Bacterial Genetics

What are the two general mechanisms bacteria use to adjust to new circumstances?

Regulation of gene expression and genetic change.

What are the two mechanisms of genetic change in bacteria?

Mutation (changes in existing nucleotide sequence) and horizontal gene transfer (movement of DNA from one organism to another).

The process by which genetic changes are passed to progeny is known as _.

vertical gene transfer

Term: Genotype

The sequence of nucleotides in an organism's DNA.

Term: Phenotype

The observable characteristics of an organism, which are influenced by genotype and environmental conditions.

Why does a change in genotype in bacteria often have a direct effect on the phenotype?

Because bacteria are haploid, meaning they have only one copy of each gene and no backup.

A mutant that requires a growth factor because it can no longer synthesize it is called an _.

auxotroph

An organism that does not require growth factors and can synthesize all its necessary cellular components is called a _.

prototroph

In bacterial genetics, what is the term for the typical phenotype of strains isolated from nature?

Wild type.

What does the genetic designation Trp- indicate about a bacterial strain?

It indicates the strain is an auxotroph that cannot synthesize tryptophan.

Random genetic changes that result from normal cell processes are called _ mutations.

spontaneous

What is the typical spontaneous mutation rate for a given gene in bacteria?

Between $10^{-4}$ and $10^{-12}$ per cell division.

What is the term for a mutation that changes back to its original, non-mutated state?

Reversion.

What is the most common type of spontaneous mutation?

Base substitution.

A change of a single base pair in the DNA sequence is known as a _ mutation.

point

What is a synonymous mutation?

A base-pair substitution that results in a codon that codes for the same amino acid as the original.

What is a missense mutation?

A base-pair substitution that creates a codon for a different amino acid, often resulting in a protein that does not function normally.

What is a nonsense mutation?

A base-pair substitution that creates a stop codon, resulting in a shorter, often non-functional protein.

What type of mutation occurs when one or two nucleotide pairs are added or deleted from the DNA?

A frameshift mutation.

Why does a frameshift mutation often result in a shortened, non-functional protein?

It changes the reading frame, altering the set of codons translated, which often leads to a premature stop codon.

What is the impact of adding or deleting exactly three nucleotide pairs in a gene?

It changes one codon, resulting in one more or one less amino acid in the protein, with the impact depending on its location.

Pieces of DNA that can move from one location to another in a cell's genome are called _.

transposons (or jumping genes)

Genetic changes that occur due to an influence outside of the cell are called _ mutations.

induced

Term: Mutagen

An agent, such as a chemical or radiation, that induces genetic change.

How do alkylating agents like nitrosoguanidine cause mutations?

They add alkyl groups (e.g., a methyl group to guanine) to nucleobases, changing their base-pairing properties.

Molecules that resemble nucleobases but have different hydrogen-bonding properties are called _.

base analogs

How does the base analog 5-bromouracil induce mutations?

It resembles thymine but often base-pairs with guanine, leading to incorrect nucleotide incorporation during DNA replication.

Flat molecules that insert between adjacent bases in a DNA strand and increase frameshift mutations are known as _ agents.

intercalating

What type of DNA damage is caused by ultraviolet (UV) light?

It causes thymine dimers, which are covalent bonds between adjacent thymine bases that distort the DNA molecule.

What type of DNA damage is caused by X-rays?

X-rays cause single- and double-strand breaks in DNA, and can also alter nucleobases.

What is the function of proofreading by DNA polymerase?

It checks the accuracy of DNA synthesis, allowing the polymerase to back up, remove an incorrect nucleotide, and insert the correct one.

The repair mechanism that fixes incorrectly inserted nucleotides that escape proofreading is called _ repair.

mismatch

In base excision repair, what enzyme is responsible for removing a damaged nucleobase from the DNA?

DNA glycosylase.

What is photoreactivation (light repair)?

A DNA repair mechanism where an enzyme uses energy from light to break the covalent bonds of thymine dimers.

The repair mechanism that removes a damaged region of DNA (like a thymine dimer) in the absence of light is called _ repair.

nucleotide excision (or dark)

What is the SOS repair system in bacteria?

A last-ditch repair mechanism used for extensive DNA damage, which involves a DNA polymerase that can synthesize past damage but lacks proofreading ability, often making errors (SOS mutagenesis).

The acquisition of genes from other cells, rather than through cell division, is called _.

horizontal gene transfer (HGT)

What are the three mechanisms of horizontal gene transfer in bacteria?

Transformation, transduction, and conjugation.

Term: Bacterial Transformation

The process by which a bacterial cell takes up 'naked' DNA from the environment.

What does it mean for a recipient cell to be 'competent' in the context of bacterial transformation?

It means the cell is in a physiological state that allows it to take up DNA from the environment.

What experiment first demonstrated bacterial transformation?

Griffith's experiment in 1920 with Streptococcus pneumoniae, where living non-encapsulated cells were transformed by DNA from heat-killed encapsulated cells.

Term: Transduction

The transfer of bacterial genes from one bacterium to another by a bacteriophage (phage).

What is a transducing particle in the context of generalized transduction?

A phage particle that mistakenly packaged a fragment of bacterial DNA instead of phage DNA, which can then inject this bacterial DNA into another cell.

Term: Conjugation

The transfer of DNA between bacterial cells that requires direct cell-to-cell contact.

What type of genetic element directs its own transfer during conjugation?

A conjugative plasmid, such as the F plasmid.

What structure, encoded by the F plasmid, is required for conjugation?

The F pilus (or sex pilus).

In conjugation, a cell that contains the F plasmid is designated as , while a cell that lacks it is designated as .

$F^+$; $F^-$

What is the outcome for both cells after F plasmid transfer via conjugation?

The recipient cell becomes $F^+$ and the donor cell remains $F^+$, so both cells are now $F^+$.

What are Hfr cells?

High frequency of recombination cells, in which the F plasmid has integrated into the bacterial chromosome.

During chromosome transfer from an Hfr cell, why does the recipient cell typically remain $F^-$?

Because the chromosome usually breaks before the complete F plasmid is transferred.

What is an F' plasmid?

A plasmid formed when the F plasmid is excised from the chromosome and carries a small piece of the bacterial chromosome with it.

The concept that the total gene pool of a bacterial species consists of a core genome, accessory genome, and unique genes is known as the _.

pan-genome

In the pan-genome concept, what is the 'core genome'?

The set of genes found in all strains of a particular species.

What is a key characteristic of plasmids?

They are usually circular, double-stranded DNA molecules with an origin of replication that generally encode non-essential information.

What is the function of R plasmids?

They encode resistance to antimicrobial medications and can spread this resistance quickly among bacteria.

What are the two components of a restriction-modification system in bacteria?

A restriction enzyme that cuts foreign DNA at specific sequences, and a modification enzyme that protects the cell's own DNA by adding methyl groups.

What is the primary evolutionary purpose of restriction-modification systems?

They likely evolved as a defense mechanism against infection by bacteriophages.

What is the function of the CRISPR system in bacteria?

It's an adaptive immune system that recognizes and destroys foreign DNA, such as from a phage that has previously invaded the cell.

In the CRISPR system, what is a 'spacer'?

A short fragment of DNA from a previous phage invasion that has been integrated into the CRISPR array in the bacterial chromosome.

During a subsequent invasion, what molecule directs the CRISPR-Cas system to cut the invading DNA?

crRNAs (CRISPR RNAs), which are transcribed from the CRISPR array and are complementary to the invading DNA.