1.1.1 Cell Structure
(e) describe and interpret drawings and photographs of eukaryotic cells as seen under an electron microscope and be able to recognise the following structures: nucleus, nucleolus, nuclear envelope, rough and smooth endoplasmic reticulum (ER), Golgi apparatus, ribosomes, mitochondria, lysosomes, chloroplasts, plasma (cell surface) membrane, centrioles, flagella and cilia;
(f) outline the functions of the structures listed in (e);
(g) outline the interrelationship between the organelles involved in the production and secretion of proteins (no detail of protein synthesis is required);
(h) explain the importance of the cytoskeleton in providing mechanical strength to cells, aiding transport within cells and enabling cell movement;
PROKARYOTIC CELLS
(i) compare and contrast, with the aid of diagrams and electron micrographs, the structure of prokaryotic cells and eukaryotic cells;
(j) compare and contrast, with the aid of diagrams and electron micrographs, the structure and ultrastructure of plant cells and animal cells.
Cells
· Organisms are classified into 5 kingdoms: Plants, Animals, Fungi, Protoctists (algae and protozoa) and Prokaryotes (bacteria and blue-green algae).
· All organisms in the first 4 kingdoms listed above have EUKARYOTIC cells (cells with a nucleus).
· Organisms in the Kingdom Prokaryotes have PROKARYOTIC cells (cells without nucleus).
· Prokaryotic and Eukaryotic cells both carry out the same activities associated with living organisms, such as cell respiration and protein synthesis. However, the two cell types are structurally different in their internal organisation which is known as the cell ultrastructure.
Prokaryotes or Bacteria
The ultrastructure of Prokaryotic cells is simpler and there are no complex membrane-bound organelles (an organelle is a structure inside a cell which carries out a specific process; some are membrane-bound).
Prokaryotic cells are much smaller (approx. 1-5µm) than eukaryotic cells (approx. 20 to 100µm).Bacteria typically have one of three shapes: rods (bacilli), spheres (cocci) or spiral (spirilla). Unicellular cells often stick together forming clumps or filaments.
Reproduce rapidly (E. coli can reproduce by binary fission every 20 minutes), and diverse habitats and modes of existence make them the most abundant and diverse kingdom on Earth. Bacteria occur in almost every environment on Earth, from the bottom of the ocean floor, deep inside solid rock, to the cooling jackets of nuclear reactors. Bacterial Structure (prokaryotes)
Bacteria lack a nuclear membrane and membrane-bound organelles. All biochemical processes that normally occur in a chloroplast or mitochondrion of eukaryotes take place in the cytoplasm of prokaryotes.
There is no membrane bound nucleus or chromosomes. Bacterial DNA is circular and found in a region of the cell known as the nucleoid. Scattered within bacterial cytoplasm are numerous small loops of DNA known as plasmids. Bacterial ribosomes (70s) are smaller than eukaryotes ribosomes (80s).
Some bacteria have cilia like projections called pilli others have flagella with a different microtubule structure (9+2) than the flagella of eukaryotes.
Most have stiff cell walls containing peptidoglycan/Murein, which is unique to prokaryotes. Many have a slime capsule made up of polysaccharides. Inside the cell wall is a plasma membrane.
