bio 1 test 4

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bio 1 test 4
2012-04-29 22:10:22

ch 16, 17.1, 17.5, 18.1, 11, 20, 38.3
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  1. creaters of the double helix model
    Watson and Crick
  2. the two chemical components of chromosomes
    DNA and protein
  3. transformation
    a change in phenotype and genotype due to the assimilation of external DNA by a cell
  4. Hershey and Chase's experiment
    radioactive DNA vs. protein proved that viruses infect cells with DNA, and nucleic acids are the carriers of genetic material
  5. DNA consists of three componenets
    a nitrogenous base (the steps of the ladder), a pentose sugar (deoxyribose) and a phosphate group (backbone of the ladder)
  6. 4 bases of DNA
    adenine (A), Thymine (T), Guanine (G), Cytosine (C)
  7. Chargaff's rules (2)
    • 1. the base composition (of DNA) varies between species
    • 2. within species, the number of A and T bases are equal and the number of C and G bases are equal.
  8. how Watson and Crick found out that DNA was helical
    by looking at Rosalind Franklin's X-ray crystallography
  9. the two strands of DNA are held in their shape and together by
    hydrogen bonds between the nitrogenous bases
  10. antiparallel
    DNA runs in opposite directions-- 5'-3' and 3'-5'
  11. semiconservative model o DNA replication
    when a DNA model replicates, each of the daughter molecules will have one old strand, from the parental molecule, and one newly made strand. (Watson and Crick)
  12. conservative model of DNA replication
    that two parental strands replicate and then come back together, forming entirely new DNA for the daughter molecule and conserving the parent molecule.
  13. dispersive model of DNA replication
    all four strands of DNA following replication have a mixture of old and new DNA. (pieces and chunks)
  14. Meselson and Stahl
    figured out that the semiconservative model of DNA was the right one in a classic example of elegant experiment design
  15. origin of replication
    the "replication bubble" where DNA replication begins (one in bacteria, many in eukaryotes)
  16. replication fork
    at the end of each replication bubble--a y-shaped region where the parental strands of DNA are being unwound
  17. helicases
    enzymes that untwist the double helix at the replication forks
  18. topoisomerase
    breaks, swivels and rejoins the parental DNA ahead of the replication fork, relieving stress of unwinding
  19. primase
    synthesizes RNA primers (temporary), using the parental DNA as a template
  20. single-strand binding proteins
    stabilize the unwound parental strands
  21. DNA polymerase III
    adds a DNA nucleotide to the RNA primer and then continues adding DNA nucleotides, building the new strand
  22. DNA polymerases can only add nucleotides to the ________ end of a primer or growing DNA strand
    3' (leading strand), so a new DNA strand can elongate only in the 5'-->3' direction. .
  23. leading strand
    the DNA strand made by DNA polymerase III in the 5'-->3' direction (smooth, simpler, one piece)
  24. lagging strand
    where DNA must work along the template strand away from the replication fork, making the strand in little fragments (Okazaki fragments)
  25. little fragments of lagging strand
    Okazaki fragments
  26. okazaki fragments
    short pieces of DNA replicated on the lagging strand
  27. DNA polymerase I
    replaces temporary RNA primer fragments with DNA so the ligase can connect Okazaki fragments
  28. DNA ligase
    the connection between lagging strand Okazaki fragments
  29. mismatch repair
    enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors
  30. nuclease
    a DNA-cutting enzyme used in DNA repair--removes the damaged segment
  31. nucleotide excision repair
    teams of enzymes find damaged DNA, nucleases cut it out, polymerases fill the gap with nucleotides and ligases seal the ends to the rest of the DNA
  32. mutations
    permanent change in the DNA sequence. Can change the phenotype of the individual and, if occur in the gametes, can be passed on to the next generation. They are the basis of evolution
  33. problem with DNA replication
    the very end of the 5' end of the molecule cannot be completed, leading to shorter and shorter DNA molecules with ragged, uneven or staggered ends
  34. telomers
    ends of DNA moleules--do not contain gene, just repetitions of one short nucleotide sequence (TTAGGG) (buffer). Lengthened by telomerase
  35. telomerase
    an enzyme that catalyzes the lengthening of telomers, compensating for the shortening of DNA replication. Mostly active in zygotes.
