A Level Biology OCR (Memo P)

10 ch 3.4 chemical tests for carbs, p51

- all monosaccharides and some disaccharides (e.g. maltose & lactose) are reducing sugars, they donate electrons, reducing another molecule or chemical. benedict's test for reducing sugars, benedict's reagent (alkaline copper(ii) sulfate). place sample in boiling tube, if not liquid, grind up or blend in water, add equal volume of benedict's reagent. heat mixture gently in water bath for five minutes. reducing sugars react with copper ions in benedict's reagent, results in addition of electrons to blue Cu^2+ ions, reduces it to brick red Cu + ions, brick red precipitate formed and indicates positive reducing sugar result. the more reducing sugar present, the more precipitate formed & the less blue Cu^2+ ions left in solution. actual colour seen is mixture of brick-red precipitate and blue unchanged Cu^2+ ions, depends on concentration of reducing sugar present. - non-reducing sugars do not react with benedict's reagent, solution remains blue after warming, indicating negative result, e.g. sucrose is most common non-reducing sugar. if sucrose is boiled with HCl, positive result when warmed with Benedict's solution, as sucrose has been hydrolysed by acid to glucose & fructose (reducing sugars). - reagent strips, used to test for presence of reducing sugars (most commonly glucose). advantage, with colour-coded chart, determines concentration of sugar. iodine test for starch, add few drops of iodine dissolved in potassium iodide solution, mix with sample. if solution changes from yellow to blue, positive & starch is present. if stays yellow, negative & starch is not present. - quantitative method to determine concentration of reducing sugar: filter placed in colorimeter, colorimeter calibrated using distilled water, benedict's test performed on range of known concentrations of sugar, resulting solutions filtered to remove precipitate, % transmission of solutions of glucose measured using colorimeter, calibration curve plotted. repeat benedict's test on unknown concentration & measure % transmission, match against curve. - biosensors, mechanism: molecular recognition, protein (enzyme/antibody) or single strand of DNA is immobilised to a surface (e.g. glucose test strip). this will interact with specific molecule under investigation. transduction, interaction causes change in a transducer, transducer detects change (e.g. in pH), produces response (e.g. release of immobilised dye on test strip / electric current in glucose-testing machine). display, produces visible qualitative/quantitative signal (e.g. particular colour on test strip or reading on test machine).

9 ch 3.3 carbohydrates, p46

- carbohydrates formula, Cx(H2O)y. carbs are saccharides/sugars, single sugar is monosaccharide (e.g. glucose, fructose & ribose), when 2 link they form disaccharide (e.g. lactose & sucrose), when 2 or more monosaccharides linked, they form polymer called polysaccharide (e.g. glycogen, cellulose & starch). - glucose is monosaccharide with 6 carbons, so hexose monosaccharide. carbons are numbered clockwise, beginning with oxygen atom within ring. 2 structural variations of glucose, alpha and beta glucose, OH groups on carbon 1 are in opposite positions. glucose molecules are polar and soluble in water, as hydrogen bonds form between hydroxyl groups and water molecules, solubility important, means glucose is dissolved in cytosol of cell. - when 2 alpha glucose molecules are side by side, the 2 hydroxyl groups interact, bonds are broken and new bonds reformed in different places, two hydrogen atoms and oxygen atom are removed from glucose monomers, forms water molecule. covalent (1,4 glycosidic) bond forms between carbons 1 and 4 on glucose molecules, molecules are joined. reaction produced maltose, disaccharide. fructose and galactose are also hexose monosaccharides. fructose + glucose = sucrose, galactose + glucose = lactose. pentode monosaccharides are sugars with 5 carbon atoms, e.g. ribose, sugar in RNA nucleotides, deoxyribose, sugar in DNA nucleotides. - many alpha glucose molecules joined by glycosidic bonds form 2 slightly different polysaccharides (starch). glucose made in plant cells stored as starch, chemical energy store. one is amylose, formed from alpha glucose joined only by 1,4 glycosidic bonds, angle of bond means long chain of glucose twists to form helix, this is further stabilised by hydrogen bonding within molecule, makes polysaccharide more compact & less soluble than glucose molecules used to make it. other type of starch, amylopectin, made by 1,4 glycosidic bonds between alpha glucose molecules, and glycosidic bonds by condensation reactions between carbons 1 & 6, means amylopectin is branched, 1,6 branching points occur every 25 glucose subunits. equivalent energy storage molecule to starch in animal and fungi is glycogen, forms more branches than amylopectin, so more compact and less space needed for it to be stored, important as animals are mobile unlike plants. cooling or branching of these polysaccharides make them compact, ideal for storage, branching also means many free ends where glucose molecules can be added or removed, speeds up process of storing & releasing glucose molecules required by the cell. overall, amylopectin & glycogen are insoluble, branched & compact, suited for storage roles. glucose is stored as starch by plants or glycogen in animals until needed for respiration, process where biochemical energy in the stored nutrients is converted into a usable energy source for the cell. to release glucose for respiration, starch & glycogen go through hydrolysis reactions, requires addition of water molecules, catalysed by enzymes. reverse of condensation reactions forming glycosidic bonds. - beta molecule unable to join in same way as alpha glucose, hydroxyl groups on carbon 1 & 4 of 2 beta-glucose molecules too far from each other to react. beta molecules can only join together and form polymer if alternate beta glucose molecules are turned upside down. when polysaccharide is formed in this way, unable to coil or form branches, straight chain molecule is formed (cellulose). cellulose molecules make hydrogen bonds with each other, form microfibrils. microfibrils join together, form macrofibrils, macrofibrils combine your form fibres. fibres strong and insoluble, used to make cell walls, difficult to break down into its monomers.

15 ch 3.9, DNA replication & genetic code, p72

- cells divide to produce more cells, for growth/repair of tissues, 2 daughter cells produces as result of cell division, both genetically identical to parent cell & to each other, therefore they contain DNA with a base sequence identical to the original. when cell prepares to divide, the 2 strands of DNA double helix separate, each strand serves as template for creation of new double-stranded DNA molecule. complementary base pairing rules ensure 2 new strands are identical to original, this process is called DNA replication. - for DNA to replicate, double-helix structure unwinds & separates into 2 strands, so hydrogen bonds holding complementary bases together must be broken. free DNA nucleotides pair with complementary bases, which are exposed after strands separate. hydrogen bonds are formed between them. the new nucleotides join to their adjacent nucleotides with phosphodiester bonds. therefore 2 new molecules of DNA are produced, each one consists of one old strand and one new strand of DNA, this is called semi-conservative replication. - DNA replication is controlled by enzymes, (class of proteins as catalysts for biochemical reactions), enzymes only able to carry out a function by recognising & attaching to specific molecules/particular parts of the molecules. before replication occurs, the 2 strands of DNA double helix unwinds & separates, carried out by enzyme DNA helicase. travels along DNA backbone, catalyses reactions that break down hydrogen bonds between complementary base pairs as it reaches them, thought of as 'unzipping'. free nucleotides pair with newly exposed bases on template strands during 'unzipping' process. second enzyme, DNA polymerase, catalyses formation of phosphodiester bonds between the nucleotides. - sequences of bases not always matched exactly, incorrect sequence may occur in newly-copied strand, these errors occur randomly & spontaneously, leads to change in sequence of bases (called mutation). - DNA is contained within the cells of all organisms, scientists determined that this molecule was the means by which genetic information was passed down from 1 generation to the next, and DNA carries 'instructions'/'blueprints' needed to synthesise the many different proteins needed by organisms. proteins are the foundation for different physical & biochemical characteristics of living things, they are made up of sequence of amino acids folded into complex structures, therefore DNA codes for a sequence of amino acids. this is called the genetic code. 'instructions' that DNA carries are contained in sequence of bases, along the chain of nucleotides that make up the 2 strands of DNA. the code in the base sequence is a simple triplet code, it is a sequence of 3 bases, (called a codon), each codon codes for an amino acid. a gene is a section of DNA that contains the complete sequence of bases (codons) to code for an entire protein. the genetic code is universal, all organisms use the same code, although sequences of bases coding for each individual protein is different. there are 4 different bases, therefore 64 different triplets/codons possible (4^3), includes start codon that signals start of a sequence that codes for a protein, if this codon is in the middle, it is methionine. there are also 3 'stop' codons that don't code for any amino acids, signals end of sequence. a single codon to signal start of a sequence ensure triplets of bases (codons) are read 'in frame', i.e. DNA base sequence is 'read' from base 1, rather than base 2 or 3, therefore genetic code is non-overlapping. there are only 20 different amino acids that regularly occur in biological proteins, therefore there are more codons than amino acids, therefore an amino acid can be coded for by multiple codons, therefore genetic code is known as degenerate.

25 ch 5.4, active transport, p112

- diffusion ultimately results in conc gradient being reduced until particles (atoms, molecules or ions) in different regions reach equilibrium. however many biological processes depend on presence of conc gradient, e.g. transmission of nerve impulses. to maintain conc gradient, particles must be moved up it at faster rate than rate of diffusion, this is an energy-requiring process called active transport. - active transport is movement of molecules/ions into or out of a cell from region of lower conc to region of higher conc, process requires energy & carrier proteins. energy is needed as particles are moved up a conc gradient, in opposite direction to diffusion, metabolic energy is supplied by ATP. carrier proteins span membranes & act as 'pumps'. general process of active transport (transport from outside to inside a cell): molecule/ion to be transported binds to receptors in channel of carrier protein on outside of cell. on inside of cell ATP binds to carrier protein & is hydrolysed into ADP & phosphate. binding of phosphate molecule to carrier protein causes protein to change shape, opens up to inside of cell. molecule/ion is released to inside of cell. phosphate molecule is released from carrier protein & recombined with ADP to form ATP. carrier protein returns to its original shape. this process is selective, specific substances are transported by specific carrier proteins. - bulk transport is another form of active transport, large molecules e.g. enzymes, hormones & whole cells (like bacteria) are too large to move through channel or carrier proteins, so are moved into & out of cell by bulk transport. endocytosis, bulk transport of material into cells, 2 types of endocytosis: phagocytosis for solids, pinocytosis for liquids, process is same for both. cell-surface membrane first invaginates (bends inwards) when it comes into contact with material to be transported, membrane enfolds the material until eventually membrane fuses, forms a vesicles. vesicle pinches off & moves into cytoplasm to transfer material for further processing within the cell, e.g. vesicles containing bacteria are moved towards lysosomes, where bacteria are digester by enzymes. - exocytosis, reverse of endocytosis, vesicles (usually formed by golgi apparatus) move towards & fuse with cell surface membrane, contents of vesicle are then released outside of cell. - energy in form of ATP is required for movement of vesicles along the cytoskeleton, changes shape of cells to engulf materials, & fusion of cell membranes as vesicles form or as they meet the cell-surface membranes.

119 ch 20.3, dihybrid inheritance

- dihybrid crosses, used to show inheritance of 2 different characteristics, caused by 2 genes, known as dihybrid inheritance. genes may be located on different pairs of homologous chromosomes. each of these genes can have 2 or more alleles. - dihybrid cross set out in similar format to monohybrid cross, however 4 alleles (2 for each characteristic) shown at each stage instead of 2. - example, inheritance of seed phenotype in pea plants, seeds can be produced in 2 different colours (yellow or green), & 2 different shapes (round or wrinkled). following codes used to represent alleles: Y, allele coding for yellow seeds (dominant), y for green (recessive), R for round, r for wrinkled. - if pea plant heterozygous for both genes (YyRr) crossed with another, expected phenotype ratio is 9:3:3:1. - actual ratio may differ from expected, because: 1, fertilisation of gametes is random process so in a small sample, a few chance events can lead to skewed ratio or 2, genes being studied are on same chromosome (these are linked genes), if no crossing over occurs alleles for the 2 characteristic will always be inherited together.

19 ch 4.2, factors affecting enzyme activity, p88

- enzymes must come in contact with substrate to catalyse reaction, enzyme must be right shape (complementary) for substrate. enzymes are complex proteins, structure can be affected by factors, e.g. temp & pH, these can cause changes in shape of active site. enzymes are more likely to come in contact with substrate if temperature & substrate concentration are increased. factors affecting enzyme action investigated by measuring the rate of reactions they catalyse. - increasing temp of reaction environment increases kinetic energy of particles, as temp increases, particles move faster & collide more frequently. in enzyme-controlled reaction, increase in temp results in more frequent successful collisions between substrate & enzyme, leads to increase in rate of reaction. temp coefficient, Q10, of a reaction/process is a measure of how much rate of reaction increases with 10°C rise in temp, for enzyme-controlled reactions this is usually 2, therefore rate of reaction double with 10°C increase. as enzymes are proteins, structure is affected by temp. at higher temps, bonds holding protein together vibrate more, as temp increases vibrations increase until bonds strain & break. breaking of these bonds results in change in precise tertiary structure of protein, enzyme has changed shape & is denatured. optimum temp is temp where enzyme has highest rate of activity, optimum temp can vary significantly. many enzymes in human body have optimum temp around 40°C, thermophilic bacteria (live in hot springs) have enzymes with optimum of 70°C, psychrophilic organisms (live in cold areas like antarctic & arctic) has enzymes with optimum below 5°C. once enzymes denature above optimum temp, decrease in rate of reaction is rapid, only needs to be slight change in shape of active site for it to no longer be complementary to substrate. this happens to all enzyme molecules at about same temp, so loss of activity is abrupt, at this point in enzyme-controlled reaction, temp coefficient (Q10) no longer applies as enzymes are denatured. decrease in rate of reaction below optimum temp is less rapid, as enzymes not denatured, but just less active. majority of living organisms have evolved to cope with living within a certain temp range, some organisms can also cope with extremes. examples of extremely cold environments are deep oceans, high altitudes & polar regions, enzymes controlling metabolic activities of organisms living in these environments need to be adapted to the cold. enzymes adapted to the cold have more flexible structures, particularly at active site, therefore are less stable than enzymes that work at higher temps. smaller temp changes will denature them. thermophiles are organisms adapted to living in very hot environments, e.g. hot springs & deep sea hydrothermal vents. enzymes present in these organisms are more stable than other enzymes, due to increased number of bonds, particularly hydrogen bonds & sulfur bridges in tertiary structure. shapes of these enzymes & active sites are more resistant to change as temp rises. - proteins, & so enzymes, are also affected by changes in pH, hydrogen bonds & ionic bonds between amino acid R-groups hold proteins in precise 3D shape, these bonds result from interaction between polar & charged R-groups present on amino acids forming primary structure. change in pH refers to change in H+ ion concentration, more H+ ions are present in low pH (acid) environments, & fewer H+ ions are present in high pH (alkaline) environments. active site is only in right shape at certain H+ ions conc, this is optimum pH for any particular enzyme, when pH changes from optimum (become more acidic/alkaline), structure of enzyme & therefore active site is altered. however if pH returns to optimum then protein resumes its normal shape & catalyse the reaction again (renaturation). when ph changes more significantly (beyond certain pH), structure of enzyme is altered irreversibly, active site is no longer complementary to substrate, & is denatured, substrate no longer binds to active site. this reduces rate of reaction. H+ ions interact with polar & charged R-groups, therefore changing conc of H+ changes degree of this interaction, interaction of R-groups with H+ ions also affect interaction of R-groups with each other. the more H+ ions present (low pH), the less the R-groups are able to interact with each other, this leads to bonds breaking & shape of enzyme changing, the reverse is true when fewer H+ ions (high pH) are present, this means shape of enzyme will change as pH changes, therefore it only functions in narrow pH range. pH conditions under which the various enzymes of the human digestive system function (optimum pHs): saliva, mouth/throat, neutral (pH 7-8), amylase, starch -> maltose. gastric juice, stomach, acidic (pH 1-2), pepsin, proteins -> polypeptides. pancreatic juice, small intestine/duodenum, slightly alkaline (pH 8), trypsin/lipase/amylase/maltose, proteins->polypeptides/triglycerides->glycerol/starch->maltose/maltose->glucose. - substrate & enzyme conc, when conc of substrate is increased, number of substrate molecules, atoms or ions in particular area/volume increases. increased number of substrate particles leads to higher collision rate with active sites of enzymes & formation of more enzyme-substrate complexes, therefore rate of reaction increases. also true when enzyme conc increased, this increases number of available active sites in particular area/volume, leads to formation of enzyme-substrate complexes at a faster rate. rate of reaction increases up to its maximum (Vmax), at this point all active sites are occupied by substrate particles & no more enzyme-substrate complexes can be formed until products are released from active sites, only way to increase rate of reaction would be to add more enzymes or increase temp. if conc of enzyme is increased, more active sites available so reaction rate rises towards higher Vmax, conc of substrate becomes limiting factor again, increasing this will once again allow reaction rate to rise until new Vmax is reached. - investigating effects of different factors on enzyme activity. catalase is an enzyme present in plant and animal tissue, makes good choice for use in investigations, as it is readily available. catalyse catalyses breakdown of H2O2 into H2O & O2. volume of O2 gas collected in set length of time can be used as measure of rate of reaction. to investigate temp, liver tissue was put in H2O2 solution, volume of oxygen released every five seconds was measured. in second experiment, liver was boiled for five mins, before placed in H2O2 solution. - serial dilution is a repeated, stepwise solution of a stock solution of known concentration, serial dilution is usually done by factors of ten to produce range of concs. serial solutions useful even if conc of initial solution is unknown as they give relative concs, serial solutions are used in many different ways, e.g. investigate effect of changing the conc of enzyme of substrate in a reaction, & determining numbers of microorganisms in a culture. 5 test tubes set up, 1ml of stock solution added to 9ml of distilled water gives 10ml of dilute solution, in which there is 1ml stock/10ml, hence 1/10 or 10 fold dilution. this step is repeated a number of times to give serial dilution. to investigate effect of different concs of catalse in rate of breakdown of H2O2, catalase rich tissues (e.g. liver/potato) is ground down to make solution. solution contains catalase released from cells. serial dilution of this solution will produce range of solutions with different relative concs of catalase. effect of the different concs on rate of reaction is investigated by adding equal volumes of a given conc of H2O2 to each solution.

