Gene

qas: question: What is a gene?
answers: text: a locus (or region) of DNA that encodes a functional RNA or protein product
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question: What is the basis of inheritance of phenotypic traits?
answers: text: The transmission of genes to an organism's offspring
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question: What influence are most biological traits under?
answers: text: polygenes (many different genes)
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question: What is one instantly visible genetic trait?
answers: text: eye colour or number of limbs
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question: What is one invisible genetic trait?
answers: text: blood type, risk for specific diseases, or the thousands of basic biochemical processes that comprise life
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question: In binary fission. when does each genome separate into daughter cells?
is_impossible: yes

question: Where do organisms inherit their genes from?
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question: What year was Mendel's work first published?
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context: 
A gene is a locus (or region) of DNA that encodes a functional RNA or protein product, and is the molecular unit of heredity.:Glossary The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits. Most biological traits are under the influence of polygenes (many different genes) as well as the gene–environment interactions. Some genetic traits are instantly visible, such as eye colour or number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that comprise life.

qas: question: What do mutations in a gene sequence lead to?
answers: text: different variants, known as alleles
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question: What do alleles do?
answers: text: encode slightly different versions of a protein
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question: What do alleles cause?
answers: text: different phenotype traits
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question: What does "having a gene" or a "good gene" typically refer to?
answers: text: having a different allele of the gene
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question: What causes genes to evolve?
answers: text: natural selection or survival of the fittest of the alleles
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question: What does transcription produce?
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question: What part of the organism is usually created which becomes a developed genetically altered organism?
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question: How does the expression of genes encoded in DNA begin?
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context: Genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a protein, which cause different phenotype traits. Colloquial usage of the term "having a gene" (e.g., "good genes," "hair colour gene") typically refers to having a different allele of the gene. Genes evolve due to natural selection or survival of the fittest of the alleles.

qas: question: What can regulatory regions of a gene be far removed from?
answers: text: its coding regions
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question: What can coding regions be split into?
answers: text: several exons
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question: What do some viruses store their genome in instead of DNA?
answers: text: RNA
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question: What are some gene products?
answers: text: functional non-coding RNAs
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question: What is a broad, modern working definition of a gene?
answers: text: any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product
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question: How can the gene nomenclature be accessed? 
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question: What are examples of a cell's external environment?
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question: What does the broad operational definition of a gene classify as gene-associated regions?
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context: The concept of a gene continues to be refined as new phenomena are discovered. For example, regulatory regions of a gene can be far removed from its coding regions, and coding regions can be split into several exons. Some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression.

qas: question: Who first suggested the existence of discrete inheritable units?
answers: text: Gregor Mendel (1822–1884)
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question: If a distinct trait in edible pea plants is mathematically described as a 2n combination, what does n represent? 
answers: text: n is the number of differing characteristics in the original peas
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question: What is one thing that Gregor Mendel was the first to demonstrate?
answers: text: independent assortment
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question: What is another thing that Gregor Mendel was the first to demonstrate?
answers: text: the distinction between dominant and recessive traits
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question: What did Gregor Mendel explain his results in terms of?
answers: text: discrete inherited units that give rise to observable physical characteristics
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question: What happens when a regulatory region binds to transcription factors?
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question: What is known as the modification of an organism's genome through biotechnology?
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question: In which type of organism do the smallest genomes occur?
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context: The existence of discrete inheritable units was first suggested by Gregor Mendel (1822–1884). From 1857 to 1864, he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring. He described these mathematically as 2n combinations where n is the number of differing characteristics in the original peas. Although he did not use the term gene, he explained his results in terms of discrete inherited units that give rise to observable physical characteristics. This description prefigured the distinction between genotype (the genetic material of an organism) and phenotype (the visible traits of that organism). Mendel was also the first to demonstrate independent assortment, the distinction between dominant and recessive traits, the distinction between a heterozygote and homozygote, and the phenomenon of discontinuous inheritance.

qas: question: What was the dominant theory of heredity prior to Mendel's work?
answers: text: one of blending inheritance
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question: Who developed the theory of inheritance known as pangenesis?
answers: text: Charles Darwin
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question: What does the term gemmule describe?
answers: text: hypothetical particles that would mix during reproduction
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question: What year was Mendel's work first published?
answers: text: 1866
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question: Who are the three scientists that claimed to have reached conclusions similar to Mendel's?
answers: text: Hugo de Vries, Carl Correns, and Erich von Tschermak
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question: What is referred to as "junk DNA"?
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question: What are mutations that lead to amino acid sequence changes but leave the protein functioning similarly called?
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question: What is the highest error rate that can occur for some RNA viruses?
is_impossible: yes
context: Prior to Mendel's work, the dominant theory of heredity was one of blending inheritance, which suggested that each parent contributed fluids to the fertilisation process and that the traits of the parents blended and mixed to produce the offspring. Charles Darwin developed a theory of inheritance he termed pangenesis, which used the term gemmule to describe hypothetical particles that would mix during reproduction. Although Mendel's work was largely unrecognized after its first publication in 1866, it was 'rediscovered' in 1900 by three European scientists, Hugo de Vries, Carl Correns, and Erich von Tschermak, who claimed to have reached similar conclusions in their own research.

qas: question: What ancient Greek word is the word 'gene' derived from?
answers: text: γένος (génos)
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question: What does the ancient Greek word 'génos' mean?
answers: text: "race, offspring"
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question: What Danish botanist coined the word 'gene'?
answers: text: Wilhelm Johannsen
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question: What was the word 'gene' used to describe in 1909?
answers: text: the fundamental physical and functional unit of heredity
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question: Who first used the word 'genetics' in 1905?
answers: text: William Bateson
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question: Where are the ribosome binding site, terminator and start and stop codons located on transcribed pre-mRNA?
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question: For what sort of organisms is the embryo normally engineered?
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question: According to Mendelian inheritance, what is part of the cause of variations in an organism's phenotype?
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context: 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.

qas: question: What was shown to be the molecular repository of genetic information by experiments in the 1940s to 1950s?
answers: text: Deoxyribonucleic acid (DNA)
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question: Who studied the structure of DNA using x-ray crystallography?
answers: text: Rosalind Franklin
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question: What two scientists published a model of the double stranded DNA molecule?
answers: text: James D. Watson and Francis Crick
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question: What is one exception to the central dogma of molecular biology?
answers: text: reverse transcription in retroviruses
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question: What is the modern study of genetics at the level of DNA known as?
answers: text: molecular genetics
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question: According to Mendelian inheritance, what is part of the cause of variations in an organism's phenotype?
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question: What is a genotype?
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question: What does DNA consist of?
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context: 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.

