CHAPTER 11- CHROMOSOME

STRUCTURE AND TRANSPOSABLE

ELEMENTS
Ultimate Storage Problem- the packaging of
tremendous amounts of genetic information into
the small space within a cell.
Transposable element- also called rider
- Are sequences that can move
about in the genome
- Played an important role in
shaping the structure of
chromosomes and genomes
Supercoiling- takes place when DNA helix is
subjected to strain by being overwound or
underwound.
- Is a partial solution to the cell’s DNA
packing problem because supercoiled
DNA occupies less space than relaxed
DNA.
o The lowest energy state for B-
DNA is when it has
approximately 10 bp per turn of
its helix
o Relaxed state- a stretch of 100
bp of DNA would assume about
10 complete turns
Positive supercoiling- Molecules that are
overrotated
Negative supercoiling- Molecules that are
underrotated
o Most DNA found in cells is
negatively supercoiled, which
has two advantages over
nonsupercoiled DNA.
Topoisomerases- enzymes that add or remove
rotations form the DNA helix by temporarily
breaking the nucleotide strands, rotating the
ends around each other, and then rejoining the
broken ends.
 - Overrotation or underrotation of a DNA
double helix places strain on the
molecule, causing it to supercoil.
Supercoiling is controlled by
topoisomerase enzymes.
- Most cellular DNA is negatively
supercoiled, which eases the separation
of nucleotide strands during replication
and transcription and allows DNA to be
packed into small spaces.
The Bacterial Chromosome
Nucleoid- when viewed with the electron
microscope, its DNA frequently appears as a
distinct clump, the nucleoid
- Confined to a definite region of the - All chromosomes have heterochromatin
cytoplasm at the centromere and telomeres.
- Heterochromatin is also present at other
Plasmids- an additional DNA in many bacteria,
specific places on some chromosomes,
in the form of small circular molecules, which
along the entire inactive X chromosome
replicates independently of the chromosome
in female mammals and throughout
Eukaryotic Chromosomes most of the Y chromosome in males.
- Individual eukaryotic chromosomes Histones- most abundant proteins in chromatin
contain enormous amounts of DNA
- High percentage of arginine and lysine
- Small, positively charged proteins
- 5 major types:
o H1
o H2A
o H2B
o H3
o H4
- All histones have a high percentage of
Chromatin- Eukaryotic DNA in the cell is arginine and lysine, positively charged
closely associated with proteins amino acids that give the histones a net
- Combination of DNA and protein positive charge.
- 2 basic types of chromatin: Nonhistone chromosomal proteins- a
o Euchromatin- undergoes the heterogenous assortment
normal process of condensation
and decondensation in the cell - Also found in eukaryotic chromosomes
cycle
o Heterochromatin- which
remains in a highly condensed
state throughout the cell cycle,
even during interphase.
The nucleosome- a core particle consisting of
DNA wrapped about two times around an
octamer of eight histone proteins(2 copies of
each of H2A, H2B, H3, H4), much like thread
wound around a spool
Chromatosome- the core particle and its
associated H1 histone
- Chromatosomes are located at regular
intervals along the DNA molecule and
are separated from one another by
Linker DNA- varies in size among cell
types
- Next level of chromatin organization
- Each chromatosome encompasses about
167 bp of DNA
Note: bp means “base pair”

Higher-order chromatin structure

- When chromatin is in a condensed form,
adjacent nucleosomes are not separated
by space equal to the length of the linker
DNA; rather, nucleosomes fold on
themselves to form a dense, tightly
packed structure
 - 2 different models propose for 30-nm - an enzyme that digests DNA
fiber:
-The ability of this enzyme to digest DNA
o Solenoid model- a linear array
depends on chromatin structure: when DNA
of nucleosomes are coiled
is tightly bound to histone proteins, it is less
o Helix model- which
sensitive to DNase I, whereas unbound
nucleosomes are arranged in a
DNA is more sensitive to digestion by
zigzag ribbon that twists or
DNase I.
supercoils
Changes in Chromatin Structure
Polytene chromosomes- unusual chromosomes
that arise when repeated rounds of DNA
replication take place without accompanying cell
division producing thousands of copies of DNA
that lie side by side
- Have provided researchers with
evidence of the changing nature of
chromatin structure.
Chromosomal puffs- localized swellings of the
chromosomes
- This occurs when polytene
chromosomes are stained with dyes,
numerous bands are revealed, in under
certain conditions.
- Each puff is a region of the chromatin
having a relaxed structure and,
consequently, a more open state. Epigenetic changes associated with
chromatin modifications
Epigenetic changes- a stable alterations of
chromatin structure that may be passed on to
cells or individual organisms
EUKARYTIC CHROMOSOMES
POSSESS CENTROMERES AND
TELOMERES
Centromere Structure
- The centromere is a constricted region
of the chromosome to which spindle
fibers attach and is essential for proper
DNase I sensitivity
chromosome movement in mitosis and
- a second piece of evidence indicating meiosis
that chromatin structure changes with
gene activity
 Shelterin- a multiprotein complex, binds to
mammalian telomeres and protects the ends
of the DNA from being inadvertently
Centromeric sequences- are the binding repaired as a double-stranded break in the
sites for the kinetochore to which spindle DNA.
fibers attach
Telomere Structure
- Telomeres are the natural ends of a
chromosome
Telomeric sequences- usually consist of
repeated units of a series of adenine or
thymine nucleotides followed by several
guanine nucleotides, taking the form 5′-(A
or T)mGn-3′, where m is from 1 to 4 and n
is 2 or more.
 heat, the two nucleotide strands separate
completely
Melting temperature (Tm)- a temperature
at which DNA denatures

