mutation

what is mutation?

mutation is a change in the:

1. sequence of DNA

2. number of chromosomes

3. structure of chromosomes in an organism

mutation

• it can occur at different scales:

  1. at a smaller scale (DNA level) → gene mutation (affects one gene) OR

  2. at a larger scale (chromosomal level) → chromosomal mutation (may affect more than one gene)

• this produces a change in the genotype which may be inherited by cells derived by mitosis or meiosis from the mutant cell

gene mutation

a gene mutation is the change in sequence of nucleotides of a gene

• it may be a change in only a single nucleotide (point mutation → single base change) or in 2 or more nucleotides

• gene mutation may change the sequence of amino acids in a polypeptide chain ⇒ primary structure

• this may affect the structure and function of the protein, and thus affect the characteristic phenotype of the organism

substitution mutation → type of gene mutation

occurs when one or more nucleotides in the nucleotide sequence of the gene is/are replaced by other nucleotide(s)

• most common type of gene mutation and is usually not as serious as deletion or insertion mutations

• substitution mutation may give rise to any of the 3 effects, depending on the position of the nucleotide affected

missense mutation → effects of substitution mutation

• nucleotide change results in a different codon that codes for a different amino acid

• these amino acids contain a different R group, with different physical and chemical properties

• the amino acid sequence of the polypeptide chain is now different

• this affects folding of polypeptide chain, resulting in altered secondary and tertiary structures and its 3D conformation

• the protein is non-functional

nonsense mutation → effects of substitution mutation

• nucleotide change results in a codon changed to a stop codon (UAA, UAG, UGA) in the mRNA

• translation of mRNA is pre-maturely halted, resulting in a truncated (shortened) polypeptide chain than original

• this affects folding of polypeptide chain, resulting in an altered secondary and tertiary structure and its 3D conformation

• the protein is non-functional

silent mutation → effects of substitution mutation

• nucleotide change results in a different codon which still codes for the same amino acid, due to genetic code being degenerate

• silent mutation has no effect on the amino acid sequence, and the polypeptide is not affected

addition/insertion mutation → type of gene mutation

insertion/addition mutation occurs when one or more nucleotide is/are added/inserted into the nucleotide sequence of the gene

deletion mutation → type of gene mutation

deletion mutation occurs when one or more nucleotide is/are removed from the nucleotide sequence of the gene

effects of insertion or deletion mutation involving 1-2 nucleotides (not a multiple of 3 nucleotides)

frame-shift mutation: a mutation occurring when the number of nucleotides inserted or deleted is not a multiple of three, resulting in the incorrect reading of the triplets from the point of insertion or deletion

1. frame-shift mutations occur when one or two nucleotide(s) is/are inserted or deleted

2. are generally more severe than substitution mutations, because the reading of the codons (reading frame) is changed from the point of mutation

   • reading frame: grouping of nucleotides in threes

• resulting protein formed may be

  1. non-functional

     • a non-functional protein is produced as ribosomes read incorrect triplets from the point of insertion or deletion ⇒ original sequence of codons on the mRNA is no longer read

     • this results in the sequence of amino acids from the point of addition/deletion being completely changed

  2. truncated/shortened

     • the new sequence of codons on the mRNA from the point of addition/deletion may consist of a premature stop codon

effects of insertion or deletion mutation involving 3 nucleotides

• effects are not as drastic as 1 or 2 nucleotides

• there is no frame-shift mutation → only an extra or a missing amino acid results

effects of gene mutation

• a change in DNA nucleotide sequence leads to a change in codon, and may/may not result in different amino acid in the polypeptide chain

• assuming the mutation results in a change in amino acid, this can lead to change in:

  1. folding to form the secondary and tertiary structures

     • change in codon may change the type of amino acid incorporated into a polypeptide chain during translation

     • depending on the property (determined by R group) and the position of changed amino acid, the final protein may be affected

     • if the amino acid is involved in the maintenance of the secondary or tertiary structure of the protein, the mutation will affect the formation of crucial bonds between R groups of amino acid residues that ensured proper folding of the polypeptide ⇒ protein loses its specific 3D conformation

