Topic 1.2- Ultrastructure of Cells
Learning Objectives:
Understandings:
• Prokaryotes have a simple cell structure without compartmentalization.
• Eukaryotes have a compartmentalized cell structure.
• Electron microscopes have a much higher resolution than light microscopes.
Applications and skills:
• Application: Structure and function of organelles within exocrine gland cells
of the pancreas and within palisade mesophyll cells of the leaf.
• Application: Prokaryotes divide by binary fission.
• Skill: Drawing of the ultrastructure of prokaryotic cells based on electron
micrographs.
• Skill: Drawing of the ultrastructure of eukaryotic cells based on electron
micrographs.
• Skill: Interpretation of electron micrographs to identify organelles and
deduce the function of specialized cells.
International-mindedness:
• Microscopes were invented simultaneously in different parts of the world at
a time when information traveled slowly. Modern-day communications have
allowed for improvements in the ability to collaborate, enriching scientific
endeavor.
Electron microscopes have a much higher resolution than light microscopes.
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The limit of resolution is the minimum distance that can be observed before two objects
merge together to form one object. The smaller the limit of resolution the higher the
resolving power.
Electron microscopes have a greater resolution (about .001 µm) when compared to a light
microscope (about 0.2 µm)
The resolution of light microscopes is limited by the wavelength of light (400-700 nm). If
the magnification becomes too great the image becomes blurry
Electrons have a much shorter wavelength so they have much greater resolution (about
200x greater than a light microscope)
Prokaryotes divide by binary fission.
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Binary fission is the form of asexual cell division that results in the reproduction of two
genetically identical prokaryotic cells.
All prokaryotic cells divide by binary fission
Here are the specific details of the functions of cell organelles
Nucleus
Known as the control center of the cell. The nucleus regulates cell activities through gene
expression. Contains the majority of the cell’s DNA. It is surrounded by a double membrane
called the nuclear envelope, which has small nuclear pores to allow molecules to move in and
out of the nucleus
Nucleolus.
The nucleolus is the nuclear subdomain that assembles ribosomal subunits in eukaryotic cells.
The nucleolar organiser regions of chromosomes, which contain the genes for pre‐ribosomal
ribonucleic acid (rRNA), serve as the foundation for nucleolar structure. The nucleolus
disassembles at the beginning of mitosis, its components disperse in various parts of the cell and
reassembly occurs during telophase and early G1 phase. Ribosome assembly begins with
transcription of pre‐rRNA. During transcription, ribosomal and non‐ribosomal proteins attach to
the rRNA. Subsequently, there is modification and cleavage of pre‐rRNA and incorporation of
more ribosomal proteins and 5S rRNA into maturing pre‐ribosomal complexes. The nucleolus
also contains proteins and RNAs that are not related to ribosome assembly and a number of new
functions for the nucleolus have been identified. These include assembly of signal recognition
particles, sensing cellular stress and transport of human immunodeficiency virus 1 (HIV‐1)
messenger RNA.
Key Concepts
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The nucleolus, whose primary function is to assemble ribosomes, is the largest structure
in the cell nucleus.
The nucleolus organizer regions of chromosomes, which harbour the genes for pre‐
rRNA, are the foundation for the nucleolus.
All active nucleoli contain at least two ultrastructural components, the nucleolar dense
fibrillar component representing early pre‐ribosomal complexes and the granular
component containing more mature pre‐ribosomal particles.
Most nucleoli in higher eukaryotes also contain fibrillar centers, which are the interphase
equivalents of the nucleolus organizer regions.
The nucleolus disassembles at the beginning of mitosis and begins to reassemble in
telophase.
Ribosome assembly begins with the transcription of pre‐rRNA by RNA polymerase I.
Ribosomal and non‐ribosomal proteins and 5S RNA associate with the pre‐rRNA during
and after transcription.
The pre‐rRNA is modified and processed into rRNA with the aid of non‐ribosomal
proteins and small nucleolar RNAs.
