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7: Patterns of Evolution Are Revealed by Changes at the Molecular Level
Population and Evolutionary Genetics
Rates of nonsynonymous
and synonymous substitutions
in mammalian genes based
on human–rodent comparisons
1 Nonsynonymous nucleotide substitutions alter
the amino acid, but synonymous ones do not.
Nucelotide substitutions per site per yearן10–9
Substitution rates are somewhat lower in the 5Ј and 3Ј
untranslated regions of a gene. As we know from Chapters
10 and 11, these regions are transcribed into RNA but do not
encode amino acids. The 5Ј untranslated region contains the
ribosome-binding site, which is essential for translation, and
the 3Ј untranslated region contains sequences that may function in regulating mRNA stability and translation; so substitutions in these regions may have deleterious effects on
organismal fitness and may not be tolerated.
The lowest rates of substitution are seen in nonsynonymous changes in the coding region, because these substitutions always alter the amino acid sequence of the protein and
are often deleterious. The highest rates of substitution are in
pseudogenes, which are duplicated nonfunctional copies of
genes that have acquired mutations. Such genes no longer
produce a functional product; so mutations in pseudogenes
have no effect on the fitness of the organism.
3 …but are much higher in
nonfunctional DNA, such
2 Rates of substitution are
lower in amino-acid-coding
regions of exons…
Rate (per site
per 109 years)
(per site per
17.17 Different parts of genes evolve at different rates. The
highest rates of nucleotide substitution are in sequences that have the
least effect on protein function.
chain (variable region)
Interferon ␣ 1
Source: After W. Li and D. Graur, Fundamentals of Molecular Evolution
(Sunderland, Mass.: Sinauer, 1991), p. 69.
In summary, there is a relation between the function of
a sequence and its rate of evolution. Higher rates are found
where they have the least effect on function.
The Molecular Clock
The neutral-mutation hypothesis is the idea that evolutionary change at the molecular level takes place primarily
through the fixation of neutral mutations (mutations that
have little or no effect on fitness) by genetic drift. The rate at
which one neutral mutation replaces another depends only
on the mutation rate, which should be fairly constant for any
particular gene. If the rate at which a protein evolves is
roughly constant with the passage of time, the amount of
molecular change that a protein has undergone can be used
as a molecular clock to date evolutionary events.
Average proportion of differences
per amino acid site
For example, we could examine the enzyme cytochrome
c in two organisms known from fossil evidence to have had
a common ancestor 400 million years ago. By determining
the number of differences in the cytochrome c amino acid
sequences in each organism, we could calculate the number
of substitutions that have occurred per amino acid site. The
occurrence of 20 amino acid substitutions since the two
organisms diverged indicates an average rate of 5 substitutions per 100 million years. Knowing how fast the molecular
clock ticks allows us to use molecular changes in cytochrome
c to date other evolutionary events: if we found that
cytochrome c in two organisms differed by 15 amino acid
substitutions, our molecular clock would suggest that they
diverged some 300 million years ago. If we assumed some
error in our estimate of the rate of amino acid substitution,
statistical analysis would show that the true divergence time
might range from 160 million to 440 million years. The molecular clock is analogous to geological dating based on the
radioactive decay of elements.
The molecular clock was proposed by Emile
Zuckerandl and Linus Pauling in 1965 as a possible means
of dating evolutionary events on the basis of molecules in
present-day organisms. A number of studies have examined
the rate of evolutionary change in proteins (Figure 17.18),
and the molecular clock has been widely used to date evolutionary events when the fossil record is absent or ambiguous. However, the results of several studies have shown that
the molecular clock does not always tick at a constant rate,
particularly over shorter time periods, and this method
Time since divergence (millions of years)
Different genes and different parts of the same gene evolve at different rates. Those parts of genes that have the least effect on
function tend to evolve at the highest rates. The idea of the molecular clock is that individual proteins and genes evolve at a constant rate and that the differences in the sequences of present-day
organisms can be used to date past evolutionary events.
✔ Concept Check 8
In general, which types of sequences are expected to exhibit the
slowest evolutionary change?
a. Synonymous changes in amino acid coding regions of exons
b. Nonsynonymous changes in amino acid coding regions of exons
500 440 400 350
270 225 180 135
Millions of years ago
17.18 The molecular clock is based on the assumption of a
The rapid growth of sequence data available in DNA databases has been a source of insight into evolutionary
processes. Whole-genome sequences also are providing
new information about how genomes evolve and the
constant rate of change in protein or DNA sequence.