Prokaryotes Summary
| Cell Inclusion | Inclusion Structure | Role of Inclusion |
| Cell wall | Rigid. Main component is a peptidoglycan called murein forming a 3D network. | Maintains cell shape and prevents lysis. |
| Cytoplasm | Gel-like ground matrix in the cell | Contains nutrient storage structures, chromosome, plasmids and ribosomes. Site of many metabolic reactions. |
| Plasma membrane | Structure is typical of all plasma membranes. There are often infoldings called MESOSOMES. | Plasma membrane controls which substances enter or leave the cell. Mesosomes are the site of aerobic respiration. |
| Flagella (sing. Flagellum) | One or more may be present. Rigid structure made of a single rod of protein fibres. Corkscrew shape. Not made of microtubules. | Enables the bacterium to swim through fluids. Acts as a helical rotor. |
| Bacterial chromosome | Single circular loop of DNA, not associated with histone proteins. | Contains several thousand genes essential for controlling the growth and metabolism of the bacterium. |
| Plasmids | Small loops of DNA in the cytoplasm, present in some bacteria. | Able to self-replicate but not associated with the main chromosome. Contain non-essential but beneficial genes such as those conferring antibiotic resistance. |
| Glycogen granules | Contain the polysaccharide glycogen. Present in the cytoplasm. | Provide a carbohydrate, energy store. |
| Lipid droplets | Contain triglycerides. Present in the cytoplasm. | Provide a lipid, energy store. |
| Ribosomes | Small (70S) free structures in the cytoplasm. Contain ribosomal RNA. | Site of protein synthesis. |
EUKARYOTS
Eukaryotic cells are larger than prokaryotes (10-100 mm). There is no cell wall, in animal cells but plants have a rigid cell wall made of cellulose.
The entire content of the cell is called protoplasm. It is further subdivided into cytoplasm (all except the contents of the nucleus).The cytoplasm consists of a fluid portion, called the cytosol, and assorted structures, collectively known as organelles such as the: nucleus, nucleolus, nuclear envelope, rough and smooth endoplasmic reticulum (ER), Golgi apparatus, ribosomes, mitochondria, lysosomes, chloroplasts, plasma (cell surface) membrane, centrioles, flagella and cilia.Each of these structures has special function/s. The number of each organelle varies from cell to cell, according to its function and can alter according to demand.
Some organelles such as chloroplasts and mitochondria, Golgi apparatus, lysosomes, and peroxisomes are membrane bound others such as the ribosomes do not have an outer membrane. Non-membranous organelles are in direct contact with the cytosol.
Membrane bound organelles are separated from the cytosol by one or more phospholipids membranes similar in structure to the cell membrane. The membrane barrier allows compartmentalisation and allows different functions to take place in each organelle. This is called division of labour.
Remember - always relate structure to function.
Cytoplasm
The cytoplasm is defined as the material between the plasma membrane (cell membrane) and the nucleus. All cell organelles are suspended within the cytoplasm.
2Fibrous proteins form the cytoskeleton within the cytoplasm, which maintain the shape of the cell as well as anchoring organelles, within the cell and controlling internal movement of structures.
The cytoskeleton consists of three principle elements: actin, intermediate fibers, and microtubules (7-25nm diameter). All three elements play a critical role in the regulation of a multitude of biological processes, including cellular plasticity (ability to keep shape), cell division, motility, intracellular transport, and signal transduction.
The Nucleus
The nucleus is found in all eukaryotic cells (with a few exception e.g. mature RBCs, phloem sieve tubes) and is the control centre of the cell. It is generally the most conspicuous structure in the cell (5mm). In electron micrographs of cells that are not dividing the nucleus appears as dark granular material. The nucleus consists of three main components:
1. double nuclear membrane
2. nucleoplasm-granular chromatin within the nuclear membrane
3. nucleolus-darker staining bodies within the nucleus
Nuclear Membrane The nuclear membrane is a double-membrane structure, separated by a space @ 20nm.Numerous pores occur in the envelope, allowing mRNA, ribosomes, hormones and other chemicals to pass through. Ribosomal components or partially assembled ribosomes and mRNA for instructions for protein synthesise are sent out via the pores.
Nucleoplasm
The nucleoplasm is not uniform; the bulk of the nucleoplasm consists of dark granular material. Since these granules readily stain with many stains they are termed chromatin.
The Nucleolus
The nucleolus is a darker staining region within the nucleus because it contains large amounts of DNA and RNA. It is the site where ribosomes are constructed.
Endoplasmic Reticulum
Endoplasmic reticulum is a mesh of interconnected membrane continuous with the nuclear membrane. It has membranous flattened sacs called cisternae. ER may be smooth in appearance (smooth ER) or studded with ribosomes (rough ER).
