MODULE 1 - CELLULAR CONTROL AND VARIATION

i.

Cellular control
A. Genetic code
1. DNA
a.

B.

C.

D.

Made up of 2 polynucleotide strands

1) DNA nucleotides form sugar-phosphate backbone
a) Nitrogenous base
i.
Hydrogen bonds between complementary bases
b) Pentose sugar
c) Phosphate group
b. Genes
1) Lengths of DNA that code for polypeptides found on chromosomes
a) Sequence of nucleotides/bases in DNA determines sequence of
amino acids
2. Triplet code
a. A sequence of three bases in DNA codes for a certain amino acid, e.g. CGG
3. Degenerate code
a. All amino acids have more than one code, except methionine
4. Stop codons
a. Dont code for amino acids, tell cells when to stop production of the protein
5. Widespread but not universal
a. Same codons code for the same amino acids in all organisms, but not always
Protein synthesis
1. Transcription
a. Production of an mRNA molecule, complementary to the DNA reference strand
b. DNA strands are separated/unzipped by DNA helicase
1) Hydrogen bonds between bases are broken
a) Free RNA nucleotides line up against exposed DNA strand
i.
Complementary bases pair up with each other
1. A on DNA pairs with U on mRNA, T with A
ii. RNA nucleotides joined together by condensation
reactions, catalysed by RNA polymerase
2. Translation
a. Production of a polypeptide using the base sequence on the mRNA
b. Takes place on a ribosome where two codons of the mRNA are exposed at a time
1) Amino acids are brought to the ribosome by tRNA molecules
a) Anticodon (3 exposed bases) binds with an mRNA codon by
complementary base pairing
i.
Anticodon determines which amino acid binds to other end
b) Condensation reaction links amino acids by peptide bonds
c) mRNA moves through ribosome and third tRNA binds with it
i.
First tRNA breaks away leaving the amino acid linked to
the one on the second tRNA
Mutations
1. Random, unpredictable changes to the base sequence of DNA
2. Substitution
a. One base swapped for another
1) Neutral effect if new triplet still codes for the same amino acid
3. Deletion/Insertion
a. Loss or gain of a base pair from DNA molecule
1) Frame shift occurs
a) All amino acids coded for beyond this point will be different
b. If the sequence of amino acids in a protein is different, then its tertiary structure is
likely to be different too and wont function properly
1) Normally harmful but sometimes it can be beneficial
a) Sickle cell anaemia
i.
Substitution in gene for haemoglobin changes its shape
Genetic control of protein production
1. Genes are only expressed in certain cell types and under certain circumstances
a. Lac operon in E. coli

1)

2)

2.

ii.

Lactose not present

a) Repressor protein coded by regulatory gene binds to operator region
i.
Prevents RNA polymerase binding to promoter region
1. Structural genes not expressed
Lactose is present
a) Lactose binds to the repressor protein and can no longer bind to
operator region, detaches itself
b) RNA polymerase can now bind to promoter region
i.
Structural genes transcribed into mRNA and translated
1. galactosidase and lactose permease produced
a. Lactose now respired

Homeobox genes
a. Genes that control the development of an animals general body plan
1) Plants and fungi have them, but are not homologous (similar) to animals
b. Contains sequence of 180 base pairs called homeobox sequence
1) Codes for sequence of 60 amino acids producing polypeptides
a) Which are transcription factors that bind to other genes
i.
Switching them on or off initiating transcription
3. Apoptosis
a. Programmed cell death
1) Important during development
a) E.g. tissue needs to be removed between fingers and toes
2) Cells contents packed tightly and engulfed by phagocytes
Meiosis and variation
A. Meiosis
1. Nuclear division that produces 4 genetically different haploid cells from a diploid cell
2. Haploid gametes fuse together during fertilisation producing a diploid zygote
a. Meiosis I
1) Interphase
a) DNA replicated so each chromosome has 2 identical copies (sister
chromatids)
2) Prophase
a) Chromosomes condense and become visible
b) Homologous chromosomes pair up forming bivalents
i.
One maternal and one paternal
c) Non-sister chromatids can cross over each other forming chiasmata
d) Nuclear envelope breaks down and centrioles form the spindle
3) Metaphase
a) Bivalents pulled to equator by microtubules of the spindle attached
to centromeres
b) Bivalents randomly arranged, so maternal or paternal could be
facing either poles
4) Anaphase
a) Homologous chromosomes in the bivalents separate, pulled apart to
opposite poles by microtubules
i.
Halves the number of chromosomes
5) Telophase
a) Nuclear envelope reforms around each set producing 2 nuclei
i.
Each with half number of chromosomes (haploid)
6) Cytokinesis
a) Plasma membrane folds inwards to form 2 haploid cells
b. Meiosis II
1) Prophase
a) Chromosomes condense and spindle develops
b) Nuclear envelope broken down again
2) Metaphase
a) Chromosomes are pulled to equator and align randomly
3) Anaphase
a) Sister chromatids are pulled to opposite poles

i.
4)

B.

