BIO

2.4.6 Explain the role of protein pumps and ATP in active transport across membranes(3).

Active transport involves the movement of substances through the membrane using energy from ATP. The advantage of active transport is that substances can be moved against the concentration gradient, meaning from a region of low concentration to a region of high concentration. This is possible because the cell membrane has protein pumps embedded it which are used in active transport to move substances across by using ATP. Each protein pump only transports certain substances so the cell can control what comes in and what goes out.

2.1.9 State that stem cells retain the capacity to divide and have the ability to differentiate along different pathways. 1

Adults have stems cells in the tissues in their bodies that need to be frequently replaced such as the skin. Stem cells have the ability to produce a wide range of cells which means that they are pluripotent. They retain their ability to divide and produce many different cells by cell division and the process of differentiation. For example, one type of stem cells in the bone marrow produce a variety of red and white blood cells.

2.4.7 Explain how vesicles are used to transport materials within a cell between the rough endoplasmic reticulum , Golgi apparatus and plasma membrane(3).

After proteins have been synthesized by ribosomes they are transported to the rough endoplasmic reticulum where they can be modified. Vesicles carrying the protein then bud off the rough endoplasmic reticulum and are transported to the Golgi apparatus to be further modified. After this the vesicles carrying the protein bud off the Golgi apparatus and carry the protein to the plasma membrane. Here the vesicles fuse with the membrane expelling their content (the modified proteins) outside the cell. The membrane then goes back to its original state. This is a process called exocytosis. Endocytosis is a similar process which involves the pulling of the plasma membrane inwards so that the pinching off of a vesicle from the plasma membrane occurs and then this vesicle can carry its content anywhere in the cell.

2.3.5 State three differences between plant and animal cells (1).

Animal cells only have a plasma membrane and no cell wall. Whereas plant cells have a plasma membrane and a cell wall. Animal cells do not have chloroplasts whereas plant cells do for the process of photosynthesis. Animal cells store glycogen as their carbohydrate resource whereas plants store starch. Animal cells do not usually contain any vacuoles and if present they are small or temporary. On the other hand plants have a large vacuole that is always present. Animal cells can change shape due to the lack of a cell wall and are usually rounded whereas plant cells have a fixed shape kept by the presence of the cell wall.

2.3.2 Annotate the diagram from 2.3.1 with the functions of each named structure.

Annotate: to add brief notes to a diagram or graph. Nucleus: This is the largest of the organelles. The nucleus contains the chromosomes which during interphase are to be found the nucleolus. The nucleus has a double membrane with pores(NP). The nucleus controls the cells functions through the expression of genes. Some cells are multi nucleated such as the muscle fibre Plasma membrane: controls which substances can enter and exit a cell. It is a fluid structure that can radically change shape. see 2.4 The membrane is a double layer of water repellant molecules. Receptors in the outer surface detect signals to the cell and relay these to the interior. The membrane has pores that run through the water repellant layer called channel proteins. Mitochondria: location of aerobic respiration and a majot synthesis of ATP region.. Double membrane organelle. Inner membrane has folds called cristae. This is the site of oxidative phosphorylation. Centre of the structure is called the matrix and is the location of the Krebs cycle. Oxygen is consumed in the synthesis of ATP on the inner membrane The more active a cell the greater the number of mitochondria. Rough endoplasmic reticulum (rER): protein synthesis and packaging into vesicles. rER form a network of tubules with a maze like structure. In general these run away from the nucleus The 'rough' on the reticulum is caused by the presence of ribosomes. Proteins made here are secreted out of the cell Ribosomes: the free ribosome produces proteins for internal use within the cell. Golgi apparatus: modification of proteins prior to secretion. proteins for secretion are modified possible addition of carbohydrate or lipid components to protein packaged into vesicles for secretion Lysozyme: Vesicles in the above diagram that have formed on the golgi apparatus. Containing hydrolytic enzymes. Functions include the digestion of old organelles, engulfed bacteria and viruses.

2.1.10 Outline one therapeutic use of stem cells.2

Bone marrow transplants are one of the many therapeutic uses of stem cells. Stem cells found in the bone marrow give rise to the red blood cells, white blood cells and platelets in the body. These stem cells can be used in bone marrow transplants to treat people who have certain types of cancer. When a patient has cancer and is given high doses of chemotherapy, the chemotherapy kills the cancer cells but also the normal cells in the bone marrow. This means that the patient cannot produce blood cells. So before the patient is treated with chemotherapy, he or she can undergo a bone marrow harvest in which stem cells are removed from the bone marrow by using a needle which is inserted into the pelvis (hip bone). Alternatively, if stem cells cannot be used from the patient then they can be harvested from a matching donor. After the chemotherapy treatment the patient will have a bone marrow transplant in which the stem cells are transplanted back into the patient through a drip, usually via a vein in the chest or the arm. These transplanted stem cells will then find their way back to the bone marrow and start to produce healthy blood cells in the patient. Therefore the therapeutic use of stem cells in bone marrow transplants is very important as it allows some patients with cancer to undergo high chemotherapy treatment. Without this therapeutic use of stem cells, patients would only be able to take low doses of chemotherapy which could lower their chances of curing the disease.

2.1.5 Calculate the linear magnification of drawings and the actual size of specimens in images of know magnification (2).

