derek-thomas/squad-v1.1-t5-question-generation huggingface dataset:
Early work in molecular genetics suggested the model that one gene makes one protein. This model has been refined since the discovery of genes that can encode multiple proteins by alternative splicing and coding sequences split in short section across the genome whose mRNAs are concatenated by trans-splicing.

Question: What model did early work in molecular genetics suggest? Question: What discovery caused the model that one gene makes one protein to be refined? Question: How do genes encode multiple proteins? Question: How are alternative splicing and coding sequences distributed? Question: In order for a gene to encode multiple proteins, how must its mRNAs be arranged?
A broad operational definition is sometimes used to encompass the complexity of these diverse phenomena, where a gene is defined as a union of genomic sequences encoding a coherent set of potentially overlapping functional products. This definition categorizes genes by their functional products (proteins or RNA) rather than their specific DNA loci, with regulatory elements classified as gene-associated regions.

Question: What sort of definition can be used to conveniently encompass the complexity of diverse phenomena? Question: What is the broad operational definition of a gene? Question: What does the broad operational definition of gene categorize genes by? Question: What does the typical definition of a gene categorize genes by? Question: What does the broad operational definition of a gene classify as gene-associated regions?
In all organisms, two steps are required to read the information encoded in a gene's DNA and produce the protein it specifies. First, the gene's DNA is transcribed to messenger RNA (mRNA).:6.1 Second, that mRNA is translated to protein.:6.2 RNA-coding genes must still go through the first step, but are not translated into protein. The process of producing a biologically functional molecule of either RNA or protein is called gene expression, and the resulting molecule is called a gene product.

Question: How many steps are required to read the information encoded in a gene's DNA and produce the specified protein? Question: What is the first step to read the information encoded in a gene's DNA and produce the protein it specifies? Question: What is the second step to read the information encoded in a gene's DNA and produce the protein it specifies? Question: What step must RNA-coding genes still go through? Question: What is the process of producing a biologically functional molecule of either RNA or protein called?
The nucleotide sequence of a gene's DNA specifies the amino acid sequence of a protein through the genetic code. Sets of three nucleotides, known as codons, each correspond to a specific amino acid.:6 Additionally, a "start codon", and three "stop codons" indicate the beginning and end of the protein coding region. There are 64 possible codons (four possible nucleotides at each of three positions, hence 43 possible codons) and only 20 standard amino acids; hence the code is redundant and multiple codons can specify the same amino acid. The correspondence between codons and amino acids is nearly universal among all known living organisms.

Question: What specifies the amino acid sequence of a protein? Question: What are sets of three nucleotides known as? Question: What does each codon correspond to? Question: What indicates the beginning and end of the protein coding region? Question: How many possible codons are there?
Transcription produces a single-stranded RNA molecule known as messenger RNA, whose nucleotide sequence is complementary to the DNA from which it was transcribed.:6.1 The mRNA acts as an intermediate between the DNA gene and its final protein product. The gene's DNA is used as a template to generate a complementary mRNA. The mRNA matches the sequence of the gene's DNA coding strand because it is synthesised as the complement of the template strand. Transcription is performed by an enzyme called an RNA polymerase, which reads the template strand in the 3' to 5' direction and synthesizes the RNA from 5' to 3'. To initiate transcription, the polymerase first recognizes and binds a promoter region of the gene. Thus, a major mechanism of gene regulation is the blocking or sequestering the promoter region, either by tight binding by repressor molecules that physically block the polymerase, or by organizing the DNA so that the promoter region is not accessible.:7

Question: What does transcription produce? Question: How does the nucleotide sequence of mRNA compare to DNA? Question: What is used as a template to generate a complementary mRNA? Question: Why does the mRNA match the sequence of the gene's DNA coding strand? Question: What is the enzyme called that performs transcription?
In prokaryotes, transcription occurs in the cytoplasm; for very long transcripts, translation may begin at the 5' end of the RNA while the 3' end is still being transcribed. In eukaryotes, transcription occurs in the nucleus, where the cell's DNA is stored. The RNA molecule produced by the polymerase is known as the primary transcript and undergoes post-transcriptional modifications before being exported to the cytoplasm for translation. One of the modifications performed is the splicing of introns which are sequences in the transcribed region that do not encode protein. Alternative splicing mechanisms can result in mature transcripts from the same gene having different sequences and thus coding for different proteins. This is a major form of regulation in eukaryotic cells and also occurs in some prokaryotes.:7.5

