Biochem-Nucleotides

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PicOlio
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118090
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Biochem-Nucleotides
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2011-11-20 15:44:37
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nucleotides nucleic acids heredity
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Ch. 17 Nucleotides, Nucleic Acids, and Heredity
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  1. heredity
    Heredity is the transfer of characteristics, anatomical as well as biochemical, from generation to generation.

    The transmission of heredity starts with the parent and is passed down at the molecular level.
  2. gene
    The unit of heredity; a DNA segment that codes for one protein or one type of RNA
  3. DNA
    Deoxyribonucleic acid carries the hereditary information.

    That is, the genes are carried in the DNA

    The macromolecule of heredity in eukaryotes and prokaryotes. it is composed of chains of nucleotide monomers of a nitrogenous base, 2-deoxy-D-ribose, and phosphate.
  4. Bases
    Purines and pyrimidines, which are components of nucleotides, DNA, and RNA
  5. The five principal bases of DNA and RNA
    • Adenine (A)
    • Guanine (G)
    • Cystosine (C)
    • Thymine (T) DNA Only
    • Uracil (U) RNA Only
  6. Both DNA and RNA contain four bases; two pyrimidines and two purines. Name them
    Purines: Adenine (A) and Guanine (G)

    • DNA Pyrimidines
    • Cytosine (C) and Thymine (T)

    • RNA Pyrimidines
    • Cytosine (C) and Uracil (U)
  7. Nucleoside
    A compound composed of ribose or deoxyribose and a base
  8. What is the sugar component of RNA?
    D-ribose

    ribonucleic acid = RNA
  9. What is the sugar component of DNA?
    2-deoxy-D-ribose

    deoxyribonucleic acid = DNA
  10. Nucleotide
    A nucleoside bonded to one, two, or three phosphate groups
  11. The building blocks (monomers) of nucleic acid chains are
    nucleotides
  12. Nucleotides are composed of what three units?
    • 1. A base
    • 2. A monosaccharide
    • 3. A phosphate
  13. What makes up a nucleoside, nucleotide, and nucleic acid?
    Nucleoside = Base + Sugar

    Nucleotide = Base + Sugar + Phosphate

    Nucleic acid = A chain of nucleotides
  14. Nucleic acid
    A polymer composed of nucleotides
  15. Double helix
    The arrangement in which two strands of DNA are coiled around each other in a screw-like fashion.
  16. DNA Double Helix
    In the DNA double helix, the two polynucleotide chains run in opposite directions. Thus, at each end of the double helix, there is one 5' -OH and one 3' -OH terminus.

    The sugar-phosphate backbone is on the outside, exposed to the aqueous environment, and the bases point inward.

    The paired bases form hydrogen bonds with each other; two for A-T and three for G-C, thereby stabilizing the double helix.
  17. Complementary base pairs
    The combination of a purine and a pyrimidine base that hydrogen bond together in DNA.
  18. Explain the 3 structures of DNA
    (Primary, Secondary, and Higher-Order)
    • Primary: -ATTGAC-
    • Secondary: Double Helix
    • Higher-Order: The way DNA coils around histones forming units called nucleosomes and is further condensed into chromatin within the body...
  19. Chromatin
    The DNA complexed with histone and nonhistone proteins that exists in eukaryotic cells between cell divisions.
  20. Solenoid
    A coil wound in the form of a helix
  21. What are the three differences in structure between DNA and RNA?
    • 1. DNA has four bases A, G, C, and T.
    • RNA has three of these bases A, G, and C but its fourth base is U, not T

    • 2. In DNA, the sugar is 2-deoxy-D-ribose.
    • In RNA, the sugar is D-ribose

    • 3. DNA is almost always double-stranded, with a helical structure.
    • There are several kinds of RNA, none of them with a repetitive double-stranded structure.
  22. mRNA
    Messenger RNA - The RNA that carries genetic information from DNA to the ribosome and acts as a template for protein synthesis.

    mRNA molecules are produced in the process called transcription and they carry the genetic information from the DNA in the nucleus directly to the cytoplasm where most of the protein is synthesized.
  23. tRNA
    Transfer RNA - The RNA that transports amino acids to the site of protein synthesis in ribosomes.
  24. rRNA
    Ribosomal RNA - The RNA complexed with proteins in ribosomes
  25. Ribosome
    Small spherical bodies in the cell made of protein and RNA; the site of protein synthesis.
  26. snRNA
    Small Nuclear RNA - Function is to help with the processing of the initial mRNA transcribed from DNA into a mature form that is ready for export out of the nucleus. A process often referred to as splicing
  27. Splicing
    The removal of an internal RNA segment and the joining of the remaining ends of the RNA molecule.
  28. Ribozymes
    RNA-based enzymes
  29. miRNA
    Micro RNA - Play important roles in cancer, stress responses, and viral infections. They inhibit translation of mRNA into protein and promote the degradation of mRNA.
  30. siRNA
    Small Interfering RNA - Small RNA molecules that are involved in degradation of specific mRNA molecules. This process serves as a protective mechanism in many species, with the siRNAs being used to eliminate expression of an undesirable gene.
  31. Name the six types of RNA and their function
    1. Transfer RNA (tRNA): Transports amino acids to site of protein synthesis

