Lecture 2

Cell structures and Cell transport

Cells
-smallest unit of matter considered as living
-structural and functional unit of life
-all living organisms contain cells
-all cells contain: plasma/cell membrane, cytoplasm (the region between the nucleus and the plasma
membrane), cytosol (gel-like substance in the cytoplasm where cell structures are suspended),
chromosomes (which contains the DNA) and ribosomes
-there are two distinct cell types prokaryotes (genetic material is found in the nucleoid region; smaller;
ex. Bacteria) and eukaryotes (genetic material is found within the nucleus, an organelle; larger in size;
ex. Human and animal cells, plant cells, yeast cell, protozoa from hay infusion)
See figure 7.5 page 167 of the book that shows the difference in structure of prokaryotes and
eukaryotes

Cell structure/organelle Structural description Function

1. Nucleus -contains a double membrane -Contains the genetic material
(inner and outer) called a nuclear -Where synthesis of mRNA
envelope. Each of the membrane (used during protein
is composed of a lipid bilayer. synthesis) occurs
The 2 membranes are 20-40nm
apart
-the nuclear envelope is
perforated by nuclear pores (a
pore/hole lined by proteins)
which controls entry and exit of
materials into/from the nucleus
-After the inner membrane of the
nuclear envelope is the nuclear
lamina made up of protein
filaments that maintains the
shape of the nucleus
-the “core” of the nucleus is
called the nucleolus which
contains the ribosomal RNA
(rRNA), and where small and
large subunits that makes up the
ribosome are synthesized, these
structures will exit the nucleus
through the nuclear pores and
will settle either in the
cytoplasm/rough ER where it will
be assembled into a ribosome
prior to protein synthesis
2. Ribosomes -contains rRNA, large and small -site for protein synthesis
subunit
-it is not considered as an
organelle since it is not
membrane-bound (not covered
by a membrane)
-can be free ribosomes those
found in the cytoplasm or they
can be bound ribosomes found in
the rough ER
The endomembrane system
(see figure 7.15 pg.179 of the book to see the relationship among members of this system)
3. Endoplasmic reticulum (ER) -made up of membranous Smooth ER
tubules (such as in Smooth ER) or -synthesis of lipids (oils,
membranous sacs called steroids, phospholipids)
cisternae (such as in Rough ER; -metabolism of carbohydrates
the cisternae are interconnected -detoxification of drugs and
to one another) poisons
-Continous with the nuclear -storage of Calcium
envelope (ex.sarcoplasmic reticulum in
-Two connected regions of the ER muscles)
a. Rough ER Rough ER
b. Smooth ER -production of secretory
proteins (ex.glycoproteins)
-production of phospholipids
-grows in place by adding
some of the phospholipids
that it synthesizes to its own
membrane
Products of the ER will leave within a transport vesicle (much like package that you order online in a
delivery truck). The transport vesicles comes from (buds from) the transitional part of the ER
(transitional ER). The transport vesicles with the products inside will now go to the golgi
appratus/bodies see figure 7.15 pg.179 of the book

4. Golgi apparatus -made up of membranous sacs -Modification of the products

called cisternae (similar to ER of the ER
howeever, this time, the -Alteration of membrane
cisternae are not physically phospholipids
connected/interconnected to -Manufacture of
one another) polysaccharides (ex.pectin)
-contains the cis face
(“receiving” side) that receives
the transport vesicle from the ER
and the trans face (“shipping”
side) that “ships” transport
vesicle (now containing the
products of the golgi or products
of both the golgi and ER) from
the golgi to other parts of the cell
-cisternal maturation model
states that the cisternae of the
golgi appratus matures from the
cis face to the trans face as it
carries products along (which can
mean that the cis face contains
“younger” cisternae and the
trans face contains “older/more
matured” cisternae)
Enzymes that are carried to the
trans face are transported back
to the cis face
The products in the transport vesicle from the golgi apparatus contains identification tags (like zip
codes in the mail) and the transport vesicle itself contains molecules that can recognize “docking site”
in the plasma/cell membrane. Upon “docking” in the cell membrane, the transport vesicle will fuse
with the cell membrane and the products that it contain will be released out of the cell see figure 7.15
pg.179 of the book

