MIC 102- Mutation and Information Transfer

What is a mutation

A permanent change in the DNA sequence. A mutation in DNA can alter RNA and protein production, leading to a neutral, beneficial, or disadvantageous phenotype.

Q: According to the lecture, what is the relationship between genotype and phenotype?

A: DNA (genotype) is transcribed into RNA, which is translated into protein. Changes in genotype can therefore alter phenotype.

Q: Do mutations arise because bacteria are exposed to antibiotics?

A: No. Mutations arise before selection. Antibiotics select for resistant mutants that already exist in the population; they do not induce the mutations.

Q: Can mutations be beneficial?

YES, Beneficial mutations contribute to diversity and adaptation.

Q: What removes disadvantageous mutations from populations?

A: Natural selection.

Q: Do antibiotics cause resistance mutations?

A: No. Resistant mutations already exist; antibiotics select for resistant cells.

Q: Why is mutation necessary for evolution?

A: Mutation creates genetic variation on which natural selection acts.

Q: Which type of error is most costly: replication, transcription, or translation?

A: DNA replication errors.

Q: Why are DNA replication errors the most serious?

A: They become permanent mutations and are inherited by daughter cells.

Q: What is a silent mutation?

A: A DNA mutation that does not change the amino acid sequence because of redundancy in the genetic code.

• Occur bc multiple codons can encode the same AA (Genetic code redundancy/wobble)

Q: What is a missense mutation? What determines its severity?

A: A mutation that changes one amino acid into another.

• A: The similarity between the original and substituted amino acids and the importance of that amino acid in protein function.

Q: What is a nonsense mutation?

A: A mutation that creates a stop codon, producing a shortened protein.

Q: What is a frameshift mutation?

A: An insertion or deletion that changes the reading frame of the gene.

Q: Before proofreading, how often does DNA polymerase incorporate the wrong nucleotide?

A: Approximately 1 error per 10⁶ base pairs.

Q: After proofreading and repair, what is the final mutation rate?

A: Approximately 1 mutation per 10¹⁰ base pairs.

Q: Which processes reduce mutation frequency after DNA polymerase makes an error?

A: Proofreading and mismatch repair.

Q: What is a mutagen?

A: An agent that increases the mutation rate.

• Increase mutation frequency about 100-1000 times

Q: What type of DNA damage is caused by ultraviolet (UV) radiation?

A: Pyrimidine dimers (such as thymine dimers) that covalently link adjacent pyrimidines on the same DNA strand.

Q: Besides radiation, what other classes of mutagens are highlighted in the lecture?

A: Chemical mutagens (e.g., base analogs), biological "mutator" strains lacking proofreading or repair, recombination events, and insertion of transposons or viral genomes.

Q: What is 5-bromouracil (5-BrU)?

A: A chemical base analog of thymine (T) that can pair with either adenine (A) or guanine (G), increasing mutation frequency.

Q: What type of mutation can 5-bromouracil (5-BrU) cause?

A: A T:A → C:G transition mutation.

Q: What is Aflatoxin B₁ (AFB₁)?

A: A potent mycotoxin that binds guanine bases in DNA, blocking replication / increasing mutation / cancer risk.

• Guanine is the DNA base targeted by aflatoxin B₁

Q: What is recombination?

A: The mixing or exchange of genetic material between DNA molecules.

Q: Between what type of DNA sequences does recombination usually occur?

A: Regions with identical (homologous) DNA sequences.

Q: Can recombination exchange entire genes or operons?

A: Both. The amount of DNA exchanged can range from small regions to entire genes or operons.

Q: What is a recombinant cell?

A: A cell whose DNA contains genetic material from different sources following recombination.

Q: What are transposons?

A: Mobile DNA elements that can move to new locations within a genome.

Q: What DNA sequences flank a transposon?

A: Inverted repeats (IRs).

Q: Besides transposase, what other genes may be carried by transposons?

A: Antibiotic resistance genes and other accessory genes.

Q: Why is a single nucleotide insertion in the middle of a coding sequence usually severe?

A: It causes a frameshift that changes all downstream codons.

Q: Why is inserting a transposon into a promoter often harmful?

A: It can disrupt promoter function and prevent transcription.

Q: What major factors determine how much a mutation affects phenotype?

A: Mutation type, mutation location, and the biological importance of the affected gene or protein

Q: What is vertical gene transfer?

A: Transmission of DNA from parent to offspring during cell division.

Q: What is horizontal gene transfer?

A: Movement of DNA between organisms that are not in a parent-offspring relationship.

• BACTERIA: “Shaking hand with someone and sharing DNA”

Q: What are the three mechanisms of horizontal gene transfer discussed in lecture?

A: Conjugation, transformation, and transduction.

Q: What is conjugation?

A: Transfer of single-stranded DNA from one living bacterium to another through a pore/channel.

• Pilus, cell-to-cell contact , both donor/recipient cells must be alive , Rolling-Circle replication

Q: What is the F factor?

A: The fertility plasmid that contains genes required for DNA transfer, including the origin of transfer and pilus assembly genes.

Q: What structure connects donor and recipient cells during Gram-negative conjugation?

A: The pilus (conjugative pilus) → Attaches to the recipient and retracts, pulling the cells together before DNA transfer

Q: Can DNA be transferred by conjugation from a dead donor to a live recipient?

A: No. A dead donor cannot perform conjugation because the process requires an active living donor cell.

Q: Can conjugation occur between distantly related bacterial species?