Rough endoplasmic reticulum is so-named because of its rough appearance due to the numerous ribosomes attached to it. It is the main site for protein synthesis. These proteins are then transported within the cisternae of the RER, either to the Golgi body or to the cell surface membrane for secretion out of the cell. RER is extensive in cells which secrete protein molecules. Cells involved in synthesis and transport have extensive network of ER. 
As the protein is synthesised it is passed into the cisternae, where it is packaged into spherical membrane-bound transport vesicles that pinch off from the tips of the endoplasmic reticulum. The transport vesicles shuttle their contents across the cytosol to the Golgi apparatus where it is modified before being exported. All cells membranes are made here, which can expand its’ own network or be exported where needed.
The smooth endoplasmic reticulum is the main site for, the synthesis of fatty acids, lipids, steroids, hormones such as testosterone and oestrogen.
Both SER and RER are also involved in detoxification.
Muscle cells have a special kind of ER called sarcoplasmic reticulum, which is involved in Ca2+ transport need for contraction.
Golgi apparatus
Golgi apparatus or Golgi complex was first observed by Italian scientist Golgi in 1898. The Golgi apparatus consists of five or six hollow curved sacs stacked one on top of each other like a series of hot water bottles or pita bread and connected so that they share a single lumen.
The stacks are constantly being formed at one end forming vesicles, which bud off from ER, and are broken down at the other end as Golgi vesicles.
Its function is to modify substances made by the endoplasmic reticulum and package them into membrane-bound vesicles. The material received by the Golgi is chemically modified; carbohydrate or lipid tags are added, rather like tags to send them off to the right destination. Golgi vesicles also make lysosomes-bags full of enzymes.
An important glycoproteins secreted by Golgi is mucin which forms mucus e.g. in root cap cells, slime, wax, gum, mucilage secretions are all released by Golgi.Golgi body are particular prominent in secretary cells such as aciner cells (secrete digestive enzyme of the pancreas into the duodenum).
Ribosomes
Ribosomes occur in both prokaryotes and eukaryotes as well as in mitochondria and chloroplasts. Eukaryotic ribosomes are slightly larger (80s) than prokaryotic, mitochondria and chloroplasts ones (70s).Ribosomes appear as tiny dark granules both floating free and attached to ER and the nuclear membrane. Both free and bound ribosomes are identical and can interchange. Often ribosomes cluster on the endoplasmic reticulum, giving it its name –rough endoplasmic reticulum- in which case they resemble a series of factories adjoining a railroad line. Ribosomes are small (20nm) dense granules of RNA and protein that manufacture proteins under the direction of the cell's DNA i.e. ribosome functions in the expression of the genetic code from nucleic acid into protein, in a process called translation. Structurally the ribosome consists of two units, a small (40S) and larger (60S) subunit.
Bound ribosomes produce secretary proteins such as hormones, which need to be transported, free ribosomes usually make protein, which is soluble and remains in the cytosol. Active cells have lots of ribosomes as compared to docile cells.
The root hair is one of the fastest growing cells in the plant. To allow this rapid growth, continuous delivery of membrane and cell wall material to the growing tip of the hair cell is required. A component part of this material is protein, which is synthesized by ribosomes along the Endoplasmic Reticulum, modified in the Golgi apparatus and packaged into vesicles. The vesicles are finally delivered to the plasma membrane by motor proteins along the cytoskeleton. How do vesicles find their target membranes? The specificity of target recognition is mediated by the interaction of v-SNARE proteins on the vesicle surface with t-SNARE proteins on the target membrane.
Mitochondria
Mitochondria are present in all eukaryotic cells where they are the main sites of respiratory activity; hence they have been termed the powerhouse of the cell. They function as the sites of energy release and ATP formation. Highly active cells, requiring much energy, characteristically have numerous large mitochondria. The number of mitochondria in a particular cell depends on the cell's energy needs.Such cells include:
Liver cells -Energy is required to drive the large and varied number of biochemical reactions taking place there.
