Pack 14 - Control of gene expression

Gene mutations
1. Usually bad but allows for variation
2. Caused by mutagenic agents
3. caused by:
  1. Chemicals
  2. High energy ionising radiation
  3. Can be random and spontaneous
4. Different types:
  1. Addition
    1. Addition of one nitrogen containing base.
  2. Deletion
    1. Removal of one nitrogen containing base.
    2. Causes frame shift mutation
  3. Substitution
    1. Nonsense mutation
      1. Base change results in formation of one of the three stop codons
    2. Mis-sense mutation
      1. Where the base change results in a different amino acid being coded for
    3. Silent mutation
      1. DNA degeneracy means it may still code for the same amino acid
  4. Inversion
    1. Piece of DNA flips over
  5. Duplication
    1. Whole codon or base duplicated
Stem Cells and Totipotency
1. Differentiation:
  1. 1. All cells contain the same genes
    1. 2. Some genes are permanently expressed in all cells (mitochondria)
      1. 3. Some genes are permanently not expressed (no insulin in small intestine
        4. Other genes are switched on and off when needed
        5. This will lead to differentiation as different proteins are expressed in various cells.
2. Stem Cells
  1. Undifferentiated cells
  2. Need to be constantly replaced
  3. Ability to divide to form copies of themselves
  4. In mammals stem cells are found in the:
    1. (for embryonic stem cells)
      1. Differentiate into al types of cells
      2. Can be used to cure things like heart damage, diabetes and blindness etc.
    2. (Umbilical cord stem cells)
      1. Blood similar to adult stem cells
    3. (placental cells)
      1. Placenta differentiate into specific cells
    4. (adult stem cells)
      1. Found in body tissue of foetus
  5. ...potent
    1. Totipotent = differentiate into all cells
      1. Zygotes
    2. Pluripotent = differentiate into most cells
      1. Embryos
    3. Multipotent = differentiate into limited cell
      1. Adults
    4. Unipotent = differentiate into single cell type
      1. e.g. retina
  6. Induced pluripotent stem cells
    1. A type of pluripotent cell produced from a unipotent cell, genetically altered in a lab with transcription factors
    2. Advantages:
      1. Can obtain stem cells from adults
      2. Produce all cell types from adult cells
      3. Able to provide original cells from patient, so no immune response
Plant tissue culture
1. Features of plant growth regulators:
  1. Wide range of effects on plant tissue
  2. Effects on a particular tissue depends upon the conc. of growth factor
  3. Same conc. affects different tissues in different ways
  4. Effect of one growth can be modified by the presence of another
  5. Growth regulators stimulate plant growth, use of in vitro development
2. In plants, many cells remain totipotent
  1. Xylem cells cannot differentiate because they have no nucleus
  2. Cells form tissue culture share same genetic material and so are clones
Regulation of transcription and translation
1. For cells to differentiate it must be switched on whilst the others are off.
2. Effects of oestrogen on transcription:
3. A transcription factor is
  1. A protein that activates or inhibits ignition of eukaryote transcription, that goes form the cytoplasm to the nucleus
4. Transcription factors:
  1. Each transcription factor moves from cytoplasm to the nucleus
    1. It has a specific site which binds to a specific base sequence of DNA called a promoter
      1. The binding of the transcription factor allows the RNA polymerase to bind which allows transcription to occur
        This causes the mRNA to be produced which is translated to produce increased amounts of protein
        The gene is said to be switched on
        When the gene is switched off the site of the DNA where the transcription factor binds is inactive
        No transcription can occur so no polypeptide synthesis
5. Oestrogen:
  1. Sex hormone
  2. Lipid soluble
    1. Allows it to enter the cell directly
  3. Stimulation of transcription factor:
    1. Oestrogen diffuses through bilayer
      1. Binds to receptor attached to transcription factor
        TF changes shape
        TF able to enter the nucleus and bind to DNA and initiate transcription
Epigenetic control of gene expression
1. Epigenetics is the process by which environmental factors can causes heritable changes in gene function without changing the base sequence of DNA
2. Features of a genome:
  1. DNA sequences do not change
    1. DNA wrapped around histones
      1. Chemicals attached to histones
        Chemicals determine shape of DNA - histone complex
        Inactive genes kept tightly packed (epigenetic silencing)
        Unwrapped regions of active genes for transcription
3. Factors that influence the epigenome in the:
  1. Foetus
    1. Signals within cells
    2. Nutrition from Mother
  2. Following birth
    1. Environment
    2. Signals within body (e.g. hormones)
  3. Controlled by increased methylation of DNA
    1. Or, decreased acetylation of associated histones
4. Acetylation
  1. Transfer of acetyl group to a molecule
    1. Acetyl co-enzyme A is the donor
      1. (de-acetylation is the reverse process)
  2. How decreased acetylation of histones reduces transcription:
    1. 1. Acetylation increases +ve charge on histones
      1. 2. This increases their attraction to phosphate groups of DNA
        3. Stronger association between DNA and histones
        4. Transcription factors unable to bind
        5. No transcription mRNA
5. Methylation
  1. Addition of methyl group (CH3) to molecule
    1. It is added to the cytosine base of DNA
  2. How increased methylation of DNA can reduce transcription:
    1. 1. Addition of methyl group to molecule
