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2010-10-26 15:24:44

test 2 review
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  1. chemotrophs
    chemical substanes as source of energy
  2. phototrophs
    light as a source of energy
  3. autotrophs
    CO2 as a source of carbon
  4. heterotrophs
    organic compounds as source of carbon
  5. organotrophs
    organic compounds as soruce of electrons
  6. lithotrophs
    inorganic compounds as source of electrons
  7. nitrogen cycle
    bacteria play critical role, such as nitrogen fixation
  8. nitrogen fixation
    conversion of N2 from the air into NH3
  9. ATP
    storage molecule for chemical enegry in all cells
  10. catabolism
  11. anabolism
  12. what produces the energy needed for anabolism?
  13. reversible reaction
    ATP is hydrolyzed to ADP + Pi + energy
  14. ATP hydrolysis
    where endergonic reactions that would not occur in living cells can be effectively promoted by coupling them into ATP hydrolysis
  15. oxidation
    loss of electrons
  16. reduction
    gain of electrons
  17. redox
    oxidation-reduction / electrons are transferred from one substace that becomes oxidized to another substance that becomes reduced.
  18. what happens in a redox reaction?
    two electrons and two hydrogen ions are transferred simultaneously
  19. electron transport chains
    proteins that are imbedded in membranes that transfer electrons and hydrogen ions in such a way that a pH gradient is generated accross the membrane
  20. chemiosmosis
    proton motive force - it drives the synthesis of ATP catalyzed by the enzyme ATP synthase when hydrogen ions pass through the enzyme.
  21. enzyme
    biological catalysts; most are proteins but some are catalytic RNAs (ribozymes)
  22. active site
    enzyme's site where the substrate binds
  23. competitive inhibitors
    compounds that compete for the binding of substrate to the enzyme
  24. allostetric site
    (distinct from the active site) where a noncompetitive inhibitor (or activator) can bind thereby affecting the activity of the enzyme
  25. feedback inhibition
    the final product of the pathway acts as a noncompetitive inhibitor of the first enzyme in the pathway.
  26. example of feedback inhibition
    some anabolic pathways (byosynthetic)
  27. what do enzymes do?
    lower activation energy needed for catalysis
  28. the activity of an enzyme is influenced by...
    pH, temperature, and the concentration of substrate
  29. what is glycolysis?
    the cleavage of glucose into two 3-carbon compounds
  30. what does the kreb's (TCA) cycle do?
    it converts acetyl-CoA into 2 CO2
  31. what does substrate level phosphorylation result in glycolysis?
    2ATP / glucose
  32. what does substrate level phosphorylation result in the Kreb's cycle?
    2GTP = 2 ATP
  33. what does oxidative phosphorylation convert by chemiosmosis?
    it converts NADH and FADH2 into ATP
  34. aerobic respiration's maximum possible energy yield for one molecule of glucose is
    38 ATP/ glucose; actual yield = 30-32 ATP/ glucose
  35. respiration
    serios of redox reactions in which an inorganic substance is the final electron acceptor. example: oxygen is this substance in aerobic respiration
  36. fermentation
    series of redox reactions in which an organic substance is the final electron acceptor. example: a small organic acid or alcohol.
  37. fermentative microbes commercially important are...
    bakers' and bewers' yeast (S. cerevisiae)
  38. fermentation's ATP yield:
  39. what can be catabolized to yield energy (ATP)
    lipids and proteins
  40. why is metabolism extensively integrated?
    so that the same or similar pathways can be used for production of energy or production of carbon chains for biosynthesis
  41. photosynthesis
    carbon fixation (CO2 added to carbohydrate) powered by ATP produced form the absorption of light by chlorophylls organized into photosystems.
  42. photosystem 1
    cyclic electron flow and does not produce oxygen
  43. photosystem 2
    noncyclic electron flow and produces oxygen
  44. where do photosystems occur?
    in chloroplasts in eukaryotes and in the plasma membranes of prokaryotes
  45. what happens in the anabolism of macromolecules?
    monomers are polymerized into polymers. for example: amino acids into proteins. nucleotides into nucleic acids. monosaccharides into polysaccharides.
  46. DNA
    genetic material in all cells and many viruses
  47. who provided evidence that DNA is the genetic material?
