BIOCHEMISTRY // CELL AND CELL MEMBRANE

Trans No.: 1

BIOCHEMISTRY

CELL AND CELL MEMBRANE: A BIOCHEMICAL APPROACH

Date: June 10, 2013

Lecturer: Dr. Allan Hilario

Transcribed by: Balondo, Cahanding, dela Cruz, Dominguez, Farillas, Frias, Montes, Uichanco
BIOCHEMISTRY
It is the frontier of science. It is not a dead science. There are
still many things unexplored in biochemistry.
Example: Human genome
Published in 1986 and only 1-2% of 33,000 enzymes working
with billions of base pairs of genomes are used and studied.
Biochemistry goes hand in hand with molecular biology.
Others call it physiological chemistry or the chemistry of life.
Understanding the biochemical aspect of cell and cell
membrane gives us the basis for what comes out as disease
or those that do not.

A.

B.

C.

Phylogeny of the Three Distinct Domains of Life

Archaebacteria

Extreme halophiles (salt-tolerant)

Methanogens

Extreme thermophiles
Eubacteria

Thermatoga

Flavobacteria

Cyanobacteria

Purple Bacteria

Gram-positive bacteria

Green nonsulfur bacteria

Eukaryotes

Animals

Plants

Ciliates

Fungi

Flagellates

Microsporidia

The macromolecule which is the first biochemical basis of life:

RNA (ribonucleic acid) Biohemical bases:
1. Informational capability to produce framework of protein
2. Protein needs to be acted upon by enzyme
Cell Introduction
Classification of All Organisms according to Energy Source
and Source of Carbon

A Comparison of Prokaryotes and Eukaryotes

Organism
Form
Organelles,
cytoskeleton,
cell division
apparatus

DNA

RNA:
Synthesis
and
maturation
Protein:
Synthesis
and
maturation
Metabolism

Endocytosis
and
exocytosis

Prokaryotes
1-10 m in size
i.e. Eubacteria,
Archaebacteria
Single-celled
Missing

Eukaryotes
10-100 m
i.e. Fungi, Plants,
Animals
Single or multicellular
Present, complicated,
specialized

Small,
circular (ALL, with
the exception of
viruses which can
have linear DNA),
no introns,
plasmids
Simple, in
cytoplasm

Large, in nucleus, many

introns (evident
difference from
prokaryotes)

Simple, coupled
with RNA
synthesis

Complicated, in the
cytoplasm, and the
rough ER

Anaerobic (i.e.
fermentation) or
aerobic, very
flexible
No

Mostly aerobic,
compartmented

*introns non-coding
sequence, not translated
Complicated, in nucleus

Yes

*enveloped by a
thick cell wall

Differentiation between an Animal and Plant Cell

Nucleolus
Nucleus
Nuclear
membrane
ER (rough,
smooth)
Golgi
apparatus
Ribosomes
Peroxisomes
Lysosomes
Cytoskeleton
Plasma
membrane
Vacuole
Cell wall
Chloroplasts
Starch
granules
Thylakoids
Plasmodesma
Glyoxysome

Animal Cell
+
+

Plant Cell
+
+

+
+
+
+

+
+

-, counterpart is the
mitochondria

+
+

-, counterparts are
gap junctions, etc.
-, lysosomes as
counterpart

+
+

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Structure of an Animal Cell

Ex. Peroxisome contains catalase (can attach a probe

with an antibody against catalase, and find it using
ELISA)
Prokaryotic cell

*Left box (yellow) percentage of the cell

*Right box (blue) quantity in the cell
*Number of mitochondrion depends on the differentiation function
of the cell

A. Isolation of Cell Organelles

Fractional Centrifugation way to differentiate the
compartments of the cell
1. Lyse the tissue
2. Sieve it through a filter membrane to remove the
debris like the whole tissue part
3. First to sediment are the nucleus and the
cytoskeleton
4. Second are the organelles mitochondria,
lysosomes, peroxisomes; plants chloroplasts
5. Third, plasma membrane and ER fragments, small
vesicles, microsomal fraction
6. Last, ribosomes, viruses, macromolecules
(polymers of carbohydrates, proteins, etc.)
B.

Ex. E. coli
Nucleodis not encapsulated
The bacteria maintains its shape through the cell wall
which contains lipopolysaccharide (LPS) which is a
membrane bound lipid (Lipid A) attached to
polysaccharides which act as endotoxin, responsible for
the symptoms of fever and shock in infected animals and
humans by gram (-) bacteria. (septicemia)

Color
Stain

Gram (+)
Blue-violet
Crystal
Violet
(Primary)

Gram (-)
Pink
Safranin

Density Gradient Centrifugation

A way to differentiate by gradient. When gradient is

known of a particular solution, the particular cellular
component will hover within that gradient, then you can
know its identity by using its marker molecules

Crowded inside with ribosomes and different solutes it

makes it easier for solute to communicate, anything that
comes in the cell is readily attached to any part of the cell
targeted
No membranes separating the organelles
The plasmid is a different set of gene, usually circular
which conveys resistance (the material that jumps from
cell to cell to prevent destruction by antibiotics)
A. Components of a Bacterial Cell
Water 60-70%
Water interacts with most substances in the cell making
its interaction with water, a classifying distinction for these
substances (Hydrophobic vs. hydrophilic)
The cell is enveloped by cell membrane serving as a
selective physical barrier
The cell is composed of supramolecular structures
capable of self-assembly
B.Inner look
Inner space of cell is crowded with macromolecules
provide non-specific stearic repulsion prevents easy
introduction of molecules inside
Macromolecules occupy 20-40% (protein is dominant)
Smaller molecules 70% of the space
Crowding affects:

