ModuIe 1: CeIIuIar ControI and Variation

(a)state that genes code for poIypeptides, incIuding enzymes;

(b) expIain the meaning of the term genetic code;
Genetic code has a number of characteristics:
- A triplet code, sequence of 3 nucleotide bases codes for an amino acid. Number of
different triplet sequences is 4 or 64 Cnly 20 amlno aclds used for proLeln synLhesls so Lhls ls
more Lhan enough
- Degenerate code. All methionine have more than one code.
- Some codes don't correspond to an amino acid but indicate stop at the end of a
polypeptide chain- these are not amino acid codes
- Widespread but not universal. So same base sequence codes for same amino acid in
any organism. Useful for genetic engineering as we can transfer a gene from one
organism into another and it will usually still produce the same protein. However there
are some variations
Ryme to remember: tri-degen-wide not uni-stopcodes

(c) describe, with the aid of diagrams, the way in which a nucIeotide sequence codes for
the amino acid sequence in a poIypeptide;
When free nucleotides are activated they have two extra phosphoryl groups attached.
Transcription of a gene the creation of a single-stranded Mrna copy of the DNA coding strand.
-free activated RNA nucleotides pair up and bind temporarily, with hydrogen bonds, to their
complementary bases on the template stand of the unwound DNA. This is catalyzed by RNA
polymerase
- the 2 extra phosphoryl groups(phosphates) are released. This releases energy for bonding
adjacent nucleotides
Mrna produced is a copy of the coding strand of DNA and complimentary to the template strand.
(d) describe, with the aid of diagrams, how the sequence of nucIeotides within a gene is
used to construct a poIypeptide, incIuding the roIes of messenger RNA, transfer RNA
and ribosomes;
Translation is the assembley of the polypeptides (proteins) at ribosomes.
Genetic code copied from dna to mrna is now translated into a sequence of amino acids.
trna hairpin shapes, have 3 exposed bases at one end where a particular amino acid can bind
and at the other end of the molecule are 3unpaired nucleotide bases(anticodon) which binds
temporarily with its complimentary codon on the mrna.
1) Molecule of mrna binds to a ribosome, 2codons (six bases) are attached to the small
subunit of the ribosome and are exposed to the large subunit. The first exposed mrna
codon is always AUG. using ATP energy and an enzyme, a trna with methionine and the
anticodon UAC forms hydrogen bonds with this codon.
2) A second trna, bearing a different amino acid, binds to the second exposed codon with
its complementary anticodon.
3) A peptide bond forms between the 2 adjacent amino acids. An enzyme present in the
ribosomal subunit, catalyses the reaction.
4) Ribosome moves along mrna reading next codon. A 3rd trna brings another amino acid
and a peptide bond forms between it and the dipeptide. The 1
st
trna leaves and is able to
collect and bring another of its amino acids
5) The polypeptide chain grows until a stop codon is reached-there are no corresponding
trnas for these 3codons(stop codons).


Protein synthesis
stage 1- TRANSCRPTON (making of mRNA)
stage 2 TRANSLATON (making of proteins)

the sequence of amino acids in a protein is critical because:
- forms the primary structure of a protein
-the primary structure determines the tertiary structure how it folds etc
- the tertiary structure (shape) is what allows a protein to function
(e) state that mutations cause changes to the sequence of nucIeotides in DNA
moIecuIes;
-DNA mutations - is a change in the amount of, or arrangement of, the genetic material in a
cell
-chromosome mutations - involves changes to parts of or whole chromosomes
(f) expIain how mutations can have beneficiaI, neutraI or harmfuI effects on the way a
protein functions;
Certain substances (mutagens) cause mutations. nclude: tar, UV light, gamma rays.
Mistakes may happen when DNA is replicating before nuclear division, by either mitosis or
meiosis.
Mutations associated with mitosis are somatic mutations and are not passed onto offspring.
But may contribute to ageing process or may lead 2 cancer.
Mutations associated with meiosis and gamete formation can be inherited(passed onto
offspring)
There are 2 main classes of DNA mutations:
-point mutations/substitutions one base pair replaces another may not have that much of
an effect as the mutation code may still code for the same amino acid as the genetic code is
degenerate
-insertion/deIetion mutations one or more nucleotide pairs are inserted or deleted from a
length of dna, which causes a frameshift likely to have a greater effect on the protein
Neutral effects
May produce no change to the organism if:
-the mutation is in a non-coding region of the DNA
- it is a silent mutation-base triplet may have changed but still codes for the same amino acid so
protein in unchanged. (genetic code is degenerate)
-the mutation causes a change to the structure of the protein, and therefore a different
characteristic, but the changed characteristic gives no particular advantage or disadvantage to
the organism
Harmful & beneficial effects
Many genetic diseases as a result of DNA mutations: sickle cell aneamia and cystic fibrosis.
-most cases of cystic fibrosis, the mutation is the deletion of a triplet of base pairs
-Sickle-cell anaemia results from a point mutation on codon 6 of the gene for the b-polypeptide
chains of heamoglobin
-Growth promoting genes are called protooncogenes. Can be changed into oncogenes by a
point mutation that alters the ability of the protooncogene to be switched off so they remain
permanently switched on. Oncogenes promote unregulated cell division- leading to a tumour
-depending on the environment, the same mutation for paler skin can be beneficial or harmful.
Environment often changes and when it does, individuals within a population who have a certain
charecteristic may be better adapted to the new environment. The well-adapted organisms can
out-compete those in the population that do not have the advantageous charecteristics. 'natural
selection'-without genetic mutations there would be no evolution
- we each have some mutations we are all mutants