121 ch 20.5, evolution

- evolution, change in inherited characteristics of a group of organisms over time. occurs due to changes in frequency of different alleles within a population. population genetics, investigates how allele frequencies change within populations over time. sum total of genes in population at any given time is known as gene pool, gene pool of population includes millions of genes but there will be variation in different alleles of a single gene. relative frequency of a particular allele in a population is called allele frequency. frequency of an allele occurring in a population is not linked to dominant or recessive characteristic, and is not fixed, it can change over time in response to changing conditions. evolution involves long-term change in allele frequencies of a population, e.g. alleles for antibiotic resistance have increased in many bacteria populations over time. biologist have developed ways to determine allele frequencies & use them in models to determine whether evolution is taking place. - calculating allele frequency - look at a gene with 2 possible alleles, A and a, frequency of A in population represented by letter p, frequency of allele a represented by q. if every individual in a population of 100 (diploid organisms) is heterozygous (Aa), frequency of each allele is 100/200 or 0.5 (50%), so p+q=1. in diploid breeding population with 2 potential alleles, frequency of dominant allele + frequency of recessive allele always equal 1, formula required for Hardy-Weinberg principle. hardy- weinberg principle - hardy-weinberg principle, models mathematical relationship between frequencies of alleles & genotypes in theoretical population that is stable and not evolving. principle states: in a stable population with no disturbing factors, allele frequencies will remain constant from one generation to the next, no evolution. completely stable population not common in real world, but still useful tool, principle provides simple model of theoretical stable population, so can measure and study evolutionary changes when they occur. principle: p^2 + 2pq + q^2 = 1, where p^2 = frequency of homozygous dominant genotype in population, 2pq = frequency of heterozygous genotype, q^2 = homozygous recessive. principle assumes theoretical breeding population of diploid organisms is large & isolated, with random mating, no mutations or selection pressure. in natural environment these conditions are uncommon, species continuously changing. e.g. peppered moths, light alleles were dominant historically, but allele frequencies changed dramatically after industrial revolution, dark alleles gave individuals advantage, now allele frequencies changed again as cities & woodlands clean again. these changes in allele frequency illustrated by principle, upsetting equilibrium eventually results in evolution. - factors affecting evolution - leads to changes in frequency of alleles in population, so affect rate of evolution: mutation, necessary for existence of different alleles in the first place, formation of new alleles, leads to genetic variation. sexual selection, increases frequency of alleles, codes for characteristics to improve mating success. gene flow, movement of alleles between populations, immigration & emigration results in changes in allele frequency within a population. genetic drift, occurs in small populations, change in allele frequency due to random nature of mutation, appearance of new allele has greater impact (more likely to increase in number) in smaller population than in much larger population, where there is greater number of alleles present in gene pool. natural selection, leads to increase in number of individuals that have characteristics to improve chances of survival, reproduction rates of these individuals increase, and frequency of alleles coding for characteristics increase, this is how changes in environment leads to evolution. - impact of small populations - gene pool of large population ensures lots of genetic diversity due to presence of many different genes & alleles, genetic diversity leads to variation within population, essential in process of natural selection. selection pressures, e.g. changes in environments, presence of new diseases, prey, competitors or human influences, lead to evolution. the population can adapt to change over time. small populations with limited genetic diversity cannot adapt to change easily, more likely to become extinct, new strain of pathogen could wipe out whole population. size of population affected by many factors, factors which limit or decrease population size are called limiting factors: density-depend factors, dependent on population size, includes competition, predation, paratism & communicable disease. density-independent factors, affect populations do all sizes in same way, includes climate change, natural disasters, seasonal change & human activities (e.g. deforestation). large reductions in population size, which lasts for at least one generation, is called population bottleneck. gene pool, along with genetic diversity, is greatly reduced and effects are seen in further generations. takes thousands of years for genetic diversity to develop in population through slow accumulation of mutations. e.g. northern elephant seals, almost hunted to extinction by 19th century, only around 20 seals left by the time hunting stopped, now has population of 30,000 but show much less genetic diversity than southern seals, that did not experience genetic bottleneck. cheetahs, thought to have experienced initial population bottleneck around 10,000 years ago, with other bottlenecks happening more recently, species now shoes low genetic diversity. cheetahs face same threat as many other african animals, e.g. habitat loss & poaching, while popuation sizes of other animals are recovering thanks to conservationists, cheetahs not recovering quickly, now close to extinction. reduced genetic diversity of cheetahs means they share 99% of alleles with other members of species, more than humans share with members of own family, mammals usually share 80% of alleles with other members of species. as a result, cheetahs showing problems of inbreeding, including reduced fertility. humans & chimpanzees split from common ancestor 6 million years ago, small groups of chimpanzees likely to show more genetic diversity than all humans alive today, it is belived that humans have experienced at least one genetic bottleneck, reducing genetic diversity, as we have evolved into present form. positive aspect of genetic bottleneck is beneficial mutations have much greater impact, leads to quicker development of new species, this is thought to have played a role in evolution of early humans. founder effect, where small populations can arise due to establishment of new colonies by a few isolated individuals, is extreme example of genetic drift. small populations have much smaller gene pools than original population, display less genetic variation. if carried to new population, frequency of any rare alleles in original population much higher in new, smaller population, therefore has much bigger impact during natural selection. afrikaner population in south africa is descended mainly from a few dutch settlers, population today has unusually high frequency of alleles causing huntington's disease. it is thought that just one of the original settlers carried the disease-causing allele. amish people of america descended from 200 germans who settled in pennsylvania in 18th century, rarely marry or have children outside own religion & therefore a closed community. a the amish have unusually high frequencies of alleles causing normally rare genetic disorder ellis-van creveld syndrome. people with syndrome are short, often have polydactyl (extra fingers of toes), abnormalities of nails & teeth, and hole between 2 upper chambers of heart. ellis-van creveld syndrome is example of founder effect caused by one couple, samuel king and his wife who settled in the area in 1744. - evolutionary forces - traits or characteristics of all living organisms show variation within populations, distribution of different variants takes form of bell-shaped curve if plotted on graph, this is known in statistics as a normal distribution. e.g. birth weight of babies, babies with average birth weight most common therefore form peak of the graph, babies with very low birth weight more prone to infections & leave babies result in difficult births, both extremes in weight reduce survival chances of baby so numbers of survivals of very small or large babies remains low, forms tails of curve. this is natural selection, or survival of the fittest, babies with average birth weight more likely to survive & reproduce than underweight or overweight babies, this is example of 'stabilising selection', because norm or average is selected for (positive selection) and extremes are selected agains (negative selection). therefore stabilising selection results in reduction of allele frequency at the extremes, and increase in average alleles. directional selection, occurs when there is change in environment & normal phenotype is no longer most advantageous. organisms less common with more extreme phenotypes are positively selected, allele frequency shifts towards extreme phenotypes & evolution occurs. e.g. changes seen in peppered moths during industrial revolution, during this period, a lot of smoke released from factories, killed lichens growing on barks of trees, soot made bark black. peppered moths originally light coloured, camouflaged by lichen from predation by birds, always a few darker moths present due to variation, but were quickly eaten and allele frequency maintained. when lichens died, trees became black and situation reversed, light coloured moths very visible and eaten, darker moths were camouflaged, over time allele frequency shifted due to natural selection and majority of peppered moths had darker colour, allele frequency shifted towards an extreme (less common) phenotype. as pollution decreased again, allele frequency of lighter coloured moths had increased. disruptive selection, extremes are selected for and norm selected against, finches observed by darwin in galápagos islands had been subjected to disruptive selection, opposite to stabilising selection when norm is positively selected. example of disruptive selection relatively rare, well-documented example involves feather colour in male lazuli buntings (birds native to north america), feather colour of young males range from bright blue to dull brown. limited nesting sites in habitat so a lot of competition between male birds to establish territories & attract female birds, dull brown males seen as non-threatening, bright blue males seen as too threatening by adult males, both brown and blue birds therefore left alone but intermediate colour attacked by adult birds, so fail to mate or establish territories. extremes are selected for and distribution of phenotypes shows 2 peaks at extremes.

17 ch 3.11, ATP, p80

- examples of processes requiring energy: muscle contraction, cell division, transmission of nerve impulses & memory formation. energy comes in many forms: heat, light, energy in chemical bonds. energy needs to be supplied in right form & quantity to processes that require it. cells require energy for 3 main types of activity; synthesis, e.g. large molecules (e.g. proteins). transport, e.g. pumping molecules/ions across cell membranes by active transport. movement, e.g. protein fibres in muscle cells that cause muscle contraction. inside cells, adenine triphosphate (ATP) supports this energy, in a way it can be used. - ATP molecule is composed of nitrogenous base, pentose sugar, & 3 phosphate groups. structure of ATP is similar to the nucleotides involved in structure of DNA & RNA. however in ATP, base is always adenine, & there are 3 phosphate groups instead of one. sugar in ATP is ribose, as in RNA nucleotides. ATP is used for energy transfer in all cels of living things, therefore it is universal energy currency. - energy is needed to break bonds & release when bonds are formed. a small amount of energy is needed to break relatively weak bond holding last phosphate group in ATP. however a large amount of energy is released when liberated phosphate undergoes other reactions involving bond formation. overall, more energy released than used, approx 30.6kJ/mol. water is involved in removal of phosphate group, so hydrolysis reaction. ATP + H2O -> ADP + Pi (inorganic phosphate) + energy. hydrolysis of ATP doesn't happen in isolation, but in association with energy-requiring reactions. reactions said to be 'coupled' as they happen simultaneously. ATP is hydrolysed into adenine diphosphate (ADP) & inorganic phosphate ion (Pi), this overall reaction releases energy. - instability of phosphate bonds in ATP means that ATP is not a good long-term energy. fats & carbohydrates better for this, energy released in breakdown of these molecules (process called cellular respiration), is used to create ATP, this occurs by reattaching a phosphate group to an ADP molecule. this process is called phosphorylation. as water is removed in this process, example of condensation reaction. due to instability of ATP, cells don't store large amounts of it. however ATP is rapidly reformed by the phosphorylation of ADP. this intercoverion of ATP & ADP happens constantly in living cells, means cells do it need a large store of ATP, therefore ATP is a good immediate energy store. - structure & properties of ATP mean it is ideal to carry out function in energy transfer: small, moves easily into, out of & within cells. water soluble, energy-requiring processes happen in aqueous environments. contains bonds between phosphates with intermediate energy, large enough to be useful for cellular reactions, but not so large that energy is wasted as heat. releases energy in small quantities, quantities suitable to most cellular needs so energy is not wasted as heat. easily regenerated, can be recharged with energy

