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Since the microscope was introduced biologists have examined the structure of living things. In most cases they have been found to be compose of cells. There are however some strange exceptions to the general cell pattern.
• Muscle Cells called fibers can be very long (300mm).
• They are surrounded by a single plasma membrane but they are multi-nucleated.(many nuclei).
• This does not conform to the standard view of a small single nuclei within a cell
Fungal Hyphae: again very large with many nuclei and a continuous cytoplasm
• The tubular system of hyphae form dense networks called mycelium.
• Like muscle cells they are multi-nucleated
• They have cell walls composed of chitin
• The cytoplasm is continuous along the hyphae with no end cell wall or membrane
Protoctista : a cell capable of all necessary functions
• Single celled organisms have
one region of cytoplasm
surrounded by a cell
• They can perform all the
functions of a differentiated
• This is an image of an amoeba. A single cell protoctista capable of all essential functions. What cell organelles can you see?
Acetabularia an extra ordinary large cell!
• This is an example of an algae
• The cells are some 7 cm long!
• This seems to contradict theory about cell size. We would expect a large surface area to volume ratio which facilitates a rapid rate of diffusion.
Bone : so much extra cellular material the basic cell structure seems lost
• There are some cells that secrete material outside of the cell membrane
• The secretions solidify and dominate the structure
• In this example the bone cell has secreted concentric layers of 'bone' largely calcium phosphates.
• The living cell is difficult to distinguish.
A virus is a non-cellular structure
• Composed of a protein coat and containing either the nucleic acid DNA or RNA
• Viruses are the smallest and simplest of the microbes.
• They are a-cellular (not made of cells) and, since they cannot reproduce (or do any of the seven characteristics of life) on their own, they are considered non-living.
• They are in fact more like complex chemicals than simple living organisms.
• Viruses are obligate parasites that can only reproduce inside host cells which get damaged in the process, leading to disease.
• Viruses are thought to have arisen from lengths of DNA that became separated from their cells.
• This is a picture of
Bacteriophage viruses .
• These are viruses that infect
bacterial rather than
• They are an important tool in
• Remember this is a protein
structure not a cell
Advantages of using a light microscope • Light microscopy has a resolution of about 200 nm, which is good enough to see cells, but not the details of cell organelles. • Specimens can be seen in color (unlike the monochrome electron micrographs) which includes staining and natural color's. • There is a wide field of view to observe the tissue structure (2mm) • Living specimens can be observed and therefore their movement can be studied
Advantages of the Electron Microscope
The electron microscope has
greater resolution (detail) and
magnification than the light
• Resolution approx = 0.25 nm
• Magnifications = x 500,000Rather than shinning light through the specimen the EM takes advantage of the short wavelength of the electron.
Rather than shinning light through the specimen the EM takes advantage of the short wavelength of the electron.
• A beam of electrons is fired from a hot metal wire and focused on the specimen by a series of electromagnets.
• The image is produced by the same principles as a TV screen. Photographs are then produced (electron micrographs)
• The Electron Microscope allows the study of the organelles of cell structure.
There are two kinds of electron microscope.
• The transmission electron microscope (TEM) works much like a light microscope, transmitting a beam of electrons through a thin specimen and then focusing the electrons to form an image on a screen or on film. This is the most common form of electron microscope and has the best resolution.
• The scanning electron microscope (SEM) scans a fine beam of electron onto a specimen and collects the electrons scattered by the surface. This has poorer resolution, but gives excellent 3-dimensional images of surfaces.
Disadvantages of the Electron Microscope :
• Specimens are dead due to preparation technique such as staining, dehydration and placement in a vacuum
• Artifacts (not natural/artificial feature)can be produced in the specimens by the preparation techniques
• No movement can be studies as specimens are dead
• Field of view is very small
Magnifies over 500,000 times Magnifies objects only up to 2000 times All images in black and white Natural color maintained Vacuum is required Vacuum is not required Preparation distorts material Material rarely distorted by preparation Lengthy and complex preparations Simple and easy preparations Large and requires special rooms Small and portable Expensive to produce electron beams Cheap to operate Expensive to buy (over 1,000,000) Cheap to purchase (100 –500) Electron Light
Comparison of Size
• In cell Biology it is most important to be able to provide details of the size of structure observed. SI units are used at all times to provide this information.
