F215 Flash Cards Pt.3

Production of penicilanic acid using an immobilised enzyme reactor

Immobilised penicillin acyclase enzyme reactors used to convert penicillin into amino penicillanic acid, which is then used as a base molecule to produce a rang eof different penicllin-type antibiotics.

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Genomics

Study of the whole set of information in the form of the DNA base sequences that occur ni the cells of organisms of a particular species. The sequenced genomes are placed on public access databases.

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What is 'junk DNA'

The non coding DNA that occupies a large amount of a genome

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Sequencing a genome - Steps

Genomes are mapped to identify where in the genome they have come from. Samples of genomes are sheared into smaller sections (shotgun approach). Placed into seperate BAC's and transferred to E.coli cells, producing copies.

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BACs

Bacterial artificial chromosones

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Clone libraries

Cells that make many copies of DNA sections.

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Sequencing a BAC section

Cells containing specific BAC are cultured. DNA extracted. Different restriction enzymes give a number of overlapping fragments. Electrophoresis. Fragments sequenced using automated process. Computer programme reassembles whole BAC segment sequence.

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Applications of comparing genomes

Identification of a protein found in all organisms gives clues to the importance of such genes to life. Comparing DNA/genes show evolutionary relationships. Modelling effects of changes to DNA/genes can be carried out.

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Electrophoresis - Steps

DNA samples treated with restriction enzymes to cut them into fragments. DNA samples places into wells cut into -ve electrode end. Gell immersed in tank of buffer sol. Electric current passed through for time. Positions shown by dye

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Electrophoresis - Theory

DNA is -ve charged due to phosphoryl groups. Attracted to +ve electrode. Shorter move further than longer.

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Southern Blotting

Nylon sheet placed over gel, covered in paper towel, pressed and left overnight. DNA fragments transfer onto sheet.

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DNA Probes

Short single stranded piece of DNA complementary to a DNA section that is being investigated

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How is a DNA probe labelled?

Radioactive marker (32P) revealed by exposure to photographic film. Flourescent marker that emits colour on exposure to UV light.

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Annealing

Htdrogen-bonding between complementary base pairs when sections of single stranded DNA or RNA join together.

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Uses of DNA probes

Locate a desired gene. To identify the same gene on a variety of different genomes. Identify presense/absence of an allele for a particular genetic disease.

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What factors of DNA do PCR rely on?

Antiparallel backbone strands. Strands that have a 5'(prime) aend and 3'(prime) end. Grows only from 3' end. Complementary base pairing.

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Steps of PCR

Double stranded DNA sample mixed with DNA polymerase and free nucleotides.. Heat to 95°C -strands seperate. Add primers. Reduce temp to 55°C-primers anneal. Raised to 72°C (opt for DNA pol). DNA pol binds to and extends primers using free base nucl.

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Thermophillic enzyme

Enzyme that is not denatured by extreme temperatures.

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What thermophilic bacterium is DNA polymerase derived from?

Thermus aquaticus, which lives in springs of up to 90°C

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Automated DNA sequencing

Primer anneals at 3' ed of template strand, allowing DNApol to attach. Adds free base nucl. Strand grows. Modified nucleotide tagged with colour inserted, enzyme thrown off and rection stops. Fragments vary in size. Laser reads colour sequence. Voila

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Recombinant DNA

Section of DNA, often in the form of a plasmid, which is formed by joining DNA sections from 2 different sources

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Cutting DNA

Use a restriction enzyme (restriction endonuclease) used to cut through DNA where a specific base sequence occurs (restriction site). Enzyme catalyses hydrolisis, breaks sug-phos backbone. Gives a staggered cut, leaving stick ends.

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Sticky ends

Formed when DNA is cut using a restriction enzyme. Short run of unpaired, exposed bases seen at the end of the cut section. Complimentary sticky ends can anneal as part of recombining DNA fragments.

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Recombining DNA fragments

DNA ligase catalyses condensation reaction between p-s backbone.

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Requirement for recombining DNA fragments

Both fragments need to have been originally cut with same restriction enzyme. Means sticky ends are complementary and allows bases to pair and H bond together

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Reasons for carrying out genetic engineering

Improving a feature of recipient organism. Engineering organisms that can synthesise useful products.