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The nucleolus has numerous other functions including assembly of signal recognition
particles, modification of transfer RNAs and sensing cellular stress
Nuclear envelope
The nuclear envelope of a cell is a barrier layer that envelopes the contents of the nucleoplasm in
the cells of eukaryotes. Recent research has indicated that the nuclear envelope is not roughly
spherical, as often depicted, but has clefts that dive into the rounded structure to form valley-like
channels and tubules. The nuclear envelope keeps the contents of the nucleus, called the
nucleoplasm, separate from the cytoplasm of the cell. The all-important genetic material, mainly
the DNA is kept separate and relatively safe from the chemical reactions taking place in the
cytoplasm. The separation also makes it possible for chemicals in the nucleus to (1) prepare for
and take part in the replication of genetic material prior to nuclear division and, (2) manufacture
different types of RNA for export to the cytoplasm.
Nuclear pores
A nuclear pore is a minute opening or passage way through the nuclear envelope. It connects the
nucleoplasm (nucleus) with the cytoplasm. The opening is ‘plugged’ with an amazing biological
valve that only permits selected chemicals to move into and out of the nucleus. The pore operates
rather like a turnstile or ticket gate. Those entering the event area will need a ticket to operate the
stile or gate. Small items can be passed through the turnstile but people with large items need
special facilities. The turnstile therefore not only controls the flow but is also selective. The
ticket operating the turnstile, like certain proteins entering a nuclear pore, carries important
destination information. It might be something like “Yankee Stadium, Stand 4, Row E, Seat 32″.
Without this detailed information access is denied. In cell biology terms this entry information
consists of a short protein sequence called a ‘nuclear localization signal’
Ribosomes
A ribosome is a cell organelle. It functions as a micro-machine for making proteins. Ribosomes
are composed of special proteins and nucleic acids. The TRANSLATION of information and the
Linking of AMINO ACIDS are at the heart of the protein production process. A ribosome,
formed from two subunits locking together, functions to: (1) Translate encoded information from
the cell nucleus provided by messenger ribonucleic acid (mRNA), (2) Link together amino acids
selected and collected from the cytoplasm by transfer ribonucleic acid (tRNA). (The order in
which the amino acids are linked together is determined by the mRNA) and, (3) Export the
polypeptide produced to the cytoplasm where it will form a functional protein.
Ribosomes are found ‘free’ in the cytoplasm or bound to the endoplasmic reticulum (ER) to form
rough ER. In a mammalian cell there can be as many as 10 million ribosomes. Several ribosomes
can be attached to the same mRNA strand, this structure is called a polysome. Ribosomes have
only a temporary existence. When they have synthesized a polypeptide the two sub-units
separate and are either re-used or broken up.
Ribosomes can join up amino acids at a rate of 200 per minute. Small proteins can therefore be
made fairly quickly but two to three hours are needed for larger proteins such as the massive
30,000 amino acid muscle protein titin.
Ribosomes in prokaryotes use a slightly different process to produce proteins than do ribosomes
in eukaryotes. Fortunately this difference presents a window of molecular opportunity for attack
by antibiotic drugs such as streptomycin. Unfortunately some bacterial toxins and the polio virus
also use it to enable them to attack the translation mechanism.
Rough endoplasmic reticulum (rER)
This is an extensive organelle composed of a greatly convoluted but flattish sealed sac that is
continuous with the nuclear membrane. It is called ‘rough’ endoplasmic reticulum because it is
studded on its outer surface (the surface in contact with the cytosol) with ribosomes. These are
called membrane bound ribosomes and are firmly attached to the outer cytosolic side of the ER.
About 13 million ribosomes are present on the RER in the average liver cell. Rough ER is found
throughout the cell but the density is higher near the nucleus and the Golgi apparatus.
Ribosomes on the rough endoplasmic reticulum are called ‘membrane bound’ and are
responsible for the assembly of many proteins. This process is called translation. Certain cells of
the pancreas and digestive tract produce a high volume of protein as enzymes. Many of the
proteins are produced in quantity in the cells of the pancreas and the digestive tract and function
as digestive enzymes.