qas: question: When was the first sequence of a gene determined?
answers: text: In 1972
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question: What was the first gene to be sequenced?
answers: text: the gene for Bacteriophage MS2 coat protein
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question: Who developed chain termination DNA sequencing in 1977?
answers: text: Frederick Sanger
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question: What did the devlopment of the chain termination DNA sequencing method do for the sequencing process?
answers: text: improved the efficiency of sequencing and turned it into a routine laboratory tool.
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question: What project used an automated version of the Sanger method in its early stages?
answers: text: the Human Genome Project
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question: What causes the specificity of base pairing?
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question: What sort of variants did the Human Genome Project indicate that many of the measured transcripts were?
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question: Why does the mRNA match the sequence of the gene's DNA coding strand?
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context: 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.

qas: question: In what time span were the theories to integrate molecular genetic with Darwinian evolution developed?
answers: text: the 1930s and 1940s
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question: What are the theories that integrate molecular genetics with Darwinian evolution called?
answers: text: the modern evolutionary synthesis
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question: Who proposed an evolutionary concept of the gene as a unit of natural selection?
answers: text: George C. Williams
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question: What is the definition of the concept of the gene as a unit of natural selection?
answers: text: "that which segregates and recombines with appreciable frequency."
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question: Who popularized ideas emphasizing the centrality of genes in evolution?
answers: text: Richard Dawkins
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question: What specialized enzyme is responsible DNA replication?
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question: In genetic linkage, what sort of point is extremely unlikely to occur?
is_impossible: yes

question: What has become a common research tool with model organisms?
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context: 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.

qas: question: What do the vast majority of living organisms encode their genes in?
answers: text: long strands of DNA (deoxyribonucleic acid)
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question: What does DNA consist of?
answers: text: a chain made from four types of nucleotide subunits
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question: What type of sugar composes part of the DNA molecule?
answers: text: a five-carbon sugar (2'-deoxyribose)
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question: What are the four bases used in nucleotide subunits?
answers: text: adenine, cytosine, guanine, and thymine
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question: Besides the sugar and the four bases, what else does DNA consist of?
answers: text: a phosphate group
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question: When paired with any other allele for the same trait, what do dominant alleles give rise to?
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question: In what type of organism will the offspring be a genetic copy or clone of the parent organism?
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question: What is used as a template to generate a complementary mRNA?
is_impossible: yes
context: 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

qas: question: What is the backbone of a DNA double helix made of?
answers: text: phosphate-sugar
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question: What base pairs with thymine?
answers: text: adenine
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question: What base does guanine pair with?
answers: text: cytosine
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question: What causes the specificity of base pairing?
answers: text: adenine and thymine align form two hydrogen bonds, whereas cytosine and guanine form three hydrogen bonds
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question: Due to the cause of the specificity of base pairing, what must be true of the two strands in a double helix?
answers: text: The two strands in a double helix must therefore be complementary
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question: Each of a parent's two genes for each trait will sort independently into gametes according to what Mendelian principle?
is_impossible: yes

question: What is another thing that Gregor Mendel was the first to demonstrate?
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question: If the alleles on the chromatids are different, what effect arises from genetic recombination? 
is_impossible: yes
context: 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

qas: question: What causes the directionality of DNA strands?
answers: text: the chemical composition of the pentose residues of the bases
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question: What is known as the 3' end?
answers: text: an exposed hydroxyl group on the deoxyribose
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question: What is known as the 5' end?
answers: text: an exposed phosphate group
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question: What type of synthesis occurs in the 5'→3' direction?
answers: text: Nucleic acid synthesis
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question: Why does DNA replication and transcription occur in the 5'→3' direction?
answers: text: because new nucleotides are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile
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question: How do genes typically accumulate mutations over time?
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question: When do recessive alleles give rise to their corresponding phenotype?
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question: What does the definition of essential genes assume an absence of?
is_impossible: yes
context: 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

qas: question: How does the expression of genes encoded in DNA begin?
answers: text: by transcribing the gene into RNA
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question: What is RNA?
answers: text: a second type of nucleic acid that is very similar to DNA
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question: What base does RNA have in place of thymine?
answers: text: the base uracil
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question: What are codons?
answers: text: a series of three-nucleotide sequences
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question: What specifies the correspondence between codons and amino acids during protein translation?
answers: text: The genetic code
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question: What is at both ends of the transcribed pre-mRNA?
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question: How much of an asexual organism's genome is inherited from its parents?
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question: What is one instantly visible genetic trait?
is_impossible: yes
context: 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

qas: question: What is the total complement of genes in an organism or cell known as?
answers: text: its genome
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question: What does a chromosome consist of?
answers: text: a single, very long DNA helix
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question: What is encoded on a chromosome?
answers: text: thousands of genes
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question: What is the region of the chromosome at which a particular gene is located called?
answers: text: its locus
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question: What does each locus contain?
answers: text: one allele of a gene
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question: In some cases, what are the actual functional products?
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question: What is the estimate for the total number of protein coding genes on Earth?
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question: What encodes the protein or RNA product?
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context: 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.

qas: question: Where are the majority of eukaryotic genes stored?
answers: text: on a set of large, linear chromosomes
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question: Chromosomes that are packed within the nucleus in complex with histones are called what?
answers: text: a nucleosome
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question: What does the manner of DNA storage on the histone and the chemical modifications of the histone itself regulate?
answers: text: whether a particular region of DNA is accessible for gene expression
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question: What are replication origins?
answers: text: regions where DNA replication is initiated to make two copies of the chromosome
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question: Long stretches of repetitive sequence that cap the ends of the linear chromosomes are called what?
answers: text: Telomeres
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question: What are mutations that do not change the amino acid sequence called?
is_impossible: yes

question: Who studied the structure of DNA using x-ray crystallography?
is_impossible: yes

question: What is the modern study of genetics at the level of DNA known as?
is_impossible: yes
context: 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

qas: question: What are prokaryotes?
answers: text: bacteria and archaea
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question: How do prokaryotes store their genomes?
answers: text: on a single large, circular chromosome
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question: What type of chromosome do some eukaryotic organelles contain?
answers: text: a remnant circular chromosome with a small number of genes
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question: Small circles of DNA that encode only a few genes and are transferable between individuals are called what?
answers: text: plasmids
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question: What allows genes for antibiotic resistance to be passed between individual cells?
answers: text: horizontal gene transfer
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question: What year was Mendel's work first published?
is_impossible: yes

question: What is a result of deleterious mutations?
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question: What are functional copies of a gene which have a loss of function due to mutation called?
is_impossible: yes
context: 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.