(g) state that cycIic AMP activates proteins by aItering their three-dimensionaI structure
so their shape is better fit to their compIimentary roIe;
(h) expIain genetic controI of protein production in a prokaryote using the ,c operon;
AM THCK!!
(i) expIain that the genes that controI deveIopment of body pIans are simiIar in pIants,
animaIs and fungi, with reference to homeobox sequences (HSW1);
Homebox genes: control the development of the body plan of an organism, including the polarity
(head and tails ends) and the positioning of the organs.
-some genes (maternal effect genes) determine the embryos polarity. Which end is
head(anterior) and which end is tail(posterior)
-other genes segmentation genes specify the polarity of each segment
-homeotic selector genes specify the identity of each segment and direct the development of
individual body segments. these are the master genes in the control networks of regulatory
genes.
Mutations of these genes can change one body part to another.
The homeobox genes each contain a sequence of 180 base pairs (known as homebox)-this
produces polypeptides of about 60 amino acids.
Some of these polypeptides are transcription factors and they bind to genes upstream(further
along the dna) and initiate transcription, so regulating the expression of other genes.
The homebox genes are arranged in clusters known as Hox clusters:
--drosophila has 2 hox clusters
--vertebrates have 4 clusters, of 9-11 genes located on separate chromosomes
The homebox genes are activated in the same order as they are expressed along the body of
the organism, from head to tail
They are expressed in specific patterns in certain stages during the development of the embryo,
in both vertebrates and invertebrates.
(j) outIine how apoptosis (programmed ceII death) can act as a mechanism to change
body pIans.
Cells should undergo approx 50 mitotic divisions then undergo a series of biochemical reactions
which leads 2 an orderly and tidy cell death.
Sequence of events:
-enzymes break down the cell cytoskeleton
-the cytoplasm becomes dense, with organelles tightly packed.
-the cell surface membrane changes and small bits called blebs form
-chromatin condenses and the nuclear envelope breaks. DNA breaks into fragments.
-the cell breaks into vesicles that are taken up by phagocytosis.

Whole process occurs very quickly
ntegral part of animal and tissue development-tightly regulated
During limp development, apoptosis causes the digits (fingers and toes) to separate from each
other
Billions of cells per day undergo apoptosis
Controlled by cell signaling
Not enough apoptosis leads to the formation of tumours
Too much leads to cell loss and degeneration
(a) describe, with the aid of diagrams and photographs, the behaviour of chromosomes
during meiosis, and the associated behaviour of the nucIear enveIope, ceII membrane
and centrioIes. (Names of the main stages are expected, but not the subdivisions of
prophase);
Meiosis is a reduction division. The resulting daughter cells have half the original number of
chromosomes. They are haploid and can be used for sexual reproduction.
nvolves 2 separate divisions meiosis and meiosis
Both involve PMAT stages
nterphase before meiosis where the DNA replicates-so each chromosome consists of
2identical sister chromatids, joined at the centromere. (long phase cell grows and carries out
its functions and replicates its DNA)
Meiosis HOMOLOGOUS PARS SEPERATE
!rophase I chromosomes come together in their homologous pairs (matching pairs) to form a
bivalent. Each member of the pair has the same genes at the same loci, each pair consists of
one maternal and one paternal chromosome
Non sister chromatids wrap around each other and attach at points called chiasmata
They may swap sections of chromatids with one another in a process called crossing over
(exchange alleles of non-sister chromatids)
Nucleolus disappears and the nuclear envelope disintegrates
A spindle forms. t is made of protein microtubules
Metaphase I bivalents line up across the equator of the spindle, attached to spindles fibres at
the centromeres, homologous pairs separate
The bivalents are arranged randomly (random assortment) with each member of a homologous
pair facing opposite poles
Anaphase I homologous chromosomes in each bivalent are pulled by the spindle fibres to the
opposite poles with their new crossing over 'chiasmata'
Telophase I 2new nuclear envelopes form

Meiosis SSTER CHROMATDS SEPERATE
!rophase II new spindle fibres form at right angles to previous spindle axis
f nuclear envelope has reformed, it breaks down again
Metaphase II chromosomes arrange themselves on the equator of the spindle. The
chromatids of each chromosome are randomly assorted
Anaphase II centromeres divide and the chromatids are pulled to opposite poles
Telophase II nuclear envelopes reform around the haploid daughter nuclei, in animals the
2cells now divide to give 4haploid cells.

(b) expIain the terms
ee a version of a gene, a gene is a length of DNA that codes for one or more polypeptides.
An allele of the gene has a difference in the DNA base sequence that is expressed as
(translates into) a slightly different polypeptide
Locus is the position of a gene on a chromosome
Phenotype observable charecterisitcs of an organism
Genotype alleles present within cells of an individual for a particular trait/characteristic, the
genetic makeup of an organism
Domin,nt characteristic in which the allelle responsible is expressed in the phenotype even in
those with heterozygous genotypes. (2different alleles for a specific gene)
Codomin,nt A charecteristic where both alleles of the same gene contribute to the phenotype
of a heterozygote
Recessive; characteristic in which the allele responsible is only expressed in the phenotype if
there is no dominant allelle present or another identical allele for the same gene
Link,ge genes for different charecteristics(atleast 2 genes or more) that are present at different
loci on the same chromosome are linked. Normally inherited together because they do not
segregate independently at meiosis unless chiasmata have formed between them. Linkage
reduces the number of phenotypes resulting from a cross
Crossing-over is when lengths of DNA are swapped from one chromatid to another. Non-sister
chromatids wrap around each other very tightly at chiasmata. Produces new combinations of
alleles on the chromatids which will eventually become chromosomes in the daughter cells.
omozygous - an organism with 2 identical alleles for a particular gene e.g. CrCr
eterozygous - an organism with 2 different alleles of the same gene e.g CrCw
Dihybrid cross - 2genes/charecteristics cross

Examiner tip: there are no genes coding for genetic diseases. Genes code for proteins that are
part of the organisms structure or for an enzyme to regulate a metabolic pathway. Genetic
diseases may be the result of altered alleles that produce altered proteins.

