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E. Coli bacteria

E. Coli bacteria. Red blood cell. Plant cell. ameoba. Eukaryotic cell. SEM images. _. +. +. _. Glycerol subunit. double bond. cholesterol. DPPC. 1-palmitoyl-2-oleoyl-PC. 1,2-di-palmitoyl-glycero-3 phosphocholine. 16:0/18:1. 16:0/16:0. Nanotech Application of DPPC (Coe Group).

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E. Coli bacteria

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  1. E. Coli bacteria Red blood cell Plant cell ameoba Eukaryotic cell

  2. SEM images

  3. _ + + _ Glycerol subunit double bond cholesterol DPPC 1-palmitoyl-2-oleoyl-PC 1,2-di-palmitoyl-glycero-3 phosphocholine 16:0/18:1 16:0/16:0

  4. Nanotech Application of DPPC (Coe Group) shiny side Ni mesh dull side Ni mesh Thickness Ni mesh 10 mm Cu-coated 10 mm before Cu-coated monolayer trilayer

  5. DPPC metal glycerol chiral carbon trilayer monolayer

  6. DPPC chiral carbon metal

  7. Control of Optical Transmission Through Microchannels 20o 30o 35o 40o 45o 50o 55o 60o 65o 70o 75o 20o Optical Polarized Microscope Images of Hexadecanethiol/Hydrated DPPC vs Temperature Schematic of Coated Mesh

  8. PM3 optimized Gramicidin A monomer (membrane structure). 15 amino acids, alternating L and D, coil into a nanochannel. A single-stranded, helical dimer (HD) spans a membrane allowing ion transport. O atoms (dark) of C=O groups line the ion channel. Williams et al., Nanotechnology, 15 S495-S503 (2004)

  9. C=O stretch, 16 different stretches, Amide I bands

  10. Halobacterium halobrium discovered by Dieter Oesterhelt, Walther Stoeckenius and A. Blaurock in 19711 Bacteriorhodopsin (BR) discovered by Dieter Oesterhelt and Walther Stoeckenius in 19732 colonies framed by the main chromosome with the external plasmids. it is divided into one large chromosome with 2,014,239 bp and 2 small replicons pNRC100 (191,346 bp) and pNRC200 (365,425 bp). O2 present they are red-pigmented4 as in a saline pond at a salt work near San Quentin, Mexico Halobacterium halobium sp. NRC-1 is a salt-loving (Halophiles) archaebacterium that inhabits natural salt lakes and areas where seawater is evaporated to produce salt3. BR in high concentrations but lacking O2 over San Francisco Bay4,11 is purple, called purple membranes Red Halobacteria in Owens Salt Lake in Owens Valley, California5 Halobacterium salinarum (electron microscope image)90.5-1.2 um x 1.0-6.0 um in size10 Great Salt Lake in Utah, the Dead Sea, or Lake Magadi in Southern Kenya's Maasai land

  11. Halobacterium salinarum (electron microscope image)90.5-1.2 um x 1.0-6.0 um in size10 light H+ H+ Purple membrane = 2-D crystalline bacteriorhodopsin lattice ADP flagellae ATP Sensor rhodopsins SR I and SR II ATP-synthase H+

  12. Archaea, common name for a group of one-celled organisms, many of which do not require oxygen or sunlight to live17. Certain archaebacteria, members of a group of primitive bacteria-like organisms, carry out photosynthesis in a different manner. The mud-dwelling green sulfur and purple sulfur archaebacteria use hydrogen sulfide instead of water in photosynthesis. These archaebacteria release sulfur rather than oxygen, which, along with hydrogen sulfide, imparts the rotten egg smell to mudflats. Halobacteria, archaebacteria found in the salt flats of deserts, rely on the pigment bacteriorhodopsin instead of chlorophyll for photosynthesis. These archaebacteria do not carry out the complete process of photosynthesis; although they produce ATP in a process similar to the light-dependent reaction and use it for energy, they do not produce glucose. Halobacteria are among the most ancient organisms, and may have been the starting point for the evolution of photosynthesis17.

