Outline

• Introduction
• Biochemistry of Amino Acids
• Biochemistry of Proteins
• Portrait of Allosteric Protein
• Enzymes
 Outline
• Biochemistry of Carbohydrates
• Glycoproteins and Glycosaminoglycan
• Biochemistry of Lipids
• Biological Membranes
• Bioenergetics and Oxidative
Phosphorylation
• Basic Concepts of Metabolism
 Outline
• Biochemistry of Carbohydrates
• Glycoproteins and Glycosaminoglycan
• Biochemistry of Lipids
• Biological Membranes
• Bioenergetics and Oxidative
Phosphorylation
• Basic Concepts of Metabolism
 Biological membranes and transport
Objectives:
- Recognize the basic structural elements, physical properties and molecular constituents of
biological membranes.
- Understand different types of membrane movements
- Know different types of proteins present at biological membranes
- Understand the mechanisms of solute transport across the membrane
Physical properties of Biological membranes
self sealing, flexibility, selectivity
The molecular constituents of Biological membranes
-different compositions of lipid membranes
- micelle, lipid bilyar, liposome
- Membrane proteins Integral proteins, peripheral proteins
Solute transport across the membrane
- Passive transport
- Facilitated diffusion
- Active transport
Different Examples for solute transport across the biological membranes.
- Aquaporin
- Glucose transport
- Chloride-Bicarbonate transport
- Sod-Pot transport
Ion selective channels
Ionophores
 Biological membranes and transport
Membrane:
- Define the external boundaries and regulate the molecular traffic across that these
boundaries.
- In eukaryotic cells, they can divide the internal spaces into compartments to segregate
processes and components
- They organize complex reaction sequences,
They are important in cell- cell communication
-within the cell, membranes organize cellular processes as energy transduction in
mitochondria and chloroplast

Physical properties of membranes

1-   flexibility: allows the shape changes in the cell growth and movements (as the
amoeboid movement)
2-   self sealing: ability to break and to reseal without the leak of the cellular
components, as in the case of exocytosis (two membranes can fuse) or endocytosis (one
single compartment divide to give two sealed compartments)

3- selectively permeable, they can retain certain compounds and ions within cells and within
specific cellular compartments while excluding others

*Membranes are not absolutely passive barriers

They include different proteins specialized for catalyzing various cellular processes
 A lipid bilayer is the basic structural element of membranes
Structural lipids are insoluble in water  when they are mixed with water, they will
form microscopic lipids aggregates in a phase separate from the aqueous surrounding.
Depending on the precise conditions and the nature of lipids three types of lipid
aggregate are formed Micelle, Bilayer, Liposome

Micelle: spherical structure, the molecules are arranged with hydrophobic regions
aggregated in the interior, excluding the water and the hydrophilic head groups at the
surface in contact with water

Micelle formation is favored

when the cross-sectional area
of the head group is greater
than that of the acyl side
chain, as free fatty acids,
lysophospholipids, detergents

Single tailed lipids tend to form micelles

Bilayer
Two lipid monolayers form a two-dimensional sheet,
bilayer formation occurs readily when the cross-sectional
areas of the head group and the acyl side chain are
similar, as in glycerphosphlipids and sphingolipids, the
hydrophobic portions in each monolayer, excluded from
water, interact with each other. The hydrophilic head
groups interact with water at each surface of the bilayer.

The two hydrocarbon tails of

glycerophospholipids and spingolipids tend
to form bilayers or liposomes

Liposome
Because the hydrophobic regions at the
edges of the bilayer are in contact with
water, the bilayer sheet is relatively
unstable and spontaneously fold back on
itself to form a hollow sphere called
liposome. These vesicles enclose water
creating a a separate water compartment
*membrane lipids are asymmetrically
distributed between the monolayers of
the bilayer
 Mobility of Lipid Molecules

