HOLY TRINITY COLLEGE
IB BIOLOGY –STUDY GUIDE: CELLS 1
1.
Outline the premises of the Cell Theory and discuss the evidence that justifies
those, using examples.
2.
Search info about the “spontaneous generation theory” or “abiogenesis”.
When was this theory proven wrong (refuted)?
3.
State special cases regarding the Cell Theory.
4.
State that unicellular organism carries out all the functions of life.
5.
Explain the importance of the surface area to volume ratio as a factor limiting
cell size. Investigate examples of very big or very small organisms and the adaptations
they had developed to cope with size (elephant, pygmy shrew, etc).
6.
Compare the relative sizes of molecules, cell membrane thickness, viruses,
bacteria, organelles and cells, using the appropriate SI unit.
7.
Calculate the linear magnification of drawings and the actual size of
specimens in images of known magnification.
8.
State that multicellular organisms show emergent properties. Read the
following:
IB Syllabus: 'Emergent properties arise from the interaction of the component parts;
the whole is greater than the sum of the parts'.
'I define life as....a whole that this pre-supposed by all its parts' S. Coleridge
Systems biologists attempt to put together the parts that make up a system and then
observe the properties of that 'emerge' from the system but which could not have
predicted from the parts themselves.
As a model consider the electric light bulb. The bulb is the system and is
composed of a filament made of tungsten, a metal cup, and a glass container. We
can study the parts individually how they function and the properties they posses.
These would be the properties of tungsten, the properties of the metal cup and
the properties of the glass container. When studied individually they do not allow
the prediction of the properties of the light bulb. Only when we combine them to
form the bulb can these properties be determined. There is nothing supernatural
about the emergent properties rather it is simply the combination of the parts
that results in new properties being shown.
Emergence and reductionism
2
The approach of the physical sciences is to reduce an inanimate phenomenon to its
constituent parts and that knowledge of these will explain the phenomena as a whole.
The parts do not vary (otherwise there would be more parts) and these are
predictable within the laws and principles that describe them. Since the smallest
parts are predictable then the system as a whole is predictable. No new properties
will arise from the sum of the parts, this is explanatory reductionism.
Biological systems need a different approached, population thinking, which
acknowledges the role of variation in a population. Consequently the
deterministic laws and theories of the physical sciences do not apply to all aspects
of biological systems. The ‘parts’ of the living system vary on both a phenotypic
level and at the level of the genetic program. This is an important feature of the
biological system (compared to the non-living) that it is not just affected by the
physiochemical laws but also by a genetic program.
Theory reduction is the concept that theories and laws in one science field are simply
special cases of theories which are to be found in the physical sciences.
Emergence is the occurrence of unexpected characteristics or properties in a
complex system. These properties emerge from the interaction of the ‘parts’ of
the system. Remember that biology insists on a population thinking so that we
know the interacting ‘parts’ vary in themselves and therefore their ‘emerging’
properties can only be generalised. One of the classic examples cited is to think of
the emergent properties of water (fluidity) that cannot be predicted from
knowledge of the constituent gases hydrogen and oxygen. On a biological scale
consider the current debate about the nature of human consciousness or the
origin of life itself.
1
Concise Oxford English Dictionary 10th edition revised: (2002), Oxford University
Press: New York
2
Mayr, E (2004) What Makes Biology Unique? Cambridge University Press:
Cambridge
9.
Explain that cells in multicellular organisms differentiate to carry out
specialized functions by expressing some of their genes but not others. To see
different types of cells, visit: www.bu.edu/histology/m/index.htm
10.
State that stem cells retain the capacity to divide and have the ability to
differentiate along different pathways.
11.
Outline one therapeutic use of stem cells. Search for information and bring it
to class.
STUDY GUIDE: CELLS 2
Draw and label a diagram of the ultrastructure of Escherichia coli (E. coli) as
an example of a prokaryote and identify the internal structures.
13.
Describe in the prokaryotic cell diagram the functions of each named
structure.
14.
State that prokaryotic cell divide by binary fission.
15.
Draw and label a diagram of the ultrastructure of a liver cell as an example of
an animal cell and identify the internal structures
16.
Describe in the eukaryotic cell diagram the functions of each named
structure.
17.
Compare prokaryotic and eukaryotic cells.
