Molecular biology (topics 2, 7, 8)

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core: topic 2; AHL: topic 7, topic 8.1

143 Terms

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molecular biology
field of study focusing on investigating biological activity on molecular level
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organic compounds
compounds containing carbon found in living things (except for carbides, carbonates, carbon oxides, cyanides)
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what properties allow carbon to form many diverse compounds?
* the ability to form 4 covalent bonds
* the bonds are stable
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main function of carbohydrates
* source of energy
* recognition molecule in cells
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main functions of lipids
* main component of the cell membrane
* long-term energy storage
* signalling molecule
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main function of nucleic acids
* genetic material
* instructions for the synthesis of proteins
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main function of proteins
* involved in catalysis
* structural molecules
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vitalism
organic molecules could __only__ be synthesised by living systems
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how was vitalism disproved?
* in 1828
* heating an inorganic salt produced urea
* artificial synthesis of urea proves that organic compounds can be produced artificially
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metabolism
the totality of chemical processes that occur within a living organism in order to maintain life
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functions of metabollic reactions
* provide a source of energy for cellular processes
* enable the production and assimilation of new materials within the cell for its use
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anabolism
reactions resulting in the building up of larger molecules from simpler ones
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catabolism
the reactions resulting in breaking up larger molecules into smaller ones
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monosaccharides are joined via…
glycosidic bonds
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amino acids are joined via
peptide bonds
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glycerol and fatty acids are joined via
ester linkages
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nucleotides are joined via
phosphodiester bonds
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examples of trace elements
Ca, P, Fe, Na, S
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function of calcium
neurotransmitter release from synapses, muscle contractions
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functions of iron
hemoglobin - needed for oxygen transport
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function of sodium
sodium potassium pump, generation of nerve impulses in neurons
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functions of phosphorus
make up cell membranes and nucleic acids
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function of sulphur
found in some amino acids, allow disulphide bridges in proteins to form
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what is the benefit of water’s dipolarity?
forming polar associations with other compounds, being the essential medium of life and the universal solvent
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properties of water
thermal, cohesive/adhesive, solvent properties
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thermal properties
* due to strong intermolecular hydrogen bonds that require a lot of energy before they can be broken
* high heat capacity. high heat of evaporation
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application of the thermal properties of water: sweat
* input of energy required to change water from liquid to gas
* energy is provided by the surface of the skin when it’s hot
* as skin gives out its heat to evaporate water, it becomes cooler
* high heat capacity = good coolant
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cohesion
the ability of like molcules to stick together
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adhesion
the ability of dissimilar molecules to stick together (e.g. water sticks to the surface)
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surface tension
* possible thanks to cohesion and adhesion
* hydrogen bonding is so strong that it allows the surface of water to resist low external force
* thanks to this, small organisms such as insects can move on the surface of water
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capillary action
* attraction to charged polar surfaces allows water to flow in the directtion opposing gravitational forces
* necessary to transport water up the stem in plants via the transpiration stream
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solvent properties
* universal solvent
* dissolves polar substances, ions
* the attraction of water can weaken the intermolecular forces, which causes the atoms of certain compounds to fall apart
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the name of the reaction joining two sugar monomers (monosaccharides)
condensation
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monosaccharides
* one sugar unit
* typically taste sweet
* immediate energy source for cells
* glucose, fructose, galactose
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disaccharides
* two sugar units
* can be soluble in water, used in transport
* sucrose, maltose, lactose
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polysaccharides
* many sugar units
* energy storage, cell recognition, structural support
* cellulose, glycogen, starch
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cellulose
* structural function - cell wall in plants
* made of beta-glucose
* indigestible for most animals, except for ruminants
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what is the difference between alpha-glucose and beta-glucose?
