Genetics Final, Young Fall ’09, 150 pts. Name:______________________Due midnight, 12/9/09 by email (subject line must include “321m”), -or- 4:30 in the Biology Office

1. (20 pts) You are a genetic counselor and are presented with a family in which a disease is present as indicated below. You’ve isolated DNA from each family member shown and have obtained PCR primers for the region surrounding a common SNP (114A>C, A being the wt nucleotide). Cycle sequencing confirms that mutations in this family are caused by this transition / transversion (underline the correct one, 2 pts) at nucleotide 114. You buy ASOs to detect sequence at 114.

1a. (2 pts) What is the mode of inheritance, based on the pedigree?

1b. Target DNA from each individual was obtained with PCR, and blotted to replicate blots (blot 1 and blot 2). Blot 1 was hybridized with a labeled 11C ASO and blot 2 with a labeled wt ASO. Fill in the circles on each blot that would show positive hybridization. For circles for which there isn’t enough information, indicate the probability of it being positive. (or indicate, by underlining, bold, etc. for email submission.)

2. (10 pts) Starting with no sequence information, use the following words only (and comma), to succinctly describe how to identify a gene that functions in mouse veromonasal tissue and clone it, including the promoter and all introns. You may use a word more than once, or not at all. mouse genomic transcriptase scan identify isolate make that hybridizes veromonasal create extract detect cDNA tissue mRNA a probe library from laser clone target the

reverse use to from , microarray

blot 1

I1 II1 II2 II3 II4 II8 III8 IV1 IV2blot 2

I1 II1 II2 II3 II4 II8 III8 IV1 IV2

3. (12 pts) For the following questions, use the amino sequence, in tandem with the codon usage table, on the Reference Page (it's the last page on your exam, and can be detached as you won't be asked to hand it in). The 638 amino acid sequence represents the complete human growth factor protein as deduced from a cDNA. Single letter amino acid designations refer to specific codons

(i.e. M = Met: AUG).

Note: Use the topmost codon if the code is degenerate at that position.

a. (2 pts) How many DNA base pairs code for the protein?

b. (6 pts) Design 12 base pair DNA primers that you can use to PCR amplify the entire gene.

5' - ___________________________ 3' 5' - ____________________________ 3'

c. (2 pts) How long (in base pairs) is the PCR product from 3b, given a complete cDAN acts as the template?

d. (2 pts) You also have genomic DNA with the whole HGF gene. You use your PCR primers on the genomic template and get a PCR product that is nearly twice as long as the PCR product in 3c. I one word, why?

4. (16 pts) Consider Fig. 4. Detection of

viruses in isolated nasal lavage from Wang et al., Microarray-based detection and genotyping of viral pathogens, PNAS 99(24).

a. (4 pts) Is this an image of a (underline correct answer)….

i. Microarray ii. Microchip iii. Neither

b. (6 pts) How was the target obtained in the RV16/HeLa Amplified portion of this figure?

c. (6 pts) What was the probe used for the RV16 (+/-) section of the figure. How was it chosen for inclusion in this experiment, and how was it made?

5. (18pts) Use the following sequenced DNA as a template for PCR:

5'-ATGCATGCGA GTAGTCGTGT AGTCGATGTA CTGCATGTTT ACGTCGTAGT GGTACGATGT |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||3'-TACGTACGCT CATCAGCACA TCAGCTACAT GACGTACAAA TGCAGCATCA CCATGCTACA

61 91 AGTCGATGTA CTGCATGTTT AAGTCGTAGT AAGCTTATGT GTACGTGTGA TGCTGCTAGT |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| TCAGCTACAT GACGTACAAA TTCAGCATCA TTCGAATACA CATGCACACT ACGACGATCA

131 TACTGACGTG TTACGTGCTA GTACGTGTGA TGCTGCTAGT GTACGTGCAT GTTACTTTGT-3' |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ATGACTGCAC AATGCACGAT CATGCACACT ACGACGATCA CATGCACGTA CAATGAAACA-5'

a. Circle a pair of 20 base sequences that would be used for PCR primers to amplify a 100 bp DNA product containing the G/C base pairs at position 93.

b. (4 pts) Write the nucleotide sequence for each primer in 5' - 3' orientation,

Primer 1: 5' - __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ - 3'

Primer 2: 5' - __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ - 3'

c. (2 pts) Exactly how long will the predominant PCR product be after 41 rounds?

___________bp

d. (6 pts) Position 93 (G) is the third base in a codon (codon table on back page) that codes for lysine, and has been found to be a highly polymorphic site that when mutated may be lethal. Design 15 base pair ASOs that will hybridize to DNA from individuals who carry a lethal mutation as heterozygotes, give the mutant sequence that will be recognized (indicate 5’, 3’ orientation), and circle the base that is diagnostic:

ASO (wt): 5' - __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ - 3'

ASO (mutant): 5' - __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ - 3'

Mutant Sequence: ____- __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ - ____

e. (6 pts) The AAGCTT at positions 91-96 is a palindrome recognized by the restriction enzyme HindIII. Draw the results of a Southern blot with DNA subjected to HindII digestion, and hybridized with labeled wt DNA.

