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Chapter 2 Answers
2. Both Avery et al. and Hershey and Chase tried to pinpoint the biochemical source of
the genetic material; the specific ways in which they did this, however, differed in several
respects.
Avery et al. used an indirect, functional approach to identify the genetic material. For
example, their assay was based entirely upon the ability to render rough bacteria virulent.
Also, they demonstrated the essential role of nucleic acids in the process not by showing that
nucleic acids were sufficient for the transforming activity, but by showing that they were
simply necessary. The destruction of nucleic acids in their sample using nucleases was
enough to eliminate the transforming ability.
In contrast, Hershey and Chase took a more direct, physical approach to finding the
genetic material. At that time, scientists already had a relatively clear understanding as to
what molecules were present in many viruses. This allowed Hershey and Chase to ask which
molecules are physically transmitted by the virus to the bacterial cell upon infection. To do
this, they used two different radioactive labels to specifically tag both the protein and nucleic
acid components of the virus, and then asked which of these components ends up in the
bacterial cell following infection and in the progeny phage. Their assay was thus based on the
detection of a specific radioactive isotope in the infected cells (and their descendents), rather
than on any functional property of the cells following infection.
3. The absence of a role for nucleic acids was demonstrated by treating the material
responsible for the disease with agents that destroy nucleic acids, such as nucleases or UV
irradiation. While these treatments should destroy whatever nucleic acids are present in the
material, they were found to have no effect on infectivity. In contrast, methods designed to
eliminate proteins in the material, such as treatment with phenol or proteases, were capable of
reducing the infectivity.
4. Chargaff examined the relative proportions of adenine, cytosine, guanine, and thymine
in DNA, and made the key discoveries that the different nucleotides were not all present at the
same concentrations in cells; that their relative levels differed in different organisms; and that
adenosine and thymine, and cytosine and guanine, are present at similar levels. This work
suggested that the genetic information may be somehow encoded by the precise arrangement
of the different nucleotides within the DNA.
5. The high-quality X-ray diffraction images obtained by Wilkins and Franklin suggested
that DNA was helical and was composed of more than one polynucleotide chain. This
knowledge helped Watson and Crick narrow down the possibilities in their work on modeling
the structure of DNA.
7. See Figure 2-7 for a depiction of the polymerase reaction. The sequence of the new
strand of DNA is determined by the sequence of the template DNA. This was demonstrated
by incubating DNA of varying nucleotide composition in the presence of polymerase and
nucleoside triphosphates. The nucleotide composition of the DNA strand produced in this
reaction precisely mirrors that of the DNA originally added to the reaction mixture.
8. The conclusion that DNA must not be the template for protein synthesis was made
based on the observation in eukaryotic cells. In these cells, DNA is exclusively present in the
nucleus, yet protein synthesis occurs in the cytoplasm. It was postulated that some sort of
intermediate molecule must carry the information from the nucleus to the site of protein
synthesis.
RNA was identified as the likely template because of its presence in the cytoplasm,
and because, given the structural similarity of RNA to DNA, it was easy to imagine how the
DNA sequence could be copied as RNA, which could then move to the cytoplasm. Also, the
development of cell-free extracts allowed researchers to isolate the various cellular
components that are required for protein synthesis, and this indicated the importance of RNA
in the process. Definitive evidence for the activity of mRNA in protein synthesis was
provided by observations in T4 infected cells, where it was found that, upon infection, RNA is
produced that has an identical base composition to the T4 DNA, and that this RNA binds to
ribosomes, leading to protein synthesis.
9. One major difference lies in the structure of the sugar moiety of the nucleic acid:
ribonucleic acids include a hydroxyl group at the 2’ carbon of the sugar moiety, whereas the
2’ carbon of deoxyribose has only hydrogen. A second difference is that RNA contains the
base uracil, whereas DNA contains thymine. Finally, DNA is almost exclusively present in
its double-stranded form in vivo, whereas RNA is largely single-stranded.
