Biology is the study of life - and life on Earth is extremely diverse, from microscopic single celled organisms, to enormous multicellular mammals. To make things a little easier life is 'classified' into five kingdoms and each kingdom can be defined by its own characteristic kind of cell.
So, what are cells?
"Cells are units of life - the smallest units that can be considered alive".
All living organisms are made of cells: -
When it comes to classifying cells, the biggest division is between the cells of the prokaryotic kingdom (Bacteria) and those of the other four kingdoms (Animals, Plants, Fungi and Protoctista), which are all Eukaryotic cells.
All cells from each of these 5 kingdoms has its fundamental differences.
(Like whether it has a cell wall or not, if it has a cell wall what is it composed of?
Does the cell contain organelles?
if so which organelles? etc...).
You will have to be able to compare and contrast cells, their structures functions and organelles.
Before moving onto the video lessons covering concepts such as the Eukaryotic cell cycle, mitosis, meiosis and what it means to be diploid... Let's run through the generalised structure of a Eukaryotic cell and the structure and function of organelles.
Prokaryotic cells are smaller and simpler than eukaryotic cells, and you can find out more about their structure, function and division on the prokaryotic cells page.
What is Cytoplasm?
(Cyto = cell; plasm = colourless fluid). Cytoplasm is the colourless solution within the cell (enclosed by the plasma membrane). Cytoplasm is the fluid which contains enzymes for important metabolic reactions to take place; for example important biochemical reactions such as glycolysis (part of cellular respiration) take place in they cytoplasm of cells. Also contained in the cytoplasm are sugars, salts, amino acids, nucleotides… just about everything needed for the cell to function.
When discussing cytoplasm, you’ll most likely come across the term cytosol - which is sometimes used synonymously with cytoplasm, - however this is incorrect!
Cytoplasm and Cytosol are not the same!
Cytosol is essentially just the liquid part of the cytoplasm - i.e. cytosol is the intracellular fluid that contains organic molecules and cytoskeleton filaments, water and salts. It is probably easiest to think of cytosol as the fluid part of cells without the organelles. Whereas cytoplasm is the fluid part of cells that contains organelles and where many biochemical reactions take place.
What is a cell Nucleus?
The Nucleus (found in eukaryotic cells) is the largest organelle. The Nucleus is surrounded by a nuclear envelope - a double membrane which contains nuclear pores. Nuclear pores are ‘holes’ within the nuclear membrane. The nuclear pores contain proteins which control the exit of substances from the nucleus, e.g. mRNA and ribosomes.
Since the Nucleus is an organelle, with its own nuclear membrane separating it from the cytoplasm of the cell, the fluid part of the nucleus has its own name -it is called nucleoplasm. The nucleoplasm is full of substance called chromatin - a DNA / protein complex which contains the genes of the organism. During cell division chromatin becomes condensed - it becomes shorter and thickens into discrete observable chromosomes.
Also identifiable within the nucleuses is darker region of chromatin - this is called the nucleolus and is involved in making ribosomes.
What are Ribosomes?
Your textbook answer to this should always be “Ribosomes are the sites of protein synthesis”.
Ribosomes are the smallest and most numerous cellular organelles and are the sites of protein synthesis, and are often found in groups called polysomes. Ribosomes are composed of protein and rRNA (ribosomal RNA) and as previously discussed are manufactured in the nucleolus of the nucleus.
Ribosomes can be found in the cell either ‘free floating’ in the cytoplasm, where they make proteins for the cell's own use. Or ribosomes can be found attached to rER (the Rough Endoplasmic reticulum - so called because of its association with ribosomes). When attached to the rER ribosomes make proteins which are exported from the cell.
Ribosomes are composed of 2 subunits, a larger and smaller subunit. The larger subunit is further organised into sites (known as E, P and A) these sites are where tRNA (transfer RNA ‘docks’ when transferring and connecting amino acids when building polypeptides (during protein synthesis this part of the process is known as Translation). The smaller subunit is the binding site for mRNA (messenger RNA) which contains the codons that complementary base pair with the anticodons located on tRNA. Later in your A-Level biology you’ll have to apply the structure and function of ribosomes and their role in protein synthesis (translation).
