Lecture 9: Chromosome Structure & DNA

Sequence

• Viral / Bacterial chromosomes

• Eukaryotic chromosomes
• Specialized chromosomes

Reading: Chpt. 12

Chromosomes Take On Many Forms

Circular or Linear?
- Bacterial chromosomes - circular
- Eukaryotic chromosomes - linear

DNA or RNA?
Free living cells use DNA
Many viruses use RNA - single or double strands

E. coli Nucleoid DNA

Nucleoid = cytosolic regions where DNA is stored
- nucleoid = DNA + proteins
- Proteins are DNA-binding proteins
- Majority are made of histone-like proteins

Fig. 12.3
 Organellar Genomes Are Circular

Endosymbiosis Theory - Mitochondria and Chloroplasts

evolved from free living bacteria

Genomes are reminiscent of

bacterial DNA
- circular
- gene structure
- DNA replication

Polytene chromosomes
• Occur in Salivary glands of some insects
• DNA has been replicated many times but strands not
separated (no anaphase or cell division)
• Many copies of homologous chromosomes side-by-side
• “Puffs” are DNA (genes) actively transcribed

How Can A Nucleus “Hold” 3 billion bp of DNA?

46 chromosomes = 6.6 x 109 bp
- 1.8 m of DNA in each human cell
- must be packed efficiently to fit
- must be accessible for gene expression

DNA is packaged by Nucleosomes

- Similar to how thread is around spools
- many levels of packaging condenses
chromosome, as seen during mitosis
 Chromatin is DNA plus Protein
Nucleosomes
-“beads on string” of DNA

- Every 200 bp

- Core made of histone

proteins

- DNA wrapped twice

Fig. 12.8

Nucleosomes Contain Histone Proteins

Histone proteins conserved in all eukaryotes
- Nearly identical in all eukaryotes
- Positively charged proteins
- Bind to all DNA with equal affinity

Chromatin Is Packaged Via Fiber-Folding Model

Levels of Packaging
1. 2 nm “naked” DNA

2. 11 nm fiber
- nucleosomes

3. 30 nm fiber
termed “solenoid”

4. Looped fiber

Fig. 12.9
 Two Types of Chromatin in Interphase
Euchromatin DNA
- less condensed (11 nm fiber)
- does not stain as well
- contains expressed genes
Heterochromatin DNA
- Highly condensed (“packaged”) DNA (30 nm fiber)
- stains darkly
- contains unexpressed DNA
- centromeres
- telomeres
- one X chromosome in females - “barr body”

Lecture 9: Chromosome Structure & DNA

Sequence

• Centromere & telomeres

• Repetitive DNA

Reading: Chpt. 12

Chromosome Staining to Get Unique Banding

Stained chromosomes have Unique pattern of Bands
- stained bands unique to each chromosomes
- homologous chromosomes have same pattern
C-banding
- Giemsa stain
- heterochromatin / centromeres stain dark
Q-banding
- Quinacrine fluorescent stain
- heterochromatin / centromeres stain dark
G-banding - Most common staining method
- Treat chromosomes with trypsin (protease)
- Giemsa stain
 G-Banding for Karyotyping Chromosomes

G-bands are used to identify homologous pairs

- homologous pairs lined up

Fig. 12.12

G-banding Used to “Map” Chromosomes

Bands on p and q arm were given designator numbers
- genes are mapped onto these banding regions

Fig. 12.13

Eukaryotic Genomes Contain Many Different

Types of Repetitive DNA
In Humans, greater than 50% of genome is repetitive
Different Types of Repetitive DNA
 Different Types of Repetitive DNA in Genome
Some types are generally called “satellite” DNA
Most repetitive DNA is not within any genes
Fig. 12.14

Mini and Micro-Satellite DNA Have been used for

Phylogenetic and Forensic Analysis

- Mini-satellite DNA:
- 10 - 100 bp in tandem repeats
- Variable Number Tandem Repeats (VNTR)
- Sometimes used for forensics & genotyping

- Micro-satellite DNA:
- 2 - 4 bp tandem repeats
- These are the “Short Tandem Repeats” (STRs)
- Current method for forensics & genotyping

Neither have any known function in human genome

What is Satellite DNA?

- DNA centrifuged in CsCl gradient
- DNA sediments differently depending on density
- G-C rich DNA is denser than A-T rich DNA

Fig. 11.15
 Centromeres Have Some Repetitive DNA
- precise sequences that make up centromeres have
been determined in yeast (fungi)
- Termed “Cen” sequences (see Fig. 11.17)
- Can be stained by in situ hybridization

Fig. 19.16
(mice)

Mini and Micro-Satellite DNA Have been used for

Phylogenetic and Forensic Analysis

- Minisatellite DNA:
- 15 - 100 bp in tandem repeats
- Variable Number Tandem Repeats (VNTR)
- Used for forensics & genotyping

- Microsatellite DNA:
- 2 - 4 bp repeated in tandem
- Include, di-, tri-, and tetra-nucleotide repeats
- Used for forensics & genotyping

Neither type have a known function

Pseudogenes are Common in Eukaryotes

- In addition to repetitive DNA, there is single-copy
DNA that is is not part of a gene

- Pseudogenes make up part of this repetitive DNA

- Non-functional copies of genes
- Some result from unequal crossing over
- Mutations accumulate blocking expression

- Reverse transcription of mRNA can make pseudogene

- Common cause of pseudogenes
- Makes DNA copy from mature mRNA
- These lack introns (key feature) and promoters
- Not expressed