(a) Relation between the rate of amino acid substitution and time
since divergence, based in part on amino acid sequences of ␣hemoglobin from the eight species shown in part b. The constant rate of
evolution in protein and DNA sequences has been used as a molecular
clock to date past evolutionary events. (b) Phylogeny of eight species
and their approximate times of divergence, based on the fossil record.
Population and Evolutionary Genetics
ψζ ψα2 ψα1
Gγ Aγ ψβ1
β-Globin gene cluster
α-Globin gene cluster
17.19 Human globin genes constitute a multigene family
that has evolved through successive gene duplications.
processes that shape the size, complexity, and organization
Gene duplication New genes have also evolved through
the duplication of whole genes and their subsequent divergence. This process creates multigene families—sets of genes
that are similar in sequence but encode different products. For
example, humans possess 13 different genes found on chromosomes 11 and 16 that encode globinlike molecules, which
take part in oxygen transport (Figure 17.19). All of these genes
have a similar structure, with three exons separated by two
introns, and are assumed to have evolved through repeated
duplication and divergence from a single globin gene in a distant ancestor. This ancestral gene is thought to have been most
similar to the present-day myoglobin gene and first duplicated
to produce an ␣/␤-globin precursor gene and the myoglobin
gene. The ␣/␤ gene then underwent another duplication to
give rise to a primordial ␣-globin gene and a primordial ␤globin gene. Subsequent duplications led to multiple ␣-globin
and ␤-globin genes. Similarly, vertebrates contain four clusters
of Hox genes, each cluster comprising from 9 to 11 genes. Hox
genes play an important role in development.
Some gene families include genes that are arrayed in
tandem on the same chromosome; others are dispersed
among different chromosomes. Gene duplication is a common occurrence in eukaryotic genomes; for example, about
5% of the human genome consists of duplicated segments.
Gene duplication provides a mechanism for the addition
of new genes with novel functions; after a gene duplicates,
there are two copies of the sequence, one of which is free to
change and potentially take on a new function. The extra
copy of the gene may, for example, become active at a different time in development or be expressed in a different tissue
or even diverge and encode a protein having different amino
acids. However, the most common fate of gene duplication is
that one copy acquires a mutation that renders it nonfunc-
tional, giving rise to a pseudogene. Pseudogenes are common
in genomes of complex eukaryotes; the human genome is
estimated to contain as many as 20,000 pseudogenes.
Whole-genome duplication In addition to the duplication of individual genes, whole genomes of some organisms
have apparently duplicated in the past. For example, a comparison of the genome of the yeast Saccharomyces cerevisiae
with the genomes of other fungi reveals that S. cerevisiae or
one of its immediate ancestors underwent a whole-genome
duplication, generating two copies of every gene. Many of
the copies subsequently acquired new functions; others
acquired mutations that destroyed the original function and
then diverged into random DNA sequences. Whole-genome
duplication can take place through polyploidy.
Horizontal gene transfer Most organisms acquire their
genomes through vertical transmission—transfer through
the reproduction of genetic information from parents to offspring. Most phylogenetic trees assume vertical transmission
of genetic information. Findings from DNA sequence studies
reveal that DNA sequences are sometimes exchanged by horizontal gene transfer, in which DNA is transferred between
different species. This process is especially common among
bacteria, and there are a number of documented cases in
which genes are transferred from bacteria to eukaryotes. The
extent of horizontal gene transfer among eukaryotic organisms is controversial, with few well-documented cases. Horizontal gene transfer can obscure phylogenetic relationships
and make the reconstruction of phylogenetic trees difficult.
New genes may evolve through the duplication of genes and
through the duplication of whole genomes. Genes can be passed
among distantly related organisms through horizontal gene transfer.
• A Mendelian population is a group of interbreeding, sexually
reproducing individuals, whose set of genes constitutes the
population’s gene pool. A population’s genetic composition
can be described by its genotypic and allelic frequencies.
The Hardy–Weinberg law describes the effects of reproduction
and Mendel’s laws on the allelic and genotypic frequencies of a
population. When a population is large, randomly mating, and
free from the effects of mutation, migration, and natural
selection, the allelic frequencies do not change and the
genotypic frequencies stabilize after one generation in the
Hardy–Weinberg equilibrium proportions p2, 2pq, and q2,
where p and q equal the frequencies of the alleles.
Nonrandom mating affects the frequencies of genotypes but
not those of alleles. Inbreeding increases the frequency of
homozygotes while decreasing the frequency of heterozygotes.
Recurrent mutation eventually leads to an equilibrium, with
the allelic frequencies being determined by the relative rates of
forward and reverse mutation.
Migration, the movement of genes between populations,
increases the amount of genetic variation within populations
and decreases the number of differences between populations.
