Final projectIn this class, we have discussed the various techno.docx

Final project
In this class, we have discussed the various technologies
humans use to convert energy into practical forms, the physical
principles and equations underlying these technologies, and
their impacts on the environment and humans. We have
discussed human energy use world-wide and have often
examined energy use in detail in the United States. In this
project, you will analyze the use of energy by a non-US
country. Write a report analyzing the use of energy by a
particular country (Japan) both quantitatively and qualitatively.
Questions that are worth addressing include: What is the total
consumption rate of primary energy, both total (in terawatts)
and per capita (in kilowatts per person)? What is the percentage
contributed to this total consumption by each primary energy
source, and how does this compare both to the US and to the
world as a whole? What is the current rate of CO2emission (in
kilograms per year), both total by the country and per capita?
How does this compare both to the US and to the world as a
whole (provide US and world-wide total rate of energy
consumption and per capita rate of energy consumption)? What
fraction of the country’s total primary energy consumption is
used to produce electricity (as opposed to being used directly)?
Which factors explain the country’s energy portfolio relative to
other countries (for example, natural resources available, policy
choices)? Which if any policies do the country have to reduce
its greenhouse gas emissions? What long-term plans or goals
does the country have for its energy portfolio? Your report
should include both quantitative analysis (e.g. combining total
numbers with population numbers to determine per capita
numbers; comparing numbers for this country with the US and
with the world) and qualitative analysis. You should focus on
reporting and analyzing the facts of the country’s current and
planned future energy usage. It should not be in the style of a
persuasive essay in which you advocate for particular choices in

energy usage. Your report should be between 1500and 2000
words(approximately3-4 pages depending on font and spacing).
Up to one additional page can be used for figures (tables,
charts, graphs, or other graphics). No such figures are required.
References should be provided for all the information you use,
and they will not be included in the word count. You can use
whatever format you like for the references, as long as it is self-
consistent and provides all information necessary to find the
reference(include URL for web sites, along with the date you
accessed the site).
Instructions You must read these first.
This assignment is divided into sections, each labeled with a
major topic. The questions were written using the key concepts
and especially the essential skills from each lecture, so while
the questions can be a bit detailed, they are exactly targeted to
our course content.
I recommend that you start by trying to answer each question
without outside resources. Then, you may consult the text,
lecture notes, and other outside resources to complete your
answers. It is essential and required that your answers be your
own work and in your own word. Any diagrams (which are
encouraged) need to be your own, just as they would be on an
in-class exam. Do not share you own answers, or use another
student’s answers, to complete this exam. Also, avoid trying to
do a sentence-by-sentence paraphrasing of material from an
outside source. If you need to use an outside source, study that
source, then put it away, and then write your answer from your
own knowledge.
You will submit your answer through Turnitin.com. Of course,
Turnitin.com will detect outright cut-and-paste copying, which
will be treated as cheating on a major assignment. I expect (and

hope) to see none, or very little of that. Turnitin.com will also
highlight cases in which answers are much too close to an
outside source – this occurs when a student attempts to reword
sentences from their sources. Because swapping and shuffling
words can be done with little of the information being
understood, I will omit regions that Turnitin.com marks as
having very high similarity to other sources while reading your
answers. I will consider that to be not doing the assignment
correctly. This isn’t something that you have to worry about if
you have your outside sources closed while you write your
answers.
This is not a term paper. The time required to actually write the
exam, not counting time spent on outside resources, should be
on the order of what we would spend on an in-class exam (given
that you won’t have the added pressure of a timer clicking down
towards zero, I’d expect it to take about 90 minutes to write
these answers). The questions almost all ask you to do the same
things that the essential skills in lecture told you that you would
be expected to be able to do. The best way to submit your
answers is to put them right into this document, just below the
matching question. Both your text and inserted diagrams are
very welcome. There will be a submission link on Canvas for
the completed exam.
Key Concepts:
0-1. _________________ is the genetic material in all living
organisms.
0-2. DNA synthesis during DNA replication, like all biological
nucleic acid synthesis, is always ____’____’ on the synthesized

strand.
0-3. All DNA polymerases require a(n) _______________
(either DNA or RNA) with a _____’-hydroxyl group, and all
require single-stranded ________________ to copy.
0-4. All living organisms initiate DNA replication at origins,
and then replication proceeds _________________ from that
origin.
0-5. Replicative DNA polymerases, in addition to their
____’____’ synthesis activity, have a 3’5’ _____________
activity that can remove recent synthesis mistakes.
0-6. ___________ are functional sequences within
chromosomal dsDNA that direct the synthesis of a product,
either an RNA or a protein.
0-7. ________________ is the synthesis of an RNA from a
DNA template.
0-8. Transcription, like all biological nucleic acid synthesis, is
always ____’____’ on the synthesized strand.
0-9. Transcription and translation are ____________ in
prokaryotes (but not in eukaryotes).
0-10. Eukaryotes have ____ nuclear RNA polymerases that
transcribe different classes of genes -for example,
RNA polymerase _____ transcribes protein-coding genes, along
with some types of functional RNAs.
0-11. Translation is the synthesis of a __________ from
information in a(n) _________.
0-12. ________ act as adaptors in translation, with one end

