Genetics: Chromosome Organization

Chromosomes:

• Structures that contain the genetic material (DNA)• Genome – complete set of genetic material in a particular cell

In bacteria – typically a single circular chromosomeIn eukaryotes – one complete set of nuclear chromosomes* also have a mitochondrial genome and a chloroplast genome in plants

What is the function of chromosomal sequences?• The synthesis of RNA and proteins• The replication of chromosomes• Proper segregation of chromosomes• Compaction of chromosomes to fit in living cells

Viruses in general

• Viruses contain a protein coat (capsid) and genetic material• Some, like bacteriophages, also contain a

sheath, base plate, and tail fibers.• Many eukaryotic viruses may have an

envelope with spike proteins• Viruses are NOT CELLULAR (no energy-

producing enzymes, ribosomes, or organelles), must RELY ON HOST CELLS• Most have limited host ranges

Viral genomes

• Genome can be DNA or RNA but not both• May be single-stranded or double-stranded• Can be linear or circular

How are viral genomes packaged?• Some are self-assembled – nucleic

acids and proteins spontaneously bind to each other (TMV)• Some like bacteriophages require

help from scaffolding proteins

Bacterial Chromosomes

• Highly compacted found in area(s) called the nucleoid• No membrane around chromosomes• Typically single circular chromosome but can have many copies (may

be linear however), may have plasmids• A few million bps in length• Have one origin of replication• Most genes code for structures but many repetitive sequences used

for DNA folding, replication, regulation, etc.

Prokaryotes havea single origin ofreplication.

Plasmid Map

How does the DNA fit into the cell?• DNA compacted 1000 fold• Forms loop domains • DNA supercoiling

Eukaryotic Chromosomes

• Eukaryotic cells have one or more sets of linear chromosomes• More DNA than prokaryotic cells• Located in a nucleus• DNA has to be compacted by binding to proteins to form chromatin (can change shape between loose and compact for gene expression)• Size of genome not related to complexity of organisms.

Functionally important regions for replication and segregation:• Many origins of replication – initiate DNA replication• Centromeres – for segregation, appears as a constricted region,

function as a site for kinetochores to link chromosomes to the spindle region• Telomeres – at ends of linear chromosomes, • prevent chromosomal rearrangements such as translocations• Prevent chromosome shortening by digestion by exonucleases and during

replication

Composition of eukaryotic genome• Unique nonrepetitive sequences found only a few times• Moderately repetitive sequences (rRNA genes), some come from

transposons (jumping genes)• Highly repetitive sequences – ex Alu family in humans; some are

interspersed and some are together – tandom repeats commonly found in centromeres

Type Occurence Example

Unique, nonrepetitive Found once or a few times Structural genesIn humans, 40% of genome

Moderately repetitive 100 to several 1000 times rRNA, histones, transposons

Highly repetitive 10,000 to one million times

Short sequences, some repeat in tandem array (repeats), often found in centromeres, function not known, ex Alu family in humans (names for cut by AluI re.)

How is sequence complexity evaluated

• DNA strands are heated to separate them.• Strands are allowed to renature, amount depends on concentration

of complementary partners that reattach• Highly-repetitive sequences faster because many copies• Denoted on a cot curve graph

Fitting DNA into the cell

• In humans, all of the DNA in a single cell would stretch to more than 1 meter• That has to fit into a nucleus with a diameter of around 2-4

microns• HOW?

Levels of compaction of DNA

• Nucleosomes – beads on a string, wrap DNA around histones

Nucleosomes compacted into a 30 nm fiber

Radial looped domains and further compacting into chromosomes at M phase

Heterochromatin and euchromatin – determine if gene expression is occurring or if DNA is active

Not active - centromeres, telomeres

Euchromatin and Heterochromatin..

• Histone tails have three types of modification including acetylation (Ac), phosphorylation (p), and methylation (Me). Euchromatin (a) is the loosely packed state that most histone tails are attached by acetyl groups. Heterochromatin (b) is the tightly packed state that most histone tails are attached by methyl groups