Key Issues:

1. What is the significance of compartmentalization within the cell?

2. What is the significance of taking apart the cell?
3. What is the significance of using a more powerful microscope to study cells?

Hypotheses:
1. Compartmentalization allows the cell to carry out its functions efficiently.
2. Compartmentalization facilitates distribution of labour within the cell.
3. It allows the compartments to be identified and observed in more detail.
4. A more powerful microscope will allow for the structures within the cell to be seen in greater
detail.

Student Generated Learning Objectives:

1. Describe the ultrastructure of the eukaryotic cell.
Nucleus (6 m)
Largest organelle of the cell often located in the central part of the cytoplasm.
Enclosed in a double layered nuclear membrane (nuclear envelope). This membrane
separates the nucleoplasm ( fluid inside nucleus) from the cytoplasm (fluid outside the
nucleus).
Usuall corresponds to the shape of the cell it is found in.
Contains 1. Nucleolus/ nucleoli (produces ribosomal subunits). Small ribosomal subunit
reads RNA (Translation). Large ribosomal sub unit joins a.a to form a polypeptide chain.
2. Chromatin (DNA): efficiently packages DNA into small volume to fit into nucleus of
the cell and protect the DNA structure and sequence. Packaging DNA into chromatin
allows for mitosis/ meiosis, prevents chromosome breakage and controls gene expression
and DNA replication.
Nuclear Envelope perforated by pores (3000 4000): facilitates communication between
nucleus and cytoplasm; transport/ regulation of movement of molecules from nucleus to
cytoplasm e.g carbohydrates, lipids, ribosomes.
Ployribosomes attached to outermembrane of nuclear enevelope (produces many
polypeptides via several ribosomes translating a single mRNA).

Cytoplasm
Fluid component of cytoplasm is cytosol (pH 7.2). Cytosol makes up about 70% of the
cell volume and is a complex mixture ofcytoskeleton filaments, dissolved molecules, and
water. The cytosol's filaments include the protein filaments such as actin
filaments and microtubules that make up the cytoskeleton, as well as soluble proteins and
small structures such as ribosomes, proteasomes.
Ribosomes (20- 30 nm)

Ribosome is composed of rRNA and about 80 different proteins. It usually occur in two
subunits, large and small subunits. The rRNA of the ribosome is synthesised in the
nucleus while its protein is synthesised in the cytosol. Ribosomes are involved in protein
synthesis. While cytosolic proteins (free proteins) are synthesised by polyribosomes,
secretory and endoplasmic reticulum proteins are synthesised on the membrane of rough
endoplasmic reticulum.
Mitochondrion
Mitochondria are membrane-bound enzyme storage organelles. Mitochondrial enzymes
are involved in aerobic respiration, in which Pyruvate is oxidised to carbon dioxide and
water, leading to the production of: ATP (15 times more than Glycolysis) and Heat
energy for maintenance of body temperature The mitochondrion is enclosed in two
sheets of membrane. An outer sieve-like unfolded membrane and An inner membrane
which is thrown into long fingerlike folds called cristae. The number of cristae
corresponds to the cells energy needs. The space between the two membranes is the
intermembranous space while the space deep to the inner membrane is referred to as the
matrix.
Mitochondria are eosinophilic, elongated rod-like organelles measuring 0.5 to 1 micron
in diameter and 5 to 10 micron in length. They are wildly distributed in all cells but
occur abundantly in cell with very high energy needs (Heart muscles and kidney cells).
Integral proteins of the outer and inner membrane provide channels for selective passage
of small molecules, while Enzymes in the matrix and on the surface of the inner
membrane are involved in the production of ATP and heat for the cell.
The Matrix also contains Chromosomes, DNA, Ribosomes, Messenger RNA and
Transfer RNA which are utilized in the synthesis of small amount of proteins for use
within the matrix.

Lysosome

Membrane bound organelle. Interior pH 5.

Hydrolytic enzymes present in lysosome breaks down bacteria, denatured proteins
(Intralysosomal digestion).
Extracellular digestion e.g osteoclast breaking down bone matrix releasing minerals for
remodelling.
Autophagosome: Organelles and certain cytoplasmic components might become enclosed
in membrane and subsequently fused with lysosome to form Autolysosome. This
phenomena is referred to as Autophagy.
Hetrolysosome: This is the product of the fusion of lysosome with membrane-bound
endocytosed material. External structure> endocytosis> material fused with lysosome.
Residulal body: This is heterolysosome containing indigestible materials such as
lipofuscin granules of the neuron and heart muscles.