Calculate means find a numerical answer showing the relevant stages in the working (unless instructed not to do so). On an image of a specimen it is useful to show how much larger/smaller the image is than the real specimen. This is called magnification. Exercise 1: Find a leaf, any leaf around 10-15 cm in length. a) Draw the leaf exactly the same size as the it is in life, add the vein patterns and note the vein pattern at the edges of the leaf. b) Make sure you measure length and breadth of the leaf. c) Add labels for structure d) If you know the name of the species of plant that the leaf comes from add this information. e) A a title 'A diagram to show the structure of a Helianthus spp. leaf'. f) Finally add the magnification as x 1 in the right hand bottom corner of the diagram (but prominent). Exercise 2: Increasing the magnification. a) You must now draw the leaf again but this time doubling every measurement b) Compete your diagram with the label x 2. Exercise 3: Decreasing the magnification a) You must now draw the leaf again but this time half all measurement and dimension. b) Add the label x 0.5 c) This means that all dimension have been decreased by one half of the original value. Calculate magnification from an image: 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 = measured length of the image /measured length of the specimen Length of the actual specimen = length on the image/ magnification ( e.g. rose leaf = image length 4.2cm/ magnification 0.82 = 5cm real length Scale Bars: images often carry a scale bar which is a horizontal line drawn on the image. The scale bar shows how long the line is in the real specimen. This example shows a plant cell. The scale bar indicates the length of 10 microns = 10um Notice that 10 um is about the vertical length of the diameter of the nucleus. All other measurements from the image are made relative to this scale bar. If you measure the actual length of the nucleus in this image and there is a scale bar you can calculate the magnification of the image. See the formula above if you require assistance.

2.2.2 Annotate the diagram from 2.2.1 with the functions of each named structure.

Cell Wall: Made of a 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. Cytoplasm: Contains all the enzymes needed for all metabolic reactions, since there are no organelles. Ribosome: 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. Nucleoid: Is the region of the cytoplasm that contains DNA. It is not surrounded by a nuclear membrane. DNA is always a closed loop (i.e. a circular), and not associated with any proteins to form chromatin. Flagella: These long thread like attachments are generally considered to be for movement. They have an internal protein structure that allows the flagella to be actively moved as a form of propulsion. The presence of flagella tends to be associated with the pathogenicity of the bacterium. The flagella is about 20nm in diameter. This structure should not be confused with the eUkaryotic flagella seen in protoctista. Pilli: These thread like projections are usually more numerous than the flagella. They are associated with different types of attachment. In some cases they are involved in the transfer of DNA in a process called conjugation or alternatively as a means of preventing phagocytosis. 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. Plasmids: Extra-nucleoid DNA of up to 400 kilobase pairs. Plasmids can self-replicate particularly before binary fission. They are associated with conjunction which is horizontal gene transfer. It is normal to find at least one anti-biotic resistance gene within a plasmid. This should not be confused with medical phenomena but rather is an ecological response to other antibacterial compounds produced by other microbes. Commonly fungi will produce anti-bacterial compounds which will prevent the bacteria replicating and competing with the bacteria for a resource. conjugation Direct contact between bacterial cells in which plasmid DNA is transferred between a donor cell and a recipient cell. There is no equal contribution to this process, no fertilisation and no zygote formation. It cannot therefore be regarded as sexual reproduction.

2.2.2 Annotate the diagram from 2.2.1 with the functions of each named structure.

Cell wall: Protects the cell from the outside environment and maintains the shape of the cell. It also prevents the cell from bursting if internal pressure rises. Plasma membrane: Semi-permeable membrane that controls the substances moving into and out of the cell. It contains integral and peripheral proteins. Substances pass through by either active or passive transport. Cytoplasm: Contains many enzymes used to catalyze chemical reactions of metabolism and it also contains the DNA in a region called the nucleoid. Ribosomes are also found in the cytoplasm. Pili: Help bacteria adhere to each other for the exchange of genetic material. Flagella (singular flagellum): Made of a protein called flagellin. Helps bacteria move around by the use of a motor protein that spins the flagellum like a propeller. Ribosomes: They are the site of protein synthesis. Contributes to protein synthesis by translating messenger RNA. Nucleoid: Region containing naked DNA which stores the hereditary material (genetic information) that controls the cell and will be passed on to daughter cells.

2.1.4 Compare the relative sizes of molecules, cell membrane thickness, viruses, bacteria, organelles and cells, using the appropriate SI unit. (3)

Compare: means to Give an account of similarities and differences between two (or more) items, referring to both (all) of them throughout. We depend on the microscope for our observation of cellular structures. Observations of this type are for the most part dependable but we must consider the introduction of 'artifacts' by those processes that prepare the material for microscopy. These artifacts are a consequence of specimen dehydration, contrast enhancement (staining), radiation and microscope function. These artifacts can lead to image or data distortions and misinterpretation. Relative sizes: 1. molecules (1nm). 2. cell membrane thickness (10nm). 3. virus (100nm). 4. bacteria (1um). 5. organelles (less 10um). 6. cells (<100 um). 7. generally plant cells are larger than animal cells. nm= nanometer (10-9m) um= micrometer (10-6m) Molecules of Biological significance are around 1 nm in size where as the cell membrane is about ten times thicker at 10nm. Where as a virus is ten times larger again at around 100nm. where as a bacteria is ten times larger again at around 1 um. where as a eukaryotic animal cell is is ten time larger again at around 10 um. where as a eukaryotic plant cell is ten times larger again at around 100 um.

2.4.4 Define diffusion and osmosis (1).

Diffusion is the passive movement of particles from a region of high concentration to a region of low concentration. Osmosis is the passive movement of water molecules, across a partially permeable membrane, from a region of lower solute concentration to a region of higher solute concentration.

