F215 Control, Genomes and Environment

Cellular Control
1. Genes code for polypeptides, including enzymes
2. Genetic Code
  1. Instructions for the construction of proteins
  2. Triplet code
    1. 3 bases code for an amino acid
  3. Degenerative code
  4. Stop codons
  5. Widespread but not universal
3. Transcription
  1. The DNA base sequence is copied onto mRNA by complementary base pairing
  2. mRNA to ribosome. Using ATP and an enzyme, a tRNA with amino acid and anticodon forms hydrogen bonds with the mRNA codon
    1. 2nd tRNA with different amino acid binds to next exposed codon with complementary anticodon
      1. Peptide bonds form between adjacent amino acids - catalysed by an enzyme
        Ribosome moves to next codon on mRNA, 3rd tRNA brings amino acid, peptide bonds form, forming a tripeptide
        Polypeptide chain grows until a stop codon is reached
4. Translation
  1. mRNA attaches to ribosome and tRNA pairs with mRNA to bring the right amino acid to the correct place in a protein
5. Mutations cause changes to the sequence of nucleotides in DNA molecules
  1. Beneficial
    1. Changes sequence of amino acids and therefore the phenotype, but gives organism advantageous characteristic
  2. Neutral
    1. Mutation in a non coding region of DNA - a silent mutation
  3. Harmful
    1. Changes sequence of amino acids and therefore the phenotype, the resulting characteristic is harmful
6. Cyclic AMP activates proteins by altering there 3D structure
7. Lac Operon
  1. Regulatory gene controls and affects the expression of the structural gene
    1. Regulatory genes make a repressor protein which is a transcription factor that switches a structural gene on and off
    2. Structural genes make enzymes, polypeptides or protein
  2. Lactose absent...
    1. Regulator gene expressed, repressor protein synthesised - has two binding site - on to lactose, one to the operator region
      1. The promoter region is blocked (RNA polymerase normally binds
        RNA polymerase cannot bind so structural genes cannot be transcribed into mRNA
        Genes cannot be translated and the enzymes cannot be synthesised
  3. Lactose present...
    1. Lactose binds to repressor protein
      1. Shape of repressor protein changes
        Repressor protein cannot bind to operator region
        RNA polymerase is able to bind to promoter
        Z and Y are transcribed and mRNA is made
        Bacteria can now use the lactose permease enzyme to take up lactose, the hydrolyse it to glucose and galactose using the B-Galactosidae enzyme - can then be used for respiration
8. Body Plans
  1. Homeotic (regulatory) genes form the homeobox sequence that codes for a gene product which binds to DNA and initiates transcription
    1. Little mutation due to their importance
9. Apoptosis
  1. Cell death
  2. Ensures cells produced by mitosis = cell death
  3. Enzymes break down cell cytoplasm
    1. Cytoplasm becomes dense with tightly packed organelles
      1. Blebs form on the cell surface membrane
        Chromatin condenses and nuclear envelope breaks. DNA fragments
        Cell breaks down into vesicles that are taken up by pagocytosis
Meiosis and Variation
1. Meiosis
  1. Meiosis 1
    1. Prophase ! - chromosomes condense,, pair up (homologous), crossing over, centrioles move to spindle, nuclear envelope breaks down.
