Genetics

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Genes

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The basic unit of heredity. Composed of DNA and are located on chromosomes.

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Alleles

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Alternative forms in which a gene may exist.

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Genotype

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The genetic makeup of an individual.

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Phenotype

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The physical manifestation of the genetic makeup. Some correspond to a single genotype, while others correspond to several different genotypes.

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Mendelian Genetics

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Describes the basic principles of genetics through experimentation with the garden pea. The study of inheritance of individual pea traits through genetic crosses. Mendel took true-breeding individuals with different traits, mated them, and statistically analyzed the inheritance of the traits in the progeny.

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Mendel’s 1st Law

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The Law of Segregation. Genes exist in alternative alleles. An organism has two alleles for each inherited trait – one inherited from each parent. The two alleles segregate during meiosis, resulting in gametes that carry only one allele for any given inherited trait. If two alleles in an individual differ, only one will be dominant and the other will be recessive. Homozygous defines organisms that contain two copies of the same allele, while heterozygous defines organisms that carry two different alleles. Mendel’s Law of Dominance shows the dominant allele being expressed in the phenotype.

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Monohybrid Cross

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A cross between two true-breeding pea plants, one with purple flowers and the other with white. Only one trait is being studied – monohybrid. The individuals being crossed are the Parental (P Generation) and the progeny generations (Filial or F generations). The purple flower parent has the genotype PP and is homozygous dominant, while the white flower parent has the genotype pp and is homozygous recessive. When crossed, they produce F1 plants that are 100% heterozygous (Pp) and all the F1 progeny have the purple flower phenotype.

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Punnett Square

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A way of predicting the genotypes expected from any give cross. It indicates all the potential progeny genotypes, and the relative frequencies of the different genotypes and phenotypes can be easily calculated. PP x Pp = F1 genotype: 100% Pp (heterozygous); F1 phenotype: 100% purple flowers. Pp x Pp = F2 genotype: 1:2:1; F2 phenotype: 3:1, purple:white

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Mendel’s 2nd Law

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The Law of Independent Assortment. Dihybrid cross – a cross that involves parents differing in two traits as long as the genes are on separate chromosomes and assort independently during meiosis. Genes on the same chromosome will stay together unless crossing over occurs. Crossing over exchanges information between chromosomes and may break the linkage of certain patterns. (e.g. red hair is typically linked with freckles, but there are some blondes and brunettes with freckles as well). Example: a purple-flowered tall pea plant is crossed with a white-flowered dwarf pea plant; both plants are doubly homozygous. Each trait assorts individually in a 3:1 ratio, as in a monohybrid cross. There are 9 purple tall and 3 purple dwarfs, for a total of 12 purple; and there are 3 white tall and 1 white dwarf, for a total of 4 white. The purple:white ratio is 12:4 = 3:1. Likewise, the tall:dwarf ratio is 3:1. The cross looks like this TtPp x TtPp and produces 4 different phenotypes.

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Non-Mendelian Patterns

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The source of complications involving the relationship between genotype and phenotype. Includes: incomplete dominance and codominance.

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Incomplete Dominance

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Some progeny phenotypes are blends of the parental phenotypes. (e.g. flower color in snapdragons (SD): homozygous dominant red SD x homozygous recessive white SD = 100% pink progeny in the F1 generation). When F1 progeny are self-crossed, they produce red, pink, and white progeny 1:2:1. An allele is incompletely dominant if the phenotype of the heterozygote is an intermediate of the phenotypes of the homozygotes.

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Codominance

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Occurs when multiple alleles exist for a given gene and more than one of them is dominant. Each dominant allele is fully dominant when combined with a recessive allele, but when two dominant alleles are present, the phenotype is the result of the expression of both dominant alleles simultaneously (e.g. the inheritance of ABO blood groups in humans). Blood type is determined by three different alleles: IA, IB, and i. Only two alleles are present in any single individual, but the population contains all three alleles. IA and IB are dominant to i. Individuals whoa re homozygous IB or heterozygous IAi have blood type A; individuals who are homozygous IB or heterozygous IBi have blood type B; and individuals who are homozygous ii have blood type O. However, IA and IB are codominant; individuals who are heterozygous IAIB have a distinct blood type, AB, which combines characteristics of both the A and B blood groups.

