AP Biology Problem Set #5: Genetics and DNA

Name ________KEY_________________ Period 1 ! " 5 # $

Reminder: Problem Sets are individual assignments. You are welcome to discuss these questions with your classmates, however your answers should be your own. Use your own words. Any academic code violations will result in a zero on this assignment and a note in your academic record.

1. A grandmother is trying to determine who the father of her granddaughter is. Her daughter has type A blood. The granddaughter has type B blood. What are the possible blood types of the father of this child? _______ AB or A____________ Show your wor ! %&e mot&er co'ld be BB ()B)B* or B+ ()Bi* b't since t&e grandda'g&ter is A, t&en t&e mot&er m'st be B+ (since s&e m'st gi-e &er da'g&ter an + allele, not a B*. %&e grandda'g&ter co'ld be A+ () Ai* or AA ()A)A*, b't since t&e mom &as B ty/e blood, &er da'g&ter m'st be A+. %&is means t&e grandda'g&ter &as to get an A allele 0rom &er 0at&er. So t&e 0at&er co'ld be A+, AA, or AB1t&is means t&e 0at&er2s blood ty/es co'ld be A or AB. ". Hemophilia is a recessi#e se$%lin ed trait. Specifically& the allele that codes for this disease is found on the ' chromosome ('h). *ndi#iduals with this disorder are unable to form blood clots properly and often run the ris of bleeding to death from in+uries that might normally be considered minor. A couple would li e to now if the child they are e$pecting could be born with hemophilia. The mother,s genotype is ' H'h. The father,s genotype is 'H- and he does not hemophilia. a) .$plain what a se$%lin ed trait is. How is this different from a se$%limited trait? A se3 lin4ed trait is a trait 5&ose alleles are 0o'nd on a se3 c&romosome. A se36llimited trait is one t&at may not be on t&e se3 c&romosomes b't is ty/ically e3/ressed based on t&e se3 o0 t&e indi-id'al. b) What are the possible genotypes for the couple,s children? 787&, 787&, 7&Y, 78Y c) What is the / chance that their child will ha#e hemophilia if it is a girl? ______9:_______ d) What is the / chance that their child will ha#e hemophilia if it is a boy? ______59:________ 0. -ou are gi#en the following 1*2.A3 strand of 42A that is 5666 base pairs long. The sites on the 42A where #arious restriction en7ymes will recogni7e and cut are indicated below! 6%%%%%%%%%%%%%%%%%%%%896 (BamH*)%%%%%%%%%%%%%%%1566 (Hind***)%%%%%%"666 (BamH*)%%%%%%%%%%0166 (Hind***)%%%%%%5666 a) How many 42A fragments would result from a BamH* digest? _ !__ b) How many 42A fragments would result from a Hind*** digest? _ !___ What would their si7es be? $59, 1 59, #999 What would their si7es be? 1;99, 1!99, "<99

:. *n fruit flies& the phenotype for eye color is determined by a certain locus. E indicates the dominant allele and e indicates the recessi#e allele. The cross between a male wild%type fruit fly and a female white%eyed fruit fly produced the following offspring. Wild%type ;ale Wild%type <emale White%eyed ;ale White%eyed <emale Brown%eyed <emale <1 6 :9 99 6 1 The wild%type and white%eyed indi#iduals from the <1 generation were then crossed to produce the following offspring. Wild%type ;ale Wild%type <emale White%eyed ;ale White%eyed <emale Brown%eyed <emale <" "0 01 "" ": 6 a) 4etermine the genotypes of the original parents (= generation) and e$plain your reasoning. -ou may use =unnett s>uares to enhance your description& but the results from the =unnett s>uares must be discussed in your answer. ?enotypes of original parents! __________ 7EY, 7e7e _____________ .$planation! %&is is a se36lin4ed trait (notice &o5 all t&e 0emales are 5ildty/e and t&e males &a-e 5&ite eyes in t&e 0irst generation*. =&en yo' constr'ct t&e P'nnett s>'are 0or t&is, it res'lts in t&e a//ro/riate ratios t&at matc& 5&at yo' get in t&e second generation (?1*. )0 yo' cross t&e c&ildren 0rom t&e cross toget&er yo' s&o'ld get ratios t&at matc& t&e ? generation.

