BS 50 Genetics and Genomics Week of Oct 24

Transcription

1 BS 50 Genetics and Genomics Week of Oct 24 Additional Practice Problems for Section Question 1: The following table contains a list of statements that apply to replication, transcription, both, or neither. In each empty box, put a check mark if that statement applies to replication or transcription. The new strand is made 5 to 3. The new strand is made 3 to 5. The new strand is identical to the template strand, with the exception of U s replacing T s. The new strand is complementary to the template strand. The template strand is RNA. The product is DNA. The product is RNA. An RNA primer is required to initiate synthesis. Synthesis of the new strand is initiated at a promoter. The process is done only during the S-phase of the cell cycle. The process is done only during the G1-phase of the cell cycle. Replication Transcription

2 2) In a eukaryote, how can insertion of a 500bp piece of DNA into a gene result in a) a truncated protein? b) a larger than normal, non-functional protein? c) a nascent RNA that is 500 bp longer than normal, but a wild-type protein? d) production of an mrna transcript that is 1500bp longer than normal? e) failure to transcribe any RNA at all?

3 3. You are studying a gene in E. coli that specifies a protein, part of whose sequence is: ala pro trp lys glu lys cys his You recover a series of mutants for this gene that show no enzyme activity. Isolating and sequencing the mutant products, you find the following protein sequences (assume each is the result of a single nucleotide change): Mutant 1: ala pro trp arg glu lys cys his Mutant 2: ala pro trp Mutant 3: ala pro trp ile glu lys cys his Mutant 4: ala pro trp lys lys asn val thr a. How many different mrna sequences could code for the given wild-type protein sequence? b. For each mutant, what type of mutation has occurred? c. What is the codon for the lysine at the fourth listed position in the wild-type protein sequence (the bold lys)? Show your work.

4 Question 4 (25 pts) You are interested in studying transcription factors and have developed an in vitro system using a segment of DNA that is transcribed under the control of a eukaryotic promoter. The transcription of this DNA occurs when you add purified RNA polymerase II, TFIID (the TATA box binding factor), and TFIIB and TFIIE (which bind to RNA polymerase), and nucleotide triphosphates. You perform a series of experiments that compare the efficiency of transcription in this defined system with the efficiency of transcription in a crude nuclear extract (isolated nuclei are broken open and all their contents are mixed with the various templates). 147 TATA Deleted templates RNA DNA added Nuclear extract Purified system undeleted deletion = low efficiency transcription 81 deletion = high efficiency transcription 50 deletion = no transcription 11 deletion 0 0 i) Why does the deletion that leaves only 11 bases ( 11) upstream of start cause the absence of transcription? ii) Explain the observed transcriptional efficiency of the various templates in the crude nuclear extract system and the difference in transcriptional efficiency between the crude nuclear extract and the defined system.

5 iii) None of these templates show tissue-specific expression when used to create transgenic animals. Why not? What would be needed to allow tissue-specific expression to be observed? 5) Define the following terms: a) pre-mrna (aka nascent RNA): b) mrna: c) intron: d) exon: e) splicing: f) capping: g) polyadenylation : h) alternative splicing:

6 Question 6 (18 pts) The gene you are studying has 3 exons and 2 introns with the following sizes: size exon 1 1 kb exon 2 exon 3 intron 1 intron 2 2 kb 3 kb 1.5 kb 2.5 kb Draw a diagram of the DNA using the line below. Below your diagram, draw the mature, processed mrna (roughly to scale). Where appropriate, indicate the location of each intron and exon, the 5 UTR, the 3 UTR, the TATA box, the 5 cap, the start codon, the stop codon, and the polya tail.