• The following diagram provides an approximation of the sizes of different structures
On an image of a specimen it is useful to show how much
larger/smaller the image is than the real specimen. This is
To calculate magnification
using a ruler measure the size of a large clear feature on the image
• measure the same length on the specimen
• convert to the same units of measurement
Magnification = length on the image /length on the specimen
Length of the actual specimen = length on the image/Magnification
• In this example the image of a Rose leaf the magnification is X 0.83
• This tells us the image is smaller than the real specimen.
• The length of the real specimen = picture length/ 0.83 or 4.2cm/0.82 = 5.0 cm
• A scale bar is a line added to a drawing, diagram or photograph to show the actual size of the structures.
• The scale bar in the picture allows you quickly to determine the approximate size of a feature.
• The main feature in the micrograph is a nucleus with a dark region called the nucleolus.
• Using the picture estimate the size of the nucleus and its nucleolus.
Surface area : Volume ratio and cell size
All organisms need to exchange substances such as food, waste, gases and heat with their surroundings. These substances must be exchanged between the organism and its surroundings.
As the size of a structure increases the surface area to volume ratio decreases.
Therefore the rate of exchange (diffusion/radiation) decreases.
This is true for organelles,cells, tissues, organs and organisms.
The rate of exchange of substances therefore depends on the organism's surface area that is in contact with the surroundings.
The exchange depends on the volume of the organism, so the ability to meet the requirements depends on , which is known as the surface area : volume ratio
• As organisms get bigger their volume and surface area both get bigger, but not by the same amount.This can be seen by performing some simple calculations concerning different-sized organisms.
1 2 3 1 cm 10 cm 100 cm Assume we have 3 cubes: With sizes: What will happen to ratio between V and S.A. as their size increases?
Ratio of V:S.A. 1 cm 3 1 000 cm 3 1 000 000 cm 3 6 cm 2 600 cm 2 60 000 cm 2 6 0.6 0.06 Ratio (S.A./V) 100 cm 3 10 cm 2 1 cm 1 S.A. (6x 2 ) Volume (x 3 ) Side Length Cube
Conclusions: •As the organism gets bigger its surface area : volume ratio decreases Example 2
A unicellular organism is a
single cell that can carry
out all those functions of
life that are necessary to
survive separately from
other cells. They can rely
on large SA:Vol ratios for
The cell is specialized
internally to obtain nutrition; carry out respiration
and to reproduce.
As has been already noted some biologists regard
such organisms as 'acellular'. Such biologist regard
cells as inter dependant units and not independent as
these specialized unicellular organisms
All organisms must carry out functions of life.
MOVEMENT – Intracellular and/or extracellular
RESPIRATION – Gas exchange. Not always O 2 and CO 2
NUTRITION – Need raw materials, i.e.- food, water, minerals
‘ Mr. Smullen’ also carries out the functions of life!
Multi-cellular organisms are large and have to specialize parts of their structure to complete the various functions that are characteristic of life.
Cells within a multi cellular organism specialize their function.
Specialized 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.
Tissues, Organs and Organ Systems
Cell differentiation leads to higher levels of
During the process of cell specialization
A process called differentiation occurs.
In the cells of the tissue some genes are
expressed and others are suppressed.
1.) A tissue is a group of similar cells performing a particular function. Simple tissues are composed of one type of cell, while compound tissues are composed of more than one type of cell. Some examples of animal tissues are:
• epithelium (lining tissue)
• connective, skeletal
Some examples of plant tissues are:
2.) An organ is a group of physically-linked different tissues working together as a functional unit. For example the stomach is an organ composed of epithelium, muscle, glandular and blood tissues.
3.) A system is a group of organs working together to carry out a specific complex function. Humans have seven main systems: the circulatory, digestive, nervous, respiratory, reproductive, urinary and muscular-skeletal systems.
Topic 1.2 Prokaryotic Cells
Prokaryotic Cell: general structure
The structural difference between the Prokaryotes and the Eukaryotes are so significant that some biologist think that these two groups merit the status of Super Kingdoms.
The main distinguishing feature between the Prokaryotes and Eukaryotes is the lack of a true nucleus in the former.
