Drug Tanzeum Diseases Diabetes Gene and Gene Product glucagon-like peptide (GLP)-1 fusion protein Gene ID GCG Structure 3IOL 1. Report on Gene and Related Protein (3-4 pages) (30 pts) (details on navigation of PubMed site in separate Power Point) a. The name and gene code for your gene product/protein. b. Determine chromosome location of your gene. Paste a picture of the chromosome from MAP VIEWER into your report and describe. c. Identify the size of the coding region of your gene, include a link to the GENE page, and explain what the coding region is. Note: your gene sequence may be very long, do not cut and paste the sequence into your report. d. Determine the intron /exon structure of your gene including the number of introns and exons. Cut and paste a schematic diagram of your gene into the report, indicate position of introns, and exons, and provide a caption for the figure that describes how the sequence of the primary mRNA transcript is related to the gene (DNA) sequence. e. Identify the sequence of the mature mRNA and copy this sequence into your report with the appropriate link to this sequence. (Note: the mRNA sequence will actually be shown as a “complementary DNA” or “cDNA.” The sequence given in the database is an exact copy of the mRNA sequence, except that it has T instead of U. ) Explain how this sequence is derived from the sequence of the coding region identified above. f. Identify the Open reading frame in the mature mRNA (Coding sequence, CDS) Find the START codon, STOP codon, and highlight the open reading frame. Explain where translation begins and ends. g. Translate the first ten amino acids of the Open Reading Frame. h. Identify the protein sequence, and copy this sequence into your report with a link to the appropriate page. Check the first ten amino acids of the database protein sequence against the ten amino acids you translated above. i. Compare your (human) gene sequence with the same gene sequence from other species. Copy a representative portion of the sequence alignment into your report that shows the similarities/differences between the human protein sequence and the homologous protein sequence from at least one other species. (Note: sequences will align if you use the Courier font). Explain how the similarity/difference in sequences explains the similarities and differences between species. j. Paste a picture of the secondary (worm view) and tertiary (space filling) structures of your protein into your report. Note: structures have not been determined for all proteins, so you may have been given an identifier for a similar protein. Describe things about the structure, for example features of the shape, charge, or hydrophobicity. Genome database assignment and stepwise instructions Goal: improve student understanding of relationship between genes, protein(gene products), and biological functions. The exercise: Each student will be assigned a gene product/protein that will be di ...

1. Drug Tanzeum
Diseases Diabetes
Gene and Gene Product glucagon-like peptide (GLP)-1 fusion
protein
Gene ID GCG
Structure 3IOL
1. Report on Gene and Related Protein (3-4 pages) (30 pts)
(details on navigation of PubMed site in separate Power Point)
a. The name and gene code for your gene product/protein.
b. Determine chromosome location of your gene. Paste a picture
of the chromosome from MAP VIEWER into your report and
describe.
c. Identify the size of the coding region of your gene, include a
link to the GENE page, and explain what the coding region is.
Note: your gene sequence may be very long, do not cut and
paste the sequence into your report.
d. Determine the intron /exon structure of your gene including
the number of introns and exons. Cut and paste a schematic
diagram of your gene into the report, indicate position of
introns, and exons, and provide a caption for the figure that
describes how the sequence of the primary mRNA transcript is
related to the gene (DNA) sequence.
e. Identify the sequence of the mature mRNA and copy this
sequence into your report with the appropriate link to this
sequence. (Note: the mRNA sequence will actually be shown as
a “complementary DNA” or “cDNA.” The sequence given in
the database is an exact copy of the mRNA sequence, except
that it has T instead of U. ) Explain how this sequence is
derived from the sequence of the coding region identified
above.
f. Identify the Open reading frame in the mature mRNA (Coding
sequence, CDS) Find the START codon, STOP codon, and

