IB Biology SL Study Guide PDF

STUDY GUIDE: SL www.ib-academy.nl ib-academy.nl  Biology SL Study Guide Available on www.ib-academy.nl Author: Design...

STUDY GUIDE: SL www.ib-academy.nl ib-academy.nl  Biology SL Study Guide Available on www.ib-academy.nl Author: Design Typesetting LATEX.guru This work may be shared digitally and in printed form, but it may not be changed and then redistributed in any form. Copyright © 2023, IB Academy Version: BioSL.3.0.220620 This work is published under the Creative Commons BY-NC-ND 4.0 International License. To view a copy of this license, visit creativecommons.org/licenses/by-nc-nd/4.0 This work may not used for commercial purposes other than by IB Academy, or parties directly licenced by IB Academy. If you acquired this guide by paying for it, or if you have received this guide as part of a paid service or product, directly or indirectly, we kindly ask that you contact us immediately. Daltonlaan 400 www.ib-academy.nl 3584 BK Utrecht [email protected] The Netherlands +31 (0) 30 4300 430 INTRODUCTION Welcome to the IB Academy Study Guide for Biology Standard Level. We are proud to present our study guides and hope that you will find them helpful. They are the result of a collaborative undertaking between our tutors, students and teachers from schools across the globe. Our mission is to create the most simple yet comprehensive guides accessible to IB students and teachers worldwide. We are firm believers in the open education movement, which advocates for transparency and accessibility of academic material. As a result, we embarked on this journey to create these study guides that will be continuously reviewed and improved. Should you have any comments, feel free to contact us. In this Biology SL guide we present everything that is vital for your final exam. Each section is clearly marked relating to the topics of the syllabus. The material is summarised in short texts that include various definitions, images, examples and labelled diagrams which will help you with your studies. This study guide also contains useful tips and info boxes that will assist you along the way, telling you which components are important for your exams. For more information and details on our revision courses, be sure to visit our website at ib-academy.nl. We hope that you will enjoy our guides and best of luck with your studies. IB Academy Team 3 TABLE OF CONTENTS 1. Cell biology 7 2. Molecular biology 31 3. Genetics 59 4. Ecology 89 5. Evolution and biodiversity 101 6. Human physiology 115 5  TABLE OF CONTENTS 6 CELL BIOLOGY 1 1.1. Cell theory 8 – Sizes of cells – Cell properties – Examples of stem cell use 1.2. Cells and membrane 15 transport – Eukaryotic and prokaryotic cells – Cell membrane – Membrane transport – Osmolarity 1.3. Origin of cells 24 – Pasteur’s soup – Formation of organic molecules – Endosymbiotic theory 1.4. Cell division 25 – Cell cycle – Phases of mitosis 7  CELL BIOLOGY Cell theory 1.1 Cell theory A 1. All organisms are composed of cells: B microscopic examination of many organisms has shown that they are all composed of cells; unicellular organisms are still composed of one cell that performs all functions of life. 2. Cell is the basic unit of life: cell as a whole can perform the functions of life, while its individual components cannot. 3. All cells originate from a pre-existing cell: spontaneous generation of cells is not possible; C a cell needs to divide to create another cell. Even though most organisms fit well into the first two points of the cell theory (A and B), some organisms and tissues seem to contradict it. Muscle fibres are fused, elongated cells with multiple nuclei and as such differ from the common definition of a cell (C). Similarly, fungal hyphae often don’t contain dividing walls and are made up multiple fused thread-like cells (D). D 8  CELL BIOLOGY Cell theory 1 7 Functions of life car- ried out by cells 1 Nutrition If these are hard to remember, think about the following: 2 Metabolism Every living being has to eat 1 , process the 3 Excretion food it has eaten 2 and excrete the waste 3 , take in the signals from the environment and 4 Response respond to them 4 , accordingly make sure that it is well balanced 5 (food-wise, heat wise, etc.) 5 Homeostasis and finally, use all that to grow 6 and pass on 6 Growth its genes 7. 7 Reproduction. Example: Paramecium is a unicellular organism widely used as an example of a Example functional unit of life. The Paramecium: Is surrounded by cilia that allows it to move. (Response) Engulfs food via a specialized membranous feeding groove called a cytostome. (Nutrition) Encloses food particles in small vacuoles with enzymes for digestion. (Metabolism) Removes solid waste via an anal pore and liquid wastes are pumped out through contractile vacuoles. (Excretion) Allows essential gases to enter and exit the cell via diffusion. (Homeostasis) Grows in size and divides asexually (fission) (Reproduction and growth) 9  CELL BIOLOGY Cell theory 1.1.1 Sizes of cells Surface area to volume ratio Surface Area: of a cell is related to the rate of exchange of materials or how fast/slow a cell takes in food/gasses and excretes wastes products. The higher the surface area, the higher the exchange rate as there is more physical membrane where exchange can happen. Volume: of a cell is related to the rate of metabolic reactions occurring in a cell or how much nutrient processing and waste production is occurring in a cell at a given time. The higher the volume of a cell, the higher the metabolic rate as the more nutrients are needed/used and thus more waste produced. Cell growth is limited by two features of the cell: surface area and volume. When the cell volume increases, the surface area increases comparably less. This limits the size of a cell because: the cell must be able to transport enough food/waste through the surface compared to the food needs/excrement production, which is determined by the cell volume. This is linked to cell division, as following a period of growth a cell will divide in order to increase the surface area to volume ratio and function more effectively. In addition, some cells increase their surface area to volume ratio by creating folds in the plasma membrane, which creates more surface area to cope with a large exchange of materials. This can be seen in the cells of the intestinal lining. Microvilli vs. Figure 1.1: Microvilli increases surface area for exchange. 