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Assignment 6 Overview In this assignment, your program will simulate protein synthesis from DNA. Specifically, it reads a DNA string from a file specified on the command line, synthesizes the protein that would be created from this DNA string by the human ribosome, and writes that protein's representation to the standard output stream The details of the assignment are specified in the Detailed Requirements section below. The Backgrouned section that follows is a short tutorial on the subject of protein synthesis. This assignment will give you experience in using hashes and in processing text using Perl's pattern-matching capabilities. Background A DNA string, also called a DNA strand, is a finite sequence consisting of the four lowercase letters a, c, g and t in any order. The four letters stand fo Nucleotides, which are the molecular units from which DNA and RNA are composed, are also called bases A special enzyme called RNA polymerase uses the information in DNA to create RNA. A RNA string or RNA strund is a finite sequence consisting of the four lowercase letters a, c, g, and u. The a, c, and g h the same names as they do in DNA, but the u represents uracil When DNA is transcribed to RNA by RNA polymerase, each thymine base is converted to uracil. Hence RNA strings have u's wherever DNA has t's. r the four nucleotides: adenine, cytosine, yuanine, and thymine. RNA in turn serves as a template for the construction of proteins, which are sequences of amino acids Proteins are synthesized within the ribosomes of living cells by a process called trunslation. In translation, the RNA string is read in three-letter groups called codons. Each codon codes for a particular amino acid. For example, guu codes for valine, and uca codes for cysteine. Let us count how many possible three-letter sequences there are in which each letter can be a, c, g, or t. There are four choices for the first letter, four independent choices for the second letter, and four for the third, so there are 43- 64 different codons. On the other hand, there are only 20 different amino acids. Some amino acids are coded for by multiple codons. For example, uca, ucc, ucg, and ucu all code for cysteine. Some codons do not code for any amino acids; they are stop codons. Their purpose is to temporarily terminate protein synthesis while reading the RNA string. There are three such stop codons: uaa, ung, and uga. When a stop codon is reached in the RNA string, protein synthesis is paused. The RNA continues to be read, but amino acids are not created until it sees a special start endon. When it finds a start codon, translation begins again. This is very much like the way that the Perl compiler treats the comments in your Perl programs. As it reads your program, it translates it into executable instructions until it finds comment start character #-The # tells the compiler to stop cmpiling, and the next newline daracter tells it to start conpiling again. The # acts like a stop code and the new line, like a start code. The start codon in RNA is aug, which also codes for methionine (Met). Thus, not all of a RNA string is translated into protein; there are large regions that are gaps in the translation oss. As the RNA is read, when a gnp is reached, it is skipped over until a start colon is found. These gaps are sometimes much larger than the non-gaps in the RNA. As the ribosome reads the RNA, it splices together the separate pieces that it has translated. As an example, the RNA strand gguuuauggucucuga as the following sequence of codons