      1. Metaphase 1 - homologous pairs (random assortment) line up along centre, attach to spindle by centromeres (attach at chiasmata)
        Anaphase 1 - spindles contract, pulling pairs apart the the poles (chiasmata seperates)
        Telophase 1 - nuclear envelope reforms, cytoplasm divides, two haploid daughter cells produced
    2. 2 haploid daughter cells
  2. Meiosis 11
    1. Daughter cells undergo prophase 11, metaphase 11, anaphase 11 and telophase 11
      1. Anaphase 11 - sister chromatids are seperated - each new daughter cells inherit one chromatid from each chromosome
    2. 4 haploid daughter cells
2. Key Words
  1. Allele - an alternative to a gene
  2. Locus - specific position on a chromosome, occupied by a specific gene
  3. Phenotype - observable characteristics of an organism
  4. Genotype - the combination of alleles possessed by an organism
  5. Dominant - characteristic in which the allele responsible is expressed in the phenotype, even in those with heterozygous genotypes
  6. Codominant - a characteristic where both alleles contribute to the phenotype
  7. Recessive - characteristic in which the allele responsible is only expressed in the phenotype when there is no dominant allele present. It is not expressed when heterozygous and the expression is masked by the dominant allele
  8. Linkage - genes for different characteristics that are present at different loci on the same chromosome are linked
  9. Crossing over - during prophase 1 crossing over means each daughter cell contains chromatids with different combination of alleles due to the exchanging of alleles when in close proximity
3. Independant Assortment
  1. Different combinations of maternal and paternal chromosomes goo into each cell - each cell ends up with a different combination of alleles
  2. Meiosis
    1. Crossing over "shuffles" alleles
    2. Random distribution and subsequent segregation of maternal and paternal chromosomes in the homologous pairs during meiosis 1 leads to genetic reassortment
    3. Random distribution and segregation of the chromatids at meiosis 11 leads to a genetic reassortment
    4. Random mutations
  3. Fertilisation
    1. Random combinations of two sets of chromosomes, one from each of two genetically unrelated individuals
4. Genetic Diagrams
  1. Sew Linkage
    1. Haemophilia
  2. Codominance
    1. Blood type
5. Epistasis
  1. The interaction of different gene loci so that one gene locus makes or suppresses the expression of another gene locus
  2. The gene products are usually enzymes in a multi-enzyme pathway where the product of one reaction is the substrate for the next
  3. Recessive - the homozygous presence of a recessive allele prevents the expression of another allele at a second locus
  4. Dominant - a dominant allele at one gene locus masks the expression of alleles at the second gene locus
  5. Recessive - 9 : 3 : 4
  6. Dominant - 13 : 3
6. Chi-squared
  1. The smaller the value, the more certain that the difference between observed and expected data is due to chance and is therefore not a significant difference
  2. Using a table....
    1. if the value is smaller than the table value, the null hypothesis can be accepted - any difference is due to chance and therefore not significant
    2. If the value is larger than the value on the table, the null hypothesis is rejected - any difference is significant and not due to chance
7. Variation
  1. Discontinuous
    1. Qualitative differences between phenotypes - they fall into clearly distinguishable categories with no intermediates
    2. Different alleles at a single gene locus have large effects on the phenotype
    3. Different gene loci have different effects on the trait
    4. E.G. Blood type
  2. Continuous
    1. Quantitative differences between phenotypes - there is a wide range of variation within the population with no distinct categories
    2. E.G. Height
    3. Different alleles at the same gene locus have small effects
    4. Different gene loci have the same effect on the trait
    5. A large number of gene loci may have a combined effect on the trait
  3. Phenotypic variation - both genotype and environment contribute
  4. Variation is essential in selection so that when the environment changes, some individuals will be better adapted to the change - they will survive and pass on the advantageous alleles
  5. Environmental factors - impact on natural selection
    1. Unchanging conditions - stabilising selection maintains existing adaptions and so maintains existing allele frequencies
    2. Changing conditions - directional selection alters allele frequencies
  6. Genetic Drift - a change in allele frequency that occurs by chance because only some organisms in each generation reproduce - particularly noticeable in small populations
  7. Isolating Mechanisms
    1. Geographical, seasonal and reproductive barriers
  8. The biological species concept
    1. A species is a groups of similar organisms that can interbreed and produce fertile offspring and is reproductively isolated from other groups
