Download Lipids Some lipid structures Micelles/Bilayers Examples

Lipids
Some lipid structures
• Organic compounds
• Amphipathic
• Hydrophobic interactions are important
Head
group
– Polar head group (hydrophilic)
– Non-polar tails (hydrophobic)
• Lots of uses
–
–
–
–
O
HO
Carboxyl
group
C
Energy storage
Membranes
Hormones
Vitamins
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Tail
group
air
H2 C
CH2
H2 C
CH2
H2 C
water
Hydrocarbon
chain
CH3
monolayer
Fatty acid
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Micelle
Inside-out
(in nonpolar
solvent)
Lipid bilayer
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Examples
Micelles/Bilayers
Lipid micelles
•Lipid is an amphipathic molecule,
but rarely exists as a monomer.
Lipid bilayers
Water
No water
Lipids and water form
tiny compartments
Serine
Phosphate
Hydrophilic heads interact with water
Hydrophobic tails interact with each other
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Hydrophilic
heads interact with water
© 2004-5 Seth Copen Goldstein
Red blood cells
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Relative Permeabilities
Using Lipids as Membranes
Phospholipid bilayer
Planar bilayers: Artificial membranes
Water
O2, CO2, N2
Hydrophobic molecules
Water
Lipid
bilayer
Small, uncharged polar molecules
H2O, glycerol
Large, uncharged polar molecules
Glucose, sucrose
Ions
H+,Na+,NCO3–,
Ca2+,CL-,Mg2+,K+
Membrane is selectively permeable
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DNA/RNA/Proteins
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DNA
• Why study?
• Here are just the basic basics
• DNA
– made up of double strands of adenine (A),
guanine (G), cytosine (C) and thymine (T)
– Pair up: C-G, A-T
• RNA
– Single stranded
– U for T
• Proteins do the work
• DNA -> RNA -> Proteins
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© 2004-5 Seth Copen Goldstein
H-bonds
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Protein
Levels of Structure
• Linear polymer of amino acids linked
by peptide bonds
• Average 200 amino acids, can be >1K
• Complex structure
– Primary structure – sequence of AAs
– Secondary structure – local
arrangements
– Tertiary structure – how the local
structures pack in 3D
– Quaternary structure – how chains fold
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Forces determining structure
•
•
•
•
Amino Acids
Van der Waals .4 – 4 KJ/mol
Hydrogen bonds 12-30 KJ/mol
Ionic bonds
20 KJ/mol
Hydrophoic interactions <40KJ/mol
• 20 natural ones
• Formed from
–
–
–
–
–
Central carbon
Amino group
Carboxyl group
H
Side-chain
• Only difference is
side-chain
• Polar/non-polar
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Alanine
Cysteine
Aspartic AciD
Glutamic Acid
Phenylalanine
Glycine
Histidine
Isoleucine
Lysine
Leucine
Methionine
AsparagiNe
Proline
Glutamine
ARginine
Serine
Threonine
Valine
Tryptophan
Tyrosine
Ala A
Cys C
Asp D
Glu E
Phe F
Gly G
His H
Ile I
Lys K
Leu L
Met M
Asn N
Pro P
Gln Q
Arg R
Ser S
Thr T
Val V
Trp W
Tyr Y
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Secondary structures
Using all this info
• Alpha helix
• Beta Sheet
• Loop regions
• Protein-based memory
• DNA as wires
• DNA-based assembly
– Often binding sites
– Often hydrophilic
– Come between alpha’s and beta’s
– Templates
– Smart-glue
– tiles
• Represented as ribbon diagrams
– Coiled – alpha
– Arrow – beta
– Thin - loops
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VHL protein
Stebbins et al, Science, 284:455.
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DNA as wires
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DNA-templates for wires
• DNA is conducting, 1986 and on
– π-bonding
– D-A, holes, Hopping
• DNA is insulator, 1999 and on
– λ-bridge between oligos on gold
– Insulator
– Lower T -> more insulating
• DNA is semiconductor, 2000 and on
– Consider series of quantum dots
– Maybe difference in fermi-level with contacts
• Conclusion?
