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AS Biology Unit 2
page 1
Heckmondwike Grammar School Biology Department
Edexcel A-Level Biology B
Contents
Cell Theory .............................................................................. p3
Eukaryotic Cells ...................................................................... p4
Prokaryotic Cells .................................................................... p9
Microscopy ............................................................................... p14
Cell Membranes ...................................................................... p19
Transport across Cell Membranes ..................................... p21
Diffusion ........................................................................ p22
Osmosis ........................................................................ p23
Active Transport ......................................................... p26
Bulk Transport ............................................................ p27
These notes may be used freely by biology students and teachers.
I would be interested to hear of any comments and corrections.
Neil C Millar ([email protected]) June 2016
Y12
Unit 1 Biochemistry
Unit 2 Cells
Unit 3 Reproduction
Unit 4 Transport
Unit 5 Biodiversity
Unit 6 Ecology
Y13
HGS Biology A-level notes
Unit 7 Metabolism
Unit 8 Microbes
Unit 9 Control Systems
Unit 10 Genetics
NCM/2/16
AS Biology Unit 2
page 2
Biology Unit 2 Specification
2.01 Cells, Tissues and Organs
Cell theory is a unifying concept that states that
cells are a fundamental unit of structure, function
and organisation in all living organisms. In
complex organisms, cells are organised into
tissues, organs, and organ systems.
2.02 Eukaryotic Cells
The ultrastructure of eukaryotic cells and the
functions of organelles, including: nucleus,
nucleolus, 80S ribosomes, rough and smooth
endoplasmic reticulum, mitochondria, centrioles,
lysosomes,
Golgi
apparatus,
cell
wall,
chloroplasts, vacuole and tonoplast.
2.03 Prokaryotic Cells
The ultrastructure of prokaryotic cells and the
structure of organelles, including: nucleoid,
plasmids, 70S ribosomes and cell wall. Distinguish
between Gram positive and Gram negative
bacterial cell walls. Be able to distinguish between
Gram positive and Gram negative bacterial cell
walls and why each type reacts differently to
some antibiotics.
HGS Biology A-level notes
2.04 Microscopy
How magnification and resolution can be
achieved using light and electron microscopy.
The importance of staining specimens in
microscopy.
2.05 Cell Membranes and Transport
The structure of the cell surface membrane with
reference to the fluid mosaic model.
 How passive transport is brought about by:
diffusion; facilitated diffusion (through carrier
proteins and protein channels); osmosis. How
the properties of molecules affects how they
are transported, including solubility, size and
charge.
 Water potential = turgor pressure + osmotic
potential.
 The process of active transport, including the
role of ATP.
Phosphorylation of ADP
requires energy and that hydrolysis of ATP
provides an accessible supply of energy for
biological processes.
 Large molecules can be transported into and
out of cells through the formation of vesicles,
in the processes of endocytosis and
exocytosis.
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AS Biology Unit 2
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HGS Biology A-level notes
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AS Biology Unit 2
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Cells
Cell Theory
All living things are made of cells. Cells were first seen in dead
plant tissue in 1665 by Robert Hooke (who named them after
monks' cells in a monastery), and living cells were first
observed by Leeuwenhoek a few years later using a primitive
microscope. However it wasn’t until two centuries later that
scientists realised that all living organisms were composed of
cells, when Schleiden and Schwann proposed cell theory in
1838.
Cell theory states that:
1. All organisms are composed of one or more cells. All the
processes of life (e.g. growth, metabolism, reproduction)
take place within cells.
2. Cells are the smallest units that can be alive.
3. New cells are always formed by division of old cells and new living cells cannot be spontaneously
generated. The first cells must have evolved from non-living structures 4 billion years ago, but the
development of “life” took place gradually over millions of years, so there was no definable first cell.
Unicellular and Multicellular Organisms
Some organisms are made of just a single cell (e.g. bacteria, algae, protozoa, yeast). In these unicellular
organisms, the single cell carries out all the process of life. But most organisms are multicellular. They are
composed of many cells, which are differentiated to carry out different tasks.
Prokaryotic and Eukaryotic Cells
Cells can be classified into two large groups:
