Topic 1 Cell Biology Notes

Topic 1 Cell Biology 1.1 Introduction to Cells 1.1 U1 According to the cell theory, living organisms are composed of cells. The Cell Theory  All living things are composed of cells (or cell products)  The cell is the smallest unit of life  Cells only arise from pre-existing cells 1.1 U2 Organisms consisting of only one cell carry out all functions of life in that cell. Students are expected to be able to name and briefly explain these functions of life: nutrition, metabolism, growth, response, excretion, homeostasis and reproduction. Unicellular organisms must carry out at least seven functions of life  Metabolism - The web of all the enzyme-catalyzed reactions in a cell e.g. respiration  Response – the ability to react to changes in the environment  Homeostasis - The maintenance and regulation of internal cell conditions, e.g. water and pH  Growth – Irreversible increase in size  Excretion - The removal of metabolic waste  Reproduction - Producing offspring, either sexually or asexually  Nutrition - Feeding by synthesis of organic molecules (e.g. photosynthesis) or the absorption of organic matter 1.1 U3 Surface area to volume For metabolism to continue, reactants used in metabolism must be absorbed and the waste products must be removed ratio is important in  Material exchange is a function of the plasma membrane – larger surface area to volume the limitation of cell ratio means that the cell can act more effectively as there is more membrane to serve size. every unit of volume that requires change  Hence, the rate of metabolic reactions are proportional to the surface area to volume ratio of the cell Benefits of larger SA:Vol ratio  Diffusion pathways are shorter – molecules travel less to get in/out of cell, less time and energy (if it is active transport) is consumed  Concentration gradients are easier to generate – makes diffusion more efficient As a cell grows, volume (units3) increases faster than surface area (units2), leading to a decreased SA:Vol ratio  If metabolic rate exceeds the rate of exchange of vital materials and wastes (low SA:Vol ratio), the cell will eventually die Cells maintain their SA:Volume ratio by:  Dividing and remaining small to maintain a high SA:Volume ratio  Cells and tissues specialised for gas and material exchange will increase their surface area to optimise material transfer o Intestinal tissue of the digestive tract may form a ruffled structure (villi) to increase the surface area of the inner lining o Alveoli within the lungs have membranous extensions called microvilli, which function to increase the total membrane surface 1.1 U4 Multicellular organisms have properties that emerge from the interaction of their cellular components. Multicellular organisms are capable of completing functions that unicellular organisms could not undertake – this is due to the collective actions of individual cells combining to create new synergistic effects (emergent properties)  Cells → Tissues → Organs → Organ systems 1.1 U5 Specialized tissues can develop by cell differentiation in multicellular organisms. All specialized cells and the organs constructed from them have developed as a result of differentiation 1.1 U6 Differentiation involves Differentiation is the process during development whereby newly formed cells become more the expression of some specialised and distinct from one another as they mature  All (diploid) cells of an organism share an identical genome – each cell contains the entire genes and not others in a cell’s genome.   set of genetic instructions for that organism The activation of different instructions (genes) within a cell by chemical signals will cause it to differentiate As a result of gene expression the cell’s metabolism and shape changes to carry out a specialized function (cell differentiation) The capacity of stem cells to divide and differentiate along different pathways is necessary in embryonic development and also makes stem cells suitable for therapeutic uses. When a cell differentiates and becomes specialised, it loses its capacity to form alternative cell types 1.1 A1 Questioning the cell theory using atypical examples, including striated muscle, giant algae and aseptate fungal hyphae. Striated muscle fibers  Muscle cells fuse to form fibers that may be very long (>300mm)  Consequently, they have multiple nuclei despite being surrounded by a single, continuous plasma membrane  Challenges the idea that cells always function as autonomous units Aseptate fungal hyphae  Fungi may have filamentous structures called hyphae, which are separated into cells by internal walls called septa  Some fungi are not partitioned by septa and hence have a continuous cytoplasm along the length of the hyphae  Challenges the idea that living structures are composed of discrete cells Giant Algae  Certain species of unicellular algae may grow to very large sizes (e.g. Acetabularia may exceed 7 cm in length)  Challenges the idea that larger organisms are always made of many microscopic cells 1.1 A2 Investigation of functions of life in Paramecium and one named photosynthetic unicellular organism. Paramecium:  Metabolism – most metabolic pathways happen in the cytoplasm  Response – the wave action of the cilia moves the paramecium in response to changes in the environment, e.g. towards food.  Homeostasis – contractile vacuole fill up with water and expel through the plasma membrane to manage the water content  Growth – after consuming and assimilating biomass from food the paramecium will get larger until it divides.  