      1. 2. Added to cytosine base of DNA
        3. Prevents binding of transcription factors
        4. Attracts proteins that condense DNA-histone complex making DNA inaccessible to transcription factors
6. How does DNA-histone complex association affect transcription?
  1. Weak association:
    1. Complex less condensed
      1. Easier access for transcription factors
        Increased transcription
  2. Strong association:
    1. Complex more condensed
      1. No access for transcription factors
        Prevented transcription
7. Twin Studies:
  1. Twins have been used to study influence of either the genome or the environment to humans
  2. Identical twins may have different gene expression due to epigenetics (e.g. methylation)
Epigenetics and Inheritance
1. Epigenetics and disease:
  1. How can epigenetics trigger cancer formation:
    1. In healthy cells normally there is no methylation near promoters
      1. Regions are highly methylated in cancer cells
        Genes which should be active, are therefore switched off.
        Occurs in early development cancer
        People with inherited cancer have increased methylation in this type of gene
2. Epigenetic Therapy:
  1. Treatments:
    1. Drugs inhibit enzymes involve in histone acetylation or DNA methylation - can re-activate genes
      1. Drugs need to be carefully targeted - other wise risk of cancer
  2. Diagnostics
    1. Identify level of DNA methylation and histone acetylation at early stage of disease
Effect of RNA interference on gene expression
1. In eukaryotes and some prokaryotes, the translation of mRNA can be inhibited by breaking down the mRNA before translation can occur.
2. The mechanism of siRNA:
  1. 1. An enzyme cuts large strands of double stranded RNA into small sections called siRNA
    1. 2. One of the two siRNA combines with an enzyme
      1. 3. The siRNA molecule guides the enzyme to the mRNA by pairing up bases with complementary ones in section of the RNA molecule
        4. Once in position the enzyme cuts mRNA into small sections
        5. The mRNA is no longer capable if being translated into a polypeptide
        6. Gene expression now no longer occurs
Epigenetics and Cancer
1. What is cancer?
  1. Group of diseases caused by damage to the genes that regulate mitosis and the cell cycle
  2. Generally derived from a single cell
  3. Unrestrained growth of cells
  4. Group of abnormal cells develops and continuously grows in size
  5. Benign = Stays in one location
  6. Malignant = can break off and cause additional damage
  7. Steps in mutation that create a cancer cell:
    1. Initiation mutation:
      1. Creation of uncontrolled mitosis
    2. Mutation in descendant cell changes subsequent cells to be different from normal
2. Genetic control of cell division:
  1. Proto-oncogenes:
    1. Stimulate cell divison
    2. How a proto-oncogene can become permanently expressed (form oncogene):
      1. 1. Gene for growth factor permanently expressed, stimulating cell division
      2. 2. Receptor protein on cell surface membrane permanently activated, even in absence of growth factor, stimulating cell division
      3. The result of this produces oncogenes which affect cell division in two ways:
        The receptor protein can be permanently activated so that cell division is on even in the absence of growth factors
        The oncogene may code for excessive amounts of the growth factor, cell division is stimulated
  2. Tumour suppressor genes:
    1. Slow down cell division, repair mistakes in DNA and initiate cell death
    2. If it becomes mutated it will be inactivated so cell division will increase, forming a tumour
  3. 3 features of a tumour
    1. Divide continuously
    2. Originates from a single cell
    3. Cells continue to divide and not die
Genome Project
1. Bioinformatics:
  1. Science of collecting and analysing complex biological data such as genomes via use of algorithms
2. Electrophoresis:
  1. DNA fragments of different sizes have an electric charge (DNA=-ve) so it moves to the +ve, further fragment = smallest
3. DNA Sequencing:
  1. Whole Genome Shotgun:
    1. 1. Cut DNA into small sequences
      1. 2. Use computer algorithms to align overlapping segments
        3. Assemble the entire genome
    2. Advantages:
      1. Allows terminators and other components to be run in one pot instead of 4
      2. Use colours to distinguish between different terminators
      3. Less labour intensive
      4. Faster turnaround
  2. Original sequencing process was Sanger sequencing
  3. Role of Dideoxyribose nucleotides:
    1. Different shapes to deoxyribose nucleotides and so cause the DNA chain to terminate
  4. Role of primer:
    1. Short piece of DNA that gives DNA polymerase something to attach DNA nucleotides to
4. Single Nucleotide polymorphisms: (SNP's)
  1. Single base variations in the genome associated with disease and other disorders
5. Genome = Genetic material of an organism
6. Proteome = All of proteins produced in a given cell by a genome
7. Human Microbiome project (bacteria)
  1. Help cure disease - gives insight to metabolism of organism
  2. Find useful genes - clean up pollutants and make biofuels
8. Determining the proteome in prokaryotes is easier than in eukaryotes because:
  1. Only one circular piece of DNA, not associated to histones
  2. None of the non-coding portion of DNA that are found in eukaryotes
9. Determining the genome and proteome in more complex organisms is difficult because:
  1. Many non-coding genes
  2. Many genes involved in regulating other genes
  3. Slight variation in DNA sequences between individuals of same species

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Pack 14 - Control of gene expression

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