10. CELL BIOLOGY Cell theory 1 Example surface area (SA) and volume (V ) calculation Example Imagine a cell as a cube with sides of length a. The surface area (SA) can be calculated by adding the SA SAs of the six faces of the cube and the volume (V ) by multiplying the sides. a SA = 6 × a 2 and V = a3 Now, compare the growth of cells, starting with a = 1, a = 5 and a = 10. size of 1 size of 5 size of 10 side= a a= 1 a= 5 a= 10 SA= 6 × a 2 SA= 1 SA= 150 SA= 600 V = a3 V=1 V = 125 V = 1000 Up to a certain size the SA still exceeds the V , and the cell would be able to import and export enough materials to sustain its life. But as the cell grows bigger the volume will exceed the SA, at which point the cell cannot transport enough materials in and out of the cell to keep up with its food needs/waste production. Typical cell sizes Cells have different sizes, from one organism to another as well as within an organism. This difference arises from the different cell functions and needs. The following scheme should help you compare the sizes of different cells: molecules cell membrane virus prokaryotes organelles eukaryotes 1 nm 10 nm 100 nm 1 µm 10 µm 100 µm 11  CELL BIOLOGY Cell theory Calculating magnification Most cells are invisible to the naked eye therefore we use microscope magnification to be able to see them. Image of the cell = real cell size × magnification. Real cell size Example Exam question: Image of a cell, measurable by a ruler. Magnification in the corner. Calculate the real size of the cell in the picture or the magnification factor Solution: Image of the cell = real cell size × magnification therefore Image of the cell Real cell size = magnification Numbers worked out. Remember to always use the same units 1 mm = 1000 micrometers (µm) Microscopes An electron microscope has a far greater resolving power than a conventional light microscope, meaning an electron microscope can be used to create images of smaller objects with greater resolution. The limit of resolution is determined by the wavelength of the incident light/electrons. And since the wavelength of electrons is much smaller than that of visible light, they can be used to view objects much smaller and in much more detail. 12  CELL BIOLOGY Cell theory 1 1.1.2 Cell properties In multicellular organisms, each cell has its own function and cooperates with other cells to form an organism. Emergent properties Emergent properties are properties that emerge from the interaction of the individual cell components creating new functions. Multicellular organisms can realize a number of complex functions that individual cells cannot perform on their own by collaborating with one another.. You can easily visualize this by thinking about how individual cardiac cells form Example tissues that work together to create an organ (the heart). Then the heart together with tissues that formed vessels can function as the vascular system, transporting blood across the body. The latter cannot be done by one single cell, but is possible by the collective actions of many cells together. Finally, different systems can create an organism, like a human, who can also perform several functions that a single cell could not do on its own. muscle cardiac heart vascular human cell tissue organ system organism 13  CELL BIOLOGY Cell theory Cell differentiation Although all cells possess the same genes, expressed genes are the ones that are “switched on” while all other genes are “switched off”. Cell differentiation is the process whereby different genes are put on “lockdown” to reach a very specific cell type with particular functions brought by the available active genes. Stem cells Undifferentiated cells that can divide and have the capacity to differentiate into any cell type and thus acquire any function. Therapeutic sources of stem cells include umbilical cord blood, bone marrow and human embryonic stem cells 1.1.3 Examples of stem cell use. Stargardt disease Example Stargardt disease is a degenerative disease of the eye (retinal cells) leading to blindness. Human embryonic stem cells are obtained from unsuccessful in vitro fertilizations. These cells are differentiated in the lab towards retinal cells and injected into the eye of patients. The new cells replace the degenerate cells in the retina and restore vision. Leukaemia Example Leukaemia is the cancer of white blood cells (immune cells). Human cord blood is collected after childbirth. The cord blood contains stem cells that differentiate into white blood cells. A patient with leukaemia is irradiated and given chemotherapy to kill all cancerous white blood cells. The killed cells are then replaced by the matching cord blood cells which are able to differentiate into all kinds of white blood cells in the patient 14  CELL BIOLOGY Cells and membrane transport 1 1.2 Cells and membrane transport 1.2.1 Eukaryotic and prokaryotic cells The main distinctions between the eukaryotic and prokaryotic cells relate to their size and complexity. Prokaryotes, also known as bacteria, are unicellular organisms with a simple, non-compartmentalized structure. Eukaryotes, which can be unicellular or multicellular organisms, are usually bigger with a complex organelle based function and compartmentalization. Compartmentalization means to have structures wrapped around a membrane, creating different discrete compartments. This allows regions in the cell to have specific functions and environments.. Lysosomes Example Lysosomes are membrane bound organelles responsible for the digestion of materials. In order to break down materials they need to have a very acidic pH of around 4.5–5. This pH is achieved with hydrogen pumps in the organelle’s membrane that pump protons inside the organelle. Without compartmentalization, this specific concentrated acidic environment would not be possible, and would disrupt normal cell functioning. 15  CELL BIOLOGY Cells and membrane transport Prokaryotic cells Make sure you can pili draw and clearly label this yourself! cell wall plasma membrane plasmid nucleoid (naked DNA) 70S ribosomes cytoplasm flagella Figure 1.2: Prokaryotic cell. The bold structures in the table are shared Table 1.1: Functions of prokaryotic cells. between the Structure Function prokaryotic and eukaryotic cells. Capsule Protection Cell wall Protection and pressure maintenance Cell membrane Transport of materials Cytoplasm Contains enzymes, food... , medium for cellular processes Ribosomes Protein synthesis Nucleoid DNA containing area not enclosed by a membrane Plasmid Extra genetic material (e.g., antibiotic resistance genes) Pili Communication, DNA exchange, attachment Flagellum Movement 16 CELL BIOLOGY Cells and membrane transport 1 Eukaryotic cells eu = good/true  → organisms with a nucleus karyon = nucleus centrioles Make sure you can draw and label this mitochondria yourself! lysosome nuclear envelope nucleolus nucleus rough ER ribosome plasma membrane Golgi apparatus cytoplasm smooth ER Figure 1.3: Eukaryotic Cell. There are two types of eukaryotic cells: pancreatic cell (animal) and mesophyll cell (plant). Table 1.2: Comparison of animal cell and plant cell. Animal Plant Structure Function cell cell Ribosome Protein synthesis ✓ ✓ Rough endoplasmic reticulum Protein modifications ✓ ✓ Golgi apparatus Protein packaging ✓ ✓ * Mitochondrion Site of cell respiration ✓ ✓ * Nucleus Contains chromosomes (DNA) ✓ ✓ Lysosome Degradation enzyme storage ✓ ✓ Centrioles Chromosome separation during mitosis ✓ ✗ Vacuole Food and water storage ✓ ✓ Cell Wall Maintenance of cell pressure ✗ ✓ * Chloroplast Site of Photosynthesis (food production) ✗ ✓ * Centrosomes Contain microtubules, move to opposite ✓ ✓ poles during mitosis division * indicates double membrane bounded organelles. 17  CELL BIOLOGY Cells and membrane transport Comparison of eukaryotic cells and prokaryotic cells Table 1.3: Comparison of prokaryotic cells and eukaryotic cells. Prokaryotic Cell Eukaryotic Cell Naked DNA DNA wrapped around DNA in nucleoid DNA enclosed by a nuclear region DNA circular DNA linear No membrane bound structures Membrane bound structures such as mitochondria, ER, Golgi apparatus present which compartmentalize functions Plasmids present No plasmids Mitochondria not present Mitochondria always present Ribosomes smaller (70S) Ribosomes larger (80S) Remember that in a compare and contrast question in the exam, you only get a point for differences if you give the alternative for each thing being compared. So it is not enough to say Prokaryotes have DNA at the nucleoid region, but you must also mention that Eukaryotes have DNA enclosed in the nuclear membrane. Besides in their structure, the two types of cells also differ in their mode of division. Eukaryotic cells divide by mitosis (discussed later) while prokaryotic cells divide by binary fission. 