    Griffith's transformation experiment
  48. where does vertical transmission DNA occur?
    cell division
  49. where does horizontal transmission of DNA occur?
    within a generation
  50. why is DNA a duplex molecule?
    it is a molecule consisting of two strands - polymers of nucleotides attached by phophodiested bonds. each strand has 5' to 3' polarity
  51. duplex DNA
    it is antiparallel wit respect to the polarity of the two strands
  52. DNA structure
    4 bases (ACGT); form base pairs (AT and GC); two strands are complementary with respect to base pairing
  53. what doest he major groove of the double helix of duplex DNA do?
    it is where sequence-specific DNA binding proteins bind
  54. DNA replication
    separation of the two strands of parental DNA and copying as templates resulting in the synthesis of two new strands of daugter DNA
  55. what is the main enzyme in DNA replication?
    DNA polymerase; other important enzymes: primase and DNA ligase
  56. where do most of the ATP used by cells go?
    in the synthesis of proteins
  57. lagging strand of DNA
    DNA synthesis is discontinuous
  58. leading strand of DNA
    DNA synthesis is continuous
  59. circular DNA
    it has only one origin of DNA replication
  60. large linear chromosomal DNA
    many origins of DNA replications
  61. nucleid acid synthesis
    (both DNA and RNA) proceed in the 5' to 3' direction
  62. telomeres
    repeated DNAs on both ends of eukaryotic chromosomes
  63. how are telomeres generated?
    by the action of telomerase (enzyme that copies RNA in making DNA)
  64. transcription
    synthesis of RNA complementary to the template strand of DNA in the gene
  65. RNA polymerase
    enzyme that catalyzes the polymerization of ribonucleotides into RNA
  66. where does the RNA polymerase bind to?
    a sequence of DNA called the promoter
  67. who has a RNA polymerases?
    E.Coli has one that syntesizes mRNA, rRNA and tRNA; eukaryotes have separate RNA polymerases for each of them
  68. what happens to bacteria related genes?
    they are clustered together and transcribed into plycistronic mRNAs that are translated into several proteins
  69. what happens in eukaryote's genes?
    they are transcirbed individually into monocistronic RNAs that are translated into one protein
  70. exons
    eukaryotic genes coding sequences
  71. introns
    eukaryotic genes noncoding sequences that separate exons
  72. what is the first product of transcription in eukaryotes?
    heterogeneous nuclar RNA (jmRNA) - must be spliced (by sliceosomes) to remove introns
  73. sliceosomes
    complex of small nuclear RNAs and proteins; they perform splicing
  74. what is the triplet code that is universal in biology?
    genetic code
  75. protein product of the gene
    3 nucleotides in mRNA encode one amino acid i nthe protein product of the gene
  76. how many common amino acids are in proteins?
  77. how many codons are in proteins?
  78. why is the genetic code said to be degenerated?
    more than one codon per amino acid
  79. what is the start codon?
  80. what are the stop codons?
  81. what does tranfer RNAs have?
    an anticodon that matches the sequence in the codon.
  82. how are amino acids attached to tRNAs?
    by aminoacyl-tRNA synthetases (requires ATP)
  83. what is the peptidyl transferase activity in protein synthesis in bacteria?
    23S rRNA
  84. what is the peptidyl transferase activity in protein synthesis in eukaryotes?
    28S rRNA
  85. catalytic RNAs
    they catalyze the formation of peptide bonds between amino acids
  86. where does protein synthesis occur on the ribosome in bacteria?
    70S bacteria
  87. wher does protein synthesis occur on the ribosome in eukaryotes?
    80S eukaryotes
  88. what is requried for protein synthesis?
    protein initiation factors (IFs), elongation factors (EFs) and GTP
  89. what do protein release factors (RFs) bind to?
    stop codons and mediate termination of protein synthesis
  90. chaperones
    specific proteins that some proteins require to fold. (protein folding may occur spontaneously)
  91. how is gene expressino regulated?
    at the level of transcription by proteins biding to specific sequences of DNA
  92. where does regulation occur?
    at the level of translation, especially in eukaryotes. mRNA splicing can also be regulated
  93. constitutive genes
    always expressed
  94. inducible genes
    function in catabolism; not expressed but can be turned on
  95. repressible genes
    function in anabolism; expressed but can be turned off
  96. how is the lac operon regulated?
    by a repressor that binds to an operator. (like the trp operon)
  97. what happens when the repressor is bound?
    transcription is blocked
  98. how does transcription occur?
    when lactose (inducer) is present and binds to the repressor and causes it to change shape so that it can't bind to DNA
  99. how is the trp operon regulated?
    by a repressor that binds to an operator. (like the lac operon)
  100. what happens when tryptophan (corepressor) is present?