All eukaryotic ribosomes are the larger, "80S", type, whereas prokaryotes, mitochondria and chloroplasts contain the smaller “70S” type.
What is Rough Endoplasmic Reticulum (rER)?
Rough Endoplasmic Reticulum is similar to sER (smooth endoplasmic reticulum), however in appearance rER looks ‘studded’ and ‘rough’ due its association with numerous ribosomes. It is the ribosomes that give rER its ‘rough’ appearance. The associated ribosomes are the sites of proteins synthesis and as the polypeptides are made, the proteins are processed in the rER (the proteins are enzymatically modified, adding carbohydrates to the polypeptide chain for example). Once modified the proteins can be “packaged” in the Golgi ready to be exported from the cell.
What is Smooth Endoplasmic Reticulum (sER)?
Smooth Endoplasmic Reticulum (sER) is a series of folded membrane channels which are involved in synthesising and transporting of materials, primarily lipids, needed by the cell.
What is the Golgi Apparatus (Golgi Body)?
Golgi is another series of flattened membrane vesicles, formed from the endoplasmic reticulum. However, the role of Golgi bodies is to transport proteins from the rER to the cell membrane for export. Parts of the rER containing proteins fuse with one side of the Golgi body (the part of the Glogi that is closely associated with rER is known as the “Cis face” of the Golgi), whilst at the other side (called the “Trans face”) small Golgi vesicles are released. The Golgi vesicles, which appear to “bud off” from the Golgi move towards the cell membrane. At the cell membrane these small Golgi vesicles fuse with the cell membrane and release their contents via exocytosis.
What are Lysosomes?
Lysosomes are small membrane-bound vesicles which are formed in the rER. Lysosomes contain digestive enzymes their function is to break down unwanted chemicals, toxins, organelles and even whole cells, so that the materials can be recycled by the cell. Lysosomes also fuse with vacuoles and digest the contents contained with them.
What are Vacuoles?
Vacuoles are membrane-bound organelles which resemble little ‘sacs’ containing water, dilute solutions of salts and other solutes. Most cells can have small vacuoles that are formed as required, but plant cells typically have one large permanent vacuole that can fill most of the cell. These large permeant vacuoles found in plant cells are filled with cell sap (water, sugars, and mineral salts). They are very important in keeping the cell turgid. Some unicellular protoctists have feeding vacuoles for digesting food, or contractile vacuoles for expelling water.
What is the Cytoskeleton?
A cells cytoskeleton is a network of protein fibres which extend throughout all eukaryotic cells. The Cytoskeleton is used for support, transport and motility. Attached to the cell membrane, the cytoskeleton provides the cell with structural integrity, helping maintain the overall shape and structure of the cell. Additionally, the cytoskeleton plays an important role holding organelles in position. The cytoskeleton is a ‘network’ of protein fibres, of which there are 3: -
2) Intermediate filaments and
Each of these protein fibres has a corresponding motor protein that can move along the protein fibre carrying cargo such as organelles, chromosomes or other cytoskeleton fibres.
It is these cytoskeletal motor proteins which are responsible for cellular actions such as: -
- chromosome movement during mitosis.
- cytoplasm cleavage during cell division.
- cilia and flagella movements,
- cell crawling (e.g. amoeba movement due to pseudopodia) and
- muscle contraction in animals.
- cytoplasmic streaming (cytoplasmic streaming is the movement or flow of cytosol in cells - particularly in in plant cells - to allow for the transport of molecules around the cell).
What are centrioles?
Centrioles are a pair of short microtubules involved in cell division. Before cell division the
centriole replicates itself and the two centrioles move to opposite poles (opposite ends) of the cell. Here at each pole of the cell the centrioles initiate spindle formation which organises and separates the chromosomes during cell division. (see mitosis for more detail).
