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Topic 5
Topic 5
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.
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) 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 {-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 ;
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
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
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;
Succession 3.3.13
{carbon dioxide and methane / both / they / eq} are greenhouse gases ;
{trap / absorb} {heat / infra-red / long wave radiation / eq} / eq ;
idea of reflected from Earths surface / re-radiation ; mean temperature of Earths 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
Hybrid inviability;
individuals produced from mating species are not healthy and do not survive
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
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 ;
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
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
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
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 dont get pollinated which will
reduced their numbers, and the insects dont 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 youngor insect life cycles speed up so that larvae or adults are
produced before the food plants
Seeds may not germinate if dont get the cold stimulus from a cold winter; over-wintering stages of
insect pests wont 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
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 ;
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 ;
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 ;
Proteomics
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)
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 ;
Gene mutation
Vaccines
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 ;
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
Antibiotic limited
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
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
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
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.
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
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
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
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
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)
DNA profiling
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
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;