Theme 4 Module 4: DNA Mutations

Theme 4, Module 4: DNA mutations

Learning Objectives

• Identify the types of mutations that can be found in DNA molecules.
• Examine the mechanisms in which DNA can be repaired.
• Understand how mutations can lead to variation in the genome.

Unit 1: How Common Are Mistakes?

• Changes in genetic information (mutations) can affect protein structure and function, leading to devastating cellular consequences or beneficial adaptations.
• Mutations are responsible for the genetic differences among organisms and are considered the source of genetic variation.
• Mutations can arise due to:
  • Environmental factors.
  • Spontaneous mutations.
  • Errors during DNA replication.
• Errors in DNA replication can lead to nucleotide-level changes. If not corrected, these incorrect nucleotides can be used as a template in subsequent replication rounds, propagating the mutation.
• Spontaneous mutations are the most common, arising randomly without a known cause.
• Mutation is a rare event for any given nucleotide.
• Mutation rates vary across organisms, with viruses having a much higher mutation rate than multicellular animals. RNA viruses have the highest mutation rate among viruses.
• The higher mutation rate in RNA viruses is attributed to:
  • The delicate nature of the RNA backbone, making it more prone to damage.
  • The lack of proofreading capability in RNA genomes.

Somatic vs. Germline Mutations

• Genetic information can be mutated in somatic or germline cells.
• Somatic mutations:
  • Occur in somatic cells and are passed on to daughter cells through cell division, leading to a patch of mutated cells.
  • The earlier a somatic mutation occurs in development, the larger the spread of mutated cells.
  • Somatic mutations are not passed on to progeny.
• Germline mutations:
  • Occur in germ cells (cells that produce new offspring).
  • Are passed on to every cell in the developing embryo.

Random vs. Directed Mutations: Lederberg Experiment

• Experiment by Joshua and Esther Lederberg (1952) demonstrated that mutations, such as antibiotic resistance in bacteria, are random and not directed by the environment.
• Experimental setup:
  • Bacteria were grown into colonies on a non-selective agar plate (plate 1).
  • The colony arrangement from plate 1 was "stamped" onto a cloth and then onto a selective plate containing penicillin (plate 2).
  • This stamping process (replica plating) preserves the relative arrangement of colonies.
• Observations:
  • Only a few colonies from plate 1 survived on the penicillin plate (plate 2).
  • The Lederbergs hypothesized that these colonies carried a mutation conferring penicillin resistance.
• Question: Did exposure to penicillin cause the antibiotic resistance, or did the mutation exist beforehand?
• Follow-up Experiment:
  • Bacteria from a suspected mutant colony on the original non-selective plate (plate 1) were isolated and cultured in a medium containing penicillin.
  • The result was a pure culture of antibiotic-resistant bacteria.
• Conclusion:
  • The penicillin-resistance mutation existed in the bacterial population before exposure to penicillin.
  • Mutations create random genetic variation, which may include beneficial changes like antibiotic resistance.
  • The environment does not create mutations but selects for pre-existing beneficial mutations.

Unit 2: DNA Repair

• Spontaneous and induced mutations occur frequently.
• Uncorrected mutations can lead to cell death, cancer, aging, and disease.
• DNA damage can be caused by mutagens (radiation or chemicals) that increase the probability of mutations.
• Most DNA damage can be corrected by specialized repair enzymes.
• DNA ligase: repairs breaks in the DNA backbone.

DNA Repair Mechanisms

• Proofreading by DNA polymerase: corrects mismatched nucleotide pairs during DNA replication.
• Mismatch Repair:
  • Scans DNA for mismatches, which create kinks in the DNA molecule.
  • Proteins recognize these kinks and initiate repair.
  • A nuclease cleaves the mismatched DNA backbone some distance from the mismatch.
  • Another enzyme removes successive nucleotides, including the mismatched nucleotide.
  • DNA polymerase and DNA ligase synthesize new DNA to fill the gap, ensuring complementarity to the template strand.
• Base Excision Repair:
  • Addresses the incorporation of uracil (characteristic of RNA) into DNA.
  • DNA uracil glycosylase cleaves uracil from the deoxyribose sugar, leaving a bare sugar.
  • AP endonuclease cleaves the backbone on either side of the base-less area.
  • DNA synthesis, facilitated by DNA polymerase and DNA ligase, adds a new, properly matched nucleotide base.
• Nucleotide Excision Repair
  • Removes and replaces multiple damaged nucleotide bases, unlike mismatch repair, which corrects single nucleotide pair mismatches.
  • Damaged bases signal enzymes to cleave the DNA backbone flanking the damaged region.
  • DNA synthesis fills the excised gap with correctly matched nucleotides, complementary to the template strand.