Centromeres divide so each chromatid is now a

chromosome

Telophase
a) Nuclear membranes reform, chromosomes decondense -> nuclei
5) Cytokinesis
a) 4 haploid cells produced (half of original chromosomes)
i.
Has 1 chromatid/chromosome from each homologous pair
3. Produces genetic variation
a. Key terms
1) Locus
a) Location of gene on a chromosome
2) Allele
a) An alternative version of a gene
b) Code for different version of the same characteristic
3) Genotype
a) Alleles an organism has, the genetic makeup
4) Phenotype
a) Characteristics the alleles produce
b) Determined by genotype and can be observed
b. Crossing over
1) Non-sister chromatids exchange alleles during prophase I
2) They break and re-join at chiasmata
c. Independent assortment of chromosomes
1) Bivalents align randomly on equator
a) Either maternal or paternal chromosomes may face either pole
i.
Combination of maternal and paternal chromosomes
migrating to either pole is random
ii. Gametes that are produced contain a mixture of alleles
d. Fertilisation
1) Combining 2 sets of chromosomes, one from paternal one from maternal
Genetics and inheritance
1. Single gene inheritance
a. Key terms
1) Recessive allele
a) Only effects phenotype when dominant allele isnt present
2) Dominant allele
a) Effects phenotype whether or not recessive is present
3) Homozygous
a) Organism has the same two alleles of a gene
4) Heterozygous
a) Organism has two different alleles of a gene
b. Hardy-Weinberg principle
1) Used to calculate allele frequencies in a population
2) P is the frequency of dominant allele
a) p is dominant homozygous
3) q is the frequency of recessive allele
4) 2pq is heterozygous individuals
c. Codominance
1) No dominant and no recessive characteristic
2) Both alleles contribute to the phenotype
d. Sex linkage
1) X chromosome is much larger than Y chromosome
a) Has many genes not present on Y
i.
Said to be sex-linked because inheritance of the genes
depends on gender
b) If gene has recessive allele, condition is more common in males as
only 1 recessive allele is needed on X chromosome as males only
have XY instead of XX
2. Dihybrid inheritance
1) Looking at inheritance of two genes at the same time

b.

c.

d.

C.

2) 9 : 3 : 3 : 1 ratio of phenotypes from two parents that are heterozygous

Autosomal linkage
1) Genes on the same chromosome tend to be inherited together
2) Their loci are very close to each other
a) Rare that crossing over will occur between the two genes
i.
If it does it produces recombinants
Epistasis
1) Interaction of different gene loci so that one gene locus makes or suppresses
the expression of another gene locus
2) Recessive
a) Homozygous presence of recessive allele prevents expression of
another allele at a second locus
b) Dominant allele of one gene needed for second gene to be expressed
3) Dominant
a) Dominant allele at one gene locus masks expression of alleles at
second gene locus
b) No dominant alleles of one gene for second gene to be expressed
Chi-squared test
1) Used to determine whether observed results of a cross (O) differ significantly
from the expected results (E)
2) 5% (0.05) critical value is used and degrees of freedom (n-1)
a) If value of x is smaller than number in the table
i.
More certain any differences are due to chance and there is
no significant different between E and O
b) If value is larger
i.
Null hypothesis rejected difference is significant and not
due to chance

Variation
1. Discontinuous
a. Phenotypes fall into one of a few distinct categories, e.g. blood groups
b. Caused by presence of dominant allele producing one phenotype
c. Influenced by one gene or small number of genes
2. Continuous
a. No distinct categories, a continuous range of values between 2 extremes, e.g. height
b. Involved a number of genes interacting together
c. At least 2 alleles for each gene and a number of genes affecting the phenotype means
its likely a lot of variations occur
3. Environmental causes
a. Variations in exposure to certain environmental conditions
b. Not inherited or passed on, and cause continuous variation, e.g. body mass
4. Genetic causes
a. Differences in the sequence of DNA caused by random mutations
b. Passed onto future generations and cause discontinuous, e.g. eye colour
5. Natural selection
a. Without variation between individuals, none will be better adapted to survive and
reproduce passing their genes on, and selection doesnt occur (no evolution)
b. Gene pool
1) The range of all the alleles in a population
c. Stabilising selection
1) Environment stays constant there will be no evolutionary change
a) Any change away from the well-adapted form is unlikely to be
successful and pass on the alleles
d. Evolutionary selection
1) Environment changes and places selection pressure on a species
a) Favours certain alleles giving selective advantages to them
i.
Better adapted, higher chance of passing on alleles
1. Higher proportion of next generation have allele
a. Increasing allele frequency
e. Genetic drift
1) Allele frequencies change (evolution) by chance instead of natural selection

2)

3)
4)
D.

E.

i.