  2. function of the protein

     • in an enzyme, if the amino acid that is affected is involved as a catalytic/contact residue of the active site ⇒ enzyme is non-functional

       • if it is a non-structural amino acid, the folding and function is not affected

• assuming the change in codon results in a premature STOP codon (UAA, UAG, UGA), the length of the polypeptide will be shortened (truncated)

  • resulting in early termination of translation

  • resultant polypeptide chain will be truncated (shortened) and may lead to a change in the secondary and tertiary structure of the protein and affect its function

sickle cell anaemia

• in a normal adult, haemoglobin (Hb A) is a quaternary protein → tetramer of 2 different types of polypeptide chains, 2 α-globin chains and 2 β-globin chains

• the α and β chains are coded by 2 different genes found on 2 different chromosomes

• caused by substitution mutation

effects of the DNA substitution mutation → sickle cell anaemia

1. change in the gene coding for β-globin chain

   • a point mutation (single nucleotide substitution mutation) occurs in the gene coding for the β-globin chain/ β-globin gene

   • the nucleotide thymine is replaced by adenine in the DNA template strand

2. change in amino acid sequence of polypeptide chain

   • as a result of the point mutation, the 6th codon in the mRNA is changed

   • glutamic acid (glutamate) amino acid in the chain is replaced by valine

3. change in properties of mutated haemoglobin (Hb S) → sickle cell haemoglobin

   • the R group of glutamate is hydrophilic while that of valine is hydrophobic

   • this change results in the formation of a mutated haemoglobin molecule

   • Hb S has a hydrophobic region on the surface of the protein, due to hydrophobic amino acid residue, valine

   • in low oxygen concentration, the Hb S haemoglobin molecules interact with one another via hydrophobic interactions to crystallise into rod-like fibres ⇒ Hb S is less efficient in carrying oxygen, resulting in anaemia

4. change in shape of red blood cell

   • rod-like fibres of the Hb S distort the normal circular, biconcave disc shape of the red blood cell into sickle shape, which blocks blood vessels

effects of sickle cell anaemia

• this interferes with blood circulation and deprives organs of oxygen

  • organs become damaged and may lead to death

  • sickle-shaped red blood cells also have a short life span, and are brought to the spleen to be destroyed

  • the spleen may become enlarged due to the accumulation of the sickle-shaped red blood cells

genetic basis of sickle-cell anaemia

• it is an autosomal recessive disorder → located on non-sex chromosomes

• affected individuals are homozygous for the mutant allele, having two copies of the mutant allele, one inherited from the father and another from the mother

• heterozygous individuals, having one copy of the mutant allele and one copy of the normal allele are said to be sickle cell trait → may exhibit symptoms

  • individuals with sickle cell trait have selective advantage in geographical areas where malaria is endemic and will be able to survive in malaria-prone areas ⇒ heterozygote advantage

chromosomal mutation

refers to changes in the number or structure of chromosomes

aneuploidy (2n ± 1) → change in the number of chromosomes

• number of chromosomes is no longer in exact multiples

• occurs due to non-disjunction which is the:

  • failure of a pair (or pairs) of homologous chromosomes to separate during anaphase I of meiosis OR

  • failure of chromatids of one (or more) chromosomes to separate during anaphase II of meiosis

• when these gametes are fertilised with a normal haploid gamete (n), the resultant zygote may have:

  1. trisomy (2n + 1): a condition where there are 3 copies of the same chromosome instead of the usual 2 copies (homologous chromosomes)

     • e.g. Down syndrome, where there is an extra chromosome 21 (Trisomy 21)

  2. monosomy (2n - 1): a condition where there is only 1 copy of a chromosome instead of the usual 2 copies (homologous chromosomes)

non-disjunction

• non-disjunction: an error in meiosis or mitosis, in which both members of a pair of homologous chromosomes or both sister chromatids fail to separate and did not move apart to opposite poles

