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The Complexity of EukaryoticGenomes

-genomes of most eukaryotes are larger

and more complex than those of prokaryotes

- However, the genome size of manyeukaryotes 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.

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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 genesThe introns are then removed by splicing to form the mature mRNA.

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-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 inevolution.

-introns may have helped accelerate evolution by facilitating recombination between

protein-coding regions (exons) of different genesa process known as exon shuffling.

(recombination between introns of different genes would result in new

genes containing novel combinations of protein-coding sequences)

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Table 9-1. Classification of Eukaryotic DNA

Protein-coding genes

Solitary genesDuplicated and diverged genes (functional gene

families and nonfunctional pseudogenes)

Tandemly repeated genes encoding rRNA, 5S rRNA,

tRNA, and histones

Repetitious DNASimple-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

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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 genefamilies while most prokaryotic genes are represented only once in the genome

Figure 4.5. Globin gene families

Members of the human - and -

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 tononfunctional gene copies

(pseudogenes).

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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 inend-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

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-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 orpaternity 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.

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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 100,000different 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 onthe 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

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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 thegenome 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 endonucleaseAluI.

-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.-AlthoughAlu 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 repeatapproximately 50,000 times in the genome.

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-L1 sequences are transcribed and at least some encode

proteins, but likeAlu sequences, they have no known function in cell

physiology.

-bothAlu and L1 sequences are examples oftransposable

elements, which are capable of moving to different sites in genomicDNA.

- some of these sequences may help regulate gene

expression, but mostAlu and L1 sequences appear not to make a

useful contribution to the cell.

-they may have played important evolutionary roles bycontributing 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 eukaryoticcell.

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The Number of Genes in Eukaryotic Cells

Organism Genome size (Mb)a Protein-coding

sequence (percent)b

Number ofgenesb

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 theE. coli, S. cerevisiae, C. elegans, andDrosophila genomic sequences

and estimated for the human genome.

Table 4.1. The Numbers of Genes in Cellular Genomes

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*Nature431, 931-945 (21 October 2004) | doi:10.1038/nature03001Finishing theeuchromatic sequence of the human genome

Latest information:

-2.85 billion nucleotides interrupted by only 341 gaps.

-encode only 20,00025,000 protein-coding genes.

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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

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-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 m).

Chromatin

-complexes between eukaryotic DNA and proteins

-major proteins of chromatin are the histones

small proteins containing a highproportion of basic amino acids (arginine and lysine) that facilitate

binding to the negatively charged DNA molecule.

- five major types of histonescalled

H1, H2A, H2B, H3, and H4which are very similar among different species of

eukaryotes

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Histonea Molecular weight Number ofamino

acids

Percentage Lysine +

Arginine

H1 22,500 244 30.8H2A 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.

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-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 basepairs.

Chromosomal DNA and Its Packaging in

the Chromatin Fiber

S l id

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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 onemolecule of H1.

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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.

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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. Heterochromatinis 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 bestudied using the light microscope

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However, euchromatin is interrupted by stretches ofheterochromatin, 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 enormoustangle 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 stilllinked together . The constricted

region indicates the position of the

centromere. Note the difference in

scales.

E h DNA M l l Th t F Li Ch M t C t i C t

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Each DNA Molecule That Forms a Linear Chromosome Must Contain a Centromere,

Two Telomeres, and Replication Origins Figure 4-22. The three DNAsequences required to produce a

eucaryotic chromosome that can be

replicated and then segregated at

mitosis. Each chromosome hasmultiple 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.

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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 todaughter cells.

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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 isreplicated 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

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Figure 4-11. The banding patterns of

human chromosomes. Chromosomes 122

are numbered in approximate order of size.

A typical human somatic (non-germ line)

cell contains two of each of thesechromosomes, plus two sex

chromosomestwo 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 areincompletely 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.

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Karyotype-Full set of chromosomes of a cell arranged with respect to size, shape, and number.

Figure 1-30. The genome ofE. coli.(A) A

cluster ofE. colicells. (B) A diagram of the E.

coligenome of 4,639,221 nucleotide pairs (for

E. colistrain K-12). The diagram is circular

because the DNA ofE. coli, like that of otherprocaryotes, forms a single, closed loop.

Protein-coding genes are shown as yellowor

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 transcribedfrom 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

Figure 4-13 The genome of S

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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 involvingscientists 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 constrictionpresent on each chromosome

represents the position of its

centromere . (B) A small region of

chromosome 11, highlighted in redin

part A, is magnified to show the high

density of genes characteristic of thisspecies. 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 12,147,813nucleotide airs lon .

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Figure 4-16. Scale of the human genome. Ifeach 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, aprotein-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

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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 ina 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 tenfoldexpansion. 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.

Table 4-1. Vital Statistics of Human Chromosome 22 and the Entire Human Genome

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CHROMOSOME 22 HUMAN GENOME

DNA length 48 106 nucleotide pairs* 3.2 109

Number of genes approximately 700 approximately 30,000Smallest 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 numerousdeletion mutations that prevent its proper expression. Most pseudogenes arise from the duplication of a functional gene

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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 (1000200,000 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 yetb d

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