Download Human Genetics Portfolio - Johnny El-Rady

PCB 4663 Spring 2016 Project
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PCB 4663 SPRING 2016
PROJECT
DESCRIPTION
 The project consists of a course portfolio with two sections. It is worth a total of 25 points,
which will constitute 12.5% of your total course grade.
SECTION I:
Question 1 (3 points)
Your BFF is a red-headed, left-handed, blue-eyed girl. She finds out that you are
taking Human Genetics and wants you to explain to her the genetic basis of her three
traits. So, your task is to provide her with the most up-to-date explanation, to the extent
that is possible. You have to do so in 400-500 words.
Question 2 (5 points)
A hypothetical genetic disease, Nanunanu syndrome, is caused by a deficiency of the
enzyme nazrat which is involved in the formation of skin. Affected individuals have skin which
is strikingly hyperextensible, fragile, and has a tendency to bruise quite easily. Mork OrKool and
Mindy McCool are planning to start a family. They visit a genetic counselor and provide him
with the following information:
1. Mork’s parents are normal, and so are his three older sisters.
2. Mindy’s parents are normal, but she has a younger brother who has Nanunanu syndrome.
3. Mork’s father has an older sister who has the disease. Their parents are normal.
4. Mindy’s father has two younger sisters, who are fraternal twins and normal. Their parents
are also normal.
a.
Construct the pedigree that encompasses three generations of the OrKools and McCools.
b. Which of the following modes of inheritance can be excluded: autosomal dominant,
autosomal recessive, Y linked, X-linked dominant, and X-linked recessive? For each mode that
you excluded, indicate the specific individual (e.g. II-1, III-2, etc.) that led you to that decision.
c.
Using the symbols N/n, assign genotypes to the extent that is possible.
d. What is the probability that Mork and Mindy’s first child will have Nanunanu syndrome?
Assume Mork’s mother is homozygous.
e.
If Mork and Mindy have a child, what is the probability that it will be normal?
Assume Mork’s mother is homozygous.
PCB 4663 Spring 2016 Project
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Question 3 (3 points)
a. Consider a normal 46,XY male and a normal 46,XX female. Diagram ALL possible
types of non-disjunction of the sex chromosomes that can occur in each case. Assume that only a
single chromosome (or chromosome pair) fails to disjoin properly in any one division.
b. The most common form of mosaicism in Klinefelter syndrome is XXY/XY. Diagram
two ways by which this can occur?
Question 4 (5 points)
On the faraway planet of Humouranus lives an organism called Bim nailliuqra. The
genetics of this organism is remarkably similar to that of humans. Indeed, the gene
expression in Bim follows the same basic pattern in humans, with the following
exceptions:
1) Transcription initiation always occurs at an Adenine.
2) Transcription termination always occurs via a rho-independent mechanism
(similar to that of bacteria).
3) Translation initiation always occurs at the first AUG of the mRNA.
4) UGA is not a stop codon; Rather, it encodes the 21st amino acid jertzine (jer).
The genetic code of this organism, with the three-letter and one-letter amino acid
abbreviations is:
2nd position of codon
U
C
1st
A
G
UUU
UUC
UUA
UUG
CUU
CUC
CUA
CUG
AUU
AUC
AUA
AUG
GUU
GUC
GUA
GUG
U
Phe, F
Phe, F
Leu, L
Leu, L
Leu, L
Leu, L
Leu, L
Leu, L
Ile, I
Ile, I
Ile, I
Met, M
Val, V
Val, V
Val, V
Val, V
UCU
UCC
UCA
UCG
CCU
CCC
CCA
CCG
ACU
ACC
ACA
ACG
GCU
GCC
GCA
GCG
C
Ser, S
Ser, S
Ser, S
Ser, S
Pro, P
Pro, P
Pro, P
Pro, P
Thr, T
Thr, T
Thr, T
Thr, T
Ala, A
Ala, A
Ala, A
Ala, A
UAU
UAC
UAA
UAG
CAU
CAC
CAA
CAG
AAU
AAC
AAA
AAG
GAU
GAC
GAA
GAG
A
Tyr, Y
Tyr, Y
Stop
Stop
His, H
His, H
Gln, Q
Gln, Q
Asn, N
Asn, N
Lys, K
Lys, K
Asp, D
Asp, D
Glu, E
Glu, E
UGU
UGC
UGA
UGG
CGU
CGC
CGA
CGG
AGU
AGC
AGA
AGG
GGU
GGC
GGA
GGG
G
Cys, C
Cys, C
Jer, J
Trp, W
Arg, R
Arg, R
Arg, R
Arg, R
Ser, S
Ser, S
Arg, R
Arg, R
Gly, G
Gly, G
Gly, G
Gly, G
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G
3rd
