Essential Cell Biology 5th edition

A:24 Answers
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.
ANSWER 9–12 Computer algorithms that search for exons
are complex, as you might imagine. To identify unknown
genes, these programs combine statistical information
derived from known genes, such as:
1. An exon that encodes protein will have an open reading
frame. If the amino acid sequence specified by this
open reading frame matches a protein sequence in any
database, there is a high likelihood that it is an authentic
exon.
2. The reading frames of adjacent exons in the same gene
will match up when the intron sequences are omitted.
3. Internal exons (excluding the first and the last) will have
splicing signals at each end; most of the time (~98%)
these will be AG at the 5′ ends of the exons and GT at
the 3′ ends.
4. The multiple codons for most individual amino acids are
not used with equal frequency. This so-called coding
bias, which varies from one species to the next, can be
factored in to aid in the recognition of true exons.
5. Exons and introns have characteristic length
distributions. The median length of exons in human
genes is about 120 nucleotide pairs. Introns tend to be
much larger: a median length of about 2 kb in genomic
regions of 30–40% GC content, and a median length of
about 500 nucleotide pairs in regions above 50% GC.
6. The initiation codon for protein synthesis (nearly always
an ATG) has a statistical association with adjacent
nucleotides that seem to enhance its recognition by
translation factors.
7. The terminal exon will have a signal (most commonly
AATAAA) for cleavage and polyadenylation close to its
3′ end.
The statistical nature of these features, coupled with the
low frequency of coding information in the genome (1.5%
for humans) and the high frequency of alternative splicing
(estimated to occur in 95% of human genes), makes it
difficult for an algorithm to correctly identify all exons. As
shown in Figure 9−36, these bioinformatic approaches are
usually coupled with direct experimental data, such as those
obtained from full-genome RNA sequencing (RNA-Seq).
ANSWER 9–13 It is often not a simple matter to determine
the function of a gene, nor is there a universal recipe for
doing so. Nevertheless, there are a variety of standard
questions whose answers help to narrow down the
possibilities. Below we list some of these questions.
In what tissues is the gene expressed? If the gene is
expressed in all tissues, it is likely to have a general function.
If it is expressed in one or a few tissues, its function is
likely to be more specialized, perhaps related to the
specific functions of the tissues. If the gene is expressed
in the embryo but not the adult, it probably functions in
development.
In what compartment of the cell is the protein found?
Knowing the subcellular localization of the protein—nucleus,
plasma membrane, mitochondria, etc.—can also help to rule
out or support potential functions. For example, a protein
that is localized to the plasma membrane is likely to be a
transporter, a receptor or other component of a signaling
pathway, a cell adhesion molecule, etc.
What are the effects of mutations in the gene? Mutations
that eliminate or modify the function of the gene product
can provide important clues to function. For example,
if the gene product is critical at a certain time during
development, mutant embryos will often die at that stage or
develop obvious abnormalities.
With what other proteins does the encoded protein
interact? In carrying out their function, proteins often
interact with other proteins involved in the same or closely
related processes. If an interacting protein can be identified,
and if its function is already known (through previous
research or through the searching of databases), the range
of possible functions can often be narrowed.
Can mutations in other genes alter effects of mutation in
the unknown gene? Searching for such mutations can be
a very powerful approach to investigating gene function,
especially in organisms such as bacteria and yeast, which
have simple genetic systems. Although much more
difficult to perform in the mouse, this type of approach
can nonetheless be used. The rationale for this strategy
is analogous to that of looking for interacting proteins:
genes that interact genetically—so that the doublemutant
phenotype is more selective than either of the
individual mutants—are often involved in the same process
or in closely related processes. Identification of such an
interacting gene (and knowledge of its function) would
provide an important clue to the function of the unknown
gene.
Addressing each of these questions requires specialized
experimental expertise and a substantial time commitment
from the investigator. It is no wonder that progress is made
much more rapidly when a clue to a gene’s function can be
found simply by identifying a similar gene of known function
in the database. As more and more genes are studied, this
strategy will become increasingly successful.
ANSWER 9–14 In a 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).
ANSWER 9–15 All of these mechanisms contribute to
the evolution of new protein-coding genes. A, C, D, 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 B is also correct.
ANSWER 9–16
A. Because synonymous changes do not alter the amino
acid sequence of the protein, they usually do not affect
the overall fitness of the organism and are therefore not
selected against. By contrast, nonsynonymous changes,
which substitute a new amino acid in place of the original
one, can alter the function of the encoded protein and
change the fitness of the organism. Since most amino
acid substitutions probably harm the protein, they tend
to be selected against.
B. Virtually all amino acid substitutions in the histone
H3 protein are deleterious and are therefore selected
against. The extreme conservation of histone H3 argues