romikgosai/squad_modified_2 huggingface dataset:
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.

Q1: What type of organism has relatively gene dense chromosomes?
A1: prokaryotes
Q2: Regions of DNA that serve no obvious function are often found in what type of organism?
A2: eukaryotes
Q3: What is referred to as "junk DNA"?
A3: DNA without an identified function
Q4: What percentage of the human genome is made of protein coding DNA?
A4: barely 2%
Q5: What percentage of bases in the human genome are expressed by protein coding DNA
A5: 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.

Q1: Often, how large a part of the structure of a gene is the protein coding sequence?
A1: often only a small part
Q2: What often plays only a small part in the structure of a gene?
A2: the actual protein coding sequence
Q3: What is one of the many elements that the structure of a gene consists of?
A3: DNA regions that are not transcribed
Q4: What is another element of the structure of a gene?
A4: untranslated regions of the RNA
Q5: What elements does the structure of a gene consist of?
A5: 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

Q1: What do all genes contain that is required for their expression?
A1: a regulatory sequence
Q2: How is a promoter sequence recognized?
A2: by transcription factors and RNA polymerase
Q3: What results when genes have more than one promoter?
A3: messenger RNAs (mRNA) that differ in how far they extend in the 5' end
Q4: What does a "strong" promoter sequence do?
A4: bind the transcription machinery well
Q5: What does a "weak" promoter sequence do?
A5: 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.

Q1: How do regulatory regions act?
A1: by binding to transcription factors
Q2: What happens when a regulatory region binds to transcription factors?
A2: the DNA to loop
Q3: How do enhancers increase transcription?
A3: by binding an activator protein
Q4: What happens after an enhancer binds an activator protein?
A4: helps to recruit the RNA polymerase to the promoter
Q5: What causes DNA to be less available for RNA polymerase?
A5: 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.

Q1: What is at both ends of the transcribed pre-mRNA?
A1: untranslated regions
Q2: Where are the ribosome binding site, terminator and start and stop codons located on transcribed pre-mRNA?
A2: untranslated regions
Q3: What do most eukaryotic open reading frames contain?
A3: untranslated introns
Q4: What dictates the splice sites to generate the final mature mRNA?
A4: The sequences at the ends of the introns
Q5: What encodes the protein or RNA product?
A5: 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

Q1: What are most prokaryotic genes organized into?
A1: operons
Q2: What are multiple protein coding sequences transcribed as?
A2: a unit
Q3: What sort of functions do the products of operon genes typically have?
A3: related functions
Q4: What type of network are the products of operon genes typically involved with?
A4: the same regulatory network
Q5: What type of coding sequences do prokaryotic genes typically have?
A5: 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.

Q1: What is an example of a regulatory region of a gene that does not have to close to the coding sequence?
A1: enhancers
Q2: Why do some regulatory regions of a gene not have to be close to the coding sequence?
A2: because the intervening DNA can be looped out to bring the gene and its regulatory region into proximity
Q3: What part of a gene can be much larger than its exons?
A3: a gene's introns
Q4: How do regulatory regions on different chromosomes operate in order to allow regions on different chromosomes to come into contact with one another?
A4: in trans
Q5: Where can regulatory regions be found?
A5: 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.

Q1: What model did early work in molecular genetics suggest?
A1: the model that one gene makes one protein.
Q2: What discovery caused the model that one gene makes one protein to be refined?
A2: the discovery of genes that can encode multiple proteins
Q3: How do genes encode multiple proteins?
A3: by alternative splicing and coding sequences
Q4: How are alternative splicing and coding sequences distributed?
A4: split in short section across the genome
Q5: In order for a gene to encode multiple proteins, how must its mRNAs be arranged?
A5: 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.

Q1: What sort of definition can be used to conveniently encompass the complexity of diverse phenomena?
A1: A broad operational definition
Q2: What is the broad operational definition of a gene?
A2: a union of genomic sequences encoding a coherent set of potentially overlapping functional products
Q3: What does the typical definition of a gene categorize genes by?
A3: their specific DNA loci
Q4: What does the broad operational definition of gene categorize genes by?
A4: their functional products (proteins or RNA)
Q5: What does the broad operational definition of a gene classify as gene-associated regions?
A5: 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.

Q1: How many steps are required to read the information encoded in a gene's DNA and produce the specified protein?
A1: two steps are required
Q2: What is the first step to read the information encoded in a gene's DNA and produce the protein it specifies?
A2: the gene's DNA is transcribed to messenger RNA (mRNA)
Q3: What is the second step to read the information encoded in a gene's DNA and produce the protein it specifies?
A3: mRNA is translated to protein
Q4: What step must RNA-coding genes still go through?
A4: the first step
Q5: What is the process of producing a biologically functional molecule of either RNA or protein called?
A5: 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.