Most likely in smaller populations

a) Just by chance one or two individuals have better breeding success
than others
i.
Their alleles become more common
1. Unlucky individuals that didnt have offspring
lose their alleles
a. Gene pool changes
Large populations arent effected by small changes in allele frequency
Natural disasters wiping out large % of populations
a) By chance result in a higher proportion of individuals with a certain
allele making it more common than before

Speciation
1. Formation of a new species through reproductive isolation
a. Members of same species no longer able to interbreed freely
1) Genetic changes do not spread throughout the whole species
a) One population has changes no seen in other
2. Isolating mechanisms
a. Geographical (ecological) isolation
1) Organisms separated by physical barrier, e.g. mountain range or river
a) Prevent populations from mixing and breeding together
b. Seasonal (temporal) mechanisms
1) Variation in timing of breeding season so populations are not synchronised
2) Not active at the same time of day
c. Reproductive mechanisms
1) Changes in courtship rituals
2) Different sizing of reproductive organs
3) Slight biochemical change making sperm and egg not compatible
3. Species concepts
a. Biological species concept
1) Group of organisms that can interbreed freely to produce fertile offspring
2) Cannot be used for asexual organisms or with fossils
b. Phylogenetic (evolutionary) species concept
1) Group of organisms that share many characteristics (morphology,
physiology, embryology and behaviour)
a) Uses many sources including DNA sequencing
2) However, can be significant variation between individuals in a species
a) Males and females make look different
b) Caterpillar looks different from butterfly
Selection
a. Selection pressure causes allele frequencies to change
2. Natural selection
a. Alleles giving selective advantages to individuals make them more likely to survive
and breed
1) Passing on alleles to next generation
b. Selective forces are abiotic and biotic aspects of the environment
c. Takes a long time unless environment changes dramatically
3. Artificial selection
a. Individuals with desirable alleles selected to breed
1) Passes on desirable characteristics to future generations
a) Only 1-2 characteristics chosen and proceeds quickly
b. Selective forces are humans
4. Modern dairy cow
a. High milk yielding females selected and bulls that have high yield female offspring
b. Sperm from bull delivered to many females by artificial insemination
1) Only a few bulls needed, and sperm can be frozen
c. Repeated with offspring and milk yield increases

MODULE 2 BIOTECHNOLOGY AND GENE TECHNOLOGIES

Cloning in plants and animals
1. A clone is an exact, genetically identical copy of the parent

B.

C.

D.

E.

Natural vegetative propagation

1. Asexual reproduction in plants
a. Produces genetically identical plants known as clones
1) Useful is sexual reproduction fails or is not possible
2) Offspring have all the genetic information to survive in the environment
3) Lack of genetic variation
a) Unable to adapt to changes in environment
i.
If one plant is vulnerable to pathogen, all will be
2. Runners
a. Horizontal stems that grow along the surface or just below
1) Sometimes take root and grow a new vertical stem, e.g. strawberry plants
3. Root suckers/basal sprouts
a. Similar to runners, but produce stems at intervals along roots
1) May form as a result of damage to parent plant
a) Suckers grow in circle around old trunk, called clonal patch
b) Elm trees produce root suckers helping them survive Dutch elm
disease
4. Bulbs and tubers
a. Specialised underground stems become swollen from which new plants grow
Artificial vegetative propagation
1. Taking cuttings
a. Stem is cut between leaf joints (nodes)
1) Cut end dipped in plant hormones, encouraging root growth and is planted
2) Forms a new plant which is a clone of original parent plant
2. Grafting
a. Section of shoot is joined to already growing root and stem (rootstack)
1) Graft grows and is genetically different from rootstack
3. Tissue culture/micropropagation
a. Small piece of tissue taken from meristem in shoot tip called explant
1) Placed on nutrient growth medium
a) Cells divide forming mass of undifferentiated cells called a callus
2) Growth medium and explants are sterilised to kill bacteria or fungi, which
would destroy explants
3) Single callus cells can be removed from the mass and placed on medium
contain plant hormones encouraging shoot growth
a) Growing shoots transferred onto different growth medium
containing different conc. of hormones encouraging root growth
4) Growing plants transferred to greenhouse to be acclimatised
a) Eventually will be planted outside
Plant cloning in agriculture
1. Produce clones of plants that are difficult to reproduce by seed
2. Crops have predictable characteristics with same harvesting and processing times
3. Lack of genetic variation
a. Entire crop is vulnerable to the same diseases, pests or environmental conditions
Cloning animals
1. Non-reproductive cloning
a. Production of genetically identical cells
b. Used to test potential new drugs or to research involvement of genes in diseases
c. Growing stem cells for research or treatment of disease
d. Growing tissue in culture to replace damaged tissues or organs
2. Reproductive cloning
a. Production of genetically identical complete organisms
b. Splitting embryos
1) Cell from a developing embryo can be separated with each one producing
genetically identical organism
c. Nuclear transfer
1) Fusion of a nucleus from a differentiated body cell with enucleated egg cell
a) Divides by mitosis as a normal zygote would
i.
Using the genetic information from the inserted nucleus
d. Advantages

e.

ii.

Biotechnology
1.

B.