Question: Where does transcription occur in prokaryotes? Question: If the transcription is very long, where on the RNA may translation begin? Question: Where does transcription occur in eukaryotes? Question: Where does a eukaryote store the cell's DNA? Question: What is the RNA molecule produced by the polymerase known as?
Translation is the process by which a mature mRNA molecule is used as a template for synthesizing a new protein.:6.2 Translation is carried out by ribosomes, large complexes of RNA and protein responsible for carrying out the chemical reactions to add new amino acids to a growing polypeptide chain by the formation of peptide bonds. The genetic code is read three nucleotides at a time, in units called codons, via interactions with specialized RNA molecules called transfer RNA (tRNA). Each tRNA has three unpaired bases known as the anticodon that are complementary to the codon it reads on the mRNA. The tRNA is also covalently attached to the amino acid specified by the complementary codon. When the tRNA binds to its complementary codon in an mRNA strand, the ribosome attaches its amino acid cargo to the new polypeptide chain, which is synthesized from amino terminus to carboxyl terminus. During and after synthesis, most new proteins must folds to their active three-dimensional structure before they can carry out their cellular functions.:3

Question: What is the process by which a mature mRNA molecule is used as a template for synthesizing a new protein called? Question: What does a ribosome consist of? Question: What is a ribosome responsible for? Question: How is the genetic code read? Question: How many unpaired bases does each tRNA have?
Genes are regulated so that they are expressed only when the product is needed, since expression draws on limited resources.:7 A cell regulates its gene expression depending on its external environment (e.g. available nutrients, temperature and other stresses), its internal environment (e.g. cell division cycle, metabolism, infection status), and its specific role if in a multicellular organism. Gene expression can be regulated at any step: from transcriptional initiation, to RNA processing, to post-translational modification of the protein. The regulation of lactose metabolism genes in E. coli (lac operon) was the first such mechanism to be described in 1961.

Question: When are genes expressed? Question: What are examples of a cell's external environment? Question: What are examples of a cell's internal environment? Question: At which step can gene expression be regulated? Question: What example of post-translational modification of a protein was first described in 1961?
A typical protein-coding gene is first copied into RNA as an intermediate in the manufacture of the final protein product.:6.1 In other cases, the RNA molecules are the actual functional products, as in the synthesis of ribosomal RNA and transfer RNA. Some RNAs known as ribozymes are capable of enzymatic function, and microRNA has a regulatory role. The DNA sequences from which such RNAs are transcribed are known as non-coding RNA genes.

Question: What is first copied into RNA as an intermediate in the manufacture of the final protein product? Question: In some cases, what are the actual functional products? Question: What sort of synthesis occurs when the RNA molecules are the actual functional products? Question: What sort of function are ribozymes capable of? Question: What are the DNA sequences from which ribozymes are transcribed known as?
Some viruses store their entire genomes in the form of RNA, and contain no DNA at all. Because they use RNA to store genes, their cellular hosts may synthesize their proteins as soon as they are infected and without the delay in waiting for transcription. On the other hand, RNA retroviruses, such as HIV, require the reverse transcription of their genome from RNA into DNA before their proteins can be synthesized. RNA-mediated epigenetic inheritance has also been observed in plants and very rarely in animals.

Question: In what form do some viruses store their entire genome? Question: Why do the cellular hosts of some viruses not have to wait for transcription to synthesize their proteins? Question: What is one type of an RNA retrovirus? Question: What sort of transcription does the genome of HIV require before its proteins can be synthesized? Question: Besides viruses, where has RNA-mediated epigenetic inheritance been observed?
Organisms inherit their genes from their parents. Asexual organisms simply inherit a complete copy of their parent's genome. Sexual organisms have two copies of each chromosome because they inherit one complete set from each parent.:1

Question: Where do organisms inherit their genes from? Question: How much of an asexual organism's genome is inherited from its parents? Question: How many copies of each chromosome does a sexual organism have? Question: Why do sexual organisms have two copies of each chromosome? Question: How many sets of chromosomes does a sexual organism inherit from each parent?
According to Mendelian inheritance, variations in an organism's phenotype (observable physical and behavioral characteristics) are due in part to variations in its genotype (particular set of genes). Each gene specifies a particular trait with different sequence of a gene (alleles) giving rise to different phenotypes. Most eukaryotic organisms (such as the pea plants Mendel worked on) have two alleles for each trait, one inherited from each parent.:20

Question: What sort of characteristics are described by an organism's phenotype? Question: According to Mendelian inheritance, what is part of the cause of variations in an organism's phenotype? Question: What is a genotype? Question: What specifies a particular trait with a different sequence of alleles? Question: How many alleles do most eukaryotic organisms have for each trait?
Alleles at a locus may be dominant or recessive; dominant alleles give rise to their corresponding phenotypes when paired with any other allele for the same trait, whereas recessive alleles give rise to their corresponding phenotype only when paired with another copy of the same allele. For example, if the allele specifying tall stems in pea plants is dominant over the allele specifying short stems, then pea plants that inherit one tall allele from one parent and one short allele from the other parent will also have tall stems. Mendel's work demonstrated that alleles assort independently in the production of gametes, or germ cells, ensuring variation in the next generation. Although Mendelian inheritance remains a good model for many traits determined by single genes (including a number of well-known genetic disorders) it does not include the physical processes of DNA replication and cell division.

