CPSC 445 - Assignment 1 (covers Module 1)

released Tue, 06/01/24; due Tue, 06/01/31, 9:30 (just before the beginning of class)

1 DNA, RNA, Proteins [15 marks]

Consider the following (incomplete) eukaryotic mRNA sequence:

5'-AACAUGUGUGUCAUCCGUCUGACU...CCUUACUUUUCUCAGGGCGCAUAAUC-3'

(a) What is the corresponding complementary DNA sequence? [5 mark]

(b) What is the amino-acid sequence of the corresponding gene product (protein) under the assumption that the 5' end of the sequence shown above corresponds to the 5' end of the mRNA? (Use the standard three letter abbreviations for amino acids.) [5 marks]

(c) Sketch out the structure of the genomic DNA sequence from which this (mature) mRNA may have been transcribed (indicate all major elements). [5 marks]

2 Genetic Code [35 marks]

As a reading assignment, you have studied Douglas Hofstadter's article 'The Genetic Code: Arbitrary?'.

(a) Briefly outline the thought experiment which is provided to support the hypothesis that the genetic code is arbitrary. (No more than 200 words.) [10 marks]

(b) Briefly outline the major objections to the hypothesis that the genetic code is arbitrary, as discussed in the article itself, including the postscriptum. (No more than 200 words.) [10 marks]

(c) Based on your knowledge of molecular biology, can you elaborate the objections from part b, lending them even more credibility? Can you think of additional objections to Hofstadter's hypothesis that are not mentioned in the article? (No more than 200 words.) [15 marks]

3 Laboratory techniques [20 marks]

Please answer the following questions concisely and in your own words.

(a) What is a blunt cutter? [2 marks]

(b) What is the basic idea behind restriction mapping (no more than 50 words)? [5 marks]

(c) How are antibiotic resistence genes used in the context of cloning? [3 marks]

(d) What is the role of primers in PCR? [2 marks]

(e) How is gel electropheresis used in the context of DNA sequencing (Sanger method)? [3 marks]

(f) Give a high-level outline of an algorithm that simulates what happens to each DNA strand in one of the test tubes used in the Sanger sequencing method at a symbolic level. [5 marks]

General remarks:

The assignment has to be handed in on the date it is due before 9:30. To ensure fairness, late hand-ins will generally not be accepted (exceptions can only be made for officially documented medical reasons). Please hand your solution to Holger at the beginning of class.
This assignment should take you no longer than about 1.5-2 hours to complete, if you have good knowledge of the topics covered and did all reading assignments. However, don't wait until the last minute relying on this estimate - it might not apply to you (or anyone at all), you might need additional time to consult the literature, etc.
While cooperation between students - especially between CS and non-CS students - is encouraged, each student is expected to work out the actual solutions to the problems individually and hand in their own assignment. In other words: help each other, but do not copy solutions.
Feel always free to contact Holger, Baharak or Mohammad if you feel you need further help than can be provided by your fellow students.