The document summarizes key aspects of eukaryotic genome complexity. It notes that while eukaryotic genomes are generally larger than prokaryotic genomes, genome size does not correlate directly with genetic complexity. Much of the increased size of eukaryotic genomes is due to noncoding sequences, including introns within genes and repetitive sequences between genes. Introns account for much more DNA than exons in higher eukaryotes. Other factors contributing to large eukaryotic genomes include repeated genes and families, as well as mobile repetitive elements like transposons. The DNA is tightly packaged into chromatin and condensed into linear chromosomes for mitosis.

1. The Complexity of Eukaryotic
Genomes
-genomes of most eukaryotes are larger
and more complex than those of prokaryotes
- However, the genome size of many
eukaryotes does not appear to be
related to genetic complexity.
- Much of the complexity of eukaryotic
genomes thus results from the abundance of
several different types of noncoding
sequences, which constitute most of the DNA
of higher eukaryotic cells.
Figure 4.1. Genome size The range of sizes of
the genomes of representative groups of
organisms are shown on a logarithmic scale.

2. Introns and Exons
-some of the noncoding DNA in eukaryotes is accounted for by long DNA sequences
that lie between genes (spacer sequences)
-large amounts of noncoding DNA are also found within most eukaryotic genes. Such
genes have a split structure in which segments of coding sequence (called exons)
are separated by noncoding sequences (intervening sequences, or introns)
Figure 4.2. The structure of eukaryotic genes
The introns are then removed by splicing to form the mature mRNA.

3. -On average, introns are estimated to account for about ten times more DNA than exons in
the genes of higher eukaryotes. (eg.human gene that encodes the blood clotting protein
factor VIII. This gene spans approximately 186 kb of DNA and is divided into 26 exons. The
mRNA is only about 9 kb long, so the gene contains introns totaling more than 175 kb).
-introns are clearly not required for gene function in eukaryotic cells.
-most introns have no known cellular function, although a few have been found to encode
functional RNAs or proteins.
-generally thought to represent remnants of sequences that were important earlier in
evolution.
-introns may have helped accelerate evolution by facilitating recombination between
protein-coding regions (exons) of different genes—a process known as exon shuffling.
(recombination between introns of different genes would result in new
genes containing novel combinations of protein-coding sequences)

4. Table 9-1. Classification of Eukaryotic DNA
Protein-coding genes
Solitary genes
Duplicated and diverged genes (functional gene
families and nonfunctional pseudogenes)
Tandemly repeated genes encoding rRNA, 5S rRNA,
tRNA, and histones
Repetitious DNA
Simple-sequence DNA
Moderately repeated DNA (mobile DNA elements)
Transposons
Viral retrotransposons
Long interspersed elements (LINES; nonviral
retrotransposons)
Short interspersed elements (SINES; nonviral
retrotransposons)
Unclassified spacer DNA

5. Gene Families and Pseudogenes
-another factor contributing to the large size of eukaryotic genomes is
that some genes are repeated many times.
-many eukaryotic genes are present in multiple copies, called gene
families while most prokaryotic genes are represented only once in the genome
Figure 4.5. Globin gene families
Members of the human α- and β-
globin gene families are clustered on
chromosomes 16 and 11, respectively.
Each family contains genes that are
specifically expressed in embryonic,
fetal, and adult tissues, in addition to
nonfunctional gene copies
(pseudogenes).

6. Repetitive DNA Sequences
-3 classes based on the number of times nucleotide sequence is
repeated within the population of DNA fragments
a. Highly Repeated DNA Sequences
- sequences present in at least 105 copies per genome (1-10% of total
DNA)
- typically short and present in clusters in which the given sequence
repeats itself over and over again w/out interruption
- the sequence is said to be present in tandem (sequence arranged in
end-to-end manner)
1. Satellite DNAs
- short sequences about 5 to a few hundred base pairs in
length(form very large clusters each containing up to several million
base pairs of DNA)
- base composition of the said DNA segments is different
from the bulk of the DNA that fragments contg. the sequence that
can be separated into a distinct ”satellite” band during density
gradient centrifugation
- localization of satellite DNA within centromeres of
chromosomes

7. -precise function of satellite DNA remains a mystery
2. Minisatellite DNAs
-sequences range from about 12 to 100 base pairs in length and are
found in clusters contg as many as 3000 repeats.
-occupy considerably shorter stretches of the genome than the
satellite sequences
-tend to be unstable, and the number of copies of a particular
sequence often increase or decrease from one generation to the next (the
length of a particular minisatellite locus is highly variable in the population
even among the same members of the same family
-used to identify individuals in criminal or
paternity cases thru the technique of DNA
fingerprinting
Use of PCR in forensic science.
Hypervariable microsatellite sequences (such as
variable number of tandem
repeats, or VNTR) are identified by PCR.