1) High valued, desired animals can be cloned in large numbers

2) Rare animals cloned for preservation
3) Genetically modified animals producing drugs can be quickly reproduced
Disadvantages
1) Low success rates
2) Problems with health, shorter life expectancies
3) Ethical issues
4) Genetic uniformity makes species unlikely to adapt to changes

Industrial use of microorganisms to carry out processes

a. Food
1) Cheese, bread, beer, yoghurt and single celled proteins
b. Medicinal drugs
1) Penicillin and insulin
c. Treating waste products
1) Water and sewage treatment
Using microorganisms
1. Reasons
a. Grown or used anywhere, making process independent of climate
b. Reproduce quickly even at low temperatures
c. Reproduce asexually so all offspring are identical
d. Few ethical issues
e. Genetically engineered to produce specific products
f. Grown using waste products otherwise useless or toxic
2. Closed culture growth
a. Follows a sigmoid curve
b. Lag phase
1) Production of enzymes
2) Absorption of nutrients
3) Reproduction and growth very slow as cells acclimatise
c. Exponential (log) phase
1) Rapid reproduction rate, population doubles every generation
2) No limiting factors and few cells die
3) Length depends on space and nutrients available
d. Stationary (stable) phase
1) Constant/stable population as death rate = reproduction rate
2) Nutrient levels decrease and waste products build up (CO)
e. Death/decline phase
1) Death rate exceeds reproduction rate
2) Population declines, possibly to 0
3) Waste products and other metabolites build up, limited nutrients
3. Continuous culture
a. Nutrients are added and products are removed at set intervals
1) Culture is maintained at exponential phase
a) Difficult and expensive to achieve
2) High growth rates as nutrients in high supply
3) More efficient as fermenter always in use
4) Used for primary metabolites
a) Insulin and single celled proteins
5) Contamination causes huge volumes of product to be lost, expensive
4. Batch culture
a. Starter population supplied with fixed amount of nutrients and left to grow
1) Products extracted at the end of time period
b. Easy to set up and maintain
c. Slower growth rate because nutrients decline
d. Less efficient as it isnt always in use
e. Used for secondary metabolites
1) Wine, beer, yoghurt
f. Contamination only causes one batch to be lost
5. Metabolites

a.

Primary
1) Substances produced by an organism as part of its normal growth
a) Proteins, enzymes and alcohol
b. Secondary
1) Produced by organisms after main population growth
a) Not essential to survival of organism
b) Not all produce them
c) Produced when nutrients in short supply and growth slows down
d) Antibiotics, penicillin
6. Manipulation of growth conditions in fermentation vessel
a. Temperature
1) Optimum to maintain metabolic rates
a) Not too hot or it denatures enzymes
2) Cold water used to cool down exergonic reactions producing heat
b. pH
1) Kept at optimum to ensure enzyme action continues as required
a) Too high/low reduces activity of enzymes
c. Oxygen
1) Sufficient supply needed for aerobic respiration processes
2) Products achieved through anaerobic respiration have no oxygen supply
a) Alcohol
d. Nutrients/substrates
1) Correct nutrients added at the right times
a) Depends on whether its batch or continuous and if primary or
secondary metabolites are needed
e. Agitation
1) Stirring or mixing to prevent microorganisms settling at bottom of fermenter
a) This would reduce activity and growth rate
2) Rotating paddle or bubbling of oxygen from base
7. Asepsis
a. Stops contamination of unwanted microorganisms in culture
1) Kill culture microorganisms
2) Use required products for their own metabolism
3) Spoil end product with toxic by-products
4) Compete with culture population for nutrients and space
a) Reducing growth rate and yield
b. Methods
1) Washing, disinfecting and steam cleaning all equipment
2) Polished stainless steel fermenters that prevent microbes sticking to surfaces
3) Sterilisation of nutrients before they are added to fermenter
a) Steam or heat treatment
4) Oxygen need to be free from microbes using filters
C. Immobilising enzymes
1. Enzymes fixed in place
a. Do not mix freely with substrate and are not lost in the process
b. Do no contaminate end product and can be reused many times straight away
c. Damage by extreme conditions unlikely as theyre protected by immobilising material
2. Adsorption
a. Enzymes held in place on a surface (glass or carbon) by hydrophobic/ion/covalent
bonding
3. Entrapment
a. Enzymes trapped in gel beads or between cellulose fibres
b. Substrate and product molecules can pass through material to reach enzyme
1) Enzyme cannot pass through into solution
4. Membrane separation
a. Physically separated from substrate by partially permeable membrane
b. Substrate/product pass through barrier, but enzymes cant
iii. Genomes and gene technologies
A. Polymerase chain reaction (PCR)
1. Mixture of the DNA sample, free nucleotides, primers and DNA polymerase is set up

a.

B.

C.

D.