1.2.2 Cell membrane Cell membrane Cell membranes are an assembly of different components that encloses cells. This includes phospholipids, cholesterol, proteins, and lipoproteins. Phospholipids molecules composed of a glycerol head with a negatively charged phosphate group and two hydrocarbon lipid tails. This makes phospholipids amphipathic, meaning that they have two opposite properties: Their heads are hydrophilic (water loving) making them polar. Their tails are hydrophobic (water hating) making them non-polar. Make sure you can draw and label a phospholipid diagram (Figure 1.4). 18 CELL BIOLOGY Cells and membrane transport 1 Phosphate group P Glycerol head Hydrophilic (polar) Hydrocarbon tail Hydrophobic (non-polar) Figure 1.4: Phospholipid diagram. This will usually give you an extra point in essay questions concerning the plasma membrane. Notice the head / tail structure of the phospholipid: their amphipathic properties cause them to spontaneously arrange into a bilayer in an aqueous environment. This is due to the fact that water is polar, and therefore the hydrophobic, non-polar portion of the phospholipids will want to be shielded from water by the hydrophilic, polar heads of the phospholipids. Due to these interactions, the plasma membrane is very stable but is said to be fluid. This means that the tails will always be facing tails, and the heads will always face outside, but the position of individual phospholipids in a layer may change. This property of the membrane also allows it to hosts a variety of other molecules, like proteins and cholesterol. This makes it look like a mosaic. glycoprotein peripheral protein protein channel phospholipid hydrophobic tails hydrophilic head integral protein cholesterol Figure 1.5: Phospholipid molecules form a phospholipid bilayer, which together with proteins and cholesterol forms cell membranes. 19  CELL BIOLOGY Cells and membrane transport Cholesterol keeps the fluidity of the membrane constant at a variety of temperatures. When it is cold, it increases fluidity and when hot, it makes the membrane more rigid. This is important to maintain a constant environment for cellular processes to occur. Integral Proteins span the lipid bilayer and are permanently attached to it by polar interactions with the phospholipid heads and nonpolar interactions with the tails. These can be for example receptors or transport proteins. Peripheral Proteins are attached to the inner or outer side of the membrane by non-covalent interactions with the surface of the membrane or other integral proteins. These are for example enzymes attached to the outside of cells. Membrane proteins fulfill various functions: Channel Carrier Recognition Receptor Enzymatic Figure 1.6: Phospholipid molecules form a phospholipid bilayer, which together with proteins and cholesterol forms cell membranes. 20 CELL BIOLOGY Cells and membrane transport 1 1.2.3 Membrane transport The lipid bilayer membrane is semi-permeable and selective, which means that Semi-permeable: only certain molecules (small, polar) can freely cross the membrane Selective: with the use of transport proteins, it can select what comes in and out and what does not Recall that the main function of the plasma membrane is transport. Generally, transport is defined as passive or active. Active transport movement of molecules from an area of lower concentration to an area of higher concentration, with the use of energy (against the concentration gradient) Passive transport movement of molecules from an area of higher concentration to an area of lower concentration (down the concentration gradient) Passive transport is further divided into two types of diffusion, simple and facilitated. Simple diffusion passive transport of molecules through a membrane, without the need of protein channels (oxygen diffusion) Facilitated diffusion passive transport of molecules facilitated by channel or carrier proteins (sodium transport, calcium transport) Osmosis is a form of passive transport that only refers to the movement of water. The water, like other particles in passive transport, moves from the area where there is more of it, to the area where there is less of it. However, osmosis is defined in terms of the concentration of dissolved molecules: Osmosis movement of water from the area of low solute concentration to the area of high solute concentration. 21  CELL BIOLOGY Cells and membrane transport Active transport, like (passive) facilitated diffusion requires proteins. However, these proteins use energy in form of ATP to pump molecules against their concentration gradient. There are two types of active transport: Primary: direct use of metabolic energy for transport of molecules against concentration gradient. Secondary: coupling the movement of one molecule against the concentration gradient with the movement of another along the concentration gradient of the second molecule, often created by primary active transport. Sodium-potassium pump is such a protein, and can be found in many cells including neurons. This pump is described in more detail in the “Human physiology” chapter, but now consider the following points: sodium potassium pump is an integral protein that uses ATP to transport molecules across a membrane; it transports sodium out of the cell, and potassium into the cell; it works against the concentration gradients of both sodium and potassium; for every three sodium molecules it transports out, two potassium molecules are transported in. You should consider two more types of active transport that involve vesicle transport, rather than protein pumps. Exocytosis Exocytosis: Transport of molecules in secretory vesicles that fuse with the plasma membrane upon contact to release the contents outside of the cell Endocytosis transport of molecules into the cell through invagination of the plasma membrane and formation of the phospholipid vesicle containing the molecule. 22 CELL BIOLOGY Cells and membrane transport 1 1.2.4 Osmolarity Osmolarity Is a measure of solute concentration (osmol/L) in a given system. A system can be a Petri dish, a cell, an organism, etc. Hypotonic low osmolarity, or low solute concentration, meaning that the system loses water Hypertonic high osmolarity, or high solute concentration, meaning that the system will gain water Imagine a potato cube in a water bath. Mind you that the potato has a much smaller volume compared to that of the water tank. Hypotonic The ratio of solutes to water inside the potato is much higher than that same ratio in a water bath. The bath is hypotonic compared to the potato. The water moves from the bath into the potato, Recall that in osmosis, the water moves from making the potato swell. where there is more of it to where there is The ratio of water to solute in the potato is the same less of it as the one in the bath. Hypertonic The water bath is more saturated with its solute compared to the potato. The bath is a hypertonic solution compared to the potato. The water inside the potato will pass into the water bath, trying to dilute it to the same concentration as in the potato. The potato will shrink, its ratio of solute to water will increase and the osmolarities will be balanced. 