  36. nucleoid
    the dense region of DNA in a bacterium
  37. Histones
    proteins responsible for the first level of DNA packing in chromatin (H1, H2A, H2B, H3 and H4)
  38. nucleosomes
    "beads on a string". Consists of DNA wound twice around a protein core composed of 2 each H2A, H2B, H3 and H4. Tails extend out like jacks.
  39. H1 histone
    involved in interactions between histone tails, linker DNA and other neucleosomes--packs nucleosomes into a thick cord
  40. looped domains
    the loops formed when the huge cord made by H1 interactions attaches to a chromosome scaffold made of proteins
  41. metaphase chromosomes
    the last stage of chromatin packing, compressed from looped domains to produce the characteristic metaphase chromosome.
  42. gene expression
    the process by which DNA directs the synthesis of proteins
  43. two stages of gene expression
    transcription and translation. Occur in all organisms.
  44. Beadle and Tatum
    bread mold, Neurospora crassa. Identified mutants that could not survive on minimal media and found the amino acids they needed. One-gene-one-enzyme hypothesis
  45. one gene-one enzyme hypothesis
    the function of a gene is to dictate the production of a specific enzyme. Eventually became one gene-one polypeptide hypothesis
  46. differences between RNA and DNA
    RNA contains ribose sugar instead of deoxyribose and has the nitrogenous base uracil rather than thymine. RNA is usually a single strand.
  47. transcription
    the synthesis of RNA using information in the DNA. mRNA makes a copy of the DNA material.
  48. mRNA
    messenger RNA, which carries a genetic message from the DNA to the protein-synthesizing machinery of the cell.
  49. Translation
    synthesis of a polypeptide using the mRNA message transcribed from the DNA.
  50. sites of DNA translation
  51. primary transcript
    the initial RNA transcript from any gene
  52. central dogma
    • DNA--->RNA--->Protein
    • genes program protein synthesis via genetic messages in the form of mRNA.
  53. codon
    triplet of nucleotides that codes for an amino acid. usually written in the 5'-3' direction
  54. triplet code
    the genetic instructions for a polyeptide chain are written in the DNA as a series of nonoverlapping, three-nucleotide words. All organisms use the same code, indicating that we were all related once. It also means that different organisms can read the DNA of other organisms, so tobacco plant grows with firefly gene and jellyfish-pig glows.
  55. template strand
    the DNA strand that is transcripbed for each gene--it provides the pattern for the sequence of nucleotides in and RNA transcript
  56. mutations
    changes to the genetic information of a cell (or virus), responsible for the huge diversity of genes found among organisms, becaues mutations are the ultimate source of new genes
  57. point mutations
    changes in a single nucleotide pair of a gene
  58. large-scale mutations
    changes that affect long segments of DNA, such as chromosomal rearrangements
  59. small-scale mutations
    changes of a few nucleotide pairs (or one)
  60. genetic disorder or hereditary disease
    a mutation that has an adverse effect on the phenotype
  61. nucleotide pair substitution
    replacement of one nucleotide and its partner with another pair of nucleotides (sometimes does nothing, due to redundancy of genetic code--silent mutation)
  62. silent mutation
    a change with no observable effect on the phenotype (can occur outside genes as well)
  63. missense mutations
    substitutions that change one amino acid to another. May have little effect on the protein. Changes that still make sense, just not the right sense
  64. nonsense mutation
    a change that turns an amino acid codon into a stop codon--causes translation to be terminated prematurely--usually leads to nonfunctional proteins
  65. Insertions
    additions of nucleotide pairs in a gene. Can have a disastrous effect on the resulting protein, altering the entire sequence (since it's in threes, an add changes ALL the threes). Causes a frameshift mutation
  66. deletion
    removal of nucleotide pairs in a gene. Can have a disastrous effect on the resulting protein, altering the entire sequence (since it's in threes, an add changes ALL the threes). Causes a frameshift mutation
  67. frameshift mutation
    changes the reading frame of the genetic message--the triplet grouping of nucleotides. It will occur every time there is an insertion or deletion not in a multiple of three. Everything below the mutation will be read differently, resulting in extensive missense, nonsense and premature termination. Protein is almost certain to be nonfunctional
  68. spontaneous mutations
    when an incorrect nucleotide is added to a growing chain during replication and the error is not corrected, but is passed down as a template for the next round.
