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2014-02-21 10:56:40
sfsu biochem

biochem eam questions
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  1. nucleotides (2)
    • DNA
    • RNA
  2. amino acids
  3. monosaccharides
  4. lipids
    do not form polymers but aggregate
  5. 4 kinds of bio-molecules
    • nucleotides
    • amino acids
    • monosaccharides
    • lipids
  6. 2 molecules of life
    • nucleotides
    • amino acids
  7. 2 energy molecules
    • monosaccharides
    • lipids
  8. What is DNA and RNA
    polymers of nucleosides that are linked together by phosphodiester bonds
  9. what is a nucleoside
    5 carbon sugar
  10. a nucleoside can be either or
    • ribose
    • deoxyribose
  11. the deoxy/ribose are linked to one of these nitrogenous bases
    • purine
    • pyrimidine
  12. nucleoside residues can be linked together by phosphodiester bonds between 3' C of one sugar and 5' C of another to form polynucleotides
  13. difference between DNA and RNA
    • nucleoside sugar  (deoxy and ribo)
    • *The 2' C on ribo has a hydroxyl group, the deoxy does not
  14. the purine bases found in both DNA and RNA link to the sugar on the 1' C
    Pyrimidine found in DNA does the same
  15. ATP is a
  16. The tri-phosphate from ATP is linked to which carbon on then sugar
    5' C
  17. The sequence of bases in the other DNA of a double helix is
  18. why are the bases considered complimentary
    because from Erwin Chargaff's studies he concluded that certain DNA bases were of a 1:1 ratio of each other
  19. what are the names of the purines found in both DNA and RNA
    • Adenine
    • Guanine
  20. which bases are found in DNA
    • A, C, T, G
    • A, U, G, C
  21. 2 differences between uracil and thymine
    • thymine and uracil have the same structure but has an extra methyl
    • uracil is in RNA thymine is in DNA
  22. how many hydrogen bond donors/acceptors in guanine? adenine? cytosine? thymine?
    • G = 2D/1A
    • A = 1D/1A
    • T = 1D/1A
    • C = 1D/2A
  23. which C is linked to the base
  24. nucleoside?
    • sugar + base
    • sugar + base + phosphate group
  25. antiparallel
    one strand runs one way while the opposite strand runs the other
  26. coding strand (sense)
    mRNA formed from the template is complimentary to the template
  27. template strand (antisense)
    acts as the template for mRNA, the strand that is copied
  28. CTD acronym
    C-terminal domain
  29. what is CTD
    a region that has a highly conserved set of seven amino acids that is repeated 52 times in vertebrates
  30. the repeating heptad of amino acids in CTD forms a tail like structure that later on bind factors involved in RNA processing and modification
  31. why is initiation in eukaryotic transcription the most critical step
    b/c if there is no initiation it wont happen, and also if its not in the correct location it wont occur
  32. TATA box is located on which strand
    coding strand
  33. bases upstream are given a + #
    bases downstream are given a - #
  34. what is a promoter
    a sequence of DNA commonly located upstream from the start of the gene which provides info used by RNA pol
  35. what pol is involved in the syn of most ribosomal RNA
    RNA pol I
  36. which pol is involved in mRNA production
    RNA pol II
  37. what RNA type is likely to be involved in associating with amino acids
  38. 3 core promoter elements
    • Inr
    • TATA box/BRE upstream
    • MTE/DPE downstream
  39. another element of eukaryotic promoters
    upstream/downstream elements enhancers or silencers
  40. 3 kinds of up/downstream elements-enhancers or silencers
    • GC box (-40)
    • CAAT box (-110)
    • CRE
  41. BRE
    • B- recognition element
    • motif 10 element
    • downstream promoter element
    • cAMP response element
  42. dNTP needs = conc of A/C/U/T/GTP to create RNA
  43. functions of the transcription initiation step
    is to orient RNA pol near the Inr site
  44. When the TATA binding protein straddles DNA, it will start to bend the DNA
  45. what is the function of TFIID during elongation phase of transcription
    this factor isn't involved in elongation as it remains at the promoter region
  46. 3 components regarding CTD
    • region is composed of a repeating AA heptad
    • region forms a tail like structure
    • region is involved in RNA processing
  47. what is the first step in forming the pre-initiation complex
    association of TBP/TFIID with the promoter element TATA
  48. TFIIH is a critical switch from the initiation phase to the elongation phase. why?
    TFIIH unwinds the DNA and phosphorylates the CTD
  49. when the polymerase leaves the promoter region, does the pol move upstream or downstream from the Inr site?
  50. after the sequence AAUAAA is encountered by the pol, what happens to the CTD?
    its dephosphorylated
  51. TFIIA function
    binds to TFIID and stabilizes TBP-DNA interactions
  52. TFIIB function
    binds to TFIID and TFIIF, thus assisting in directing RNA pol promoter region
  53. TFIID function
    the factors has many proteins and contains TBP which will bind to the TATA box
  54. TFIIE function
    helps to recruit TFIIH
  55. TFIIF function
    binds to RNA pol and directs to promoter region
  56. TFIIH functions (2)
    • helicase activity that unwinds the DNA
    • has kinase activity which phosphorylates the CTD
  57. TBP function
    is located in the TFIID and binds to the TATA box
  58. In the promoter region of a hypothetical gene, which strand will the RNA Pol II use as a template strand
    in order to find out which strand will the RNA pol II use, you must look for the TATA in the strand which means there is a TATA box in the sequence
  59. TFIIB is one of the 6 general eukaryotic transcriptions factors, the function of this factor is (2)
    • helps RNA pol II to position itself near the Inr thru factor F
    • to stabilize the TBP (TFIID) DNA interaction
  60. during elongation, when RNA is synthesizing at the 5' end, we tend to use these 3
    • ATP
    • UTP
    • GTP
  61. TFIIF helps the RNA pol II to keep going
  62. enhancers and activators function
    increase the amount of specific transcript produced
  63. transcription of a specific gene can be regulated
  64. where are enhancers located
    are upstream elements
  65. what are the 2 upstream regulatory elements and what are they known as
    • SRE
    • E box
    • DNA sequences (enhancers)
  66. the 2 activators of transcription and what are they known as
    • SREBP
    • USF
    • activators
  67. mediator protein function
    links enhancers and activators to the basic transcription machinery by a DNA looping mechanism
  68. The DNA looping mechanism function
    enhances the rebinding to the promoter for multiple rounds of transcription
  69. before transcripts can be translated, what 3 modifications are needed to occur
    • 5' capping
    • splicing
    • 3' polyadenylation
  70. 5' capping and function
    as the RNA comes out a "cap" is placed on the 5' end to prevent it from being degraded
  71. what is the "cap"
    a methyl group is the cap that prevents degrading
  72. the 5' capping make the end of the transcripts look different, so it throws off exonuclease preventing it from recognizing the end so it will then prevent or slow down the rate at which it is degraded
  73. There are 42 splice sites in FAS
  74. splicing process function
    removes introns and connects exons
  75. the end of the exon contains the sequence
    the beginning of the intron contains the sequence
    • AG
    • GU
  76. mRNA function
    the seq dictates the AA seq of proteins
  77. rRNA function
    make up the ribosomes
  78. tRNA function
    delivers amino acids to the site of the protein synthesis
  79. snRNA function
    forms complexes with proteins to form snRNPs that is involved in RNA splicing, polyadenylation rxns, and other unknown functions
  80. enzyme that synthesizes mRNA
    RNA polymerase
  81. which RNA pol is involved in synthesizing
    18S rRNA
    • II
    • I
    • III
  82. 2 structural features of
    • contains 2 heterocyclic rings
    • contain 4 ring N