2. highlight the open reading frame. Explain where translation
begins and ends.
g. Translate the first ten amino acids of the Open Reading
Frame.
h. Identify the protein sequence, and copy this sequence into
your report with a link to the appropriate page. Check the first
ten amino acids of the database protein sequence against the ten
amino acids you translated above.
i. Compare your (human) gene sequence with the same gene
sequence from other species. Copy a representative portion of
the sequence alignment into your report that shows the
similarities/differences between the human protein sequence and
the homologous protein sequence from at least one other
species. (Note: sequences will align if you use the Courier
font). Explain how the similarity/difference in sequences
explains the similarities and differences between species.
j. Paste a picture of the secondary (worm view) and tertiary
(space filling) structures of your protein into your report. Note:
structures have not been determined for all proteins, so you may
have been given an identifier for a similar protein. Describe
things about the structure, for example features of the shape,
charge, or hydrophobicity.
Genome database assignment and stepwise instructions
Goal: improve student understanding of relationship between
genes, protein(gene products), and biological functions.
The exercise:
Each student will be assigned a gene product/protein that will
be discussed in class during the pathways or electricity portions
of the course. The assignment will be to:

3. Complete a digital laboratory project that involves retrieving
information about the gene, mRNA, and protein from genome
databases at the National Center for Biotechnology Information.
Research the expression and function of the gene
product/protein
Leaning Objectives:
Successfully navigate genome databases and retrieve
information on genes and gene products.
Distinguish gene (DNA) sequences, mRNA sequences, and
protein sequences.
Understand relationship between gene sequences, mRNA
sequences, and proteins.
Compare proteins sequences of humans and other species and
explain significance of observed homology.
Connect gene sequence and the structure of the gene product to
biological function and the regulation of these functions.
Understand the role of gene sequences and gene products in
maintaining health and the origin of disease.
This document
This document describes the genome database assignment and
report and provides step-by-step instructions . The instructions
are illustrated with an example of the gene and gene product for
glucagon, GCG, a hormone involved in maintaining adequate
levels of sugar in the blood.
Deliverables
Rough draft of Genome Section of the Final Paper by end of
Genome Unit
Corrected Genome Section as part of the Final Paper submission
during the last class.
Genome database collection:

4. The name and gene code for your gene product/protein.
Determine chromosome location of your gene. Paste a picture of
the chromosome from MAP VIEWER into your report and
describe.
Identify the size of the coding region of your gene, include a
link to the GENE page, explain what the coding region is. Note:
your gene sequence may be very long, do not cut and paste the
sequence into your report.
Determine the intron /exon structure of your gene including the
number of introns and exons. Cut and paste a schematic
diagram of your gene into the report, indicate position of
introns, and exons, and provide a caption for the figure that
describe how the sequence of the primary mRNA transcript is
related to the gene (DNA) sequence.
Identify the sequence of the mature mRNA and copy this
sequence into your report with the appropriate link to this
sequence. (Note: the mRNA sequence will actually be shown as
a “complementary DNA” or “cDNA.” The sequence given in
the database is an exact copy of the mRNA sequence, except
that it has T instead of U. ) Explain how this sequence is
derived from the sequence of the coding region identified
above.
Identify the Open reading frame in the mature mRNA (Coding
sequence, CDS) Find the START codon, STOP codon, and
highlight the open reading frame. Explain where translation
begins and ends.
Translate the first ten amino acids of the Open Reading Frame.
Identify the protein sequence, and copy this sequence into your
report with a link to the appropriate page. Check the first ten
amino acids of the database protein sequence against the ten
amino acids you translated above.
Compare your (human) gene sequence with the same gene
sequence from other species. Copy a representative portion of
the sequence alignment into your report that shows the
similarities/differences between the human protein sequence and
the homologous protein sequence from at least one other

5. species. (Note: sequences will align if you use the Courier
font). Explain how the similarity/difference in sequences
explains the similarities and differences between species.
Paste a picture of the secondary (worm view) and tertiary
(space filling) structures of your protein into your report. Note:
structures have not been determined for all proteins, so you may
have been given an identifier for a similar protein. Describe
things about the structure, for example features of the shape,
charge, or hydrophobicity.
Go to www.pubmed.gov
Find the “GENE” database from the drop down SEARCH menu.
Enter your gene code or the name of the gene and the word
“human” or “Homo sapiens” in the search box. Hit GO.
Click on the entry indicated by your gene code
4
Review the information on your gene. Research additional
information on your gene and its gene product (protein) online.
Wikipedia is an acceptable source for this information. All
sequence information (below) must be retrieved from the NCBI
database.
Scroll down and click on the link Map Viewer, located on the
right hand side under links.
5