• The general size of a prokaryotic cell is about 1-2 um.
• Note the absence of membrane bound organelles
• There is no true nucleus with a nuclear membrane
• The ribosome's are smaller than eukaryotic cells
• The slime capsule is used as a means of attachment to a surface
• Only flagellate bacteria have the flagellum
• Plasmids are very small circular pieces of DNA that maybe transferred from one bacteria to another.
Function of Prokaryotic cell structures
Cell Wall •Made of 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.
Mesosome •A tightly-folded region of the cell membrane containing all the membrane-bound proteins required for respiration and photosynthesis.
• Can also be associated with the nucleoid.
• This is now thought to be an artifact of the electron microscope and not a real structure.
Cytoplasm •Contains all the enzymes needed for all metabolic reactions, since there are no organelles
Ribosome's •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.
Naked DNA •Nucleoid is the region of the cytoplasm that contains DNA. It is not surrounded by a nuclear membrane. DNA is always circular (i.e. a closed loop), and not associated with any proteins to form chromatin. Sometimes confusingly referred to as the bacterial chromosome
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.
Bacteria have a large range of different
metabolic reactions at their disposal, far more
than in the eukaryotes, who are confined to
just respiration or photosynthesis.
1. Fermentation :
• sometimes these bacteria oxidize organic molecules like glucose. In many instances they metabolize as far as lactic acid or alcohol molecules making them useful to fermentation industry
• Many bacteria are photosynthetic and use the same process of photosynthesis as plants. These phototrophic bacteria were some of the earliest forms of life on the planet, and their metabolic reactions increased the oxygen content of the atmosphere from 1% to 20%.
3. Nitrogen Fixing
• obtain their energy by oxidizing inorganic compounds like ammonia, nitrite, methane or hydrogen sulphide. These bacteria use a variety of unusual metabolic reactions and many are able to synthesise carbohydrates from carbon dioxide – the chemosynthetic bacteria.
Topic 1.3 Eukaryotic cells
The nucleus is generally a very conspicuous membrane-bound organelle. It contains most of the genes that control the entire cell.
It averages ~ 5 um in diameter
It is enclosed by a nuclear envelope
It contains chromosomes/chromatin
• Mitochondria is the site of aerobic respiration.
• The matrix is the site of the Krebs cycle
• Oxidative phosphorylation occurs on the cristae membrane
• Very active cells usually have a lot of mitochondria e.g. muscle cel
Controls what enters and leaves the cell.Function & structure are covered in more detail in section
Rough Endoplasmic Reticulum
• A complex interconnected network of membrane tubes.
• The surface is covered in ribosomes where proteins are made for secretion
• Unattached ribosomes make proteins for internal use.
• Ribosome size measured in Svedberg (S) units; derived from sedimentation in ultracentrifuge
• Ribosomes made of 40S and 60S subunits, assemble into 80S ribosome
• Contains many enzymes for general metabolism
• Compartment in which foodstuffs enter and from which wastes leave cell
• Modification of proteins for secretion
1. Intermembrane Space - separates the two membranes.
2. Thylakoids - Are flattened sacs inside the chloroplast. They segregate the interior of the chloroplast into 2 compartments:
Chlorophyll is located in the thylakoid membrane.
They are stacked together (grana).
Stroma - photosynthetic rxns that convert chemical energy into sugars. The stroma is a viscous fluid outside the thylakoids
CO 2 + H 2 O + light C 6 H 12 O 6 + O 2
• The vacuole is a storage area in plants for amino acids and sugars (sap).
• The tonoplast is a membrane like the plasma membrane it controls what enters and leaves the vacuole
• The cell wall supports plant tissue
• Composed of a fully permeable wall of cellulose
• Important structure in establishing turgidity
Prokaryotic vs Eukaryotic cells
Comparison of Plant and Animal Cells
Composition of the plant cell wall
• This image shows the fibrous structure of cellulose
• Cellulose is composed of a linear chain of glucose molecules. The molecules attached to each other by hydrogen bonds
• The molecules are arranged in to bundles called fibers. The fibers provide the cell with tensile strength. This allows the development of high pressures within the cell (turgid).
Some differences between plant and animal cells.
