Genetics Vocab chapts. 2, 3, 4, 5, 6, 7, 11, 12,

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Genetics Vocab chapts. 2, 3, 4, 5, 6, 7, 11, 12,
2012-05-09 16:15:57
Genetics chapters

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  1. Chromosomes
    structures found in nuclei that are carriers of hereditary information, composed of proteins and nucleic acids (RNA and DNA)
  2. Mutation
    • heritable change in the genetic material
    • Ex: Griffith's transformation experiment with Smooth and Rough strains
  3. Nucleases
    Samples of mixtures are treated separately with two different kinds of nucleases, which are enzymes that degrade the nucleic acids and are then tested to see if they can transform
  4. Bacteriophages
    • viruses that attack bacteria
    • Ex: Hershey and Chase experiment with T2 = DNA must be the material responsible for the function and reproduction of phage T2
  5. Nucleotides
    monomers that make up RNA and DNA, each one consists of a pentose (5 carbon) sugar, a nitrogenous base, and a phosphate group

    • DNA pentose sugar = deoxyribose
    • RNA pentose sugar = ribose
  6. nucleoside
    combination of a sugar and a base
  7. Antiparallel DNA
    strands are oriented in opposite directions, with one strand in the 5' to 3' direction and the other strand in the 3' to 5' direction

    5' is the head of the chain and the 3' is the tail
  8. complementary base pairs
    A-T and G-C base pairs are the only ones that can fit the physical dimensions of the helical model and their arrangement fits Chargaff's rules
  9. Genome
    the full amount of genetic material found in a virus, prokaryotic cell, eukaryotic organelle, or in one haploid set of a haploid organism's chromosomes...may be RNA or DNA

    nucleotides --> genes --> chromosomes --> genome
  10. Topoisomerase
    The amount and type of supercoiling DNA is controlled by topoisomerase -- enzymes that are found in all organelles
  11. Histones and Nonhistones
    Two major types of proteins associated with DNA in chromatin. Both types of proteins play an important role in determining the physical structure of the chromosome

    -Histones (H1, H2A, H2B, H3, H4) are the most abundant proteins in chromatin and are small and basic with a net positive that facilitates their binding to negatively charged DNA

    -Nonhistones are much less abundant and are acidic proteins with a negative charge, they include proteins that play a part in DNA replication, DNA repair, transcription, and recombination
  12. Nucleosomes
    beads of the chromatin fiber and thr basic structural units of eukaryotic chromatin, they are about 11 nm in diameter and consists of a core of eight histone proteins

    Nucleosomes are connected by strands of linker DNA
  13. Euchromatin
    Chromosomes or regions of chromosomes that show the normal cycle of chromosome condensation and decondensation in the cell cycle and most of the genome of an active cell is in the form of Euchromatin

    • -Euchromatic DNA is actively transcribed and genes can be expressed
    • -Transcription usually occurs in Euchromatin and not in heterochromatin
  14. Heterochromatin
    Contrasting to Euchromatin because the chromosomes or chromosomal regions usually remain condensed and genes within heterochromatin are usually transcriptionally inactive

