Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

366 Chapter 6: How Cells Read the Genome: From DNA to Protein
in the chemical differences between them. Ribose, like glucose and other simple
carbohydrates, can be formed from formaldehyde (HCHO), a simple chemical
which is readily produced in laboratory experiments that attempt to simulate
conditions on the primitive Earth. The sugar deoxyribose is harder to make, and
in present-day cells it is produced from ribose in a reaction catalyzed by a protein
enzyme, suggesting that ribose pre-dates deoxyribose in cells. Presumably,
DNA appeared on the scene later, but then proved more suitable than RNA as
a permanent repository of genetic information. In particular, the deoxyribose in
its sugar-phosphate backbone makes chains of DNA chemically more stable than
chains of RNA, so that much greater lengths of DNA can be maintained without
breakage.
The other differences between RNA and DNA—the double-helical structure of
DNA and the use of thymine rather than uracil—further enhance DNA stability by
making the many unavoidable accidents that occur to the molecule much easier
to repair, as discussed in detail in Chapter 5 (pp. 271–273).
Summary
From our knowledge of present-day organisms and the molecules they contain, it
seems likely that the development of the distinctive autocatalytic mechanisms fundamental
to living systems began with the evolution of families of RNA molecules
that could catalyze their own replication. DNA is likely to have been a late addition:
as the accumulation of protein catalysts allowed more efficient and complex cells to
evolve, the DNA double helix replaced RNA as a more stable molecule for storing the
increased amounts of genetic information required by such cells.
What we don’t know
• How did the present relationships
between nucleic acids and proteins
evolve? How did the genetic code
originate?
• The information carried in genomes
specifies the sequences of all proteins
and RNA molecules in the cell,
and it determines when and where
these molecules are synthesized.
Do genomes carry other types of
information that we have not yet
discovered?
• Cells go to great length to correct
mistakes in the processes of DNA
replication, transcription, splicing,
and translation. Are there analogous
strategies to correct mistakes in the
selection of which genes are to be
expressed in a given cell type? Could
the great complexity of transcription
initiation in animals and plants reflect
such a strategy?
Problems
Which statements are true? Explain why or why not.
6–1 The consequences of errors in transcription are
less severe than those of errors in DNA replication.
6–2 Since introns are largely genetic “junk,” they do not
have to be removed precisely from the primary transcript
during RNA splicing.
6–3 Wobble pairing occurs between the first position
in the codon and the third position in the anticodon.
6–4 During protein synthesis, the thermodynamics of
base-pairing between tRNAs and mRNAs sets the upper
limit for the accuracy with which protein molecules are
made.
+ + – –
Figure Q6–1 Supercoils around a moving RNA polymerase (Problem
6–6).
6–7 You have attached an RNA polymerase molecule
to a glass slide and have allowed it to initiate transcription
on a template DNA that is tethered to a magnetic bead as
shown in Figure Q6–2. If the DNA with its attached magnetic
bead moves relative to the RNA polymerase as indicated
in the figure, in which direction will the bead
Problems p6.02/6.02
rotate?
6–5 Protein enzymes are thought to greatly outnumber
ribozymes in modern cells because they can catalyze
a much greater variety of reactions and all of them have
faster rates than any ribozyme.
Discuss the following problems.
6–6 In which direction along the template must the
RNA polymerase in Figure Q6–1 be moving to have generated
the supercoiled structures that are shown? Would
you expect supercoils to be generated if the RNA polymerase
were free to rotate about the axis of the DNA as it
progressed along the template?
fluorescent
beads
RNA
glass slide
DNA
magnet
magnetic
bead
RNA
polymerase
Figure Q6–2 System for
measuring the rotation of DNA
caused by RNA polymerase
(Problem 6–7). The magnet
holds the bead upright (but
doesn’t interfere with its
rotation), and the attached
tiny fluorescent beads allow
the direction of motion to
be visualized under the
microscope. RNA polymerase is
held in place by attachment to
the glass slide.