BIOCHM E3 C9 FINAL

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BIOCHM E3 C9 FINAL
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BIOCHM E3 C9 FINAL
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  1. RNA
    synthesis is called ----- AND OCCURS WHERE?
    • RNA
    • synthesis is called transcription (in nucleus)
  2. The total RNA transcripts for an organism is its --------
    transcriptome
  3. RNA synthesis is called transcription (in nucleus) and involves complementary base pairing of --------- to
    ribonucleotides

    • DNA bases-messenger
    • RNA
  4. Each new RNA is a -----
    transcript
  5. The -------- is the entire set of proteins synthesized
    proteome
  6. -------- -------- is the process by which cells
    control the timing of gene product synthesis in response to environmental or
    developmental cues
    Gene expression
  7. ---------- refers to the sum total of low
    molecular weight metabolites produced by the cell
    Metabolome.

    • TCA PRODUCTS.
    • SIGNATURE MOLECULES THAT STATE A PROCESS IS OCCURING. THINK FRUIT BREATH AND DIABETIC.
  8. Several RNA molecules participate directly in the synthesis of protein, or-----------.
    translation
  9. ------------- specifies the primary protein sequence
    Messenger RNA (mRNA)
  10. ------- delivers the specific amino acid
    Transfer RNA (tRNA)
  11. ------- molecules are components of ribosomes
    Ribosomal RNA (rRNA)
  12. DEFINE THE CENTRAL DOGMA
    • generally how the flow of information works in all organisms, except some
    • viruses have RNA genomes and use reverse transcriptase to make DNA (e.g., HIV)
  13. TRANSCRIPTION/ TRANSLATION. WHEN DO THEY OCCUR?
    • TRANSCRIPT...BTWN DNA---> RNA
    • TRANSLATION RNA------->PROTEIN
  14. T OR F?
    Artificial selection for certain physical traits in domesticated animals and plants has
    been used for thousands of years
    TRUE
  15. The field of genetics began in the ------ century
    19TH
  16. Early in the ------- century, scientists recognized that physical traits are inherited as discrete
    units (genes)
    20TH
  17. ---------- were also identified as the carriers of genetic information (contained genes)
    Chromosomes
  18. DNA structure was elucidated in ------ by James Watson and Francis Crick, and
    Wilkins/Franklin
    1953
  19. WHO IDENTIFIED TRANSFORMATION?
    • FRED GRIFFITH 1928.
    • THINK SMOOTH AND ROUGH.
    • though few accepted his discovery—uptake of DNA by bacteria-virulence reincorporated into non-virulent strain. DNA LIVES AFTER BACTERIA DIES.
  20. WHO AND WHEN reported the identification of Griffith’s transforming principle as DNA
    -Everyone was still not convinced
    1944, Oswald Avery
  21. WHO AND WHEN demonstrated the different functions of protein and DNA with their T2 bacteriophage experiment, that DNA was accepted as the genetic material.
    1952 Hershey and Chase
  22. The ----------experiment confirmed DNA as the transforming principle
    Hershey-Chase experiment
  23. Information used to construct the model of DNA:
    (WHAT'S IT MADE OF)
    Chemical and physical dimensions of deoxyribose SUGAR, nitrogenous bases, and phosphate.
  24. Chargaff’s rules)—does not apply to RNA—Why??
    SINGLE STANDED AND URASEL.
  25. EACH DNA TURN IS HOW LONG?
    3.3 nm (33 anstroms)
  26. LENGHT BETWEEN BASES.
    0.33nm (3.3 ANSTROMS)
  27. THE LENGTH BEWTEEN THE TWO POLYNUCLEOTIDE STRANDS. (SPACE IN THE MIDDLE BTW RAILS)
    2.4nm (24 ANSTROMS)
  28. T OR F ?
    DNA is composed of two polynucleotide
    strands forming a double helix
    TRUE
  29. BASE ARE HYDROPHOBIC?
    YES
  30. PHOSDISEATER IS HYDROPHILLIC ?
    WHERE IS IT, INSIDE OR OUT?
    • YES.
    • OUTSIDE.
    • HYDRATION SPHERES.
  31. DNA consists of two polynucleotide strands that wind around each other to form a -------- -------- double helix
    RIGHT HANDED. CLOCKWISE FROM VIEWER
  32. NORMAL B-DNA OR WATSON & CRICK DNA MODELS TURN WHICH WAY?
    RIGHT HANDED. CLOCKWISE FROM VIEWER
  33. Z-DNA SPINS WHICH WAY?
    LEFT HANDED
  34. WHAT THE HELL IS A-DNA?
    • COMPACT B-DNA.
    • DEHYDRATED.
  35. DEFINE Nucleotide
    • one sugar
    • one base
    • one phosphate
  36. DEFINE Nucleoside
    one sugar + one base
  37. DIFFERENCE BETWEEN NUCLEOTIDE AND NUCLESIDE?
    Nucleotide = one sugar,one base, one phosphate.

