

condensins

Selective localization of two interphase chromosomesChromosome 18 (red) and 19 (turquoise)

Specific regions of interphase chromosomes in close proximity to the nuclear envelope

Two different regions of chromosome 2 (yellow and magenta) close to the nuclear envelop (green)

• Chromosomes are decondensed during interphase and hard to visualize

• Lampbrush chromosomes of vertebrate oocytes and polytene chromosomes in the giant secretory cells of insects are exceptions, revealing the global organization of chromosome

• Gene expression needs the decondensation of chromosome loops

• Euchromatin and heterochromatin• Telomere and centromere are general heterochromatin• Chromosomes are spatially organized and deposited in

nucleus• Mitotic chromosomes are condensed and organized.

Summary