b) The brown%eyed female in the <1 generation resulted from a mutational change. .$plain what a mutation is& and discuss two types of mutations that might ha#e produced the brown%eyed female in the <1 generation. A m'tation is a c&ange in t&e DNA se>'ence. %&is co'ld res'lt in a bro5n eyed 0ly beca'se it co'ld it mig&t c&ange t&e /rotein /rod'ced (5&ic& 5o'ld res'lt in a di00erent color eye* or it co'ld also res'lt in a non0'nctional /rotein (5&ic& 5o'ld also c&ange t&e a//earance o0 eye color* 9. -ou are wor ing in a plant lab trying to find the genes responsible for pigmentation (color) of the yellow pigment of the plant. -our predicted pathway is! .n7yme 1 @ompound 1 %%%%%%%%%%%%%%%%%%%%%A @ompound " (colorless) (orange) .n7yme ; %%%%%%%%%%%%%%%%%%A @ompound 0 (yellow)

-ou call the two alleles that produce functional en7yme 1 and ;. l and m alleles produce no functional en7yme. -ou assume that one functional copy of an en7yme is sufficient to cataly7e the reaction. To test your predictions& you cross two plants of genotypes! 1l;m $ 1l;m What would the colors of the progeny be (and in what ratios)? <@1# yello5, !@1# orange, A colorless Show your Wor ! BC Bm lC lm BC BBCC BBCm BlCC BlCm Bm BlCm BBmm lBCm Blmm lC BlCC BlCm llCC llCm lm BlCm Blmm llCm llmm

B. Cne of the most common uses of restriction analysis is to detect 3<1=. This stands for 3estriction <ragment 1ength =olymorphism. Simply put& this method ta es ad#antage of differences in the 42A of indi#iduals that result in different restriction sites when treated with specific restriction en7ymes. After the 42A has been digested with the appropriate en7ymes and run on an agarose gel& a So't&ern Blot is performed to allow for further analysis. The steps of a Southern Blot are! *. The gel is soa ed in a basic solution to denature (separate) the 42A strands. **. Then the 42A is transferred from the gel to a piece of nylon membrane. The spacing and position of the 42A is maintained in the transfer from the gel to the membrane. ***. The membrane is incubated with radioacti#e /robes to detect specific 42A fragments. A probe is a piece of 42A that is complementary to the strand of 42A you are trying to detect. A radioacti#e tag is added to the probe so that scientists can see which fragments the probe binds to. Dsually& probes are thousands of base pairs long. *E. After incubation with the probe& unbound probe is washed away. E. The membrane is put with '%ray film to detect where the radioacti#e probes bound to the membrane. The de#eloped '%ray film is called an a'toradiogra/&. E*. oa ed in a basic solution to denature (separates) the 42A strands. E**. Then the 42A is transferred from the gel to a piece of nylon membrane. The spacing and position of the 42A is maintained in the transfer from the gel to the membrane. E***. The membrane is incubated with radioacti#e /robes to detect specific 42A fragments. A probe is a piece of 42A that is complementary to the strand of 42A you are trying to detect. A radioacti#e tag is added to the probe so that scientists can see which fragments the probe binds to. Dsually& probes are thousands of base pairs long. *'. After incubation with the probe& unbound probe is washed away. '. The membrane is put with '%ray film to detect where the radioacti#e probes bound to the membrane. The de#eloped '%ray film is called an a'toradiogra/&.

a) -ou are as ed to design a probe to hybridi7e to the following segment of 42A! 9, AT?@TA@?A@@ 0, What should the se>uence for the probe be? Dont forget to label the 5 and 3 ends of the DNA. !2 %ADGA%GD%GG 52 b) As a lab technician& part of your +ob is to ma e sure the probes you are using are appropriate for the 42A you are trying to detect. -ou are wor ing with the following sample of 42A (only one strand is shown)! 9, AT@@?@TAAT?GD@?AT@TAAT?@TA@?A@@T@TA@?TTTA@AATATA?GD@TA?@TA?@TT@?AT@?@T@ 0, i. Suppose you were to cut the 42A shown abo#e with the en7yme HaeIII. The recognition se>uence for this en7yme is 9, ??@@ 0,. The en7yme cuts between the ? and @ bases. *n the strand of 42A abo#e& draw line(s) to show where the en7yme would cut. W.11