(d) expIain how meiosis and fertiIisation can Iead to variation through the independent
assortment of aIIeIes;
- Crossing over during prophase , to shuffle alleles
- Genetic reassortment due to the random distribution and subsequent segregation of the
maternal and paternal in the homologous pairs during meiosis
Each gamete gets a different mixture of maternal and paternal chromosomes
- Genetic reassortment due to the random distribution segregation of the sister chromatids at
meiosis
-random mutation - dna mutations during interphase, chromosome mutations too. f mutation
occurs in sperm or egg that are used in fertilization then the mutated gene will be present in
every cell of the offspring.
-fertiIisation randomly combines 2 sets of chromosomes, one from each of 2 genetically
unrelated individuals. Millions of sperms, all genetically different, any one can fertilise the egg.
(e) use genetic diagrams to soIve probIems invoIving sex Iinkage and codominance;
Charecterisic is Sex linked is the gene that codes for it is found on one of the sex chromosomes
(X and Y).
The gene is always represented by a single letter, with upper case for the dominant allele and
lower case for the recessive allele
where there is codominance (both alleles contribute to the phenotype) the gene is represented
by an upper case letter and alleles in superscript
always provide a key with ur genetic diagrams and indicate which symbol relates to which allelle
n humans, males are heterogametic (XY) and females are homogametic (XX)
(f) describe the interactions between Ioci (epistasis). (Production of genetic diagrams is
not required);
Epistasis is the interaction of different gene loci so that one gene locus masks or suppresses
the expression of another gene locus
Not inherited it is an interaction between 2 gene loci
The genes involved may control the expression of one phenotypic characteristic in one of the
following ways:
Work against each other(antagonistically) resulting in masking
The homozygous presence of a recessive allele may prevent the expression of another allele at
a second locus the alleles at the 1
st
locus are epistatic and alleles at the 2
nd
locus are
hypostatic.
Recessive epistasis e.g. homozygous aa
Dominant epistasis occurs when a dominant allele at one gene locus masks the expression of
the alleles at a second gene locus . e.g. presence of aIIeIe D
May work together in a complimentary fashion. work together to form
something new (e.g. a new characteristic)


(g) predict phenotypic ratios in probIems invoIving epistasis;
All epistatic ratios are variations on the normal 9:3:3:1 ratio from a dihybrid inheritance of 2
unlinked genes. Remember:
O A :3:4 ratio suggests recessive epistasis
O A 12:3:1 ratio or a 13:3 ratio suggests dominant epistasis
O A :7 ratio suggests epistasis by compIimentary action
(h) use the chi-squared (
2
) test to test the significance of the difference between
observed and expected resuIts. (The formuIa for the chi-squared test wiII be provided);
Test to find out if the difference between observed categorical data (data in categories) and
expected data is small enough to be due to chance. Raw counts must be used, not percentages
nor ratios.
Tests null hypothesis. Assumption- there is no statistically significant difference between the
observed and expected numbers
-The bigger the value of X the more certain we are that there is a significant difference between
observed and expected values
-The smaller the value, the more certain we are that the difference between observed and
expected is due to chance
(i) describe the differences between continuous and discontinuous variation;
Discontinous variation Continuous variation
"ualitative differences between phenotypes "uantitative difference between phenotypes
Clearly distinguishable categories Wide range of variation within the population
No intermediate values No distinct categories
e.g Either male/female e.g. Height/ body mass of humans
Act in an epistatic way Polygenic
Monogenic

(j) expIain the basis of continuous and discontinuous variation by reference to the
number of genes which infIuence the variation;
Both types of variation may be the result of more than one gene.
-->However, in discontinuous variation, if there is more than one gene involved, the genes
interact in an epistatic way where one gene masks or influences the expression of another
gene.
Monogenic- discontinuous variation where there may only be one gene involved-Characteristic
coded for by one gene
Different alleles at a single gene locus have large effects on the phenotype
Different gene loci have different effects on the phenotype e.g. codominance, dominance and
recessive patterns
n continuous variation traits controlled by 2 or more genes, each provides an additive
component to the phenotype.
Different alleles of each gene have a small effect on the phenotype
!olygenic- large number of genes combined determine the phenotype. These genes are
unlinked on different chromosomes.
(k) expIain that both genotype and environment contribute to phenotypic variation. (No
caIcuIations of heritabiIity wiII be expected);
Environmental factors may limit the expression of a gene e.g. shortage of water, light, minerals
The expression of polygenic traits is influenced more by the environment than the expression of
monogenic traits
(I) expIain why variation is essentiaI in seIection;
When the eniroment changes, those individuals well adapted survive, reproduce, passing on
their advantageous alleles to their offsprings. Many of the traits
(m) use the Hardy-Weinberg principIe to caIcuIate aIIeIe frequencies in popuIations
(popuIation genetics)(HSW1);
We observe the phenotype (and not the genotype) of individuals. To measure the frequency of
an allele, we need to know:
1) The mechanism of inheritance. e.g codominance, recessive, dominant
2)how many different alleles of the gene for that trait are in the population













(n) expIain, with exampIes, how environmentaI factors can act as stabiIizing or
evoIutionary forces of naturaI seIection;
Evolution the process of gradual change in the inherited traits passed from one generation to
the next within a population. t results in formation of new species.
Stabilizing selection a type of natural selection in which the allele & genotype frequency within
population stays the same because the organisms are already well adapted to the environment.