Unit 3: Mutations in Nucleotide Sequence

• Despite DNA repair mechanisms, mutations can escape repair and persist in the genome.
• Mutations can be small point mutations (single nucleotide changes) or large-scale mutations (changes in large chromosomal regions).
• Point mutations can arise during DNA replication when proofreading mechanisms fail.
• The fidelity of DNA replication retains point mutations in a population of dividing cells.
• Single Nucleotide Polymorphisms (SNPs): the most common type of point mutation, involving the substitution of one base pair for another.

Types of Point Mutations

• Missense Mutations: a single nucleotide pair base change that results in a change in the amino acid sequence.
  • Can have serious consequences, as seen in sickle-cell anemia, caused by a single nucleotide substitution that leads to a valine instead of a glutamate in the beta-globin protein.
• Synonymous (Silent) Mutations: alters a nucleotide pair but does not change the amino acid due to the redundancy of the genetic code.
• Nonsense Mutations: changes a codon for an amino acid into a stop codon, resulting in premature termination of translation and a shorter, often nonfunctional protein. The mutation leads to a shorter polypeptide sequence than the one that is encoded for in the normal gene.

Insertions and Deletions

• Insertion mutations: one or more extra nucleotides are inserted into replicating DNA.
• Deletion mutations: one or more nucleotides are skipped or removed during DNA replication.
• The impact of insertions/deletions in protein-coding regions depends on the size of the change.
  • Deletion of three nucleotides can result in a missing amino acid.
  • Insertion of six nucleotides can lead to the insertion of two amino acids.
  • Example: Cystic fibrosis is caused by a three-nucleotide deletion in the CFTR transporter gene, leading to a nonfunctional protein and thick, sticky mucus.
• Frameshift Mutations: occur when the number of inserted or deleted nucleotides is not a multiple of three.
  • Lead to improper grouping of nucleotides into codons downstream of the mutation.
  • Result in a massive missense mutation, often ending in premature termination.
  • Almost certainly lead to nonfunctional proteins.

Unit 4: Chromosomal Mutations

• Chromosomal mutations affect larger DNA regions and cause visible changes in chromosome structure.
• Four major types of chromosomal mutations:
  • Deletions
  • Duplications
  • Inversions
  • Reciprocal Translocations

Types of Chromosomal Mutations

• Deletions: loss of a chromosomal fragment, leading to the loss of genes. Loss of the centromere can result in the loss of the entire chromosome.
  • Deletions in embryos often lead to death or fatal abnormalities.
• Duplications: regions of a chromosome are duplicated during DNA replication.
  • Duplicated genes may confer an advantage and potentially lead to the formation of new genes through duplication and divergence.
• Inversions: the normal order of a gene sequence is reversed; a chromosome fragment breaks off and reattaches in the reverse order.
  • Inversions do not usually lead to serious consequences since all genes are present.
  • Small inversions are common and contribute to chromosomal evolution.
• Translocations: a portion of one chromosome attaches to a non-homologous chromosome; two non-homologous chromosomes exchange terminal fragments.
  • Reciprocal translocations often occur in noncoding regions and may not disrupt gene function.
  • Problems can arise during gamete formation if homologous chromosomes do not pair and move together correctly due to the translocation, leading to developmental abnormalities.

Unit 5: Variation and Gene Evolution

• Gene families can arise from gene duplication and mutation.
• Beta-globin gene family: an example of a gene family that arose due to multiple rounds of gene duplication and sequence divergence.
  • Consists of five different genes expressed at various times during development.
  • All genes have the same function: to bind and carry oxygen in red blood cells.
  • The evolution of the beta-globin gene dates back 200 million years when a single duplication event led to the evolution of prenatal and adult globin genes.
  • Even within the same gene family, there are characteristic differences among the beta-globin genes of humans.
  • The two gamma globin genes found in fetuses are nearly identical in amino acid sequence, yet expressed at different levels. The sequences of all gene family members are identical enough to support the possibility that the existing globin genes arose through multiple duplication and divergence events.

Module Summary

• Random mutations are common in DNA.
• Cells have various repair mechanisms to fix mutations, but some mutations persist and are the basis for gene evolution and adaptation.
• This leads to the variation that exists when comparing across many genomes.