Genetic drift is change in allelic frequencies due to chance
factors. Genetic drift arises when a population consists of a
small number of individuals, is established by a small number
of founders, or undergoes a major reduction in size. Genetic
drift changes allelic frequencies, reduces genetic variation
within populations, and causes genetic divergence among
Natural selection is the differential reproduction of genotypes;
it is measured by the relative reproductive successes (fitnesses)
• Evolution is genetic change taking place within a group of
organisms. It is a two-step process: (1) genetic variation arises
and (2) genetic variants change in frequency. Anagenesis refers
to change within a single lineage; cladogenesis is the splitting
of one lineage into two.
A species can be defined as a group of organisms that are
capable of interbreeding with one another and are
reproductively isolated from the members of other species.
Species are prevented from exchanging genes by reproductive
isolating mechanisms, either before a zygotes has formed
(prezygotic reproductive isolation) or after a zygote has
formed (postzygotic reproductive isolation).
Allopatric speciation arises when a geographic barrier
prevents gene flow between two populations. Sympatric
speciation arises when reproductive isolation exists in the
absence of any geographic barrier.
Evolutionary relationships (a phylogeny) can be represented by
a phylogenetic tree, consisting of nodes that represent organisms
and branches that represent their evolutionary connections.
Two different approaches to constructing phylogenetic trees
are the distance approach and the parsimony approach.
Different parts of the genome show different amounts of
genetic variation. In general, those parts that have the least
effect on function evolve at the highest rates.
The molecular-clock hypothesis proposes a constant rate of
nucleotide substitution, providing a means of dating
evolutionary events by looking at nucleotide differences
Genome evolution takes place through the duplication of
genes to form gene families, whole-genome duplication, and
the horizontal transfer of genes between organisms.
genetic rescue (p. 430)
Mendelian population (p. 430)
gene pool (p. 430)
genotypic frequency (p. 431)
allelic frequency (p. 431)
Hardy–Weinberg law (p. 433)
Hardy–Weinberg equilibrium (p. 433)
inbreeding (p. 436)
equilibrium (p. 437)
migration (gene flow) (p. 437)
sampling error (p. 438)
genetic drift (p. 438)
effective population size (p. 439)
founder effect (p. 439)
genetic bottleneck (p. 439)
fixation (p. 440)
fitness (p. 440)
selection coefficient (p. 441)
directional selection (p. 441)
overdominance (p. 441)
underdominance (p. 442)
evolution (p. 443)
anagenesis (p. 443)
cladogenesis (p. 443)
species (p. 444)
biological species concept (p. 444)
reproductive isolating mechanism
prezygotic reproductive isolating
mechanism (p. 444)
postzygotic reproductive isolating
mechanism (p. 444)
speciation (p. 445)
allopatric speciation (p. 445)
sympatric speciation (p. 445)
phylogeny (p. 448)
phylogenetic tree (p. 448)
node (p. 449)
branch (p. 449)
rooted tree (p. 449)
molecular clock (p. 451)
multigene family (p. 453)
Population and Evolutionary Genetics
Answers to Concept Checks
7. Genetic drift can bring about changes in the allelic frequencies
of populations and lead to genetic differences among
populations. Genetic differentiation is the cause of postzygotic
and prezygotic reproductive isolation between populations that
leads to speciation.
1. What is a Mendelian population? How is the gene pool of a
Mendelian population usually described?
2. What are the predictions given by the Hardy–Weinberg law?
*3. What assumptions must be met for a population to be in
4. Define inbreeding and briefly describe its effects on a
5. What determines the allelic frequencies at mutational
*6. What factors affect the magnitude of change in allelic
frequencies due to migration?
7. Define genetic drift and give three ways in which it can
arise. What effect does genetic drift have on a population?
*8. What is effective population size? How does it affect the
amount of genetic drift?
9. Define natural selection and fitness.
10. Briefly describe the differences between directional
selection, overdominance, and underdominance. Describe
the effect of each type of selection on the allelic frequencies
of a population.
*11. Compare and contrast the effects of mutation, migration,
genetic drift, and natural selection on genetic variation
within populations and on genetic divergence between
*12. What are the two steps in the process of evolution?
13. How does anagenesis differ from cladogenesis?
*14. What is the biological species concept?
15. What is the difference between prezygotic and postzygotic
reproductive isolating mechanisms?
16. What is the basic difference between allopatric and
sympatric modes of speciation?
*17. Briefly describe the difference between the distance
approach and the parsimony approach to the reconstruction
of phylogenetic trees.
18. Outline the different rates of evolution that are typically
seen in different parts of a protein-encoding gene. What
might account for these differences?
*19. What is the molecular clock?