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o Biochemical reaction rates

o Protein folding
o Protein-protein binding
o Chromosome structure
o Gene expression
o Signal transduction
*Why crowding takes less time to interact due to less
distance between cells
Proteins becomes super complexes
o act as biological machines that perform work
when motor protein subunits bind and hydrolyze
nucleotides such as ATP
o ATP universal currency of cells
Energy-induced changeproduce conformational and
orderly change in shape of the adjacent subunits causing
movement (work)
All cells have the inherent ability to interpret and
response to signal from its environment and adjacent
cells through signal transduction (ability of the cell to
respond to stimuli from the environment)

TWO MAJOR PARTS OF THE CELL

1. Cytoplasm
Portion of the cell enclosed by the cell membrane and
outside the nucleus
Where the cellular organelles are found which are
membrane-bound or the macromolecules and other
ribosomes which are not membrane-bound
These organelles are not just simply floating but are linked
together by the cytoskeleton of the cell
Cytosol: fluid portion of the cytoplasm; where most of the
biochemical processes occur
These include glycolysis, gluconeogenesis, fatty acid
synthesis, protein synthesis, part of urea cycle and purine
metabolism an amino acid synthesis, NADPH production
(pentose phosphate pathway; malic enzyme), isoprenoid
and sterol synthesis (early stages), fatty acid synthesis
But not all cells will do that. There are differentiation of cells
where only gluconeogenesis is present and ketogenesis is
absent.
Nucleoplasm: the cytosol in the nucleus

C. Biochemical Reactions of the Cytoplasm

Pentose phosphate pathway

Gluconeogenesis

Protein biosynthesis

Fatty acid biosynthesis

Glycolysis, etc.
*In prokaryotes, everything happens in the cytoplasm

Cytoskeleton
- a network of protein scaffolding
- maintains the shape of the cell
- serves as tracts for movement of organelles
- These filamentous protein polymers are categorized into
3 types depending on its size with differing functions:
1. Microfilaments (6-8 nm)
2. Intermediate filaments (10 nm)
3. Microtubules (25 nm)
- The protein scaffolding assembles as polymers from
protein subunits.
- What is that recurring theme from the prokaryotes to the
eukaryotes? SELF- ASSEMBLY (They have the same
characteristics that make them assemble. The noncovalent factors that make them assemble: London
forces, stearric, Van der Waals, hydrogen bond, dipoledipole, ionic bond.)

These characteristics are recurring theme in both prokaryotes

as exemplified by a bacterial cell and eukaryotes as
exemplified by an animal cell.

Metabolism is the totality of cellular activities that

generates energy for cellular function, (1) conversion of
micronutrients, (2) polymerization of various monomeric
components of macromolecules and (3) synthesis and
degradation of various macromolecules various and
specialized cellular functions.

Anabolism is the synthesis of macromolecules from its

monomeric units usually for storage.
- needs reducing equivalents

Catabolism is the degradation of macromolecules to its

monomeric units usually for energy production, entrance
to other metabolic pathways or disposal.
- an oxidative process

CELLULAR ORGANIZATION
Eukaryotic cell
Coming from the three germ layers:
1. Ectoderm producing the external
2. Mesoderm mesenchymal
3. Endoderm mostly neural tissue
There are over 200 cell types in the human body.

1.

Microfilaments
Actin

most abundant protein in eukaryotic cells

the protein component of microfilaments

occurs in two forms: a monomolecular form (Gactin, globular actin) and polymer (F-actin,
filamentous actin)

G-actin is an asymmetrical molecule with a

mass of 42 kDa, consisting of two domains.

As the ionic strength increases, G actin

aggregates reversibly to form F actin, a helical
homopolymer. G actin carries a firmly bound
ATP molecule that is slowly hydrolyzed in F
actin to form ADP. Actin therefore also has
enzyme properties (ATPase activity: It
hydrolyzes ATP to ADP and organic phosphate).

Myosin is the globular protein that interacts with

actin in myocytes for muscle contraction.

It is present in all cells not just in the muscles.

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Toxin found in Amanita

phalloides mushroom inhibits
decay by binding to the
negative polarity.

Mold toxin inhibits

polymerization by
binding to the positive
polarity

(Refer to the figure above) This is the single monomer of actin

and when they polymerize, they become F actin. The negative
end which is actually negative in its electric capacity is
inhibited by phalloidin, a toxin. The positive end is inhibited by
cytochalasin. These two can be used to prevent the formation
of actin so the cell will die, especially in cancer cells.
2.

Intermediate filaments
The intermediate filament belongs to five related
protein family with cell type-specificity. These include:
1. Cytokeratins (ectoderm)
2. Desmin (ectoderm)
3. Vimentin (mesoderm)
4. Glial fibrillary acidic protein (GFAP) (endoderm;
in the glial cells of the nervous tissue)
5. Neurofilament (endoderm)
These proteins have a rod-shape structure at the
center called super helix configuration.
The intermediate filament is produced from 8
protofilaments.
-

3.