18.
State three differences between plant and animal cells.
19.
Outline two roles of extracellular components: cell wall and extracellular
matrix.
20.
Answer “Chapter 1 Questions” page 24 in the book.
12.
CALCULATING MAGNIFICATION
1.
STOMACH CELL: Magnification of the micrograph: X 8000. Calculate the width
of the cell.
2.
LIVER CELL: Using the scale bar, calculate the real size of structures P and M
in µm. Which is the magnification of the micrograph
3.
PLANT CELL: Using the scale bar, calculate the real size of one chloroplast
and the width of the vacuole in µm. Which is the magnification of the micrograph??
4.
SMALL INTESTINE CELL: Using the scale bar, calculate the real size of the
nucleus in µm. Which is the magnification of the micrograph?
5.
PANCREAS CELL: Using the scale bar, calculate the real size of the lysosome in
µm. Which is the magnification of the micrograph?
6.
ANIMAL CELL NUCLEUS: Magnification: X 8500. Which is the nucleus real size?
7.
ONION CELL X40: Calculate the size of the nucleus in µm.
8.
ONION CELL X10: Calculate the length of a cell in µm.
9.
PLANT CELL: Magnification: X 5500. Calculate the size of the nucleus and
chloroplasts in µm.
10.
CHLOROPLAST: Calculate the length of the starch granules. Which is the
magnification?
1. CELL THEORY
The cell is the smallest unit of life capable of surviving independently
 A cell can perform all metabolic processes
 Organelles need other organelles for their successful function. Example:
mitochondria that has DNA and can replicate and carry out metabolism, but
needs products from the cytoplasm to begin aerobic respiration.
 Virus: intracellular compulsory parasite. Consists of a loop of DNA or RNA
surrounded by a protein capsule. Replicates by using the host cell DNA. Can´t
perform metabolic processes.
All living organisms consist of cells, at least one.
 Unicellular organisms: all prokaryotes and some eukaryotes as Proctista.
 Bacteria: rudimentary cells, few organelles, no true nucleus.
 Proctista: complex cells, membrane bounded organelles, larger than the
average cell. Some scientists consider them “acellular”
All cell come from other pre-existing cells
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Cells carry out a form of cell division to form new cells. This process of cell
replication in eukaryotes is called mitosis and in prokaryotes is called binary
fission. The parental cell divides to produce identical daughter cells.
This aspect of cell theory suggests that all cells therefore have a common
ancestor, the original ancestral cell form which all other cells have arisen by
descent. (origin of cellular life).
This relationship of common ancestor therefore suggests that all organisms
are related
Cell theory replaces the idea of spontaneous generation o abiogenesis in
which inanimate matter reassembles itself into living form. This was believed
to be the origin of diseases that spontaneously arose and killed so many
people.
Francesco Redi, Agostino Bassi, John Snow and Louis Pasteur worked to state
that diseases were caused by microscopic organisms that multiplied inside
humans.
2. STATE SPECIAL CASES REGARDING THE CELL THEORY.
Muscle cells: multinucleated, but surrounded by one cell membrane. Very long
(300mm)
Fungal hyphae cells: multinucleated, but surrounded by one cell membrane and cell
wall made of chitin. Many hyphae form a micellium.
More examples???? Bone cells, red blood cells, some white blood cells
3. STATE THAT UNICELLULAR ORGANISM CARRIES OUT ALL THE
FUNCTIONS OF LIFE.
Unicellular organisms: they perform all metabolic processes, different from typical
cells that need others to divide functions (specialization). Metabolic processes
performed by a unicellular organism:
a. metabolism which includes respiration the synthesis of ATP.
b. response to a change in the environment
c. homeostasis the maintenance and regulation of internal cell conditions.
d. growth which for a unicellular organism means an increase in cell size and
volume.
e. reproduction which for the unicellular organism is largely asexual through cell
division to form a clone.
f. nutrition which means either the synthesis of organic molecules or the absorption
of organic matter.
SURFACE AREA/VOLUME RATIO
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As the size of a structure increases the surface area to volume ratio
decreases.
This can be seen by performing some simple calculations concerning differentsized organisms.
All cells need to exchange substances such as food, waste, gases and heat
with their surroundings.
