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7. Studying genetic diversity in species.
As we know the knowledge of gene structure is extremely important for gene manipulation as well as for understanding basic principles of life. The common structure of a gene is shown below.
| Sequence Element | Function |
| Promoter | To target RNA polymerase to DNA and to start transcription of a mRNA copy of the gene sequence. |
| Transcription terminator | To instruct RNA polymerase to stop transcription. |
| Shine-Dalgarno sequenceand translation start | S-D sequence in mRNA will load ribosomes to begin translation. Translation almost always begins at an AUG codon in the mRNA (an ATG in the DNA becomes an AUG in the mRNA copy). Synthesis of the protein thus begins with a methionine. |
| Coding Sequence | Once translation starts, the coding sequence is translated by the ribosome along with tRNAs which read three bases at a time in linear sequence. Amino acids will be incorporated into the growing polypeptide chain according to the genetic code. |
| Translation Stop | When one of the three stop codons [UAG (amber), UAA (ochre), or UGA] is encountered during translation, the polypeptide will be released from the ribosome. |
Example: A gene coding sequence that is 1,200 nucleotide base pairs in length (including 1200 the ATG but not including the stop codon) will specify the sequence of a protein/= 3400 amino acids long. Since the average molecular weight of an amino acid is 110 da, this gene encodes a protein of about 44 kd, the size of an average protein.
Classically, genes are identified by their function. That is, the existence of the gene is recognized because of mutations in the gene that give an observable phenotypic change.
Historically, many genes have been discovered because of their effects on phenotype. Now, in the era of genomic sequencing, many genes of no known function can be detected by looking for patterns in DNA sequences. The simplest method which works for bacterial and phage genes (but not for most eukaryotic genes as we will see later) is to look for stretches of sequence that lack stop codons. These are known as open reading frames or ORFs. This works because a random sequence should contain an average of one stop codon in every 21 codons. Thus, the probability of a random occurrence of even a short open reading frame of say 100 codons without a stop codon is very small (61/ 64)100 = 8.2 x 10-3
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