Discussion on Zoroastrianism, Buddhism, and Classical Hinduism

read and write a paper about history and religion
“Zoroastrianism, Buddhism, and Classical Hinduism all developed out a religious world that is represented by the hymns of the Rig Vedas. Please use the Vedas, and Uppanishads, the Bhagavat Gita, and primary sources for Zoroastrianism and Buddhism to show how each new religion changed from Vedic religion.”sources are attached6 pages double space

Midterm 2
Take Home Part
Three old transport
stories.
This booklet is the take home portion of our second midterm. It is worth 52 points, but I will tally your score
as if it were 50. So there is a bit of a buffer.
This portion of the test will need to be submitted by 11/23 at the end of the day (ie 11:59 PM). As before,
there will be a corresponding link to a test form in the assignment tab in which you can input your answers
for grading. There will not be an attempt limit on the test file , but as before it might be easier to just mark
your answers as you go along using the booklet and then input your answers into the test submission form
when you are done. The reason for having this part of the midterm divided between an assignment booklet
and a test answer entry form is that the test features of iLearn don’t readily allow for a complex layout of
figures, etc. But if the answers are inputted into the testing application they can be automatically scored.
The rules are that you can use any source of information: class materials, study notes, information on the
internet. But you may not work collaboratively either with each other, a person outside the class, or a proxy
on the internet that actively responds to questions.
So, to do the take home portion, open this booklet, answer the questions, and when you are done, input your
answers by launching the test submission form.
There will be a separate test link deployed for the in-class part of the exam on Monday Nov. 23. It will show
up in your assignment content area as a separate test.
Good luck.
Instructions
STORY 1
In which Mary Moore and Gunter Blobel almost figure out how nuclear import
works. Their model would have been right, if they had chosen to study nuclear
export instead of import. This story presents some data up front, so hang with it.
The questions basically ask if you understand how nuclear transport works.
The story is based on this
paper. Old papers like this
are often behind paywalls.
You should not need to read
the paper to answer the
questions. But if you want
to access it, the paper will
be posted in a folder in
“Course Materials” on the
iLearn site.
As the title indicates, Blobel’s lab was one of the
ones that discovered Ran was required for
nuclear import.
Their assay for nuclear import was based on the
strategy depicted in the diagram. A detergent
called digitonin has the useful property of
disrupting (ie poking holes in) the plasma
membrane, but it leaves the nuclear membranes
intact.
Under these conditions Ran and import
receptors diffuse out of the nucleus because
disrupting the plasma membrane creates a large
concentration gradient across the nuclear
membrane.
The key is that Moore and Blobel can now add
back fractions (cytosolic extracts in the diagram)
to the permeabilized cells to reconstitute
transport. In other words, what do you have to
add back to get transport to work again?
The green proteins are
fluorescently labelled NLS cargo
proteins to visualize transport.
Moore found two cytosolic fractions, called A
and B, were both needed to restore nuclear
import in the permeabilized cells.
(a) shows just the permeabilized cells with
fluorescently labelled NLS cargo proteins.
The dark hole in the middle of the cells is
the nucleus-no transport.
(b) shows adding just fraction A. Now the
cargo localizes strongly to the outside of
the nuclear pores, producing the ring of
fluorescence around the nucleus. A small
amount of import into the nucleus is also
observed.
(c) shows adding just fraction B. No effect. B
by itself looks just like (a).
(d) shows adding fractions A and B together.
Now transport works great. The glowing
nuclei indicate virtually complete
transport of NLS cargo into the nucleus.
Based on already published work, it was clear that fraction A contained nuclear
import receptors. They bind the fluorescent NLS cargo proteins and then bind to
FG-nups on the cytoplasmic side of the nuclear pore complex. That is what
produces the ring of fluorescence around the nucleus. But the receptor/cargo
complexes by themselves have only limited ability to perform transport .
Moore showed that fraction B contained Ran, an important discovery. But she also
found that fraction B must contain something else besides Ran. If they just added
fraction A + purified Ran (which would have been complexed with GDP) they only
got inefficient transport. But if they added fraction A + purified Ran + a small
amount of fraction B, transport now worked great.
So their observations indicated fraction B must contain at least two factors required
for efficient nuclear transport: Ran and something else.
What proteins are in fractions A and B?
Moore tried to figure out the role of Ran GTP binding and
hydrolysis in performing transport. It was confusing.
(a) Add Fraction A, + purified Ran, + a small amount of
fraction B, + no nucleotide. Just a bit of transport.
(b) Add fraction A, + purified Ran,+ a small amount of
fraction B, + GTP. Transport works great.
(c) Add fraction A, + purified Ran, + a small amount of
fraction B, + non-exchangeable analogue of GDP. Just
a bit of transport, like adding no nucleotide in (a).