24 ch 5.3, diffusion, p108

- exchange of substances between cells & their environment or between membrane-bound compartments within cells & cell cytosol, defined as either active (requires metabolic energy) or passive. all movement requires energy, however passive movement utilises energy from natural motion of particles, rather than energy from another source. diffusion is net/overall movement of particles (atoms, molecules or ions) from region of higher conc to region of lower conc, it is a passive process, continues until there is a concentration equilibrium between the 2 areas. equilibrium means balance or no different in concentrations. diffusion happens because particles in gas/liquid have kinetic energy (they are moving), this movement is random and an unequal distribution of particles will eventually become an equal distribution. equilibrium doesn't mean particles stop moving, just the movements are equal in both directions. for this reason cells are generally microscopic, movement of particles within cells depends on diffusion & a large cell would lead to slow rates of diffusion, reactions wouldn't get substrates they need quickly enough or ATP would be supplied too slowly to energy-requiring processes. - factors affecting diffusion: temperature, higher temperature, higher rate of diffusion, because particles have more kinetic energy & move at higher speeds. concentration difference, greater difference in concentration between 2 regions, faster rate of diffusion, because overall movement from higher conc to lower conc is larger. conc difference is said to be conc gradient, which goes from high to low conc, diffusion takes place down conc gradient, takes a lot more energy to move substances up a conc gradient. so far diffusion in absence of a barrier/membrane has been considered, this is simple diffusion. rate of diffusion is calculated by distance travelled over time, & volume filled over time. distance travelled over time isn't affected by changes in surface area, whilst volume over time varies depending on surface area. to investiagte how rare of diffusion is affected by surface area: use different sized agar blocks containing phenolphthalein (turns pink in alkali), agar blocks are immersed in solution of NaOH and distance it diffused is measured with ruler. - diffusion across membranes involved particles passing through phospholipid bilayer, only happens if membrane is permeable to the particles, non-polar molecules e.g. oxygen (O2) diffuse through freely down concentration gradient. hydrophobic interior of the membrane repels substances with positive/negative charge (ions), so cannot easily pass through, polar molecules e.f. water (H2O) with partial positive & negative charges can diffuse through membranes, but at very slow rate. small polar molecules pass through more easily than larger ones. therefore membranes are described as partially permeable. rate at which molecules/ions diffuse across membranes is affected by: surface area, larger the area of an exchange surface, higher the rate of diffusion. thickness of membrane, thinner the exchange surface, higher the rate of diffusion. - phospholipids bilayers are barriers to polar molecules & ions, however membranes contain channel proteins through which polar molecules & ions can pass. diffusion across a membrane through protein channels is called facilitated diffusion. membranes with proteins channels are selectively permeable, as most protein channels are specific to one molecule/ion. facilitated diffusion can also involve carrier proteins, which change shape when specific molecule binds, in facilitate diffusion movement of molecules is down a conc gradient & doesn't require external energy. rate of facilitated diffusion is dependent on temp, conc gradient, membrane surface area & thickness, but also affected by number of channel proteins present, the more protein channels, the higher rates of diffusion overall. - cell membranes are complex structures involved in active & passive transport of ions & molecules, hydrophobic & hydrocarbon core of membrane is barrier to ions & large polar molecules, but allows passage of non-polar molecules. cells are too small & cell membranes too thin to use in practical investigations, therefore dialysis tubing is used as substitute membrane, model enables us to investigate effects of temp & conc on rate of diffusion across membranes. dialysis tubing is partially permeable, pores are a similar size to those on a partially permeable membrane, therefore small molecules like water can pass through it, but larger molecules like starch cannot fit through the pores. tubing is therefore a barrier to large molecules. a model cell can be simulated by tying one end of section of tubing, filling with a solution, then tying other end, 'cell' is then placed into another solution, solutions could contain different sizes or concentrations of solute molecules. changes in conc of solute molecules, both inside & outside model cells, is measured over time, rates of diffusion across tubing can then be calculated. glucose is a small molecule which can cross tubing, benedict's solution is used to test for presence of glucose, can also be used to estimate concentration. starch molecules are large & will not cross tubing, iodine is used to test for presence of starch. water is a small molecule, will pass through tubing while other solutes e.g. sucrose will not, model cells can be placed in solutions with different solute concs. rate of osmosis is calculated using changes in volume/mass of model cells over time. rates of diffusion at different temps is also calculated using water bath, to change temp of model cell, other variables e.g. conc must be then kept constant.

120 ch 20.4, phenotypic ratios

- expected ratios of phenotypes easily calculated as long as dominant and recessive alleles are known. actual numbers may vary from expected to some extent, because process is random but differences should mot be large. the larger the sample, the closer the numbers will be to expected ratio. - linkage - ratios observed in many dihybrid crosses differ significantly from expected, often due to linkage (meaning genes are located on same chromosome), e.g. sex linkage (effects of sex linkage seen in haemophilia & colourblindness). when linked genes are found on one of the other pairs of chromosomes (not sex chromosomes), it's called autosomal linkage. linked genes tend to be inherited together as one unit, as there's no independent assortment during meiosis unless alleles are separated by chiasmata. linked genes can't undergo random 'shuffling' of alleles during meiosis & expected ratios aren't produced in offspring as they are effectively inherited as a single unit. e.g. body colour & wing length, are linked characteristics in fruit flies, allele B responsible for brown body & is dominant to b for black body, allele V is responsible for long wings & is dominant to v for short wings. fly with genotype BbVv crossed with bbvv, expected ratio is 1:1:1:1, observed is 5:1:1:5. homozygous parent can only produce bv gametes, heterozygous parent produces mainly BV & bv gametes as alleles are linked. heterozygous parent will produce a few bV and Bv gametes, due to crossing over, results in separation of some linked genes, this results in small number of flies with brown & short, and black & long characteristics, these are called recombinant offspring (they have different combinations of alleles than either parent). the closer the genes are on the chromosome, the less likely they are to be separated during crossing over & the fewer recombinant offspring produced. recombination frequency is measure of amount of crossing over in meiosis, recombination frequency = (number of recombinant offspring)/total number of offspring. recombination frequency of 50% indicates no linkage and genes are on separate chromosomes. less than 50% indicates gene linkage & random process of independent assortment is hindered. degree of crossing over determined by how close genes are on a chromosome, as degree of crossing over reduces the recombination frequency also decreases, therefore the closer the genes are on a chromosome the less likely they are to be separated during crossing over & vice versa. recombination frequencies for a number of characteristics coded for by genes on the same chromosome can be used to map genes on the chromosome, a recombination frequency of 1% indicates 1 map unit on a chromosome. - chi-squared test - observed & expected results from a genetic cross will almost always be different due to chance. the number of observations made determines how chance affects results. it is important to know whether differences are due to chance or if there is another reason (significant differences). chi-squared test, statistical test to measure size of the difference between expected & observed results, helps determine whether differences are significant or not, by comparing the sizes of differences & number of observations. chi-squared test conventionally used to test null hypothesis, null hypothesis is there is no significant difference between expected & observed results, therefore differences due to chance. calculated chi-squared values are used to find probability of difference being due to chance alone. χ² = Σ(O-E)²/E. large chi-squared values means a statistically significant difference between observed & expected results & probability this is due to chance is low, there must be another reason for unexpected results. the number of categories being compared in investigation affects size of chi-squared value, degrees of freedom is number of comparisons being made i& is calculated as n-1, where n is number of categories or possible outcomes (phenotypes) present in analysis. e.g. looking at yellow and green peas, 2 categories, therefore 1 degree of freedom. if calculated χ² value is less than critical value found in a table at 5% significance, no sufficiently strong evidence to reject null hypothesis, therefore accept null hypothesis, no significant difference between observed & expected. if calculated χ² value is greater than critical value, reject null hypothesis, some other factor, outside original expectation, likely to be causing significant difference between expectation & observation. minimum value that gives 5% probability is called critical value, critical value increases as degrees of freedom increases. - epistasis - interaction of genes at different loci, gene regulation is form of epistasis, regulatory genes control activity of structural genes (e.g. lac operon). gene interaction also occurs in biochemical pathways. originally thought that all genes expressed independently, therefore effects of phenotype seen, now known that many genes interact epistatically, it is the result of these interactions that are seen in phenotypes of organisms, characteristics of plants & animals that show continuous variation involve multiple genes & epistasis occurs frequently. e.g. a biochemical pathway involves enzymes a, b, c & d, required to produce pigment responsible for colour of a flower petal. 4 genes a, b, c & d need to be expressed to produce these enzymes, if one is not expressed then 1 step will be missing, and petal won't have expected colour. lack of enzyme normally produced when gene a, b or c is expressed means the intermediate molecule necessary for next reaction in sequence was not produced, results in lack of substrate for the next enzyme in the pathways so expression of this gene is not observed in phenotype. gene is effectively 'masked' by lack of expression of previous gene in pathway. if enzyme d not produced precursor D is not converted to a pigment, therefore it is often hard to observe expression of genes a, b and c in phenotype. disabled gene d is likely to mask their expression. gene affected by another gene is called hypostatic, gene that affects expression of another gene is epistatic. - dominant & recessive epistasis - epistatic gene may influence activity of other genes, as a result of the presence of dominant or recessive alleles, e.g. if presence of 2 recessive alleles at a gene locus led to the lack of an enzyme, it is known as recessive epistasis. dominant epistasis, if a dominant allele results in gene having effect on another gene, this happens if epistatic gene coded for an enzyme that modified one of the precursor molecules in the pathway. next enzyme in pathway then lacks suitable substrate molecule so pigment is again not produced. all genes in the sequence effectively 'masked'. - labrador colours - produced as result of pigment melanin being deposited in skin & fur, one gene codes for production of pigment and has alleles B (dominant, black pigment produced) and b (recessive, brown pigment produced). a second gene codes for where the pigment is deposited and, again, has two alleles E (dominant, pigment deposited in skin & fur) and e (recessive, skin only). the colour of a lab varies depending on alleles present at each locus, genes are not expressed independently so this is example of epistasis. gene at the E locus is epistatic to the hypostatic gene at the B locus. yellow coat of labs is example of recessive epistasis and ranges from deep gold to pale blond.

16 ch 3.10, protein synthesis, p76

- gene (section of DNA that contains complete sequence of codons for entire protein), is transcribed into RNA molecules, & then translated into specific amino acid sequence. DNA is contained within double membrane (nuclear envelope), protects DNA from damage in cytoplasm. - protein synthesis occurs in cytoplasm at ribosomes, but chromosomal DNA molecule too large to leave nucleus, to supply coding information needed to determine protein's amino acid sequence. therefore base sequences of a gene need to be copied & transported to site of protein synthesis (ribsoome), process is called transcription, produces shorter molecules of RNA. - transcription results in different polynucleotide, but has similarities with DNA replication. section of DNA that contains gene unwinds & unzips, by DNA helicase, beginning at start codon, involves breaking hydrogen bonds between bases. only one of 2 strands of DNA contains code for protein to be synthesised (sense strand), runs from 5' to 3'. other strand (3' to 5') is complementary copy of sense strand, doesn't code for protein (antisense strand), & acts as template strand during transcription, so that the complementary RNA strand formed carried the same base sequence as the sense strand. free RNA nucleotides pair with complementary bases exposed on antisense strand, when DNA unzips, thymine bade replaced by uracil base, so RNA uracil binds to adenine on DNA template strand. phosphodiester bonds are formed between RNA nucleotides by enzymes RNA polymerase. transcription stops at end of gene, short strand of RNA is called messenger (m)RNA, has same base sequence as bases making up gene on DNA, except uracil base instead of thymine. mRNA then detaches from DNA template, leaves nucleus through nuclear pore, DNA double helix reforms. mRNA molecule travels to ribosome in cell cytoplasm for translation in protein synthesis. - in eukaryotic cells, ribosomes made up of 2 subunits (1 large, 1 small), subunits composers of almost equal amounts of protein & form of RNA (ribosomal (r)RNA), rRNA is important in maintaining structural stability of protein synthesis sequence, & plays biochemical role in catalysing reaction. after leaving nucleus, mRNA bonds to specific site on the small subunit of the ribosome, ribosome holds mRNA in position while it is decided/translated, into sequence of amino acids. this process is called translation. transfer (t)RNA is another form of RNA, necessary for translation of mRNA, is composed of a strand of RNA folded so that 3 bases (anticodon) are at one end of the molecule. this anticodon binds to a complementary codon on mRNA, follows normal base pairing rule. tRNA molecules carry amino acid corresponding to that codon. when tRNA anticodon bind to complementary codons along mRNA, amino acids are brought together in correct sequence, to form primary structure of the protein coded for by mRNA. this doesn't happen all at once, amino acids are added one at a time, polypeptide chain (protein) grows as this happens. ribosomes act as binding site for mRNA, & tRNA catalyse assembly of the protein. - overall (translation): mRNA binds to small subunit of ribosome at its start codon (AUG). tRNA with complementary anticodon (UAC) binds to mRNA start codon, tRNA carries amino acid methionine. another tRNA with anticodon UGC, carrying corresponding amino acid (threonine), binds to next codon on mRNA (ACG), maximum of 2 tRNAs can be bound at same time. first amino acid, methionine, is transferred to amino acid (threonine) on second tRNA by formation of peptide bond, catalysed by enzymes peptides transferase, an rRNA component of the ribosome. ribosome moves along the mRNA, releases the first tRNA, the second tRNA becomes the first. stage 3 (another tRNA with corresponding amino acid, binds to mRNA codon) to 5 repeated, with another amino acid added each time, process keeps repeating until ribosome reaches end of mRNA at stop codon, & polypeptide is released. as amino acids are joined together, forming primary structure of protein, they fold into secondary & tertiary structures, folding & bonds formed are determined by amino acid sequence in indy structure. protein may undergo further modifications at Golgi apparatus, before fully functional, and ready to carry out specific role, for which it has been synthesised. many ribosomes can follow on mRNA behind the first, so multiple identical polypeptides can be synthesised simultaneously.

13 ch 3.7, types of proteins, p64

- globular proteins, compact water soluble, usually spherical, form when proteins fold into tertiary structure in a way that hydrophobic R-groups on amino acids are kept away from aqueous environment. hydrophilic R-groups are on outside of protein, so globular proteins soluble in water, solubility important for the many different functions of globular proteins, essential for regulating many processes, e.g. muscle contraction, chemical reactions & immunity. insulin is globular protein, hormone, involved in regulation of blood glucose concentration. hormones are transported in bloodstream, need to be soluble. hormones also have to fit into specific receptors on cell-surface membranes to have their effect, therefore need precise shapes. - conjugated proteins, globular proteins with non-protein component, prosthetic group. proteins without prosthetic group are simple proteins, there are different types of prosthetic groups. lipids/carbs can combine with proteins, forms lipoproteins/glycoproteins. metal ions & molecules derived from vitamins also form prosthetic groups. haem groups are examples of prosthetic groups, contain iron(ii)ions, catalase & haemoglobin both contain haem groups. - haemoglobin is the red, O2-carrying pigment found in RBC, quaternary protein made from 4 polypeptides, 2 alpha and 2 beta subunits. each subunit contains prosthetic haem group, iron(ii) ions present in haem groups able to combine reversibly with O2 molecule, enables haemoglobin to transport O2 around the body. haemoglobin can pick up O2 in lungs & transport it to cells that need it, where it is released. catalase is an enzyme, enzymes catalyse reactions, increases reaction rates, each enzyme is specific to particular reaction/type of reaction. catalase is a quaternary protein, contains 4 haem prosthetic groups, presence of iron(ii) ions in prosthetic groups allow catalase to interact with H2O2, speeds up breakdown. H2O2 is byproduct of metabolism, but damages cells & cell components if it accumulates, catalase makes sure H2O2 is broken down. - fibrous proteins, formed from long, insoluble molecules, due to presence of high proportion of amino acids with hydrophobic R-groups in primary structures. contains limited range of amino acids, usually with small R-groups. amino acid sequence in primary structure is usually repetitive, leads to organised structures reflected in roles of fibrous proteins. fibrous proteins make strong, long molecules, folded into complex 3D shapes, like globular proteins. - keratin, group of fibrous proteins present in hair, skin & nails, has large proportion of the sulfur-containing amino acid, cysteine. results in strong disulfide bonds, makes strong, inflexible & insoluble materials, degree of disulfide bond determines the flexibility, hair contains fewer bonds making it more flexible than nails, which contain more bonds. unpleasant smell produced when hair/skin is burnt is due to presence of large quantities of sulfur in the proteins. elastin, fibrous protein found in elastic fibres (& small protein fibres), elastic fibres are present in walls of blood vessels & alveoli in lungs, gives structures flexibility to expand when needed, but also return to normal size. elastin is a quaternary protein, made from many stretchy molecules (called tropoelastin). collagen, fibrous protein, connective tissue found in skin, tendons, ligaments & nervous system. there are a number of different forms, but all are made up of 3 polypeptides wound together, forms long & strong rope-like structure, like rope, collagen is flexible.