Striated muscle cells -Energy is needed for muscle contraction, especially where this is rapid e.g. flight muscle of insects.
Sperm tails - provide energy to propel the sperm.
Nerve cells -Mitochondria are especially numerous adjacent to synapses where they provide the energy needed for the production and release of transmitter substances.
Intestinal epithelial cells -Many mitochondria occur beneath the microvilli on these cells to provide energy for the absorption of digested food by active transport.
Mitochondrial Structure· Size and shape vary and can alter, ranging from 1-10 mm.
· Mitochondria are also involved in the synthesis of lipids.
· Mitochondria have double membrane (6-10nm apart).
· The outer membrane is smooth but the inner membrane is folded to form cristae in order to increase its surface area.
The inner membrane is the site for respiratory process. In the centre of the mitochondrion, inside the inner membrane, is the mitochondrial matrix that contains enzymes, ribosomes, granules, and strands of DNA. Cellular respiration occurs in the matrix.
Mitochondria are unusual organelles in two ways. First of all, in their matrix they have their own unique DNA (called mitochondrial DNA (mDNA). This mitochondrial DNA, along with the ribosomes in the matrix, means that mitochondria can manufacture some of its own proteins.
Mitochondria and endosymbiosis
According to one theory, mitochondria (and chloroplasts) are the descendants of bacteria that invaded cells millions of years ago. Instead of digesting the smaller organisms the large one and the smaller one entered into a type of symbiosis known as mutualism, wherein both organisms benefit and neither is harmed. This relationship became so strong that now eukaryotic cells cannot survive without mitochondria (likewise photosynthetic eukaryotes cannot survive without chloroplasts), and the endosymbionts cannot survive outside their hosts.
Supporting evidence for this theory is the fact that mitochondria and chloroplast both contain DNA (many copies-12% cell’s DNA) and ribosomes. The ribosomes are the type found in prokaryotes (70S). The second unusual characteristic of mitochondria is their ability to replicate themselves even when the cell to which they belong is not undergoing cell division. This process is aided by the presence of mitochondrial DNA that allows the organelles to direct their own duplication. 
Cells such as exercising muscle cells, which are subjected to increased energy demands over a period of time, may meet the demand for more ATP by increasing the number of mitochondria in their cytoplasm.Lysosomes
Lysosomes are small spherical liquid filled storage vesicles (0.1-0.5 µm diameter) surrounded by a single membrane. Lysosomes are the intracellular digestive system.
They contain powerful enzymes that break down all types of biomolecules.
Cells use the enzymes in lysosomes to destroy damaged organelles, to kill bacteria, inside the cell, and occasionally to dissolve extracellular support material, such as the hard calcium carbonate portion of bone.
As many as 50 types of enzymes have been identified in lysosomes from different types of cells. The enzymes contained within the vesicle are synthesised in the RER and transported to the Golgi where they are modified, membrane bound, which later bud off and are called primary lysosomes (1°) which may fuse with other vesicles to form 2° lysosomes.
Because the enzymes of lysosomes are so powerful, one of the questions that puzzled researchers was why these enzymes do not normally destroy the cell that contains them. What they discovered was that lysosomal enzymes are activated only by very acid conditions, 1000 times more acid than the normal cytoplasm. When the lysosomes are first pinched off from the Golgi apparatus, their interior pH is about the same as that of the cytosol, 7.0-7.3. The enzymes are inactive at this pH. Their inactivity serves as a form of insurance: if the lysosome breaks or accidentally releases the enzyme; it will not harm the cell.
However, as the lysosome sits in the cytoplasm, it accumulates H+ ions and the pH inside the lysosome drops to 4.8-5.0, and the enzymes are activated. Once this has occurred, the enzymes are capable of breaking down various biomolecules.