• these failures can occur because spindle fibres may not have attached properly to the centromere ⇒ gametes with one extra chromosome (n + 1) or one less chromosome (n - 1) will be produced

polyploidy (extra set of chromosomes) → change in the number of chromosomes

refers to cells having one or more extra sets of chromosomes (e.g. 3n, 4n)

• occurs when a 2n zygote fails to divide after replicating its DNA due to:

  • failure of complete cytokinesis OR

  • failure of spindle fibres to attach to sister chromatids, thus the sister chromatids are not pulled to opposite poles during mitosis (non-disjunction)

• such mutations will mostly be lethal in animals

• in plants, such mutations are not lethal

  • the artificial induction of polyploidy is a common technique to overcome the sterility of a hybrid species during plant breeding

• e.g.: triticale is the hybrid of wheat and rye

  • it combines sought-after characteristics of the parents, but the initial hybrids are sterile

  • after polyploidization, the hybrid becomes fertile and can thus be further propagated to become triticale

  • hybrid is sterile (infertile) because the chromosomes from wheat are not homologous and cannot pair during meiosis

deletion → change in the structure of chromosome

this involves the loss of a segment of the chromosome → shorter chromosome which is missing certain genes

inversion → change in the structure of chromosome

• occurs when a segment of chromosome breaks off and reattaches to the chromosome in the reverse orientation

• as a result, the normal sequence of the genes is reversed

• in some cases, when one of the chromosomes breaks within a gene whose function is critical to the organism → lethal gene mutation ⇒ death of the organism

translocation → change in the structure of chromosome

• a segment of one chromosome breaks off and joins another non-homologous chromosome

• translocation can be:

  • reciprocal → non-homologous chromosomes exchange fragments OR

  • non-reciprocal → a chromosome transfers a fragment without receiving a fragment in return

duplication → change in the structure of chromosome

• a segment of a chromosome replicates so that a set of genes is repeated ⇒ amount of gene product increases, and this may affect the phenotype

• duplications may arise from the

  • incorporation of a region from a homologous chromosome OR

  • unequal crossing-over during meiosis I

comparison between gene mutation and chromosomal mutation

point of comparison	gene mutation	chromosomal mutation
changes to DNA	change in sequence of DNA	change in structure or number of chromosomes
number of gene loci affected	involves only one gene locus	involves multiple gene loci
mechanism involved in the mutation	brought about by deletion, insertion or substitution of one or more nucleotides	brought about by deletion, duplication, inversion or translocation of several gene loci on a chromosome due to non-disjunction during meiosis I or meiosis II
how it gives rise to genetic variation	forming new alleles • some new alleles may result in new proteins with novel functions	by reshuffling of alleles on a chromosome
changes to chromosome number	does not change chromosome number	changes chromosome number through polyploidy or aneuploidy
frequency	more frequent • genes outnumber chromosomes by several thousand to one	less frequent
evolutionary importance	of evolutionary importance because acquisition of new alleles increases gene pool for natural selection to operate	generally of lower evolutionary importance because it only reshuffles alleles already existing in the gene pool however, polyploidy may give rise to new species in some cases
examples	sickle cell anaemia • due to substitution of one nucleotide (T to A in the DNA template strand)	Down syndrome • due to an extra chromosome 21

bioethics

• ethics: a field of study that looks at the moral basis of human behaviour and attempts to
  determine the best course of action in the face of conflicting choices

• bioethics: a subfield of ethics that is applied to the life sciences → aims to help society
  make decisions about how to best use scientific knowledge and policy decisions
  regarding medicines and treatments

• the first step in the study of bioethics is to recognize and define what the ethical question
  is → usually is a decision that is difficult to make, with multiple alternate solutions

  • these solutions all have their pros and cons ⇒ no solution which satisfies all
    individuals involved as the solutions involve conflicting moral choices

• e.g.: should individuals who donate an organ choose who their organ should go to? should parents select the sex of their child in advance?