(d) Add fraction A, + purified Ran, + a small amount of
fraction B, + a non-hydrolysable analogue of GTP. Now
absolutely no transport is observed, and the ability of
the receptors to cluster NLS cargo on the cytoplasmic
side of the nuclear pores is completely disrupted.
It is worth mentioning that GTP in (b) and GTP analogs
in (c) and (d) are small enough to diffuse in and out of
the nucleus through nuclear pores. RCC1 will still be
present in the nucleus.
(a)
(b)
(c)
(d)
QUESTION 1
3 pts. From what you learned about nuclear transport, why would the addition of
non-hydrolysable GTP disrupt the ability of receptors to cluster cargo proteins
around the cytoplasmic side of nuclear pores?
A) Ran with non-hydrolysable GTP would concentrate receptors in the nucleus.
B) Ran with non-hydrolysable GTP would displace receptors from their NLS cargo.
C) Ran with non-hydrolysable GTP would not be able to bind to cargo receptors.
QUESTION 2
3 pts. From what you learned about nuclear transport, how does Ran-GDP in the
cytoplasm most efficiently get back into the nucleus to undergo nucleotide exchange.
A) Ran-GDP can interact with FG-nups like a receptor protein.
B) Ran-GDP can piggy-back on NLS cargo proteins.
C) Ran-GDP can bind to a specialized transport receptor.
D) Ran-GDP is not recycled back to the nucleus.
To try and figure things out, Blobel’s lab eventually purified the second factor in fraction
B. The found that the second factor bound tightly to Ran-GDP and was a protein with a
molecular mass of ~15 kDa (ie 15,000 Daltons). However, they never quite figured out
what the second protein was doing.
QUESTION 3
4 pts. From what you learned about nuclear transport and Moore’s data, what was
the identity of the second protein in fraction B? The average molecular mass of an
amino acid is 110. Note that this provides a second way to derive the answer.
A) RAG1, the Ran GAP (587 amino acids long)
B) RCC1, the Ran GEF (445 amino acids long)
C) NTF2 (127 amino acids long)
D) KAP1, an abundant nuclear transport receptor (514 amino acids long)
QUESTION 4
2 pts. After researching this story and writing the questions, I realized there was a
second to last sentence at the end of one of the supplement slides that I had
forgotten to delete from the previous year. Because of that, I thought I needed to
provide two different ways to answer question 3. The sentence also happens to
contains the answer to question 3. Find and write the sentence below. This is the
where the additional two points comes from.
The picture on the left is the nuclear transport model Moore and Blobel
proposed in their paper. The picture on the right illustrates our current
understanding of nuclear transport.
QUESTION 5
2 pts. The cargo receptor (fraction A) recognizes an NLS-bearing substrate in the
cytoplasm.
A) Consistent.
B) Inconsistent.
The sentences below are from the Moore and Blobel paper describing how they thought
transport might work. It is interesting to look back and see what they got right and what
they got wrong. For each statement, is it consistent or inconsistent with our current
understanding of how nuclear transport works?
QUESTION 6
2 pts. Ran-GTP associates with cargo-receptor complexes in the cytoplasm, stimulating
transport into the nucleus.
A) Consistent.
B) Inconsistent.
QUESTION 7
2 pts. Movement of the receptor/cargo complex through the nuclear pore might be
driven by a series of association/disassociation reactions involving sequential
interaction with nuclear pore complex proteins that are present in multiple copies.
A) Consistent.
B) Inconsistent.
QUESTION 8
2 pts. After entry of the receptor/cargo complex into the nucleus, Ran GTP hydrolysis
stimulates release of cargo.
A) Consistent.
B) Inconsistent.
STORY 2
In which Peter Walter and Gunter Blobel race against a competitor to purify the SRP.
This story is based on these
two old papers. You
shouldn’t need to read them
to answer the questions.
But if you want to access
them, they will be posted in
a folder in “Course
Materials” on the iLearn site.
By the early 1980s, researchers had deduced that their must be a factor, which
ultimately came to be called the SRP, that performed two tasks. First, it
paused translation of proteins that were to be secreted or inserted into the ER
membrane. Second, it was required for ribosomes to dock with the ER so the
protein could be transported through a translocator.
Blobel’s co-author on the papers describing his original ER transport assays was a guy
named Bernhard Dobberstein. Dobberstein now had his own lab in Heidelberg and
the two labs were competing against each other (in a friendly way) to purify the SRP.
Amount of protein translated,
% of maximum
Peter Walter appeared to have
successfully purified the SRP.
This graph shows his purified
SRP could perform the first job
of the SRP, blocking translation.
I have re-labelled the axes for
clarity. This was done by just
adding the SRP to a translation
extract, no rough ER
microsomes were present.
The SRP appeared to block
translation of some proteins but
not others. Increasing the SRP
concentration had no effect on
translation of a mRNA encoding ahemoglobin (GLO). But increasing
SRP did block translation of a
protein called pre-prolactin (pPL).
