Chromosome Organization and Molecular Structure

Chromosomes are the structures that contain the genetic material They are complexes of DNA and proteins The genome comprises all the genetic material that an organism possesses In bacteria, it is typically a single circular chromosome In eukaryotes, it refers to one complete set of nuclear chromosomes Note: Eukaryotes possess a mitochondrial genome Plants also have a chloroplast genome Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

DNA sequences are necessary for The main function of the genetic material is to store information required to produce an organism The DNA molecule does that through its base sequence DNA sequences are necessary for 1. Synthesis of RNA and cellular proteins 2. Replication of chromosomes 3. Proper segregation of chromosomes 4. Compaction of chromosomes So they can fit within living cells Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

VIRAL GENOMES Viruses are small infectious particles containing nucleic acid surrounded by a capsid of proteins For replication, viruses rely on their host cells ie., the cells they infect Most viruses exhibit a limited host range They typically infect only specific types of cells of one host species Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Bacteriophages may also contain a sheath, base plate and tail fibers General structure of viruses

Viruses with a simple structure may self-assemble During an infection process, mature viral particles need to be assembled Viruses with a simple structure may self-assemble Genetic material and capsid proteins spontaneously bind to each other Example: Tobacco mosaic virus Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

A typical bacterial chromosome contains a few thousand different genes Bacterial chromosomal DNA is usually a circular molecule that is a few million nucleotides in length Escherichia coli  ~ 4.6 million base pairs Haemophilus influenzae  ~ 1.8 million base pairs A typical bacterial chromosome contains a few thousand different genes Structural gene sequences (encoding proteins) account for the majority of bacterial DNA The nontranscribed DNA between adjacent genes are termed intergenic regions Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

A few hundred nucleotides in length Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

The looped structure compacts the chromosome about 10-fold To fit within the bacterial cell, the chromosomal DNA must be compacted about a 1000-fold This involves the formation of loop domains The looped structure compacts the chromosome about 10-fold The number of loops varies according to the size of the bacterial chromosome and the species E. coli has 50-100 with 40,000 to 80,000 bp of DNA in each Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

DNA supercoiling is a second important way to compact the bacterial chromosome Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

EUKARYOTIC CHROMOSOMES Eukaryotic species contain one or more sets of chromosomes Each set is composed of several different linear chromosomes The total amount of DNA in eukaryotic species is typically greater than that in bacterial cells Chromosomes in eukaryotes are located in the nucleus To fit in there, they must be highly compacted This is accomplished by the binding of many proteins The DNA-protein complex is termed chromatin Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Has a genome that is more than twice as large as that of Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Required for proper segregation during mitosis and meiosis Eukaryotic chromosomes contain many origins of replication approximately 100,000 bp apart Required for proper segregation during mitosis and meiosis Kinetochore proteins link the centromere to the spindle apparatus Prevent chromosome sticky ends which could lead to translocations and shortening

Repetitive Sequences Sequence complexity refers to the number of times a particular base sequence appears in the genome There are three main types of repetitive sequences Unique or non-repetitive Moderately repetitive Highly repetitive Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Repetitive Sequences Unique or non-repetitive sequences Found once or a few times in the genome Includes structural genes as well as intergenic areas In humans, make up roughly 41% of the genome Moderately repetitive Found a few hundred to a few thousand times Includes Genes for rRNA and histones Origins of replication Sequences that regulate gene expression and translation Transposable elements Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Repetitive Sequences Highly repetitive Found tens of thousands to millions of times Each copy is relatively short (a few nucleotides to several hundred in length) Some sequences are interspersed throughout the genome Example: Alu family in humans Represents 10% of human genome Found every 5-6000 bp Other sequences are clustered together in tandem arrays Example: AATAT and AATATAT sequences in Drosophila These are commonly found in the centromeric regions Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Introduction to chromatin structure Chromatin is a complex made up of DNA and proteins. The proteins consist of the basic histone proteins and some nonhistone proteins.

Histone proteins are basic They contain many positively-charged amino acids Lysine and arginine These bind with the phosphates along the DNA backbone Histone proteins have a globular domain and a flexible, charged amino terminus or ‘tail’ There are five types of histones H2A, H2B, H3 and H4 are the core histones Two of each make up the octamer H1 is the linker histone Binds to linker DNA Also binds to nucleosomes But not as tightly as are the core histones Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Diameter of the nucleosome Vary in length between 20 to 100 bp, depending on species and cell type Diameter of the nucleosome Overall structure of connected nucleosomes resembles “beads on a string” This structure shortens the DNA length about seven-fold Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Play a role in the organization and compaction of the chromosome Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Regular, spiral configuration containing six nucleosomes per turn Irregular configuration where nucleosomes have little face-to-face contact Regular, spiral configuration containing six nucleosomes per turn Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

The nuclear matrix is hypothesized to be an intricate fine network of irregular protein fibers plus many other proteins bound to these fibers. This structure is very dynamic and complex. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

The third mechanism of DNA compaction involves the formation of radial loop domains Matrix-attachment regions Scaffold-attachment regions (SARs) or 25,000 to 200,000 bp MARs are anchored to the nuclear matrix, thus creating radial loops Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Further Compaction of the Chromosome 1 1 1 6 4 2 2 5 5 3 3 2 3 6 5 4 6 Z 2 1 4 2mm 3 Z 5 Z (a) Metaphase chromosomes (b) Chromosomes in the cell nucleus during interphase Each of seven types of chicken chromosomes is labeled a different color. Each occupies a specific territory during interphase. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

There are two types of heterochromatin Constitutive heterochromatin Regions that are always heterochromatic Permanently inactive with regard to transcription Usually contain highly repetitive sequences Facultative heterochromatin Regions that can interconvert between euchromatin and heterochromatin Example: Barr body formation during development in female Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

The levels of compaction leading to a metaphase chromosome

Compaction level in euchromatin During interphase most chromosomal regions are euchromatic Compaction level in heterochromatin

Metaphase Chromosomes Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

The condensation of a metaphase chromosome by condensin The number of loops has not changed However, the diameter of each loop is smaller During interphase, condensin is in the cytoplasm Condensin binds to chromosomes and compacts the radial loops Condensin travels into the nucleus The condensation of a metaphase chromosome by condensin Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Cohesins along chromosome arms are released The alignment of sister chromatids via cohesin Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display