Genes and Chromosomes

Genes Code for Proteins

One gene: One enzime
One gene : One
polypeptide
or RNA

 Dominance
is explained
by the
properties
of mutant
proteins

Mutations in the
same gene cannot
complement

Mutations: Loos of
function or gain of
function

Recombin
ation
ocurrs by
physical
exchange
of DNA

 The code genetic is triplet

Every sequence hasthree possible
reading frames

Several
processes are
required to
express the
protein product
of a gene

 Proteins are trans acting

Sites on DNA are cis acting

THE INTERRUPTED GENE

 Some genes possess only one o few

introns

Some DNA sequences code for more than

one polypeptide

Some exons can be equated with protein

functional domains

The Content of the Genome:

The genome
The transcriptome
The proteome
The interactome

Figure 05.01: A point mutation that affects a restriction site is detected

by a difference in restriction fragment lengths.

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.

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.

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.

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.

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.

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.

Courtesy of Eishi Noguchi,

Drexel University College of
Medicine.
Courtesy of Carolyn B.
Courtesy of Rocky
Marks and David H. Hall, Mountain Laboratories,
Albert Einstein College of NIAID, NIH
Medicine, Bronx, NY.

Courtesy of Keith
Weller/USDA.

Photo of intracellular
bacterium courtesy of
Gregory P. Henderson
and Grant J. Jensen,
California Institute of
Technology.

Genome sequences and gene

numbers

Photodisc.

Figure 06.01: The minimum gene number required for any type of
organism increases with its complexity.

Prokaryotic Gene Numbers Range Over an

Order of Magnitude
The minimum number of
genes for a parasitic
prokaryote is about 500;
for a free-living
nonparasitic prokaryote it
is about 1500.

Figure 06.02: Genome sizes and gene

numbers are known from complete
sequences for several organisms.

Figure 06.03: The number of genes in bacterial and archaeal genomes is

proportional to genome size.

Total Gene Number Is Known for Several

Eukaryotes
There are 6000 genes in yeast; 21,700 in a nematode
worm; 17,000 in a fly; 25,000 in the small plant
Arabidopsis; and probably 20,000 to 25,000 in mice and
humans.

Figure 06.04: The number

of genes in a eukaryote
varies from 6000-40,000
but does not correlate with
genome size or the
organism complexity.

Figure 06.05: The S. cerevisiae genome of 13.5 Mb has 6000 genes, almost
all uninterrupted.

Total Gene Number Is Known for Several

Eukaryotes

Figure 06.06: Functions of Drosophila genes based on comparative

genomics of twelve species.

Adapted from Drosophila 12 Genomes

Consortium, Evolution of genes and genomes
on the Drosophila phylogeny, Nature 450
(2007): 203218.

How Many Different Types of Genes Are

There?
The sum of the number of unique genes and the number
of gene families is an estimate of the number of types of
genes.
Figure 06.07: Many
genes are
duplicated, and as
a result the
number of different
gene families is
much less than the
total number of
genes.

How Many Different Types of Genes Are

There?
orthologous genes
(orthologs) Related
genes in different
species.
The minimum size of
the proteome can be
estimated from the
number of types of
genes.
Figure 06.09: Fruit fly genome can be
divided into genes present in all
eukaryotes, genes present in all
multicell eukaryotes, genes specific to
flies.

The Human Genome Has Fewer Genes

Than Originally Expected
Only 1% of the human genome consists of exons.
The exons comprise ~5% of each gene, so genes (exons
plus introns) comprise ~25% of the genome.
The human genome has 20,000 to 25,000 genes.

Figure 06.11: Genes occupy 25% of the

human genome, but protein-coding
sequences are only a small part of this
fraction.

The Human Genome Has Fewer Genes

Than Originally Expected

Figure 06.12: The average human gene is 27 kb long and has nine exons,
usually comprising two longer exons at each end and seven internal
exons.

The Human Genome Has Fewer Genes

Than Originally Expected
~60% of human genes are alternatively spliced.
Up to 80% of the alternative splices change protein
sequence, so the proteome has ~50,000 to 60,000
members.

