The structure of a chloroplast – 3.3.

 Thylakoid: LDR (Light-dependent reaction) takes place; contains chlorophyll and other
photosynthetic pigments; electron carriers
 Granum: A stack of thylakoids joined to one another - provides site for LDR; large surface area.
 Stroma: Fluid surrounding thylakoids; site of the LIR (Light-independent reaction) + contains all
enzymes for LIR (including RuBisCO)
 Thylakoid space: Fluid within the thylakoid membrane sacs; contains enzymes for photolysis of
water
 Outer Membrane: Smooth; freely permeable to molecules like Carbon Dioxide and Water, many
open channel proteins
 Inner Membrane: Contain transporter molecules e.g. sugars and protein; permeable to many
substances which need to enter or leave the cell.

Role in relation to photosynthesis – 3.3.2

 Membranes / (disc) shape provides large surface for light absorption;
 layering of membrane allows a lot of pigment;
 (permeable) membrane allows diffusion of gases / carbon dioxide;
 membranes provide surface for attachment of electron / hydrogen acceptors;
 stroma / matrix containing enzymes for Calvin cycle / light–independent reactions ;
Photosynthesis reaction – 3.3.3

ADP and Reduced NADP production (light dependent reaction) – 3.3.4

 light {raises energy level of / excites electrons} / absorbed by {PSI / PSII / photosystem} ;
 pass through carriers;
 energy {released / transferred / eq} ;
 ATP formed from ADP + P;
 In context of producing reduced NADP / formed with electrons
 splitting of water / photolysis / water;
 water supplies protons/H+ ions to reduce NADP

More advanced mark scheme of the above

ADP and reduced NADP usage (Calvin Cycle/Light-independent reaction) – 3.3.6
 RuBP converted to GP;
 RuBP as carbon dioxide acceptor/combines with carbon dioxide;
 catalysed by rubisco;
 GP converted to triose phosphate/TP/GALP;
 this reaction is a reduction;
 reduced NADP provides hydrogen;
 ATP provides energy;
 some triose phosphate/TP/GALP converted to glucose/carbohydrate;
 some triose phosphate used to produce RuBP
 ATP supplies phosphate for this reaction;

Light-independent reaction; continued synthesis – 3.3.6

 5C/RuBP combines with CO2;
 to form 3C compound / TP / GP;
 catalysed by rubisco;
 using ATP;
 and reduced NADP / eq;
 2 molecules of 3C compound/ TP / GP form hexose;
 all RuBP is regenerated;
 10 molecules of 3C/TP/GP form 6 molecules of 5C/RuBP;

Application to starch
 idea of conversion (of GP / Z) to GALP / eq ;
 using ATP and reduced NADP / eq ;
 idea of conversion (of GALP) to {glucose / hexose} eq ;
 (which is) α glucose ;
 reference to formation of glycosidic bonds ;
 these bonds are 1-4 and 1-6 (glycosidic bonds) / eq ;
 by condensation ;
 ref to amylose and amylopectin ;
 credit details of amylose e.g. straight chain, 1-4 bonds ;
 10.credit details of amylopectin e. branched, 1-4 and 1-6 bonds ;

Synthesis of Cellulose
 GALP is a 3C molecule / eq ;
 reference to formation of {glucose / hexose/ 6C sugar} (from GALP) ;
 idea of enzymes involved in the synthesis of {glucose / cellulose} ;
 idea that cellulose consists of {ß-glucose / beta glucose } ;
 joined by glycosidic bonds / eq;
 reference to 1-4 (bonds) ;
 reference to condensation reactions (between glucoses) ;
 idea that cellulose is a long chain molecule e.g. polysaccharide, polymer ;
 {unbranched / eq} molecule ;

Electron Transport Chain – 3.3.4

 electron transport chain accepts excited electrons;
 from chlorophyll / photosystem;
 electrons lose energy along chain;
 ATP produced;
 from ADP and Pi;
 reduced NADP formed;
 when electrons (from transport chain) and H+ combine with NADP;
 H+ from photolysis;

Non-Cyclic Photophosphorylation

 electrons from PS I;
 also pass onto an electron carrier / combine with the hydrogen ions (from the water);
 reduce NADP to NADPH;

Cyclic photophosphorylation
 reference to large amounts of NADPH;
 electron from PS I is passed to the electron carriers;
 used in PS II;
 ATP is formed;
 electrons return to PS I to fill the space;

GPP/NPP – 3.3.7
 NPP =GPP – plant respiration
 Net primary productivity = potential energy plant has stored
 Gross primary productivity = amount of energy produced by a plant
 energy lost as heat / eq ;
 provide energy for {active transport / any other named energy-requiring process} ;
 NPP is {(stored) energy / energy available for next trophic level / eq} ;

Efficiency –3.3.8
 Energy Stored / NPP of Plant x 100 = Efficiency
 Between levels: net productivity of level / previous level x 100

Why only 10% is transferred to the next trophic level – 3.3.8

 Plants respire products of photosynthesis / eq ;
 Reference to gross primary production (GPP) and net primary production (NPP) ;
 Not all of {producers / plants} eaten / inedible plant material / dead leaves / underground
parts ;
 Energy losses in animals from {respiration / metabolism} ;
 Energy losses in {excretory materials / urine} ;
 Energy losses in {egested materials / faeces} ;
 Energy losses due to {movement / death / reproduction / other reasonable
suggestion} ; [all must be qualified]

