BIO/CSC 295 2009F Bioinformatics

Class 10: Protein Alignments (1)

Back to Gene Alignments (4). On to Protein Alignments (2).

This outline is also available in PDF.

Held: Tuesday, 29 September 2009

Summary: We consider how our techniques for aligning DNA sequences might change as we think about aligning protein sequences.

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Notes on Proteins

BioConcept Questions from Chapter 4

Since the chapter seems fairly straightforward, we'll go over the BioConcept questions. [From St. Clair and Visick, p. 90.]

1. Suppose a mutation changes a codon in a gene from GUA to GAA. What is the corresponding amino-acid change?

2. What are two ways in which this small change in DNA can produce a drastic change in the function of the protein encoded by this gene?

3. Even though this mutation changes only a single nucleotide, it is rarely observed when comparing actual genes from different organisms. Why isn't it more common?

4. The enzyme lactase is found in your small intestine and coverts lactose from dairy products into two simple sugars. The active site of this protein, where the enzyme binds and breaks the lactose, is made up of several amino acids, and as you would expect, mutations that change these amino acids often affect the function of the enzyme. But, some mutations that change amino acids far from the active site also drastically affect enzyme function. What could explain the effect of these mutations?

5. Some mutation in HBB produce beta-globin proteins that appear to have exactly the same three-dimensional conformation as normal beta-globins. Yet, these mutations produce hemoglobin molecules that do not function properly. Can you think of a possible explanation?

6. Suppose a gene's coding sequence begins with ATGCTCCGGCAAAGG.... A gene in another organism begins with the sequence ATGTTAAGAAACCGT..., so there does not seem to be much sequence similarity. Would our conclusion be different if this were a protein alignment? (Hint: Translate the two sequences before answering the question.)

Sequence Alignment: From Nucleotides to Amino Acids

PAM Matrices

Disclaimer: I could not track down the original PAM paper, and the variety of online resources are surprisingly inconsistent in their descriptions.

Back to Gene Alignments (4). On to Protein Alignments (2).

Disclaimer: I usually create these pages on the fly, which means that I rarely proofread them and they may contain bad grammar and incorrect details. It also means that I tend to update them regularly (see the history for more details). Feel free to contact me with any suggestions for changes.

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Samuel A. Rebelsky,

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