qas: question: What type of organism has relatively gene dense chromosomes?
answers: text: prokaryotes
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question: Regions of DNA that serve no obvious function are often found in what type of organism?
answers: text: eukaryotes
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question: What is referred to as "junk DNA"?
answers: text: DNA without an identified function
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question: What percentage of the human genome is made of protein coding DNA?
answers: text: barely 2%
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question: What percentage of bases in the human genome are expressed by protein coding DNA
answers: text: about 80%
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question: In order for a gene to encode multiple proteins, how must its mRNAs be arranged?
is_impossible: yes

question: Each of a parent's two genes for each trait will sort independently into gametes according to what Mendelian principle?
is_impossible: yes

question: What is the degree of sequence similarity between homologous genes called?
is_impossible: yes
context: 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.

qas: question: Often, how large a part of the structure of a gene is the protein coding sequence?
answers: text: often only a small part
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question: What often plays only a small part in the structure of a gene? 
answers: text: the actual protein coding sequence
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question: What is one of the many elements that the structure of a gene consists of?
answers: text: DNA regions that are not transcribed
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question: What is another element of the structure of a gene?
answers: text: untranslated regions of the RNA
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question: What elements does the structure of a gene consist of?
answers: text: DNA regions that are not transcribed as well as untranslated regions of the RNA
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question: What are genes that result from divergence of the genes after a speciation event called?
is_impossible: yes

question: Each of a parent's two genes for each trait will sort independently into gametes according to what Mendelian principle?
is_impossible: yes

question: The duplication and transmission of genetic material from one generation of cells to the next is the basis for what?
is_impossible: yes
context: 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.

qas: question: What do all genes contain that is required for their expression?
answers: text: a regulatory sequence
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question: How is a promoter sequence recognized?
answers: text: by transcription factors and RNA polymerase
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question: What results when genes have more than one promoter?
answers: text: messenger RNAs (mRNA) that differ in how far they extend in the 5' end
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question: What does a "strong" promoter sequence do?
answers: text: bind the transcription machinery well
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question: What does a "weak" promoter sequence do?
answers: text: bind poorly and initiate transcription less frequently
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question: What is encoded on a chromosome?
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question: In binary fission. when does each genome separate into daughter cells?
is_impossible: yes

question: If the transcription is very long, where on the RNA may translation begin?
is_impossible: yes
context: 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

qas: question: How do regulatory regions act?
answers: text: by binding to transcription factors
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question: What happens when a regulatory region binds to transcription factors?
answers: text: the DNA to loop
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question: How do enhancers increase transcription?
answers: text: by binding an activator protein
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question: What happens after an enhancer binds an activator protein?
answers: text: helps to recruit the RNA polymerase to the promoter
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question: What causes DNA to be less available for RNA polymerase?
answers: text: silencers bind repressor proteins
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question: What are mutations that have no effect on an organism's phenotype called?
is_impossible: yes

question: What causes the specificity of base pairing?
is_impossible: yes

question: What sort of variants did the Human Genome Project indicate that many of the measured transcripts were?
is_impossible: yes
context: 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.

qas: question: What is at both ends of the transcribed pre-mRNA?
answers: text: untranslated regions
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question: Where are the ribosome binding site, terminator and start and stop codons located on transcribed pre-mRNA?
answers: text: untranslated regions
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question: What do most eukaryotic open reading frames contain?
answers: text: untranslated introns
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question: What dictates the splice sites to generate the final mature mRNA?
answers: text: The sequences at the ends of the introns
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question: What encodes the protein or RNA product?
answers: text: the splice sites to generate the final mature mRNA
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question: When are genes expressed?
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question: Which organism acts as a single non coding RNA gene?
is_impossible: yes

question: In which type of organism do the smallest genomes occur?
is_impossible: yes
context: 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.

qas: question: What are most prokaryotic genes organized into?
answers: text: operons
is_impossible: no

question: What are multiple protein coding sequences transcribed as?
answers: text: a unit
is_impossible: no

question: What sort of functions do the products of operon genes typically have?
answers: text: related functions
is_impossible: no

question: What type of network are the products of operon genes typically involved with?
answers: text: the same regulatory network
is_impossible: no

question: What type of coding sequences do prokaryotic genes typically have?
answers: text: multiple protein-coding sequences
is_impossible: no

question: Who proposed an evolutionary concept of the gene as a unit of natural selection?
is_impossible: yes

question: Who popularized ideas emphasizing the centrality of genes in evolution?
is_impossible: yes

question: In cell division, what two cells are created? 
is_impossible: yes
context: 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

qas: question: What is an example of a regulatory region of a gene that does not have to close to the coding sequence?
answers: text: enhancers
is_impossible: no

question: Why do some regulatory regions of a gene not have to be close to the coding sequence?
answers: text: because the intervening DNA can be looped out to bring the gene and its regulatory region into proximity
is_impossible: no

question: What part of a gene can be much larger than its exons?
answers: text: a gene's introns
is_impossible: no

question: How do regulatory regions on different chromosomes operate in order to allow regions on different chromosomes to come into contact with one another?
answers: text: in trans
is_impossible: no

question: Where can regulatory regions be found?
answers: text: different chromosomes
is_impossible: no

question: Which organism acts as a single non coding RNA gene?
is_impossible: yes

question: What does the broad operational definition of a gene classify as gene-associated regions?
is_impossible: yes

question: What does transcription produce?
is_impossible: yes
context: 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.

qas: question: What model did early work in molecular genetics suggest?
answers: text: the model that one gene makes one protein.
is_impossible: no

question: What discovery caused the model that one gene makes one protein to be refined?
answers: text: the discovery of genes that can encode multiple proteins
is_impossible: no

question: How do genes encode multiple proteins?
answers: text: by alternative splicing and coding sequences
is_impossible: no

question: How are alternative splicing and coding sequences distributed?
answers: text: split in short section across the genome
is_impossible: no

question: In order for a gene to encode multiple proteins, how must its mRNAs be arranged?
answers: text: concatenated by trans-splicing.
is_impossible: no

question: What does DNA consist of?
is_impossible: yes

question: What are prokaryotes?
is_impossible: yes

question: What are examples of a cell's internal environment?
is_impossible: yes
context: 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.

qas: question: What sort of definition can be used to conveniently encompass the complexity of diverse phenomena?
answers: text: A broad operational definition
is_impossible: no

question: What is the broad operational definition of a gene?
answers: text: a union of genomic sequences encoding a coherent set of potentially overlapping functional products
is_impossible: no

question: What does the typical definition of a gene categorize genes by?
answers: text: their specific DNA loci
is_impossible: no

question: What does the broad operational definition of gene categorize genes by?
answers: text: their functional products (proteins or RNA)
is_impossible: no

question: What does the broad operational definition of a gene classify as gene-associated regions?
answers: text: regulatory elements
is_impossible: no

question: How can the gene nomenclature be accessed? 
is_impossible: yes

question: How many genes are essential for Escherichia coli?
is_impossible: yes

question: What is the highest error rate that can occur for some RNA viruses?
is_impossible: yes
context: 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.

