Download Starch Blocker - Genomics Help

Starch Blocker
There is a type of diet pill known as a “starch blocker” sold under various trade names
such as “Phase 2,” “Phaseolamin,” and “Phaseolean.”
Look for it on the Web. Are the claims on these websites likely to be true?
The starch blocker is a protein extracted from kidney beans, so the FDA (Food and Drug
Administration) does not consider it a drug. Therefore, there are no laws regulating the
claims of effectiveness as a weigh loss agent. Many people could stand to loose a few
pounds, but they can’t give up eating starchy foods. Think like a scientist. How can we
investigate further?
These starch blocker pills contains an alpha-amylase inhibitor extracted from bean (or
wheat seeds). The alpha-amylase inhibitor is a protein (a lectin) that binds to the natural
alpha-amylase enzyme and inactivates it.
Questions:
1) Is the “starch blocker” likely to work as claimed to reduce calorie intake from
starchy foods?
What happens to starch that is eaten and not broken down by alpha-amylase?
2) Do bacteria have alpha-amylase enzymes? How about E. coli (a bacteria found in
the human gut)?
[Query: “alpha-amylase” in GenBank, BLAST against bacterial database]
Does this change your answer to question #1?
a. Get the sequence of the human alpha amylase protein from the protein
section of GenBank: http://www.ncbi.nlm.nih.gov/
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b. Use the human amylase protein sequence as the query in a BLAST
search against the Bacterial section of GenBank (use protein-protein
BLAST): http://www.ncbi.nlm.nih.gov/BLAST/
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On the protein-protein BLAST web page, scroll down to the “Options for advanced
blasting” section and choose Bacteria [ORGN] from the pulldown menu where it says
“or select from:”
The advanced options “select from” menu also includes Escherichia coli as a choice of
organism to limit the search.
c. Design an experiment to see if E. coli bacteria can grow on starch as
their only energy source.
d. Design an experiment to see if starch blocker pills prevent E. coli from
digesting starch.
3) What if the starch blocker works too well? Are there any dangerous effects caused
by a lack of alpha amylase enzyme? A geneticist would look to see if there are
any human genetic diseases associated with mutations of alpha amylase? [Look
up “alpha amylase” in the OMIM database at the NCBI website.
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4) These amylase inhibitors have been shown to slow the uptake of glucose into the
blood after a starch-rich meal. This may be beneficial to people with Type II
diabetes (effectively reduces the glycemic index). How might this work?
5) Beans are well known to cause “gastric distress” for some people. (There is a
product known as “Beano” which aids in the digestion of unusual starch
molecules found in beans.) Is it likely that the “starch blocker” will cause similar
symptoms?
6) Do humans have a protein similar to bean amylase inhibitor?
There are many ways to locate this information, but since this is a well-known
protein that is not found in humans, the SwissProt database is a good choice to get
detailed information about the protein without wading through too many
irrelevant matches. Go to the SwissProt Full text search page and type in “alphaamylase inhibitor” in the keyword search box. Check “Swiss-Prot” but uncheck
“TrEMBL”, then hit the submit button.
http://us.expasy.org/cgi-bin/sprot-search-ful
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This brings up a page with a list of about 42 matching proteins. However, there are only 3
from bean (Phaseolus vulgaris). Alpha-amylase inhibitor 1 (LEA1-PHAVU) is probably
the protein found in the commercial starch blocker products. Click on the link to LEA1PHAVU to bring up a screen with a lot of information about this protein.
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Scan the whole page, down to the bottom, where you will find a link to “P02873 in
FASTA format.” This will give you the protein sequence in a simple text format – copy
the sequence into a file on your computer (open a text editor, or word processor).
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The SwissProt “NiceProt” view page has a button at the top for a Quick BlastP
Search, which will compare the Alpha-AI-1 gene to every other protein in the
SwissProt database. The result of this search will show you that this gene has good
matches only to other plant lectin proteins. However, this BLAST tool is not very
flexible. The BLAST tool at the NCBI website provides many more options. \
Use the Advanced Options to limit the BLAST search to humans (Homo sapiens).
[Can you recognize a bad BLAST match?]
How many plants have similar proteins? [BLAST, limit to plants]
7) What is the likely role of the amylase inhibitor in plants (think about ecology)?