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Interfacial Nanowire Assembly
DNA as “glue”
Selectivity
– 4n unique sequences for oligo of length n
– base pairing determines thermodynamic stability
Au surface
Versatility
Au surface
– sequence
– 5’ or 3’ terminal -SH, -NH2, biotin, etc.
Reversibility
– temperature, base
1
• Challenges:
– Gravity
– High interfacial tension
– Incompatible with DNA, high salt
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58oC
48oC
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36
•
•
•
•
38oC
36
21
1
2
1
1
1
2
1
1
1
1
1
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Necessary components of raft
assembly:
cross-section view:
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2
3
1
2
1
2
1
Temperature-programmed Raft
Assembly
bird’s eye view:
70oC
3
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Hybridization-compatible interface
DNA-coated nanowires at the interface
Hybridization-driven nanowire assembly
Thermal control over assembly process
5’
Deterministic rafts will be assembled at
the aq/aq interface via sequential
assembly of nanowires harboring
decreasing lengths of oligonucleotides A
and A´ as the sample is cooled.
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HS-C12H24-TTG AGA CCG TTA AGA
CGA GGC AAT CAT GCA ATC CTG 3’
Length
36-mer
21-mer
18-mer
15-mer
9-mer
Tm
75oC
61oC
51oC
41oC
28oC
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DNA-directed assembly at the
interface?noncomplementary
Aqueous-aqueous interfaces
•
•
•
•
•
polymeric solutes, few weight %
particles collect at interface
low, tunable interfacial tensions
compatible with DNA, high salt
stable up to 95oC
Minutes after
removal from
shaker
complementary
hybridization-induced nanowire
assembly at the aq/aq interface
PEG/Au Colloid
• 70-nm Au nanowires
• MESA-derivatized
• PEG/dextran ATPS
• hybridization buffer
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lecture 5-sa 15-398
interface
1.0
solution
1.0
0.5
1.2
0.4
0.2
interface
1.0
• Surface dilution of proper DNA
sequence decreases Tm
• We can control coverage from 1-5 x
1013 strands/cm2 (40-150/particle)
• This approach can be used to tailor
Tm’s for temperature-programmed
assembly
surface diluted w/ polyA
0.3
0.8
0.6
0.4
0.2
0.1
solution
50
55
60
65
70
Temperature (Deg. C)
© 2004-5 Seth Copen Goldstein
1.5
0.8
0.2
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2.0
1.0
1.2
Absorbance
1.4
Absorbance
Nanowire concentration at
the interface favors assembly
1.6
Controlling Tm by surface dilution
0.0
0.0
– Higher Tm than solution-prepared counterparts
– Large aggregates lead to high scattering
– Observe greater change upon melting
• more DNA was hybridized
• interface concentrates nanowires for assembly
Absorbance at 540nm
Nanowire rafts removed from interface
Absorbance at 260nm
Melt curves for interface and
solution assemblies
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0.5
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• DNA-coated nanowires at aq/aq
interface – form reflective
interface after gentle agitation
0.1
Dextran
40
50
60
Temperature (deg C)
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-0.1
70
Tm = 51 oC
© 2004-5 Seth Copen Goldstein
Tm = 55 oC
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Potential-Assisted Raft
Positioning
2 distinct
melting events
80°C
°C
40
60 °C
2
raft side-view
1
Initial proof-of-concept for temperatureprogrammed assembly
“landing pad”
•
•
•
•
•
0.00
dA
0.05
0.10
Absorbance @540 nm
0.5
1.0
Temperature-controlled Dissociation
40
50
60
70
80
Temperature (deg C)
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12-nm Au nanoparticles
A, B = 12 mers
90
C, D = 18 mers
© 2004-5 Seth Copen Goldstein
lithographically-defined “landing pads”
derivatize with complementary DNA
hold at positive potential
allow rafts to hybridize to pads
reverse potential for stringency
“landing pad”
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DNA Tiles
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raft side-view
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