0.2 Historical Introduction II
0.2 Historical Introduction II
• It was natural to be curious about what is the molecular/chemical nature of these genes?
• And how they function?
• The realization that chromosomes have both nucleic acids and protein wasn’t helpful since the
structure of neither was understood.
• The most fruitful speculations was concerning the fact that genes need to duplicate.
• How a complicated molecule which carry such diverse types of information could be precisely
copied to yield exact replicas?
• How could such information be coded?
• What could be the nature of such molecule which is mostly stable, but can also succumb to
spontaneous mutation that is permanent in nature?
• Many Physicist/Mathematicians became intrigued but enough details was not known to say
anything.
Preliminary Attempts To Find A Gene–Protein Relationship
• As it was observed that many of the functions in the cells were performed by proteins, it was
suspected that genes effect proteins.
• The most fruitful early endeavors to find a relationship between genes and proteins examined the
ways in which gene changes affect which proteins are present in the cell.
• It soon became clear that genes with simple metabolic functions would be easier to study than
genes affecting gross structures like eyes and wings.
• Based on a study of a hereditary disease affecting amino acid metabolism, English physician
Archibald E. Garrod suggested in 1909, that genes work by controlling the synthesis of specific
enzymes (the one gene–one enzyme hypothesis).
• However, no assurance could be given either that most genes control the synthesis of proteins, or
that all proteins are under gene control.
Nature of Genetic Information
• Until the mid-1940s, there appeared to be no direct way to attack the chemical essence of the
gene.
• It was known that chromosomes possessed a unique molecular constituent, deoxyribonucleic
acid (DNA).
• Despite this, there was no way to show that DNA carried genetic information, or was serving as a
scaffold.
• It was generally assumed that genes would be composed of amino acids because they appeared
to be the only biomolecules with sufficient complexity to convey genetic information.
• By early 1940s, research was generating increasingly strong evidence supporting the 30-year-old
hypothesis of Archibald E. Garrod that genes work by controlling the synthesis of specific
enzymes.
• Thus, given that all known enzymes had been shown to be proteins, the key problem was how
genes participate in the synthesis of proteins.
• The simplest hypothesis was that genetic information within genes determines the order of the
20 different amino acids within the polypeptide chains of proteins. How is it coded?
Nature of Genetic Information
• Initial guess was that there are enzymes that determine the order of each amino acid added to a
polypeptide chain.
• However, such scheme would require, for the synthesis of a single type of protein, as many
ordering enzymes as there are amino acids in the respective protein.
• But because all enzymes known at that time were themselves proteins (we now know that RNA
can also act as an enzyme), still additional ordering enzymes would be necessary to synthesize
the ordering enzymes.
• Chicken and egg problem?
• Fortunately, limitations in chemistry knowledge did not deter researchers from doing genetic
experiments with chemically simple molds, bacteria, and viruses.
Nature of Genetic Information
• The idea that DNA might be the key genetic molecule emerged from studies on pneumonia-
causing bacteria.
• In 1928 English microbiologist Frederick Griffith made the startling observation that non-virulent
strains of the bacteria became virulent when mixed with their heat-killed pathogenic
counterparts.
• That such transformations form non-virulence to virulence represented hereditary changes was
shown by using descendants of the newly pathogenic strains to transform still other non-
pathogenic bacteria.
• ⇒ when pathogenic cells are killed by heat, their genetic components remain undamaged.
• Moreover, once liberated from the heat-killed cells, these components can pass through the cell
wall of the living recipient cells and undergo subsequent genetic recombination with the
recipient’s genetic apparatus.
lele of the capsule gene is present, a capsule is formed around the cell
that is necessary for pathogenesis (the formation of a capsule also gives a
smooth appearance to the colonies formed from these cells). When the R
capS
(capsule gene) chromosome
capsule
heat to kill
capS fragment
released capS
pathogenic
S (smooth) cell capS
capR capR recombination capS
and cell division
• Pathogenicity reflects the action of the capsule gene, which codes for a key enzyme involved in
given gene is usually less than 1%.