What are Mitochondria?
Mitochondria are “sausage-shaped organelles” typically about 8μm long. Within the mitochondria is the “space” enclosed by the inner membrane - this “space” is called the mitochondrial matrix, and it is here within the mitochondrial matrix where 70S ribosomes and small circular strands of mitochondrial DNA(mtDNA) can be found. Structurally mitochondria are surrounded by a double membrane: the outer membrane is relatively simple and permeable. Whilst the inner membrane is slightly more complex. This highly folded inner membrane, forms the inner membrane structures called cristae. Cristae of course provide the inner mitochondria membrane with a large surface area - and it is here where ATP synthesis occurs. Mitochondria are where aerobic respiration takes place in all eukaryotic cells.
What are Chloroplasts?
Chloroplasts are where photosynthesis takes place. Thus, chloroplasts are only found in photosynthetic organisms (e.g. plants and algae). Similar to mitochondria, chloroplasts are enclosed by a double membrane. However, chloroplasts also have a third membrane called the thylakoid membrane. The thylakoid membrane is folded into thylakoid disks, which are then stacked into structures knows as grana. The thylakoid membrane contains chlorophyll and other photosynthetic pigments arranged in photosystems, and is the site of photosynthesis and ATP synthesis. The space between the inner membrane and the thylakoid is called the stroma. Chloroplasts also contain starch grains, ribosomes (70S) and circular DNA.
What is a Cell Membrane?
The cell membrane (aka. the Plasma Membrane or phospholipid bilayer) is a thin, flexible layer around the outside of all cells. Cell membranes are composed of phospholipids and proteins. Cell membranes separate the contents of the cell (intracellular environment) from the outside (extracellular environment). Cell membranes regulate, that is they control the entry and exit of materials. The cell membrane (i.e. The fluid mosaic model) will be discussed in greater detail later.
What is a Cell Wall?
Cell walls are a thick layer consisting of a network of fibres - outside of the cell membrane. Cell walls are there to provide strength and rigidity, and whilst the cell wall gives a cell strength it is still freely permeable to solutes (unlike cell membranes).
Plant cell walls are made mainly of cellulose, (plant cell walls can also contain hemicellulose, pectin, lignin and other polysaccharides). Plant cell walls are built up in three layers called the primary cell wall, the secondary cell wall and the middle lamella. Channels through plant cell walls called plasmodesmata link the cytoplasm of adjacent cells.
Fungal cell walls are made of chitin (pronounced Kai-Tin - Not Shittin’ as many of my students liked to say!). Chitin is a complex of fibrous polysaccharides and also forms the exoskeleton of arthropods.
Animal cells DO NOT have a cell wall (though they do have a layer of carbohydrate outside the cell membrane called glycocalyx).
What is Microvilli?
Microvilli are small finger-like extensions of the cell membrane found in certain cells, for example epithelial cells of the intestine. Microvilli increase the surface area for absorption of materials. They are just visible under the light microscope and are described a as a “brush border.”
What is Undulipodium?
Undulipodium is a long flexible tail present in some eukaryotic cells. The Undulipodium is used for motility. A undulipodium is an extension of the cytoplasm, surrounded by the cell membrane, and is full of microtubules and motor proteins so is capable of complex swimming movements.
Cilia are identical in structure to undulipodia, but are much smaller and there are usually very many of them - cilia typically resemble short microscopic hairlike structures which vibrate allowing for movement (e.g. in ciliated protists) or “beating” and “vibrating” creating a flow / propulsion in the surrounding fluid - e.g. in the respiratory tract where they help filter out microorganisms, dust and other particles breathed in from the air.
The Cell Membrane - The Fluid Mosaic Model.
The cell membrane / plasma membrane surrounds all living cells. It cannot be overemphasised just how important cell membranes are, since they control how substances can move into and out of cells. Cell membranes are also responsible for many other things too. Membranes that surround the nucleus and other organelles (e.g. mitochondria) are almost identical to the cell membrane, and are composed of phospholipids, proteins and carbohydrates arranged what is commonly known as the fluid mosaic model (conceived in 1972 by Nicolson and Singer).
