CHROMOSOME STRUCTURE &

DNA ORGANIZATION

Bacterial & Viral Chromosomes

• Viruses

– DNA or RNA

– SS or DS

– Linear or circular

• Bacteria

– Circular DNA

– DS DNA

– 1 chromosome; possibly multiple plasmids

Bacterial & Viral Chromosomes

• Universal problem

– How is the vast amount of genetic material

contained?

Fig. 12-3

Bacterial & Viral Chromosomes

• Viruses

– Genetic material tightly packed into capsid

– Functionally inert until released into host

• Bacteria

– DNA compacted into nucleoid

– Associated with DNA-binding proteins

Clicker question

• A)

• B)

• C)

• D)

Eukaryotic Chromosomes

• Humans

– Longest human chromosome = #1

• Unfolded ~10 cm

– All chromosomes unfolded ~2 m

– Cell nucleus ~5-8 m diameter

Eukaryotic Chromosomes

Fig. 12-11

Chromatin Structure

• Chromatin is a stable, ordered complex of DNA and protein

• Histones = major class of basic proteins in chromatin fibers – Positively charged

– Associate with phosphates in DNA backbone

• Five major types of histones are found in chromatin:

H1, H2A, H2B, H3 and H4

• Histones of different species are similar = conserved

Histones

H2A, H2B, H3, H4:

Form octamers (=2 tetramers)

– Associate with 147 bp of

DNA

H1 subunits associate with linker

DNA between nucleosomes

Fig. 11-11

Nucleosomes

Fig. 11-10

Eukaryotic Chromosomes

– Solenoid formation

• Coil of nucleosomes

– Looped domains

• Coil of solenoids

• Chromatin

– Chromatid formation

• Prophase of mitosis (or meiosis)

Fig. 11-11

Forms of Chromatin

• How does the degree of chromatin folding

affect transcription?

Forms of Chromatin

• Heterochromatin

– Compact regions

– Rich in satellite DNA

– Low in gene content

– Higher degree of folding

– Genetically inactive

• Centromeres & telomeres – repetitive sequences

• Introns

• Most of Barr bodies

Forms of Chromatin

• Euchromatin

– Less condensed

– High gene content (active “structural” genes)

– More diffuse (less folding)

• Satellite DNA

– Highly repetitive non-coding DNA sequences

Genome Organization in

Eukaryotes • Most of the genome does not encode

functional genes

So what is most of the DNA?

Fig. 12-13

Centromeric & Telomeric DNA

• Satellite DNA

– Short sequences repeated many times

– CEN regions all very similar

• 170 bp in tandem arrays up to 1M bp

– Telomere regions

• Short tandem repeats

Fig. 12-16

Middle Repetitive Tandem

Repeats • No known function in genome

– Often used as forensics markers

• Minisatellites

– VNTRs (variable number tandem repeats)

– 15-100bp sequences

– Form tandem repeats 1000-5000bp long

– Within & between genes

• Microsatellites

– Dinucleotides - (CA)n

Transposable Elements

• No known genomic function

• Able to move to different locations within

the genome

• SINEs (short interspersed elements)

– <500bp; present 500,000+ times in genome

– Alu family

• >5% of human genome

• Origin? RNA element dispersed through genome

via reverse transcriptase

Transposable Elements

• No known genomic function

• Able to move to different locations within

the genome

• SINEs (short interspersed elements)

• LINEs (long interspersed elements)

– L1 family

• >5% of human genome

• Retrotransposon

– Portion of L1 codes for reverse transcriptase

– L1 transcribed RT makes DNA complement new L1

integrated into new site on chromosome

Mitochondria & Chloroplasts

• mtDNA & cpDNA

– Circular DS DNA • Few associated proteins

• Small genomes

• Multiple copies

– Code for certain products essential for transcription/translation, cellular respiration & photosynthesis

– Involves unique ribosomes

• Endosymbiont hypothesis

mtDNA

mtDNA

• Introns & gene repetitions

sequences typically absent

• Replication dependent on nuclear

enzymes

• Respiratory proteins

– Quaternary structure derived from

nuclear and mt transcripts

Fig. 12-5

cpDNA

• Contains introns & repetitive sequences

• Larger genome & more copies than in

mitochondria