    • Two types of heterochromatin
    • 1. constitutive: present in all cells on both homologous chromosomes of a pair
    • 2. facultative: varies in state in different cell types and at different stages, sometimes from one homologous chromosome to another
  15. Telomere
    Specific set of sequences at the end of a linear chromosome, stabalizes the chromosome and is required for replication, each chromosome has two ends = two telomeres
  16. Centromere
    region of a chromosome containing DNA sequences to which mitotic and meiotic spindle fibers attach, the centromere is responsible for accurate segregation of replicated chromosomes
  17. Semiconservative model
    from Watson and Crick: if the DNA molecule was untwisted and the two strands separated, each strand could act as a template for the synthesis of a new, complementary strand of DNA that could then be bound to the parental strand
  18. Conservative model
    the two parental strands of DNA remain together or pair again after replication and, as a whole, serve as a template for the synthesis of new progeny DNA double helices. In this model, one of the two DNA molecules is the parental double-stranded DNA molecule and the other is made of all new material
  19. DNA polymerase I and DNA polymerase III
    • -Both are necessary for replication
    • -Both replicate DNA is the 5' to 3' direction
    • -Both have 3' to 5' exonuclease activity, which means they can remove nucleotides from the 3' end of a DNA chain = proofreading
    • -Only DNA polymerase I had 5' to 3' exonuclease activity and can remove either RNA or DNA nucleotides from the 5' end
  20. Template Strand
    the segments of single strands in the replication bubble on which the new strands are made, in accordance with complementary base-pairing rules
  21. Replication Fork
    When DNA untwists to expose the two single-stranded template strands for DNA replication, a Y-shaped structure called a replication fork forms and moves in the direction of untwisting the DNA. When DNA untwists there are two replication forks: two Y's joined together at their tops to form a replication bubble and each moves bidirectionally
  22. DNA helicase
    Helicase unwinds the double helix and are loaded onto the DNA by DNA helicase loader proteins, helicase untwists the DNA in both directions from the origin of replication by breaking the hydrogen bonds between the bases
  23. DNA primase
    forms a complex called the primosome and is important in DNA replication because DNA polymerase cannot initiate the synthesis of a DNA strand, they can only add nucleotides to a preexisting strand
  24. RNA primer
    DNA primase (modified RNA polymerase) synthesizes a short RNA primer to which new nucleotides are added by DNA polymerase. The RNA primer is removed later and replaced with DNA
  25. Single-stranded DNA binding proteins
    binds to each single-stranded DNA, stabalizing them and preventing them from reforming double-stranded DNA by complementary base pairing, prevents reassociation of complementary bases
  26. Okazaki Fragments
    The fragments of lagging strand DNA made in semidiscontinuous replication. When DNA is synthesized continuously on the leading strand and synthesized discontinuously on the lagging strand, each Okazaki fragment starts with a new RNA primer and are eventually joined into a continuous DNA strand
  27. DNA ligase
    makes phosphodiester bond to seal the nicks left on the lagging strand
  28. Origin Recognition Complex
    The initiator protein in eukaryotes, the ORC binds to two different regions at one end of the replicator and recruits other replication proteins, one of those proteins is needed for DNA unwinding
  29. Telomerase
    maintains chromosome lengths by adding telomere repeats to one strand (the one with the 3' end) which serves as a template on previous DNA replication at each end of a linear chromosome. The complementary strand to the one synthesized by telomerase must be added by the regular replication machinery
  30. Pleiotropic
    When one gene influences multiple phenotypic traits. A mutation in a pleiotropic gene may have an effect on some or all traits at the same time and this can be a problem when selection on one trait favors one specific version of the allele, while the selection on the other trait favors another allele
  31. Phenylketonuria (PKU)
    • This enzyme is necessary to metabolize the amino acid phenylalanine (Phe) to the amino acid tyrosine. Phenylalanine is needed to make proteins but too much can be harmful and excess is further metabolized into tyrosine
    • -Has pleiotropic effects and people with PKU cannot make tyrosine
  32. Albinism
    Caused by an autosomal recessive mutation and is caused by a mutation in the gene for tyrosinase = enzyme used to convert tyrosine to DOPA from which skin pigment melanin comes from
  33. Tay-Sachs disease
    autosomal recessive genetic disorder caused by a genetic mutation in the HEXA gene on human chromosome 15
  34. Amniocentesis
    How to find out whether a fetus is normal or not by taking a sample of amniotic fluid because the fluid contains cells that the fetus's skin has "sloughed off" and the cells can then be cultured in the lab and then examined for protein or enzyme alterations or deficiencies
  35. Transcription
    synthesis of DNA to RNA
  36. Translation
    Synthesis of RNA to protein, conversion of mRNA base-sequence information into the amino acid sequence of a polypeptide
  37. Central Dogma
    Watson and Crick: DNA --> RNA --> Protein

