molecular genetics

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kaitiek09
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259587
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molecular genetics
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2014-02-28 12:31:20
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sfsu molecular genetics
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  1. units in a nucleic acid
    nucleotide
  2. 3 components of nucleic acid
    • 5 C sugar
    • phosphate group
    • nitrogenous base
  3. deoxyribonucleotides have a d in front of them. Examples dAMP or dGMP
    RNA does not have an r in front of its ribonucleotides. Examples AMP, GMP
  4. when the phosphate attaches to the 5 C sugar, it creates a
    phosphodiester bond
  5. DNA is generated from which end to the other located on which terminus
    generated from 5'-3' and is located on the OH terminus
  6. what 2 types of bonds are found in the nucleic acid structure
    • hydrogen
    • Van der Waals
  7. proximity of atoms in van der waals interactions causes temporary polarization leading to an interaction
  8. in Van der Waals interactions
    1) far apart
    2) close together
    3) over lap
    • 1) there is no attraction
    • 2) some attractive interaction
    • 3) repulsive interaction
  9. this type of bond allows for the bases to stack along the nucleic acid chain
    van der waals
  10. hydrogen bonds occur between
    purines and pyrimidines
  11. opposite strand of DNA is the reverse complimentary.
    This allows for various secondary structures in RNA to become stem loops
  12. the stacking of adjacent base pairs in DNA causes there to be hydrophobicity within the double helix
  13. chargaffs rules of DNA (4)
    • base composition varies in species
    • DNA specimens isolated from diff tissues of the same species have the same composition
    • base composition of DNA does not change
    • # of A=T # of C=G
  14. one helical turn
    34 A(angstroms)= 10.5 base pairs
  15. DNA is a right handed helix
  16. 3 alternate forms of DNA duplexes
    Right handed helix (2)
    Left handed helix (1)
    • B-DNA
    • A-DNA
    • Z-DNA
  17. 3 examples of functional RNA with a secondary structure
    • tRNA
    • Riboswitches
    • rRNA
  18. loops occur when there is imperfect pairing within double helix pattern in RNA
  19. 2 factors that aid in RNA stabilization
    • hydrogen bonds other than between nitrogenous bases
    • binding of metal ions to allow for tighter binding of molecules through protection from phosphate backbone negative charge
  20. Gregor Mendel findings
    organisms contain some heritable trait that can be passed from parent to progeny
  21. 3 findings of Walter Sutton
    • X theory of inheritance
    • connection between X and Mendel's particles of heredity
    • X exists in pairs (diploids)
  22. Thomas Hunt Morgan experiment and his findings
    studied fruit flies and proved scientific evidence for the X theory of inheritance
  23. the scientific community thought that the proteins associate with the X were heritable trait
  24. 2 Thomas Hunt Morgan findings
    • evidence for the X theory of inheritance
    • sex linked genes
  25. Fredrick Griffith findings
    an unknown molecule can be passed from one strain of bacteria to another
  26. Avery, Macleod, and McCarthy finding
    showed that DNA was the heritable trait from generation to generation
  27. what did Avery, Macleod, and McCarthy do and what did they find
    repeated Avery's experiment with Strep pneumonia and found that DNA was heritable trait from generation to generation
  28. Avery's experiment
    DNA from heat killed smooth strain and rough strain was mixed and injected into the mouse. The mouse dies.
  29. 4 symptoms of sickle cell anemia
    • organ damage due to lack of blood flow
    • anemia
    • pain, delayed growth, strokes, etc.
    • life span reduced by 30 years
  30. type of Hb and the amino acid and nucleotide sequence
    • A:
    • Pro-Glu-Glu
    • -CCT-GAG-GAG

    • B:
    • Pro-Val-Glu
    • -CCT-GTG-GAG
  31. sickle cell blood cells are stiff and angular in shape which causes them to become stuck in capillaries
  32. factors that can denature DNA strands (3)
    • temperature
    • salt concentraion
    • pH
  33. relatedness between different species can be determined by
    how they form hybrid duplexes
  34. hybrid duplexes- the more E required the separate a duplex, the closer two organisms are related.