2.1.2 Discuss the evidence for the cell theory. 3

Discuss: Give an account including, where possible, a range of arguments for and against the relative importance of various factors, or comparisons of alternative hypotheses. a. All living things are made of cells: When living things are observed under the microscope they consistently appear to be composed of cells. However, there are a number of examples that do not conform to the standard notion of what a cell looks like at the microscopic level. Exceptions the that test the rule of cell theory: Muscle cells: challenges the idea that a cell has one nucleus. Muscle cells have more than one nucleus per cell Muscle Cells called fibres 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 Cells: challenges the idea that a cell is a single unit. 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: Challenges the idea that a cell is specialised to a single function. Yet, the protoctista can carry out all functions of life. A cell capable of all necessary functions Amoeba Single celled organisms have one region of cytoplasm surrounded by a cell membrane. The protoctista cell is unusual in that it performs all functions. Such cells are usually much larger than other cells such that some biologist consider them 'acellular', that is, non-cellular. This is an image of an amoeba. A single cell protoctista capable of all essential functions. What cell organelles can you see?

2.1.8 Explain that cells in multicellular organisms differentiate to carry out specialized functions by expressing some of their genes but not others. 3

Every cell in a multicellular organisms contains all the genes of that organism. However, the genes that are activated vary from cell to cell. The reason we have different types of cells in our body (the cells in your eyes are not the same as the ones that make up your hair) is because different genes are activated in different cells. For example, the gene that produces keratin will be active in hair and nail cells. Keratin is the protein which makes up hair and nails. Genes encode for proteins and the proteins affect the cell's structure and function so that the cell can specialize. This means cells develop in different ways. This is called differentiation. Differentiation depends on gene expression which is regulated mostly during transcription. It is an advantage for multicellular organisms as cells can differentiate to be more efficient unlike unicellular organisms who have to carry out all of the functions within that one cell.

2.4.6 Explain the role of protein pumps and ATP in active transport across membranes(3).

Explain means to give a detailed account of causes, reasons or mechanisms. Molecules are moved against the concentration gradient from a region of their low concentration to a region of their high concentration. Active mean that the membrane protein 'pump' requires energy (ATP) to function The source of energy is ATP is produced in cell respiration Transported molecules enter the carrier protein in the membrane. The energy causes a shape change in the protein that allows it to move the molecule to the other side of the membrane. The sodium-potassium, pump that creates electro-chemical gradient across the cell membrane of all cells. Cells are -ve charged on the inside relative to the outside. This pump is modified in the nerve cell to create some of the electrochemical phenomena seen in nerve cells.

2.1.8 Explain that cells in multicellular organisms differentiate to carry out specialized functions by expressing some of their genes but not others (3).

Explain means to give a detailed account of causes, reasons or mechanisms. An interesting parallel with economic theories is that the larger collective economic group the greater the number of specialisms, (Adam Smith) a rough guide which is found to hold true in living systems. As a general principle then we find that the larger a multicellular organisms become the more diversity and differentiated specialisms there are within the organism. Rather than all cells carrying out all functions, tissues and organs specialise to particular functions. These organs and systems are then integrated to give the whole organism (with its emergent properties). Differentiation: Cells within a multi cellular organism specialise their function. Specialised 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. What is the benefit of differentiation and specialisation of tissues rather than all tissues carrying out all functions? In a multi cellular organism specialisation is more efficient than the generalised plan when competing for a specific resource. Consider the role of water transport through the plant: In higher plants we have specialisation to for a tubular system called the xylem. This is more efficient way of water transport than simply been passed by the mass movement of water from cell to cell. In the xylem water can be moved very efficiently from underground to the canopy of the highest trees at very little cost to the plant. If there is no specialised tissue for carrying water then the plant would rely on the movement of water by mass flow of diffusion which is very slow. The plant is therefore limited in size and therefore cannot compete with larger species. The study of how animal cells become specialised is called embryology. This study area in biology has been developing very fast in recent time. Some of the discoveries about why some embryonic cells become nerves, muscles or blood cells has led to new ideas about the evolution of life. The new discipline is called evolutionary developmental biology or 'Evo-devo'. The following text is a great introduction to what will become one of the most important aspects of biology for this new century

2.16 Explain the importance of the surface area to volume ratio as a factor limiting cell size (3).

Explain means to give a detailed account of causes, reasons or mechanisms. As the size of a structure increases the surface area to volume ratio decreases. Reasoning: This can be seen by performing some simple calculations concerning different-sized organisms. The rate of exchange of substances therefore depends on the organism's surface area that is in contact with the surroundings. Reason: as organisms get bigger their volume and surface area both get bigger, but not by the same amount. The volume increases as the cube but the area of the surface only increases by the square. Conclusions: As the organism gets bigger its surface area : volume ratio decreases This rule is a limiting factor for cell size. As the cell gets bigger the ratio decreases If the ratio decreases the rate of exchange decreases Example: gas exchange of oxygen for respiration. A cell which respires aerobically demands oxygen for the process. Oxygen is obtained form the surrounding environment such as water or blood (depends on the cell). Oxygen diffuses across the cell membrane. More membrane more diffusion (Surface area= increases by the 2). Bigger cell (Volume = increases by the 3). However the ratio of surface area2 : volume 3 is decreasing Therefore the volume of oxygen obtained for each unit of cell volume is actually decreasing Cells must not get too big because they cannot obtain sufficient oxygen to satisfy the demands of the cell. why cells are small (reasoning): Size as a limiting Factors for cell because: A big cell needs more oxygen than a little cell Big cells need to have more oxygen diffusion across the cell membrane. But the big cell has relatively small surface area compared to its volume i.e. the surface area: volume ratio is small. What ever other benefits a cell might gain from being big, it cannot become larger than is limited by the rate of gas exchange. This reasoning can be applied to nutrients and to waste, anything that is exchanged across the cell surface. Try preparing a reason why size is a limiting factor for: Obtaining nutrient (glucose) Excretion of waste molecules ( urea, ammonia, carbon dioxide).

2.4.7 Explain how vesicles are used to transport materials within a cell between the rough endoplasmic reticulum , Golgi apparatus and plasma membrane(3).