    -transcription and then translation
  38. mRNA
    messenger RNA that codes from an amino acid sequence of a polypeptide, translation of an mRNA produces a polypeptide
  39. rRNA
    ribosomal RNA with ribosomeal proteins, makes up the ribosomes where mRNA is translated
  40. tRNA
    Transfer RNA brings amino acids to ribosomes during translation
  41. snRNA
    small nuclear RNA with proteins, forms complexes that are used in eukaryotic RNA processing to produce functional mRNAs
  42. Promoter
    initiation of transcription is at the promoter, a sequence upstream of the start of the gene that encodes the RNA and RNA polymerase interacts with the promoter and the promoer sequence binds and orients the RNA polymerase to start transcribing
  43. Terminator
    specifies where transcription stops
  44. Concensus sequence
    the base found most frequently at each position

    -Bacteria: -35 region = TTGACA; -10 region = TATA
  45. RNA polymerase I
    in eukaryotes, its located in the nucleolus and catalyzes the synthesis of three of the RNAs found in the ribosome
  46. RNA polymerase II
    in eukaryotes is located in the nucleoplasm and synthesizes messenger RNAs and some snRNAs
  47. RNA polymerase III
    in eukaryotes is located in the nucleoplasm and synthesizes transfer RNAs, 5S rRNA, and the snRNAs not made by RNA polymerase II
  48. Promoter-proximal elements
    • are upstream from the TATA box and are important for determining how and when a gene is expressed (activators and enhancers
    • Ex: CAAT box and GC box
  49. General Transcription Factors (GTFs)
    accurate initiation of transcription of a protein-coding gene involves the assembly of RNA polymerae II and a number of other proteins (GTFs) on the core promoter

    GTFs bind first and recruit RNA polymerase to form a complex
  50. Introns/Exons
    -Introns: intervening sequence that is not translated into an amino acid sequence, introns must be excised from each pre-mRNA to produce a mature RNA that can be translated into the encoded polypeptide

    -Exons: coding sequence that includes the 5' and 3' UTRs as well as the amino acid-coding portions
  51. PolyA polymerase
    adds A nucleotides to the 3' end of the RNA using ATP as the substrate to produce the polyA tail, which is required for efficient export of the mRNA from the nucleus to the protein
  52. polyA site
    site in the RNA transcript that is about 10 to 30 nucleotides downstream of the polyA consensus sequence
  53. mRNA splicing
    mRNA splicing removed introns and pre-mRNAs and exons joined in the nucleus, occurs in the spliceosome
  54. RNA editing
    involves the posttranscriptional insertion or deletion of nucleotides or the conversion of one base to a result, the functional RNA molecule has a base sequence that does not match the base-pair sequence of its DNA coding sequence
  55. Polypeptides
    proteins are made up of polypeptides, which are composed of smaler building blocks called amino acids
  56. Peptide Bond
    amino acids of a polypeptide are joined by this bond, which is a covalent bind formed between the carboxyl group of one amino acid and the amino acid group of an adjacent amino acid
  57. Genetic Code
    Triplet code that is a set of three nucleotides (codon) in mRNA
  58. Frameshift Mutations
    When mutations occur in the amino acid-coding part of a gene, if a single base pair is deleted or inserted, the code is different and so is the reading frame and become a new set of amino acids
  59. Nonsense codons, stop codons, chain determining codons
    the three nucleotide anticodon pairs with the codon in the mRNA used to specify the end of translation of a polypeptide chain
  60. Wobble hypothesis
    Proposed by Francis Crick: occurs in the anticodon and since 61 sense condons specify amino acids in the mRNA, a total of 61 tRNA molecules could have the appropriate anticodons and less exact base pairing occurs
  61. Anticodon
    three-nucleotide sequence that pairs with a three-nucleotide codon sequence in mRNA by complementary base pairing during translation and is important for the growing of the polypeptide chain
  62. Aminoacyl-tRNA synthease
    The correct amino acid is attached to the tRNA by this enzyme in the process of aminoacylation (charging) to produce an aminoacyle-tRNA (charged tRNA)
  63. Shine-Dalgarno Sequence
    A ribosomal binding site in the mRNA, generally located 8 basepairs upstream of the start codon AUG. The Shine-Dalgarno sequence exists both in bacteria and archaea, This sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning it with the start codon. The complementary sequence (CCUCCU), is called the anti-Shine-Dalgarno sequence and is located at the 3' end of the 16S rRNA in the ribosome.
  64. Peptidyl Transferase
    Forms peptide links between adjacent amino acids using tRNAs during the translation process of protein biosynthesis and Peptidyl transferase activity is carried out by the ribosome
  65. Translocation
    In the last step in the elongation cycle, the ribosome moves one codon along the mRNA toward the 3' end. In bacteria, translocation requires the activity of another protein elongation factor
  66. Release Factor (RF)
    The ribosome recognizes a stop codon with the help of the protein release factors, which mimick the shape and function of tRNA including the regions that read the codons and then initiate a series of specific termination events
  67. Chromosomal Mutations
    changes involving the whole chromosome or sections of them
  68. point mutations
    broad type of change in the genetic material that involves a change of one or a few base pairs and may change the phenotype or the organism if it occurs within the coding region of a gene or in the sequences regulating the gene
  69. Gene mutations
    mutations that affect the function of genes and can alter the phenotype by changing the function of a protein
  70. Mutation
    process by which the sequence of base pairs in a DNA molecule is altered and may result in a change to either a DNA base pair or a chromosome. A cell with a mutation is a mutant cell
  71. Types of Point Mutations
    -Base-pair substitution: a change from one base pair to another in DNA (transitition and transversion mutations)