• The lipid bilayer itself is stable but individual molecules have a great freedom
of motion
• Rarely will a lipid molecule transfer across a bilayer in a process termed
transverse diffusion or flip – flop
• However, lipids are very mobile in the plane of the bilayer and move in a
process called lateral diffusion this randomizes the positions of the lipid
molecules in few seconds
• The interior of a bilayer is in constant motion
 Temperature Dependence of the Fluidity of a Bilayer
• The interior of the bilayer is fluid because the hydrocarbon chain of fatty acid are in
constant motion produced by rotation about C-C bonds of the acyl chains.
The degree of fluidity depend on the lipid composition and temperature:
• At low temp. bilayer becomes a gel -like solid Paracrystalline state
• at high temp.  lipids undergo rapid motion and the bilayer becomes more fluid

• The transition temperature : the temp above which the

paracrstalline changes into fluid and it is characteristic to
the membrane and depend on the lipid composition

• The transition temperature is dependant on chain length

and the degree of saturation of
its component fatty residues
• Cholesterol broadens the temperature range of the phase
transition:The rigid structure of the sterol nucleus has two
effect on the fluidity of the membrane
-Below the Trans. Temp
-Above the Trans. Tem
Sterols moderate the extremes of solidity and fluidity of
membranes
 The Molecular constituents of membranes

• Lipids and proteins and some carbohydrates as part of glycoprotein and

glycolipids.
• The relative proportions of protein and lipids vary with the type membrane
reflecting the diversity of biological role.
e.g. Plasma membrane of mitochondria contains more protein than lipid; many
enzyme-catalyzed processes take place there.
while Mylelin sheath = plasma membrane of neurons act as electrical insulator
 contains high % of lipids.
* The lipid and protein composition of membranes from different sources vary
reflecting the biological activity.
 The supramolecular architecture of membranes
Common properties
• Biological membranes are impermeable to most polar or charged solutes but
permeable to non-polar compounds
• 5-8 nm thickness

-fluid mosaic model for the structure of biological membranes

• Phospholipids and sterols form a lipid bilayer in which the non-polar regions face each
other at the core of the bilayer and the polar head groups face outward.

• The proteins are embedded at irregular intervals fixed with hydrophobic

interactions between lipids and hydrophobic domains in the proteins

• lipids and protein form a fluid mosaic, because most of their interactions are not
covalent this leave the lipid and protein molecules move freely laterally in the
membrane

• The orientation of the protein is asymmetric; the proteins exposed at one side are
different from those at the other side
• Some proteins present at on side, others have domains exposed at the two sides
 Membrane Structure & Assembly

Fluid Mosaic Model

• Lipids and proteins can undergo rotational and lateral
movement
• 30 - 90% of membrane proteins are freely mobile
• Membranes are asymmetric
* Lateral Asymmetry
– Proteins can associate and cluster in the plane of the membrane -
they are not uniformly distributed in many cases
– Lipids can cluster in the plane of the membrane - they are not
uniformly distributed
* Transverse asymmetry
– N-terminus is often extracellular whereas C-terminus is
intracellular
– In most cell membranes, the composition of the outer monolayer
is quite different from that of the inner monolayer
 Membranes are full of proteins

- Can be 20-80% protein (dry wt.)

- In eukaryotes, different membranes differ in their protein composition
- Proteins can be associated with membranes with different ways

Association of proteins with membranes

- Integral (intrinsic): = proteins that pass

through membrane, largely buried within the
membrane and can be exposed on both
membrane faces, they are tightly bound to
membranes by hydrophobic interactions,
removable only by agents that interfere with
hydrophobic interactions, as detergents,
organic solvents or denaturants. Detergents can
form a micelle like structure around the protein
molecule
Integral membrane proteins
• Attachment of an integral protein to a membrane requires protein
has one or more hydrophobic domains that can span the lipid
bilayer. Most often, these are a-helical domains.
• Integral proteins are amphiphlies
• Oligosaccharides can be linked covalently to the integral proteins
at the outer face; out side the membrane
• The protein segment inserted into the membrane can vary in
structure.
• Serve as transporters, ion channels, receptors and
play important role in cell fusion , cell-cell recognition