 Prokaryotic cells do not have a nucleus, or any interior compartments
 Eukaryotic cells do have a nucleus, and various other interior compartments, called organelles.
We'll examine these two kinds of cell in detail, based on structures seen in electron micrographs. These
show the individual organelles inside a cell.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
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Eukaryotic Cells
Eukaryotic cells contain a nucleus and numerous other cell organelles.
cell wall
small vacuole
cell membrane
Golgi body
cytoskeleton
rough
endoplasmic
reticulum
large vacuole
chloroplast
nucleus
mitochondrion
nucleoplasm
nucleolus
nuclear envelope
80S ribosomes
smooth
endoplasmic
reticulum
nuclear pore
lysosome
centriole
undulipodium
Not all eukaryotic
cells have all the
parts shown here
10 µm
Cell Membrane (or Plasma Membrane)
This is a thin, flexible layer round the outside of all cells made of phospholipids and proteins. It separates
the contents of the cell from the outside environment, and controls the entry and exit of materials. The
structure and function of the membrane is examined in detail on p19.
HGS Biology A-level notes
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AS Biology Unit 2
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Nucleus
This is the largest organelle. It is roughly spherical and surrounded by
a nuclear envelope, which is a double membrane with nuclear pores
– large holes containing proteins that control the exit of substances
from the nucleus. The interior is called the nucleoplasm, which is full
nuclear
envelope
RER
nucleolus
of chromatin – the DNA/protein complex. During cell division the
observable
nuclear pore
chromosomes. The nucleolus is a dark region of chromatin, involved
nucleoplasm
(containing
chromatin)
chromatin
becomes
condensed
into
discrete
in making ribosomes.
Mitochondrion (pl. Mitochondria)
This is a sausage-shaped organelle (8µm long), and is where aerobic
outer membrane
respiration takes place and ATP is synthesised in all eukaryotic cells
inner membrane
(anaerobic respiration takes place in the cytoplasm). Cells that use a
matrix
lot of energy (like muscle cells) have many mitochondria.
Mitochondria are surrounded by a double membrane: the outer
membrane is simple and quite permeable, while the inner membrane
is highly folded into cristae, which give it a large surface area. The
space enclosed by the inner membrane is called the mitochondrial
matrix, and contains small circular strands of DNA. The inner
crista (fold in
inner membrane)
stalked particles
(ATP synthase)
ribosomes
DNA
membrane is studded with stalked particles, which are the enzymes
that make ATP.
Chloroplast
Bigger and fatter than mitochondria, chloroplasts are where
photosynthesis takes place, so are only found in photosynthetic
organisms (plants and algae). Like mitochondria they are enclosed by
a double membrane, but chloroplasts also have a third membrane
called the thylakoid membrane. The thylakoid membrane is folded
into thylakoid disks, which are then stacked into piles called grana.
The space between the inner membrane and the thylakoid is called
the stroma. The thylakoid membrane contains chlorophyll and
chloroplasts also contain starch grains, ribosomes and circular DNA.
outer membrane
inner membrane
thylakoid
membrane
granum
(thylakoid stack)
stalked particles
(ATP synthase)
starch grain
stroma
Chloroplasts are the most common type of plastids, which are organelles with double membranes, found in
all plant and algae cells. The other types of plastid are not used for photosynthesis, but are usually storage
organelles, such as amyloplasts, which store starch. Plastids can multiply inside eukaryotic cells by fission
(splitting), just like bacterial cells.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 7
Ribosomes
These are the sites of protein synthesis. Ribosomes are the smallest and most
numerous of the cell organelles, but, unlike most other organelles, are not
enclosed in a membrane. Ribosomes are either found free in the cytoplasm,
where they make proteins for the cell's own use, or they are found attached to
the rough endoplasmic reticulum, where they make proteins for export from
the cell. All eukaryotic ribosomes are of the larger, "80S", type.
Endoplasmic Reticulum (ER)
This is a series of membrane channels involved in synthesising and transporting materials.
 Rough Endoplasmic Reticulum (RER) is studded with numerous
cisternae
ribosomes, which give it its rough appearance. The ribosomes synthesise
proteins, which are processed in the RER (e.g. by enzymatically modifying
ribosomes
the polypeptide chain, or adding carbohydrates), before being exported
from the cell via the Golgi Body.
 Smooth Endoplasmic Reticulum (SER) does not have ribosomes and is used to process materials, mainly
lipids, needed by the cell.
Golgi Body (or Golgi Apparatus)
Another series of flattened membrane vesicles, formed from the