    • contains 1 heterocyclic ring
    • contains only 2 ring N
  83. minor groove vs major groove
    minor groove is the groove inside while the major groove is the groove on the outside of the double helix
  84. RNA pol synthesizes pre-rRNA
  85. RNA pol synthesizes tRNA and small RNAs
  86. is a segment of a gene that does not code for a product
  87. is a DNA sequence that begins with a start codon and ends with a stop
  88. is a DNA segment that is transcribed and processed to produce a specific protein
  89. is a gene segment that appears in the mature mRNA
  90. is a small cDNA sequence, synthesizes from mRNA and sequences that can be used t identify a particular gene
    expressed sequence tag
  91. contains genes for related proteins and regions that function in gene transcription
  92. polyadenylation can occur before and after mRNA splicing
    pol adds polyadenylate tail to the mRNA while it is still in the nucleus
    polyadenylation tail helps to protect the mRNA from exonucleases
  93. splicesosome consists of 5 small RNA molecules and many associated proteins splicing occurs while the mRNA is still in the nucleusone mRNA can sometimes code for more than one protein by splicing alternative sites
  94. translation
    process involved in converting mRNA sequence into proteins
  95. proteins like RNA and DNA are polymers made up of AA linked together in an order specified the RNA seq
  96. splicesome
    is a # of snrps that remove introns and joins exons
  97. which is the purpose of the 3' tail (2)
    • increases half life
    • ensure effective transport of RNA out of the nucleus
  98. AA are linked together by
    amide bonds aka peptide bonds
  99. the code in RNA requires at least 3 bases to describe all 20 AA because 3 is the number of bases that would cover all 20 AA
  100. function of tRNA (2)
    • bind to the codon
    • bind to the correct AA
  101. the 3' of the anticodon binds to AA that will recognize the codon
  102. inosine is frequently found in the 5' end of the anticodon
  103. wobble
    the third position of the codon
  104. tRNA (anticodon) binds to mRNA (codon)
    • G
    • U
    • CU
    • AG
    • CAU
  105. how to compact the DNA double helix into a chromatid
    • wound around histones octamers forming nucleosomes which then
    • are linked together by histone protein (H1) forming beads on a string motif
    • the nucleosome beads are supercoiled to form 30nm fibers
    • fibers are then looped, compressed, and coiled to form chromatid
  106. miRNA (micro)
    alters gene expression
  107. small interfering RNA (siRNA) (2)
    • alters gene expression
    • used to describe synthetically made RNAs and mRNA and naturally occurring RNAs
  108. p site function (2)
    • binds the tRNA molecule that is attached to the growing peptide chain
    • site that binds peptidyl-tRNA
  109. a site function
    site that binds the aminoacyl-tRNA
  110. e site
    may be bound to deacylated tRNA
  111. is a DNA segment that begins with a start and ends with a stop codon (nonsense)
  112. contains genes for related proteins and regions that function in gene transcription
  113. is a small cDNA seq, synthesized from mRNA and sequenced, that can be used to identify a particular gene
    expressed sequence tag
  114. 5' capping has which nucleoside added
  115. nucleoside is connected to the mRNA through
    triphosphate linkage
  116. the added nucleotide is modified by methylation at
    N atom
  117. mRNA is modified by 5' capping methylation of
    ribose residues at the 2' hydroxyl position
  118. Why at the eukaryotic promoters A and T rich and not G and C rich
    because it takes less E to break a part the bonds of A and T. If G and C rich than it will take more time and E to break the strands
  119. the 3' end of the tRNA links to
    a specific amino acid in the cyto
  120. the anti-codon loop base pairs with
    a codon on the mRNA
  121. Aminoacylation of tRNA requires
    aminoacyl tRNA synthetase
  122. 3 structures translation requires
    • mRNA transcript
    • charged tRNA
    • a ribosome protein assembly plant.
  123. Large subunit 60s
    3 RNAs
    # of proteins
    • 28s rRNA
    • 5.8s rRNA
    • 5s rRNA