    -Missense mutation: a gene mutation in which a base-pair change causes a change in an mRNA codon so that a different amino acid is inserted into the polypeptide

    -Nonsense mutation: gene mutation in which a base-pair change alters an mRNA codon for an amino acid to a stop (nonsense) codon

    -Neutral Mutation: no detectable changes in the function of the protein

    -Silent mutation: the base pair is changed but it still codes for the same amino acid

    -Frameshift mutation: results in a nonfunctional protein and may generate new stop codons
  72. Deamination
    the removal of an amino group from a base, like how the deamination of cytosine produces uracil, which is not a normal base in DNA
  73. Carcinogens
    mutations from chemicals that result in tumorous or cancerous growth and typically are base-pair substitutions that produce missense or nonsense mutations
  74. Auxotrophic mutant
    mutant that is unable to make a particular molecule essential for growth and are most readily detected in microorganisms like E. coli and yeast
  75. Mismatch repair by DNA polymerase proofreading
    When an incorrect nucleotide is inserted, the polymerase often detects the mismatched base pair and corrects the area by "backspacing" to remove the wrong nucleotide and then resuming synthesis in the forward direction
  76. Repair of UV induced pyrimidine dimers
    Through light repair, UV light-induced thymine dimers are reverted directly to the original form by exposure to UV light
  77. Base excision repair
    Damaged single bases or nucleotides are most commonly repaired by removing the base or the nucleotide involved and then inserting the correct base or nucleotide. In base excision repair, a glycoslyase enzyme removes the damaged base from the DNA by cleaving the bond between the base and the sugar and the phosphodiester backbone
  78. Nucleotide excision repair
    this system in E.coli involves four proteins and corrects other serious damage-induced distortions of the DNA helix
  79. Methy-directed mismatch repair
    mismatched base pairs left after DNA replication can be corrected by methyl-directed mismatch repair. It recognizes mismatch base pairs, excises the incorrect base, and then carries out repair synthesis, after replication the parental DNA strand has a methylated A in the GATC sequence
  80. Insertion sequences (IS)
    simplest transpoable element found in bacteria and contains only genes required to mobilize the element and insert it into a new location in the genome
  81. Transposase
    The transposition of the IS element requires an enzyme encoded by the IS element = transposase
  82. Transposons
    Like an IS element, contains genes for the insertion of the DNA segment into the chromosome and mobilization of the element in other locations on the chromosome. A transposon is more complex than an IS element because it contains additional genes
  83. Reverse transcriptase
    enzyme that enters the cell as part of the virus particle and is an RNA-dependent DNA polymerase, meaning that the enzyme uses an RNA template to produce a DNA copy
  84. Monohybrid Crosses
    crosses between true-breeding strains of peas that had alternative forms of a single trait
  85. Reciprocal crosses
    • Mating that are done both ways
    • ex: smooth female X wrinkled male
    • AND
    • wrinkled female X smooth male
  86. Principle of Segregation
    Mendel proposed: recessive traits, which are masked in the F1 from a cross between two true-breeding strains, reappear in a specific proportion in the F2...when genes separate from eachother, half the gametes carry one allele, and half carry the other
  87. Wild-type allele
    the functional allele of a gene that predominates in the population of an organis, found in the "wild" and they usually encode a product for a particular biological function
  88. Loss-of-function mutations
    if a mutation in a gene causes the protein product of a gene to be absent, or non-functioning, then the function is likely to be lost or decreased and these mutations are usually recessive
  89. Mendel's 2nd law, principle of independent assortment
    factors for different pairs of traits assort independently of one another, pairs of alleles for genes on different chromosomes segregate independently in the formation of gametes
  90. Dihybrid crosses
    The F1 are heterozygous for two pairs of alleles at two differnt loci, which are dihybrids and a cross between two of these of the same type = dihybrid crosses
  91. Null hypothesis
    there is no real different between the observed data and the predicted data in a chi-square test
  92. Proband
    the affected individual through whom the pedigree is discovered
  93. Recessive Traits
    • many human traits are knwn to be caused by homozygosity for mutant alleles that are recessive to the normal allele and such recessive mutant alleles produce mutant phenotypes because of a loss-of-function
    • -Ex: albinism
  94. Dominant Traits
    Dominant mutant alleles may produce mutant phenotypes because of a gain-of-function mutations that result in gene products with new functions
  95. Homologous and Nonhomologous Chromosomes
    • -Homologous: members of a chromosome pair in diploid organisms that contain the same genes and that pair during meiosis
    • -Nonhomologous: chromosomes that contain different genes and that do not pair during meiosis
  96. Autosomes
    Chromosomes other than sex chromosomes
  97. metacentric chromosome
    has the centromere at about the center so the chromosome appears to have two approximately equal arms
  98. Mitosis
    nuclear division and the cycle of growth in the cell cycle
  99. Cell Cycle
    consists of two phases: M-phase and interphase, which is made up of three separate phases: G1, S, G2. Chromosome replication takes place in interphase and then mitosis occurs, resulting in the distribution of a complete chromosome set to each of two progency nuclei