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Transgenic organism

Contains DNA that has been added to its cells as a result of genetic engineering

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Forming a recombinant plasmid and inserting into bacteria

Cut the Plasmid and gene with same restriction enzyme (complementary sticky ends). Treat with ligase to form recombinant plasmid. Mix plasmid with bacterial cells in presence of calcium salts. Transgenic bacteria formed.

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Bacterial Conjugation definition

Exchange of genetic material. Copies of plasmid DNA passed between.

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Bacterial Conjugaton steps

Conjugation tube forms between donor and recipient. Enzyme nicks plasmid. Plasmid DNA replication. Free DNA moves through tube. Replication of DNA in recipient. Cells move apart, plasmid forms a circle.

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Steps in producing human insulin

mRNA for insulin. Reverse transcriptase used to synthesis template DNA strand. DNApol and free nucl. Second strand built. Forms cDNA. Unpaired nucleotides added to give sticky ends comp to plasmid. Put in plasmid -> bacteria -> insulin.

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Human insulin 3 colonies that could have grown

1. Not taken up plasmid. 2. Taken up plasmid that's not sealed up to its original plasmid (not insulin one).3.The ones that have taken up the recombinant plasmid - transformed bacteria

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Identification of transformed bacteria by replica plating- preparation

Plasmids chosen that are resistant two to different antibiotic chemicals (ampicillin, tetracyline). Resistance genes known as genetic markers. Plasmid cut, restriction site in middle of tetracyline gene. Gene taken up, gene is broken:no resistance

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Identification of transformed bacteria by replica plating - comparison

Bacteria grown on standard nutrient agar. Cells put into agar with ampicillin-only those that have taken up plasmid grow. Transferred to tetracyline treated agar - those that have plasmid without insulin grow.

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Biofortified

High than normal concentration of a particular nutrient (golden rice = beta-carotene)

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Golden rice case study

B-carotene needed for Vit A. Gene for production in endosperm turned off. Genes inserted code for enzxmes (pyhtoene synthase+Ctr 1 enzyme). Inserted near to specific promoter sequence. Accumulates B in endosperm.

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Problems with Golden Rice

Reduces biodiversity. Human food safety unkown. Contamination of wild rice populations.

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Gene therapy

Whena functioning allele of a particular gene is inserted into a cell that lacks it

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Somatic Cell

Biological cell forming the bod of an organism

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Somatic cell gene therapy -Augmentation

Inheritance of faulty alleles to loss of a functional gene product (polypeptide). Engineer a functioning copy into relevant specialised cells. Means polypeptide is synthesised normally

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Somatic cell gene therapy - Killing specific cells

Eliminate certain populations of cells. Use genetic techniques to make cancer cells express genes to produce proteins (cell surface antigens). Makes cell vulnerable to attack by immune system. Could lead to targeted cancer treatments.

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Germline

Gives rise to the gametes of organisms that reproduce sexually.

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Germline cell gene therapy

Engineering a gene into sperm, egg, zygote means as the organism grows, every cell contains a copy of the engineered gene. The functioning allele of transgenic animals can be passed onto offspring.

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Why is germline illegal?

An idvertant modification of DNA introduced into germline could create new human disease or interfere with human evolution in an unexpected way. Permanent modifications to the human genome raises moral, ethical, social foshizzle.

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Xenotransplantation

Transplantation of cell tissues or organs between animals of different species

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Allotransplantation

Transplantation of cell tissues or organs between animals of same species

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Community

All of the populations of different species that live in the same place at the same time, and can interact with each other.

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Ecosystem

Any group of living organism and non-living things occuring together, and the interrelationships between them.

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Biotic Factors

A factor created by a living thing or any living component within an environment in which the action of the organism affects the life of another organism - food supply, predation, disease.

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Abiotic factors

Non-living components of an ecosystem - pH, temp, soil type etc.

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Primary consumers

Herbivores, feed on plants

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Secondary consumers

Carnivores, feed on herbivores

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Tertiary consumers

Carnivores, feed on secondary carnivores.

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Trophic leve

Level at which an organism feeds in a food chain

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What does the arrow in a food chain show?

The direction of energy transfer

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Measuring efficiency of energy transfer

Pyramids of biomass. Pyramids of energy. Pyramids of energy.

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Steps behind pyramid of biomass

Areas of bar proportional to dry mass of organisms at each trophic level. (Organisms put into oven at 80*C). Wet mass can be used to protect ecosystem damage.