20 ch 4.3, enzyme inhibitors, p94

- important to keep cellular conditions (e.g. pH & temp) within narrow limits so enzyme activity is not delayed, ensures reactions can happen at rate fast enough to sustain living processes, e.g. respiration. also important reactions don't happen too fast, as leads to build-up of excess products, living processes rarely involve just one reaction but are complex, multi-step reaction pathways. these pathways need to be closely regulated to meet needs of living organisms without wasting resources. - the different steps in reaction pathways are controlled by different enzymes, controlling activity of enzymes at crucial points in these pathways regulates rate & quantity of product formation. enzymes can be activated by cofactors or inactivated by inhibitors. inhibitors are molecules that prevent enzymes from carrying out normal function of catalysis, or slow them down, there are 2 types of enzyme inhibition (competitive & non-competitive). - competitive inhibition: molecule-part of molecule with similar shape to substrate of enzyme can fit into active site of the enzyme, blocks substrate from entering active site, prevents enzyme catalysing reaction. enzyme can't carry out function and is inhibited. non-substrate molecule that binds to active site is a type of inhibitor, substrate & inhibitor molecules present in solution compete for each other to bind to active sites in a given time, slows rate of reaction. therefore these are competitive inhibitors, degree of inhibition depends on relative concs of substrate, inhibitor or enzyme. most competitive inhibitors only bind temporarily to active site of enzyme, so effect is reversible. however there are some exceptions, e.g. aspirin. competitive inhibitor reduced rate of reaction for given conc of substrate, but doesn't change Vmax of enzyme it inhibits. if substrate conc is increased enough, there is so much more substrate than inhibitor that original Vmax can still be reached. example of competitive inhibitor used in synthesis of cholesterol, statin. statins are prescribed to help people reduce blood cholesterol conc, hjgj blood conc levels can result in heart disease. aspirin irreversible inhibits active site of COX enzymes, prevents synthesis of prostaglandins & thromboxane, chemicals responsible for producing pain & fever. - non-competitive inhibition: inhibitor binds to enzyme at location other than active site (called allosteric site). binding of inhibitor causes tertiary structure of enzyme to change, therefore active site shape changes, active site no longer has complementary shape to substrate, so unable to bind to enzyme. enzyme can't carry out its function and is inhibited. as inhibitor doesn't compete with substrate, it is non-competitive inhibition. increasing conc of enzyme or substrate will not overcome effect of non-competitive inhibitor. however increasing conc of inhibitor will decrease rate of reaction, as more active sites become unavailable. binding of inhibitor may be reversible or non-reversible, irreversible inhibitors cannot be remove from part of enzyme they are attached to, often very toxic but not always. organophosphate used as insecticides & herbicides irreversible inhibit enzyme acetyl cholinesterase, enzyme necessary for nerve impulse transmission, this can lead to muscle cramps/paralysis & death if accidentally ingested. proton pump inhibitors (PPIs) are used to treat long-term indigestion, irreversibly block an enzyme system responsible for secreting H+ ions into the stomach. this makes PPIs effective in reducing production of excess acid, which can lead to formation of stomach ulcers if left untreated. - end product inhibition, term used for enzyme inhibition that occurs when product of reaction acts as inhibitor to enzyme that produces it, serves as negative-feedback control mechanism for reaction. excess products are not made & resources not wasted, is example of non-competitive reversible inhibition. respiration is a metabolic pathway, results in production of ATP. glucose is broken down in number of steps, first step involves addition of 2 phosphate groups to glucose molecule, addition of second phosphate group (results in initial breakdown of glucose molecule) is catalysed by enzyme phosphofructokinase (PFK), this enzyme is competitively inhibited by ATP, therefore ATP regulates its own production. when levels of ATP are high, more ATP binds to allosteric site on PFK, prevents addition of second phosphate group to glucose, glucose is not broken down & ATP is not produced at same rate. as ATP is used up, less binds to PFK & enzymes can catalyse addition of second phosphate group to glucose, respiration resumes, leads to production of more ATP.

3 ch 2.3, more microscopy, p19

- in light microscopy, increased magnification can be achieved easily using appropriate lenses, but if image becomes blurred no more detail will be seen. resolution is limiting factor - in electron microscopy, beam of electrons with wavelength of less than 1nm is used to illuminate specimen. more detail of cell ultra structure is seen as electrons have smaller wavelength than light waves. they produce image with magnifications of up to x500,000 and still have clear resolution - electron microscopes very expensive and only used in controlled environment in a dedicated spaced. specimens damaged by electron beam and preparation process is complex so artefacts can be produced - artefact is visible structural detailed caused by processing the specimen and is not a feature of the specimen. can happen in light or electron microscopy, e.g. when preparing for light microscopy, air bubbles when placing cover slip on slide. in electron microscopy, change in cell ultra structure occurs due to processing, e.g. loss of continuity in membranes, distortion of organelles and empty spaces in cytoplasm of cells. - two types of electron microscope: transmission electron (TEM), beam of electrons transmitted through specimen and focused to produce an image (similar to light microscopy). best resolution, 0.5nm. scanning electron microscope (SEM), beam of electrons sent across surface of specimen and reflected electrons collected to produce 3D image of surface, valuable information for knowing appearance of different organisms, 3-10nm. - optical microscopes use visible light to illuminate specimens and lens to produce magnified image. fluorescent microscopes use higher light intensity, longer wavelengths, less energy, to illuminate and magnify specimen that is treated with fluorescent chemical. fluorescence is absorption and re-radiation of light. - laser scanning confocal microscope move a a single spot of focused light across specimen. causes fluorescence from components labelled with a dye. emitted light from specimen filtered through pinhole aperture, only light radiated from very close to focal plane is detected, as light emitted from other parts of specimen would reduce resolution and cause blurring. unwanted radiation doesn't pass through pinhole and not detected. laser used instead of light to get higher intensities, improves illumination. - very thin sections of specimen are examined and light elsewhere is removed, high resolution achieved. spot illuminating specimen moved across specimen and 2D image produced. 3D image produced when creating images at different focal planes. - laser scanning non-invasive, used for diagnosis of eye disease, endoscopic procedures, can see distribution of molecules within cells so used for development of drugs, virtual biopsies for skin cancer - beamsplitter is dichroic mirror, only reflects one wavelength (from laser) but allows other wavelengths (from sample) to pass through. positions of two pinholes lets light waves from laser (illuminating sample) follow same path as light waves radiated when sample fluoresces, means they have same focal plane hence confocal

7 ch 3.1 biological elements, ions & polymers, p42

- ions in solutions are electrolytes. - positive cations: calcium (Ca2+), nerve impulse transmission, muscle contraction. sodium (Na+), nerve impulse transmission, kidney function. potassium (K+), nerve impulse transmission, stomata opening. hydrogen (H+), catalysis of reactions, pH determination. ammonium (NH4+), production of nitrate ions by bacteria. - negative anions: nitrate (NO3-), nitrogen supply to plants for amino acid & protein formation. hydrogen carbonate (HCO3-), maintenance of blood pH. chloride (Cl-), balance positive charge of sodium & potassium ions in cells. phosphate (PO4 3-), cell membrane formation, nucleus acid & ATP formation, bone formation. hydroxide (OH-), catalysis of reactions, pH determination - carbohydrates, CHO. lipids, CHO. proteins, CHONS. nucleic acids, CHONP. - biological molecules often polymers. polymers are long-chain molecules made up of multiple individual molecules (monomers) i'm repeating pattern. in carbs, monomers are sugars (saccharides), in proteins, monomers are amino acids.

18 ch 4.1, Enzyme action, p84

- life processes involve chemical reactions, need to happen fast. in lab/industry, reactions demand very high temps & pressures, however extreme conditions not possible in living cells as they would damage cell components, therefore reactions catalysed by enzymes. enzymes are biological catalysts, they are globular proteins, they interact with substrate molecules, causes them to react at faster rates without need for harsh environmental conditions, without enzymes many processes necessary to life would not be possible. - role of enzymes, living organisms need to be built and maintained, involves synthesis of large polymer-based components, e.g. cellulose forms walls of plant cells & long protein molecules form contractile filaments of muscle in animals. different cell components are synthesised & assembles into cells, these form tissues, organs & eventually while organism. chemical reactions required for growth are anabolic (building up) reactions, catalysed by enzymes. energy is constantly required for majority of living processes, includes growth. energy is released from large organic molecules (e.g. glucose), in metabolic pathways that consist of many catabolic (breaking down) reactions. catabolic reactions are also catalysed by enzymes. these large organic molecules are obtained from digestion of food, made up of larger molecules (e.g. starch). digestion is also catalysed by enzymes. reactions rarely happen in isolation, but as part of multi-step pathways. metabolism is the sum of all different reactions & reaction pathways happening in a cell/organism, only happens as result of control & order imposed by enzymes. like reactions in lab, speed at which different cellular reactions proceed varies considerably, is usually dependent of environmental conditions. temp, pressure & pH may have effect on rate of chemical reaction. enzymes can only increase rate of reactions up to a certain point (Vmax, maximum initial velocity/rate of enzyme-catalysed reaction). - mechanism of enzyme action, molecules in solution move & collide randomly, for reaction to happen, molecules need to collide in right orientation. when high temps & pressures are applied, speed of molecules increases, therefore number of successful collisions & overall rate of reaction increases. many different enzymes are produced by living organisms, as each enzyme catalyses 1 biochemical reaction, of which there are 1000s in a cell, this is known as specificity of enzymes. energy needs to be supplied for most reactions to start, called activation energy. sometimes amount of energy needed is so large, that it prevents reaction from happening under normal conditions. enzymes help molecules collide successfully, therefore reduce activation energy required. there are 2 hypothesis for how enzymes do this: lock and key, area within tertiary structure of enzyme (active site) has shape that is complementary to shape of specific substrate molecule, like only right key fits into lock, only specific substrate will "fit" active site of enzyme, this is lock & key hypothesis. when substrate is bound to active site, enzyme-substrate complex is formed. substrate(s) react & product(s) are formed in enzyme-product complex. product(s) are released, leaves enzyme unchanged & able to take part in subsequent reactions. substrate is held by enzyme so that right atom-groups are close enough to react, R-groups within active site of enzyme also interact with substrate, forms temporary bonds. these put strain on bonds within substrate, which helps reaction. induced-fit, more recently, evidence suggest active site of enzyme changes shape slightly as substrate enters, called induced-fit hypothesis, is modified version of lock and key hypothesis. initial interaction between enzyme & substrate is relatively weak, but the weak interactions rapidly induce changes in enzyme's tertiary structure, strengthens binding, & puts strain on substrate molecule. this weakens bond(s) in substrate, therefore lowers activation energy for reaction. - enzymes have essential role in both structure & function of cells & whole organisms, synthesis of polymers from monomers, e.g. making polysaccharides from glucose, requires enzymes. enzymes that act within cells are intracellular enzymes. H2O2 is toxic product of many metabolic pathways, enzyme catalase ensures H2O2 is broken down to O2 & H2O quickly, prevents accumulation. found in both animal & plant tissues. all reactions happening within cells need substrates (raw materials) to make products needed by organism, these raw materials need to be constantly supplied by cells to keep up with the demand. nutrients (components necessary for survival & growth) present in the diet/environment of the organism, supply these materials. nutrients are often in form of polymers, e.g. proteins & polysaccharides, these large molecules cannot enter cells directly through cell-surface membrane, need to be broken down into smaller components first. enzymes are released from cells to break down large nutrient molecules into smaller molecules, in process of digestion. these enzymes are extra cellular enzymes, they work outside of cell that made them. in some organisms (e.g. fungi), they work outside body. both single-celled & multicellular organisms rely on extracellular enzymes to make use of polymers for nutrition. single-celled organisms (e.g. bacteria & yeast) release enzymes into immediate environment, enzymes break down larger molecules (e.g. proteins) & the smaller molecules produced (e.g. amino acids & glucose) are then absorbed by the cells. many multicellular organisms eat food to gain nutrients, although nutrients are taken into digestive system, large molecules still have to be digested so small molecules can be absorbed into bloodstream. from there, they are transported around body to be used as substrates in cellular reactions. example of extracellular enzymes involved in digestion in humans are amylase & trypsin. - digestion of starch, begins in mouth & continues in small intestine, starch is digested in 2 steps, involves 2 different enzymes. different enzymes needed, as each enzyme only catalysed one specific reaction: 1) starch polymers partially broken down into maltose (disaccharide), enzyme involved in this stage is amylase. amylase is produced by salivary glands & pancreas, released in saliva into the mouth, & in pancreatic juice into small intestine. 2) maltose then broken down into glucose (a monosaccharide), enzyme involved is maltose, maltose is present in small intestine. glucose is small enough to be absorbed by cells lining digestive system & subsequently absorbed into bloodstream. digestion of proteins, trypsin is a protease, type of enzyme that catalyses digestion of proteins into smaller peptides, which is then broken down further into amino acids by other processes. trypsin is produced in pancreas & released with pancreatic juice into small intestine, where it acts on proteins. amino acids produced by the action of protease are absorbed by cells lining digestive system, then absorbed into bloodstream.

11 ch 3.5 lipids, p54

- lipids (fats & oils), fats solid at room temp, oils liquid at room temp. lipid molecules contain C, H & O, are non-polar, as electrons in outer orbital than form the bonds, are more evenly distributed than in polar molecules, therefore no positive & negative areas within molecules, therefore insoluble in water, (oil & water don't mix). lipids are large, complex molecules, macromolecules, not built from repeating units (like monomers & polysaccharides). - triglycerides, made from one glycerol molecule & 3 fatty acids. glycerol is alcohol, fatty acid is carboxylic acid (has -COOH), both contain OH groups. OH groups interact, forms 3 water molecules & ester bonds between the 3 fatty acids and glycerol molecule (esterification). type of condensation reaction. to break down triglycerides, 3 water molecules needed to reverse reaction that formed the triglyceride, example of hydrolysis reaction. saturated fatty acid chains, no double bonds present between carbon atoms, all carbon atoms have maximum number of bonds between hydrogen atoms. unsaturated fatty acid chains, double bonds between some carbon atoms. monounsaturated, only one double between carbon atoms. polyunsaturated, 2 or more double bonds. presence of double bonds cause kink or bend in molecule, therefore cannot pack closely together, therefore liquid at room temp rather than solid, therefore unsaturated triglycerides described as oils rather than fats. plants contain unsaturated triglycerides, normally occur as oils, healthier in human diet than saturated triglycerides or fats. some evidence that in excess, saturated fats lead to coronary heart disease, but evidence is inconclusive. any type of fat in excess can lead to obesity, puts strain on heart. - phospholipids, modified triglycerides that contain C, H, O & P. inorganic phosphate ions (PO4 3-) found in every cell, phosphate ions have extra electrons so are negatively charged, therefore are soluble in water. one fatty acid chain in a triglyceride molecule is replaced with phosphate group to make phospholipid. phospholipids unusual, due to their length, have non-polar end/tail (fatty acid chains) and charged end/head (phosphate group). non-polar tails repelled by water, but mix readily with fat, hydrophobic. charge heads (NOT polar), interact with and is attracted to water, hydrophilic. therefore forms layer on surface of water with phosphate heads in water, fatty acid tails sticking out of water, therefore are called surface active agents, (surfactants). also form two-layered sheet formations, bilayer, all hydrophobic tails point inwards towards centre of sheet, protected from water by hydrophilic heads. due to bilayer, phospholipids have key role in forming cell-surface membranes, they can separate aqueous environment in cells, environment usually exists as cytosol within cells. thought that this is how cells were first formed and later on membrane-bound organelles. - sterols, aka steroid alcohols, type of lipid in cells, not fats or oils and little in common with them structurally. complex alcohol molecules, has a 4 carbon ring structure with hydroxyl group at one end. like phospholipids, have dual hydrophobic/hydrophilic characteristics, OH group is polar and hydrophilic, rest of molecule is hydrophobic. cholesterol is a sterol, body manufactures cholesterol primarily in liver and intestines, important in formation of cell membranes, positioned between phospholipids, with hydroxyl group at periphery of the membrane. adds stability to cell membranes, regulates fluidity by keeping membranes fluid at low temperatures, stop them becoming too fluid at high temperature. Vitamin D; steroid hormones & bile all manufactured using cholesterol. - lipids, due to non-polar nature, have biological roles: membrane formation & creation of hydrophobic barriers, hormone production, electrical insulation for impulse transmission, waterproofing (e.g. birds' feathers & plant leaves). lipids, particularly triglycerides, have important role in long-term energy storage. stored under skin and around vital organs, also provide: thermal insulation to reduce heat loss (e.g. in penguins), cushioning to protect vital organs (e.g. heart & kidneys), buoyancy for aquatic animals (e.g. whales). lipids can be identified by emulsion test, sample is mixed with ethanol, resulting solution is mixed with water and shaken. white emulsion forms as a layer on top of solution, indicates presence of a lipid. if solution remains clear, test is negative.