10. The central dogma states that genetic information flows from DNA to RNA to protein.
In other words, DNA stores the genetic information within the chromosomes in the nucleus.
This information is transcribed onto RNA, which then exits the nucleus, and the RNA is then
translated into protein. Even though the dogma is almost always valid, exceptions have been
found such as the copying of DNA from RNA templates during the life cycle of retroviruses.
11. Before Crick’s proposal that an adaptor molecule might intervene between mRNA and
amino acids, scientists had speculated that RNA may fold into precise three-dimensional
forms that specifically recognize particular amino acids. Crick rejected this suggestion as
unlikely, because RNA bases are mostly hydrophilic, yet the side chains of numerous amino
acids are hydrophobic. In addition, the strong structural similarity between certain amino acid
side chains made it difficult to imagine how different RNA structures could accurately
distinguish between them.
The adaptor was ultimately found to be tRNA.
12a. These three types of RNA differ in multiple respects. For example, both rRNA and
tRNA are quite different from mRNA in terms of size and complexity. tRNA molecules are
quite small (less than 100 nucleotides), and are relatively uniform in sequence. rRNA
molecules are rather large and fall into several discrete sizes, and are also relatively uniform
in sequence. mRNA, in contrast, is extremely diverse, both in terms of size—ranging from
very small messages of less than 100 nucleotides to very large messages of many thousands—
and in terms of complexity, as the collection of mRNA sequences in the cell must be
sufficiently diverse to code for all of the different proteins made in the cell. Also, the GC
content of rRNA is relatively high. Finally, the abundance of the three types differs within
the cell, with rRNA making up some 85 percent of the total RNA, tRNA about 10 percent,
and the rest being mRNA.
b. Whereas rRNA binds directly and stably to the ribosomal proteins, mRNA only
interacts transiently with already assembled ribosomes. Also, while a given rRNA molecule
forms part of a single ribosome, a single mRNA molecule can associate with multiple
ribosomes (forming a polyribosome).
13. The codons must have sufficient complexity to be able to code for all 20 amino acids
used during protein synthesis. Codons of only two nucleotides could only specify (42) 16
different combinations and would therefore not be sufficient to specify all of the amino acids.
While four-nucleotide codons would be possible, there would be a great excess of potential
codons compared to the number of different amino acids. This would both needlessly
increase the size of the genome and also require the cell to wastefully produce a much larger,
but unnecessary, number of different tRNA species.
14. Mutant classes C and F should show very little phenotypic difference from the wild-
type gene, whereas classes A, B, D, and E should show a mutant phenotype. In these classes,
the addition of one, two, four, or five nucleotides would change the reading frame of the
coding sequence, altering the identity of all subsequent amino acids and almost certainly
destroying the function of the encoded protein. In contrast, the addition of three or six
nucleotides (in classes C and F) would not change the reading frame but would simply add
one or two amino acids to the protein sequence. While this may have some effect on the
protein’s activity, it is likely that the protein would still function even with these extra amino
acids.
The fact that insertions of any number of nucleotides that is not a multiple of 3 causes
a mutant phenotype indicates that the codons must consist of three nucleotides.
15. They created synthetic RNA molecules of a known sequence, added them to a cell-free
translation system, and examined the amino acid sequence of the proteins that were produced.
The first such molecule they made was poly-U, or UUUUU…, which gave rise to a
polypeptide composed exclusively of the amino acid phenylalanine.
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underneath it a Campo Santo,—a depository for their dead.
The adventurous merchant ships a cargo for some distant port, Rat
goes with it. Great Britain plants a colony in Botany Bay, Van
Diemen's Land, or at the Swan River, Rat takes the opportunity for
colonizing also. Ships are sent out upon a voyage of discovery. Rat
embarks as a volunteer. He doubled the Stormy Cape with Diaz,
arrived at Malabar in the first European vessel with Gama,
discovered the new world with Columbus and took possession of it at
the same time, and circumnavigated the globe with Magellan and
with Drake and with Cook.
