Anatomy and Function of a Gene: Dissection Through Mutation III

  1. Fine structure mapping
    • Fine structure mapping: recombination mapping of mutations in the same gene; in some bacteriophage experiments, fine structure mapping can resolve mutations in adjacent nucleotides
    • Monoploid: describing cells, nuclei, or organisms that have a single set of unpaired chromosomes. For diploid organisms, monoploid and haploid are synonymous
  2. Cistron
    a term sometimes used as a synonym for complementation group or gene
  3. Deletions are mutations that remove _______ nucleotide pairs along a DNA molecule. In crosses between bacteriophages carrying deletions of the corresponding region, no _____ ____ ________ progeny can arise, because neither ________ carries the proper info at the location of the ________
    • adjacent or contiguous 
    • wild type recombinant progeny
    • chromosome
    • mutation
  4. However, if the mutation lies outside the region deleted from the homologous chromosome, _____ _____ progeny can appear. This is true whether the mutation is a _____ mutation affecting one or a few nucleotides, or a large ______
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    • wild type
    • point 
    • deletion
  5. Crosses between any uncharacterized mutation and known deletions thus immediately reveal?
    Whether the mutation resides in the region deleted from the other phage chromosome, providing a rapid way to find the general location of a mutation
  6. Some sites within a gene spontaneously mutate more frequently than others and as a result are known as _____ ______
    • mutations hotspots
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  7. What does the existence of hotspots suggest?
    certain nucleotides can be altered more readily than others
  8. Treatment with ________ also turns up hotspots but because they have specificities for particular nucleotides, the highly mutable sites that turn up with various _______ are often at _______ positions in a gene than the hotspots resulting from _______ mutation
    • mutagens
    • mutagens
    • different positions
    • spontaneous
  9. Benzer's experiments imply, the molecular machinery responsible for mutation and recombination does not discriminate between those nucleotides that are _______ (within a gene) and those that are ______ (between genes)
    • intragenic 
    • intergenic
  10. The main distinction between DNA within and DNA outside a gene is that the array of nucleotides composing a gene has evolved a function that determines _________
  11. In the 1940s, George Beadle and Edward Tatum carried out a series of experiments on the bread mold Neurospora crassa that demonstrated a direct relationship between genes and the enzymes that catalyze specific biochemical reaction. Their strategy was simple: (2-story)
    pg 234 middle left
  12. auxotroph 
    • auxotroph: A nutritional mutant microorganism that requires supplementation with substances not needed by wild-type strains
    • prototroph: a cell that does not require the addition of a substance. It is a wild-type cell that can grow on minimal medium alone
  13. Isolation of arginine auxotrophs (4-story)
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    pg 234 bottom left to top right
  14. They next asked whether any of the mutant Neurospora strains could grow in minimal medium supplemented with any of three known intermediates (orinthine, citrulline, and arginosuccinate) in the biochemical pathway leading to ______, instead of with _______ itself
    • arginine
    • arginine
  15. This test would identify Neurospora mutants able to convert the ________ compound into _______. Beadle Tatum compiled a table describing which arginine auxotrophic mutants were able to grow on minimal medium supplemented with each of the ________
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    • intermediate
    • arginine 
    • intermediates
  16. On the basis of the results, Beadle and Tum proposed a model fo how Neurospora cells synthesize arginine. In the linear progression of biochemical reactions by which a cell constructs arginine from the constituents of minimal medium, each intermediate is both the _____ of one step and the ______ for the next
    • product
    • substrate
    • (green pic)
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  17. Each reaction in the precisely ordered sequence is catalyzed by a specific ______, and the presence of each _______ depends on one of the four ______ genes.
    • enzyme 
    • enzyme
    • ARG
  18. A mutation in one gene blocks the pathway at a particular step because the cell lacks the corresponding enzyme and thus cannot make ______ on its own.
