Genetics and Gene Regulation: DNA Mutations, Operons, and Transcription

What is a gene?

A specific nucleotide sequence in DNA that codes for a functional product (protein or RNA).

Define allele.

An alternative form of a gene that arises from differences in the nucleotide sequence.

What does phenotype refer to?

The observable physical or physiological traits of an organism, determined by its genotype and environment.

What is the primary source of genetic variation?

Mutations, which are heritable changes in the genetic information.

What are spontaneous mutations?

Natural errors that occur during DNA replication or due to chemical instability of DNA.

What is a replication error?

An incorrect nucleotide insertion by DNA Polymerase that is not fixed by proofreading.

What is strand slippage?

A phenomenon in repetitive DNA sequences where the template or new strand loops out, causing insertions or deletions.

What is depurination?

The spontaneous loss of a purine base (A or G) from the nucleotide, leaving an apurinic site.

What happens during deamination?

The spontaneous loss of an amino group from a base, such as Cytosine converting to Uracil.

What are chemical mutagens?

Agents that damage DNA bases by adding or eliminating functional groups.

What is the role of UV radiation as a mutagen?

It promotes the formation of covalent bonds between adjacent pyrimidines, creating distortions in the DNA.

What is proofreading in DNA repair?

A mechanism where DNA Polymerase checks and corrects newly added nucleotides during replication.

What is mismatch repair (MMR)?

A system that corrects errors that escaped proofreading by recognizing and repairing mismatches in DNA.

What is nucleotide excision repair (NER)?

A DNA repair mechanism that removes bulky lesions that distort the double helix.

What are point mutations?

Base substitutions that can lead to silent, missense, or nonsense mutations.

What is a silent mutation?

A nucleotide change that results in the same amino acid being incorporated.

What is a missense mutation?

A nucleotide change that results in a different amino acid being incorporated.

What is a nonsense mutation?

A change that converts an amino acid codon into a STOP codon, terminating translation prematurely.

What is a frameshift mutation?

A mutation caused by the insertion or deletion of nucleotides that shifts the reading frame of the ribosome.

What is a loss-of-function mutation?

A mutation that results in the protein losing its ability to perform its biochemical job.

What is a gain-of-function mutation?

A mutation that results in the protein acquiring a new property or activity.

What are restriction enzymes?

Bacterial enzymes that act as 'molecular scissors' to cut DNA at specific recognition sequences.

What is the significance of restriction fragment length polymorphism (RFLP)?

It allows for the detection of different alleles based on the lengths of DNA fragments produced by restriction enzyme digestion.

Why is gene regulation important?

To conserve energy and resources by preventing the production of unnecessary proteins.

What is the doubling time for bacteria?

Less than 30 minutes, indicating their short cell cycles.

What is the role of mutagens?

Agents that induce mutations, either chemically or physically.

What is the function of DNA Polymerase I in DNA repair?

It fills in gaps during DNA repair using the old strand as a guide.

What happens during a loss-of-stop mutation?

A STOP codon is changed to an amino acid codon, leading to continued translation and potentially a gain-of-function.

What is the typical doubling time for bacteria?

Less than 30 minutes.

What is the most efficient control mechanism in bacteria?

Transcription control, as it is the farthest upstream.

What are the two types of transcription factors?

Activators (stimulate transcription) and Repressors (block transcription).

What is the lac operon a model for?

Metabolic efficiency in E. coli.

Under what conditions are the genes of the lac operon expressed?

When lactose is present and glucose levels are low.

What type of mRNA is produced by the lac operon?

Polycistronic mRNA, which encodes multiple proteins.

What is the role of the repressor in the lac operon?

It binds to the operator to block RNA polymerase from accessing the promoter.

What is the inducer molecule for the lac operon?

Allolactose, which is an isomer of lactose.

What happens to the lac operon when lactose is present?

Allolactose binds to LacI, causing it to release the operator and allowing transcription.

What is the role of cAMP in the lac operon regulation?

cAMP binds to CRP, enhancing RNA polymerase recruitment when glucose is low.

What is the trp operon a model for?

Biosynthetic (anabolic) control of tryptophan synthesis.

What is the default state of the trp operon?

ON, and it is turned OFF when tryptophan is abundant.

What is the role of DNA methylation in gene regulation?

It silences genes by adding methyl groups to DNA, blocking transcription.

What is the function of histone acetylation?

It loosens chromatin structure, allowing access for RNA polymerase.

What are non-coding RNAs, such as miRNAs, involved in?

RNA interference, blocking translation or directing mRNA destruction.

What are the two life cycles of bacteriophages?

Lytic cycle (immediate replication) and Lysogenic cycle (silent passenger).

What occurs during the lytic cycle of a bacteriophage?

Early genes stop host transcription and stimulate viral replication.

What is the role of the repressor in the lysogenic cycle?

It binds to regulatory sequences to prevent expression of lytic genes.

What is the TATA box in eukaryotic promoters?

A sequence rich in A-T pairs that helps initiate transcription.

What are enhancers in eukaryotic gene regulation?

Regulatory sequences that bind transcriptional activators to enhance transcription.

What is the mediator complex in eukaryotic transcription?

It bridges the enhancer-bound activator and the basal transcription apparatus.

What is the function of general transcription factors (GTFs)?

They bind to most promoters to form the basal transcription apparatus.

What is the role of the co-repressor in the trp operon?

Tryptophan binds to trpR, increasing its affinity for the operator to block transcription.

What is the effect of deacetylation on histones?

It restores the positive charge, tightening DNA binding and silencing genes.

What is the significance of chromatin structure in eukaryotic gene regulation?

It determines the accessibility of DNA for transcription.

What is the primary function of transcription factors?

To control the access of RNA polymerase to the promoter.

What is the role of the operator in the lac operon?

It is the regulatory sequence where the repressor binds to inhibit transcription.

What happens to the trp operon when tryptophan levels are low?

The trpR repressor is inactive, allowing the operon to be ON.