• in consideration of any ethical question, it is important to examine the facts available and assess what additional information is needed

four principles of bioethics

1. respect for autonomy: everyone has inherent worth and dignity. it is a person’s right to make their own choices

2. beneficence: maximising the benefits of the outcome

3. non-maleficence: minimising the harms of the outcome. together with beneficence, it considers how to act in everyone’s best interest while doing no harm

4. justice: everyone should be treated fairly and equitably. it requires that everyone receive their fair share of resources and opportunity

bioethical arguments

1. identify the ethical question

2. identify facts and questions that remain

3. identify stakeholders and bioethical principles to apply

4. constructing a strong justification

   • a clearly-stated position (claim) that relates directly to the ethical question

   • reference to important facts and science content of the case → evidence

   • reference to one or more principles of bioethics → reasoning

prenatal screening for trisomy-21 (down syndrome) → case study

1. uchal translucency (NT) measurement

   • uses ultrasound to measure the thickness of the fluid-filled area at the back of the baby’s neck at 11 to 14 weeks of pregnancy → detection rate is 80%.

2. maternal serum screening

   • the mother’s blood is measured for alpha-fetoprotein (AFP) and human chorionic gonadotrophin (HCG), produced by the baby and the placenta at 15 to 20 weeks of pregnancy → mums with low AFP and high levels of HCG have a higher risk of having
     a baby with Down syndrome → detection rate is 66%

• NT and maternal serum screening can be combined and performed at 11 to 14 weeks, increasing the detection rate to 90% → recommended test in singapore

• in singapore, screening tests are optional and are offered to all mothers regardless of age. the screening tests do not confirm if the child will have Down syndrome but only indicate the risk of them having it. Parents can then decide if they wish to have a confirmatory test

• if the screening test shows that the risk of Down syndrome is significantly high, the child is screen positive. however, being screen positive does not mean that the child has Down
  syndrome. If the risk is high enough, further confirmatory tests can be carried out to obtain fetal cells

• these tests are usually invasive and carries a risk of miscarriage:

  1. Chorionic villus sampling (CVS)

     • a biopsy of the placenta → a tissue sample of the placenta (containing a mixture of maternal and fetal cells) is obtained through the vagina or abdomen and is usually performed at 10 to 13 weeks

       • carries a higher rate of miscarriage compared to amniocentesis but can also be used to test other genetic disorders

  2. amniocentesis

     • involves putting a needle into the amniotic sac under ultrasound guidance and drawing out amniotic fluid containing fetal cells for testing → performed at 15 to 20 weeks

       • carries a low risk of miscarriage and is more accurate than CVS

• once the fetal cells are obtained, genetic testing can be performed on the fetal cells to confirm trisomy-21, the genetic tests are:

  1. karyotype analysis to check chromosomes for large chromosomal abnormalities

  2. chromosome microarray analysis (CMA) to check for microdeletions (smaller
     chromosomal abnormalities) & chromosomal translocation

• other genetic tests can be carried out on fetal cells, such as whole exome sequencing and DNA sequencing for specific mutations in the DNA, which can identify other genetic disorders

arguments for prenatal genetic screening → case study

1. prevents the birth of children with severe, lifelong disability

   • using the bioethical principles of beneficence and non-maleficence, this allows the government to make more financial savings for the betterment of the country’s economy

   • using the bioethical principles of beneficence and non-maleficence, parents can prevent their child from suffering from intellectual disabilities and physical ailments. at the same time, they will have an easier time looking after the child, and the fear of their child not being able to be independent would also be removed

2. women have the right to make decisions regarding the fetus

   • using the bioethical principle of respect for autonomy, a pregnant woman has the rights to know if the fetus has Down syndrome and the rights to decide what to do after knowing it

3. allows for early intervention, which can enhance the ability of newborns with Down syndrome

   • using the bioethical principles of beneficence and non-maleficence, parents will be able to prepare in advance to introduce early interventions for their newborn, which will allow them to have a better prospect in life

arguments against prenatal genetic screening

1. with less women going for pre-natal screening, there will be less abortion of fetus with Down syndrome and as such, there will be more individuals with Down syndrome

