DNA is made of a double helix structure that can separate into single strands. In eukaryotes, DNA is found in the nucleus as linear chromosomes and in mitochondria and chloroplasts as small circular molecules. DNA contains the genetic information of an organism and can undergo processes like replication, transcription, and translation. Chromosomes are organized structures containing DNA, and the human genome contains over 3 billion nucleotide base pairs organized into 23 chromosome pairs.

2. DNA is the stuff our genes are made of…
 The organization of total sum of genetic information
(or genome) of an organism is in the form of double-
stranded DNA, except that viruses may have single-
stranded DNA, single-stranded RNA or double-
stranded RNA genomes.
 In many viruses and prokaryotes, the genome is a
single linear or circular molecule.
 In eukaryotes, the nuclear genome consists of linear
chromosomes (usually as a diploid set) and the
mitochondrial and chloroplast (in plants) genomes
are small circular DNA molecules.
 In 1952, Watson and Crick proposed that DNA is a
double helix which is known to have alternative
forms.

4. (a) The B form of DNA
has ≈10.5 base pairs per helical turn. Adjacent stacked base pairs
are 0.36 nm apart. (b) The more compact A form of DNA has 11
base pairs per turn and exhibits a large tilt of the base pairs with
respect to the helix axis. (c) Z DNA is a left-handed double helix.

5. DNA supercoils can be removed by
cleavage of one strand. (a) EM of SV40
viral DNA. When the SV40 circular
DNA is isolated, the DNA duplex is
underwound and assumes the
supercoiled configuration. (b) If a
supercoiled DNA is nicked, the strands
can rewind, leading to loss of a
supercoil. Topoisomerase I catalyzes
this reaction and also reseals the
broken ends. All the supercoils in
isolated SV40 DNA can be removed by
the sequential action of this
enzyme, producing the relaxed-circle
conformation.

7. In general,
genome
size
increases
with the
complexity
of
organism.

8. 1. Base stacking interactions - hydrophobic interactions resulting from
the individual base pairs’ stacking on top of each other in the nonpolar
interior of the double helix, electrostatic forces between nearest-
neighbor base pairs, and from van der Waals forces between the
bases.
2. Deoxyribose sugar- this is less reactive because of C-H bonds.
Consequently, DNA has smaller grooves which hinder attachment of
damaging enzymes that attack DNA.
3. Hydrogen bonds- the sum of all the H-bonds between the paired bases
leads to a stabilizing "zipper effect.“
4. Protective "twisting" of the DNA helix and flexibility of the two strands
- although the bases cannot rotate freely about the axis of their bonds
with each other, they are able to rotate around their bonds with the
sugars. This area of rotation is like a joint on a human arm. In
DNA, there are several flexible bonds:
a. bonds between oxygen and phosphorus in phosphate groups
b. bonds linking the phosphate groups to the sugar rings
c. bonds which link the sugar rings to the aromatic bases
5. Interaction with histones- chains of DNA become even more stable, as
they entwine with histones. DNA ribbons coil around histones for
protection, like a string on a spool.

9.  The bacterial chromosome is
localized in the nucleoid
region of the cell (no nucleus)
and is looped into negative
coils.
 The loops are 50,000 to
100,000 bps in length (similar
to eukaryotic chromosomes)
which are held in place by
RNA and small basic (histone-
like) proteins.
 Plasmids, small negatively
supercoiled circular DNA
molecules, carry usually non-
essential genes (often drug
resistance).

10.  A chromosome is formed from a
single, enormously long DNA molecule that
contains a linear array of many genes.
 The human genome contains 3.2 × 109 DNA
nucleotide pairs, divided between 22 different
autosomes and 2 sex chromosomes.

11. Chromosomal banding patterns and multicolor FISH are
used to analyze human anomalies
Characteristic chromosomal translocations are associated with
certain genetic disorders and specific types of cancers. In nearly
all patients with chronic myelogenous leukemia, the leukemic
cells contain the Philadelphia chromosome, a shortened
chromosome 22 [der (22)], and an abnormally long chromosome
9 [der (9)]. These result from a translocation between normal
chromosomes 9 and 22.

12. Comparative studies reveal that human genomes contain genes in
the same order as another mammal, a feature called conserved
synteny. Using chromosome banding/ painting, the phylogenetic
history of our own chromosomes maybe reconstructed by
comparing them with those from other mammals.

13. DNA in a eukaryotic chromosome contains genes, many
replication origins, one centromere, and two telomeres.
These sequences ensure that the chromosome can be
replicated efficiently and passed on to daughter cells.