Photosynthetic inefficiency
 idea of reflection ;
 reference. to {incorrect / eq } {wavelength / colour / frequency} ;
 idea of {not hitting the {chloroplast / chlorophyll}} / it is transmitted ;
 idea of light being in excess e.g. at max. photosynthesis so more light can be used

Carbon Cycle
 carbon dioxide taken in as a result of photosynthesis / more photosynthesis than respiration;
 idea that carbon is fixed/incorporated into compounds in the trees;

Biofuels – 3.3.9
 reference to biofuels being (possibly)carbon neutral ;
 idea that {plants / crops} are used for biofuels ;
 idea that carbon dioxide used for photosynthesis (by plants / in production of
 biofuels) ;
 idea of using biofuels to replace fossil fuels

Biofuels not being carbon neutral

 idea that biofuel production may (overall) results in more carbon dioxide in the
 atmosphere ; OR idea that carbon neutral means that the carbon dioxide produced equals the
carbon dioxide used ;
 idea of forests as carbon {sinks / eq} ;
 idea that {clearing land / deforestation} results in (net) increase in carbon dioxide (in
atmosphere) ;
 (less plants means) less carbon dioxide {removed / used / eq} by photosynthesis ;
 {burning / eq} trees would produce carbon dioxide ;
 idea that (increased) decomposition produces carbon dioxide;
 idea of using {(fossil) fuels / petrol / diesel} by {lorries / machinery / eq}produces carbon dioxide
;
 {burning /eq} of biofuels produces carbon dioxide ;

Re-forestation
 reference to the planting of new trees ;
 more carbon dioxide removed from atmosphere / eq ;
 by photosynthesis ;
 Carbon (dioxide) is used in forming permanent plant tissues / biomass / plant structures;
 Carbon is incorporated in organic molecules / named e.g.;
More carbon in soil (carbon sinks) due to less ploughing / farming
 Less oxygen can enter the soil (from the air);
 For saprobionts / soil microorganisms / bacteria / fungi / decomposers / correctly named soil
organisms;
 For use in aerobic respiration;
 Less breakdown of organic matter / humus / dead plants / dead animals / other e.g.;
 Less carbon dioxide released / formed;

Factors: Abiotic / biotic – 3.3.10

 Biotic factors – The living elements of a habitat which affect the ability of an organism to survive
there. These include: Predation; finding a mate; territory; parasitism & disease.
 Abiotic factors – The non-living elements of the habitat of an organism. These include: edaphic
factors; light; temperature; oxygen availability; wind and water currents.

Niche in relation to distribution / abundance – 3.3.12

 idea of a niche e.g. organisms exist where conditions that make their role exist
 lack of habitat / insects means certain organisms won’t be able to live there
 two species occupying {same / similar } niches will compete ;
 less species (both) will survive ;

Succession – 3.3.13

 reference to lichens and mosses as pioneer community ;

 able to grow in {little / no} soil / eq ;
 (that) breaks up (rock) fragments / forms {thin / shallow / eq} soil;
 reference to {plants / eq} with {small / short / eq} roots ;
 (able to) grow in {thin / shallow / eq} soil / eq ;
 idea that changes in soil structure enable {trees / shrubs} to grow / eq ;
 general points:
 reference to soil able to {hold / retain / contain / eq} {water / minerals} ;
 as plants {lose leaves / die / decay / eq} ;
 reference to {organic matter / humus / eq} {increases / released / eq} ;
 reference to competition effects ;

Temperature / Greenhouse gases

 {carbon dioxide and methane / both / they / eq} are greenhouse gases ;
 {trap / absorb} {heat / infra-red / long wave radiation / eq} / eq ;
 idea of reflected from Earth’s surface / re-radiation ; mean temperature of Earth’s surface
increases / eq
Presyzgotic reproductive barriers – 3.3.22

o Habitat isolation;
o populations occupy different habitats in the same area so do not meet to breed

o Temporal isolation;
o species exist in the same area but are active for reproduction at different times

o Mechanical isolation;
o reproductive organs don't fit together

o Behavioural isolation;
populations do not respond to each other's reproductive displays or signals

o Gametic isolation;
o male and female gametes from two populations are not {compatible / eq}
o credit example e.g. the pollen of one species cannot form tube on stigma of other species

Postzygotic reproductive barriers – 3.3.22

 Hybrid sterility;
 healthy individuals produced from mating of two different species cannot reproduce
 credit example e.g. a mule is the infertile offspring of a horse and a donkey

 Hybrid inviability;
 individuals produced from mating species are not healthy and do not survive

 Low hybrid zygote vigour;

 zygotes fail to develop properly;
 idea that zygotes do not survive during the embryonic development;
 idea that surviving zygotes result in offspring with severe abnormalities;
 so cannot reproduce;

Barriers/Isolation – 3.3.22
 idea of no {(inter) breeding / reproduction / mating / eq}
 (because) {geographical / physical} barrier / eq ;
 idea of different behaviour ;
 idea of incompatible genitalia ;
 idea of each population having a {discrete / eq} gene pool e.g. restricted gene flow, different
mutations, different alleles

Speciation – (Geographic Isolation) – 3.3.22

 isolation of two populations; barrier (sea, land, mountain)
 variation already present due to mutations;
 different environmental conditions / selection pressures;
 selection of different features and hence different alleles;
 populations become (genetically) different;
 different frequency of alleles;
 separate gene pools / no interbreeding; breed together;
 if fertile offspring, then same species; infertile offspring, then different species

Farming Effects on Succession

 e.g. crops are planted (not native plants);
 these compete with native plants;
 ploughing returns to bare soil;
 destroys herbaceous plants/tree/shrub seedlings;
 grazing by farm animals;
 destroys herbaceous/shrub seedlings/communities.