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Sex Determination

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In sexually differentiated species, most chromosomes exist as pairs of homologues called autosomes, but sex is determined by a pair of sex chromosomes. All humans have 22 pairs of autosomes. Females have a pair of homologous X chromosomes, and males have a pair of heterologous chromosomes X and Y. The sex chromosomes pair during meiosis and segregate during the first meiotic division. Since females can produce only gametes containing the X chromosome, the gender of a zygote is determined by the genetic contribution of the male gamete; if it carries an X chromosome, the zygote will be female. For every mating there is a 50:50 male:female ratio. Genes that are located on the X or Y chromosome are called sex linked. In humans, most sex-linked genes are located on the X chromosome, though some Y-linked traits have been found (e.g. hair on the outer ears).

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Sex-Linkage

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In humans, females have two X chromosomes and males only one resulting in recessive genes that are carried on the X chromosome producing the recessive phenotypes whenever they occur in males since no dominant allele is present to mask them. The recessive phenotype will be much more frequently found in males (e.g. sex-linked recessives in humans are the genes for hemophilia and color-blindness). Since males pass the X chromosome only to their daughters, affected males cannot pass the trait to their male offspring. Unless the daughter also receives the gene from her mother, she will be a phenotypically normal carrier of the trait. Since all of the daughter’s male children will receive their only X chromosome from her, half of her sons will receive the recessive sex-linked allele. Thus, sex-linked recessives generally affect only males; they cannot be passed from father to son, but can be passed from father to grandson via a daughter carrier and skipping a generation.

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Drosophila Melanogaster

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AKA the fruit fly has provided several advantages for genetic research. It reproduces often (short life cycle), it reproduces in large numbers (large sample size), its chromosomes are large and easily recognizable in size and shape, its chromosomes are few (4 pairs, 2n=8), and mutations occur relatively frequently. Using this specie, scientists have elucidated the patterns of embryological development, discovering how genes expressed early in development can affect the adult organism.

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Environmental Factors

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Affect the expression of a gene. (e.g. Drosophila with a given set of genes have crooked wings at low temperature, but straight wings at higher temperatures). Temperature also influences the hair color of the Himalayan hare. The same genes for color result in white hair on the warmer parts of the body and black hair on colder parts. If the naturally warm portions are cooled, the hair will grow in black.

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Genetic Problems

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Genetic replication is very accurate, but chromosome number and structure can be altered by abnormal cell division during meiosis, or by mutagenic agents. Problems include: nondisjunction, chromosomal breakage, and mutations.

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Nondisjunction

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The failure of homologous chromosomes to separate properly during meiosis I, or the failure of sister chromatids to separate properly during meiosis II. The resulting zygote might either have three copies of that chromosome (trisomy – somatic cells will have 2N+1 chromosomes), or might have a single copy of that chromosome (monosomy – somatic cells will have 2N-1 chromosomes). Example of trisomy is Down syndrome, which is caused by trisomy of chromosome 21. Most monosomies and trisomies are lethal, causing the embryo to randomly abort early in pregnancy. Nondisjunction of the sex chromosomes may also occur, resulting in individuals with extra or missing copies of the X and/or Y chromosomes.

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Chromosomal Breakage

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May occur randomly or be induced by environmental factors, such as mutagenic agents and X-rays. The chromosome that loses a fragment is said to have a deficiency.

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Mutations

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Changes in the genetic information of a cell, coded in the DNA. Alterations in the somatic cells can lead to tumors, while alterations in the gametes will be transmitted to the offspring. Most occur in regions of DNA that do not code for proteins and are silent. Ones that do not change the sequence of amino acids in proteins are often recessive and deleterious.