endoplasmic reticulum. Its job is to transport proteins destined for
extracellular use from the ER to the cell membrane for export. Parts of the
RER containing proteins fuse with one side of the Golgi body membranes
to form cisternae, while at the other side small vesicles bud off from the
cisternae and move towards the cell membrane, where they fuse, releasing
their contents to the outside of the cell by exocytosis.
Vacuoles
These are membrane-bound sacs containing water or dilute solutions of salts
and other solutes. Most cells can have small vacuoles that are formed as
required, but plant cells usually have one very large permanent vacuole that
fills most of the cell, so that the cytoplasm (and everything else) forms a thin
layer round the outside. Plant cell vacuoles are surrounded by a membrane
called the tonoplast and filled with cell sap. They help to keep the cell rigid, or turgid. Some unicellular
protoctists have feeding vacuoles for digesting food, or contractile vacuoles for expelling water.
HGS Biology A-level notes
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AS Biology Unit 2
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Lysosomes
These are small membrane-bound vesicles formed from the RER containing a
cocktail of digestive enzymes. They are used to break down unwanted
chemicals, toxins, organelles or even whole cells, so that the materials may be
recycled. They can also fuse with a feeding vacuole or a phagosome to digest
its contents.
Cytoskeleton
This is a network of protein fibres extending throughout all eukaryotic cells,
used for support, transport and motility. The cytoskeleton is attached to the
cell membrane and gives the cell its shape, as well as holding all the organelles in
position. The cytoskeleton is also responsible for all cell movements, such as
cell division, cilia and flagella, cell crawling and muscle contraction in animals.
Centrioles
There are always two centrioles found near the nucleus. They are part of the
cytoskeleton and are used in cell division to make the spindle fibres that move the
chromosomes. Centrioles are found in animal cells, but not in plants, fungi or
prokaryotes.
Cilia, Flagella and Microvilli
These are different finger-like extensions of the cell membrane containing
cytoskeleton proteins so they can move.
 Cilia are short and numerous and are used for moving the cell (e.g. ciliates)
or for moving the extracellular fluid (e.g. trachea).
 Flagella are longer than the cell, there are usually only one or two of them
and they are used for motility (e.g. sperm).
 Microvilli are short extensions found in certain cells such as in the epithelial
cells of the intestine and kidney, where they increase the surface area for
absorption of materials.
Cytoplasm (or Cytosol)
This is the solution within the cell membrane. It contains enzymes for glycolysis (part of respiration) and
other metabolic reactions together with sugars, salts, amino acids, nucleotides and everything else needed
for the cell to function.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 9
Cell Wall
This is a thick layer outside the cell membrane. Almost all cells have cell walls, made of different materials:
 Plant cell walls are made of cellulose
 Fungal cell walls are made of chitin
 algal cell walls are made of glycoproteins
 diatom cell walls are made of silica
 bacterial cell walls are made of peptidoglycan
 archaean cell walls are made of S-layer proteins
Only animal cells do not have a cell wall. Cell walls are used to give strength and rigidity to cells and to
resist osmotic lysis. They are made of a network of fibres that give strength but are freely permeable to
solutes (unlike membranes). A wickerwork basket is a good analogy.
Plant cell walls are composed of three layers:
1. The middle lamella is a layer of pectins on the outside of the
cell wall that glues adjacent cells together.
2. The primary cell wall is a thin layer of cellulose microbfibrils
(unit 1), laid down while the cell is growing. The primary cell
wall is flexible, so that is can expand as the cell grows.
3. The secondary cell wall is a thick layer built up inside the
primary cell wall once the cell has stopped growing. It is made of cellulose microbfibrils (unit 1)
embedded in a matrix made of hemicellulose and pectin, and provides most of the strength of the cell. In
xylem vessels the secondary cell wall also contains lignin for strength and waterproofing, and these
lignified cell walls form woody tissue (unit 4).
Plant cell walls are usually studded with channels called plasmodesmata (singular plasmodesma), which link
the cytoplasms of adjacent cells, forming a symplast (a continuous cytoplasm, see unit 4). This symplast
allows solutes to diffuse freely between cells without crossing any membranes.
HGS Biology A-level notes
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AS Biology Unit 2
page 10
Comparison of different types of Eukaryotic Cell
Fungi
Plants
Animals
Nucleus
Mitochondria






