D1.3 - MUTATIONS AND GENE EDITING

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what is a gene

a section of DNA that encodes for a specific trait

outline what gene mutation is and how it occurs

definition: mutation is a change in nucleotide sequence of a section of DNA that encodes for a specific trait

how it occurs: it occurs through a point mutation which is when a single nucleotide is added, deleted or changed (base substitutions, insertions and deletions (aka frameshift mutations)

outline what gene mutation is caused by

• caused by mutagens and proofreading errors

  • DNA replication: DNA polymerase fails to detect and remove the incorrectly paired nucleotide during DNA replication

  • repair: incorrect nucleotide failed to be removed during mismatch repair

    • replication and repair errors contribute to mutations

  • mutagen: agent that induces permanent change to genetic material of organism

    • raditation: x-ray, uv light radiation

    • chemical: reactive o2 species, mustard gas, nitrous acid

    • biological: viruses, bacteria

explain base substitution mutations (aka - single nucleotide polymorphisms)

• specific type of mutation where one nucleotide base in the DNA sequence is replaced by another

  • 3 types: silent, missense, nonsense

missense - beneficial/neutral: DNA change does not alter amino acid sequence of polypeptide chain (genetic code degenerate, certain codons may code for same amino acid)

missense - beneficial/neutral or harmful: DNA change alters a single amino acid sequence of polypeptide chain (eg. sickle cell anaemia: CTC → CAC, glutamine → valine)

nonsense - harmful: DNA change creates premature STOP codon, resulting in a truncated polypeptide

why is single nucleotide polymorphism the result of base substitution mutations?

this is because of the degeneracy of the genetic code as they may or may not change a single amino acid in a polypeptide

• single specific nucleotide changed in a large proportion of population, can identify genetic markers and causes for disease condition

explain frameshift mutations (insertions/deletions)

• the addition or deletion of a single base of DNA

  • shifts the reading frame in translation - single nucleotide frameshifts usually result in non-functioning proteins

    • all the codons “downstream” are changed

      • can dramatically change an amino acid sequence

      • have a significant impact on cellular activity - ceases the likelihood of a functioning polypeptide

explain sickle cell anaemia which is mutation that resulted in a changed protein structure

• caused by base substitution mutation at the 6th codon for beta chan haemoglobin

• DNA sequence changes from CTC→CAC, mRNA changes from GAG→GUG so the 6th amino acid changes from glutamic acid to valine

  • alters the structure of haemoglobin (from globular to fibrous), forming insoluble fibrous strands which _ the ability to carry O2 efficiently resulting in reduced O2 level supplied in tissues

  • erythrocyte RBC changes shape to a sickle shape

• sickle RBC are more rigid, viscous and easily aggregated making it easier to block smaller blood vessels

• recessive trait so it requires two copies of mutant allele

  • only one mutant allele: carriers → increased protection from malaria infection

mutation is random

• they occur anywhere in the genome

  • some nucleotide bases are more prone to mutations

  • C→U spontaneously and requires repair

  • cells have no deliberate mechanism for mutating their DNA

  • there is no natural mechanism that is known for making a deliberate change to a particular base with the purpose of changing a trait

mutations in somatic cells

• somatic cells: all the cells in the body except for germ cells

  • mutations in somatic cells can cause disease (such as cancer) during a persons lifetime

    • would not be passed on to offspring

mutations in germ cells

• germ cells: cells that give rise to eggs or sperm

  • mutations in germ cells can lead to mutations in gametes (sperm/egg)

    • can be passed onto offspring

    • inherited mutations can have various effects on the offspring

mutation as a source of genetic variation

• mutation is an original source of all genetic variation (alleles)

  • they can be either neatral, harmful or beneficial, but in the long term: they are essential for adapting to environmental changes and developing adaptations by natural selection

what is gene knockout?

gene knockout is a technique used for investigating the function of a gene by changing it to make it inoperative allowing scientists to learn about its function by its absence

explain how the library of gene knockout organisms are utilised in research by scientists

• scientists use a library of genetically engineered gene knockout organisms to understanding gene function

  • gene knockout organisms exist to act as model organisms for research purposes

    • mice with allergies, diabeties, cancer

    • libraries of bacteria, yeast, fruit flies, zebrafish

      • scientists observing the phenotypes (observable traits) of knockout organisms provide insights into gene function

explain how CRISPR-Cas9 is utilised in gene editing

• precisely cuts DNA at desired sequences

  • creates mutations in specific genes

OR

• allow new sequences to be inserted

  • natural DNA repair processes take over

state one example on how CRISPR-Cas9 is applied in gene editing

scientists managed to slow the growth of cancer cells by targeing a protein called Tudor-SN that helps with cell division which could help inhibit fast-growing cells

NOS 1: explain how commercial genetic tests can yield information about potential future health and disease risk

• without expert interpretation, this information could be problematic

  • misinterpretation/misunderstanding

  • anxiety

  • uninformed decisions

  • family & social impacts

  • lack of counseling or comprehensive healthcare

NOS 2: explain why certain potential uses of CRISPR raise ethical issues that must be addressed before implementation

• scientists across the world are subject to different regulatory systems

  • therefore, there is an international effort to harmonize regulation of the application of genome editing technologies such as CRISPR

explain how hypotheses can account for conserved or highly conserved sequences in genes

• conserved sequences are identical or similar across a species or a group of species

  • highly conserved sequences are identical or similar over long periods of evolution

• scientists have come up with a few hypothesis’s as to why this exists

  • HYPOTHESIS 1: genes’ proteins are so fundamental to life, that mutations and variations don’t survive and persist

  • HYPOTHESIS 2: the genes have had low mutation rates