  13. The sequence of bacteriorhodopsin6,12 (CP) The protein/lipid ratio is 75:25 Aspartic Acid (Asp) (EC) Arginine (Arg) Lysine (Lys)

  14. Wt ~ 26 kDa Volume=83 nm3 5 nm 45 Å or 0.0045 mm

  15. trans 9 11 7 5 13 4 8 10 15 12 6 3 14 2 1 Lysine (Lys) hn = 568 nm 9 7 11 5 13 4 8 10 cis 6 12 14 3 1 2 15 Lysine (Lys)

  16. Photocycle of Bacteriorhodopsin6-7 BR568= hn Photoisomerized to 13-cis a 9-cis pathway19-20 J600 8-10 ms 500 fs O640 Protonated all-trans 5 ps K590 Retinal Quantum Efficiency in methanol 15.0% 0.5 ms 2 ms Retinal Quantum Efficiency in BR 67.0-64.0% N550 Solar Panels Efficiency 22.0%13 L550 2 ms 70 ms M412 (CP) H+in M412 (EC) H+out De- and reprotonated of the Schiff base

  17. Possible applications for long term recording, 3-D data and holographic storage19. BR568= hn Blue light to revert back Q380 Thermal relaxation 8-10 ms P490 O640 Photochemical activation 7 9 5 red pulse 4 10 8 6 9-cis pathway 11 12 3 1 2 14 13 15

  18. Bacteriorhodopsin makes ATP by ATP-synthase. It converts the energy of the light into an electrochemical proton gradient (H+ ions transferring across the membrane). The proton gradient that results is used to drive ATP synthesis by use of the ATP-synthase complex. This modification allows bacteria to live in low oxygen but rich light regions. The H+ ions that are produced are then transported outside of the cell. “This results in a potential energy gradient similar to that produced by charging a flashlight battery”. The force the potential energy gradient produces is called a proton motive force that can accomplish a variety of cell tasks including converting ADP into ATP8.

  19. Proposed mechanism of light driven proton pumping and conformational changes of bacteriorhodopsin7.

  20. Applications of BR16 ID card with an optical data memory made from BR. In the purple colored data strip, more than 1 MB of digital data may be stored permanently A holographic camera for non-destructive Testing using BR films as rewriteable Optical recording media. Prevent counterfeiting ID-card as a novel security system

  21. An important protein in the rod cell: Rhodopsin15 Microscope images of Rod cells of a Zebrafish15 Wt ~ 40 kDa ~1 mm across 10 mm across Cone cells important for color detection21 Red cones (560-566 nm max sensitivity) Green cones (540-545 nm max sensitivity) Blue cones (440 nm max sensitivity)

  22. References and Sources used: 1Oesterhelt, D. & Stoeckenius, W. (1971) Nature New Biol. 233, 149-152 and Blaurock, A.E. & Stoeckenius, W. (1971) Nature New Biol. 233, 152-155 2Dieter Oesterhelt and Walther Stoeckenius, Functions of a new Photoreceptor Membrane Proc. Nat. Acad. Sci. USA. 70, No 10, pp 2853-57, 1973 3http://biology.kenyon.edu/Microbial_Biorealm/archaea/halobacterium/halobacterium.html 4http://www.ucmp.berkeley.edu/archaea/archaealh.html 5http://waynesword.palomar.edu/plsept98.htm 6http://www.biochem.mpg.de/oesterhelt/ 7Lubert Stryer Biochemistry 4th Edition, W.H. Freeman and Company, New York, 1995 8http://www.creationresearch.org/crsq/articles/36/36_1/atp.html 9http://www.biochem.mpg.de/oesterhelt/genomics/Intro_Hsal.html 10http://soils1.cses.vt.edu/ch/biol_4684/Microbes/halo.html 11picture provide by Ruth Anderson 12http://www.ks.uiuc.edu/Research/Method/quant_sim/

