The Interrupted Gene Flashcards

Describe the interrupted gene and the relationship between DNA and mature RNA
Describe how the base composition of introns and exons can differ and the four base composition rules
Explain the ways in which exons and introns can be organized including variation in size and location
Explain how introns and exons vary from each other and under what conditions.
Describe how one gene can encode multiple proteins
Describe how exon and intron organization can be related to protein domains
Explain gene families and their origins

Interrupted gene: A gene in which the coding sequence is not continuous due to the presence of introns.
Primary (RNA) transcript: The original unmodified RNA product corresponding to a transcription unit.
RNA splicing: The process of excising introns from RNA and connecting the exons into a continuous mRNA.
Intron: A segment of DNA that is transcribed, but later removed from within the transcript by splicing together the sequences (exons) on either side of it.
Mature transcript: A modified RNA transcript. Modification may include the removal of intron sequences and alterations to the 5′ and 3′ ends.
Interrupted genes are expressed via a precursor RNA. Individual coding regions are separated in the gene. The length of the precursor RNA defines the region of the gene.

Introns are removed by RNA splicing, which occurs in cis in individual RNA molecules.
Mutations in exons can affect polypeptide sequence.
Mutations in introns can affect RNA processing and hence may influence the sequence and/or production of a polypeptide.
Exons remain in the same order in mRNA as in DNA, but distances along the gene do not correspond to those of mRNA or polypeptide products.

The four “rules” for DNA base composition are the first and second parity rules, the cluster rule, and the GC rule.
Exons and introns can be distinguished on the basis of all rules except the first.
The second parity rule suggests an extrusion of structured stem-loop segments from duplex DNA, which would be greater in introns.
The rules relate to genomic characteristics, or “pressures,” that constitute the genome phenotype.

Introns can be detected when genes are compared with their RNA transcription products by either restriction mapping, electron microscopy, or sequencing.
cDNA: A single-stranded DNA complementary to an RNA, synthesized from it by reverse transcription in vitro.
Comparison of the restriction maps of cDNA and genomic DNA for mouse β-globin.
The positions of introns are usually conserved when homologous genes are compared between different organisms.
The lengths of the corresponding introns may vary greatly.
Introns usually do not encode proteins.
Mammalian genes for DHFR have the same relative organization of rather short exons and very long introns.

Comparisons of related genes in different species show that the sequences of the corresponding exons are usually conserved, but the sequences of the introns are much less similar.
Introns evolve much more rapidly than exons because of the lack of selective pressure to produce a polypeptide with a useful sequence.

Under positive selection, an individual with an advantageous mutation survives (i.e., is able to produce more fertile progeny) relative to others without the mutation.
Due to intrinsic genomic pressures, such as that which conserves the potential to extrude stem-loops from duplex DNA, introns evolve more slowly than exons that are under positive selection pressure.

Most genes are uninterrupted in S. cerevisiae but are interrupted in multicellular eukaryotes.
Most genes are uninterrupted in yeast, but most genes are interrupted in flies and mammals.
Exons are usually short, typically encoding fewer than 100 amino acids.
Exons encoding for polypeptides are usually short.
Introns are short in unicellular/oligocellular eukaryotes but can be many kb in multicellular eukaryotes.
The overall length of a gene is determined largely by its introns.
Introns range from very short to very long.

The use of alternative initiation or termination codons allows multiple variants of a polypeptide chain.
Overlapping gene: A gene in which part of the sequence is found within part of the sequence of another gene.
Two proteins can be generated from a single gene by starting (or terminating) expression at different points.
Different polypeptides can be produced from the same sequence of DNA when the mRNA is read in different reading frames (as two overlapping genes).
Two genes might overlap by reading the same DNA sequence in different frames.
Otherwise identical polypeptides, differing by the presence or absence of certain regions, can be generated by differential (alternative) splicing when certain exons are included or excluded.
This can take the form of including or excluding individual exons, or of choosing between alternative exons.
Alternative splicing uses the same pre-mRNA to generate mRNAs that have different combinations of exons.

Proteins can consist of independent functional modules the boundaries of which, in some cases, correspond to those of exons.
Immunoglobulin light and heavy chains are encoded by genes whose structures correspond to the distinct domains in the protein.
The exons of some genes appear homologous to the exons of others, suggesting a common exon ancestry.
The LDL receptor gene consists of 18 exons. Triangles mark the positions of introns.

Gene family: A set of genes within a genome that encodes related or identical proteins or RNAs.
The members were derived by duplication of an ancestral gene followed by accumulation of changes in sequence between the copies.
Most often the members are related but not identical.
Superfamily: A set of genes all related by presumed descent from a common ancestor, but now showing considerable variation.
A set of homologous genes (homologs) should share common features that preceded their evolutionary separation.
The rat insulin gene with one intron evolved by loss of an intron from an ancestor with two introns.
All globin genes have a common form of organization with three exons and two introns, suggesting that they are descended from a single ancestral gene.
The exon structure of globin genes corresponds to protein function, but leghemoglobin has an extra intron in the central domain.
Intron positions in the actin gene family are highly variable, which suggests that introns do not separate functional domains.
Actin genes vary widely in their organization.

Genetic information includes not only that related to characters corresponding to the conventional phenotype, but also that related to characters (pressures) corresponding to the genome “phenotype.”
In certain contexts, the definition of the gene can be seen as reversed from “one gene-one protein” to “one protein-one gene.”
Positional information might be important in development.
Sequences transferred “horizontally” from other species to the germ line could land in introns or intergenic DNA and thence transfer “vertically” through the generations.
Some of these might be involved in intracellular non-self-recognition.