Unit 1: Biochemistry
Chapter 1: The Molecules of Life
Chapter 2: The Cell and its Components
Chapter 2: The Cell and Its Components

Overview
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Structures and functions of eukaryotic cells
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Organelles
Cell membrane
The transport of substances across the cell membrane
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Diffusion
Osmosis
Active transport
Membrane-assisted transport
Section 2.1: Structures and Functions of
Eukaryotic Cells
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Animals, plants, fungi, and protists are composed of
eukaryotic cells
All eukaryotic cells have these characteristics:

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A membrane-bound nucleus that contains the DNA
A cell membrane composed of a phospholipid bilayer
The cell interior is filled with jelly-like cytoplasm, which
consists of everything outside the nucleus but within the cell
membrane
The Nucleus
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The nucleus contains DNA, which replicates the genetic
information of the cell
Each molecule of DNA in the nucleus combines with an
equal mass of protein to form a chromosome

The number of chromosomes in the nucleus varies from
species to species
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Ex: Humans have 46 chromosome, while mosquitoes have 6
Chromosomes are visible only in dividing cells
In a non-dividing cell, chromatin represents the unfolded
state of chromosomes
The Endoplasmic Reticulum
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The nuclear envelope is connected to a complex of
membrane-bound tubules and sacs called the
endoplasmic reticulum (ER)
The ER regions that synthesize proteins are studded
with ribosomes, which are composed of proteins
and RNA
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
These regions are called rough endoplasmic reticulum
The rough ER ribosomes assemble proteins that
become part of membranes or are exported from the
cell

Proteins that function in the cytosol, on the other hand, are
made by ribosomes that are freely suspended there.
The Endoplasmic Reticulum
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Regions of the ER that have no ribosomes are called
smooth endoplasmic reticulum
The smooth ER synthesizes lipids and lipid-containing
molecules
The smooth ER also performs other functions
depending on the type of cell

Ex: In the liver, smooth ER helps detoxify drugs and alcohol.
Ribosomes


The ribosomes of eukaryotes have different
structures and mechanisms compared with those of
prokaryotes
This is why antibiotics that kill bacteria cells do not
harm the cells of the body

Ex: Tetracycline is an antibiotic that inhibits protein synthesis
in prokaryotic ribosomes, but does not affect protein
synthesis in human cells
The Endomembrane System: Protein
Modification and Transport
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The endomembrane system acts to synthesize, modify,
and transport proteins and other cell products
It also compartmentalizes the cell so that particular
functions are restricted to specific regions
This system consists of the nuclear envelope, the
endoplasmic reticulum, the Golgi apparatus, and vesicles.
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The Golgi apparatus is a stack of curved membrane sacs that
packages, processes, sorts, and distributes proteins, lipids, and other
substances within the cell
Vesicles are membrane-enclosed sacs used for transport and
storage
Functions of the Endomembrane System
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The endomembrane system modifies and transports
proteins
On the rough ER, polypeptides are produced by bound
ribosomes and are extruded into the lumen
The polypeptides travel through the lumen to the
smooth ER, there they are stored and processed
When proteins are ready for transport, pieces of
smooth ER pinch off to form vesicles containing the
protein
Functions of the Endomembrane System
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Vesicles from the smooth ER travel across the cell to
the cis face (entry face) of the Golgi apparatus, where
they merge with the membrane of the Golgi apparatus
and release their contents into the interior
In the Golgi apparatus, some proteins are stored and
others are modified further
When the modified proteins are ready for transport,
pieces of the Golgi apparatus pinch off from the trans
face (exit face) to form vesicles
These vesicles transport the proteins to the cell
membrane, or to other destinations within the cell
Additional Functions of the Endomembrane
System

In animal cells, the Golgi apparatus also produces
lysosomes
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Lysosomes contain more than 40 enzymes that
catalyze hydrolysis reactions
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Membrane-enclosed sacs containing digestive enzymes
Break down macromolecules into smaller molecules
Break down parts of the cell that are old or no longer
needed
Break down bacteria and other foreign particles that have
been ingested by the cell
The enzymes in lysosomes function best at the acidic
pH of around 5
Peroxisomes

Peroxisomes are also membrane-enclosed sacs
containing enzymes, but they differ from lysosomes in
two major ways:


Lysosomes are produced by the Golgi apparatus, while
peroxisomes are produced by the endoplasmic reticulum.
Lysosome enzymes catalyze hydrolysis reactions, while
peroxisome enzymes catalyze redox reactions (they are
oxidases)
Peroxisomes
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
Peroxisomes break down many biological molecules
and some toxic molecules
Peroxisomes in some cells synthesize molecules
Many of the reactions that take place in peroxisomes
produce toxic hydrogen peroxide, H2O2