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Steps behind pyramids of energy

Burning organisms in a calorimeter and work out how much heat energy released per gram.

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Productivity

Rate at which energy passes through each trophic level in a food chain.

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Gross Primary productivity

Total amount of energy fixed by photosynthesis - net flux of carbon from atm. to plants, per unit time. (MJ m-2 yr-1)

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Net pp

Rate at which carbohydrate accumulates in the tissue of plants of an ecosystem. Measured in dry organic mass (kg

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Net pp equation

Net pp = primary productivity - respiratory heat loss

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Succesion

Directional change in a community of organisms over time.

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Succesion example

Pioneer community (algae and lichens), rotting of organisms gives soil for larger plants, succed pioneer community. Climax community reached.

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Quadrat records?

Distribution or abundance.

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Population size of a species equation

Pop size = mean no. of individuals in species in quadrat/ fraction of total habitat are covered.

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Transect type

Line (species touching tape). Belt (quadrat at regular intervals next to line [interrupted], move quadrat along [continupus])

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Decomposers

Saprotrophs- feed by secreting enzymes onto food, absorb digested nutrients through outer wall

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Nitrogen fixation

Plants can't use N directly, needs fixed nitrogen NH4+ & NO3-

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Nitrogen fixing bacteria

Rhizobium, lives in root nodules of beans/peas. Mutualistic relationship (Give N, get C compounds). Proteins (leghaemoglobin) absorb oxygen in nodules and keep anaerobic conditions)

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Nitrification

Chemoautotrophic bacteria in soil, absorb ammonium ions. Gain energy by oxidising ammonium to nitrites or nitrites to nitrates. only happens in well aerated soil for O2.

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Denitrification

Bacteria convert nitrates to nitrogen gas. Use nitrates for O2 where they live in anaerobic conditions. Make N20 + N2.

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Competition

where resources are in inadequate amounts ti satisfy the needs of all the individuals who depend on the resource.

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Intraspecific comp

Between individuals of same species. Better adapted survive. Pop. drops -comp reduces - pop. increases and vice verse

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Interspecific comp

Between individuals of deifferent species. Affect both pop. size & distribution.

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Coppicing

Cutting a tree trunk close to the ground to encourage new growth. New shoots grow again.

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Pollarding

Cutting trunk higher so that deer don't eat emerging shoots of coppiced stems.

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Rotational Coppicing

Divide wood into sections. Cut a section each year. New stems grown by the time you return. Reduces succesion and lets light down to the ground.

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Conservation

Maintenance of biodiversity; diversity between species, genetic diversity within species. Maintenance of habitats and ecosystems.

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Economic and social reasons for conservation

Species provide valuable food resource. Drugs in natural envirnnments. Natural predators of pests act as biological control agents.

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What does conservation involve?

Raise carrying capacity by providing extra food. More indivuals to enlarge pop. Restrict dispersal of individuals by fencing. Control predators and poachers. Vaccinate individuals against disease.

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Galapogos Problems

Habitat disturbance. Over exploitation of resources. Introduced species.

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Tropism

directional growth responses in which the direction of response is determined by the direction of the external stimulus.

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Types of tropisms

Photo (shoot grow towards light). Geo (roots grow towards gravity. Chemo (pollen tubes grow down style to ovum). Thigmo (shoots of climbing plants wind around plants or solid structures and gain support.

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How do plant hormones move around?

Active transport. Diffusion. Mass flow in phloem sap/xylem vessels

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Auxins

Promote cell elongation. Inhibit growth of side shoots and leaf abscission.

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Cytokinis

Promote cell division

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Gibberelins

Promote seed germination and growth of stems

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Abscisic acid

Inhibit seed germination and stem growth.

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Ethene

Promotes fruit ripening

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Meristems

Growth points in a plant where immature cells are still capable of dividing.

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Apical meristems

Tips of roots and shoot - getting longer

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Lateral Bud

Buds - gives rise to side shoots

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Lateral

Cylinder near outside of roots/shoots - shoots getting wider.

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Intercalary meristems

Between nodes. Growth between nodes makes shoots longer.

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Phototropism

Shoot bends towards light. Shaded side elongates faster. Auxins tranported to shaded side. Promote increase in rate of elongation.

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Stopping Shedding Leaves

Cytokinins stop deciduous trees senescing. Makes leaf act as a sink for p

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F215 Flash Cards Pt.3

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