Reproduction – The nucleus can divide to support cell division by mitosis, reproduction is often asexual  Excretion – the plasma membrane control the entry and exit of substances including expulsion of metabolic waste  Nutrition – food vacuoles contain organisms the paramecium has consumed 1.1 U7 Chlorella or Scenedesmus are suitable photosynthetic unicells, but Euglena should be avoided as it can feed heterotrophically. Stem cells are unspecialised cells that have two key qualities: 1. Self Renewal – They can continuously divide and replicate 2. Potency – They have the capacity to differentiate into specialised cell types There are four main types of stem cells present at various stages of human development:  Totipotent – Can form any cell type, as well as extra-embryonic (placental) tissue (e.g. zygote)  Pluripotent – Can form many cell type (e.g. embryonic stem cells)  Multipotent – Can differentiate into a number of closely related cell types (e.g. haematopoietic adult stem cells)  Unipotent – Cannot differentiate, but are capable of self-renewal (e.g. progenitor cells, muscle stem cells Chlorella:  Metabolism – most metabolic pathways happen in the cytoplasm  Response – the wave action of the cilia moves the algae in response to changes in the environment, e.g. towards light.  Homeostasis – contractile vacuole fill up with water and expel through the plasma membrane to manage the water content  Growth – after consuming and assimilating biomass from food the algae will get larger until it divides.  Reproduction – The nucleus can divide to support cell division, by mitosis (these cells are undergoing cytokinesis)  Excretion – the plasma membrane control the entry and exit of substances including the diffusion out of waste oxygen  1.1 A3 Use of stem cells to treat Stargardt’s disease and one other named condition. Nutrition – photosynthesis happens inside the chloroplasts to provide the algae with food Stem cells can be used to replace damaged or diseased cells with healthy, functioning ones This process requires:  The use of biochemical solutions to trigger the differentiation of stem cells into the desired cell type  Surgical implantation of cells into the patient’s own tissue  Suppression of host immune system to prevent rejection of cells (if stem cells are from foreign source)  Careful monitoring of new cells to ensure they do not become cancerous Stargardt’s disease  A genetic disease due to a recessive mutation of a gene that causes a membrane protein used for active transport in retina cells to malfunction  Photoreceptor cells (light detectors) in the retina degenerate, ultimately resulting in progressive vision loss, to the point of blindness  Treated by replacing dead cells in the retina with functioning ones derived from stem cells Leukemia  Type of cancer that produces abnormally large numbers of white cells  To remain healthy in the long run, the patient must be able to produce the white blood cells needed to fight the disease  Fluid is removed from the bone marrow, to extract adult stem cells – only have the potential of producing blood cells  A high dose of chemotherapy drugs is given to the patient, to kill all the cancer cells in the bone marrow, which disables the bone marrow’s ability to produce blood cells  The stem cells are then returned to the patient’s body, re-establishes themselves in the patient’s bone marrow, multiply and start to produce red and white blood cells 1.1 A4 Ethics of the therapeutic use of stem cells from specially created embryos, from the umbilical cord blood of a new-born baby and from an adult’s own tissues. Differentiation Ease of extraction Ethics of extraction Tumour risk Genetic damage Compatibility Embryonic stem cells Almost unlimited growth potential, can differentiate into any type in the body Can be obtained from excess embryos generated by IVF programs Removal of cells from the embryo kills it Cord blood stem cells Adult stem cells Limited capacity to differentiate into different cell types – less growth potential than embryonic stem cells Easily obtained and stored, however limited quantities of stem cells Difficult to obtain as there are very few, and are buried deep in tissues Umbilical cord is discarded at birth whether or not stem cells are harvested Lower risk of development Removal of stem cells does not kill the adult form which the cells are taken More risk of becoming tumour cells Less chance of genetic damage than adult cells Likely to be genetically different to the patient Due to accumulation of mutations through the life of the adult, genetic damage can occur Fully compatible with the patient as the stem cells are genetically identical – no rejection problems occur The ethical considerations associated with the therapeutic use of stem cells will depend on the source  Using multipotent adult tissue may be effective for certain conditions, but is limited in its scope of application  Stem cells derived from umbilical cord blood need to be stored and preserved at cost, raising issues of availability and access  The greatest yield of pluripotent stem cells comes from embryos, but requires the destruction of a potential living organism 1.1 S1 Use of a light microscope to investigate the 1mm = 1000 m structure of cells and tissues, with drawing of cells. Calculation of the magnification of drawings and the actual size of structures and ultrastructures shown in drawings or micrographs. Scale bars are useful as a way of indicating actual sizes in drawings and micrographs. 