Stretch of the protein most likely

to be EXTRACYTOPLASMIC
 Association of proteins with membranes

- Peripheral (extrinsic) associated with membrane

through electrostatic interactions and hydrogen
bonding with the polar head groups of membrane
lipid or with hydrophilic domains in the integral
proteins, they can be released by relatively mild
treatments that interfere with electrostatic
interactions or break H-bonds
(eg. changes in ionic strength or pH, removal of Ca 2+
by chelator, urea)
They serve as regulators of membrane bound
enzyme or may limit the mobility of integral
proteins

PROTEIN
-linked-Lipid: some proteins I
C=O
released by treatment with PI- NH
CH2

specific phospho-lipase C: cleaves CH2

P
a “glycosyl phosphatidyl-inositol”
sugars
membrane anchor attached at
COOH terminus of some proteins P inositol

PL-C
 Lipid-anchored proteins
Thioester-linked
16:0 palmitate

- Note sidedness
Amide-linked - The lipid anchors are added to a protein
14:0 myristate after a protein has been made
(at N-terminus)
- Always attached to a C-terminal residue
- Examples: surface antigens, adhesion
molecules
Thioether-linked
15 or 20 carbon
isoprenoid on
C-terminal Cys
GlcN
Amide link between
ethanolamine N and
C-terminal aa of
protein

cytoplasm Extra cytoplasmic

 Membrane protein movements
-Many proteins can are free to diffuse laterally in the plane
of the bilayer and are in constant motion
*Fusion of a mouse cell with a human cell result in the
randomization of the membrane proteins from the two cells

-Some membrane
proteins associate
together to form large
aggregate can't move

-Other protein are linked

to to internal structures
that prevent their free
diffusion
 Membrane fusion

Biological membrane is able to undergo

fusion with another membrane without
losing its integrity.
Exocytosis, endocytosis, cell division,
fusion of the egg and sperm cells and the
entry of many viruses into the host cells,
all involve the fusion of two membranes
without loss of continuity.
Specific fusion requires that
1- the two membranes recognize each
other
2- their surfaces become closely
opposed, removal of the water associated
with the polar head groups.
3- Their bilayer structures become
locally disrupted and the two bilayers
fuse to form a single continuous bilayer
 Solute transport across Membranes
- Cells must i) import raw materials for biosynthesis and energy production
ii) export by-products of metabolism
- Non-polar gases such as O2, hydrophobic molecules such as steroid hormones, and small, non-polar
molecules can enter and leave a cell by diffusing through the membrane.

-The hydrophobic core of a lipid bilayer is a barrier to polar and charged molecules

- Import/export occurs across permeable membranes and mediated by proteins as trans-

membrane channels, carriers, pumps

• The diffusion of a substance between two sides of a membrane thermodynamically

resembles a chemical equilibration.

• The difference in the concentration of a substance on two sides of a membrane

generates a chemical potential difference
• The movement of ions across a membrane also results in a charge difference generating
an electrical potential difference
 Transport may be mediated or non-mediated

Non-mediated transport occurs through simple diffusion where the rate of diffusion
depends on the concentration gradient and the substances solubility in the membrane’s
non-polar core
– O2, N2 , CO2 and methane and steroids diffuse readily

Mediated transport is classified

into two categories depending on
the thermodynamics of the system

1. Passive –mediated transport or

facilitated diffusion. Molecules
flow
from high concentrations to low
concentrations

2. Active transport. A molecule is

transported against its
concentration gradient. This
endergonic process must be coupled
with an exergonic process to make
it thermodynamically
favorable.
*Passive transport
Simple diffusion
A solute moves from a region of high concentration to one of low concentration by simple
diffusion
-The difference in the solute concentration across the membrane is called chemical gradient

- When ions of opposite charge are separated by a permeable membrane, there is a

transmembrane electrical gradient, = membrane potential (in volts or millivolts)
-Membrane potential produces a force that drives ion movements to make the potential equal
zero
-The direction in which a charged solute tends to move spontaneously across a membrane
depends on both the chemical gradient (= difference in [solute]) and the electrical gradient
across the membrane
-Together, these two factors are referred to as the electrochemical gradient or
electrochemical potential.
 Membranes as permeability barriers
Simple Diffusion
- Non-polar cores of bilayers make them very impermeable to most ionic and polar
substances and proteins (water molecules traverse membranes slowly).