98 ch 17.1, energy cycles, p460

- living organisms have to be active to survival organisms grow, respond to changes in environment & deal with threats from other organisms, they have to find or make food & reproduce. all this activity depends on metabolic reactions & processes continually taking place in individual cells. examples of metabolic activities amongst many include: active transport, essential for uptake of nitrates by root hair cells, loading sucrose into sieve tube cells, selective reabsorption of glucose & amino acids

2 ch 2.2, magnification, p15

- magnification is how many times larger the image is than the actual size of object, but doesn't increase amount of detail that can be seen, so resolution needs to be increased, resolution determines amount of detail that can be seen, the higher the resolution the more details are visible. resolution is ability to see individual objects as separate entities. resolution is limited by diffraction of light. - structures in specimens are very close to each other and light reflected from individual structures overlap due to diffraction. so structures are no longer seen as separate and detail is lost. - in optical microscopy structures closer than half the wavelength of light cannot be seen resolution can be increased by using beams of electrons with wavelengths thousands of times shorter than light. electron beams still diffracted but shorter wavelength means structures can be much closer before they overlap. so structures much smaller and closer together can be seen separately without diffraction blurring image - magnification = size of image/actual size of object - to measure size of sample under microscope, use eyepiece graticule, true magnification of different lenses of microscope varies slightly from magnification stated, therefore every microscope must be calibrated individually using eyepiece graticule & slide micrometer. eyepiece graticule is glass disc marked with fine scale of 1 to 100, scale has no units, remains unchanged whichever objective lens is in place, relative size of division, however, increases with each increase in magnification, so need to know what divisions the represent at different magnifications to measure specimens. scale on graticule at each magnification is calibrated using stage micrometer. stage micrometer is microscope slide with very accurate scale in micrometers (um) engraved on it, scale marked on micrometer is usually 100 divisions = 1mm, so 1 division = 10um. eyepiece graticule scale is calibrated for each objective lens separately, once all 3 lenses calibrated, if same cell is measured using 3 different lenses, same actual measurement should be obtained each time. method: put stage micrometer in place & eyepiece graticule in eyepiece. get scale on micrometer slide in clear focus. align micrometer scale with scale in eyepiece, take a reading from 2 scales. if 20 divisions on eyepiece graticule = 10 divisions on stage micrometer = 100um, 1 division on eyepiece graticule = 5um & magnification factor = 5x.

117 ch 20.1, patterns of inheritance & variation, p520

- members of different species usually clearly different from each other, members of same species rarely identical, therefore variation important feature of organisms. variation arises due to mutations (random & constant changes in genetic code). variation essential for natural selection process, therefore evolution. variation occurs as result of environmental & genetic variation, majority of cases determine organism's characteristics (e.g. chlorosis in plants & body mass of animals) - chlorosis - most plants programmed to produce large quantities of chlorophyll (green pigment vital for photosynthesis & gives leaves green colour), however some plants suffer from chlorosis, causes leaves to look pale/yellow, occurs when cells not producing normal amount of chlorophyll, lack of chlorophyll reduces ability of plant to make food by photosynthesis. most plants with chlorosis have normal genes for chlorophyll production, change in phenotype due to environmental factors, different environmental factors have different effect on physiology but same change in phenotype: lack of light, e.g. when gardening tool left on lawn, in absence of light plants reduce chlorophyll production to conserve resources so chlorosis only occurs where plants get no light. mineral deficiencies (lack of iron/magnesium), iron needed by cofactor by some enzymes that and chlorophyll, magnesium found in chlorophyll molecule, if either elements are lacking in soil, plants can't make chlorophyll & gradually all leaves become yellow. virus infections, when viruses infect plants they interfere with metabolism of cells, common symptom is yellowing in infected tissues as they can no longer support synthesis of chlorophyll. in summary, genetic factors in plant are likely to code for green leaves but environmental factors play key role in final leaf appearance. - animal body mass - body mass of animals within species varies, organism's body mass determined by genetic & environmental factors, in most cases dramatic variations e.g. obesity & being severely underweight are result of environmental factors, e.g. amount of food & exercise, or presence of disease affects body mass. being extremely overweight/underweight causes health problems for an animal. occasionally obesity caused by genetic factors, e.g. mutation on chromosome 7, causes change in fat deposition pattern in body. gene acts in conjunction with other genes that regulate energy balance, results in animal with mutation to grow 35-50% fatter by middle age than a normal animal would. - creating genetic variation - genetic variation is created by versions of genes inherited from parents, most genes have number of different possible alleles proteins variants. individual mixture of alleles inherited by organism influences characteristics they display, combination determined by sexual reproduction, involves meiosis (formation of gametes) & random fusion of gametes at fertilisation. results in vast genetic variation seen between individuals of same species. for most genes in body, 2 alleles add inherited (1 from each parent), alleles may be same or different versions of gene. genotype (combination of alleles an organism inherits for a characteristic) is genetic make-up of organism in respect of that gene. observable characteristics of organism are phenotype, actual characteristics that an organism displays are also influences by environment. changes environment makes to person's phenotype not inherited, they are modifications, only mutations (change in DNA) in gametes can be passed on to offspring. not always possible to determine organism's genotype from its phenotype due to dominance of particular alleles, dominant allele is version of allele always expressed if present, therefore individual showing dominant characteristic in phenotype could have 1 or 2 copies of dominant gene (can't tell from appearance), however recessive allele is only expressed if 2 copies of allele present in organisms, therefore with individual with recessive phenotype, genotype can be determine (must have 2 alleles coding for recessive phenotype). key terms to describe organism's genotype for particular characteristic: homozygous, have 2 identical alleles for characteristic, organism could be homozygous dominant (2 alleles for dominant phenotype) or homozygous recessive (2 alleles for recessive phenotype). heterozygous, have 2 different alleles for characteristic, in this case only allele for dominant phenotype expressed. - continuous & discontinuous variation - variation of characteristic displayed within species divided into 2 groups (continuous & discontinuous), in discontinuous individual falls into distinct groups (e.g. blood groups) & normally only one gene is involved & environment has little to no effect. in continuous, there are 2 extremes, every degree of variation possible in between (e.g. height or weight), many genes are involved & environment has large effect. continuous: characteristic that can take any value within range, genetic & environmental cause, polygenes (controlled by many genes), e.g. lead surface area, animal mass, skin colour. discontinuous: characteristic only appears in specific (discrete) values, mostly genetic cause, one or 2 genes, e.g. blood group, albinism, round/wrinkled pea shape.

22 ch 5.1, plasma membranes, structure & function of membranes, p103

- membranes are structures that separate contents of cells from environment, they also separate the different areas within cells (organelles) from each other & the cytosol. some organelles are divided further by internal membranes. the formation of separate membrane-bound areas jn a cell is called compartmentalisation, compartmentalisation is vital to a cell as metabolism includes many different & often incompatible reactions. containing reactions in separate parts of the cell allows the specific conditions required for cellular reactions (e.g. chemical gradients) to be maintained, & protects vital cell components. - all membranes in a cell have the same basic structure, cell surface membrane which separates cell from its external environment is known as plasma membrane. membranes are formed from a phospholipid bilayer, hydrophilic phosphate heads of phospholipids from both the inner & outer surface of a membrane, sandwiches the fatty acid tails of the phospholipids to form a hydrophobic core inside the membrane. cells normally exist in aqueous environments, inside of cells & organelles are also usually aqueous environments. phospholipid bilayers are perfectly suited as membranes, as the outer surfaces of the hydrophilic phosphate heads can interact with water. - membranes were seen for the first time following invention of electron microscopy, which allowed images to be taken at higher magnification & resolution, images taken in 1950s showed membranes as 2 black parallel lines, supported earlier theory that membranes were composed of a lipid bilayer. in 1972, american scientists Singer & Nicolson proposed a model, building upon earlier lipid-bilayer model, in which proteins occupy various positions in the membrane. model is known as the fluid-mosaic model because the phospholipids are free to move within the layer, relative to each other (they are fluid), giving the membrane flexibility, & because proteins embedded in the bilayer vary in shape, size & position (in the same way as tiles of a mosaic). this model forms the basis of our understanding of membranes today. - plasma membranes contain various proteins & lipids, type & number of which are particular to each cell type. the components of plasma membranes play an important role in the functions of the membrane, & the cell/organelle they are part of: membrane proteins, have important roles in various functions of membranes, there are 2 types of proteins in cell-surface membrane (intrinsic & extrinsic proteins). intrinsic proteins, or integral proteins, are transmembrane proteins embedded through both layers of a membrane, they have amino acids with hydrophobic R-groups on their external surfaces, these interact with hydrophobic core of the membranes, keeping them in place. channel & carrier proteins are intrinsic proteins, they are both involved in transport across the membrane. channel proteins provide a hydrophilic channel, allows the passive movement of polar molecules & ions down a concentration gradient through membranes. they are held in position by interactions between the hydrophobic core of the membrane and the hydrophobic R-groups on the outside of proteins. carrier proteins, have important role in both passive transport (down conc gradient) & active transport (against conc gradient) into cells. this often involves the shape of the protein changing. glycoproteins are intrinsic proteins, embedded in cell-surface membrane with attached carbohydrate (sugar) chains of varying lengths and shapes. glycoproteins play a role in cell adhesion (when cells join together to form tight junctions in certain tissues) & as receptors for chemical signals. when the chemical binds to the receptor, it elicits a response from the cell, this may cause a direct response or set off a cascade of events inside the cell. this process is known as cell communication/cell signalling, examples include: receptors for neurotransmitters, e.g. acetylcholine at nerve cell synapses, binding of the neurotransmitters triggers or prevents an impulse in next neurone. receptors for peptide hormones, e.g. insulin & glucagon, affects uptake & storage of glucose by cells. some drugs act by binding to cell receptors, e.g. beta-blockers, used to reduce the response of the heart to stress. extrinsic proteins or peripheral proteins are present in one side of the bilayer, they normally have hydrophilic R-groups on their outer surfaces & interact with the polar heads of the phospholipids, or with intrinsic proteins. they can be present in either layer & some move between layers. cholesterol is a lipid with a hydrophilic end & hydrophobic end, like a phospholipid, it regulates the fluidity of membranes. cholesterol molecules are positioned between phospholipids in a membrane bilayer, with hydrophilic end interacting with heads & hydrophobic end interacting with tails, pulling them together. in this way cholesterol adds stability to membranes without making them too rigid. cholesterol molecules prevent membranes becoming too solid by stopping phospholipid molecules from grouping too closely & crystallising. - like enzymes, proteins in membranes forming organelles, or present within organelles, have to be in particular positions for chemical reactions to take place, e.g. the electron carries & the enzyme ATP synthase have to be in correct position within cristae (inner membrane of mitochondrion) for the production of ATP in respiration). the enzymes of photosynthesis are found on the membrane stacks within the chloroplasts.

23 ch 5.2, factors affecting membrane structure, p107

- membranes control passage of different substances into & out of cells (and organelles), if membranes lose their structure, they lose control of this & cell processes will be disrupted. a number of factors affect membrane structure, e.g. temp & presence of solvents. - phospholipids in cell membrane are constantly moving, when temp is increased, phospholipids have more kinetic energy & will move more, this makes membrane more fluid & it begins to lose its structure. if temp continues to increase, cell will eventually break down completely. loss of structure increases permeability of the membrane, making it easier for particles to cross it. carrier & channel proteins in membrane are denatured at higher temps, these proteins are involved in transport across membrane, therefore as they denature, membrane permeability is affected. - water, a polar solvent, is essential in formation of the phospholipid bilayer, non-polar tails of phospholipids are orientated away from water, forms bilayer with hydrophobic core. the charged phosphate heads interact with water, helps keep the bilayer intact. many organic solvents are less polar than water, e.g. alcohols, or non-polar, e.g. benzene. organic solvents dissolve membranes, disrupting cells. this is why alcohols are used in antiseptic wipes, alcohols dissolve membranes of bacteria in a wound, killing them & reducing risk of infection. pure/very strong alcohol solutions are toxic as they destroy cells in the body, less concentrated solutions of alcohols, e.g. alcoholic drinks, won't dissolve membranes but still cause damage. the non-polar alcohol molecules enter cell membrane & presence of these molecules between the phospholipids disrupts the membrane. - when membrane is disrupted, it becomes more fluid & more permeable. some cells need intact cell membranes for specific functions, e.g. transmission of nerve impulses by neurones (nerve cells). when neuronal membranes are disrupted, nerve impulses are no longer transmitted as normal. this also happens to neurones in the brain, explains changes seen in peoples' behaviour after consuming alcoholic drinks. - beetroot cells contain betalain, red pigment, because of this they are useful for investigating effects of temp & organic solvents on membrane permeability. when beetroot cells membranes are disrupted, red pigment is released & surrounding solution is coloured. amount of pigment released into solution is related to disruption of cell membranes. to investigate effect of temp on permeability of cell membranes: five small pieces of beetroot of equal size are cut using cork borer. beetroot pieces are thoroughly washed in running water, the. placed in 100ml of distilled water in a water bath. temp of water bath is increased in 10°C intervals. samples of the water containing beetroot are taken 5mins after each temp is reached, absorbance of each sample is measured using colorimeter, with a blue filter. light first passes through a filter and then the sample, intensity of light hitting the detector is recorded. experiment repeated 3 times. each time with fresh beetroot pieces & a mean is calculated for each temperature.