Space (for plants to grow, or for animals to defend a feeding territory and to rear young),
availability of food, light, minerals, water, predation and infection by pathogens. These factors
offer environmental resistance.
f environmental resistance is great enough, the population size will shrink. This reduces
competition and the population will grow. As it increases, there will be more intraspecific
competition for resources such as food, shelter and mates so the population size falls again
$election pressure environmental factor that confers greater chances of survival to
reproductive age on some members of the population- natural selection to keep things the way
they are stabilizing selection.
f the environment changes, the selection pressure also changes.
DirectionaI seIection leads to evolutionary change, it is an evoIutionary force of natural
selection

Examiner tip: when answering "'s about selection, always refer to increasing chances of
favourable alleles (not genes) being passed onto offspring's

(o) expIain how genetic drift can cause Iarge changes in smaII popuIations;
Genetic drift: the change in allele frequency in a population, as some alleles pass onto the next
generation and some disappear. This causes some phenotypic traits to become rarer or more
common.
Reduces genetic variation
May lead to the production of a new species
May reduce the ability of a population to survive in a new environment
As the size of population decreases, the degree of fluctuation will increase (genetic drift)

p represents the frequency of the dominant allele
q represents the frequency of the recessive allele
q is the frequency of the genotype (male)
p is the frequency of the genotype (female)
2pq is the frequency of the genotype assuming random mating within the population, where any 2
individuals of (pq) mate with each other.
p + 2pq + q
Within the population, the frequency of alleles, p+q=1/100%
Within the population, the frequency of genotypes, p + 2pq + q=1/100%
Remember: 2 aIIeIes for each gene so doubIe for each person when finding aIIeIe frequency

(p) expIain the roIe of isoIating mechanisms in the evoIution of new species, with
reference to ecoIogicaI (geographic), seasonaI (temporaI) and reproductive (GSR)
mechanisms;
Mechanisms that divide populations of organisms into subgroups
Geographical barriers: rivers, mountain range
Seasonal barriers: climate change throughout a year
Reproductive mechanisms: members may not be able to physically mate, genitals may be
incompatible
(q) expIain the significance of the various concepts of the species, with reference to the
-bioIogicaI species concept
Is a group of similar organisms that can interbreed and produce fertile offspring and is
reproductively isolated from other such groups
Problematic when biologists want to classify living organisms that do not reproduce sexually
also some members of the same species may look very different from each other. Some
species males look different from the females. Some isolated populations, may appear very
different from each other.
-phyIogenetic (cIadistic/evoIutionary) species concept (HSW1);
is a group of organisms that have a similar morphology(shape), physiology (biochemistry),
embryology (stages of development) and behavior, and occupy the same ecological niche.
Any group of organisms with similar haplotypes is called a cIade. Assumes that classification of
living of living organisms corresponds to their phylogenetic descent (evolutionary ancestry)
Focuses on evolution (phylogenetic relationships) between species
Uses Rna and Dna sequencing
Places great importance on using objective and quantitative (molecular) analysis
(r) compare and contrast naturaI seIection and artificiaI seIection;
NaturaI seIection ArtificiaI seIection
Mechanism for evolution Humans select the organisms with useful
characteristics
Best adapted to environments likely to survive
and reproduce
Humans allow those with useful characteristics
to breed and prevent the ones without the
characteristics from breeding
Nature/environment is doing the selecting Humans have a significant effect upon the
evolution of these populations or species
The genetic processes are the same. E.g. meiosis, DNA replication

(s) describe how artificiaI seIection has been used to produce the modern dairy cow and
to produce bread wheat (%riticum ,estivum) (HSW6a, 6b).
Modern dairy cow
Humans selected animals for docility, meat, milk production, and to survive in the environment
with high milk yields
Repeatedly selecting cows with high milk yields and allowing them to breed over many
generations.
- Each cow's milk yield is measured and recorded
- The progeny of bulls is tested to find which bulls have produced daughters with high milk
yields
- Only a few good-quality bulls need to be kept as the semen from one bull can be
collected and used to artificially inseminate many cows
- Some elite cows are given hormones so they produce many eggs
- The eggs are fertilized in vitro (in glass) and the embryos are implanted into surrogate
mothers
- These embryos could also be a cloned and divided into many more identical embryos
- This way few elite cows can produce more offspring than they would naturally
Bread wheat
Resistance to fungal infections, high protein content, straw (stem) stiffness, increased yield
ncludes the wild and domestic species of the wheat
- Domestification and artificial selection of wild species, which altered the phenotype but
not the chromosome number.
- Sterile Hybrid with wild grass
- Mutation that doubled the chromosome number to form emmer wheat
- Emmer wheat sterile hybrid with goat grass
- Mutation that doubled the chromosome number
- Common wheat form a hexaploid (2or more sets of chromosomes in a cell or organism
6)
- Spring wheat is grown where winters are colder (Europe), the grains are harder and
have a higher protein content, making them suitable for bread

ModuIe 2: BiotechnoIogy and Gene TechnoIogies
(a) outIine the differences between reproductive and non-reproductive cIoning;
Reproductive cIoning Non- reproductive



(b) describe the production of naturaI cIones in pIants using the exampIe of vegetative
propagation in eIm trees;
O heaIthy eIm has minimaI root suckers
O EIm shows signs of stress, more suckers are produced
O Suckers grow in a circIe around big eIm- CIonaI patch
O The patch wiII extend as far as recourses permit
O AsexuaI reproduction wiII mean eventuaIIy the offspring wiII get the disease

(c) describe the production of artificiaI cIones of pIants from tissue cuIture;
O A smaII expIant is taken from meristem tissue
O This is pIaced in nutrient medium which stimuIates mitosis
O A batch of undifferentiated ceIIs caIIed a caIIus is formed
O The caIIus is put onto a medium that produces roots, and shoot
O They are transferred onto steriIe soiI and accIimatized

(d) discuss the advantages and disadvantages of pIant cIoning in agricuIture (HSW6a,
6b, 7c);
Advantages D|sadvantages
O ,any vers|ons can be made from one
p|ant
O a||uses can be genet|ca||y eng|neered
O an be produced a|| year round and
transported a|| over
O A|| coned p|ants w||| be suscept|b|e to
same d|sease
O Iery |abour |ntens|ve




