Chapter 1: Cell Biology 1. Introduction to cells 2. Ultrastructure of cells 3. Membrane structure 4. Membrane transport 5. The origin of cells 6. Cell division Introduction to cells Understandings: 1. According to cell theory, living organisms are composed of cells. 2. Organisms consisting of only one cell conduct all functions of life in that particular cell. E.g.: Paramecium, Amoeba, certain bacteria, etc. 3. Surface area to volume ratio is important in the limitation of cell size: This might be important since the surfaces of cells are exchange surfaces, which are used for nutrient uptake, excretion, etc. An analogous example will be that a human needs large lung to support a large body. 4. Multicellular organisms have properties that emerge from the interactions of their cellular components. 5. Specialised tissues can develop by cell differentiation in multicellular organisms. The conversion of stem cells to more specialised cells such as brain cells/ neurons. 6. Differentiation involves the expression of some genes and not others in a cell’s genome. 7. The capacity of stem cells to divide and differentiate along different pathways is necessary in embryonic development. This also makes stem cells useful for therapeutic treatment. Applications: 1. Questioning the cell theory using atypical examples, including striated muscle, giant algae and aseptate fungal hyphae. 2. Investigation of functions of life in Paramecium and one named photosynthetic unicellular organism. 3. Use of stem cells to treat Stagardt’s disease and one other named condition. 4. 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. Nature of Science: 1. Looking for trends and discrepancies. Trying to identify organisms which do not conform to cell theory. 2. Ethical implications of stem cell research Skills: 1. Use of a light microscope to investigate the structure of cells and tissues. 2. Drawing cell structures as seen with the light microscope. 3. Calculation of the magnification of drawings from the actual size of structures shown in drawings or micrographs. Ahh, now that the formalities are done. Let us move on to the content: 1. 2. 3. 4. Every living cell has a membrane. Each cell contains genetic information. Chemical processes occur inside the cell, these are catalysed by enzymes. Cells have a system of energy release. Holistic and Reductionist approach of Biology. A holistic approach considers the effects of the whole organisms and the environmental context. Whereas a reductionist approach attempts to explain all biological phenomena in terms of their underlying biochemical and molecular processes. A light microscope is one of the most important biological apparatuses. It consists of several pieces, which I will now try to delineate. A stage is attached to the microscope stand. On this stage the specimen is placed. This specimen can be placed in a petri dish or a glass microscope slide. A bulb underneath the transparent portion of the stand, illuminates the specimen, passing the light in an upward direction. This light is received by the objective lens. Of these there are usually three of different magnification. All of which are placed on a rotating turret. This light from the objective lens passes through the eyepiece lens, where the observer can then place their eye and view the image. However, it is unlikely that the image will be clear on first viewing. Hence, the microscope is equipped with two knobs, which adjust the focus of the image. The coarse-focusing knob and fine-focusing knob. The difference between these two, can easily be understood by their names. Some interesting types of cells which can be viewed on a light microscope are as follows: 1. Moss leaf cells. Which should be around 10 to 15 micrometres in width. The slide can be prepared using methylene blue dye or even plain old water. 2. Banana cells. A pretty large cell which may be around 0.1 millimetres (100 micrometres) in length. An iodine solution may be used. 3. Mammalian liver cells. You will need cut liver. Cut liver from poultry is satisfactory. A methylene blue dye will be needed. 4. Leaf lower epidermis 5. Human cheek cells. Scraping inner cheek with a cotton bud. 6. White blood cells. A pin prick of blood should be smeared on the slide. A Leishman’s stain can be used for preparation. Leishman’s stain is methylene blue with certain additives. It marks out the white blood cells, and other non-RBC components of blood (it does not mark platelets as well). An interesting idea is that of looking at urine under a microscope, and looking at the number of WBC’s, RBC’s and platelets, and doing analysis on that. Urine tests could also be used. This could be done for an IA. Notes for drawing of diagrams: 1. Thin, clean, sharp lines. 