romikgosai/squad_modified huggingface dataset:
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

Questions and answers:
['
Q: What do the vast majority of living organisms encode their genes in?
A: long strands of DNA (deoxyribonucleic acid)', '
Q: What does DNA consist of?
A: a chain made from four types of nucleotide subunits', "
Q: What type of sugar composes part of the DNA molecule?
A: a five-carbon sugar (2'-deoxyribose)", '
Q: What are the four bases used in nucleotide subunits?
A: adenine, cytosine, guanine, and thymine', '
Q: Besides the sugar and the four bases, what else does DNA consist of?
A: a phosphate group']
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

Questions and answers:
['
Q: What is the backbone of a DNA double helix made of?
A: phosphate-sugar', '
Q: What base pairs with thymine?
A: adenine', '
Q: What base does guanine pair with?
A: cytosine', '
Q: What causes the specificity of base pairing?
A: adenine and thymine align form two hydrogen bonds, whereas cytosine and guanine form three hydrogen bonds', '
Q: Due to the cause of the specificity of base pairing, what must be true of the two strands in a double helix?
A: The two strands in a double helix must therefore be complementary']
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

Questions and answers:
['
Q: What causes the directionality of DNA strands?
A: the chemical composition of the pentose residues of the bases', "
Q: What is known as the 3' end?
A: an exposed hydroxyl group on the deoxyribose", "
Q: What is known as the 5' end?
A: an exposed phosphate group", "
Q: What type of synthesis occurs in the 5'→3' direction?
A: Nucleic acid synthesis", "
Q: Why does DNA replication and transcription occur in the 5'→3' direction?
A: because new nucleotides are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile"]
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

Questions and answers:
['
Q: How does the expression of genes encoded in DNA begin?
A: by transcribing the gene into RNA', '
Q: What is RNA?
A: a second type of nucleic acid that is very similar to DNA', '
Q: What base does RNA have in place of thymine?
A: the base uracil', '
Q: What are codons?
A: a series of three-nucleotide sequences', '
Q: What specifies the correspondence between codons and amino acids during protein translation?
A: The genetic code']
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.

Questions and answers:
['
Q: What is the total complement of genes in an organism or cell known as?
A: its genome', '
Q: What does a chromosome consist of?
A: a single, very long DNA helix', '
Q: What is encoded on a chromosome?
A: thousands of genes', '
Q: What is the region of the chromosome at which a particular gene is located called?
A: its locus', '
Q: What does each locus contain?
A: one allele of a 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

Questions and answers:
['
Q: Where are the majority of eukaryotic genes stored?
A: on a set of large, linear chromosomes', '
Q: Chromosomes that are packed within the nucleus in complex with histones are called what?
A: a nucleosome', '
Q: What does the manner of DNA storage on the histone and the chemical modifications of the histone itself regulate?
A: whether a particular region of DNA is accessible for gene expression', '
Q: What are replication origins?
A: regions where DNA replication is initiated to make two copies of the chromosome', '
Q: Long stretches of repetitive sequence that cap the ends of the linear chromosomes are called what?
A: Telomeres']
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.

Questions and answers:
['
Q: What are prokaryotes?
A: bacteria and archaea', '
Q: How do prokaryotes store their genomes?
A: on a single large, circular chromosome', '
Q: What type of chromosome do some eukaryotic organelles contain?
A: a remnant circular chromosome with a small number of genes', '
Q: Small circles of DNA that encode only a few genes and are transferable between individuals are called what?
A: plasmids', '
Q: What allows genes for antibiotic resistance to be passed between individual cells?
A: horizontal gene transfer']
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.

Questions and answers:
['
Q: What type of organism has relatively gene dense chromosomes?
A: prokaryotes', '
Q: Regions of DNA that serve no obvious function are often found in what type of organism?
A: eukaryotes', '
Q: What is referred to as "junk DNA"?
A: DNA without an identified function', '
Q: What percentage of the human genome is made of protein coding DNA?
A: barely 2%', '
Q: What percentage of bases in the human genome are expressed by protein coding DNA
A: about 80%']
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.

Questions and answers:
['
Q: Often, how large a part of the structure of a gene is the protein coding sequence?
A: often only a small part', '
Q: What often plays only a small part in the structure of a gene? 
A: the actual protein coding sequence', '
Q: What is one of the many elements that the structure of a gene consists of?
A: DNA regions that are not transcribed', '
Q: What is another element of the structure of a gene?
A: untranslated regions of the RNA', '
Q: What elements does the structure of a gene consist of?
A: DNA regions that are not transcribed as well as untranslated regions of the RNA']
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

Questions and answers:
['
Q: What do all genes contain that is required for their expression?
A: a regulatory sequence', '
Q: How is a promoter sequence recognized?
A: by transcription factors and RNA polymerase', "
Q: What results when genes have more than one promoter?
A: messenger RNAs (mRNA) that differ in how far they extend in the 5' end", '
Q: What does a "strong" promoter sequence do?
A: bind the transcription machinery well', '
Q: What does a "weak" promoter sequence do?
A: bind poorly and initiate transcription less frequently']
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.

Questions and answers:
['
Q: How do regulatory regions act?
A: by binding to transcription factors', '
Q: What happens when a regulatory region binds to transcription factors?
A: the DNA to loop', '
Q: How do enhancers increase transcription?
A: by binding an activator protein', '
Q: What happens after an enhancer binds an activator protein?
A: helps to recruit the RNA polymerase to the promoter', '
Q: What causes DNA to be less available for RNA polymerase?
A: silencers bind repressor proteins']
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.

