Mutations: Effects, Inheritance, and Consequences

Mutations

• A mutation constitutes a change in the nucleotide sequence of DNA.
• Mutations usually result in reduced or lack of function of RNAs and proteins.
• Evolution via mutations has led to more species, better adapted species, and more complex organisms.
• Mutations are heritable if unrepaired before DNA replication, ensuring daughter cells inherit the change.
• Mutations happen randomly, not due to selective pressure, but some may result in organisms that are better adapted to certain conditions.

Luria and Delbrück experiment

• Illustrated that mutations occur randomly
• Involves bulk flask of bacteria and individual cultures plated with T1 phage

Classification of Mutations

• Very large mutations resemble chromosomal aberrations.
  • This involves changes in hundreds of thousands or even millions of nucleotides.
  • Can be observed through a microscope.
• There are intermediate mutations, like those caused by transposable elements.
  • Includes changes in hundreds of nucleotides.
• Small mutations are referred to as point mutations.
  • Point mutations strictly refer to changes of a single nucleotide in a sequence.

Point Mutations

• Substitutions entail transitions and transversions.
  • Transitions: purine to purine or pyrimidine to pyrimidine (G 🡪 A, A 🡪 G, C 🡪 T, T🡪 C).
  • Transversions: purine to pyrimidine or pyrimidine to purine (A 🡪 T, A 🡪 C, C 🡪 G, T 🡪 A).
• Insertions that add nucleotides to the sequence
• Deletions that remove nucleotides from the sequence

Silent Mutation

• These terms only apply to mutations in the open reading frame part of a gene
• Does not change the amino acid sequence

Missense Mutation

• Results in a change in the amino acid sequence

Nonsense Mutation

• Results in a premature stop codon in the amino acid sequence

Insertion Mutation

• Will typically change the amino acid sequence

Deletion Mutation

• Will also change the amino acid sequence

Frame-Shift Mutations

• Insertions or deletions of nucleotides in a number that is not a multiple to three within the Open Reading Frame (ORF).

Classification of mutations based on functional changes

• Loss-of-function mutations lead to the cell losing some function.
  • May occur due to changes causing reduced protein functionality of the protein or lower levels of protein being produced which reduces its impact.
  • These mutations may occur in any part of a gene like the promoter region, 5'-UTR region, or in the introns.
• Gain-of-function mutations lead to the cell gaining function.
  • Generally occur due to higher levels of protein production,.
  • Can rarely occur due to an amino acid sequence change that results in acquiring a new function.
  • These mutations generally occur in the regulatory regions of a gene, like promoters.
• Loss-of-function mutations are more common than gain-of-function mutations.

Forward and Reversion Mutations

• Includes a forward, and original mutation.
• Needs a second mutation that restores the original function in the cell.
  • True reversion restores original function by restoring the gene sequence or the encoded protein.
  • Suppression restores original function, without restoring the original squence.
    • Intragenic Suppression- the 2nd mutation occurs in same gene as the original mutation
    • Intergenic Suppression- 2nd mutation occurs in a different gene than the original.
  • If the original is a deletion, the reversion must be an insertion, but not necessarily in the same position.
  • If the original is an insertion, the reversion must be a deletion, but not necessarily in the same position.
  • Sequence mutations are from easier to harder to revert: - Deletions/insertions - Transitions - Transversions

Spontaneous Mutations

• DNA replication errors can occur. However, DNA polymerases usually have proofreading ability based on their 3' to 5' exonuclease activity.
• Tautomeric forms of the bases can result in DNA polymerase leaving the wrong base in the new strand. The tautomeric form still pairs with a base of the other type, purine with pyrimidine and vice versa. These cause transition mutations.
• Slippage or sliding of the template or new strand by repeated sequences will lead to deletions or insertions respectively. The ORF can have a frame-shift mutation if the repeat is not a trinucleotide or a number of bases that is a multiple of three.
• The breakage of bind between deoxyribose and purine can spontaneously occur
• Deamination is the removal of an amino group, most commonly from cytosine

Hot Spots

• Sequences that accumulate a higher number of mutations than others
  • Sequences with repeats will cause more mutations due to strand slippage
  • Sequences with a high proportion of methylated cytosines may also cause more mutations.

Induced mutations

• Radiation can cause induced mutations:
  • Includes high energy, ionizing isotopes (for example X-rays) that can break phosphodiester bonds and cause abnormalities like deletions, inversions, translocations.
  • Includes lower energy isotopes (for example UV rays) that often cause the formation of thymine dimers.

Ames Test

• Used to determine if a compound is mutagenic Tests his- mutants of Salmonella typhimurium.

Everyday Mutagens

• Heterocyclic amines (HAs)
  • Found when meats are overcooked of barbecued
  • Liver enzymes will modify HAs to make compounds bind with and form adducts with DNA.
  • Adducts may result in made during DNA replication and mutations
• Nitrosamines are found in food (beer, fish, meat, and cheeses) as produced from nitrites in food, and they also form from tobacco nicotine. They bind to DNA forming adducts resulting in mistakes made during DNA replication.
• Polycyclic aromatic hydrocarbons (PAHs) are produced by the incomplete burning of fossil fuels, or in cooked meats. Similar to the others, they will bind to DNA and form adducts, as well.
• Mutagens used in research include Base analogs, Base modifying agents, Intercalating agents

Mutagens Used in Research to Produce Mutations

• Base analogs
  • 5-Bromouracil is a thymine analog (B-A base pairing)
  • Amino purine is an analog of adenine (A-T base pairing)
• Base modifying agents:
  • deaminating agent
  • hydroxylating agent
  • alkylating agent
• Intercalating agents include ethidium bromide or proflaine.

Base-Modifying Agents

• Deaminating agents- for example, nitrous acid

  • Can convert adenine to hypoxanthine to pair with cytosine, cytosine to uracil to pair with adenine.

• Hydroxylating agents- for example, hydroxylamine

  • Cytosine mutates to hydroxylaminocytoine to pair with adenine.

• Alkylating agents- for example, Ethyl methane sulfonate (EMS)

  • Guanine mutates to ethylguanine to pair with thymine, thymine to ethylthymine to pair with guanine

Intercalating agents

• Intercalating agents like ethidium bromide or proflavin.

Genetic Code

• Common and spontaneous mutations in genetics are: transversions
• Induced mutagens in research will cause: transitions