- A small molecule/ion must first shed its hydration shell of water, then become
dissolved in the hydrocarbon core of the membrane, then diffuse through the core, and
become rehydrated on the other side.

- Although the energy used to strip the solute of its hydration shell is regained as the
compound is rehydrated on the other side of the membrane i.e. the consumed energy in
the passive diffusion is is zero, the need to remove a coordination shell of water
molecules creates a very high activation energy (DG‡ )
 Facilitated diffusion
- Transmembrane passage of polar
compounds is made possible by
proteins that lower the activation energy
(by providing an alternative path for
specific solutes through the bilayer)

- Membrane proteins that speed the

movement of a solute across the membrane by
facilitating diffusion is called transporters or
permeases .

- Transporters bind substrates specifically

through many weak, non-covalent
interactions,
replacing water.

- The -ve free energy change associated with

these interactions (DGbinding)
counterbalances
the +ve free energy change for
dehydration
of the solute (DGdehydration), and lowers DG‡
for transmembrane passage.
 Non-mediated and mediated/facilitated transport

1. Passive diffusion 2. Carrier-mediated transport

Not saturable Saturable (like enzyme)
Rate increases w. concentration i) No energy required:
difference across membrane “facilitated diffusion” or “passive transport”
ii) Energy required:
“active transport”
 Three General classes of transport system
- Transporters differ in the number of solutes transported and in the direction in
which each is transported

- This classification, however, tells us nothing about whether these are energy-
requiring or energy-independent processes.
 Facilitated Diffusion Examples
1)Aquaporins, 2) Glucose transport, 3) chloride and bicarbonate
Aquaporins form hydrophilic transmembrane channels for the passage of water
Aquaporins (AQPs): a family of integral proteins that provide channels for rapid movement of
water molecule across plasma membranes in a variety of specialized tissue.membranes of
erythrocytes and proximal renal tubule cells are rich in aquaporins
Aquaporins are type III integral proteins with six transmembrane helical segments, four
monomers form tetrameric transmembrane channel lined with hydrophilic side chains and
having a diameter of 3 A to allow the passage of water molecules
AQPs reduce the activation energy for the passage of water  water moves in the channels
in a continuous stream
Example: Glucose transporter of Erythrocyte mediates passive transport of glucose
(GluT1)
Glucose enters the erythrocyte by facilitated diffusion via specific glucose transporter.
Glucose transporter is integral protein and exists in two conformations T1, with the glucose-
binding site exposed on the outer surface of the plasma membrane and T2 with the binding
site at the inner surface

T in conformation 1: Glc-binding site

exposed on outer surface of membrane

1. Glc binds to specific site,

lowering activation energy for….

2. Conformational change from

Sout.T1 to Sin.T2, which “brings about”
passage of Glc through the membrane

3. Glc released from T2 into cytosol

4. T2 returns to T1 conformation

Note: transport process is fully reversible: Glucose can’t be

accumulated in cells at Concentrations higher than in the
medium.

Transporter achieves equilibration of Glucose at a much

higher rate
Example: Chloride and bicarbonate are co-transported across the erythrocyte
membrane
The chloride-bicarbonate exchanger(anion exchange protein) is an integral protein that
mediate mediates the simultaneous movement of two anions: for each HCO3 ion that moves
in one direction, one Cl ion moves in the opposite direction.

The coupling of Cl and HCO3

movement is obligatory, the absence
of Cl, the transport of bicarbonate
stops,
 Active transport
- Results in accumulation of a solute above the equilibrium point because of the movement of
the molecules against an electrochemical gradient

- Thermodynamically unfavorable (endergonic process): occurs only when coupled (directly or

indirectly) to an energy-yielding (exergonic) process.