20

40

60

80

100

wt hetero-zygote

homo-zygotemutant

bp

6. (11 pts) Consider Fig. 3 Two-dimensional gel electrophoresis of proteins from the cytosolic fraction of human from Intra- and Interspecific Variation in Primate Gene Expression Patterns, Science(296). A. Human, B. Chimpanzee. Check all correct answers…

6a. (4 pts) The spot labeled “5” in 3A and 3B (underline all correct answers),

…is expressed more highly in chimpanzees than in humans,

…is expressed more highly in humans than in chimpanzees,

…has different 1o sequence in the two species,

…has similar 1o sequence in the two species.

6b. (4 pts) The spot labeled “13” in 3A and 3B (underline all correct answers),

…is expressed more highly in chimpanzees than in humans,

…is expressed more highly in humans than in chimpanzees,

…has different 1o sequence in the two species,

…has similar 1o sequence in the two species.

6c. (3 pts) The “spots” are (underline all correct answers),

i. mRNA ii. cDNA iii. Genomic DNA iv. Proteins v. Probes vi. Targets

7a. (4 pts) Considering virus detection, what’s the difference between a primer used in a multiplexed PCR reaction with a primer used in a degenerate PCR reaction?

7b. (4 pts) What’s the most common G6PD deficient mutant found in African populations?

What are the amino acid changes?

8. (12 pts) Consider Fig. 1 Targeted deletion of a cluster of V1r genes from Deficient pheromone responses in mice lacking a cluster of vomeronasal receptor genes, Nature (419).

a. (4 pts) What are V1r genes?

b. (4 pts) Why wereV1ra,b genes selected for this reverse genetic study?

c. (4 pts) On what basis were the V1r genes clustered for this diagram?

i. DNA array data ii. DNA sequence data iii. DNA map data iv. Behavior analysis

9. (12 pts) Consider Fig. 2. Distance trees representing the relative extent of expression changes among three primate species and three tissues as assayed by the DNA arrays from Intra- and Interspecific Variation in Primate Gene Expression Patterns, Science(296).

a. (4 pts) What was the target in this experiment?

___________________

b. (4 pts) What was the probe in this experiment?

i. cDNA, ii. genomic DNA,iii. mRNA iv. all of these

c. (4 pts) What is different between Fig. 1a and Fig. 2 in this paper?

i. probes are longer in Fig. 1 ii. probes are longer in Fig. 2

iii. targets are longer in Fig. 1 iv. targets are longer in Fig. 2

Fig. 1aFig. 1a.

Fig. 2

10. (18 pts) Consider Fig. 1. Metabolic defect in hereditary fructose intolerance fromThe genetic consequences of our sweet tooth, Nature Reviews Genetics (3).

a. (4 pts) Circle the main compound

that builds up in patients with HFI.

b. (4 pts) Underline the enzymatic step(s) in this diagram that are genetically blocked in persons with Hereditary Fructose Intolerance (HFI).

c. (6 pts) Place stars beside compounds that do not accumulate in patients with HFI, compared with wt.

d. (6 pts) Fructokinase activity is eventually inhibited by high levels of fructose-1-phosphate. After an HFI event, which of the following sugars would be safe for the affected individual to consume (circle all possible answers), if they want to get better?

i. Glucose ii. Fructose iii. Sucrose iv. Lactose

11. (13 pts ) The following represents a genomic map of a mutant gene. The wild-type version of the gene lacks the BamH1 site on the second exon. The probe homology region is shown below the scale (100 bp per tick, all map points not falling on a tick are at 50 bp). You have genomic DNA and full length cDNA, and cut them with BamH1.

wt mut wt mut ladder genomic genomic cDNA cDNA

You run the samples on a gel, blot and probe. Complete this blot by creating a ladder, and

Probe

indicating the locations of any fragments that hybridize. If you can’t draw for email, just tell me the sizes.

1 mdfwqllltl alagssdafs gseataails rapwslqsvn pglktnsske pkftkcrspe 61 retfschwtd evhhgtknlg piqlfytrrn tqewtqewke cpdyvsagen scyfnssfts 121 iwipyciklt snggtvdekc fsvdeivqpd ppialnwtll nvsltgihad iqvrweaprn 181 adiqkgwmvl eyelqykevn etkwkmmdpi lttsvpvysl kvdkeyevrv rskqrnsgny 241 gefsevlyvt lpqmsqftce edfyfpwlli iifgifgltv mlfvflfskq qrikmlilpp 301 vpvpkikgid pdllkegkle evntilaihd sykpefhsdd swvefieldi depdektees 361 dtdrllssdh ekshsnlgvk dgdsgrtscc epdiletdfn andihegtse vaqpqrlkge 421 adllcldqkn qnnspyhdac patqqpsviq aeknkpqplp tegaesthqa ahiqlsnpss 481 lsnidfyaqv sditpagsvv lspgqknkag msqcdmhpem vslcqenflm dnayfceada 541 kkcipvaphi kveshiqpsl nqediyitte slttaagrpg tgehvpgsem pvpdytsihi 601 vqspqgliln atalplpdke flsscgyvst dqlnkimp

Reference Page