Geographical isolation #2 (animals – in this case, birds)

 idea of geographical isolation e.g. physical barrier between Corsican and mainland birds /
allopatric speciation ;
 idea that there are different selection pressures (between Corsica and the mainland);
 an example of selection pressure e.g. food source, different habitats ;
 idea that mutations occurred ;
 Idea that this results in adaptation to the conditions ;
 these {alleles /genes} passed on (to offspring);
 idea of change in gene pool e.g. increasing frequency of (these) alleles, changes in gene pool ;
 reference to reproductive isolation (of Corsican nuthatches from mainland nuthatches) ;
 idea that birds on mainland could live in all regions as there is no restriction on gene flow ;

Natural selection to allele frequency – 3.3.21

 variation present in (original population);
 best adapted individuals more likely to survive;
 (these reproduce and) pass on genes (to next generation/offspring);
 more/increase (in frequency) of these alleles/genes;
 Individuals within a species may show a wide range of variation ;
 Predation, disease and competition result in differential survival and reproduction ;

Speciation -- common ancestry (plant-related) –

 reference to original population increasing in size and spreading into a wider diversity of
{habitats / eq} ;
 reference to mutations ;
 leading to diversity in flowering times / eq ;
 (and) other plant features / eq ;
 reference to reproductive isolation ;
 restriction in gene flow / eq ;
 between extremes of population / eq ;
 reference to different environmental factors in each region ;
 each region has different selection pressures / eq ;
 idea of plants adapted to a region ;
 reference to survival and breeding ;
 reference to change in allele frequencies (over time) ;
 (leads to) differences between gene pools / eq ;

Succession – 3.3.13

 reference to lichens and mosses as pioneer community ;

 able to grow in {little / no} soil / eq ;
 (that) breaks up (rock) fragments / forms {thin / shallow / eq} soil;
 reference to {plants / eq} with {small / short / eq} roots ;
 (able to) grow in {thin / shallow / eq} soil / eq ;
 idea that changes in soil structure enable {trees / shrubs} to grow / eq ;
 general points:
 reference to soil able to {hold / retain / contain / eq} {water / minerals} ;
 as plants {lose leaves / die / decay / eq} ;
 reference to {organic matter / humus / eq} {increases / released / eq} ;
 reference to competition effects ;
 ref to climax ;

Primary succession – Starts with an empty inorganic surface. The first plants are opportunists or
pioneer species. These organisms penetrate the rock surface causing it to break leading to the
production of humus. Humus over time forms soil. Grasses and ferns establish root systems. More
soil develops. The diversity of species increases until a climax community is reached; biodiversity is
constant

Secondary succession – Starts with soil but no vegetation. For example when rivers shift the courses,
after fires and flood. The number of species is high from the start. The time to get to a climax
community is dependent on a number of factors such as temperature, rainfall and soil fertility. A
plagioclimax community is often reached.

Changing communities

 Reference to removal of grazer (whatever is referred to in the text) / eq ;

 Allows {new / different / eq} {species / plants} to {grow / colonise } ;
 Reference to {competitive effects / change in soil /eq} ;
 Will go through several stages / eq;
 Reference to succession ;
 Reference to climatic climax / eq ;
 Change in species composition / different food {web /chains} / eq;
Global warming – 3.3.14

 reference to {fires / burning / eq} produces carbon dioxide

 which is a greenhouse gas ;
 idea that these gases {build up / remain / form a layer / increase} in (upper) atmosphere;
 which {absorb / trap / eq} {heat energy / infrared / IR / eq} ;
 reflected from earth’s surface ;
 idea that increased levels of these gases increase the greenhouse effect ;
 idea that (mean) temperature of earth’s {surface / atmosphere} is increasing ;
 idea that less carbon dioxide {removed / used / eq} by photosynthesis ;

Factors Limiting the size of the Climax Community

 named nutrient availability;
 numbers of producers providing energy (for a food chain);
 light intensity affecting the rate of photosynthesis;
 disease killing (weaker) members of species;
 space for nest building / niches;
 reproductive rate balancing death rate;
 competition for a named limited resource;
 (intra and interspecific) competition explained;
 predation described;

Effect of temperature increase on enzyme reactions – 3.3.16

 Rate of reaction increases;
 Increasing temperature increases rate of movement of molecules/kinetic energy;
 Collide more often/substrate enters active site more often/more enzyme-substrate complexes
formed;
 Up to optimum;
 Rate of reaction decreases;
 High temperatures cause denaturation/loss of tertiary structure/3D structure;
 By breaking H bonds (not peptide bond);
 Active site altered/substrate cannot bind/fit/ ;

Effect of increased temperature for animals (from global warming)

 ref to global warming {raising / eq} temperature ;
 metabolic {reactions / processes / eq} speed up
 rate of growth {rises / increases / eq} / eq ;
 life cycle becomes {faster / eq }
 (then) up to optimum / eq ;
 metabolic { processes / reactions / eq } {fall / slow down / eq } ;
 rate of growth falls / eq ;
 life cycle slows down / eq ;

Effect of global warming on distribution – 3.3.15

 reference to changing conditions / credit example e.g. rising temperatures ;
 idea that temperature may be too high ;
 reference to organisms {migrating / moving / eq} ;
 reference to change of {biodiversity / eq } ;
 reference to the increased competition effects ;
 reference to range of organisms {expanding / growing / increasing / eq} ;
 idea that plants can move less easily than animals (accept converse) ;
 (so) the animals / plants survive more / less / eq ;