Chloroplast



80S ribosome



Vacuoles



Cytoskeleton



Centriole



Plasma membrane

(chitin)

(cellulose)

Cell Wall

Cell Organisation
In multicellular organisms the eukaryotic cells are specialised to perform different functions. Thousands of
different types of cell have been described, such as red blood cells, smooth muscle cells, adipose cells, B
lymphocytes, osteocytes, motor neurones, ova, ciliated epithelial cells, endocrine cells, hepatocytes,
palisade mesophyll cells, guard cells, root hair cells, cambium, and countless more.
Eukaryotic cells are arranged into:
 A tissue is a group of similar cells performing a particular function. Simple tissues are composed of one
type of cell, while compound tissues are composed of more than one type of cell. Animal tissues include
epithelium (lining tissue), connective, nerve, muscle, blood, glandular. Plant tissues include epidermis,
meristem, vascular, mesophyll, cortex.
 An organ is a group of physically-linked different tissues working together as a functional unit. For
example the stomach is an organ composed of epithelium, muscular, glandular and blood tissues. A plant
leaf is also an organ, composed of mesophyll, epidermis and vascular tissues.
 An organ system is a group of organs working together to carry out a specific complex function. Humans have seven main systems: the circulatory, digestive, nervous, respiratory, reproductive, urinary and
muscular-skeletal systems.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 11
Prokaryotic Cells
Prokaryotic cells are smaller than eukaryotic cells and do not have a nucleus or indeed any membranebound organelles. The prokaryotes comprise the bacteria and archaea (see unit 2). Prokaryotic cells are
much older than eukaryotic cells and they are far more abundant (there are ten times as many bacteria
cells in a human than there are human cells). The main features of prokaryotic cells are:
 Cytoplasm. Contains all the enzymes needed for
all metabolic reactions, since there are no
organelles
 Ribosomes. The smaller “70S” type, all free in
the cytoplasm and never attached to membranes.
Used for protein synthesis.
 Nucleoid. The region of the cytoplasm that
contains DNA. It is not surrounded by a nuclear
membrane.
 DNA. Always circular (i.e. a closed loop), and not
associated with any proteins to form chromatin.
Sometimes
referred
to
as
the
bacterial
chromosome to distinguish it from plasmid DNA.
 Plasmid. Small circles of DNA, separate from the main DNA loop. Used to exchange DNA between
bacterial cells, and also very useful for genetic engineering (see unit 3).
 Plasma membrane. Made of phospholipids and proteins, like eukaryotic membranes.
 Cell Wall. This is a thick layer outside the cell membrane used to give a cell strength and rigidity and
resist osmotic lysis. Made of peptidoglycan (not cellulose), which is a glycoprotein (i.e. a
protein/carbohydrate complex, also called murein). There are two types of cell wall: Gram-positive and
Gram-negative (see next page).
 Capsule. A thick polysaccharide layer outside of the cell wall. Used for sticking cells together, as a food
reserve, as protection against desiccation and chemicals, and as protection against phagocytosis. In some
species the capsules of many cells fuse together forming a mass of sticky cells called a biofilm. Dental
plaque is an example of a biofilm.
 Flagellum. A rigid rotating helical-shaped tail used for propulsion. The motor is embedded in the cell
membrane and is driven by a H+ gradient across the membrane. The bacterial flagellum is quite different
from the eukaryotic flagellum.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
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The Bacterial Cell Wall
There are two kinds of bacterial cell wall, which are identified by the Gram Stain technique when observed
under the microscope. Gram positive bacteria stain purple, while Gram negative bacteria stain pink. The
technique was discovered by Christian Gram in 1884 and is still used today to identify and classify bacteria.
We now know that the different staining is due to two types of cell wall:
Gram Positive cell wall Gram Negative cell wall
(stains purple) (stains pink)
Gram positive bacteria have a thick peptidoglycan
cell wall outside their cell membrane. The cell
wall is very strong and allows these bacteria to
withstand severe physical conditions. There may
be a capsule outside the cell wall.
Gram negative bacteria have a more complex
structure, with a thin layer of periplasm (like
cytoplasm but outside the cell), a thin
peptidoglycan cell wall, and then a second, outer
membrane, which contains lipopolysaccharides
instead of phospholipids in its outer layer. This
layer resists antibiotics and lysozyme enzymes, so
gram negative bacteria are more difficult to kill.
The Gram Stain
A microscope slide is prepared with a sample of the bacteria to be examined. There are four steps in the
Gram staining technique:
1. The microscope slide is flooded with crystal violet (the primary stain), which binds to the peptidoglycan
cell wall, staining all bacterial cells purple.
2. The slide is flooded with iodine. This binds to crystal violet in the cell wall and fixes it, making it difficult
to wash out.
3. The slide is washed with ethanol. The ethanol dissolves the outer lipopolysaccharide membrane of
gram-negative cells, whose peptidoglycan cell wall is so thin that the crystal violet is washed out. The
peptidoglycan cell wall of gram-positive cells is so thick that the crystal violet cannot be washed out, so
these cells remain purple.
4. The slide is flooded with safranin (the counter-stain), which stains the thin peptidoglycan cell wall of
gram-negative cells pink.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 13
Bacteria Cells and Antibiotics
Antibiotics are antimicrobial chemicals produced naturally by other microbes (usually fungi or bacteria) and
used to treat bacterial infections. Antibiotics are so useful because they are selectively toxic i.e. they kill
bacteria growing in human tissue without killing the host human cells. Antibiotics do this by inhibiting
enzymes that are unique to prokaryotic cells, such those involved in synthesising the bacterial cell wall or
70S ribosomes. For example:
 penicillin (and related antibiotics ampicillin, amoxicillin and methicillin) Inhibits an enzyme involved in the
