Mutations and gene expression

• what is a mutation?

  a change in the order or amount of DNA nucleotides in a sequence
• how does substitution mutation effect the codon?

  one base in a codon changes
• how does a substitution mutation effect the primary structure of the protein?

  - no change in the amino acid sequence (due to degenerative code) -- (silent substitution)

  - one amino acid in the sequence changes (mis-sense) -- change in an intron doesnt affect protein

  - code for a stop codon so continuation of the amino acid sequence / polypeptide production stops (non-sense)
• how does a substitution mutation effect the function of a protein?

  - silent substitution = functions normally

  - mis-sense substitution = may function e.g. the amino acid change may not lead to significant share change or the change may be located at a point that does not affect functioning (not at active site on enzyme) , may be non functional or change function

  - non-sense substitution = early in chain = non functional , late in chain = may function as normal
• how does an addition mutation effect the codon?

  one additional base in the DNA base sequence, change in all codons after this point -- frame shift
• how does addition mutation effect the primary structure of the protein?

  change in many amino acids after the first codon change
• how does addition mutation effect the function of the protein?

  non-functional protein or change in function
• how does a deletion mutation effect the codon?


  one less base in the DNA sequence, change in all codons after this point -- frameshift
• how does a deletion mutation effect the primary structure of the protein?


  change in many amino acids after the first codon change
• how does a deletion mutation effect the function of the protein?

  non-functional protein or change in function
• how does a translocation mutation effect the codon?

  a sequence of bases moves to a different part of the DNA changing the sequence of codons at the new location
• how does a translocation mutation effect the primary structure of the protein?

  large number of amino acids changes in a polypeptide
• how does a translocation mutation effect the function of a protein?

  usually a non- functional protein
• how does a inversion mutation effect a codon?

  a series of nucleotides are reversed. Two or three nucleotides inverting leads to one codon change. A large number of nucleotides give a greater number of codons that are changed
• how does a inversion mutation effect a primary structure of the protein?

  one amino acid change if a small number of nucleotides are inverted or a stop codon could be created at the wrong location In a gene. Many amino acids change and possibility of a stop cidid if a larger number of nucleotides are inverted

  - change in an intron so not involved in the making of a protein
• how does a inversion mutation effect the function of a protein?

  usually a non-functional protein
• what are consequences of mutations?

  - genetic conditions - sickle cell anaemia, cystic fibrosis

  - non-functional enzymes due to a change in the shape of the active site

  - non-functional receptor due to a change in the shape of the receptor site

  - metabolic blocks - failure to make a substrate due to a faulty gene and its resultant non-functional enzyme. No substrate for the next functional enzyme e.g. epitasis

  - new alleles so increase in variation

  - new allele may lead to a phenotype with a selective advantage - natural selection and speciation are possible

  - antibiotic resistance / pesticide resistance

  - cancer due to the formation of oncogenes or the failure of a tumour repressor gene to produce a functional protein
• what are stem cells?

  unspecialised cells that will divide and differentiate into specialised cells
• what potency?


  ability to differentiate
• what are totipotent stem cells?

  cells that have the capability to differentiate into any type of cell of the body and into placental cells
• what are pluripotent stem cells?


  cells that can differentiate into any type of body cell
• what are multipotent stem cells?


  cells that can different into a few different types of cells
• what are unipotent stem cells?

  cells that can only differentiate into one type of cell
• what are induced pluripotent stem cells?

  body cells that can be reverted to pluripotent which can divide and differentiate into any type of body cell
• why are IPS cells better than growing embryonic stem cells?

  - IPS cell will only contain your antigens so there's a lower chance of it being rejected

  - less ethical issues
• how are IPS cells produced?

  - use virus to put genes into cells
• what is an issue with using viruses to make IPS cells?

  - may add viral genes into the IPS cell genomes
• why do prokaryotes not have transcription factors?

  because they dont have a nucleus
• how does oestrogen activate transcription factor?

  - Oestrogen is lipid soluble, it moves into the cell via simple diffusion.

  - in the cytoplasm, oestrogen binds to a complementary shaped oestrogen receptor.

  - This oestrogen receptor is a transcription factor.

  - The binding of oestrogen leads to a change in tertiary structure

  - The transcription factor enters the nucleus and binds to the promoter (has a complementary shape to the base sequence of the promotor).

  - The binding of the transcription factor enables RNA polymerase to bind.

  - Transcription occurs and mRNA is produced.

  - Translation can then occur, and a protein is produced / the gene is expressed.
• how does a transcription factor stimulate transcription?