How Are Genes and Other Sequences

Distributed in the Genome?
Repeated sequences (present in more than one copy)
account for >50% of the human genome.
The great bulk of repeated sequences consists of copies
of nonfunctional transposons.
There are many duplications
of large chromosome regions.

Figure 06.14: The largest component of

the human genome consists of
transposons.

The Y Chromosome Has Several

Male-Specific Genes
The Y chromosome has ~60 genes that are expressed
specifically in the testis.
The male-specific genes are present in multiple copies in
repeated chromosomal segments.
Gene conversion between multiple copies allows the
active genes to be maintained during evolution.
Figure 06.15: The Y
chromosome consists of Xtransposed regions, Xdegenerate regions, and
amplicons.

How Many Genes Are Essential?

Not all genes are
essential. In yeast and
flies, deletions of <50% of
the genes have
detectable effects.
When two or more genes
are redundant, a
mutation in any one of
them may not have
detectable effects.

Figure 06.16: Essential

yeast genes are found in
all classes.

How Many Genes Are Essential?

We do not fully understand the persistence of genes that
are apparently dispensable in the genome.

Figure 06.17: A
systematic analysis of
loss of function for
86% of worm genes
shows that only 10%
have detectable
effects on the
phenotype.

About 10,000 Genes Are Expressed at

Widely Differing Levels in a Eukaryotic Cell
mRNAs expressed at low levels overlap extensively
when different cell types are compared.
housekeeping gene A gene that is (theoretically)
expressed in all cells because it provides basic functions
needed for sustenance of all cell types.

The abundantly expressed mRNAs are usually

specific for the cell type.
luxury gene A gene encoding a specialized function,
(usually) synthesized in large amounts in particular cell
types.

~10,000 expressed genes may be common to most

cell types of a multicellular eukaryote.

6.10 Expressed Gene Number Can Be

Measured En Masse
DNA microarray technology allows detailed comparisons
of related animal cells to determine (for example) the
differences in expression between a normal cell and a
cancer cell.

Figure 06.22: Heat map of 59

invasive breast tumors from
women who breastfed 6
months (red lines) or who
never breastfed (blue lines).

Image courtesy of Rachel E. Ellsworth, Clinical

Breast Care Project, Windber Research Institute.

 Clusters and Repeats

gene family
pseudogenes
gene cluster

7.1 Introduction
satellite DNA DNA that consists of many
tandem repeats (identical or related) of a short
basic repeating unit.
minisatellite DNAs consisting of tandemly
repeated copies of a short repeating sequence, with
more repeat copies than a microsatellite but fewer
than a satellite.
The length of the repeating unit is measured in tens of base
pairs.
The number of repeats varies between individual genomes.

Unequal Crossing Over Rearranges Gene

Clusters
When a genome contains a cluster of genes with
related sequences, mispairing between
nonallelic loci can cause unequal crossing over.
This produces a deletion in one recombinant
chromosome and a corresponding duplication in the
other.

Unequal Crossing Over Rearranges Gene

Clusters

Figure 07.04: Gene number can be changed by unequal crossing over.

Unequal Crossing Over Rearranges Gene

Clusters
Different thalassemias are
caused by various deletions
that eliminate - or -globin
genes.
The severity of the disease
depends on the individual
deletion.
Figure 07.05: -thalassemias
result from various deletions
in the -globin gene cluster.

Mammalian Satellites Consist of

Hierarchical Repeats

Figure 07.17: The alignment of eighth-repeats shows that each quarterrepeat consists of an and a half.

Minisatellites Are Useful for Genetic

Mapping
The variation between microsatellites or minisatellites
in individual genomes can be used to identify heredity
unequivocally by showing that 50% of the bands in an
individual are inherited from a particular parent.
variable number tandem repeat (VNTR) Very short
repeated sequences, including microsatellites and
minisatellites.

Minisatellites Are Useful for Genetic

Mapping

Figure 07.20: Alleles may differ

by number of repeats at a
minisatellite locus, so digestion
generates restriction fragments
that differ in length.

Chromosomes

 Centromere

 Telomeres

 Nucleosome

Dos copias

Tetramero H3H4

Dimero H2AH2B