Carbohydrates stored as starch. Carbohydrates stored as glycogen. Stores large amounts of liquid (juice). Larger size of cell. Central Vacuole X Does not store large amounts of liquid. Smaller size of cell. Rigid, cannot easily change shape. Cell Wall X Flexible, can easily change shape. Can produce its own food. Chloroplast X Cannot produce its own food Plant Cells Structure Animal Cells
Topic 1.4: Cell Membrane
1.4.1 Fluid mosaic model
• Fluid because it can change shape but also because the phospholipids can change position in the same plane
• Mosaic as the membrane has protein molecules embedded and attached to its surface
• This model accounts for the behavior observed in cell membranes. Like a any good model it also predicts some characteristics.
• The phospholipids are arranged in a bilayer, with their polar, hydrophilic phosphate heads facing outwards, and their non-polar, hydrophobic fatty acid tails facing each other in the middle of the bilayer.
• This hydrophobic layer acts as a barrier to all but the smallest molecules(oxygen & Carbon Dioxide), effectively isolating the two sides of the membrane.
• Phospholipids can exchange position in the horizontal plane but not the vertical.
Hydrophobic ‘ afraid of water’ Hydrophilic ‘ loves water’
• Usually span from one side of the phospholipid bilayer to the other.
• Proteins that span the membrane are usually involved in transporting substances across the membrane
• These proteins sit on one of the surfaces (peripheral proteins). They can slide around the membrane very quickly and collide with each other, but can never flip from one side to the other.
• Proteins on the inside surface of plasma membrane are often involved in maintaining the cell's shape, or in cell motility.
• They may also be enzymes, catalysing reactions in the cytoplasm
Usually involved in cell recognition which is part of the immune system. They can also acts as receptors in cell signaling such as with hormones. These are extracellular components
Binds together lipid in the plasma membrane reducing its fluidity as conferring structural stability
1.4.2 Phospholipid Properties
The 'head's have large phosphate groups, thus they are hydrophilic (attract water) or polar. These section are suited to the large water content of the tissue fluid and cytoplasm on opposite sides of the membrane.
• The fatty acid tails are non-charged, hydrophobic and repel water. This creates a barrier between the internal and external 'water' environments of the cell. The 'tails' effectively create a barrier to the movement of charged molecules
1.4.2 Phospholipid Properties
• The individual phospholipids are attracted through their charges and this gives some stability. They can however move around in this plane
• The stability of the phospholipid can be increased by the presence of cholesterol molecules.
Membrane Protein Functions
These proteins span the membrane from one side to another. They allow the movement of large molecules across the plasma membrane. Included within this are the passive and active membrane pumps
These proteins (B in diagram) may detect hormones arriving at cells to signal changes in function. They may also be involved in other cell and substance recognition as in the immune system.
Integral in the membrane they may be enzymes e.g. ATP Synthetase, Maltase
Diffusion and Osmosis
• The movement of particles is caused by the kinetic energy possessed by the particle
• The direction of movement is random
• Observing groups of particles they appear to move from regions of high concentration to regions of low concentration
• However, most biological diffusion takes place through membranes and involves sources, sinks and diffusion gradients
Diffusion vs. Mixing
Diffusion is very important over the small scale of things
Most of what we observe directly is mixing
If we put a droplet of cream in coffee and stir very carefully, we can see that the droplet is drawn out – and only blends in with mixing
Diffusion is the passive movement of particles from a region of high concentration to a region of low concentration (down a concentration gradient), until there is an equal distribution.
Osmosis is the passive movement of water molecules, across a partially permeable membrane, from a region of lower solute concentration (high water concentration) to a region of higher solute concentration (low water concentration).
High Concentration Low Concentration Diffusion moves down the concentration gradient just like a ball rolling down a hill. It cannot roll uphill without energy.
Passive transport across membranes in terms of diffusion.
Requires no energy
Moves from down the concentration gradient
Some molecules pass through the membrane
Some molecules use channels for facilitated diffusion
Effects of osmosis on cells:
The examples illustrate the problems that organisms will have if
they live in:
• concentrated solutions (hypertonic)
• dilute solutions (hypotonic)
Most organism have a mechanism to deal with these difficulties.
These are studied through out the course. How do you maintain
isotonic conditions for your tissues?
