The structure of the cell, as it relates to functions ... · Schematic diagram of an animal cell...
Transcript of The structure of the cell, as it relates to functions ... · Schematic diagram of an animal cell...
There are several important themes that transcends the
chemistry and bring the importance of understanding the
cell biological differences between eukaryotes and
prokaryotes.
These themes are all part of the evolution of eukaryotes.
The evolution of internal membrane structures gives rise
to the organelles referred to as the cytomembranes,
while the other group belongs to the endosymbionts.
How they arose and how the endosymbionts evolved
has changed greatly since Lyn Margulis original thesis.
What is the advantages of compartmentation? What drove the evolution of compartmentation?
Schematic diagram of an animal cell accompanied by electron micrographs of its organelles. The biochemistry of these organelles are universal. And in many ways similar if not identical to that of prokaryotes.
The model of a cell,
but do all cells fit the
model?
Why do eukaryotes
evolve
comparmentation of their
Chemistry into membr
bound
orangelles?
The three types of cytoskeletal
filaments: actin filaments,
microtubules, and intermediate
filaments. Cellular structures can
be labeled with an antibody (that
recognizes a characteristic protein)
covalently attached to a fluorescent
compound. The stained structures
are visible when the cell is viewed
with a fluorescence microscope. (a)
Endothelial cells from the bovine
pulmonary artery. Bundles of actin
filaments called “stress fibers” are
stained red; microtubules, radiating
from the cell center, are stained
green; and chromosomes (in the
nucleus) are stained blue.
Simulated cross section of an E. coli cell magnified around one
million fold. So, how much free water is there in a cell?
The cell
membrane
; 1. What are the
functions of the
cell membrane?
2. Why is it a
plasma
membrane?
3. What is the origin
of the plasma
membr?
The plasma membranes of cells contain combinations of glycosphingolipids and protein receptors organized in glycolipoprotein microdomains termed lipid rafts. These membr microdomains, compartmentalize cellular processes by serving to organize the assembly of proteins in the membr.
The recent lipid rafts definition state that lipid rafts are very small (10-200 nm),
heterogeneous, highly dynamic, sterol- and sphingolipid- enriched domain [Pike, L., Rafts defined: a report on the Keystone Symposium on Lipid Rafts and Cell Function. The Journal of Lipid Research,
2006. 47(7): p. 1597.]. Therefore, we can indicate lipid rafts as saturated phospholipid and
cholesterol-containing regions that depleted from the cholesterol-poor or unsaturated
phospholipid regions. In the present, we have believed that lipid rafts involve many
biological functions such as signaling, recruitment of specific proteins and endocytosis.
With this point of view, biological membranes are not only cell barrier but also behave like a platform of biochemical reactions.
CHRISTIAN DE DUVE Laboratory of Physiological Chemistry University of Louvain, Belgium and The Rockefeiler Institute, New York, N. Y., U.S.A.
CD4
Lck
Ras Raf-1
MKK
Ras/MAPK signaling
ERK-1.2
CD3
TCR CD28
fyn
Grb-2 SOS
NFATc
PiP2 InsP3 + DAG
PLC
[Ca2+]
Calcium signaling
calcineurin
PI3-K
p85
p110
PKC signaling
JNK
PKC
Grb-2
ZAP-70 Lck
p75
3
2 1
I-kβ
NF-kβ
NF-kβ
Differential cytokine genes transactivated
AP-1 NFAT
NFAT Fos/Jun (AP-1)
Shc
Cbl
Vav C3G
p116 Crk1
Separation of functional complexes of the respiratory
chain. The outer mitochondrial membrane is first removed
by treatment with the detergent digitonin. Fragments of
inner membrane are then obtained by osmotic rupture of
the mitochondria, and the fragments are gently dissolved
in a second detergent. The resulting mixture of inner
membrane proteins is resolved by ion-exchange
chromatography into different complexes (I through IV) of
the respiratory chain, each with its unique protein
composition (see Table 19-3), and the enzyme ATP
synthase (sometimes called Complex V). The isolated
Complexes I through IV catalyze transfers between
donors (NADH and succinate), intermediate carriers (Q
and cytochrome c), and O2, as shown. In vitro, isolated
ATP synthase has only ATP-hydrolyzing (ATPase), not
ATP-synthesizing, activity.
• Where do all of these
pathways arise from?
• Why are most of the
genes for these
pathways in the
nucleus?
• If many of these genes
are not α-protobacterial
then where did they
arise form?
• Was the mitochondria
free living or parasitic?
Structure of the water molecule. (a) The dipolar nature of the H2O molecule
is shown in a ball-and-stick model; the dashed lines represent the nonbonding
orbitals. There is a nearly tetrahedral arrangement of the outer-shell electron
pairs around the oxygen atom; the two hydrogen atoms have localized partial
positive charges (δ+) and the oxygen atom has a partial negative charge (δ–).