Proteasomes

cytoplasmic protein complexes.

Identifies faulty proteins (no benefit to the cell), degrades them to amino acids to form
better proteins or even terminates some enzymatic proteins. Ubiquintin molecules forms a
complex with the protein which needs to be altered and with the aid of ATP, breaks down
the protein.
Peroxisome
Peroxisomes are membrane-bound organelles which contain various enzymes and utilise
oxygen without the production of ATP. Measuring about 0.5 micron in diameter they
oxidise organic substrate by the removal of hydrogen ions, leading to the production of
H2O2. This is immediately broken down by peroxisomal catalase to prevent its toxic
effect on the cell. The oxygen atom released from this process is utilized in oxidation of
other potentially toxic substances/drugs in the liver (Ethyl alcohol) and kidneys.
Peroxisomes are also implicated in lipid metabolism (Beta oxidation of long-chain [18
carbon and over] fatty acids).
Endoplasmic Reticulum
made up of anastomosing network of intercommunicating channels/cisternae/sacs
enclosed in a continuous membrane. Extension of tubes into nuclear pores facilitates
communication.
RER is prominent in protein synthesising cells such as; Pancreatic acinar cells, cells of
the endocrine glands, plasma cells, fibroblast etc. Proteins synthesised in RER are stored
in Lysosomes or granules; stored temporarily before exocytosis or used as integral
membrane proteins.
SER involved in synthesis phospholipids and cholesterol used in all cellular membranes
including membranes of organelles.
Golgi Apparatus
complex of smooth membranous saccule usually located between the apical membrane
and the nucleus of the secretory cell. Within its saccule are various enzymes implicated in
processing proteins synthesised in the endoplasmic reticulum. The Golgi apparatus
receives transport vesicles containing proteins from the endoplasmic reticulum and
packages modified proteins into condensing vesicles for transportation to other organelle
or to the cell membrane for release of modified proteins as secretory products. Protein
modification occurring in the Golgi apparatus includes concentration, glycosylation,
sulfation, phosphorylation and proteolysis. Vesicle attaches to membrane, breaks up,
releases out of cell (exocytosis).
Cytoskeleton
composed of a complex of microtubules, microfilaments (Actin Filaments), and
Intermediate Filaments.
Microtubules: tubular protein subunits involved in cellular shape, cell division, intra and
extra cellular movements and transport of substances in the cytoplasm of the cell.
Cytoplasmic microtubules for intracellular transport of materials including organelles.
Centrioles which are involved in cell division. Mitotic spindles which are involved in cell
division. Cilia and Flagella which are motile structures implicated in cellular motion.

Microfilaments: Microfilament is a double-stranded helix of globular protein subunits

which is widely distributed in all body cells and is involved in the structural integrity and
contractility of the cell as well as movement of organelles in the cytosol. Actin filaments
are also implicated in cell cleavage during cell division.
Intermediate filaments: strength, protection and for structural integrity e.g. Keratin of
epithelial cell for strength and protection.
Centrosome/ Centrioles: The centrosome is the region of the cytosol situated between the
nucleus and the Golgi apparatus. It accommodates the Centrioles which are two
cylindrical shaped microtubular structures oriented at right angles to one another. Each
cylinder is made up of nine triplets of parallel microtubules. Centrioles are implicated in
organising the microtubules of the cell as in the organization of mitotic spindles during
cell division. They also form the basal bodies of cilia and flagella.
Inclusion Bodies
transitory residents of the cytoplasm not involved in cell metabolism and do not survive
cell division. They comprise mainly accumulated metabolites, lipid droplets and pigments
and are sporadically distributed in body cells. E.g. Fat droplet of the adipocytes, liver
cells and cells of the adrenal cortex. Pigments: These include: Lipofuscin, golden-brown
pigments which are found only in stable and non-dividing cells where they accumulate
progressively with age and thus used to determine cells age. They derived from the
residual bodies following lysosomal digestion.

