Download BSCI 410-Liu Homework#1 Key Spring 05 1 1. (8 points) The

BSCI 410-Liu
Homework#1 Key
Spring 05
1. (8 points) The following is a list of mutational changes. For each of the specific
mutations indicate which type of mutation best describes the change. Sometimes, more
than one term could be used to describe each of the following statement (such as
transition, transversion, translocation, insertion, deletion etc.).
(1) An A-T base pair is changed to a T-A pair.
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transversion
(2) An A-T base pair in the wild type gene is changed to a G-C pair.
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transition
(3) The sequence of AAGCTTATCG is changed to AAGCTATCG.
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deletion
(4) The sequence AACGTTATCG is changed to AATGTTATCG.
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transition
(5) The sequence AAGCTTATCG is changed to AAGCTTTATCG.
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insertion
(6) The sequence AACGTCACACACACATCG is changed to AACGTCACATCG.
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deletion
(7) The gene map in a given chromosome arm is changed from bog-rad-fox1fox2-try-duf to bog-rad-fox2- fox1-try-duf.
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Inversion
(7) The gene map in a chromosome is changed from bog-rad-fox1-fox2-try-duf to
bog-rad-fox1-met1-qui-txu-sqm.
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Translocation
2. (10 points) Design a mutagenesis screen to isolate mutations involved in the
biosynthesis of cytosine in yeast? Note: such a mutant is expected to be lethal.
See fig 7.20
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Mutagenize (and then induce meiosis)
2
Grow in complete media
2
Transfer (replica-plating) to minimal media
2
Those that fail to grow in minimal media will be tested in the next step
2
Test for growth in minimal media supplemented with cytosine to
confirm. Those that fail to grow in minimal media (MM) but can now
grow in MM supplemented with cytosine will be the mutants we want.
3. (20 points) Briefly compare and contrast following pairs of terms:
1. Auxotroph and Prototroph
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Auxotroph: Strain requires growth factors not normally needed by
Wt cells for viability
2
Prototroph: Strain which does not require any special growth factors
(usually WT)
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BSCI 410-Liu
Homework#1 Key
Spring 05
2. Complete medium and Minimal medium
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Complete medium: Contains all nutrients necessary for growth
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Minimal medium: Contains only a carbon source (usually glucose),
inorganic salts and water.
3. Mutagenesis screen and Mutagenesis selection
2
Selection: Conditions set up so only the mutant of interest will survive
(use death vs. growth to select)
2
Screen: Both Wt and mutant organisms are present (ie. survive) and
require one to look through all of them to identify the mutant of
interests.
4. Haploinsufficient and dominant negative mutations
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Haploinsufficiency is very rare and occurs when a phenotype is
observed in individuals heterozygous for a loss-of-function allele (or
null) and its phenotype is similar to homozygous loss-of-function
mutants.
2
Dominant negative mutations are those in which a mutant protein
product interferes (poisons) with the wild type product. Often this
occurs in cases in which there are multiple subunits of a protein, and
a mutation in one subunit interferes with the activity of the entire
protein complex. An individual heterozygous for the dominant gainof-function mutation exhibits a phenotype similar to homozygous lossof-function.
5. Retrotransposons and Transposons
2
Retrotransposons: Use a reverse transcribed RNA intermediate to
transpose to a new location, and has a polyA tail at one or LTR at
both ends. Still maintain the original (starting) retrotransposon (ie.
increase in copy number rapidly).
2
Transposons: Requires no RNA intermediate, short inverted repeats
at end. It may excise itself and insert itself into a new location (no net
gain of the transposon).
4. (8 points) Wild type mouse with normal pigmentation is grey in color. Albino means
white (no pigment at all). The following mutations (m1, m2, m3, and m4) affecting
pigment synthesis in mouse are identified. They all affect the activity of the same gene.
Given the following genotype as well as corresponding phenotype, could you describe
the type of mutations using following terms: "recessive-null", "dominant-gainoffunction", "dominant-negative", "hypomorphic", "hypermorphic", and "neomorphic".