Questions and answers:
['
Q: What is at both ends of the transcribed pre-mRNA?
A: untranslated regions', '
Q: Where are the ribosome binding site, terminator and start and stop codons located on transcribed pre-mRNA?
A: untranslated regions', '
Q: What do most eukaryotic open reading frames contain?
A: untranslated introns', '
Q: What dictates the splice sites to generate the final mature mRNA?
A: The sequences at the ends of the introns', '
Q: What encodes the protein or RNA product?
A: the splice sites to generate the final mature mRNA']
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

Questions and answers:
['
Q: What are most prokaryotic genes organized into?
A: operons', '
Q: What are multiple protein coding sequences transcribed as?
A: a unit', '
Q: What sort of functions do the products of operon genes typically have?
A: related functions', '
Q: What type of network are the products of operon genes typically involved with?
A: the same regulatory network', '
Q: What type of coding sequences do prokaryotic genes typically have?
A: multiple protein-coding sequences']
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.

Questions and answers:
['
Q: What is an example of a regulatory region of a gene that does not have to close to the coding sequence?
A: enhancers', '
Q: Why do some regulatory regions of a gene not have to be close to the coding sequence?
A: because the intervening DNA can be looped out to bring the gene and its regulatory region into proximity', "
Q: What part of a gene can be much larger than its exons?
A: a gene's introns", '
Q: How do regulatory regions on different chromosomes operate in order to allow regions on different chromosomes to come into contact with one another?
A: in trans', '
Q: Where can regulatory regions be found?
A: different chromosomes']
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.

Questions and answers:
['
Q: What model did early work in molecular genetics suggest?
A: the model that one gene makes one protein.', '
Q: What discovery caused the model that one gene makes one protein to be refined?
A: the discovery of genes that can encode multiple proteins', '
Q: How do genes encode multiple proteins?
A: by alternative splicing and coding sequences', '
Q: How are alternative splicing and coding sequences distributed?
A: split in short section across the genome', '
Q: In order for a gene to encode multiple proteins, how must its mRNAs be arranged?
A: concatenated by trans-splicing.']
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.

Questions and answers:
['
Q: What sort of definition can be used to conveniently encompass the complexity of diverse phenomena?
A: A broad operational definition', '
Q: What is the broad operational definition of a gene?
A: a union of genomic sequences encoding a coherent set of potentially overlapping functional products', '
Q: What does the typical definition of a gene categorize genes by?
A: their specific DNA loci', '
Q: What does the broad operational definition of gene categorize genes by?
A: their functional products (proteins or RNA)', '
Q: What does the broad operational definition of a gene classify as gene-associated regions?
A: regulatory elements']
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.

Questions and answers:
["
Q: How many steps are required to read the information encoded in a gene's DNA and produce the specified protein?
A: two steps are required", "
Q: What is the first step to read the information encoded in a gene's DNA and produce the protein it specifies?
A: the gene's DNA is transcribed to messenger RNA (mRNA)", "
Q: What is the second step to read the information encoded in a gene's DNA and produce the protein it specifies?
A: mRNA is translated to protein", '
Q: What step must RNA-coding genes still go through?
A: the first step', '
Q: What is the process of producing a biologically functional molecule of either RNA or protein called?
A: gene expression']
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.

Questions and answers:
["
Q: What specifies the amino acid sequence of a protein?
A: The nucleotide sequence of a gene's DNA", '
Q: What are sets of three nucleotides known as?
A: codons', '
Q: What does each codon correspond to?
A: a specific amino acid', '
Q: What indicates the beginning and end of the protein coding region?
A: a "start codon", and three "stop codons"', '
Q: How many possible codons are there?
A: There are 64 possible codons (four possible nucleotides at each of three positions, hence 43 possible codons)']
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

Questions and answers:
['
Q: What does transcription produce?
A: a single-stranded RNA molecule known as messenger RNA', '
Q: How does the nucleotide sequence of mRNA compare to DNA?
A: complementary to the DNA from which it was transcribed', "
Q: What is used as a template to generate a complementary mRNA?
A: The gene's DNA", "
Q: Why does the mRNA match the sequence of the gene's DNA coding strand?
A: because it is synthesised as the complement of the template strand", '
Q: What is the enzyme called that performs transcription?
A: an RNA polymerase']
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

Questions and answers:
['
Q: Where does transcription occur in prokaryotes?
A: in the cytoplasm', "
Q: If the transcription is very long, where on the RNA may translation begin?
A: at the 5' end of the RNA", '
Q: Where does transcription occur in eukaryotes?
A: transcription occurs in the nucleus', "
Q: Where does a eukaryote store the cell's DNA?
A: in the nucleus", '
Q: What is the RNA molecule produced by the polymerase known as?
A: the primary transcript']
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

Questions and answers:
['
Q: What is the process by which a mature mRNA molecule is used as a template for synthesizing a new protein called?
A: Translation', '
Q: What does a ribosome consist of?
A: large complexes of RNA and protein', '
Q: What is a ribosome responsible for?
A: carrying out the chemical reactions to add new amino acids to a growing polypeptide chain', '
Q: How is the genetic code read?
A: via interactions with specialized RNA molecules called transfer RNA (tRNA)', '
Q: How many unpaired bases does each tRNA have?
A: three']