23  CELL BIOLOGY Origin of cells 1.3 Origin of cells 1.3.1 Pasteur’s soup A prior belief was that cells could spontaneously arise from the assembly of inorganic matter. However, Louis Pasteur disputed the belief of spontaneous formation of life in the 19th century. In his simple experiment, he filled two flasks with nourishing soup, a medium highly nutritious for microorganisms to thrive, and then sterilized them. One flask had a straight open neck, while the other had a curved opened neck. Within a week, the straight-necked soup was spoiled and the curved-necked soup was as good as it was on the first day. Day 1 Day 7 The germs found in the spoiled soup, could be found at the entrance of the curved necked, where they got stuck. Therefore, the mould, fungi and bacteria were able to enter the soup from the environment, but were not able to assemble from thin air in the sealed container. 1.3.2 Formation of organic molecules In order to form cells, first we have to form (relatively) complex molecules. The Miller–Urey experiment showed that: water vapour, ammonia and methane, all found in the early atmosphere, could have spontaneously assembled into amino acids and carbon compounds, in the presence of electricity (lightning); if some of the compounds formed at that time on earth were phospholipids, they would have naturally assembled into bilayers, forming early membranes; the formation of nucleic acids such as RNA would have given rise to early enzymatic activities, protein assembly and the first genetic information. 24 CELL BIOLOGY Cell division 1 1.3.3 Endosymbiotic theory Next, this theory assumes that more complex eukaryotic cells have evolved from the prokaryotic cells through a symbiotic process. Symbiosis is a mutually favourable coexistence of two organisms. The theory suggests that a larger anaerobic prokaryotic cell could have engulfed a smaller aerobic cell, and started coexisting with it. The large cell was supplying the smaller one with food, while the smaller cell was converting the food into energy for the larger cell → symbiosis.This would have given rise to mitochondria and chloroplasts. Unlike the rest, these organelles are bounded by a double membrane. The two membranes would be the vesicle from endocytosis and the cell membrane of the engulfed cell. Mitochondria and chloroplasts contain plasmid-like, circular DNA (characteristic of prokaryotes) that has genes independent from those found in the eukaryotic nucleus. These are thought to be conserved genes from the original engulfed cell. 1.4 Cell division Mitosis is the division of the cell’s nucleus into two identical daughter nuclei containing the same number of chromosomes as the mother cell. cleavage furrow centrosome spindle microtubules chromosomes equator prophase metaphase anaphase telophase The function of mitosis is to create two genetically identical daughter cell with the genome of the mother cell. The process involves replication (=duplication) of DNA (all chromosomes). In order for separation of duplicated DNA to work, the DNA (normally 25  CELL BIOLOGY Cell division a very long molecule) needs to supercoil. Replication is said to be proofread and checked for errors by the cell’s machinery. Remember that mitosis occurs only in eukaryotic cells, while prokaryotic cells divide by binary fission. Cytokinesis is the division of the cell’s cytoplasm and organelles that directly follows mitosis In plant and animal cells, the process of cytokinesis differs. In plant cell, the kinesis results from the transport of vesicles to the cell equator leading to their eventual fusion and formation of the plasma membrane. The vesicles bring cellulose to form the cell wall around the newly formed plasma membrane. In animal cells, the division of cytoplasm is a result of an invagination of the plasma membrane. Actin and myosin are the contractile fibres that create this invagination called cleavage furrow. 1.4.1 Cell cycle From its formation, until division, each cell goes through several phases of the life cycle. G1 is the phase in which cells spend the majority of their lifespan: this is the period of growth and performance of its daily functions. S is the phase that occurs once the cell has decided to undergo mitosis: this is the period of DNA synthesis (replication) G2 is the phase where the cell does its last preparations for mitosis: during G2, the cell duplicates its organelles and prepares enzymes and proteins needed for mitosis A tip to remember the phases is to know them as G(rowth)1, S(ynthesis of DNA), and G(rowth)2. Cyclins are proteins that regulate the cell cycle. The name cyclin should help you remember that the concentrations of these proteins go through cycles or vary throughout the cell cycle in response to internal and external signals. An increase or decrease in the concentration of cyclins will influence the progression of the cell cycle. Cyclins comprise the cell cycle checkpoints 26 CELL BIOLOGY Cell division 1 The first cell cycle check point occurs between G1 and S phase Another checkpoint occurs during S phase before the beginning of DNA replication If the cyclins are not produced or activated, the cell cannot pass a cell cycle checkpoint Cyclin dependent kinases (CDKs) are enzymes whose activity is dependant on the concentrations of cyclins. It is CDKs which ultimately allow progression through a stage of the cycle via phosphorylation specific molecules. Despite this tightly regulated cell cycle system, some cells manage to escape the checkpoints and form tumours. Cancer is the result of uncontrollable cell division and tumours are the aggregates of cancerous cells. Mutagens are agents that cause mutations in the DNA. Some of these mutations can be missed by proofreading machinery leading to gene mutations UV light is a known mutagen that cause high rate of DNA mutations that can often not be repaired Oncogenes are genes of each cell that are responsible for normal cell division. They are called oncogenes, because a mutation in these genes can lead to the formation of cancer If these genes are mutated, they often lead to cancer Proto-oncogenes are oncogenes that in their mutated state become overactivated and promote cell division leading to tumour formation Tumour suppressor genes are genes that negatively regulate the cell cycle, so when mutated, they fail to prevent uncontrollable cell divisions Metastasis refers to the movement of the primary cancerous cells to a new formation where they continue to form tumours. 