8. 3. Microsatellite DNAs
-shortest sequences (1 to 5 base pairs long) and are typically
present in small clusters of about 10 to 40 base pairs in length
-scattered quite evenly thru the DNA – more than 100,000
different loci are present in the human genome
b. Moderately Repeated DNA Sequence
- moderately repeated fraction of the genomes of plants and animals
- vary from about 20 to more than 80% of the total DNA, depending on
the organism
- sequences that are repeated within the genome anywhere from a few
times to tens of thousands of times.
- sequences that code for known gene products, either RNAs or proteins,
and those that lack a coding function
1. Repeated DNA Sequences with Coding Functions
-includes genes that code for ribosomal RNA as well as those
that code for histones (impt. chromosomal proteins)
-the repeated sequences that code for each of these products
are typically identical to one another and located in tandem array

9. 2. Repeated DNAs that Lack Coding Functions
-the bulk of the moderately repeated DNA fraction does not
encode any type of product
-repetitive DNA sequences are scattered throughout the
genome rather than being clustered as tandem repeats (i.e. interspersed
thruout the genome as individual elements).
-can be grouped into two classes:
a. SINEs (short intesrpersed elements)
-major SINEs in mammalian genomes are
Alusequences, so-called because they usually contain a single
site for the restriction endonuclease AluI.
-Alu sequences are approximately 300 base pairs long,
and about a million such sequences are dispersed throughout
the genome, accounting for nearly 10% of the total cellular
DNA.
-Although Alu sequences are transcribed into RNA,
they do not encode proteins and their function is unknown.
b. LINEs (long interspersed elements)
-major human LINEs (which belong to the LINE 1, or L1,
family) are about 6000 base pairs long and repeat
approximately 50,000 times in the genome.

10. -L1 sequences are transcribed and at least some encode
proteins, but like Alu sequences, they have no known function in cell
physiology.
-both Alu and L1 sequences are examples of transposable
elements, which are capable of moving to different sites in genomic
DNA.
- some of these sequences may help regulate gene
expression, but most Alu and L1 sequences appear not to make a
useful contribution to the cell.
-they may have played important evolutionary roles by
contributing to the generation of genetic diversity.
3. Nonrepeated DNA Sequences
- are present in a single copy in the genome which includes genes that exhibit
Mendelian patterns of inheritance
-always localize to a particular site on a particular chromosome
-contains by far the greatest amount of genetic information
-include DNA sequences that code for virtually all proteins other thanhistones
-even if these sequenes are not present in multiple copies, genes that code for
polypeptides are usually members of a family of related genes(this is true for globins,
actins, myosins, collagens, tubulins, integrins and most other proteins in a eukaryotic
cell.

11. The Number of Genes in Eukaryotic Cells
Organism Genome size (Mb)a Protein-coding
sequence (percent)b
Number of genesb
E. coli 4.6 90 4,288
S. cerevisiae 12 70 5,885
C. elegans 97 25 19,099
Drosophila 180 13 13,600
Human 3,000 3 *100,000
a Mb = millions of base pairs.
b Determined from the E. coli, S. cerevisiae, C. elegans, and Drosophila genomic sequences
and estimated for the human genome.
Table 4.1. The Numbers of Genes in Cellular Genomes

12. *Nature 431, 931-945 (21 October 2004) | doi:10.1038/nature03001Finishing the
euchromatic sequence of the human genome
Latest information:
-2.85 billion nucleotides interrupted by only 341 gaps.
-encode only 20,000–25,000 protein-coding genes.

13. Chromosomes and Chromatin
Organism Genome size (Mb)a Chromosome numbera
Yeast (Saccharomyces cerevisiae) 12 16
Slime mold (Dictyostelium) 70 7
Arabidopsis thaliana 130 5
Corn 5,000 10
Onion 15,000 8
Lily 50,000 12
Nematode (Caenorhabditis elegans) 97 6
Fruit fly (Drosophila) 180 4
Toad (Xenopus laevis) 3,000 18
Lungfish 50,000 17
Chicken 1,200 39
Mouse 3,000 20
Cow 3,000 30
Dog 3,000 39
Human 3,000 23
a Both genome size and chromosome number are for haploid cells. Mb = millions of base pairs.
Table 4.2. Chromosome Numbers of Eukaryotic Cells

