Ch 9 Flashcards
In this chapter, it is argued that genetic variability is beneficial for a species because it enhances that species’ ability to adapt to changing conditions. Why, then, do you think that cells go to such great lengths to ensure the fidelity of DNA replication?
When it comes to genetic information, a
balance must be struck between stability and change. If the
mutation rate were too high, a species would eventually die
out because all its individuals would accumulate mutations
in genes essential for survival. And for a species to be
successful—in evolutionary terms—individual members must
have a good genetic memory; that is, there must be high
fidelity in DNA replication. At the same time, occasional
changes are needed if the species is to adapt to changing
conditions. If the change leads to an improvement, it
will persist by selection; if it is neutral, it may or may
not accumulate; but if the change proves disastrous, the
individual organism that was the unfortunate subject of
nature’s experiment will die, but the species will survive
Why do you suppose that horizontal
gene transfer is more prevalent
in single-celled organisms than in
multicellular organisms?
In single-celled organisms, the genome is
the germ line and any modification is passed on to the next
generation. By contrast, in multicellular organisms, most
of the cells are somatic cells and make no contribution to
the next generation; thus, modification of those cells by
horizontal gene transfer would have no consequence for the
next generation. The germ-line cells are usually sequestered
in the interior of multicellular organisms, minimizing their
contact with foreign cells, viruses, and DNA, thus insulating
the species from the effects of horizontal gene transfer.
Nevertheless, horizontal gene transfer is possible for
multicellular organisms. For example, the genomes of some
insect species contain DNA that was horizontally transferred
from bacteria that infect them.
Highly conserved genes such as those for ribosomal RNA are present as clearly recognizable relatives in all organisms on Earth; thus, they have evolved very slowly over time. Were such genes “born” perfect?
It is unlikely that any gene came into
existence perfectly optimized for its function. Ribosomal
RNA genes presumably varied a great deal when they
first appeared on Earth. But this would have been at the
very early stage of a common ancestral cell (see Figure
9–23). Since then there has been much less leeway for
change since ribosomal RNA (and other highly conserved
genes) play such a fundamental role in living processes.
Nonetheless, the environment an organism finds itself in is
changeable, so no gene can be optimal indefinitely. Thus
we find there are indeed significant differences in ribosomal
RNAs among species.
Many transposons move within a genome by replicative mechanisms (such as those shown in Figure 9–24B). They therefore increase in copy number each time they transpose. Although individual transposition events are rare, many transposons are found in multiple copies in genomes. What do you suppose keeps the transposons from completely overrunning their hosts’ genomes?
Each time another copy of a transposon
is inserted into a chromosome, the change can be either
neutral, beneficial, or detrimental for the organism. Because
individuals that accumulate detrimental insertions would
be selected against, the proliferation of transposons is
controlled by natural selection. If a transposon arose that
proliferated uncontrollably, it is unlikely that a viable host
organism could be maintained. For this reason, most
transposons have evolved to transpose only rarely. Many
transposons, for example, synthesize only infrequent bursts
of very small amounts of the transposase that is required for
their movement.
Discuss the following statement: “Viruses exist in the twilight zone of life: outside cells they are simply dead assemblies of molecules; inside cells, however, they are alive.”
have no metabolism, do not communicate
with other viruses, and cannot reproduce themselves.
They thus have none of the attributes that one normally
associates with life. Indeed, they can even be crystallized.
Only inside cells can they redirect normal cellular
biosynthetic activities to the task of making more copies of
themselves. Thus, the only aspect of “living” that viruses
display is their capacity to direct their own reproduction
once inside a cell.
Mobile genetic elements, such as the Alu sequences, are found in many copies in human DNA. In what ways could the presence of an Alu sequence affect a nearby gene?
Mobile genetic elements could provide
opportunities for homologous recombination events,
thereby causing genomic rearrangements. They could
insert into genes, possibly obliterating splicing signals and
thereby changing the protein produced by the gene. They
could also insert into the regulatory region of a gene, where
insertion between an enhancer and a transcription start
site could block the function of the enhancer and therefore
reduce the level of expression of a gene. In addition, the
mobile genetic element could itself contain an enhancer and
thereby change the time and place in the organism where
the gene is expressed.
Discuss the following statement: “Mobile genetic elements
are parasites. They are harmful to the host organism and
therefore place it at an evolutionary disadvantage.”
With their ability to facilitate genetic
recombination, mobile genetic elements have almost
certainly played an important part in the evolution of
modern-day organisms. They can facilitate gene duplication
and the creation of new genes via exon shuffling, and they
can change the way in which existing genes are expressed.
Although the transposition of a mobile genetic element
can be harmful for an individual organism—if, for example,
it disrupts the activity of a critical gene—these agents of
genetic change may well be beneficial to the species as a
whole.
Human Chromosome 22 (48 × 106 nucleotide pairs in
length) has about 700 protein-coding genes, which average
19,000 nucleotide pairs in length and contain an average
of 5.4 exons, each of which averages 266 nucleotide
pairs. What fraction of the average protein-coding gene is
converted into mRNA? What fraction of the chromosome
do these genes occupy?
About 7.6% of each gene is converted
to mRNA [(5.4 exons/gene × 266 nucleotide pairs/exon)/
(19,000 nucleotide pairs/gene) = 7.6%]. Protein-coding
genes occupy about 28% of Chromosome 22 [(700 genes ×
19,000 nucleotide pairs/gene)/(48 × 106 nucleotide pairs) =
27.7%]. However, over 90% of this DNA is made of introns
(True/False) The majority of human DNA is unimportant
junk. Explain your answer.