27  CELL BIOLOGY Cell division 1.4.2 Phases of mitosis Mitosis consists of 4 phases that can be distinguished under the microscope. Due to supercoiling of the DNA, the chromosomes become visible and can be tracked during these phases. Prophase DNA supercoils, chromosomes condense and become visible. centrosome Nuclear envelope breaks down. Spindle microtubules start forming at the poles of the cell. chromosomes The cell contains double the Figure 1.7: Prophase: nuclear envelope is DNA compared to its G1 fractured, chromosomes are becoming thick, phase, the same number of centrioles are located and the poles of the cell. chromosomes. Begins after S phase has occurred Metaphase spindle microtubules Chromosomes align at the equator equator of the cell. Figure 1.8: Metaphase: chromosomes lo- Spindle microtubules attach cated at the equator of the cell, each X to the centromeres (centres representing a chromosome, and they’re of the chromosome). ordered in one single row. Spindle fibres originate at the poles and attach to centres of X-es each pole, with one chromosome having one spindle from each pole. 28 CELL BIOLOGY Cell division 1 Anaphase Sister chromatids (legs of each chromosomes, containing identical copies of DNA) are pulled to opposite poles by spindle microtubules. Now there is an equal Figure 1.9: Anaphase: fibres are shortening number of chromosomes towards the poles, and dragging one leg of (DNA molecules) at each the X towards the pole. Equal number of pole, but overall, the cell chromosome legs are moving to each pole. now has double the number of chromosomes compared to prophase. Telophase cleavage furrow Chromosomes begin to uncoil as the nuclear envelope reforms around them. The cell contains two identical nuclei and awaits Figure 1.10: Telophase: two nuclei beginning the division of cytoplasm and to form at each pole, and the chromosomes organelles (= Cytokinesis). uncoiling and becoming longer. When observing a tissue or a group of cells under a microscope, it is easy to calculate the rate of division of the cells/tissue in question. This is done by the following formula: number of cells undergoing mitosis Mitotic index = total number of cells 29  CELL BIOLOGY Cell division 30 MOLECULAR BIOLOGY 2 2.1. Molecules to metabolism 33 – The carbon atom: the core of organic compounds – Metabolism 2.2. Water 35 – Water: molecular and chemical characteristics – Thermal, cohesive, adhesive, and solvent properties of water – Hydrophilic vs. hydrophobic substances 2.3. Carbohydrates and lipids 38 – Carbohydrates – Lipids 2.4. Proteins 43 – Amino acids: the building blocks of proteins – The peptide bond: from amino acids to polypeptides – Functions of proteins – Proteomes: the fingerprints of cells 2.5. Enzymes 46 – Concepts and definitions – Influencing enzyme activity: temperature, pH and substrate concentration 31  MOLECULAR BIOLOGY 2.6. Structure of DNA and 48 RNA – Nucleotide structure – DNA vs. RNA – The formation of the DNA double helix 2.7. DNA replication, 51 transcription and translation – DNA replication – Transcription: from gene to messenger RNA (mRNA) – Translation: making functional proteins from mRNA sequences 2.8. Cell respiration 54 – Cell respiration: substrates and products – Anaerobic cell respiration – Aerobic cell respiration 2.9. Photosynthesis 54 – Photosynthesis – Light spectrum and chlorophyll – Production of oxygen by photolysis – The Calvin cycle: using energy to form carbohydrates and other carbon compounds – Rate-limiting factors of photosynthesis 32 MOLECULAR BIOLOGY Molecules to metabolism 2 2.1 Molecules to metabolism 2.1.1 The carbon atom: the core of organic compounds The field of molecular biology aims to explain living processes in terms of the chemical substances involved. The most frequently occurring chemical elements in living things are carbon, hydrogen, oxygen and nitrogen. Carbon (C) in particular is a very important element in the study of living things, as: all organic compounds contain C (few exceptions like CO2 and CO) C can form four covalent bonds, and thus allows for the formation of a wide variety of stable and complex compounds some of these organic compounds essential for life include carbohydrates, proteins, lipids and nucleic acids. A diagram of these four types of molecules can be found in Figure 2.1. Amino acids Ribose C5 H10 O5 ( D) Glucose C6 H12 O6 ( ) 7 H H O OH OH H N C C OH H C H O OH H C H 5 6 Amino group Carboxyl group R C H H C C O 4 1 H 5 H Side chain H H C C C C 3 2 4 OH H 1 OH OH HO OH C C 3 2 Fatty acids (long C chains) H OH H H H H H H O C C C C C C C H Skill: Identify molecular HO diagrams of these structures as H H H H H H amino acids, sugars (ribose and glucose) and lipids (fatty acids) Or (short form) Skill: Draw molecular diagrams O of amino acids (top left), ribose (top centre), glucose (top right)
C CH2 n CH3 OH and a saturated fatty acid (bottom left) Figure 2.1: Molecular diagrams. 33  MOLECULAR BIOLOGY Molecules to metabolism 2.1.2 Metabolism Metabolism is a web of all the enzyme-catalysed reactions in a system (e.g., cell or organism). Metabolic pathways can consist of chains or cycles, and can be anabolic or catabolic. Anabolism Synthesis of complex molecules from simpler ones, for example, the formation of macromolecules from monomers by condensation reactions. Anabolism is associated with condensation reactions, which consist of the removal of a water molecule each time a monomer is added to a polymer chain or another monomer. E.g., amino acids → polypeptide + water. Catabolism The breakdown of complex molecules into simpler ones, for example, the hydrolysis of macromolecules into monomers. Catabolism is associated with hydrolysis, which consists of the addition of water molecules to break down a polymer. E.g., dipeptide + water → 2 amino acids.. Urea: endogenous molecule or artificially produced toxic compound? Example O C H2 N NH2 urea In earlier days, organic molecules were believed to be solely synthesized in living organisms. Because urea is an organic compound synthesized in the kidneys as a waste product, it was believed to only be an endogenous molecule. In the early 1800s however, researchers first managed to synthesize artificial urea using silver isocyanate and ammonium chloride. Nowadays it is used as a nitrogen-releasing fertilizer, as well as in the automobile industry and for medical use. 34 MOLECULAR BIOLOGY Water 2 2.2 Water 2.2.1 Water: molecular and chemical characteristics Water is an essential molecule for life on Earth. It is a polar molecule that consists of 2 hydrogen atoms bound by covalent bonds to an oxygen atom. The principle of covalent bonding consists of sharing of electrons between atoms. It is this bonding gives water its most important characteristic for living organisms: being polar. This polarity arises as water has a slightly positively charged pole where the hydrogen atoms are located and a slightly negatively charged pole where the oxygen atom is located. Polar molecule is a molecule that has an uneven distribution of charges across the molecule. For example, it is more negative at one end and more positive at another. Non-polar molecule is a molecule that has an even distribution of charges across the molecule, so no positive or negative poles are formed Due to the polarity of water molecules, the small negative charge on the oxygen atom has the ability to attract the slightly positively charged hydrogen atoms in nearby hydrogen atoms from other molecules. This attraction leads to the formation of hydrogen bonds between molecules and can explain a number of properties of this molecule, including thermal, cohesive, adhesive and solvent properties. It is important to remember that in water, covalent bonds are formed between a hydrogen and an oxygen of the same molecule, while hydrogen bonds are found between a hydrogen from one molecule and an oxygen from another 2.2.2 Thermal, cohesive, adhesive, and solvent properties of water Thermal properties High specific heat capacity: large amounts of energy are needed to raise the water’s temperature. Hydrogen bonds are said to be the strongest of the weak bonds as they restrict movement, meaning it takes a lot of energy to break them down 35  MOLECULAR BIOLOGY Water H Hydrogen is Oxygen is slightly O slightly positive negative H H Hydrogen bond Covalent bond O H O H H Figure 2.2: Diagrams showing the molecular structure of water (top) and the hydrogen bonds between two water molecules (bottom). High latent heat of vaporization: hydrogen bonds between water molecules in a liquid form make it very hard for single molecules to escape as vapour. The energy necessary to break these hydrogen bonds and vaporize water is very high compared to other liquids (100 °C). When water vaporizes, a large release of energy occurs, causing a cooling effect on the surface upon which the water used to rest. The concept of sweating as a cooling effect demonstrates this: all the energy used to break hydrogen bonds is released, cooling the skin. High latent heat of fusion: water at 0 °C must lose a lot of energy before forming ice crystals. Water expands as it freezes and therefore ice can float upon its surface. Cohesive properties Water molecules can stick to each other through the formation of hydrogen bonds between the hydrogen of one and the oxygen of another water molecule. Can explain the formation of water droplets, why some organisms can “walk on water”, etc. Adhesive properties Water can adhere to charged surfaces through the formation of hydrogen bonds due to its polarity. 