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Today…

Genome 351 , 4 April 2014, Lecture 2. Today…. DNA is the genetic material. Structure of DNA reveals a digital code. Replication of DNA. DNA in chromosomes. Where do the proteins come from?. Each cell division requires a doubling of the amount of protein.

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Today…

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  1. Genome 351, 4 April 2014, Lecture 2 Today… DNA is the genetic material Structure of DNA reveals a digital code Replication of DNA DNA in chromosomes

  2. Where do the proteins come from? Each cell division requires a doubling of the amount of protein. And each daughter cell has to be capable of generating new proteins. This heritability is reflected in the transmission of traits. In some cases these traits could be shown to be the result of specific protein defects. Scientists knew the heritability resided in chromosomes in the nucleus.

  3. Base PO4 Sugar Two varieties of large base: A and G Base PO4 Sugar Two varieties of small base: T and C DNA (deoxyribonucleic acid) is a simple and boring molecule • Long polymer • Similar in all life forms • Four subunits Each subunit has three parts: a sugar ring, a phosphate and a base How could this hold the secret of life?

  4. Subunits link together to form polymer Proportions of subunits (A, C, G, T) are roughly 1/4 each Long chains with no activity, no shapes

  5. Subunits link together to form polymer By contrast, proteins consist of 20 different subunits (with unique chemical properties) They fold into a variety of different structures with different activities

  6. DNA, not protein, is the genetic material In the 1940’s Avery, MacLeod and McCarty showed that pure DNA could change bacterial traits. Animation describing in more detail that DNA is the basis of heredity: http://www.dnaftb.org/dnaftb/17/concept/

  7. Avery, MacLeod and McCarty’s Experiments heat-killed virulent + live nonvirulent non-virulent pneumococcus virulent pneumococcus heat-killed virulent Conclusion: a heritable factor from the dead virulent strain is transferred to the live non-virulent strain.

  8. Avery, MacLeod and McCarty’s Experiments The purified heritable factor looked a lot like DNA: Also: the heritable factor was destroyed by DNA-degrading treatments; The heritable factor was unaffected by protein-degrading treatments But it was bacteria, and DNA was so simple!

  9. Wilkins and Franklin show DNA is double stranded & helical

  10. Chargaff showed that there are correlations in the A/T & G/C content of DNA Chargoff’s rules: (1). DNA from any organism: A content = T content G content = C content (2). The A/T and G/C ratios vary in different organisms e.g., humans: A+T = 40%; G+C = 60% E. Coli: A+T = 50%; G+C = 50%

  11. Watson and Crick solve the structure of DNA In 1953 At the 40th anniversary

  12. Watson and Crick realize the bases face inward and pair with one another G C A T

  13. G C A T Watson and Crick realize the bases face inward and pair with one another

  14. Other illustrations of the double helical arrangement of the bases

  15. DNA as an information storage device • Backbone keeps the order of bases constant • Base-pairing means one strand contains the information of two • Replication provides exact copies for each daughter cell • Bases can be ‘read’ like letters on a page!

  16. DNA as an information storage device • Instead of a 2-bit code like computers, DNA is a 4-bit code. • Both strands can be read. • Each copy of the human genome contains 3 billion base pairs (6 billion bases); the diploid genome contains 6 billion base pairs (12 billion bases) • Each copy of the human genome is over a yard long! • A 12 Gbyte hard drive in a nucleus a few microns across!!

  17. Some conventions for designating DNA 5’ 5’ 3’ 3’ 5’pApCpTpGpTpGpCpAOH3’ 3’HOTpGpApCpApCpGpTp5’ 5’pApCpTpGpTpGpCpAOH3’ 5’ACTGTGCA3’ ACTGTGCA