All peroxisomes contain the enzyme catalase, which breaks
down hydrogen peroxide into water and oxygen gas.
Vesicle and Vacuoles
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“Vesicle” is used to describe
membrane-bound sacs used
for the transport and
storage of substances in the
cell
Vesicles form by pinching off
from cell membranes and
organelle membranes
They can also fuse with cell
membranes and organelle
membranes to release their
contents
Vesicles and Vacuoles



Plant cells contain a single
large vesicle, called a
vacuole
Stores water, ions, sugars,
amino acids, and
macromolecules
Also contains enzymes that
break down macromolecules
and cell wastes
Vesicles and Vacuoles


The quantity of water in the vacuole determines the
turgor pressure, or internal pressure, of the plant cell
A full vacuole presses against the cell wall, making the cell
rigid


Source of rigidity in the flexible stems of herbaceous plants.
Without enough water, the vacuole will shrink and pull
away from the cell wall

This is why unwatered plants wilt
Chloroplasts and Mitochondria
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Cells that perform photosynthesis contain one to
several hundred chloroplasts
Chloroplasts contain the photosynthetic pigment
chlorophyll, which absorbs light energy as part of
photosynthesis

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Photosynthesis converts carbon dioxide and water into
energy-rich organic molecules through redox reactions
Chloroplasts are membrane-bound organelles
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Filled with a thick liquid called stroma
Stroma surrounds thylakoids, which contain chlorophyll in
their membranes
A stack of thylakoids are called a granum (plural: grana).
Chloroplasts and Mitochondria

Mitochondria break down high-energy organic
molecules to convert stored energy into usable
energy
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Mitochondria have a smooth outer membrane and a
folded inner membrane.
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Provides the energy needed for all activities and chemical
reactions within the cell
The folds of the inner membrane are called cristae, and the
fluid-filled space in the inner membrane is called the matrix.
Both mitochondria and chloroplasts contain some of
their own DNA, which encodes some of their own
proteins
The Cell Wall and Cytoskeleton

Cells of plants, fungi, and many types of protists have
a cell wall, which provides protection and support
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All cells contain an internal network of protein fibres
called the cytoskeleton
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The composition varies with the type of cell, but it’s usually
a combination of polysaccharides, glycoproteins, or both
The fibres of the cytoskeleton extend throughout the
cytoplasm, providing structure and anchoring the cell
membrane and organelles in place
Vesicles and organelles move along these fibres
In some cells, cytoskeleton fibres form appendages that
enable the cell to propel itself
Cilia and Flagella


Cilia and flagella are appendages that develop on the
outside of some eukaryotic cells
Composed of an internal shaft made of microtubules
covered with an outer membrane that is a continuation
of the cell membrane
Cilia and Flagella
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If there are just one or two longer appendages, they
are called flagella
Flagella are like tails, and their whip-like movement
propels cells
Ex: A human sperm cell has a single flagella
Cilia and Flagella

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
If there are many shorter appendages, they are called
cilia
In unicellular protists the wave-like motion of cilia
enable them to move
In multicellular organisms, cells that line the upper
respiratory tract have cilia
The Cell Membrane

All living cells exist in an aqueous medium
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For a unicellular organism, this medium might be pond water
For the cells of a multicellular organism, the aqueous
medium is the extracellular fluid that surrounds all cells
The contents of the cells are physically separated
from the environment by the cell membrane
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Functions as a selective, dynamic cellular boundary
Are incredibly thin
If it fails to function properly, cellular processes fail and the
cell dies
The Cell Membrane
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Maintains the integrity of the cell by regulating the
passage of molecules and ions into and out of the cell
In the early 1900s researchers noticed that lipidsoluble molecules entered cells more rapidly than
water-soluble molecules
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This led them to believe that lipids were a component of
cell membranes
By 1925, chemical analysis had demonstrated that
phospholipids are a component of cell membranes and
are arranged in a bilayer
The Cell Membrane
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The presence of lipids cannot account for all
properties of the cell membrane
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Ex: Some non-lipid molecules can pass through it
In the 1940s, researchers hypothesized that proteins
are part of the membranes and proposed a model in
which a phospholipid bilayer is sandwiched between
two continuous layers of proteins
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This model was confirmed through electron microscopy in
the 1950s
But a suitable model linking the structure and properties of
membranes to various functions remained elusive
The Cell Membrane
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In 1972, two American biologists, Jonathan Singer and
Garth Nicholson, proposed a model for membranes that
remains in use today
They visualized proteins inserted into the phospholipid
bilayer with their non-polar segments in contact with the
non-polar interior of the bilayer and the polar portions
protruding from the membrane surface
In this fluid mosaic model, an assortment of proteins
and other molecules (in other words, “the mosaic”) floats
in or on the fluid phospholipid bilayer
Features of the Fluid Mosaic Model
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According to the fluid mosaic model, each layer of a
membrane bilayer is composed of various
macromolecules
Phospholipids act as the “scaffolding” in which proteins
and other macromolecules are embedded
Membrane lipids are held together by weak
intermolecular forces so the molecules in a membrane
can move around freely