Each situation listed below could sometimes be described by more than one terms
(1) m1/+ grey mouse
m1/m1 albino mouse
2
recessive-null, hypomorph, or loss of function
(2) m2/+ albino mouse
m2/m2 albino
2
dominant negative or haploid-insufficient
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Homework#1 Key
2
(3) m3/+ Black (darker than normal)
m3/m3 Black
hypermorph or dominant gain-of-function
2
(4) m4/+ Redish brown (unusual color)
m4/m4 Redish brown
neomorph
Spring 05
5. (10 points) You have isolated five recessive maize mutants (d1-d5) which are
defective in pigment biosynthesis. While wild type kernels are Red (R) in color; these d1d5 mutant kernels are Yellow (Y) in color. To test if any of these mutations are allelic to
each other, you did pairwise crosses among all five mutations and observed F1
phenotypes, which are summarized in the table below. How many genes are represented
by these five mutations? How are these five mutations grouped into different genes?
d1 d2 d3 d4 d5
d1 Y R R Y R
d2
Y R R R
d3
Y R Y
d4
Y R
d5
Y
(R: red; Y: Yellow)
2.5
2.5
2.5
2.5
d1=d4
d3=d5
d2 different from rest
3 genes
6. (14 points) The intermediates A, B, C, D, E, and F all occur in the same biochemical
pathway. G is the product of the pathway and mutants 1 through 7 are all G- (ie. fail to
produce G). The following table shows which intermediates will promote growth in each
of the mutants. Arrange the intermediates in order of their occurrence in the pathway, and
indicate the step in the pathway at which each mutant strain is blocked. + in the table
indicates that the strain will grow if given that substance, an O means lack of growth.
Supplement
Mutant A B C D E F G
1 + + + + + O +
2 O O O O O O +
3 O + + O + O +
4 O + O O + O +
5 + + + O + O +
6 + + + + + + +
7 O O O O + O +
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Homework#1 Key
Spring 05
F D A C B E G
1
5 3
4
7 2
1 pnt for each correct letter and number
7. (10 points) Ethylene is a plant hormone that facilitate fruit ripening. Two types of
tomato mutants were isolated that either could not ripen even when exposed to ethylene
treatment or could ripen even without ethylene treatment. To determine the epistatic
relationship among these mutations, double mutants were constructed and their
phenotypes were observed and summarized below.
Gene names Single mutant phenotype:
never red (nrd): Form green tomatos even after ethylene treatment
never ripen (nrp): Form green tomatos even after ethylene treatment
always ripen (ar): Form red tomatos even without ethylene treatment
(nrd, and nrp are defective in different genes).
Gene names Double mutant phenotype:
nrd ar: Form green tomatos even after ethylene treatment
nrp ar: Form red tomatos even without ethylene treatment
What is the regulatory relationship among these three genes? (Draw the regulatory
pathway starting with “Ethylene” and ending with “tomato ripening”. Use arrows to
indicate positive regulations and bars ( )to indicate negative regulations.
Ethylene (arrow) nrp (bar) ar (bar) nrd (arrow) red tomatoes
2pnts for each correct gene placement in pathway
1pnt for each correct arrow or bar placed in pathway (and ethylene and red tomatoes
being in the correct places in the pathway)
8. (8 points) Name and describe what type of transposable element each of the following
is:
(1).Ty1 transposon from yeast.
2
Retrotransposon, uses RNA intermediate
(2). P-element from drosophila,
2
Transposon, does not require an RNA intermediate
(3). Ac/Ds from maize
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Transposon
Ac: activator, autonomous
Dc: dissociation, non autonomous
Inverted repeats at end
(4). T-DNA from agrobacteria,
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BSCI 410-Liu
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Homework#1 Key
Spring 05
Inserts into host DNA upon agrobacteria infection, can cause transformation
9. (12 points) What kinds of effect on DNA each of following mutagens could cause?
(1) UV irradiation
2
thymine – thymine dimmer
(2) X-ray
2
double stranded DNA break, causing inversions, deletions or other
rearrangements
(3) EMS
2
Chemical change (alkylating agents) causing transitions
(4) Proflavin
2
Intercalation causes insertions and deletions (frameshifts)
(5) Nitrous acid
2
Deaminating agent causes transitions
(6) Transposon insertion
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inserts different nucleic acids into a gene and can disrupt frame, change
encoding, introduce stops, alter splicng etc.
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