  69. mutagens
    chemical and physical agents that interact with DNA in ways that cause mutations. Include nucleotide analogs (similar to normal DNA but pair incorrectly in replication), agents that interfere with correct replication by inserting themselves and distorting the double helix, or causing chemical changes in bases that change their pairing properties
  70. nucleotide analogs
    chemical mutagen--chemicals that are similar to normal DNA nucleotides but pair incorrectly during DNA replication
  71. regulation of enzyme production
    the end product turns genes off or on, much like negative feedback inhibition.
  72. promoter
    a site where RNA polymerase can bind to DNA and begin transcription
  73. coordinately controlled
    genes that are grouped together by function onto one transcription unit and therefore have a single "on-off" switch.
  74. operator
    the DNA segment that is the on-off switch. Positioned within the promoter or sandwiched between it and the enzyme-producing genes. Controls the access of RNA polymerase to the gens.
  75. operon
    the operator, the promoter and the genes they control--the entire stretch of DNA required for enzyme production for the pathway.
  76. repressor
    protein that switches off the operon. it binds to the operator and blocks attachment of RNA polymerase to the promotor, preventing the transcription of the genes. It is specific to the operator of a particular operon
  77. regulatory gene
    produces the repressor. It is located a ways away and has its own promoter. expressed continuiously at a low rate.
  78. corepressor
    a small molecule that cooperates with a repressor protein to switch an operon off
  79. repressible operon
    an operon that's transcription is usually on but can be inhibited when a specific small molecule binds allosterically to a regulatory protein
  80. inducible operon
    usually off but can be stimulated (induced) when a specific small molecule interacts with a regulatory protein (lac operon)
  81. beta-galactosidase
    the enzyme that splits lactose into glucose and galactose. Part of the lac operon
  82. lacI
    regulatory gene for lac operon. Outside the operon, codes for an allosteric repressor protein that can switch off the operon by binding to the operator
  83. inducer
    specific small molecule that inactivates the repressor (allolactose)
  84. inducible enzymes
    enzymes whose synthesis is induced by a chemical signal (the enzymes of the lactose pathway are induced by allactose) (usually catabolic)
  85. repressible enzymes
    enzymes that are stopped or repressed by a chemical signal (tryptophan) (usually anabolic)
  86. cyclic AMP (cAMP)
    a small organic molecule that ainteract with an allosteric regulatory protein. Accumulates when glucose is scarce in lac-operon. Also is the second messenger between epinephrine and glycogen breakdown.
  87. activator
    a protein that binds to DNA and stimulates transcription of a gene. A regulatory protein in positive gene regulation
  88. lac-operon
    under both positive and negative control: negative by the lac repressor (determines whether lactose is used at all) and positive by CAP (controls the rate of lac transcription). Both an on-off switch and a volume control.
  89. signal transduction pathway
    the steps required to turn a recieved signal into a specific cellular response
  90. local regulators
    signals that influence cells only in the vicinity (growth factor)
  91. growth factor
    a local regulator that stimulates nearby target cells to grow and divide
  92. the three stages of recieving cellular conversation
    • Reception (detection of a signaling molecule from outside)
    • Transduction (converts the signal to a form that can bring about cellular response)
    • Response (the transduced signal triggers a response)
  93. signal reception
    only certain target cells detect and react to a particular molecule. A receptor protein allows it to "hear" the molecule--attach to a particularly shaped part, like a ligand. Often it changes shape, which activates the pathway.