If a puncture or tear occurs in a membrane, molecules will
quickly rearrange themselves to seal the rupture
Features of the Fluid Mosaic Model

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The lipid bilayer structure of membranes can be
explained based on chemical principles and the
properties of phospholipids
A phospholipid molecule has a hydrophilic polar “head”
and two hydrophobic non-polar “tails”.
When placed in water, phospholipids spontaneously
form structures where the heads cluster together,
facing the water molecules, while the tails are shielded
from the water
Features of the Fluid Mosaic Model
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The heads interact with the water molecules and each
other using intermolecular interactions (ex: hydrogen
bonding)
The tails are held together by hydrophobic interactions
The heads end up facing out and the tails face inward,
away from the aqueous environment
The Fluidity of a Phospholipid Bilayer
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At room temperature, a phospholipid bilayer has a
viscosity similar to vegetable oil
This fluidity is an important property
If it is too fluid, it permits too many molecules to diffuse
in and out of the cell
If it is not fluid enough, it prevents too many molecules
from crossing
The Fluidity of a Phospholipid Bilayer


The factors that affect fluidity include:
Temperature


As temperature increases, the bilayer becomes increasingly
fluid until it is unable to act as a barrier
As temperature decreases, the bilayer solidifies into a gel-like
state
The Fluidity of a Phospholipid Bilayer

Presence of double bonds in the fatty acid “tails”

Double bonds form “kinks” in a fatty acid tail that cause fatty
acids to be less tightly packed and more fluid
The Fluidity of a Phospholipid Bilayer

Fatty acid “tail” length

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Longer fatty acid tails have more intermolecular attractions
and hold together more tightly, thus reducing fluidity
The most common tail length is 16-18 carbon atoms
The Fluidity of a Phospholipid Bilayer
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The presence of cholesterol in
cell membranes also affects
fluidity
At room temperature and higher,
cholesterol increases the
intermolecular forces in the
membrane and holds it more
tightly together, thus reducing
fluidity
At lower temperatures,
cholesterol molecules break up
the packing that occurs as
phospholipids solidify into a gel,
increasing fluidity
The Functions of Proteins in a Phospholipid
Bilayer
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Two types of proteins are associated with
membranes:
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Integral proteins are embedded in the membrane
Peripheral proteins are more loosely and temporarily
attached to the outer regions of the membrane or to
integral proteins
Peripheral proteins and some integral proteins help
to stabilize membranes, and hold them in place by
linking them with the cytoskeleton of the cell
The Functions of Proteins in a Phospholipid
Bilayer
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Membrane proteins also determine the function of
the membrane by performing the following functions:
Transport


Proteins play an essential role in transporting substances
across the cell membrane
Reaction catalysis

Enzymes in cell membranes carry out chemical reactions
The Functions of Proteins in a Phospholipid
Bilayer
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Cell recognition
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The carbohydrate chains that protrude from glycoproteins on
the outer layer of the cell membrane enable cells to
“recognize” each other.
Signal reception and transduction
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Receptor proteins in cell membranes bind to signal molecules
and change shape as a result
This initiates a cellular response to the signal, enabling cells to
receive and respond to signals from the brain and other organs
Section 2.2: The Transport of Substances
Across a Cell Membrane
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The cell membrane can regulate the passage of
substances into and out of the cell, because it is semipermeable
Processes that enable substances to move in and out of
cells without an input of energy are referred to as
passive transport
Some ions and molecules can move passively across the cell
membrane easily because of a concentration gradient
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A difference between the concentration on the inside of the
membrane and the concentration on the outside of the
membrane
Three types of passive transport are diffusion, osmosis, and
facilitated diffusion
Passive Transport by Diffusion
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
The net movement of ions and molecules (i.e.
solutes) from a region of higher concentration to a
region of lower concentration is called diffusion
Net movement of the solutes will continue until the
concentration is the same in all regions
Passive Transport by Diffusion
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
In the context of cells, diffusion involves differences in
the concentration of solutes on either side of a cell
membrane
The two factors that determine whether diffusion
occurs across cell membranes are:
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
Relative concentrations of the solutes inside and outside the
cell
How readily a molecule or ion can cross the membrane
Passive Transport by Diffusion