Question: Where can alleles be located in order to be either dominant or recessive? Question: When paired with any other allele for the same trait, what do dominant alleles give rise to? Question: When do recessive alleles give rise to their corresponding phenotype? Question: When do alleles assort independently? Question: What are gametes?
The growth, development, and reproduction of organisms relies on cell division, or the process by which a single cell divides into two usually identical daughter cells. This requires first making a duplicate copy of every gene in the genome in a process called DNA replication.:5.2 The copies are made by specialized enzymes known as DNA polymerases, which "read" one strand of the double-helical DNA, known as the template strand, and synthesize a new complementary strand. Because the DNA double helix is held together by base pairing, the sequence of one strand completely specifies the sequence of its complement; hence only one strand needs to be read by the enzyme to produce a faithful copy. The process of DNA replication is semiconservative; that is, the copy of the genome inherited by each daughter cell contains one original and one newly synthesized strand of DNA.:5.2

Question: What does the growth, development, and reproduction of organisms rely on? Question: In cell division, what two cells are created? Question: What specialized enzyme is responsible DNA replication? Question: Why does the sequence of one strand completely specify the sequence of its complement? Question: What one word characterizes the process of DNA replication?
After DNA replication is complete, the cell must physically separate the two copies of the genome and divide into two distinct membrane-bound cells.:18.2 In prokaryotes (bacteria and archaea) this usually occurs via a relatively simple process called binary fission, in which each circular genome attaches to the cell membrane and is separated into the daughter cells as the membrane invaginates to split the cytoplasm into two membrane-bound portions. Binary fission is extremely fast compared to the rates of cell division in eukaryotes. Eukaryotic cell division is a more complex process known as the cell cycle; DNA replication occurs during a phase of this cycle known as S phase, whereas the process of segregating chromosomes and splitting the cytoplasm occurs during M phase.:18.1

Question: What is one thing the cell must do once DNA replication is compete? Question: What is another thing the cell must do once DNA replication is complete? Question: In binary fission, what shape is each genome? Question: In binary fission. when does each genome separate into daughter cells? Question: Compared to the rates of cell division in eukaryotes, with what speed does binary fission occur?
The duplication and transmission of genetic material from one generation of cells to the next is the basis for molecular inheritance, and the link between the classical and molecular pictures of genes. Organisms inherit the characteristics of their parents because the cells of the offspring contain copies of the genes in their parents' cells. In asexually reproducing organisms, the offspring will be a genetic copy or clone of the parent organism. In sexually reproducing organisms, a specialized form of cell division called meiosis produces cells called gametes or germ cells that are haploid, or contain only one copy of each gene.:20.2 The gametes produced by females are called eggs or ova, and those produced by males are called sperm. Two gametes fuse to form a diploid fertilized egg, a single cell that has two sets of genes, with one copy of each gene from the mother and one from the father.:20

Question: The duplication and transmission of genetic material from one generation of cells to the next is the basis for what? Question: Why do organisms inherit the characteristics of their parents? Question: In what type of organism will the offspring be a genetic copy or clone of the parent organism? Question: In what type of organism will a specialized form of cell division called meiosis produce cells called gametes? Question: What are the gametes produced by females called?
During the process of meiotic cell division, an event called genetic recombination or crossing-over can sometimes occur, in which a length of DNA on one chromatid is swapped with a length of DNA on the corresponding sister chromatid. This has no effect if the alleles on the chromatids are the same, but results in reassortment of otherwise linked alleles if they are different.:5.5 The Mendelian principle of independent assortment asserts that each of a parent's two genes for each trait will sort independently into gametes; which allele an organism inherits for one trait is unrelated to which allele it inherits for another trait. This is in fact only true for genes that do not reside on the same chromosome, or are located very far from one another on the same chromosome. The closer two genes lie on the same chromosome, the more closely they will be associated in gametes and the more often they will appear together; genes that are very close are essentially never separated because it is extremely unlikely that a crossover point will occur between them. This is known as genetic linkage.