Explain means to give a detailed account of causes, reasons or mechanisms. Cells will manufacture molecules for secretion outside of the cell. Some of these secretion molecules are complex combinations of proteins, carbohydrates and lipids. The base protein is coded for by a gene whose expression begins the process. The animation below picks up the process with the protein already synthesised in the rough endoplasmic reticulum. The animation plays very slowly so that the sequence can be followed. 1. Protein is already synthesised and present in the rER. 2. The protein is moved through the rER and modified. 3. A spherical vesicle is formed form the end of the rER with the protein inside. 4. The vesicle migrates to the golgi apparatus. 5. Vesicle and golgi membranes fuse. The protein is released into the lumen of the golgi apparatus. 6. The golgi modifies the protein further by adding lipid or polysaccharides to the protein. 7. A new vesicle is formed from golgi membrane which then breaks away. The vesicles migrates to the plasma membrane. 8. The vesicle migrates to the plasma membrane fuses and secretes content its contents out of the cell. A process called exocytosis.

2.4.5 Explain passive transport across membranes by simple diffusion and facilitated diffusion (3).

Explain means to give a detailed account of causes, reasons or mechanisms. The passive movement implies that there is no expenditure of energy in moving the molecules from one side of the membrane to the other: However the molecules themselves possess kinetic energy which accounts for why they are in movement. The membrane therefore 'allows' the molecules to pass through without needing to add any additional energy to the kinetic energy already possessed by the particles. Particles will in fact pass in both directions but over all the emerging pattern is that molecules move from a region of their high concentration to a region of their low concentration. Some molecules are so small that they pass through the membrane with little resistance This includes Oxygen and Carbon Dioxide Lipid molecules (even though very large) pass through membranes with very little resistance also. Larger molecules (red) move passively through the membrane via channel proteins These proteins(grey) have large globular structures and complex 3d-shapes The shapes provide a channel through the middle of the protein, the 'pore' The channel 'shields' the diffusing molecule from the non-charged/ hydrophobic/ non-polar regions of the membrane.

2.4.2 Explain how the hydrophobic and hydrophilic properties of phospholipids help to maintain the structure of the cell membranes (3)

Explain means to give a detailed account of causes, reasons or mechanisms. This model of the bilayer's has the proteins removed for clarity. 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 meaning they 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 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.

2.3.5 State three differences between plant and animal cells (1).

LOOK AT CHART 2 State:means to give a specific name, value or other brief answer without explanation or calculation. Only three differences from this list are required. Plant cell electron micrographs and images are provided at this stage although not specified at this point in the syllabus Chloroplast: Note: double membrane internal thylakoid membranes which contain the chlorophyll. Stroma where the calvin cycle fixes CO2 into carbohydrates, oils or starch. Vacuole: The vacuole is a storage area for organic solute such as sugars and amino acids. The vacuole is surrounded by a membrane called the tonoplast which has essentially the same type of structure as the plasma membrane. Cell Wall: Plant cell walls are composed of cellulose (2.3.6) In the electron micrograph we can see cytoplasmic connections through adjacent cells. These are called plasmodesmata.

2.3.4 Comparison of prokaryotic and eukaryotic cells (3).

LOOK AT CHART 2 compare means to give an account of similarities and differences between two (or more) items, referring to both (all) of them throughout.

2.2.3 Identify structures from 2.2.1 in electron micrographs of E. coli.

LOOK AT PAPER 2 1. Note the double membrane of this E. coli . This feature means that the cells do not retain the dark blue stain used in microscopy. They are therefore known as Gram-negative this contrast with Gram-positive single membrane bacteria. 2. There is some evidence in the image of pilli which are the surrounding light grey masses. 3. In the cytoplasm of the bacterium there are no visible organelles which is consistent with how we expect a prokaryote cell to appear. 4. The nucleoid region is not seen well in this particular image but is clearer in the next image.

2.3.3 Identify structures from 2.3.1 in electron micrographs of liver cells.(2)

LOOK AT PIC 2 Identify: To find an answer from a given number of possibilities. To identify structures within an electron micrograph it is necessary to know the scale at which the image has been taken. Look around the image to find the nucleus and then the mitochondria. In a plant cell there will also be the cell wall, chloroplasts and the vacuole to identify. Nucleus: In an electron micrograph the nucleus will be the largest of the organelles. In this image there is a dark stained region called the nucleolus which is the location of the DNA. The membrane has pores which allow the entry of cell signal molecules, nucleotides and the exit of mRNA. Generally the nucleus appears spherical however there are cells in which the nucleus has more unusual shape such as the multi-lobbed white blood cells. Plasma membrane: This image shows the junction between two liver cells. The image has been manipulated for clarity to see the two adjoining plasma membranes. Notice the mitochondria to the left and the rER to the right of the membranes. Mitochondria: This micrograph of a mitochondria shows: Double outer membrane Folded inner membrane called the cristae. Matrix of the mitochondria These features are common to all mitochondria. Notice the rER above the mitochondria for scale and the dark granules of glycogen below the organelle. Endoplasmic reticulum (rER). The rER runs vertical in the image. Note the dark spots which are the ribosomes. A cell with a great deal of rER is producing proteins for secretion outside of the cell. The network of endoplasmic tubules allows proteins to be moved around within the cytoplasm before final packaging and secretion. Golgi apparatus: The golgi apparatus in the diagram forms a stack of membrane envelopes on top of each other. Vesicles containing proteins fuse with the structure. The proteins are modified inside the apparatus usually with the addition of non-protein substances. Lysosome: simple membrane bound vesicle containing hydrolytic enzymes produced in the golgi apparatus. used to digest engulfed bacteria or viruses or old organelles used to digest macromolecules hydrolytic enzymes are retained within the vesicle membrane to prevent autodigestion of the cell. Boston University Histology this site is a great source of histological diagram including those of the liver cell (syllabus specified).