  94. adenylyl cyclase
    converts ATP to cAMP in response to epinephrine, ont he way to glycogen breakdown when stimulated by a receptor protein
  95. Ephinephrine pathway
    binds to a G protein-coupled receptor, which activates a G protein (GTP) which activates Adenylyl cyclase which turns ATP into cAMP which turns into protein kinase A which provides a cellular response
  96. protein kinase A
    usually activated by cAMP. phosporylates various other proteins, depending on the cell. Leads to cellular responses
  97. Ca2+
    a very widely used 2nd messenger (more than cAMP). Usually concentration is very low in cytosol (pumped out) and higher in ER. A small change in # of ions can make a huge difference in percentage. Released from ER by inositol triphosphate (IP3) and diacylglycerol (DAG)
  98. signal transduction of epinephrine (numerary response)
    1 receptor=1000 G-protein molecules. Eventually 108 molecules of glucose 1-phosphate make for a huge rush of energy from one ephinephrine molecule
  99. scaffolding proteins
    large relay proteins to which several other relay proteins are simultaneously attached
  100. phosphodiestrerase
    enzyme that converts cAMP to AMP
  101. GTPase
    enzyme that hydrolyzes bound GTP--happens in G protein
  102. apoptosis
    controlled cell suicide, programmed cell death.
  103. G-proteins and tyrosine kinases similarities
    Both G protein-coupled receptors and receptor tyrosine kinases are transmembrane receptors that have a binding domain located on the extracellular side of the plasma membrane. The binding of a signaling molecule to these receptors is the first step in a signaling pathway. However, what happens after a signaling molecule binds is different for each receptor.
  104. G-proteins
    An activated G protein-coupled receptor activates a G protein inside the cell, which involves the release of GDP and the binding of GTP. The activated G protein then activates an associated enzyme, leading to a cellular response.Many signal molecules, such as neurotransmitters and many hormones, act through G-protein-linked receptors. This kind of receptor spans the cell membrane, and as you might guess, it works through a protein called a G protein. When the signal molecule binds to the receptor, the receptor becomes activated. It is now able to activate a specific G protein by causing GTP to displace GDP on the G protein. The activated G protein then binds to another protein, usually an enzyme, and alters its activity. Then the G proteinhydrolyzes its GTP and reverts to its inactive form— ready to respond to another signal.
  105. Tyrosine Kinases
    Receptor tyrosine kinases form dimers after binding signaling molecules. The tyrosines are then phosphorylated, fully activating the receptor. Each phosphorylated tyrosine can bind a relay protein, each of which can trigger a transduction pathway. In this way, a single signaling-molecule binding event can trigger multiple signal transduction pathways and thus multiple cellular responses. Binding of signal molecules causes two polypeptides to join, activating parts of each that act as tyrosine-kinase enzymes, which then phosphorylate tyrosines in the tail of the other polypeptide.The receptor protein is now recognized by specific relay proteins inside the cell. One receptor tyrosine kinase may activate several relay proteins at once, triggering several different effects within the cell.
  106. ligand-gated ion channels
    They are protein pores in the plasma membrane that allow or block the passage of certain ions through the membrane. For example, this occurs when one neuron signals another via a neurotransmitter. The signal molecule attaches to a site on the ion channel protein. This changes the shape of the protein, opening a channel through the membrane. Ions flow through the channel, and the change in ion concentration triggers a cellular response.
  107. intracellular receptors
    Some signal molecules actually enter target cells and act on intracellular receptors— proteins located inside the target cell. Steroid hormones like testosterone and estrogen act on intracellular receptors. Nonpolar molecules like steroids and thyroid hormones are able to pass through the plasma membrane and bind to a receptor protein in the cytoplasm or nucleus of a target cell. The activated receptor triggers a change in the cell. Steroids cause receptors to turn genes on and off
  108. transcription factor
    By binding to DNA it triggers the transcription of a specific gene
  109. recombinant DNA
    DNA molecules formed when segments of DNA from two different sources (even different species) are combined in vitro (test tube).
