Biofizyka

Biofizyka
3. Komórka eukariotyczna
jako reaktor chemiczny
Michał Kurzyński
Uniwersytet Adama Mickiewicza
Wydział Fizyki
(a)
(b)
j¹dro
organelle
cytoplazma
hialoplazma
b³ona cytoplazmatyczna
b³ona cytoplazmatyczna
1
rzêska (krótka)
wiæ (d³uga)
centriole
g³adkie
retikulum endoplazmatyczne
ziarno
j¹dro
wodniczka
szorstkie
retikulum endoplazmatyczne
tylakoid
aparat Golgiego
mitochondrium
chloroplast
egzosom
lizosom
œciana komórkowa
endosom
Eukaryotic cell: a system of
•membranes,
•cytoskeleton,
•and chromatin.
First approximation: only membranes. Reactions
within compartments and transport across
membranes between compartments. The both are
catalyzed by protein enzymes or channels. Channels
formally act as enzymes. Coupling of the free energy
donating with the free energy accepting processes.
Second approximation: soft matter (liquid-like and
solid-like regions). Active viscoelastic medium.
2
Metabolism of eukaryotic cell
• Cell nucleus: nucleic acid synthesis
• Lysosomes: catabolic reactions: hydrolysis
• Mitochondrial matrix: Krebs cycle, fatty acid degradation
• Chloroplast stroma: Calvin cycle
• Internal membrane of mitochodria: oxidative phosphoryl.
• Thylacoid membrane of chloroplasts: photophosphoryl.
• Rough reticulum membrane : protein synthesis
• Smooth reticulum membrane: lipid biosynthesis
• Golgi apparatus: polysaccharyde synthesis
skrobia, glikogen
P
H
H
P
P
nukleotydy
H
fosfolipidy
H
P
H
P
H
H
P
H
sterydy
aminokwasy
H
P
P
H
H
H
porfiryny
P
H
3
E
kT
4.2 ×10 −21 J = 4.2 pN ⋅ nm = 2.5 kJ/mol
300 K
hν
1/1.6 ×10 −13 s = 6 ×1012 s −1 = 6 THz
hcλ−1
220 cm −1
eϕ
25 meV
4
Enzyme classification
• Oxidoreductases
• Transferases
• Hydrolases
• Lyases
• Isomerases
• Ligases (synthethases)
5
Catalysis:
(a)
R
acid
(b)
O
H
C
X
O
+
H
H
base
O
B
R
(c)
--
electrophylic
O
C
X
O
H
R
+
(d)
nucleophylic
2+
O
Zn
X
C
O
A
--
R
H
H
H
--
C
X
Nu
O
H
H
intramolecular
-
O
H3C
OH
C
O
O
H HOOC
H
H3C
C
O
O
H2 HOOC
O
H
HOOC
H
6
Serine or cysteine proteases (e.g. chymotripsin or papain)
EH + AcX
EH . AcX
O
O
R
C
Nu
X
R
H
C
OX
Nu H
B
EAc + XH
R
+
B
Nu
R
H
C
O
Nu
O
R
X
H
+
B
EH . AcOH
EAc + H2O
O
C
O- H
R
H
C
B
Nu
O
H
R
O
H
C
O
Nu- H
+
B
C
X
Nu
H
B
EH + AcOH
O
H
C
O
Nu
H
R
+
B
B
Proton relay triad
N
N
H
H
O
R
C
X
H
N
N
H
O
-
O
Nu
C
Ser or Cys
C
His
C
Asp
7
(a)
(b)
(c)
(d)
E
P
R
M
J
J+
bA
- J-
8
(a)
(b)
1
J+_
J+_
k +_
1
k +_
0
[R]0
0
1
K +_
1
[R]0
0
[E]
[E]0
(a)
0
0
(b)
[A]
9
Singer-Nicholson
`fluid mosaic model’
(1972)
An amended and
updated version
(clustering of proteins)
D. M. Engelman,
Nature 438, 578 (2005)
10
Aquaporin water channel
homotetramer
Asp-Pro-Ala and aromatic-Arg regions
after B.L. de Groot & H. Grubmueller, Curr. Opin. Struct. Biol. 15, 176 (2005)
The Grotthuss mechanism for proton conductivity
in an acid (b) and a base (b)
(a)
(b)
H
+ O
H
H
H
O
H
H
O
O
H
+ O
H
O
O
H
- O
H
O
H
H
H
H
H
- O
H
H
H
H
H
O
H
H
H
H
O
H
H
H
O
O
O
H
H
H
O
H
H
11
The mechanism of water permeation through aquaporin channel
B. L. de Groot & H. Grubmueller, Science 294, 2353 (2001)
KcsA potassium channel
(a)
(b)
select. filter
outer helix
inner helix
C
N
after D. A. Doyle et al.,Science 280, 69 (1998)
12
Voltage-dependent gating – paddle rotation mechanism
Voltage-dependent gating – ball on a chain mechanism
13
Voltage-gated sodium channel
Cryo-electron microscopy
out
interior
after C. Sato et al.., Nature 409, 1047 (2001)
(a)
Acetylcholine-gated sodium channel
(b)
after N. Unwin, J. Mol. Biol. 346, 967 (2005)
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