Lysosomes act as the digestive system of the cell. They break up bacteria or old organelles, such as mitochondria, and break them down into their component molecules. Under certain conditions, cells allow the enzymes of their lysosomes to come in contact with the cytoplasm, leading to self-digestion of all or part of the cell. When muscles atrophy (shrink) from lack of use or the uterus diminishes in size after pregnancy, the loss of cell mass is due to the action of lysosomes. Damaged cells will digest themselves as their lysosomes rupture. The inappropriate release of lysosomal enzymes has been implicated in certain disease states: for example, the inflammation and destruction of joint tissue in rheumatoid arthritis.
In the inherited conditions known as lysosomal storage diseases, lysosomes are not effective because they lack specific enzymes. As a result, harmful waste products accumulate, disrupting the normal function of cells, often with fatal results. One of the best-known lysosomal storage diseases is the inherited condition known as Tay-Sachs disease. Infants who inherit, two copies of the gene for Tay-Sachs disease have lysosomes that lack enzymes that break down gangliosides- glycolipids that are an important component of nerve cells. As a result, gangliosides accumulate in the cells of the brain, causing the cells to swell and degenerate. The infants exhibit symptoms of nervous system dysfunction, including blindness and loss of coordination, and most die in early childhood.Centrioles
Centrioles are bundles of microtubules that direct the movement of DNA strands during cell division. Centrioles are present in most animal cells as well as in lower organisms such as fungi and some algae. They have not been observed in plants.
Centriole occur in pairs, arranged at right angles to each other, in a densely staining region called centrosome near the nucleus and the Golgi and appear to organise the spindle formation in cell division. Cells that have lost their ability to undergo cell division, such as mature nerve cells, lack centrioles.
Each centriole is a cylindrical bundle (diameter 0.15-0.2mm and about 0.3-0.5mm long), formed from a ring of 27 hollow microtubules, arranged in nine triplets.
At the beginning of nuclear division the centrioles replicate and migrate to opposite poles of the cell. The spindle forms, on which the chromosomes align.It is these microtubules, which control the separation of chromosomes and the chromatids.
Although higher plants lack centrioles the spindle is still formed.
Cell (Plasma) Membrane
The cell membrane (also called the plasma membrane) separates the inside of the cell from the surrounding extracellular fluid. It is an extremely effective barrio but also controls traffic BOTH in and out of the cell.
The cells of the body are surrounded by a dilute salt solution known as the extracellular fluid (ECF) [extra-, outside]. This is the external environment of the cell from which the cell gains its nutrients and into which the cell puts its wastes and the chemicals that it uses to communicate with other cells.
The protoplasm (all material inside the cell) is enclosed in a semi or partially/selectively permeable membrane. If it was freely permeable life would not be possible! Electron microscopic examinations of cell membranes revealed it to appear as a triple layer, 6-8 nm thick. Structurally, the membrane is a bilayer (double layer) and appears as two dark lines separated by a lighter region, giving it trilaminar appearance. This layering is termed a bilayer and an electron microscopic technique known as freeze-fracturing is able to split the two layers.
The plasma membrane both isolates the cell from its external environment and allows selective movement of molecules in and out. It serves as both a gateway and a barrier. Since most cell organelles are also surrounded by PM it also isolates the cell organelles, compartmentalizing them from the rest of the cell content, allowing for specialised activity. The nucleus, also enclosed in a double-layered membrane, is suspended in the cytoplasm, as are all other cell organelles. The structure of all cell membranes is the same. The main components of the PM are phospholipid and proteins, with some carbohydrates and cholesterol. Integrated amongst the phospholipids are proteins molecules, studded like raisins in a slice of bread, which are arranged so that their hydrophilic areas "stick out" into the cells interior and outside of the cell. The proteins float in a sea of phospholipids and appear as a mosaic floor and the arrangement is described as fluid mosaic model.
The most common molecule in the model is the phospholipid, which has a polar (hydrophilic) head and two nonpolar (hydrophobic) tails. The phospholipid is an amphipathic molecule-meaning it has both hydrophobic and hydrophilic regions. The phospholipids are aligned with their nonpolar (hydrophobic) tails pointing inwards and their polar (hydrophilic) heads pointing outwards. Some proteins penetrate the whole layers (integral proteins), others are partially embedded (extrinsic or peripheral proteins). Water and small ions can cross the membrane without hindrance but larger molecules and charged ions are restricted.