5. Lysosomes -a membranous sac -functions in processes such as

-contains hydrolytic enzymes autophagy and phagocytosis
 that works best at an acidic pH (figure 7.13, page 177)
(excessive leakage of this enzyme
inside the cell can cause
self-digestion of the cell)
-the hydrolytic enzyme, which is
a protein, is a product of the ER
(specfically rough ER which
contains ribosomes, the site for
protein synthesis)
-the lysosome itself is derived
from the trans face of the golgi
apparatus
Answer concept check 7.4 page 178 of the book
6. Vacuoles -are large vesicles derived from -Central vacuole in plants
the ER and golgi apparatus contains the cell sap and is a
repository of inorganic ions
and is important in the growth
of the plant cell
-Food vacuole which plays a
role in phagocytosis
-Contractile vacuole in
unicellular eukaryotes such as
protozoa from hay infusion, it
pumps out excess water from
the cell

-It can act as lysosome in

plants and fungi since it can
contain hydrolytic enzymes
-can contain proteins such as
in seeds
-can contain poisonous
compounds
-can contain pigments
7. Mitochondria -found in nearly all eukaryotic -functions in cellular
cells (animals, plants, fungi and respiration
other unicellular eukaryotes
-contains a double membrane
(outer membrane which is
smooth and inner membrane
which is convoluted or has
infoldings). The two membranes
are separated by the
intermembrane space
-contains cristae or the folds
inside
-contains the mitochondrial
matrix that contains the
enzymes, mitochondrial DNA
(thus the mitochondria can
self-replicate), and ribosomes

8. Chloroplast -double-membrane bound -functions in photosynthesis in

organelle like the mitochondria plants
-Contains interconnected
 membranous sacs called
thylakoids (the plate-like
structure) that when stacked is
called a granum/grana.
-Contains the stroma (similar to
the mitochondrial matrix) that
contains the chloroplast DNA,
ribosomes and enzymes
-Chloroplast contains the
pigment chlorophyll
-Chloroplast is a member of a
family of plant organelles called
plastids. Other members are
amyloplast which stores starch
and chromoplast which stores
other pigments
Answer concept check 7.5 page 182 of the book
9. Peroxisomes -bound by a single membrane
like the lysosome
10. Cytoskeleton Components of the cytoskeleton
1. Microtubules (made up of
protein tubulin)
2. Microfilaments (made up of
protein actin)
3. Intermediate filaments (made
up of several proteins such as
keratin)
(see table 7.1 page 183 of the
book)
-use oxygen to break down
acid used during cellular
respiration
-detoxifies alcohol and other
harmful compounds by
transferring hydrogen from
these compounds/substances
and adding it to Oxygen. This
process leads to another toxic
compound, Hydrogen
peroxide (H2O2). However,
peroxisomes contain enzymes
that can convert H2O2 into
water
Glyoxysomes- specialized
peroxisomes that functions in
the conversion of fatty acids
to sugar in seeds of plants
(since seeds are not yet
capable of synthesizing sugar
through photosynthesis)
Microtubules
-maintains and support shape
of the cell
-functions for cell motility, it is
the “track” where motor
proteins that carries an
organelle (ex. Transport
vesicles) “walks”
-During cell division,
microtubules that “moves”
chromosomes are supplied by
the centrosome. Within the
centrosome is the centriole
made up of microtubules
arranged in a ring of 9 triplets
of microtubules
(see figure 7.22 page 184 of
the book)
-component of the cilia and
flagella, microtubules within
are arranged in a “9+2”
structure. The basal body
which is kind of the
intersection or meeting point
between the flagella/cilia and
the cell also contains
microtubules arranged in
“9+0” structure
(see figure 7.24 page 186 of
the book)

*Cilia and flagella differ in

number per cell (flagella
usually one per cell while cilia
is in large number), length
(flagella are usually longer,
while cilia are usually shorter)
and beating pattern (flagella
undulates while the cilia
moves in back and forth
motion much like a broom)
(see figure 7.23 page 185 of
the book)