  110. biotechnology
    the manipulation of organisms or their components to make useful products (selective breeding, microorganisms to make wine and cheese, and genetic engineering)
  111. genetic engineering
    the direct manipulation of genes for practical purposes
  112. plasmids
    small circular DNA molecules that reproduce separately from the bacterial chromosome--has only a small number of genes that may be useful in a particular environment but may not be required for survival or reproduction usually
  113. recombinant bacterium
    a bacterial cell that has had an altered plasmid (recombinant DNA molecule) inserted into it.
  114. gene cloning
    the production of multiple copies of a single gene
  115. 2 purposes of gene cloning
    • to amplify or make many copies of a particular gene
    • to produce a protein product
  116. restriction enzymes or restriction endonucleases
    enzymes that cut DNA molecules at a limited number of specific locations. Protect bacterial cell by cutting up foreign DNA from other organisms or phages. Very specific at recognizing a particular short DNA sequence (restriction site) and cutting it
  117. restriction site
    a particular short DNA sequence recognized by a restriction enzyme. Most are symmetrical when read in a 5'-3' direction and are usually 4-8 nucleotides long
  118. restriction fragments
    the pieces between restriction sites--left intact when cuts are made by restriction enzymes
  119. sticky end
    the single-stranded end of the double-stranded fragments made by useful restriction enzymes. Can form hydrogen-bonded base-pairs with other, complimentary sticky ends. These bonds are made permanent by DNA ligase
  120. DNA ligase
    permanently attaches DNA, such as two "sticky ends" of restriction fragments left over from restriction enzymes or two Okazaki fragments
  121. cloning vector
    the original plasmid before any foreign DNA is added. A DNA molecule that can carry foreign DNA into a host cell and replicate there
  122. X-gal turns blue with
    uninterrupted lacZ--did not take up foreign DNA
  123. ampR is
    ampocillin resistance. Gene on bacterial plasmid used to weed out bacteria that did not take up a plasmid
  124. gel electrophoreisis
    used for separating nucleic acids or proteins that differ in size, electrical charge or other physical properties--use restriction enzymes to cut, so different results must come from different
  125. DNA is _________charged
    negatively, so it will move toward the positive electrode in electrophoresis
  126. short molecules move _________than long ones in electrophoresis
    faster/farther toward positive electrode, or anode
  127. proof that corn is man-made
    the kernels are permanently attached to the cob and can 't spread, and enclosed by the husk. Corn would die out if not for people. Also, original plant was Teosynthae
  128. Triticale
    a hybrid of rye and wheat that has the yield and quality of bread yeast and the cold, moisture and acidity tolerance of rye. It grows well in marginal soil.
  129. two definitions of plant biotechnology
    • innovations in the use of plants or substances derived from them to make products of use to humans
    • use of GM organisms in agriculture and industry
  130. Golden Rice
    a transgenic rice variety supplimented with two daffodil genes that enable it to produce grain containing beta-carotene (precurser to vitamin A)
  131. bt maize
    corn that is poisonous to insects but non-toxic to humans. has 90% less cancer-causing and birth-defect-causing fungal toxin (fumonisin)
  132. cassava
    a root-vegetable that is the staple for 800 million of the poorest people on the planet. Scientists have enriched protein, iron and beta-carotene and have nearly removed the cyanide content from the roots, while making them twice the size.
  133. biofuels
    fuel made by fermenting plants. Could supplant fossil fuels in the near future
  134. concerns of GMOs
    • human health: could transfer allergens into unexpected foods (scientists are removing allergen-causing genes from foods now)
    • effects on non-target organisms: (Monarch butterfly effect) (actually insecticides sprayed on normal maize are more dangerous to the butterflies)
    • transgene escape: crop-to-weed hybridization. "superweed" (looking into making all males sterile or putting gene into chloroplast DNA so it can't travel unexpectedly, self-pollination)