1. BioPhysics 101 Biology section #2 Sept. 30 2003 Today’s topics: Dogmas Operons Cis and Trans Haplotypes

2. Transcription For a given gene, only one strand of the DNA serves as the template for transcription. An example is shown below. The bottom (blue) strand in this example is the template strand, which is also called the minus (-) strand,or the sense strand. It is this strand that serves as a template for the mRNA synthesis. The enzyme RNA polymerase synthesizes an mRNA in the 5' to 3' direction complementary to this template strand. The opposite DNA strand (red) is called the c oding strand, the non-template strand, the plus (+) strand, or the anti- sense strand. The easiest way to find the corresponding mRNA sequence (shown in green below) is to read the c oding, non-template, plus (+), or anti-sense strand directly in the 5' to 3' direction substituting U for T. PLUS (anti-sense) STRAND:5' T G A C C T T C G A A C G G G A T G G A A A G G 3' MINUS (sense) STRAND:3' A C T G G A A G C T T G C C C T A C C T T T C C 5‘ mRNA STRAND:5' U G A C C U U C G A A C G G G A U G G A A A G G 3' Plus strand, Minus strand, Sense Strand, Anti-sense strand.

3. Prokaryotic cell

4. Eukaryotic cell

5. Tree of life

6. CharacteristicEuacteriaArchaeaEukarya nuclear envelopeabsent present membrane-enclosed organelles absent present peptidoglycan in cell wallpresentabsent membrane lipidsunbranched hydrocarbons some branched hydrocarbons unbranched hydrocarbons RNA polymeraseone kindseveral kinds initiator amino acid for start of protein synthesis formyl-methioninemethionine intronsabsent present in some genes present antibiotic sensitivity growth inhibited by streptomycin and chloramphenicol not inhibited by these antibiotics A comparison of the three domains of life.

7. The central dogma At what stage do prokaryotes and eukaryotes differ?

8. Eukaryote central dogma

9. Operons: DNA segment = protein sequence + control circuitry

10. RNA polymerase transcription

11. Prokaryotic vs Eukaryotic RNA PolII

12. Transcription initiation: get bent

13. Prokaryotic Transcription initiation

14. Eukaryotic transcription initiation

15. Eukaryotic pre-initiation

16. Eukaryotic mRNA packaging.

17. What is this?

18. mRNA nuclear export

19. Nuclear pore

20. lacZ: Beta- galactosidase The E. coli Lactose operon

21. Lactose transporter: lacY

22. V-class proton pumps

23. P-class pumps

24. F-class proton pumps

25. Cell membrane receptors for hormones, neurotransmitters, odors, and light.

26. The potassium channel

27. Cis/Trans effect testing for markers in the E. coli lac operon using a plasmid. Cis/Trans testing in haploid organisms

28. Genotypes vs. Haplotypes Consider a diploid organism, such as a mouse (two copies of each gene per cell). Consider two mouse markers M A, and M B, that are biallelic (two known alleles for each). Represent the alleles as A, a, B, and b. For a mouse cell with the genotype AaBb, there are two possible haplotypes: Haplotype (AB, ab)Haplotype (Ab, aB) *Haplotypes ignore the (maternal, paternal) chromosome labels

29. If one or more of the markers was cis acting: The haplotype (AB, ab) would result in the phenotype L. The haplotype (Ab, aB) would result in the phenotype l. Cis vs. Trans Using our mouse example, suppose the linked markers M A, and M B, both influence a phenotype controlling hair length. Furthermore, assume that the wild type alleles A and B are dominant: The genotypes AAbb, aaBB and aabb would all result in the phenotype l. The genotype AABB would result in the phenotype L. The genotype AaBb would result in the phenotype L if both markers were dominant and trans acting. Cis and Trans are terms that express a relationship between two linked markers that influence a given phenot The genotypes AAbb, aaBB and aabb would all result in the phenotype l. ype.