The rough ER working with membrane bound ribosomes takes polypeptides and amino acids
from the cytosol and continues protein assembly including, at an early stage, recognizing a
‘destination label’ attached to each of them. Proteins are produced for the plasma membrane,
Golgi apparatus, secretory vesicles, plant vacuoles, lysosomes, endosomes and the endoplasmic
reticulum itself. Some of the proteins are delivered into the lumen or space inside the ER whilst
others are processed within the ER membrane itself. In the lumen some proteins have sugar
groups added to them to form glycoproteins. Some have metal groups added to them. It is in the
rough ER for example that four polypeptide chains are brought together to form hemoglobin.
Smooth endoplasmic reticulum (sER)
Smooth ER is more tubular than rough ER and forms a separate sealed interconnecting network.
It is found fairly evenly distributed throughout the cytoplasm. It is not studded with ribosomes
hence ‘smooth ER’.
Smooth ER is devoted almost exclusively to the manufacture of lipids and in some cases to the
metabolism of them and associated products. In liver cells for example smooth ER enables
glycogen that is stored as granules on the external surface of smooth ER to be broken down to
glucose. Smooth ER is also involved in the production of steroid hormones in the adrenal cortex
and endocrine glands Smooth ER – the detox stop - Smooth ER also plays a large part in
detoxifying a number of organic chemicals converting them to safer water-soluble products.
Large amounts of smooth ER are found in liver cells where one of its main functions is to
detoxify products of natural metabolism and to endeavor to detoxify overloads of ethanol derived
from excess alcoholic drinking and also barbiturates from drug overdose. To assist with this,
smooth ER can double its surface area within a few days, returning to its normal size when the
assault has subsided.
Golgi Apparatus
Golgi apparatus(or complex, or body, or ‘the ‘Golgi’) is found in all plant and animal cells and is
the term given to groups of flattened disc-like structures located close to the endoplasmic
reticulum. The number of ‘Golgi apparatus’ within a cell is variable. Animal cells tend to have
fewer and larger Golgi apparatus. Plant cells can contain as many as several hundred smaller
versions. The Golgi apparatus receives proteins and lipids (fats) from the rough endoplasmic
reticulum. It modifies some of them and sorts, concentrates and packs them into sealed droplets
called vesicles. Depending on the contents these are dispatched to one of three destinations:
Destination 1: within the cell, to organelles called lysosomes.
Destination 2: the plasma membrane of the cell
Destination 3: outside of the cell
Mitochondria
.Mitochondrion (plur: mitochondria) – energy converter, determinator, generator (of reactive
oxygen chemicals), enhancer, provider of genetic history and, controversially, an aid to boost the
success rate in infertility treatment.
Mitochondria are organelles that are virtually cells within a cell. They probably originated
billions of years ago when a bacterial cell was engulfed when visiting what was to become a host
cell. The bacterial cell was not digested and stayed on in symbiotic relationship. A true story of a
visitor that stayed on and on……forever. Like many visitors the guest bacterium contributes
something towards its keep; the mitochondrion has certainly made sure its presence is felt. In
addition to the features mentioned below mitochondria also take part in reactions concerning
fatty acid metabolism, the urea cycle and the biosynthesis of the heme part of hemoglobin.
Mitochondria, using oxygen available within the cell convert chemical energy from food in the
cell to energy in a form usable to the host cell. The process is called oxidative phosphorylation
and it happens inside mitochondria. In the matrix of mitochondria the reactions known as the
citric acid or Krebs cycle produce a chemical called NADH. NADH is then used by enzymes
embedded in the mitochondrial inner membrane to generate adenosine triphosphate (ATP). In
ATP the energy is stored in the form of chemical bonds.