35
S-labeled THE DOUB
coat protein
DNA
of helical molecules was developed by William Cochran
H. Crick, and Vladimir Vand. This theory made it easy to te
DNA structures on a trial-and-error basis. The correct solution,
mentary double helix (see Chapter 4), was found in 1953 by
multiplication of James D. Watson, then working in the laboratory of Max P
• While work was proceeding on the X-ray analysis of protein structure, a smaller number of viral chromosome
and production
John Kendrew in Cambridge, United Kingdom. Their arrival at
answer depended largely on finding the stereochemically mos
scientists were trying to solve the X-ray diffraction pattern of DNA (makes sense as protein got all
of new phage
configuration compatible with the X-ray diffraction data of W
Franklin.
the limelight initially). In the double helix, the two DNA chains are held together by
release of bonds (a weak noncovalent chemical bond; see Chapter 3) betw
• The first diffraction patterns were taken in 1938.
new progeny
particles
of bases on the opposing strands (Fig. 2-6). This base pairi
specific: the purine adenine only base-pairs to the pyrimidine
whereas the purine guanine only base-pairs to the pyrimidine
• It was in the early 1950s that high-quality X-ray diffraction photographs were taken by Maurice
2-3 Demonstration that only
FIGURE
In double-helical DNA, the number of A residues must be eq
Wilkins and Rosalind Franklin, in the UK. the DNA component of the bacterio-
phage T2 carries the genetic information
and that the protein coat serves only as a
• These photographs suggested not only that the underlying DNA structure was helical
protective shell.
but that it was composed of more than one polynucleotide chain—either two or
three.
• At the same time, the covalent bonds of DNA were being unambiguously
established.
• In 1951, thanks to Linus Pauling’s work on 𝛼 helix protein motif, an elegant theory of
diffraction of helical molecules was developed by Francis Crick, among others. 2-4 The key X-ray photograph involved in the elucidation of the D
FIGURE
• The correct solution, a complementary double helix was found in 1953 by 1953,Crick and
This photograph, taken by Rosalind Franklin at King’s College, London, in the win
confirmed the guess that DNA was helical. The helical form is indicated by
• By 1949 his data showed not only that the four different nucleotides are not present in equal
matography” to analyze the nucleotide composition of DNA. By
1949 his data showed not only that the four different nucleo-
thymine (T) residues, and the number of guanine (G) residues
equaled the number of cytosine (C) residues. In addition, re-
amounts, but also that the exact ratios of the four nucleotides vary from one species to another.
tides are not present in equal amounts, but also that the exact gardless of the DNA source, the ratio of purines to pyrimidines
ratios of the four nucleotides vary from one species to another was always approximately 1 ( purines ¼ pyrimidines). The fun-
• Chargaff’s experiments also showed that the relative ratios of the four bases were not random.
(Box 2-1 Table 1). These findings opened up the possibility
that it is the precise arrangement of nucleotides within a DNA
damental significance of the A ¼ T and G ¼ C relationships
(Chargaff’s rules) could not emerge, however, until serious at-
molecule that confers its genetic specificity. tention was given to the three-dimensional structure of DNA.
• The fundamental significance of the A = T and G = C relationships (Chargaff’s rules) could not
Chargaff’s experiments also showed that the relative ratios of
emerge, however, until serious attention was given to the three-dimensional structure of DNA.
the four bases were not random. The number of adenine (A)
cha-
ruc-
dels
epli-
peri-
tahl
dels,
ated
dispersive semiconservative conservative
• Showed that the two strands of the double helix permanently bacteria growing in 15N;
all DNA is heavy
transfer
to 14N medium
continued growth
in 14N medium
• One can then separate heavy DNA from lighter DNA by light 14N-15N heavy
creating density gradients in cesium chloride in a centrifuge. DNA hybrid DNA DNA
solution centrifuged at
• DNA molecules, in which both strands are heavy (H-H DNA) 140,000 x g for ~48 hr
Transcription Translation
Duplication DNA RNA Protein.