Water builds up on the side of the solute. The net flow will stop when it comes to equilibrium.
If the water were allowed to flow until it stopped, we would see that the water had risen.
We could alternatively apply a piston to the top of the water on the solute side and apply pressure.
In either case, the pressure needed to stop the water flow is called the osmotic pressure .
Animal Cells and Osmotic Pressure
All cells have thin delicate membranes – animal cells have only plasma membrane
They respond to differences in external solute concentration and osmotic pressure
If isotonic (usually 0.9% w/vol NaCl), no change in shape
If hypertonic (high salt) then shrinks
If hypotonic (low salt) then expands and can lyse
Plant Cells and Osmotic Pressure
In plants, hypotonic solutions produce osmotic pressure that produces turgor pressure
Turgor means “tight or stiff owing to being very full”
Keeps plant upright; in hypertonic conditions plants wilt
Requires energy, in the form of ATP, or adenosine triphosphate
Molecules are ‘pumped’ across the membrane UP the concentration gradient
Pumps fit specific molecules
The pump changes shape when ATP activates it, this moves the molecule across the membrane
Vesicles are used to transport materials within a cell between the rough endoplasmic reticulum, Golgi apparatus and plasma membrane. The fluidity of the membrane allows it to change shape, break and reform during endocytosis and exocytosis.
Exocytosis the mass movement OUT of the cell by the fusion of a vacuole and the membrane
Endocytosis the mass movement INTO the cell by the membrane ‘pinching’ into a vacuole
Topic 1.5 Cell Division
Cellular division in eukaryotic cells.
Chromatin is arranged into chromosomes.
Cell grows in size.
Is cellular cloning.
Cell Cycle : the ‘life cycle’ of a cell.
There are 2 phases:
M phase (mitotic phase)
Telophase & cytokinesis
The non-dividing phase in a cell
Lasts about ~ 90% of the cell cycle.
The cell grows and replicates DNA preparing for Mitosis.
There are three periods:
3 periods of Interphase
1. G o – a cell functioning as normal
2. G1 phase – first growth phase
3. S phase- synthesis of DNA
4. G2 phase- 2 nd growth phase
Mitosis is a reliable process. Only one error occurs
Per 100,000 cell divisions.
The nucleolus disappears.
Chromatin condenses into visible chromosomes.
There are two sister chromatids held together by a centromere.
The mitotic spindle forms in the cytoplasm.
The nuclear envelope disappears.
Spindle fibers extend from each pole to the cell’s equator.
Spindle fibers attach to the centromeres.
Chromosomes are lined up in the equator (middle) of the cell.
This is called the metaphase plate .
Characterized by movement. It begins when pairs of sister chromatids pull apart.
Sister chromatids move to opposite poles of the cell.
Chromosomes look like a “V” as they are pulled.
At the end of anaphase, the two poles have identical number and types of chromosomes.
Telophase and Cytokinesis
Microtubules elongate the cell.
Daughter nuclei begin to form at the two poles.
Nuclear envelopes re-form.
Cells split their cytoplasm.
It is basically the opposite of prophase.
Role of Mitosis
• Growth : Multicellular organisms increase their size through growth. This growth involves increasing the number of cells through mitosis. These cells will differentiate and specialize their function.
• Tissue Repair : As tissues are damaged they can recover through replacing damaged or dead cells. This is easily observed in a skin wound. More complex organ regeneration can occur in some species of amphibian.
• Asexual Reproduction : This the production of offspring from a single parent using mitosis. The offspring are therefore genetically identical to each other and to their “parent”- in other words they are clones. Asexual reproduction is very common in nature, and in addition we humans have developed some new, artificial methods
The mass of cells produced from this uncontrolled cell division is called a tumor. There are two major types of tumor:
Benign Tumors this is a
mass of cancerous cells that do not invade other areas of the body. These are not as dangerous to health but may still require removing to prevent effects on neighboring tissue
2. Malignant Tumors is a mass of cancer cells that may invade surrounding tissues or spread to distant areas of the body. Cancer cells replace normal functioning cells in distant sites:
e.g. replacing blood forming cells in the bone marrow, replacing bones leading to increased calcium levels in the blood, or in the heart muscles so that the heart fails.