  19. How does supplementing the medium with any intermediate that occurs beyond the blocked reaction restore growth?
    because the organism has all the enzymes required to convert the intermediate to arginine
  20. Why doesn't supplementation with an intermediate that occurs before the missing enzyme work
    because the cell is unable to convert the intermediate into arginine
  21. Each mutation ______ the cell's ability to make an enzyme capable of catalyzing a certain reaction. By inference, then, each gene controls the synthesis or activity of an enzyme, or as stated by Beadle and Tatum:
    • abolishes
    • One gene, one enzyme: broadly true but not broad enough. Many proteins aren’t enzymes. Some proteins are multimeric to be active.
  22. All of the amino acids have certain basic features, encapsulated in what form?
  23. The -COOH of amino acids aka the ______ ______ is, as the name implies, acidic; the -NH2 component, aka the ______ group is ______. The R refers to _____ ______ that distinguish each of the amino acids
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    • carboxylic acid
    • amino group
    • basic
    • side chains
  24. An R group can be as simple as a hydrogen atom (in the amino acid ______) or as complex as a benzene ring as in __________. Some side chains are relatively ________ and nonreactive, others are ______, and still others are ______
    • glycine
    • phenylalanine
    • neutral 
    • acidic
    • basic
  25. The chemical properties that enable structural proteins to give a cell its shape, or enzymes to catalyze specific reactions, are a direct consequence of the ______, ______, and _______ order of amino acids in the protein
    identity, number, and linear
  26. Sickle cell anemia (5-story)
    pg 236
  27. The glutamic acid-to-valine change affects the _______ of hemoglobin within the red blood cell. At low concentrations of oxygen, the ______ _______ sickle cell form of hemoglobin aggregates into _____ chains that deform the red blood cell
    • solubility
    • less soluble
    • long chain
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  28. Despite the uniform nature of protein construction a string of amino acids joined by ______ bonds (each _______ folds into a unique three-dimensional shape)
    • peptide bonds
    • polypeptide
  29. Biochemists often distinguish between four levels of protein structure: ______, ______, _____ and _______. The first three of these apply to any one ________ ______, while the quaternary level describes _______ ______ within a protein complex
    • primary, secondary, tertiary and quaternary
    • polypeptide chain
    • multiple polypeptide
  30. Primary structure
    The linear sequence of amino acids within a polypeptide
  31. Each unique primary structure places constraints on how a chain can arrange itself in _____ ______ space. Because the R group distinguishing the 22 amino acids have dissimilar ______ _______, some amino acids form _______ bonds or ________ bonds when brought into proximity with other amino acids
    • three dimensional
    • chemical properties 
    • hydrogen bonds or electrostatic bonds
  32. Nonpolar amino acids, for example, may become associated with each other by interactions that ______ them from water in localized hydrophobic regions. As another example, two cysteine amino acids can form _______ ______ bridges (-S-S-) through the _______ of their -SH groups
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    • hide
    • covalent disulfide bridges
    • oxidation
  33. The primary structure determines three dimensional shape by generating ________ ________
    secondary structure
  34. secondary structure
    Image Upload 9
    localized region of a polypeptide chain with a characteristic geometry, such as an α-helix or β-pleated sheet
  35. ________ structure is responsible for other folds and twists that together with ________ structure produce the ultimate three-dimensional ______ ______ of the entire polypeptide
    Image Upload 10
    • Primary 
    • Secondary
    • tertiary structure
  36. Tertiary structure
    Native configuration
    • Tertiary structure: the ultimate 3D shape of a polypeptide
    • Native configuration: the way a long chain of amino acids naturally folds in three-dimensional space under physiological conditions
  37. Types of interactions that help stabilize native configuration
    • hydrogen bonds
    • electrostatic bonds
    • hydrophobic interactions
    • disulfide bridges 
    • etc
  38. It is worth repeating that primary structure (amino acid sequence) directly determines _______ and _______ structure. The info required for the chain to fold into its native config is inherent in its ____ ______ of amino acids
    • secondary and tertiary
    • linear sequence
  39. In one example of this principle, many proteins unfold, or become _______, when exposed to urea and mercaptoethanol or to increasing heat or pH. These treatments disrupt the interactions that normally stabilize the ________ and _______ structures
    • denatured
    • secondary and tertiary
  40. When conditions return to normal, many proteins spontaneously refold into their _______ _______ without help from other agents. No other info beyond the _______ ______ is needed to achieve the proper three-dimensional shape of such proteins
    • native configuration 
    • primary structure
  41. Certain proteins, such as ______ that promotes black-and-white vision, consist of a ________ polypeptide. Many other, however, such as the lens crystallin protein, which provides rigidity and transparency to the lenses of our eyes, or the hemoglobin molecule described earlier, are composed of ____ or ______ polypeptide chains that associate in a specific way
    • rhodopsin 
    • single
    • two or more
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  42. The individual polypeptides in an aggregate are known as _______, and the complex of subunits is often referred to as a ______. 