Enzyme cuts between the bolded blue bases

ii. iii. -ou run the 42A that you ha#e digested with HaeIII on an agarose gel. -ou get the results shown to the right (the well is on the top of the gel photo)! -ou denature the 42A from the gel and transfer it onto a nylon membrane. -ou incubate the membrane with the probe you made in part (a). 4raw an arrow to the 42A fragment(s) on the gel that the probe will bind to. See arro5 The same nylon membrane can be used with another probe. The membrane is sub+ected to high temperatures to detach the e$isting probe from the membrane. The probe is washed off then the membrane is incubated and hybridi7ed with a new probe. Suppose you incubate the membrane with the following probe! 0, ?AT@?AA?@TA? 9, Which 42A fragment(s) will this new probe bind to? @ircle the fragment(s) on the gel that this new probe will bind to. %&e 0ragment t&at t&e DNA 5ill bind to 5ill be 52 D%AGD%%DGA%D !2 . Dircled in t&e diagram.

i#.

8. 3<1= is fre>uently used to detect different alleles and genetic mutations. Suppose there is an autosomal genetic disease called SF2S that is caused by a recessi#e allele (a) of the Dwk7 gene. The Dwk7 gene has a BamHI restriction site on either side of it. 8. 3<1= is fre>uently used to detect different alleles and genetic mutations. Suppose there is an autosomal genetic disease called SF2S that is caused by a recessi#e allele (a) of the Dwk7 gene. The Dwk7 gene has a BamHI restriction site on either side of it. As a genetic counselor& your +ob is to ad#ise couples about the ris their children might ha#e of de#eloping SF2S. A couple comes to you and gi#es you the following information! 2either of them has SF2S The husband had a baby brother who died from SF2S at age 0. There has ne#er been any incidence of SF2S in the wife,s family. The allele that causes SF2S can be detected by 3<1=. -ou ta e blood samples from the couple and do 3<1= analysis on their 42A for the mutation that causes SF2S. Along with the couple,s 42A& you also run a sample of 42A from an indi#idual that you now has SF2S. -ou digest each 42A sample with BamHI and run the results on an agarose gel. -ou do a Southern Blot with a probe that hybridi7es to a portion of the Dwk7 gene. Then you ma e an autoradiograph of the results. These autoradiograph results are shown on the following page!

W.11S

1ane 1 G Husband 1ane " G Wife 1ane 0 G *ndi#idual with SF2S 1ane : G Si7e Standard (896& 966& :"9& 066& "66)

a) Based on these results& what is the genotype of the husband? ___AA___ What is the genotype of the wife? ___Aa ______

b) *f this couple were to ha#e a child what is the / chance that heHshe would ha#e SF2S? __ 9:______
Show your wor .

c) What are the chances that a child of this couple will be a carrier for SF2S? ___ 59:_____ Show your wor .

d) -ou construct a pedigree for the couple. Dsing the information the couple ga#e you as well as the results of the autoradiograph& fill in the pedigree below with the correct genotype for each family member. -ou do not need to fill in the genotypes for the couple,s future children. KEY
Half shaded

male future child

Half shaded

female

indi#idual with SF2S (shaded) indi#idual without SF2S (unshaded) carrier for SF2S

Yo' can2t 4no5 t&e 5i0e2s /arents2 genoty/es1neit&er can be aa b't at least one o0 t&em (or bot&* &as to be a carrier (Aa*.

e) When you loo at the agarose gel under DE light& this is what you see!
1ane 1 G Husband 1ane " G Wife 1ane 0 G *ndi#idual with SF2S 1ane : G Si7e Standard (896& 966& :"9& 066& "66)