Changing rainfall patterns

 some areas will get increased rainfall, including torrential rainstorms  flooding
 other areas will get less rain

Changes is seasonal cycles

 warmer winters/warmer earlier spring
 dry seasons may last longer
 warmer autumns/shorter winters

Global warming and decomposition

 As temperatures of soils increase enzyme activity of decomposers increases
 so more decomposition of dead organic matter in soil occurs.
 products of decomposition are used by the decomposers for respiration
 which itself increases as a result of the warmer temperatures
 so more CO2 (and methane) is released

Why reduction in fossil fuels may not lead to less chance of global warming
 carbon dioxide produced {by using / in production of / eq} fossil fuels / eq ;
 no (direct) evidence that increased carbon dioxide leads to global warming / eq ;
 reference to carbon dioxide released from {other processes / named process} ;
 idea of removal of {carbon sinks / named example / eq} (also) leads to increase in carbon dioxide
;
 stated example of any other greenhouse gas released from another source e.g. CFC, water
vapour, methane ;
 description of source e.g. ruminant animals, paddy fields, melting ice, clearance of peat
land ;
 idea of natural {cycles / events / phenomena / eq} may be involved (in global warming) e.g.
solar, volcanoes ;
 idea of evidence from past is being used ;
 idea of {(past evidence) is not in indicator of future events / limitations of (climatic)
 models} ;
 idea that scientists may be biased ;
 description of bias e.g. employed by {company / country} with vested interest, self-promotion
 specific example of problem with / disadvantage of} alternative source of energy
Not a mark scheme but a developed answer on why temperature increases affects organisms

• Enzyme activity is temperature-sensitive; increases in temperature increase rate of reactions

• Rate of photosynthesis could increase so more energy fixed so increasing growth; this may give
competitors an advantage so one species may increase and another decrease

• This may mean more food for some species of primary consumer and less for others, with the
consequent changes in prey abundance/choice for predators so altering the dynamics of food webs

• Means rate of photosynthesis may be sufficient to support growth further north because it is now
warmer. But temperature may be too high in the southern limits so enzyme rates increase
differently and metabolic sequences become chaotic; increased temperature may increase
respiration >p/s so less growth possible; high temps reduce amount of water so p/s decreases, so a
plants distribution may shift northwards, and increased p/s there may mean these plants now grow
better and outcompete other species

• May alter the synchronisation between life cycles in the environment e.g. flowers may be
produced before their insect pollinators have hatched, so flowers don’t get pollinated which will
reduced their numbers, and the insects don’t get their food so their numbers decrease too

• Or food plants have grown earlier and so died off before caterpillars appear from eggs laid by
butterflies so numbers of butterflies could decrease, and birds that depend on caterpillars have less
food with which to raise their young…or insect life cycles speed up so that larvae or adults are
produced before the food plants

• Seeds may not germinate if don’t get the cold stimulus from a cold winter; over-wintering stages of
insect pests won’t get killed leading to pest epidemics in the following year

• But natural selection will operate too so that, in any population with some individuals with the
combinations of genes to enable them to survive long enough to breed will do so, so more of the
offspring inherit the genes so the population becomes adapted to the changing conditions e.g.
insects hatch earlier too so they remain in synchronisation with their food plants
Evidence for global warming

Why peat bogs?

 Provides information from long periods ago / specified time e.g. ice age ;
 Peat formed when plant material dies but does not decompose / eq ;
 ref to successive layers [qualified e.g. lowest layers are the oldest: pollen trapped in peat layers]
;
 Use of carbon dating techniques can establish the age of the layers ;

Use of pollen records from peat bogs

 idea that each plant produces a characteristic and recognisable type of pollen ;
 idea that that more pollen there is of a particular species in particular layers of a peat core the
more common it was at the time the peat was laid down ;
 Using knowledge of the present day distribution of species and climate scientists know that
particular species of plants survive in particular climatic conditions ;
 idea that scientists can infer what the climatic conditions were likely to be when the pollen was
deposited ;

Dendrochronology
 ref to tree rings;
 ref to tree ring growing yearly / eq ;
 idea that tree rings can be dated by counting inwards ;
 idea that thicker / wider tree rings reflects amount of growth ;
 in warmer conditions the rings are thicker (better growth) ;
 scientists can see what the climate is like each year ;

Temperature record reliability

 Records only go back to mid C16
 Early records not reliable
 Inaccurate equipment (only mercury thermometers)
 Records only collected in a few places
 Modern records more reliable: accurate equipment; data-logging/computers allows vast
numbers of readings to be collected and processed
 Records taken from many parts of the world
Extrapolation of Data / Evidence / Scientific conclusions
Extrapolation
 ref / idea of extending the line of best fit through existing data into the future ;
 idea that this model assumes there is enough data to establish the trend accurately ;
 idea that this model assumes that present trends continue e.g. fossil fuel use, no changes in
control of emissions ;

Limitations
 limited data;
 records do not go back far enough / eq ;
 models assume existing trends will continue;
 limited knowledge of the global climate so models are only approximations ;
 not all factors involved e.g. major volcanic events, snow cover ;
 limitations of computing resources ;
 future changes in use of fossil fuels ;

Actions taken to reduce global warming

 Increase in biofuels
 Some farmers support;
 Government fund farming crops ;
 Some drivers support;
 Price of biofuels is lower than oil-based fuels ;
 Some consumers may disagree ;
 Food shortages ;
 Some conservationists disagree ;
 Forests need to be cleared ;