The Doctor thought there was no creature to which you could trace
back so many persons in civilized society by the indications which
they afforded of habits acquired in their prænatal professional
education. In what other vehicle, during its ascent could the Archeus
of the Sailor have acquired the innate courage, the constant
presence of mind, and the inexhaustible resources which
characterise a true seaman? Through this link too, on his progress
towards humanity, the good soldier has past, who is brave, alert and
vigilant, cautious never to give his enemy an opportunity of
advantage, and watchful to lose the occasion that presents itself.
From the Rat our Philosopher traced the engineer, the miner, the
lawyer, the thief, and the thief-taker,—that is, generally speaking:
some of these might have pre-existed in the same state as moles or
ferrets; but those who excelled in their respective professions had
most probably been trained as rats.
1 SHAKSPEARE.
CHAPTER CCXXX.
I think it not impertinent sometimes to relate such accidents as may seem no better
than mere trifles; for even by trifles are the qualities of great persons as well disclosed
as by their great actions; because in matters of importance they commonly strain
themselves to the observance of general commended rules; in lesser things they
follow the current of their own natures.
“In Saxonia, near unto Halberstad, was a man that also had a
Killcrop, who sucked the mother and five other women dry, and
besides devoured very much. This man was advised that he should
in his pilgrimage at Halberstad make a promise of the Killcrop to the
Virgin Mary, and should cause him there to be rocked. This advice
the man followed, and carried the Changeling thither in a basket. But
going over a river, being upon the bridge, another Devil that was
below in the river called, and said, Killcrop! Killcrop! Then the child in
the basket, (which never before spake one word) answered ho, ho!
The Devil in the water asked further, whither art thou going? The
child in the basket said, ‘I am going towards Halberstad to our Loving
Mother, to be rocked.’ The man being much affrighted thereat, threw
the child with the basket over the bridge into the water. Whereupon
the two Devils flew away together, and cried, ho, ho, ha! tumbling
themselves one over another and so vanished.
Mr. Cottle has made this the subject of a lively eclogue; but if that
gentleman had happened upon the modern edition of Luther's
Colloquia Mensalia, or Divine Discourses at his Table, instead of the
old one, this pleasant poem would never have been written, the
account of the Killcrops being one of the passages which the modern
editor thought proper to omit. His omissions are reprehensible,
because no notice is given that any such liberty has been taken; and
indeed a paragraph in the introductory life which is prefixed to the
edition might lead the reader to conclude that it is a faithful reprint;
that paragraph saying there are many things which, for the credit of
Luther, might as well have been left out, and proceeding to say, “but
then it must be considered that such Discourses must not be brought
to the test of our present refined age; that all what a man of Luther's
name and character spoke, particularly at the latter part of his life,
was thought by his friends worth the press, though himself meant it
only for the recreation of the company; that he altered many opinions
in his progress from darkness to light; and that it is with a work of this
kind, as with the publishing of letters which were never intended for
the press; the Author speaks his sentiments more freely, and you are
able to form a true idea of his character, by looking, as it were, into
his heart.” Nevertheless there are considerable omissions, and as
may be supposed of parts which are curious, and in a certain sense
valuable because they are characteristic. But the reprint was the
speculation of a low publisher, put forth in numbers, and intended
only for a certain class of purchasers, who would read the book for
edification. The work itself deserves farther notice, and that notice is
the more properly and willingly bestowed upon it here, because the
original edition is one of the few volumes belonging to my venerable
friend which have passed into my possession, and his mark occurs
frequently in its margin.