Repository and cellular localization of storage replication

and expression of genetic information
Contains 99%of cell DNA (1% in the mitochondria)

Structure:
1. Nuclear Envelope- separates the nucleus from the
cytoplasm; hastwo separate bilayer membranes (one
inside the other)
The outer membrane is continuous w/ the ER of the
cell cytoplasm
The space between the two membranes is
continuous with the space inside the ER
2. Nuclear Pores- controls the movement of substances
between the nucleus and cytoplasm
3. Nucleolus- contains RNA and proteins of the types found
in ribosomes
Has no limiting membrane
4. Nucleoplasm- highly viscous liquid surrounding the
chromosomes and nucleoli
5. Chromatin- composed of DNA and other proteins that
make up the nucleus
6. Chromosomes- contains most of the cells hereditary
units (genes) that controls cell structure and its activities
Functions:
Control center of the cell
Contains large amounts of DNA
Transmits genetic information
Directs protein synthesis in cytoplasm via various RNA
forms
Contains enzymes for DNA repair, replication,
transcription, and mRNA production
Pathways that occurs in the nucleus:
1. Replication
a. Nucleus -99%
b. Mitochondria -1%
2. Transcription
3. Translation
+
4. Biosynthesis of NAD

Tubulins
The basic components of the tube-shaped
microtubules are and tubulin (53 and 55 kDa).
Thirteen protofilaments form a ring-shape and
polymerize to form a long tube.
Important during mitosis.
Nucleolus- ONLY part where rRNA is synthesized
Euchromatin- transcribing part; white part in the electronmicrograph
Heterochromatin -dense part; dark part
ORGANELLES

1.Mitochondria
Powerhouse of the cell where, most not all, ATP is
produced
Self-replicating

2. Nucleus

Largest organelle

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*phospholipids produced in SER are immediately incorporated in
the bilayer of the SER itself for the formation of transport /ER
vesicles and replenish the cell membrane bilayer
3. Golgi Apparatus
Responsible for the packing of proteins in vesicles to be
exported out of the cell

Primitive prokaryotic cell engulfed the bacterium (animalaerobic; plant-cyanobacterium) which resulted to the
double-membrane structure called mitochondria (for
animal and chloroplast for plants).
Explains why mitochondria contains circular DNA which is
also present in the bacterium

1.
2.

cis face - fusion of areas of Golgi with ER

trans face - site for packaging and sorting

Functions:
Receives protein from rER via coated vesicles to be
further processed, packed and released into the
cytoplasm as vesicles
Synthesizes certain carbohydrates not formed in the ER
such as hyaluronic acid and chondroitin sulfate
4. Lyososomes
Contains nucleases, proteases, glcosidases, lipases,
phosphatases, sulfatases, phospholipases
All macromolecules that gets into the lysosomes (very
acidic in nature) are either catabolised for salvage usage or
for waste disposal

Structures:
Originates from the Golgi apparatus
Acidic at pH 4.5
Membrane bound vesicles dispersed in the cytoplasm
Contains digestive enzymes (hydrolase) and bactericidal
agents (ex. lysozyme and lysoferrin)
Stuctures:
1. Outer membrane porous
2. Inner membrane selectively porous
3. Cristae-where electron transport chain and oxidative
phosphorylation occur; contains enzymes required for ATP
synthesis
4. Intermembrane space
5. Matrix

Functions:
Degradative via endocytosis towards:
a. Damaged cell structures
b. Food particles ingested
c. Unwanted materials (ex. bacteria)
-

Proteins-major macromolecule content of mitochondria

Pathways in the mitochondria:
1. Tricarboxylic Acid Cycle (Krebs Cycle)
2. Beta-Oxidation
3. Part of the Urea Cycle
4. Respiratory Chain
5. ATP Synthesis
Transport Systems in the Mitochondria:
1. Citrate-Malate Shuttle
2. Carnitine Shuttle
3. Glyerophosphate huttle
4. Malate shuttle
2.
A.

Rough and Smooth Endoplasmic Reticulum

Rough ER: Granular Endoplasmic Reticulum

Flattened sacs of ER studded with ribosomes (where
protein synthesis occurs) giving its rough appearance
Functions:
Protein synthesis via ribosomes
mRNA translational and post-translational modification
of proteins

B.

Smooth ER: Granular Endoplasmic Reticulum

Tubular sacs of ER with no ribosomes attached
Functions:
Site of lipid and cholesterol synthesis
Drug detoxification
Calcium reservoir for cell signaling
Conversion of hydrophobic into water soluble molecules

Responsible for tissue regression after long periods of

inactivity
Responsible for autolysis after cell damage

5. Peroxisomes
Degrades peroxides because of the enzyme oxidases
present in it

Structures:
Membrane bound
Forms by self replication
Budding off from the sER
Contains oxidases instead of hydrolases
Functions:
Membrane-bound vesicles containing oxidative enzymes for:
Detoxifying harmful substances
Oxidation of fatty acids
Pathways in Peroxisomes:
1. Fatty Acid Oxidation (alpha, beta, omega)
2. Synthesis of certain membrane lipids
3. Purine catabolism
4. Generation and breakdown of NaOH

CELL MEMBRANE
Emerged with most polar charged substances but allows
the hydrophobic substances or the non polar substance
A 5 to 10 nanometers in thickness
Appears trilaminar structure when viewed in electron
microscope.
1.

Trilaminar
Actual picture of the lipid bilayer under the electron
microscope
Dense part of phosphate group in phospholipid
Less dense is the tail of the phospholipid

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II.

2.