1.2 Ultrastructure of Cells 1.2 U1 1.2 U2 Prokaryotes have a simple cell structure without compartmentalization. Prokaryotes are organisms whose cells lack a nucleus ('pro' = before; 'karyon' = nucleus) Prokaryotic Features Prokaryotic cells will typically contain the following cellular components:  Cytoplasm – internal fluid component of the cell  Nucleoid – region of the cytoplasm where the DNA is located (DNA strand is circular and called a genophore)  Plasmids – autonomous circular DNA molecules that may be transferred between bacteria (horizontal gene transfer)  Ribosomes – complexes of RNA and protein that are responsible for polypeptide synthesis (prokaryote ribosome = 70S)  Cell membrane – Semi-permeable and selective barrier surrounding the cell  Cell wall – rigid outer covering made of peptidoglycan; maintains shape and prevents bursting (lysis)  Capsule – a thick polysaccharide layer used for protection against desiccation (drying out) and phagocytosis  Flagella – Long, slender projections containing a motor protein that enables movement (singular: flagellum)  Pili – Hair-like extensions that enable adherence to surfaces (attachment pili) or mediate bacterial conjugation (sex pili) Eukaryotes are organisms whose cells contain a nucleus (‘eu’ = good / true; ‘karyon’ = Eukaryotes have a compartmentalized cell nucleus)  They have a more complex structure and are believed to have evolved from prokaryotic structure. cells (via endosymbiosis)  Their chromosomes are bund by a nuclear envelope consisting of a double layer of membrane  Eukaryotic cells are compartmentalised by membrane-bound structures (organelles) that perform specific roles Animal Cell Plant Cell The advantages of being compartmentalized:  Efficiency in metabolism - enzymes and substrates are localized and much more concentrated  Localized conditions - pH and other such factors can be kept at optimal levels. The optimal pH level for one process in one part of the cell  Toxic/ damaging substances can be isolated - e.g. digestive enzymes (that could digest itself) are stored in lysozymes  Numbers and locations of organelles can be changed - dependent on the cell's requirements 1.2 U3 1.2 A1 Electron microscopes have a much higher resolution than light microscopes. Structure and function of organelles within exocrine gland cells of the pancreas and within palisade mesophyll cells of the leaf. Resolution is the shortest distance between two points that can be distinguished Beams of electrons have a much shorter wavelength than light, so electron microscopes have a much higher resolution  Electron microspores have a resolution that is 200 times greater than light microscopes  Light microscopes reveal the structure of cells, but electron microscopes reveal the ultrastructure Structure Phospholipid bilayer embedded with proteins Function Semi-permeable and selective barrier surrounding the cell Double membrane structure with folded inner membrane (cristae), fluid inside (matrix) Two subunits made of RNA and protein; larger in eukaryotes (80S) than prokaryotes (70S) Double membrane structure with pores; contains DNA associated with histone proteins Site of aerobic respiration (ATP production) Rough endoplasmic reticulum Golgi apparatus A network of flattened membrane sacs (cisternae) that are studded with ribosomes (rough ER) Consists of flattened membrane sacs called cisternae Vesicles Lysosomes Single membrane with fluid inside Single membrane structures formed by the golgi apparatus, containing high concentration of digestive enzymes Microtubules are cylindrical fibres. Protein synthesized by the ribosomes of the rER passes into its cisternae and is then carried by vesicles Involved in the sorting, storing, modification and export of secretory products Transport material inside the cell Break down ingested food in vesicles using digestive enzymes Plasma membrane Mitochondrion Ribosomes Nucleus Microtubules and Site of polypeptide synthesis (this process is called translation) Stores genetic material (DNA) as chromatin; nucleolus is site of ribosome assembly Radiating microtubules form spindle centrioles (animals only) Cilia and flagella Chloroplast (plants only) Vacuoles Cell wall (plants only) 1.2 A2 Prokaryotes divide by binary fission. 1.2 S1 Drawing of the ultrastructure of prokaryotic cells based on electron micrographs. Drawings of prokaryotic cells should show the cell wall, pili and flagella, and plasma membrane enclosing cytoplasm that contains 70S ribosomes and a nucleoid with naked DNA. Centrioles form an anchor point for microtubules during cell division. Also present inside cilia and flagella Whip like structures projecting from the cell surface. Contain a ring of nine double microtubules and two central ones Double membrane structure with internal stacks of membranous discs (thylakoids) Fluid-filled internal cavity surrounded by a membrane External outer covering made of cellulose fibres and move chromosomes during cell division Cilia and flagella can be used for locomotion Site of photosynthesis – manufactured organic molecules are stored in various plastids Maintains hydrostatic pressure Provides support and mechanical strength; prevents excess water uptake Prokaryotes reproduce asexually using the process of binary fission 1. The DNA is replicated semi conservatively 2. The two DNA loops attach to the membrane 3. The membrane elongates and pinches off (cytokinesis) forming two separate cells 4. The two daughter cells are genetically identically (clones) 1.2 S2 Drawing of the ultrastructure of eukaryotic cells based on electron micrographs. Drawings of eukaryotic cells should show a plasma membrane enclosing cytoplasm that contains 80S ribosomes and a nucleus, mitochondria and other membrane-bound organelles are present in the cytoplasm. Some eukaryotic cells have a cell wall. 1.2 S3 Interpretation of electron micrographs to identify organelles and deduce the function of specialized cells. 