The phospholipids that from cell membranes arrange in a particular way, due to their amphiphilic nature, remember from the phospholipids lesson how phospholipids form cell membranes. The phospholipids form a bilayer the with their polar (hydrophilic) phosphate heads facing outwards, and their non-polar (hydrophobic) fatty acid tails facing each other in the middle of the phospholipid bilayer. It is the hydrophobic fatty acid tails that form a “layer” in the middle of the bilayer which acts as a barrier to all but the smallest molecules. It is this 'barrier' which effectively isolates the two sides of the cell membrane.
Cell membranes can have phospholipids with different fatty acid tails too, which affects the rigidity / flexibility of the membrane. Animal cell membranes also contain cholesterol which can link to the fatty acids and provide stability, thus, strengthening the cell membrane.
The phospholipid bilayer is thin, flexible and in constant motion - the phospholipids move in a range of ways, rotating in situ, swapping positions with neighbours and even “jumping” from one side of the membrane to the other - in a manoeuvre called the “flip flop”. It is of course this “fluidity” of the phospholipid bilayer that gave rise its “fluid” name in Singer and Nicholson's "fluid mosaic model".
The “mosaic” part is simply due to the fact that embedded within the phospholipid bilayer are proteins. The proteins "float" in the phospholipid membrane forming channels and receptors for molecules that warrant entry or exit from cells, and don’t forget the carbohydrates that extend out from the proteins too. These carbohydrates have functional parts to play as cell surface receptors, and other roles which we’ll get to shortly.
The proteins embedded within the phospholipid bilayer usually span from one side of the phospholipid bilayer to the other (integral proteins), but can also sit on one of the surfaces of cell membranes (peripheral proteins). The proteins can slide around the membrane, moving very quickly and colliding with one another, but can never flip from one side to the other (like phospholipids can!) Cell membrane proteins have hydrophilic regions in contact with the water on the outside of cell membranes (these hydrophilic regions are composed of hydrophilic amino acids). The proteins also have hydrophobic regions (composed of hydrophobic amino acids) in contact with the fatty chains which form the inside part of the cell membrane. Proteins make up approximately 50% of the mass of cell membranes and are responsible for most of the membrane's functional properties (i.e. regulation / transport of substances into and out of the cell).
Proteins that span the membrane are usually involved in transporting substances across the membrane.
Proteins on the inside surface of cell membranes are often attached to the cytoskeleton and are involved in maintaining the cell's shape and aid in cell motility. Some of these proteins maybe enzymes that catalyse specific reactions.
Proteins on the outside surface of cell membranes typically act as receptors -
These proteins have specific binding sites where hormones or other molecules bind - triggering cellular events. These proteins may also be involved in cell signalling, cell recognition and enzyme activities - like in digestive processes, e.g. maltase is a membrane bound enzyme that hydrolyses the disaccharide maltose into two alpha-glucose molecules.
Carbohydrates are not just digested either… some carbohydrates play functional roles and are found on the outer surface of all eukaryotic cell membranes. These carbohydrates are attached to the cell membrane proteins and sometimes directly to the phospholipids. Proteins with carbohydrates attached have specific names - they are called glycoproteins, (“glyco” referring to the carbohydrate portion and “protein” referring to, well the protein part)…
Phospholipids with carbohydrates attached also have special names - these are called glycolipids. (the same convention of naming applies - “glyco” meaning the carbohydrate bit and “lipid” meaning the phospholipid part.
The carbohydrates that associate with cell membranes are short polysaccharides composed of a variety of different monosaccharides. Together they form a cell “coat” or glycocalyx outside the cell membrane (once again naming conventions remain consistent here too - the “glyco” meaning carbohydrate and “calyx” is of Greek origin meaning “case” or “enclosure”. So, the glycocalyx is involved in protection and cell recognition - Antigens, for example the ABO antigens on blood cells are usually cell-surface glycoproteins.
