Genetic Biology

1. You are in a lab that is studying the process of DNA replication. You are particularly interested to know what exactly happens at the replication fork. To answer this question, you have set up a series of DNA replication reactions in test tubes using physiological buffers and conditions. However, the student that you have hired to help you has accidentally set up every reaction incorrectly. For each scenario below, indicate if DNA replication will be affected by the mistake and explain why or why not. A. No DNA Polymerase was added b) rNTPs were added instead of dNTPs c) No primase was added d) Only dNTPs were added (no rNTPs) 2. The nucleic acid from various viruses was extracted... click for more

Construction of genetic map on the basis of transfer of genes during conjugation

Four Hfr stains of E. coli are known to transfer their genetic material during conjugation in different sequences. Given the time of entry of the markers into the F- recipient: A. Construct a genetic map that includes all of these markers. (12 points) B. Label the time distance between adjacent gene pairs. (11 points) C. Indicate the points at which the F factor is located for each of the strains. (4 points) Hfr Strain 1 Markers arg thy met thr - - Times in min 15 21 32 48 - - Hfr Strain 2 Markers mal met thi thr try - Times in min: 10 17 22 33 57 - Hfr Strain 3 Markers phe his bio azi thr thi Times in min ... click for more

Promoter sequence retrieval and pre-processing

Question 1: Promoter sequence retrieval and pre-processing Your biologist collaborator just conducted ChIP-chip experiments of transcription factor gene with ID YNL216W on Saccharomyces cerevisiae (budding yeast), and identified the promoter of 100 genes as the binding target of this factor (attached as data2.txt). These sequences are ranked according to p-values, so the first one is the most confident. Go to RSA-tools: http://rsat.ulb.ac.be/rsat/ to download the promoter of these genes. Use default upstream sequence options, and don’t worry if the sequence of a few promoters can not be retrieved. You might need to do a little manual editing to get the sequences in good FASTA format. ... click for more

Motif finding

Question 2: Motif finding Try a number of motif-finding algorithms covered in the lab, and try different parameters. What good motif can you find from the sequence? Here are some useful hints for the analysis (depends on the software you are using): • Motif width ~ 13, and search in both strands of the DNA • Ask each algorithm to report the best 3-10 motifs • Each sequence contains 0-n copies of the motif • If possible, specify the background as yeast (or S. cerevisiae) intergenic or yeast genome • If the same motif was reported by different algorithms, it is likely real and good a) What is the motif consensus (most frequent nucleotide at each position)? b) Select the single m... click for more

GO analysis

Question 3: GO analysis Now you know YNL216W is regulating these 100 genes, you want to ask what function it really has. One thing you can do is to perform GO analysis and which GO term is enriched in these 100 genes. This can be achieved at FuncAssociate: http://llama.med.harvard.edu/cgi/func/funcassociate Paste in your 100 genes, select the correct genome, and leave everything else as default. a) What are the most significantly enriched GO terms (in numbers)? b) Based on the most significantly enriched GO terms, can you summarize with less than 5 words what YNL216W regulates? c) Another thing to check is Saccharomyces Genome Database (SGD), do a quick search on YNL216W. On the res... click for more