rajpurkar/squad huggingface dataset:
Title: Gene

The word gene is derived (via pangene) from the Ancient Greek word γένος (génos) meaning "race, offspring". Gene was coined in 1909 by Danish botanist Wilhelm Johannsen to describe the fundamental physical and functional unit of heredity, while the related word genetics was first used by William Bateson in 1905.

Question: What ancient Greek word is the word 'gene' derived from?
Answer: γένος (génos)

Question: What does the ancient Greek word 'génos' mean?
Answer: "race, offspring"

Question: What Danish botanist coined the word 'gene'?
Answer: Wilhelm Johannsen

Question: What was the word 'gene' used to describe in 1909?
Answer: the fundamental physical and functional unit of heredity

Question: Who first used the word 'genetics' in 1905?
Answer: William Bateson
Title: Gene

Advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid (DNA) was shown to be the molecular repository of genetic information by experiments in the 1940s to 1950s. The structure of DNA was studied by Rosalind Franklin using X-ray crystallography, which led James D. Watson and Francis Crick to publish a model of the double-stranded DNA molecule whose paired nucleotide bases indicated a compelling hypothesis for the mechanism of genetic replication. Collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, which is transcribed from DNA. This dogma has since been shown to have exceptions, such as reverse transcription in retroviruses. The modern study of genetics at the level of DNA is known as molecular genetics.

Question: What was shown to be the molecular repository of genetic information by experiments in the 1940s to 1950s?
Answer: Deoxyribonucleic acid (DNA)

Question: Who studied the structure of DNA using x-ray crystallography?
Answer: Rosalind Franklin

Question: What two scientists published a model of the double stranded DNA molecule?
Answer: James D. Watson and Francis Crick

Question: What is one exception to the central dogma of molecular biology?
Answer: reverse transcription in retroviruses

Question: What is the modern study of genetics at the level of DNA known as?
Answer: molecular genetics
Title: Gene

In 1972, Walter Fiers and his team at the University of Ghent were the first to determine the sequence of a gene: the gene for Bacteriophage MS2 coat protein. The subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing and turned it into a routine laboratory tool. An automated version of the Sanger method was used in early phases of the Human Genome Project.

Question: When was the first sequence of a gene determined?
Answer: In 1972

Question: What was the first gene to be sequenced?
Answer: the gene for Bacteriophage MS2 coat protein

Question: Who developed chain termination DNA sequencing in 1977?
Answer: Frederick Sanger

Question: What did the devlopment of the chain termination DNA sequencing method do for the sequencing process?
Answer: improved the efficiency of sequencing and turned it into a routine laboratory tool.

Question: What project used an automated version of the Sanger method in its early stages?
Answer: the Human Genome Project
Title: Gene

The theories developed in the 1930s and 1940s to integrate molecular genetics with Darwinian evolution are called the modern evolutionary synthesis, a term introduced by Julian Huxley. Evolutionary biologists subsequently refined this concept, such as George C. Williams' gene-centric view of evolution. He proposed an evolutionary concept of the gene as a unit of natural selection with the definition: "that which segregates and recombines with appreciable frequency.":24 In this view, the molecular gene transcribes as a unit, and the evolutionary gene inherits as a unit. Related ideas emphasizing the centrality of genes in evolution were popularized by Richard Dawkins.

Question: In what time span were the theories to integrate molecular genetic with Darwinian evolution developed?
Answer: the 1930s and 1940s

Question: What are the theories that integrate molecular genetics with Darwinian evolution called?
Answer: the modern evolutionary synthesis

Question: Who proposed an evolutionary concept of the gene as a unit of natural selection?
Answer: George C. Williams

Question: What is the definition of the concept of the gene as a unit of natural selection?
Answer: "that which segregates and recombines with appreciable frequency."

