Mutations and Gene Technologies

• substitution: one base is replaced for another
• insertion: one or more bases is added
• deletion: one or more bases is removed
• inversion: a sequence of bases is reversed
• neutral effect:

  • The mutation changes a base in a triplet but the amino acid that the triplet codes for doesn’t change. This happens because some amino acids are coded for by more than one triplet
  • The mutation produces a triplet that codes for a different amino acid but the amino acid is chemically similar to the original so it functions like the original amino acid.
  • The mutated triplet codes for an amino acid not involved with the protein’s function
• mutagenic agents:

  • Some chemicals delete or alter bases.
  • Some types of radiation change DNA structure.
  • Some chemicals are a similar shape to bases and can become incorporated into the DNA strand during replication.
• the two types of genes that lead to cancer:

  • Mutations which inactivate tumour-suppressor genes – these genes stop uncontrolled cell division by coding for proteins which inhibit mitosis or trigger apoptosis. If the tumour suppressor gene is inactivated, the protein isn’t produced, resulting in uncontrolled cell division.
  • Mutations which activate proto-oncogenes – these genes stimulate cell divisions by coding for proteins which trigger mitosis. If the proto-oncogene is overactive, cells divide uncontrollable, leading to the formation of a tumour. 
• benign tumour: non-cancerous and grow slowly. They’re covered in fibrous tissue that stops them from invading other parts of the body. They are not usually harmful, although they can cause blockages and put pressure on organs. Some benign tumours become malignant.
• malignant tumours:

  cancerous. They grow quickly and spread around the body, invading multiple tissues.
• cancer cells distinct features:

  • Express different antigens on their cell membrane
  • Larger, darker nuclei
  • Divide by mitosis more frequently
  • Irregular shape
  • Don’t produce all the proteins that a cell needs to function properly
  • Don’t respond to growth-regulating processes
• Epigenetics:

  • the addition or removal of chemical 'tags' onto DNA or histone proteins
  • can be caused by environmental factors
  • changes the structure of the chromosome - making it more or less accessible to RNA polymerase
• accessibility to RNA Polymerase:

  • more open the structure of the chromosome - more accessible - gene switched on
  • less open the structure of the chromosome - less accessible - gene switched off
• the two main types of epigenetic 'tags':

  • methyl groups
  • acetyl groups
• DNA methylation:

  Methyl groups can be added directly onto the DNA. They attach to a region of DNA called the CpG site - this is where a cytosine is found next to a guanine. The addition of a methyl group makes the DNA less accessible to the proteins involved in transcription. The gene is switched off 
• Histone Acetylation:

  Chromosomes are made up of chromatin, DNA wrapped around histone proteins. Chromatin can be tightly wound or more loosely wound. The more condensed the chromatin, the less accessible to transcription proteins. The addition of acetyl groups to histones causes the chromatin to be less condensed, more accessible and activating the gene. The removal of acetyl groups makes chromatin highly condensed form, which is less accessible so represses transcription of the gene. Histone deacetylases enzymes remove acetyl groups from histones causing reduced gene expression. 
• cause of uncontrolled cell division:

  • increased methylation of tumour suppressor genes
  • reduced methylation of proto-oncogenes
• Cancer treatments: drugs that reduce DNA methylation are used in chemotherapy for types of cancer that are caused by hypermethylation of tumour suppressor genes. Drugs which inhibit HDACs are also being used to treat some types of cancer. This prevents deacetylation and allows genes to remain switched on. however, hard to make drugs that target only cancer cells
• oestrogen in cancer:

  Increased exposure to oestrogen is thought to increase the risk of breast cancer. This may be because:

  • Oestrogen stimulates cell division in breast cells. If cells are dividing more frequently, there is more opportunity for mutation to take place.
  • If a mutation does happen, oestrogen may help the mutated cells to replicate faster, helping tumours to form quickly.
  • Oestrogen may even introduce mutations directly into the DNA of breast cells.
• Stem Cells:

  Stem cells are unspecialised cells which have the ability to become specialised cells, The process by which a stem cell is converted from an unspecialised cell to a specialised cell is called cell differentiation. Stem cells have an unlimited capacity to divide and can produce lots more stem cells by mitosis. The ability of stem cells to undergo differentiation is called potency.
• totipotent: totipotent cells have the ability to divide into any type of cell
• pluripotent: pluripotent cells can divide into any type of cell except the extraembryonic cells.
• Multipotent: these cells can divide into a handful of different cell types
• unipotent: these cells can only divide into one type of cell
• Gene Expression:

