Biofizyka molekularna

2. Szczególne własności wody

Michał Kurzyński Uniwersytet Adama Mickiewicza

Wydział Fizyki

O

H

HH

H

H

H

H

H

H

H

OO

O

O

wiązanie wodorowe (~10 – 20 kJ/mol)

około 20 razy słabsze od wiązania kowalencyjnego

http://www-ssrl.slac.stanford.edu/nilssongroup/images/structure_liquid.jpg

http://www-ssrl.slac.stanford.edu/nilssongroup/images/structure_ice.jpg

Struktura loduuporządkowana ale rzadka

Struktura ciekłej wodygęsta ale nieuporządkowana

http://www.camptaichi.com/blog/wp-content/uploads/snowflakes-and-tai-chi.jpg

Warunek minimum energii swobodnej F = E – TS :Trzy stany skupienia wody

Mars >

Wenus ^http://www.canadianmanufacturing.com/coatings/images/content/features/BelzonaRudderCavitation/ruddersFigure1.jpg

Warunek minimum energii swobodnej F = E – TS :Rozpuszczalność w wodzie

Hydrofile – lubią wodę

• Cząsteczki tworzące wiązania wodorowe z wodą(np. alkohole, cukry), nie zaburzają sieci wiązańwodorowych, nie zmieniają ani entropii ani energii

• Cząsteczki nie tworzące wiązań wodorowych ale posiadające ładunek elektryczny lub moment dipolowy (np. aniony i kationy soli), obniŜająentropię ale takŜe energię

TSEF −=

Hydrofoby – nie lubią wody

Cząsteczki, które nie tworzą wiązań wodorowych ani nie mają ładunku elektrycznego czy momentu dipolowego (np. węglowodory), woda dookoła nich porządkuje się tworząc lokalne „góry lodowe”

Amfifile – zarówno składniki lubiące wodę („głowy”) jak i nie lubiące wody („ogony”)

Dobrze się czują na granicy wody i oleju (surfaktanty)

A jak zachowują się w czystej wodzie?

micellespherical

cylindrical(0D)(1D)

bilayer (2D)

spinodal

binodal

concentration0.0

A B

Tc

1.0

tem

per

ature

Mixing of two phases

• homogeneous mixture (solution)

• heterogeneous mixture (coexistence of two phases)

• dispersive mixture (surfactants lower the free energy of interphase borders)

Dispersive mixtures (colloids)

• continuous phase

• dispersed phase – colloid particles of diameter

from 5 nm (lipid micelles, protein domains, tRNAs containing some 3x103 atoms)

to 500 nm (suspension: Brownian force stronger than

gravitation, simultaneously visible light wavelength: particles invisible under optical microscope but diffraction effects possible: Tyndall effect, play of color)

emulsion sol

fog

disp. phase: gas liquid solid

con

t. p

hase

:so

lid

liq

uid

g

as

foam

gel

vesicle

lamelle

invertedmicellarstructure

perforated lamelar structure

liposome

2D crystal2D liquid

disp. struct.: gel

liquid cryst.

solid cryst.

dispersive struct.: sol

water content0.0 1.0

tem

per

atu

re

www.susqu.edu/brakke/evolver/examples/periodic/periodic.html

Perforowana struktura lamelarnadzieli przestrzeń na dwa rozłączne obszary• regularna (np. powierzchnia Schwarza• nieregularna (np. „koszmar hydraulika”)

Kevin Cappis 2004 (www.surrealplaces.com)

(d)

H ON

H

O

N

(c)

S

SCa

i

Ca

j

(a)

H

O

f

c

y

O H

H

Ca

i

Ri

Ca

i+1C

a

i-1 N

N

(b)

HO Ca

i

Ca

i-1

N

O

yf

w

H

Ca

i+1N

Białka – liniowe polimery aminokwasów

http://www.denizyuret.com/students/vkurt/thesis-main_dosyalar/image010.jpg

Wiązania wodorowe – struktura αααα

http://cmgm.stanford.edu/biochem/biochem201/Slides/Protein%20Structure/

http://www.denizyuret.com/students/vkurt/thesis-main_dosyalar/image012.jpg

Wiązania wodorowe – struktury ββββ

http://cmgm.stanford.edu/biochem/biochem201/Slides/Protein%20Structure/

O

NH2

CH3

CH3

O

NH2

CH3

CH3

O

NH2

CH3

O-

NH2

O

O

_

O

NH2

OH

O

NH2

OH

CH3

O

O

NH2

NH2

O

O

NH2

NH2

O O

O-

NH2

_

O

NH2

NH3

+

NH2

+

O

NH

NH2

NH2

+

O

NH2

SCH

3

O

NH2

CH3

CH3

O

NH2OH

O

NH2

Asp (D) Glu (E)

