Chromosome Organization & Molecular Structure

Chromosomes & Genomes Chromosomes complexes of DNA & proteins – chromatin Viral – linear, circular; DNA or RNA Bacteria – single, circular Eukaryotes – multiple, linear Genome The genetic material that an organism possesses Nuclear genome Mitochondrial & chloroplasts genome

Infectious particles containing nucleic acid surrounded by protein capsid Rely on host cell for replication, transcription, translation Exhibit limited host range Genomes size bp Viroids – nucleic acid & bound protein Bacteriophage – simple viruses of prokaryotes Viruses – intricate, encapsulated nucleic acid May have membrane envelope Viruses

Some Virus Structures Phage Capsid protein TMV

In a region called the nucleoid DNA in direct contact with cytoplasm Bacterial Chromosomes

Chromosomal DNA is compacted ~ 1000 fold to fit within cell

Size Escherichia coli ~ 4.6 million bp Haemophilus influenzae ~ 1.8 million bp Composition E coli ~6000 genes Genes encoding proteins for related functions arranged in operons Intergenic regions nontranscribed DNA Single origin of replication (Ori) Bacterial Chromosomes

Prokaryotic Gene (Operon) Structure Stop Codon TAA, TAG, TGA Regulatory Elements Cistron 1 Coding Sequence= ORF +1 ATG Stop Codon TAA, TAG, TGA ATG Coding Sequence= ORF Cistron 2 Promoter & Operator DNA Terminator sequence Regulatory & Coding Sequence Unit = Operon Protein A Protein B Structural or Coding Sequences Regulatory Sequences

Eukaryotic species contain one or more sets of linear chromosomes Chromosomes in nucleus highly compacted to fit DNA packaged by proteins DNA-protein complex is chromatin Eukaryotic Chromosomes

Eukaryotic Gene Structure Promoter/ Enhancer Transcriptional Regulatory Elements Translation Start Codon ATG Exon1 Exon2Exon3 Translation Stop Codon TAA, TAG, TGA Transcription start site Transcription termination site

Histone proteins basic (+ charged lysine & arginine) amino acids that bind DNA backbone Four core histones in nucleosome Two of each of H2A, H2B, H3 & H4 Fifth histone, H1 is the linker histone Nucleosomes

Beads on a String Overall structure of connected nucleosomes resembles “beads on a string” Shortens DNA length ~ seven-fold

Nucleosomes associate to form solenoid structure 30 nm in diameter Compaction due to Histone H1 Nucleosomes Compact to 30 nm Fiber 10-54

Figure 10.21

Nuclear Matrix Association nuclear matrix proteins Arrange 30nm chromatin fiber into domains/loops

Matrix proteins form metaphase chromosomes

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

Interphase chromosome degrees of compaction Euchromatin Less condensed regions Transcriptionally active 30 nm fiber in radial loop domains Heterochromatin Tightly compacted regions Transcriptionally inactive Radial loop domains condensed Often repetitive sequences Heterochromatin vs Euchromatin

Types of Heterochromatin Figure Constitutive heterochromatin Always heterochromatic Always transcriptionally inactive Facultative heterochromatin Converts btwn euchromatin & heterochromatin Example: Barr body

Long, linear DNA molecules 3 types of sequences required for chromosome maintenance Origins of replication (many) Centromere (1) Telomeres (2) Eukaryotic Chromosome Organization Centromere Kinetochore proteins Origin of replication Telomere Genes Repetitive seqs

Chromosome Organization Genes located between centromere & telomeres 100s – 1000s of genes lower eukaryotes (i.e. yeast) Genes short Few introns higher eukaryotes (i.e. mammals) Genes long Many introns Non-gene sequences Repetitive DNA Telomere Centromere Satellite Transposons

Genome Organization

Unique Sequences non-repetitive sequences Found once or a few times in the genome Includes genes (regulatory & structural)

Sequence complexity related to # of times a particular sequence exists in genome 2 general types Moderately repetitive Highly repetitive (low complexity) Repetitive Sequences

Moderately repetitive 100 – 1000 copies tRNA, rRNA & histones genes Origins of replication Repetitive Sequences

Highly repetitive copies Each copy relatively short Microsatellites (VNTRs) mono-hepta nucleotide repeats AGAGAGAGAGAGAGAG CCAACCAACCAACCAACCAACCAACCAA Retroelements Transposable elements Some sequences are interspersed throughout the genome Example: Alu family in humans (retrotransposon) Other sequences are clustered together in tandem arrays Example: centromeric satellite & telomeric regions Repetitive Sequences

DNA fractions Absorbance* Satellite DNA Density

C o t ½ Measures Complexity Highly Repetitive Moderately Repetitive Unique

Repetitive Sequences on Chrom 22

Centromere probe rDNA probe Telomere probe Alu repeat probe