Chapter 5
The Content of
the Genome
5.1 Introduction
• genome – The complete set of sequences in the
genetic material of an organism.
– It includes the sequence of each chromosome plus
any DNA in organelles.
• transcriptome – The complete set of RNAs
present in a cell, tissue, or organism.
– Its complexity is due mostly to mRNAs, but it also
includes noncoding RNAs.
5.1 Introduction
• proteome – The complete set of proteins that is
expressed by the entire genome.
– The term is sometimes used to describe the
complement of proteins expressed by a cell at any
one time.
• interactome – The complete set of protein
complexes/protein–protein interactions present
in a cell, tissue, or organism.
5.2 Genomes Can Be Mapped at Several
Levels of Resolution
• Linkage maps are based on the frequency of
recombination between genetic markers.
• Restriction maps are based on the physical distances
between markers.
• Molecular characterization of mutations can be used to
reconcile linkage maps with physical restriction maps.
5.3 Individual Genomes Show Extensive
Variation
• Polymorphism may be detected at the phenotypic level
when a sequence affects gene function, at the restriction
fragment level when it affects a restriction enzyme target
site, and at the sequence level by direct analysis of DNA.
• The alleles of a gene show extensive polymorphism at
the sequence level, but many sequence changes do not
affect function.
Figure 05.01: A point mutation that affects a restriction site is detected by a difference in
restriction fragment lengths.
5.3 Individual Genomes Show Extensive
Variation
• restriction fragment length polymorphism
(RFLP) – Inherited differences in sites for
restriction enzymes (for example, caused by
base changes in the target site) that result in
differences in the lengths of the fragments
produced by cleavage with the relevant
restriction enzyme.
– They are used for genetic mapping to link the genome
directly to a conventional genetic marker.
5.3 Individual Genomes Show Extensive
Variation
Figure 05.03: A restriction polymorphism can be
used as a genetic marker to measure
recombination distance from a phenotypic
marker.
Figure 05.04: If a restriction marker is associated with a phenotypic characteristic, the
restriction site must be located near the gene for the phenotype.
5.3 Individual Genomes Show Extensive
Variation
• single nucleotide polymorphism (SNP) – A
polymorphism (variation in sequence between
individuals) caused by a change in a single
nucleotide.
– SNPs are responsible for most of the genetic variation
between individuals.
5.4 RFLPs and SNPs Can Be Used for
Genetic Mapping
• RFLPs and SNPs can be the basis for linkage
maps and are useful for establishing parent–
offspring relationships.
• haplotype – The particular combination of
alleles in a defined region of some chromosome;
in effect, the genotype in miniature.
– Originally used to describe combinations of major
histocompatibility complex (MHC) alleles, it now may
be used to describe particular combinations of
RFLPs, SNPs, or other markers.
5.4 RFLPs and SNPs Can Be Used for
Genetic Mapping
• DNA fingerprinting – A technique for analyzing
the differences between individuals of the
fragments generated by using restriction
enzymes to cleave regions that contain short
repeated sequences, or by PCR.
– The lengths of the repeated regions are unique to
every individual.
– The presence of a particular subset in any two
individuals can be used to define their common
inheritance (e.g., a parent–child relationship).
5.5 Eukaryotic Genomes Contain Both
Nonrepetitive and Repetitive DNA
Sequences
• The kinetics of DNA reassociation after a genome has
been denatured distinguish sequences by their
frequency of repetition in the genome.
• Polypeptides are generally encoded by sequences in
nonrepetitive DNA.
• Larger genomes within a taxonomic group do not contain
more genes but have large amounts of repetitive DNA.
5.5 Eukaryotic Genomes Contain Both
Nonrepetitive and Repetitive DNA
Sequences
Figure 05.05: The proportions of different sequence
components vary in eukaryotic genomes.
• A large part of
moderately
repetitive DNA may
be made up of
transposons.
5.6 Eukaryotic Protein-Coding Genes Can
Be Identified by the Conservation of Exons
• Conservation of exons can be used as the basis for
identifying coding regions by identifying fragments
whose sequences are present in multiple organisms.