14. -genomes of prokaryotes are contained in single chromosomes, which are
usually circular DNA molecules.
-the genomes of eukaryotes are composed of multiple chromosomes, each
containing a linear molecule of DNA.
-DNA of eukaryotic cells is tightly bound to small basic proteins (histones) that
package the DNA in an orderly way in the cell nucleus(total extended length of
DNA in a human cell is nearly 2 m, but this DNA must fit into a nucleus with a
diameter of only 5 to 10 μm).
Chromatin
-complexes between eukaryotic DNA and proteins
-major proteins of chromatin are the histones
small proteins containing a high
proportion of basic amino acids (arginine and lysine) that facilitate
binding to the negatively charged DNA molecule.
- five major types of histones—called
H1, H2A, H2B, H3, and H4—which are very similar among different species of
eukaryotes

15. Histonea Molecular weight Number of amino
acids
Percentage Lysine +
Arginine
H1 22,500 244 30.8
H2A 13,960 129 20.2
H2B 13,774 125 22.4
H3 15,273 135 22.9
H4 11,236 102 24.5
a Data are for rabbit (H1) and bovine histones.
Table 4.3. The Major Histone Proteins
-histones are extremely abundant proteins in eukaryotic cells; together, their
mass is approximately equal to that of the cell's DNA.

16. -not found in eubacteria (e.g., E. coli), but Archaebacteria, do contain histones that
package their DNAs in structures similar to eukaryotic chromatin.
-the basic structural unit of chromatin, the nucleosome, consisting of DNA (≈146-bp
segment of DNA )wrapped around a histone core.
Figure 4.8. The organization of chromatin in nucleosomes
(A) The DNA is wrapped around histones in nucleosome core
particles and sealed by histone H1. Nonhistone proteins
bind to the linker DNA between nucleosome core particles.
The linker DNA between the nucleosome core particles is
preferentially sensitive, so limited digestion of chromatin
yields fragments corresponding to multiples of 200 base
pairs.
Chromosomal DNA and Its Packaging in
the Chromatin Fiber

17. Figure 4.10. Chromatin fibers The packaging of
DNA into nucleosomes yields a chromatin fiber
approximately 10 nm in diameter. The chromatin is
further condensed by coiling into a 30-nm fiber,
containing about six nucleosomes per turn.
Solenoid structure
Figure 4.9. Structure of a
chromatosome (A) The nucleosome
core particle consists of 146 base
pairs of DNA wrapped 1.65 turns
around a histone octamer consisting
of two molecules each of H2A, H2B,
H3, and H4. A chromatosome
contains two full turns of DNA (166
base pairs) locked in place by one
molecule of H1.

18. Figure 4.11. Model for the packing of chromatin and the
chromosome scaffold in metaphase chromosomes. In
interphase chromosomes, long stretches of 30-nm chromatin
loop out from extended scaffolds. In metaphase
chromosomes, the scaffold is folded into a helix and further
packed into a highly compacted structure, whose precise
geometry has not been determined.

19. The chromatin in chromosomal regions that are not being transcribed exists
predominantly in the condensed, 30-nm fiber form. The regions of chromatin actively
being transcribed are thought to assume the extended beads-on-a-string form
Euchromatin -Decondensed, transcriptionally active interphase chromatin.
Most of the euchromatin in interphase nuclei appears to be in the form of 30-nm fibers,
organized into large loops containing approximately 50 to 100 kb of DNA. About 10% of
the euchromatin, containing the genes that are actively transcribed, is in a more
decondensed state (the 10-nm conformation) that allows transcription
Heterochromatin-Condensed, transcriptionally inactive chromatin. Heterochromatin
is transcriptionally inactive and contains highly repeated DNA sequences, such as
those present at centromeres and telomeres.
As cells enter mitosis, their chromosomes become highly condensed so that they can
be distributed to daughter cells. The loops of 30-nm chromatin fibers are thought to
fold upon themselves further to form the compact metaphase chromosomes of mitotic
cells, in which the DNA has been condensed nearly 10,000-fold (Figure 4.11). Such
condensed chromatin can no longer be used as a template for RNA synthesis, so
transcription ceases during mitosis. Electron micrographs indicate that the DNA in
metaphase chromosomes is organized into large loops attached to a protein scaffold
Metaphase chromosomes are so highly condensed that their morphology can be
studied using the light microscope

20. However, euchromatin is interrupted by stretches of heterochromatin, in which 30-nm fibers
are subjected to additional levels of packing that usually render it resistant to gene
expression. Heterochromatin is commonly found around centromeres and near telomeres,
but it is also present at other positions on chromosomes.
Figure 4-21. A comparison of
extended interphase chromatin with
the chromatin in a mitotic
chromosome. (A) An electron
micrograph showing an enormous
tangle of chromatin spilling out of a
lysed interphase nucleus. (B) A
scanning electron micrograph of a
mitotic chromosome: a condensed
duplicated chromosome in which the
two new chromosomes are still
linked together . The constricted
region indicates the position of the
centromere. Note the difference in
scales.