PCB 4663 Spring 2016 Project
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A cloned gene from Bim is given the name fun (function unknown). The following DNA
sequence, shown in the 5′ → 3′ orientation, was obtained from the non-template strand of the
gene:
1
CAATATGGAC GGCTAACGAC GAATACGCAG ATCCGGTAAC GGCTCCAGAC
51
CTAATGTGGC CATATAAAAG AGGCCAGTAG CAGGAATGGC CCTTCCCTGG
101 ACTGCCGGTT TGTCGCGGCT AACGGCAGTG TAGGAGGCCG ATGGAGAACA
151 TCAACGATGC CAGAAAATAA GAGACATCCG GGGAAACATG AATAGGAGGC
201 TACTGGATAA CACACATAAC GTAAGGGGAG AATTAATGCC CCGGGATGAA
251 GCTATTCATC CTTTTTTTCG CCGATGTTGA CATGCACTAC GTTGCAATGT
a.
Predict the sequence of the mRNA transcript of this gene. Discuss your reasoning.
b. What is the amino acid sequence of the Fun protein? Use the single-letter
abbreviations for the amino acids.
Six different mutants are found to produce a Fun protein whose primary structure is three
times longer than that of the wildtype protein. Sequence analyses revealed interesting
results: All six mutants produce mutant Fun proteins with identical amino acid sequences;
and all of them differ in only one or two nucleotides from each other, with all the
differences occurring in the same codon. The differences in DNA sequence between the
mutant and wildtype fun genes are shown below. (Key: R = purine and Y = pyrimidine)
Mutant 1 = A single R-to-Y base substitution.
Mutant 2 = A Y insertion and an R deletion.
Mutant 3 = A Y insertion, an R deletion, and a single R-to-Y base substitution.
Mutant 4 = A Y insertion, an R deletion, and a single R-to-Y base substitution.
Mutant 5 = A Y insertion, an R deletion, and a single R-to-R base substitution.
Mutant 6 = A Y insertion, an R deletion, and a single R-to-R base substitution.
c.
What is the cause of this larger Fun protein?
d. What is its amino acid sequence? Use the single-letter abbreviations for the amino
acids.
e.
Predict the different base(s) between each of the six mutants and the wildtype fun
gene? Explain how you got to your answers.
PCB 4663 Spring 2016 Project
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Question 5 (3 points)
The competition “Autosomal Idol” is underway! It is designed to select the most important
autosome out of the 22 found in humans. Only three can make it to the finals, where the whole
nation will get to vote, and your task is to select those three. So, research all 22 human
autosomes as best as you can, and choose what you believe are the three most “important” ones.
You then are asked to write 1-page essays in the form of an “autobiography”. In other words, the
essay has to be written in the first tense, where the chromosome in question is highlighting the
reasons why s/he needs to be chosen as “Autosomal Idol”. You need to write three such
persuasive essays, one for each chromosome you chose. Note: Each has to be 300-400 words.
SECTION II:
Part A – Articles R Us (4 points)
 Consists of 12 newspaper/magazine articles published this semester! These articles have
to be related to biological issues/concepts that are pertinent to this course. For example: a
discovery, advance, therapy, or ethical issue in genetics. Each article (or a photocopy of it)
should be pasted on a sheet or sheets of paper. Alongside the article will be a typed paragraph
that summarizes the article, and another that provides your interpretation of it.
 The articles have to be compiled according to these rules:
- All articles must come from newspapers/magazines catering to the general public.
- At least four different sources must be used.
- No more than six articles can come from the internet.
- No more than two articles can come from the same issue of the newspaper/magazine.
- At least one article has to come from January.
- At least three articles have to come from each of February, March and April.
- No two articles can be about the same specific topic.
Part B – Laughter is the Best Medicine (2 points)
 Consists of 6 cartoons published this semester! Each cartoon (or its photocopy) should be
pasted on a sheet of paper along with a typed paragraph that includes the reasons the cartoon is
pertinent to this class.