2. No rulers. Cells, organisms, etc. are all products of organic nature. Nature does not have any straight lines; organic forms will also be irregular. So, you should also not use rulers in your drawings. 3. Do not overlap lines, for this is a sin. Magnification: A typical school microscope has three levels of magnification. 1. *40 (Low power) 2. *100 (Medium power) 3. *400 (High power) You must also remember the formula, which although intuitive, may be confusing in times of stress and trouble: Magnification = Size of Image Actual size of specimen Please keep in mind the units of both the image and actual size. Outliers in the eyes of cell theory: 1. Striated Muscle Cells 1. Abnormally long. 30mm when compared to the average of 0.03 mm for human cells. 2. Have many nuclei, sometimes several hundred. 2. a. b. c. Aseptate fungi hyphae Septa - Cross walls which divide fungal hyphae into cell-like sections. Aseptate (A-septa-ate) - Fungi which does not have septa. Each hypha is like an uninterrupted tube-like structure. 3. a. Acetabularia or Giant Algae These unicellular algae can grow to lengths of 100 mm. Functions of life: 1. 2. 3. 4. 5. 6. 7. Nutrition Metabolism Growth Response Excretion Homeostasis Reproduction Limitations on cell size. The surface area to volume ratio is important in the limitation of cell size. The metabolic rate is proportional to the volume of the cell. The surface area to volume ratio is important for the following reasons: 1. Nutrient and substance intake. 2. Excretion. 3. Heat management. The Paramecium is one of the most common examples of a single celled organisms: Some of its features are as follows: 1. Asexual reproduction 2. Food vacuoles 3. Cell membrane 4. Contractile vacuoles which store water 5. Cilia Chlamydomonas is a unicellular alga that lives in soil and freshwater. 1. Has both cell wall and cell membrane? Cell wall is freely permeable, whilst the cell membrane is not. 2. 2 flagella 3. Light sensitive eyespot allows it to sense the brightest light. Contractile vacuoles are water, highly translucent sacs. Flagella are long, whilst cilia are short hairs. Multicellular Organisms Groups of cells cooperating and living with each other are not considered to be multicellular organisms. Emergent properties are the characteristics of the whole organism. Differentiation involves the expressions of some genes and not others in a cell’s genome. There are 220 cell types in the human body, all of these cells have the same set of genes.4 There are approximately 25000 genes in the human genome. Gene expressions is when a gene is being used in a cell. Stem cells Zygote is when the sperm and egg fuse. Embryo is formed when the zygote divides into two cells. Stem cells can be used for therapeutics because: Ultrastructure of cells Understanding: 1) 2) 3) 4) Prokaryotes have a simple cell structure without compartments Eukaryotes have a compartmentalized cell structure. Prokaryotes divide by binary fission. Electron microscopes have a much higher resolution than light microscopes. Nature of Science: 1) Developments in scientific research follow improvements in apparatus: the development of the electron microscope led to greater understanding of cell structure. Applications: 1) The structure and function of the organelles within exocrine gland cells of the pancreas. 2) The structure and function of organelles within the palisade mesophyll cells of the leaf. Skills: 1) Drawing the ultrastructure of prokaryotic cells based on electron micrographs. 2) || of eukaryotic cells || 3) Interpretation of electron micrographs to identify organelles and deduce the function of specialised cells.’ Light microscopes cannot be used to image structures smaller than 0.2 micrometres. Many biological structures are smaller than this with the example of the cell membrane which 0.01 micrometres thick. Electron microscopes can image until 0.001 micrometres. Resolution is making the separate parts of an object distinguishable by eye. Light microscopes are limited by the wavelength of light. 1.22*Wavelength/Aperture. Prokaryotes (Pro-Kernel, Before-Casing) 1) 2) 3) 4) 5) Have a peptidoglycan cell wall. No internal organelles, except 70 S (Svedberg Units) Ribosomes. Have a nucleoid, which appears as a lighter region in a micrograph. They undergo Binary Fission. Have a plasma membrane Garlic Hungama Garlic cells store a chemical called alliin in their cell vacuoles. While they store Alliinase, an enzyme, in another part of the cell. Alliinase converts allin to allicin, which is the compound which gives garlic its distinctive smell and flavour. However, this reaction can only occur when garlic is cut into, or bitten into, and when garlic cells are damaged. Hence to get the garlic flavour, garlic must be cut or crushed., it cannot be used whole. Eukaryotes. (Eu-Kernel, easily formed-casing) Cell Organelles: 1. THE NUCLEUS