binding an mRNA codon by complementary base pairing, and
the other end delivering the amino acid.
0-13. A special tRNA, the _________ tRNA, is required to
deliver the first amino acid during translation initiation - this
tRNA is unique in that it enters the ribosome at the ____ site.
0-14. ________________________________ attach the amino
acid to the 3’-end of the tRNA, and there is one of these
for each ______________.
0-15. Polypeptides and the coding region of genes are colinear
– the coding sequence of a gene or mRNA can be read
__________ to give the primary sequence of a polypeptide
_________.
Genetics:
1-1A. We are going to analyze the genetics of coat color in
using three randomly chosen mice from our colony.
Male – has black fur
Female #1 – has brown fur
Female #2 – has brown fur
We set up two crosses and get the indicated offspring:
Female #1 (brown) X Male (black) all offspring have
brown fur
Female #2 (brown) X Male (black) ½ of offspring
have brown fur, and ½ of offspring have black fur

What is the simplest (and the most likely) genetic explanation
for these results?
How many genes appear to be controlling coat color in
these crosses? __________________
Which of the phenotypes is dominant?
__________________
Using capital B and small b as allele symbols, write the
genotypes for each of these mice:
Male – _________
Female #1 – __________
Female #2 – __________
1-1B. A man and woman are both of normal pigmentation, but
both have one parent who is albino (they lack skin and hair
pigmentation). Albinism is an autosomal recessive trait.
Using symbols and terms consistent with Mendelian genetics,
what is the genotype of the man in this cross? _________
Using symbols and terms consistent with Mendelian genetics,
what is the genotype of the woman in this cross? _________
What is the probability that their first child will have normal
pigmentation? ____________

What is the probability that their first child will be a girl with
normal pigmentation? ____________
What is the probability that their first TWO children will be
albino? ______________
1-2. As a genetic counselor, you routinely advise couples about
the possibility of genetic disease in their offspring based on
their family histories. This morning you met with an engaged
couple, both of whom are phenotypically normal. The man,
however, has a brother who died of Duchenne-type muscular
dystrophy, an X-linked recessive condition that usually results
in death before the age of 20. His prospective bride, whose
family has no history of the disease, is worried that the couple’s
sons or daughters might inherit this muscular dystrophy.
How would you advise this couple? What would you tell
them about the risk that one of their sons or one of their
daughters will inherit this muscular dystrophy? Be specific.

The sister of this same man described above (remember, his
brother had muscular dystrophy) is planning to marry his
fiancé’s brother (this brother does not have muscular dystrophy
nor any family history of the condition). How would you advise
this second couple? What would you tell them about the risk
that one of their sons or one of their daughters will inherit this
muscular dystrophy? Again, be specific.
1-3A. The pedigree below traces the inheritance of a common,
polymorphic trait in humans (hair color, or something else that
varies frequently in the population). Individuals with the trait
are indicated by filled-in circles or squares.
Does this trait appear to be autosomal, or does it appear to be
X-linked? _____________________

Does this trait appear to be dominant, or does it appear to be
recessive? _____________________
Based on your answers to those two questions, add genotypes to
each of the symbols above if you can determine what the
genotype is.
1-3B. The pedigree that follows is for the human trait called
osteopetrosis, which is characterized by bone fragility and
dental abscesses.
Is the gene that affects bone and tooth structure autosomal or X-
linked? _______________________
Is this trait dominant or recessive?
_________________________
On the pedigree, circle or highlight each of the symbols for
each of the individuals who you can determine to be carriers
(heterozygous) for the gene controlling this trait.
DNA Replication
2-1. In your own words, summarize the experiment the Avery,
MacLeod, and McCarty performed to show that DNA served as
the genetic material in bacteria. You will need to outline the
procedure that they used and the results that they observed. Be
especially clear on the reasoning they used to conclude that
DNA, not RNA or protein, served as the genetic material

2-2. In the 1950’s Matthew Meselson and Franklin Stahl did an
experiment in which they took bacteria that had grown for many
generations in medium containing the stable nitrogen isotope
15N, and transferred them into medium containing only the 14N
isotope of nitrogen. They purified DNA from these bacteria at
time zero (before transfer to 14N) and after 1 and 2 rounds of
DNA replication in 14N medium.
When they analyzed the density of DNA molecules at time zero
(before bacterial had been in the 14N medium), what did they
observe?
When they analyzed the density of DNA molecules after one
round of DNA replication, what did they observe?

