Biology Chapter 3

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amrish2990
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Biology Chapter 3
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2013-04-26 00:16:48
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Molecular Biology
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Molecular Biology
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  1. Nucleosome
    A structure composed of two coils of DNA wrapped around on octet of histone proteins. The nucleosome is the primary form of packaging of eukaryotic DNA.
  2. Nucleoside
    A structure composed of a ribose molecule linked to one of the aromatic bases. In a deoxynucleoside, the ribose is replaced with deoxyribose.
  3. Nucleotide
    A nucleoside with one or more phosphate groups attached. Nucleoside triphosphates (NTPs) are the building blocks of RNA and are also used as energy molecules, especially ATP. Deoxynucleoside triphosphates (dNTPs) are the building blocks of DNA; in these molecules, the ribose is replaced with deoxyribose.
  4. Okazaki fragments
    Small fragments of DNA produced on the lagging strand during DNA replication; joined later by DNA ligase to form a complete strand.
  5. Operator
    A specific DNA nucleotide sequence where transcriptional regulatory proteins can bind.
  6. Operon
    A nucleotide sequence on DNA that contains three elements: a coding sequence for one or more enzymes, a coding sequence for a regulatory protein, and upstream regulatory sequences where the regulatory protein can bind. An example is the lac operon found in prokaryotes.
  7. Origin of replication
    The specific location on a DNA strand where replication begins. Prokaryotes typically have a single origin of replication, while eukaryotes have several per chromosome.
  8. 5' cap
    A methylated guanine nucleotide added to the 5' end of eukaryotic mRNA. The cap is necessary to initiate translation of the mRNA.
  9. Adenine
    • One of the four aromatic bases found in DNA and RNA; also a component of ATP, NADH, and FADH2. Adenine is a purine; it pairs with thymine (in DNA) and with uracil (in RINA). 
    • A2T(U)
    • G3C

    • Pyrimidines: Cytosine & Thymine
    • Purines: Adenine & Guanine
  10. Amino acid acceptor site
    The 3' end of a tRNA molecule that binds an amino acid. The nucleotide sequence at this end is CCA.
  11. Aminoacyl tRNA
    A tRNA with an amino acid attached. This is made by an aminoacyl-tRNA synthetase, an enzyme that is specific to the amino acid being attached.
  12. Anticodon
    A sequence of three nucleotides (found in the anticodon loop of tRNA) that is complementary to a specific codon in mRNA. The codon to which the anticodon is complementary specifies the amino acid that is carried by that tRNA.
  13. Antiparallel orientation
    The normal configuration of double-stranded DNA in which the 5' end of strand is paired with the 3' end of the other.
  14. A site
    Aminoacyl-tRNA site; the site on a ribosome where new amino acid is added to a growing peptide.
  15. Chromatin
    DNA that is densely packed around histone proteins. The genes is heterochromatin are generally inaccessible to enzymes and are turned off.
  16. Chromosome
    A single piece of double stranded DNA; part of the genome of an organism. Prokaryotes have circular chromosomes and eukaryotes have linear chromosomes.
  17. Codon
    A group of three nucleotides that is specific for a particular amino acid, or that specifies "stop translating."
  18. Cytosine
    One of the four aromatic bases found in DNA and RNA. Cytosine is a pyrimidine, it pairs with guanine. 

    • Pyrimidines: Cytosine & Thymine
    • Purines: Adenine & Guanine
    • A2T
    • G3C
  19. DNA polymerase
    Also called DNA pol, this is the enzyme that replicates DNA. Eukaryotes have a single version of the enzyme, simply called DNA pol; prokaryotes have three versions, called DNA pol I, DNA pol II, and DNA pol III.
  20. Downstream
    Toward the 3' end of an RNA transcript (the 3' end of the DNA coding strand). Stop codons and (in eukaryotes) the poly-A tail are found "downstream."
  21. Euchromatin
    DNA that is loosely packed around histones. This DNA is more accessible to enzymes and the genes in euchromatin can be activated if needed.
  22. Exon
    A nucleotide sequence in RNA that contains protein-coding information. Exons are typically separated by introns (intervening sequences) that are spliced out prior to translation.
  23. formylmethionine (fMET)
    A modified methionine used as the first amino acid in all prokaryotic proteins.
  24. Frameshift mutation
    A mutation caused by an insertion or deletion of base pairs in a gene sequence in DNA such that the reading frame of that gene (and thus the amino acid sequence of the protein) is altered.
  25. Genetic Code
    The "language" of molecular biology that specifies which amino acid corresponds to which three-nucleotide group.
  26. Genome
    All the genetic information in an organism; all of an organism's chromosomes.
  27. Guanine
    One of the four aromatic bases found in DNA and RNA. Guanine is a purine; it pairs with cytosine.