Here the arrows indicate the directions proposed for the transfer of genetic
• The Adaptor Hypothesis: It was
information. Therealized by Crick
arrow encircling DNA that it that
signifies willDNA
be isdifficult for Nucleotides to
the template
for its self-replication. The arrow between DNA and RNA indicates that
distinguish between the
RNA 20 amino
synthesis acids.
(called transcription) is directed by a DNA template. Corre-
spondingly, the synthesis of proteins (called translation) is directed by an
• Crick thus proposed that prior toMost
RNA template. incorporation into
importantly, the last twoproteins, amino acids
arrows were presented as uni- are first attached to
specific adaptor molecules,
directional;which in turn
that is, RNA possess
sequences unique
are never surfaces
determined thattem-
by protein can bind specifically to
plates nor was DNA then imagined ever to be made on RNA templates.
bases on the RNA templates.
The idea that proteins never serve as templates for RNA has stood the test
of time. However, as we will see in Chapter 12, RNA chains sometimes do
Discovery of Transfer RNA
• This led to the seminal discovery that prior to their incorporation into proteins, amino acids are
first attached to transfer RNA (tRNA) molecules (accounts for some 10% of all cellular RNA).
• Crick had indeed previously speculated that his proposed “adaptors” might be short RNA chains,
because their bases would be able to base-pair and “read” the appropriate groups on the RNA
molecules that served as the templates for protein synthesis
The Paradox of the Nonspecific-Appearing Ribosomes
• Early on, the cellular site of protein synthesis was pin-pointed to be the ribosomes.
• Ribosomes contain both RNA and proteins (About 85% of cellular RNA is found in ribosomes).
• Amount of ribosomes in the cell is greatly increased in cells engaged in large-scale protein
synthesis (e.g. rapidly growing bacteria).
⇒ Ribosomes are responsible for protein synthesis.
• Initially ribosomal RNA (rRNA) was thought to be the template for ordering amino acids.
• But it can’t be: the RNAs and proteins are all the same in all ribosomes.
• Moreover, base composition of rRNA was seen to be high in G and C in all known bacteria, plants,
and animals, despite wide variations in the AT/GC ratios of their respective DNA.
Discovery of Messenger RNA (mRNA)
• In 1960, work on bacteriophage and also in E.coli evidence for a separate messenger class of RNA,
• Only a few percent of total cellular RNA is mRNA; easy to understand why it was first overlooked.
Enzymatic Synthesis of RNA upon DNA Templates
• As mRNA was being discovered, the first of the enzymes that transcribe RNA using DNA templates
was being independently isolated: RNA polymerases
• These enzymes function only in the presence of DNA.
• Direct evidence that DNA lines up the correct ribonucleotide precursors came from seeing how
the RNA base composition varied with different DNA molecules: In every case, the RNA AU/GC
ratio was roughly similar to the DNA AT/GC ratio.
• By this time, there was firm evidence for the postulated movement of RNA from the DNA-
containing nucleus to the ribosome-containing cytoplasm of eukaryotic cells.
• By briefly exposing cells to radioactively labeled ribonucleotides, then adding a large excess of
unlabeled ribonucleotides (a “pulse chase” experiment), mRNA synthesized during a short time
window was labeled.
• They were observed to be created in the nucleus, and then transported to cytoplasm.
Establishing the Genetic Code
• Given the existence of 20 amino acids but only four bases, groups of several nucleotides must
somehow encode a given amino acid.
• Group of 2 gives?
• Group of 3 gives?
• The assumption of colinearity was important: It held that successive groups of nucleotides along a
DNA chain code for successive amino acids along a given polypeptide chain.
• A mutational analysis on bacterial proteins, carried out in the early 1960s by Charles Yanofsky and
Sydney Brenner showed that colinearity does exist.
• Also, genetic analyses by Brenner and Crick, in 1961, first established that groups of three
nucleotides are used to specify individual amino acids.
Establishing the Genetic Code
38 Chapter 2
third position
first position
Gln
CUG CCG CAG CGG G
triplet. AUU ACU AAU AGU U
Asn Ser
AUC Ile ACC AAC AGC C
A Thr
AUA ACA AAA AGA A
Lys Arg
AUG Met ACG AAG AGG G