Molecular Biology Week 10 Study Notes PDF

Molecular Biology Week 10: Study Notes In week 10, students study genetic mutations: what they are, and how they occur. We also look at their impact on human health and how scientists deliberately insert mutations into genes to gain a better understanding of how pro...

Molecular Biology Week 10: Study Notes In week 10, students study genetic mutations: what they are, and how they occur. We also look at their impact on human health and how scientists deliberately insert mutations into genes to gain a better understanding of how proteins work. You will be expected to write supplementary study notes for these units and they will need to be submitted at the end of the week. ________________________________________________________________________________ DNA repair – proofreading Briefly discuss DNA repair: how many errors DNA polymerases make, how they are repaired, and what the consequences of unrepaired errors are. There are many errors that DNA polymerases can make like mismatch repair (MMR), base excision repair (BER), nucleotide excision repair (NER), and homologous recombination and non-homologous end joining. MMR is a system that identifies and repairs base mismatches or small insertions or deletions that occur during DNA replication. BER is a repair pathway that fixes small, non-bulky lesions of bases by removing the damaged base and replacing it with the correct one. NER removes bulky lesions by excising a segment of the DNA strand and filling it with the correct one. Homologous recombination uses a sister chromatid as a template while non-homologous end joining joins the broken ends directly but sometimes can lead to errors. The consequences of the unrepaired errors is that the genes that are involved in the cell cycle control the suppressor genes that can lead to mutations and then the accumulation of these mutations can lead to genetic diseases or cancer or cell death. Mutations There are two types of mutations: Gene Mutations – these occur at the gene level and involve simple substitutions, additions, or deletions. Chromosomal Mutations – these result in changes to the actual chromosomes. Changes can occur in the structure of chromosomes or the number of chromosomes. Use the following table to document what each of the different types of mutations are. You may use text and/or images. Type Descriptor Silent mutation (Gene mutation) A mutation in which a change in a single nucleotide does not change the amino acid that it is coded for. Example: UCU → UCC (both code for Serine). Conservative missense (Gene mutation) A mutation resulting in a different amino acid being incorporated, but the new amino acid has similar properties. Example: Glutamate (Glu) → Aspartate (Asp). Non-conservative missense (Gene mutation) A mutation that replaces an amino acid with one that has different properties, potentially altering protein function. Example: Glutamate (Glu) → Valine (Val). Nonsense (Gene mutation) A mutation that changes a codon into a stop codon, prematurely terminating protein synthesis. Example: UGG → UGA (stop). Frameshift (substraction or insertion) A mutation caused by insertion or deletion of nucleotides not in multiples of three, changing the reading frame and (Gene mutation) potentially resulting in a nonfunctional protein. Example: Addition of "A" in AUG → AAGUG. Substitution (transition and Transition tranversion) Replacement of one purine with another (A ↔ G) or one pyrimidine with another (C ↔ T). (Gene mutation) Transversion Replacement of a purine with a pyrimidine (A/G ↔ C/T) or vice versa. Duplication (Chromosomal sequence) A segment of the chromosome is copied and inserted into the genome, resulting in extra genetic material. Deletion (Chromosomal sequence) A segment of a chromosome is removed or lost, potentially eliminating essential genes  Inversion A chromosome segment is reversed end to end, altering the (Chromosomal sequence) gene's orientation but not its amount. Translocation (Chromosomal sequence) A segment of one chromosome is transferred to another chromosome, which may be reciprocal or unbalanced. Monosomy A condition where a chromosome is missing in a diploid organism, resulting in 2n-1 chromosomes. Example: Turner syndrome Trisomy A condition where an extra chromosome is present in a diploid organism, resulting in 2n+1 chromosomes. Example: Down syndrome Induced mutations What is the difference between a spontaneous and an induced mutation? Spontaneous mutation is naturally occurring this often arises from errors in DNA replication or natural background radiation whereas induced mutation is cause by external agents (mutagens) like a physical, chemical or biological factor that interacts with the DNA and increases the mutation rates. Provide one example each for a physical, chemical, and biological mutagen. Physical: Ultraviolet radiation that causes thymine dimers in DNA that leads to errors during replication. Chemical: Nitrous acids that deaminates adenine and cytosine that causes them to mispair during DNA replication Biological: Some viruses like HPV that can integrate into the host genome and disrupt the normal cellular regulation potentially leading to cancer. Complete the following table on the different causes of cancer, their relative occurrence and description. Relative occurrence Description Random errors 60%-70% Mutations occurring randomly during DNA replication or cell division, unrelated to inheritance or environment. Environmental 25%-30% Happens by the exposure to external factors such as smoking tobacco, UV radiation which leads to damage of DNA or increased likelihood of mutations. Inherited 5%-10% Caused by mutations in the germline DNA that passed from the parents to their offsprings, these mutations often affect the tumor suppressor genes or the DNA repair genes. Using Mutations for Research Scientists deliberately induce mutations so they can examine how it affects protein structure and function. One of the ways this is done is through site-directed mutagenesis. The technique uses PCR to amplify plasmid DNA (containing the mutation). That mutation is then transformed into the cell for expression. In your pre-concept pages, an example was provided of how a scientist deliberately changed an amino acid from proline to alanine. Complete the following table, annotating what is happening at each step. Annotations / descriptors The original plasmid A circular DNA molecule that serves as the starting template for introducing mutations. Typically contains the gene of interest and selectable markers. Primer Design Specific oligonucleotide primers are designed to introduce the desired mutation (e.g., substitution, insertion, or deletion). Primers are complementary  to the plasmid, with the mutation incorporated into their sequence. Elongation DNA polymerase extends the primers, synthesizing a new DNA strand complementary to the template, including the mutation into the newly synthesized plasmid. Amplification The mutated plasmid is amplified through polymerase chain reaction (PCR), producing copies of the plasmid containing the desired mutation. Mutated plasmid The final product after amplification and transformation into bacteria for replication. The plasmid now contains the intended mutation and can be used for downstream applications, such as protein expression or functional studies. You have studied various diseases in this unit. Document some brief facts about the disease and the types of mutations involved in the following table. Disease Brief facts (symptoms, treatments, the type of mutation) Sickle Cell anaemia - Symptoms: Fatigue, pain crises, organ damage, anaemia due to sickle- shaped red blood cells. - Treatments: Blood transfusions, hydroxyurea, gene therapy. - Type of Mutation: A single nucleotide substitution (missense mutation) in the HBB gene (GAG → GTG), causing glutamic acid to be replaced by valine in haemoglobin. Cystic Fibrosis - Symptoms: Thick mucus production affecting lungs and digestive system, recurrent infections, difficulty breathing. - Treatments: Physiotherapy, antibiotics, CFTR modulators.  - Type of Mutation: Most common mutation is ΔF508, a deletion of three nucleotides in the CFTR gene leading to loss of phenylalanine at position 508 Turner Syndrome - Symptoms: Short stature, delayed puberty, infertility, heart defects. - Treatments: Growth hormone therapy, estrogen replacement therapy. - Type of Mutation: Monosomy (45,X); a chromosomal disorder where one X chromosome is missing in females. Downs syndrome - Symptoms: Intellectual disability, characteristic facial features, heart defects, hypotonia. - Treatments: Supportive therapies (speech, physical, occupational therapy), educational interventions. - Type of Mutation: Trisomy 21; presence of an extra copy of chromosome 21. A cancer of your This section can be completed after Tutorial A. It is not needed for your choosing pre-tutorial work but will be needed for your final study notes. (Based on the faulty gene studies from Tutorial A)