1.3 Membrane Cell Structure 1.3 U1 Phospholipids form Structure of Phospholipids:  Consist of a polar head (hydrophilic) composed of a glycerol and a phosphate molecule bilayers in water due to  Consist of two non-polar tails (hydrophobic) composed of fatty acid (hydrocarbon) the amphipathic chains properties of  Because phospholipids contain both hydrophilic (water-loving) and lipophilic (fatphospholipid loving) regions, they are classed as amphipathic molecules. Amphipathic phospholipids have hydrophilic and hydrophobic properties. The phosphate heads are attracted to water but the hydrocarbon tails are attracted to each other, but not to water  Because of this, the phospholipids become arranged into double layers, with the hydrophobic tails facing inwards towards each other and the hydrophilic heads facing the water on either side  This double layer is called the phospholipid bilayer Properties of the Phospholipid Bilayer:  The bilayer is held together by weak hydrophobic interactions between the tails  Hydrophilic / hydrophobic layers restrict the passage of many substances  Individual phospholipids can move within the bilayer, allowing for membrane fluidity and flexibility  This fluidity allows for the spontaneous breaking and reforming of membranes (endocytosis / exocytosis) 1.3 U2 Membrane proteins are Proteins  Integral proteins are permanently embedded, many go all the way through and are diverse in terms of polytopic (many surface), integral proteins penetrating just one surface are monotopic structure, position in  Peripheral proteins usually have a temporary association with the membrane, they can the membrane and be monotopic or attach to the surface function. Glycoproteins  Are proteins with an oligosaccharide (few sugar) chain attached  They are important for cell recognition by the immune system and as hormone receptors Functions of Membrane Proteins Transport: Protein channels (facilitated) and protein pumps (active) Receptors: Peptide-based hormones (insulin, glucagon, etc.) Anchorage: Cytoskeleton attachments and extracellular matrix Cell recognition: MHC proteins and antigens Intercellular joinings: Tight junctions and plasmodesmata Enzymatic activity: Metabolic pathways (e.g. electron transport chain) 1.3 U3 Cholesterol is a component of animal Cholesterol is a component of animal cell membranes, where it functions to maintain integrity and mechanical stability cell membranes.     1.3 A1 Cholesterol is a type of lipid, but not a fat or oil Most of a cholesterol molecule is hydrophobic and therefore is attracted to the hydrophobic hydrocarbon tails in the centre of the membrane One end of the cholesterol molecule has a hydroxyl (-OH) group which is hydrophilic and attracted to the phosphate heads of the periphery of the membrane They are therefore amphipathic and are positioned between phospholipids in the membrane The hydrophobic hydrocarbon tails usually behave as a liquid, but the hydrophilic phosphate Cholesterol in mammalian heads act more like a solid  Overall the membrane is fluid as the components of the membrane are free to move membranes reduces membrane fluidity and It is important to regulate the degree of fluidity: permeability to some  Membranes need to be fluid enough so that the cell can move and the required solutes. substances can move across the membrane  If too fluid however the membrane could not effectively restrict the movement of substances across itself Cholesterol’s role in membrane fluidity  Cholesterol disrupts the regular packing of the hydrocarbon tails of phospholipid molecules, so prevents them crystallising and behaving as a solid  It restricts the molecular motion and therefore the fluidity of the membrane  It reduces the permeability to hydrophilic particles such as sodium ion and hydrogen ions  Due to its shape cholesterol can help membranes to curve into a concave shape, which helps the formation of vesicles during endocytosis 1.3 S1 Drawing of the fluid mosaic model. Drawings of the fluid mosaic model of membrane structure can be two dimensional rather than three dimensional. Individual phospholipid molecules should be shown using the symbol of a circle with two parallel lines attached. A range of membrane proteins should be shown including glycoproteins. 1.3 S2 When viewed under a transmission electron microscope, membranes exhibit a Analysis of evidence characteristic 'trilaminar’ appearance (3 layers – two dark outer layers and a lighter inner region) from electron microscopy that led to the proposal of the Electron Micrograph of Plasma Membrane Davson-Danielli model. Danielli and Davson proposed a model whereby two layers of protein flanked a central phospholipid bilayer  The model was described as a 'lipo-protein sandwich’, as the lipid layer was sandwiched between two protein layers  The dark segments seen under electron microscope were identified (wrongly) as representing the two protein layers 1.3 S3 Analysis of the falsification of the Davson-Danielli model that led to the SingerNicolson model. Structure of membrane proteins  Protein extracted from the membranes were very varied in size and globular in shape – unlike the type of structural protein that would form uniform and continuous layers on periphery of the membrane  The phospholipid