21. Each DNA Molecule That Forms a Linear Chromosome Must Contain a Centromere,
Two Telomeres, and Replication Origins Figure 4-22. The three DNA
sequences required to produce a
eucaryotic chromosome that can be
replicated and then segregated at
mitosis. Each chromosome has
multiple origins of replication, one
centromere, and two telomeres.
Shown here is the sequence of events
a typical chromosome follows during
the cell cycle. The DNA replicates in
interphase beginning at the origins of
replication and proceeding
bidirectionally from the origins across
the chromosome. In M phase, the
centromere attaches the duplicated
chromosomes to the mitotic spindle
so that one copy is distributed to each
daughter cell during mitosis. The
centromere also helps to hold the
duplicated chromosomes together
until they are ready to be moved
apart. The telomeres form special
caps at each chromosome end.

22. Figure 4.17. Assay of a centromere
in yeast Both plasmids shown
contain a selectable marker (LEU2)
and DNA sequences that serve as
origins of replication in yeast (ARS,
which stands for autonomously
replicating sequence). However,
plasmid I lacks a centromere and is
therefore frequently lost as a result
of missegregation during mitosis. In
contrast, the presence of a
centromere (CEN) in plasmid II
ensures its regular transmission to
daughter cells.

23. replication origin- Location on a DNA molecule at which duplication of the DNA begins.
Centromere- Constricted region of a mitotic chromosome that holds sister chromatids
together. It is also the site on the DNA where the kinetochore forms that captures
microtubules from the mitotic spindle.
Telomere-End of a chromosome, associated with a characteristic DNA sequence that is
replicated in a special way. Counteracts the tendency of the chromosome otherwise to
shorten with each round of replication. (From Greek telos, end.)
-perform another function: the repeated telomere DNA sequences, together
with the regions adjoining them, form structures that protect the end of the chromosome
from being recognized by the cell as a broken DNA molecule in need of repair.
Figure 4.19. Structure of a telomere
Telomere DNA loops back on itself to
form a circular structure that protects
the ends of chromosomes

24. Figure 4-11. The banding patterns of
human chromosomes. Chromosomes 1–22
are numbered in approximate order of size.
A typical human somatic (non-germ line)
cell contains two of each of these
chromosomes, plus two sex
chromosomes—two X chromosomes in a
female, one X and one Y chromosome in a
male. The chromosomes used to make
these maps were stained at an early stage
in mitosis, when the chromosomes are
incompletely compacted. The horizontal
green line represents the position of the
centromere, which appears as a
constriction on mitotic chromosomes; the
knobs on chromosomes 13, 14, 15, 21, and
22 indicate the positions of genes that code
for the large ribosomal RNAs (discussed in
Chapter 6). These patterns are obtained by
staining chromosomes with Giemsa stain,
and they can be observed under the light
microscope.

25. Karyotype- Full set of chromosomes of a cell arranged with respect to size, shape, and number.
Figure 1-30. The genome of E. coli. (A) A
cluster of E. coli cells. (B) A diagram of the E.
coli genome of 4,639,221 nucleotide pairs (for
E. coli strain K-12). The diagram is circular
because the DNA of E. coli, like that of other
procaryotes, forms a single, closed loop.
Protein-coding genes are shown as yellow or
orange bars, depending on the DNA strand
from which they are transcribed; genes
encoding only RNA molecules are indicated by
green arrows. Some genes are transcribed
from one strand of the DNA double helix (in a
clockwise direction in this diagram), others
from the other strand (counterclockwise).
The Sequences of Complete Genomes

26. Figure 4-13. The genome of S.
cerevisiae (budding yeast). (A) The
genome is distributed over 16
chromosomes, and its complete
nucleotide sequence was determined
by a cooperative effort involving
scientists working in many different
locations, as indicated (gray, Canada;
orange, European Union; yellow,
United Kingdom; blue, Japan; light
green, St Louis, Missouri; dark green,
Stanford, California). The constriction
present on each chromosome
represents the position of its
centromere . (B) A small region of
chromosome 11, highlighted in red in
part A, is magnified to show the high
density of genes characteristic of this
species. As indicated by orange, some
genes are transcribed from the lower
strand ,while others are transcribed
from the upper strand. There are
about 6000 genes in the complete
genome, which is 12,147,813
nucleotide pairs long.