The important thing to remember is that cell membranes are more complex that just a simple lipid bilayer allowing things into and out of cells. Rather, cell membranes are “Fluid” - that is to say they are in constant motion and they are “mosaic” - that is, cell membranes are embeddedwith a variety of proteins, enzymes, glycoproteins and glycolipids - all playing essential roles in cell regulation cell recognition, cell signalling, and many many more important cellular events.
A Level Biology - Cell Fractionation and differential centrifugation.
When studying the structure and function of cells, biologists use many techniques. Microscopy / electron microscopy being at the top of the essential skills list. Microscopy of course allows scientists to gain information about the relative size and structure of cells and their organelles.
But how do biologists isolate organelles and study their structures and functions?
Cell fractionation and differential centrifugation is used to isolate sub-cellular organelles in order to study their structures and functions… Here you'll learn exactly how and why cell fractionations is done and why certain steps in the procedure are necessary.
Firstly, as with all a-level biology topics it’s a good idea to familiarise yourself with the vocabulary used - and an understanding of the key terms used here is essential.
So, to begin - Create a flash card to learn and revise each of the following key words.
Define the following terms: -
Cell | Tissue | Fractionation | Differential,
Centrifugation | Homogenate | Supernatant,
Precipitate | Buffer | Isotonic
If you need help define any of these (check out the glossary) and of course keep reading as you’ll come across these terms in context as we go through cell fractionation and differential centrifugation.
What’s in a name?
Well by now you know how to define “cell” (“the basic unit of living organisms”) and you most likely know what “fractionation” means, but let’s break it down anyway.
Fraction - “a small (or tiny) part of ‘something’
Fractionation - “a procedure which separates ‘something’ into smaller parts (i.e. into “fractions”).
So, in this case, cell fractionation is literally “a procedure that separates cells into smaller parts” i.e. breaking cells down into their constituent parts, such as mitochondria, endoplasmic reticulum, chloroplasts, ribosomes, etc…
Easy right… so how is cell fractionation done?
Let’s take a look at each step of the cell fractionation and centrifugation procedure… (by the way you can download the cell fractionation worksheet help with your revision).
Cell fractionation - The Procedure.
Cell Fractionation and Ultracentrifugation Step 1:
The sample is chilled in ice-cold, buffered, isotonic solution.
Note: “The Sample “ could be any tissue sample - i.e. liver tissue, lung, tissue, pancreatic tissue, plant tissue… whatever - so its a good idea you can define “tissue” as its a question commonly associated with this procedure in exams.
Cell Fractionation and Ultracentrifugation Step 2:
The tissue (e.g. liver, heart, leaf, etc) is homogenised in an ice-cold, isotonic, buffered solution.
Note: The sample is homogenised in order to “break open” the cells and release the organelles into the solution.
Cell Fractionation and Ultracentrifugation Step 3:
The mixture (homogenate) is filtered to remove any larger pieces of tissue not broken up by homogeniser (the blender) and any cell debris. The result is a solution consisting ‘free' organelles.
Cell Fractionation and Ultracentrifugation Step 4:
This solution (the homogenate) is now centrifuged at low speed. Any cellular debris is forced to the bottom of the tube. This is called "the pellet" (or sediment). The solution above this pellet is the supernatant, and consists of all the other (less dense) organelles. The supernatant is decanted (carefully poured) into a new tube. The pellet can be resuspended if needed (i.e. if the pellet consists of mitochondria we would want to re-suspend it in cold, buffered, isotonic solution for isolation and further study.
Cell Fractionation and Ultracentrifugation Step 5:
The solution (supernatant) is now centrifuged at a higher speed. The larger (more dense) organelles are forced to the bottom of the tube, again forming “the pellet”. The supernatant is decanted ready for the next round of centrifugation and the pellet can be removed and can be resuspended too if required.