6. Identify the chromosome containing your gene sequences and
copy and paste the schematic of the chromosome showing the
location of the gene sequences for your gene.
Go back to the Gene page
6
Move your curser over the exons (green) to highlight
transcription unit for your gene.
Then click on GenBank. This link will take you to the database
entry describing the gene sequence for your gene.
There is no step #10
7
The length of the gene sequence will be given at the top of this
page. Scroll to the bottom, and you will find the entire gene
sequence (coding region only)..
Scroll to the bottom, and you will find the coding region of your
gene. This may be very (very) long. Copy the link for this
sequence into your report .
Identify the bases that are included in the mature mRNA by
looking in the left margin for information indicated by mRNA.
. For example, the mRNA for glucagon is comprised of bases
exons. Identify how many exons are in the genes. Identify the
sequences that are in the introns (e.g. the intervening
sequences) and the number of introns. Number the nucleotides

7. at the beginning of each exon and intron in your schematic.
(Note: if your gene has more than 10 exons, include only the
first ten in your schematic.)
8
13. Draw a schematic of your gene indicating the total length
and positions of introns (blue in previous view) and open
reading frame/coding sequence (red in previous view). The
length of the gene sequence is shown under “gene.” The
positions of exons within the coding region is shown under
mRNA as the sequences that are “joined” to form the mature
mRNA. The sequences that will comprise the open reading
frame (coding sequence) are shown under “CDS .”
9
To access the mature mRNA sequences, click on /transcript_id=

8. “XX XXXXX.XX
10
11
Scroll down and you will find the mature mRNA sequence.
Identify the length of the gene and look at the gene sequence at
the bottom of the page. Compare the length of this mRNA
sequence to the length of the genomic sequence identified
above. Copy and paste the mRNA sequence into your report.
(Note: even though mRNA is comprised of A, G, C, and U , it is
traditional to show all sequences using the DNA code – A, G, C,
and T. The reason for this is that it is technically hard to work
with RNA in the laboratory, so most experimental work is done
by coping RNA in to DNA to make a copy of the RNA – called
a cDNA.)
Look in the left margin for information designated as CDS
(Coding Sequence). This will identify the first and last bases of
the open reading frame. Identify the first base in the sequence
and confirm that it is a START codon. Identify the last base of
the coding serquence and identify which of the three possible

9. STOP codons is used. Highlight (color or italics) the region
between the START and STOP codons that represents the open
reading frame. Using the tables given below, translate the first
ten codons following the START codon using the code on the
next slide.
12
Click on Graphics at the top of the previous screen. Copy a
screen shot of the graphical representation of the mature mRNA
sequence into your report.
14
Go back to the page with the sequence of the gene.
15
Scroll down an click on /protein_id=“NP XXXX.XX

10. 16
This page has information on the protein sequence – primary
structure – of the protein. Copy the link into your report.
Scroll down to the protein sequence. Copy the protein sequence
(in one letter code) into your report using the table on the next
slide. Check the ten amino acids you translated above with the
sequence shown. Are they the same?
17
Return to the GENE page.
Click on HomoloGene in the right margin under links
19
This page will show related genes from other species in the

11. database. Species include: Homo sapiens=human, Pan
troglodytes=chimpanzee, Canis lupus familiaris=dog, Bos
Maurus=cow, Mus musculus=mouse, Rattus norvegicus=rat,
Gallus gallus=chicken, Danio rerio=zebrafish.
Scroll down to protein alignments, and click on “Multiple
Alignment”
20
Compare this human protein sequence with that of other related
specieCut and paste the alignment of the first 50 amino acids
into your report. Hint: you may want to reduce the font and
change it to one with even spacing (e.g. Courier) to keep things
aligned. Replace the sequence code at left with the common
name of the species. Comment on how similar or dissimilar the
sequences are to human sequence.
21
Click on Multiple Alignments
28. Find the “Structure” database from the drop down SEARCH
menu. Enter your Structure # and Hit GO.
29. Click on the picture that appears.

12. 30. Double click on Structure View in Cn3D (below the
picture).
31. The secondary structure of the protein will be displayed .
You can turn this picture using your cursor to examine the
structure. Copy this picture into your report.
32. To view the tertiary structure of the protein, use the drop
down menu under “Style” and
click on “Rendering shortcuts and then “Space Fill”. You
can also color amino acids by charge using the drop down menu
under “Style “ and click on “Coloring Shortcuts” and “Charge”.
Copy and paste this picture in your report.