A: Yes. Some conjugative plasmids can be transferred between very distantly related bacterial species.

Q: During conjugation, does the donor transfer an entire plasmid at once?

A: No. A single DNA strand is transferred while rolling-circle replication replaces the missing strand in the donor.

Q: Which bacterium was presented as "Nature's bioengineer"?

A: Agrobacterium tumefaciens.→ infect plant cells and transfer a defined sequence of their DNA to the plant cell by infection

• Transfer the Ti (tumor-inducing) plasmid. → Causes plant cells to divide/produce compounds that serve as preferred carbon source

Q: What is transformation?

A: Uptake of naked DNA from the environment by a bacterial cell

• “Funeral pass” → DNA usually comes from dead (lysed) bacterial cells

Q: Does transformation require direct cell-to-cell contact?

A: No. DNA is taken up directly from the environment.

Q: Griffith’s transformation experiment

Bacterial species: Streptococcus pneumoniae,

• Strain of S. pneumoniae more virulent
  A: The smooth (S) strain

• Strain of S. pneumoniae less virulent?
  A: The rough (R) strain

Q: Why is the smooth (S) strain more virulent than the rough strain?

A: Because it possesses a protective capsule.

Q: What happened when live rough cells were injected into mice?

A: The mice survived → Rough (R) cells don’t have a protective capsule, the mice’s immune system kills the virus

Q: What happened when live smooth cells were injected into mice?

A: The mice died → Smooth (S) cells have a protective capsule against the mice’s immune system.

Q: What happened when heat-killed smooth cells were injected alone?

A: The mice survived. → Denatures the smooth cell’s protective capsule, mice’s immune system protected it against the virus

Q: What happened when live rough cells were mixed with heat-killed smooth cells?

A: The mice died because the rough cells acquired DNA from the dead smooth cells and became virulent.

Q: What was Griffith's "transforming principle"?

A: DNA released from dead cells transformed living cells.

Q: What important conclusion did Griffith's experiment demonstrate?

• Traits can be acquired through DNA exchange.

• DNA can be exchanged between organisms

Q: Why did the rough bacteria become virulent?

A: They incorporated DNA containing the capsule genes from dead smooth bacteria.

Q: Would Griffith's experiment have worked if Streptococcus pneumoniae were not naturally competent?

A: No. Without natural competence, the rough cells could not have taken up DNA released from the dead smooth cells.

Q: What is competence?

A: The ability of a bacterial cell to actively take up foreign DNA from the environment.

Q: Is competence always present?

A: No. It is often transient and inducible.

• About 1% of bacteria are actually naturally competent under permissive conditions

Q: What conditions can induce natural competence according to the lecture?

A: High cell density and DNA damage.

Q: What barriers must DNA overcome during transformation?

A: DNA must cross the cell envelope (cell membrane, outer membrane if present, and peptidoglycan), and negatively charged DNA must approach the negatively charged bacterial surface.

Q: Why is transformation generally inefficient without competence?

A: DNA cannot easily cross the bacterial cell envelope or overcome electrostatic repulsion from the negatively charged cell surface.

Q: What structure was shown "harpooning" DNA from the environment during transformation?

A: A type IV pilus.

Q: What is artificial competence?

A: Laboratory methods that temporarily make bacterial cells capable of taking up DNA.

Q: What happens to the bacterial membrane during artificial competence?

A: Temporary pores are formed that allow DNA to enter the cell.

Q: Can artificially competent bacteria take up both linear and circular DNA?

A: Yes

Q: What are the two major methods used to induce artificial competence?

A: Electroporation (Shock) and chemical competence(Ca²).

Q: What is electroporation?

A: A technique that uses a brief electrical pulse to create temporary pores in the cell membrane, allowing DNA to enter.

Q: What is chemical competence?

A: A laboratory method that uses chemicals (usually calcium ions, Ca²⁺) followed by heat shock to allow DNA uptake.

Q: What is transduction?

A: Horizontal gene transfer in which a bacteriophage transfers bacterial DNA from one bacterium to another.

• “Viral pass” → Bacterial DNA is transferred by a virus (bacteriophage)

Q: From what type of donor cell does the bacteriophage obtain bacterial DNA during transduction?

A: An infected bacterium that is lysed.

• A bacteriophage packages the bacterial DNA during transduction

Q: During transduction, does the donor bacterium make direct contact with the recipient?

A: No. The bacteriophage serves as the carrier of the DNA.

Q: Which horizontal gene transfer mechanism requires direct cell-to-cell contact/ a living donor cell?

Conjugation→ pilus/ cell-to-cell contact/ rolling-cycle

Q: Which horizontal gene transfer mechanism uses naked DNA?

Transformation → “Funeral pass”

Q: Which horizontal gene transfer mechanism uses a bacteriophage?

Transduction → “Viral pass”

Q: What are the two major ways bacteria acquire new genetic information?

A: Mutation and horizontal gene transfer.

Q: Which process creates entirely new DNA sequence changes?

A: Mutation.

Q: Which process moves pre-existing DNA between bacteria?

A: Horizontal gene transfer (conjugation, transformation, or transduction).

Q: Match each mechanism with its nickname from lecture.

• Conjugation

• Transformation

• Transduction

• Conjugation → "Living pass" (live donor → live recipient through a pilus/channel)

• Transformation → "Funeral pass" (naked DNA from dead cells)

• Transduction → "Viral pass" (DNA transferred by a bacteriophage)