  35. nucleic acid is transferred to nitrocellulose membrane by capillary action
  36. 3 radioactive isotopes typically used in molecular biology
    • 32P
    • 33P
    • 35S
  37. fluorescent probes not as sensitive as radioactive isotopes
  38. mediator proteins function
    • interacts with the transcription apparatus
    • also helps promote future transcripts
  39. 4 protein structures
    • 1
    • 2
    • 3
    • 4
  40. primary structure
    amino acid sequence
  41. secondary structure
    alpha helix
  42. tertiary helix
    folded peptide chain
  43. quaternary structure
    assembled subunits
  44. R groups of the AA sequence of a 1 structure allows for
    variation in protein structure and function
  45. 4 groups on an amino acid
    • hydrogen
    • amino group
    • carboxyl
    • R
  46. R groups dictate
    type of protein folding
  47. hydrophilic AA are located
    hydrophobic AA are located
    • exterior
    • interior
  48. bonds between amino acid
    peptide bonds
  49. peptides synthesize from
    N to C terminal
  50. peptides
    polypeptides
    polypeptide chain
    • 4-10
    • 10-100
    • +100
  51. 3 types of protein secondary structure and what are they due to
    • due to hydrogen bonding
    • alpha helix
    • beta sheet
    •  loop/turn
  52. a protein involved in DNA rep has all 3 forms of secondary structure
  53. interactions involved in the tertiary structure (3)
    • hydrophobic interactions
    • polar
    • ionic
  54. the interactions of the tertiary structure are mediated by
    the r-groups of the amino acid in the polypeptide
  55. tertiary structure
    polypeptide chain folded into a 3D orientation of all the diff secondary structures
  56. quaternary structure
    structure produced by the interaction of multiple polypep of a protein
  57. homodimer
    same subunits
  58. heterodimer
    different subunits
  59. not all proteins have a quaternary structure
    amount of subunits also depends on the protein
  60. human hemoglobin quaternary structure is
    heterotetramer
  61. interactions involved in tert and quat structure are
    disulfide bridges form between 2 cysteines to bind two protein subunits
  62. protein domains
    independent folding units within the protein
  63. proteins can have 1+ domains, the larger the pro the more domains
    are important because they have certain functions
  64. DNA binding protein function
    regulate how gene is expressed
  65. motifs are defined by
    a proteins supersecondary structure
  66. 3 protein domains that have specialized functions and can be found in proteins involved in DNA binding
    • helix turn helix
    • leucine zipper
    • zinc finger
  67. 3 factors effecting protein structure, resulting in altered protein function
    • chaperones
    • ligands and substrates
    • alternating protein function (results in conformation changes)
  68. what are prions
    plaques in the brain that form due to misfolded PrP protein that is protease resistant
  69. PrP
    PrPc
    • protein resistant protein
    • normal protein in brain
  70. PrPsc and function
    misfolded protein that form aggregates and creates plaques in brain
  71. reverse transcription
    RNA transcribing back into DNA
  72. how prions defy central dogma
    a misfolded protein can cause a normal folded protein to become misfolded and it is not reversible
  73. in bacteria transcription and translation are coupled
  74. template DNA strand is reverse complimentary
    coding strand is the complimentary of the RNA
  75. in the direction of transcription, the nucleotides are added to the 3' end
  76. holoenzyme
    apoprotein + sigma factor
  77. a typical bacterial promoter is recognized by the
    -10 and -35 consensus sequence
  78. Upstream promoter element is bound by the alpha subunit of RNA pol
  79. sigma 70
    house keeping genes`
  80. typical bacterial promoter between the -10 and -35 is only recognized by
    sigma 70
  81. sigma 38
    sigma 28
    sigma 32