Primers are short pieces of DNA complementary to bases at the start of DNA
fragments
b. DNA polymerase is an enzyme that creates new DNA strands
2. Heated to 95C to break hydrogen bonds in DNA forms single strands
a. Cooled to 50-65C so that primers can bind (anneal) to strands
1) Forms double stranded section allowing DNA polymerase to bind to
3. Heated to 72C so DNA polymerase can line up free DNA nucleotides along template strands
a. Complementary base pairing means new complementary strands are formed
1) 2 new copies of DNA fragment are formed
a) Each PCR cycle doubles amount of DNA
Restriction enzymes
1. Restriction endonuclease enzymes are specific to DNA
a. Wide range of them, each with different active site thats specific to a particular
sequence of nucleotides (restriction site)
1) Usually palindromic sequences that consist of antiparallel base pairs
2. Shape of restriction site is complementary to enzymes active site
3. If restriction sites are on either side of DNA fragment needed, restriction enzymes can separate
it from rest of DNA
4. Enzyme catalyses hydrolysis reaction
a. Breaking sugar-phosphate backbone of DNA
5. Sequence of unpaired and exposed nucleotides are left after cutting, called sticky ends
a. Can be used to bind (anneal) DNA fragment to another length of DNA with
complementary sticky ends
Gel electrophoresis
1. Technique of separating pieces of DNA according to their length
2. Gel contains wells
a. Sample of DNA is placed into these
1) Covered in buffer solution to conduct electricity
2) Florescent tag added to all DNA fragments so they can be viewed with UV
b. Electrical current passed through the gel
1) DNA fragments negatively charged
a) Move towards positive electrode at far end of gel (anode)
i.
Small DNA fragments move faster and travel further
1. DNA separates according to size
2. DNA fragments can be viewed under UV light
Genetic engineering
1. Transformed/transgenic organisms
a. Have recombinant DNA
1) DNA formed by joining together DNA from different sources
2. Fragment inserted into vector
a. DNA fragment containing gene required is isolated by using restriction enzymes and
inserted into vector DNA
1) Vector is something used to transfer DNA into a cell
a) Plasmids found in bacteria, bacteriophages are used
b. Same restriction enzyme used to cut open vector DNA
1) So that sticky ends of the vector are complementary to stick ends of DNA
fragment
c. Vector DNA and DNA fragment mixed together with DNA ligase
1) Joins up sugar-phosphate backbone through ligation
d. Leaves recombinant DNA (vector dna + dna fragment)
3. Vector transfers gene into bacteria
a. Vector with the recombinant Dna is used to transfer the gene into bacterial cells
b. Plasmids
1) Bacterium placed in calcium chloride to increase cell wall permeability
a) Plasmids added to mixture and heated to encourage cells to take in
vector
c. Bacteriophage
1) Infects the bacterium by injecting its DNA into it
a) DNA of phage integrates into the bacterium DNA
d. Bacteria become transformed or transgenic

4.

Identification of transformed bacteria

a. Not all bacteria take up the vector
b. Marker genes inserted into vectors at the same time as desired genes
1) Meaning transformed bacteria contain both
c. Marker gene can code for antibiotic resistance
1) Bacteria grown on agar plates containing antibiotics, so only cells with
marker genes will survive and grow
d. Marker gene can code for fluorescence
1) When agar plate is placed under UV light only transformed bacteria will
fluoresce
5. Insulin
a. Insulin used to be from dead pigs, now genetically engineered bacteria manufacture it
b. Gene for human insulin is identified and isolated using restriction enzymes
c. Plasmid cut open use same R.enzyme
1) Insulin gene inserted into plasmid (forming recombinant DNA)
d. Plasmid taken up by bacteria and transformed bacteria identified using marker genes
e. Bacteria grown in fermenter
1) Human insulin produced as bacteria grow and divide
a) Extracted and purified so it can be used in humans
f. Advantages
1) More effective than animal insulin
a) Less chance of rejection or allergic reaction
2) Cheaper and faster to produce
a) More reliable and large supply
3) No ethical or moral issues using it compared to dead animals LOL (not lol.)
6. Golden Rice
a. Genetically engineered rice to contain beta carotene
1) Used to produce Vitamin A in the body
a) Used to reduce deficiency in S.Asia and Africa
7. Xenotransplantation
a. Transplant of organs from one species to another
b. Pigs and sheep can be engineered to make xenotransplantation easier
1) Genes for cell surface proteins found on human cells inserted into animal
embryo
a) Animal produces these proteins and less chance of rejection
c. Animal genes making cell surface proteins are remove or inactivated
1) Doesnt produce them, reducing risk of rejection
8. Gene therapy
a. Treating genetic disorders by inserting new genes
1) Does not replace genes, rather it adds to the genome
b. Somatic cell gene therapy
1) Adding genes into a body cell so that the cell can produce a specific protein
a) Doesnt affect offspring
c. Germ line gene therapy
1) Treating a fertilised egg
a) All cells in organism will possess the required gene that will be
passed onto offspring
9. Ethical concerns
a. Possible spread of antibiotic resistant genes used as markers
b. Reduction of genetic variation if only certain GM crops are grown
c. Spread of genes for resistance to pests or herbicides from crops to weeds
1) Making them superweeds
d. Suffering to farm animals if the genes introduced adversely affect their metabolism or
health
e. Simply do not know what risks may exist
10. DNA probes
a. Short length of single stranded DNA
1) Used to identify genes with a specific sequence
b. Labelled
1) Radioactive label