Question: When can an event called genetic recombination or crossing-over sometimes occur? Question: If the alleles on the chromatids are the same, what effect arises from genetic recombination? Question: If the alleles on the chromatids are different, what effect arises from genetic recombination? Question: Each of a parent's two genes for each trait will sort independently into gametes according to what Mendelian principle? Question: In genetic linkage, what sort of point is extremely unlikely to occur?
DNA replication is for the most part extremely accurate, however errors (mutations) do occur.:7.6 The error rate in eukaryotic cells can be as low as 10−8 per nucleotide per replication, whereas for some RNA viruses it can be as high as 10−3. This means that each generation, each human genome accumulates 1–2 new mutations. Small mutations can be caused by DNA replication and the aftermath of DNA damage and include point mutations in which a single base is altered and frameshift mutations in which a single base is inserted or deleted. Either of these mutations can change the gene by missense (change a codon to encode a different amino acid) or nonsense (a premature stop codon). Larger mutations can be caused by errors in recombination to cause chromosomal abnormalities including the duplication, deletion, rearrangement or inversion of large sections of a chromosome. Additionally, the DNA repair mechanisms that normally revert mutations can introduce errors when repairing the physical damage to the molecule is more important than restoring an exact copy, for example when repairing double-strand breaks.:5.4

Question: What is it called when errors occur in DNA replication? Question: What is the lowest error rate that occurs in eukaryotic cells? Question: What is the highest error rate that can occur for some RNA viruses? Question: What can small mutations be caused by? Question: What can larger mutations be caused by?
When multiple different alleles for a gene are present in a species's population it is called polymorphic. Most different alleles are functionally equivalent, however some alleles can give rise to different phenotypic traits. A gene's most common allele is called the wild type, and rare alleles are called mutants. The genetic variation in relative frequencies of different alleles in a population is due to both natural selection and genetic drift. The wild-type allele is not necessarily the ancestor of less common alleles, nor is it necessarily fitter.

Question: What is it called when multiple different alleles for a gene are present in a species's population? Question: What can some alleles give rise to? Question: What is a gene's most common allele known as? Question: What are rare alleles called? Question: What is one cause of the genetic variation in relative frequencies of different alleles in a population?
Most mutations within genes are neutral, having no effect on the organism's phenotype (silent mutations). Some mutations do not change the amino acid sequence because multiple codons encode the same amino acid (synonymous mutations). Other mutations can be neutral if they lead to amino acid sequence changes, but the protein still functions similarly with the new amino acid (e.g. conservative mutations). Many mutations, however, are deleterious or even lethal, and are removed from populations by natural selection. Genetic disorders are the result of deleterious mutations and can be due to spontaneous mutation in the affected individual, or can be inherited. Finally, a small fraction of mutations are beneficial, improving the organism's fitness and are extremely important for evolution, since their directional selection leads to adaptive evolution.:7.6

Question: What are mutations that have no effect on an organism's phenotype called? Question: What are mutations that do not change the amino acid sequence called? Question: What are mutations that lead to amino acid sequence changes but leave the protein functioning similarly called? Question: What is a result of deleterious mutations? Question: What does the directional selection of beneficial mutations lead to?
Genes with a most recent common ancestor, and thus a shared evolutionary ancestry, are known as homologs. These genes appear either from gene duplication within an organism's genome, where they are known as paralogous genes, or are the result of divergence of the genes after a speciation event, where they are known as orthologous genes,:7.6 and often perform the same or similar functions in related organisms. It is often assumed that the functions of orthologous genes are more similar than those of paralogous genes, although the difference is minimal.

Question: What are genes with a most recent common ancestor called? Question: What is one reason for homologs to appear? Question: What are genes that occur from duplication within an organism's genome called? Question: What are genes that result from divergence of the genes after a speciation event called?
The relationship between genes can be measured by comparing the sequence alignment of their DNA.:7.6 The degree of sequence similarity between homologous genes is called conserved sequence. Most changes to a gene's sequence do not affect its function and so genes accumulate mutations over time by neutral molecular evolution. Additionally, any selection on a gene will cause its sequence to diverge at a different rate. Genes under stabilizing selection are constrained and so change more slowly whereas genes under directional selection change sequence more rapidly. The sequence differences between genes can be used for phylogenetic analyses to study how those genes have evolved and how the organisms they come from are related.

Question: What does comparing the sequence alignment of genes' DNA measure? Question: What is the degree of sequence similarity between homologous genes called? Question: How do genes typically accumulate mutations over time? Question: Under what type of selection are genes constrained so they change more slowly? Question: What type of analyses can the sequence differences between genes be used for?