    Define Quaternary structure
    • subunits 
    • multimer
    • Quaternary structure: the 3D config of subunits in a multimer of a complex protein
  43. The same forces that stabilize the native form of a polypeptide also contribute to the maintenance of ________ structure
    quaternary structure
  44. In some multimers, the two or more interacting subunits are ______ polypeptides and their chains are encoded by ______ gene. In other multimers, by contrast, more than one kind of polypeptide makes up protein. The ______ polypeptides in these multimers are encoded by ______ genes
    • identical 
    • one
    • different 
    • different
  45. Alterations in just one kind of ______, caused by a mutation in _____ gene, can affect the function of a ________
    • subunit
    • one
    • multimer
  46. An example is an X-linked mutation in mice and humans that incapacitates several different proteins all known as ______ ______ (IL). Why does such a mutation cause the life-threatening condition known as X linked severe combined immune definciency (XSCID)
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    • interleukin receptors
    • because all of these receptors are essential to the normal function of the immune system cells that fight infection
  47. The polypeptides of complex proteins can assemble into extremely large structure capable of changing with the needs of the cell. State an example
    The microtubules that make up the spindle during mitosis are gigantic assemblages of mainly two polypeptide: α-tubulin and β-tubulin
  48. The cell can organize these subunits into very long hollow tubes that _____ and ______ as needed at different stages of the cell cycle
    • grow and shrink
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  49. People perceive light through neurons in the ______ at the back of the eye. These neurons are of two types: ______ and _____
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    • retina
    • rods and cones
  50. The rods, which make up 95% of all light-receiving neurons, are stimulated by ______ light over a range of wavelengths.
  51. At ________ light intensities, the rods become _______ and no longer send ______ info to the brain. This is when the ______ take over processing wavelengths of ______ light that enable us to see color
    • higher 
    • saturated
    • meaningful
    • cones
    • bright
  52. The cones come in three forms name them
    • one specializes in the reception of red light
    • a second in the reception of green
    • a third in the reception of blue
  53. For each phtoreceptor cell, the act of reception consists of ______ photons from light of a particular wavelength, ________ info about the number and energy of those photons to electrical signals, and ___________ the signals via the optic nerve to the brain. *This allows us to see over 1 million colors
    • absorbing
    • transducing 
    • transmitting
  54. The protein that receives photons and triggers the processing of info in rod cells is ______. It consists of a single ________ _______ containing 348 amino acids that snakes back and forth across the ______ _______
    • rhodopsin
    • single polypeptide chain
    • cell membrane
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  55. One lysine within the chain associates with retinal, a carotenoid pigment molecule that actually absorbs _______. The amino acids in the vicinity of the retinal connstitute rhodopsin's _____ ______; by positioning the retinal in a particular way, they determine its response to _____
    • photons
    • active site
    • light
  56. Each rod cell contains approximately 100  million molecules of _______ in its specialized membrane
    • rhodopsin
    • *the gene governing the productino of rhodopsin is on chromosome 3
  57. The protein that receives and initiates the processing of photons in the blue cones is a relative of rhodopsin, also consisting of a ______ _____ _____ containing 348 amino acids and also encompassing one molecule of retinal
    single polypeptide chain
  58. Slightly less than ______ of the 348 amino acids in the blue-receiving protein are the same as those found in ________; the rest are different and account for the _______ light-receiving ability of the protein
    Image Upload 16