the location of one of the OH groups (they are isomers)
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starch
* energy storage in plants
* composed of alpha-glucose
* amylose: linear, helical, only 1-4 linkages, less soluble, preferred as energy storage since it takes up less space
* amylopectin: branched, additional 1-6 linkages, more soluble
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glycogen
* energy storage polysaccharide formed in the liver of animals
* composed of alpha-glucose with both 1-4 and 1-6 linkages, so it is branched
* branching every 10 subunits
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condensation reaction
* takes away one water molecule
* requires two monomers to form a dimer
* energy is required
* enzymes are required to speed up the process
* consists of bond-making
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hydrolysis
* breaks down a large molecule into a smaller ones
* releases energy
* requires enzymes
* one molecule of water is added, as bonds are broken
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saturated fatty acids
have NO double bonds - have the maximum number of hydrogen atoms attached
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unsaturated fatty acids
have double bonds, can be monounsaturated or polyunsaturated
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cis vs trans isomers of fatty acids
* cis isomers have hydrogens attached on the same side of the double bond
* trans isomers have hydrogens on opposite sides of the double bond
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what are triglycerides?
* largest class of lipids
* function as long-term energy storage molecules
* made up of glycerol and three fatty acids joined by an ester linkage during condensation (3 molecules of water are formed)
* animals store triglycerides as fats (solids) and plants as oils (liquids)
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lipid health risks
* trans and unsaturated increase blood cholesterol
* found in sweets, candies, pizza, beef, etc.
* raise LDL levels, which carry the cholesterol from the liver to the rest of the body
* hardening and narrowing of arteries by deposition
* this will restrict blood flow
* if coronary arteries are clogged, coronary heart disease may occur
* obesity
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(SODAS) comparison of lipids and carbohydrates
* Storage (long-term) is carried out more by lipids
* Osmolality - lipids have a lower effect on the osmotic pressure of a cell
* Digestion and utilisation is easier in the case of carbohydrates
* ATP yield is greater for lipids, as they store more energy per gram (twice as much)
* Solubility is greater for carbohydrates, so they are easier to transport in the bloodstream
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formula for BMI
BMI=\[mass in kg\]/\[height in m squared\]
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who is BMI not suitable for?
* pregnant women
* athletes
* BMI should not be used as a diagnostic tool, but rather one of many tests
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function of lipids (SHIPS)
* Storage of energy for long-term use
* Hormonal roles (steroids such as estrogen)
* Insulation - both thermal and electrical
* Protection of internal organs
* Structural components of cells, e.g. phospholipids or cholesterol
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generalised structure of an amino acid
* NH2 amine group
* COOH carboxyl group
* H atom
* interchangeable R group
* all bound to a central carbon atom
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why do all amino acids have the interchangeable R groups?
* they have distinct chemical properties
* it causes the protein to fold up in a specific pattern, giving it distinct function
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peptide bond formula
O=C-N-H
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primary structure of proteins
the sequence of amino acids that determines the folding of proteins
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secondary structure of proteins
* folded, stable structure resulting from the presence of hydrogen bonds
* alpha-helix - coil/spiral structure
* beta-pleated sheet - directionally-oriented staggered strand
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tertiary structure of proteins
* three-dimensional
* influenced by interactions such as: ionic interactions, hydrogen bonding, disulphide bridges, polar associations
* functional
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quaternary structure of proteins
* more than one polypeptide chain linked to each other
* may also have a prosthetic group that can be inorganic
* haemoglobin - haeme groups
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denaturation of proteins
it is a change in the structure of proteins which usually results in the permament loss of functions and biological properties
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denaturation by heat
* may disrupt hydrogen bonds that fold the protein
* loss of folding = loss of functionality
* in humans, the optimum temperature is around 37 degrees Celsius
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denaturation by pH fluctuations
* change in pH alters the structure, which means that its solubility or overall shape will change
* optimum pH differs for each protein
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conversion from genes to polypeptides
transcription - making mRNA based on DNA in the nucleus

translation - mRNA transcript used to link amino acids together at the ribosomes
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one gene codes for how many polypeptides?
