IB DP Bio - A 2.2 Cell Structure - Student Notes
IB DP Bio - A 2.2 Cell Structure - Student Notes
IB DP Bio - A 2.2 Cell Structure - Student Notes
2 SL Cell structure
Guiding Questions
“What are the features common to all cells and the features that differ? ”
Syllabus Objectives
Students should be aware that deductive reason can be used to generate predictions from theories. Based on
Cells as the basic structural
A2.2.1 cell theory, a newly discovered organism can be predicted to consist of one or more cells.
unit of all living organisms
Students should have experience of making temporary mounts of cells and tissues, staining, measuring sizes
Microscopy skills & using an eyepiece graticule, focusing with coarse & fine adjustments, calculating actual size & magnification,
A2.2.2
calculating magnification producing a scale bar & taking photographs.
Developments in Include the advantages of electron microscopy, freeze fracture, cryogenic electron microscopy, and the use of
A2.2.3
microscopy fluorescent stains & immunofluorescence in light microscopy.
Structures common to cells Typical cells have DNA as genetic material and a cytoplasm composed mainly of water, which is enclosed by a
A2.2.4 plasma membrane composed of lipids. Students should understand the reasons for these structures.
in all living organisms
Include these cell components: cell wall, plasma membrane, cytoplasm, naked DNA in a loop and 70S
ribosomes. The type of prokaryotic cell structure required is that of Gram-positive eubacteria such as Bacillus
A2.2.5 Prokaryote cell structures and Staphylococcus. Students should appreciate that prokaryote cell structure varies. However, students are not
required to know details of the variations such as the lack of cell walls in phytoplasmas and mycoplasmas.
Students should be familiar with features common to eukaryote cells: a plasma membrane enclosing a
compartmentalized cytoplasm with 80S ribosomes; a nucleus with chromosomes made of DNA bound to
A2.2.6 Eukaryote cell structures histones, contained in a double membrane with pores; membrane-bound cytoplasmic organelles including
mitochondria, endoplasmic reticulum, Golgi apparatus and a variety of vesicles or vacuoles including lysosomes;
and a cytoskeleton of microtubules and microfilaments.
Processes of life in Include these functions: homeostasis, metabolism, nutrition, movement, excretion, growth, response to stimuli
A2.2.7 and reproduction.
unicellular organisms
Differences in eukaryotic Include presence and composition of cell walls, differences in size & function of vacuoles, presence of
A2.2.8 cell structure between chloroplasts and other plastids, and presence of centrioles, cilia and flagella.
animals, fungi and plants
Atypical cell structure in Use numbers of nuclei to illustrate one type of atypical cell structure in aseptate fungal hyphae, skeletal muscle,
A2.2.9
eukaryotes red blood cells and phloem sieve tube elements
Students should be able to identify cells in light or electron micrographs as prokaryote, plant or animal. In
Cell types and cell
electron micrographs, students should be able to identify these structures: nucleoid region, prokaryotic cell wall,
A2.2.10 structures viewed in light nucleus, mitochondrion, chloroplast, sap vacuole, Golgi apparatus, rough and smooth endoplasmic reticulum,
and electron micrographs
chromosomes, ribosomes, cell wall, plasma membrane and microvilli.
Students should be able to draw and annotate diagrams of organelles (nucleus, mitochondria, chloroplasts, sap
Drawing and annotation
vacuole, Golgi apparatus, rough and smooth endoplasmic reticulum and chromosomes) as well as other cell
A2.2.11 based on electron
structures (cell wall, plasma membrane, secretory vesicles and microvilli) shown in electron micrographs.
micrographs
Students are required to include the functions in their annotations.
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Cells as the basic structural unit of all living organisms
Are they all biological cells? Discuss with a partner: nope, even if one of them does contain a living organism
Cell theory:
Scientists have agreed on some key principles for cells to be biologically defined as cells. These principles can be
summarized as the cell theory and are based on 3 main pillars. Can you elaborate on each of them?
multicellular
cells are the smallest units of life -> organelles carry out
survive alone
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water containing all those enzymes
Structures common to cells in all living organisms: etc...
-------- DNA
In addition to these basic principles of life, there are some
structures which are common to cells in all living
organisms. They all have a cell membrane, genetic
material and cytoplasm.
ribosomes
(needed to produce proteins)
cells will divide, genetic material will give info to all metaboli=
=sm and to cell division.
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Microscopy skills & calculating magnification
In order to visualize cells it is best to use a microscope with a decent enough magnification. In schools, typically
a light microscope is good enough to view plant and animal cells accurately enough.
arm (to carry it)
Label the parts of the microscope:
ocular lesnses
revolver
fine F.K
light source
stage manip.
the base
light switch
Magnification:
When using microscopes to measure cells sizes, there are two different magnifications to consider.