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Mutagenic Agents

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Agents that induce mutations including cosmic rays, X-rays, ultraviolet rays, radioactivity, and chemical compounds such as colchicine (inhibits spindle formation causing polyploidy) and mustard gas. They are also typically carcinogenic.

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Mutation Types

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In a gene mutation, nitrogen bases are added, deleted, or substituted creating different genes; inappropriate amino acids are inserted into polypeptide chains, and a mutated protein is produced. Mutations are genetic errors with the wrong base or no base on the DNA at the particular position.

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Phenylketonuria (PKU)

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A genetic disorder that is a molecular disease caused by the inability to produce the proper enzyme for the metabolism of phenylalanine. A degradation product (phenylpyruvic acid) accumulates.

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Sickle-cell Anemia

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A genetic disorder that is a disease which red blood cells become crescent-shaped because they contain defective hemoglobin. The sickle-cell hemoglobin carries less oxygen. This disease is caused by a substitution of valine (GUA or GUG) for glutamic acid (GAA or GAG) because of a single base pair substitution in the gene coding for hemoglobin.

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Molecular Genetics

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Genes are composed of DNA, which contains information coded in the sequence of its base pairs, providing the cell with a blueprint for protein synthesis. These proteins regulate all life functions. DNA has the ability to self-replicate, crucial for cell division and organismal reproduction. DNA is the basis of heredity; self-replication ensures that its coded sequence will be passed on to successive generations. DNA is mutable and can be altered under certain conditions. Changes in DNA are stable and can be passed from generation to generation providing the basis for evolution.

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Structure of DNA

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The basic unit of DNA is the nucleotide, which is composed of deoxyribose (a sugar) bonded to both a phosphate group and a nitrogenous base. There are two types of bases: purines and pyrimidines. Purines in DNA are adenine (A) and guanine (G). Pyrimidines are cytosine (C) and thymine (T). A DNA molecule is a double-stranded helix with the sugar-phosphate chains on the outside of the helix and the bases on the inside. T always forms two hydrogen bonds with A, and G always forms three hydrogen bonds with C. This base-pairing forms “rungs” on the interior of the double helix that link the two polynucleotide chains together. This is known as the Watson-Crick DNA Model. Since G is triple bonded to C, the higher the G/C content of DNA, the more tightly bound the two strands of DNA will be.

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DNA Replication

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The double-stranded DNA molecule unwinds and separates into two single strands. Each strand acts as a template for complementary base-pairing in the synthesis of two new daughter helices. Each new daughter helix contains an intact strand from the parent helix and a newly synthesized strand; thus DNA replication is semiconservative. The daughter DNA helices are identical in composition to each other and to the parent DNA.

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The Genetic Code

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DNA consists of 4 “letters”: A, T, C, and G and 20 “words” or amino acids. The DNA letters must be translated by mRNA to produce the 20 words in the amino acid language (Triplet code). The base sequence of mRNA is translated as a series of triplets, otherwise known as codons. A sequence of three consecutive bases codes for a particular amino acid (e.g. the codon GGC = glycine and GUG = valine). The genetic code is universal for almost all organisms. The code contains synonyms because most amino acids have more than one codon specifying them. This property is referred to as the degeneracy or redundancy of the genetic code.

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Structure of RNA

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Ribonucleic acid is a polynucleotide structurally similar to DNA except that its sugar is ribose, it contains uracil (U) (a pyrimidine) instead of thymine, and it is usually single-stranded. It can be found in both the nucleus and the cytoplasm. There are several types of RNA, all of which are involved in some aspect of protein synthesis: mRNA, tRNA, and rRNA.

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mRNA

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Messenger RNA carries the complement of a DNA sequence and transports it from the nucleus to the ribosomes, where protein synthesis occurs. It is assembled from ribonucleotides that are complementary to the “sense” strand of DNA. It has the “inverted” complementary or negative codes of the original DNA (e.g. DNA = AAC; mRNA = UUG). It is monocistronic – one mRNA strand codes for one polypeptide.