Hydrogen Bonds
• Strong dipole-dipole or charge-dipole interaction that
arises between an acid (proton donor) and a base (proton
acceptor)
• Typically 4–6 kJ/mol for bonds with neutral atoms,
and 6–10 kJ/mol for bonds with one charged atom
• Typically involves two electronegative atoms (frequently
nitrogen and oxygen)
• Hydrogen bonds are strongest when the bonded
molecules are oriented to maximize electrostatic
interaction
• Ideally the three atoms involved are in a line
Directionality of the hydrogen bond. The attraction between the partial electric charges
(see Figure 2-1) is greatest when the three atoms involved in the bond (in this case O, H,
and O) lie in a straight line. When the hydrogen-bonded moieties are structurally
constrained (when they are parts of a single protein molecule, for example), this ideal
geometry may not be possible and the resulting hydrogen bond is weaker.
Hydrogen Bonding in Water
• Water can serve as both
– an H donor
– an H acceptor
• Up to four H-bonds per water molecule gives water its
– anomalously high boiling point
– anomalously high melting point
– unusually large surface tension
• Hydrogen bonding in water is cooperative
• Hydrogen bonds between neighboring molecules are
weak (20 kJ/mol) relative to the H–O covalent bonds
(420 kJ/mol)
Structure of the water
molecule. (b) Two H2O
molecules joined by a
hydrogen bond (designated
here, and throughout this
book, by three blue lines)
between the oxygen atom
of the upper molecule and
a hydrogen atom of the
lower one. Hydrogen
bonds are longer and
weaker than covalent O—
H bonds.
Water as a Solvent
• Water is a poor solvent for nonpolar
substances
– nonpolar gases
– aromatic moieties
– aliphatic chains
• Water is a good solvent for charged and
polar substances
– amino acids and peptides
– small alcohols
– carbohydrates
Water dissolves many salts
• High dielectric constant reduces attraction
between oppositely charged ions in salt
crystal; almost no attraction at large (> 40
nm) distances
• Strong electrostatic interactions between the
solvated ions and water molecules lower the
energy of the system
• Entropy increases as ordered crystal lattice is
dissolved
Water as solvent. Water dissolves many crystalline salts by hydrating their
component ions. The NaCl crystal lattice is disrupted as water molecules
cluster about the C– and Na+ ions. The ionic charges are partially neutralized, and the electrostatic attractions necessary for lattice formation are weakened.
Physics of Noncovalent Interactions
• Ionic (Coulombic) Interactions
– Electrostatic interactions between permanently charged species, or
between the ion and a permanent dipole
• Dipole Interactions
– Electrostatic interactions between uncharged, but polar molecules
• van der Waals Interactions
– Weak interactions between all atoms, regardless of polarity
– Attractive (dispersion) and repulsive (steric) component
• Hydrophobic Effect
– Complex phenomenon associated with the ordering of water molecules
around nonpolar substances
Noncovalent interactions do not involve sharing a pair of electrons. Based
on their physical origin, one can distinguish between:
Ionization of Water
• O-H bonds are polar and can dissociate heterolytically
• Products are a proton (H+) and a hydroxide ion (OH–)
• Dissociation of water is a rapid reversible process
• Most water molecules remain un-ionized, thus pure water has very low
electrical conductivity (resistance: 18 M•cm)
• The equilibrium is strongly to the left
• Extent of dissociation depends on the temperature
H2O H+ + OH-
Proton Hydration
• Protons do not exist free in solution.
• They are immediately hydrated to form hydronium (oxonium)
ions.
• A hydronium ion is a water molecule with a proton associated
with one of the non-bonding electron pairs.
• Hydronium ions are solvated by nearby water molecules.
• The covalent and hydrogen bonds are interchangeable. This
allows for an extremely fast mobility of protons in water via
“proton hopping.”
Proton Hydration
• Protons do not exist free in solution.
• They are immediately hydrated to form hydronium (oxonium)
ions.
• A hydronium ion is a water molecule with a proton associated
with one of the non-bonding electron pairs.
• Hydronium ions are solvated by nearby water molecules.
• The covalent and hydrogen bonds are interchangeable. This
allows for an extremely fast mobility of protons in water via
“proton hopping.”
Proton hopping. Short
“hops” of protons between
a series of hydrogen-bonded
water molecules result in an
extremely rapid net
movement of a proton over
a long distance. As a
hydronium ion (upper left)
gives up a proton, a water
molecule some distance
away (lower right) acquires
one, becoming a hydronium
ion. Proton hopping is much
faster than true diffusion and
explains the remarkably high
ionic mobility of H+ ions
compared with other
monovalent cations such as
Na+ and K+.
Proton Hopping