    Nucleoside = one sugar + one base.
  38. Nucleotides are linked by --------
    • 3′,5′-phosphodiester bonds.
    • —look at the sugar counting from the anomeric
    • carbon.
  39. THE 3'-5' PHOSPHODIESTER BONDS WHAT TWO THINGS?
    • 3′-hydroxyl of one nucleotide to the
    • 5′-phosphate of another
  40. WHY IS DNA CALLED "DEOXY"?
    MISSING OH ON THE 2ND CARBON OF THE 3' END.
  41. The------------- nature of the two strands allows
    hydrogen bonds to form between the nitrogenous bases
    antiparallel
  42. NAME THE 2 PURINE BASE PAIRS
    ADENINE AND GUANINE.

    • LOOK AT THE END OF THE WORD.
    • PURINE = INE.
  43. NAME THE THREE PYRIMDINE BASES.
    • thymine
    • cytosine
    • URACAIL.
    • CAUGHT UNDER THE PRYAMID.
  44. HOW MANY HYDROGEN BONDS BETWEEN G-C
    3
  45. HOW MANY HYDROGEN BONDS BETWEEN A-T ?
    2
  46. One turn of the double helix spans ------ nm and consists of ----- base pairs
    • 3.3 nm
    • 10.3 base pairs
  47. DEFINE Base stacking.
    • bases are nearly planar and
    • stacked, allowing for weak van der Waals forces between the rings
  48. DEFINE Hydration
    water interacts with the structure of DNA to stabilize structure-18-19 molecules of water/nucleotide.
  49. DEFINE Electrostatic interactions.
    destabilization by negatively charged phosphates of sugar-phosphate backbone are minimized by the shielding effect of water, Mg2+, and basic proteins such as histones. pKa of phosphodiester ~ 2.
  50. Xenobiotics, and thermal fluctuations CAN FUCK WITH DNA. WHAT ARE THEY?
    • Think environmental toxins, Cancer
    • drugs, heating, etc..

    • C CAN BIND TO A.
    • TAUTOMERIC SHIFT.
  51. WHAT WOULD CAUSE A TRANSITION MUTATION?
    • TAUTOMERIC SHIFT.
    • HYDROGEN MOVES AND C CAN BIND WITH A.
    • AKA POINT MUTATION.
  52. Tautomeric shifts are spontaneous changes to nucleotide base structure:
    Amino to ----- and keto to ------ groups.
    • Amino to imino
    • keto to enol
    • AIKE
  53. T OR F?
    The imino form of adenine does not pair with thymine; it pairs with cytosine.
    TRUE
  54. Overuse of x-rays, CT scans now may
    contribute to cancer. HOW?
    The most common UV-induced products are thymine-thymine dimers
  55. thymine-thymine dimers LOOK LIKE WHAT?
  56. NAME 3 Nonalkylating agents
    • Benzo(a)pyrenes in cigarette smoke forms adducts (STICK).
    • Preservatives (NaNO2) in meats deaminates bases (charred cured meats and cured meats)
  57. DEFINE Intercalating agents
    • certain planar molecules that can distort DNA by inserting themselves between
    • the stacked bases.
    • -Causes Base pair deletion or addition
    • -Cancer drug—doxorubicin (adriamycin)
    • -Acridine
    • - “Ethidium bromide”
  58. Ethidium bromide IS WHAT TYPE OF AGENT?
    INTERCALATING
  59. Xenobiotics classes include:
    (NAME 2)
    • 1. Base analogues. Structures similar to bases and can be incorporated into DNA.
    • MAINSTEY CANCER DRUG