    49 proteins
  124. small subunit 40s
    # of proteins
    18s rRNA

    33 proteins
  125. 2 tRNAs for met
    • tRNA met
    • tRNAi met
  126. 1 difference
    1 similarity

    between tRNAi met and tRNA met
    tRNAi met is used at the start AUG

    both have the same anti codon for AUG (CAU)
  127. 3 steps of translation and their function
    • initiation - orient the RNA transcript in the correct position
    • elongation - to make the peptide bond
    • termination - cleave the peptide and release ribosome to begin process again
  128. transpeptidation function
    A reaction involving the transfer of one or more amino acids from one peptide chain to another
  129. ribozyme is located where
  130. ribozyme function
    a molecule of RNA that functions as an enzyme such as by catalyzing the cleavage of other RNA molecules
  131. ribonucleic acid enzyme = ribozyme
  132. degenerate
    a code in which several code words have the same meaning
  133. enzymes involved in 5' capping?
    poly a tail
    • guanylyltransferase and methyltransferase
    • poly a polymerase
  134. what type of reactions are involved in splicing
  135. 2 acid amino acids
    3 basic amino acids
    • aspartate glutamate
    • histidine lysine arginine
  136. 1 codon = 3 nucleotides = 1 AA
  137. degenerate
    means that some of the AA are coded by more than one codon, its redundant
  138. enzyme involve in attaching the correct AA to the correct RNA
    aminoacyl-transfer RNA synthetase
  139. 4 types of ribosomal RNA
    • 16s
    • 18s
    • 28s
    • 5.8s
  140. translocation
    move the peptide attached to the tRNA from the A site to P site.
  141. A site needs to be open to accept the next AA
  142. Why does the A site need to be protected from water
    because if exposed than it could hydrolize the ester bond which will release the peptide from tRNA
  143. How many elongation rounds would be necessary to synthesize a peptide that has 523 amino acids
  144. how many hi bonds (minimum) must be hydrolyzed to synthesize a peptide that has 523 amino acid?
    • 2092
    • 523 x 4
  145. The number of elongation cycles depends directly on
    depends on the number of amide bonds you have to make
  146. peptide grows in what direction
    N>C 5>3
  147. what steps of elongation require energy in the form of GTP hydrolysis
  148. the ribosome moves along the RNA in what direction
    C>N 3>5
  149. What factor is associated with the transpeptidation step
  150. what factor is associated with the translocation step
  151. Function of castor beans in translation
    prevents EF1 and 2 from binding, thus inactivating the ribosome
  152. how many ATP equivalents are needed to charge tRNA
  153. IF2
    • escort tRNAi met into the P site of 40s
    • 1 hi bond
  154. IF3 (2)
    • prevent 60s from binding to the small subunit
    • helps bind mRNA
    • none
  155. EF1
    • delivers charged tRNA to the A site
    • 1 hi E
  156. EF2 (3)
    • translocates ribosomes
    • moves peptide-tRNA from the A site to the P site
    • moves mRNA down the 3' end
    • 1 hi E
  157. RF1
    recognizes stop codons
  158. RF3
    • promotes dissociation of RF1 peptide and mRNA from ribosome
    • 1 hi E bond
  159. chloramphenicol function on translation
    blocks a site
  160. erythromycin function on translation
    inhibits translocation
  161. puromycin function on translation
    causes premature chain termination