    In G1, the cell prepares for DNA and chromosome replication, which occurs in the S stage. In G2, the cell prepares for cell division
  100. Sister Chromatids
    The DNA of each chromosome is replicated is the S phase, giving two exact copies that are held together by the replicatied but unseparated centromeres
  101. Daughter Chromosomes
    • Later, the centromeres separate and the sister chromatids become daughter chromosomes so in a diploid cell there are pairs of homologous chromosomes.
    • When the DNA of a pair of homologous chromosomes replicates in interphase, the result is two pairs of sister chromatids and after the centromeres separate, two pairs of daughter chromosomes are produced
  102. Prophase
    in the G2 stage of the cell cycle, the chromatids condense so they gradually appear shorter and mitotic spindle assembles outside of the nucleus
  103. Prometaphase
    nuclear envelope breakdown and at the end of prophase and before metaphase and the developing of the spindle in the nucleus, kinetochore are the sites for the attachment of the chromosomes to spindle microtubules and they bind to each centromere
  104. Metaphase
    kinetochore microtubules oritent chromosomes so that their centromeres become aligned at the metaphase plate
  105. Anaphase
    the joined centromeres of sister chromatids separate, giving rise to two daughter chromosomes and the sister chromatids separate and daughter chromosomes move to opposite poles by shortening microtubules attachmed to kinetochores
  106. Telophase
    the two sets of daughter chromosomes are assembled into two groups at opposite ends of the cell and the chromosomes begin to unncoild and assume the elongated state, spindle microtubles disappear and the nucleolus reforms
  107. Cytokinesis
    division of cytoplasm and follows after telophase, it cleaves cell into two daughter cells
  108. crossing-over
    the reciprocal physical exchange of chromosome segments at corresponding positions along pairs of homologous chromosomes, the position where crossing over occurs is randomand vary from one meiosis to another
  109. Genetic recombination
    caused by crossing over, with a combination of alleles that differs from the combination which it started
  110. Chiasma
    the result of crossing-over becomes visible during diplonema as this cross-shaped structure, at each chiasma the homologous chromosomes are very tightly associated
  111. Meoisis
    two successive division of a diploid nucleus after only one DNA replication cycle, occurs only at a special point in an organism's life cycle, in animals it results in the formation of haploid gametes (egg and sperm)
  112. Meoisis I
    Meoisis 1: chromosome number is reduced from diploid to haploid

