romikgosai/squad_modified huggingface dataset:
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.

Questions and answers:
['
Q: When are genes expressed?
A: only when the product is needed', "
Q: What are examples of a cell's external environment?
A: available nutrients, temperature and other stresses", "
Q: What are examples of a cell's internal environment?
A: cell division cycle, metabolism, infection status", '
Q: At which step can gene expression be regulated?
A: at any step', '
Q: What example of post-translational modification of a protein was first described in 1961?
A: The regulation of lactose metabolism genes in E. coli']
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.

Questions and answers:
['
Q: What is first copied into RNA as an intermediate in the manufacture of the final protein product?
A: A typical protein-coding gene', '
Q: In some cases, what are the actual functional products?
A: the RNA molecules', '
Q: What sort of synthesis occurs when the RNA molecules are the actual functional products?
A: the synthesis of ribosomal RNA and transfer RNA', '
Q: What sort of function are ribozymes capable of?
A: enzymatic function', '
Q: What are the DNA sequences from which ribozymes are transcribed known as?
A: non-coding RNA genes']
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.

Questions and answers:
['
Q: In what form do some viruses store their entire genome?
A: in the form of RNA', '
Q: Why do the cellular hosts of some viruses not have to wait for transcription to synthesize their proteins?
A: Because they use RNA to store genes', '
Q: What is one type of an RNA retrovirus?
A: HIV', '
Q: What sort of transcription does the genome of HIV require before its proteins can be synthesized?
A: reverse transcription', '
Q: Besides viruses, where has RNA-mediated epigenetic inheritance been observed?
A: in plants and very rarely in animals']
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

Questions and answers:
['
Q: Where do organisms inherit their genes from?
A: from their parents', "
Q: How much of an asexual organism's genome is inherited from its parents?
A: a complete copy", '
Q: How many copies of each chromosome does a sexual organism have?
A: two copies of each chromosome', '
Q: How many sets of chromosomes does a sexual organism inherit from each parent?
A: one complete set from each parent', '
Q: Why do sexual organisms have two copies of each chromosome?
A: because they inherit one complete set 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

Questions and answers:
["
Q: According to Mendelian inheritance, what is part of the cause of variations in an organism's phenotype?
A: variations in its genotype", "
Q: What sort of characteristics are described by an organism's phenotype?
A: observable physical and behavioral characteristics", '
Q: What is a genotype?
A: particular set of genes', '
Q: What specifies a particular trait with a different sequence of alleles?
A: Each gene', '
Q: How many alleles do most eukaryotic organisms have for each trait?
A: two alleles 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.

Questions and answers:
['
Q: Where can alleles be located in order to be either dominant or recessive?
A: at a locus', '
Q: When paired with any other allele for the same trait, what do dominant alleles give rise to?
A: their corresponding phenotypes', '
Q: When do recessive alleles give rise to their corresponding phenotype?
A: when paired with another copy of the same allele', '
Q: When do alleles assort independently?
A: in the production of gametes', '
Q: What are gametes?
A: germ cells']
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

Questions and answers:
['
Q: What does the growth, development, and reproduction of organisms rely on?
A: cell division', '
Q: In cell division, what two cells are created? 
A: identical daughter cells', '
Q: What specialized enzyme is responsible DNA replication?
A: DNA polymerases', '
Q: Why does the sequence of one strand completely specify the sequence of its complement?
A: Because the DNA double helix is held together by base pairing', '
Q: What one word characterizes the process of DNA replication?
A: semiconservative']
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

Questions and answers:
['
Q: What is one thing the cell must do once DNA replication is compete?
A: physically separate the two copies of the genome', '
Q: What is another thing the cell must do once DNA replication is complete?
A: divide into two distinct membrane-bound cells', '
Q: In binary fission, what shape is each genome?
A: circular', '
Q: In binary fission. when does each genome separate into daughter cells?
A: as the membrane invaginates to split the cytoplasm', '
Q: Compared to the rates of cell division in eukaryotes, with what speed does binary fission occur?
A: extremely fast']
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

Questions and answers:
['
Q: The duplication and transmission of genetic material from one generation of cells to the next is the basis for what?
A: molecular inheritance', "
Q: Why do organisms inherit the characteristics of their parents?
A: cells of the offspring contain copies of the genes in their parents' cells", '
Q: In what type of organism will the offspring be a genetic copy or clone of the parent organism?
A: In asexually reproducing organisms', '
Q: In what type of organism will a specialized form of cell division called meiosis produce cells called gametes?
A: In sexually reproducing organisms', '
Q: What are the gametes produced by females called?
A: eggs or ova']
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.

Questions and answers:
['
Q: When can an event called genetic recombination or crossing-over sometimes occur?
A: During the process of meiotic cell division', '
Q: If the alleles on the chromatids are the same, what effect arises from genetic recombination? 
A: no effect', '
Q: If the alleles on the chromatids are different, what effect arises from genetic recombination? 
A: reassortment of otherwise linked alleles', "
Q: Each of a parent's two genes for each trait will sort independently into gametes according to what Mendelian principle?
A: independent assortment", '
Q: In genetic linkage, what sort of point is extremely unlikely to occur?
A: a crossover point']
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

Questions and answers:
['
Q: What is it called when errors occur in DNA replication?
A: mutations', '
Q: What is the lowest error rate that occurs in eukaryotic cells?
A: 10−8 per nucleotide per replication', '
Q: What is the highest error rate that can occur for some RNA viruses?
A: 10−3', '
Q: What can small mutations be caused by?
A: DNA replication', '
Q: What can larger mutations be caused by?
A: errors in recombination']
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.