Double Nuclear Membrane Chromatin Dense Chromatin Dense Chromatin Nuclear Pores ENDOPLASMIC RETICULUM Cisterna Ribosomes Lysosome Mitochondrion Free Ribosomes Vacuoles and Vesicles Chloroplast Microtubules and centrioles Cilia and flagella 1.3 Membrane Structure Amphipathic substances are substances with both hydrophobic and hydrophilic properties, Hydrophilic part is the phosphate group. Hydrophobic part consists of two hydrocarbon chains. This is in line with what is taught in the chemistry syllabus. Organic compounds are insoluble in water, and only soluble in other organic compounds. Phospholipid bilayer Hydrophilic phosphate head Hydrophobic carbon chain Membrane proteins Functions of membrane proteins: • • • • • Hormone Binding sites (Hormone receptors): E.g.: Insulin receptor Immobilized enzymes with active sites outside: E.g.: In the small intestine Cell adhesion to form tight junctions between groups of cells in tissues and organs cell to communication, for example receptors for neurotransmitter at synapses Channels for passive transportation to allow hydrophilic particles across by facilitated diffusion Pumps for active transport which use ATP to move particles across the membrane. Hormone: Thyroid stimulating hormone (Blue/Red) Peripheral Hormone receptor (Purple) Integral Phospholipid Bilayer (Grey) G-protein: Conveys the hormonal message to the cell interior. (Orange) Peripheral • • Integral proteins: o Often Hydrophobic (At least on part of their surface) o Embedded in hydrocarbon chains in the centre of the membrane. o Many are transmembrane o They may have hydrophilic parts projecting out through the phosphate heads on either side. Peripheral Proteins o Often hydrophilic o Hence, no embedded in the membrane o Often attached to the surface of integral proteins o However, this attachment is reversible. o Some have a single hydrocarbon chain attached to them which is inserted into the membrane, anchoring the protein to the membrane surface. Cholesterol in membranes: • • Lipid Steroid Cholesterol in mammalian membranes reduces membrane fluidity and permeability to some solutes. 1.4 Membrane Transport The fluidity of membranes allows materials to be taken into cells by endocytosis and released by exocytosis. Cell membrane engulfs substance/material, it detaches to form a vesicle. Vesicles move materials within cells. Exocytosis is the taking fusion into the plasma membrane, and then out of the cell. Exo-cyto-osis: Exo (Exit), Cyto (Relate to cell activity), Osis (Process) Endo-cyto-osis: Endo (Entrance) || Simple diffusion: Particles move across membranes by simple diffusion, facilitated diffusion, osmosis and active transport. Paramecium Diffusion of oxygen into the Eye (Cornea) 1) 2) 3) 4) Simple Diffusion Facilitated Diffusion Osmosis Active Transport Facilitated Diffusion There are channels made out proteins in the plasma membrane. Osmosis Diffusion for water. Movement of water molecules from a region of lower solute concentration to a region of higher solute concentration (through a partially permeable membrane). Transmission of nervous impulses by means of facilitated diffusion by use of potassium channels. To ensure proper functioning of facilitated diffusion channels, appropriate concentration gradient must be maintained. This is done using a sodium-potassium active transport pump system. This is delineated below: The interior of the pump is open to the axon, three sodium ions enter the pump and attach to its binding site. ATP transfers a phosphate group, this causes the pump to change shape and close. ATP becomes ADP. The interior of the pump opens to the outside of the axon, the three sodium ions are released. Two potassium ions enter the pump, and bind to their active sites. Binding of the two ions, leads to a release of the phosphate group which causes the pump to open to the interior of the axon, Facilitated diffusion using potassium channels. Two potassium ions are released, the cycle repeats. Isotonic has same osmolarity Hypertonic has greater osmolarity. (Hyper-tension- High blood pressure) Hypotonic has lower osmolarity. (Hypo-tension- Low blood pressure) 1.5 The Origin of Cells Cells can only be formed by division of pre-existing cells. Explanations for the origin of cells: • Production of Carbon compounds such as sugars and amino acids. o Stanley Miller and Harold Urey passed steam through a mixture of methane, hydrogen and ammonia. This mixture was thought to be representative of the atmosphere of the early Earth. • Assembly of carbon compounds into polymers. o A possible site for the origin of the first carbon compounds is around deep sea vents. They contain gushing hot water carrying reduced inorganic chemicals such as iron sulphide. This may have been an energy source for the assembly of these carbon compounds into