20. What is a multigene family? What processes produce
21. Define horizontal gene transfer. What problems does it
cause for evolutionary biologists?
Application Questions and Problems
22. How would you respond to someone who said that models
are useless in studying population genetics because they
represent oversimplifications of the real world?
*23. Voles (Microtus ochrogaster) were trapped in old fields in
southern Indiana and were genotyped for a transferrin
locus. The following numbers of genotypes were recorded,
where T E and T F represent different alleles.
T ET E
T ET F
T FT F
Calculate the genotypic and allelic frequencies of the transferrin locus for this population.
24. Jean Manning, Charles Kerfoot, and Edward Berger studied
the allelic frequencies at the glucose phosphate isomerase
(GPI) locus in the cladoceran Bosmina longirostris. At one
location, they collected 176 animals from Union Bay in
Seattle, Washington, and determined their GPI genotypes
by using electrophoresis (J. Manning, W. C. Kerfoot, and
E. M. Berger. 1978. Evolution 32:365–374).
Determine the genotypic and allelic frequencies for this
25. A total of 6129 North American Caucasians were blood
typed for the MN locus, which is determined by two
codominant alleles, LM and LN. The following data were
Carry out a chi-square test to determine whether this
population is in Hardy–Weinberg equilibrium at the
26. Most black bears (Ursus americanus) are black or brown in
DATA color. However, occasional white bears of this species appear
in some populations along the coast of British Columbia.
Kermit Ritland and his colleagues determined that white
coat color in these bears results from a recessive mutation
(G) caused by a single nucleotide replacement in which
guanine substitutes for adenine at the melanocortin-1
receptor locus (mcr1), the same locus responsible for red
hair in humans (K. Ritland, C. Newton, and H. D. Marshall.
2001. Current Biology 11:1468–1472). The wild-type allele at
this locus (A) encodes black or brown color. Ritland and his
colleagues collected samples from bears on three islands and
determined their genotypes at the mcr1 locus.
a. What are the frequencies of the A and G alleles in these
b. Give the genotypic frequencies expected if the
population is in Hardy–Weinberg equilibrium.
c. Use a chi-square test to compare the number of
observed genotypes with the number expected under
Hardy–Weinberg equilibrium. Is this population in
Hardy–Weinberg equilibrium? Explain your reasoning.
27. Genotypes of leopard frogs from a population in central
Kansas were determined for a locus (M) that encodes the
enzyme malate dehydrogenase. The following numbers of
genotypes were observed:
a. Calculate the genotypic and allelic frequencies for this
b. What would the expected numbers of genotypes be if
the population were in Hardy–Weinberg equilibrium?
28. Full color (D) in domestic cats is dominant over dilute color
(d). Of 325 cats observed, 194 have full color and 131 have
a. If these cats are in Hardy–Weinberg equilibrium for
the dilution locus, what is the frequency of the dilute
b. How many of the 194 cats with full color are likely to be
29. Tay–Sachs disease is an autosomal recessive disorder.
Among Ashkenazi Jews, the frequency of Tay–Sachs disease
is 1 in 3600. If the Ashkenazi population is mating
randomly for the Tay–Sachs gene, what proportion of
the population consists of heterozygous carriers of the
*30. The human MN blood type is determined by two
codominant alleles, LM and LN. The frequency of LM in
Eskimos on a small Arctic island is 0.80. If the inbreeding
coefficient for this population is 0.05, what are the expected
frequencies of the M, MN, and N blood types on the island?
31. Pikas are small mammals that live at high elevation in the
talus slopes of mountains. Most populations located on
mountain tops in Colorado and Montana in North America
are isolated from one another, because the pikas don’t
occupy the low-elevation habitats that separate the
mountain tops and don’t venture far from the talus slopes.
Thus, there is little gene flow between populations.
Furthermore, each population is small in size and was
founded by a small number of pikas. A group of population
geneticists propose to study the amount of genetic
variation in a series of pika populations and to compare
the allelic frequencies in different populations. On the
bases of the biology and the distribution of pikas, predict
what the population geneticists will find concerning the
within- and between-population genetic variation.
32. Two chromosomal inversions are commonly found in
populations of Drosophila pseudoobscura: Standard (ST)
patterns, particularly in regard to the role of cladogenesis in
and Arrowhead (AR). When treated with the insecticide
DDT, the genotypes for these inversions exhibit
overdominance, with the following fitnesses:
What will the frequencies of ST and AR be after
equilibrium has been reached?