Ser (S) Thr (T)

Asn (N) Gln (Q)

Lys (K) Arg (R)

O

NH2

NH

NH

+

O

NH2NH

His (H)

Phe (F)

Ile (I)

Val (V) Leu (L)

Ala (A)

Tyr (Y)

Trp (W)

Met (M)

Gly (G)Pro (P)Cys (C)O

NH

O

NH2

SH

strukturalne

kw

aso

we

za

sa

do

we

hydrofilowe hydrofobowe

(a) (b)

(d)(c)

http://www.mpibpc.mpg.de/home/grubmueller/gallery/album_aquaporine/bild1/dimerplot.jpg

http://4.bp.blogspot.com/-2-9OvXqIPBQ/T7xPGyRKiMI/AAAAAAAAAog/DpLJe07ISzg/s1600/Picture1.jpg

Proteins in membrane

Bi

Bi+1

O

a

b

z

e

d

g

O

1’2’3’

4’

5’

X

O

X

P

OO

O

-

O

P

OO

O

-

O

N

NN

NN

H

H

H

H

N

N

N

OH

H

H

N

NN

N

N

O

H

H

H

H

N

N

O

O

R

H

H

cytozyna (C)

adenina (A)

guanina (G)

tymina (T) R = CH3

uracyl (U) R = H

Kwasy nukleinowe DNA i RNA– liniowe polimery nukleotydów, pary Watsona-Cricka

DNA – dwa łańcuchy

http://www.bio.miami.edu/tom/courses/protected/MCB6/ch04/4-03.jpg

http://www.cgm.cnrs-gif.fr/michel/images/fig1.gif www.cgm.cnrs-gif.fr/michel/images/fig2.jpg

Rybozym (enzym zbudowany z RNA)

Rybosom

RNA + białka,częściowo w wodzieczęściowo w błonie

Kompleksy kwasów nukleinowych z białkami

http://www.beckman.illinois.edu/news/releases/images/release0914073.jpg

Nukleosom

DNA + białka,podstawowyskładnik strukt.chromatynyw jądrze komórk.

http://www.leavethelightson.info/data/site/nucleosome.png

Molecular structure of water and oxygen

H O2

water

HO OH_

hydrogen superoxide superoxide radical molecular oxygen

(d) (e) (f)

O

HO

H

.. ..

....

O O_. .

O

.. ..

....

O..

.

CH4

methane

(a) (b) (c)

hydroxyl radical

H

C

H

H

H

....

....

HO O_ .

.. ..

....

H

.. ..

O

H

OH

-

O

O

....

..

.. ..

.-

H

.. ..

..

.. ..

O

.

.

.

H O2 2

.OH

OH_

.OH

H O2

H O2

Fe2+

Fe3+

Fe3+

Fe2+

H + e+ _

e_

2H + e+ _

H + e+ _

O2

._

O2O2

._

Photolysis of water

• interstellar matter • living organisms after γγγγ or X irradiation• planet atmospheres after UV irradiation

(if no ozone shell)

hydroxyl and superoxide radicals

History of the three similar planets: Venus, Earth and Mars

• formed 4.6 billion years ago as a result of accretion of the dust component of the gaseous dusty cloud being the origin of the Solar System

• after the end of Big Bombardment, 3.9 billion years ago, the early gaseous envelope of the volcanic and cometic origin differentiates into gaseous Atmosphere (mainly CO2) and liquid Ocean (mainly H2O)

However, the latter history is different

http://www.universetoday.com/wp-content/uploads/2009/07/venuswater-250x199.jpg

Venus

• Green house effect of CO2

– evaporation of water• Photolysis of water onto O2 and H2, the escape velocity for the latter• Blow out of O2 by solar wind (no magnetosphere)• However, still plate tectonics

Venus Express, 2008

http://www.universetoday.com/wp-content/uploads/2008/05/falsecolor.jpg

Venus Express, 2008

The present atmosphere

P = 9,2 MPa, T = 470 oC

CO2 – 96,5 %N2 – 3,5 %H2O – 0,002 %SO2 – 0, 015 %

Dense clouds of H2SO4

Mars

http://www.wdcgc.spri.cam.ac.uk/news/mars/hubble.jpg

http://esamultimedia.esa.int/images/marsexpress/212-010705-1343-6-3d-01-CraterIce_H.jpg

At present, ice of H2O

• in polar caps – since ~5 mln. years, alternating layers of dust and ice deposited every ~100 thousend years (Earth glaciations?)

