Molecular Genetics Exam 3, Tuesday, Nov. 22, 2005page 1 of 5
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Your name:
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Define the following terms (5 points each):
RISC
RNA-induced silencing complex. Complex of proteins that bind to siRNA or miRNA, unwind it, and inhibit transcription and/or translation of RNA that is complimentary to the bound miRNA or siRNA.
U1 snRNP
A small nuclear ribonuleoprotein containing U1 snRNA. It is involved in splicing / splice site recognition. U1 snRNP binds to the 5’ end of the intron and forms part of the spliceosome.
Haploinsufficiency
A form of dominance in which the heterozygote does not produce enough protein for a normal phenotype. An individual heterozygous for a wild-type and a null allele will have an abnormal phenotype.
Shine-Dalgarno sequence
A portion of the ribosome binding site in prokaryotes, the Shine-Dalgarno sequence is a 6 nucleotide mRNA sequence just upstream from the start codon. It is important for ribosome binding and the initiation of translation.
1. (10 points) Compare and contrast chromatin associated with actively transcribed genes and chromatin associated with inactive genes (Name at least 3 differences between them).
See lecture 13, slide 33. Each correct difference was assigned 3 pts; full credit was given when at least 3 clear differences were listed with no incorrect statements.
Though it is listed on lecture 13, slide 33, credit was not given for a difference being gene activity vs no gene activity. This is stated directly in the question and credit is not given for restating what is stated in the question.
This pedigree shows a family affected by an autosomal dominant genetic disease.
Genotypes for three markers, A, B and C, are shown
The genotypes are:
1 ______
Molecular Genetics Exam 2 Monday, April 8, 2002page 1 of 4
Your name ______
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I-1A1,2 B1,2 C1,2
I-2A3,3 B3,3 C3,3
II-1A1,3 B2,3 C1,3
II-2A4,4 B4,4C1,3
III-1A1,4 B2,4 C1,3
III-2A3,4 B3,4 C3,3
III-3A1,4 B3,4 C3,3
III-4A1,4 B2,4 C1,1
III-5A3,4 B3,4 C1,1
1 ______
Molecular Genetics Exam 3, Tuesday, Nov. 22, 2005page 1 of 5
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Your name:
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2. (5 points). Indicate the phase of alleles in individual II-1 by showing his haplotypes.
There are four possibilities. They are A1 B2 C1 /A3 B3 C3; A1 B2 C3 /A3 B3 C1 ;
A1 B3 C1 /A3 B2 C3 and A1 B3 C3 /A3 B2 C1
A1 B2 C1 /A3 B3 C3
3. (5 points) For each individual in the third generation, indicate whether they are recombinant, nonrecombinant or indeterminate (meaning that you can't tell, that this was an uninformative meiosis) for paternal alleles at the loci A and B.
(i.e. Was the meiosis informative and, if so, was there recombination)?
III-1Nonrecombinant
III-2Nonrecombinant
III-3Recombinant
III-4Nonrecombinant
III-5Nonrecombinant
4. (5 points) For each individual in the third generation, indicate whether they are recombinant, nonrecombinant or indeterminate (meaning that you can't tell, that this was an uninformative meiosis) for paternal alleles at the loci B and C.
(i.e. Was the meiosis informative and, if so, was there recombination)?
III-1Indeterminate
III-2Nonrecombinant
III-3Nonrecombinant
III-4Nonrecombinant
III-5Recombinant
5. (5 points) For each individual in the third generation, indicate whether they are recombinant, nonrecombinant or indeterminate (i.e. you can't tell; the result of an uninformative meiosis) for alleles at the loci A and C.
III-1Indeterminate
III-2Nonrecombinant
III-3Recombinant
III-4Nonrecombinant
III-5Recombinant
6. (5 points) Which gene (A, B or C) is most likely to lie between the other two?
B
7. (5 points) What is the lod score for linkage between A and B with = 0?
Log10 (0) or -∞ was given full credit. Partial credit was given if correct equation was written down but improperly implemented.
8. (5 points)
Which locus (A, B or C or none) has the highest lod score for linkage to the disease gene with = 0?
A (lod score is ~1.5, but it was not necessary for full credit)
9. (5 points) Does observing association between alleles at two loci (LD) imply that these loci are linked? (yes or no) No, population stratification can cause associtation.
10. (8 points) Explain the yeast two-hybrid technique for analysis of interactions between and among proteins. Include explanation of how you would use the technique to find new interacting proteins, how you would use it to find which amino acids in your favorite protein are required for it to bind its partner and what it tells you about transcriptional regulation in eukaryotes.
3 pts for good explanation of the technique (partial credit for less complete or nearly accurate explanations)
2 pts for explanation of using the technique to find new interacting proteins
2 pts for explanation of using the technique to determine which amino acids are important for binding
1 pt for indicating that this technique demonstrates the separability of the DNA binding and activation functional domains in transcription (this may have been implicit in a good/full explanation).
11. (10 points)
Define, compare and contrast siRNAs and miRNAs. Spell out the abbreviations, explain what they do, how they work and what species have them.
siRNA: small interfering RNAs (1pt)
miRNA: microRNAs (1pt)
Both are bound by the RISC complex and act to degrade, or blocktranslation of, mRNAs to which they are complementary. Both thereforework by base-pairing to an mRNA target. (2pts)
Differences between them are that 1) miRNAs are produced by the cell (1pt),from miRNA genes, and are processed from precursors. 2) miRNAs aremore likely to result in translational arrest without degradationwhile 1) siRNAs are normally produced from double-stranded precursors (1pt)and 2) siRNAs are more likely to result in mRNA degradation (1pt).
These RNAs arefound in eukaryotes (animals and plants, but also some unicellulareukaryotes). (2pts)
Points may have been given for other correct details.
12. (12 points) You study the mouse. A colleague sends you an unusual allele of your favorite gene that causes the ears to be long and hang down. You find that it is fully dominant. No other allele of your gene (and you have several) has this phenotype. How likely is it that this allele is null, hypomorphic, hypermorphic, neomorphic or antimorphic (your answer should consider each case separately). You have a null allele and you have a duplication (a normal copy of the wild-type gene on another chromosome). What experiments would you do to determine the type of allele you have?
The following table indicates the likelihood / possibility that the new dominant allele (Dom) is each type of allele. It then give the offspring phenotypes expected for crosses of Dom/Dom individuals with Null/Null and Dom/Dom with +/+, +/+.
Allele Type / Likely / Possible / Exp 1: Dom/Null / Exp 2: Dom/+, +/+Null / No / N.A. / N.A.
Hypomorphic / No / N.A. / N.A.
Hypermorphic / Yes / Reduced phenotype / Increased phenotype
Neomorphic / Yes / Same phenotype / Same phenotype
Antimorphic / Yes / Result unknown / Reduced phenotype (more like wild-type)
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