    • Pyrimidines: Cytosine & Thymine
    • Purines: Adenine & Guanine
    • A2T
    • G3C
  28. Gyrase (DNA gyrase)
    A prokaryotic enzyme used to twist the single circular chromosome of prokaryotes upon itself to form supercoils. Supercoiling helps to compact prokaryotic DNA and make it sturdier.
  29. Helicase
    An enzyme that unwinds the double helix of DNA and separates the DNA strands in preparation for DNA replication.
  30. Histones
    Globular proteins that assist in DNA packaging in eukaryotes. Histones form octamets around which DNA is wound to form a nucleosome.
  31. hnRNA
    Heterogeneous nuclear RNA; the primary transcript made in eukaryotes before splicing.
  32. Inducible enzyme
    An enzyme whose transcription can be stimulated by an abundance of its substrate.
  33. Intron
    A nucleotide sequence that intervenes between protein-coding sequences. In DNA, these intervening sequences typically contain regulatory sequences, however in RNA they are simple spliced out to form the mature (translated) transcript.
  34. Lagging strand
    The newly forming daughter strand of DNA that is replicated in a discontinuous fashion, via Okazaki fragments that will ultimately be ligated together; the daughter strand that is replicated in the opposite direction that the parental DNA is unwinding.
  35. Leading Strand
    The newly forming daughter strand of DNA that is replicated in a continuous fashion; the daughter strand that is replicated in the same direction that parental DNA is unwinding.
  36. Ligase
    An enzyme that connects two fragments of DNA to make a single fragment; also called DNA ligase. This enzyme is used during DNA replication and is also used in recombinant DNA research.
  37. Missense mutation
    A point mutation in which a codon that specifies an amino acid is mutated into a codon that specifies a different amino acid.
  38. Monocistronic mRNA
    mRNA that codes for a single type of protein, such as is found in eukaryotic cells.
  39. mRNA
    Messenger RNA; the type of RNA that is read by a ribosome to synthesize protein.
  40. Nonsense mutation
    A point mutation in which a codon that specifies an amino acid is mutated into a stop (nonsense) codon.
  41. Peptidyl transferase
    The enzymatic activity of the ribosome that catalyzes the formation of a peptide bond between amino acids. It is thought that the rRNA of the ribosome possesses the peptidyl transferase activity.
  42. Point mutation
    A type of mutation in DNA where a single base is substituted for another.
  43. Poly-A tail
    A string of several hundred adenine nucleotides added to the 3' end of eukaryotic mRNA.
  44. Polycistronic mRNA
    mRNA that codes for several different proteins by utilizing different reading frames, nested genes, etc. Polycistronic mRNA is a characteristic of prokaryotes.
  45. Primase
    An RNA polymerase that creates a primer (made of RNA) to initiate DNA replication. DNA pol binds to the primer and elongates it.
  46. Promoter
    The sequence of nucleotides on a chromosome that activate RNA polymerase so that transcription can take place. THe promoter is found upstream of the start site, the location where transcription actually begins.
  47. P site
    Peptidyl-tRNA site; the site on a ribosome where the growing peptide (attached to a tRNA) is found during translation.
  48. Purine bases
    Aromatic bases found in DNA and RNA that are derived from purine. They have a double-ring structure and include adenine and guanine.

    • Pyrimidines: Cytosine & Thymine
    • Purines: Adenine & Guanine
    • A2T
    • G3C
  49. Pyramidine bases
    Aromatic bases found in DNA and RNA that have a single-ring structure. They include cytosine, thymine and uracil.