There is a large smear of 42A in e#ery laneI *t,s nothing li e the clear bands you saw in the autoradiograph. Why is this? .$plain why the gel and the autoradiograph are so different. (Hint! thin about the probe) %&e gel s&o5s yo' all o0 t&e DNA. %&e a'toradiogra/& 'ses a s/eci0ic /robe, so it only lig&ts '/ t&e one se>'ence o0 DNA t&at com/lements t&e /robe. f) -ou suspect that the mutation that causes SF2S might be a point mutation in which a single nucleotide is mutated in the Dwk7 gene. What is the significance of this mutation? Specifically& how does it allow the 3<1= to show who has the SF2S allele and who will ha#e the normal allele? Since it is a /oint m'tation, t&at means t&ere is only one n'cleotide di00erent bet5een t&e A and a allele DNA se>'ences. %&is one m'tation m'st introd'ce a ne5 restriction site 0or Bam8). %&is means t&e A allele gets c't into only one /iece by Bam8) (since it c'ts on eit&er side o0 t&e gene* and t&e a allele is c't into /ieces (on eit&er side and t&en once in t&e middle. =&en t&e /robe binds, it binds to all o0 t&e A allele b't it only binds to t&e !99 b/ /iece o0 t&e a allele a0ter it is c't.

g) Based on the autoradiograph& how many base pairs long is the Dwk7 gene? __599___ bp h) A diagram of the a allele of the Dwk7 gene is shown below. *ndicate any BamHI restriction sites on the diagram and shade in the area where the probe binds during the Southern Blot. 1abel the right side of the diagram as total length of the gene. 1 9 Probe binds &ere !99 (a allele only* 599 599 bp

%&e lines re/resent 5&ere Bam8) 5ill c'ts, t&e n'mbers re/resent 5&ere it 5ill c't 5. 3<1= can also be used to determine paternity and show how indi#iduals are related to one another. A man comes to your lab because he belie#es that his wife has been unfaithful and is carrying another man,s child. After obtaining 42A from the wife and the fetus she is carrying& you do 3<1= analysis for a polymorphism on chromosome " (called 4"S::). The autoradiograph is shown below. @ould this man really be the father of the fetus? ___ YES________ .$plain your answer. %&e 0et's &as a combination o0 alleles 0rom mot&er and 0at&er (one allele 0rom eac& /arent*. So i0 yo' loo4 at t&e a'toradiogra/&, yo' can see t&at t&e mot&er and c&ild &a-e one allele in common. %&ere is also anot&er allele t&at t&e c&ild &as in common 5it& t&e alleged 0at&er (circled*, so t&is man co'ld be t&e 0at&er o0 t&e 0et's.

J. As the newest member of San <rancisco,s elite @S* s>uad& you are assigned a burglary case in which there are 0 possible suspects. When the burglar fled the scene of the crime& heHshe cut himHherself on a bro en window and left behind some blood. After obtaining a court order to get the 42A of all three suspects& you do 3<1= analysis on the suspects, 42A and the blood found at the crime scene. -ou use " different probes on the same nylon membrane (" separate hybridi7ations). The combined autoradiograph (of all " hybridi7ations) is seen below.

1ane 1 % Si7e Standard 1ane " % Suspect K1 Blood 1ane 0 % Suspect K" Blood 1ane : % Suspect K0 Blood 1ane 9 % Si7e Standard 1ane B % Home Cwner Blood 1ane 8 % @rime Scene Blood 1ane 5 % 2egati#e @ontrol (non%suspect) 1ane J % Si7e Standard

a) Based on the autoradiograph& which suspects can be ruled out as 2CT being the burglar? .$plain your answer.
S's/ects #1 and can be r'led o't. %&eir DNA does not matc& t&e crime scene DNA.

b) Which suspect is most li ely the burglar? .$plain your answer. S's/ect #!1t&e DNA matc&es t&e crime scene DNA 0or t&ese

/robes.

c) Why is it necessary to use more than one probe when doing 42A profiling li e this? %ec&nically, many /eo/le2s DNA co'ld matc& 0or only one /robe. By testing more /robes, it decreases t&e c&ances t&at t&ey 5o'ld all matc& i0 t&e DNA came 0rom di00erent /eo/le. So t&e more /robes yo' test, t&e more certain yo' can be t&at t&e DNA came 0rom t&e same so'rce (i0 it matc&es* d) Dsing this autoradiograph alone& can we be 166/ certain that one of the suspects (A& B& or @) is the burglar who left hisHher blood at the crime scene? Why or why not? No, yo' can2t be 199: certain. +nly /robes 5ere tested. Core /robes m'st be tested in increase certainty since t&e more /robes are tested, t&e less t&e : c&ance t&at t5o di00erent /eo/le 5o'ld be t&e same in t&at many locations o0 t&eir DNA.