2.4.1 Draw and label a diagram to show the structure of membranes (1).

LOOK AT PIC 2 & CHART 2 Draw: To represent by means of pencil lines.

2.4.3 List the functions of membrane proteins (1).

List means to give a sequence of names or other brief answers with no explanation. LOOK AT CHART 2

2.16 Explain the importance of the surface area to volume ratio as a factor limiting cell size (3).

Many reactions occur within the cell. Substances need to be taken into the cell to fuel these reactions and the wast products of the reactions need to be removed. When the cell increases in size so does its chemical activity. This means that more substances need to be taken in and more need to be removed. The surface area of the cell is vital for this. Surface area affects the rate at which particles can enter and exit the cell (The amount of substances that it takes up from the environment and excretes into the environment), whereas the volume affects the rate at which material are made or used within the cell, hence the chemical activity per unit of time. As the volume of the cell increases so does the surface area however not to the same extent. When the cell gets bigger its surface area to volume ratio gets smaller. To illustrate this we can use three different cubes. The first cube has a side of 1 cm, the second 3 cm and the third 4 cm. If we calculate the surface area to volume ratio we get: Cube 1 Surface area: 6 sides x 12 = 6 cm2 Volume: 13 = 1 cm3 Ratio = 6:1 Cube 2 Surface area: 6 sides x 32 = 54 cm2 Volume: 33 = 27 cm3 Ratio = 2:1 Cube 3 Surface area: 6 sides x 42 = 96 cm2 Volume : 43 = 64 cm3 Ratio = 1.5:1 As we can see the cube with the largest surface area and volume has the smallest surface area to volume ratio. If the surface area to volume ratio gets too small then substances won't be able to enter the cell fast enough to fuel the reactions and wast products will start to accumulate within the cell as they will be produced faster than they can be excreted. In addition, cells will not be able to lose heat fast enough and so may overheat. Therefor the surface area to volume ratio is very important for a cell.

2.4.3 List the functions of membrane proteins (1).

Membrane proteins can act as hormone binding sites, electron carriers, pumps for active transport, channels for passive transport and also enzymes. In addition they can be used for cell to cell communication as well as cell adhesion.

2.4.5 Explain passive transport across membranes by simple diffusion and facilitated diffusion (3).

Membranes are semi-permeable which means that they allow certain molecules through but not others. The molecules can move in and out through passive transport which is a method that does not require any input of outside energy. It can either be done by simple diffusion or facilitated diffusion. Molecules will go from a region of high concentration to a region of low concentration as they move randomly and eventually become evenly distributed within the system if they are permeable to the membrane. Simple diffusion involves the diffusion of molecules through the phospholipid bilayer while facilitated diffusion involves the use of channel proteins embedded in the membrane. The cell membrane is hydrophobic inside so hydrophobic (lipid soluble) molecules will pass through by simple diffusion whereas hydrophilic molecules and charged particles will use facilitated diffusion. Water moves through by osmosis which is also by passive transport. Osmosis involves the movement of water molecules from a region of low solute concentration, to a region of high solute concentration. So if the solute concentration is higher inside the cell than outside the cell, water will move in and vice versa.

2.1.7 State that multicellular organisms show emergent properties (1).

Multicellular organisms show emergent properties. For example: cells form tissues, tissues form organs, organs form organ systems and organ systems form multicellular organisms. The idea is that the whole is greater than the composition of its parts. For example your lungs are made of many cells. However, the cells by themselves aren't much use. It is the many cells working as a unit that allow the lungs to perform their function.

2.1.10 Outline one therapeutic use of stem cells (2).

Outline means to give a brief account or summary. 1.Non-Hodgkins Lymphoma is a cancerous disease of the lymphatic system. Outline of the disease. 1. patient requires heavy does of radiation and or chemotherapy. This will destroy health blood tissue as well as the diseased tissue. 2. Blood is filtered for the presence of peripheral stem cells. Cells in the general circulation that can still differentiate into different types of blood cell otherwise known as stem cells. 3. Bone marrow can be removed before treatment. 4. Chemotherapy supplies toxic drugs to kill the cancerous cells. 5. Radiation can be used to kill the cancerous cells. In time however the cancerous cells adapt to this treatment so that radiation and chemotherapy are often used together. 6. Post radiation/ chemotherapy means that the patients health blood tissues is also destroyed by the treatment. 7. Health stem cells or marrow cells can be transplanted back to produce blood cells again top You may wish to think about more elaborate forms of stem cell therapy. The following information provides an introduction to these technologies. 2. Embryonic Stem cell therapy this animation is an excellent introduction to the use of embryonic stem cell for therapies. 3. Therapeutic cloning . This is a method of obtaining ES cells from someone who has already been born. These stem cells can be used to treat the individual without generating an immune response. The human body recognizes and attacks foreign cells, including stem cells. This is a serious barrier to stem cell therapy. The process of therapeutic cloning is shown in this diagram. It begins by taking a somatic (body) cell from the individual. The somatic cell is fused with an egg that has had its nucleus removed. The resulting cell is genetically identical to the individual because it contains the DNA from the individual's somatic cell. The new cell behaves like a fertilized egg and develops into a blastocyst. ES cells can be harvested from the blastocyst and grown in culture. These ES cells could be used to treat the individual without encountering resistance from his or her immune system. Notice that we do not not refer to this type of blastocyst as an embryo. This is because, technically speaking, an embryo is the result of the union of an egg and a sperm, which has not happened in this case. ¨ 1. The patient requires the replacement of some diseased tissue. First we obtain a health cell from the same patient. 2. At the same time we require a human egg cell. This is mainly as the cell retains the tendency to divide unlike the sample tissue from the patient. 3. The nucleus is removed from the egg and discarded. The cell body itself is retained. 4. The nucleus of the patients cell is removed and retained. The cell body of the patients cell is discarded. 5. The nucleus from the patients cell is transferred to the enucleated cell body. 6. The cells then stimulated to divide forming a clone. 7. The cell mass forms a blastocyst. 8. The inner cell mass becomes a source of totipotent stem cells. Totipotent means they are capable of being stimulated to become one of any type of cell. 9. Cells are stimulated using differentiation factors to become the type of cell required for therapy. 10. Therapy would require the transfer of the new healthy cell to the patient. In therapeutic cloning these cells have the same immune system identity as the patient therefore there is not immune rejection problem. It is important that this technique is not confused with embryonic stem cell cultures or with reproductive cloning.