bilayer was insoluble (indicating hydrophobic surfaces) Fluorescent antibody tagging  Membrane proteins from two different cells were tagged with red and green fluorescent markers respectively  When the two cells were fused, the markers became mixed throughout the membrane of the fused cell  This demonstrated that the membrane proteins could move and did not form a static layer (as per Davson-Danielli) Freeze-etched electron micrographs  Rapid freezing of cells and then fracturing them – fracture occurs along lines of weakness  Revealed irregular rough surfaces within the membrane  These rough surfaces were interpreted as being transmembrane proteins, demonstrating that proteins were not solely localised to the outside of the membrane structure 1.4 Membrane Transport 1.4 U1 Particles move across membranes by simple diffusion, facilitated diffusion, osmosis and active transport. Cellular membranes possess two key qualities:  They are semi-permeable (only certain materials may freely cross – large and charged substances are typically blocked)  They are selective (membrane proteins may regulate the passage of material that cannot freely cross) The polar heads are attracted to other polar molecules and the non-polar tails repel any polar molecules, preventing passage of ions through the membrane. Passive Transport   Passive transport involves the movement of material along a concentration gradient (high concentration ⇒ low concentration) Because materials are moving down a concentration gradient, it does not require the expenditure of energy (ATP hydrolysis) Diffusion is the net movement of molecules from a region of high concentration to a region of low concentration  This directional movement along a gradient is passive and will continue until molecules become evenly dispersed (equilibrium)  Small and non-polar (lipophilic) molecules will be able to freely diffuse across cell membranes (e.g. O2, CO2, glycerol) The rate of diffusion can be influenced by a number of factors, including:  Temperature (affects kinetic energy of particles in solution)  Molecular size (larger particles are subjected to greater resistance within a fluid medium)  Steepness of gradient (rate of diffusion will be greater with a higher concentration gradient) Osmosis is the net movement of water molecules across a semi-permeable membrane from a region of low solute concentration to a region of high solute concentration (until equilibrium is reached)  Water is considered the universal solvent – it will associate with, and dissolve, polar or charged molecules (solutes)  Because solutes cannot cross a cell membrane unaided, water will move to equalise the two solutions  At a higher solute concentration, there are less free water molecules in solution as water is associated with the solute  Osmosis is essentially the diffusion of free water molecules and hence occurs from regions of low solute concentration Solutions may be loosely categorised as hypertonic, hypotonic or isotonic according to their relative osmolarity  Solutions with a relatively higher osmolarity are categorised as hypertonic (high solute concentration ⇒ gains water)  Solutions with a relatively lower osmolarity are categorised as hypotonic (low solute concentration ⇒ loses water)  Solutions that have the same osmolarity are categorised as isotonic (same solute concentration ⇒ no net water flow) Aquaporin is an integral protein that acts as a pore in the membrane that speeds the movement of water molecules Facilitated diffusion is the passive movement of molecules across the cell membrane via the aid of a membrane protein  It is utilised by molecules that are unable to freely cross the phospholipid bilayer (e.g. large, polar molecules and ions)  This process is mediated by channel proteins Active Transport Active transport uses energy to move molecules against a concentration gradient  This type of movement across a membrane is not diffusion and energy is needed to carry it out (ATP) Active transport involves the use of carrier proteins (called protein pumps due to their use of energy)  A specific solute will bind to the protein pump on one side of the membrane  The hydrolysis of ATP (to ADP + Pi) causes a conformational change in the protein pump  The solute molecule is consequently translocated across the membrane (against the gradient) and released 1.4 U2 The fluidity of membranes allows materials to be taken into cells by endocytosis or released by exocytosis. Endocytosis – the taking in of external substances by forming a vesicle  Inward pouching of the plasma membrane, pinched off to form a vesicle containing the external material  Phagocytosis (solid substance ingestion) and Pinocytosis (liquid substances ingested) Exocytosis – the release of substances from a cell (secretion)  Vesicle fuses with the plasma membrane, the contents are then outside membrane  Digestive enzymes are released from gland cells exocytosis  Exocytosis can also be used to expel waste products or unwanted materials 1.4 U3 Vesicles move materials within cells. the by Vesicles can be used to move materials around inside cells An example of moving the vesicle contents occurs in the secretory cells  Protein is synthesized by ribosomes on the rough endoplasmic reticulum and accumulates inside the rER  Vesicles containing the protein bud off the rER and carry them to the Golgi apparatus  The vesicles fuse with the Golgi apparatus, which processes the protein into its final form  When this has been done, vesicles bud off the Golgi apparatus and move to the plasma membrane, where the protein is secreted 1.4 A1 Structure and function of sodium–potassium pumps for active transport and potassium channels for facilitated diffusion in axons. An axon is part of a neuron with the function of conveying messages rapidly from one part of the body to another in an electrical form called a nerve impulse  A nerve impulse involves rapid movements of sodium and then potassium across the axon membrane The sodium-potassium pump follows a repeating cycle of steps that result in three sodium ions being pumped out of the axon and two potassium ions being pumped in  Each time the pump goes around this cycle it uses one ATP 1. 