36 MOLECULAR BIOLOGY Water 2 Solvent properties Water is an excellent solvent for other polar molecules that attract the charged poles of water molecules (e.g., inorganic molecules with positive or negative charges, polar organic molecules, enzymes, etc.). Water can form bonds around other polar compounds, such as NaCl, separating them. Compounds and molecules that dissolve in water are referred to as hydrophilic. Water can also form hydrogen bonds around molecules whose elements are tightly bonded and thus acts as an ideal transport medium for polar molecules (like glucose in blood) 2.2.3 Hydrophilic vs. hydrophobic substances Hydrophilic (“water-loving”) are all molecules that can readily dissolve in water and can freely associate with it by forming intramolecular bonds. These include polar molecules and ionic compounds Hydrophilic compounds can readily dissolve in water. Hydrophobic (“water-hating”) are all molecules that cannot associate with water molecules or easily dissolve in it. These include large and non-polar molecules. These molecules tend to be insoluble in water. The hydrophilic and hydrophobic nature of compounds, as well as the solvent property of water, are essential in the transport of molecules in blood for example (which has a high water content). Below is the mode of transport of various important molecules based on their solubility in water: Glucose and amino acids are polar, so they can be freely transported and dissolved in blood. Cholesterol and fats are non-polar so they are transported in small droplets called lipoproteins, where these non-polar molecules are coated by phospholipids and proteins, which are in turn, polar themselves. Oxygen is non-polar, and while some molecules can dissolve in water, they are not sufficient to supply the entire body, therefore, most oxygen is transported in the blood bound to haemoglobin. A good molecule used to illustrate the importance of the polarity of water and hydrogen bonding for living organisms is methane. 37  MOLECULAR BIOLOGY Water Methane, as opposed to water, has four hydrogens bound to its central atom (in this case a carbon). This causes methane to have an even distribution of charges across the molecule, or a tetrahedral Lewis structure in comparison to water’s bent Lewis structure, making it non-polar. This non-polarity gives methane very different properties than those previously discussed for water, and these can demonstrate the vital role of the polarity of water. The latter is shown in Figure 2.3. Water Methane H O H C H H H H Bent Tetrahedral Figure 2.3: Water vs. Methane.. Comparing thermal properties of water and methane Example Property Methane Water Explanation Melting point =182 °C 0 °C Ice melts at a much higher temperature: hydrogen bonds restrict the movement of water molecules and heat is needed to overcome this. Specific heat 2.2 J/(g °C) 4.2 J/(g °C) Water’s heat capacity is higher: hydrogen capacity bonds restrict movement so more energy is stored by moving molecules of water than methane. Latent heat of 760 J/g 2257 J/g Water has much higher heat of vaporization vaporization: much heat energy is needed to break hydrogen bonds and allow a water molecule to evaporate. Boiling point =160 °C 100 °C Water’s boiling point is much higher: heat energy is needed to break hydrogen bonds and allow water to change from a liquid to a gas 38 MOLECULAR BIOLOGY Carbohydrates and lipids 2 2.3 Carbohydrates and lipids 2.3.1 Carbohydrates Carbohydrates are organic molecules composed of hydrogen, oxygen, and carbon atoms. Monosaccharides are the monomers of carbohydrates, and are therefore the building blocks of more complex carbohydrates. Monomer is the building block or basic unit of a class of compounds that can be polymerized to make larger compounds Dimer is a compound made from the bonding of two monomers Polymer is two or more repeated monomers from a class of compounds bound together, forming a more complex molecule The most important carbohydrates from monomers to polymers are shown in the table bellow: monomer = monosaccharide dimer = disaccharide polymer = polysaccharide Table 2.1 Monosaccharide Glucose (G) Fructose (F) Galactose (Ga) Disaccharides Maltose (G+G) Sucrose (G+F) Lactose (G+Ga) Polysaccharides Cellulose Glycogen Starch/Amylose/Amylopectin (all polymers of G) 39  MOLECULAR BIOLOGY Carbohydrates and lipids 2.3.2 Lipids Lipids are hydrophobic compounds that have important functions in: Long term energy storage. Heat insulation. Buoyancy. Shock absorption The main monomers of lipids are fatty acids: long hydrocarbon chains with a carboxyl group at the end. Fatty acids may be: Saturated: all the carbon atoms in the fatty acid chain are connected by single covalent bonds, so the number of hydrogen atoms connected to each carbon cannot be increased. Monounsaturated: there is one double bond between two carbon atoms in the fatty acid chain. Polyunsaturated: there is more than one double bond between the carbons in the fatty acid chain. Unsaturated fatty acids can be: Trans unsaturated: hydrogen atoms are bonded to carbon on the opposite sides of the double bond. Cis unsaturated: hydrogen atoms are bonded to carbon on the same side of the double bond. There are three main classes of lipids: phospholipids (important membrane components) steroids (cholesterol and hormones) and triglycerides (long-term energy storage). We will look at the formation of triglycerides, important in energy storage, by means of a condensation reaction. H O H O H C OH HO C H C O C O O H C OH + HO C −−→ H C O C + 3H2 O O O H C OH HO C H C O C H H glycerol three fatty acids triglyceride Figure 2.4: Triglyceride formation. 40  MOLECULAR BIOLOGY Carbohydrates and lipids 2 Both lipids and carbohydrates are suitable for energy storage. However, each is more suitable for a specific function: Carbohydrates Lipids More easily digested than lipids, Can store more energy per gram good for energy storage that than carbohydrates → better for needs to be more rapidly released. long term energy storage. Soluble in water → easier to Not soluble in water, also harder transport in blood. to break down and transport around the body (build-up of high energy content fats).. Health issues associated to trans- and saturated fatty acids Example Trans fats have been banned in several countries in the world, as there is a positive correlation between a diet high in trans fats and coronary heart disease. Saturated fats have also been shown to have a positive correlation (albeit, weaker than trans fats) with the incidence of coronary heart disease. However, many of the tested populations do not fit these findings, so evidence must be carefully evaluated before banning products and establishing anti trans or saturated fat campaigns. 