The control of gene expression

• Gene mutation


  A change in the base sequence of DNA
• Mutagenic agent


  A factor that increases rate of mutation, eg. ultraviolet (UV) light or alpha particles
• How a gene mutation can lead to the production of a non-functional protein or enzyme

  1. Changes sequence of base triplets in DNA so changes sequence of codons on mRNA

  2. Changes sequence of amino acids in the encoded polypeptide

  3. Changes position of hydrogen / ionic / disulphide bonds (between amino acids)

  4. Changes tertiary structure (shape) of protein

  5. Enzymes - active site changes shape so substrate can't bind, enzyme-substrate complex can't form

  
• Types of gene mutations

  • Substitution
  • Addition
  • Deletion
  • Duplication
  • Inversion
  • Translocation
• Not all gene mutations affect the order of amino acids
• Why a change in amino acid sequence is not always harmful

  • May not change tertiary structure of protein (if position of ionic / disulphide / H bonds don't change)
  • May positively change the properties of the protein, giving the organism a selective advantage
• Frameshift


  • A frameshift occurs when gene mutations (eg. addition, deletion, duplication or translocation) change the number of nucleotides / bases by any number not divisible by 3
  • This shifts the way the genetic code is read, so all the DNA triplets / mRNA codons downstream from the mutation change
  • The sequence of amino acids encoded changes accordingly and the effects on the encoded polypeptide are significant
• If a multiple of 3 bases is added / removed there won't be a frameshift, but extra / less triplets will result in extra / less amino acids in the encoded polypeptide
• A frameshift could also lead to production of a stop codon (that doesn't code for amino acids so terminates translation), resulting in a shorter polypeptide
• Stem cells


  • Undifferentiated / unspecialised cells capable of:
  • Dividing (by mitosis) to replace themselves indefinitely
  • Differentiating into other types of (specialised) cells
• How stem cells become specialised during development

  1. Stimuli lead to activation of some genes (due to transcription factors - see 8.2.2)

  2. So mRNA is transcribed only from these genes and then translated to form proteins

  3. These proteins modify cells permanently and determine cell structure / function

  
• Totipotent cells


  • Occur for a limited time in early mammalian embryos
  • Can divide AND differentiate into any type of body cell (including extra-embryonic cells eg. placenta)
• Pluripotent cells


  • Found in mammalian embryos (after first few cell divisions)
  • Can divide AND differentiate into most cell types (every cell type in the body but not placental cells)
• Multipotent cells


  • Found in mature mammals
  • Can divide AND differentiate into a limited number of cell types
• Unipotent cells


  • Found in mature mammals
  • Can divide AND differentiate into just one cell type
• How stem cells can be used in the treatment of human disorders

  1. Transplanted into patients to divide in unlimited numbers

  2. Then differentiate into required healthy cells (to replace faulty / damaged cells)
• How induced pluripotent stem (iPS) cells are produced

  1. Obtain adult somatic (body) cells (non-pluripotent cells or fibroblasts) from patient

  2. Add specific protein transcription factors associated with pluripotency to cells so they express genes associated with pluripotency (reprogramming)

  3. Culture cells to allow them to divide by mitosis

  
• Evaluation of the use of stem cells in treating human disorders

  • For:
  • Can divide and differentiate into required healthy cells, so could relieve human suffering by saving lives and improving quality of life
  • Embryos are often left over from IVF and so would otherwise be destroyed
  • iPS cells unlikely to be rejected by patient's immune system as made with patient's own cells
  • iPS cells can be made without destruction of embryo and adult can give permission
  • Against:
  • Ethical issues with embryonic stem cells as obtaining them requires destruction of an embryo and potential life (embryo cannot consent)
  • Immune system could reject cells and immunosuppressant drugs are required
  • Cells could divide out of control, leading to formation of tumours / cancer
• Transcription factors


  • Proteins which regulate (stimulate or inhibit) transcription of specific target genes in eukaryotes
  • By binding to a specific DNA base sequence on a promoter region

  
• How transcription can be regulated using transcription factors


  1. Transcription factors move from cytoplasm to nucleus

  2. Bind to DNA at a specific DNA base sequence on a promoter region (before / upstream of target gene)

  3. This stimulates or inhibits transcription (production of mRNA) of target gene(s) by helping or preventing RNA polymerase binding