27. Figure 4-16. Scale of the human genome. If
each nucleotide pair is drawn as 1 mm as in
(A), then the human genome would extend
3200 km (approximately 2000 miles), far
enough to stretch across the center of Africa,
the site of our human origins (red line in B). At
this scale, there would be, on average, a
protein-coding gene every 300 m. An average
gene would extend for 30 m, but the coding
sequences in this gene would add up to only
just over a meter.
The Human Genome

28. Figure 4-15. The organization of genes on a human
chromosome. (A) Chromosome 22, one of the smallest
human chromosomes, contains 48 × 106 nucleotide pairs
and makes up approximately 1.5% of the entire human
genome. Most of the left arm of chromosome 22 consists
of short repeated sequences of DNA that are packaged in
a particularly compact form of chromatin
(heterochromatin), which is discussed later in this chapter.
(B) A tenfold expansion of a portion of chromosome 22,
with about 40 genes indicated. Those in dark brown are
known genes and those in light brown are predicted
genes. (C) An expanded portion of (B) shows the entire
length of several genes. (D) The intron-exon arrangement
of a typical gene is shown after a further tenfold
expansion. Each exon (red) codes for a portion of the
protein, while the DNA sequence of the introns (gray) is
relatively unimportant. The entire human genome (3.2 ×
109 nucleotide pairs) is distributed over 22 autosomes and
2 sex chromosomes (see Figures 4-10 and 4-11). The term
human genome sequence refers to the complete
nucleotide sequence of DNA in these 24 chromosomes.
Being diploid, a human somatic cell therefore contains
roughly twice this amount of DNA. Humans differ from
one another by an average of one nucleotide in every
thousand, and a wide variety of humans contributed DNA
for the genome sequencing project. The published human
genome sequence is therefore a composite of many
individual sequences.

29. Table 4-1. Vital Statistics of Human Chromosome 22 and the Entire Human Genome
CHROMOSOME 22 HUMAN GENOME
DNA length 48 × 106 nucleotide pairs* 3.2 × 109
Number of genes approximately 700 approximately 30,000
Smallest protein-coding gene 1000 nucleotide pairs not analyzed
Largest gene 583,000 nucleotide pairs 2.4 × 106 nucleotide pairs
Mean gene size 19,000 nucleotide pairs 27,000 nucleotide pairs
Smallest number of exons per gene 1 1
Largest number of exons per gene 54 178
Mean number of exons per gene 5.4 8.8
Smallest exon size 8 nucleotide pairs not analyzed
Largest exon size 7600 nucleotide pairs 17,106 nucleotide pairs
Mean exon size 266 nucleotide pairs 145 nucleotide pairs
Number of pseudogenes** more than 134 not analyzed
Percentage of DNA sequence in exons
(protein coding sequences)
3% 1.5%
Percentage of DNA in high-copy
repetitive elements
42% approximately 50%
Percentage of total human genome 1.5% 100%
* The nucleotide sequence of 33.8 × 106 nucleotides is known; the rest of the chromosome consists primarily of very short
repeated sequences that do not code for proteins or RNA.
** A pseudogene is a nucleotide sequence of DNA closely resembling that of a functional gene, but containing numerous
deletion mutations that prevent its proper expression. Most pseudogenes arise from the duplication of a functional gene
followed by the accumulation of damaging mutations in one copy.

30. Figure 4-17. Representation of the nucleotide sequence content of the human genome.
LINES, SINES, retroviral-like elements, and DNA-only transposons are all mobile genetic
elements that have multiplied in our genome by replicating themselves and inserting the
new copies in different positions. Mobile genetic elements are discussed in Chapter 5. Simple
sequence repeats are short nucleotide sequences (less than 14 nucleotide pairs) that are
repeated again and again for long stretches. Segmental duplications are large blocks of the
genome (1000–200,000 nucleotide pairs) that are present at two or more locations in the
genome. Over half of the unique sequence consists of genes and the remainder is probably
regulatory DNA. Most of the DNA present in heterochromatin, a specialized type of
chromatin (discussed later in this chapter) that contains relatively few genes, has not yet
been sequenced.