synthesis of peptidoglycan for bacterial cell wall. This weakens the cell wall, killing bacterial cells by
osmotic lysis. The penicillins can’t easily cross cell membranes, so they are only effective against Grampositive bacteria (since the peptidoglycan cell wall is exposed) but not against Gram-negative bacteria
(since the wall is behind the outer membrane).
 Streptomycin, tetracycline and erythromycin inhibit enzymes in 70S ribosomes. This stops protein
synthesis so prevents cell division. These antibiotics are equally effective against Gram-positive and
Gram-negative bacteria, since they both contain the same 70S ribosomes.
These effects are reflected in the concentration of antibiotics required to treat bacterial infections, shown
on this chart:
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 14
Summary of the Differences between Prokaryotic and Eukaryotic Cells
Prokaryotic Cells
Eukaryotic cells
small cells (< 5 µm)
larger cells (> 10 µm)
always unicellular
often multicellular
no nucleus
or any membrane-bound organelles
always have nucleus
and other membrane-bound organelles
DNA is linear and associated with proteins
to form chromatin
DNA is circular, without proteins
ribosomes are small (70S)
ribosomes are large (80S)
no cytoskeleton
always has a cytoskeleton
motility by rigid rotating flagellum,
made of flagellin
motility by flexible waving undulipodium,
made of tubulin
cell division is by binary fission
cell division is by mitosis or meiosis
reproduction is always asexual
reproduction is asexual or sexual
huge variety of metabolic pathways
common metabolic pathways
Endosymbiosis
Prokaryotic cells are far older and more diverse than eukaryotic cells. Prokaryotic cells have probably been
around for 3.5 billion years, while eukaryotic cells arose only about 1 billion years ago. It is thought that
eukaryotic cell organelles like nuclei, mitochondria and chloroplasts are derived from prokaryotic cells that
became incorporated inside larger prokaryotic cells. This idea is called endosymbiosis, and is supported by
these observations:
 organelles contain circular DNA, like bacteria cells.
 organelles contain 70S ribosomes, like bacteria cells.
 organelles have double membranes, as though a single-membrane cell had been engulfed and surrounded
by a larger cell.
 organelles reproduce by binary fission, like bacteria.
 organelles are very like some bacteria that are alive today.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 15
Microscopy
Of all the techniques used in biology microscopy is probably the most important. The vast majority of living
organisms are too small to be seen in any detail with the human eye, and cells and their organelles can only
be seen with the aid of a microscope. Microscopes have two properties: magnification and resolution.
Magnification and Resolution
 Magnification is a dimensionless number, usually written as a magnification factor, e.g. x100. It is simply
indicates how much bigger the image is that the original object. By using more lenses, microscopes can
magnify by a larger amount, but the image may get more blurred, so this doesn't always mean that more
detail can be seen.
 Resolution is a distance, usually measured in nm. It is the smallest separation at which two separate
objects can be distinguished, or resolved. For example if the resolution of a microscope is 50nm, then
objects closer together than 50nm cannot be seen as separate objects. The resolution of a microscope
is ultimately limited by the wavelength of light used (400-600nm for visible light), so to improve
resolution waves with a shorter wavelength is needed. This is how electron microscopes gain
resolution.
This chart shows the effect of magnification and resolution on the appearance of two small objects.
Low resolution
(a large distance)
High resolution
(a small distance)
Low
magnification
High
magnification
There are three common kinds of microscope:
1. Light (or optical) microscope
2. Transmission electron microscope (TEM)
3. Scanning electron microscope (SEM)
HGS Biology A-level notes
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AS Biology Unit 2
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1. The Light Microscope
Light, or optical, microscopes are the oldest,
simplest
and
most
widely-used
form
of
microscopy. Specimens are illuminated with visible
light, which is focused using glass lenses and
viewed using the eye or photographic film. Most
light microscopes have three lenses: a condenser
lens to focus the light onto the specimen; an
objective lens to magnify the image; and an
eyepiece lens to focus the image on the eye. The
total magnification of a microscope is given by the
product of the objective and eyepiece lenses. The
resolution of a light microscope is about 200nm,
but special optical techniques (like fluorescence
microscopy and interference microscopy) can
improve this limit down to 1nm.
Specimens can be living or dead but need to be thin so that enough light can be transmitted through them.
Most biological specimens will then be invisible, so they usually need to be coloured with a chemical stain
to make them stand out. Some common stains are:
 Iodine to stain starch in plant cells
 Methylene blue or acetic orcein to stain DNA in nuclei
 Toluidine blue to stain lignin in xylem cell walls
 Phalloidin to stain the cytoskeleton
2. The Transmission Electron Microscope (TEM)
The Transmission Electron Microscope (TEM) uses a beam of electrons, rather than electromagnetic
radiation, to "illuminate" the specimen. This may seem strange, but electrons behave like waves and can
easily be produced (using a hot wire), focused (using electromagnets) and detected (using a phosphor
screen or photographic film). A beam of electrons has an effective wavelength of less than 1nm, so can be
used to resolve small sub-cellular ultrastructure. The development of the electron microscope in the 1930s
revolutionised biology, allowing organelles such as mitochondria, ER and membranes to be seen in detail for
the first time.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 17
Electron microscope specimens need to be very thin,
and to prevent them breaking the specimens have to be
embedded in plastic. Biological specimens are usually
transparent to electrons, so they also have to be stained
with electron-dense heavy metal compounds such as
gold, osmium or even uranium salts. These stains aren’t
coloured, so electron microscope image are always