28 ch 6.2, mitosis, p124

- mitosis is term used to describe entire process of cell division in eukaryotic cells, actually refers to nuclear division, essential state in cell division. mitosis ensures both daughter cells produced when parental cell divides are genetically identical (except in rare events when mutations occur), each new cell will have exact copy of DNA present in parent cell & same number of chromosomes. mitosis is necessary when all daughter cells must be identical, this is the case during growth, replacement & repair of tissues in multicellular organisms, e.g. animals, plants & fungi. mitosis, also necessary for asexual reproduction, which is production of genetically identical offspring from 1 parent in multicellular organisms, includes plants, fungi & some animals, and also eukaryotic single-celled organisms, e.g. amoeba species. prokaryotic organisms, e.g. bacteria, don't have nucleus & reproduce asexually by different process (binary fission). before mitosis occurs, all DNA in nucleus is replicated during interphase. each DNA molecule (chromosome) is converted into 2 identical DNA molecules (called chromatids). 2 chromatids are joined together at region called centromere, it's necessary to keep chromatids together during mitosis so they can be precisely manoeuvred & segregated equally, one each into 2 new daughter cells. four stages of mitosis, prophase, metaphase, anaphase, telophase, described separately but in fact they flow seamlessly. each phase can be viewed & identified using light microscope, dividing cells can be easily obtained from growing root tips of plants. root tips are treated with chemical to allow cells to be separated, then they are squashed to form single layer of cells on microscope slide. stains that bind DNA are used to make chromosomes clearly visible. - prophase: chromatin fibres (complex made of various proteins, RNA & DNA) begin to coil & condense to form chromosomes, to take up stain & become visible under light microscope. nucleolus, distinct area of nucleus responsible for RNA synthesis, disappears. nuclear membrane begins to break down. protein microtubules form spindle-shaped structures, links poles of the cell. fibres forming spindle are necessary to move chromosomes into correct positions before division. in animal & some plant cells, 2 centrioles migrate to opposite poles of cell, entrapped are cylindrical bundles of protein that help in formation of spindle. spindle fibres attach to specific areas on the centromeres & start to move the chromosomes to the centre of the cell. by end of prophase, nuclear envelope disappeared. - metaphase: chromosomes are moved by spindle fibres to form plane in centre of cell, called metaphase plate, then held in position. - anaphase: centromeres holding together pairs of chromatids in each chromosome divide. chromatids are separated, pulled to opposite poles of cell by shortening spindle fibres. characteristic 'V' shape of chromatids moving towards poles, is a result of them being dragged by centromeres through liquid cytosol. - telophase: chromatids have reached poles & are now called chromosomes, the 2 new sets of chromosomes assemble at each pole & nuclear envelope reforms around them. chromosomes start to uncoil & nucleolus is formed. cell division (cytokinesis) begins. cytokinesis, actual division of cell into 2 separate cells, begins during telophase. in animal cells, cleavage furrow forms around middle of cell, cell-surface membrane is pulled inwards by cytoskeleton until close enough to fuse around middle, forms 2 new cells. plant cells, have cell walls so not possible for cleavage furrow to be formed. vesicles from golgi apparatus begin to assemble in same places, as where metaphase plate was formed. vesicles fuse with each other & cell-surface membrane, this divides the cell into 2. new sections of cell wall then form along new sections of membrane (if dividing cell wall form before daughter cells are separated, they immediately undergo osmotic lysis from surrounding water).

14 ch 3.8, nucleic acids, p68

- nucleic acids contain the elements C, H, O, N & P, nucleic acids are large polymers formed from many nucleotides (monomers) linked together in a chain. individual nucleotide is made up of: pentose monosaccharide (sugar), contains 5 carbon atoms. phosphate group (-PO4 ^2-), inorganic molecule that is acidic and negatively charged. nitrogenous base, complex organic molecule, contains 1 or 2 carbon rings & nitrogen. nucleotides are linked together by condensation reactions to form a polynucleotide (polymer). the phosphate group at the 5th carbon of the pentose sugar (5'), of one nucleotide, forms covalent bonds with the hydroxyl (OH) group at the 3rd carbon (3'), of an adjacent nucleotide. bonds are called phosphodiester bonds. this forms long, strong sugar-phosphate backbone, with a base attached to each sugar. the phosphodiester bonds are broken by hydrolysis (reverse of condensation), releases individual nucleotides. - DNA is deoxyribonucleic acid, is deoxyribose (sugar with one less oxygen than ribose). nucleotides in DNA have 1 of 4 different bases, therefore there are 4 different DNA nucleotides. the 4 bases are divided into purines & pymidines. purines, larger bases, contain double carbon ring structures, adenine (A) & guanine (G). pyrimidines, smaller bases, contain single carbon ring structures, thymine (T) & cytosine (C). DNA molecule varies in length from a few nucleotides to millions. DNA molecule is made of 2 strands of polynucleotides, coiled into helix, known as DNA double helix. the 2 strands of double helix are held together by hydrogen bonds between the bases, each strand has phosphate group (5') at one end, and hydroxyl group (3') at other end. the 2 parallel strands are arranged so they run in opposite directions, therefore are antiparallel. the pairing between the bases allows DNA to be copied and transcribed, key properties of the molecule of heredity. - bases bind in very specific way, adenine (A) & thymine (T) able to form 2 hydrogen bonds, always join with each other. cytosine & guanine form 3 hydrogen bonds, so also only bind to each other (complementary base pairing), therefore a small pyrimidine base always binds to larger print base. this arrangement maintains constant distance between the DNA backbones, results in parallel polynucleotide chains. complementary base pairing means DNA always has equal amounts of adenine & thymine, and equal amounts of cytosine & guanine, this was determined by Watson & Crick long before detailed structure of DNA was determined. the sequence of bases along a DNA strand carries the genetic information of an organism, in form of a code. - RNA is ribonucleic acid, has important role in transfer of genetic information, DNA stores all of the genetic information needed by an organism, this is passed on from generation to generation. however the DNA of each eukaryotic chromosome is a very long molecule, comprises many hundreds of genes, therefore unable to leave nucleus to supply the info directly to sites of protein synthesis. therefore, the relatively short section of a DNA molecule corresponding to a single gene is transcribed, into a similarly short messenger RNA (mRNA) molecule. each individual mRNA is shorter than the whole chromosome of DNA. RNA is a polymer composed of many nucleotide monomers. RNA nucleotides are different to DNA nucleotides, pentose sugar is ribose rather than deoxyribose, and thymine base is replaced with uracil base, like thymine, uracil is a pyrimadine, forms 2 hydrogen bonds with adenine, therefore base pairing rules still apply when RNA nucleotides bing to DNA, when making copies of particular sections of DNA. the RNA nucleotides form polymers in the same way as DNA nucleotides, (by formation of phosphodiester bonds in condensation reactions). RNA polymers formed are small enough to leave the nucleus & travel to ribosomes, as they are central to process of protein synthesis. after protein synthesis, RNA molecules are degraded in cytoplasm, phosphodiester bonds are hydrolysed, RNA nucleotides are released & reused. - DNA extraction procedure: grind sample in pestle & mortar, this breaks down cell walls. mix sample with detergent, this breaks down cell membrane, releases cell contents into solution. add salt, this breaks hydrogen bonds between the DNA & H2O molecules. add protease enzyme, this breaks down proteins associated with DNA in the nuclei. add layer of alcohol (ethanol) on top of sample, this causes DNA to precipitate out of solution. DNA is seen as white strands, forms between the layer of sample & layer of alcohol, DNA can be picked up by spooling it onto glass rod.

26 ch 5.5, osmosis, p114

- osmosis is a particular type of diffusion, specifically diffusion of water across a partially permeable membrane, as with all types of diffusion, it is a passive process & energy isn't required. - solute is substance dissolved in solvent (e.g. water), forms a solution, amount of solute in certain volume of aqueous solution is concentration. water potential is pressure exerted by water molecules as they collide with membrane/container, measured in units of pressure pascals (Pa) or kilopascals (kPa). symbol for water potential is psi ψ. pure water is defined as having water potential of 0kPa (at standard temp & pressure (25°C & 100kPa), this is highest possible value for water potential, as presence of solute in water lowers the water potential below zero. all solutions have negative water potentials, the more concentrated the solution, the more negative the water potential. when solution of different concs (& therefore different water potentials), are separated by partially permeable membrane, water molecules can move between solution but solutes cannot, there will be a net movement of water from solution with higher water potential (less concentrated) to solution with lower water potential (more concentrated), this continues until water potential is equal on both sides of the membrane (equilibrium). - diffusion of water into solution leads to increase in volume of this solution, if solution is in a closed system, e.g. a cell, this results in increase in pressure. this pressure is called hydrostatic pressure, & has same units as water potential, kPa. at cellular level, this pressure is relatively large & potentially damaging. if animal cell is placed in solution with higher water potential than that of cytoplasm, water moves into cell by osmosis, increases hydrostatic pressure inside cell. all cells have thin cell-surface membranes (approx 7nm) & no cell walls, cell-surface membrane can't stretch much & can't withstand increased pressure, it breaks & cell bursts, an event called cytolysis. if animal cell is placed in solution with lower water potential than that of cytoplasm, it loses water to solution by osmosis down water potential gradient, this causes reduction in volume of the cell, & cell-surface membrane to 'pucker', referred to as cremation. to prevent either cytolysis or cremation, multicellular animals usually have control mechanisms to make sure cells are continuously surrounded by aqueous solutions with equal water potential (isotonic), in blood the aqueous solution is blood plasma. - like animal cells, plant cells contain variety of solutes, mainly dissolved in a large vacuole. however, unlike animals, plants are unable to control water potential of fluid around them, e.g. roots usually surrounded by almost pure water. plant cells have strong cellulose walls surrounding cell-surface membrane, when water enters by osmosis, increased hydrostatic pressure pushes membrane against rigid cell walls, this pressure against cell wall is called turgid. as turgid pressure increases, is resists entry of further water & cell is said to be turgid. when plant cells are placed in solution with lower water potential than their own, water is lost from cells by osmosis, leads to reduction in volume of cytoplasm, eventually pulls cell-surface membrane away from cell wall, cell is said to be plasmolysed. - to investigate osmosis in plant cells, pieces of potato/onion placed into sugar/salt solutions with different concs, therefore different water potentials. water moves into/out of cells depending on water potential of solution, relative to water potential of plant tissue. as plant tissue gains or loses water, it increases/decreases in mass & size, & vice versa. to investigate osmosis in animal cells, chicken eggs without their shells are placed in different concs of sugar syrup, over time osmosis takes place & there will be net movement of water into/out of the eggs, depends on conc of syrup they were in. (if egg is hard boiled for easier handling, this damages membrane).

12 ch 3.6 structure of proteins, p59

- peptides are polymers made of amino acid molecules (the monomers), proteins consist of 1 or more polypeptides arranges abs complex macromolecules, have specific biological functions. all proteins contain C, H, O and N. all amino acids have same basic structure, different R-groups result in different amino acids. 20 different amino acids commonly found in cells, 5 non-essential, bodies make them from other amino acids, 9 essential, can only be obtained from foods, 6 conditionally essential, only needed by infants and growing children. amino acids join when amine and carboxylic acid groups (connected to central carbon atom) react. R-groups not involved at this point. OH in carboxylic acid group of one amino acid reacts with H in amine group of another, peptide bond is formed and water is produced (condensation reaction), produces dipeptide. when many amino acids are joined by peptide bonds, polypeptide is formed, reaction is catalysed by enzymes peptides transferase (present in ribosomes, site of protein synthesis). different R-groups of the amino acids making up a protein are able to interact with each other (R-group interactions), forms different types of bond. Bonds lead to long chains of amino acids (polypeptides), folds into complex structures (proteins). presence of different sequences of amino acids leads to different structures with different shapes produced. specific shapes of proteins are vital for the many different functions proteins have in living organisms. - thin layer chromatography (TLC) used to separate & identify individual components of a mixture, including mixture of amino acids in solution. 2 phases: stationary phase, & mobile phase which involves organic solvent. mobile phase picks up amino acids and moves through stationary phase, & amino acids are separated. in stationary phase, thin layer of silica gel (or other adhesive substance) is applied to a rigid surface, e.g. sheet of glass or metal. amino acids then added to one end of gel, then end is submerged in organic solvent. organic solvent moves through silic gel (mobile phase). rate at which different amino acids in organic solvent move through silica gel, depends on interactions (hydrogen bonds) they have with silica in stationary phase, and solubility in mobile phase. therefore different amino acids move different distances in same time period, resulting in them separating out. procedure: wear gloves, draw pencil line on chromatography plate, 2cm from bottom, only handle plate by the edges. mark 4 equally spaced points along pencil line, spot amino acid solution onto first pencil mark using capillary tube, & allow spot to dry, label spot with pencil. spot 3 remaining marks with known amino acids. place plate into a jar containing the solvent, solvent is no more than 1 cm deep, then close jar. leave plate in solvent until it reaches 2cm from top, remove plate and draw pencil line along solvent front, allow plate to dry. spray plate in fume cupboard with ninhydrin spray. amino acids react with ninhydrin, and purple/brown colour is produced. mark the centre of each spot present with pencil. - levels of protein structure: primary structure, sequence in which amino acids are joined. directed by information carried in DNA. specific amino acids in sequence influences how polypeptide folds to give protein's final shape, this determines its function. only peptide bonds involved in primary structure. secondary structure, O, H & N atoms of basic, repeating structure of amino acids interact (R-groups not involved at this stage). H-bonds may form in amino acid chain, pulls it into a coil shape (alpha helix). polypeptide chains may lie parallel to one another, joined by H-bonds, forms sheet-like structures. pattern formed by individual amino acids causes structure of appear pleated (beta-pleated sheets). secondary structure is result of H-bonds & forms at regions along protein molecules, depends on amino acid sequences. tertiary structure, protein folds into final shape, includes sections of secondary structure. coiling/folding of sections of proteins into secondary structures brings R-groups of different amino acids closer together, therefore close enough to interact, therefore further folding of sections occur. interactions that occur between R-groups: hydrophobic & hydrophilic interactions, weak interactions between polar & non-polar R-groups. hydrogen bonds, weakest of bonds formed. ionic bonds, stronger than hydrogen bonds, form between oppositely charged R-groups. disulfide bonds, covalent & strongest of bonds, only form between R-groups containing sulfur atoms. this produces variety of complex-shaped proteins, with specialised characteristics & functions. quarternary structure, results from association of 2 or more individual proteins (subunits), interactions between subunits are same as in tertiary structure, except between different protein molecules, rather than within 1 molecule. the protein subunits can be identical or different, enzymes often consist of 2 identical subunits, whereas insulin (a hormone) has 2 different subunits. haemoglobin (protein required for O2 transport in blood) has 4 subunits, 2 sets of identical subunits. - proteins are assembles in aqueous environment of cytoplasm, the way a protein folds also depends on whether R-groups are hydrophilic or hydrophobic. hydrophilic groups are on inside of molecule, shielded from water in cytoplasm. peptides are created by amino acids linking together in condensation reactions to form peptide bonds, proteases are enzymes that catalyse reerse reaction, turns peptides into constituent amino acids. water molecule is used to break peptide bond (hydrolysis reaction), reforms amine and carboxylic acid groups. - peptide bonds form violet complexes with copper ions in alkaline solutions. biuret test, add 3cm^3 of liquid sample, mix with equal volume of 10% NaOH solution 1% CuSO4 solution added a few drops at a time, until sample turns blue. solution mixed & left to stand for 5 mins. positive test, purple.