    • half 
    • rhodopsin
    • specialized
  59. Similarly related to rhodopsin are the red-and green- receiving proteins in the red and green cones. These are also polypeptides associated with retinal and embed in  the cell membrane, although they are both slightly _______ at 364 amino acids in length
  60. Like the blue protein, the red and green proteins differ from rhodopsin in nearly _____ of their amino acids; they differ from each other in only ______ amino acids out of every hundred
    • half 
    • four
  61. The genes for the red and green proteins both reside on the _____ ______ in a tandem head-to-tail arrangement. Most individuals have one red gene and one to three green genes on their _____ ______
    • X chromosome
    • X chromosome
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  62. The similarities in structure and function among rhodopsin and the three rhodopsin related photoreceptor proteins suggests that the genes encoding these polypeptides arose by duplication of an ______ ______ gene and then divergence through accumulation of _______
    • original photoreceptor
    • mutations
  63. Many of the mutations that promoted the ability to see color must have provided selective advantages to their bearers over the course of evolution
  64. The red and green genes are the most ______, differing by less than _____ nucleotides out of every hundred. This fact suggests they diverged from each other in the relatively ______ evolutionary past
    • similar 
    • five
    • recent
  65. The less pronounced amino acid similarity of the red or green proteins with the blue protein, and the even lower relatedness between rhodopsin and any color photoreceptor, reflect ______ duplication and divergence
  66. At least 29 different single nucleotide substitutions in the rhodopsin gene cause an autosomal dominant vision disorder known as ______  _______ that begins with an early loss of _____ function, followed by a ______ progressive degeneration of the _______ retina
    • retinitis pigmentosa
    • rod
    • slow
    • peripheral
  67. Here we see the _______ of the amino acids affected by these mutations. These amino acid changes result in abnormal rhodopsin proteins that either do not _____ properly or, once ______ are unstable.
    Image Upload 18
    • location 
    • fold
    • folded
  68. Although normal rhodopsin is an essential structural element of rod cell membranes, these nonfunctional _______ proteins are retained in the body of the cell, where they remain unavailable for ________ into the membrane. Rod cells that cannot incorporate enough _______ into their membranes eventually die
    • mutant 
    • insertion
    • rhodopsin
  69. Depending on how many rod cells die, partial or complete _______ ensues
  70. People with normal color vision have a single ____ gene; some of these normal individuals also have a single adjacent _____ gene, while others have _____ or even _____ green genes
    • red
    • green 
    • two 
    • three
  71. Their proximity and high degree of homology (red and green) make these genes unusually prone to an error in meiotic recombination called _______ _______ ______
    unequal crossing over
  72. When homologous chromosomes associate during meiosis, two ______ _______ DNA sequences that are _______ to each other, like the red and green photoreceptor genes, can pair with each other _________
    • closely related
    • adjacent 
    • incorrectly
  73. If recombination takes place between the mispaired sequences, photoreceptor genes may be _____, _______ or _______.
    deleted, added or changed
  74. A variety of ____ _____ events produce DNA containing no red gene, no green gene, various combos of green genes, or hybrid red-green genes
    • unequal recombination events 
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  75. These different DNA combos account for the large majority of known aberrations in red-green color perception, with the remaining abnormalities stemming from ____ mutations
  76. Why do people with no red or no green gene perceive red and green as the same color?
    Because the accurate perception of red and green depends on the differing ratios of red and green light processed.
Card Set
Anatomy and Function of a Gene: Dissection Through Mutation III
Ch 7