1. Basic biology: A Review

2. Which half are you? Half of you will already know >90% of this material-- your challege will be to stay awake enough to catch the <10% you don't know Half of you will know <10% of what we will talk about-- your challege will be to learn an enormous amount of material in a short 2.5 hour lecture.

3. Genomes Constructed from DNA (mostly) Sizes Human = ~ 3.2 GB Drosophilla (fruit fly) = ~ 137 MB Bacteria (M. tuberculosis) = 4.4 MB HIV = 9181bp

6. Genome made up of chromosomes Humans have 23 chromosomes Flys have 4 chromosomes Bacteria have 1 chromosome D. McDonald Seattle Laboratory of Pathology

7. Chromosomes have genes The density of genes on a chromosome can be quite variable Chromosome 19-- 23 genes per million bp Chromosome 13-- 5 genes per million bp Gene length An average human gene size(spliced) is around 3000bp

8. "non-functional" regions 3-10% may actually code for a protein LINES -Long Interspersed Nuclear elements Transposable elements AT rich regions SINES - Short.... Alu, Mariner elements Transposable elements Repeats

9. Transcription Allows the flow of information from genes to the end product (mostly) proteins RNA the working copy of genetic information RNA is a "copy" of DNA Single stranded Condensed, all of the "filler" is taken out Translated into proteins

10. Introns and Exons

11. Other mRNA modifications Splicing removing intons, splicing exons Capping Adding a 'G' in reverse orientation to the 5 prime end Polyadenylation not coded in the DNA ~200 A's added to the 3 prime end of mRNA

12. From genes to proteins

13. What makes a protein Amino acids are linked together to make a peptide, which is extended and folded into a functional protein. 20 amino acids Several classes of amino acids Some substitutions can be tolerated in the overall structure of the protein (sometimes)

14. From sequence to structure So a protein is a chain of amino acids... How is the structure formed Due to the interaction of amino acids with adjacent amino acids as well as interaction of groups of amino acids with the surrounding environment. Computer modeling software exists to predict this structure They typically do not do a good job

15. Summary of information flow DNA to RNA to Amino acid (protein) Complications: How does DNA or RNA get made? How is the replication of DNA from generation to generation handled? What controls which gene gets made first or how many copies of a protein are made?

16. Replication of DNA One could envision several methods of replication conservative or semi- conservative.... Important considerations: errors, start and stop points, mechanics...

17. DNA replication

18. Transcription Factors and Binding Sites RNA polymerase is ~ 1.6 X 10 -8 meters long Human DNA when streched out and tied togther would stretch 1.8 meters Polymerase needs to cover a huge area, quickly and accurately Not all of the DNA is as accessable as others How to find the genes that need to be transcribed quickly?

19. Context Transcription -The conversion of DNA information to RNA information. Happens before splicing Mechanism for transcription is RNA polymerase. Followed by translation - The conversion of RNA information to amino acid sequence

20. RNA polymerase >10 subunits Several types I-III Type II is involved in "gene" transcription. Type I and III transcribe ribosomal and transfer RNA

21. Characteristics of transcription (eukaryotic) Usually positive regulation Usually a single transcripted gene

22. How transcription elements are discovered Use of a reporter system Procedural, makes the enzyme assay routine Artifacts present, not all factors will be present Chop off the DNA until you get a change in the reporter enzyme levels Mutate a potential site (Single bp changes) Consensus sequences

23. Promoters vs Enhancers Characteristics of each Promotors <200 bp from start Enhancers < 'several kb' May end up closer due to bending Typically more global regulatory elements, tissue or time specifc. Enhancers several closely packed sites Promotors more dispersed Both consist of < 10 bp elements

24. Enhancers Can be either upstream or downstream. Could change density of supercoiling. Provid an entry site for the polymerase. Anchor the DNA at a place within the cell for access.

25. Questions about translation Punctuation? Size of frame, 20 amino acids 4 different bp-- need more than one bp to encode each amino acid M. Nirenberg and H. Matthael broke the code ~10 years after the structure was discovered

26. Codons?

27. tRNA

29. Finding your way on molecules 5 prime end is the start of DNA 3 prime end is the end of DNA N terminal is the start of a protein C terminal is the end of a protein

30. Proteins Primary-> secondary -> tertiary structure -> quartenary There are several common protein motifs Beta sheet alpha helix cystines

31. Mutation Common themes in mutation point mutation transition G or C -> A or T transversion A T -> TA or GC -> CG recombination transposition deletion

32. Severity of mutation No effect point mutants in particular can be silent (no change to AA) can have minimal effect - not critical to protein function Major effect insertions which inactivate a protein can be reversed Deletions

33. SNPs Single nucleotide polymorphisims The human genomic sequence even without errors is an approximation Normal variation in sequence is several million per person Can be important in drug tolerance and disease prevelence questions