Microfilaments
-bear tension (“pulling
forces”)
-can be found in the microvilli
(like projections) of the
intestine
-functions in muscle
contraction, movement of
amoeba, a unicellular
eukaryote, and cytoplasmic
streaming or movement of cell
contents in a plant cell
(see figure 7.26 page 187 of
the book)

Intermediate filaments
-larger than microfilaments,
smaller than microtubules in
terms of diameter
-specialized for bearing
tension (“pulling forces”)
-can also be found in the
microvilli of the intestine
11. Cell wall in plant cells
12. Extracellular Matrix (ECM)
in animal cells
(see figure 7.28 page 189 of the
book)
13. Cell junctions
(in between cells)
-thicker than the cell membrane
-primary cell wall is thick and
flexible found in younger plants
-secondary cell wall added
between the cell membrane and
the primary cell wall usually
found in woody plants.
-In between two plant cells, is a
“space” called the middle lamella
which glues the cells together. It
contains the polysaccharide
pectin
-main component are
glycoproteins such as collagen
Plant cells
Plasmodesmata
-perforations in the cell wall of
plant cells
Animal cells
Tight Junctions
Desmosomes (anchoring
junctions) that are connected to
the cytoplasm through the help
of intermediate filaments
Gap junctions (communicating
junctions) that are pores
surrounded by membrane
proteins
(see figure 7.30 page 190 of the
book)
-protects and supports the
cell, maintains cell shape,
prevents excessive uptake of
water
-supports the cell (similar to
the function of cell wall in
plant cells)
-for adhesion
-movement and regulation
Plant cells
Plasmodesmata
-acts as channel that connects
cell and where water, small
solutes, sometimes RNA and
proteins can pass freely from
cell to cell
Animal cells
Tight junctions
-prevents leakage of
extracellular fluid (fluid
outside of the cell) across a
particular cell layer
-reason why our skin is
watertight
Desmosomes
-Fastens cells together into a
strong sheet
-Sometimes, rupture of
 desmosomes can cause
muscle tear.

Gap junctions
-more like the plasmodesmata
in plant cells
-where ions, sugars and other
small molecules can pass from
one cell to another

Cell structures present in animal cells, absent in plant cells- lysosomes, centrosomes, flagella
Cell structures present in plant cells, absent in animal cells- chloroplast, central vacuole, cell wall

Endosymbiont Theory (proposed by Lynn Margulis, 1938-2011)

This theory tries to explain/proposes that chloroplast where derived from cyanobacteria
(photosynthetic bacteria) while the mitochondria where derived from proteobacterium. This can be
further supported by the fact that the mitochondria and choloroplast has their own DNA thus they can
self-replicate and ribosomes for protein synthesis

‘
Cell membrane
-It is composed of lipids (specifically phospholipids and cholesterol), proteins (integral or peripheral
proteins) and carbohydrates
-the most abundant lipids are phospholipids which are amphipathic meaning, they have both the
hydrophilic and hydrophobic parts.

This image
depicts the fluid
mosaic model
which tellls us
that the
membrane
proteins are
embedded like a
mosaic in a fluid
bilayer of
phospholipids

Why is the cell membrane “fluid”?

-The membrane is held together by hydrophobic interactions
-It is “fluid” because the phospholipids in a cell membrane can move sideways (this occurs rapidly),
sometimes the phospholipids can also “flip-flop” from one phospholipid layer to another (for example
one phospholid below can go up to the upper phospholipid layer while another one can go down to
the lower layer of phospholipid)
-Membrane proteins can also move slowly, while some are immobile held by microfilaments from the
extracellular matrix (ECM)
-This “fluidity” can be affected by temperature and the reaction is based on the fatty acid or lipids
present in the membrane

As temperature decreases, phospholipids settle in a

densely packed arrangement until it solidifies. This can
occur due to saturated fatty acid in the hydrophobic tail of
the phospholipid. However, presence of unsaturated fatty
acid in the hydrophobic tail of the phospholipid can
prevent packing thus making the membrane more fluid

The cell membrane cannot be solid since it can affect

permeability and it can inactivate enzymes, too much
fluidity is also not good because it affects protein function.
Thus cholesterol is present in the membrane to act as a
buffer that can hinder too much fluidity or solidification at
certain temperatures
Function of membrane proteins