qas: question: How many steps are required to read the information encoded in a gene's DNA and produce the specified protein?
answers: text: two steps are required
is_impossible: no

question: What is the first step to read the information encoded in a gene's DNA and produce the protein it specifies?
answers: text: the gene's DNA is transcribed to messenger RNA (mRNA)
is_impossible: no

question: What is the second step to read the information encoded in a gene's DNA and produce the protein it specifies?
answers: text: mRNA is translated to protein
is_impossible: no

question: What step must RNA-coding genes still go through?
answers: text: the first step
is_impossible: no

question: What is the process of producing a biologically functional molecule of either RNA or protein called?
answers: text: gene expression
is_impossible: no

question: What is it called when multiple different alleles for a gene are present in a species's population?
is_impossible: yes

question: Why does the mRNA match the sequence of the gene's DNA coding strand?
is_impossible: yes

question: What does a chromosome consist of?
is_impossible: yes
context: 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.

qas: question: What specifies the amino acid sequence of a protein?
answers: text: The nucleotide sequence of a gene's DNA
is_impossible: no

question: What are sets of three nucleotides known as?
answers: text: codons
is_impossible: no

question: What does each codon correspond to?
answers: text: a specific amino acid
is_impossible: no

question: What indicates the beginning and end of the protein coding region?
answers: text: a "start codon", and three "stop codons"
is_impossible: no

question: How many possible codons are there?
answers: text: There are 64 possible codons (four possible nucleotides at each of three positions, hence 43 possible codons)
is_impossible: no

question: How many essential genes does Saccharomyces cerevisiae have?
is_impossible: yes

question: What is the highest error rate that can occur for some RNA viruses?
is_impossible: yes

question: What is known as the modification of an organism's genome through biotechnology?
is_impossible: yes
context: 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.

qas: question: What does transcription produce?
answers: text: a single-stranded RNA molecule known as messenger RNA
is_impossible: no

question: How does the nucleotide sequence of mRNA compare to DNA?
answers: text: complementary to the DNA from which it was transcribed
is_impossible: no

question: What is used as a template to generate a complementary mRNA?
answers: text: The gene's DNA
is_impossible: no

question: Why does the mRNA match the sequence of the gene's DNA coding strand?
answers: text: because it is synthesised as the complement of the template strand
is_impossible: no

question: What is the enzyme called that performs transcription?
answers: text: an RNA polymerase
is_impossible: no

question: What is one thing the cell must do once DNA replication is compete?
is_impossible: yes

question: In some cases, what are the actual functional products?
is_impossible: yes

question: What is the modern study of genetics at the level of DNA known as?
is_impossible: yes
context: 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

qas: question: Where does transcription occur in prokaryotes?
answers: text: in the cytoplasm
is_impossible: no

question: If the transcription is very long, where on the RNA may translation begin?
answers: text: at the 5' end of the RNA
is_impossible: no

question: Where does transcription occur in eukaryotes?
answers: text: transcription occurs in the nucleus
is_impossible: no

question: Where does a eukaryote store the cell's DNA?
answers: text: in the nucleus
is_impossible: no

question: What is the RNA molecule produced by the polymerase known as?
answers: text: the primary transcript
is_impossible: no

question: What is one characteristic that varies widely between organisms?
is_impossible: yes

question: What does the typical definition of a gene categorize genes by?
is_impossible: yes

question: Which organism acts as a single non coding RNA gene?
is_impossible: yes
context: 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

qas: question: What is the process by which a mature mRNA molecule is used as a template for synthesizing a new protein called?
answers: text: Translation
is_impossible: no

question: What does a ribosome consist of?
answers: text: large complexes of RNA and protein
is_impossible: no

question: What is a ribosome responsible for?
answers: text: carrying out the chemical reactions to add new amino acids to a growing polypeptide chain
is_impossible: no

question: How is the genetic code read?
answers: text: via interactions with specialized RNA molecules called transfer RNA (tRNA)
is_impossible: no

question: How many unpaired bases does each tRNA have?
answers: text: three
is_impossible: no

question: What are prokaryotes?
is_impossible: yes

question: What is another thing the cell must do once DNA replication is complete?
is_impossible: yes

question: What does the directional selection of beneficial mutations lead to?
is_impossible: yes
context: 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

qas: question: When are genes expressed?
answers: text: only when the product is needed
is_impossible: no

question: What are examples of a cell's external environment?
answers: text: available nutrients, temperature and other stresses
is_impossible: no

question: What are examples of a cell's internal environment?
answers: text: cell division cycle, metabolism, infection status
is_impossible: no

question: At which step can gene expression be regulated?
answers: text: at any step
is_impossible: no

question: What example of post-translational modification of a protein was first described in 1961?
answers: text: The regulation of lactose metabolism genes in E. coli
is_impossible: no

question: What do most eukaryotic open reading frames contain?
is_impossible: yes

question: When do recessive alleles give rise to their corresponding phenotype?
is_impossible: yes

question: What are mutations that lead to amino acid sequence changes but leave the protein functioning similarly called?
is_impossible: yes
context: 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.

qas: question: What is first copied into RNA as an intermediate in the manufacture of the final protein product?
answers: text: A typical protein-coding gene
is_impossible: no

question: In some cases, what are the actual functional products?
answers: text: the RNA molecules
is_impossible: no

question: What sort of synthesis occurs when the RNA molecules are the actual functional products?
answers: text: the synthesis of ribosomal RNA and transfer RNA
is_impossible: no

question: What sort of function are ribozymes capable of?
answers: text: enzymatic function
is_impossible: no

question: What are the DNA sequences from which ribozymes are transcribed known as?
answers: text: non-coding RNA genes
is_impossible: no

question: What are mutations that lead to amino acid sequence changes but leave the protein functioning similarly called?
is_impossible: yes

question: What is the backbone of a DNA double helix made of?
is_impossible: yes

question: What sort of transcription does the genome of HIV require before its proteins can be synthesized?
is_impossible: yes
context: 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.

qas: question: In what form do some viruses store their entire genome?
answers: text: in the form of RNA
is_impossible: no

question: Why do the cellular hosts of some viruses not have to wait for transcription to synthesize their proteins?
answers: text: Because they use RNA to store genes
is_impossible: no

question: What is one type of an RNA retrovirus?
answers: text: HIV
is_impossible: no

question: What sort of transcription does the genome of HIV require before its proteins can be synthesized?
answers: text: reverse transcription
is_impossible: no

question: Besides viruses, where has RNA-mediated epigenetic inheritance been observed?
answers: text: in plants and very rarely in animals
is_impossible: no

question: Where are the majority of eukaryotic genes stored?
is_impossible: yes

question: How can the gene nomenclature be accessed? 
is_impossible: yes

question: When did techniques begin to be developed to add, remove and edit genes?
is_impossible: yes
context: 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.