2. 3. 4. 5. 6. The interior of the pump is open to the inside of the axon; three sodium ions enter the pmp and attach to their binding sites ATP transfers a phosphate group from itself to the pump; this causes the pump to change shape and the interior is then closed The interior of the pump opens to the outside of the axon and three sodium ions are released Two potassium ions from outside can then enter and attach to their binding sites Binding of potassium causes release of the phosphate group; this causes the pump to change shape again so that it is again only open to the inside of the axon The interior of the pump opens to the inside of the axon and the two potassium ions are released; sodium ions can then enter and bind to the pump again 1.4 A2 1.4 S1 Tissues or organs to be used in medical procedures must be bathed in a solution with the same osmolarity as the cytoplasm to prevent osmosis. Estimation of osmolarity in tissues by bathing samples in hypotonic and hypertonic solutions. Osmosis experiments are a useful opportunity to stress the need for accurate mass and volume measurements in scientific experiments In solutions with higher osmolarity (hypertonic solution), water leaves the cells by osmosis so their cytoplasm shrinks in volume, causing indentations  Conversely, in a solution with lower osmolarity (hypotonic) the cells take in water by osmosis and swell up, and may eventually burst Both hypertonic and hypotonic solutions therefore damage human cells  In a solution with same osmolarity as the cells (isotonic) , water molecules enter and leave the cell at the same rate so they remain healthy  It is therefore important for any human tissues and organs to be bathed in an isotonic solution during medical procedures  Usually an isotonic sodium chloride solution is used, which is called normal saline 1.5 Origin of Cells 1.5 U1 Cells can only be formed by division of pre-existing cells. Cells only arise from the division of preexisting cells  Mitosis – duplication of the DNA and the nucleus, results in genetically identical diploid daughter cells  Meiosis – cell division in parents, generates haploid gametes (sex cells) Students should be aware that the 64 codons Other evidences of the cell theory in the genetic code have 1. Cells are highly complex structure and no mechanism has been found for producing cells form simpler subunits the same meanings in nearly all organisms, but 2. All known examples of growth, be it of a tissue, an organism population, are all a result of cell division that there are some minor variations that are 3. Viruses are produced from simpler subunits, but they do not consist of cells, and they can only be produced inside the host cells that they have infected likely to have accrued 4. Genetic code is universal each of the 64 codons (a codon is a combination of 3 DNA since the common origin of life on Earth. bases) produces the same amino acid in translation, regardless of the organism Base pairs (ATGC) → codon (3 base pairs) → genes (many codons) → Chromosome (many genes) 1.5 U2 The first cells must have arisen from nonliving material. There is evidence that suggest complex structures arising in a series of stages over logn periods of time. There are hypotheses of how some of the main stages could have occurred: 1. Non-living synthesis of simple organic molecules:  Miller and Urey recreated the conditions of pre-biotic Earth in a closed system  They passed steam through a mixture of methane, hydrogen and ammonia (representative of the atmosphere of the early Earth)  Electrical discharges were used to stimulate lightning  They found that amino acids and other carbon compounds needed for life were produced 2. Assembly of these organic molecules into polymers:  A possible site for the origin of the first carbon compounds is around deep-sea vents (cracks in the Earth’s surface)  They are characterized by gushing hot water carrying reduced inorganic chemicals  These chemicals represent readily accessible supplies of energy, a source of energy for the assembly of carbon compounds into polymers 3. Formation of membranes to package the organic molecules  Experiments have shown that phospholipids natural assemble into bilayers, if conditions are correct.  Formation of the bilayer creates an isolated internal environment which allows optimal conditions, e.g. for replication or catalysis to be maintained. 