When they analyzed the density of DNA molecules after two
rounds of DNA replication, what did they observe?
What was the major conclusion from the Meselson-Stahl
experiment?
2-3. Add each of these proteins, correctly labeled, to this
replication fork. Note that the arrowheads in the figure indicate
the direction of synthesis.
Do Distribute or Post Any Part of These Problems
Name _____________________
I know I’m asking for a 2-deminsional drawing of
a 3-deminsional movie, but do your best
to capture the functions of these components.
DNA helicase

SSB protein
primase
topoisomerase
DNA polymerase I
DNA polymerase III
DNA ligase
Now, label the following-
both 5’ and both 3’ ends of the parent DNA molecule
leading strand
lagging strand
an RNA primer
an Okazaki fragment
Transcription:
3-1. In this question you will summarize the process of
transcription initiation as it occurs in E. coli.
Define “promoter”. Be clear about what it is and what its
function is.
Distinguish between the functions of the core of RNA
polymerase and of the sigma subunit of RNA polymerase.

Describe the steps in initiation of transcription as in occurs in
E. coli. Be sure to keep the steps in order, and highlight the
roles of the promoter and the sigma subunit in your
descriptions.

3-2. This diagram shows the structure of a typical protein
coding gene in a eukaryote (such as us humans).
On the gene diagram, clearly label the introns and the exons.
Clearly indicate the start and the end of each exon. No credit
for ambiguous answers.
In the space below the gene, draw the primary transcript that
RNA polymerase II would synthesize (note that +1 marks the
transcription start site).
Below the primary transcript, show and label each step in the
processing of the primary transcript to produce the final mRNA.
Be careful to keep your drawing correctly lined-up with the
gene above it. For this diagram, one of the main things I will
be looking at is which parts of the gene remain in the final
mRNA, and the main way I will judge that is how well lined-up
the partially processed RNAs are with the gene.
On your final mRNA, label the 5’and 3’ ends, the 5’-UTR and
the 3’-UTR, and the protein coding sequence.

Translation:
4-1. In order for translation to occur, the ribosome must
assemble on an mRNA and begin recruiting tRNAs, all before
the first peptide bond is formed. List the steps involved in
translation initiation in E. coli, starting with a newly
synthesized mRNA, and ending just before the first peptide
bond is formed. Each step can be stated in one sentence, but
make an effort to be specific in what is happening. (For
example, you wouldn’t just say a tRNA binds the ribosome –
it’s important whether that tRNA binds at the A-site or at the P-
site, so include that information.)

4-2. Here is a short region of the DNA for a gene. This short
sequence shows the start codon, which is underlined and bolded.
This is only a short piece near the start of a gene, so the stop
codon isn’t included.
5’ – . . . A A G C T A T G C A G G C C T C A G C A A C
A . . . – 3’
3’ - . . . T T C G A T A C G T C C G G A G T C G T T G
T . . . – 5’
Write the sequence of the encoded mRNA. Be sure to label the
5’ and 3’ ends of the mRNA.
Write the sequence of the encoded polypeptide chain. Be sure
to label the amino- and carboxy-ends.
Rewrite (or copy-paste) the DNA sequence I gave you above,
but include an example of a synonymous mutation.
Now, write the sequence of the polypeptide chain encoded by
the mutated gene region you just wrote.

but include an example of a misense mutation.
but include an example of a nonsense mutation.
but include an example of a frameshift mutation.

4-3. To demonstrate an understanding of translation elongation,
we’ll start somewhere in the middle of translation of a
polypeptide. At this moment, the entire ribosome (the small
and large subunits) is bound to the mRNA, and there is a tRNA
bound at the P-site. Attached to the 3’-end of this tRNA is the
start of the polypeptide-
Amino-Met-Leu-Ser-Ala-Phe-tRNA
At this starting point, there is no other tRNA bound to the
ribosome, and the next codon is 5’-UGG-3’
When the next tRNA binds to the ribosome, what amino acid
will be attached to that tRNA?
And for that next tRNA, write the sequence of the anticodon
that is part of that tRNA.
5’ - __ __ __ -3’
And for that tRNA, at which of the tRNA binding sites on the
ribosome will it bind?
At the moment that the ribosome forms the next peptide bond,
what will the sequence of the newly extended peptide be? Use
the same format that I used when I gave you the initial peptide
sequence, but include the new amino acid in the sequence.

And at that moment when the ribosome forms the next peptide
bond (the one you just showed in the previous part of this
question), at which site of the ribosome will the tRNA carrying
that peptide be bound?
Eventually, translation will need to end and the completed
polypeptide must be released. Briefly explain how this
translation termination occurs.

Final projectIn this class, we have discussed the various techno.docx

Recommended

Recommended

More Related Content

Similar to Final projectIn this class, we have discussed the various techno.docx

Similar to Final projectIn this class, we have discussed the various techno.docx (15)

More from tjane3

More from tjane3 (20)

Recently uploaded

Recently uploaded (20)

Final projectIn this class, we have discussed the various techno.docx