polymers. • Formation of membranes. o If phospholipids or other amphipathic carbon compounds were among the first carbon compounds, they would have naturally assembled into bilayers. Experiments have shown that these bilayers readily form vesicles resembling the plasma membrane of a small cell. • Development of a mechanism for inheritance o Living organisms currently have genes made of DNA and use enzymes as catalaysts. To replicated DNA and be able to pass genes on to offspring enzymes are needed. However, for enzymes to be made genes are needed. The solution may be RNA was genetic material. Like DNA, RNA stores information. However, it is self-replicating and also acts as a catalyst. Endosymbiosis theory for origin or mitochondria, nucleus and chloroplasts. 1.6 Cell Division Mitosis is the division of the nucleus into two genetically identical daughter nuclei. Phases of mitosis: 1) 2) 3) 4) Prophase Metaphase Anaphase Telophase Interphase: Interphase is a very active phase of the cell cycle with many processes occurring in the nucleus and cytoplasm. • • • There is an increase in the numbers of mitochondria in the cytoplasm. Interphase has three phases G1, S phase and G2. Cells which are not going to divide, to not enter S phase. Rather they enter the G0 phase. Supercoiling of chromosomes. Chromosomes condense by supercoiling during mitosis. Histones and enzymes are responsible for supercoiling, Phases of mitosis: Prophase: • • • • • Chromosomes undergo supercoiling. The nucleolus breaks down. Microtubules grow from structures called Microtubule organising centre (MTOC). A spindle shaped array links the poles of the cell. At the end of prophase the nuclear membrane breaks down Metaphase: • • • Microtubules continue to grow and attach to centromeres on each chromosome. The two attachment points on opposite sides of each centromere, each side is attached to a different pole. The microtubules are tugged upon / shortened at the centromeres to test whether the arrangement is correct. Anaphase: • • T the start, each centromere divides, allowin the pair of sister chromadis to separate. Microtubules, rapidly pull them towards the poles of the cell, Telophase: • • • The chromatids which have reached the poles are called chromosomes. They are pulled into a tight group near the MTOC. The chromosomes uncoil and a nucleolus is formed. Cytokinesis: The process of cell division. Cyclins are involved in the control of the cell cycle. Cyclins bind to enzymes called cyclin-dependant kinase. The kinases 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. Tumour formation and cancer: Mutagens, oncogenes and metastasis are involved in the development of primary and secondary tumours. The few genes that can cause cancer after mutating are known as oncogenes. Metastasis is the movement of cells from a primary tumour to set ip secondary tumours in other parts of the body. Molecular Biology 1. 2. 3. 4. 5. 6. 7. 8. 9. Molecules to metabolism Water Carbohydrates and lipids Proteins Enzymes Structure of DNA and RNA DNA replication, transcription and translation= Cell respiration Photosynthesis Molecules to metabolism Living organisms use 4 main classifications of organic compounds: • • • • Carbohydrates o Consist of carbon, hydrogen and oxygen. o Hydrogen to oxygen ration is 2:1. Lipids o Broad class of molecules insoluble in water. They include: steroids, waxes and fatty acids and triglycerides. Proteins o Composed of one or more chain or amino acids. o Contain Carbon, hydrogen, nitrogen and oxygen. However, two of the twenty amino acids contain Sulphur. Nucleic Acids o Chains of subunits called nucleotides. o Contain carbon, hydrogen, oxygen, nitrogen and phosphorus. o Two main types are: ▪ DNA (Dioxyribonucleic acid) ▪ RNA (Ribonucleic acid) To draw: • Ribose • Glucose • Saturated fatty acids • Amino acids Anabolism: Anabolism is the synthesis of complex macromolecules from simples molecules including the formation of macromolecules from monomers by condensation reaction. • Protein synthesis using ribosomes • DNA synthesis and replication. • Photosynthesis including production of glucose from carbon dioxide and water. • Synthesis of complex carbohydrates including starch, cellulose and glycogen. Catabolism: Catabolism is the breakdown of complex molecules into simples molecules including the hydrolysis of macromolecules into monomers • Digestion of food in the mouth, stomach and small intestine. • Cell respiration in which glucose or lipids are oxidies to carbon dioxide and water. • Digestion of complex carbon compounds in dead matter by decomposers. Water Water molecules are polar and hydrogen bonds form between them. Hydrogen bonding and bipolarity explain the adhesive, cohesive, thermal and solvent properties of water. Substances can be hydrophilic or hydrophobic.