41  MOLECULAR BIOLOGY Carbohydrates and lipids. Determining the body mass index (BMI) Example Because of the natural variation in size between adults, weighing someone does not provide a clear indicator of body mass. The body mass index is a screening tool to identify possible weight problems, and it can be calculated using the following formula: where: mass in kg BMI = Body mass index Conclusion (height in meters)2 Below 18.5 Underweight 18.5 to 24.9 Normal weight 25.0 to 29.9 Overweight 30.0 or more Obese A nomogram can also be used to calculate BMI, by drawing a line that connects the height and weight lines, the BMI measure is indicated by the scale in the middle. mass (kg) height (cm) 160 120 150 140 125 130 120 130 110 135 100 90 140 80 145 Obese 150 70 30 28 50 (kg) 26 Overweight 155 BMI = = 20.81 60 24 1.552 (m) 22 Normal weight 160 20 165 50 18 170 175 40 Underweight 180 110 (kg) 10 185 BMI = = 32.49 1.842 (m) 190 30 195 200 205 210 20 215 body mass index 42 MOLECULAR BIOLOGY Proteins 2 2.4 Proteins 2.4.1 Amino acids: the building blocks of proteins Amino acids, containing a carboxyl, an ammine and an R group, are the monomers of proteins that when linked together by peptide bonds form complex proteins. Proteins are important organic molecules that carry out major functions in cells and in the extracellular space. Although there are only 20 different amino acids, millions of proteins exist as these monomers can be linked in any given sequence This means that if you have a protein made of n amino acids, there are 20n different proteins that may be made. The specific sequence of each protein is coded for in the genetic material of the organism. As we will see later in the chapter, DNA is transcribed into mRNA and later translated by ribosomes into polypeptide chains. The Central Dogma of molecular biology states that there is a sequential transfer of information where DNA is transcribed into RNA, which in turn is translated into proteins. 43  MOLECULAR BIOLOGY Proteins From amino acids to polypeptides, there are 4 discrete levels of organization recognizable in proteins. amino acids Primary structure Consists of a string of amino acids (the amino acid sequence) pleated sheet alpha helix Secondary structure Formation of alpha helices and beta pleated sheets. This organization is stabilized by the formation of hydrogen bonds. Tertiary structure pleated sheet Formation of the 3D structure of the polypeptide. This occurs due to interactions between the R groups of the alpha helix amino acids. These include: disulphide bridges, hydrogen bonds, van der waal interactions, and ionic bonds. Quaternary structure Multiple polypeptide chains combined to form a single protein. Figure 2.5: Protein organisation. 44 MOLECULAR BIOLOGY Proteins 2 2.4.2 The peptide bond: from amino acids to polypeptides Figure 2.6 is a diagram showing the formation of a dipeptide (a 2-amino acid molecule) via a condensation reaction, and the breakdown of a dipeptide into two amino acids. The condensation reaction creates a covalent, peptide bond between the carboxyl group of one amino acid and the amino group of the other, and results in the release of a water molecule. In the hydrolysis reaction (Figure 2.7), water is added in order to break the peptide bond. You need to be able to identify the peptide peptide bond! bond H H O H H O H O H H H O H N C C OH H N C C OH N C C N C C amino carboxyl H OH group R R R R group side chain H O H O H H H O H H H H O H H O H O N C C N C C H N C C OH H N C C OH H OH R peptide R R R bond Figure 2.6: Condensation. Figure 2.7: Hydrolysis. 2.4.3 Functions of proteins Table 2.2 depicts some of the major functions proteins carry out in an organism, as well as specific examples for each function. Table 2.2: Protein functions. Function Example Details Shape Structural Collagen Strenghen bone, tendon and skin Fibrous Transport Hemoglobin Bind oxygen in the lungs and transports to other Globular tissues Movement Actin Involved in the contraction of muscles Fibrous Defence Immunoglobulins Acts as antibody Globular 45  MOLECULAR BIOLOGY Enzymes 2.4.4 Proteomes: the fingerprints of cells Proteome is the entire set of proteins expressed by a genome, cell, tissue, or organism at a given time. While the genetic make up of an organism is the same in all cells, each tissue or individual cell shows variable gene expression and thus different proteins are created. The proteome of individuals within the same species is quite similar (as the genetic make up is also similar), however, each individual has a unique proteome (like a fingerprint, which can be similar but never identical to other individuals). 2.5 Enzymes 2.5.1 Concepts and definitions Enzymes are globular proteins that function as biological catalysts that speed up chemical reactions in biological processes. Substrates are substances acted upon by enzymes. Active site is the region on the enzyme to which substrates bind and where catalysis occurs. The activity of enzymes relies on the concepts of molecular motion and collision, in other words, substrates and enzymes must “collide” with one another due to their individual motion (kinetic energy). The more collisions between enzyme and substrate, the faster the reaction occurs. Enzymes speed up reactions without getting consumed by the process, meaning they can speed up many reactions. There are two main models that aim to explain the mechanism of action of enzymes: The Lock-and-key model: the substrate and enzyme have shapes that make them fit perfectly with each other. Thus, each enzyme catalyses a specific reaction The Induced-fit model: as substrate and enzyme approach each other, their interactions make them shift physical conformation so that they fit perfectly with one another. 46 MOLECULAR BIOLOGY Enzymes 2 2.5.2 Influencing enzyme activity: temperature, pH and substrate concentration Enzyme activity increases as temperature increases, Temperature often doubling with every 10 °C rise. This is because collisions between substrate and active site happen Enzyme activity more frequently at higher temperatures due to faster molecular motion. Enzymes are proteins, therefore at high temperatures they are denatured and stop working. This is because heat causes vibrations inside enzymes which break bonds needed to maintain the structure of the Temperature enzyme. Enzyme activity is reduced as pH increases above the pH optimum because the conformation of the enzyme is altered more and more. Above a certain pH the Enzyme activity alkalinity denatures the enzyme and it does not catalyze the reaction at all. Enzyme activity is reduced as pH increases above the optimum because the conformation of the enzyme is altered more and more. Above a certain pH the alkalinity denatures the enzyme and it does not pH catalyze the reaction at all. At low substrate concentrations, enzyme activity Substrate increases steeply as substrate concentration increases. concentration This is because random collisions between substrate and active site happen more frequently with higher Enzyme activity substrate concentrations. At high substrate concentrations most of the active sites are occupied, so raising the substrate concentration has little effect on enzyme activity. A plateau is reached when enzymes