  Within each cell, certain genes will be activated and others will be inactivated. Only the activated genes are transcribed into mRNA which is translated into protein. The particular proteins that are formed will modify the cell by changing its structure and controlling cellular processes. These changes cause the cell to become specialised.
• Stem Cells in Medicine:

  • used to treat certain diseases
  • Stem cell transplants are given to patients with leukaemia as leukaemia destroys stem cells so transplants replace these
  • Research is being carried out to develop ways of growing whole organs from stem cells. The organs can then be transplanted into the patient to replace organs that have been damaged or are diseased.
• adult stem cells:

  • found in bone marrow of adults
  • limited potency
  • multipotent
• embryonic stem cells:

  • in human embryos
  • pluripotent
  • more useful but ethical implications
• induced pluripotent stem cells: made by taking adult stem cells and reprogramming them into a stem cell state using a cocktail of transcription factors. The transcription factors cause the adult cells to express genes for pluripotency. The transcription factors are introduced into cells by packaging them in a virus, which then infects the adult cells. the most useful type of stem cell in research. They don’t have ethical baggage, can be used to make any cell type. They can be made from a patient’s own cells. They are genetically identical to the patient, reducing the risk of rejection.
• Transcription Factors:

  they activate and deactivate genes. TFs which activate genes are called activators whereas TFs which deactivate genes are referred to as repressors. Activators work by binding to the beginning of the gene and helping RNA polymerase to bind and transcribe the gene. Repressors work by binding to the gene and blocking RNA polymerase from binding.
• transcription factors, Oestrogen:

  Oestrogen works by binding to an oestrogen receptor to form an oestrogen-oestrogen receptor complex. Oestrogen is a steroid hormone so it can cross the cell membrane and get inside the nucleus. Once there, it binds to specific sites on DNA, either activating or inhibiting the expression of its target genes.
• RNA interference:

  RNA interference is when small strands of RNA bind to messenger RNA to form a double-stranded structure. This prevents the mRNA from being translated into proteins and prevents the gene from being expressed.

  two types, small interfering RNA, microRNA
• small interfering RNA:

  • Double-stranded siRNA binds to proteins in the cytoplasm and unwinds.
  • A single strand of siRNA binds to the target mRNA – the siRNA will have a complementary sequence to its target so will only bind to specific mRNAs.
  • The proteins that are bound to the siRNA chop the mRNA into fragments.
  • The small mRNA fragments are moved into a processing body for degradation.
• MicroRNA:

  • Unlike siRNA, miRNA isn’t completely complementary to its target mRNA so it is less specific.
  • miRNA binds to proteins in the cytoplasm
  • The miRNA-protein complex binds to the target mRNA and blocks the ribosome from translating the mRNA.
  • The mRNA is moved into a processing body and is either stored or degraded.
• Genome:

  all the genes present in an organism
• Proteome: all of the proteins present in an orgasim
• genome sequencing basics

  • can't sequence accurately long DNA so needs to be made into shorter fragments
  • once we know sequence we can determine amino acid sequence
  • this then can determine proteome
• Genetic engineering:

  to sequence the genome, you first have to chop it up into smaller pieces because the sequencing method won’t work on a big section of DNA in one go. Scientists also need to produce DNA fragments if they want to take a useful gene from one species and place it in another species.
• transgenic:

  the modified organisms
• restriction enzymes:

  • Restriction enzymes - enzymes that cut double-stranded DNA at specific recognition sequences.
  • These sites are palindromic – they read the same backwards and forwards.
  • When the restriction enzyme detects its recognition sequence, it cuts DNA in one of two ways – either straight down the middle, creating ‘blunt ends’ or in a zig-zag fashion, creating ‘sticky ends’
  • Scientists analyse the DNA to determine which recognition sites are present either side of the gene of interest. They will then use the corresponding enzymes to extract the gene from the longer section of DNA.
• 'sticky ends':

  Sticky ends are overhangs of single-stranded DNA at the ends of the fragment.