Question: Who popularized ideas emphasizing the centrality of genes in evolution?
Answer: Richard Dawkins
Title: Gene

The vast majority of living organisms encode their genes in long strands of DNA (deoxyribonucleic acid). DNA consists of a chain made from four types of nucleotide subunits, each composed of: a five-carbon sugar (2'-deoxyribose), a phosphate group, and one of the four bases adenine, cytosine, guanine, and thymine.:2.1

Question: What do the vast majority of living organisms encode their genes in?
Answer: long strands of DNA (deoxyribonucleic acid)

Question: What does DNA consist of?
Answer: a chain made from four types of nucleotide subunits

Question: What type of sugar composes part of the DNA molecule?
Answer: a five-carbon sugar (2'-deoxyribose)

Question: What are the four bases used in nucleotide subunits?
Answer: adenine, cytosine, guanine, and thymine

Question: Besides the sugar and the four bases, what else does DNA consist of?
Answer: a phosphate group
Title: Gene

Two chains of DNA twist around each other to form a DNA double helix with the phosphate-sugar backbone spiralling around the outside, and the bases pointing inwards with adenine base pairing to thymine and guanine to cytosine. The specificity of base pairing occurs because adenine and thymine align form two hydrogen bonds, whereas cytosine and guanine form three hydrogen bonds. The two strands in a double helix must therefore be complementary, with their sequence of bases matching such that the adenines of one strand are paired with the thymines of the other strand, and so on.:4.1

Question: What is the backbone of a DNA double helix made of?
Answer: phosphate-sugar

Question: What base pairs with thymine?
Answer: adenine

Question: What base does guanine pair with?
Answer: cytosine

Question: What causes the specificity of base pairing?
Answer: adenine and thymine align form two hydrogen bonds, whereas cytosine and guanine form three hydrogen bonds

Question: Due to the cause of the specificity of base pairing, what must be true of the two strands in a double helix?
Answer: The two strands in a double helix must therefore be complementary
Title: Gene

Due to the chemical composition of the pentose residues of the bases, DNA strands have directionality. One end of a DNA polymer contains an exposed hydroxyl group on the deoxyribose; this is known as the 3' end of the molecule. The other end contains an exposed phosphate group; this is the 5' end. The two strands of a double-helix run in opposite directions. Nucleic acid synthesis, including DNA replication and transcription occurs in the 5'→3' direction, because new nucleotides are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile.:27.2

Question: What causes the directionality of DNA strands?
Answer: the chemical composition of the pentose residues of the bases

Question: What is known as the 3' end?
Answer: an exposed hydroxyl group on the deoxyribose

Question: What is known as the 5' end?
Answer: an exposed phosphate group

Question: What type of synthesis occurs in the 5'→3' direction?
Answer: Nucleic acid synthesis

Question: Why does DNA replication and transcription occur in the 5'→3' direction?
Answer: because new nucleotides are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile
Title: Gene

The expression of genes encoded in DNA begins by transcribing the gene into RNA, a second type of nucleic acid that is very similar to DNA, but whose monomers contain the sugar ribose rather than deoxyribose. RNA also contains the base uracil in place of thymine. RNA molecules are less stable than DNA and are typically single-stranded. Genes that encode proteins are composed of a series of three-nucleotide sequences called codons, which serve as the "words" in the genetic "language". The genetic code specifies the correspondence during protein translation between codons and amino acids. The genetic code is nearly the same for all known organisms.:4.1

Question: How does the expression of genes encoded in DNA begin?
Answer: by transcribing the gene into RNA

Question: What is RNA?
Answer: a second type of nucleic acid that is very similar to DNA

Question: What base does RNA have in place of thymine?
Answer: the base uracil

Question: What are codons?
Answer: a series of three-nucleotide sequences

Question: What specifies the correspondence between codons and amino acids during protein translation?
Answer: The genetic code
Title: Gene

The total complement of genes in an organism or cell is known as its genome, which may be stored on one or more chromosomes. A chromosome consists of a single, very long DNA helix on which thousands of genes are encoded.:4.2 The region of the chromosome at which a particular gene is located is called its locus. Each locus contains one allele of a gene; however, members of a population may have different alleles at the locus, each with a slightly different gene sequence.

Question: What is the total complement of genes in an organism or cell known as?
Answer: its genome

Question: What does a chromosome consist of?
Answer: a single, very long DNA helix

Question: What is encoded on a chromosome?
Answer: thousands of genes

Question: What is the region of the chromosome at which a particular gene is located called?
Answer: its locus

Question: What does each locus contain?
Answer: one allele of a gene
Title: Gene

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?
Answer: on a set of large, linear chromosomes

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

Question: What does the manner of DNA storage on the histone and the chemical modifications of the histone itself regulate?
Answer: whether a particular region of DNA is accessible for gene expression

Question: What are replication origins?
Answer: regions where DNA replication is initiated to make two copies of the chromosome

Question: Long stretches of repetitive sequence that cap the ends of the linear chromosomes are called what?
Answer: Telomeres
Title: Gene