The other dense part is the other polar group in the

inner layer
Lipid Bilayer

Characteristic of the membrane

PROTEIN MOVEMENT

FLUID MOSAIC MODEL

1972 by Singher and Nicolson
Lipid bilayer wherein the lipid layer is DYNAMIC. There is a
lot of movement in the inner and outer leaves.
Proteins and other structures in the bilayer moves. They
float in a sea of lipids.

Integral membrane proteins are inserted into the lipid

bilayer, whereas peripheral proteins arebound to the
membrane indirectly by protein-protein interactions. Most
integral membraneproteins are transmembrane proteins,
with portions exposed on both sides of the lipid bilayer.The
extracellular portions of these proteins are usually
glycosylated, as are the peripheralmembrane proteins
bound to the external face of the membrane.

1.

2.

3.
4.

LIPID CONTENT OF PLASMA MEMBRANE

Major content of the lipid bilayer is PHOSPHOLIPIDS
POLAR: Phosphate group; head
NON-POLAR: Fatty acyl chain; tail
Arranged in such a way that the outer polar group is in
contact with the outer matrix and the inner polar group is in
contact with the cytoplasm.
Middle contains the non-polar acyl chains of both tails.
They are attached by non-covalent bonds due to their
stearic attraction.
In general, most commonly found are: Phospholipids,
sphingolipids and cholesterol.

*Is the lipid content of plasma membrane constant in all cell types?
No, they vary.

I.

CELL MEMBRANE MOTION STUDIES

LIPID MOVEMENT

Cells from two different species (human and mouse, blue

and pink respectively) are tagged with fluorescent
antibodies that react with membrane proteins.
These cells are induced to fuse by exposure to Sendai
virus. The proteins from the two parent cells are localized
to two separate halves of the hybrid cell initially.
Within a few minutes, they begin to intermix.
After around 40 minutes, they are now randomly
distributed in the plasma membrane.
PROTEINS IN THE CELL MEMBRANE

GLYCOPROTEINS: outer leaflet

Oligosaccharides: outer leaflet

Important for signal transduction and recognition

Antigen-antibody binding
FUNCTIONS OF THE CELL MEMBRANE

The bounding function of the membrane gives the cell its

shape and separates itself from other cells and external
environment.
When there is actual anchorage of any protein in the cell,
there is less movement.
CELL MEMBRANE LIPID COMPOSITION

1.
2.

3.

4.

The cell was reacted with fluorescent probe to label the

lipids of the cell membrane (first step).
Second step shows the fluorescent labeled cell
membrane and its appearance in the fluorescence
microscope.
In the third step, an intense laser beam bleaches a small
area of the cell membrane and its appearance
microscopically.
In time, the unbleached phospholipids diffuse into the
bleached area (therefore, movement).

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It can be generalized that the inner leaflet contains

phosphatidylserine.
Tricylglycerol or neutral fat is not present in cell membranes
with only a few exceptions.
Cholesterol is exclusively found in animal cell membranes.
When present in plants, they are called steroids.

2.

Lipid bilayer

Basic structural element of the cell membrane.

3.

Vesicle/Liposome

Two layers of lipid bilayer engulfing an aqueous

environment.
Presence of an aqueous cavity inside the inner membrane.

CELL MEMBRANE COMPOSITION IN DIFFERENT CELLS

TYPES

NERVE CELL PLASMA MEMBRANE

o Sphingomyelin is high because it serves as an
insulator (i.e. myelin sheath)

MITOCHONDRIA
o high in proteins because these proteins are enzymes
responsible for oxidative phosphorylation and the
electron transport chain

CARDIOLIPIN

only specialized lipid that is antigenic;

present in the mitochondria

proof of endosymbiosis

SELF-ASSEMBLY OF PHOSPHOLIPIDS
Phospholipids when placed in an aqueous solution can
assemble itself in different ways.

1.

Micelle

CELL MEMBRANE FLUIDITY

The most important characteristic of the fluid mosaic model
is its fluidity.
Fluidity refers to the viscosity of the lipid bilayer or the
degree by which the bilayer resists movement.

Hydration of polar heads and the tails aggregate in the

center
No cavity inside
Individual units are wedge-shaped (cross section of
head greater than that of side chain)

Factors Affecting Membrane Fluidity

1. Temperature
Higher temp, higher fluidity
2.

Unsaturated Fatty Acid Content

More unsaturated fat, more fluid

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Cell Membrane Self-Sealing

Presence of double bonds, therefore kinks in
This is for the maintenance of cell membrane integrity. Two types:
hydrophobic tail.
a. Lateral diffusion of lipid contents for small disruptions
The kinks cant provide an ordered structure by
b. Energy requiring process through Ca2+ for larger tear
stacking.
due to mechanical stress
3. Cholesterol (paradoxical)
Cell Membrane Selective Permeability

Aliphatic: polar and nonpolar

The hydrophobic hydrocarbon chains in lipid bilayer

Paradoxical way by which it provides fluidity.

provide an impervious barrier for ionic and polar
substances.
Cell Membrane Fluidity

Specific proteins - regulate the passage of ionic and polar

Viscosity of the lipid bilayer or the degree of resistance of

substances in and out of the cell so that polar groups
membrane components to move.
cannot pass through easily the cell membrane but
hydrophobic groups can easily diffuse:
Factors:

Water - aquaporins
1. Temperature: higher T, more fluid

Polar substances - shed hydration shell

2. Content of unsaturated FA: higher content, more fluid
3. Content of cholesterol: when cholesterol interacts with

Large molecules and ions - transport system such as

unsaturated/short-chain fattyacyl PL results to less
protein membrane
fluidity; when cholesterol interacts with spingolipids and
long-chain fattyacyl PL tends to make it more fluid.
Cell Membrane Lipid Movement
1.