“I will make no long excursion here, but a short apology for one that
deserved well of the reformed Religion. Many of our adversaries
have aspersed Luther, with ill words, but none so violent as our
English fugitives, because he doth confess it that the Devil did
encounter him very frequently, and familiarly, when he first put pen to
paper against the corruptions of the Church of Rome. In whose
behalf I answer: much of that which is objected I cannot find in the
Latin Editions of his works which himself corrected, although it
appears by the quotations some such things were in his first writings
set forth in the Dutch language. 2. I say no more than he confesseth
ingenuously of himself in an epistle to Brentius, his meaning was
good, but his words came from him very unskilfully, and his style was
most rough and unsavoury. St. Paul says of himself, that he was
rudis sermone, rude in speech. But Luther was not so much ἰδιώτης
τῷ λόγῳ the word used in Saint Paul, as ἄγροικος, after his Dutch
Monastical breeding, and his own hot freedom. By nature he had a
boisterous clownish expression; but for the most part very good
jewels of doctrine in the dunghills of his language. 3. If the devil did
employ himself to delude and vex that heroical servant of God, who
took such a task upon him, being a simple Monk, to inveigh against
errors and superstitions which had so long prevailed, why should it
seem strange to any man? Ribadaneira sticks it among the praises
of his founder Ignatius Loiola, that the Devil did declaim and cry out
against him, (believe it every one of you at your leisure,) and why
might not the Devil draw near to vex Luther, as well as roar out a
great way off against Loiola? I have digrest a little with your patience,
to make Luther's case appear to be no outrageous thing, that weak
ones may not be offended when they hear such stuff objected out of
Parsons, or Barclay, or Walsingham, or out of Bellarmine himself. If
Beelzebub was busy with the Master, what will he be with the
Servants? When Christ did begin to lay the first corner stone of the
Gospel, then he walked into the wilderness to be tempted of the
Devil.”1
1 HACKET'S SERMONS.
CHAPTER CCXXXI.
Tertull. Apologet. cap. 39. The primitive Christians ate and drank
to satisfy nature, and discoursed at their Tables of the Holy
Scriptures, or otherwise, as became those that knew God did
hear them, ut non tam cœnam cœnaverint, quam disciplinam.
The original Collection was first published three and thirty years after
Luther's death, consequently not till most of those persons from
whose reminiscences it professes to be compiled, had past away.
The book therefore is far from carrying with it any such stamp of
authenticity as Boswell's Life of Johnson, which in that respect, as
well as for its intrinsic worth is the Ana of all Anas. But though it may
have been undertaken upon book-making motives, there seems no
reason to suppose that the task was not performed faithfully by the
Doctors Clearstream and Goldsmith, according to their judgment,
and that much which had lightly or carelessly fallen from such a man
as Luther was likely to be carefully preserved, and come into their
hands. Many parts indeed authenticate themselves, bearing so
strong a likeness that no one can hesitate at filiating them upon the
ipsissimus Luther. The editor of the modern English edition, John
Gottlieb Burckhardt, D.D., who was Minister of the German Lutheran
Congregation in the Savoy, says, “the Book made a great noise at its
first appearance in 1569. Some indeed have called its authenticity in
question; but there is no reason to doubt of the testimony of Dr. John
Aurifaber; and indeed the full character of Luther's free manner of
speaking and thinking is seen almost in every line. The same manly,
open, bold and generous spirit breathes through the whole, as is felt
in reading the compositions which he published himself in his life
time. There is a pleasing variety of matters contained in these
discourses, and many fundamental truths are proposed in a familiar,
careless dress, and in Luther's own witty, acute manner; for which
reason it is as much entertaining to popular capacities as to men of
genius. Many good Christians have found it to be of great benefit for
establishing their souls in the knowledge and practice of truth, and of
the good old way; and since many weeds grow up from time to time
in the Church, this book handed down to posterity, will be a standing
test of sound doctrines, which our forefathers believed, and of such
wise principles on which they acted at, and after the Reformation.”