Integral proteins- spans the cell membrane (ex. Transmembrane protein, a type of integral protein)
and they penetrate up to the hydrophobic interior of the cell membrane. The region of the integral
protein that penetrates the hydrophobic interior of the membrane is made up of 20-40 non-polar
amino acids arranged in an α helix (remember the four protein structures, α helix or β pleated sheet
are secondary structure of proteins). Some integral proteins can also have hydrophilic channels (much
like tunnels within its body) where hydrophilic substance like water can pass through

Peripheral proteins- unlike integral proteins these proteins do not span/penetrate the cell membrane
and are only loosely bound in the outside, sometimes in the exposed end of the integral protein (see
figure above)

For the function of different membrane proteins, see figure 8.7 page 200 of the book

Function of membrane carbohydrates

-Carbohydrates usually short branched chains made up of 15 sugar units

can covalently bind to proteins (glycoprotein) or lipids (glycolipids)
-These carbohydrates are important for cell-to-cell recognition (or simply
that one cell can recognize that another cell is part of that body and not a
foreign body)

Sidedness and synthesis of the cell membrane

Read the steps in figure 8.9 page 201 of the book
Permeability of the cell membrane
Substances that can easily Substances that can’t easily
pass through pass through

Transport proteins
-Transport proteins allow passage of hydrophilic substances across the membrane.
-A transport protein is specific for the substance it moves.
Examples:
a) channel proteins
b) carrier proteins

a. Channel proteins
-They have a hydrophilic channel that certain molecules or ions can use as a tunnel
Examples:
1. Aquaporins, for facilitated diffusion of water between cells
2. Ion channels that open or close in response to a stimulus (gated channels).

b. Carrier proteins
-They bind to molecules and change shape to shuttle them across the membrane.
e.g. GLUT1 (glucose transporter 1) facilitates the transport of glucose across the plasma membranes
of mammalian cells
Concentration gradient
The difference in solute concentration between adjacent regions of solution is called the
concentration gradient.

I. Passive Transport
-Passive transport is the diffusion of a substance across a membrane
with no energy investment.
-Diffusion is the tendency for molecules to spread out evenly into the
available space: from High to Low solute concentrations until dynamic
equilibrium is reached where number of solute is “equal” in both sides
(simply, like students (students=solute) in a crowded area in the library
moving to an area with less students, logically and in real life, this is
favorable, to study in a less crowded area)
-Simple diffusion, facilitated diffusion and osmosis are all under passive
transport since no energy is required to do these processes

A. Simple diffusion B. Facilitated diffusion

-No energy investment/ no ATP needed -No energy investment/ no ATP needed
-Movement from high to low solute -Movement from high to low solute
concentrations concentrations
-Uses “facilitators” specifically transport
proteins either channel or carrier proteins
Used by smaller molecules Large molecules
Ex. CO2, O2, H2O* Ex. Glucose, using the carrier protein glucose
transporter
*Note that facilitated diffusion of water can also occur through the use of channel proteins called
aquaporin (ex. Cells of the renal tubule, secretory glands and red blood cell)

C. Osmosis
-This time, water will move along a concentration gradient and not the solute
-Osmosis is the diffusion of water across a selectively permeable membrane
-Water moves from an area of lower solute concentration to an area of higher solute concentration
(water moves to an area of higher solute concentration in order to dilute or to lower the concentration
or number of solute in that area until the concentration or number of solute in both area are more
similar)
Tonicity is the ability of a solution to cause a cell to gain or lose water. When explaining/answering
whether a cell will gain or lose water in a solution, the principle of osmosis is used (water moves from
an area of lower to higher solute concentration)

1. Isotonic Solution 2. Hypertonic solution 3. Hypotonic solution

What will happen to the cell
when placed in an isotonic
solution? Will it gain or lose
water?
This solution contains equal
concentration of solute
molecules compared to the
inside of the cell (Example,
outside of the cell there is 10%
salt, and inside of the cell there
is 10% salt)
What will happen to the cell
when placed in an hypertonic
solution? Will it gain or lose
water?
This solution contains higher
concentration of solute
molecules compared to the
inside of the cell (Example,
outside of the cell there is 20%
salt, and inside of the cell there
is 10% salt)
What will happen to the cell
when placed in an hypotonic
solution? Will it gain or lose
water?
This solution contains lower
concentration of solute
molecules compared to the
inside of the cell (Example,
outside of the cell there is 10%
salt, and inside of the cell there
is 20% salt)