Rotation

2. Lateral diffusion - very fast

3. Flip flop - very slow that enzymes are needed

Cell Membrane Asymmetry

The inner and outer leaflets of the lipid bilayer differ in
composition

Components of phospholipid that needs enzyme:

1. Flippase
- P-type ATPase
- Allows one polar head group to go the other side
- Requires energy
2. Floppase
- ABC transporters
- Inner leaflet to the other side
- Requires energy
3. Scramblase
- Moves either way

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Cell Membrane Proteins
Cell Membrane Microdomains
These are for transfer of solute. The latter cannot enter the lipid Examples:
bilayer because it is polar.
1. Lipid Raft

Classification:
1. Integral proteins
Embedded in and/or pass through the lipid bilayer
Extracted only through disruption of the cell membrane
with organic solvents or detergents
Amino group in cytoplasm or extracellular side
Traverse the membrane in a certain manner wherein
the hydrophobic part of the segment of the polypeptide
traverse in certain type of manner the cell membrane
making a ionic channel wherein solutes can pass
through
Allow hydrophobic interaction with lipid bilayer
Most have alpha-helical structures with 15 to 20 aa
Have bulky side chains: alanine, leucine, isoleucine,
phenylalanine, and valine
May have several helices that pass through the
membrane in serpentine manner
2.

3.

Transmembrane proteins (but not integral proteins)

Beta-pleated sheet is the secondary structure:
a. FepA-ion transport for bacteria
b. OmpLA-phospholipase in E. coli
c. Maltoporin- transport in E.coli
d. In human: porins in outer membrane
mitochodria

Thickened portion of the lipid bilayer comprising

about 50% and rich in cholesterol and sphingolipids
Rich in sphingolipids and cholesterol where the GPIanchoring protein can be seen
Important in anchorage and cell-cell interaction and
signaling

2.

Caveola

Curved lipid raft, due to the action of caveolin, a protein

which dimerizes with other caveolin through its fatty acyl
and cholesterol moities, producing a strain and causing
the cell membrane to invaginate.
Important in various cellular process involving membrane
breakage and sealing, and signal transduction.

of

Peripheral proteins
Bound to the membrane through non-covalent
interaction with integral proteins
Covalently bound to several mechanism: myristic,
palmitic, prenyl group, glycosylphosphatidylinositol
anchors (GPI-anchors) in lipid rafts
Can also be found in extracellular

Hydropathy plot - a graph determining the sequence of amino

acid in polypeptide will have a certain hydrophobicity

Endocytosis and Exocytosis

For bigger substances to transport
a.

Microdomains - 50% of proteins in cell membrane

Endocytosis - the entrance of substances, smaller

macromolecules, and other debris through a cell
membrane mediated engulfment without leakage of

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cell contents or without the loss of cellular membrane
integrity

Diffusion

Simple diffusion without membrane protein

- movement of solutes down its electrochemical
gradient due random thermal movement or simply
because the solute is permeable through the lipid
bilayer because it is small enough and/or
hydrophobic

Facilitated diffusion
- movement of solutes down its electrochemical
gradient through either transporters or ion channels
(membrane proteins)

How do transporters allow the passage of hydrophobic

solute?
For proteins to transverse the lipid bilayer, they have to
interact with the hydrophobic core within the chain of the
sequence of amino acids protrudes out the hydrophilic part,
e.g. the hydrogen and nitrogen, making the core ionic in
nature so hydrophilic solute can pass through
By lowering the energy of activation of the solute (ex.
+
hydrated Na
ion needs much energy to pass
through the membrane but transporters lower the free
energy change)
Passive and Active Transport

b.

Cell Moembrane Transport

Transfer of solutes and information across membranes
1.
2.
3.
4.
5.

Exocytosis - the release of substances, smaller

macromolecules,and other substances for transport to
othe issues and cells through a celmembrane mediated
release without leakage of cell contents or without the
loss of cellular membrane integrity

Diffusion
Simple diffusion (passive and facilitated)
Cross-membrane movement of large molecules
Endocytosis
Exocytosis
Signal transmission across membrane

Cell surface receptors

1) Signal transduction (glucagon cAMP)
2) Signal internalization (coupled with endocytosis like
LDL receptos, Insulin
and Glut transporters)
Movement to intracellular receptors (steroid hormones,
thyroid hormones, retinoids, Vit. D hydrophobic in
nature so they do not need transport proteins; easily
pass through the membrane)

Free diffusion H2, CO2, urea, O2

Facilitated diffusion downhill but does not need energy

Creation of Electrochemical Gradient

Depends on the chemical gradient
(or the difference of
solute concentration or its ratio C2/C1) and the
transmembrane electrical gradient, Vm in millivolts. Solutes
follow the 2nd law of thermodynamic where it tends to
assume spontaneously the greatest randomness and the
lowest energy

Comparison between Transporters and Ion channels

Transporter- alternating gates
- Binds molecule and ion with high specificity
- Undergoes conformational change to let the transported
ion enter the other side of the membrane
- Saturable/ acts like an enzyme
- Involves active and passive transport (facilitated
diffusion)
2. Ion Channels single gate
- Show some specificity for the solute but does not act like
an enzyme and only forms pores which open and close
with less conformational change
- Non-saturable
- Involve mostly facilitated diffusion
1.