On the other hand the book afforded as much gratification to the
enemies of Luther, as to his admirers. Bayle after noticing some of
the monstrous calumnies with which the Papists assailed his
memory, proceeds to say, La plûpart de ces medisances sont
fondées sur quelques paroles d'un certain livre publié par les amis
de Luther, ausquelles on donne un sens tres-malin, et fort éloigné de
la pensée de ce Ministre. Ce n'est pas qu'il ne faille convenir qu'il y
eut une très-grande imprudence à publier une telle compilation. Ce
fut l'effet d'un zêle inconsideré, ou plútôt d'une preoccupation
excessive, qui empêchoit de conoître les defauts de ce grand
homme. In like manner Seckendorf, whom Bayle quotes, says it was
compiled with little prudence, and incautiously published, but upon
its authenticity (as far as any such collection can be deemed
authentic) he casts no suspicion.
“Whereupon I took the said Book before me, and many times began
to translate the same, but always I was hindered therein, being
called upon about other business; insomuch that by no possible
means I could remain by that work. Then about six weeks after I had
received the said Book, it fell out, that I being in bed with my Wife,
one night between twelve and one of the clock, she being asleep but
myself yet awake, there appeared unto me an Antient Man, standing
at my bed-side, arrayed all in white, having a long and broad white
beard, hanging down to his girdle-stead; who, taking me by my right
ear, spake these words following unto me. Sirrah! Will not you take
time to translate that Book which is sent unto you out of Germany? I
will shortly provide for you both place and time to do it! And then he
vanished away out of my sight. Whereupon being much thereby
affrighted, I fell into an extreme sweat, insomuch that my Wife
awaking, and finding me all over wet, she asked me what I ailed, I
told her what I had seen and heard; but I never did heed nor regard
visions, nor dreams. And so the same fell soon out of my mind.
CHAPTER CCXXXII.
No son ever regarded the memory of his father with more reverential
affection than this last of the Doves. There never lived a man, he
said, to whom the lines of Marcus Antonius Flaminius, (the sweetest
of all Latin poets in modern times, or perhaps of any age,) could
more truly be applied.
Vixisti, genitor, bene, ac beate,
Nec pauper, neque dives; eruditus
Satis, et satis eloquens; valente
Semper corpore, mente sanâ; amicis
Jucundus, pietate singulari.
He was far however from thinking that those who are born to all the
advantages, as they are commonly esteemed, of rank and fortune,
are better placed for the improvement of their moral and intellectual
nature, than those in a lower grade. “Fortunatos nimium sua si bona
nôrint,” he used to say of this class, but this is a knowledge that they
seldom possess; and it is rare indeed to find an instance in which the
high privileges which hereditary wealth conveys are understood by
the possessors, and rightly appreciated and put to their proper use.
The one, and the two talents are
in general more profitably occupied than the five; the five indeed are
not often tied up in a napkin, but still less often are they faithfully
employed in the service of that Lord from whom they are received in
trust, and to whom an account of them must be rendered.
2 COWPER.
3 TASSO RINALDO.
il figlio
Del tale, ed il nipote del cotale,
Natò per madre della tale.4
Naboth has been named in relating this, but the reader will not
suppose that I have any intention of comparing the great proprietor
to Ahab,—or to William the Conqueror. There was nothing unjust in
his proceedings, nothing iniquitous; and (though there may have
been a great want of proper feeling) nothing cruel. I am not aware
that any hardship was inflicted upon the families who were ejected,
farther than the inconvenience of a removal. He acted as most
persons in the same circumstances probably would have acted, and
no doubt he thought that his magnificent habitation was greatly
improved by the demolition of the poor dwellings which had
neighboured it so closely. Farther it may be said in his justification
(for which I would leave nothing unsaid) that very possibly the
houses had not sufficient appearance of neatness and comfort to
render them agreeable objects, that the people may have been in no
better state of manners and morals than villagers commonly are,
which is saying that they were bad enough; that the filth of their
houses was thrown into the road, and that their pigs, and their
children who were almost as unclean, ran loose there. Add to this if
you please that though they stood in fear of their great neighbour,
there may have been no attachment to him, and little feeling of good
will. But I will tell you how Dr. Dove would have proceeded if he had
been the hereditary Lord of that Castle and that domain.