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The rate of exchange of substances therefore depends on the cell´s surface
area that is in contact with the surroundings.
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All cells perform metabolic processes to keep life on.
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The rate of metabolism therefore depends on the cell´s volume
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As cells get bigger their volume and surface area both get bigger, but not by
the same amount.
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The surface area/volume ratio applies also to the size of organisms
COMPARE THE RELATIVE SIZES OF MOLECULES, CELL MEMBRANE THICKNESS,
VIRUSES, BACTERIA, ORGANELLES AND CELLS, USING THE APPROPRIATE SI UNIT.
Relative sizes:
1. Molecules (1nm).
2. Cell membrane thickness (10nm).
3. Virus (100nm).
4.
5.
6.
7.
Bacteria (1um).
Organelles (less 10um).
Cells (<100 um).
Generally plant cells are larger than animal cells.
CALCULATE THE LINEAR MAGNIFICATION OF DRAWINGS AND THE ACTUAL SIZE OF
SPECIMENS IN IMAGES OF KNOWN MAGNIFICATION.
Methods for calculating magnification:
 Use of scale bars: They indicate the real length of a structure. Calculate the
length of the scale bar with your ruler and convert it to the scale bar units.
Divide them and obtain the magnification or measure other structures in the
micrograph.
 Magnification: Indicates how many times bigger the micrograph or drawing in
comparison with the real size is. Measure the size of the structure with your
ruler and calculate the real size taking into account how many times bigger it
is shown.
STATE THAT MULTICELLULAR ORGANISMS SHOW EMERGENT PROPERTIES.
Read text.
EXPLAIN THAT CELLS IN MULTICELLULAR ORGANISMS DIFFERENTIATE TO CARRY
OUT SPECIALIZED FUNCTIONS BY EXPRESSING SOME OF THEIR GENES BUT NOT
OTHERS.
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What is the benefit of differentiation and specialisation of tissues rather than
all tissues carrying out all functions?
Specialised cells have switched on particular genes (expressed) that correlate
to these specialist functions.
These specific gene expressions produce particular shapes, functions and
adaptations within a cell.
Therefore a muscle cell will express muscle genes but not those genes which
are for nerve cells.
The study of how cells become specialised is called embryology. This study
area in biology has been developing very fast in recent time. Some of the
discoveries about why some embryonic cells become nerves, muscles or blood
cells has led to new ideas about the evolution of life. The new discipline is
called evolutionary developmental biology or 'Evo-devo'.
STATE THAT STEM CELLS RETAIN THE CAPACITY TO DIVIDE AND HAVE THE ABILITY
TO DIFFERENTIATE ALONG DIFFERENT PATHWAYS.
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A stem cell retains the capacity to divide and has the ability to
differentiate along different pathways.
A stem cell is able to divide but has not yet expressed genes to
specialise to a particular function. Under the right conditions stem
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cells can be induced to express particular genes and differentiate into
a particular type of cell.
Stem cells can be obtained from a variety of different places including
the blastocyte. Adults still posses’ stem cells in some organs but much
less so than a child. Even the placenta can be a useful source of stem
cells.
OUTLINE ONE THERAPEUTIC USE OF STEM CELLS. SEARCH FOR INFORMATION AND
BRING IT TO CLASS.
Non-Hodgkins Lymphoma is a
cancerous disease of the
lymphatic system.
1. Patient requires heavy doses
of radiation and or
chemotherapy. This will destroy
health blood tissue as well as the
diseased tissue.
2. Blood is filtered for the
presence of peripheral stem
cells. Cells in the general
circulation that can still
differentiate into different types
of blood cell.
3. Bone marrow can be removed
before treatment.
4. Chemotherapy supplies toxic drugs to kill the cancerous cells.
5. Radiation can be used to kill the cancerous cells but in time they adapt to this
treatment so that radiation and chemotherapy are often used together.
6. Post radiation/ chemotherapy the patients health blood tissues is also destroyed.
7. Health stem cells or marrow cells can be transplanted back to produce blood cells
again
You may wish to think about more elaborate forms of stem cell therapy. The
following information provides an introduction to these technologies.
2. Embryonic Stem cell therapy this animation is an excellent introduction to the
use of embryonic stem cell for therapies.