A.

Uniport, Symort, Antiport

Glucose - through passive transport and a uniport which is
used in transporting glucose in the cell through the influence
of insulin

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(uphill)
Glucose - may also be transported together with sodium into Secondary Active transport- occurs when endergonic
cell as a symport type of facilitated transport
transport of one solute is coupled to an exergonic (downhill)
flow of a different solute that was originally pumped uphill a
Chloride-bicarbonate exchanger of the RBC membrane - primary active transport
allows the transport of bicarbonate without changing the
membrane potential in opposite direction with chloride ions
and increases the carbon dioxide carrying capacity of blood

B.

C.

Aquaporins
Water channels that only allow the passage of water
molecules in the membranes of RBC and cells of the
collecting ductules of the kidney
Mutation in some of these channel proteins may cause
Nephrogenic Diabetes Insipidus [a disorder in which a
defect in the small tubes (tubules) in the kidneys causes a
person to pass a large amount of urine].

Comparison between Ionotropic Channels and Ionophores

Ionotropic Channels
Receptors that acts as
channels and do not need
a secondary messenger

a.
b.

c.
a.
b.
c.
d.

Acetylcholine- Na+ and

Ca2+
Serotonin and
Glutamate-K+, Na+,
Ca2+
Glycine-Cl specific
channels
Dendrotoxin (mamba
+
snake)- K
Tetrodotoxin (puffer
fish)- Na+
Cobrotoxin and alpha
conotoxinAcetylcholine receptor
ion channel

Ionophores
Non-receptor compounds that
produce channels or pores in the
cell. If it produces pores or
channels in bacteria they serve as
anti-bacterial.
While if they cause production of
pores or channels on cell
membranes of human cells, they
cause injury or disease.
Valinomycin-K+ channels
Monensin-Na+ channels
Gramicidin-folding creates hollow
channels

Diptheria toxin and activated

complement- create large cellular
pores causing lysis
Alpha-hemolysis (Strep.), leak out
ATP

TERMS

Diagram (directly) above summarizes

transport mechanisms.

cell membrane

Active transport - the diffusion of molecules and ions against its

Importance of Ion Channels
electrochemical gradient with the use of energy which is mostly
supplied by ATP; its protein transporter has an ATPase activity
Venom of animals like snakes targets the ion channels instead of
hydrolyzing ATP to ADP producing the needed energy.
proteins of metabolism. If it wanted to take down another organism,
Primary Active Transport - the solute accumulation coupled it would inhibit the others glycolytic pathway. Ion channels and the
directly to an exergonic chemical reaction such as breakdown of metabolic pathway are both composed of proteins (enzymes n the
metabolic pathway). *In science the straight forward line going to
ATP

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the answer is the easiest and most correct one*. In the
evolutionary sense it is always through the conservation that our
species (or other species) perpetuate. Animals with poisons want
to make their venom more effective by targeting ion channels
since even when targeting those alone the venom will already
affect numerous parts of the body. In the case of action potentials,
when these are disturbed/interrupted an animal/human may be
paralyzed right away. Paralysis due to targeting proteins of the
glycolytic pathway may take more time compared to the immediate
paralysis by disruption of ion channels.
Cell Membrane Transport
Some types of ATP-deriven Active Transporters
Type
Example
Cellular Location
Sarcoplasmic
2+
Ca ATPase
Reticulum
P-Type
Plasma or cell
+ +
N -K ATPase
membrane
mt ATPase
synthase of
F-Type
Mitochondria
oxidative
phosphorylation
The ATPase that
pumps protons
Lysosomal and
V-Type
into lysosomes
synaptic vesicular
and synaptic
membranes
vesicles
Plasma or cell
CFTR protein
membrane
ABC
Transported
Plasma or cell
MDR I protein
membrane
Some of the types of ATPase (from Harper) are listed on the
table above. The most important to remember is your
sarcoplasmic reticulum, a specialized form of endoplasmic
reticulum in the myocyte. This facilitates occurrence of muscle
contraction.

An action potential is one that causes the repolarization of the cell

membrane of the axon which may lead to activation of postsynaptic vesicles of the post-synaptic neurons, or the contraction
of muscles which is brought about by the ionic composition within
the cell and the external environment. In the following Table 40-1,
we find that the extracellular fluid is very high in sodium (140
+
mmol/L) however the intracellular fluid only has 10 mmol/L of Na .
+
The potassium (K ) on the other hand is very high in the
intracellular fluid (140 mmol/L) while very low (only 4 mmol/L) in
extracellular fluid. There is a discrepancy between sodium and
potassium levels. Mataas ang sodium sa labas, mababa sa loob;
mataas naman ang potassium sa loob, mababa sa baba.
Similarly so, Calcium is like Sodium and Chloride because they
are depolarizing ions. Remember this, the sodium, calcium, and
chloride ions are depolarizing.