The conclusions made

 judged on reliability of data

 evidence ;
 bias ;
 example e.g. vested interest
Evidence for evolution

Proteomics

 study of the size / shape / amino acid sequence of proteins ;

 amino acid sequence is coded for by DNA sequence ;
 similar DNA sequences;
 similar amino acid sequences ;
 more closely related ;
 organisms that diverged away more recently have similar proteins ;
 less time has passed for changes to occur ;

Genomics (the study of DNA)

 look at the sequence of bases in genes ;

 the more distantly related two species are the more differences there will be due to the
accumulation of mutations over time ;
 Analysed by DNA hybridisation, DNA profiling, DNA molecular clocks ;

Validation

 Scientific journals;
 Share theories / eq ;
 Replication of results indications reliability and validity ;
 Peer review ;
 Check for validity ;
 Scientific conferences
 Ref to questions being asked or discussions ;
 Ensures validity
Nature of genetic code – 3.4.2

 Triplet code;
 some reference / idea that each amino acid is coded for by three {nucleotides / bases} ;
 credit any quoted example / idea that 12 {nucleotides / bases} code for 4 amino acids;
 Non-overlapping;
 idea that each {triplet is discrete / each base is only used once in a triplet / eq } ;
 idea that AAT + AAC + CAG + TTT (whatever quoted example) gives 4 (distinct) {triplets / codes} ;
 degenerate;
 idea that more than one code can be used for a {particular amino acid/ stop code} ;
 idea that only the first two of 3 bases count in determining the amino acid ;
 idea the last base is altered then polypeptide remains the same ;
 idea that mutations have less effect ;
 2AAT and AAC code for leucine (example from text)

Features of a gene which enables it to code for a protein

 Gene is a (length) of DNA;
 Gene is a sequence of bases/chain of nucleotides;
 Triplet (base) code/read in three‟s;
 On sense/coding strand;
 Triplet coding for amino acid;
 Degenerate code; non-overlapping; start/stop code;
 Sequence of triplets/bases code for protein;

Protein synthesis (more simple) – 3.4.3

 Sequence of bases is the code;
 DNA strands separate/Hydrogen bonds break;
 Producing mRNA/scription (linked to mRNA production);
 Role of RNA polymerise;
 Complementary base pairing;
 mRNA attaches to ribsome/rER;
 tRNA bring amino acid;
 anticodons of tRNA complementary to condons on mRNA/ translation;
 amino acids join by peptide bonds/condensation reaction;

Transcription
 DNA strands {separate / unzip / eq} ;
 idea that one DNA {strand / eq} used as template (to form mRNA) / eq ;
 from free nucleotides / eq ;
 reference to complementary base pairing ;
 reference to hydrogen bonding ;
 correct reference to {RNA-polymerase / DNA helicase} ;
 credit correct sequence of bases on {mRNA / DNA} ;

Translation
 reference to specific amino acid attachment to tRNA ;
 idea that anticodon (on tRNA) {attaches / binds / lines up / eq} to the {codon / triplet} on mRNA ;
 example quoted using the information in the diagram e.g. tRNA with alanine has CGA
 anticodon which binds to GCU on mRNA ;
 idea that two tRNA held in ribosome (at any one time) ;
 reference to formation of peptide {bonds / links} (between adjacent amino acids) ;
 reference to peptidyl transferase ;
 process continues until the stop codon (for which there is no tRNA) ;
 polypeptide released into the rER ;

Why only 1% of genetic info is transcribed

 Only some genes transcribed;
 only one strand transcribed;
 different protein/enzyme required by different cells;
 intron ref/some DNA does not code/non sense codes/junk DNA;
 stutter sequences/repeat DNA;

Post-transcriptional processing of mRNA.

 Genes have coding regions (exons) and non-coding regions (introns).

 Whole gene is transcribed into mRNA.
 Introns then ‘cut out’ leaving just the exon sections.
 Exons spliced together to make functional mRNA; the exons can be sliced together in different
ways so that several types of mRNA are produced which will be translated into several different
proteins; this is called post-transcriptional processing
 So one gene  several related proteins [this is a form of molecular amplification]

Immune response to only certain bacteria

 reference to protein nature of {antigens / antibodies} ;

 antigens are specific (to each bacteria) / eq ;
 antibodies need to be {complementary / specific} (to the antigen) ;
 idea that {binding / eq} can take place ;
 (some bacteria) have {different / changed} antigens / eq ;
 idea that this is a primary infection ;
 reference to {mucus / slime} {coat /capsule} (of bacterial cells) (in terms of phagocytosis) ;
 idea that some bacteria are inside body cells ;
 idea of antibodies already present e.g through passive immunity
Double-stranded molecule

 (Double-stranded because made of) two strands ;

 (strands joined) by hydrogen bonds (between bases ) ;
 (polynucleotide) of {many / eq} nucleotides ;
 (nucleotides) linked by phospho(di)ester bonds / eq ;

Gene mutation

 the {change / eq} in DNA ;

 ref to {change / deletion / addition / duplication / substitution / eq} of {bases / nucleotides} ;

Vaccines

 idea of using {virus / PCV2} as vaccine ;

 which is {modified / attenuated / harmless / similar / part of / eq} ;
 idea that the vaccine contains the antigen ;
 reference to stimulation of {humoral / eq} immunity ;
 idea of {activation / proliferation} of (specific) {B cell / T cell / lymphocyte} ;
 reference to production of (B / T) memory cells ;
 idea that body now able to produce (specific) antibody {faster / at higher concentration / eq} on
another exposure to PCV2 ;