    • 2. Alkylating agents. cause alkylation (adding carbon chains) and cross-linking of bases. Base pair incorrectly, leading to transition or transversion mutations--pyrimidine substitutes
    • for purine or vice versa).
  60. Base pair incorrectly, leading to transition or transversion mutations--pyrimidine substitutes
    for purine or vice versa).
    WHAT TYPE DNA DAMAGE IS THIS CLASSIFED BY?
    • XENOBIOTICS CLASS
    • ALKYLATING AGENTS
  61. DEFINE transition mutations
    • pyrimidine for pyrimidine or purine for purine.
    • a type of point mutation, a single base pair change.
  62. DEFINE Transversion mutations
    • pyrimidine for purine or vice versa, can also be point.
    • THINK "VER" AS IN reVERse.
  63. DEFINE depurination.
    loss of purine base
  64. DEFINE deamination
    loss of amine
  65. When DNA is underwound, it twists to the right to relieve strain, causing -------------- ------------.
    negative supercoiling
  66. DNA Winds around itself to form an ---------- ------------ and has stored energy in the form of torque
    interwound supercoil
  67. Makes reversible cuts that allow the supercoiled segments to unwind.
    topoisomerases
  68. ----------- that forms during strand separation can be relieved by a class of enzymes called topoisomerases.
    Supercoiling (positive)
  69. ---- contain genes that are packaged into --------
    • DNA
    • chromosomes
  70. E. coli Prokaryotic OR eukaryotic?
    AND WHAT TYPE OF DNA?
    • Prokaryotes-
    • circular DNA molecule that is extensively looped and coiled, EVEN Supercoiled
    • DNA complexed with a protein core
  71. In the nucleoid of Bacteria, the chromosome is attached to the protein core in at least 40 places. WHY?
    This structural feature limits the unraveling of supercoiled DNA.
  72. Prokaryotic Genomes size- usually considerably --------DNA and fewer genes than eukaryotic genomes.
    • LESS.
    • THINK E. COLI
  73. Prokaryotic Genomes ARE DIFFERENT THAN EUKARYOTIC IN 3 WAYS NAME THEM.
    • 1. Genome size
    • 2. Coding capacity- compact and continuous genes
    • 3. Gene expression- genes organized into operons
  74. Set of related genes which are regulated as a unit
    CALLED WHAT?
    OPERONS
  75. ------------- often contain plasmids,
    which are usually small and circular DNA with additional genes (e.g., antibiotic
    resistance)
    Prokaryotes
  76. NAME 2 TYPES OF DNA
    GENOMIC AND PLASMID
  77. Each eukaryotic chromosome consists of a----- ----- DNA molecule complexed with histone proteins (basic proteins) to form nucleohistone
    single, linear DNA
  78. DEFINE CHROMATIN
    combination of eukaryotic linear DNA and proteins that make up the contents of the nucleus of a cell.
  79. DEFINE NUCLEOHISTONE
    eukaryotic chromosome a single, linear DNA molecule complexed with histone proteins (basic proteins).
  80. WITH THE EUKARYOTIC GENOME GENES ARE INTERRUPTED BY ------ ------ which can be removed by splicing from the primary RNA transcript
    NONCODING INTRONS EXPRESSED AS EXONS
  81. NONCODING INTRONS EXPRESSED AS --------
    EXONS
  82. Existence of ---- & ------- allows eukaryotes to produce more than one protein from each gene
    • introns (removed sequences)
    • exons (expressed sequences)
  83. -------- ------- allows for various combinations of exons to be joined to form different mRNAs
    Alternative splicing
  84. --------------- -----------are those sequences that do not code for polypeptide primary sequence or RNAs
    Intergenic sequences
  85. T OR F?
    Of the 3,200 Mb of the human genome, only 38% comprise genes and related sequence
    TRUE
  86. Over 60% of the human genome is ------- SEQUENCE.
    intergenic sequences—do not code for gene products-called “junk DNA” but not really appropriate term.
  87. -------------- are DNA sequences in which multiple
    copies are arranged next to each other
    Tandem repeats (satellite DNA)
  88. Certain tandem repeats play structural
    roles like------------- & ---------------.
    centromeres and telomeres.
  89. DEFINE telomeres
    REPEATING SEQUENCES ON THE END OF DNA DEGRAD OVER TIME, EXECPT IN CANCER CELLS, THEY CAN REPROGRAM AND CURCUMVENT IT.
  90. NAME 2 SHORT TANDEM REPEATS AND THEIR SIZE
    • microsatellites (1-4 bp)
    • minisatellites (10-100 bp)