He would have considered that this village was originally placed
there for the sake of the security which the Castle afforded. Times
had changed and with them the relative duties of the Peer and of the
Peasantry: he no longer required their feudal services, and they no
longer stood in need of his protection. The more therefore, according
to his “way of thinking,” was it to be desired, that other relations
should be strengthened and the bonds of mutual goodwill be more
closely intertwined. He would have looked upon these villagers as
neighbours, in whose welfare and good conduct he was especially
interested, and over whom it was in his power to exercise a most
salutary and beneficial influence; and having this power he would
have known, that it was his duty so to use it. He would have
established a school in the village, and have allowed no ale-house
there. He would have taken his domestics preferably from thence. If
there were a boy who by his gentle disposition, his diligence and his
aptitude for learning gave promise of those qualities which best
become the clerical profession, he would have sent that boy to a
grammar school, and afterwards to college, supporting him there in
part, or wholly, according to the parents' means, and placing him on
his list for preferment, according to his deserts.
If there were any others who discovered a remarkable fitness for any
other useful calling, in that calling he would have had them instructed
and given them his countenance and support, as long as they
continued to deserve it. The Archbishop of Braga, Fray Bartolomen
dos Martyres, added to his establishment a Physician for the poor.
Our friend would in like manner have fixed a medical practitioner in
the village,—one as like as he could find to a certain Doctor at
Doncaster; and have allowed him such a fixed stipend, as might
have made him reasonably contented and independent of the little
emolument which the practice of the place could afford, for he would
not have wished his services to be gratuitous where there was no
need. If the parish to which the village belonged was too extensive,
or the parochial Minister unwilling, or unable to look carefully after
this part of his flock, his Domestic Chaplain, (for he would not have
lived without one) should have taken care of their religious
instruction.
In his own family and in his own person he would have set his
neighbours an example of “whatsoever things are honest,
whatsoever things are just, whatsoever things are pure, whatsoever
things are lovely, whatsoever things are of good report.” And as this
example produced its sure effects, he would have left the Amateurs
of Agriculture to vie with each other in their breeds of sheep and
oxen, and in the costly cultivation of their farms. It would have been,
not his boast, for he boasted of nothing;—not his pride, for he had
none of
it was out of the root of Christian humility that all his virtues grew,—
but his consolation and his delight to know that nowhere in Great
Britain was there a neater, a more comfortable village than close to
his own mansion; no where a more orderly, a more moral, a more
cheerful, or a happier people. And if his castle had stood upon an
elevation commanding as rich a survey as Belvoir or Shobden, that
village when he looked from his windows, would still have been the
most delightful object in the prospect.
5 BEAUMONT AND FLETCHER.
I have not mentioned the name of the old Quaker in my story; but I
will preserve it in these pages because the story is to his honour. It
was Joshua Dickson. If Quakers have (and certainly they have) the
quality which is called modest assurance in a superlative degree that
distinguishes them from any other class of men, (it is of the men only
that I speak) they are the only sect, who as a sect, cultivate the
sense of conscience. This was not a case of conscience, but of
strong feeling assuming that character under a tendency to
madness.
When Lord Harcourt about the same time removed the village of
Nuneham, an old widow Barbara Wyat by name, earnestly intreated
that she might be allowed to remain in her old habitation. The
request which it would have been most unfeeling to refuse, was
granted; she ended her days there, and then the cottage was pulled
down: but a tree which grew beside it, and which she had planted in
her youth, is still shown on the terrace at Nuneham, and called by
her name. Near it is placed the following Inscription by that amiable
man the Laureate Whitehead. Like all his serious poems it may be
read with pleasure and profit,—though the affecting circumstance
which gives the anecdote its highest interest is related only in a note.
6 The Classical reader will be aware that the Author of these lines had Claudian's “Old
Man of Verona” in his mind's eye, as Claudian had Virgil's “Corycian Old Man.”—
Georg. iv. 127.