1. Magnification of the
microscope, which is the
magnification of the image
when viewed down a
microscope.
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1. Determining the size of a cell using an eyepiece graticule:
Eyepiece graticule scale in Eyepiece graticule scale over a human We will not know the actual size of the
birds eye perspective when cheek epithelial cell. The cell lies between eyepiece units until the eyepiece graticule scale
looking through the 40 and 60 on the scale. We therefore say it is calibrated. To calibrate the eyepiece graticule
microscope. measures 20 eyepiece units in diameter scale, a miniature transparent ruler called a
(the difference between 60 and 40). stage micrometer scale is placed on the
microscope stage and is brought into focus.
Worked example:
_________
1 mm 1000microm. 32 units >>>> 1 unit = 31.25nanom.
> aka 26 micrometers for S. V. A. magnification x4 (x40) range: 3125microm.
> aka 32 micrometers for G. R.
1000microm. 26 units >>>> 1unit = 38.46microm.
magnification x4 (x40) range: 3848microm.
In 1mm we have 1000micrometers
a. What is the total scale length of the eyepiece graticule shown above_________
690 μm
b. What is the length of one minor/small division of the eyepiece graticule therefore: _______
6.9 μm
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Activity:
1. Collect a microscope and place the stage micrometer on the stage of your microscope.
2. Start with the lowest power of magnification (4x objective lens) and search for the stage micrometer
ruler with a scale of 1DIV = 0.01mm.
3. Once you have both little rulers in focus, change the power of magnification first to 10x, then to 40x.
Each time, make sure you can focus in on both rulers.
4. Calibrate the eyepiece graticule by following these steps:
a. Align the stage micrometer with the eyepiece graticule.
b. Measure the total length of the eyepiece scale as in the worked example above.
What is the total scale length of the eyepiece graticule at your magnification_________ μm
What is the length of one minor division of the eyepiece graticule therefore: _______ μm
5. Remove the stage micrometer you used in the previous exercise from the stage of the microscope.
6. Peel a single layer of onion cells from the of an onion, mount it on a glass slide, add a drop of water and
cover it with a cover slip. Dab off any excess water with a tissue.
7. Place the microscope slide on the stage of your microscope and start focusing in using the smallest
power of magnification (4x). Increase the power of magnification to 40x and focus on a few cells.
8. Accurately draw one onion cell on a piece of paper (or in the space provided on the next page). Write
down the cell size of your onion cell you measure using the eyepiece graticule. Repeat the same
procedure with a plant cell (or another suitable sample).
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2. Calculating magnification of a cell drawing:
Combining our knowledge of how to deduce the actual size of a specimen we viewed under the microscope
with our drawing skills of a biological sample, we can now work out at which magnification we have actually
drawn the image:
1. Using the image, you have just produced, draw a straight line below the cell to measure the total length
in cm or mm, just like shown in the example below.
Practice examples :
1. If a red blood cell has a diameter of 8 µm and a student shows it with a diameter of 40 mm in a drawing,
what is the magnification of the drawing?
A. × 0.0002
B. × 0.2
C. ×5
D. × 5000 (Total 1 mark)
2. A student observes and draws an Amoeba, using the high power lens of a microscope. The diameter of the
drawing is 100 mm. The actual diameter of the Amoeba is 100 µm. What is the magnification of the drawing?
A. 0.001
B. 100
C. 400
D. 1000 (Total 1 mark)
3. A sperm cell has a tail 50µm long. A student draws it 75mm long. What is the magnification?
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3. Calculating magnification using scale bars
Calculate the magnification of the image and explain how you went on about to do this: :
Practice examples:
How can these scale bars be used to calculate the magnification of the images?
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4. Calculating the actual size of a specimen using the scale bar:
Scale bars can not only be used to calculate the magnification of the image, but also the actual size of the
organism seen in the image. What is the actual size of the weevil?
Calculate the actual size of the cell if you know the magnification of the image:
1. Measure the length of the specimen
2. Re-arrange the formula:
3. Divide the measured length (in the most appropriate units) by the magnification.
Worked example:
1. Measure the length of the weevil in the picture.
2. Write down the magnification of the image you have calculated before: ___________________
2. Re-arrange the equation from above or use the triangle to work out the actual size of the weevil:
You could also calculate the actual size by factoring the scale bar length against the length of the weevil. Can
you show how to do that?
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Practice examples:
1. A student views an image of a cell magnified 350 times. The image is 250mm long. What is the actual
length of the sample in the image?
2. The image below shows a student’s drawing of a plant cell. Based on their measurements with the
eyepiece graticule the student calculated the magnification of the drawing. Unfortunately they lost the
calclulations showing measured and actual sizes. Work out the real size of the plant cell.