typically one
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what is the purpose of alternative splicing of genes
producing multiple polypeptide variants
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what is the purpose of genetic mutations
producing multiple polypeptide variants
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proteome
the totality of proteins expressed within a cell, tissue or organism at a certain time; usually significantly larger than the number of genes
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functions of proteins (SHITS ME)
* Structure - collagen (component of connective tissue in animals), spider silk (fiber used to make webs)
* Hormones - insulin (lowers blood sugar), glucagon (raises blood sugar)
* Immunity - immunoglobulins (antibodies produced by plasma cells that target specific antigens)
* Transport - haemoglobin (transporting oxygen, found in red blood cells)
* Sensation - rhodopsin (a pigment in the photoreceptor cells of the retina that is responsible for the detection of light)
* Movement - actin (thin filaments involved in the contraction of muscle fibres), myosin (thick filament involved in the contraction of muscle fibres)
* Enzymes - rubisco (enzyme involved in the light-independent stage of photosynthesis)
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fibrous vs globular proteins (SPADES)
* Shape: long and narrow/spherical
* Purpose: structural/function
* Acid sequence: repetitive amino acid sequence/irregular
* Durability: less affected by pH or temp changes/more influenced
* Examples: keratin, fibrin, actin, myosin, elastin/rubisco, haemoglobin, immunoglobulins
* Solubility: insoluble/soluble
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enzymes
globular proteins that act as biological catalysts and speed up chemical reactions by lowering the activation energy; they remain unchanged or unconsumed at the end of the reactions, which is why they can be reused
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active site
the region of the enzyme to which the substrate binds
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enzymes are…
substrate specific - they complement each other in terms of shape and chemical properties
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how does enzyme catalysis work?
* typically in aqueous solutions
* substrate binds to enzyme and forms enzyme-substrate complex
* enzyme catalyses the conversion, forming enzyme-product complex
* dissociation of enzyme and product
* enzyme can catalyse further reactions as it is left intact
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how can the rate of catalysis be increased?
* increased temperature to increase the kinetic energy of molecules
* increasing the concentration of substrates and enzymes
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what is the purpose of enzyme immobilisation?
* fixed to a static surface in order to improve the efficiency of the catalysed reaction
* Enzyme concentrations are conserved as the enzyme is not dissolved – hence it can be retained for reuse
* Separation of the product is more easily achieved as the enzyme remains attached to the static surface
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production of lactose-free milk
* The lactase is purified from yeast or bacteria and then bound to an inert substance (such as alginate beads)
* Milk is then repeatedly passed over this immobilised enzyme, becoming lactose-free
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advantages of lactose-free milk
* As a source of dairy for lactose-intolerant individuals
* As a means of increasing sweetness in the absence of artificial sweeteners (monosaccharides are sweeter tasting)
* As a way of reducing the crystallisation of ice-creams (monosaccharides are more soluble, less likely to crystalise)
* As a means of reducing production time for cheeses and yogurts (bacteria ferment monosaccharides more readily)
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the lock and key model
* According to the lock and key model, the enzyme’s active site complements the substrate precisely
* The substrate fits a particular active site like a key fits into a particular lock
* This theory of enzyme-substrate interaction explains how enzymes exhibit *specificity* for a particular substrate
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induced fit model for enzymes
* the active site will undergo a __conformational change__ when exposed to a substrate to improve binding
* It explains how enzymes may exhibit *broad specificity* (e.g. lipase can bind to a variety of lipids)
* It explains how catalysis may occur (the conformational change stresses bonds in the substrate, increasing reactivity)
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metabolic pathways
* typically organised into chains or cycles of enzyme-catalysed reactions


* allow for a greater level of regulation, as the chemical change is controlled by numerous intermediates
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activation energy
the minimum amount of energy required for a reaction to occur
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competitive inhibition
* substance binds to the enzyme’s active site
* the substance is chemically and structurally similar to the substrate
* substrate cannot bind to the enzyme due to the blocked active site
* increasing substrate concentration can solve the problem
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non-competitive inhibition
* inhibitor binds to an allosteric site - not active site