The major barrier to crossing a biological membrane
is the hydrophobic interior that repels polar
molecules (but not non-polar molecules)
If a concentration difference exists for a non-polar
molecule, it will move across the membrane until the
concentration is equal on both sides

Movement in both directions still occurs, but there is no net
change in either direction
Passive Transport by Diffusion
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
Factors that affect the rate of diffusion are:
Molecule size
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Molecule polarity
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The larger the molecule, the more difficult it is for it to diffuse
across a membrane
The rate of diffusion decreases as molecule size increases
Small polar molecules diffuse across membranes more slowly
than non-polar molecules of the same size
The rate of diffusion is lower for polar molecules
Molecule or ion charge

Charged molecules and ions cannot diffuse across cell
membranes
Passive Transport by Diffusion

Temperature and pressure can also affect the rate of
diffusion


At higher temperatures, molecules have more energy and
can move faster, thus increasing the rate of diffusion
At higher pressures, molecules are forced across the
membrane and the rate of diffusion increases
Passive Transport by Osmosis

Movement of water molecules across biological
membranes is called osmosis
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Water molecules move because the membrane is
impermeable to the solute
In order for osmosis to occur, solute concentrations
must differ on either side of the membrane
Water molecules move in or out of the cell, along the
concentration gradient, until their concentrations on
both sides of the membrane are equal

At that time, water molecules continue to move in and out,
but there is no net movement of water.
Passive Transport by Osmosis
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
The regulation of water entry is crucial to cells
The aqueous cytoplasm is a solvent for cellular
molecules and ions
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
Cells must maintain enough water to enable cellular
processes
Cells also interact with extracellular fluid, the
composition of which is constantly changing
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If too much water enters the cell, it swells
If too much water leaves the cell, it shrinks
Each response can affect the ability of a cell to function
Passive Transport by Osmosis
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
The concentration of all solutes in a solutions
determines its osmotic concentration
If two solutions have unequal osmotic concentrations:
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The solution with the higher solute concentration is
hypertonic (hyper = “more than”)
The solution with the lower solute concentration is
hypotonic (hypo = “less than”)
When two solutions have the same osmotic concentration,
they are isotonic (iso = “equal”)
Passive Transport by Facilitated Diffusion
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Many important molecules required by cells cannot easily
cross the plasma membrane
These molecules can still enter the cell by diffusion
through specific channel proteins or carrier proteins
embedded in the plasma membrane
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
But there must be a higher concentration of the molecule
outside the cell than inside
This process of diffusion that is mediated by a membrane
protein is called facilitated diffusion
Passive Transport by Facilitated Diffusion
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
Channel proteins have a hydrophilic interior that provides
an aqueous channel through which polar molecules can
pass when the channel is open
Carrier proteins, in contrast to channels, bind specifically
to the molecule they assist, much like an enzyme binds to
its substrate
Channel protein
Carrier protein
Channel Proteins
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Channel proteins form highly specific channels
through the cell membrane
The structure of a channel protein determines which
particles can travel through it.
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A channel protein has a tubular shape which is composed of
one or more helixes
The exterior of a channel protein is usually composed of
amino acids with non-polar side chains that interact with the
non-polar interior of the cell membrane, anchoring the
protein in place
The shape and size of the hole through a channel protein
determines the shape and size of particles that can pass
through it
Channel Proteins
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Some channel proteins remain open all the time
Others have gates that the cell can open or close to
allow or prevent the passage of particles
Different types of gates open or close in response to
a variety of signals, such as hormones, electric charge,
pressure, or even light
In general, channel proteins permit the passage of
ions or polar molecules
Carrier Proteins
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Carrier proteins bind to specific molecules, transport
them across the membrane, and then release them
on the other side
Because they bind to the molecules they’re
transporting, carrier proteins change shape while
transporting molecules
Usually transport ions or small polar molecules, but can
also transport larger molecules (ex: glucose)
They bind to only a few molecules at a time, so carrier
proteins have lower rates of diffusion than channel
proteins
Carrier Proteins
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The exterior of carrier proteins is usually composed
of non-polar amino acids that interact with the nonpolar interior of the membrane
The interior of a carrier protein is lined with amino
acids that can bind to the particle to be transported
Malfunctions in carrier proteins can cause a variety of
diseases.