1. Calculate the actual sizes of a) one mitochondrion and b) the biggest skin cell using the scale bars:
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Development in microscopy:
Many of the most interesting biological events and structures are smaller than the unaided human eye can see.
In fact, human eyes have a resolution of about 100 µm. On the chart below, notice that of all the structures
listed, only the plant cell is within our resolution--just barely.
Light microscopes only magnify images up to ca. 1000 times. This is due to the wavelengths of light which
only allow to distinguish between two points to a certain limit. Why are electron microscopes better used to
view very small specimen or samples?
because they can magnify up to a million times thanks to the beams of electrons with shorter wavelengths, instead
of light
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Resolution:
10 micrometers = 10000 nm
light microscopes
only work in
the visible light
spectrum.
the radiation (the type of light or energy source) used to view the
sample.
Objects much smaller than the wavelength of the radiation being used do not interrupt the waves, and so are
not detected. A microscope with a more powerful magnification will not increase the resolution any further. It
will increase the size of the image, but objects closer than about 200nm will still only be seen as one point.
Read through the information on the different types of microscopes below and complete the table:
Electron microscopes
Light (optical microscopes)
Transmission (TEM) Scanning (SEM)
it's more accessibile -> cheaper magnifies up to 1 million times
Advantages
dead tissue
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1. The light microscope
The light microscope doesn’t have
a very high resolution and only
allows cells or bigger structures to
be visualized. This limit is due to
the wavelength of light (400-
700nm). In other words, optical
microscopes cannot resolve 2
points closer together than the
wavelength of light used, so cells
which are smaller than. Cells
observed under a light microscope
can be alive and show their natural
composition, colors, movement,
and appearance. Magnification is
ca. 1000 – 5000x.
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Development in microscopy – Staining of samples:
Even though electron microscopy allows for a high resolution, detail, and higher magnifications, it comes with
the disadvantage of only producing black and white images. Techniques in staining and improved visualization
technology have helped to produce even more advanced images.
The table below gives you an overview over different staining procedures:
Staining with methylenblue
Molecules in cells are colorless when
fewed under the electon microscope, so
stains such as methylene blue to bind
DNA or RNA can be used to visualize the
nucleus ot cytoplasm.
Fluorescent staining
Fluorescent microscopy uses a much
higher intensity light to illuminate the
sample, which then excites flourescently
stained specimen. This emits light at a
longer wavelength.
Immunofluorescent staining
Immunofluorescence uses cells of the
immune system (antibodies) which are
equipped with a flourescent marker.
Upon binding to a target a fluorescent
image can be produced.
Cryogenic microscopy
This preparation technique in
microscopy is used for researching the
structure of proteins. The frozen protein
solution of interest is placed in an
electron microscope and patterns of
many differently orientated proteins are
produced. Using computer algorithms, a
3D image can be created.
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Freeze-fracture of cells
Freeze-fracture electron microscopy is
used to produce images of surfaces
within cells. Rapid freezing of cells in
liquified propane (-190°C) and
subsequent fracturing allows the cell to
be broken along lines of weakness,
including the centre of membranes. Any
structures which appeared globular are
transmembrane proteins.
Which cell structures are stained when using a dye such as methylenblue?
stains such as methylene blue to bind DNA or RNA can be used to visualize the nucleus ot cytoplasm.
visualize them.
Cryogenic microscopy is a new technique which has given insight into the way structures are visualized. Can
you describe how cryogenic microscopy is different from common staining techniques, and what the
advantages of this method are?
cryogenics microscopy freezes a proteins and utilizes advanced comuter algorithms to artificially form a 3D structure
of the protein, at the moment where it is frozen. this allows a scientist to cliearly see the changefrom one form of to
another as they carry out their function, since they are practically frozen in time
Freeze-fracture of cells and subsequent viewing under the microscope has provided information about the
surfaces and plasma membranes of cells – which was important for the understanding of transport
mechanisms in and out of the cell.
Explain how and why cell membranes can easily split apart:
we are using an instant freezing agent, so the weak attractions are breaking down; so inside of the cell, they will
orientate themselves naturally because the hydrophobic tails will split (because the bonds are broken)
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Prokaryotic and Eukaryotic cells:
At one time it was common practice to try to classify all living organisms as either animals or plants. With
advances in our knowledge of living things, it has become obvious that the living world is not that simple. Fungi
and bacteria, for example, are very different from animals and plants, and from each other. Eventually it was
discovered that there are two fundamentally different types of cell.
simpler structures
electron microscope
(prokariotes are much
smaller than eukariotes)
Draw a diagram of the bacillus bacteria and outline cell structures such as plasma membrane, cell wall,
nucleoid, cytoplasm and 70S ribosomes.