2) Fluorescent label, detected using UV light

Probes mixed with fragmented DNA in suspension
1) Probe binds with DNA fragment
a) DNA fragments then separated by gel electrophoresis
d. Probes can be poured on to gel electrophoresis plate after DNA fragments have been
separated
1) Allows probes to bind to complementary sequence
a) Identifies where on the electrophoresis plate the desired gene is
11. Gene sequencing
a. Chain-termination method
1) Used for fragments up to 750bp long
2) Following added to 4 tubes
a) DNA fragment
b) DNA primer
c) DNA polymerase enzyme joining DNA nucleotides together
d) Free DNA nucleotides
e) Fluorescently labelled modified nucleotides
i.
Normal, except once added to a DNA strand no more bases
can be added after it
ii. Different modified nucleotide added to each tube
3) Tubes undergo PCR
a) Many different length strands
i.
Each one terminates at a different point, depending on
which nucleotide
b) DNA fragments separated by electrophoresis
i.
Visualised under UV light
c) Complementary base sequence can be read from the gel
i.
Reading bands from bottom to the top
ii. Original sequence will be opposite of this sequence
b. BACs bacterial artificial chromosomes
1) Used to sequence whole genomes
a) Genome cut into smaller fragments of ~100k bp using restriction
enzymes
i.
Inserted into BACs
1. Manmade plasmids
a. Each fragment in separate plasmid
ii. BACs inserted into bacteria
1. Grown in culture to clone many copies of DNA
b) DNA extracted from bacteria and cut into shorter fragments using
restriction enzymes
c) Fragments separated by gel electrophoresis
i.
Each fragment is sequenced by chain termination method
ii. Sequence is produced by computer systems
MODULE 3 ECOSYSTEMS AND SUSTAINABILITY
c.

i.

Ecosystems
A. Key terms
1. Biotic factors
a. How living organisms in an ecosystem affect each other
1) Food supply, predation and disease
2. Abiotic factors
a. Effects of non-living components of an ecosystem
1) Temperature, pH and soil type
3. Niche
a. Role that each species plays in an ecosystem
4. Habitat
a. Place where an organism lives
5. Population
a. All the organisms of one species that can live in the same place at the same time
b. Can interbreed freely
6. Community

a. All the populations of different species living in the same place at the same time
Ecosystem
a. Group of living organisms and non-living things occurring together and the
interrelationships between them
b. Always changing, not static they are dynamic
B. Trophic levels
1. Stages in a food chain occupied by a particular group of organisms, a.k.a feeding levels
2. Producers
a. Autotrophs converting energy from environment and inorganic matter into chemical
energy in the form of complex organic molecules
1) Used in growth or as substrates for respiration
b. Phototrophs
1) Plants using suns energy to convert inorganic matter into carbs
c. Chemotrophs
1) Bacteria using chemical energy and heat to convert inorganic into complex
3. Consumers
1) Digest complex organic molecules made by autotrophs, using to growth or
respiration
b. Primary consumers
1) Herbivores that feed on plants
c. Secondary consumers
1) Feed on primary consumers
d. Tertiary consumers
1) Feed on secondary consumers
4. Decomposers
a. Organisms that feed on waste or dead organic matter
1) Gain energy through digesting and respiring complex molecules in the matter
a) Cause decay and food to go off
MODULE 4 RESPONDING TO THE ENVIRONMENT
Plant responses
A. Why do plants need to respond?
1. All organisms need to respond to changes in their internal or external environment
a. Changes are stimuli and responses are to increase survival chances
1) Avoiding predation
2) Abiotic stress
a) Not enough water or light
B. Tropisms
1. A tropism is a directional growth response
a. Direction of response determines by direction of external stimulus
2. Phototropism
a. Response to light
1) Shoots show positive phototropism and grow towards light
3. Geotropism
a. Response to gravity
b. Shoots show negative geotropism and grow away from gravity
c. Roots show positive and grow towards
C. Plant hormones
a. Coordinate plant responses, also called plant growth regulators
b. Do not have endocrine glands and have different effects on different tissues
2. Auxin
a. Coordinates response to light
b. Produced in tip of growing shoot
c. Increases growth by promoting elongation of the cells
1) Hydrogen ions are pumped into the cell wall to lower pH
a) Softens the cell wall allowing extra stretching
d. Shoot bends towards light source
1) Auxin in higher concentrations on shaded side of shoot
a) Cells on shaded shade elongate more making it grow more and bend
D. Apical dominance
1. Refers to inhibition of lateral shoots further down the shoot by the apical bud
7.

i.

a. Auxin produced at tip of shoot (apex) inhibiting growth of side shoots

Evidence
a. Removal of apical bud allows lateral buds to grow
b. Chemicals that inhibit auxin transport allows lateral bud growth
c. Plant grows taller lateral buds grow at bottom of shoot
1) Further away from the apical bud
a) Lower conc. of auxin and growth is less inhibited
d. Auxin promotes production of abscisic acid which inhibits lateral bud growth
E. Gibberellins
1. Elongation of the stem is stimulated by gibberellins
2. Genetically dwarf plants treated with gibberellic acid elongate stems considerably
F. Leaf loss (abscission)
1. Deciduous plants shed their leaves each year
a. Abscission zone is a region of cells at end of leaf stalk that responds to hormones
2. Auxin produced in leaf inhibits abscission by making cells insensitive to ethene
3. Cytokinins enter the leaf and prevent ageing of leaves
a. When conc. falls the leaf ages and turns brown
1) Called senescence which stops production of auxin in the leaf
a) Abscission zone becomes sensitive to ethene
i.
Stimulates production of cellulase in abscission zone
1. Digests cell walls and leaf falls off
G. Commercial uses of plant hormones
1. Auxins
a. To promote root growth in cuttings
b. To produce seedless fruit
c. As a selective weed killer
2. Cytokinins
a. Delay leaf senescence to avoid vegetables discolouring
b. Promote bud and shoot growth during tissue culture
c. Promote growth of lateral buds
3. Ethene
a. Speed up fruit ripening and promote fruit drop
4. Gibberellins
a. Improve shape and size of fruit
b. Speed up seed production during breeding
Animal responses
A. Why animals need to respond
1. Respond to their internal or external environment to stay alive through nerves and hormones
2. Avoid predation; Find food; Increase chances of reproduction; Temperature regulation; Homeo
B. Nervous system
a. Detects environmental changes and brings about suitable responses to those changes
b. Receptors all over body to detect stimuli, both internal and external
2. Central
a. Brain and spinal cord
3. Peripheral
a. Somatic
1) All receptors, sensory and motor neurones supplying skeletal muscles
b. Autonomic
a) Coordinates the unconscious responses involved in homeostasis
b) Only motor neurones and mostly unmyelinated
2) Sympathetic
a) Pre-ganglion neurones are short
b) Post ganglion neurones are long
i.
Secrete noradrenaline at synapse between neurone and
effector
1. Increased heart rate
2. Pupil dilation
3. Increased ventilation rate
4. Increases activity, to prepare for activity
c) Active at times of stress
2.