3. Therapeutic cloning . This is a method of obtaining ES cells from someone who
has already been born. These stem cells can be used to treat the individual without
generating an immune response. The human body recognizes and attacks foreign
cells, including stem cells. This is a serious barrier to stem cell therapy.
The process of therapeutic cloning is shown in this diagram. It begins by taking a
somatic (body) cell from the individual. The somatic cell is fused with an egg that
has had its nucleus removed. The resulting cell is genetically identical to the
individual because it contains the DNA from the individual’s somatic cell. The new
cell behaves like a fertilized egg and develops into a blastocyst. ES cells can be
harvested from the blastocyst and grown in culture. These ES cells could be used to
treat the individual without encountering resistance from his or her immune system.
Notice that we do not not refer to this type of blastocyst as an embryo. This is
because, technically speaking, an embryo is the result of the union of an egg and a
sperm, which has not happened in this
case. ¨
1. The patient requires the replacement
of some diseased tissue. First we obtain a
health cell from the same patient.
2. At the same time we require a human
egg cell. This is mainly as the cell retains
the tendency to divide unlike the sample
tissue from the patient.
3. The nucleus is removed from the egg
and discarded. The cell body itself is
retained.
4. The nucleus of the patients cell is
removed and retained. The cell body of
the patients cell is discarded.
5. The nucleus from the patients cell is
transferred to the enucleated cell body.
6. The cells then stimulated to divide
forming a clone.
7. The cell mass forms a blastocyst.
8. The inner cell mass becomes a source
of totipotent stem cells. Totipotent
means they are capable of being
stimulated to become one of any type of
cell.
9. Cells are stimulated using differentiation factors to become the type of cell
required for therapy.
10. Therapy would require the transfer of the new healthy cell to the patient. In
therapeutic cloning these cells have the same immune system identity as the patient
therefore there is not immune rejection problem.
It is important that this technique is not confused with embryonic stem cell cultures
or with reproductive cloning.
PROKARYOTIC CELLS
The general size of a prokaryotic cell is
about 1-2 um.
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Note the absence of membrane
bound organelles
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There is no true nucleus with a
nuclear membrane
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The ribosome's are smaller than
eukaryotic cells
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The slime capsule is used as a
means of attachment to a surface
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Only flagellate bacteria have the flagellum
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Plasmids are very small circular pieces of DNA that maybe transferred from
one bacteria to another.
top
2.2.2 Function of the Prokaryotic cell parts
Cell Wall:
Made of a murein (not cellulose), which is a glycoprotein or peptidoglycan (i.e. a
protein/carbohydrate complex). 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 is still used today to identify and classify bacteria. We now know that the
different staining is due to two types of cell wall
Plasma membrane:
Controls the entry and exit of substances, pumping some of them in by active
transport.
Cytoplasm:
Contains all the enzymes needed for all metabolic reactions, since there are no
organelles.
Ribosome:
The smaller (70 S) type are all free in the cytoplasm, not attached to membranes
(like RER). They are used in protein synthesis which is part of gene expression.
Nucleoid:
Is the region of the cytoplasm that contains DNA. It is not surrounded by a nuclear
membrane. DNA is always a closed loop (i.e. a circular), and not associated with any
proteins to form chromatin.
Flagella:
These long thread like attachments are generally considered to be for movement.
They have an internal protein structure that allows the flagella to be actively moved
as a form of propulsion. The presence of flagella tends to be associated with the
pathogenicity of the bacterium. The flagella is about 20nm in diameter. This
structure should not be confused with the eUkaryotic flagella seen in protoctista.
Pilli:
These thread like projections are usually more numerous than the flagella. They are
associated with different types of attachment. In some cases they are involved in the
transfer of DNA in a process called conjugation or alternatively as a means of
preventing phagocytosis.
Slime Capsule:
A thick polysaccharide layer outside of the cell wall, like the glycocalyx of
eukaryotes. 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 in a colony fuse together forming a mass of sticky cells
called a biofilm. Dental plaque is an example of a biofilm.
Plasmids:
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Extra-nucleoid DNA of up to 400 kilobase pairs. Plasmids can self-replicate
particularly before binary fission.
They are associated with conjunction which is horizontal gene transfer.
It is normal to find at least one anti-biotic resistance gene within a plasmid.