    • -prophase I: homologous chromosomes pair with eachother and crossing-over occurs
    • -Metaphase I: kinetochore microtubules align each chromosome pair on the metaphase plate, align independently
    • -Anaphase I: chromosomes in each tetrad separate and begin migrating toward opposite poles, sister chromatids remain joined after metaphase whereas they separate in mitosis
    • -Telophase I: chromosomes, each with two sister chromatids, complete migration to the poles and new nuclear envelopes form,
    • -Cytokinesis: chromosomes do not replicate before meiosis II
  113. Meoisis II
    • -Prophase II: chromosomes condense and spindle forms
    • -Metaphase II: movement of the kinetochore microtubules alignes the chromosomes on metaphase plate
    • -Anaphase II: centromeres separate and the now-daughter chromosomes are pulled to the opposite poles of the spinlde, one sister chromatid of each pair goes to one pole and the other goes to the opposite pole
    • -Telophase II: the chromosomes begin condensing, a nuclear envelope forms around each set of chromosomes, and cytokinesis takes place. After telophase II, the chromosomes continue decondensing

    *end product = four haploid cells from one original diploid cell and because of crossing-over the chromosomes are not exact copies of the original chromosome
  114. Chromosome theory of inhertitance
    states that genes are located on chromosomes because of Walter Sutton recognizing that the transmission of chromosomes from one generation to the next closely paralleled the pattern of inheritance of Mendelian factors from one generation to the next
  115. Heterogametic sex
    • This is what males are called because the male produces two kinds of gametes with respect to sex chromosomes (X or Y)
    • -Ex: flies
  116. Homogametic sex
    this is what females are called because the female produces only one type of gamete (X)
  117. Mutant alleles
    variants of a wilf-type strain arise from mutational changes of the wild-type alles that produce these mutant alleles, which result in strains with mutant characteristics and may be dominant or recessive to the wild-type
  118. Hemizygous
    • This is what the condition in X-linked genes in males is called because the gene is present only once is the organism and there is no homologous gene in the Y
    • Ex: white eyed drosphila males have an X chromosome with a white allele and no other allele of that gene in their genomes
  119. Sex-linked or X-linked
    Morgan's crosses in dropshila involved eye-color characteristics that we now know are coded for by a gene found on the X chromosome. These characteristics and the genes that give rise to them are sex-linked because the gene locus is part of the X chromosome
  120. Nondisjunction
    can involve either autosomes or the sex chromosomes and results when homologous chromosomes or daughter chromosomes fail to move to opposite poles at anaphase

    • -Primary nondisjunction: when it occurs in an individual with a normal set of chromosomes
    • -Secondary nondisjunction: occurs in the progencies of females that are produced by primary nondisjunction
  121. Aneuploidy
    An abnormal condition in which one or more whole chromosomes of a normal set of chromosomes are missing or are present in more than the usual number of copies
  122. Turner Syndrome
    In humans, XO individuals with the normal two sets of autosomes are female and sterile and they exhibit Turner Syndrome. Individuals with this disorder have only one sex chromosome (X chromosome) and only have 45 chromosomes because they are aneuploidy
  123. Klinefelter Syndrome
    nondisjunction can also result in the generation of XXy humans, who are male with this syndrome. These males are 47, XXY which means they have an extra chromosome
  124. Barr Body
    the somatic cell nuclei of normal XX females contain a highly condensed mass of chromatin named the Barr body and are not found in the normal nuclei of XY males.
  125. Epigenic
    • A heritable change in gene expression that occurs without a change in DNA sequence
    • -Ex: X inactivation = silencing of one X chromosome
  126. X-linked recessive trait
    • a trait resulting from a recessive mutant allele carried on the X chromosome and involve X-linked recessive alleles
    • -Ex: hemophilia
  127. X-linked dominant trait
    a trait resulting from a dominant mutant allele carried on the X chromosome, only a few X-linked dominant traits have been identified