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tRNA

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Transfer RNA is a small RNA found in the cytoplasm which aids in the translation of mRNA’s nucleotide code into a sequence of amino acids. It brings amino acids to the ribosomes during protein synthesis. There is at least one type of it for each amino acid; there are approx. 40 known types of it. In transcription, it recognizes both the amino acid and the mRNA codon. One end of tRNA contains a three-nucleotide sequence, the anti-codon, which is complementary to one of the mRNA codons; the other end is the site of amino acid attachment. Each amino acid has its own aminoacyl-tRNA synthetase, which has an active site that binds to both the amino acid and its corresponding tRNA, catalyzing their attachment to form an aminoacyl-tRNA complex.

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rRNA

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Ribosomal RNA is a structural component of ribosomes and is the most abundant of all RNA types. It is synthesized in the nucleolus.

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Transcription

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The process whereby information coded in the base sequence of DNA is transcribed into a strand of mRNA which leaves the nucleus through nuclear pores. The remaining events of protein synthesis occur in the cytoplasm.

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Ribosomes

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Composed of two subunits (consisting of proteins and rRNA), one large and one small, that bind together only during protein synthesis. They have three binding sites: one for mRNA, and two for tRNA: the P site (peptidyl-tRNA binding site) and the A site (aminoacyl-tRNA complex binding site). The P site binds to the tRNA attached to the growing polypeptide chain, while the A site binds to the incoming aminoacyl-tRNA complex.

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Polypeptide Synthesis

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Divided into three distinct stages: initiation, elongation, and termination. Synthesis begins when the ribosome binds to the mRNA near its 5’ end. The ribosome scans the mRNA until it binds to a start codon (AUG). The initiator aminoacyl-tRNA complex, methionine-tRNA, base pairs with the start codon. In elongation, hydrogen bonds form between the mRNA codon in the A site and its complementary anti-codon on the incoming aminoacyl-tRNA complex. A peptide bond is formed between the amino acid attached to the tRNA in the A site and the met attached to the tRNA in the P site. Following peptide bond formation, a ribosome carries uncharged tRNA in the P site and peptidyl-tRNA in the A site. They cycle is completed by translocation, in which the ribosome advances 3 nucleotides along the mRNA in the 5’ to 3’ direction. In a concurrent action, the uncharged tRNA from the P site is expelled and the peptidyl-tRNA from the A site moves into the P site. The ribosome then has an empty A site ready for entry of the aminoacy

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Cytoplasmic Inheritance

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DNA is found in chloroplasts and mitochondria and other cytoplasmic bodies. These cytoplasmic genes may interact with nuclear genes and are important in determining the characteristics of their organelles. Drug resistance in many microorganisms is regulated by cytoplasmic DNA known as plasmids that contain one or more genes.

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Bacterial Genome

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Consists of a single circular chromosome located in the nucleoid region of the cell. Many bacteria also contain smaller circular rings of DNA called plasmids, which contain accessory genes. Episomes are plasmids that are capable of integration into the bacterial genome.

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Replication

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Replication of the bacterial chromosome begins at a unique origin of replication and proceeds in both directions simultaneously. DNA is synthesized in the 5’ and 3’ direction.

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Genetic Variance

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Bacterial cells reproduce via binary fission and proliferate very rapidly under optimal conditions. Although binary fission is asexual, bacteria have three mechanisms for increasing the genetic variance of a population: transformation, conjugation, and transduction.

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Transformation

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The process by which a foreign chromosome fragment (plasmid) is incorporated into the bacterial chromosome via recombination, creating new inheritable genetic combinations.