    sigma 24
    sigma 54
    • starvation/stationary growth phase
    • flagellar structure and movement
    • heat shock
    • extracytoplasmic stress
    • N uptake and metabolism
  82. sigma 54 is the only sigma factor that requires ATP at an AAA+ protein to create an open complex
  83. in elongation, small aborted RNA transcripts are produced until the promoter is cleared
  84. 2 methods of termination of transcription in bac
    • RHO dependent
    • RHO independent
  85. how RHO independent works (4)
    • hairpin on 15-20 nt forms before transcription term
    • a series of UUU follows the hairpin
    • trans is stalled
    • RNA pol dissociates
  86. how RHO dependent works (4)
    • RHO helicase binds to the rut site
    • movement of RHO requires ATP
    • RHO moves in the 5'-3' direction towards RNA pol
    • RNA pol dissociate from DNA
  87. pol II core promoter key components (4)
    • TATA box
    • TBP
    • TFIID
    • TFIIB
  88. the formation of the pre-initiation complex is mediated by
    transcription factors
  89. transcription initiation steps (5)
    • TFIID and TBP bind to tata
    • TFIIB binds to TBP and DNA
    • TFIIA stabilizes complex (not always required)
    • TFIIF bind pol to other TF
    • TFIIE and TFIIH creates a closed DNA complex before being unwound and opened by TFIIH
  90. 2 functions of mediator complex
    • allows for interaction between upstream activators and enhancers and TF
    • increases the rate of assembly for the initiator complex
  91. elongation factors allow for the continuous generation of RNA
  92. modifications to mRNA regulate mRNA stability
  93. function of the 5' cap
    methylated guanosine base protects the 5' phos end of the mRNA from being recognized by exonucleus
  94. 3 characters of capping enzyme
    • occurs during transcription
    • only in mRNA
    • helps recruit capped mRNA to ribo
  95. why does capping only occur in mRNA
    due to association of capping enzyme to RNA pol II CTD
  96. 3 steps of poly a tail addition
    • Pol II transcribes poly A addition sites
    • polyA factors bind the polyA signal, initiating mRNA cleavage
    • PAP syn the polyA tail, PABP protects the tail from degradation
  97. polyA factors are associated with
    CTD
  98. Where the polyA tail added
    at cleaved 3'OH by polyA pol
  99. PABP is recruited to prevent degradation of the tail
  100. bonds types and chemical interactions in DNA (4)
    • hydrogen
    • van der waals
    • phosphodiester bonds
    • glycosidic bonds
  101. bond types and chemical interactions in RNA (4)
    • Hydrogen
    • phosphodiester
    • glycosidic bond
    • van der waals
  102. bond types and chemical interactions in peptide
    amide bond
  103. bond types and chemical interactions in primary protein
    peptide bonds (amino acids)
  104. bond types and chemical interactions in secondary protein
    hydrogen bonds
  105. bond types and chemical interactions in tertiary protein (3)
    • hydrogen bonds
    • disulfide bonds
    • r-group interactions
  106. bond types and chemical interactions in quaternary bonds (2)
    • hydrophobic
    • hydrophilic interactions
  107. Chargaff's rules 4
    • base composition of DNA varies
    • DNA of same species have same base comp
    • base comp of given species does not change
    • the sum of the # of purines = the sum of the # of pyrimidines
  108. the R groups of the protein allows for these 3
    • variation in protein structure
    • variation in protein function
    • dictates the type of protein folding
  109. protein domains
    are independent folding units within the protein
  110. *proteins can have more than 1 domain, the larger the protein, the more domains it has*
  111. A protein domain is a conserved part of a given protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain.
  112. Each domain forms a compact three-dimensional structure and often can be independently stable and folded.
  113. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions.