(e) describe how artificiaI cIones of animaIs can be produced;
SpIitting embryo NucIear transfer
O get egg and sperm from high vaIue
parents
O artificiaI insemination- grow zygote
to 16 weeks
O spIit into 4 segments, ceIIs are gen.
identicaI
O each ceII segment pIaced into
surrogate mothers
O Remove ceIIs and cuIture
O Remove ovum (different sheep) and
remove nucIeus
O use cuItured ceII and nucIeus
O PIace in oviduct in sheep
O Recover earIy embryo and pIace in
surrogate mother


(f) Discuss the advantages and disadvantages of cIoning animaIs (HSW4, 6a, 6b, 7c).
Advantages Disadvantages
O High vaIue animaIs can be found
in high numbers
O Can be geneticaIIy engineered
O Rare animaIs can be preserved
O AnimaI weIfare
O &nIikeIy to adapt to
environmentaI changes
O &ncIear if nucIear transfer
animaIs wiII remain heaIthy.


(a) state that biotechnoIogy is the industriaI use of Iiving organisms (or parts of Iiving
organisms) to produce food, drugs or other products (HSW6a);

BiotechnoIogy is the industriaI use of Iiving organisms (or parts of Iiving organisms) to
produce things that benefit humans

(b) expIain why microorganisms are often used in biotechnoIogicaI processes;

O Grow quickIy and easiIy
O Production of chemicaIs that can be harvested
O Can be geneticaIIy modified for specificity
O Can be grown on recycIed materiaIs
(c) describe, with the aid of diagrams, and expIain the standard growth curve of a
microorganism in a cIosed cuIture;


























(d) Describe how enzymes can be immobiIized;

Adsorbtion
O Mixed with support and bind via H-bonding, hydrophobic interactions, enzymes
can be Ieaked off due to weak bonding, can give high reaction rates

CovaIent bonding
O Enzymes are bonded onto an insoIubIe materiaI, not many enzymes can be
bonded this way- Iess Ieakage

Entrapment
O Enzymes trapped in their naturaI state, reaction rates are sIow. CovaIent and
adsorbtion are better methods.

Membrane separation
O Enzymes are physicaIIy separated by a partiaIIy permeabIe membrane, substrate
moIecuIes pass through the membrane

(f) ExpIain why immobiIized enzymes are used in Iarge-scaIe production;
This done to make peniciIIinic acid.






























(g) compare and contrast the processes of continuous cuIture and batch cuIture;


Batch cuIture Continuous cuIture
O f one mixture is contaminated onIy
one batch is disposed of
O Not very efficient
O Easy to set up and maintain
O f mixture is contaminated the whoIe
produce is Iost
O DifficuIt to set up an maintain
O Very efficient

(h) describe the differences between primary and secondary metaboIites;

Primary metaboIites
O foIIow the growth curve of the cuIture, substances produced that is apart of an
organisms naturaI growth, e.g. enzymes

secondary metaboIites
O Substances produced that are not a part of the normaI growth- begins after the
main growth period. OnIy a few organisms produce this.


(i) expIain the importance of manipuIating the growing conditions in a fermentation
vesseI in order to maximize the yieId of product required;
O An optimum temperature- k.e
O The correct type of nutrient added at the correct time- so primary and secondary
metaboIites can be made
O Sufficient oxygen- aerobic conditions
O Optimum PH- enzymes rate of reaction, active site

(i) expIain the importance of asepsis in the manipuIation of microorganisms.
Asepsis is important because growth of any unwanted microorganisms may;
O Compete for nutrients and reduce yieId of product,
O Produce primary or secondary metaboIites that are toxic to the cuIture,
O Produce toxic chemicaIs and
O SpoiI the product

(a) outIine the steps invoIved in sequencing the genome of an organism;

O Genomes are mapped
O SampIes are broken into smaIIer sections
O SampIes pIaced into BAC
O Specific BAC's are cuItured
O Restriction enzymes cut them up into fragments
O EIectrophoresis separates fragments
O Then genome is sequenced by computers

(b) outIine how gene sequencing aIIows for genome-wide comparisons between
individuaIs and between species (HSW7b);

O ModeIing changes can be carried out
O Comparing simiIar pathogenic and non pathogenic genomes shows the sections
which pose risk
O DNA of individuaIs can be anaIyzed

(c) define the term recombin,nt DN;
O DNA from two different organisms that has been joined together.

(d) expIain that genetic engineering invoIves the extraction of genes from one organism,
or the manufacture of genes, in order to pIace them in another organism (often of a
different species) such that the receiving organism expresses the gene product
(HSW6a);
O Genetic engineering invoIves the extraction of genes from mRNA, his gene is the
pIaced into a vector and the vector pIaced in a host ceII. The gene can be modified
before inserted into the vector. The host ceII synthesizes the gene.
O Gene put in by;
O ViraI transfer
O EIectrophoration
O Microinjection



(e) describe how sections of DNA containing a desired gene can be extracted from a
donor organism using restriction enzymes;
O Restriction enzymes cut the gene at a specific gene sequence and the cut end
(done by hydroIysis of bonds) is known as a sticky end, which has a unique shape
depending on the restriction enzyme used.