• zoo blot – The use of Southern blotting to test the ability
of a DNA probe from one species to hybridize with the
DNA from the genomes of a variety of other species.
• Human disease genes are identified by mapping and
sequencing DNA of patients to find differences from
normal DNA that are genetically linked to the disease.
5.6 Eukaryotic Protein-Coding Genes Can
Be Identified by the Conservation of Exons
• exon trapping –
Inserting a genomic
fragment into a
vector whose
function depends on
the provision of
splicing junctions by
the fragment.
Figure 05.06: A special splicing vector is
used for exon trapping.
5.7 The Conservation of Genome
Organization Helps to Identify Genes
• Methods for identifying functional genes are not perfect
and many corrections must be made to preliminary
estimates.
• Pseudogenes must be distinguished from functional
genes.
Figure 05.07: Exons of
protein-coding genes are
identified as coding
sequences flanked by
appropriate signals.
5.7 The Conservation of Genome
Organization Helps to Identify Genes
• There are extensive syntenic relationships between the
mouse and human genomes, and most functional genes
are in a syntenic region.
• synteny – A relationship between chromosomal regions
of different species where homologous genes occur in
the same order.
Figure 05.08: Mouse chromosome 1
has 21 segments 1-25 Mb in length
syntenic with regions corresponding to
parts of six human chromosomes.
5.7 The Conservation of Genome
Organization Helps to Identify Genes
• expressed sequence tag (EST) – A short sequenced
fragment of a cDNA sequence that can be used to
identify an actively expressed gene.
5.8 Some Organelles Have DNA
• Mitochondria and chloroplasts
have genomes that show nonMendelian inheritance.
Typically they are maternally
inherited.
• Organelle genomes may
undergo somatic segregation in
plants.
Figure 05.10: DNA from the sperm enters the oocyte to
form the male pronucleus in the egg, but all the
mitochondria are provided by the oocyte.
5.8 Some Organelles Have DNA
• extranuclear genes – Genes that reside outside the
nucleus, in organelles such as mitochondria and
chloroplasts.
• Comparisons of human mitochondrial DNA suggest that
it is descended from a single population that existed
~200,000 years ago in Africa.
5.9 Organelle Genomes Are Circular DNAs
That Encode Organelle Proteins
• Organelle genomes are usually (but not always)
circular molecules of DNA.
– Mitochondrial DNA (mtDNA)
– Chloroplast DNA (cpDNA or ctDNA)
• Organelle genomes encode some, but not all, of
the proteins used in the organelle.
Figure 05.11: Mitochondrial
genomes have genes encoding
(mostly complex I–IV) proteins,
rRNAs, and tRNAs.
5.9 Organelle Genomes Are Circular DNAs
That Encode Organelle Proteins
• Animal cell mtDNA is extremely compact and typically
encodes 13 proteins, 2 rRNAs, and 22 tRNAs.
• D loop – A region of the animal mitochondrial DNA
molecule that is variable in size and sequence and
contains the origin of replication.
• Yeast mtDNA is 5× longer than animal cell mtDNA
because of the presence of long introns.
5.9 Organelle Genomes Are Circular DNAs
That Encode Organelle Proteins
Figure 05.12: Human mitochondrial DNA
has 22 tRNA genes, two rRNA genes, and 13
protein-coding regions.
5.10 The Chloroplast Genome Encodes
Many Proteins and RNAs
• Chloroplast genomes vary in size, but are large enough
to encode 50 to 100 proteins as well as rRNAs and
tRNAs.
Figure 05.14: The chloroplast
genome in land plants encodes 4
rRNAs, 30 tRNAs, and ~60 proteins.
5.11 Mitochondria and Chloroplasts Evolved
by Endosymbiosis
• Both mitochondria and
chloroplasts are descended from
bacterial ancestors.
• Most of the genes of the
mitochondrial and chloroplast
genomes have been transferred
to the nucleus during the
organelle’s evolution.
Figure 05.15: Mitochondria originated by a endosymbiotic
event when a bacterium was captured by a eukaryotic cell.