Questions and answers:
["
Q: What is it called when multiple different alleles for a gene are present in a species's population?
A: polymorphic", '
Q: What can some alleles give rise to?
A: different phenotypic traits', "
Q: What is a gene's most common allele known as?
A: the wild type", '
Q: What are rare alleles called?
A: mutants', '
Q: What is one cause of the genetic variation in relative frequencies of different alleles in a population?
A: genetic drift']
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

Questions and answers:
["
Q: What are mutations that have no effect on an organism's phenotype called?
A: silent mutations", '
Q: What are mutations that do not change the amino acid sequence called?
A: synonymous mutations', '
Q: What are mutations that lead to amino acid sequence changes but leave the protein functioning similarly called?
A: conservative mutations', '
Q: What is a result of deleterious mutations?
A: Genetic disorders', '
Q: What does the directional selection of beneficial mutations lead to?
A: adaptive evolution']
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.

Questions and answers:
['
Q: What are genes with a most recent common ancestor called?
A: homologs', "
Q: What is one reason for homologs to appear?
A: gene duplication within an organism's genome", "
Q: What are genes that occur from duplication within an organism's genome called?
A: paralogous genes", '
Q: What are genes that result from divergence of the genes after a speciation event called?
A: orthologous genes']
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.

Questions and answers:
["
Q: What does comparing the sequence alignment of genes' DNA measure?
A: The relationship between genes", '
Q: What is the degree of sequence similarity between homologous genes called?
A: conserved sequence', '
Q: How do genes typically accumulate mutations over time?
A: by neutral molecular evolution', '
Q: Under what type of selection are genes constrained so they change more slowly?
A: stabilizing', '
Q: What type of analyses can the sequence differences between genes be used for?
A: phylogenetic']
The most common source of new genes in eukaryotic lineages is gene duplication, which creates copy number variation of an existing gene in the genome. The resulting genes (paralogs) may then diverge in sequence and in function. Sets of genes formed in this way comprise a gene family. Gene duplications and losses within a family are common and represent a major source of evolutionary biodiversity. Sometimes, gene duplication may result in a nonfunctional copy of a gene, or a functional copy may be subject to mutations that result in loss of function; such nonfunctional genes are called pseudogenes.:7.6

Questions and answers:
['
Q: What is the most common source of new genes in eukaryotic lineages?
A: gene duplication', '
Q: What creates copy number variation of an existing gene in the genome?
A: gene duplication', '
Q: What are the genes that result from eukaryotic gene duplication called?
A: paralogs', '
Q: What type of copy can gene duplication sometimes result in?
A: nonfunctional', '
Q: What are functional copies of a gene which have a loss of function due to mutation called?
A: pseudogenes']
De novo or "orphan" genes, whose sequence shows no similarity to existing genes, are extremely rare. Estimates of the number of de novo genes in the human genome range from 18 to 60. Such genes are typically shorter and simpler in structure than most eukaryotic genes, with few if any introns. Two primary sources of orphan protein-coding genes are gene duplication followed by extremely rapid sequence change, such that the original relationship is undetectable by sequence comparisons, and formation through mutation of "cryptic" transcription start sites that introduce a new open reading frame in a region of the genome that did not previously code for a protein.

Questions and answers:
['
Q: What is a gene whose sequence shows no similarity to existing genes called?
A: De novo or "orphan" genes', '
Q: What is the estimate of the number of orphan genes in the human genome?
A: 18 to 60', '
Q: How do the lengths of orphan genes compare to most eukaryotic genes?
A: typically shorter', '
Q: How does the structure of orphan genes compare to most eukaryotic genes?
A: simpler in structure', '
Q: What is one primary source of orphan protein-coding genes?
A: gene duplication followed by extremely rapid sequence change']
Horizontal gene transfer refers to the transfer of genetic material through a mechanism other than reproduction. This mechanism is a common source of new genes in prokaryotes, sometimes thought to contribute more to genetic variation than gene duplication. It is a common means of spreading antibiotic resistance, virulence, and adaptive metabolic functions. Although horizontal gene transfer is rare in eukaryotes, likely examples have been identified of protist and alga genomes containing genes of bacterial origin.

Questions and answers:
['
Q: What is the  transfer of genetic material through a mechanism other than reproduction known as?
A: Horizontal gene transfer', '
Q: In what type of organism is horizontal gene transfer a common source of new genes?
A: prokaryotes', '
Q: What is one trait that horizontal gene transfer is a common means of spreading?
A: antibiotic resistance', '
Q: In what type of organism is horizontal gene transfer rare?
A: eukaryotes', '
Q: What is one example of horizontal gene transfer in eukaryotes?
A: alga genomes containing genes of bacterial origin']
The genome size, and the number of genes it encodes varies widely between organisms. The smallest genomes occur in viruses (which can have as few as 2 protein-coding genes), and viroids (which act as a single non-coding RNA gene). Conversely, plants can have extremely large genomes, with rice containing >46,000 protein-coding genes. The total number of protein-coding genes (the Earth's proteome) is estimated to be 5 million sequences.

Questions and answers:
['
Q: What is one characteristic that varies widely between organisms?
A: genome size', '
Q: In which type of organism do the smallest genomes occur?
A: viruses', '
Q: What is the smallest number of protein coding genes that a virus can have?
A: 2', '
Q: Which organism acts as a single non coding RNA gene?
A: viroids', '
Q: What is the estimate for the total number of protein coding genes on Earth?
A: 5 million']