Overview
This learning module is divided into activities that support student learning about amino
acid structure, the relationship of primary conformation to function, the use of molecular
data to infer phylogeny and the effect of amino acid substitutions to function.
Activity 1
Use molecular model kit to build and convert a hydrocarbon to an amino acid by
replacing hydrogen atoms with functional groups
Activity 2
Classify amino acids based on their R groups.
Activity 3
Compare conserved to variable amino acid regions within hemoglobin beta chains
across select species using MEGA software
Activity 4
Utilize MEGA software to predict outcome of amino acid substitutions on protein
function.
Activity 5
Construct a phylogenetic tree with MEGA.
Preparation
Textbook: CAMPBELL BIOLOGY, Ninth edition, (or any that cover the topics listed
below)
Chapter 1.2 Evolution- unity and diversity of life
Chapter 4.2 Carbon bonding, 4.3 Functional groups
Chapter 5.4 Proteins, 5.5 Nucleic acids
Chapter 14.4 Mendelian traits – Cystic fibrosis, Sickle cell disease (Evolution)
Download MEGA-MD
Copy:
General structure of amino acids sheet (class set)
Specific structure of amino acids classification sheet (group or partner sets)
Sickle Cell Anemia information
Student set of activities instructions
Sickle Cell Anemia
A hemoglobin molecule consists of four subunits, 2 alpha and 2 beta, produced from
two different genes. Each of the genes codes for the synthesis of a specific
polypeptide. The sequence of amino acids (primary conformation) dictates how the
polypeptide will fold (secondary and tertiary conformations) to form a subunit. The
subunits interact to form the functional protein (quaternary conformation). Each subunit
contains an iron atom that can bind an oxygen molecule. The iron is part of what is
termed a heme group, and the protein subunits are globular, hence the name
hemoglobin.
Amino acid sequences for hemoglobin vary across species, and even within a species
there are differences from one member to another. Some of the changes do not affect
the function of the protein; others do, and are heritable. Those substitutions can be
related to specific genetic disorders.
Mutation in the hemoglobin beta chain gene is the basis of sickle cell anemia. It causes
a non-synonymous amino acid substitution of valine instead of the native glutamic acid.
That change affects the shape of the molecule, and its ability to function. The resulting
hemoglobin molecules stick together and form long, rigid molecules. The rigid protein
bends causing red blood cells to have a sickle shape. These cells die prematurely
causing anemia, they also block small blood vessels causing pain and organ damage.
Uncharacterized Amino Acids
Lesson
Opening Discussion what are student conceptions and misconceptions about amino
acids.
1. What do you already know about amino acids?
2. What kind macromolecule molecule are they used for to build in living things?
3. What is the basic molecular structure of an amino acid?
4. What makes each one different from the others?
Homework
Students build a table with the molecular structure and functional properties of the
seven Biologically Important Chemical Groups (pages 64-65).
Activity 1
Using molecular model kits students to build a glycine molecule sequentially from a
methane molecule.
1. Build a methane molecule, observe how the hydrogens are attached to the
central carbon (alpha) atom, and the tetrahedral shape of the molecule.
2. Separately build an amino group and a carboxyl group.
3. Remove a hydrogen from one bond of the alpha carbon in the methane molecule
and replace it with an amino group. If this molecule was within a cell what would
the characteristic of the molecule be now (polar or nonpolar, charged or neutral,
acidic or basic)? Explain.
4. Remove the hydrogen on the opposite side of the alpha carbon and replace it
with the carboxyl group. The simplest amino acid, glycine, is now constructed. If
this molecule was within a cell what would the overall characteristic of the
molecule be (polar or nonpolar, charged or neutral)? Explain.
Activity 2
In class without the textbook, in pairs (or small groups), using the chart of
uncharacterized amino acid structures and the homework, develop a scheme (based on
the functional groups) and categorize the amino acids. If time permits students can
share and compare their scheme and rationale with other partners (or groups).
Discussion
Re-ask original questions, and lead further discussion:
1. Are amino acids interchangeable in the primary conformation of a polypeptide?
2. What impact would a change in primary conformation have on protein folding?
3. What kinds of things do you think can cause a change in the amino acid
sequence?
Activity 3
Phillips 66 collaborative activity – After students read hemoglobin handout and pages
277-8, Sickle –Cell Disease, for discussion divide into four groups of six from different
parts of the room), ask a specific question about the readings, give them six minutes to
discuss.
Download and open MEGA-MD from http://www.mypeg.info/ Project the following steps
on the overhead projector as students perform them on the student computers.
When the Mutation Diagnosis window will appears, click the Wizard button.
The Mutation Explorer Window has two tabs, Gene Search and Prediction Data.
Type hemoglobin into the search box on the Gene Search tab and click search. There
will be a brief delay until the search for the gene is complete. The results will be
displayed in the area below.
At the gene HBB, NP_000509, click the Diagnose Variant link at the far right. After a
brief delay the Sequence Data Explorer window will appear displaying alignment of the
gene sequence across a variety of species.
On the tool bar, click on C to view sites that are conserved across these species.
Conserved sequences are highlighted.
For comparison, click on V to view the variable sites.
Discussion
1. What part of the protein do you think is represented by the conserved
sequences?
2. What might cause the sequences to change over time?
3. Note the similarities across the primate species. Compare them those of other
species. Do you think the changes in amino acid sequence can be used to infer
phylogeny? If so how? If not, why not?
Activity 4
Predict outcome of a mutation in hemoglobin amino acid sequences.
Procedure
Open MEGA-MD, a prompt window will appear. Click on Wizard.
The Mutation Explorer Window will appear. It has two tabs labeled Gene Search and
Prediction Data.
Type hemoglobin into the search box on the Gene Search tab and click Search. After a
brief delay, search for the gene is complete. The results will be displayed in the area
below.
At the gene HBB, NP_000509, click the Diagnose Variant link at the far right on the
toolbar. After a brief delay the Sequence Data Explorer window will appear displaying
alignment of the gene sequence across a variety of species.
From this window you can investigate how changing an amino acid anywhere within the
sequence of the hemoglobin beta chain will affect the function of the protein. Move to
position 7 in the chain and then on the Diagnose Variant link select Valine.
The Detail View screen appears and provides information indicating whether the amino
acid substitution is predicted to be likely deleterious, deleterious or neutral at position
seven in the protein. The consensus prediction comes from information gathered from
several prediction tools.
Near the bottom you will find Coordinate Info. block that provides the location and
position of the gene on the human chromosome, the nucleotide and amino acid
position, as well as the wild type nucleotide and the mutant nucleotide responsible for
the change in amino acid. Explore further by changing amino acid locations and
selected amino acid mutations in conserved and variable positions.
Activity 5
Generate a phylogenetic tree that will provide the native amino acid for this (or any)
position across the species, click on the Explore Ancestors link and select Infer
Ancestral Seqs (ML).
A tree will be generated listing the native the amino acid for that position across species
.
Discussion
1. Based on that data, is the amino acid at position seven conserved or variable
within primate species?
2. How does it compare with that position in other species? Explain what that infers
about phylogeny.
3. What is the wild type amino acid at position 7
4. What is the consensus prediction for a substitution of valine at that position?
5. What is the difference in the R groups between the wild type amino acid and
valine?
This mutation is the basis of sickle cell anemia.