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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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slide1

E. Coli bacteria

Red blood cell

Plant cell

ameoba

Eukaryotic cell

slide6

_

+

+

_

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

slide8

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

slide9

DPPC

metal

glycerol

chiral carbon

trilayer

monolayer

slide10

DPPC

chiral carbon

metal

slide11

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

slide14

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)

slide18

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

slide19

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+

slide20

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.

slide21

The sequence of bacteriorhodopsin6,12

(CP)

The protein/lipid ratio is 75:25

Aspartic Acid (Asp)

(EC)

Arginine (Arg)

Lysine (Lys)

slide24

Wt ~ 26 kDa

Volume=83 nm3

5 nm

45 Å or 0.0045 mm

slide25

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)

slide26

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

slide27

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

slide28

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.

slide29

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

slide30

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

slide31

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)

slide32

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/

slide33

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.

slide38

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

slide46

1RHI.pdb

4RHV.pdb

Rhinovirus Coat Proteins, PDB files

slide48

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