SRP (Activity units/25 microliters.
QUESTION 9
1 pt. Following any transport steps, where does a-hemoglobin (HBA1) function?
A) Inside the cell in the cytoplasm.
B) It is inserted into the plasma membrane.
C) It is secreted.
D) In the ER.
QUESTION 10
1 pt. Following any transport steps, where does prolactin (PRL, the processed
form of pre-prolactin) function?
A) Inside the cell in the cytoplasm.
B) It is inserted into the plasma membrane.
C) It is secreted.
D) In the ER.
QUESTION 11
3 pts. The SRP specifically blocks the translation of pre-prolactin because preprolactin has a ___________________ at the NH2 end of the protein.
If necessary, search on HBA1 at the Human
Protein Atlas; https://www.proteinatlas.org/
If necessary, seach on PRL at the Human
Protein Atlas; https://www.proteinatlas.org/
Here is one troubling thing you may have noticed regarding Blobel’s classic
experiments. Blobel found that if he added microsomes AFTER translation, no
transport was observed. But translation of the full-length protein still occurred.
So, if the SRP was present in Blobel’s original translation extract, and, as Walter
showed, the SRP blocked translation when microsomes were not present, why
was Blobel able to observe the full-length protein being synthesized? Shouldn’t
translation have been blocked, and therefore the protein just absent?
Blobel’s competitor eventually published a paper that provided a solution to this apparent
conundrum. The abstract of the paper is on the next slide (and the full paper is on the
iLearn site although you should not need it).
QUESTION 12
3 pts. Which statement from the abstract explains why Blobel was able to observe a
secreted protein being synthesized in his translation extracts without rough ER
microsomes?
A) Docking of SRP/ribosome complexes with the ER allows translation to resume.
B) If docking sites aren’t present, SRP arrest of translation is transient rather than stable.
C) The SRP can arrest translation at multiple sites on the protein.
D) The SRP blocks translation of both secretory and membrane proteins.

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Walter than examined whether the purified SRP could do it’s second job, namely
mediating transport into the ER. He set up the following reactions.
His reactions contained:
1) Purified ER microsomes.
2) A translation extract that (unlike Blobel’s original extracts) did NOT contain SRP.
3) His purified SRP fraction to see if it worked.
He set up the reactions in paired sets of tubes. At different times after starting
the reaction he took one tube from each set and spun it in a centrifuge so that
the microsomes pelleted to the bottom. The other tube in each set served as a
“no spin” control. He then removed the top half of the supernatant from both
tubes and allowed translation to continue for about half an hour. A stunning
artwork showing the “spin” and “no spin” tubes is on the next slide.
Blue ribosomes translating mRNA, orange rough ER microsomes, green SRP. If you have
worked in a bio lab before, you know the pipet tips are yellow. Magically delicious.
pPL
PL
_ + _ +
0 min 7 min
1 2 3 4
Time between starting reaction
and doing the spin (min)
Spin (+) or control (-)
Then, of course, Walter ran a gel. Below is my representation of a key figure from his
paper. He observed the expected processing of pre-prolactin (pPL) to prolactin (PL) in
his no spin control samples (lanes 1 and 3). If he centrifuged the tubes, he only saw
full length pPL (lanes 2 and 4). The longer he waited to do the spin, the less pPL he
saw (compare the intensity of the pPL band in lanes 2 and 4).
QUESTION 13
3 pts. Why aren’t the processed PL fragments observed in the “+ spin” reactions
shown in lanes 2 and 4.
A) The SRP blocks translation of the PL but not the pPL mRNA.
B) Signal peptidase is not functional in the spin reactions.
C) Transport into the ER never occurs in the spin reactions.
D) The PL fragments are present in the microsomes at the bottom of spin tubes.
QUESTION 14
4 pts. Why does the abundance of the pPL band decline in the spin reactions
between 0 and 7 min? ONE SENTENCE.
I’ve always wanted to ask some variation of the following question. This figure
from the MBoC text shows internal START and STOP signals for a seven pass transmembrane protein. The initial START transfer will be placed in HH1 of Sec61 in
what we called orientation 2 (also, on review supplement, orientation b). This
orientation of an internal START also acts as a STOP transfer, causing the ribosome
to immediately detach from Sec61.
But what if we just swap the orientation of the charged residues as shown above?
QUESTION 15
2 pts. Will the second hydrophobic alpha-helical region indicted by the
arrow now act as a START or as a STOP transfer?
A) START transfer
B) STOP transfer
C) A START/STOP transfer
D) It depends on the orientation of + charged residues around the second
helical region.
QUESTION 16
2 pts. After swapping the charged residues, how many trans-membrane
passes will the protein now have?
A) 6
B) 7
C) 8
D) Can’t be determined from the information given.