qas: question: Where do organisms inherit their genes from?
answers: text: from their parents
is_impossible: no

question: How much of an asexual organism's genome is inherited from its parents?
answers: text: a complete copy
is_impossible: no

question: How many copies of each chromosome does a sexual organism have?
answers: text: two copies of each chromosome
is_impossible: no

question: How many sets of chromosomes does a sexual organism inherit from each parent?
answers: text: one complete set from each parent
is_impossible: no

question: Why do sexual organisms have two copies of each chromosome?
answers: text: because they inherit one complete set from each parent
is_impossible: no

question: When do alleles assort independently?
is_impossible: yes

question: What is the highest error rate that can occur for some RNA viruses?
is_impossible: yes

question: What is one trait that horizontal gene transfer is a common means of spreading?
is_impossible: yes
context: 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

qas: question: According to Mendelian inheritance, what is part of the cause of variations in an organism's phenotype?
answers: text: variations in its genotype
is_impossible: no

question: What sort of characteristics are described by an organism's phenotype?
answers: text: observable physical and behavioral characteristics
is_impossible: no

question: What is a genotype?
answers: text: particular set of genes
is_impossible: no

question: What specifies a particular trait with a different sequence of alleles?
answers: text: Each gene
is_impossible: no

question: How many alleles do most eukaryotic organisms have for each trait?
answers: text: two alleles for each trait
is_impossible: no

question: Why does the sequence of one strand completely specify the sequence of its complement?
is_impossible: yes

question: What can regulatory regions of a gene be far removed from?
is_impossible: yes

question: What indicates the beginning and end of the protein coding region?
is_impossible: yes
context: 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

qas: question: Where can alleles be located in order to be either dominant or recessive?
answers: text: at a locus
is_impossible: no

question: When paired with any other allele for the same trait, what do dominant alleles give rise to?
answers: text: their corresponding phenotypes
is_impossible: no

question: When do recessive alleles give rise to their corresponding phenotype?
answers: text: when paired with another copy of the same allele
is_impossible: no

question: When do alleles assort independently?
answers: text: in the production of gametes
is_impossible: no

question: What are gametes?
answers: text: germ cells
is_impossible: no

question: What techniques can be used to alter the genomes of an adult organism to treat genetic disease?
is_impossible: yes

question: What does each codon correspond to?
is_impossible: yes

question: Who studied the structure of DNA using x-ray crystallography?
is_impossible: yes
context: 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.

qas: question: What does the growth, development, and reproduction of organisms rely on?
answers: text: cell division
is_impossible: no

question: In cell division, what two cells are created? 
answers: text: identical daughter cells
is_impossible: no

question: What specialized enzyme is responsible DNA replication?
answers: text: DNA polymerases
is_impossible: no

question: Why does the sequence of one strand completely specify the sequence of its complement?
answers: text: Because the DNA double helix is held together by base pairing
is_impossible: no

question: What one word characterizes the process of DNA replication?
answers: text: semiconservative
is_impossible: no

question: What is referred to as "junk DNA"?
is_impossible: yes

question: What sort of DNA repair is created by modern genetic engineering techniques?
is_impossible: yes

question: What type of coding sequences do prokaryotic genes typically have?
is_impossible: yes
context: 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

qas: question: What is one thing the cell must do once DNA replication is compete?
answers: text: physically separate the two copies of the genome
is_impossible: no

question: What is another thing the cell must do once DNA replication is complete?
answers: text: divide into two distinct membrane-bound cells
is_impossible: no

question: In binary fission, what shape is each genome?
answers: text: circular
is_impossible: no

question: In binary fission. when does each genome separate into daughter cells?
answers: text: as the membrane invaginates to split the cytoplasm
is_impossible: no

question: Compared to the rates of cell division in eukaryotes, with what speed does binary fission occur?
answers: text: extremely fast
is_impossible: no

question: What is one reason for homologs to appear?
is_impossible: yes

question: Which organism acts as a single non coding RNA gene?
is_impossible: yes

question: What can some alleles give rise to?
is_impossible: yes
context: 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

qas: question: The duplication and transmission of genetic material from one generation of cells to the next is the basis for what?
answers: text: molecular inheritance
is_impossible: no

question: Why do organisms inherit the characteristics of their parents?
answers: text: cells of the offspring contain copies of the genes in their parents' cells
is_impossible: no

question: In what type of organism will the offspring be a genetic copy or clone of the parent organism?
answers: text: In asexually reproducing organisms
is_impossible: no

question: In what type of organism will a specialized form of cell division called meiosis produce cells called gametes?
answers: text: In sexually reproducing organisms
is_impossible: no

question: What are the gametes produced by females called?
answers: text: eggs or ova
is_impossible: no

question: What discovery caused the model that one gene makes one protein to be refined?
is_impossible: yes

question: What is the basis of inheritance of phenotypic traits?
is_impossible: yes

question: Why does the mRNA match the sequence of the gene's DNA coding strand?
is_impossible: yes
context: The duplication and transmission of genetic material from one generation of cells to the next is the basis for molecular inheritance, and the link between the classical and molecular pictures of genes. Organisms inherit the characteristics of their parents because the cells of the offspring contain copies of the genes in their parents' cells. In asexually reproducing organisms, the offspring will be a genetic copy or clone of the parent organism. In sexually reproducing organisms, a specialized form of cell division called meiosis produces cells called gametes or germ cells that are haploid, or contain only one copy of each gene.:20.2 The gametes produced by females are called eggs or ova, and those produced by males are called sperm. Two gametes fuse to form a diploid fertilized egg, a single cell that has two sets of genes, with one copy of each gene from the mother and one from the father.:20

qas: question: When can an event called genetic recombination or crossing-over sometimes occur?
answers: text: During the process of meiotic cell division
is_impossible: no

question: If the alleles on the chromatids are the same, what effect arises from genetic recombination? 
answers: text: no effect
is_impossible: no

question: If the alleles on the chromatids are different, what effect arises from genetic recombination? 
answers: text: reassortment of otherwise linked alleles
is_impossible: no

question: Each of a parent's two genes for each trait will sort independently into gametes according to what Mendelian principle?
answers: text: independent assortment
is_impossible: no

question: In genetic linkage, what sort of point is extremely unlikely to occur?
answers: text: a crossover point
is_impossible: no

question: What is a gene?
is_impossible: yes

question: What are prokaryotes?
is_impossible: yes

question: What sort of transcription does the genome of HIV require before its proteins can be synthesized?
is_impossible: yes
context: During the process of meiotic cell division, an event called genetic recombination or crossing-over can sometimes occur, in which a length of DNA on one chromatid is swapped with a length of DNA on the corresponding sister chromatid. This has no effect if the alleles on the chromatids are the same, but results in reassortment of otherwise linked alleles if they are different.:5.5 The Mendelian principle of independent assortment asserts that each of a parent's two genes for each trait will sort independently into gametes; which allele an organism inherits for one trait is unrelated to which allele it inherits for another trait. This is in fact only true for genes that do not reside on the same chromosome, or are located very far from one another on the same chromosome. The closer two genes lie on the same chromosome, the more closely they will be associated in gametes and the more often they will appear together; genes that are very close are essentially never separated because it is extremely unlikely that a crossover point will occur between them. This is known as genetic linkage.