118 ch 20.2, monogenic inheritance, p524

- performing genetic cross - genetic cross, shows how genes are passed from one gen to next, most commonly shows inheritance of single gene (monogenic inheritance). performing genetic cross, key steps (ensures diagram explains full what is happening to genes of organism during fertilisation): 1 state phenotype of both parents, 2 state genotype of both parents, by assigning letter code to represent alleles of the gene being studied (capital dominant, lower case recessive), 3 state gametes of each parent (circle letters), 4 use punnett square to show results of random fusion of gametes during fertilisation, 5 state proportion of each genotype produced among offspring, 6 state corresponding phenotype for each possible genotype. homozygous genetic cross - organisms that contain homozygous alleles for gene known as 'true breeding'/pure individuals, result is 100% of offspring are heterozygous (offspring known as F1 generation). heterozygous genetic cross - take 2 offspring from heterozygous F1 generation, offspring produced are F2 generation (1:2:1 genotype, 3:1 phenotype ratio). - codominance - when 2 alleles occur for a gene, both are equally dominant, both alleles are expressed in phenotype of organism if present. example in snapdragon flowers: allele codes for red flowers, codes for production of enzyme which catalysed production of red pigment from a colourless precursor. allele codes for white flowers, codes for altered version of enzyme which does not catalyse production of the pigment therefore white flowers. in this example 3 colours can be produced, red if plant is homozygous for allele coding for production of red pigment, white if plant is homozygous for allele coding for no pigment production, pink if plant is heterozygous, single allele present coding for red pigment produced enough pigment to produce pink flowers. genetic cross, letter is chosen to represent the gene (e.g. C for colour of flowers), second letter as a superscript represents different alleles, e.g. C^R for red flowers, C^W for white flowers. - multiple alleles - when genes have more than 2 versions. however as organism carries only 2 versions of the gene (one on each of homologous chromosomes), only 2 alleles present in individual. blood group is determined by gene with multiple alleles, immunoglobulin gene codes for production of antigens on surface of RBC, 3 alleles of this gene: I^A, results in production of antigen A, I^B, production of antigen B, I^O, production of neither antigen. I^A and I^B codominant, I^O recessive to both of other alleles, different combinations of these alleles result in 4 blood groups: A-group I^A I^A or I^A I^O, B-group I^B I^B or I^B I^O, AB-group I^A I^B, O-group I^O I^O. parents with I^A I^O and I^B I^O can produce offspring with any 4 of the blood groups, with equal chance. - determining sex -in humans, mammals & many different species, sex is genetically determined, humans have 23 pairs of chromosomes with varying sizes & shapes, in 22 pairs both members of the pair are the same, but 23rd pair (sex chromosomes) are different. human females have 2 X chromosomes, male has X & Y, X chromosome contains many genes not involved in sexual development, Y chromosome very small and contains almost no genetic information, but carries gene causing embryo to develop as a male. sex linked, meaning when characteristics are determined by genes on sex chromosomes, as Y chromosome smaller than X chromosome, there are a number of genes that males only have 1 copy of, therefore any characteristic caused by a recessive allele on a section of the X chromosome, with that gene missing in the Y chromosome, occurs more frequently in males, as many females will also have a dominant allele present in their cells. - haemophilia - example of sex-linked genetic disorder, patients with haemophilia have blood which clots extremely slowly due to absence of a protein blood-clotting factor (majority of cases, this is factor VIII), therefore injury can result in prolonged bleeding, which if left untreated is potentially fatal. if male inherits recessive allele that codes for haemophilia (on X chromosome), they can't have a corresponding dominant allele on Y chromosome, so develop the condition. as a result, vast majority of haemophilia sufferers are male, females who are heterozygous for haemophilia coding gene are carriers. they don't suffer from disorder but may pass allele to their children, can result in birth of son with haemophilia. when showing inheritance of sex-linked gene, alleles are shown linked to sex-chromosomes they are found on. haemophilia linked to X chromosome, therefore X^H used to represent 'healthy' allele, X^h used to represent recessive allele coding for haemophilia (through non-production of blood-clotting protein). Y is used to represent Y chromosome, has no allele attached to it as it doesn't carry gene producing specific blood-clotting protein. if carrier female & normal male have children, 25% normal female, 25% normal male, 25% normal carrier female, 25% haemophilic male. however, affected male can pass faulty allele to daughters, results in then becoming carriers.

5 ch 2.5, ultrastructure and function of plant cell components, p33

- plant cells rigid unlike animal cells, all plants have cellulose cell wall, cell wall surrounds cell-surface membrane, cell wall made of cellulose (complex carbohydrate), freely permeable so substances pass in and out of cell through cellulose wall. cell walls of plant cell give it shape, contents of cell press against cell wall making it rigid. supports cell and plant as a whole, cell wall also defence mechanism, protects contents of cell against invading pathogens. - vacuoles, membrane-lined sacs in cytoplasm containing cell sap. many plants have large permanent vacuole, maintains turgor so contents of cell push against cell wall and maintain rigid framework for cell - membrane of vacuole is tonoplast, selectively permeable so some small molecules pass through but others cannot, vacuoles appearing in animal cells are small and transient (not permanent). - chloroplasts, organelles responsible girl photosynthesis of plant cells, found in cells of green parts of plants (leaves and stems, not in roots). have double membrane structure like mitochondria, fluids enclosed in chloroplast is stroma, have internal network of membranes which form flattened sacs called thylakoids. several thylakoids stacked together is called granum, grana are joined by membranes called lamellae, grana contain chlorophyll pigments, where light-dependent reactions occur during photosynthesis. starch produced by photosynthesis present as starch grains. - chloroplasts also contain DNA and ribosomes, like mitochondria. chloroplasts therefore able to make their own proteins. internal membranes provide large surface area needed for enzymes, proteins and pigment molecules, necessary for photosynthesis

6 ch 2.6, ultrastructure and function of prokaryotic and eukaryotic cells, p35

- prokaryotic cells earliest forms of life, adapted to living in extremes of salinity, pH and temperature (extremophiles). found in hydrothermal vents and salt lakes, similar environment to those that made up early Earth, usually domain of Archaea and found in soil and human digestive system. always unicellular with relatively simple structure, DNA not contained in nucleus, have few organelles, organelles not membrane-bound. - DNA in prokaryotes fundamentally same as eukaryotes but packaged differently, prokaryotes only have one molecule of DNA (one chromosome), supercooled to make it more compact. genes on chromosome grouped into operons, meaning a number of genes are switched on and off at same time. ribosomes in prokaryotic cells smaller than in eukaryotic cells, relative size determined by rate at which they settle, or form sediment, in solution. larger eukaryotic ribosomes are 80s, smaller prokaryotic ribosomes are 70s. both necessary for protein synthesis, but eukaryotic ribosomes involved in formation of more complex proteins. - flagella or prokaryotes thinner than equivalent structure of eukaryotes, doesn't have 9+2 arrangement, energy to rotate the filament that forms flagellum supplies by chemiosmosis, not ATP as in eukaryotic cells. flagellum is attached to cell membrane of bacterium by a basal body, rotated by molecular motor. cell wall made of peptidoglycan/murein, complex polymer formed from amino acids and sugars. - eukaryotic cells more complex than prokaryotic cells, DNA present in nucleus and exists as multiple chromosomes, which are supercooled, each one wraps around proteins called histones, forms a complex for efficient packaging, complex is called chromatin, chromatin coils and condensed to form chromosomes. eukaryotic cells have membrane-bound organelles including mitochondria and chloroplasts, organisms of plant, animals, fungi and protoctist kingdoms all composed of eukaryotic cells, many are multicellular. prokaryotic/eukaryotic: no nucleus/has nucleus, circular DNA/linear DNA, DNA organisation- proteins fold and condense DNA/DNA associated with histone proteins, extra chromosomal DNA- circular DNA called plasmids/only present in certain organelles (chloroplasts & mitochondria), organelles non membrane-bound/both membrane-bound and non-membrane bound, cell wall peptidoglycan/fungi chitin, plants cellulose, not present in animals, ribosomes smaller 70s/larger 80s, cytoskeleton present/present more complex, reproduction binary fission/asexual or sexual, cell type unicellular/unicellular and multicellular, cell-surface membrane present/present

4 ch 2.4, eukaryotic cell structure, p26

- prokaryotic, single celled organisms with single undivided internal area (cytoplasm) filled with cytosol (made of water, salts & organic molecules). eukaryotic, membrane-bound nucleus & cytoplasm with membrane-bound cellular components - metabolism, synthesis and breaking down of molecules, take place in cytoplasm. cytoplasms separates from external environment with cell-surface membrane. cytoplasm divided into different membrane-bound compartments (organelles), provides distinct environments and conditions for different cellular reactions. membranes, selectively permeable, effectively control movement of substances in and out of cells and organelles, but fragile - nucleus, contain genetic information in the form of DNA. DNA directs synthesis of all proteins required by the cell (the protein synthesis occurs outside of nucleus at ribosomes). therefore DNA controls metabolic activities in this way as many of these proteins are enzymes needed for metabolism to take place. DNA contained in double-membrane (nuclear envelope), protected from damage in cytoplasm. nuclear envelope has nuclear pores, allows molecules to move into and out of nucleus. DNA too large to leave nucleus to site of protein synthesis in cytoplasm, so transcribed to smaller RNA molecules, exported through nuclear pores. DNA uses proteins called histones to form complex called chromatin, chromatin coils and condensed to form structures called chromosomes, chromosomes only visible when cells prepare to divide. Nucleolus, area within nucleus, responsible for ribosome production. composed of proteins and RNA, RNA used to produced ribosomal RNA (rRNA), ribosomal RNA combined with proteins to form ribosomes necessary for protein synthesis - mitochondria, site of final stages of cellular respiration, has energy stored in bonds of organic molecules which is made available for cell to use, by converting it and producing ATP. number of mitochondria relative to how much energy the cell uses, more active cells have more mitochondria. mitochondria have double membrane, inner membrane highly folded to form cristae, fluid interior is matrix. membrane forming cristae contains enzymes used in aerobic respiration. mitochondria contains some DNA (mtDNA), produces own enzymes and reproduces themselves - vesicles, membranous sacs, for storage and transport. consist of a single membrane with fluid inside. vesicles used to transport materials inside the cell. lysosomes are specialised forms of vesicles, contain hydrolytic enzymes, responsible for breakdown of waste material in cells, including old organelle, break down pathogens ingested by phagocytic cells in immune system, role in apoptosis/cell death - cytoskeleton, present throughout the cytoplasm, network of fibres for shape and stability of cell, organelles held in place by cytoskeleton and it controls cell movement of organelles within cells. cytoplasm has 3 components. microfilament, contractile fibres formed from actin protein, responsible for cell movement and cell contraction during cytokinesis (when cytoplasm of single eukaryotic cell divided into two daughter cells). microtubules, globular tubulin proteins polymerise to form tubes, form scaffold-like structure that determines shape of cell, act as tracks for movement of organelles, including vesicles, around the cell. spindle fibres that physically segregate chromosomes in cell division have microtubules. intermediate fibres, give mechanical strength to cells, help maintain their integrity. - centrioles, component of cytoskeleton present in most eukaryotic cells except flowering plants and most fungi, composed of microtubules. 2 associates centrioles form the centrosome, involved in assembly and organisation of spindle fibres during cell division. in flagella and cilia, centrioles have a role in positioning of these structures - flagella (whip-like), cilia (hair-like), extensions that protrude from some cell types. flagella longer than cilia but cilia are usually present in much greater numbers. flagella used primarily to enable cell mobility, in some cells used as sensory organelle to detect chemical changes in cell's environment. cilia mobile or stationary: stationary cilia present on surface of many cells, function in sensory organs such as nose. mobile cilia beat in rhythmic manner and create a current, causes fluids or objects adjacent to the cell to move. e.g. in trachea to move mucus away from the lungs (keeps airways clean), & in fallopian tunes to move egg cells from ovary to uterus. each cilium contains 2 central microtubules (black circles) surrounded by 9 pairs of microtubules, 9+2 arrangement, pairs of parallel microtubules slide over each other causing cilia to move in beating motion. - cell synthesises proteins for internal use and for secretion (transport out of cell). ribosomes, ER & golgi apparatus closely linked for different roles within the cell. cytoskeleton plays key role in coordinating protein synthesis. endoplasmic reticulum is network of membranes enclosing flattened sacs (cisternae), connected to the outer membrane of nucleus. two types: smooth ER, responsible for lipid and carb photosynthesis, and storage. rough ER, has ribosomes bound to surface, responsible for synthesis and transport of proteins. secretory cells, which release hormones or enzymes, have more RER than cells that don't release proteins. ribosomes, free-floating in cytoplasm or attached to ER, forms rough ER, not surrounded by a membrane, constructed of RNA molecules made in nucleolus of cell. ribosomes are site of protein synthesis. mitochondria and chloroplasts, and prokaryotic cells contain ribosomes. golgi apparatus, similar in structure to smooth ER, compact structure consists of cisternae and doesn't contain ribosomes. modifies proteins and packaged them into vesicles, can be secretory vesicles if proteins are to leave cell, or lysosomes if staying in cell - protein production: proteins synthesised on ribosomes bound to ER, pass into cisternae and are packaged into vesicles. vesicles containing newly synthesised proteins move towards golgi apparatus along cytoskeleton. vesicles fuse with cis face of golgi and proteins enter, proteins are modified and leave golgi in vesicles from trans face. secretory vesicles carry proteins to be released from the cell, vesicles move towards cell-surface membrane and fuse, release contents by exocytosis. some vesicles form lysosomes, contain enzymes for use in cell.

1 ch 2.1, microscopy, p8

- sample preparation, depends on resolution desired - dry mount: solid specimens viewed whole/cut into very thin sections w/ blade knife (sectioning). specimen placed on centre of slide & cover slip placed over. e.g. hair, pollen, insect parts (whole), muscle tissue & plants (sectioned) - wet mount: specimens suspended in liquid (water/immersion oil). cover slip placed on at angle. e.g. aquatic life & other living organisms - squash slides: wet mount & lens tissue to press down cover slip. avoid damage to cover slip by squashing sample between 2 slides, care taken to avoid breaking cover slip when pressed. e.g. soft samples, root tips for cell division - smear slides: edge of slide to smear sample for thin even coating on other slide. cover slip placed over sample. e.g. blood for cells in blood - in light microscopy, sample illuminated all at once from below and observed from above, images have low contrast as most cells don't absorb a lot of light. resolution limited by wavelength & diffraction (bending of light as it passes close to edge of object) of light. cytosol (aqueous interior of cells) and other cell structures often transparent - stains increase contrast as different components in cell take up stains to different degrees, increase in contrast allows components to become visible and identifiable - prepare sample for staining: air dry and heat-fix by passing through flame. specimen sticks to slide and takes up stains. crystal violet / methylene blue positive so attracted to negatively charged materials in cytoplasm so stains cell components. congo red / nitros in negatively charged so repel negative cytosol. dyes stay outside cells so left unstained and contrast with stained background (negative stain technique) - differential staining distinguishes between 2 types of organisms otherwise hard to identify or different organelles of single organism within tissue sample: gram stain technique to separate bacteria into gram-positive & gran-negative. crystal violet applied to bacterial specimens on slide, then iodine to fix the dye, then washed with alcohol. gram-positive bacteria retains the crystal violet stain to appear blue or purple in microscope. gran-negative bacteria have thinner cell walls so lose the stain, stained with safranin dye (counterstain). gran-negative appears red. gram-positive susceptible to penicillin which inhibits formation of cell walls and gram-negative not susceptible. acid-fast technique used to differentiate Mycobacterium species from other bacteria. lipid solvent carries carbolfuchsin dye into cells, then cells washed with dilute acid-alcohol solution. Mycobacterium not affected by acid-alcohol and retain carbolfuschin stain and appear bright red. other bacteria lose stain and exposed to a methylene blue stain (blue) - pre-prepared slide production: fixing, chemicals like formaldehyde used to preserve specimens in near-natural state. sectioning, specimens dehydrated with alcohol then placed in mould with wax or resin to form hard block and sliced with thin knife (microtome). staining, specimens treated with multiple stains to show different structures. mounting, specimens secured to microscope slide and cover slip placed on top. chemicals can be toxic and risk assessment needed - light microscopy, easily available, cheap, observe living organisms & dead prepared specimens - microscopes allow to discover details of cell's structures & functions - compound light microscope has 2 lenses: objective placed near specimen, eyepiece through which specimen is viewed, objective magnifies image which is magnified again by eyepiece - compound reduces chromatic aberration and allows for higher magnitude than simple light microscope - opaque specimens illuminated from above