The cell will neither gain or lose Water will move from an area Water will move from an area
water, it will stay the same of lower (inside of the cell) to of lower (outside of the cell) to
higher (outside of the cell) higher (inside of the cell) solute
solute concentration concentration

Results to a normal animal cell
or “flaccid” plant cell
Water will move out of the cell,
thus, the cell will lose water
Results to crenation (shrinkage)
of animal cell and plasmolysis
in plant cell
Water will move into the cell,
thus, the cell will gain water
Results to cytolysis (death by
bursting in animal cell) and
turgor pressure in plant cell
(the pressure exerted by fluid to
a structure that contains it)

When enough turgor pressure

builds up inside, the water
stops diffusing. The amount of
turgor that stops osmosis is
called osmotic pressure.

II. Active Transport

-Active transport moves substances against their concentration gradient (L-->H solute conc.)
-Active transport requires energy, usually in the form of ATP
-Active transport is performed by specific membrane carrier proteins (ion pumps) that use ATP
energy to change shape, thereby pumping the solute across the membrane.
Why would the cell do something that is kind of “unfavorable”? spending energy and going against
the concentration gradient (like a student going to a crowded place in the library when there are
available spaces in another area)

For example,sugars outside of the cell needs to get inside to

be used as a raw material for certain processes like cellular
respiration. Sugar can go inside using facilitated diffusion
(movement of solutes from an area of higher to lower solute
concentration with the help of a transport protein)

However, movement along a concentration gradient such as

in diffusion will “stop” when a dynamic equilibrium is
reached (equal amount of solute on both sides). What if, the
cell needs more sugar?

This time, active transport will be used, solutes will be

moved from an area of lower to higher solute concentration,
against the concentration gradient and ATP is used. This is
kind of, in a sense, unfavorable going somewhere where
there is already a higher number of solutes but then again,
this is because, in this situation, the cell needs more

How are ions transported across the cell membrane?

-Ions (charged) can’t easily pass through the hydrophobic interior of the cell membrane because they
have little affinity to it given that the hydrophobic tail of phospholipids that make up the interior is
uncharged. Thus, transport proteins are used.
-There are more positive charges outside the cell and more negative charges inside of the cell
(cytoplasmic side of the cell) thus, there is a concentration gradient. Because of this gradient, ions can
pass through using facilitated diffusion, a “type” of passive transport. Positive charges outside of the
cell (area of higher concentration of positive charges) can go down its concentration gradient to inside
of the cell (area of lower concentration of positive charges) (see orange arrow). Meanwhile, negative
charges inside of the cell (area of higher concentration of negative charges) can go down its
concentration gradient to outside of the cell (area of lower concentration of negative charges) (see
blue arrow)
Extracellular (outside of the cell) Cytoplasmic side of membane (inside of the cell)
+ -
+ -
+ -
+ -
+ -
+ -

Diagram 1
Let’s use Sodium (Na+) and Potassium (K+) as example:

-Outside of the cell, concentration of Na+ is

higher and K+ is lower
-Inside of the cell, concentration of Na+ is
lower and K+ is higher

Normally, if active transport or ion/electrogenic pumps are not used, this is what will happen

-Na+ can move (or diffuse,facilitated diffusion using transport proteins) inside the cell since it is an
area of lower Na+ concentration (see blue arrow in the diagram above) (Diffusion- movement of a
solute from an area of higher to lower concentration)
-Also, since Na+ is positive and inside the cell is more negative in charge, it can attract Na+ inside
-Thus, there are two “forces” that can influence Na+ entry into the cell, the opposing charges between
Na+ and negative charges inside the cell, and the concentration gradient (area of higher Na+
concentration outside and area of lower Na+ concentration inside the cell), thus, collectively, these
two “forces” that affects ion movement is what we call the electrochemical gradient