Q1: What specifies the amino acid sequence of a protein?
A1: The nucleotide sequence of a gene's DNA
Q2: What are sets of three nucleotides known as?
A2: codons
Q3: What does each codon correspond to?
A3: a specific amino acid
Q4: What indicates the beginning and end of the protein coding region?
A4: a "start codon", and three "stop codons"
Q5: How many possible codons are there?
A5: 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

Q1: What does transcription produce?
A1: a single-stranded RNA molecule known as messenger RNA
Q2: How does the nucleotide sequence of mRNA compare to DNA?
A2: complementary to the DNA from which it was transcribed
Q3: What is used as a template to generate a complementary mRNA?
A3: The gene's DNA
Q4: Why does the mRNA match the sequence of the gene's DNA coding strand?
A4: because it is synthesised as the complement of the template strand
Q5: What is the enzyme called that performs transcription?
A5: 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

Q1: Where does transcription occur in prokaryotes?
A1: in the cytoplasm
Q2: If the transcription is very long, where on the RNA may translation begin?
A2: at the 5' end of the RNA
Q3: Where does transcription occur in eukaryotes?
A3: transcription occurs in the nucleus
Q4: Where does a eukaryote store the cell's DNA?
A4: in the nucleus
Q5: What is the RNA molecule produced by the polymerase known as?
A5: 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

Q1: What is the process by which a mature mRNA molecule is used as a template for synthesizing a new protein called?
A1: Translation
Q2: What does a ribosome consist of?
A2: large complexes of RNA and protein
Q3: What is a ribosome responsible for?
A3: carrying out the chemical reactions to add new amino acids to a growing polypeptide chain
Q4: How is the genetic code read?
A4: via interactions with specialized RNA molecules called transfer RNA (tRNA)
Q5: How many unpaired bases does each tRNA have?
A5: three
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.

Q1: When are genes expressed?
A1: only when the product is needed
Q2: What are examples of a cell's external environment?
A2: available nutrients, temperature and other stresses
Q3: What are examples of a cell's internal environment?
A3: cell division cycle, metabolism, infection status
Q4: At which step can gene expression be regulated?
A4: at any step
Q5: What example of post-translational modification of a protein was first described in 1961?
A5: 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.

Q1: What is first copied into RNA as an intermediate in the manufacture of the final protein product?
A1: A typical protein-coding gene
Q2: In some cases, what are the actual functional products?
A2: the RNA molecules
Q3: What sort of synthesis occurs when the RNA molecules are the actual functional products?
A3: the synthesis of ribosomal RNA and transfer RNA
Q4: What sort of function are ribozymes capable of?
A4: enzymatic function
Q5: What are the DNA sequences from which ribozymes are transcribed known as?
A5: 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.

Q1: In what form do some viruses store their entire genome?
A1: in the form of RNA
Q2: Why do the cellular hosts of some viruses not have to wait for transcription to synthesize their proteins?
A2: Because they use RNA to store genes
Q3: What is one type of an RNA retrovirus?
A3: HIV
Q4: What sort of transcription does the genome of HIV require before its proteins can be synthesized?
A4: reverse transcription
Q5: Besides viruses, where has RNA-mediated epigenetic inheritance been observed?
A5: 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

Q1: Where do organisms inherit their genes from?
A1: from their parents
Q2: How much of an asexual organism's genome is inherited from its parents?
A2: a complete copy
Q3: How many copies of each chromosome does a sexual organism have?
A3: two copies of each chromosome
Q4: How many sets of chromosomes does a sexual organism inherit from each parent?
A4: one complete set from each parent
Q5: Why do sexual organisms have two copies of each chromosome?
A5: 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

Q1: According to Mendelian inheritance, what is part of the cause of variations in an organism's phenotype?
A1: variations in its genotype
Q2: What sort of characteristics are described by an organism's phenotype?
A2: observable physical and behavioral characteristics
Q3: What is a genotype?
A3: particular set of genes
Q4: What specifies a particular trait with a different sequence of alleles?
A4: Each gene
Q5: How many alleles do most eukaryotic organisms have for each trait?
A5: 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.

Q1: Where can alleles be located in order to be either dominant or recessive?
A1: at a locus
Q2: When paired with any other allele for the same trait, what do dominant alleles give rise to?
A2: their corresponding phenotypes
Q3: When do recessive alleles give rise to their corresponding phenotype?
A3: when paired with another copy of the same allele
Q4: When do alleles assort independently?
A4: in the production of gametes
Q5: What are gametes?
A5: 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

Q1: What does the growth, development, and reproduction of organisms rely on?
A1: cell division
Q2: In cell division, what two cells are created?
A2: identical daughter cells
Q3: What specialized enzyme is responsible DNA replication?
A3: DNA polymerases
Q4: Why does the sequence of one strand completely specify the sequence of its complement?
A4: Because the DNA double helix is held together by base pairing
Q5: What one word characterizes the process of DNA replication?
A5: semiconservative