This statement is probably true. For
example, nearly half our DNA is composed of defunct
mobile genetic elements. And only about 9% of the human
genome appears to be under positive selection. However,
it is possible that future research will uncover a function for
some portion of our seemingly unimportant DNA.
Mobile genetic elements make up nearly half of the human
genome and are inserted more or less randomly throughout
it. However, in some spots these elements are rare, as
illustrated for a cluster of genes called HoxD, which lies on
Chromosome 2 (Figure Q9–10). This cluster is about
100 kb in length and contains nine genes whose differential
expression along the length of the developing embryo helps
establish the basic body plan for humans (and for other
animals). Why do you suppose that mobile genetic elements
are so rare in this cluster? In Figure Q9–10, lines that project
upward indicate exons of known genes. Lines that project
downward indicate mobile genetic elements; they are so
numerous they merge into nearly a solid block outside
the HoxD cluster. For comparison, an equivalent region of
Chromosome 22 is shown.
The HoxD cluster is packed with complex
and extensive regulatory sequences that direct each of its
genes to be expressed at the correct time and place during
development. Insertion of mobile genetic elements into the HoxD cluster is thought to be selected against because it
would disrupt proper regulation of its resident genes
An early graphical method for comparing nucleotide
sequences—the so-called diagon plot—still yields one of the best visual comparisons of sequence relatedness.
An example is illustrated in Figure Q9–11, in which the
human β-globin gene is compared with the human cDNA
for β globin (which contains only the coding portion of the
gene; Figure Q9–11A) and to the mouse β-globin gene
(Figure Q9–11B). Diagon plots are generated by comparing
blocks of sequence, in this case blocks of 11 nucleotides
at a time. If 9 or more of the nucleotides match, a dot is
placed on the diagram at the coordinates corresponding to
the blocks being compared. A comparison of all possible
blocks generates diagrams such as the ones shown in Figure
Q9–11, in which sequence similarities show up as diagonal
lines.
A. F rom the comparison of the human β-globin gene with
the human β-globin cDNA (Figure Q9–11A), can you deduce
the positions of exons and introns in the β-globin gene?
B. Are the exons of the human β-globin gene (indicated
by shading in Figure Q9–11B) similar to those of the mouse
β-globin gene? Identify and explain any key differences.
C. Is there any sequence similarity between the human
and mouse β-globin genes that lies outside the exons?
If so, identify its location and offer an explanation for its
preservation during evolution.
D. Did the mouse or human gene undergo a change of
intron length during their evolutionary divergence? How can
you tell?
A. The exons in the human β-globin gene correspond to
the positions of sequence similarity (in this case identity)
with the cDNA, which is a direct copy of the mRNA and
thus contains no introns. The introns correspond to the
regions between the exons. The positions of the introns
and exons in the human β-globin gene are indicated
in Figure A9–11A. Also shown (in open bars) are
sequences present in the mature β-globin mRNA (and in
the gene) that are not translated into protein.
B. From the positions of the exons, as defined in Figure
A9–11A, it is clear that the first two exons of the
human β-globin gene have counterparts, with similar
sequence, in the mouse β-globin gene (Figure A9–11B).
However, only the first half of the third exon of the
human β-globin gene is similar to the mouse β-globin
gene. The similar portion of the third exon contains
sequences that encode protein, whereas the portion
that is different represents the 3ʹ untranslated region
of the gene. Because this portion of the gene does not
encode protein (nor does it contain extensive regulatory
sequences), its sequence is not constrained and the
mouse and human sequences have drifted apart.
C. The human and mouse β-globin genes are also similar at
their 5ʹ ends, as indicated by the cluster of points along
the same diagonal as the first exon (Figure A9–11B).
These sequences correspond to the regulatory regions
upstream of the start sites for transcription. Functional
sequences, which are under selective pressure, diverge
much more slowly than sequences without function.
D. The diagon plot shows that the first intron is nearly the
same length in the human and mouse genes, but the
length of the second intron is noticeably different (Figure
A9–11B). If the introns were the same length, the line
segments that represent sequence similarity would fall
on the same diagonal. The easiest way to test for the
colinearity of the line segments is to tilt the page and
sight along the diagonal. It is impossible to tell from this
comparison if the change in length is due to a shortening
of the mouse intron or to a lengthening of the human
intron, or some combination of those possibilities.
9-14 Why do you expect to encounter a stop codon about every
20 codons or so in a random sequence of DNA?
In a very long, random sequence of
DNA, each of the 64 different codons will occur with equal
frequency. Because 3 of the 64 are stop codons, they will be
expected to occur on average every 21 codons
(64/3 = 21.3).
9-16 Which of the processes listed below contribute significantly
to the evolution of new protein-coding genes?
A. Duplication of genes to create extra copies that can
acquire new functions.
B. F ormation of new genes de novo from noncoding DNA
in the genome.
C. H orizontal transfer of DNA between cells of different
species.
D. M utation of existing genes to create new functions.
E. S huffling of protein domains by gene rearrangement
All of these mechanisms contribute to
the evolution of new protein-coding genes. A, B, C, and
E were discussed in the text. Recent studies indicate that
certain short protein-coding genes arose from previously
untranslated regions of genomes, so choice D is also
correct.