monochrome (though the images can be coloured
artificially using computer software).
The biggest problem with electron microscopy is that
there must be a vacuum inside the electron microscope
(or the electron beam would be scattered by the air
molecules), so it can't be used for living organisms.
Specimens can also be damaged by the electron beam,
so delicate structures and molecules can be destroyed. There is always a concern that structures observed
by an electron microscope are artefacts (i.e. due to the preparation process and not present in the real
cell), but improvements in technique have eliminated most of these.
3. The Scanning Electron Microscope (SEM)
The scanning electron microscope (SEM)
works in a very different way to other
microscopes. It scans a fine beam of
electrons onto a specimen and detects the
electrons scattered back by the surface.
The scattered electron signal is then
converted
into
a
computer-generated
image of the surface of the specimen. These
images are fantastically detailed but do not
have very high magnification.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 18
Comparison of Different Microscopes
Light Microscope
Advantages  good magnification (1000x)
 can use living specimens
 colour images
Limitations
 poor resolution (200nm)
 can’t see organelles
 specimens must be stained
TEM
 high magnification
(5 000 000x)
 very good resolution
(1nm)
SEM
 gives 3-dimentional images
 don’t need thin sections
 vacuum, so can’t use living
specimens
 resolution not as good as
TEM (10nm)
 complex specimen
preparation – specimens
need to be very thin and
embedded in plastic
 can’t see internal
structures
 no colour
 specimens can be damaged
by electron beam, causing
artefacts.
Uses
 tissues, cells and small
organisms
 cell organelles, prokaryotes  surfaces of living and nonand viruses
living specimens
 videos
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 19
Magnification Calculations
Microscope drawings and photographs (micrographs) are usually magnified, and you have to be able to
calculate the true size of the object from the image. There are two ways of doing this:
1. Using a Magnification Factor
Sometimes the image has a magnification factor on it. The formula for the magnification is:
For example, if this drawing of an object is 40mm long and the magnification is
x1000, then the object's true length is T =
I
M
=
40mm
1000
= 0.04mm = 40μm.
Always convert your answer to appropriate units, usually µm for cells and
x 1000
organelles.
Sometimes you have to calculate the magnification. For example, if this drawing
of an object is 40mm long and its true length is 25µm, the magnification of the
drawing is: M=
I
T
=
40 000μm
25μm
= 1600. Remember, the image and true lengths
must be in the same units. Magnifications can also be less than one (e.g. x 0.1), which means that the
drawing is smaller than the actual object.
2. Using a Scale Bar
Sometimes the picture has a scale bar on it. You can easily judge rough sizes by seeing how many scale bars
fit into the object, but to work out a size accurately, you first use the scale bar to calculate the
magnification, then you apply this magnification to the object.
For example, if this 5µm scale bar is 10mm long, then the magnification is:
M=
I
T
=
10 000μm
5μm
= 2000. Therefore if this drawing of an object is 40mm long
the object's true size is: T =
I
M
=
40mm
2000
= 0.02mm = 20μm. This makes sense,
5µm
as we can fit about four scale bars into the object.
It's good to have a rough idea of the size of objects, to avoid silly mistakes. A mitochondrion is not 30mm
long! Scale bars make this much easier than magnification factors.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 20
The Cell Membrane
The cell membrane (or plasma membrane) surrounds all living cells, and is the cell's most important
organelle. It controls how substances can move in and out of the cell and is responsible for many other
properties of the cell as well. The membranes that surround the nucleus and other organelles are almost
identical to the cell membrane. Membranes are composed of phospholipids, proteins and carbohydrates
arranged as shown in this diagram.
peripheral
protein on
outer surface
carbohydrate
attached to
protein
phospholipid
fatty acid chains
polar head
part of
cytoskeleton
peripheral
protein on
inner surface
integral protein
forming a channel
The phospholipids form a thin, flexible sheet, while the proteins "float" in the phospholipid sheet like
icebergs, and the carbohydrates extend out from the proteins. This structure is called a fluid mosaic
structure because all the components can move around (it’s fluid) and the many different components all fit
together, like a mosaic.
The phospholipids are arranged in a bilayer (i.e. a double layer), with their polar, hydrophilic phosphate
heads facing out towards water, and their non-polar, hydrophobic fatty acid tails facing each other in the
middle of the bilayer. This hydrophobic layer acts as a barrier to most molecules, effectively isolating the
two sides of the membrane. Different kinds of membranes can contain phospholipids with different fatty
acids, affecting the strength and flexibility of the membrane, and animal cell membranes also contain
cholesterol linking the fatty acids together and so stabilising and strengthening the membrane.
The proteins usually span from one side of the phospholipid bilayer to the other (integral proteins), but
can also sit on one of the surfaces (peripheral proteins). They can slide around the membrane very quickly
and collide with each other, but can never flip from one side to the other. The proteins have hydrophilic
amino acids in contact with the water on the outside of membranes, and hydrophobic amino acids in
HGS Biology A-level notes
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AS Biology Unit 2
page 21
contact with the fatty chains inside the membrane. Proteins comprise about 50% of the mass of
membranes, and are responsible for most of the membrane's properties.
 Transport proteins. Most transport of small molecules across the
membrane take place through integral proteins. This transport includes
facilitated diffusion and active transport (more details below).
 Receptor proteins. Receptor proteins must be on the outside surface of
cell membranes and have a specific binding site where hormones or other