    it binds to the repressor and activates itso that it bind to the operator sequence of DNA
  101. negative regulation
    inhibition of transcription
  102. positive regulation
    stimulation of transcription
  103. what type of regulation does the lac operon exhibit?
    both: negative by the repressor and positive by the CAP- cAMP
  104. what happens when glucose levels are low?
    adenlyl cyclase converts ATP into cyclic AMP (cAMP) + PPi. then, cAMPbiind to the catabolite activator protein (CAP) to form a functional complex that binds to DNA and stimulates the binding of RNA polymerase to its promoter
  105. what eliminates the mRNAs from being translated into proteins?
    small nuclar RNAs (siRNAs) bind to m RNAs and cause them to be degraded by a nuclease (dicer)
  106. how can novel sequences be yied?
    DNA sequence recombination
  107. mutation
    change in the sequence of nucleotides in DNA.
  108. why are mutations caused?
    by chemicals (mutagens) or electromagnetic radiation (UV or x-rays)
  109. point mutations
    changes in one base pair in the DNA
  110. missense mutations
    change a codon into a codon for another amino acid
  111. nonsense mutations
    change a codon for an amino acid into a stop codon
  112. silent muations
    chagne a codon for an amino acid into another codon for the same amino acid
  113. when do thymine-thymine dimers occur?
    when DNA absorbs UV light?
  114. what enzymes correct damage to DNA?
    repair enzymes: excision repair and mismatch repair
  115. who does an excision repair serve?
    any DNA sequence
  116. who does mismatch repair serve?
    newly replicated DNA only
  117. how do repair enzymes work?
    they remove damaged DNA segments, polymerization of nucleotides to fill in the gap, and DNA ligation
  118. carcinogens
    chemicals that cause cancer; mutagens in the Ames test that measures the frequency of reversion of a his- mutation to the wild type, his+.
  119. auxotroph
    nutritional mutant
  120. where does homologous recombination occur?
    between related DNA sequeces
  121. where does site-specific recombination occur?
    at specific sites
  122. plasmids
    small circular DNAs with their own origin of DNA replication. they replicate independently of baterial chromosomal DNA
  123. F factor
    plasmid that is requried for conjugation; the F factor itself is transferred; it can integrate into the bacterial chromosomal resulting in a Hfr (high frequency of recombination) cell.
  124. what kind of F factor is donor E. Coli?
  125. what kind of F factor is recipient E. Coli?
  126. what can an Hfr corss with?
    an F- cell; chromosomal genes are transferred
  127. transposon
    mobile sequence of DNA; they harbor genes for drug resistance
  128. transformation
    uptake and integration of DNA. (occurs in high frequencies in bacteria)
  129. transduction
    uptake and incorporation of DNA mediated by a virus
  130. generalized transduction
    encapsidation of a piece of bacterial DNA into a virus particle
  131. recombinant DNA
    DNA from two sources that is spliced together
  132. restriction enzymes
    cut DNA at specific sequences (palindromes); many have been isolated from different microbes.
  133. vector
    sequence of DNA that can be used for the formation of recombinant DNA
  134. cloning vector
    production of DNA inserts
  135. expression vectors
    prodcution of the proein product of that gene
  136. complimentary DNA (cDNA) produced from mRNA by reverse transcriptase
  137. selectable marker
    gene for resistance to an antibiotic; used to ensure that transformed bacteria contain the recombiant DNA desired
  138. libraries
    series of cloned DNAs (genomic, cDNA)
  139. DNA fragments
    separated by size by agarose gel electrophoresis
  140. The Southern blot
    comibnes the separation of DNA by size with the detection of specific DNA sequences by hybridization (allowing mixed duplexes to form between a test DNA or probe and the DNA being studied)
  141. polymerase chain reaction (PCR)
    way to aplify DNA
  142. how does polymerase chain reaction works?
    it uses oligonucleotide primers and Taq DNA polymerase (thermostable) in a thermocycler to produce many copies of DNA in a test tube
  143. DNA sequencing by Sanger method
    it uses dideoxynucleotides as chain terminators
  144. how are results analyzed in the Sanger method?
    by polycrylamide gel electrophoresis
  145. GenBank
    public database where tens of billions of nucleotides of DNA sequences are available
  146. genome
    consist of all genes in an organism
  147. microarrays
    many genes can be analyzed simultaneously
  148. what represents all proteins in an organism?
    the proteome
  149. how can proteome be analyzed?
    by a two-dimensional gel electrophoresis