(f) outIine how DNA fragments can be separated by size using eIectrophoresis (HSW3);
O DNA treated with restriction enzymes
O SampIes pIaced into weIIs at the anode side of the geI pIate
O Current passed through DNA traveIs to Cathode side
O arge fragments take Ionger to pass through smaIIer are faster

(g) describe how DNA probes can be used to identify fragments containing specific
sequences;
O DNA probes are compIimentary to the DNA being anaIyzed, as it is singIe
stranded the DNA anneaIs to it making that section visibIe.
O Radioactive marker probe or &V marker probe
O Probes are usefuI because;
O Can identify the same gen in ANY species
O ocation of a specific gene
O Can identify the presence of absence of an aIIeIe for genetic disease

(h) outIine how the poIymerase chain reaction (PCR) can be used to make muItipIe
copies of DNA fragments;
O DNA sampIes mixed with DNA nucIeotides & DNA poIymerase
O Heated to C- breaks H bonds
O Primers added, and mixture cooIed to C to aIIow anneaIing, primers bind to DNA
O Heat to 72C-optimum temp 4 DNA poIymerase
O DNA poIymerase reaches other end of strand then new strand forms.
O Repeat cycIe-exponentiaI increase

(j) expIain how isoIated DNA fragments can be pIaced in pIasmids, with reference to the
roIe of Iigase;
O &sefuI gene cut using restriction enzymes
O PIasmid is cut with same restriction enzymes forming compIimentary sticky ends
O PIasmid mixed with gene and Iigase enzyme, forming a recombinant pIasmid
O igase cIoses up the pIasmid

(k) state other vectors into which fragments of DNA may be incorporated;
O Virus genomes
O Yeast ceII chromosomes
O iposomes

(I) expIain how pIasmids may be taken up by bacteriaI ceIIs in order to produce a
transgenic microorganism that can express a desired gene product;
O Adding nutrience, caIcium saIts and suitabIe bacteria, treating with heat shock
(temp Iowered to freezing then increased to 40C, this is an inefficient process)
O Some bacteria take up the pIasmid can now be described as transformed and
transgenic

(m) describe the advantage to microorganisms of the capacity to take up pIasmid DNA
from the environment;
O This speeds up antibiotic resistance between popuIations
O Contribute to genetic variation
O Genes expressed ensure naturaI seIection passes on gene to Iater generations.

(n) outIine how genetic markers in pIasmids can be used to identify the bacteria that
have taken up a recombinant pIasmid;
O . Coi have two genetic markers amp
R
and tet
R

O Recombinant pIasmid cuts into tet
R
and deactivates it antibiotic capabiIities
O The other one however does work
O PIacing bacteria in amp
R
KiIIs those which have taken up no pIasmid
O PIacing bacteria in tet
R
wiII kiII those which have the recombinant pIasmid
O CoIonies con now be identified and grown on Iarge scaIe

(o) outIine the process invoIved in the genetic engineering of bacteria to produce human
insuIin;
O Extract mRNA
O &se reverse transcriptase to obtain compIimentary DNA
O Add DNA poIymerase and free nucIeotides to the DNA
O orms the tempIate strand
O cDNA gene
O unpaired nucIeotides are added to the cDNA to form compIimentary sticky ends
O pIasmids cut open with restriction enzymes are mixed with cDNA and Iigase
enzyme
O Bacteria mixed with pIasmids and cuItured.


(p) outIine the process invoIved in the genetic engineering of 'GoIden Rice
TM
' (HSW6a);
O insertion of two genes into endosperm
O These are inserted into promoter sequence that switches on genes for
endosperm deveIopment.
O So they are now expressed as the endosperm grows.




























(q) outIine how animaIs can be geneticaIIy engineered for xenotranspIantation (HSW6a,
6b);
O Pigs have been engineered to Iack enzyme o-1'3-transferase, which causes
rejection of organs in humans
O Human enzyme nuIeotidase grafted into pig ceII cuIture. t reduces the number of
immune ceIIs that resuIt in xenotranspIantation rejection

(r) expIain the term gene ther,py;
O The techniques of moIecuIar gene technoIogy that can be used to treat some
genetic disorder












(s) expIain the differences between somatic ceII gene therapy and germ Iine ceII gene
therapy;

























(t) discuss the ethicaI concerns raised by the genetic manipuIation of animaIs (incIuding
humans), pIants and microorganisms (HSW4, 6a, 6b, 7c).
O ReIigious beIiefs
O ears of unforeseen effects
O Growing GM pIants compete with naturaI one and damage the environment
O Wrong to taper with naturaI genotype



















ModuIe 3: Ecosystems and SustainabiIity

(a) define the term ecosystem;
all the living organisms and all the non-living components in a specific habitat and their
interactions. Components of an ecosystem: habitat, population, community
(b) state that ecosystems are dynamic systems; change all the time, population sizes rise
and fall, either very slightly or very noticeably
(c) define the terms
biotic f,ctor;
the living organisms in an ecosystem can affect each other food supply, predation, disease
,biotic f,ctor;
the effects of the non-living components of an ecosystem !h, temperature, soil
(d) define the terms
Producer;
Autotrophic organisms (plants, protoctists & some bacteria) that convert light energy to chemical
energy, which they then supply to consumers
Consumer;
Living organisms that feed on other living organisms
Primary consumers are herbivores who feed on plants
Primary consumers eaten by carnivorous secondary consumers
Secondary consumers eaten by carnivorous tertiary consumers
Decomposer;
Organisms (bacteria, fungi and some animals) that feed on dead organic matter, releasing
molecules, minerals and energy that then become available to other living organisms in that
ecosystem.
%rophic eve;
The level at which an organism feeds in a food chain

(e) describe how energy is transferred though ecosystems;
Within an ecosystem, living organisms are usually members of more than one food chain, and
often feed at different trophic levels in different chains. Drawing these food chains together as a
food web helps to understand how energy flows through the whole ecosystem. Energy is not
recycled- it flows through the ecosystem.