2.3.6 Outline two roles of extracellular components. 3

Outline means to give a brief account or summary. a) Plant cell wall. Found around all plant cells Composed of cellulose. Maintains the shape of the cell. Provides structural support against the force of gravity. prevents excessive uptake of water by the cell b) Animal extracellular matrix i) Basement membrane: a secretion formed from collagen and glycoproteins joined together by a third 'linkage' protein. Their exact composition varies form tissue to tissue. Support: the membrane surrounds the tissues of lines ducts. It provides structural support for the integrity of the tissue or organ. Usually found as the basal lamina or basement membrane of epithelial cells. Filter : The basement membrane of the kidney glomerulus provides the effective barrier for ultrafiltration Vascular niche : Interestingly cells often require a base on which to organise before they will form proper tissue. There are implications here for developmental biology, tissue repair, stem cell therapies and cancer treatment. ii) Interstitial matrix: Bone has a matrix which includes collagen with a calcium phosphate. Other tissues are surrounded by a matrix composed of a kind of gel that provides support for the tissue.

2.1.1 Outline the cell theory. 2

Outline: To give a brief account or summary. All living things are made of cells. Cells are the smallest unit of life. Existing cells have come from other cells. Stated in this way Cell Theory might be attributed to Schleiden and Schwann (1838). Robert Hooke first coined the term 'cell' after observing the structure of cork in 1655. The first observation of living cells was by Anton van Leeuwenhoek in 1674.

2.4.2 Explain how the hydrophobic and hydrophilic properties of phospholipids help to maintain the structure of the cell membranes (3)

Phospholipid molecules make up the cell membrane and are hydrophilic (attracted to water) as well as hydrophobic (not attracted to water but are attracted to other hydrophobic tails). They have a hydrophilic phosphate head and two hydrophobic hydrocarbon tails. Cell membranes are made up of a double layer of these phospholipid molecules. This is because in water the hydrophilic heads will face the water while the hydrophobic tails will be in the center because they face away from the water. The phospholipid bilayer makes the membrane very stable but also allows flexibility. The phospholipid in the membrane are in a fluid state which allows the cell to change it's shape easily.

2.2.4 State that prokaryotic cells divide by binary fission (1).

Prokaryotic cells divide by binary fission. Binary fission is a method of asexual reproduction involving the splitting of the parent organism into two separate organisms.

2.3.4 Comparison of prokaryotic and eukaryotic cells (3).

Prokaryotic cells have naked DNA which is found in the cytoplasm in a region named the nucleoid. On the other hand, eukaryotes have chromosomes that are made up of DNA and protein. These chromosomes are found in the nucleus enclosed in a nuclear envelope. Prokaryotes do not have any mitochondria whereas eukaryotes do. Prokaryotes have small ribosomes (70S) compared to eukaryotes which have large ribosomes (80S). In prokaryotes there are either no or very few organelles bounded by a single membrane in comparison to eukaryotes which have many of them including the Golgi apparatus and the endoplasmic reticulum.

2.1.4 Compare the relative sizes of molecules, cell membrane thickness, viruses, bacteria, organelles and cells, using the appropriate SI unit (3)

Remember: 1 millimeter (mm) = 10-3 meters 1 micrometer (μm) = 10-3 millimeters 1 nanometer (nm) = 10-3 micrometers A molecule = 1 nm Thickness of cell membrane = 10 nm Viruses = 100 nm Bacteria = 1μm Organelles = up to 10 μm Eukaryotic cells = up to 100 μm

2.3.2 Annotate the diagram from 2.3.1 with the functions of each named structure.

Ribosomes: Found either floating free in the cytoplasm or attached to the surface of the rough endoplasmic reticulum and in mitochondria and chloroplast. Ribosomes are the site of protein synthesis as they translate messenger RNA to produce proteins. Rough endoplasmic reticulum: Can modify proteins to alter their function and/or destination. Synthesizes proteins to be excreted from the cell. Lysosome: Contains many digestive enzymes to hydrolyze macromolecules such as proteins and lipids into their monomers. Golgi apparatus: Receives proteins from the rough endoplasmic reticulum and may further modify them. It also packages proteins before the protein is sent to it's final destination which may be intracellular or extracellular. Mitochondrion: Is responsible for aerobic respiration. Converts chemical energy into ATP using oxygen. Nucleus: Contains the chromosomes and therefore the hereditary material. It is responsible for controlling the cell.