33. The fruit fly Drosophila melanogaster normally feeds on
DATA rotting fruit, which may ferment and contain high levels of
alcohol. Douglas Cavener and Michael Clegg studied allelic
frequencies at the locus for alcohol dehydrogenase (Adh) in
experimental populations of D. melanogaster (D. R. Cavener
and M. T. Clegg. 1981. Evolution 35:1–10). The experimental
populations were established from wild-caught flies and
were raised in cages in the laboratory. Two control
populations (C1 and C2) were raised on a standard
cornmeal–molasses–agar diet. Two ethanol populations (E1
and E2) were raised on a cornmeal–molasses–agar diet to
which was added 10% ethanol. The four populations were
periodically sampled to determine the allelic frequencies of
two alleles at the alcohol dehydrogenase locus, AdhS and
AdhF. The frequencies of these alleles in the experimental
populations are shown in the graph.
35. Michael Bunce and his colleagues in England, Canada, and
the United States extracted and sequenced mitochondrial
DNA from fossils of Haast’s eagle, a gigantic eagle that was
driven to extinction 700 years ago when humans first
arrived in New Zealand (M. Bunce et al. 2005. Plos Biology
3:44–46). Using mitochondrial DNA sequences from living
eagles and those from Haast-eagle fossils, they created the
following phylogenetic tree. On this phylogenetic tree,
identify (a) all terminal nodes; (b) all internal nodes;
(c) one example of a branch; and (d) the outgroup.
Frequency of AdhS
10 15 20 25 30 35 40 45 50
a. One the basis of these data, what conclusion might you
draw about the evolutionary forces that are affecting the
Adh alleles in these populations?
b. Cavener and Clegg measured the viability of the
different Adh genotypes in the alcohol environment
and obtained the following values:
Using these relative viabilities, calculate relative fitnesses for
the three genotypes.
34. The following illustrations represent two different patterns
of evolution. Briefly discuss the differences in these two
Black hawk eagle
36. The Barton Springs salamander is an endangered species
found only in a single spring in the city of Austin, Texas.
There is growing concern that a chemical spill on a nearby
freeway could pollute the spring and wipe out the species.
To provide a source of salamanders to repopulate the spring
in the event of such a catastrophe, a proposal has been made
to establish a captive breeding population of the salamander
in a local zoo. You are asked to provide a plan for the
establishment of this captive breeding population, with the
goal of maintaining as much of the genetic variation of the
species as possible in the captive population. What factors
might cause loss of genetic variation in the establishment of
the captive population? How could loss of such variation be
prevented? With the assumption that only a limited number
of salamanders can be maintained in captivity, what
procedures should be instituted to ensure the long-term
maintenance of as much of the variation as possible?
37. Explain why natural selection may cause prezygotic
reproductive isolating mechanisms to evolve if postzygotic
reproductive isolating mechanisms are already present, but
natural selection can never cause the evolution of
postzygotic reproductive isolating mechanisms.
acentric chromatid Lacks a centromere; produced when crossing over
takes place within a paracentric inversion. The acentric chromatid
does not attach to a spindle fiber and does not segregate in meiosis
or mitosis; so it is usually lost after one or more rounds of cell
acrocentric chromosome Chromosome in which the centromere is
near one end, producing a long arm at one end and a knob, or
satellite, at the other end.
activator See transcriptional activator protein.
addition rule States that the probability of any of two or more
mutually exclusive events occurring is calculated by adding the
probabilities of the individual events.
additive genetic variance Component of the genetic variance that can
be attributed to the additive effect of different genotypes.
adenine (A) Purine base in DNA and RNA.
adenosine-3Ј,5Ј-cyclic monophosphate (cAMP) Modified nucleotide
that functions in catabolite repression. Low levels of glucose
stimulate high levels of cAMP; cAMP then attaches to CAP, which
binds to the promoter of certain operons and stimulates
A-DNA Right-handed helical structure of DNA that exists when little
water is present.
allele One of two or more alternate forms of a gene.
allelic frequency Proportion of a particular allele in a population.
allopatric speciation Arises when a geographic barrier first splits a
population into two groups and blocks the exchange of genes
between them. Compare sympatric speciation.
allopolyploidy Condition in which the sets of chromosomes of a
polyploid individual possessing more than two haploid sets are
derived from two or more species.
allosteric protein Protein that changes its conformation on binding
with another molecule.
alternative processing One of several pathways by which a single premRNA can be processed in different ways to produce alternative
types of mRNA.
alternative splicing Process by which a single pre-mRNA can be
spliced in more than one way to produce different types of mRNA.