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Many proteins may have carbohydrates chains (glycoproteins) attached to them. The exact amount of and the type of phospholipid and protein vary from cell to cell depending on its function and are modified according to the cell needs.
These, along with carbohydrates attached to the integral proteins (glycoproteins), are thought to function in self-recognition. Cholesterol is another important component of cell membranes embedded in the hydrophobic areas of the inner (tail-tail) region. Its bulky structure hinders the regular packing, reducing its fluidity at moderate temperatures but prevents the membrane from solidifying at low temperatures. It decreases permeability, preventing leakage of polar molecules. It mechanically stabilizes the membrane. It pulls together the chains of fatty acids in phospholipids, limiting their movement, but not making them solid. It limits uncontrolled leakage of small molecules such as water and ions in and out of the membranes. Thus cholesterol is an important constituent of cell membranes. It allows flexibility of the membrane, which is important because vesicles are forever forming, fusing and rupturing. Most bacterial cell membranes do not contain cholesterol.
Vacuoles and Vesicles
Vacuoles are bound by a single-membrane and are found in most plant cells and many unicellular animals. Many organisms will use vacuoles as storage areas. The single membrane of a plant vacuole is known as a tonoplast. Vesicles are like vacuoles but much smaller and are found manly in animal cells. Function is storage, transport within and to the outside of the cell.The Cell Wall
Animal cells and most single celled organisms (Proctists) do not have cell walls but plants, bacteria, fungi and some Proctists do have a cell wall.Plant cells have a variety of chemicals incorporated in their cell walls, most common being cellulose. Bacteria have cell walls containing peptidoglycan. Fungi and many Proctists have cell walls, but their cell walls do not contain cellulose, rather a variety of other chemicals (chitin for fungi). Some plant cells also have lignin and other chemicals embedded in their secondary walls.
Cells are interconnected by plasmodesmatas, through their thick walls.Cells communicate chemically with each other through the plasmodesmatas.
Chloroplasts
Chloroplasts contain many different types of accessory pigments, depending on the taxonomic group of the organism being observed. They also contain chlorophyll, the green pigment necessary for photosynthesis to occur. Chloroplasts occur in large numbers in palisade cells of leaves.
They are disc shaped structures and range from 2-5 mm. Inside are membranous sacs, thylakoids (collectively a stack of thylakoids are a granum (plural - grana) floating in a fluid termed the stroma. Chlorophyll molecules trap light and are located on the thylakoids.
Like mitochondria, chloroplasts have their own DNA, termed cpDNA and ribosomes (70S). Also present in the chloroplast are starch grains and fat droplets. Chloroplasts of Green Algae (Protista) and Plants (descendants of some Green Algae) are thought to have originated by endosymbiosis of a prokaryotic alga similar to living Prochloron (Prochlorobacteria).
Leukoplasts store starch, sometimes protein or oils. Chromoplasts store pigments associated with the bright colours of flowers and/or fruits.| Table 1: Comparison of features of prokaroytic and eukaryotic cells | ||
| | Prokaryotes | Eukaryotes |
| Typical organisms | ||
| Typical size | ~ 1-10 µm | |
| Type of nucleus | nucleoid region; no real nucleus | real nucleus with double membrane |
| DNA | circular (usually) | |
| RNA-/protein-synthesis | coupled in cytoplasm | RNA-synthesis inside the nucleus protein synthesis in cytoplasm |
| 70S | 80S | |
| Cytoplasmatic structure | very few structures | highly structured by endomembranes and a cytoskeleton |
| none | one to several dozen (though some lack mitochondria) | |
| none | ||
| Organization | usually single cells | single cells, colonies, higher multicellular organisms with specialized cells |
| Binary fission (simple division) | ||
