1. Selfish DNA
Honors Genetics

2. DNA – Genes and the Rest Genic ( Gene containing portion of DNA) -
Genes are viewed as “ORFS” – Open Reading Frames – These are determined by a start
3’ TAC and a stop ATT5’
Genes account for 25% of our DNA
In a gene there are coding regions
Exons
Between the Exons there are intervening sequences called Introns

3. What is the product of a Gene ?
Proteins – All types such as transmembrane proteins , transport proteins, immune proteins, messenger proteins, enzymes, channels, toxins, developmental proteins
( hox), transcription factors, and many more
RNAs – m RNA ( intermediate in protein synthesis), t RNA required for protein synthesis, r RNA( ribosomal RNA’s), RNAi, antisense RNAs, micro RNAs, snurps, spliceosome RNAs and many more

4. ORF

5. What is a Gene?

6. Gene Expression

7. Spliceosome – editing the primary transcript

8. Intron Borders

9. DNA to Protein
Only 1% of DNA actually defines the structure of genes and proteins
Out of 46 chromosomes containing 30,00-50,000 genes only 1% is actively engaged in keeping you alive

10. Making a Protein

11. Genes are grouped in islands on chromosomes
Genes are in clusters on chromosomes
What is between – the space between the genes contains DNA that has survived through evolution
It is believed to be the substance of mutations – contributing to change in the change for both the positive and negative

12. Genes were thought to be fixed in one location on a chromosome
17q31.2

13. Barbara McClintock discovered “ jumping genes”
Jumping genes are referred to as mobile
They have the ability to change their position and jump from one chromosome to another
Jumping genes are also called TRANSPOSONS

14. The Original Jumping Genes

15. Transposons
1) IS - insertion sequence. Inverted repeats + transposase gene
2) Composite transposon. Two IS elements + antibiotic resistance gene(s)
3) Noncomposite transposon. Inverted repeats + transposase gene + antibiotic resistance gene(s)

16. Transposon Action

17. Transposon structure

18. Transposable elements and the new meaning of mutation

19. Retrotransposons
Retrotransposons move by a "copy and paste" mechanism but in contrast to the transposons described above, the copy is made of RNA, not DNA.
The RNA copies are then transcribed back into DNA — using a reverse transcriptase — and these are inserted into new locations in the genome.
Many retrotransposons have long terminal repeats (LTRs) at their ends that may contain over 1000 base pairs in each.
Like DNA transposons, retrotransposons generate direct repeats at their new sites of insertion. In fact, it is the presence of these direct repeats that often is the clue that the intervening stretch of DNA arrived there by retrotransposition. About 40% of the entire human genome consists of retrotransposons.

20. Sines ( Short Interspersed elements)
SINEs are short DNA sequences (100–400 base pairs) that represent reverse-transcribed RNA
Alus - Thousands of our Alu elements occur in the introns of structural genes.

22. Alu Action
ALU elements have been accumulating in the human genome throughout primate evolution, reaching a copy number of over a million per genome. However, most of these Alu copies are not identical and can be classified into several subfamilies (reviewed in DEININGER and BATZER ).
These different subfamilies of Alu elements were generated once mutations occurred within the "master" or "source" gene that actively retroposed at different rates and time periods of primate evolution (DEININGER et al ).
Currently, the Alu retroposition rate is reduced by 100-fold from its peak early in primate evolution (SHEN et al ). The vast majority of the Alu elements present in the human genome inserted before the radiation of extant humans and are therefore observed in all individuals in the human population.

23. Microsatellites
Studies show that microsatellites, tandem repeat sequences abundant in the genomes of higher eukaryotes, contain reiterating A-rich loci, which are involved in the higher-order organization of the chromatin
Other studies have shown satellites consisting of about 1 million copies of a 221-bp tandem repeat unit has been localized in the centromeres of 58 of the 64 horse chromosomes
Many hundreds of studies have implicated mutations in satellites, minisatellites, and microsatellites, in diseases which show genetic linkage, including studies on Crohn's disease

24. What is Selfish DNA?
The theory that we creatures exist for the preservation of genes and are nothing more than their throwaway survival machines.
Natural selection means the differential survival of the “ fittest”
Does natural selection “ choose” the most fit individuals or the most fit genes?

25. What are the characteristics of Selfish DNA?
They have been called "junk" DNA and "selfish" DNA.
"selfish" because their only function seems to make more copies of themselves and
"junk" because there is no obvious benefit to their host.

26. Some theories on Alus
Some of these contain sequences that when transcribed into the primary transcript are recognized by the spliceosome.
These can then be spliced into the mature mRNA creating a
new exon, which will be transcribed into a new protein product.
Alternative splicing can provide not only the new mRNA (and thus protein) but also the old.
In this way, nature can try out new proteins without the risk of abandoning the tried-and-true old one.

27. Alternative splicing

28. Alternative Splicing