Download Alignment Table

Implementing Vision and Change Using Concept-Driven Teaching Strategies
NSF RCN-UBE Grant #0957205
Designing Scientific Teaching Tools for BMB Education
UC Santa Barbara
February 8, 2014
BMB Alignment Table Template
Please save this template as a separate working document for your group, with the filename as:
Alignment LocationAbbr LastNameA LastNameB LastNameC LastNameD.docx
(e.g., Alignment USD Garcia Nguyen Smith Thompson.docx)
Designed by:
Davon Callander
Sara Olson
Thomas Schmidt
Selected Aspect of BMB:
A1 Foundational Concepts
Keywords:
Search terms relevant to your alignment
Initial Overall Learning Goal:
Understand how nonsense, missense, and silent mutations affect characteristics of the resulting
polypeptide.
Initial Specific Learning Objective:
Students should be able to convert a DNA sequence into amino acid sequence and identify how
mutations affect protein composition. Given a DNA sequence, students should translate into
protein and identify effects of mutations on protein structure/function.
Overall Learning Goal: Understand nonsense, missense, and silent mutations and how they
may affect characteristics of the resulting polypeptide.
Specific
Learning Objective
Specific
Learning Assessment
Specific
Learning Strategy
POGIL-type exercise centered
on the insulin A chain – use
medical relevance (diabetes)
to hook student interest.
Provide DNA sequence for
insulin A chain. Embedded in
this sequence are alternative
start codons with nearby stops
(LO2).
1. Use a codon table to
convert a DNA codon into
an amino acid. (Low)
Provide a DNA sequence with
several positions highlighted
2. Identify a correct reading
where specific mutations could
frame start and stop
occur. Students will need to
codons to identify the
identify the correct reading
correct reading frame.
frame (with correct start
(Mid)
codon), use the codon chart to
determine amino acid changes
3. Distinguish among
or protein truncations, and
missense, nonsense, and predict how that mutation may
silent mutations. (But arrive affect polypeptide
at this objective using
characteristics.
higher order cognitive
skills.) (Mid-High)
Provide an amino acid
4. Predict how a given
mutation will affect the
characteristics of the
resulting polypeptide.
(High)
5.
sequence and introduce a
“spin” on the normal condition.
Students need to design
mutations to the provided aa
sequence that would allow the
protein to be happy.
A codon table is provided so
students can translate the
DNA sequence into amino
acids (LO1).
Highlight specific nucleotides
in the sequence that can be
mutated. Students determine
which amino acid changes will
occur, if any. Depending on
which changes are present,
students discuss the effect on
the polypeptide (aa change,
truncation, no change, etc.)
(LO3).
Provide a table that classifies
aa’s into polar, nonpolar,
charged, etc. Students predict
how the mutations affect the
character of the polypeptide.
For example, changing Arg 
Asp would have a much more
dramatic effect than Arg  Lys
(LO4)
Assessment:
Design your assessment here, and be sure to include the answer or scoring rubrics.
Criteria
Low
Intermediate
Mastery
Didn’t quite get to this
Strategy:
POGIL-type activity that should take 30-40 minutes.
1. Provide DNA sequence for insulin A chain. Embedded in this sequence are alternative start
codons with nearby stops (LO2).
2. A codon table is provided so students can translate the DNA sequence into amino acids
(LO1).
3. Highlight specific nucleotides in the sequence that can be mutated. Students determine
which amino acid changes will occur, if any. Depending on which changes are present,
students discuss the effect on the polypeptide (aa change, truncation, no change, etc.) (LO3).
4. Provide a table that classifies aa’s into polar, nonpolar, charged, etc. Students predict how
the mutations affect the character of the polypeptide. For example, changing Arg  Asp
would have a much more dramatic effect than Arg  Lys (LO4)
Based on the attached Codon Table convert the following DNA sequence to the amino
acid sequence.
Insulin Sequence:
*
AATCATGGGCATCGTCGAACAATGTTGTACCTCAATCTGTTCACTTTATCAACTTGATAATTATTGTAATGAGGCTATGAT
#
#
#
# #
#
G
T
C
T G
C
1
2
3
4 5
6
Give the amino acid sequence:
Identify the mutations:
1.
2.
3.
4.
5.
6.
Convert the sequence below to its nt sequence without referencing to the nt
sequence above. (Due the wobble effect it will lead to a class discussion)
Insulin A Chain:
CCTSICS
A patient comes into the doctor with a truncated form of the insulin A chain. The
resulting sequence is shown below, can you introduce a mutation to into problem #1
to cause this truncation?
M
G
I
V
E
Q
C
C
T
S
I
C
S
L
Y
Extra Credit:
Can you come up with an idea how to change the amino acid composition without
changing the nt sequence at the DNA level based on the figure below.
(*note: looking for an answer about deamination)