chemicals can bind to form a hormone-receptor complex (like an enzymesubstrate complex). This binding then triggers other events in the cell
membrane or inside the cell.
 Enzymes. Enzyme proteins catalyse reactions in the cytoplasm or outside
the cell, such as maltase in the small intestine (more in digestion).
 Recognition proteins. Some proteins are involved in cell recognition.
These are often glycoproteins, such as the A and B antigens on red blood cell
membranes.
 Structural proteins. Structural proteins on the inside surface of cell
membranes and are attached to the cytoskeleton. They are involved in
maintaining the cell's shape, or in changing the cell's shape for cell motility.
Structural proteins on the outside surface can be used in cell adhesion –
sticking cells together temporarily or permanently.
The carbohydrates are found on the outer surface of all eukaryotic cell membranes, and are attached to
the membrane proteins or sometimes to the phospholipids. Proteins with carbohydrates attached are
called glycoproteins, while phospholipids with carbohydrates attached are called glycolipids.
Remember that a membrane is not just a lipid bilayer,
but comprises the lipid, protein and carbohydrate parts.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 22
Movement across Cell Membranes
The job of the cell membrane is to control what materials can enter and leave cells. There are five main
methods by which substances can move across a cell membrane:
Passive transport methods
Active transport methods
1. Lipid Diffusion
4. Active Transport
2. Facilitated Diffusion
5. Bulk transport
3. Osmosis (Water Diffusion)
Passive Transport Methods
Passive processes do not require any energy, other than the thermal energy of the surroundings.
Substances move around randomly within cells due to thermal motion, and if there is a concentration
difference between two places then the random movement results in a substance diffusing down its
concentration gradient from a high to a low concentration. This process is called diffusion.
Passive transport is simply diffusion across a cell membrane, so does not require metabolic energy and is
simply driven by thermal energy. Substances diffuse in both directions across a membrane, but there is a
net movement down a concentration gradient.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 23
1. Lipid Diffusion (Simple Diffusion)
A few substances can diffuse directly through the lipid bilayer part of the membrane. The only substances
that can do this are hydrophobic (lipid-soluble) molecules such as steroids, and a few extremely small
hydrophilic molecules, such as H2O, O2 and CO2. For these molecules the membrane is no barrier at all.
Since lipid diffusion is a passive process, no energy is involved and substances can only move down their
concentration gradient. Lipid diffusion cannot be switched on or off by the cell.
2. Facilitated Diffusion.
Facilitated Diffusion is the diffusion of substances across a membrane through a trans-membrane transport
protein molecule. The transport proteins tend to be specific for one molecule, so substances can only
cross a membrane that contains an appropriate protein. This is a passive diffusion process, so no energy is
involved and substances can only move down their concentration gradient. There are two kinds of
transport protein:
 Channel Proteins form a water-filled pore or channel in the membrane. This allows charged substances
to diffuse across membranes. Most channels can be gated (opened or closed), allowing the cell to
control the entry and exit of ions. In this way cells can change their permeability to certain ions. Ions
like Na+, K+, Ca2+ and Cl- diffuse across membranes through specific ion channels.
 Carrier Proteins have a binding site for a specific solute and constantly flip between two states so that
the site is alternately open to opposite sides of the membrane. The substance will bind on the side
where it at a high concentration and be released where it is at a low concentration. Important solutes
like glucose and amino acids diffuse across membranes through specific carriers. Sometimes carrier
proteins have two binding sites and so carry two molecules at once. This is called cotransport, and a
common example is the sodium/glucose cotransporter found in the small intestine (see next page). Both
molecules must be present for transport to take place.
HGS Biology A-level notes
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AS Biology Unit 2
page 24
3. Osmosis (Water Diffusion)
Osmosis is the diffusion of water across a membrane. Water can diffuse across a membrane in two ways:
partly through the phospholipid bilayer (an example of lipid diffusion) and partly through protein channels
called aquaporins (an example of facilitated diffusion).
As we’ve seen, diffusion takes place down a concentration gradient but, as the solvent in all cells, the total
concentration of water is very high (about 55mol L-1) and it never changes. However, much of this water is
not free to diffuse, since it is bound to solvent molecules as a hydration shell. The more concentrated the
solution, the more solute molecules there are in a given volume, and the more water molecules are bound
in hydration shells, so the fewer free water molecules there are. Two different solutions can be separated
by a cell membrane, since membranes are partially-permeable (i.e. the solvent water molecules can pass
through easily, but larger solute molecules cannot). So if there is a concentration difference of solutes
across a membrane, there will also be a concentration difference of free water molecules across the
membrane, so water will diffuse across. This is osmosis. In osmosis water diffuses from a more dilute
solution to a more concentrated solution across a partially-permeable membrane.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 25
Water Potential
Osmosis can be quantified using water potential, so we can calculate which way water will move. Water
potential is a force and is measured in units of pressure (Pa, or usually kPa), and the rule is that water
always "falls" from a high to a low water potential (in other words it's a bit like gravity potential or
electrical potential). It is abbreviated by the symbol w or just  (the Greek letter psi, pronounced "sy").
Water potential is made up of two components: pressure potential (p) and solute potential (s).
water potential