Structure of antibodies
 reference to glycoprotein ;
 credit detail of structure e.g. specific (3D) shape, L and H regions, Y-shape, 4 (peptide) chains,
disulphide bridges between peptides, hinge region ;
 reference to {antigen-binding site / variable region / Fab (region) / eq };
 idea of antibodies have a {similar / constant / Fc / eq } region;
 produced by plasma cells / present on B cells ;
 role of antibody described e.g. opsonisation, immobilisation, agglutination, lysis ;

Bacteria vs Viruses – 3.4.8

 bacteria are cells, viruses are {not / particles} ;

 idea of bacteria surrounded by {cell wall /slime / capsule } , viruses surrounded by {protein /
capsids / envelope} ;
 bacteria have { plasmids / ribosomes / other named structure} , viruses do not have {plasmids /
ribosomes / other named structure } ;
 bacteria (genome) are DNA, viruses can be DNA or RNA ;
 bacterial DNA is double-stranded, viral genetic material is single (or double) stranded / eq ;
 idea that bacteria have {circular / eq} genetic material, viruses have {linear / straight} genetic
material ;
Decomposition by microbes

 ref to {microorganisms / microbes / bacteria /fungi / eq} ;

 ref to respiration of (microorganisms / bacteria /fungi / eq) ;
 ref to aerobic / anaerobic (respiration) ;
 converts {organic compounds / eq} to carbon dioxide / eq ;
 converts {nitrogen compounds / proteins / amino acids/ urea} to ammonia / eq ;

Another

 Role of Microbes/Fungi
 extracellular digestion;
 by secretion of enzymes;
 hydrolysis/breakdown/digestion of carbon compounds;
 respiration (by bacteria);
 releasing carbon dioxide;
 taken up by the plant during photosynthesis

Bactericidal vs. Bacteriostatic

 idea of antibiotic is used to {control / kill / prevent reproduction of / eq} bacteria ;
 bacteriostatic prevent {reproduction / division / multiplication / growth / eq} of bacteria;
 bactericidal {destroy / kill / eq} bacteria ;

Antibiotic – limited

 reference to antibiotic acting as selective pressure ;

 reference to some bacteria resistant (to antibiotic) ;
 idea that resistant bacteria survive and {reproduce / pass on resistance / pass on
gene / eq};
 idea that antibiotic no longer effective ;
 reference to some infections cannot be treated with antibiotics

The protection against microorganisms

 Skin flora;
 Outcompete for nutrients ;
 Outcompete for space ;
 Ref to secretion of enzymes / chemicals / eq ;
 Keratin ;
 which forms a physical barrier / eq ;
 Stomach acid ;
 ref to low pH / acidic conditions ;
 Gut ;
 Lysozyme ;
 Destroy cell walls ;
HIV

 {glycoprotein / gp120} on virus / eq ;

 binds with {receptors / CD4} / eq ;
 on (surface) membrane of lymphocytes / eq ;
 viral RNA enters the lymphocyte / eq ;
 viral RNA used to produce viral DNA (in lymphocyte) / eq ;
 by action of reverse transcriptase ;
 ref to integrase ;
 ref to formation of new viruses ;
 lymphocyte destroyed when new viruses {bud out of / leave} the cell / eq ;
 T killer {cells / lymphocytes} destroy T helper {cells / lymphocytes} / eq ;

Pulmonary Tuberculosis – transmission/infection

 (Bacteria transmitted in) droplets / aerosol;
 (Bacteria) engulfed / ingested by phagocytes / macrophages;
 (Bacteria) encased in named structure e.g. wall / tubercle / granuloma / nodule;
 (Bacteria) are dormant / not active / not replicating;
 If immunosuppressed, bacteria activate / replicate / released;
 Bacteria destroy alveoli / capillary / epithelial cells;
 (Leads to) fibrosis / scar tissue / cavities /calcification;
 (Damage) leads to less diffusion /less surface area / increases diffusion distance;
 (Activation / damage allows bacteria) to enter blood / spreads (to other organs);
 Accept symptoms e.g. bloody coughing / mucus, inflammation;

Interferon

• Cells infected with virus secrete a protein called interferon (a type of cytokine)
• attaches to membranes of surrounding cells.
• this triggers the cells to make their own antiviral proteins which inhibit synthesis of viral proteins
so no new viruses can be produced, so limiting infection.
• Also stimulates virus-infected cells to ‘self-destruct’
Significance

• Interferon system reacts very quickly to viral infection

• This limits the infection until the slower acting specific immune response kicks in to take over.

Phagocytosis
 Phagocyte attracted to bacteria by chemicals / recognise antigens on bacteria as foreign;
 Engulf/ingest bacteria;
 Bacteria in vacuole / vesicle;
 Lysosome fuses with / empties enzymes into vacuole;
 Bacteria digested / hydrolysed;
Inflammation

• Damage/infection causes damaged mast cells (cells found in connective tissue) to release
hisamine
• causes vasodilation of the arterioles nearby so more blood flows to area of infection
• also increases permeability of capillaries so more tissue fluid forced out -> localised swelling
• Phagocytes can squeeze out of capillaries into the tissues to destroy the bacteria to limit
infection.