are working at full capacity at their maximum rate Substrate concentration 47  MOLECULAR BIOLOGY Structure of DNA and RNA. The use of lactase in the production of lactose-free milk Example Many enzymes are used in industrial processes (for instance, in the food industry). Enzymes are often immobilized on a surface and employed in large concentrations to catalyse a wide range of biochemical reactions. A common example is the use of enzyme lactase in the production of lactose-free milk. Lactose is the disaccharide in milk that many people are intolerant to as they do not produce the enzyme lactase to break it down. Often times milk and other milk products are treated with immobilized lactase, and lactose is broken down prior to consumption. The resulting monosaccharides are easier to digest by lactose-intolerant people, and result in a sweeter flavour (less artificial additives needed). The use of the enzyme also speeds up the production of fermented products like yogurt and cheese. Immobilized lactase can be used in much larger concentrations and can resist larger changes in pH and temperature compared to endogenous lactase. The immobilized enzymes can also be reused, and the products are not contaminated with enzymes (easier to introduce and remove from the sites of reaction. 2.6 Structure of DNA and RNA 2.6.1 Nucleotide structure Nucleic acids are the biomolecules responsible for information storage, essential to all forms of life. The two major types of nucleic acids DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are essential compounds involved in gene expression in cells. RNA and DNA polymers consist of repeated units of nucleotides, which are in turn made of a 5 carbon sugar linked to a phosphate group at carbon 5, and to one of five nitrogenous bases (adenine, guanine, thymine, uracil and cytosine) at carbon 1. The overall nucleotide structure is shown in Figure 2.8. Skill: Draw a simple diagram of the phosphate group structure of single nucleotides (you may P use simple circles for the phosphate, C5 pentagons for the sugar [deoxyribose or O nitrogenous base ribose] and rectangles for the base). C4 C1 C3 C2 deoxyribose sugar Figure 2.8: Nucleotide structure. 48 MOLECULAR BIOLOGY Structure of DNA and RNA 2 The nucleotide can have either a ribose (RNA) or a deoxyribose (DNA) pentose sugar. These differ in the presence or absence of an oxygen molecule. This oxygen molecule makes ribose a less stable molecule than deoxyribose, due to the fact that oxygen has high electronegativity, meaning that it really wants to more electrons. This instability causes RNA to be single stranded while DNA can be double stranded. HOCH2 O OH HOCH2 O OH 5 5 C H H C C H H C 4 1 4 1 H C C H H C C H 3 2 3 2 OH H OH OH Deoxyribose Ribose Figure 2.9: Deoxyribose and ribose. 2.6.2 DNA vs. RNA Both types of nucleic acids share structural similarities, but also significant differences: RNA DNA Contains a 5-carbon sugar Contains a 5-carbon sugar Sugar is called ribose Sugar is called deoxyribose Single-stranded molecule Double-stranded molecule Contains bases adenine (A), Contains bases adenine (A), uracil (U), cytosine (C), and thymine (T), cytosine (C), and guanine (G) guanine (G) 49  MOLECULAR BIOLOGY Structure of DNA and RNA 2.6.3 The formation of the DNA double helix DNA is composed of a double stranded helix of DNA nucleotides. Each strand of DNA is held together by covalent bonds that form between the phosphate group of one nucleotide to carbon 3 of the neighbouring nucleotide. This forms a single-stranded backbone. The DNA double strand is then achieved by the formation of hydrogen bonds between the nitrogenous bases of two nucleotide strands. Base pairing in DNA is complementary, meaning that one base can only bind to a specific complementary base: Adenine (A) binds to thymine (T) → 2 hydrogen bonds. Cytosine (C) binds to guanine (G) → 3 hydrogen bonds. The two DNA strands are antiparallel, in other words, they run in opposite directions (where one strand has a 5′ end, the complementary strand has a 3′ end). The diagram shows the structure of the DNA double helix, showing two joined antiparallel DNA strands bound together by complementary base pairing of adenine with thymine (2 H-bonds); and cytosine and guanine (3 H-bonds). nucleotides 5′ 3′ P 3′ O 5′ A T 5′ O 3′ P P 3′ deoxyribose O 5′ G C 5′ O phosphate group 3′ P P 3′ O phosphodiester bond 5′ T A 5′ O 3′ P P hydrogen bond 3′ O 5′ C G 5′ O 3′ P ′ 3 5′ nitrogenous bases Figure 2.10: DNA structure. 50  MOLECULAR BIOLOGY DNA replication, transcription and translation 2 2.7 DNA replication, transcription and translation 2.7.1 DNA replication During the DNA replication process, one double stranded DNA molecule gives rise two daughter DNA molecules. This process is said to be semi-conservative, meaning that each new DNA double helix contains one newly synthesized daughter strand and one strand from the original parent DNA strand, which serves as a template to ensure that both new strands are identical. Essentially, part of the original DNA is conserved at each replication step. Below is a brief description of the process of DNA replication: Takes place during the synthesis (S) phase of the cell cycle. Helicase unwinds the double helix and separates the two DNA strands by breaking hydrogen bonds. The two parent strands that emerge from this process serve as templates for the new daughter strands to be synthesized. Enzyme DNA polymerase can then link free nucleotides to the template strands by complementary base pairing. Note that DNA polymerase can only add nucleotides at the 3′ end of a growing strand. Two identical daughter DNA strands are created, resulting in two semi-conservative double stranded DNA helices.. Taq DNA polymerase: production of multiple copies of DNA by polymerase Example chain reaction (PCR) This technique has been one of the greatest biotechnological developments in DNA research. It allows scientists to amplify desired regions of DNA in very little time. PCR consists of the following steps: 1. Isolate the desired region of DNA (using restriction enzymes). 2. Introduce it in a mixture containing free nucleotides, primers and Taq DNA polymerase. 3. The mixture is heated up to 90 °C to separate the DNA strands of the original template. 4. Temperature is then reduced to 55 °C to allow for primer annealing to the now separated strands. 5. Taq polymerase (isolated from thermophiles, organisms that can survive at very high temperatures) works optimally at 72 °C, so the mix is heated to this temperature to enhance the formation of new double-stranded copies of the original DNA. 6. Process is repeated several times until the DNA is amplified. 51  MOLECULAR BIOLOGY DNA replication, transcription and translation 2.7.2 Transcription: from gene to messenger RNA (mRNA) Transcription is the synthesis of mRNA copied from the DNA base sequences present in an organism’s chromosomes. The sections of DNA that code for polypeptides are called genes, but in order for these polypeptides to be expressed, machinery located outside the nucleus is needed. Thus, a messenger RNA (mRNA) molecule carries the “message” from Skill: While you must the DNA to the cytoplasm. Below is the explanation of the process of transcription: be able to determine the mRNA sequence that will result from a RNA polymerase unwinds the area of the DNA to be transcribed. given DNA sequence, RNA polymerase catalyses the addition of free RNA nucleotides using one of the it is essential that you newly s