 The cartoons have to be compiled according to these rules:
- At least two different sources (newspapers/magazines) must be used
- No cartoon can come from the internet
- No more than two cartoons can come from the same issue
- No more than two cartoons can come from the same cartoon strip
 Note: The cartoons can also be drawn! As long as they are original.
PCB 4663 Spring 2016 Project
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INSTRUCTIONS
1. Again, it is your choice to work individually or as part of a group. The group has to be
between 2 and 5 students. No Exceptions! Note: All students in a group will get the same grade,
provided they have contributed to the project to the best of their abilities. Each member of the
group will have to sign a “Statement of Cooperation” that will be turned in with the project.
2. The project should be typed and neat. You will lose points otherwise.
3. Points will be deducted for mechanical problems such as
- speling mistakes
- the use of of repeated words
- grammatical errors you might have make
4. Points will also be deducted for answers that are NOT accompanied by an explanation.
Whenever appropriate, you cannot just provide the answer: you have to describe how you got it!
5. Points will be deducted if you do not follow any of the instructions given for the creation and
submission of the project.
6. The articles and cartoons will be graded mainly on: their pertinence to the course, the
thoughtfulness of your interpretations, originality, and neatness.
7. The project should show no signs of PLAGIARISM. If there is such evidence, you may earn a
zero for the entire project.
8. Deadlines:
a. Friday, February 19 = All groups must be formed by this date. Please try to give your
group a name that has a nice ring to it. For example, Mendel’s Maniacs! The group also
has to email me ([email protected]) with the group’s name and members.
b. Friday, March 25 = All groups or individuals must turn in a “progress report”. This
consists of a 1-2 page typed narrative outlining how far you have come to answering the
questions and compiling the articles/cartoons.
c. Wednesday, April 27 = Projects are due by 3 PM.
PCB 4663 Spring 2016 Project
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CITATIONS
To maintain consistency among all projects, I ask that you arrange your sources
alphabetically using the following citation styles:
a. Books:
- Eg:
Author(s). Date. Title. Publisher: City, State (or Country). Pages used.
Klug, W. S., and Cummings, M. R. 2005. Essentials of Genetics.
5th edition. Prentice Hall: Upper Saddle River, NJ. pp. 1-16.
b. Journal Article:
- Eg:
Author. Date. Article title. Magazine Title. Issue number: pages.
McKusick, V. A. 1988. The new genetics and clinical medicine.
Hosp. Pract. 23: 177-191.
c. Web Resources: Title of the Site. Name of the creator/editor (if given).
Date of Electronic Publication or latest update. Name of Sponsoring
Institution or Organization. Date of Access. URL.
- Eg:
Evaluation of Genetic Testing. Centers for Disease Control and
Prevention. 2015. Accessed on October 7, 2015.
http://www.cdc.gov/genomics/gtesting/index.htm
d. Cartoons
Last Name, First Name of Artist. "Title of Comic Strip." Publication Name.
Date of Publication: page number.
- Eg:
Piraro, Dan. “Bizzaro”. Tampa Bay Times. January 20, 2016: 3F.
SUBMISSION
 The project is due by 3 PM on Wednesday, April 27th. Late projects will NOT be accepted!
 Each group or individual will submit a binder (of some sort or other) that contains a hard copy
of the project. (Note: Groups need to attach the signed “Statement of Cooperation”).
 An electronic copy has to be submitted via Turnitin. If you are in a group, only one student
needs to submit the file via their Canvas account. It should be saved in this format:
PCB4663_Spring2016_Group name_Project
or PCB4663_Spring2016_Lastname-Firstname_Project, if you are working individually.
 If you have any questions or problems about this project, please don’t hesitate to contact me.
GOOD LUCK!
PCB 4663 Spring 2016 Project
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PCB 4663
SPRING 2016
PROJECT
Group Name =
.
Statement of Cooperation
We, the undersigned, hereby swear, under the conditions of the Honor System, that we have
participated fully and to the best of our abilities to complete the group project for Human
Genetics (PCB 4663).
Name (Please Print)
Signature
1.
1.
2.
2.
3.
3.
4.
4.
5.
5.
Note: Please attach this form to the finished Project, and turn them in by the due date.