4. Formation of polymers that can self-replicate (enabling inheritance)  DNA though very stable and effective at storing information is not able to self-replicate – enzymes are required  However, RNA can both store information and self-replicate - it can catalyze the formation of copies of itself and hence are speculated to be the genetic material used in early Earth  In ribosomes RNA is found in the catalytic site and plays a role in peptide bond formation 1.5 U3 The origin of eukaryotic cells can be explained by the endosymbiotic theory. Evidence for the endosymbiotic theory is expected. The origin of eukaryote cilia and flagella does not need to be included. Endosymbiotic theory explains the existence of several organelles of eukaryotes. The theory states that the organelles (e.g. mitochondria and chloroplasts) originated as symbioses between separate single-celled organisms. Development of the Nucleus  A prokaryote grows in size and develops folds in its membrane to maintain an efficient SA:Vol  The infoldings are pinched off forming an internal membrane  The nucleoid region is enclosed in the internal membrane and hence becomes the nucleus Development of Mitochondria  An aerobic proteobacterium enters a larger anaerobic prokaryote (possibly as prey or a parasite)  It survives digestion to become a valuable endosymbiont (An endosymbiont is a cell which lives inside another cell with mutual benefit)  The aerobic proteobacterium provides a rich source of ATP to its host enabling it to outcompete other anaerobic prokaryotes  As the host cell grows and divides so does the aerobic proteobacterium therefore subsequent generations automatically contain aerobic proteobacterium  The aerobic proteobacterium evolves and is assimilated and to become a mitochondrion Evidence for Endosymbiosis Mitochondria and chloroplasts are both organelles suggested to have arisen via endosymbiosis  Evidence that supports the extracellular origins of these organelles can be seen by looking at certain key features: Component Membranes Antibiotics Division DNA Ribosomes 1.5 A1 Evidence from Pasteur’s experiments that spontaneous generation of cells and organisms does not now occur on Earth. Evidence Some organelles have double membranes Susceptible to antibiotics Reproduction occurs via a fission-like process Has own DNA which is naked and circular (like prokaryotic DNA structure) Have ribosomes which are 70S in size Louis Pasteur experimented whether sterile nutrient broth (everything that is needed for a living organism) to determine if life can be generated spontaneously Method:  Two experiments were set up  In both, Pasteur added nutrient broth to flasks and bent the necks of the flasks into Sshapes  Each flask was then heated to boil the broth in order to kill all existing microbes  After the broth had been sterilized, Pasteur broke off the swan necks from the flasks in Experiment 1, exposing the nutrient broth within them to air from above  The flasks in Experiment 2 were left alone Results  The broth in experiment 1 turned cloudy whilst the broth in experiment 2 remained clear  Microbe growth only occurred in experiment 1 This suggested that spontaneous generation of life no longer occurs on Earth, and that life only arises from pre-existing life forms 1.6 Cell Division 1.6 Mitosis is division of Mitosis is the nuclear division by which replicated copies of a cell’s DNA are organized into U1 the nucleus into two genetically identical daughter nuclei. The sequence of events in the four phases of mitosis should be known. To avoid confusion in terminology, teachers are encouraged to refer to the two parts of a chromosome as sister chromatids, while they are attached to each other by a centromere in the early stages of mitosis. From anaphase onwards, when sister chromatids have separated to form individual structures, they should be referred to as chromosomes. chromosomes. Reasons for Cell Division  Growth - cells can only get to a certain SA:Vol ratio  Asexual reproduction - certain eukaryotic organisms ay reproduce asexually by mitosis and for single celled organisms, cell division  Tissue repair - damaged tissue can recover by replacing dead or damaged cells  Embryonic development - a fertilised egg will undergo mitosis and differentiation in order to develop into an embryo The cell cycle is the series of events through which cells pass to divide and create two identical daughter cells. Chromosome and Chromatid  A chromosome is the condensed form of DNA which is visible during mitosis (via microscopy)  As the DNA is replicated during the S phase of interphase, the chromosome will initially contain two identical DNA strands  These genetically identical strands are called sister chromatids and are held together by a central region called the centromere Interphase DNA is present as uncondensed chromatin (not visible under microscope)  DNA is contained within a clearly defined nucleus  Centrosomes and other organelles have been duplicated  Cell is enlarged in preparation for division Prophase  DNA supercoils and chromosomes condense (becoming visible under microscope)  Chromosomes are comprised of genetically identical sister chromatids (joined at a centromere)  Paired centrosomes move to the opposite poles of the cell and form microtubule spindle fibres  The nuclear membrane breaks down and the nucleus dissolves Metaphase  Microtubule spindle fibres from both centrosomes connect to the centromere of each chromosome  Microtubule depolymerisation causes spindle fibres to shorten in length and contract  This causes chromosomes to align along the centre of the cell (equatorial plane or metaphase plate) Anaphase  Continued contraction of the spindle fibres causes genetically identical sister chromatids to separate  Once the chromatids separate, they are each considered an individual chromosome in their own right  The genetically identical chromosomes move to the opposite poles of the cell Telophase  Once the two chromosome sets arrive at the poles, spindle fibres dissolve  Chromosomes decondense (no longer visible under light microscope)  Nuclear membranes reform around each chromosome set  Cytokinesis occurs concurrently, splitting the cell into two 1.6 U2 Chromosomes condense by supercoiling during mitosis.    