qas: question: What is it called when errors occur in DNA replication?
answers: text: mutations
is_impossible: no

question: What is the lowest error rate that occurs in eukaryotic cells?
answers: text: 10−8 per nucleotide per replication
is_impossible: no

question: What is the highest error rate that can occur for some RNA viruses?
answers: text: 10−3
is_impossible: no

question: What can small mutations be caused by?
answers: text: DNA replication
is_impossible: no

question: What can larger mutations be caused by?
answers: text: errors in recombination
is_impossible: no

question: What is one characteristic that varies widely between organisms?
is_impossible: yes

question: What is the degree of sequence similarity between homologous genes called?
is_impossible: yes

question: What techniques can be used to alter the genomes of an adult organism to treat genetic disease?
is_impossible: yes
context: DNA replication is for the most part extremely accurate, however errors (mutations) do occur.:7.6 The error rate in eukaryotic cells can be as low as 10−8 per nucleotide per replication, whereas for some RNA viruses it can be as high as 10−3. This means that each generation, each human genome accumulates 1–2 new mutations. Small mutations can be caused by DNA replication and the aftermath of DNA damage and include point mutations in which a single base is altered and frameshift mutations in which a single base is inserted or deleted. Either of these mutations can change the gene by missense (change a codon to encode a different amino acid) or nonsense (a premature stop codon). Larger mutations can be caused by errors in recombination to cause chromosomal abnormalities including the duplication, deletion, rearrangement or inversion of large sections of a chromosome. Additionally, the DNA repair mechanisms that normally revert mutations can introduce errors when repairing the physical damage to the molecule is more important than restoring an exact copy, for example when repairing double-strand breaks.:5.4

qas: question: What is it called when multiple different alleles for a gene are present in a species's population?
answers: text: polymorphic
is_impossible: no

question: What can some alleles give rise to?
answers: text: different phenotypic traits
is_impossible: no

question: What is a gene's most common allele known as?
answers: text: the wild type
is_impossible: no

question: What are rare alleles called?
answers: text: mutants
is_impossible: no

question: What is one cause of the genetic variation in relative frequencies of different alleles in a population?
answers: text: genetic drift
is_impossible: no

question: What does the typical definition of a gene categorize genes by?
is_impossible: yes

question: What are prokaryotes?
is_impossible: yes

question: What sort of transcription does the genome of HIV require before its proteins can be synthesized?
is_impossible: yes
context: When multiple different alleles for a gene are present in a species's population it is called polymorphic. Most different alleles are functionally equivalent, however some alleles can give rise to different phenotypic traits. A gene's most common allele is called the wild type, and rare alleles are called mutants. The genetic variation in relative frequencies of different alleles in a population is due to both natural selection and genetic drift. The wild-type allele is not necessarily the ancestor of less common alleles, nor is it necessarily fitter.

qas: question: What are mutations that have no effect on an organism's phenotype called?
answers: text: silent mutations
is_impossible: no

question: What are mutations that do not change the amino acid sequence called?
answers: text: synonymous mutations
is_impossible: no

question: What are mutations that lead to amino acid sequence changes but leave the protein functioning similarly called?
answers: text: conservative mutations
is_impossible: no

question: What is a result of deleterious mutations?
answers: text: Genetic disorders
is_impossible: no

question: What does the directional selection of beneficial mutations lead to?
answers: text: adaptive evolution
is_impossible: no

question: What does the definition of essential genes assume an absence of?
is_impossible: yes

question: What is another for which  organisms have been modified for?
is_impossible: yes

question: What can some alleles give rise to?
is_impossible: yes
context: Most mutations within genes are neutral, having no effect on the organism's phenotype (silent mutations). Some mutations do not change the amino acid sequence because multiple codons encode the same amino acid (synonymous mutations). Other mutations can be neutral if they lead to amino acid sequence changes, but the protein still functions similarly with the new amino acid (e.g. conservative mutations). Many mutations, however, are deleterious or even lethal, and are removed from populations by natural selection. Genetic disorders are the result of deleterious mutations and can be due to spontaneous mutation in the affected individual, or can be inherited. Finally, a small fraction of mutations are beneficial, improving the organism's fitness and are extremely important for evolution, since their directional selection leads to adaptive evolution.:7.6

qas: question: What are genes with a most recent common ancestor called?
answers: text: homologs
is_impossible: no

question: What is one reason for homologs to appear?
answers: text: gene duplication within an organism's genome
is_impossible: no

question: What are genes that occur from duplication within an organism's genome called?
answers: text: paralogous genes
is_impossible: no

question: What are genes that result from divergence of the genes after a speciation event called?
answers: text: orthologous genes
is_impossible: no

question: What is the RNA molecule produced by the polymerase known as?
is_impossible: yes

question: What is first copied into RNA as an intermediate in the manufacture of the final protein product?
is_impossible: yes

question: What is one thing the cell must do once DNA replication is compete?
is_impossible: yes
context: Genes with a most recent common ancestor, and thus a shared evolutionary ancestry, are known as homologs. These genes appear either from gene duplication within an organism's genome, where they are known as paralogous genes, or are the result of divergence of the genes after a speciation event, where they are known as orthologous genes,:7.6 and often perform the same or similar functions in related organisms. It is often assumed that the functions of orthologous genes are more similar than those of paralogous genes, although the difference is minimal.

qas: question: What does comparing the sequence alignment of genes' DNA measure?
answers: text: The relationship between genes
is_impossible: no

question: What is the degree of sequence similarity between homologous genes called?
answers: text: conserved sequence
is_impossible: no

question: How do genes typically accumulate mutations over time?
answers: text: by neutral molecular evolution
is_impossible: no

question: Under what type of selection are genes constrained so they change more slowly?
answers: text: stabilizing
is_impossible: no

question: What type of analyses can the sequence differences between genes be used for?
answers: text: phylogenetic
is_impossible: no

question: What did the devlopment of the chain termination DNA sequencing method do for the sequencing process?
is_impossible: yes

question: If the alleles on the chromatids are different, what effect arises from genetic recombination? 
is_impossible: yes

question: How does the expression of genes encoded in DNA begin?
is_impossible: yes
context: The relationship between genes can be measured by comparing the sequence alignment of their DNA.:7.6 The degree of sequence similarity between homologous genes is called conserved sequence. Most changes to a gene's sequence do not affect its function and so genes accumulate mutations over time by neutral molecular evolution. Additionally, any selection on a gene will cause its sequence to diverge at a different rate. Genes under stabilizing selection are constrained and so change more slowly whereas genes under directional selection change sequence more rapidly. The sequence differences between genes can be used for phylogenetic analyses to study how those genes have evolved and how the organisms they come from are related.