   • using the bioethical principles of beneficence and non-maleficence, with more individuals with Down syndrome, there will be more resources and services provided for them to allow them to lead a long and satisfying life

2. the issue should not be preventing Down syndrome, but rather overcoming and fixing society and its biases and discrimination to better accommodate these individuals

   • using the bioethical principle of respect for autonomy, individuals with Down syndrome should be considered individuals with worth and value. Down syndrome should not be prevented by abortion for society to be free of genetic defects. rather, they are members of society and should be treated as such

   • using the bioethical principle of justice, all individuals have a right to life. aborting fetuses with Down syndrome ends their life, removing the possibility of them living a fulfilling life. additionally, some of the testing carries a significant
     risk of miscarriage, endangering the life of the fetus

3. individuals with Down syndrome are seen by their families as individuals with unique personality traits and quirks who love and are loved and deserve a long and satisfying life

   • using the bioethical principle of justice, individuals with Down syndrome should not be discriminated against, society should not be trying to prevent Down syndrome

explain why changing a single base in the gene coding for a protein may have a major effect on the function of a protein [faq] → generic protein

• DNA mutation: the single base change in the DNA (i.e. substitution mutation)

• effect on the mRNA: this changes a codon in the mRNA after transcription

• effect on the amino acid sequence of the protein: this results in a different amino acid with a different R group upon translation. for example, a hydrophilic amino acid could be replaced by a hydrophobic amino acid. the amino acid sequence / primary structure of the polypeptide is now different

• effect on the folding of the protein and property: this affects the secondary structure or tertiary structure of the polypeptide / folding of the polypeptide into its 3D conformation / shape. hence, the property of the protein (e.g. solubility) is different

• effect on the function of the protein: the protein may become non-functional

explain why changing a single base in the gene coding for a protein may have a major effect on the function of a protein [faq] → stop codon is created

• DNA mutation: the single base change in the DNA (i.e. substitution mutation)

• effect on the mRNA: this changes original codon in the mRNA to a stop codon (e.g. UAA, UGA, UAG)

• effect on the amino acid sequence of the protein: this results in premature termination of translation and gives rise to a truncated / shortened polypeptide. the amino acid sequence / primary structure of the polypeptide is now different

• effect on the folding of the protein and property: this in turn affects the secondary structure or tertiary structure of the protein / folding of the polypeptide chain into its 3D conformation

• effect on the function of the protein: the protein may become non-functional

explain why changing a single base in the gene coding for a protein may have a major effect on the function of a protein [faq] → enzyme is involved

• DNA mutation: the single base change in the DNA (i.e. substitution mutation)

• effect on the mRNA: this changes a codon in the mRNA

• effect on the amino acid sequence of the protein: this results in a different amino acid with a different R group upon translation. the amino acid sequence / primary structure of the polypeptide is now different

• effect on the folding of the protein and property: this affects the 3D conformation of the active site such that its shape is no longer complementary to shape of its substrate. enzyme-substrate complex cannot form

  • if the original amino acid is a contact residue at the active site, this mutation may affect the binding of the substrate to the active site. Enzyme-substrate complex cannot form

  • if the original amino acid is a catalytic residue at the active site, this mutation may affect the enzyme ability to act on bonds in substrate

• effect on the function of the protein: the enzyme becomes non-functional

explain why inserting or deleting a single base in the gene coding for a protein may have a major effect on the function of a protein

• DNA mutation: the single base insertion / deletion in the DNA (i.e. insertion / deletion mutation)

• effect on the mRNA: this results in frameshift mutation in which the reading of codons (i.e. reading frame), from the point of mutation onwards is changed

• effect on the amino acid sequence of the protein: this results in different amino acids upon translation. the amino acid sequence / primary structure of the polypeptide is now different

• effect on the folding of the protein and property: this affects the secondary structure or tertiary structure of the polypeptide / folding of the polypeptide into its 3D conformation. hence, the property of the protein (e.g. solubility) may be affected

• effect on the function of the protein: the protein becomes non-functional