  114. Factors effecting protein structure, altering protein function
    • chaperones
    • ligands and substrates
    • prions
  115. What allows for the strength between the two strand of DNA
    the number of hydrogen bonds
  116. what allows for the strength in n RNA molecule with secondary structures
    motifs that are protein domains with special functions
  117. motifs are defined  by
    proteins supersecondary structure
  118. Motifs can be found in proteins involving
    DNA binding
  119. how do the factors affect protein structure which alter protein function
    when chaperones, ligands or substrates bind to the protein resulting in conformational changes cause the protein function to alter, sometimes to the point of nonfunctional
  120. effect on molecular biology
    DNA is a genetic material
  121. what are the differences in the structure of the tRNA, mRNA, and rRNA molecules
    The mRNA is the messenger RNA and has a secondary structure, tRNA is transfer RNA and has a tertiary structure, rRNA is secondary structure
  122. LacI
    LacZ
    LacY
    LacA
    • lac repressor
    • beta-galactosidase
    • galactoside permease
    • thiogalactoside transacetylase
  123. what 2 do you need to get a positive regulator
    cAMP receptor protein + cAMP
  124. increase in glucose = adenylate cyclase decrease in ATP and cAMP
  125. riboswitches
    are RNA elements that undergo a shift in structure in response to binding of a regulatory molecule
  126. Riboswitch RNAs control a broad range of genes in bacterial species, including                     those involved in metabolism or uptake of amino acids, cofactors, nucleotides, and metal ions
  127. riboswitches functions in bacterial control gene expression by
    binds a metabolite to the riboswitch causing the shine dalgarno sequence to segregate from gene expression, which prevents translation
  128. riboswitches in bacterial control gene expression
    translation on
    translation off
    • shine dalgarno sequence free when metabolite signal is absent
    • shine dalgarno sequence is unavailable when the metabolite signal is present
  129. activators function
    DNA binding proteins that increase gene transcription of a gene or a set of genes
  130. repressor
    DNA-binding protein that regulates the expression of one or more genes by binding to the operator and blocking the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes
  131. 3 differences between Pro and Euk ribosomes
    • 70s subunit for pro while euk has a 80s subunit
    • ribosomes are syn in cytoplasm in pro, euk ribosomes are syn in cytoplasm and nucleus
    • 8 kinds of proteins and 5 kinds of RNA in euk, pro 3 kinds of RNA and 50 kinds of proteins
  132. large subunit pro and euk
    small subunit pro and euk
    #s and function
    • 50s 30s
    • 60s 40s
    • su = genetic code is read
    • lu = where peptide chains are formed
  133. type of reaction occurring during polypeptide synthesis
    peptidyl transferase reaction
  134. function of northern blot
    study gene expression by the detection of RNA or isolated mRNA
  135. function of southern blots
    to detect a specific DNA sequence in DNA samples
  136. 5 steps in northern and southern blotting
    • get a nucleic acid sample and place it into the agarose gel
    • run agarose gel electrophoresis
    • transfer the results o the nitrocellulose membrane
    • then hybridize with nucleic acid probe
    • then an autoradiogram reveals which fragments separated into strands with the probe
  137. how can southern blots help to detect sickle cell anemia
    • restriction enzymes cut DNA at specific sequences "CCTnAGG"
    • separate the DNA fragments generated using gel electrophoresis
    • design a nucleic acid probe for the beta globin gene to detect the mutant and wild type beta globin gene
  138. 2 ways to create a nucleic acid probe
    • end labeled dATP*
    • incorporated into the sequence dATP* + dCTP*
  139. purpose of gel electrophoresis
    is to separation and analysize DNA, RNA and proteins and their fragments, based on their size and charge
  140. how gel electrophoresis is performed
    The DNA samples are loaded onto the gel and an electric current is applied to the gel. DNA is negatively charged because of all the phosphate groups in the backbone of the DNA. Therefore, DNA is attracted to the positive electrode. As the pieces of DNA move through the gel, they were feel resistance. Larger pieces of DNA will move at a slower rate than smaller fragments of DNA. This allows the separation of different sizes of DNA fragments. A DNA ladder is loaded into one of the wells as a scale to compare the different base pairs of the DNA.
  141. 3 cons for GMO
    • cell division is random so we are not always guaranteed to have a some rice with the beta carotene gene in the rice stalk
    • why don't we use a gene from the rice stalk since instead of using another gene from daffodil and a bacteria
    • commercialization, even though its made affordable now, that when later on when its in higher demand they can charge more
  142. 3 pros for GMO
    • Vitamin A is involved in avariety of functions throughout the body such as vision, immune function,embryonic development and reproduction, bone metabolism, etc. With the lack ofvitamin A for adults and children over the age of being breast fed, these functions are being altered for the worst.
    • People are ignorant aboutbiotechnology. A poll was taken and 25% of people believed your genes could bealtered when you consume a GM fruit. While 59% of others thought tomatoes hadcontained no DNA.
    • According to a study takenin Bangladesh where adult women and children had eaten the new golden rice(GR2). Women are recommended to intake 500 micrograms per gram of vitamin Awhile children under 7 need 450 micrograms per gram. When the studies weretaken and adult women and children consumed GR, they actually exceeded theamount they needed to intake daily by 200% for women and 112% for children

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