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Dynamic Probes of Physical States in Live Cells Presented by Dr. Brett Helms,

Dynamic Probes of Physical States in Live Cells Presented by Dr. Brett Helms, Molecular Foundry Lawrence Berkeley National Laboratories Berkeley, California Part of AMSEC ’ s MAD Seminar Series M aterials S cience S eminar Monday, April 11th

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Dynamic Probes of Physical States in Live Cells Presented by Dr. Brett Helms,

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  1. Dynamic Probes of Physical States in Live Cells Presented by Dr. Brett Helms, Molecular Foundry Lawrence Berkeley National Laboratories Berkeley, California Part of AMSEC’s MAD Seminar Series Materials Science Seminar Monday, April 11th 5:15pm in CF110 / Refreshments at 5:00pm in CF110

  2. Dideoxy sequencing animation • http://spine.rutgers.edu/cellbio/assets/flash/dideoxy.htm • http://www.dnalc.org/view/15479-Sanger-method-of-DNA-sequencing-3D-animation-with-narration.html

  3. Table 3-3

  4. PCR Animation • http://www.dnalc.org/resources/animations/pcr.html • http://www.dnalc.org/view/15507-The-cycles-of-the-polymerase-chain-reaction-PCR-3D-animation-with-no-audio-.html

  5. Figure 3-16

  6. Introducing mutations

  7. What are stem cells? • Non-specialized cells that have the capacity to divide in culture and differentiate into more mature cells with specialized functions. • Adult stem cells (ASCs), embryonic stem cells (ESCs).

  8. How do you clone an animal?

  9. A decade of reproductive cloning 1996 1998 2000 2001 2003 Who’s next???? 2005

  10. Many (all?) fates possible Limited set of fates possible Embryonic stem cells (ESCs) Adult stem cells (ASCs)

  11. Ionic properties of amino acids impart ionic properties to proteins • in general these are SURFACE properties (i.e. charged sidechains are on solvent-exposed outside of folded structure) • affect protein-ligand binding (e.g. DNA-binding proteins) or catalysis • average charge on protein is an important consideration in the design of a purification process

  12. Models Models from Cal Lutheran PDB files

  13. Ionic properties of amino acids impart ionic properties to proteins • in general these are SURFACE properties (i.e. charged sidechains are on solvent-exposed outside of folded structure) • affect protein-ligand binding (e.g. DNA-binding proteins) or catalysis • average charge on protein is an important consideration in the design of a purification process

  14. pKa3 pKa2 pKa1

  15. Other Properties of Amino Acids • Stereochemistry (all biosynthetic proteins made up of L-isomer) • Hydropathy (partitioning between polar and nonpolar solvents as indicator of polarity) these two properties are major determinants of peptide conformation

  16. Example of a protein sequence MANSKINKQL DKLPENLRLN GRTPSGKLRS FVCEVCTRAF ARQEHLKRHY RSHTNEKPYP CGLCNRCFTR RDLLIRHAQK IDSGNLGETI SHTKKVSRTI TKARKNSASS VKFQTPTYGT PDNGGSGGTV LSEGEWQLVL HVWAKVEADV AGHGQDILIR LFKSHPETLE KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH HEAELKPLAQ SHATKHKIPI KYLEFISEAI IHVLHSRHPG DFGADAQGAM NKALELFRKD IAAKYKELGY G N-terminus C-terminus

  17. VVP page 150 “nonpolar” “polar”

  18. VVP Fig 6-1 p 125

  19. VVP Fig 5-1 p 94 C-termini N-termini

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