.Chloroplast
Plant chloroplasts are large organelles (5 to 10 μm long) that, like mitochondria, are bounded by
a double membrane called the chloroplast envelope. In addition to the inner and outer
membranes of the envelope, chloroplasts have a third internal membrane system, called
the thylakoid membrane. The thylakoid membrane forms a network of flattened discs called
thylakoids, which are frequently arranged in stacks called grana. Because of this three-membrane
structure, the internal organization of chloroplasts is more complex than that of mitochondria. In
particular, their three membranes divide chloroplasts into three distinct internal compartments:
(1) the intermembrane space between the two membranes of the chloroplast envelope; (2)
the stroma, which lies inside the envelope but outside the thylakoid membrane; and (3) the
thylakoid lumen.
.Cytoplasm
The cytoplasm consists of all of the contents outside of the nucleus and enclosed within the cell
membrane of a cell. This includes the cytosol and in euckaryotic cells, organelles such as
mitochondria and ribosomes. Also located within the cytoplasm is the cytoskeleton, a network of
fibers that help the cell maintain its shape and give it support.
Cytoskeleton
The cytoskeleton is the overall name given to protein filaments and motor proteins (also called
molecular motors) in the cell. These protein filaments form an enormous three dimensional (3D)
meshwork. Filaments can be cross linked to other similar filaments, and to membranes, by means
of accessory proteins. This inter-linking greatly increases rigidity. Some filaments are used as
track ways for motor proteins to transport cargoes. All cells, except those of most bacteria,
contain components of the cytoskeleton. They help the cell remain rigid but also help it move
and change its shape when instructed to do so. Components of the cytoskeleton also enable cilia,
flagella and sperm to move, cell organelles to be moved and positioned, and muscles to function.
During cell division these components also assist by pulling the daughter chromosomes to
opposite ‘poles’ in the dividing process. Throughout the life of the cell various molecules and
cargo containing vesicles are transported around the cell by motor proteins. These move along
the protein filaments using them as track ways rather like a railway locomotive runs on rail
tracks.
There are three groups of movers, the motor proteins: kinesin, dynein and myosin, and three
main groups of shapers, the protein filaments: microtubules, intermediate filaments and actin
filaments.
Cytosol
The cytosol is the main component of the cytoplasm, the fluid that fills the inside of the cell. The
cytoplasm is everything in the cell except for the cytoskeleton and membrane-bound organelles.
Both structures, the cytoskeleton and cytosol, are "filler" structures that do not contain essential
biological molecules but perform structural functions within a cell. The cytosol often comprises
more than 50% of a cell's volume. Beyond providing structural support, the cytosol is the site
wherein protein synthesis takes place
Centrosome
The centrosome is located in the cytoplasm usually close to the nucleus. It consists of two
centioles — oriented at right angles to each other — embedded in a mass of amorphous material
containing more than 100 different proteins.
It is duplicated during S phase of the cell cycle. Just before mitosis, the two centrosomes move
apart until they are on opposite sides of the nucleus. As mitosis proceeds, microtubules grow out
from each centrosome with their plus ends growing toward the metaphase plate. These clusters
of microtubules are called spindle fibers.
Centiole
Found only in animal cells and some lower plants, a centriole is composed of short lengths of
microtubules lying parallel to one another and arranged around a central cavity to form a
cylinder. In animal cells centrioles are located in, and form part of, the centrosome where they
are paired structures lying at right angles to one another. In this context they are possibly
involved in spindle assembly during mitosis. The centrosome is positioned in the cytoplasm
outside the nucleus but often near to it. A single centriole is also to be found at the basal end of
cilia and flagella. In this context it is called a ‘basal body’ and is connected with the growth and
operation of the microtubules in a cilium or flagellum. A centriole is composed of short lengths
of microtubules arranged in the form of an open-ended cylinder about 500nm long and 200nm in
diameter. The microtubules forming the wall of the cylinder are grouped into nine sets of bundles
of three microtubules each
Veslicles
Vesicles are small, membrane-bound spheres whose contents are isolated from the surrounding
cytoplasm. Extremely important for the movement of material within cells, vesicles are formed
by membrane budding from organelles such as the endoplasmic reticulum and Golgi complex,
and can be moved along cytoskeletal elements by motor proteins. Endocytotic vesicles bud from
the plasma membrane of the cell, bringing surface membrane and material to the interior, and
exocytotic vesicles fuse with the plasma membrane, releasing their contents to the outside world.