  18. Some DNA sequence from the CF gene ATTCATTGTAGAGATGCCGAACGGGGGTCTAGAGCTTGCCTTTTCGGGGTCTCTCCCGTCCTTCT

  19. Some DNA sequence from the CF gene ATTCATTGTAGAGATGCCGAACGGGGGTCTAGAGCTTGCCTTTTCGGGGTCTCTCCCGTCCTTCT CCATCCTCCTTATCTCCTGGGCTGCCCCCTCTCCCCCCGCGCCCCGCTCTCCCTGGCTCGCCCGG GCCTAGGGCGCCGCCTGCAGTTGCGCGCGGCCGCCTCTAGATGGAACTTTCTCACCAACGCAAGG CCCGGCCGGAGCAGCTACCCGGGAGCTGGGCGGCGAGGGGCTACTTTCTCTCATTCCGGCGGGTG CAGGATCGGGGGGCCTGGGCAGTAACTAGTGGGGAGGAGCGCTGGACTGTGCACGTCGAGCCCGG CAGGTTTCCGCATGCGGCATGCGAAGGGAATCCCGAGGTTTCCCTGCAGAACCCGAGCACGGCTC CCCCGGAGTTTCCTGCCCCGCGTCTGCGGCTCCTTGAATCATCTCAATAAAATGACCGTCCCGGT AGCCACCCATGCCCCTTCCTGCGCAGTGCCCGCAGCGGACCGCGCTGTGTGGTACCTCGAGCCCT GGGGACTCTGTTGCACGCGTCCCTCAGACCCTCGGGGGCGGGGAGTGGGGAGACAATCGCCAGAG CCGCGGGGCGGGACAAATGGCGGAACCGCCGCGCGGCGCCAGGCAAACTTTGCAAGGGAACCGCG CGGCTTGCCGGCTCTACTTTAAGCATTCCCGAAAAGAAAGCATGTGGCGGGACACTTGTCATCTA CCATGTGTTATTCTCGGTGACGCTTTCTGGAGCTGTGTTCACCGGGGACCCGGGCTCGCGGGTGC TGCCCGCTGTGCTCGGGCGGGCGTCGCGCCTCCCCGCGCCGGTCCCGGGCTCGCCAGGCAGCCGG AGCCGCTGGGCTCCTCCACAACCATATTCCTTCTTCTACCGCTCCCGCTTCTTCCCACCCTCTCA How is all of this information copied and transmitted faithfully (i.e., without errors) during cell division and gamete formation? Another 275 pages like this for all of the CF gene; Another 3.3 million pages like this for the entire human genome sequence For more go to http://www.ncbi.nlm.nih.gov/blast/Blast.cgi Click on ‘nucleotide search’ and copy in sequence.

  20. Mitosis (somatic cell division) Meiosis (formation of sperm and eggs) “It has not escaped our notice that the specific pairing we have postulated suggests a possible copying mechanism for the genetic material” Watson & Crick (1953) Nature171 (more on these topics next week)

  21. “It has not escaped our notice that the specific pairing we have postulated suggests a possible copying mechanism for the genetic material” Watson & Crick (1953) Nature171

  22. Watson & Crick’s proposed DNA copying mechanism: semi-conservative DNA replication Two strands separate and each acts as a template for the synthesis of a new strand. A is placed opposite T, G is placed opposite C, T with A and C with G.

  23. DNA replication movie http://www.contexo.info/DNA_Basics/replication%20move.htm

  24. How is the 6 billion bp of human DNA packed into a nucleus? Chromosomes! Each chromosome contains a single DNA double helix stretching from one end to the other! Human chromosome 1 is ~150 mm long, but condensed to < 6 microns. 1 human cell has 2 meters of DNA (end-to-end). Proteins condense the DNA.

  25. Chromatin • Composed of DNA and associated proteins • DNA winds around histone proteins • (nucleosomes) • Other proteins wind DNA more tightly to form a chromosome

  26. 1 chromatid = 1 double-stranded DNA molecule A human Chromosome shortly before cell division Sister chromatids are the two copies of the DNA double helix after replication

  27. Human Chromosomes Each chromosome has its own characteristic appearance variations in folding  distinctive banding patterns (when stained); chromosomes can also be distinguished by size from 1 individual karyotype: picture of human chromosome set 22 pairs of autosomes 2 sex chromosomes

  28. Chromosome appearance is reproducible… …even between species Left-to-right: chr 1 & 2, human, chimp, gorilla, orangutan

  29. Cancer cell (XX) Karyotyping with “chromosome paints” Hybridization with a color-coded set of chromosome-specific probes (color-coded staining for different chromosomes) Normal cell (XX)

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