The overall pressure on water.
 can be positive or negative.
If two compartments are
separated by a partiallypermeable membrane, then
water diffuses from the higher
to the lower water potential.
=
=
pressure potential
p
Hydrostatic pressure due to an
external force. p is usually
positive, which means a
compression force (e.g. due to a
cell wall) but it can be negative,
which means a tension force (e.g.
in xylem vessels). Pressure
potential used to be known as
turgor pressure, and this term is
sometimes still applied to plant
cells.
+
+
solute potential
s
Pressure due to dissolved
solutes. The higher the solute
concentration, the lower the
solute potential. s is always
negative since pure water has
s = 0, and any solute decreases
s. Solute potential used to be
known as osmotic pressure or
osmotic potential, but these
terms are obsolete.
In this experiment a Visking tube is used a partially permeable membrane that lets water through but not
solute molecules. The experiment illustrates the use of the water potential equation.
A Visking tube bag containing salt solution is
placed in a beaker of pure water. The beaker is
open to the air, so there are no external forces
on the water, so p=0 and since pure water has
s =0 then overall s =0. The Visking bag is
floppy (flaccid) so is not generating any pressure
so p=0, but the salt solution has a s =-200kPa,
so the overall =-200kPa. So water enters the bag
by osmosis, down its water potential gradient.
As water enters the bag it dilutes the salt, raising
s to -100kPa. The incoming water expands the
bag till it can expand no more, and it applies a
compression force resisting further entry of water
(p =+100kPa). At equilibrium the positive
pressure potential balances the negative solute
potential so the water potential is zero and there
is no net movement of water.
We can use water potential to understand the behaviour of cells in different surroundings or solutions.
There are three situations:
A hypotonic solution
A solution with a lower solute concentration, or higher s, than the cell.
A hypertonic solution
A solution with a higher solute concentration, or lower s, than the cell.
A isotonic solution
A solution with the same solute concentration and s as the cell.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 26
Cells without cell walls (animal cells)
Since animal cells don’t have a cell wall, there is rarely an external force acting on them, so p is almost
always zero. Animal cells burst in a hypotonic solution (osmotic lysis) and shrink in a hypertonic solution.
The crinkled shape is due to the cytoskeleton.
Cells with cell walls (plant, fungi and bacteria cells)
Cell walls are strong so can apply an external force to the cell, increasing s. In a hypotonic solution plant
cells swell until they reach a dynamic equilibrium where the positive pressure potential exactly balances the
negative solute potential, so the overall water potential is zero and there is no net movement of water. The
cell is turgid and this is the normal state for healthy plant cells. Turgor provides support for leaves and nonwoody stems. In isotonic solutions p=0 and the cells are flaccid. In hypertonic solutions plant cells act like
animal cells, shrinking and pulling away from the cell wall. This is called plasmolysis and would kill the cell.
HGS Biology A-level notes
NCM/2/16
AS Biology Unit 2
page 27
Active Transport Methods and ATP
Active processes need energy. All the processes that need energy in a cell (including active transport) use a
molecule called adenosine triphosphate (ATP) as their immediate source of energy. ATP is synthesised
from ADP and phosphate (Pi) using energy released from glucose in respiration in mitochondria.
respiration
ADP + Pi
active transport
ATP
The hydrolysis (splitting) of ATP back to ADP and Pi releases energy, which can be used to drive processes
like muscle contraction, biosynthesis, and active transport. Active transport therefore involves protein
molecules that are ATPase enzymes, which catalyse this hydrolysis of ATP to release the energy.
4. Active Transport
Active transport is the pumping of substances across a membrane by a trans-membrane protein pump
molecule, using energy from ATP. These transport proteins are ATPase enzymes, and they have an ATPase
active site on their cytoplasm side. The protein binds a molecule of the substance to be transported on one
side of the membrane, changes shape using energy from ATP splitting, and releases the molecule on the
other side. The proteins are highly specific, so there is a different protein pump for each molecule to be
transported. Active transport always occurs in the same direction and can transport substances up their
concentration gradient.
A common active transport pump is the sodium/potassium
ATPase (Na/K pump), found in all animal cell membranes.
This pump continually uses ATP to actively pump sodium
ions out of the cell and potassium ions into the cell. This
creates ion gradients across the cell membrane, which can
be used to regulate water potential and drive other process.
HGS Biology A-level notes
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AS Biology Unit 2
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5. Bulk Transport
Membrane proteins can only transport fairly small
molecules, like ions, glucose and amino acids. But
cells also need to transport large macromolecules
like proteins and polysaccharides and even small
cells. These large objects are transported by bulk
transport using membrane vesicles. The synthesis,
movement and fusion of the vesicles require
metabolic energy in the form of ATP, so this is
another active transport process. Transport into a
cell is called endocytosis and transport out of a cell
is called exocytosis.
Endocytosis
A part of the membrane folds to form a pocket that deepens and pinches shut to form a vesicle containing
whatever material was captured outside the cell.
 Endocytosis of large particles in suspension (such as microbial cells, viruses, dust particles and cellular
debris) is called phagocytosis (“cell eating”). Phagocytosis is used by large white blood cells called
phagocytes to engulf and destroy pathogens in the blood (unit 8). They also recycle dead and damaged
red blood cells. The vesicle, called a phagosome, often fuses with a lysosome so that the lysozyme
enzymes can digest the engulfed particles into small soluble molecules. These molecules are then
recycled for cell growth.
 Endocytosis of small volumes of extra-cellular fluid with its dissolved solutes is called pinocytosis (“cell
drinking”). Many unicellular protoctists feed this way, and human cells take up cholesterol-containing
lipoproteins (LDLs) from the blood by pinocytosis.
Exocytosis
This is the reverse of endocytosis. A membrane vesicle fuses with the cell membrane so that its contents
are released to the outside. The vesicle is usually formed from the endoplasmic reticulum and the Golgi
apparatus, where proteins, lipids and other substances are synthesised and processed for export.
Exocytosis is used by secretory cells to secrete hormones into the blood and digestive enzymes into the
intestine, and by nerve cells to release neurotransmitter chemicals at synapses (Y13). Exocytosis is also
used by plant cells to export the proteins and carbohydrates needed to make the cell wall.
HGS Biology A-level notes
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AS Biology Unit 2
page 29
Effect of concentration difference on rate of transport
The three kinds of transport can be distinguished experimentally by the effect of solute concentration on
its rate of transport:
 Lipid diffusion shows a linear relationship. The greater
then concentration difference the great the rate of
diffusion (see Fick’s law, unit 4)).
 Facilitated diffusion has a curved relationship with a
maximum rate. At high concentrations the rate is
limited by the number of transport proteins.
 Active transport has a high rate even when there is no
concentration difference across the membrane. Active
transport stops if cellular respiration stops, since there
is no ATP.
Summary of Membrane Transport
method
uses energy?
which part of
membrane?
specific?
concentration
gradient
Lipid Diffusion

phospholipid bilayer


Osmosis

phospholipid bilayer


Facilitated Diffusion

proteins


Active Transport

proteins


HGS Biology A-level notes
NCM/2/16