Ion Channels and Electrical Signals in Excitable Cells

The membranes of nerve cells contain well-studied ion channels
that are responsible for the generation of action potentials. The
activity of these channels is controlled by neurotransmitters; hence,
channel activity can be regulated (Murray, R.K., Bender, K.M.,
Kennelly, P.J., Rodwell, V.W., Weil, P.A., 2012).
Ion channels are open transiently and thus are gated. Gates can
be controlled by opening or closing. In ligand-gated channels, a
specifc molecule binds to a receptor and opens the channel.
Voltage-gated channels open (or close) in response to changes in
membrane potential. Mechanically-gated channels respond to
mechanical stimuli like pressure or touch (Murray, R.K., Bender,
K.M., Kennelly, P.J., Rodwell, V.W., Weil, P.A., 2012).
Characteristics of ion channels are listed in Tables 40-4 and 40-5
of Harper.
Dr. Hilario introduced the ion-gated channels just to give us the
principle behind them (but this would be discussed in more detail
in physiology). And asked the question: What kind of transport is
this (Sodium-potassium ATPase)? Anti-core, primary active
transport! For the action of this transporter, for every three
potassium ions out, enters two sodium ions (see schematic
diagram that follows).

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BIOCHEMISTRY // CELL AND CELL MEMBRANE

membrane

There is an imbalance: there is negativity inside the cytoplasm and

positivity outside it. This is the membrane potential which is about
50 to 70 mV. So any perturbation in the cell membrane like
pinching or any injury or stimulation will cause the leakage of
sodium through the sodium channels where it goes inside causing
depolarization of the membrane (Ano yung tatlong ion na nag-dedepolarize? Those are sodium, chloride, and calcium ions). So this
time sodium depolarizes the membrane. It goes through the
membrane until it reaches the neuromuscular junction. It will then
depolarize the vesicle that releases the Acetylcholine (ACh) which
will then attach to the receptor in the post-synaptic axon.
Depolarization of sodium will continue until it reaches the
neuromuscular junction and release the calcium through the Ttubule so that it propagates the action potential.

Problem with cystic fibrosis: secretions are thick because theres a

mutation in the gene encoding the CFTR protein which is a
chloride transporter. When chloride passes through the ion
channel what comes with it? Sodium does. Water follows sodium.
Water hydrates the lining of the respiratory membrane. Without
water, the lining becomes thick; bacteria tend to be trapped in it.
Most of cystic fibrosis patients die of pneumonia.

DISEASES INVOLVING ION CHANNEL DEFECTS

The neuron starts the action potential. Its the same membrane in
the diagrammatic scheme (see second to the last page). It goes to Table 11-7 below lifted from Dr. Hilarios lecture notes. Note
the neuromuscular junction and the muscle contracts causing the emphasized items.
movement. If you look at the very small part of the axon, it would
reach the neuromuscular junction and the neuron will act on the
skeletal muscle.
You can see the release of the neurotransmitter, ACh in the
diagram, so that it would act on the post-synaptic vesicles. Postsynaptic vesicles will then continue the action potential wherein
sodium depolarizes the cell membrane. The acetylcholine binds to
the receptor of the motor end plate of the neuromuscular junction.
This depolarizes the cell membrane of the muscle fiber and going
to the tubules releasing the calcium from the sarcoplasmic
reticulum. The T-tubules are invaginations of the cell membrane.
The same sodium channel acts on the membrane. It then releases
the calcium. When theres calcium it will stimulate the troponin until
it works its way through actin-myosin binding so that there is
movement. The sarcomere shortens thus causing the contraction.
It moves along until it provides you the movement. Sodium is the
one that leads the action potential. Chloride and calcium also
depolarizes while potassium hyperpolarizes.
This diagram presents Ach as a receptor in a ligand-gated channel
(two images in the last page). The others formerly presented are
ion-gated channels.
DISEASES INVOLVING ABNORMALITIES OF MEMBRANES
Table 40-7 from Harpers lists diseases involving abnormalities in
Cell Membranes. Those enclosed in red rectangles are the ones
emphasized by Dr. Hilario.

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For the ion channel defects, we have the sodium-gated channel for 3.
hyperkalemic periodic paralysis (Dr. Hilario doesnt want us to
know the clinical part here. Just associate it with ion channels so
that you can at least know the relevance of studying these
diseases in relation to the ion channels). Ion channels defects of
skeletal muscle responsible for the clinical entity: hyperkalemic
periodic paralysis.
ARTIFICIAL MEMBRANES AND THEIR IMPORTANCE

4.

The Phospholipid (PL) may be attached to an antibody where

drug delivery may be target-oriented.
Anything may be attached to phospholipids which are ionic
parts of the cell membrane. You can attach protein which
attach to antibodies so you can target whatever you want to
target (most especially cancer cells).
Studies and researches on the activity and property of various
lipid and protein components of the cell membrane will soon
be made possible.

References:
Dr. Allan Hilario Lecture and Notes
Murray, R.K., Bender,K.M., Kennelly, P.J., Rodwell, V.W.,
th
Weil, P.A. (2012). Harpers Illustrated Biochemistry (29
ed.). North America: McGraw Hill Companie, Inc.

Images:
When you look at the solution of aliphatic hydrocarbons in solution
with aqueous membranes you will find the electron micrograph like
this (as in image above). Each layer is a bilipid layer. When you
subject this to ultrasound frequency but mostly sonication, it
creates a vesicle-like structure where there is an aqueous cavity
inside. But still it is bounded by the lipid bilayer.

Dr. Allan Hilario Lecture and Notes

http://www.zoology.ubc.ca/~gardner/synapses%20%20presynaptic.htm
http://www.cnsforum.com/imagebank/item/rcpt_sys_nic_ag1/de
fault.aspx

IMPORTANCE OF ARTIFICIAL MEMBRANES

1.