• in frozen lakes at the bottom of craters

Positive feedback both for freezing and melting of water

The increase (decrease) in surface coverage by snow and ice turns increase (decrease) of albedo thus decrease (increase) in absorption of solar radiation energy.

The most effective on equator

Possible mechanism of the Snowball Planet state

Triggered and stopped by changes in CO2 concentration

Carbon dioxide sinks

• weathering of rocks

Continents: CaSiO3 + 2 CO2 + H2O ���� SiO2 + Ca2+ + 2 HCO3-

Ocean: Ca2+ + CO32- ���� CaCO3

• photosynthesis

Carbon dioxide sources

• volcanoes eruptions

• respiration, men activities

http://www.distantworlds.wz.cz/DisWorlds1-2/Solarsys/Zivmars_soubory/image005.jpg

http://www.astro.virginia.edu/class/oconnell/astr121/im/mars-w-water-fuse-apr03-sm.jpg

In the past (3.8 billion years ago) liquid water in Vastilas Borealis of a volume comparable to the Earth’s Ocean• Great river valeys• Relics of river deltas• Origin of some mineralsIs there still liquid water under the polar cups?

The present atmosphere

P = 6 hPa, T = - 63 oC

CO2 – 95,3 %N2 – 2,7 %CO – 1,8 %H2O – 0,03 %

http://rst.gsfc.nasa.gov/Sect19/mars.jpg

Hubble Space Telescope, 2003

Cause of water lack• assimilating CO2 by Ca2+

• snowball planet period• stop of plate tectonics• photolisis of H2O • assimilating O2 by Fe2+

Europa

the fourth-largest moon of Jupiter(Galileo, 1996,Hubble, 2016)

By ESA/Hubble, CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=52031182

Enceladus six-largest moon of Saturn (Cassini, 2005, 20015 )

Liquid water both in ocean, in atmosphere and on continents

The present atmosphere:

P = 0.1 MPa, T = 0 oC

N2 – 78 %O2 – 21 %Ar – 1 %CO2 – 0.04 %H2O – 0.40 %

http://www.losgazquez.com/blog/wp-content/uploads/2007/12/earth-from-space.jpg

Earth

http://cdn.phys.org/newman/gfx/news/2013/7-paleontologi.jpg

photolysis 2H2O ���� 2Η2Η2Η2Η2222 + Ο+ Ο+ Ο+ Ο2222

replaced by photosynthesis ΗΗΗΗ2222Ο + Ο + Ο + Ο + CΟΟΟΟ2222 ���� CH2O + O2

and next respiration CH2O + O2 ���� H2O + CO2

No life without water

No water witout life (?)

History after the Great Bombardment

• 3.8 billion years ago – change of 13C / 12C isotope proportion on Greenland (origin of life?)• 3.5 billion years ago – stromatolites (photosynthetic revolution?)• 2.7 billion years ago – unquestrionable fossils of cyanobacteria• 2.4 – 2.2 billion years ago – early Protozoic glaciation (the first Snowball Earth?)• 2.2 billion years ago – iron formations Fe3+

• 2.1 billion years ago – aerobic bacteria, mitochondria• 850 - 550 million years ago – the one before last Pangea, late Protozoic glaciation (the second Snowball Earth?)• 510 million years ago – Cambrian explosion

Beginning of life

• Primordial soup: H2, CH4, NH3, H2O

• Meteorites

• Black smokers (acidic sea vents)

• White smokers (alkaline sea vents)

http://www.redorbit.com/media/gallery/national-science-foundation-gallery/183_53b0b292cd83b84b0d674620b3d97074.jpg

Deep sea vents life in the Mid-Atlantic Ridge

http://media1.s-nbcnews.com/j/MSNBC/Components/Photo/new/130111-LifePhoto-hmed-1205p_files.grid-5x2.jpg

Black smokers

Acidic H2S – energy source for life

Wachtershauser (1988 – 1992)

SH2 CH O2

CO2FeS2 H2S (ocean)

(vent) O2

1_2

Lost City (hydrothermal field) http://www.nsf.gov/od/lpa/news/press/01/pr0156.htm

White smokers

Alkaline reductor Fe2+(OH)-2 –

source of H2 and CH4 – reacts with acidic water HCO3

-

CaCO3 is formed

Michael Russel (1988)