B Cells
 B lymphocytes produce antibodies/involved in humoral response;
 Macrophages present antigens;
 (specific) B lymphocytes recognise/bind to antigen; increase in numbers by mitosis;
 produce plasma cells (which make antibodies);
 antibodies bind to and clump/ agglutinate virus; memory cells produced by 1st exposure/cloned
on 2nd exposure;

T cells
 T lymphocytes involved in cell mediated immunity;
 T lymphocytes(helpers) produce chemicals;
 which aid B lymphocyte cloning;
 encourages phagocytes to engulf clumped virus;
 killer T cells kill virus infected cells;
 memory cells produced by 1st exposure/cloned on 2nd exposure

Production of plasma cells

 reference to humoral (immune) response ;
 reference to {phagocytosis / eq} by{phagocytes /named phagocyte} ;
 reference to macrophages as { antigen-presenting cells / APCs} (to T helper cells) ;
 reference to B cells as { antigen-presenting cells / APCs} (to itself) ;
 idea that T helper cells release cytokines for B cell {activation / stimulation} ;
 idea of B cells {forming clones / dividing /eq} (to form B effector cells) ;
 reference to {differentiation of B cells into plasma cells / formation of plasma cells from B cells}
(subsequent to cloning)

Role of memory cells

 On further exposure to same microorganism;

 Antigen recognised;
 Faster response;
 Greater production of antibodies;
B memory cells are formed so that if the body is infected by the same pathogen again, antibodies
specific to that pathogen can be produced quicker.

B effector cells proliferate to Plasma cells which secrete antibodies and present antibodies on their
MHC proteins for recognition by the CD4 receptors on T helper cells

T helper cells direct and activate other immune system cells. They produce cytokines which
stimulate B cells to proliferate and produce B memory cells and B effector cells.

T memory cells – cloned cells which remain in the body and rapidly become active if the same
antigen is encountered again.

T killer cells bind to infected cells and interact with the cell membrane to destroy the infected cell
and pathogens with it.

Types of body immunity

Natural active immunity - The immunity which results from natural infection of the body and the
production of antibodies by the immune system.

Natural passive immunity - Immunity which results from passing naturally from a mother to her baby
via the placenta, in the colostrum and in the milk.

Artificial passive - immunity which results when antibodies formed in one individual are extracted
and injected into another individual

Artificial active – immunity induced by the use of a small amounts of antigen (vaccine) to trigger an
active immune response

An ‘evolutionary arms race’ exists between pathogens and drug developers

 Drug developers produce new drugs effective against pathogens (bacteria or viruses)
 These drugs provide a selection pressure;
 Rapid multiplication pathogens produces many with mutations
 Any pathogen with mutations that make them resistant to the drug will be more likely to survive
and reproduce; susceptible pathogens killed, resistant ones survive and increase
 Drugs now ineffective against resistant pathogens
 Drug developers have to create new drugs.

Hygiene
 ref to hand washing regimes for {doctors / nurses / medical staff / visitors} ;
 particularly when dealing with open {wounds / eq} / eq ;
 ref to wearing suitable clothing ;
 ref to antiseptic (solutions) readily available ;
 named antiseptic e.g. gels, pastes, alcohol rubs ;
 ref to {isolation of suspected cases / screening of admissions} / eq ;
 ref to {controls / monitors} use of antibiotics / eq ;
 fewer {patients / visitors} passing in and out ;
Use of body temperature
Body temp = deep core temp, measured deep inside the body (often using a long
thermoprobe pushed into the liver
 Mean body temperature = 36.8oC
 Due the heat released by metabolic reactions e.g. respiration.
 On death these metabolic reactions stop so no heat is produced
 So cooling will occur

Estimate of time of death influenced by factors affecting rate of cooling e.g.

 Environmental temperature
 Body size (SA/vol relationship)
 Body position e.g. surface area exposed to cooling
 Clothing

Degree of muscle contraction

On death
 Muscles initially relaxed
 Once oxygen supply depleted respiration ceases so ATP production stops.
 Lack of ATP results in cross-links between muscle contractile proteins becoming
fixed
 Muscles become stiff = rigor mortis so limbs remain fixed in position
 Most bodies have complete rigor mortis 6 – 9 hrs after death
Extent of decomposition

Causes of decomposition
Autodigestion or autolysis due to action of hydrolytic enzymes (= self-digestion!) begins
about 4 mins after death!
 In gut
 from lysosomes in cells
Causes breakdown of body tissues

Action of bacteria
 From gut especially, later those from outside which invade through natural openings
or wounds,
 Initially aerobic bacteria but these use up oxygen so replaced by anaerobic bacteria
which cause putrefaction

Extent of decomposition depends on time and temperature

Forensic entomology
This is especially useful when the body has been dead for more than a few days, because the
features that are normally used to determine the time of death, like temperature or rigor
mortis, are no longer helpful

Many types of fly will lay their eggs in a dead body because it is a source of food for the
larvae (maggots). Eggs can be laid on the skin, in body openings, e.g. nose, ears, mouth or
in wounds

How maggots are useful

 Identification of the stage of development at the ambient temperature can give an
estimate of age and hence time since the eggs were laid and hence the time of death
 The time taken for eggs to hatch can also give an indication of when the eggs were
laid and hence the time of death.
 The age of the maggot, and hence when the eggs were laid can be determined by
measuring the fully extended length of the maggot and the ambient temperature

Assumptions made to make this method useful:

 Temp has been fairly constant
 Flies found the body to lay eggs soon after death

Insect succession used to date a body:

 As the body decomposers it undergoes changes which may make it more attractive
to other species.
 The flies etc which feed on the body also bring about changes in it that also make
attractive to other species.
 Decomposition follows a predictable sequence, so do the insect species found over
time.
Experiment-based questions
Quadrats and Sampling

