AP Biology Ancillary Lab Signaling Molecules
Pages 126-140
Name: _______________________ Date: ________ Period: _________
All organisms MUST take in/make its own food and break down materials to create a
source of energy for the cell to maintain homeostasis.* (There are some exceptions to this
statement that have recently been discovered.) Homeostasis is to maintain organism and stay
organized (and perhaps to grow larger and replicate). Each cell gives off waste products and
other products that “may” help the single cell or multi-celled organism to be successful. Each
waste product or other products are either the result of breaking down food or foreign material,
or created “by accident” as a form of signaling or communication with other cells or organisms.
Moreover, all cells have a collection of receptor molecules on their cell surface that can bind to
waste products or “other” products created by other cells or bacterium.
A side fact is that present scientists now know that certain symbiotic bacteria that live
inside us play important roles in digestion, protection against other “bad” bacteria, behavior, as
well as affecting/modifying signaling pathways and metabolic pathways! When bacterial
populations are changed or upset by pathogenic (disease causing) bacteria or antibiotics, this can
causes illnesses that we NOW know can be ameliorated (made better) by bacterial transplants
(i.e. see fecal transplants/Internet).
How do all these bacterial create these various effects in our bodies? These bacterium
release waste products and other products (signal molecules?). The compounds and products that
are released can be made up of carbohydrates, cholesterol (and cholesterol-like compounds),
proteins, lipids, and combinations of many of those just listed (example: lipoproteins,
glycoproteins, polysaccharides…). Each of these molecules may be associated with other
molecules when released or hook up with other molecules after they are released. The point of
all of this is really --- how do these molecules “actually attach” to other molecules or receptors
to cause a single reaction or a set of cascading reactions (see text pages 134-135). The answer
lies in a simple experiment that we will do in class.
All molecules and compounds are made up of individual atoms with covalent bonding,
ionic bonding, hydrogen bonding, Van der Waal forces, and other attractive forces. We will be
focusing in on the simplest attractive forces that rule most of the interactive forces between
molecules and their receptors, protein enzymes and their substrates, and ribozymes and
their substrates. These are positive charges and negative charges. We confine ourselves to
these because they are easy to understand and control most interactions between molecules in the
cell and the body! Proteins are the work-horse molecules of the cell and in multi-cellular
organisms. Proteins are made up of building blocks called
amino acids. There are twenty different naturally occurring
amino acids in the human body (to date there are 22
naturally occurring on Earth-24 if you count artificially
created amino acids). Amino acids are separated into four
(or five*) groups: Non-polar, polar/uncharged, charged,
and special function (proline, methionine, and cysteiene)
(*the last group refers to “aromatic” which can be grouped
into non-polar and polar uncharged---see page 42 of text).
The portions of the amino acids that are in the “white”
squares (ibid page 42) are the “R” groups. The “R” groups
are those that are responsible for the majority of
Page 2 (Cont. Ancillary Lab/Signaling molecules AP Bio.)
interactions with receptors. The “R” groups point away
from the center of the protein molecule in a 3-dimensional
shape (see page 43 shows protein “R” groups binding to
other parts of the protein and picture to right-shows “R”
groups helping to bind the enzyme to a substrate). We
can somewhat mimic this interaction in our classroom.
If you understand this concept of positive binding
to (attracted to) negative charges-and nonpolar (Van der
Waals) interaction, then all other reactions in the cell and body simply build off of this simple
concept.
You will take out a large sheet of paper and draw one of the following symbols (VERY
large- fill entire paper); +, or -, or 0 (zero). Our teacher will arbitrarily separate you into two
groups. You will line up randomly across from another student and display your “symbol”. Now
will write down the charges facing one another below: (boxes represent the “R” groups of amino
acids that make up the protein/enzyme or the substrate receptor)
Protein/enzyme molecule
Substrate or receptor molecule
1.) In the blue boxes put the appropriate symbol and in the red boxes put the appropriate symbol
for the amino acid directly across from it. (10 pts.)
2.) Now place an arrow that will force them apart if they are the same charge:
Place these arrows if they will be forced together:
Page 3 (Cont. Ancillary Lab/Signaling molecules AP Bio.)
Place this symbol if there is no effect:
(That is-neither moves away from each
other, or toward one another.) (5 pts. each)
Using what you learned moving chains of proteins in class and looking up competitive and
non-competitive inhibitors in your book AND Internet…construct the following molecules
with the correct charges for questions 3 and 4.
3.) Using the boxes referred to as the “active site” in the diagram below, construct a Shaped
molecule (label it “C”) with appropriate charges that would constitute a competitive inhibitor: (5
pts.)
Allosteric
Site
Active
Site
4.) Using the boxes referred to as the “allosteric site” in the diagram below, construct a Shaped
molecule (label it “N”) with appropriate charges that would constitute a non-competitive
inhibitor: (5 pts.)
Answer the following multiple choice questions on this handout only and hand this lab in for
credit (make sure your name is on this sheet so I can give you proper credit.(5 pts.@)
_____ 5.) Why would certain bacterium or other cells produce proteins or signal molecules?
a.) to tell other cells there is food nearby
b.) to tell other cells if there is danger nearby
c.) to tell other cells to “stay away”
d.) this could be accidental and have to reason
e.) all of the above could be true
Page 4 (Cont. Ancillary Lab/Signaling molecules AP Bio.)
______ 6.) Looking up the “R” groups in the following pairs of amino acids, which two “R”
groups of the named amino acids would attract?
a.) Arg-Lys b.) Asp-Glu c.) His-Glu d.) Ala-Lys e.) Ile-Arg
_____ 7.) What is “induced fit” when we are discussing enzyme/substrate interaction? (Internet)
a.) when the enzyme and substrate come together and their “R” groups are all the same charge
b.) when the enzyme and substrate come together and the “R” groups are opposite charges and
cause a conformational change so the shapes fit
c.) when the enzyme and substrate come together and the “R” groups cause no discernible
change in shape even though the “R” groups of opposite charges
d.) When the enzyme inhibits the substrate through an allosteric site
_____ 8.) Of the following bonds that can form between “R” groups, which is the STRONGEST
bond? (Internet)
a.) Van der Waal forces b.) hydrogen bonds c.) ionic bonds d.) covalent bonds
_____ 9.) Why would a bacterial cell have a receptor for a waste product of another bacterial
cell?
a.) could glean information that there is food available to be broken down and move toward that
site
b.) could be repelled by this waste product (could be toxic)
c.) could be a signal to turn on or turn off a gene
d.) the receptor could have been “made by accident” and have no real function
e.) all of the above could be correct
_____ 10.) Of all the amino acids listed below, which would be most accepted into the center of
a bi-lipid membrane?
a.) Trp b.) Pro c.) Asn d.) Gln e.) His
Date: ________________________________
Lesson Plan for Handout #16 A/P Biology
Objective: TLWD the ability to determine how molecules attach and interact, especially
enzyme/protein molecules with receptor/substrate molecules, using polar, positive charges and
negative charges when student demonstrate the movement of protein chains in the lab
demonstration/interaction. Moreover, students will be able to explain the difference between
competitive inhibitors and non-competitive inhibitors when investigating these during the lab
and looking up examples of these on the Internet and on the handout.
Content: Positive, negative and non polar interaction between “R” groups of amino acids in
enzyme/substrate interactions and protein/receptor interactions.
Method: Animated lab “walk-through demonstrating the attractive forces of “R” groups of
different compounds coming together.
Homework: Complete Lab Signaling Handout
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