Ames test Test in which special strains of bacteria are used to evaluate
the potential of chemicals to cause cancer.
amino acid Repeating unit of proteins; consists of an amino group, a
carboxyl group, a hydrogen atom, and a variable R group.
aminoacyl (A) site One of three sites in a ribosome occupied by a
tRNA in translation. All charged tRNAs (with the exception of the
initiator tRNA) first enter the A site in translation.
aminoacyl-tRNA synthetase Enzyme that attaches an amino acid to a
tRNA. Each aminoacyl-tRNA synthetase is specific for a particular
amphidiploidy Type of allopolyploidy in which two different diploid
genomes are combined, so that every chromosome has one and only
one homologous partner and the genome is functionally diploid.
anagenesis Evolutionary change within a single lineage.
anaphase Stage of mitosis in which chromatids separate and move
toward the spindle poles.
anaphase I Stage of meiosis I. In anaphase I, homologous
chromosomes separate and move toward the spindle poles.
anaphase II Stage of meiosis II. In anaphase II, chromatids separate
and move toward the spindle poles.
aneuploidy Change from the wild type in the number of chromosomes;
most often an increase or decrease of one or two chromosomes.
anticodon Sequence of three nucleotides in tRNA that pairs with the
corresponding codon in mRNA in translation.
antiparallel Refers to a characteristic of the DNA double helix in
which the two polynucleotide strands run in opposite directions.
apoptosis Programmed cell death, in which a cell degrades its own
DNA, the nucleus and cytoplasm shrink, and the cell undergoes
phagocytosis by other cells without leakage of its contents.
archaea One of the three primary divisions of life. Archaea consist of
unicellular organisms with prokaryotic cells.
artificial selection Selection practiced by humans.
autopolyploidy Condition in which all the sets of chromosomes of a
polyploid individual possessing more than two haploid sets are
derived from a single species.
autoradiography Method for visualizing DNA or RNA molecules
labeled with radioactive substances. A piece of X-ray film is placed
on top of a slide, gel, or other substance that contains DNA labeled
with radioactive chemicals. Radiation from the labeled DNA
exposes the film, providing a picture of the labeled molecules.
autosome Chromosome that is the same in males and females; nonsex
auxotroph Bacterium or fungus that possesses a nutritional mutation
that disrupts its ability to synthesize an essential biological
molecule; cannot grow on minimal medium but can grow on
minimal medium to which has been added the biological molecule
that it cannot synthesize.
backcross Cross between an F1 individual and one of the parental (P)
bacterial artificial chromosome (BAC) Cloning vector used in bacteria
that is capable of carrying DNA fragments as large as 500 kb.
bacterial colony Clump of genetically identical bacteria derived from a
single bacterial cell that undergoes repeated rounds of division.
bacteriophage Virus that infects bacterial cells.
Barr body Condensed, darkly staining structure that is found in most
cells of female placental mammals and is an inactivated X
base See nitrogenous base.
base analog Chemical substance that has a structure similar to that of
one of the four standard bases of DNA and may be incorporated
into newly synthesized DNA molecules in replication.
base-excision repair DNA repair that first excises modified bases and
then replaces the entire nucleotide.
base substitution Mutation in which a single pair of bases in DNA is
B-DNA Right-handed helical structure of DNA that exists when water
is abundant; the secondary structure described by Watson and
Crick and probably the most common DNA structure in cells.
bidirectional replication Replication at both ends of a replication
bioinformatics Synthesis of molecular biology and computer science
that develops databases and computational tools to store, retrieve,
and analyze nucleic acid and protein sequence data.
biological species concept Defines a species as a group of organisms
whose members are capable of interbreeding with one another but
are reproductively isolated from the members of other species.
Because different species do not exchange genes, each species
evolves independently. Not all biologists adhere to this concept.
biotechnology Use of biological processes, particularly molecular
genetics and recombinant DNA technology, to produce products
of commercial value.
bivalent Refers to a synapsed pair of homologous chromosomes.
blending inheritance Early concept of heredity proposing that
offspring possess a mixture of the traits from both parents.
branch Evolutionary connections between organisms in a phylogenetic
branch point Adenine nucleotide in nuclear pre-mRNA introns that
lies from 18 to 40 nucleotides upstream of the 3Ј splice site.
broad-sense heritability Proportion of the phenotypic variance that
can be attributed to genetic variance.
catabolite activator protein (CAP) Protein that functions in catabolite
repression. When bound with cAMP, CAP binds to the promoter
of certain operons and stimulates transcription.
catabolite repression System of gene control in some bacterial
operons in which glucose is used preferentially and the
metabolism of other sugars is repressed in the presence of glucose.
cDNA (complementary DNA) library Collection of bacterial colonies
or phage colonies containing DNA fragments that have been
produced by reverse transcription of cellular mRNA.
cell cycle Stages through which a cell passes from one cell division to
cell theory States that all life is composed of cells, that cells arise only
from other cells, and that the cell is the fundamental unit of
structure and function in living organisms.
