Chromosome Structure and Benjamin A. Pierce GENETICS A Conceptual Approach FIFTH EDITION CHAPTER 11 Chromosome Structure and Organelle DNA © 2014 W. H. Freeman and Company

Large Amounts of DNA Are Packed into a Cell DNA must be tightly packed to fit in small spaces (Fig. 11.1) Supercoiling Positive supercoiling, Figure 11.2 (b) Negative supercoiling, Figure 11.2 (c) Topoisomerase: The enzyme responsible for adding and removing turns in the coil.

Figure 11.2 Supercoiled DNA is overwound or underwound, causing it to twist on itself.

The Bacterial Chromosome Most bacterial genomes have a single circular DNA molecule

Figure 11.3 Bacterial DNA is highly folded into a series of twisted loops.

Organelle DNA Has Unique Characteristics Mitochondria and chloroplasts contain DNA Encodes some polypeptides used by the organelle, rRNA, and some tRNAs

Organelle DNA Has Unique Characteristics Endosymbiotic theory: proposes that mitochondria and chloroplasts were once free-living bacteria Both organelles are similar to eubacteria, and DNA sequences found within them are also similar to eubacteria

Organelle DNA Has Unique Characteristics Uniparental inheritance of organelle-encoded traits Animal mtDNA inherited almost exclusively from female parent Replicative segregation Each cell has hundreds to thousands of organelles Heteroplasmic cells: organelles segregate randomly

Traits Encoded by mtDNA Petite mutations in yeast Neurospora mutations Human diseases: MERRF, LHON, NARP, KSS, CEOP In plants, cytoplasmic male sterility

The Mitochondrial Genome Mitochondrial genomes are small and vary greatly (Table 11.4) Human mtDNA: circular, 16,569 base pairs; encodes two rRNAs, 22 tRNAs, and 13 proteins (Fig. 11.16) Yeast mtDNA: five times as large as human; encodes 2 rRNAs, 25 tRNAs, and 16 polypeptides (Fig. 11.17) Flowering-plant mtDNA: extensive size variation (Fig. 11.18)

The Evolution of Mitochondrial DNA High mutation rate in vertebrate mtDNA Number of genes and organization remains relatively constant Most copies of mtDNA identical

Damage to Mitochondrial DNA is Associated with Aging Many human genetic diseases associated with mtDNA appear in middle age or later Oxidative phosphorylation capacity declines with age; those with mutations in mtDNA start life with decreased oxidative phosphorylation capacity Mechanism of age-related mtDNA damage unknown

The Chloroplast Genome Many traits associated with chloroplasts exhibit cytoplasmic inheritance Chloroplasts shown to have their own DNA in 1963 Sequence very similar to DNA sequences found in cyanobacteria

Large Amounts of DNA Are Packed into a Eukaryotic Cell Chromatin structure (Table 11.1) Euchromatin Heterochromatin Histone proteins

Concept Check 2 Neutralizing their positive charges would have which effect on the histone proteins? They would bind the DNA tighter. They would separate from the DNA. They would no longer be attracted to each other. They would cause supercoiling of the DNA.

Concept Check 2 Neutralizing their positive charges would have which effect on the histone proteins? They would bind the DNA tighter. They would separate from the DNA. They would no longer be attracted to each other. They would cause supercoiling of the DNA.

Large Amounts of DNA Are Packed into a Cell Chromatin structure The nucleosome Chromatosome Linker DNA High-order chromatin structure 30 nm fiber 300 nm loops 250 nm wide fiber

Figure 11.4 Chromatin has a highly complex structure with several levels of organization.

Figure 11.5 The nucleosome is the fundamental repeating unit of chromatin.

Large Amounts of DNA Are Packed into a Cell Chromatin structure Changes in chromatin structure Polytene chromosome: created by repeated rounds of DNA replication with no cell division (Fig. 11.6) Chromosomal puffs DNase I sensitivity: correlates with gene activity (Fig. 11.7) Epigenetic changes: methylation; capable of being reversed and often due to environmental factors (Fig. 11.8)

Figure 11. 7 Chromosomal puffs are regions of relaxed chromatin where active transcription is taking place.

Figure 11. 7 Chromosomal puffs are regions of relaxed chromatin where active transcription is taking place.

Eukaryotic Chromosomes Possess Centromeres and Telomeres Centromere structure: constricted region of a chromosome where spindle fibers attach Figure 11.9 Telomere structure: ends of chromosomes; provide a means to replicate the ends of linear chromosomes

Figure 11.10 DNA at the ends of eukaryotic chromosomes consists of telometric sequences. (a) The G-rich strand at the telomere is longer than the C-rich strand. (b) In mammalian cells, the G-rich strand folds over and pairs with a short stretch of DNA to form a t-loop.

Eukaryotic DNA Contains Several Classes of Sequence Variation Organisms differ in amount of DNA per cell (C value) Denaturation Melting temperature Renaturation Types of DNA sequences in eukaryotes: Unique sequence DNA Gene family: Similar but not identical copies of unique DNA sequences that arose through duplication of an existing gene

Eukaryotic DNA Contains Several Classes of Sequence Variation Types of DNA sequences in eukaryotes: Repetitive DNA Moderately repetitive DNA: 150 ~ 300 bp long Tandem repeat sequences Interspersed repeat sequences Short interspersed elements: SINEs: Alu element Long interspersed elements: LINEs

Eukaryotic DNA Contains Several Classes of Sequence Variation Types of DNA sequences in eukaryotes: Repetitive DNA Highly repetitive DNA: less than 10 bp long Microsatellite DNA