1. Genetics: Chromosome Organization

2. Chromosomes: Structures that contain the genetic material (DNA) Genome – complete set of genetic material in a particular cell In bacteria – typically a single circular chromosome In eukaryotes – one complete set of nuclear chromosomes * also have a mitochondrial genome and a chloroplast genome in plants

3. 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

4. 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

5. Viral genomes Genome can be DNA or RNA but not both May be single-stranded or double-stranded Can be linear or circular

6. 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

7. 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.

9. Prokaryotes have a single origin of replication.

10. Plasmid Map

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

13. 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.

15. 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

17. 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

18. TypeOccurenceExample Unique, nonrepetitiveFound once or a few timesStructural genes In humans, 40% of genome Moderately repetitive100 to several 1000 timesrRNA, histones, transposons Highly repetitive10,000 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.)

19. 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

21. 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?

22. Levels of compaction of DNA Nucleosomes – beads on a string, wrap DNA around histones

23. Nucleosomes compacted into a 30 nm fiber

24. Radial looped domains and further compacting into chromosomes at M phase

25. Heterochromatin and euchromatin – determine if gene expression is occurring or if DNA is active Not active - centromeres, telomeres

26. 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