sentence-transformers/squad huggingface dataset:
Passage: The majority of eukaryotic genes are stored on a set of large, linear chromosomes. The chromosomes are packed within the nucleus in complex with storage proteins called histones to form a unit called a nucleosome. DNA packaged and condensed in this way is called chromatin.:4.2 The manner in which DNA is stored on the histones, as well as chemical modifications of the histone itself, regulate whether a particular region of DNA is accessible for gene expression. In addition to genes, eukaryotic chromosomes contain sequences involved in ensuring that the DNA is copied without degradation of end regions and sorted into daughter cells during cell division: replication origins, telomeres and the centromere.:4.2 Replication origins are the sequence regions where DNA replication is initiated to make two copies of the chromosome. Telomeres are long stretches of repetitive sequence that cap the ends of the linear chromosomes and prevent degradation of coding and regulatory regions during DNA replication. The length of the telomeres decreases each time the genome is replicated and has been implicated in the aging process. The centromere is required for binding spindle fibres to separate sister chromatids into daughter cells during cell division.:18.2

Question: Where are the majority of eukaryotic genes stored?

Question: Chromosomes that are packed within the nucleus in complex with histones are called what?

Question: What does the manner of DNA storage on the histone and the chemical modifications of the histone itself regulate?

Question: What are replication origins?

Question: Long stretches of repetitive sequence that cap the ends of the linear chromosomes are called what?
Passage: Prokaryotes (bacteria and archaea) typically store their genomes on a single large, circular chromosome. Similarly, some eukaryotic organelles contain a remnant circular chromosome with a small number of genes.:14.4 Prokaryotes sometimes supplement their chromosome with additional small circles of DNA called plasmids, which usually encode only a few genes and are transferable between individuals. For example, the genes for antibiotic resistance are usually encoded on bacterial plasmids and can be passed between individual cells, even those of different species, via horizontal gene transfer.

Question: What are prokaryotes?

Question: How do prokaryotes store their genomes?

Question: What type of chromosome do some eukaryotic organelles contain?

Question: Small circles of DNA that encode only a few genes and are transferable between individuals are called what?

Question: What allows genes for antibiotic resistance to be passed between individual cells?
Passage: Whereas the chromosomes of prokaryotes are relatively gene-dense, those of eukaryotes often contain regions of DNA that serve no obvious function. Simple single-celled eukaryotes have relatively small amounts of such DNA, whereas the genomes of complex multicellular organisms, including humans, contain an absolute majority of DNA without an identified function. This DNA has often been referred to as "junk DNA". However, more recent analyses suggest that, although protein-coding DNA makes up barely 2% of the human genome, about 80% of the bases in the genome may be expressed, so the term "junk DNA" may be a misnomer.

Question: What type of organism has relatively gene dense chromosomes?

Question: Regions of DNA that serve no obvious function are often found in what type of organism?

Question: What is referred to as "junk DNA"?

Question: What percentage of the human genome is made of protein coding DNA?

Question: What percentage of bases in the human genome are expressed by protein coding DNA
Passage: The structure of a gene consists of many elements of which the actual protein coding sequence is often only a small part. These include DNA regions that are not transcribed as well as untranslated regions of the RNA.

Question: Often, how large a part of the structure of a gene is the protein coding sequence?

Question: What often plays only a small part in the structure of a gene?

Question: What is one of the many elements that the structure of a gene consists of?

Question: What is another element of the structure of a gene?

Question: What elements does the structure of a gene consist of?
Passage: Firstly, flanking the open reading frame, all genes contain a regulatory sequence that is required for their expression. In order to be expressed, genes require a promoter sequence. The promoter is recognized and bound by transcription factors and RNA polymerase to initiate transcription.:7.1 A gene can have more than one promoter, resulting in messenger RNAs (mRNA) that differ in how far they extend in the 5' end. Promoter regions have a consensus sequence, however highly transcribed genes have "strong" promoter sequences that bind the transcription machinery well, whereas others have "weak" promoters that bind poorly and initiate transcription less frequently.:7.2 Eukaryotic promoter regions are much more complex and difficult to identify than prokaryotic promoters.:7.3

Question: What do all genes contain that is required for their expression?

Question: How is a promoter sequence recognized?

Question: What results when genes have more than one promoter?

Question: What does a "strong" promoter sequence do?

Question: What does a "weak" promoter sequence do?
Passage: Additionally, genes can have regulatory regions many kilobases upstream or downstream of the open reading frame. These act by binding to transcription factors which then cause the DNA to loop so that the regulatory sequence (and bound transcription factor) become close to the RNA polymerase binding site. For example, enhancers increase transcription by binding an activator protein which then helps to recruit the RNA polymerase to the promoter; conversely silencers bind repressor proteins and make the DNA less available for RNA polymerase.

Question: How do regulatory regions act?

Question: What happens when a regulatory region binds to transcription factors?

Question: How do enhancers increase transcription?

Question: What happens after an enhancer binds an activator protein?

Question: What causes DNA to be less available for RNA polymerase?
Passage: The transcribed pre-mRNA contains untranslated regions at both ends which contain a ribosome binding site, terminator and start and stop codons. In addition, most eukaryotic open reading frames contain untranslated introns which are removed before the exons are translated. The sequences at the ends of the introns, dictate the splice sites to generate the final mature mRNA which encodes the protein or RNA product.

Question: What is at both ends of the transcribed pre-mRNA?

Question: Where are the ribosome binding site, terminator and start and stop codons located on transcribed pre-mRNA?

Question: What do most eukaryotic open reading frames contain?

Question: What dictates the splice sites to generate the final mature mRNA?

Question: What encodes the protein or RNA product?
Passage: Many prokaryotic genes are organized into operons, with multiple protein-coding sequences that are transcribed as a unit. The products of operon genes typically have related functions and are involved in the same regulatory network.:7.3

Question: What are most prokaryotic genes organized into?

Question: What are multiple protein coding sequences transcribed as?

Question: What sort of functions do the products of operon genes typically have?

Question: What type of network are the products of operon genes typically involved with?

Question: What type of coding sequences do prokaryotic genes typically have?
Passage: Defining exactly what section of a DNA sequence comprises a gene is difficult. Regulatory regions of a gene such as enhancers do not necessarily have to be close to the coding sequence on the linear molecule because the intervening DNA can be looped out to bring the gene and its regulatory region into proximity. Similarly, a gene's introns can be much larger than its exons. Regulatory regions can even be on entirely different chromosomes and operate in trans to allow regulatory regions on one chromosome to come in contact with target genes on another chromosome.

Question: What is an example of a regulatory region of a gene that does not have to close to the coding sequence?

Question: Why do some regulatory regions of a gene not have to be close to the coding sequence?

Question: What part of a gene can be much larger than its exons?

Question: How do regulatory regions on different chromosomes operate in order to allow regions on different chromosomes to come into contact with one another?

Question: Where can regulatory regions be found?
Passage: 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?
Passage: 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 typical definition of a gene categorize genes by?

Question: What does the broad operational definition of gene categorize genes by?

Question: What does the broad operational definition of a gene classify as gene-associated regions?
Passage: 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?
Passage: 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?
Passage: 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?
Passage: 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?
Passage: 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?
Passage: 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?
Passage: 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?
Passage: 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?
Passage: 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: How many sets of chromosomes does a sexual organism inherit from each parent?

Question: Why do sexual organisms have two copies of each chromosome?
Passage: 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: According to Mendelian inheritance, what is part of the cause of variations in an organism's phenotype?

Question: What sort of characteristics are described by 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?
Passage: 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?
Passage: 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?
Passage: 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?