    Used as markers in genetic disease, forensic investigations, and kinship, UNIQUE TO EACH PERSON.
  91. Differences between DNA and RNA primary structure:NAME 3
    • 1. Ribose sugar instead of deoxyribose
    • 2. Uracil nucleotide instead of thymine
    • 3.Single stranded
  92. ADVENAGE LENGTH OF tRNA
    75 bases
  93. ----------- allows the tRNA to recognize the correct mRNA codon and properly align its amino acid for protein synthesis.
    ANTICODON
  94. WITH tRNA Amino acids are attached via specific-------- ------ ------ to the end opposite the three nucleotide anticodon.
    aminoacyl-tRNA synthetases
  95. is the most abundant RNA in living cells (80%) with a complex secondary
    structure
    Ribosomal RNA (rRNA)
  96. T OR F?
    Eukaryotes and prokaryotes are Similar
    in shape and function, both have a small and large subunit, but differ in size and chemical composition
    TRUE
  97. Eukaryotic vs prokaryotic rRNA SIZE
    Eukaryotic larger (80S) with a 60S and 40S subunit, prokaryotic smaller (70S) with 50S and 30S subunits
  98. mRNA Eukaryotic vs prokaryotic
    processed differently; eukaryotic mRNA requires 5′ capping (7-methylguanosine cap), 3′ tailing (poly A), and splicing (getting rid of introns).
  99. mRNA MAKES UP HOW MUCH OF THE TOTAL RNA?
    5%
  100. Most VIRUS capsids are----- OR -------.
    SHAPES!
    are helical or icosahedral
  101. HIV is an enveloped virus with a---------- core within its capsid
    cylindrical
  102. The HIV RNA WHER AND NAME THE TYPES.
    The core contains two copies of the RNA, reverse transcriptase, and integrase
  103. Once bound, HIV fuses with the host cell membrane and releases ------ and reverse transcriptase
    ssRNA
  104. HIV Immediately makes ssDNA from
    the viral RNA which is integrated into the host cell chromosome by the --------- enzyme
    integrase
  105. Cell death can be triggered by:
    NAME 3
    • Viral activation of apoptosis genes
    • Numerous viral particles budding at the same time
    • Massive viral release, depleting necessary components
  106. Caused by virus Rhabdoviruses..WHAT?
    RABIES
  107. T OR F ?
    Rabies occurs in more than 150
    countries and territories.Worldwide, more than 55,000 people die of rabies every year. 1-2 in US.
    TRUE
  108. T OR F?
    40% of people who are bitten by suspect rabid animals are children under 15 years of age.
    TRUE
  109. DEFINE RFLP
    • Genetic variations in minisatellites DNA sequence allow for the analysis of differences by restriction
    • fragment length polymorphisms

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