    2. Ribosomal RNA (rRNA): Combines with proteins to form ribosomes, the site of protein synthesis

    3. Messenger RNA (mRNA): Directs amino acid sequence of proteins

    4. Small nuclear RNA (snRNA): Processes initial mRNA to its mature form in eukaryotes

    5. Micro RNA (miRNA): Affects gene expression; important in growth and development

    6. Small interfering RNA (siRNA): Affects gene expression; used by scientists to knock out a gene being studied.
  32. What is the difference between exons and introns?
    Stretches of DNA that spell out (encode) the amino acid sequence to be assembled are interrupted by long stretches that seemingly do not code for anything. The coding sequences are called exons, short for "expressed sequences" and the noncoding sequences are called introns short for "intervening sequences".
  33. Exon
    Nucleotide sequence in DNA or mRNA that codes for a protein
  34. Intron
    A nucleotide sequence in DNA or mRNA that does not code for a protein
  35. Replication
    The process by which copies of DNA are made during cell division.
  36. The DNA in the chromosomes carries out two functions. What are they?
    1. It reproduces itself (replication)

    2. It supplies the information necessary to make all the RNA and proteins in the body, including enzymes.
  37. Origin of Replication
    The point in a DNA molecule where replication starts.
  38. Replication fork
    The point on a DNA molecule where replication is proceeding.
  39. In all known forms of replication, is the primer made out of RNA or DNA?
    In all known forms of replication, the primer is made out of RNA, not DNA.
  40. Where in a cell is the DNA located?
    In eukaryotic cells, DNA is located in the cell nucleus and in mitochondria.
  41. Where in a cell is the RNA located?
    RNA is synthesized from DNA in the nucleus, but further use of RNA (protein synthesis) occurs on ribosomes in the cytoplasm.
  42. What is the difference in structure between thymine and uracil?
    Thymine and uracil are both based on the pyrimidine ring. However, thymine has a methyl substituent at carbon 5, whereas uracil has a hydrogen. All of the other ring substituents are the same.
  43. What is the difference in structure between D-ribose and 2-deoxy-D-ribose?
    D-Ribose and 2-deoxy-D-ribose have the same structure except at carbon 2.

    D-Ribose has a hydroxyl group and hydrogen on carbon 2, whereas deoxyribose has two hydrogens.
  44. RNA and DNA refer to nucleic acids. Which part of the molecule is acidic?
    Neither. The name "nucleic acid" derives from the fact that the nucleosides are linked by phosphate groups, which are the dissociated form of phosphoric acid.
  45. What type of bond exists between the two phosphates in ADP?
    Anhydride bonds
  46. In RNA, which carbons of the ribose are linked to the phosphate group and which are linked to the base? What types of bonds are they?
    In RNA, carbons 3' and 5' of the ribose are linked by ester bonds to phosphates. Carbon 1 is linked to the nitrogen base with an N-glycosidic bond.
  47. How many hydrogen bonds can form between uracil and adenine?
    Two
  48. What is the nature of the interaction between histones and DNA in nucleosomes?
    Electrostatic interactions
  49. What constitutes the superstructure of chromosomes?
    The superstructure of chromosomes consists of many elements. DNA and histones combine to form nucleosomes that are wound into chromatin fibers. These fibers are further twisted into loops and minibands to form the chromosome superstructure.
  50. What are the higher-order structures of DNA that eventually make up a chromosome?
    DNA is wound around histones, collectively forming nucleosomes that are further wound into solenoids, loops, and bands.
  51. Which has the longest chains; tRNA, mRNA, or rRNA?
    rRNA
  52. Which type of RNA has a sequence exactly complementary to that of DNA?
    mRNA
  53. What kind of functions do ribozymes, in general, perform?
    Ribozymes, or catalytic forms of RNA, are involved in post-transcriptional splicing reactions that cleave larger RNA molecules into smaller, more active forms.

    For example, tRNA molecules are formed in this way.
  54. Does mRNA also have introns and exons? Explain.
    Immediately after transcription, messenger RNA contains both introns and exons. The introns are cleaved out by the action of ribozymes that catalyze splicing reactions on the mRNA.
  55. Do satellites code for a particular protein?
    No

    Satellites are short sequences of DNA that are repeated hundreds of thousands of times but do not code for any protein in RNA.
  56. A DNA molecule normally replicates itself millions of times, with almost no errors. What single fact about the structure is most responsible for this fidelity of replication?
    The specificity between the base pairs, A-T and G-C
  57. How many different bases are present in a DNA double helix?
    Four.
  58. Why is replication called semiconservative?
    In semiconservative DNA replication, the new daughter DNA helix is composed of one strand from the original (or parent) molecule and one new strand.
  59. What are helicases? What is their function?
    Helicases are enzymes that break the hydrogen bonds between the base pairs in double-helix DNA and thus help the helix to unwind. This prepares the DNA for the replication process.
  60. In which direction is the DNA molecule synthesized continuously?
    The leading strand or continuous strand is synthesized in the 5' to 3' direction.
  61. Which enzyme catalyzes the joining of Okazaki fragments?
    DNA ligase
  62. From the perspective of the chain being synthesized, in which direction does DNA synthesis proceed?
    From the 5' to the 3' direction.
  63. What is the function of endonuclease in the BER repair mechanism?
    One of the enzymes involved in the DNA base excision repair (BER) pathway is an endonuclease that catalyzes the hydrolytic cleavage of the phosphodiester backbone. The enzyme hydrolyzes on the 5' side of the AP site.
  64. Which bonds are cleaved by glycosylase?
    A beta-N-glycosidic bond between the damaged base and the deoxyribose.
  65. What 12-nucleotide primer would you use in the PCR technique when you want to amplify a gene whose end is as follows: 3'TACCGTCATCCGGTG5'?
    5'ATGGCAGTAGGC3'

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