centiMorgan Another name for map unit.
central dogma Concept that genetic information passes from DNA to
RNA to protein in a one-way information pathway.
centriole Cytoplasmic organelle consisting of microtubules; present at
each pole of the spindle apparatus in animal cells.
centromere Constricted region on a chromosome that stains less
strongly than the rest of the chromosome; region where spindle
microtubules attach to a chromosome.
centromeric sequence DNA sequence found in functional
Chargaff ’s rules Rules developed by Erwin Chargaff and his colleagues
concerning the ratios of bases in DNA.
checkpoint A key transition point at which progression to the next
stage in the cell cycle is regulated.
chiasma (pl., chiasmata) Point of attachment between homologous
chromosomes at which crossing over took place.
chromatin Material found in the eukaryotic nucleus; consists of DNA
chromatin-remodeling complex Complex of proteins that alters
chromatin structure without acetylating histone proteins.
chromatosome Consists of a nucleosome and an H1 histone protein.
chromosomal scaffold protein Protein that plays a role in the folding
and packing of the chromosome, revealed when chromatin is
treated with a concentrated salt solution, which removes histones
and some other chromosomal proteins.
chromosome deletion Loss of a chromosome segment.
chromosome duplication Mutation that doubles a segment of a
chromosome inversion Rearrangement in which a segment of a
chromosome has been inverted 180 degrees.
chromosome mutation Difference from the wild type in the number
or structure of one or more chromosomes; often affects many
genes and has large phenotypic effects.
chromosome rearrangement Change from the wild type in the
structure of one or more chromosomes.
chromosome theory of heredity States that genes are located on
cis configuration Arrangement in which two or more wild-type
genes are on one chromosome and their mutant alleles are on
the homologous chromosome; also called coupling
cladogenesis Evolution in which one lineage is split into two.
clonal evolution Process by which mutations that enhance the ability
of cells to proliferate predominate in a clone of cells, allowing the
clone to become increasingly rapid in growth and increasingly
aggressive in proliferation properties.
cloning vector Stable, replicating DNA molecule to which a foreign
DNA fragment can be attached and transferred to a host cell.
cloverleaf structure Secondary structure common to all tRNAs.
coactivator Protein that cooperates with an activator of transcription.
In eukaryotic transcriptional control, coactivators often physically
interact with transcriptional activators and the basal transcription
codominance Type of allelic interaction in which the heterozygote
simultaneously expresses traits of both homozygotes.
codon Sequence of three nucleotides that encodes one amino acid in a
coefficient of coincidence Ratio of observed double crossovers to
expected double crossovers.
cohesive end Short, single-stranded overhanging end on a DNA
molecule produced when the DNA is cut by certain restriction
enzymes. Cohesive ends are complementary and can
spontaneously pair to rejoin DNA fragments that have been cut
with the same restriction enzyme.
colinearity Concept that there is a direct correspondence between the
nucleotide sequence of a gene and the continuous sequence of
amino acids in a protein.
colony See bacterial colony.
comparative genomics Comparative studies of the genomes of
competent cell Capable of taking up DNA from its environment
(capable of being transformed).
complementary DNA strands The relation between the two
nucleotide strands of DNA in which each purine on one strand
pairs with a specific pyrimidine on the opposite strand (A pairs
with T, and G pairs with C).
complementation Two different mutations in the heterozygous
condition are exhibited as the wild-type phenotype; indicates that
the mutations are at different loci.
complementation test Test designed to determine whether two
different mutations are at the same locus (are allelic) or at
different loci (are nonallelic). Two individuals that are
homozygous for two independently derived mutations are crossed,
producing F1 progeny that are heterozygous for the mutations. If
the mutations are at the same locus, the F1 will have a mutant
phenotype. If the mutations are at different loci, the F1 will have a
complete linkage Linkage between genes that are located close together
on the same chromosome with no crossing over between them.
complete medium Used to culture bacteria or some other
microorganism; contains all the nutrients required for growth and
synthesis, including those normally synthesized by the organism.
Nutritional mutants can grow on complete medium.
concept of dominance Principle of heredity discovered by Mendel
stating that, when two different alleles are present in a genotype,
only one allele may be expressed in the phenotype. The dominant
allele is the allele that is expressed, and the recessive allele is the
allele that is not expressed.
conditional mutation Expressed only under certain conditions.
conjugation Mechanism by which genetic material may be exchanged
between bacterial cells. During conjugation, two bacteria lie close
together and a cytoplasmic connection forms between them. A
plasmid or sometimes a part of the bacterial chromosome passes
through this connection from one cell to the other.
consanguinity Mating between related individuals.
consensus sequence Comprises the most commonly encountered
nucleotides found at a specific location in DNA or RNA.