(QWC – Spelling of technical terms (shown in italics) must be correct and the answer must be
organised in a logical sequence)

 ref to {several / many / more than 2} readings ;

 ref to use of random quadrat positions ;
 description of suitable process to give random positions / eq ;
 ref to {known / stated} area of quadrat ;
 number of individuals in each quadrat {counted/ recorded} / eq ;
 description of how mean density calculated using total count e.g. total number (of each species)
divided by total area sampled ;

Brine shrimp hatch rates

 equal / same number of brine shrimp eggs in water bath ;

 reference to different temperatures ;
 reference to {volume of water / salinity / [oxygen]} as controls ;
 record number of hatches every 5 hours / eq ;
 reference to equation (number of hatches in each water bath / number of hours) ;

Seedling growth rates

 ref to height measurement of seedlings in soil tray / eq ;

 ref to {incubation / eq} at different temperatures / specified temperatures ;
 ref to {water content / light intensity / other names variable} as controls ;
 ref to change in heights / eq ;
 ref to equation (average change in seedling height per tray / incubation period} ;

DNA profiling

 DNA mixed with nucleotides, primers, DNA polymerase ;

 ref to correct temperature / 95 degrees (not ‘high’) ;
 ref to cooling / accept temperatures from 50-65 ;
 (allows) primers to {bind / join / anneal / eq} to DNA ;
 ref to complementary sequence at start ;
 mixture heated to 72 degrees ;
 idea that free nucleotides lined up by DNA polymerase;
 along template strands to produce new strands of DNA ;
 idea of repeats ;
Another set of mark schemes

Test of antibiotics
 Prepare lawn of bacteria / bacteria culture (on agar) ;
 ref to {wells / eq} filled with antibiotic mixture OR filter paper discs ;
 ref to any aseptic technique e.g. flame sterilisation with Bunsen burners ;
 ref to incubation time and temp. e.g. 24 hours at 25 degrees ;
 idea of controls e.g. volume / area / time of incubation ;
 ref to {inhibition zone / clear zone / area / eq } showing effectiveness of antibiotic (bigger zone
means more effective) ;
 ref to experimental repeats ;
 General points:
 If the inhibition zones are not circular:
 -Take different points/radii from the centre and calculate the average OR
 -Trace area with graph sheets

Another
 1. idea of bacteria distributed evenly / description of technique e.g. lawn spreading ;
 2. description of method used to apply different antibiotics at known positions e.g. multidisks,
wells in agar ;
 3. reference to control of antibiotic concentration ;
 4. reference to {sterile / aseptic} technique ;
 5. reference to incubation at a suitable temperature ;
 6. description of how effect is assessed e.g. measure {clear area / inhibition zone / eq} ;
 7. reference to replication (with same bacterium) ;
 8. reference to repetition with different bacteria ;

Describe how gel electrophoresis can be used to separate DNA fragments of different length
 The DNA is cut into fragments using restriction endonucleases.
 The DNA fragments are placed into wells in agarose gel.
 An electric current is passed through. The negatively charged DNA fragments are attracted to
the positive electrode.
 Lighter fragments are able to move faster and travel further up the gel while heavier fragments
move more slowly.
 Southern Blotting allows the fragments to be seen. An alkaline buffer is added and a nylon filter
is placed over the gel. Dry absorbent paper is used to draw the solution containing DNA
fragments to filter, leaving them as blots on the paper

DNA Analysis for closely-related species

 reference to source of DNA sample, e.g. blood, saliva, semen ;

 reference to small samples of DNA can be amplified by PCR ;
 reference to use of (restriction / eq) enzymes to {break / eq} DNA ;
 reference to use of {electro potential / potential difference / eq} ;
 reference to {treatment / staining / eq} ;
 show up as {bands / bars / eq} ;
 reference to the {number of bands / eq} that match indicates similarity of the DNA ;
 GENERAL POINTS:
 DNA profiling assumes every individual’s DNA is {unique / different} / eq ;
 apart from identical twins / eq ;
 ref to DNA profiling analyses the {introns / non-coding blocks / STR / short tandem repeats / eq}
;
 non-coding DNA {very variable / hypervariable / eq} ;
 large number of {introns / non-coding blocks / eq} ;
 idea of many {combinations / eq} (at each locus) ;

Unreliability of DNA profiling

 ref to DNA profiling has several stages ;
 ref to {artefacts / contamination / eq} can arise at any stage ;
 only {a few sequences / small portion } of DNA analysed / eq ;
 ref to possibility of two identical profiles from unrelated individuals ; {identical twins / closely-
related individuals / eq} may show same profile / eq

Other points

Importance of Repeatability
 Calculate running mean/description of running mean;
 When enough quadrats, this shows little change/levels out (if plotted as a graph);
 Enough to carry out a statistical test;
 A large number to make sure results are reliable;
 Need to make sure work can be carried out in the time available;

Use of the scattergram

 Plot graph/scatter diagram of one set of results against the other;
 Expect to see points lying close to line / Line should slope upwards/show positive correlation;
 OR
 Plot measurement against number;
 Look for overlying / corresponding points;

Use of a statistical test

 (A statistical test) determines the probability of results being due to chance;
 Enables null hypothesis/description of null hypothesis to be accepted/rejected;
 Determines whether correlation/result is significant;

Why same endonuclease

 Cuts the DNA at the same base sequence / specific points;
 Gives repeats of the same piece of DNA ;