Vesicle. is a fairly general term, and is sometimes used for more specific structures such as
endosomes. Vacuoles, lysosomes, transport vesicles, and secretory vesicles are all types of
vesicles
Lysosome
Lysosomes are membrane bounded organelles found in animal and plant cells. They vary in
shape, size and number per cell and appear to operate with slight differences in cells of yeast,
higher plants and mammals. Lysosomes contribute to a dismantling and re-cycling facility. They
assist with degrading material taken in from outside the cell and life expired components from
within the cell. Recent research suggests that lysosomes are organelles that store hydrolytic
enzymes in an inactive state. The system is activated when a lysosome fuses with another
particular organelle to form a ‘hybrid structure’ where the digestive reactions occur under acid
(about pH 5.0) conditions. From this ‘hybrid structure’ a lysosome is reformed for re-use.
Lysosomes play no part in determining which cells are eliminated. This is a function of the
processes of programmed cell death (apoptosis) and phagocytosis. Lysosomes are neither the
‘suicide bags’ nor ‘garbage disposal units’ that these evocative terms would suggest
Peroxisomes
Peroxisomes, sometimes called microbodies are generally small (about 0.1 – 1.0 µm in diameter)
organelles found in animal and plant cells. They can vary in size within the same organism.
Peroxisomes break down organic molecules by the process of oxidation to produce hydrogen
peroxide. This is then quickly converted to oxygen and water. Peroxisomes produce cholesterol
and phospholipids found in brain and heart tissue. A peroxisome protein is involved in
preventing one cause of kidney stones. In plants a type of peroxisome converts fatty acids to
carbohydrates. Peroxisomes are small rounded organelles found free floating in the cell
cytoplasm. These structures contain at least 50 enzymes and are separated from the cytoplasm by
a lipid bilayer single membrane barrier. They are called peroxisomes because they all produce
hydrogen peroxide. Here is a link to a good article relating to Lorenzo's Oil, the disease
adrenoleukodystrophy (ALD), and peroxisomes:
https://www.nabt.org/websites/institution/index.php?p=486
Vacuole
A vacuole is a membrane-enclosed fluid filled sac found in the cells of plants including fungi.
Vacuoles can be large organelles occupying between 30% and 90% of a cell by volume.
Vacuoles appear to have three main functions, they:
1. Contribute to the rigidity of the plant using water to develop hydrostatic pressure
2. Store nutrient and non-nutrient chemicals
3. Break down complex molecules.
Gap Junctions
Gap junctions are intercellular channels some 1.5–2 nm in diameter. These permit the free
passage between the cells of ions and small molecules (up to a molecular weight of about 1000
daltons).
They are cylinders constructed from 6 copies of transmembrane proteins called connexins.
Because ions can flow through them, gap junctions permit changes in membrane potential to
pass from cell to cell.
Examples:
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The action potential in heart (cardiac) muscle flows from cell to cell through the heart
providing the rhythmic contraction of the heartbeat.
At some so-called electrical synapses in the brain, gap junctions permit the arrival of an
action potential at the synaptic terminals to be transmitted across to the postsynaptic cell
without the delay needed for release of a neurotransmitter.
As the time of birth approaches, gap junctions between the smooth muscle cells of the
uterus enable coordinated, powerful contractions to begin.
Several inherited disorders of humans such as
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certain congenital heart defects and
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certain cases of congenital deafness
Plasmodesmata
Although each plant cell is encased in a boxlike cell wall, it turns out that communication
between cells is just as easy, if not easier, than between animal cells. Fine strands of cytoplasm,
called plasmodesmata, extend through pores in the cell wall connecting the cytoplasm of each
cell with that of its neighbors.