QUESTION 17
2 pts. After swapping the charged residues, will the C-terminus of the
protein now reside on the cytoplasmic or luminal side of the membrane?
A) Cytoplasmic side
B) Luminal side
C) Can’t be determined from information given.
STORY 3
In which the pathway that transports acid hydrolyases to the lysosome is discovered
even before Blobel figures out ER to Golgi transport.
You should not need
to read this paper to
answer the questions.
But if you want to
access it, it will be
posted in course
materials on iLearn.
One thing I learned in researching this exam was that the existence of the mannose-
6-phosphate (M6P) signal to transport acid hydrolyases to the lysosome was
discovered remarkably early. One reason for this is that it turns out that the M6P
sorting pathway at the trans-Golgi is rather inefficient, and 10-20% of acid
hydrolyases get secreted outside the cell, even though they are completely
functional enzymes that are tagged with M6P.
1 1 4 2
3
cis
trans
QUESTION 18
4 pts. Which pathways that we discussed from the trans-Golgi will cause acid
hydrolyases to get secreted from the cell?
A) Pathway(s) 1
B) Pathway 2
C) Pathway 3
D) Pathway 4
In keeping with the sloppy sorting, M6P receptors also end up being routed to the
plasma membrane. Because the secreted acid hydrolyases are perfectly capable of
binding to M6P receptors on the plasma membrane, it ended up being fairly easy to
work out the biochemistry. But it led to a mistaken idea that acid hydroylases were
primarily routed to lysosomes by a secretion-recapture-endocytosis pathway. First the
hydrolyases would be secreted, still bound to the receptor. Then the
receptor/hydrolyase complex would undergo endocytosis. Then the endosome would
be transported to lysosomes.
The paper that this story focuses on is definitely old-school. But it is fascinating.
Remarkably, our friend chloroquine-which was proposed to disrupt lipid rafts on the
first exam-makes another appearance. So I figured what do we have to lose, let’s write
some questions on it.
Way before COVID19 caused a return to its popularity, chloroquine had been
characterized as a so-called lysosomotropic compound, meaning a drug that screws
up lysosomal function. In fact, that is why it is an effective anti-malarial drug; it
messes up the lysosomes of the malarial parasites, and they can’t get the nutrients
they need by endocytosing metabolic supplies provided by you, the host. It’s also
why chloroquine shows variable success as an anti-viral compound for enveloped
viruses that enter the cell via the “classic” route that you learned about in Discussion.
Following endocytosis, those viruses need intact lysosome function to become
activated to fuse with the lysosomal membrane.
To figure out why chloroquine messed up
lysosomes, back in 1978 a clever assay was
designed to measure the internal pH of
lysosomes in living cells. In the experiment
shown on the graph, chloroquine was added to
cells at time 0 and washed out (W) of the
medium after 20 min.
QUESTION 19
2 pts. Based on the results how does
chloroquine affect lysosomes?
A) It causes protons to leak into lysosomes.
B) It rapidly increases the number of lysosomes.
C) It makes lysosomes have a more acidic pH.
D) It makes lysosomes have a more neutral pH.
This table shows one of their
key findings in the paper. By
comparing ”medium alone”
with “medium + chloroquine”,
it it is apparent that
chloroquine greatly increases
secretion of acid hydrolyases
outside the cell. This effect is
also observed for ammonium
chloride, another basic amine
compound.
QUESTION 20
2 pts. This is a final figure from the paper.
They devised an assay to detect Bglucuronidase (an acid hydrolyase)
binding to M6P receptors on the surface
of the cell. They took an initial
measurement of binding, then changed
the pH of the growth medium, and remeasured binding. At what pH does Bglucuronidase exhibit the greatest
detachment from the receptor?
A) 5.0
B) 7.0
C) 9.0
D) Data does not permit a conclusion.
QUESTION 21
4 pts. Based on the preceding observations and your knowledge of Golgi to lysosome
transport, what did the authors propose must be occurring to explain the effect of
chloroquine on the secretion of acid hydrolyases.
A) In the presence of chloroquine, the M6P signal cannot bind to the receptor in the
trans-Golgi, and so the hydrolyases undergo constitutive secretion.
B) In the presence of chloroquine, acid hydrolyases get routed to lysosomes by the
M6P receptor but cannot detach. Receptor/hydrolyase complexes accumulate in
lysososomes.
C) In the presence of chloroquine, acid hydrolyases get routed to lysosomes by the
M6P receptor but cannot detach. A retrieval pathway continually brings the
receptor/hydrolyase complexes the back to the Golgi, leading to increased
constitutive secretion.
D) In the presence of chloroquine, endocytosis of secreted receptor/hydrolyase
complexes is blocked, and so the hydrolyases accumulate on the outside of the cell.

 

20201121060807zoroastrianism (1) 20201121060748ancient_india (1)

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