70S are small ribosomes. (look up)
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The table below summarizes the structures and functions of a prokaryotic cell:
cell wall
Practice Question:
name Botox®.
2. What causes the cytoplasm of Clostridium to appear so dark in the electron micrograph?
the presence of ribosomes
3. This image is a longitudinal section: You can see a thin slice of the bacterium going from end to end.
What shape would you see in a transverse section (going from side to side)? circular shape
4. There is a scale bar on the micrograph. Use this to calculate the magnification of the micrograph.
22mm measured
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Eukaryote cell structure:
Eukaryotic cells are very diverse in sizes and shapes. They are more complex and typically bigger in size (15 – 100µm). Their interior is
compartmentalized, and they have many membrane-bound organelles such as mitochondria, chloroplasts, nucleus, Golgi apparatus and
Endoplasmic Reticulum. They also have larger ribosomes (80S) than prokaryotes. Eukaryotes can be grouped into 4 categories – 3 of
which we will look at in more detail: Plants, animals and fungus
Draw and label the structures of the three main types of eukaryotic cells:
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Eukaryotes: comparing animal, plant and fungal cells:
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Summary of all the important structures and functions of eukaryotic cells:
Match the cards your teacher gave you and describe the functions for each cell structure:
Organelle Structure Function
Nucleus & Nucleolus
• Contains a double membrane
• Pores (holes) in the membrane
• Holds the DNA which is associated
with histone proteins.
• Uncoiled chromosomes are
referred to as chromatin – they
stain dark in electron micrograph.
• Within the nucleus is the
nucleolus which consists of RNA
and proteins.
Mitochondrion
• Surrounded by double membrane
• Outer membrane is smooth, inner
membrane is folded/invaginated.
• The folds are called “cristae”
• Variable in shape and number
Ribosomes
• 80 S (larger than in prokaryotes)
• Composed of 2 subunits
• No membrane
• Free in the cytoplasm or bound to
Endoplasmic Reticulum (ER)
• Composed of ribosomal RNA and
protein produced in the nucleolus
of the nucleus
• Appear as dark granules
Golgi apparatus
• Only a single membrane
• Consists of flattened sacs called
cisternae, which are stacked on
top of one another
• Has two sides: a cis-side (receives
products at that site), and a trans-
side (discharges products)
• Transport vesicles bud off
• In contrast to the rER it does not
have attached ribosomes, is sited
close to the plasma membrane
and the cisternae are shorter and
more curved than those of rER
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Organelle Structure Function
Vesicles & Vacuoles
• Consist of a single membrane
with fluid inside
• Variable in size – when small:
Vesicles, when big Vacuole
• Plant cells: vacuoles are large and
permanent, often occupying more
than half of the cell.
• Animal cells: small and temporary
filled with materials or food.
Lysosomes
• Formed from Golgi vesicles which
bud off
• Spherical with single membrane
• High concentration of enzymes
(proteins) cause this organelle to
stain heavily and hence appears
dark
• Only in animal cells (plants use
vacuoles)
Cytoskeleton
• Constructed from protein fibers
like tubulin and actin, which are
used to make microtubules and
microfilaments.
Chloroplast
• Double membrane surrounding
the chloroplast
• Stacks of thylakoids inside
• Each thylakoid is a disc composed
of a flattened membrane.
• Variable shape (spherical or ovoid)
Centrioles:
• Consist of two groups of nine
triple microtubules
• Only in animal cells, not present in
plants or fungi
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Compare the structural features of prokaryotes and eukaryotes:
Prokaryotes Eukaryotes
Complexity
Genetic material
Size
Membrane
enclosed
organelles
Uni/multicellular
Size of ribosomes
Compartment-
alization
Examples
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Look at this image and analyse the structures shown. Highlight and label them correctly.
All living organisms carry out the functions of life, even unicellular organism. In multicellular organism some of
the functions are divided up between differently specialized cells.
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Although many living organism are
unicellular, they can carry out all
functions of life. The single-celled
organism Paramecium exemplifies this.
Read the following articles to research on the lifestyle and functions of life of Chlamydomonas:
https://www.seaweed.ie/algae/chlamydomonas.php and https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii
Chlamydomonas
Reproduction
Response
Excretion
Nutrition
Growth
Metabolism Just like Paramecium, Chlamydomonas uses its cytoplasm for many enzyme-controlled
reactions and metabolic pathways such as cellular respiration.
Homeostasis Chlamydomonas also have a contractile vacuole which they can use to control the water
content of the cell.
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Atypical cell structure in eukaryotes:
Do you remember the principles of the cell theory? Some cells do not necessarily comply with all of the
statements, or only under an extended perspective.
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