  23. 13http://www.qrg.northwestern.edu/projects/vss/docs/Power/2-how-efficient-are-solar-panels.html13http://www.qrg.northwestern.edu/projects/vss/docs/Power/2-how-efficient-are-solar-panels.html 14Feng Gai, K.C. Hasson, J. Cooper McDonald, Philip A. Anfinrud. Chemical Dynamics in Proteins: The Photoisomerization of Retinal in Bacteriorhodopsin, Science, Vol 27(20), March 20, 1998. 15http://www.accessexcellence.org/AE/AEC/CC/vision_background.html 16http://www.chemie.uni-marburg.de/~hampp/index_engl.htm 17http://beta.encarta.msn.com/encyclopedia_761572911_2/Photosynthesis.html 18http://www.tu-darmstadt.de/fb/ch/Fachgebiete/BC/AKDencher/energie_en.html 19Norbert Hampp. Bacteriorhodopsin as a Photochromic Retinal Protein for Optical Memories, Chem Rev., Vol. 100, 1755-1776, 2000. 20Norbert Hampp, Nathan B. Gillespie, Kevin J. Wise, Lei Ren, Jeffrey A. Stuart, Duane L. Marcy, Jason Hillebrecht, Qun Li, Lavoisier Ramos, Kevin Jordan, Sean Fyvie, and Robert R. Birge. Characterization of the Branched-Photocycle Intermediates P and Q of Bacteriorhodopsin, J. Phys. Chem B., Vol. 106, 13352-13361, 2002. 21David W. Ball. The Baseline Eyes: The Body’s Own Spectroscopes, Spectroscopy, Vol. 20(4), 36-37, April 2005.

  24. HeLa cell with rhinovirus

  25. 4RHV.pdb

  26. 4RHV.pdb HEADER RHINOVIRUS COAT PROTEIN 25-JAN-88 4RHV 4RHV 3 COMPND RHINOVIRUS 14 (/HRV$14) 4RHV 4 SOURCE HUMAN (HOMO $SAPIENS) VIRUS GROWN IN HE*LA CELLS 4RHV 5 AUTHOR E.ARNOLD,M.G.ROSSMANN 4RHV 6 REVDAT 7 15-OCT-94 4RHVF 3 REMARK CRYST1 SCALE 4RHVF 1 REVDAT 6 15-JAN-92 4RHVE 1 REMARK 4RHVE 1 REVDAT 5 15-JUL-90 4RHVD 1 REMARK 4RHVD 1 REVDAT 4 15-JAN-90 4RHVC 1 REMARK 4RHVC 1 REVDAT 3 19-APR-89 4RHVB 1 SEQRES 4RHVB 1 REVDAT 2 09-OCT-88 4RHVA 1 JRNL 4RHVA 1 REVDAT 1 16-APR-88 4RHV 0 4RHV 7

  27. 1RHI.pdb 4RHV.pdb Rhinovirus Coat Proteins, PDB files

  28. DNA 101 • 3 Components of a Nucletide • Nitrogenous base – the major bases are derivatives of 2 parent compounds • Pyrmidine – 6 member ring (containing 2 nitrogens) • Adenine (A) • Guanine (G) • guanine • Purine – 6 member ring and 5 member ring (containing 4 total nitrogens) • Thymine (T) • Cytosine (C) adenine • 3 Components of a Nucletide • Nitrogenous base – the major bases are derivatives of 2 parent compounds • Pyrmidine – 6 member ring (containing 2 nitrogens) • Adenine (A) • Guanine (G) thymine • cytosine • 2-deoxy-D-ribose – five carbon sugar residue with carbons numbered using primes to distinguish them from the carbons in the nitrogenous bases (1’ carbon attaching to nucleic acid and 5’ carbon to phosphate bridge) • Phosphate bridge – covalently links the 5’ hydroxyl of one nucleotide to the 3’ hydroxyl of another

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