Ex: Cystinurea is a hereditary disease caused by the inability
of carrier proteins to remove cystine and some other amino
acids from urine
Active Transport: Movement Against a
Concentration Gradient

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Diffusion, facilitated diffusion,
and osmosis are all passive
transport processes that move
substances down their
concentration gradients
Cells can also actively move
substances across a cell
membrane against, or up, their
concentration gradients
This process, called active
transport, requires the
expenditure of energy, usually
from ATP
Active Transport: Movement Against a
Concentration Gradient


ATP (adenosine triphosphate) is the main source of
energy in the cell
An ATP molecule is derived from an adenosine
nucleotide, but it has a triple phosphate group instead
of a single phosphate group
Primary Active Transport



Primary active transport uses ATP directly to move
molecules or ions from one side of a membrane to the
other
Ion pumps are carrier proteins that use ATP to “pump”
ions from one side of a membrane to the other, against a
concentration gradient
One of the most well studied examples is the sodiumpotassium pump


This system transports sodium ions out of the cell while
transporting potassium ions into the cell
Both processes occur against concentration gradients, so this
carrier protein requires ATP to function
Secondary Active Transport

As an ion pump functions, a difference in charge (or
electric potential) builds up across the membrane.



One side of the membrane gains a more positive or negative
charge compared to the other side, due to the accumulation of
positive or negative ions
At the same time, a concentration gradient builds up
across the membrane as the concentration of ions on
one side increases compared to the other side
The combination of a concentration gradient and an
electric potential across a membrane is called an
electrochemical gradient

This gradient stores potential energy that can be used by the
cell.
Secondary Active Transport


Secondary active transport uses an electrochemical
gradient as a source of energy to transport molecules or
ions across the cell membrane.
An example of secondary active transport is the
hydrogen-sucrose pump
Membrane-Assisted Transport

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
A cell can accumulate and excrete smaller molecules
and ions using membrane proteins
Macromolecules, however, are too large to cross the
cell membrane through a channel or by means of a
carrier protein
Instead, the cell forms vesicles to surround incoming or
outgoing material and move it across the cell
membrane through membrane-assisted transport


This transport requires energy from the cell
The two forms are endocytosis and exocytosis
Endocytosis


Endocytosis is the process by which a cell engulfs
material by folding the cell membrane around it and
then pinching off to form a vesicle inside the cell
There are three methods of endocytosis:



Phagocytosis
Pinocytosis
Receptor-mediated endocytosis
Endocytosis

Phagocytosis occurs when the material the cell takes
in is made up of discrete particles, such as an organism
or some other fragment of organic matter


Pinocytosis occurs when the material the cell takes in
is liquid


Phagocytosis literally means “cell-eating”
Pinocytosis literally means “cell-drinking”
Virtually all eukaryotic cells constantly carry out these
endocytotic processes, trapping particles and
extracellular fluid in vesicles and ingesting them
Endocytosis




Receptor-mediated endocytosis involves the use of
receptor proteins on a portion of a cell membrane
that bind with specific molecules outside the cell
The area of the cell membrane containing receptor
proteins is called a coated pit
The receptor proteins bind with molecules and the pit
folds inward to form a vesicle
The contents of the vesicle may be used by the cell or
digested by the cell, and the receptor proteins may be
recycled by the cell membrane
Exocytosis



Macromolecules and other large
particles can leave a cell by a
process called exocytosis
In exocytosis, vesicles that
contain cell products to be
released, or waste material to
be excreted, fuse with the cell
membrane and empty their
contents into the extracellular
environment.
The vesicle itself becomes part of
the cell membrane
Exocytosis


In plant cells, exocytosis is an important means of
exporting through the cell membrane the materials
needed to construct the cell wall
In animal cells, exocytosis provides a mechanism for
secreting many hormones, neurotransmitters,
digestive enzymes, and other substrates


Ex: Specialized glands secrete sebum, which is an oily
substance that lubricates human skin, hair, and eyes
Ex: Cells in the intestines of animals secrete enzymes and
acid to aid in the digestive process
Cellular Transport: A Summary
Is energy
required for
the
mechanism to
function?
No
Type of
cellular
transport
mechanism
Primary
direction of
movement of
substances
Essential
related
factor(s)
Examples of
transported
substances
Diffusion
Toward lower
concentration
Concentration
gradient
No
Facilitated
diffusion
Toward lower
concentration
Lipid-soluble
molecules, water,
gases
Some sugars and
amino acids
Yes
Yes
Yes
Channel protein
or carrier
protein and
concentration
gradient
Active transport Toward higher
Carrier protein
concentration
and energy
Endocytosis
Toward interior Vesicle
of cell
formation
Exocytosis
Toward exterior Fusion of vesicle
of cell
with cell
membrane
Sugars, amino
acids, ions
Macromolecules
Macromolecules