* conformational changes in the active site are the result, hence the active site and the substrate no longer share specificity and the substrate cannot bind
* cannot be reduced by increasing the substrate concentration
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end-product inhibition or feedback inhibition
* controlling metabolic pathways and the yield of products
* In end-product inhibition, the final product in a series of reactions inhibits an enzyme from an earlier step in the sequence
* The product binds to an allosteric site and temporarily inactivates the enzyme (via non-competitive inhibition)
* As the enzyme can no longer function, the reaction sequence is halted and the rate of product formation is decreased
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examples of feedback inhibition
* threonine → isoleucine
* Isoleucine is an **essential amino acid**, meaning it is not synthesised by the body in humans (and hence must be ingested)
* **Food sources rich in isoleucine** include eggs, seaweed, fish, cheese, chicken and lamb
* In plants and bacteria, isoleucine may be synthesised from threonine in a five-step reaction pathway
* In the first step of this process, threonine is converted into an intermediate compound by an enzyme (threonine deaminase)
* Isoleucine can bind to an allosteric site on this enzyme and function as a non-competitive inhibitor
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components of a nucleotide
* pentose sugar - deoxyribose or ribose
* phosphate group
* nitrogenous bases: G, T, U, C, A
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adenine and thymine are connected by
two hydrogen bonds
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cytosine and guanine are connected by
three hydrogen bonds
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purines
double-ringed nitrogenous bases, adenine and guanine
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pyrimidines
single-ringed nitrogenous bases, cytosine, uracil, thymine
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nucleotides are connected by what type of bond?
phosphodiester
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what does it mean that the two DNA strands are antiparallel?
they have to run in opposite directions in order to allow the base pairs to form
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why is DNA organised in a double helix?
the atoms arrange in the most energetically stable configuration as the chains lengthen
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what discoveries helped Watson and Crick develop their model of DNA structure?
* DNA is composed of nucleotides made up of a sugar, phosphate and base – *Phoebus Levene, 1919*
* DNA is composed of an equal number of purines (A + G) and pyrimidines (C + T) – *Erwin Chargaff, 1950*
* DNA is organised into a helical structure – ***Rosalind Franklin****, 1953*  *(data shared without permission)*
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what were the early DNA models proposed by W&C?
* The first model generated was a triple helix
* Early models had bases on the outside and sugar-phosphate residues in the centre
* Nitrogenous bases were not initially configured correctly and hence did not demonstrate complementarity
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what did W & C’s final DNA model represent?
* DNA strands are antiparallel and form a double helix
* DNA strands pair via complementary base pairing (A = T ; C Ξ G)
* Outer edges of bases remain exposed (allows access to replicative and transcriptional proteins)
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Rosalind Franklin’s contribution to the development of the DNA structure
The final construction of a correct DNA molecule owed heavily to the X-ray crystallography data generated by Franklin

* This data confirmed the arrangement of the DNA strands into a helical structure
* The data was shared without Franklin’s knowledge or permission and contributed profoundly to the final design
* Hence, Franklin is now recognised as a key contributor to the elucidation of DNA structure
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why can DNA replication be called a semi-conservative process?
the replicated DNA contains one newly formed strand and one that is conserved from the templete DNA molecule
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Meselson-Stahl experiment
* 1958
* Meselson and Stahl were able to experimentally test the validity of these three models using radioactive isotopes of nitrogen
* DNA molecules were prepared using the heavier 15N and then induced to replicate in the presence of the lighter 14N
* DNA samples were then separated via centrifugation to determine the composition of DNA in the replicated molecules
* The results after two divisions supported the semi-conservative model of DNA replication
* After one division, DNA molecules were found to contain a mix of 15N and 14N, disproving the conservative model
* After two divisions, some molecules of DNA were found to consist solely of 14N, disproving the dispersive model
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three hypotheses proposed prior to the Meselson-Stahl experiment about the mechanism of DNA replication
* *Conservative Model* – An entirely new molecule is synthesised from a DNA template (which remains unaltered)
* *Semi-Conservative Model* – Each new molecule consists of one newly synthesised strand and one template strand
* *Dispersive Model* – New molecules are made of segments of new and old DNA
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PCR
polymerase chain reaction, artificial method of replicating DNA under laboratory conditions