Cell Fractionation and Ultracentrifugation Step 6... 7, 8
The above process can be repeated many times, each time increasing the speed of the centrifuge (until centrifugation is ultra fast! (ultracentrifugation). This differential centrifugation technique allows us to separate (that is: differentiate) each of the sub-cellular organelles, based upon size (density).
So, which each step centrifugation separates the organelles according to their size (density).
Remember! The organelle(s) forced into the pellet through centrifugation is always dependent upon the sample you start with (i.e. animal or plant tissue - and what already exists in the sample). Make sure you read any exam questions carefully as your answers must be in context.
A Level Biology - Basic Genetics
Genetics is the study of heredity (the passing on of characteristics from one generation to the next). Genetics is concerned with a few key questions, but primarily the question
"Why do organisms look almost, but not exactly, like their parents?"
Genetics can be subdivided into 3 main areas: -
1. Mendelian Genetics (Classical Genetics). Mendelian Genetics (pioneered by Gregor Mendel: 1822-1884) is the study of heredity at the whole organism level by investigating how particular characteristics are inherited - it is in classical genetics where you learn all about Punnet Squares and investigating monohybrid and dihybrid inheritance. You can recap simple punnet squares and their application in population genetics in the Hardy-Weinberg lessons.
2. Molecular Genetics (Molecular Biology), is the study of heredity at the molecular level, thus, molecular genetics if primarily concerned with the structure, function and properties of DNA and nucleic acids. Molecular genetics also includes genetic engineering, molecular cloning, biotechnology and a whole host of cool cell biology stuff - like PCR and Genetic Fingerprinting.
3. Population Genetics, is the study of genetic differences within species and between species, including how species evolve by natural selection. Population genetics utilises statistical models (like the Hardy-Weinberg equilibrium) to investigate how characteristics evolve through populations.
In a previous section we learned all about nucleic acids: - DNA, RNA, mRNA, tRNA and also learned a bit about they key players involved in the discovery of DNA, important figures such as Crick, Watson, Franklin, Wilkins, and Chargaff…
DNA molecules are pretty big polynucleotides… So, in order to fit into the cell, DNA exists in shorter lengths and each length of DNA is tightly wrapped up with histone proteins to form a complex called chromatin. During most of the life of a cell the chromatin is dispersed throughout the nucleus and cannot be seen with a light microscope. However, parts of the chromatin will unwind so that genes on the DNA can be transcribed.
Just before cell division DNA is replicated, and more histone proteins are synthesised, so there
is temporarily twice the normal amount of chromatin. Following replication the chromatin then
coils up even tighter to form short fat bundles called chromosomes.
Chromosomes are about 100,000 times shorter than fully stretched DNA, and therefore 100,000 times thicker, so chromosomes are “large” enough to be seen under a light microscope.
Chromosome have a sort of “X” shape - this is because a chromosome contains two replicated copies of DNA - with each of ‘arms’ of the “X” being identical. Each “arm” of a chromosome is called a chromatid, and chromatids are joined together at the centromere.
DNA molecules extend form one end of a chromosome to the other, and genes are distributed along the DNA. Each gene has its own specific position on a chromosome, and this position is
known as the locus (loci) of the gene.
Some Key terms: -
Chromatin: - DNA + histones at any stage of the cell cycle.
Chromosome: - Compact, short and thick “X” shaped form of chromatin. Chromosomes are condensed forms of chromatin and are therefore visible during mitosis.
Chromatid: - single arm of an “X” shaped chromosome.
A Level Biology - Chromosome Structure and Key Terminology (i.e. Gene, Allele, Locus...)
A Level Biology - The Eukaryotic Cell Cycle
The cell cycle
There are two ways in which a cell can divide:
Organisms grow and repair by Mitosis.
Whereas Meiosis is a more complex type of cell division with 2 essential things to understand:
The (diploid) chromosomal number is halved
Genes are randomly assorted (i.e. ‘shuffled’) so that each daughter cell contains different combinations of alleles.
A Level Biology - Mitosis