Ϫ10 consensus sequence (Pribnow box) Consensus sequence
(TATAAT) found in most bacterial promoters approximately 10 bp
upstream of the transcription start site.
Ϫ35 consensus sequence Consensus sequence (TTGACA) found in
many bacterial promoters approximately 35 bp upstream of the
transcription start site.
constitutive gene A gene that is not regulated and is expressed
contig Set of overlapping DNA fragments that have been assembled in
the correct order to form a continuous stretch of DNA sequence.
continuous characteristic Displays a large number of possible
phenotypes that are not easily distinguished, such as human
continuous replication Replication of the leading strand in the same
direction as that of unwinding, allowing new nucleotides to be
added continuously to the 3Ј end of the new strand as the template
coordinate induction Simultaneous synthesis of several enzymes that
is stimulated by a single environmental factor.
core enzyme Part of bacterial RNA polymerase that, during
transcription, catalyzes the elongation of the RNA molecule by the
addition of RNA nucleotides; consists of four subunits: two copies
of alpha (a), a single copy of beta (b), and a single copy of beta
corepressor Substance that inhibits transcription in a repressible
system of gene regulation; usually a small molecule that binds to a
repressor protein and alters it so that the repressor is able to bind
to DNA and inhibit transcription.
correlation Degree of association between two or more variables.
cosmid Cloning vector that combines the properties of plasmids and
phage vectors and is used to clone large pieces of DNA in bacteria.
Cosmids are small plasmids that carry l cos sites, allowing the
plasmid to be packaged into viral coats.
cotransduction Process in which two or more genes are transferred
together from one bacterial cell to another. Only genes located
close together on a bacterial chromosome will be cotransduced.
cotransformation Process in which two or more genes are transferred
together during cell transformation.
coupling configuration See cis configuration.
crossing over Exchange of genetic material between homologous but
C value Haploid amount of DNA found in a cell of an organism.
cyclin A key protein in the control of the cell cycle; combines with a
cyclin-dependent kinase (CDK). The levels of cyclin rise and fall in
the course of the cell cycle.
cyclin-dependent kinase (CDK) A key protein in the control of the
cell cycle; combines with cyclin.
cytokinesis Process by which the cytoplasm of a cell divides.
cytoplasmic inheritance Inheritance of characteristics encoded by
genes located in the cytoplasm. Because the cytoplasm is usually
contributed entirely by only one parent, most cytoplasmically
inherited characteristics are inherited from a single parent.
cytosine (C) Pyrimidine base in DNA and RNA.
deamination Loss of an amino group (NH2) from a base.
degenerate genetic code Refers to the fact that the genetic code
contains more information than is needed to specify all 20
common amino acids.
deletion Mutation in which one or more nucleotides are deleted from
a DNA sequence.
deoxyribonucleotide Basic building block of DNA, consisting of
deoxyribose, a phosphate, and a nitrogenous base.
deoxyribose Five-carbon sugar in DNA; lacks a hydroxyl group on the
depurination Break in the covalent bond connecting a purine base to
the 1Ј-carbon atom of deoxyribose, resulting in the loss of the
purine base. The resulting apurinic site cannot provide a template
in replication, and a nucleotide with another base may be
incorporated into the newly synthesized DNA strand opposite the
dicentric bridge Structure produced when the two centromeres of a
dicentric chromatid are pulled toward opposite poles, stretching
the dicentric chromosome across the center of the nucleus.
Eventually, the dicentric bridge breaks as the two centromeres are
dicentric chromatid Chromatid that has two centromeres; produced
when crossing over takes place within a paracentric inversion. The
two centromeres of the dicentric chromatid are frequently pulled
toward opposite poles in mitosis or meiosis, breaking the
dideoxyribonucleoside triphosphate (ddNTP) Special substrate for
DNA synthesis used in the Sanger dideoxy sequencing method;
identical with dNTP (the usual substrate for DNA synthesis)
except that it lacks a 3Ј-OH group. The incorporation of a ddNTP
into DNA terminates DNA synthesis.
dihybrid cross A cross between two individuals that differ in two
characteristics—more specifically, a cross between individuals that
are homozygous for different alleles at the two loci (AA BB ϫ aa bb);
also refers to a cross between two individuals that are both
heterozygous at two loci (Aa Bb ϫ Aa Bb).
diploid Possessing two sets of chromosomes (two genomes).
directional selection Selection in which one trait or allele is favored
direct repair DNA repair in which modified bases are changed back
into their original structures.