  - enters nucleus through nuclear pore

  - binds to promotor region for a gene

  - allows RNA polymerase to bind to DNA and initiates transcription

  - (some prevent RNA polymerase from binding which inhibits transcription)
• what is a transcription factor?


  a molecule that moves from the cytoplasm to the nucleus to bind to a specific promoter region for a gene on the DNA and triggers transcription to occur

  - Transcription factors are proteins which bind to promotor regions at the start of genes.

  - has a tertiary structure that is complementary to the base sequence of the promotor

  - When the factor binds, RNA polymerase binds, and transcription is initiated.
• what is RNA interference?

  - RNA interference is a process where RNA molecules (siRNA /miRNA) prevent the expression of a gene so that a protein is not produced
• how is RNAi molecules produced?

  - The RNAi molecules are transcribed from a cell's DNA (from the 'non-coding' DNA between genes)

  - Larger double stranded molecules are first produced that are then spilt into shorter lengths of nucleotides (around 25 nucleotides long), before being made single stranded.

  - A single strand of the molecule can bind to a protein in the cytoplasm to form a complex.

  - The complex is called an RNA-induced silencing complex
• how does siRNA stop gene expression?

  - siRNA is found in prokaryotic cells.

  - The siRNA associates with an enzyme (to form an RISC). The enzyme is called RNA hydrolase.

  - The siRNA has a complementary base sequence to the mRNA for a specific protein.

  - When the siRNA binds it brings the enzyme that will then catalyse the hydrolysis of a phosphodiester bond and therefore breaks down the mRNA.

  - With no mRNA the protein is not produced, and the gene is not expressed.
• how does miRNA stop gene expression?

  - miRNA is found in eukaryotic cells.

  - The miRNA associates with a blocking protein (to form a RISC).

  - The miRNA has a complementary base sequence to mRNA.

  - (miRNAs are not as specific as siRNAs)

  - The binding of the RISC means that the mRNA can nolonger bind to a ribosome. tRNA's cannot bind so no translation occurs and the protein is not produced. Gene expression has not occurred.

  - miRNAs can move the mRNA into a processing body where it can be stored and later released so that translation can then occur.
• what is epigenetic?


  hereditary changes to gene function without altering the DNA base sequence
• how does increased acetylation lead to increased gene expression?

  - histone acetyl transferase adds acetyl groups to the amino acid lysine in histone

  - the acetyl group neutralises the charge on lysine

  - without the positive charge on the lysine within the histones, the histones have less attraction to the negative charge of DNA

  - this leads to a less condensed DNA-histone complex

  - transcription factors have access to the DNA and are able to bind to the promoter region

  - this leads to the expression of the gene as the RNA polymerase can now bind
• how does decreased acetylation lead to decreased gene expression?

  - acetyl groups are removed by histone deacetylases

  - lysine in histones have a positive charge

  - the histones are attracted to the negative charge of DNA (caused by the presence of phosphate groups in each nucleotide)

  - condensation of the DNA histone complex occurs

  - there is no access for transcription factors to bind to the promotor regions of the DNA at the start of a gene

  - the gene is not expressed
• how does increased methylation lead to decreased gene expression?

  - the addition of methyl groups to cytosine occurs

  - using the enzyme DNA methyl transferase

  - the presence of methyl groups on cytosine inhibits transcription because it prevents the binding of transcription factors to DNA as they no longer have a complementary shape to the promotor region of the DNA

  - the methyl groups also attract proteins that condense the DNA histone complex (the proteins induce deacetylation of the histones) making the DNA inaccessible to transcription factors
• how do benign and malignant tumours compare?

  - benign cells produce adhesion molecules that make them 'stick' together and they remain in the tissue as primary tumour but malignant have metastasis occurring which forms secondary tumours- benign has slow growth but malignant has faster growth- both can grow large- benign have a nucleus shape that is well defined (regular) but malignant have a nucleus shape hat is often larger and darker due to increased amount of DNA- benign cells are differentiated but malignant cells can become de-differentiated (unspecialised)- benign cells are contained with a capsule of dense tissue but malignant are not contained within a capsule- benign can be dangerous (if the tumour puts pressure on blood vessels it can cause bursting/ decreased blood flow) but malignant are dangerous- benign are often localised but malignant have widespread effects across the body- benign is removed by surgical removal but malignant needs radiotherapy or chemotherapy drugs- benign has a low chance of reoccurring but malignant has a higher chance of reoccurring