Chapter 7 The Molecular Organization of Chromosomes

Chuan-Mu Chen, Ph.D.

Professor Department of Life Sciences National Chung Hsing University

Contents
I. The Molecular Basis of Chromosomes:
(I) Genome Size and Evolutionary Complexity (II) The Supercoiling of D NA (III) The Structure of Bacterial Chromosomes

II. The Organization of Chromosomes:

(I) The Nucleosome (II) Arrangement of Chromatin Fibers (III) Polytene Chromosomes

III. The Specialty in Eukaryotic Genomes:

(I) Repetitive Nucleotide Sequences (II) Centromere and Telomere Structure

7.1

Genome Size and Evolutionary Complexity

The Genome Size: 1. The size of Viral Genomes: 10-1000 kb 2. The size of Bacterial Genomes: 1- 10 Mb 3. The size of Eukaryotic Genomes: 10- 1000 Mb C-Value Paradox:
Among multi-cellular eukaryotes, genome size often differs enormously among species with the same level of metabolic, developmental, and behavioral complexity. The lack of correlation is known as C C-value paradox. paradox

Genome size ranges over several orders of magnitude in some groups of organisms. Genome size is not correlated with developmental, metabolic, or behavioral complexity.

An Example for Genomic CValue Paradox

Japanese Pufferfish: Two-toed salamander: Pufferfish: Two 400genome size 90,000-Mb genome size 400-Mb 90,000

7.2

The Supercoiling of DNA

Topoisomerase Enzymes
Topoisomerase I Topoisomerase II

The 3D structure of an association between duplex DNA and topoisomerase I

 The action of yeast topo II untangles a pair of DNA strand by TwoTwo-set jaws jaws model.

Figure 7.3: Topoisomerase II untangles a pair of DNA molecules by cleaving one DNA duplex and passing the other duplex through the gap

7.3

The Structure of Bacterial Chromosomes

Nucleoid Nucleoid or folded chromosome chromosome in E. coli
containing a protein core, supercoiled and relaxed DNAs and some RNAs. RNAs.
Figure 7.4: Electron micrograph of an E. coli chromosome, showing the multiple loops emerging from a central region

Among 40-50 Supercoiling Loops Presented in E. coli Nucleoid

DNase

7.4

The Structure of Eukaryotic Chromosomes

The NucleosomeThe Structural Unit of Nucleosome Chromatin

Figure 7.6: Dark-field electron micrograph of chromatin showing the beaded structure at low salt concentration

Octomer of Nucleosome Core Protein

Core DNA: Linker DNA:

2020-100 bp 145145-bp

The Nucleosome Core Particle

1st Packaging 2nm doublehelix DNA 11nm histone fiber
Figure 7.8: Subunit structure of the nucleosome core particle with the DNA duplex wrapped around it

The Arrangement of Chromatin Fibers in a Chromosome

2nd Packaging 11nm 30nm chromatin fiber

3rd Packaging 30nm 300nm chromatin fiber 4th Packaging 300nm 700nm chromatin fiber

Chromatin Condensed During Metaphase

5th Packaging 700nm * Scaffold proteins 1400nm chromatid

7.5

Polytene Chromosomes

Chromocenter
Figure 7.14: Polytene chromosomes from a larval salivary gland cell of Drosophila melanogaster

Polytene Chromosomes for Cytological Maps

1. Chromosome inversion; 2. Chromosome deletion; 3. Chromosome translocation; 4. Chromosome duplication

10

7.6

Repetitive Sequences in Eukaryotic Genomes

Kinetics of DNA Renaturation Cot Curve Concentration & Genome Size

4040-kb

160160-kb

Analysis of Genome Size and Repetitive Sequences by Renaturation

C 1 = Co [1+kCot] C/Co = 1/2; Cot1/2 = 1/k

11

Analysis of Genome Size and Repetitive Sequences by Renaturation

7.7

Unique and Repetitive Sequences in Eukaryotic Genomes

Unique Sequences : 3030-75%

* singlesingle-copy gene

Highly Repetitive Sequences : 5-45%

* typically 5050-300 bp / repeat; * >105 copies / genome * Alu repeat; SINE, LINE retrotransposon

MiddleMiddle-Repetitive Sequences: 1-30%

* 1010-1000 copies / genome * Histone, Histone, tRNA genes / 2020-600 copies * PP-element, copia transposon/ transposon/ 1010-50 copies

12

Highly Repetitive Sequences Largely Located in Heterochromatin Region

* Euchromatin * Heterochromatin

7.8

Centromere and Telomere Structure

Molecular Structure of the Centromere

1. Holocentric chromosome (Diffuse Centromere) Centromere) * Present in C. elegans chromosome * Microtubules attach along the entire chromatid 2. Localized Centromere * Microtubules attach to a single kinetochore in centromere (1) Point centromeres: centromeres: S. cerevisiae (2) Regional centromeres: centromeres: most of higher eukaryotes

13

A Point Centromere From S. cerivsae

Hybridization of Human Metaphase Chromosomes with alpha-satellite using FITC -satellite :

1. Presenting in human chromosomal centromeric regions; 2. A tandem repeat sequences with a length of 170170-bp; 3. The number of alphaalpha-satellite copies in the centromeric region ranges from 5000 to 15000 depending on the chromosome.

14

Molecular Structure of the Telomere

Telomere Formation in Tetrahymena Polymerized by Telomerase The enzyme telomerase has a RNA molecule that serves as the template for telomere DNA synthesis.

Figure 7.23: Telomere formation in Tetrahymena

15

Telomere Repeat Unit is a CGCG-rich Sequence

Hoogstein base pairing

16

Models of telomere structure

THE END

17