This should not be confused with medical phenomena but rather is an
ecological response to other antibacterial compounds produced by other
microbes. Commonly fungi will produce anti-bacterial compounds which will
prevent the bacteria replicating and competing with the bacteria for a
resource.
CONJUGATION OR BINARY FISSION
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Direct contact between bacterial cells in which plasmid DNA is transferred
between a donor cell and a recipient cell.
There is no equal contribution to this process, no fertilisation and no zygote
formation. It cannot therefore be regarded as sexual reproductiON.
The process of binary fission takes place in four stage:
(a). Reproduction signal: The cell receives a signal,
of internal or external origin that initiates the cell
division.
E.coli replicates about once every 40 minutes when
incubated at 37o C. If however we increase the
concentration of carbohydrate nutrients that the cell
is supplied with then the division time can be reduced
to 20 minutes. There is a suggestion here that an
external signal (nutrient concentration) is acting as
the reproductive signal.
(b). Replication of DNA: bacterial cells have a single
condensed loop of DNA. This is copied by a process
known as semi-conservative replication to produce
two copies of the DNA molecule one for each of the
daughter cells
The replication begins at a single point on the loop of
DNA. The process proceeds around the loop until two
loop have been produced, each a copy of the original.
The process finishes at a single point on the loop of
DNA .
(c). Segregation of DNA: One DNA loop will be
provided for each of the daughter cells.
(d). Cytokinesis: Cell separation. This occurs once
the DNA loop replication and segregation is complete.
The DNA completes a process of condensing whilst the plasma membrane begins to
form a 'waist' or constriction in the middle of the cell. As the plasma membrane
begins to pinch and constrict the membrane fuses and seals with additional new
membrane also being formed.
EUKARYOTIC CELL
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N:Nucleus
PM: plasma
membrane
M: mitochondria
rER: Rough
endoplasmic
reticulum
GA: Golgi
apparatus
L: Lysosome
MV: Microvilli
Nucleus: This is the largest of the organelles. The nucleus contains the chromosomes
which during interphase are to be found the nucleolus.
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The nucleus has a double membrane with
pores(NP).
The nucleus controls the cells functions through the
expression of genes.
Some cells are multi nucleated such as the muscle
fibre
Nucleus:
In an electron micrograph the nucleus will be the largest of
the organelles.
In this image there is a dark stained region celled the
nucleolus which is the location of the DNA.
The membrane has pores which allow the entry of cell
signal molecules, nucleotides and the exit of mRNA.
Generally the nucleus appears spherical however there are
cells in which the nucleus has more unusual shape such as the multi-lobbed white
blood cells.
Plasma membrane: controls which
substances can enter and exit a cell. It is a
fluid structure that can radically change
shape.
The membrane is a double layer of water
repellant molecules.
Receptors in the outer surface detect signals
to the cell and relay these to the interior.
The membrane has pores that run from the
cytoplasm to the surrounding fluid.
Plasma membrane:
This image shows the junction between two
liver cells. The image has been manipulated
for clarity to see the two adjoining plasma
membranes.
Notice the mitochondria to the left and the
rER to the right of the membranes.
Mitochondria: location of aerobic
respiration
Double membrane organelle.
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Inner membrane has folds
called cristae. This is the site
of oxidative phosphorylation.
Centre of the structure is
called the matrix and is the
location of the Krebs cycle.
Oxygen is consumed in the
synthesis of ATP on the inner
membrane
The more active a cell the
greater the number of mitochondria.
Mitochondria:
This micrograph of a mitochondria
shows:
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Double outer membrane
Folded inner membrane
called the cristae.
Matrix of the mitochondria
These features are common to all
mitochondria. Notice the rER above
the mitochondria for scale and the
dark granules of glycogen below the
organelle.
Rough endoplasmic reticulum (rER):
Protein synthesis and packaging into
vesicles.
rER form a network of tubules with a maze
like structure.
In general these run away from the nucleus
The 'rough' on the reticulum is caused by the
presence of ribosomes.
Proteins made here are secreted out of the cell
Endoplasmic reticulum (rER).
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A cell with a great deal of rER
is producing proteins for
secretion outside of the cell.
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The network of tubules allows proteins to be moved around within the
cytoplasm before final packaging and secretion.