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?
Answer: bacteria and archaea

Question: How do prokaryotes store their genomes?
Answer: on a single large, circular chromosome

Question: What type of chromosome do some eukaryotic organelles contain?
Answer: a remnant circular chromosome with a small number of genes

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

Question: What allows genes for antibiotic resistance to be passed between individual cells?
Answer: horizontal gene transfer
Title: Gene

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?
Answer: prokaryotes

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

Question: What is referred to as "junk DNA"?
Answer: DNA without an identified function

Question: What percentage of the human genome is made of protein coding DNA?
Answer: barely 2%

Question: What percentage of bases in the human genome are expressed by protein coding DNA
Answer: about 80%
Title: Gene

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?
Answer: often only a small part

Question: What often plays only a small part in the structure of a gene? 
Answer: the actual protein coding sequence

Question: What is one of the many elements that the structure of a gene consists of?
Answer: DNA regions that are not transcribed

Question: What is another element of the structure of a gene?
Answer: untranslated regions of the RNA

Question: What elements does the structure of a gene consist of?
Answer: DNA regions that are not transcribed as well as untranslated regions of the RNA
Title: Gene

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?
Answer: a regulatory sequence

Question: How is a promoter sequence recognized?
Answer: by transcription factors and RNA polymerase

Question: What results when genes have more than one promoter?
Answer: messenger RNAs (mRNA) that differ in how far they extend in the 5' end

Question: What does a "strong" promoter sequence do?
Answer: bind the transcription machinery well

Question: What does a "weak" promoter sequence do?
Answer: bind poorly and initiate transcription less frequently
Title: Gene

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?
Answer: by binding to transcription factors

Question: What happens when a regulatory region binds to transcription factors?
Answer: the DNA to loop

Question: How do enhancers increase transcription?
Answer: by binding an activator protein

Question: What happens after an enhancer binds an activator protein?
Answer: helps to recruit the RNA polymerase to the promoter

Question: What causes DNA to be less available for RNA polymerase?
Answer: silencers bind repressor proteins
Title: Gene

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?
Answer: untranslated regions

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

Question: What do most eukaryotic open reading frames contain?
Answer: untranslated introns

Question: What dictates the splice sites to generate the final mature mRNA?
Answer: The sequences at the ends of the introns

Question: What encodes the protein or RNA product?
Answer: the splice sites to generate the final mature mRNA
Title: Gene

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?
Answer: operons

Question: What are multiple protein coding sequences transcribed as?
Answer: a unit

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

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

Question: What type of coding sequences do prokaryotic genes typically have?
Answer: multiple protein-coding sequences
Title: Gene

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?
Answer: enhancers

Question: Why do some regulatory regions of a gene not have to be close to the coding sequence?
Answer: because the intervening DNA can be looped out to bring the gene and its regulatory region into proximity

Question: What part of a gene can be much larger than its exons?
Answer: a gene's introns

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

Question: Where can regulatory regions be found?
Answer: different chromosomes
Title: Gene

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?
Answer: the model that one gene makes one protein.

Question: What discovery caused the model that one gene makes one protein to be refined?
Answer: the discovery of genes that can encode multiple proteins

Question: How do genes encode multiple proteins?
Answer: by alternative splicing and coding sequences

Question: How are alternative splicing and coding sequences distributed?
Answer: split in short section across the genome

Question: In order for a gene to encode multiple proteins, how must its mRNAs be arranged?
Answer: concatenated by trans-splicing.
Title: Gene

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?
Answer: A broad operational definition

Question: What is the broad operational definition of a gene?
Answer: a union of genomic sequences encoding a coherent set of potentially overlapping functional products

Question: What does the typical definition of a gene categorize genes by?
Answer: their specific DNA loci

Question: What does the broad operational definition of gene categorize genes by?
Answer: their functional products (proteins or RNA)

Question: What does the broad operational definition of a gene classify as gene-associated regions?
Answer: regulatory elements
Title: Gene

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?
Answer: two steps are required

Question: What is the first step to read the information encoded in a gene's DNA and produce the protein it specifies?
Answer: the gene's DNA is transcribed to messenger RNA (mRNA)

Question: What is the second step to read the information encoded in a gene's DNA and produce the protein it specifies?
Answer: mRNA is translated to protein

Question: What step must RNA-coding genes still go through?
Answer: the first step

Question: What is the process of producing a biologically functional molecule of either RNA or protein called?
Answer: gene expression