Human cells are on average less than 5 μm in diameter. Human chromosomes are 15mm to 85mm (15,000μm to 85,000 μm) in length It is therefore essential to package chromosomes into much shorter structures Condensation occurs by means of repeatedly coiling the DNA molecule to make the chromosome shorter and wider – this process is called supercoiling  This process occurs during the first stage of mitosis 1.6 U3 Cytokinesis occurs after mitosis and is different in plant and animal cells. Cytokinesis is the division of the cytoplasm and hence the cell  The division of the cell into two daughter cells (cytokinesis) occurs concurrently with telophase. Animal cells  Microfilaments pulls the plasma membrane inward  Produces cleavage furrow  When the cleavage furrow reaches the centre of the cell it is pinched apart Plant cells  During Telophase, vesicles migrate to the centre of the cell  Vesicles fuse to form tubular structures  The tubular structure merge with the plasma membrane (the cell plate)  Completes the division of the cytoplasm  Vesicles deposit substances in the lumen between the daughter cells to form the middle lamella (‘gluing’ the cells together)  Both daughter cell secrete cellulose to form their new adjoining cell walls 1.6 U4 Interphase is a very active phase of the cell cycle with many processes occurring in the nucleus and cytoplasm. Interphase The stage in the development of a cell between two successive divisions This phase of the cell cycle is a continuum of three distinct stages:  G1 – First intermediate gap stage in which the cell grows and prepares for DNA replication  S – Synthesis stage in which DNA is replicated  G2 – Second intermediate gap stage in which the cell finishes growing and prepares for cell division During interphase, the cell carries out its normal functions  DNA replication – DNA is copied during the S phase of interphase  Organelle duplication – Organelles must be duplicated for twin daughter cells  Cell growth – Cytoplasmic volume must increase prior to division  Transcription / translation – Key proteins and enzymes must be synthesised  Obtain nutrients – Vital cellular materials must be present before division  Respiration (cellular) – ATP production is needed to drive the division process 1.6 U5 Cyclins are involved in the control of the cell cycle. Cyclins are a family of proteins that control the progression of cells through the cell cycle  Cells cannot progress to the next stage of the cell cycle unless the specific cyclin reaches its threshold  Cyclins bind to enzymes called cyclin-dependent kinases  These kinases then become active and attach phosphate groups to other proteins in the cell  The attachment of phosphate triggers the other proteins to become active and carry out tasks (specific to one of the phases of the cell cycle) 1.6 U6 Mutagens, oncogenes and metastasis are involved in the development of primary and secondary tumors. Tumours are abnormal cell growths resulting from uncontrolled cell division and can occur in any tissue or organ  Diseases caused by the growth of tumours are collectively known as cancers Mutations A mutation is a change in an organism’s genetic code  A mutation in the base sequence of certain genes can result in cancer Mutagens A mutagen is an agent that changes the genetic material of an organism (either acts on the DNA or the replicative machinery) Mutagens may be physical, chemical or biological in origin:  Physical – Sources of radiation including X-rays (ionising), ultraviolet (UV) light and radioactive decay  Chemical – DNA interacting substances including reactive oxygen species (ROS) and metals (e.g. arsenic)  Biological – Viruses, certain bacteria and mobile genetic elements (transposons) Mutagens that lead to the formation of cancer are further classified as carcinogens Oncogenes An oncogene is a gene that produces the proteins that controls the cell cycle.  A mutation in the oncogene can produce proteins that may not function properly, causing uncontrolled cell cycle Metastasis Tumour cells may either remain in their original location (benign) or spread and invade neighbouring tissue (malignant)  Metastasis is the spread of cancer from one location (primary tumour) to another, forming a secondary tumour  Secondary tumours are made up of the same type of cell as the primary tumour – this affects the type of treatment required o For example, if breast cancer spread to the liver, the patient has secondary breast cancer of the liver (treat with breast cancer drugs) 1.6 A1 The correlation between smoking and A correlation in science is a relationship between two variable factors  There is a positive correlation between cigarette smoking and the death rate due to cancer incidence of cancers.    1.6 S1 Many researches show that the more cigarettes smoked per day, the higher the death rate due to cancer More than 20 chemicals found in tobacco have caused cancers in laboratory animals and humans More than 40 other chemicals found in tobacco have been identified as carcinogens Identification of phases of mitosis in cells viewed with a microscope or in a micrograph. Prophase Preparation of temporary mounts of root squashes is recommended but phases in mitosis can also be viewed using permanent slides. Metaphase Anaphase Telophase 1.6 S2 Determination of a mitotic index from a micrograph. Mitotic index - the ratio between the number of cells in a tissue and the total number of observed cells