Artificial Chromosomes Renaturation- or reannealing, which a

denatured single-stranded DNA is
- In 1983 geneticists constructed the first
slowly cooled, single stands will collide
artificial chromosomes from parts culled
and hydrogen bons will again form
from yeast and protozoans.
between complementary base pairs,
- In 1987, David Burke and Maynard
producing double-stranded DNA.
Olson (at Washington University, St.
Louis) used yeast to create much larger Hybridization- Two single-stranded
artificial chromosomes called yeast molecules of DNA from different
artificial chromosomes or YACs. sources, such as different organisms,
- Artificial chromosomes have also been will anneal if they are complementary.
made from chromosomal components of
bacteria (BACs) and mammals (MACs). Types of DNA sequences in Eukaryotes

Eukaryotic DNA contains several classes of - 3 types of sequences in eukaryotic

sequence variation DNA:
1. Unique-sequence DNA
- Eukaryotic organisms differ - A consists of sequences that are present
dramatically in the amount of DNA per only once or, at most, a few times in the
cell, a quantity termed an organism’s C genome.
value - Other genes within unique sequence
DNA are present in several similar, but
The Denaturation and Renaturation of
not identical, copies and together are
DNA
referred to as a gene family.
Denaturation- or melting, refers to when a 2. Moderately repetitive DNA
double stranded DNA in solution is heated , - Major class of repetitive DNA
the hydrogen bonds that hold the two strands - which typically consists of sequences
together are weakened and with enough from 150 to 300 bp in length (although
 they may be longer) that are repeated General Characteristics of Transposable
many thousands of times Elements
- 2 types of repeats:
o Tandem repeat sequences-
appear one after another and
tend to be clustered at particular
locations on the chromosomes.
o Interspersed repeat
sequences- are scattered
throughout the genome. An
example of an interspersed
repeat is the Alu sequence, a
200-bp sequence that is present
more than a million times and
comprises 11% of the human
genome, although it has no
obvious ceullar function.
- SINEs (short interspersed elements)-
a short repeat such as the Alu sequences
- LINEs (long interspersed elements) - a
longer interspersed repeats consisting of
several thousand base pairs
3. Highly repetitive DNA
- These short sequences, often less than
10 bp in length, are present in hundreds
of thousands to millions of copies that
are repeated in tandem and clustered in Short flanking direct repeats- from 3 to 12 bp
certain regions of the chromosome, long are present on both sides of most
especially at centromeres and telomeres. transposable elements.
- sometimes called satellite DNA, because
Terminal inverted repeats- sequences from 9
its percentages of the four bases differ
to 40 bp in length that are inverted complements
from those of other DNA sequences and,
of one another. For example, the following
therefore, it separates as a satellite
sequences are inverted repeats:
fraction when centrifuged at high
speeds. 5′–ACAGTTCAG . . . CTGAACTGT–3′
- Rarely transcribe into RNA
3′–TGTCAAGTC . . . GACTTGACA–5
Transposable Elements are DNA sequences
capable of Moving TRANSPOSITION

