The structure of the cell, as it relates to

functions. Revised Lecture # 1 2014

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.

Antigen Presenting Cell

T Cell CD 4+ CD4

TCR

MHC II

Figure 2

B7

CD28

Antigenic peptide

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