  
• How oestrogen affects transcription

  1. Oestrogen is a lipid-soluble steroid hormone so diffuses into cell across the phospholipid bilayer

  2. In cytoplasm, oestrogen binds to its receptor, an inactive transcription factor, forming an oestrogen-receptor complex

  3. This changes the shape of the inactive transcription factor, forming an active transcription factor

  4. The complex diffuses from cytoplasm into the nucleus

  5. Then binds to a specific DNA base sequence on the promoter region of a target gene

  6. Stimulating transcription of target genes forming mRNA by helping RNA polymerase to bind

  
• Oestrogen only affects target cells that have oestrogen receptors
• Epigenetics


  • Heritable changes in gene function / expression without changes to the base sequence of DNA
  • Caused by changes in the environment (eg. diet, stress, toxins)
• Epigenome


  All chemical modification of DNA and histone proteins - methyl groups on DNA and acetyl groups on histones
• Epigenetic control of gene expression in eukaryotes

  • Methylation of DNA to inhibit transcription
  • Acetylation of histones to allow transcription
  • Decreased methylation of DNA or increased acetylation of histones to stimulate transcription
  • Increased methylation of DNA or decreased acetylation of histones to inhibit transcription

  
• How methylation and acetylation can inhibit transcription

  1. Increased methylation of DNA - methyl groups added to cytosine bases in DNA

  2. So nucleosomes (DNA wrapped around histone) pack more tightly together

  3. Preventing transcription factors and RNA polymerase binding to promoter

  4. Decreased acetylation of histones increases positive charge of histones

  5. So histones bind DNA (negatively charged) more tightly

  6. Preventing transcription factors and RNA polymerase binding to promoter

  
• Environmental factors (eg. diet, stress, toxins) can lead to epigenetic changes that can stimulate / inhibit expression of certain genes and lead to disease development
• RNA interference (RNAi)


  • Inhibition of translation of mRNA produced from target genes, by RNA molecules eg. siRNA, miRNA
  • This inhibits expression of (silencing) a target gene

  
• Regulation of translation by RNA interference


  1. Small interfering RNA (siRNA) or micro-RNA (miRNA) is incorporated into / binds to a protein, forming an RNA-induced silencing complex (RISC)

  2. Single-stranded miRNA / siRNA within RISC binds to target mRNA with a complementary base sequence

  3. This leads to hydrolysis of mRNA into fragments which are then degraded OR prevents ribosomes binding

  4. Reducing / preventing translation of target mRNA into protein

  
• miRNA / siRNA within RISC binds to target mRNA

  1. Complementary base sequence

  2. Hydrolysis of mRNA into fragments

  3. Degradation of mRNA fragments

  4. Preventing ribosomes binding

  
• Reducing / preventing translation of target mRNA into protein

  
• Students should be able to interpret data provided from investigations into gene expression AND evaluate appropriate data for the relative influences of genetic and environmental factors on phenotype
• Transcription factors stimulate or inhibit transcription by helping or preventing RNA polymerase binding

  
• Oestrogen is a steroid hormone that binds to and activates oestrogen receptors, which are the actual transcription factors
• To get the mark, you need to mention whether these epigenetic modifications inhibit or allow / stimulate transcription and therefore gene expression

  
• DNA is methylated and histone proteins are acetylated
• siRNA and miRNA bind to target mRNA molecules that have been transcribed from a gene, so that they are not able to be translated

  
• Tumour


  Mass of abnormal cells resulting from uncontrolled cell division due to mutations in DNA / genes controlling mitosis
• Types of tumours


  • Malignant tumour (cancerous, can spread by metastasis)
  • Benign tumour (non-cancerous)
• Benign tumours


  • Grow slowly (cells divide less often)
  • Cells are well differentiated / specialised
  • Cells have normal, regular nuclei
  • Well defined borders and often surrounded by a capsule so do not invade surrounding tissue
  • Do not spread by metastasis (as cell adhesion molecules stick cells together)
  • Can normally be removed by surgery and they rarely return