ii.

3)

C.

D.

E.

F.

d) Neurones are linked at a ganglion just outside the spinal cord

Parasympathetic
a) Pre-ganglion neurones are long
b) Post- ganglion are short
i.
Secrete acetylcholine at synapse between effector
1. Decreasing heart rate
2. Pupil constriction
3. Decreased ventilation rate
4. Decreases activity to conserve energy
c) Most active in sleep or relaxation
d) Neurones are linked at ganglion within the target tissue

The human brain

1. Cerebrum
a. Cerebral cortex
1) Control of higher functions such as memory, language, emotions, thinking
and planning
2. Cerebellum
a. Control and coordination of movement and posture, walking, running
3. Medulla oblongata
a. Control of involuntary processes; breathing, heart rate and smooth muscle of the gut
4. Hypothalamus
a. Control of the autonomic nervous system and some endocrine glands
b. Control of homeostatic mechanisms
1) Monitors blood glucose and body temperature and water potential
Action of muscles at joints
1. Movement is achieved by coordinated action of the antagonistic muscles
a. When one muscle contracts and gets shorter the other relaxes and is extended
b. Skeletal muscles therefore work in antagonistic pairs (oppose each other)
2. Muscles stimulated by motor neurones leading from motor area of brain
a. One is attached to one or more muscle fibres, called a motor unit
1) Attached by a motor end plate or neuromuscular junction
a) Stimulate muscle fibre membrane (sarcolemma) like a synapse wud
The elbow
1. Humerus, radius and ulna join at the elbow hinge joint
2. Biceps
a. Flexor muscle that bends the joint when it contracts
3. Triceps
a. Extensor muscle that straightens the joint when contracted
4. Triceps and biceps are antagonistic, working against each other
Skeletal muscle
1. Striated muscle
a. Produced by arrangement of actin and myosin protein filaments inside muscle fibres
b. A band (dark band)
1) Made up of thicker myosin filaments held together by the M line
c. I band (lighter band)
1) Made up of thinner actin filaments that are held together by Z line
a) Distance between 2 Z lines is a sarcomere
i.
Active unit of a muscle
d. These two bands overlap
2. Each fibre has many nuclei, theyre multinucleate
a. Surrounded by membrane called sarcolemma (plasma membrane)
b. Cytoplasm is called the sarcoplasm and contains many mitochondria to supply energy
for contraction process
c. Endoplasmic reticulum is called sarcoplasmic reticulum to control contractions
3. Contraction
a. Brought about by actin and myosin filaments sliding past each other
1) Moves Z lines closer together so the sarcomeres get shorter, along with fibre
b. I band gets narrower
c. H zone gets shorter
1) Region of A band that has no overlap with actin

d.

4.

5.

6.