-For K+ since it is positive and inside the cell is more negative in charge, it can attract K+ inside
-However, since K+ concentration is already high inside the cell (Diffusion- movement of a solute from
an area of higher to lower concentration), this concentration gradient will move K+ outside of the cell
(see orange arrow)

-However, there are transport proteins that are known to maintain membrane potential/generate
voltage in the cell and thus uses active transport rather than diffusion. An example is the use of ion
pumps or electrogenic pumps

Membrane potential- it is the voltage difference across a membrane

Voltage is created by differences in the distribution of positive + and negative - ions on the two sides
of the membrane (Diagram 1, in page 13 of this handout shows that voltage is present since positive
charges are numerous on one side of the cell (outside) and negative charges are numerous in the
other (inside))
-Maintenance of membrane potential is important during transmission of electrical signals by neurons

A.Ion pumps (Electrogenic pumps)

-Primary active transport system
-Are trans-membrane protein molecules using energy (ATP) to transport ions across a plasma
membrane against their concentration gradient
-Example of electrogenic pumps are Ca2+ pump, Sodium-Potassium pump, and proton (H+) pump

Electrogenic pumps (ion pumps) generates voltage/maintains

membrane potential across the cell membrane

How does the pump generate voltage across the cell membrane? Let’s use the sodium potassium
pump as an example.
Sodium (Na+)-potassium (K+) pump
-It is considered as an example of active transport through the use of electrogenic pump which
generates voltage across the membrane
-The Na+K+ pump is the major electrogenic pump of animal cells (present in nearly all body cells)
it uses 1/3 of the cell’s available energy
-Is a cotransporter (protein that moves 2 substances at the same time; same or opposite direction)

-Use of ion pump is considered as active transport since Na+ will be pumped out of the cell (already an
area of higher Na+ concentration; Remember that for active transport, substances are moved from an
area of lower to higher solute concentration). Also, K+ is pumped into the cell where there is already
higher K+ concentration.

-Ion pumps generate voltage/maintains membrane potential in 2 ways: 1. Pumps 3 Na+ out and only
pumps in 2 K+ thus, still maintaining that the inside of the cell is more negative than positive (since
there is less positive-charged ion pumped inside). 2. Even if K+ is pumped in, it will not increase in
number that much since K+ concentration is already high inside the cell, this concentration gradient
will move K+ outside of the cell (Diffusion- movement of a solute from an area of higher to lower
concentration), thus the inside of the cell is still more negative than positive. This way, inside of the
cell is more negative, outside is more positive no matter how many positively-charged ions will get
inside, thus there will always be voltage or a difference in distribution of + and - at two sides of the
membrane through the help of ion pumps

Proton pump
-The main electrogenic pump of plants, fungi, and bacteria is a proton pump, which actively
transports protons (H+) out of the cell.
-The pumping of H+ transfers positive charge from the cytoplasm to the extracellular solution .
B. Coupled Transport
-It occurs when active transport of a solute indirectly drives the transport of another solute.
It uses ATP indirectly

III. Bulk Transport

-Small molecules and water enter or leave the cell through the lipid bilayer or by transport proteins.
-Large molecules, such as polysaccharides and proteins, cross the membrane in bulk via vesicles.
-Bulk transport across the plasma membrane occurs by exocytosis and endocytosis; it requires
energy.
A. Exocytosis (large molecules out)
-In exocytosis, transport vesicles migrate to the membrane, fuse with it, and release their contents
outside the cell.
-Many secretory cells use exocytosis to export their products.

B. Endocytosis (Large molecules in)

-In endocytosis, the cell takes in macromolecules by forming vesicles from the plasma membrane.
-Endocytosis is a reversal of exocytosis, involving different proteins.
-There are three types of endocytosis:
1. Phagocytosis (“cellular eating”)
2. Pinocytosis (“cellular drinking”)
3. Receptor-mediated endocytosis
(see figure 8.19 page 210 of the book for the description of each of the type of endocytosis)

References:
Campbell, N. Biology: A Global Approach (11th ed)

Suggested websites for some of the topics:

Biomanbio.com/cell transport
Khanacademy.com/active transport