9roducer
9rlmary consumer
Secondary consumer
1erLlary consumer
Arrows show
dlrecLlon of energy
Lransfer
(i) outIine how energy transfers between trophic IeveIs can be measured;
Draw a !yramid of biomass
-The area of the bars is proportional to the dry mass of all the organisms at that trophic level.
An ecologist would collect all the organisms and put them in an oven at 80c until all the water
has been evaporated so energy released
Or measure wet mass of the organisms and calculate the dry mass on the basis of previously
published data
onstruct a !yramid of energy
nvolves burning the organisms in a calorimeter and working out how much heat energy is
released per gram this is calculated from the temperature rise of a known mass of water
!roductivity
The rate at which energy passes through each trophic level in a food chain (MJ megajoule is
1million/10(
-drawing a pyramid of energy flow
Productivity gives an idea of how much energy is available to the organisms at a particular
trophic level, per unit area in a given amount of time (usually 1year)
At the base of the food chain, the productivity of plants is called the primary productivity -
energy captured by leaves for photosynthesis
The gross primary productivity is the rate at which plants convert light energy into chemical
energy. But energy is lost when plant respires, so less available to the primary consumer. The
remaining energy is called the net primary productivity.


(j) discuss the efficiency of energy transfers between trophic IeveIs;
at each trophic level, some energy is lost from a food chain, and is therefore unavailable to the
organism at the next trophic level.
- At each trophic level organisms need to carry out life processes. Respiration releases
energy from organic molecules like glucose. Some of this is eventually converted to heat
- Energy remains stored in dead organisms and waste material, which is then only
available to decomposers. This waste material includes parts of animals and plants that
cannot be digested by consumers
- Less energy received to living tissue at higher levels of the food chain ecologists draw
a pyramid of numbers to represent this idea
(k) expIain how human activities can manipuIate the fIow of energy through ecosystems
(HSW6b);
NPP is the rate of production of new biomass (carbohydrates) available for consumption by
heterotrophs in the ecosystem.
Humans can increase NPP- making energy conversion more efficient, reducing energy loss and
increasing crop yields.
mproving primary productivity
- Light energy can limit rate of photosynthesis. Some crops planted early to provide a
longer growing season 2 harvest more light. Others are grown under light banks
- Lack of water is important. As well as irrigating crops, drought-resistant strains have
been used.
- Temperature can limit the speed can limit the speed of chemical reactions in a plant.
Greenhouses can provide a warmer temperature for growing plants
- Lack of available nutrients, crop rotation, many field crops have been bred to be
responsive to high levels of fertilizer
- Pests, remove biomass and stored energy from the food chain. Pesticides and some
plants have been bred to be pest-resistant (same with fungi)
mproving secondary productivity
Primary consumers don't make full use of plants biomass some plants die, consumers don't
eat every part of the plant, and they don't digest everything they eat, egesting a lot of it in their
faeces. Even when food is digested and absorbed, much of the stored energy is used to keep
the animal alive, with only a small amount being stored when it grows. t is this small amount
that is available to the next consumer in the food chain- usually humans.
- A young animal invests a larger proportion of its energy into growth than an adult does.
- Selective breeding has been used to produce breeds with faster growth rates, increased
egg production and increased milk production
- Animals may be treated with antibiotics to avoid unnecessary loss of energy to
pathogens and parasites
(I) describe one exampIe of primary succession resuIting in a cIimax community;
Succession is a directional change in a community of organisms over time
Development of such a community from bare ground is known as primary succession, and
comes about as follows:
- algae and lichens begin to live on the bare rock. This is called a pioneer community
- erosion of the rock, and a build-up of dead and rotting organisms, produces enough soil
for larger plants like mosses and ferns to grow. These replace or succeed the algae and
lichens
- larger plants succeed these small plants, until a final, stable community is reached. This
is called a cIimax community.
All about building an increasingly stable environment, previous plants succeed others-bring
more nutrients and stabilizes community
(m) describe how the distribution and abundance of organisms can be measured, using
Iine transects, beIt transects, quadrats and point quadrats (HSW3);
"uadrat is a square frame used for studying ecosystems
Percentage cover, ACFOR scale
You can record simply presence or absence of each species (distribution), or you can estimate
or count the number of individuals (abundance) of each species.
Transect; a line taken across a habitat, take samples at regular intervals along the tape
ine transect at regular intervals, make a note of which species is touching the tape
Belt transect- at regular intervals, place a quadrat next to the line (interrupted belt transect) or
(continuous belt transect) place a quadrat next to the line, moving it along the line after looking
at each quadrat.
(n) describe the roIe of decomposers in the decomposition of organic materiaI;
dead and waste organic material can be broken down by decomposers these are
microorganisms such as bacteria and fungi.
Bacteria and fungi are saprotrophs;
- saprotrophs secrete enzymes onto dead and waste material
- These enzymes digest the material into small molecules, which are then absorbed into the
organism's body
- the molecules are stored or respired to release energy
f bacteria and fungi did not break down dead organisms, energy and valuable nutrients would
remain trapped within the dead organisms. By digesting dead and waste material, microbes get
a supply of energy to stay alive, and the trapped nutrients are recycled. Microorganisms have a
particularly important role to play in the cycling of carbon and nitrogen within ecosystems.
(I) describe how microorganisms recycIe nitrogen within ecosystems. (OnIy
Nitrosomon,s Nitrob,cter and Rhizobium need to be identified by name).
Nitrogen fixation
-conversion of nitrogen gas into a form which is usable by plants, such as nitrate or ammonium
ions
-Plants need a 'fixed' supply of nitrogen such as ammonium ions (NH+) or nitrate ions (NO).
Nitrogen fixation can occur when lightning strikes or through the Haber process. But these
processes only account for small amount of nitrogen fixation around world.
- Nitrogen fixing bacteria account for the rest. Many live freely in soil and fix nitrogen gas, which
is in the air within the soil, using it 2 manufacture amino acids
- Nitrogen fixing bacteria such as Rhizobium also live inside the root nodules of plants.
They have a mutuaIistic relationship with the plant, the bacteria provide the plant with
fixed nitrogen and receive carbon compounds e.g glucose in return
Proteins in the nodules absorb oxygen and keep the conditions anaerobic. Under these
conditions the bacteria use an enzyme, nitrogen reductase to reduce nitrogen gas to
ammonium that can be used by host plants
Nitrification
Happens when chemoautotrophic bacteria in the soil absorb ammonium ions (NH+%
cbemoootottopbs organlsm LhaL makes lLs own food uslng slmple lnorganlc molecules such as CC and
PC 1hey use chemlcal energy
-ammonium ions released by bacteria involved in decomposition
-chemoautotropic bacteria gain their energy by oxidizing ammonium ions to nitrites
Nitrosomon,s b,cteri,
-chemoautotropic bacteria gain their energy by oxidizing nitrites to nitrates Nitrob,cter b,cteri,
-nitrates can be absorbed from the soil by plants and used to make nucleotide bases & amino
acids.
Denitrification
Other bacteria convert's nitrates back to nitrogen gas.
When the bacteria involved are growing under anaerobic conditions, they use nitrates as a
source of oxygen for photosynthesis and produce nitrogen gas and nitrous oxide (NO)