qas: question: What is the most common source of new genes in eukaryotic lineages?
answers: text: gene duplication
is_impossible: no

question: What creates copy number variation of an existing gene in the genome?
answers: text: gene duplication
is_impossible: no

question: What are the genes that result from eukaryotic gene duplication called?
answers: text: paralogs
is_impossible: no

question: What type of copy can gene duplication sometimes result in?
answers: text: nonfunctional
is_impossible: no

question: What are functional copies of a gene which have a loss of function due to mutation called?
answers: text: pseudogenes
is_impossible: no

question: What can small mutations be caused by?
is_impossible: yes

question: What is one instantly visible genetic trait?
is_impossible: yes

question: What base does guanine pair with?
is_impossible: yes
context: The most common source of new genes in eukaryotic lineages is gene duplication, which creates copy number variation of an existing gene in the genome. The resulting genes (paralogs) may then diverge in sequence and in function. Sets of genes formed in this way comprise a gene family. Gene duplications and losses within a family are common and represent a major source of evolutionary biodiversity. Sometimes, gene duplication may result in a nonfunctional copy of a gene, or a functional copy may be subject to mutations that result in loss of function; such nonfunctional genes are called pseudogenes.:7.6

qas: question: What is a gene whose sequence shows no similarity to existing genes called?
answers: text: De novo or "orphan" genes
is_impossible: no

question: What is the estimate of the number of orphan genes in the human genome?
answers: text: 18 to 60
is_impossible: no

question: How do the lengths of orphan genes compare to most eukaryotic genes?
answers: text: typically shorter
is_impossible: no

question: How does the structure of orphan genes compare to most eukaryotic genes?
answers: text: simpler in structure
is_impossible: no

question: What is one primary source of orphan protein-coding genes?
answers: text: gene duplication followed by extremely rapid sequence change
is_impossible: no

question: What are the four bases used in nucleotide subunits?
is_impossible: yes

question: What are mutations that do not change the amino acid sequence called?
is_impossible: yes

question: What does transcription produce?
is_impossible: yes
context: De novo or "orphan" genes, whose sequence shows no similarity to existing genes, are extremely rare. Estimates of the number of de novo genes in the human genome range from 18 to 60. Such genes are typically shorter and simpler in structure than most eukaryotic genes, with few if any introns. Two primary sources of orphan protein-coding genes are gene duplication followed by extremely rapid sequence change, such that the original relationship is undetectable by sequence comparisons, and formation through mutation of "cryptic" transcription start sites that introduce a new open reading frame in a region of the genome that did not previously code for a protein.

qas: question: What is the  transfer of genetic material through a mechanism other than reproduction known as?
answers: text: Horizontal gene transfer
is_impossible: no

question: In what type of organism is horizontal gene transfer a common source of new genes?
answers: text: prokaryotes
is_impossible: no

question: What is one trait that horizontal gene transfer is a common means of spreading?
answers: text: antibiotic resistance
is_impossible: no

question: In what type of organism is horizontal gene transfer rare?
answers: text: eukaryotes
is_impossible: no

question: What is one example of horizontal gene transfer in eukaryotes?
answers: text: alga genomes containing genes of bacterial origin
is_impossible: no

question: When can an event called genetic recombination or crossing-over sometimes occur?
is_impossible: yes

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

question: What do most eukaryotic open reading frames contain?
is_impossible: yes
context: Horizontal gene transfer refers to the transfer of genetic material through a mechanism other than reproduction. This mechanism is a common source of new genes in prokaryotes, sometimes thought to contribute more to genetic variation than gene duplication. It is a common means of spreading antibiotic resistance, virulence, and adaptive metabolic functions. Although horizontal gene transfer is rare in eukaryotes, likely examples have been identified of protist and alga genomes containing genes of bacterial origin.

qas: question: What is one characteristic that varies widely between organisms?
answers: text: genome size
is_impossible: no

question: In which type of organism do the smallest genomes occur?
answers: text: viruses
is_impossible: no

question: What is the smallest number of protein coding genes that a virus can have?
answers: text: 2
is_impossible: no

question: Which organism acts as a single non coding RNA gene?
answers: text: viroids
is_impossible: no

question: What is the estimate for the total number of protein coding genes on Earth?
answers: text: 5 million
is_impossible: no

question: In some cases, what are the actual functional products?
is_impossible: yes

question: How do genes encode multiple proteins?
is_impossible: yes

question: When do recessive alleles give rise to their corresponding phenotype?
is_impossible: yes
context: The genome size, and the number of genes it encodes varies widely between organisms. The smallest genomes occur in viruses (which can have as few as 2 protein-coding genes), and viroids (which act as a single non-coding RNA gene). Conversely, plants can have extremely large genomes, with rice containing >46,000 protein-coding genes. The total number of protein-coding genes (the Earth's proteome) is estimated to be 5 million sequences.

qas: question: Since when has the number of base pairs of DNA in the human genome been known?
answers: text: the 1960s
is_impossible: no

question: What was the highest initial theoretical prediction of the number of human genes?
answers: text: 2,000,000
is_impossible: no

question: What sort of variants did the Human Genome Project indicate that many of the measured transcripts were?
answers: text: alternative variants
is_impossible: no

question: After the Human Genome Project, how many genes were encoded on the mitochondrial genome?
answers: text: 13
is_impossible: no

question: What percentage of the human genome consists of protein coding genes?
answers: text: 1–2%
is_impossible: no

question: In some cases, what are the actual functional products?
is_impossible: yes

question: Where can alleles be located in order to be either dominant or recessive?
is_impossible: yes

question: What is referred to as "junk DNA"?
is_impossible: yes
context: Although the number of base-pairs of DNA in the human genome has been known since the 1960s, the estimated number of genes has changed over time as definitions of genes, and methods of detecting them have been refined. Initial theoretical predictions of the number of human genes were as high as 2,000,000. Early experimental measures indicated there to be 50,000–100,000 transcribed genes (expressed sequence tags). Subsequently, the sequencing in the Human Genome Project indicated that many of these transcripts were alternative variants of the same genes, and the total number of protein-coding genes was revised down to ~20,000 with 13 genes encoded on the mitochondrial genome. Of the human genome, only 1–2% consists of protein-coding genes, with the remainder being 'noncoding' DNA such as introns, retrotransposons, and noncoding RNAs.