Plasmodesmata provide an easy route for the movement of ions, small molecules like sugars and
amino acids, and even macromolecules like RNA and proteins, between cells. The larger
molecules pass through with the aid of actin filaments. Plasmodesmata are sheathed by a plasma
membrane that is simply an extension of the plasma membrane of the adjoining cells. This raises
the intriguing question of whether a plant tissue is really made up of separate cells or is, instead,
a syscytinum: a single, multinucleated cell distributed throughout hundreds of tiny
compartments.
Extracellular matrix (ECM)
All cells in solid tissue are surrounded by extracellular matrix.
Both plants and animals have ECM. The cell wall of plant cells is a type of extracellular matrix.
In animals, the ECM can surround cells as fibrils that contact the cells on all sides, or as a sheet
called the basement membrane that cells ‘sit on’. Cells in animals are also linked directly to each
other by cell adhesion molecules (CAMs) at the cell surface.
ECM is composed of proteins and polysaccharides. Connective tissue is largely ECM together
with a few cells.
For cells ECM provides:
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mechanical support
a biochemical barrier
a medium for:
1. extracellular communication that is assisted by CAMs
2. the stable positioning of cells in tissues through cell matrix adhesion
3. the repositioning of cells by cell migration during cell development and
wound repair
Motor proteins
Motor proteins are the driving force behind muscle contraction and are responsible for the active
transport of most proteins and vesicles in the cytoplasm. They are a class of molecular motors
that are able to move along the surface of a suitable substrate, powered by the hydrolysis of ATP.
There are three superfamilies of cytoskeletal motor proteins. Myosin motors act upon actin
filaments to generate cell surface contractions and other morphological changes, as well as
vesicle motility, cytoplasmic streaming and muscle cell contraction. The kinesin and dynein
microtubule based motor superfamilies move vesicles and organelles within cells, cause the
beating of flagella and cilia, and act within the mitotic and meiotic spindles to segregate
replicated chromosome
Fun Animation on cell and organelles
https://youtu.be/MfopLilIOeA
Good animation on cell and organelles
https://youtu.be/fKEaTt9heNM
Advanced animation on cell and organelles - includes motor proteins
https://youtu.be/FzcTgrxMzZk
Application:
Prokaryotes divide by binary fission.
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Binary fission is the form of asexual cell division that results in the reproduction of two
genetically identical prokaryotic cells.
All prokaryotic cells divide by binary fission
Skill: Drawing of the ultrastructure of prokaryotic cells based on electron micrographs
Application: Structure and function of organelles within exocrine gland cells of the
pancreas and within palisade mesophyll cells of the leaf.
Exocrine Gland Cells of the Pancreas
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These are animal cells that are specialized to secrete large quantities of digestive
enzymes.
They will have all the organelles of an animal cell but will have many ribosomes and
rough ER to create the enzymes which are proteins and transport them outside the cell.
They have many mitochondria to supply the ATP needed for these processes.
Palisade Mesophyll cells carry out most of the photosynthesis in the leaf.
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They have many chloroplasts to allow the cell to carry out the maximum levels of
photosynthesis.
The cells are surrounded by a cell wall to hold the shape of and protect the cell and a
plasma membrane to allow substances in and out of the cell.
They also have mitochondria which are membrane-bound organelles that carry out
aerobic cellular respiration to create ATP.
They have vacuoles which are a large cavity in the middle of the cell that stores water
and dissolved substances, e.g. sugars and metabolic by-products
They are basically plant cells with many chloroplasts.
Skill: Drawing of the ultrastructure of eukaryotic cells based on electron micrographs.
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The diagram below shows an animal cell like a liver cell which contains many ribosomes,
rough endoplasmic reticulum (rER), lysosomes, Golgi apparatus, many mitochondria and
the nucleus.
Liver cells contain many mitochondria for energy and rough endoplasmic reticulum with
ribosomes for secretion purposes.
Skill: Interpretation of electron micrographs to identify organelles and deduce the function of
specialized cells.
Identify as many structures and organelles you can from the two micrographs below.
http://botit.botany.wisc.edu/Resources/Botany/Plant%20Cell/Electron%20Micrographs/General%20Cell/
Nucleus%20microbodies%20chloroplasts.jpg