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Conjugation

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Sexual mating in bacteria; it is the transfer of genetic material between two bacteria that are temporarily joined. A cytoplasmic conjugation bridge is formed between the two cells and genetic material is transferred from the donor male (+) type to the recipient female (-) type. Only bacteria containing plasmids called sex factors are capable of conjugating. The F Factor in E. Coli: bacteria possessing this plasmid are termed F+ cells, those without F- cells. During conjugation between a F+ and F- cell, the F+ cell replicates its F factor and donates the copy to the recipient, converting it to an F+ cell. Sometimes the sex factor becomes integrated into the bacterial genome. During conjugation the entire bacterial chromosome replicates and begins to move from the donor cell into the recipient cell. The conjugation bridge usually breaks before the entire chromosome is transferred, but the bacterial genes that enter the recipient cell can easily recombine with the bacterial genes already present to form novel

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Transduction

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Occurs when fragments of the bacterial chromosome accidentally become packaged into viral progeny produced during a viral infection. These virions may infect other bacteria and introduce new genetic arrangements through recombination with the new host cell’s DNA. The closer two genes are to one another on a chromosome, the more likely they will be to transduce together.

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Recombination

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Occurs when linked genes are separated by breakage and rearrangements of adjacent regions of DNA when organisms carrying different genes or alleles for the same traits are crossed.

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Gene Regulation

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The regulation of gene expression (transcription) enables prokaryotes to control their metabolism. Regulation of transcription is based on the accessibility of RNA polymerase to the genes being transcribed, and is directed by an operon, which consists of structural genes, an operator gene, and a promoter gene. Structural genes contain sequences of DNA that code for proteins. The operator gene is the sequence of non-transcribable DNA that is the repressor binding site. The promoter gene is the noncoding sequence of DNA that serves as the initial binding site for RNA polymerase. There is also a regulator gene that codes for the synthesis of a repressor molecule that binds to the operator and blocks RNA polymerase from transcribing the structural genes.

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Inducible Systems

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Systems that require the presence of a substance, called an inducer, for transcription to occur. In this system, the repressor binds to the operator, forming a barrier that prevents RNA polymerase from transcribing the structural genes. For transcription to occur, an inducer must bind to the repressor, forming an inducer-repressor complex. This complex cannot bind to the operator, thus permitting transcription. The proteins synthesized are thus said to be inducible. The structural genes typically code for an enzyme, and the inducer is usually the substrate, or a derivative of the substrate, upon which the enzyme normally acts. When the substrate (inducer) is present, enzymes are synthesized; when it is absent, enzyme synthesis is negligible. In this manner, enzymes are transcribed only when they are actually needed.

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Repressible Systems

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Systems in a constant state of transcription unless a corepressor is present to inhibit transcription. In this system, the repressor is inactive until it combines with the corepressor. The repressor can bind to the operator and prevent transcription only when it has formed a repressor-corepressor complex. Corepressors are often the end-products of the biosynthetic pathways they control. The proteins produced (usually enzymes) are said to be repressible since they are normally being synthesized; transcription and translation occur until the corepressor is synthesized. Operons containing mutations such as deletions or whose regulator genes code for defective repressors are incapable o being turned off and whose enzymes, which are always being synthesized, are referred to as constitutive.

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Bacteriophage

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A virus that infects its host bacterium by attaching to it, boring a hole through the bacterial cell wall, and injecting its DNA, while its protein coat remains attached to the cell wall. Once inside its host, the bacteriophage enters either a lytic cycle or a lysogenic cycle.

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Lytic Cycle

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The phage DNA takes control of the bacterium’s genetic machinery and manufactures numerous progeny. The bacterial cell then bursts (lyses), releasing new virions, each capable of infecting other bacteria. Bacteriophages that replicate by this cycle, killing their host cells, are called virulent. If the initial infection takes place on a bacterial lawn (a plated culture) then very shortly a plaque or clearing in the lawn occurs, corresponding to the area of lysed bacteria. The physical characteristics of a plaque are useful in identifying mutant phage strains that may arise.

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Lysogenic Cycle

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If the bacteriophage does not lyse its host cell, it becomes integrated into the bacterial genome in a harmless form (provirus), lying dormant for one or more generations. The virus may stay integrated indefinitely, replicating along with the bacterial genome. However, either spontaneously or as a result of environmental circumstances (e.g. radiation, UV light, or chemicals), the provirus can reemerge and enter a lytic cycle. Bacteria containing proviruses are normally resistant to further infection (“superinfection”) by similar phages.