Drug delivery where liposome, being hydrophobic in nature,

can easily enter the normal cell, cancer cell, and bacterial cell
So anything that can be dissolved in aqueous solution (that
you can put inside the cavity) can be transported through the
membrane so easily. Anti-cancer drugs, which are usually
hard to transport through the membrane because of their ionic
character, can be easily transported by liposome. The
importance of liposome is mainly (at the moment) for drug
delivery. Liposome being hydrophobic in nature can easily
enter the cell, i.e. cancer cells and bacterial cells. There are
liposomal preparations of doxorubicin which is a neomycin
that is anthracite-based chemotherapeutic agent for most
solid tumors, and cancer. There is also liposomal preparation
of ticarcillin and tobramycin which are used on most resistant
bacteria that resist usual preparations of those antibiotics.
With the presence of liposomal carriers they can easily
penetrate the membrane and gain access to bacteria in order
to facilitate bacterial destruction.

2.

Gene therapy liposome can easily penetrate the nucleus

that gene insert may be easily incorporated.
Gene therapy has failed before since most vectors used are
HIV viruses (retroviruses). E diba natatakot ang tao, pag
retrovirus HIV yun. So how could you prevent infection with
HIV if the vectors for gene therapy are HIV viruses? So the
first experiment for gene therapy of ADA (adenosine
deamylase) for severe combined immune deficiency disease
was cancelled.
In the future, liposomal insertion (gene insert) into the
chromosome through the nucleoplasm through the nuclear
membrane may be easily achieved through liposomal carriers.

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Metabolic
Terms
Glycolysis

Gluconeogenesis

Hexose
Monophosphate
Shunt

Glycogenolysis

Glycogenesis
Tricarboxylic
Acid Cycle or
TCA or Krebs
Cycle
Oxidative
phosphorylation
and the electron
transport chain
Lipolysis (BetaOxidation)

Definition
Breakdown of
glucose and other
hexoses to pyruvate
or lactate
Synthesis of glucose
from glucogenic
precursor
Breakdown of
glucose and other
hexoses for the
production of
reducing equivalent
and the sugar ribose
Breakdown of
glycogen into
glucose
Synthesis of
glycogen from
glucose
Central metabolic
pathway of all cells
Pathway for
producing the ATPs
from all electron
contributing
pathways for energy
needs
Degradation of fatty
acids for energy
need

Lipogenesis

Synthesis of lipids

Alpha and BetaOxidation

Same as BetaOxidation
Same as Betaoxidation

Omega-oxidation
Replication

Synthesis of DNA

Transcription

Synthesis of RNA

Translation

Synthesis of proteins

Post-translational
modification

Modification of
protein molecules
after its synthesis
Packaging of protein
either for temporary
storage or transport

Function

Cellular Location

Production of ATP for

energy need of the ell and
for lipogenesis

Cytoplasm of all cells

Use of glucose to undergo

glycolysis for energy need in
case of scarce food source

Cytoplasm of hepatocytes and

renal cells; and in special
conditions intestinal cells

Provide the reducing

equivalents for most
synthetic pathways and the
sugar backbone (ribose) for
DNA and RNA synthesis

Cytoplasm of all cells

To provide glucose readily

from its storage form
(glycogen) for energy need
To store excess glucose
from the diet in glycogen
form
To burn the acetyl-CoA
made from fat, glucose, or
CHON to make ATP in
cooperation with oxidative
phosphorylation

Cytoplasm of hepatocytes and

muscle cells
Cytoplasm of hepatocytes and
muscle cells

Mitochondria of all cells (partly

cytoplasm)

To synthesize ATPs from

electrons from NADH and
FADH

Mitochondria of all cells

To break down fatty acids

from acetyl-CoA

Mitochondria of all cells

To synthesize fatty acids

from acetyl-CoA
To breakdown FA with more
than 18 carbons
To breakdown medium and
long-chain fatty acids
To provide duplicate copies
of the DNA for cell division
To serve as a template of
nformation transfer from the
DNA of the genes and for
protein synthesis and the
other types of RNA
To synthesize protein gene
expression
To provide the protein
molecules its mature
function

Fat cells and Part of it in the

cytoplasm
Peroxisomes
Peroxisomes
Nucleus

Nucleus

(rER) cytoplasm
Multiple

To direct the release of

protein to its target of action

Golgi apparatus

Ketogenesis

Excess acetyl-CoA is
converted to ketone
bodies

To provide fuel source

especially the brain during
prolonged starvation

Matrix of mitochondria of
hepatocytes (in cytoplasm);
and in special conditions renal
cells

Urea Cycle

Cyclical pathway that

produces urea from
ammonia,CO2 and
aspartate

To dispose approximately
90% of surplus nitrogen in
the presence of excess
amino acids as in excess
intake or starvation

Hepatocytes

Protein Sorting

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Metabolic
Terms

Definition

Function

Cell Location
rER (Cytoplasm)

Amino Acid
Synthesis

The synthesis of
amino acids

To provide the amino acids

needed for protein synthesis

Amino Acid
Catabolism

Degradation of
amino acids

To provide intermediates for

energy needs and as
dependent compounds

Paanong RBC? Once nucleated

precursors of RBC are already
removed of cytoplasm, the RBC is
already complete, its just waiting
itself to die after 120 days. Only
function is to transport
haemoglobin.

Cytoplasm of all cells

Volatage-gated Channel

Ligand-gated Channel

Ligand-gated Channel

*Illustration lifted from Dr. Hilarios Lecture Notes*

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