Ribosomes: the free ribosome produces proteins
for internal use within the cell.
Golgi apparatus: modification of
proteins prior to secretion.
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proteins for secretion are
modified
possible addition of
carbohydrate or lipid
components to protein
packaged into vesicles for
secretion
Golgi apparatus:

The golgi apparatus in the
diagram forms a stack of
membrane envelopes on top of
each other.
Vesicles containing
proteins fuse with the
structure.
 The proteins are
modified inside the
apparatus usually with the addition of non-protein substances.
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Lysozyme:
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Vesicles in the above diagram that form on the Golgi apparatus.
Contain hydrolytic enzymes.
Functions include the digestion of old organelles, engulfed bacteria and
viruses.
simple membrane bound vesicle containing hydrolytic enzymes
Produced in the Golgi apparatus.
Used to digest engulfed bacteria or viruses or old organelles
Used to digest macromolecules.
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Hydrolytic enzymes are retained within the vesicle membrane to prevent auto
digestion of the cell.
Comparison of prokaryotic and eukaryotic cell structure.
Comparison of plant and animal cell structure.
Chloroplast:
Note the:double
membrane,
internal thylakoid
membranes which
contain the
chlorophyll.
Stroma where the
calvin cycle fixes
CO2 into
carbohydrates,
oils or starch.
Vacuole
The
vacuole is
a storage
area for
organic
solute
such as
sugars and
amino
acids.The
vacuole is
surrounde
by a
membrane
called the tonoplast which has essentially the same structure as the plasma
membrane.
EXTRACELLULAR COMPONENTS
Cell Wall:
Plant cell walls are composed of cellulose
In the electron micrograph we can see cytoplasmic connections through adjacent
cells. These are called plasmodesmata.
Extracellular components
a) Plant cell wall.
Found around all plant cells
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Composed of cellulose.
Maintains the shape of the cell.
Provides structural support
against the force of gravity.
prevents excessive uptake of
water by the cell
b) Animal extracellular matrix
i) Basement membrane: a secretion formed from collagen and glycoproteins joined
together by a third 'linkage' protein. Their exact composition varies form tissue to
tissue.
Support: the membrane surrounds the tissues of lines ducts. It provides structural
support for the integrity of the tissue or organ. Usually found as the basal lamina or
basement membrane of epithelial cells.
Filter : The basement membrane of the kidney glomerulus provides the effective
barrier for ultrafiltration
Vascular niche : Interestingly cells often require a base on which to organise before
they will form proper tissue. There are implications here for developmental biology,
tissue repair, stem cell therapies and cancer treatment.
ii) Interstitial matrix:
Bone has a matrix which includes collagen with a
calcium phosphate.
Other tissues are surrounded by a matrix
composed of a kind of gel that provides support
for the tissue.
HOLY TRINITY COLLEGE
IB BIOLOGY – STUDY GUIDE: CELLS 3
Membranes
21.
Draw and label a diagram to show the structure of membranes.
22.
Explain how the hydrophobic and hydrophilic properties of phospholipids help
to maintain the structure of cell membranes.
23.
List the functions of membrane proteins.
24.
Define diffusion and osmosis.
25.
Explain passive transport across membranes by simple diffusion and facilitated
diffusion.
26.
Explain the role of protein pumps and ATP in active transport across
membranes.
27.
Explain how vesicles are used to transport materials within a cell between the
rough endoplasmic reticulum, Golgi apparatus and plasma membrane.
28.
Describe how the fluidity of the membrane allows it to change shape, break
and re-form during endocytosis and exocytosis.
Cell division
29.
Outline the stages in the cell cycle, including interphase (G1, S, G2), mitosis
and cytokinesis.
30.
State that tumours (cancers) are the result of uncontrolled cell division and
that these can occur in any organ or tissue.
31.
State that interphase is an active period in the life of a cell when many
metabolic reactions occur, including protein synthesis, DNA replication and an
increase in the number of mitochondria and/or chloroplasts.
32.
Describe the events that occur in the four phases of mitosis (prophase,
metaphase, anaphase and telophase).
33.
Explain how mitosis produces two genetically identical nuclei.
34.
State that growth, embryonic development, tissue repair and asexual
reproduction involve mitosis.