21 ch 4.4, cofactors, coenzymes & prosthetic groups, p97

- some enzymes need non-protein 'helper' component to carry out function as biological catalysts, they may transfer atoms/groups from one reaction to another in multi-step pathway, or may actually form part of active site of enzyme. these components are cofactors, or if cofactor is an organic molecule, it is a coenzyme. inorganic cofactors are obtained is diet as minerals, includes iron, calcium, chloride & zinc ions. e.g. enzyme amylase, (catalyses breakdown of starch), contains chloride ion necessary for formation of correctly shaped active site. many coenzymes are derived from vitamins, a class of organic molecule found in diet, e.g. vitamin B3 is used to synthesise NAD (nicotinamide adenine dinucleotide), a coenzyme responsible for transfer of H atoms between molecule involved in respiration. NADP, which plays similar role in photosynthesis, is also derived from vitamin B3. another example is vitamin B5, used to make coenzyme A, coenzyme A is essential in breakdown of fatty acids & carbs in respiration. - prosthetic groups, haemoglobin prosthetic group is iron (Fe) ion. prosthetic groups are cofactors, required by certain enzymes to carry out catalytic function. while some cofactors are loosely/temporarily bound to enzyme protein in order to activate them, prosthetic groups are tightly bound & form permanent feature of protein, e.g. zinc ions (Zn2+) form important part of structure or carbonic anhydrase, enzyme necessary for metabolism of carbon dioxide. - many enzymes are produced in inactive form, known as inactive precursor enzymes, particularly enzymes that can cause damage within cells producing them or to tissues where they are released, or enzymes whose action needs to be controlled & only activated under certain conditions. precursor enzymes often need to undergo change in shape (tertiary structure), particularly to active site, to be activated, this can be achieved by addition of a cofactor. before a cofactor is added, precursor enzyme is called an apoenzyme. when cofactor is added & enzyme is activated, it is called a holoenzyme. sometimes change in tertiary structure is caused by action of another enzyme, e.g. protease, which cleaves certain bonds in the molecule. in some cases, change in conditions (e.g. pH/temp) results in change in tertiary structure & activates precursor enzyme. the types of precursor enzymes are called zymogens/proenzymes. when inactive pepsinogen is released into stomach to digest proteins, the acid pH causes the transformation into active enzyme pepsin. this adaptation protects body tissues against digestive action of pepsin. - blood clotting/coagulation is important biological response to tissue damage, blood-clotting process only begins when platelets aggregate at site of tissue damage. aggregated platelets release clotting factors, includes factor X. factor x is important component in blood-clotting mechanism, it is an enzyme that's dependent on cofactor vitamin K for activation. activated factor Z catalyses the conversation of prothrombin into enzyme thrombin by cleaving certain bonds in molecule, this alters its tertiary structure. thrombin is a protease & catalyses conversion of soluble fibrinogen into insoluble fibrin fibres. fibrin molecules, together with platelets, form a blood clot. this series of successive enzyme activations in blood clotting is called the coagulation cascade.

122 ch 20.6, speciation and artificial selection

- speciation, means formation of new species through process of evolution. organisms belonging to new species no longer able to interbreed to produce fertile offspring, with organisms belonging to original species. a number of events happen leading to speciation: members of a population become isolated, no longer interbreed with rest of population, results in no gene flow between 2 groups. alleles within groups continue to undergo random mutations, environment of each group different or changed (results in different selection pressures), different characteristics selected for an against. accumulation of mutations & changes in allele frequencies over many generations leads to large changes in phenotype, members of different populations become so different they are no longer able to interbreed to produce fertile offspring, now reproductively isolated and are different species. - allopathic speciation, more common form of species, happens when some members of populations separated from rest of group by physical barrier (e.g. duvet or sea), so geographically isolated. environments of different groups often different, so selection pressures result in different physical adaptations. separation of a small group results in founder effect, leads to genetic drift, further enhances differences between the populations. example of allopatric speciation is finches inhabiting galapagos island (in pacific ocean off the coast of south america), for 2 million years small groups of finches have flown to, and been stranded on, different islands. the finches, separated from finches on other islands & mainland by sea, formed new colonies on different islands. the finches have evolved and adapted to different environments, particular food sources, present on the island, and are example of adaptive radiation (means where rapid organism diversification takes place). as the finches are unable to breed with each other, new species evolved with unique beaks adapted to type of food available. some species have large blunt beaks to crack nuts, some have long thin beaks to get nectar in flowers, some have medium-sized beaks for catching insects. honeycreepers (family Drepanidinae) of islands of Hawaii are birds, a larger example of adaptive radiation, a single ancestor species has led to evolution of at least 54 species that have filled every available niche in the different islands. panama (narrow strip of land (isthmus), joins north & south america and separates atlantic & pacific oceans) was formed 3 million years ago, due to movement of tectonic plates, & results in separation of organisms that had originally occupied the same habitat when the 2 oceans were joined. originally about 15 species of snapping shrimp present, now 15 present on one side of the isthmus & 15 on the other. although shrimp from either side appear ti be identical, if males & females are mixed they will snap eat each other rather than mate. in 1995, 15 iguanas (Iguana iguana), survived hurricane in caribbean island of anguilla, these iguanas were first of their species to reach the island. if these iguanas are successful in colonising island, could be start of allopatric speciation, it could take thousands if not millions of years before this is known. - sympathetic speciation, occurs within populations that share the same habitat, happens less frequenctly than allopatric speciation, more common in plants than animals. can occur when members of 2 different species interbreed and form fertile offspring (often happens in plants). hybrid is formed, which is a new species, will have different number of chromosomes to either parent and may no longer be able to interbreed with members of either parent population. this stops gene flow & reproductively isolates hybrid organisms. examples of sympathetic speciation, fungus-farming ants & blind mole rats. fungus farming ants cultivate growth of fungi, main source of nutrition, by supplying organic material to keep fungi growing. parasitic ants have been found in one colony of these industrious ants, instead of helping in growth of fungi the parasitic ants spend their time eating the fungi & reproducing, they are sometimes ignored and at other times killed. genetic analysis shows they are genetically different from fungus-farming ants but are their descendants. they are not a species evolved in geographic isolation but within same habitat due to behavioural change. it is believed genetic division of the original species of any only happened 37,000 years ago, not long in evolutionary terms. blind mole rats live in small area of northern israel that is part igneous rock and part chalk bedrock, the different types of soils formed above bedrock support a different range of plants. blind mole rats found in both types of soil are sometimes only separated by few metres of loose soil. mole rats only interbreed with mole rats living in same type of soil, dna always is shows lack of gene flow between 2 species is already resulting in genetic differences, even though members of different groups often come into contact with each other, as there is no physical barrier. over time genetic differences could accumulate to the point mole rats from different soil types will no longer be able to interbreed and will be separate species. plants cross with plants of different species, form hybrids much more frequently than animals. indiscriminate release of large numbers of pollen grains by plants is one reason for this. hybrids are reproductively isolated from each parent specifies but can still be present in same habitat. evolution of modern wheat has involved at least 2 hybridisation events & formation of new species along the way. disruptive selection, mating preferences and other behavioural differences can result in individuals or small groups becoming reproductively isolated. however they will still be living in same habitat so gene flow (even if reduced) often interferes with process of speciation. reproductive barriers to successful interbreeding can form within populations before or after fertilisation has occurred, prezygotic reproductive barriers prevent fertilisation and formation of a zygote. postzygotic reproductive barriers, often as result of hybridisation, reduces viability or reproductive potential of offspring. - populations are usually polymorphic, means they display more than one distinct phenotype for most characteristics, the allele coding for most common or normal characteristics is called the wild type allele. other forms of that allele, resulting from mutations, are called mutants. artificial selection/selective breeding is fundamentally same as natural selection, except nature of selection pressure is applied, instead of changes in environment leading to survival of fittest, it is selection for breeding of plants or animals with desirable characteristics by farmers/breeders. farmers have been selectively breeding plants & animals since before genes were disconcerted or theory of evolution proposed, individuals with desired characteristics selected & interbred. offspring from this cross show best examples of desired traits & then selected to breed, this breeding of closely related individuals is called inbreeding, process is repeated over many generations, results in change in allele frequency within population, eventually speciation. brassica oleracea is wild mustard, selectively bred for many centuries producing number of common vegetables. - problems caused by inbreeding, limits gene pool, so decreasing genetic diversity reduces chances of population of inbred organisms evolving & adapting to changes in environment. many genetic disorders are caused by recessive alleles, e.g. cystic fibrosis, condition where digestive system & lungs are clogged with mucus. recessive alleles are not uncommon in most populations but 2 recessive alleles are needed before they are expressed & most individuals will be heterozygous. organisms closely related are genetically similar & likely to have same recessive alleles, breeding of closely related organisms therefore results in offspring with greater chance of being homozygous for recessive traits, and being affected by genetic disorders, over time this reduces ability of these organisms to survive & reproduce. results in organisms being less biologically fit, i.e. less likely to survive & produce 2 surviving offspring to replace themselves. seed banks keep samples of seeds from both wild type & domesticated varieties, important genetic resource. gene banks store biological samples other than seeds, e.g. sperm or eggs, they are usually frozen. due to problems caused by inbreeding, alleles from gene banks used to increase genetic diversity in process called outbreeding, breeding unrelated or distantly related varieties is also form of outbreeding, reduces occurrence of homozygous recessives & increases potential to adapt to environmental change.

27 ch 6.1, cell cycle, p120

- the cell cycle is highly ordered sequence of event, takes place in a cell, results in division of cell & formation of 2 genetically identical daughter cells. - in eukaryotic cells, cell cycle has 2 main phases, interphase & mitotic (division) phase. interphase: cells don't divide continuously, long periods of growth & normal working separate divisions, these periods are called interphase, & cell spends majority of its time in this phase. interphase sometimes referred to as resting phase, as cells not actively dividing, however this is not an accurate description, interphase is actually very active phase of cell cycle, when cell is carrying out all of its major functions e.g. producing enzymes & hormones, while also actively preparing for cell division. during interphase: DNA is replicated & checked for errors in nucleus. protein synthesis occurs in cytoplasm. mitochondria grow & divide, increase number in cytoplasm. chloroplasts grow & divide in plant & algal cell cytoplasm, increasing in number. normal metabolic processes of cells occur (some, e.g. cell respiration, also occur throughout cell division). 3 stages of interphase are: G1, the first growth phase, proteins used to synthesis organelles are produced & organelles replicate, cell increases in size. S, synthesis phase, DNA is replicated in nucleus. G2, the second growth phase, cell continues to increase in size, energy stores are increased, & duplicated DNA is checked for errors. - the mitotic phase is the period of cell division, cell division involves 2 stages, mitosis, nucleus divides. cytokinesis, cytoplasm divides & 2 cells are produced. G0, is name given to phase when cell leaves cycle, either temporarily or permanently, there are a number of reasons for this, including: differentiation, cell that becomes specialised to carry out a particular function (differentiated) is no longer able to divided, will carry out this function indefinitely & not enter cycle again. when DNA of cell is damaged & no longer viable, damaged cell can no longer divide & enters period of permanent cell arrest (G0), majority of normal cells only divide limited number of times & eventually become senescent. as you age, number of these cells in body increases, growing numbers of senescent cells linked with many age-related diseases, e.g. cancer & arthritis. a few types of cell that enter G0 can be stimulated to go back into cell cycle & start dividing again, e.g. lymphocytes (WBC) in an immune response. - it's vital to ensure cell only divides when it has grown to right size, replicated DNA is error-free (or is repaired), & chromosomes are in correct positions during mitosis. this is to ensure fidelity of cell division, that 2 identical daughter cells are created from parent cell. checkpoints are control mechanisms of cell cycle, they monitor & verify whether processes at each phase of cell cycle have been accurately completed, before cell is allowed to progress into next phase. - checkpoints occur at various stages of cell cycle: G1 checkpoint, this checkpoint is at end of G1 phase, before entry into S phase, if cell satisfies requirements of this checkpoint (check for: cell size, nutrients, growth factors, DNA damage), it's triggered to begin DNA replication, if not it enters a resting state (G0). G2 checkpoint, this checkpoint is at end of G2 phase, before mitotic phase, in order for this checkpoint to be passed, cell must check for number of factors (cell size, DNA replication, DNA damage), if checkpoint is passed, cell initiates molecular processes that signal beginning of mitosis. spindle assemble checkpoint (also called metaphase checkpoint), this checkpoint is at point in mitosis where all chromosomes should be attached to spindles & have aligned (check for chromosome attachment to spindle), mitosis can't proceed until checkpoint is passed.

8 ch 3.2, water, p44

- water molecules are polar, molecules with hydroxyl (OH) groups are polar, oxygen has greater share of electrons in O-H bond. positive and negative regions of water molecules attract each other and form hydrogen bonds, hydrogen bonds relatively weak interactions, hydrogen bonds break and reform between constantly moving water molecules, but occur in high numbers, gives water unique characteristics essential for life. - water has unusually high boiling point, water is small molecule and lighter than gases CO2 or O2 but is liquid at rtp, due to hydrogen bonding between water molecules, takes a lot of energy to increase temperature of water and cause water to become gaseous (evaporate). water freezes into ice, ice less dense than liquid state unlike other substances, due to hydrogen bonding. as water cools below 4°C hydrogen bonds fix position of polar molecules further apart than average distance in liquid state, produces giant, rigid but open structure, with every oxygen atom at centre of tetrahedral arrangement of H atoms, so ice floats. water is cohesive, moves as one mass as molecules are attracted to each other (cohesion), plants able to draw water up roots. water adhesive, water molecules attracted to other materials, sticks to sides of roots. water molecules more strongly cohesive to each other than to air, results in surface tension. - water acts as solvent, many solutes in an organism can be dissolved, cytosol of prokaryotes and eukaryotes mainly water, many solutes are also polar molecules (amino acids, proteins & nucleic acids). - water is an efficient transport medium within living organisms, cohesion between water molecules means when water is transported through body, molecules stick together, adhesion occurs between water molecules and other polar molecules & surfaces, effects of adhesion and cohesion results in capillary action, process where water rises up narrow tube against gravity - water acts as a coolant, helps buffer temperature changes during chemical reaction in prokaryotic and eukaryotic cells, as large amounts of energy required to overcome hydrogen bonding, maintaining constant temperatures in cellular environments important, as enzymes only active in narrow temperature range. aquatic organisms live in water and cannot survive out of it, water is stable and doesn't change temperature of become a gas easily, therefore provides constant environment. ice floats, forms surface on pond and lakes, so insulating later above water. aquatic organisms can't survive if habitat became solid. some organisms also inhabit surface of water, surface tension strong enough to support small insects (pond skaters)