      1. But not all organisms reproduce sexually, members of the same species can differ in appearance, males look different to females, isolated populations appear very different from each other
  9. The phylogenetic species concept
    1. A species is a group of organisms that have a similar morphology, physiology, embryology and behaviour, and occupy the same ecological niche
8. Hardy-Weinberg Principle
9. Selection
  1. Natural - the organism best adapted for their environment is more likely to survive, passing on the beneficial allele - this will increase in frequency in the gene pool
  2. Artificial - humans select the organisms with desirable characteristic - these are bred on
  3. Diary Cow - large milk yield, high quality, large udders, resistance to disease
    1. Milk yield is measured, bulls are tested to find out which produced daughters with high yield, semen is used to artificially inseminate many cows, eggs are fertilised in vitro and put into surrogate, embryos can then be cloned
Cloning
1. Reproductive - production of offspring which are genetically identical to the mother (nuclear transfer) or other offspring (splitting embryos)
2. Non reproductive - the use of stem cells in order to generate replacement cells, tissues or organs which may be used to treat particular diseases or conditions
3. Vegetative propagation in elm trees
  1. The English Elm Tree form a genetically isolated clone, they make pollen but rarely produce seeds and reproduce asexually - instead they spread by developing suckers from their roots (each sucker can grow into a new tree)
4. Tissue culture - use leaf/stem/root/bud using aseptic technique, cut into explants, sterilise using bleach or alcohol, place on agar (containing glucose, amino acids, nitrates, phosphates) where they form a callus, subdivide the callus and treat to induce roots and shoots, transfer to greenhouse before planting outside
5. Plant cloning
  1. Advantages - quick, disease free, uniform, reproduction of infertile plants, whole plants from GM cells, can take place anytime regardless of seasons, save extiction
  2. Disadvantages - expensive, labour intensive, microbial contamination, susceptible to same pests or diseases, no genetic variation
6. Nuclear transfer - a nucleus from an adult differentiated cell is placed in an enucleated egg cell, then the egg cell undergoes stages of development using the genetic information from the inserted nucleus
7. Splitting embryos - cells from a developing embryo are separated out, with each one going on to produce a separate, genetically identical organism
8. Animal cloning
  1. Advantages - high value animals cloned on high numbers, rare animals preserved, GM animals can be quickly reproduced
  2. Disadvantages - animal welfare, excessive uniformity (unable to adapt), questions over long term health
Biotechnology
1. The industrial use of living organisms to produce food, drugs or other products
  1. Grow rapidly in favourable conditions, production of proteins and chemicals that can be harvested from surrounding medium, can be genetically modified, low temperatures, not dependant on climate
2. Lag phase - adjustment to environment (intake of water, cell expansion, enzyme synthesis), active but not reproducing
3. Log phase - population size doubles each generation due to space available, rate depends on space/nutrients available
4. Stationary phase - nutrient levels decrease, waste products build up, death = produced, in an open system this would be the carrying capacity
5. Death phase - nutrient expansion and increased levels of toxic waste products lead to increasing death rate
6. Immobilising enzymes
  1. Absorption - enzyme molecules are mixed with immobilising support and bind to it due to a combination of hydrophobic interactions and ionic links
  2. Covalent bonding - enzyme molecules are covalently bonded to support, often by covalently linking enzymes together and to insoluble material using a cross linking agent
  3. Entrapment - enzymes are trapped (e.g. gel bead), substrate and product materials can pass through the material to the enzyme, but the enzyme cannot pass through the solution
  4. Membrane separation - enzymes are physically separated from the substrate by a partially permeable membrane
7. Continuous/batch culture
8. Primary metabolites - substances produced by an organism as part of its normal growth, the production matches growth in population
9. Secondary metabolites - substances produced by an organism that are not the main part of its normal growth, production usually begins after the main growth period so does not match growth in population
10. Asepsis - the absence of unwanted microorganisms which could: compete with the culture for nutrient and space, reduce yield of useful products, produce toxic chemicals

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F215 Control, Genomes and Environment

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