Action potential travels down the motor neurone

1) Stimulate calcium ions to enter presynaptic swelling
a) Vesicles of acetylcholine fuse with membrane releasing it to cleft
i.
Binds to receptors causing inflow of Na ions
1. Depolarise sarcolemma
e. If above threshold level action potentials transmitted along sarcolemma
1) Also transmitted down into transverse system (T-system) tubules
a) Depolarisation causes Ca channels in sarcoplasmic reticulum to
open and release Ca ions in sarcoplasm
i.
Act as secondary messenger to stimulate movement of
myofibrils
f. Myosin filaments have heads
1) Bridge the gap between actin and myosin
2) Myosin head attaches to a special binding site on actin
a) Changes shape, bends and pulls actin past myosin
i.
Making filaments slide past each other
1. Releasing ADP and Pi
b) When actin and myosin locked together, ATP joins the myosin head
i.
Broken down releasing energy
1. Separates myosin and actin
2. Moves myosin head back to starting position
ii. Creatine phosphate makes ATP in muscles
iii. Muscle tissue also has glycogen
3) Ca ions stored in sarcoplasmic reticulum
a) Released when action potential travels from motor neurones along
sarcolemma down T system tubules
i.
Bind to protein troponin which moves tropomyosin aside
1. Exposed binding sites on actin for myosin heads
Synapses and neuromuscular junctions similarities
a. Both activated by action potentials
b. Both release acetylcholine by exocytosis into the cleft
c. Receptor sites on postsynaptic membrane open Na channels to produce AP in
membrane
d. AP in postsynaptic cell, but muscle contracts for neuromuscular junctions
Muscle types
a. Voluntary muscle
1) Found attached to bone
2) Controlled by somatic nervous system
3) Contracts quickly tires easily
4) Striated
5) Cylindrical cells multinucleate
b. Involuntary muscle
1) Unstriated
2) Contracts slowly and fatigues slowly
3) Controlled by autonomic system
4) Found in walls of tubular structures such as gut blood vessels and ducts
5) Spindle shaped with a single nucleus for each cell
c. Cardiac muscle
1) Found only in heart
2) Supplied by nerves from autonomic nervous system
3) Semi-striated
4) Contracts spontaneously without fatigue
5) Cylindrical cells each with single nucleus
a) Cross bridges with other fibres to carry excitations across it all
Flight or fight response
1) Responses can be coordinated by nervous system and endocrine system
b. Sensory receptors detect environmental changes
1) Sensory neurones carry action potentials to the CNS
a) Spinal reflex action bring about rapid responses
c. Impulses also conducted to cerebrum

1)

d.

Uses association centres to make decisions about how to respond

a) Impulses sent down somatic motor neurones to skeletal muscles
i.
Brings about voluntary coordinated movement
Hypothalamus stimulated and sends impulses down sympathetic part of autonomic
nervous system to bring about changes
1) Cardiac accelerator nerve carries impulses to heart, increasing rate and stroke
2) Blood pressure is raised
3) Breathing rate and depth increases
4) Blood vessels to gut and skin constrict
5) Blood vessels to muscles dilate
6) Adrenal glands are stimulated and release adrenaline
a) Stimulated liver to release glucose and maintains other effects of
sympathetic nervous system

iii. Animal behaviour

A. Innate behaviour
1. Features
a. Genetically determined and passed on via reproduction
1) Not learnt or taught
2) Immediate survival value for young inexperienced animals in dangerous
situations
b. All members of species show this behaviour
c. Stereotyped behaviour
1) Fixed action pattern
2. Types
a. Reflex
1) Usually escape response that takes body or part of body out of harms way
quickly and automatically
2) Escape reflex of worms when touched to avoid predation
b. Taxis
1) Directional response where animal moves towards or away from stimulus
2) Shark attracted to blood in water, swims towards it to find food
3) Woodlice move away from light to be less visible to predators
c. Kinesis
1) Increased movement with no defined direction in response to a stimulus
a) Rate of movement related to intensity
b) Slows down when stimulus no longer present
2) Woodlice move about more quickly in light or dry conditions
a) Until in more suitable conditions
B. Learnt behaviour
a. Animal responses that change or adapt with experience
2. Features
a. Not present at birth
b. Not all members show the behaviour
c. Can be passed on to other members of species by observation
3. Types
a. Habituation
1) Animal learns to ignore a repeated stimulus that causes no harm
2) Avoids wasting energy in making escape responses
3) People become unaware of a continuous sound or constant smell
b. Imprinting
1) Young animals associate with another organism
2) Lorenz showed young geese recognise their own kind because they imprint
on the first thing they see that moves
a) In nature is their parent, but was replaced by Lorenz
c. Classical conditioning
1) Animal learns to associate two unrelated stimuli through repetition
2) Innate response is modified
3) Pavlov trained dogs to salivate at sound of bell
a) Salivation is a conditioned response to inappropriate stimulus
d. Operant conditioning

1)

C.

D.

Animals learn to carry out particular action in order to receive a reward

a) Or to avoid unpleasant experience
e. Latent learning
1) Animals learns its surroundings and makes use of that knowledge to escape
or find food
2) Mice/rats trained to run through a maze
f. Insight learning
1) Use of previous experience/memories to solve a problem
2) Chimps stack boxes to reach bananas normally out of reach
Social behaviour in primates
1. Advantages to living in a social group
a. Many individuals searching for food can cover a wider area
b. Many together can protect each other and fight off a predator
c. Social grooming can help to get rid of parasites
d. Young members of group can learn through observation and play
1) This is learned behaviour
Dopamine and DRD4
1. Facts
a. Neurotransmitter in the brain and a hormone
b. Involved in release of adrenaline and noradrenaline
c. >5 different dopamine receptors (DRD1-5)
1) Each one producing a different response
a) Therefore has many different responses
2. Responses to dopamine
a. Controlling motivation and learning
b. Increasing general arousal
c. Decreasing inhibition
d. Controls addictive behaviour and risk taking
3. Concentrations of dopamine
a. Too little -> Parkinsons
b. Too much -> Schizophrenia
4. Use of drugs
a. Used to block dopamine receptors to help treat addictive behaviour or impulsive
behaviour
1) ADHD, gambling etc
5. Genetics
a. Variation in alleles for dopamine receptors between individuals
1) Some people have more/less sensitive receptors than others
a) Display different behaviours than others, more risky/addictive