2.Describe the structure of the plasma membrane.

Plasmalemma (7.5nm- 10nm): External boundary of the cell. Composed of proteins,

carbohydrates, lipids, cholesterol.
Intrinsic proteins penetrate and bind tightly to the lipid bilayer, which is made up largely
of phospholipids and cholesterol and which typically is between 4 and 10 nanometers
(nm; 1 nm = 109 metre) in thickness. Extrinsic proteins are loosely bound to the
hydrophilic (polar) surfaces, which face the watery medium both inside and outside the
cell. Some intrinsic proteins present sugar side chains on the cells outer surface.
integral proteins which traverse the thickness of the membrane and peripheral
proteins which are adsorbed to the outer or inner surfaces of the membrane. Peripheral
proteins are involved in: Cell recognition and Cell interactions, Integral proteins:
Regulate passage of material and Active transport of specific molecules across the
membrane.
Phospholipid bi layer; middle is hydrophic due to non polar tails and upper are
hydrophilic because of polar heads.
Cholesterol helps maintain the fluidity of the membrane.

2. Describe the structure and properties of lipids.

Phospholipids consist of a hydrophilic (or 'water loving') head and a hydrophobic (or
'water fearing') tail. Phospholipids like to line up and arrange themselves into two parallel
layers, called a phospholipid bilayer.

Simple Lipids:
On hydrolysis gives fatty acids and alcohol (trihydric or monohydric)

Oils: Unsaturated fatty acid + glycerol.

Fats: Saturated fatty acids + glycerol,
Waxes: Fatty acids + mono or dihydric alcohol.
Simple glyceride: Contains same fatty acids. .
Mixed glyceride: Contains different fatty acids.

2) Compound lipids: (Complex lipids):

On hydrolysis gives phosphoric acid, various sugars, sphingosine, ethanolamine and
serine in addition to fatty acids and glycerol.

a) Phospholipid: Fatty acids + glycerol + phosphoric acid + nitrogenous base.

e.g. Lecithin :Fatty acids + glycerol + phosphoric acid + choline
Cephalin: Fatty acids + glycerol + phosphoric acid + ethanolamine.

b) Glycolipids: Glycerol + fatty acid + Carbohydrates (on hydrolysis)

They are sub classified as galactosyl diglyceride, cerebrosides and sulpholipids.

c) Sphingophosphoiplds: Fatty acids + sphingosine + phosphoric acid + choline.

3) Derived Lipids: Hydrolytic products of simple and compound lipids

i) Alcohols: Glycerol and other sterol

ii) Fatty acids
iii) Terpenoids

Properties: Insoluble in soluble; soluble in organic solvents. Energy Storage.

3. Describe the structure and properties of carbohydrates.

Carbohydrates consist of the elements carbon (C), hydrogen (H) and oxygen (O) with a
ratio of hydrogen twice that of carbon and oxygen. Carbohydrates include sugars,
starches, cellulose.
Monosaccharides are the simplest carbohydrates and are often called single sugars. They
are the building blocks from which all bigger carbohydrates are made. (CH2O)n e.g. glucose,
glactose, fructose.

Most sugars found in nature are disaccharides. These form when two monosaccharides
react.(Condensation) e.g. sucrose, maltose, lactose.
Monosaccharides can undergo a series of condensation reactions, adding one unit after
another to the chain until very large molecules (polysaccharides) are formed. This is

called condensation polymerisation, and the building blocks are called monomers.e.g
starch, glycogen, cellulose.
Properties: Energy