2.2.4 State that prokaryotic cells divide by binary fission (1).

State:means to give a specific name, value or other brief answer without explanation or calculation. Prokaryotic cells divide by binary fission. This is an asexual method of reproduction in which a 'parental' cell divides into two smaller but equally sized cells. The cells are genetically identical and form the basis of a reproductive clone. a little extra information for the interested reader. The process of binary fission takes place in four stage: (a). Reproduction signal: The cell receives a signal, of internal or external origin that initiates the cell division. E.coli replicates about once every 40 minutes when incubated at 37o C. If however we increase the concentration of carbohydrate nutrients that the cell is supplied with then the division time can be reduced to 20 minutes. There is a suggestion here that an external signal (nutrient concentration) is acting as the reproductive signal. (b). Replication of DNA: bacterial cells have a single condensed loop of DNA. This is copied by a process known as semi-conservative replication to produce two copies of the DNA molecule one for each of the daughter cells The replication begins at a single point (ori)on the loop of DNA. The process proceeds around the loop until two loop have been produced, each a copy of the original. The process finishes at a single point on the loop of DNA called the ter position. (c). Segregation of DNA: One DNA loop will be provided for each of the daughter cells. As the new loops form the ori site becomes attached to some contractile proteins that pull the two ori sites, and therefore the loops, to opposite ends of the cell. This is an active process that requires the bacteria to use energy for the segregation. (d). Cytokinesis: Cell separation. This occurs once the DNA loop replication and segregation is complete. The DNA completes a process of condensing whilst the plasma membrane begins to form a 'waist' or constriction in the middle of the cell. As the plasma membrane begins to pinch and constrict the membrane fuses and seals with additional new membrane also being formed.

2.1.9 State that stem cells retain the capacity to divide and have the ability to differentiate along different pathways(1).

State:means to give a specific name, value or other brief answer without explanation or calculation. A stem cell retains the capacity to divide and has the ability to differentiate along different pathways. A stem cell is able to divide but has not yet expressed genes to specialise to a particular function. Under the right conditions stem cells can be induced to express particular genes and differentiate into a particular type of cell. Stem cells can be obtained from a variety of different places including the blastocyte. Adults still posses stem cells in some organs but much less so than a child. Even the placenta can be a useful source of stem cells.

2.1.3 State that unicellular organisms carry out all the functions of life (1).

State:means to give a specific name, value or other brief answer without explanation or calculation. These organisms are able to carry out all the processes which are characteristic of living things such as: a. metabolism which includes respiration the synthesis of ATP. b. response to a change in the environment c. homeostasis the maintenance and regulation of internal cell conditions. d. growth which for a unicellular organism means an increase in cell size and volume. e. reproduction which for the unicellular organism is largely asexual through cell division to form a clone. f. nutrition which means either the synthesis of organic molecules or the absorption of organic matter.

2.1.7 State that multicellular organisms show emergent properties (1).

State:means to give a specific name, value or other brief answer without explanation or calculation. syllabus: 'Emergent properties arise from the interaction of the component parts; the whole is greater than the sum of the parts'. Systems biologists attempt to put together the parts that make up a system and then observe the properties of that 'emerge' from the system but which could not have predicted from the parts themselves. As a model consider the electric light bulb. The bulb is the system and is composed of a filament made of tungsten, a metal cup, and a glass container. We can study the parts individually how they function and the properties they posses. These would be the properties of : Tungsten Metal cup Glass container. When studied individually they do not allow the prediction of the properties of the light bulb. Only when we combine them to form the bulb can these properties be determined. There is nothing supernatural about the emergent properties rather it is simply the combination of the parts that results in new properties emerging. Emergence,reductionism and Biology 2 The approach of the physical sciences is to reduce an inanimate phenomenon to its constituent parts and that knowledge of these will explain the phenomena as a whole. The parts do not vary (otherwise there would be more parts) and these are predictable within the laws and principles that describe them. Since the smallest parts are predictable then the system as a whole is predictable. No new properties will arise from the sum of the parts, this is explanatory reductionism. Biological systems need a different approached, population thinking, which acknowledges the role of variation in a population. Consequently the deterministic laws and theories of the physical sciences do not apply to all aspects of biological systems. The 'parts' of the living system vary on both a phenotypic level and at the level of the genetic program. This is an important feature of the biological system (compared to the non-living) which is affected by both the physiochemical laws and also by a genetic program. Theory reduction is the concept that theories and laws in one science field are simply special cases of theories which are to be found in the physical sciences. Emergence is the occurrence of unexpected characteristics or properties in a complex system. These properties emerge from the interaction of the 'parts' of the system. Remember that biology insists on a population thinking so that we know the interacting 'parts' vary in themselves and therefore their 'emerging' properties can only be generalised. On a biological scale consider the current debate about the nature of human consciousness or the origin of life itself. 1Concise Oxford English Dictionary 10th edition revised: (2002), Oxford University Press: New York 2 Mayr, E (2004) What Makes Biology Unique? Cambridge University Press: Cambridge

2.1.5 Calculate the linear magnification of drawings and the actual size of specimens in images of know magnification (2).

Take a measurement of the drawing (width or length) Take this same measurement of the specimen Remember to convert units if needed to Place your values into the equation Magnification = length of drawing / length of actual specimen You can also calculate the length of the specimen if this is unknown: length of the drawing / magnification. Conversion of units: 1 centimeter = 10-2 meters 1 millimeter = 10-3 meters 1 micrometer = 10-6 meters 1 nanometer = 10-9 meters

2.1.1 Outline the cell theory. 2

The cell theory states that: All living organisms are composed of cells. Multicellular organisms (example: humans) are composed of many cells while unicellular organisms (example: bacteria) are composed of only one cell. Cells are the basic unit of structure in all organisms. Cells are the smallest unit of life. They are the smallest structures capable of surviving on their own. Cells come from pre-exsisting cells and cannot be created from non-living material. For example, new cells arise from cell division and a zygote (the very first cell formed when an organism is produced) arises from the fusion of an egg cell and a sperm cell.

2.4.8 Describe how the fluidity of the membrane allow s it to change shape, break and re-form during endocytosis and exocytosis(2).