Transposable Elements- are mobile Transposition- is the movement of a

DNA sequences found in the genomes transposable element from one location to
of all organisms another.
DNA transposons- also called Class II
transposable elements
Reverse transcriptase- a special enzyme that
takes place in RNA that is transcribed from the
transposable element (DNA) and is then copied
back into DNA.
Replicative Transposition- also called copy-
and-paste transposition
- A new copy of the transposable element
is introduced at a new site while the old
copy remains behind at the original site,
and so the number of copies of the
transposable element increases as a
Transposition through an RNA intermediate
result of transposition.
Nonreplicative Transposistion- also called cut-
and-paste transposition
- the transposable element excises from
the old site and inserts at a new site
without any increase in the number of its
copies.
- requires the replication of only the few
nucleotides that constitute the direct
repeats.
Cointegrate structure- consists of molecules
A+B fused together with two copies of the
transposable element.
- Transposition may take place through DNA or Insertion sequences- The simplest type of
an RNA intermediate. transposable element in bacterial chromosomes
and plasmids
- In replicative transposition, a new copy of the
transposable element inserts in a new location - This type of element carries only the
and the old copy stays behind; in nonreplicative genetic information necessary for its
transposition, the old copy excises from the old movement.
site and moves to a new site. - are common constituents of bacteria;
they can also infect plasmids and viruses
- Transposition through an RNA intermediate
and, in this way, can be passed from one
requires reverse transcription to integrate into
cell to another.
the target site
SEE PAGE 307- CHAPTER 11
The regulation of Transposition
- Transposable elements frequently cause
mutations and DNA rearrangements.
Many cells regulate transposition by
altering DNA or chromatin structure, by
controlling the amount of transposase
produced, or by direct inhibition of the
transposition event
Different Types of transposable Elements
Composite Transposons- Any segment of
Have characteristic structures
DNA that becomes flanked by two copies of an
insertion sequence may itself transpose.
- Each composite transposon is
designated by the abbreviation Tn,
followed by a number.
Noncomposite transposons- Some transposable
elements in bacteria lack insertion sequences
- possess a gene for transposase and have
Transposable elements in Bacteria inverted repeats at their ends
- carries genes for transposase and
- The DNA transposons found in bacteria
resolvase, plus a gene that encodes the
(there are no retrotransposons in
enzyme β-lactamase, which provides
bacteria) constitute two major groups:
resistance to the antibiotic ampicillin
o simple transposable elements,
called insertion sequences, that
carry only the information
required for movement and
o more-complex transposable
elements, called composite
transposons, that contain DNA
sequences not directly related to
transposition.
 - The delta sequences are analogous to
the long terminal repeats found in
retroviruses and contain several genes
that are related to the gag and pol genes
present in retroviruses
Ac and Ds elements in maize- Transposable
elements were first identified in maize more
than 50 years ago by Barbara McClintock

Transposable elements in Drosophila

Transposable elements in Eukaryotes
- A number of different transposable
- can be divided into 2 groups: elements are found in Drosophila
o One group is structurally similar - A number of different transposable
to transposable elements found elements are found in Drosophila are
in bacteria, typically ending in about 2900 bp long, although shorter P
short inverted repeats and elements containing deletions also exist.
transposing as DNA.
Hybrid dysgenesis- which is the sudden
o The other group comprises
appearance of numerous mutations,
retrotransposons (see Figure
chromosome aberrations, and sterility in the
11.15); they use RNA
offspring of a cross between a P+ male fly (with
intermediates, and many are
P elements) and a P− female fly (without them).
similar in structure and
movement to retroviruses (see Transposable elements in humans
pp. 227–229 in Chapter 8).
- About 45% of the human genome
Ty elements in yeast- are a family of common consists of sequences derived from
retrotransposons found in yeast; many yeast transposable elements, although most of
cells have 30 copies of Ty elements these elements are now inactive and no
longer capable of transposing.
- At each end of a Ty element are direct
- One of the most common transposable
repeats called delta sequences
elements in the human genome is Alu.
- Every human cell contains more than 1
million related, but not identical, copies
of Alu in its chromosomes

- A great variety of transposable elements

exist in eukaryotes. Some resemble
transposable elements in prokaryotes,
having terminal inverted repeats, and
transpose as DNA. Others are
retrotransposons with long direct repeats
at their ends and transpose through an
RNA intermediate.
Transposable elements have played an
important role in genome evolution
- Transposable elements have clearly
played an important role in shaping the
genomes of many organisms. Much of
the tremendous variation in genome size
found among eukaryotic organisms is
due to differences in numbers of
transposable elements.
 - Approximately 45% of the human elements have clearly evolved to serve
genome consists of remnants of useful purposes for their host cells.
transposable elements and about 50% of - These transposons are sometimes
all spontaneous mutations in Drosophila referred to as domesticated, implying
are due to transposition. that their parasitic tendencies have been
replaced by properties useful to the cell.
The evolution of Transposable Elements
The evolution of new genes through
- Transposable elements exist in all
transposons
organisms, often in large numbers. Why
are they so common? Several different - Transposable elements that employ the
ideas have been proposed to explain cut-and-paste mechanism of
their widespread presence. transposition often imprecisely excise
from the DNA.
Transposable elements as genomic parasites
- Imprecise excision may result in part of
- As we have seen, many transposble the transposon sequence being left
elements leave a copy behind when they behind when the transposon moves,
transpose to a new location (copy-and- leaving a genetic footprint of the
paste transposition) and therefore transposable element at the site of
increase in number within a genome exision.
with the passage of time.
Many transposable elements appear to be
genomic parasites, existing in large numbers
because of their ability to efficiently increase in
copy number. Increases in copy number of
transposable elements have contributed to the
large size of may eukaryotic genomes. In several
cases, transposable elements and their ability to
transpose have been adopted for specific cellular
Transposable elements and genetic variation
functions.
- The process of evolution requires the
presence of genetic variation within a
population
- Because transposable elements induce
mutations and chromosome
rearrangements, some scientists have
argued that they exist because they
generate genetic variation, which
facilitates evolutionary adaptation.
- This idea suggests that a certain amount
of genetic variation is useful because it
allows a species to adapt to
environmental change.
Domestication of Transposable elements
- Regardless of the evolutionary reasons
for their existence, some transposable