4. Discuss the correlation between compartmentalization and function of the cell.

Enclosing DNA in the nucleus protects it and allows post transcriptional modifications to
the mRNA to occur before translation into a protein takes place in the cytosol.
hydrolytic enzymes in lysosomes have a lower optimum pH - the pH of a lysosome can
be lowered by H+ ATPase pumps in the membrane pumping H+ in. pH of the interior of
the lysosome is 5. pH of cytosol is 7.2. The hydrolytic enzymes are inactive in the
cytosol. Because of the cytosols pH of 5, it allows the hydrolytic enzymes to be active
allowing it to breakdown bacteria, denatured proteins. (Intralysosomal digestion).
They are both part of the endomembrane system.
When a cell makes proteins, it starts by transcribing RNA from the DNA located inside
its nucleus. RNA is then carried out of the nucleus into the rough endoplasmic reticulum.
There, the RNA meets up with a ribosome, which are attached to the ER. Though the
process of Translation, the endoplasmic reticulum makes polypeptides, which then fold
into the proper shapes to make proteins. RER is prominent in protein synthesising cells
such as; Pancreatic acinar cells, cells of the endocrine glands, plasma cells, fibroblast etc.
Proteins synthesised in RER are stored in: Lysosomes as enzymes or Granules where they
are stored temporarily before exocytosis or Used as integral membrane proteins. The
Golgi apparatus receives transport vesicles containing proteins from the endoplasmic
reticulum and packages modified proteins into condensing vesicles for transportation to
other organelle or to the cell membrane for release of modified proteins as secretory
products.

5. Discuss the correlation between compartmentalization and metabolism of the cell.

Compartmentalization of the cell contributes to the overall enhanced efficiency of

metabolism of the cell.

6. Discuss the benefits of using more powerful microscope vs a light microscope for viewing a
eukaryotic cell.
A more powerful microscope will have a higher resolution than a light microscope.
Therefore they are able of higher magnifications e.g. transmission electron microscope up
to 10 million times mag. While light microscope has up to 1000- 2000 mag. A more
powerful microscope will allow for the visualization of structures that would normally be
not visible by optical microscopy. E.g. the very atoms that make up the compartments
and hence the cell can be seen under an electron microscope.
Allows for three dimensional visualization of compartments.

7. Discuss the processing of cells for microscopic studies.

Basic Cell Staining:

Cell staining is a technique that can be used to better visualize cells and cell components under a
microscope. By using different stains, one can preferentially stain certain cell components, such
as a nucleus or a cell wall, or the entire cell.

Permeabilization - treatment of cells, generally with a mild surfactant, which dissolves cell
membranes in order to allow larger dye molecules to enter inside the cell.e.g methanol,
acetone (organic solvents dissolve lipids from cell membranes making them permeable).
Fixation - serves to "fix" or preserve cell or tissue morphology through the preparation
process. This process may involve several steps, but most fixation procedures involve adding a
chemical fixative that creates chemical bonds between proteins to increase their rigidity.
Common fixatives include formaldehyde, ethanol, methanol, and/or picric acid. Alcohol based
fixations dehydrate cells/tissues, causing proteins to denature and precipitate in situ.
Paraformaldehyde causes covalent cross-links between molecules, effectively gluing them
together into an insoluble meshwork.
Mounting - involves attaching samples to a glass microscope slide for observation and
analysis. Cells may either be grown directly to the slide or loose cells can be applied to a slide
using a sterile technique. Thin sections (slices) of material such as tissue may also be applied
to a microscope slide for observation.

Staining - application of stain to a sample to color cells, tissues, components, or metabolic

processes. This process may involve immersing the sample (before or after fixation or
mounting) in a dye solution and then rinsing and observing the sample under a microscope.
Some dyes require the use of a mordant, which is a chemical compound that reacts with the
stain to form an insoluble, colored precipitate. The mordanted stain will remain on/in the
sample when excess dye solution is washed away.
Eosin - a counterstain to haematoxylin, this stain colors red blood cells, cytoplasmic material,
cell membranes, and extracellular structures pink or red.
Fuchsin - this stain is used to stain collagen, smooth muscle, or mitochondria.
Methylene blue - stains animal cells to make nuclei more visible.

Electron Microscopy

1. Sections of Embedded Material

Biological material contains large quantities of water. Since the TEM works in vacuum, the water must be
removed. To avoid disruption as a result of the loss of water, preserve the tissue with different fixatives.
These cross-link molecules with each other and trap them together as stable structures. The tissue is then
dehydrated in alcohol or acetone.
After that, specimen can be embedded in plastic that polymerize into a solid hard plastic block. The block
is cut into thin sections by a diamond knife in an instrument called ultramicrotome. Each section is only
50-100 nm thick.
The thin sections of your sample is placed on a copper grid and stained with heavy metals e.g. mercury,
chromium, lead. The slice of tissue can now be studied under the electron beam.