The phospholipids in the cell membrane are not solid but are in a fluid state allowing the membrane to change its shape and also vesicles to fuse with it. This means substances can enter the cell via endocytosis and exit the cell via exocytosis. The membrane then returns to its original state. In exocytosis the vesicles fuse with the membrane expelling their content outside the cell. The membrane then goes back to its original state. Endocytosis is a similar process which involves the pulling of the plasma membrane inwards so that a vesicle is pinched off it and then this vesicle can carry its content anywhere in the cell.

2.3.6 Outline two roles of extracellular components. 3

The plant cell wall gives the cell a lot of strength and prevents it from bursting under high pressure as it is made up of cellulose arranged in groups called microfibrils. It gives the cell its shape, prevents excessive water up take by osmosis and is the reason why the whole plant can hold itself up against gravity. The animal cell contains glycoproteins in their extracellular matrix which are involved in the support, movement and adhesion of the cell.

2.1.2 Discuss the evidence for the cell theory. 3

When scientists started to look at the structures of organisms under the microscope they discovered that all living organisms where made up of these small units which they proceeded to call cells. When these cells were taken from tissues they were able to survive for some period of time. Nothing smaller than the cell was able to live independently and so it was concluded that the cell was the smallest unit of life. For some time, scientists thought that cells must arise from non-living material but it was eventually proven that this was not the case, instead they had to arise from pre-exsisting cells. An experiment to prove this can be done as follows: Take two containers and put food in both of these Sterilize both of the containers so that all living organisms are killed Leave one of the containers open and seal the other closed What will happen is that in the open container mold will start to grow but in the container that was sealed no mold will be present. The reason for this is because in the open container, cells are able to enter the container from the external environment and start to divide and grow. However, due to the seal on the other container no cells will be able to enter and so no mold will develop, proving that cells cannot arise from non-living material.

2.4.8 Describe how the fluidity of the membrane allow s it to change shape, break and re-form during endocytosis and exocytosis(2).

a) Exocytosis: vesicle membrane fuses with the plasma membrane. b) Endocytosis:a vesicle is formed by the infolding of the plasma membrane In each of the cases above the membranes are able to form and break without loss of the continuity of the plasma membranes. The process is very similar to the childhood game of playing with bubbles of detergent. Bubbles are produced then they can be watched readily joining together or splitting apart. The process is readily observed in cells but proof of the mechanism was not produced until 2002 by Lin Yang and Huey Huang. Membrane fluidity: (a) The phospholipid molecules can change places in the horizontal plane. This creates the so called fluid property of the membrane. (b) Molecule exchange in the vertical plane does not occur. This maintains the integrity of the membrane. (c) Cholesterol embedded in the membrane reduces its fluidity. top Mechanism for the making and breaking of the cell membrane. The Li Yang and Huey Huang model has shown that it is the proportion of other molecules in the plasma membrane that will determine whether is opens or closes. It is suggested that the molecules that initiate membrane fusion or breakage will be:lipids;proteins and cholesterol. They derived their model by a serendipitous observations whilst performing other experiments. With x-ray diffraction patterns they showed how the phospholipids will form an hourglass shape at the point of contact. (click image for diffraction x-rays) The sequence of diagrams shows how a membrane might fuse or split and yet self-seal during a wide variety of biological situations. It has not been lost on the researchers the potential uses of this knowledge and mechanism in medical therapies. In the model: (a) Membranes approach. (b) Touching membranes note how the phospholipid heads flow together starting the process of fusion. As noted above this requires the presence of additional molecules. (c) At the point of contact there is a single lipid bilayer. (d) The pore is open and the membranes are now continuous. Mouse-over the image for evidence x-ray diffraction images.

2.4.4 Define diffusion and osmosis (1).

define means to give the precise meaning of a word, phrase or physical quantity. Diffusion: passive movement of particles from a region of high concentration to a region of low concentration. Osmosis is the passive movement of water molecules from a regions of lower solute concentration to a region of higher solute concentration DIffusion ideas: This model illustrates the main features of the process of diffusion. The movement of particles is caused by the kinetic energy possessed by the particle. The direction of movement is random. Observing groups of particles it emerges that they move from regions of high concentration to regions of low concentration. Alternatively the statement can be in terms of pressure. Movement from a region of high pressure to a region of low pressure. However, most biological diffusion takes place through membranes and involves sources, sinks and diffusion gradient. top This model shows diffusion through a membrane: The region that supplies and maintains the high concentration of particles are called the source. The place where the substances is continually removed (or changed) is called the sink. Maintaining the concentration gradient between the two areas is a feature of biological systems. A concentration gradient maintains the movement of the substance. e.g. Source = blood oxygen. Sink= respiring cell top Osmosis ideas: water moves(because they have kinetic energy) through plasma membranes pores called aquaporin. In this image of osmosis the solute is represented by the green molecules. The water is represented by the blue molecules. The water molecules have kinetic energy like other molecules. The water molecules move randomly and will if they come into contact with the membrane pass straight through. The tendency is for water to pass from lower solute (left) to higher solute (right) concentrations.

2.2.1 Draw and label a diagram of the ultrastructure of Escherichia coli (E. coli) as an example of a prokaryote (1)

look at drawing 1

2.2.1 Draw and label a diagram of the ultrastructure of Escherichia coli (E. coli) as an example of a prokaryote (1)

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2.2.3 Identify structures from 2.2.1 in electron micrographs of E. coli.

look at paper 1

2.3.1.Draw and label a diagram of the ultrastructure of a liver cell as an example of an animal cell (1).

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2.3.3 Identify structures from 2.3.1 in electron micrographs of liver cells.

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2.4.1 Draw and label a diagram to show the structure of membranes (1).

look at pic 1

2.3.1.Draw and label a diagram of the ultrastructure of a liver cell as an example of an animal cell (1).

look at pic 2