    • Pyrimidines: Cytosine & Thymine
    • Purines: Adenine & Guanine
    • A2T
    • G3C
  50. Release factor
    A cytoplasmic protein that binds to a stop codon when it appears in the A-site of the ribosome. Release factors modify the peptidyl transferase activity of the ribosome, such as water molecule is added to the end of the completed protein. This releases the finished protein from the final tRNA and allows the ribosome subunits and mRNA to dissociate.
  51. Replication
    The replication of DNA.
  52. Replication fork(s)
    The site(s) where the parental DNA double helix unwinds during replication.
  53. Replication bubbles
    Multiple sites of replication found on large, linear eukaryotic chromosomes.
  54. Repressible enzyme
    An enzyme whose transcription can be stopped by an abundance of its product.
  55. Repressor
    A regulatory protein that binds DNA at a specific nucleotide sequence (sometimes known as the operator) to prevent transcription of downstream genes.
  56. Ribosome
    A structure made of two protein subunits and rRNA; this is the site of protein synthesis (translation) in a cell. Prokaryotic ribosomes (also known as 70S ribosomes) are smaller than eukaryotic ribosomes (80S ribosomes). The S value refers to the sedimentation rate during centrifugation.
  57. RNA polymerase
    An enzyme that transcribes RNA. Prokaryotes have a single RNA pol, while eukaryotes have three; in eukaryotes, RNA pol I transcribes rRNA, RNA pol II transcribes mRNA, and RNA pol III transcribes tTRNA.
  58. rRNA
    Ribosomal RNA; the type of RNA that associates with ribosomal proteins to make a functional ribosome. It is thought that the rRNA has the peptidyl transferane activity.
  59. Semi-conservative replication
    DNA replication. Each of the parental strands is read to make a complementary daughter strand, thus each new DNA molecule is composed of half the parental molecule paired with a newly synthesized strand.
  60. Silent mutation
    A point mutation in which a codon that specifies an amino acid is mutated into a new codon that specifies the same amino acid.
  61. Single strand binding proteins
    Proteins that bind to and stabilize the single strands of DNA exposed when helicase unwinds the double helix in preparation for replication.
  62. Splicing
    One type of eukaryotic mRNA processing in which introns are removed from the primary transcript and exons are ligated together. Splicing of transcripts can be different in different tissues.
  63. Start site
    The location on a chromosome where transcription begins.
  64. Stop codon
    A group of three nucleotides that does not specify a particular amino acid, but instead serves to notify the ribosome that the protein being translated is complete. The stop codons are UAA, UGA, and UAG. They are also known as nonsense codons.
  65. Supercoiling
    A method of DNA protection utilized by prokaryotes, in which their large circular chromosome is coiled upon itself.
  66. Theta replication
    DNA replication in prokaryotes, so named because as replication proceeds around the single, circular chromosome, it takes on the appearance of the Greek letter theta.
  67. Thymine
    One of the four aromatic bases found in DNA. Thymine is a pyrimidine; it pairs with adenine.

    • Pyrimidines: Cytosine & Thymine
    • Purines: Adenine & Guanine
    • A2T
    • G3C
  68. Topoisomerase
    An enzyme that cuts one or both strands of DNA to relieve the excess tension caused by the unwinding of the helix by helicase during replication.
  69. Transition mutation
    A point mutation in which a pyrimidine is subsitututed for a pyrimidine, or a purine is substiuted for a pruine.
  70. Translation
    The process of reading a strand of mRNA to synthesize protein. Protein translation takes place on a ribosome.
  71. Transversion mutation
    A point mutation in which a pyrimidine is substituted for a purine or vice versa.
  72. tRNA
    Transfer RNA; the type of RNA that carries an amino acid from the cytoplasm to the ribosome for incorporation into a growing protein.
  73. tRNA loading
    The attachment of an amino acid to a tRNA (note that this is a specific interaction). tRNA loading requires two high-energy phosphate bonds.
  74. Upstream
    Toward the 5' end of an RNA transcript (the 5' end of the DNA coding strand). The promoter and start sites are "upstream"
  75. Uracil
    One of four aromatic bases found in RNA. Uracil is pyrimidine; it pairs with adenine.

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