Primary active transport: solute accumulation is coupled directly to the exergonic chemical
reaction, like the breakdown of ATP, oxidation reaction, absorption of sunlight.

Secondary active transport: solute accumulation is coupled indirectly to exergonic reaction

as concomitant flow of another chemical species down its electrochemicalgradient

- Ion gradient X (often Na+) is

established by 1° active transport

- Movement of ion X down its

concentration gradient provides
the energy to drive co-transport
of a second solute(s) against its
electrochemical gradient
 Secondary active transport
Secondary active transport: solute accumulation is coupled indirectly to
exergonic reaction as associated with flow of another chemical species down
its electrochemical gradient

x-inside X-outside
ATP ADP +Pi
X-outside x-inside
s-outside S-inside
=============================
s-outside + ATP S-inside + ADP +Pi
 Active transport: examples

Primary active transport example: Na+ K+ ATPase

The energy released by ATP hydrolysis drives solute movement against its electrochemical
gradient. There are several types of ATP-dependent active transporters, that called
transport ATPases which are differing in the structure, mechanism, and localization in
specific tissues and intracellular compartments

- Responsible for setting and maintaining intracellular [Na+] and [K+] in animal cells

- Internal [Na+] < external [Na+] and internal [K+] > external [K+]

= 2-subunit integral membrane protein in plasma membrane

- Antiport - three positive charges exit for every two that enter
 Na+ K+ ATPase

- For each ATP converted to ADP + Pi,

transporter moves 2 K+ into cell and 3
Na+ out

- Process creates a net separation of

charge across membrane: =
transmembrane potential (-50 to -70 mV,
inside -ve relative to outside)

- Current model: ATP-dependent

phosphorylation of the transporter
changes its conformation: transporter
cycles between: a phosphorylated form
with high affinity for for K+ and low
affinity for Na+, and a
dephosphorylated form with high affinity
for Na+ and low affinity for K+.
 Secondary active transport example: Accumulation of glucose in the
intestinal cell
Glucose and some amino acids can be accumulated in the cell by the symport with Na
+
, using the Na + gradient established by the Na + -K+ ATPase of the plasma membrane

Na + -glucose symporters take

up the glucose from the
intestine in a process driven by
the down gradient flow of the
+
Na
glucose is co-transported with *
Na+ ions across the plasma
membrane of the intestinal
cells. It passes into the blood
via (GluT2)passive glucose
transporter. The Na + -K +
ATPase continues to pump Na +

outward to maintain the

gradient of Na + that drives the
glucose uptake
 Passive Transport: Ion selective channels
Passive transport
1- Simple diffusion
2- Facilitated Diffusion
3- Ion selective channels
4- Ionophores
Ion selective channels
Ion selective channels are another mechanism for moving inorganic ions across membranes,
together with Na+-K+ pumps they regulate the cystolic concentration of ions and the
membrane potential
Ion channels are distinguished from transporters in the following
Rate of flux through ion channels is much greater than that of transporter -1
Ion channels are not saturable -2
They are “ gated” can be opened or closed in response to some cellular event. Ligand- -3
gated channels ; the binding of some molecules forces changes in the protein lead to open or
close the channel. Voltage-gated ion channels ; change in the transmembrane electrical
potential causing the ion channel to open or close
The most popular channels K+, and Na+ channels that present in neurons, heart cells, skeletal
muscles
Role of Na+-K+ channels and Na+-K+ pumps in the signal transmission of the *
??? neuron
 Passive Transport: Ionophores

Ionophores
• An ionophore is an organic molecule that binds an ion facilitating
the ions diffusion through the membrane
• Ionophores are often antibiotics of bacterial origin.
• Ionophores can act as carriers, valinonycin, or as channel formers, gramicidin A
• Ionophores can only dissipate an ion gradient
The End