(a) expIain the significance of Iimiting factors in determining the finaI size of a
popuIation;
the habitat cannot support a larger population because of factors that limit the growth in
population size Iimiting factors.
-often the factor in shortest supply
E.g. food, water, oxygen, shelter, nesting sites, competition for resources
The carrying capacity is the upper limit that these factors place on the population size

(b) expIain the meaning of the term c,rrying c,p,city; (Iook in book page 204 at diagram
on Ieft)
The maximum population size that can be maintained over a period of time in particular habitat
-at stationary phase, the population levels out at the carrying capacity of the habitat -rates of
reproduction and mortality are equal -population size remains stable, slight fluctuations due to
environmental conditions
(c) describe predator-prey reIationships and their possibIe effects on the popuIation
sizes of both the predator and the prey;
Predation can act as a limiting factor on a preys population size, which in turn can affect the
predators population
1) when the predator population gets bigger, more prey are eaten
2) the prey population then gets smaller, leaving less food for the predators
3) with less food, fewer predators can survive and their population size reduces
4) with fewer predators, fewer preys are eaten, and their population size increases
5) with more prey, the predator population gets bigger and the cycle starts again
n the wild, predators often eat more than one type of prey, and there are a number of other
limiting factors

(d) expIain, with exampIes, the terms interspecific and intr,specific competition;

-@ASL -@LSL
eLween lndlvlduals of Lhe same specles eLween lndlvlduals of dlfferenL specles
lacLors such as food supplles become llmlLed
lndlvlduals have Lo compeLe for Lhem
AffecL boLh Lhe populaLlon slze of a specles and
dlsLrlbuLlon of specles ln an ecosysLem
SllghL flucLuaLlons ln populaLlon slze durlng
sLaLlonary phase however keeps populaLlon
relaLlvely sLable
Cne may be ouLcompeLed by Lhe oLher and would
dle or become exLlncL ln Lhe hablLaL


(e) distinguish between the terms conserv,tion and preserv,tion (HSW6a, 6b);
conservation maintenance of biodiversity, involves management and reclamation
preservation usually involves protecting areas of land, as yet unused by humans, in their
'untouched' form

(f) expIain how the management of an ecosystem can provide resources in a sustainabIe
way, with reference to timber production in a temperate country;
problem- increase in human population, larger demand and exploitation,
conflict between need for resources and conservation in wood and timber production
sustainable management-means biodiversity is maintained & that wood and timber companies
can have a financially secure and sustainable supply of wood.
Coppicing involves cutting a tree trunk close to the ground to encourage new growth-
several new shoots grow from cut surface rotational coppicing- divide wood into
sections and cut one section each year
PoIIarding just cutting trunk higher up, useful when population size of deer is high, as
they like to eat the emerging shoots from a coppiced stem. Cannot reach if higher up
Any tree which is harvested is replaced by another tree
Even with extraction of timber, the forest as a whole must maintain its ecological function
regarding biodiversity, climate and mineral water cycles
Selective cutting only removing the largest most valuable trees so habitat broadly
affected only.
f each tree supplies more wood, fewer trees will need to be harvested

(g) expIain that conservation is a dynamic process invoIving management and
recIamation;
-Successful conservation requires consideration of the social and economic costs to the local
community.
-Can also involve giving legal protection to endangered species, or conserving them ex-situ in
zoos or botanic gardens
-Maintaining biodiversity in dynamic ecosystems requires careful management to maintain a
stable community, or even to reclaim an ecosystem by reversing the effects of human activity
Often easier to replace a disrupted community with a slightly different community, rather than to
rehabilitate the original community






(h) discuss the economic, sociaI and ethicaI reasons for conservation of bioIogicaI
resources (HSW6b, 7c);
Economic SociaI EthicaI
Direct economic value when
harvested valuable food
source
Aesthetic value Every species has value in its
own right
ndirect economic value e.g.
communities maintain water
quality, protect soil and break
down waste products
Natural medicines and drugs
were discovered in wild
plant species
Every living thing has a right
to survive
Ecotourism and recreation recreation
Reduction in biodiversity may
reduce climatic stability-
resulting in flooding &
associated economic costs

(i) outIine, with exampIes, the effects of human activities on the animaI and pIant
popuIations in the GaIapagos sIands (HSW6b).
The islands isolation and small population sizes provide optimal conditions for rapid evolutionary
change
Habitat disturbance Over expIoitation of
resources
ntroduced species
ncreased pollution, building,
and conversion of land for
agriculture
Harvesting whales and seals
to sell internationally
Non-native species that may
have an impact on existing
communities
Caused destruction and
fragmentation of habitats
Depletion of sea cucumber
populations has a drastic
effect on under water
ecology
Goats, brought to island
eats rock purslane (unique
species to island) and out-
competes giant tortoise food
supply
Shrubs have almost been
eradicated
outcompete local species, can
eat native species, destroy
native species habitats and
bring diseases