qas: question: What are the set of genes which are thought to be crucial for the survival of an organism?
answers: text: Essential genes
is_impossible: no

question: What does the definition of essential genes assume an absence of?
answers: text: environmental stress
is_impossible: no

question: How many genes are essential for Escherichia coli?
answers: text: 250–400
is_impossible: no

question: What fraction of Escherichia coli's essential genes are orthologs?
answers: text: Half
is_impossible: no

question: How many essential genes does Saccharomyces cerevisiae have?
answers: text: 1000 genes
is_impossible: no

question: In what time span were the theories to integrate molecular genetic with Darwinian evolution developed?
is_impossible: yes

question: What can some alleles give rise to?
is_impossible: yes

question: What is one of the many elements that the structure of a gene consists of?
is_impossible: yes
context: Essential genes are the set of genes thought to be critical for an organism's survival. This definition assumes the abundant availability of all relevant nutrients and the absence of environmental stress. Only a small portion of an organism's genes are essential. In bacteria, an estimated 250–400 genes are essential for Escherichia coli and Bacillus subtilis, which is less than 10% of their genes. Half of these genes are orthologs in both organisms and are largely involved in protein synthesis. In the budding yeast Saccharomyces cerevisiae the number of essential genes is slightly higher, at 1000 genes (~20% of their genes). Although the number is more difficult to measure in higher eukaryotes, mice and humans are estimated to have around 2000 essential genes (~10% of their genes).

qas: question: What type of genes are necessary for performing basic cell functions?
answers: text: Housekeeping genes
is_impossible: no

question: At what relative level are housekeeping genes expressed at?
answers: text: constant
is_impossible: no

question: When investigating gene expression, what type of genes are used as a control for experiments?
answers: text: housekeeping genes
is_impossible: no

question: How are some essential genes regulated?
answers: text: developmentally
is_impossible: no

question: When are some essential genes expressed?
answers: text: at certain times during the organism's life cycle
is_impossible: no

question: What was the highest initial theoretical prediction of the number of human genes?
is_impossible: yes

question: What is one reason for homologs to appear?
is_impossible: yes

question: How does the expression of genes encoded in DNA begin?
is_impossible: yes
context: Housekeeping genes are critical for carrying out basic cell functions and so are expressed at a relatively constant level (constitutively). Since their expression is constant, housekeeping genes are used as experimental controls when analysing gene expression. Not all essential genes are housekeeping genes since some essential genes are developmentally regulated or expressed at certain times during the organism's life cycle.

qas: question: What committee has established gene nomenclature for every known human gene?
answers: text: HUGO Gene Nomenclature Committee (HGNC)
is_impossible: no

question: How can the gene nomenclature be accessed? 
answers: text: through a database maintained by HGNC
is_impossible: no

question: How many symbols does each gene have?
answers: text: only one
is_impossible: no

question: With what is it preferred that symbols are kept consistent with?
answers: text: homologs in other species
is_impossible: no

question: What type of model does the mouse play a role for?
answers: text: common model
is_impossible: no

question: What is the estimate for the total number of protein coding genes on Earth?
is_impossible: yes

question: What do scientists explore by adding genes to mice with a certain gene's function disrupted?
is_impossible: yes

question: What is the degree of sequence similarity between homologous genes called?
is_impossible: yes
context: Gene nomenclature has been established by the HUGO Gene Nomenclature Committee (HGNC) for each known human gene in the form of an approved gene name and symbol (short-form abbreviation), which can be accessed through a database maintained by HGNC. Symbols are chosen to be unique, and each gene has only one symbol (although approved symbols sometimes change). Symbols are preferably kept consistent with other members of a gene family and with homologs in other species, particularly the mouse due to its role as a common model organism.

qas: question: What is known as the modification of an organism's genome through biotechnology?
answers: text: Genetic engineering
is_impossible: no

question: When did techniques begin to be developed to add, remove and edit genes?
answers: text: the 1970s
is_impossible: no

question: What sort of enzymes do recently developed genome engineering techniques use?
answers: text: engineered nuclease enzymes
is_impossible: no

question: What sort of DNA repair is created by modern genetic engineering techniques?
answers: text: targeted
is_impossible: no

question: What term refers to extensive genetic engineering of an organism?
answers: text: synthetic biology
is_impossible: no

question: What does the ancient Greek word 'génos' mean?
is_impossible: yes

question: Where are the majority of eukaryotic genes stored?
is_impossible: yes

question: Where are the ribosome binding site, terminator and start and stop codons located on transcribed pre-mRNA?
is_impossible: yes
context: Genetic engineering is the modification of an organism's genome through biotechnology. Since the 1970s, a variety of techniques have been developed to specifically add, remove and edit genes in an organism. Recently developed genome engineering techniques use engineered nuclease enzymes to create targeted DNA repair in a chromosome to either disrupt or edit a gene when the break is repaired. The related term synthetic biology is sometimes used to refer to extensive genetic engineering of an organism.

qas: question: What has become a common research tool with model organisms?
answers: text: Genetic engineering
is_impossible: no

question: What do scientists explore by adding genes to mice with a certain gene's function disrupted?
answers: text: that gene's function
is_impossible: no

question: What is an application for which organisms have been modified for?
answers: text: agriculture
is_impossible: no

question: What is another for which  organisms have been modified for?
answers: text: industrial biotechnology
is_impossible: no

question: What is yet another application for which  organisms have been modified for?
answers: text: medicine
is_impossible: no

question: What are mutations that lead to amino acid sequence changes but leave the protein functioning similarly called?
is_impossible: yes

question: What are genes with a most recent common ancestor called?
is_impossible: yes

question: What type of copy can gene duplication sometimes result in?
is_impossible: yes
context: Genetic engineering is now a routine research tool with model organisms. For example, genes are easily added to bacteria and lineages of knockout mice with a specific gene's function disrupted are used to investigate that gene's function. Many organisms have been genetically modified for applications in agriculture, industrial biotechnology, and medicine.

qas: question: For what sort of organisms is the embryo normally engineered?
answers: text: multicellular organisms
is_impossible: no

question: What techniques can be used to alter the genomes of an adult organism to treat genetic disease?
answers: text: gene therapy techniques
is_impossible: no

question: What part of the organism is usually created which becomes a developed genetically altered organism?
answers: text: the embryo
is_impossible: no

question: What can be changed in an adult organism using gene therapy techniques?
answers: text: the genomes of cells
is_impossible: no

question: What can be treated using genetic engineering?
answers: text: genetic diseases
is_impossible: no

question: How does the nucleotide sequence of mRNA compare to DNA?
is_impossible: yes

question: Besides the sugar and the four bases, what else does DNA consist of?
is_impossible: yes

question: What influence are most biological traits under?
is_impossible: yes
context: For multicellular organisms, typically the embryo is engineered which grows into the adult genetically modified organism. However, the genomes of cells in an adult organism can be edited using gene therapy techniques to treat genetic diseases.