14. 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
Human DNA, if fully extended, would have a
total length of 1.7 m. If you unwrap all the sequences in this gene
DNA you have in all your cells, you could would add up to only
reach the moon ...6000 times! just over a meter.

15. Chromosome Organization

17.  Interphase chromosomes contain both condensed
and more extended forms of chromatin
 Constitutive heterochromatin - found in the
centromere, nucleolar organizers (found in human
chromosomes 13,14,15,21, and 22), repetitive or
satellite DNA
 Facultative heterochromatin- one of the
homologues become heterochromatic, e.g. X
chromosome becomes Barr body
 Euchromatin – loosely packed, actively
transcribed regions of the chromosome.
 Chromatin structure is dynamic: by temporarily
altering its structure by using chromatin remodeling
complexes and enzymes that modify histone tail, the
cell can ensure that proteins involved in gene
expression, replication, and repair have rapid,
localized access to the necessary DNA sequences.

18. Different
chromatin
remodeling
complexes disrupt
and reform
nucleosomes. The
same complex
might catalyze both
reactions. The
DNA-binding
proteins could be
involved in gene
expression, DNA
replication, or DNA
repair.

19. Each histone can be
modified by the covalent attachment of different molecules.
Histone H3, for example, can receive an acetyl group (Ac), a
methyl group (Me), or a phosphate (P). Note that some positions
(e.g., lysine 9 and 27) can be modified in more than one way.

20. Different combinations of histone tail modifications may
constitute a type of “histone code.” Each marking conveys a
specific meaning to the stretch of chromatin on which it occurs.
Only a few of the meanings of the modifications are known.

21.  Contains
alpha
satellite
sequences
(5,000-
15,000
copies of
171 base
pair
sequences).
 Position of
centromere
 P and q
arms

22. Within the centromere
region, the actual location
where the attachment of
chromosomes to spindle
fibers occurs is called the
kinetochore and is
composed of both DNA and
a protein called CEN DNA.
It can be moved from one
chromosome to another
and still provide the
chromosome with the
ability to segregate. CEN
DNA consists of several
sub-domains, CDE-I, CDE-II
and CDE-III. Additional
analyses of the DNA and
protein components of the
centromere are necessary
to fully understand the
mechanics of chromosome
segregation.

23.  Telomeres are non-sticky
regions that prevent fusion of
chromosomes and DNAse from
degrading their ends.
 They facilitate replication
without loss of material.
 Most species have telomeric
3’G overhangs that form G-
quartets (Hoogstein base-
pairing)
 Contain tandem repeats which
are highly conserved
(TTAGGGG in man)
 These 500-3,000 repeats in
normal cells shorten with age
(biological fortune-tellers?)

26. The stability of the T-
loop is largely
dependent on the
integrity of associated
telomere-specific
proteins called the
shelterin complex.
TRF (telomeric repeat-binding factor) 1 and TRF2 bind to the
double-stranded segment of telomeric DNA. POT1 (protein
protection of telomeres 1) binds directly to the single-stranded
telomeric DNA and interacts directly with TPP1 (tripeptidyl
peptidase 1). Rap1 (repressor activator protein 1) binds TRF2, and
TIN2 (TRF1-interacting nuclear factor 2) is a central component of
the complex interacting with TRF1, TRF2 and TPP1.

27. TERRA (Telomeric
repeat-containing
RNA) Biogenesis,
telomere association
and displacement
from telomeres.
TERRA forms
telomeric
heterochromatin
which may have
roles (?) in
telomerase
regulation and in
orchestrating
chromatin
remodelling
throughout
development and
cellular
differentiation.
TERRA dysfunction
leads to RF collapse.

28. Most human cells lack
telomerase. In normal
cells that still produce
functional p53 and have
their cell-cycle
checkpoints intact, this
triggers cell death. But a
cell that has acquired a
p53 mutation may ignore
this signal and cause
massive chromosomal
damage. Some cells
reactivate
telomerase, which
restores enough
chromosomal stability for
cell survival. These
damaged cells can then
go on to accumulate the
additional mutations
needed to produce a
cancer.

29.  The mitochondria and chloroplasts also have a DNA genome
(or chromosome). These resemble procaryotic genomes
(likely due to the endosymbiotic origin of these organelles)
but are much smaller.
 The mitochondrial genome varies in size among eukaryotes
(mammals =16.5 kb & 37 genes, yeast and plants are greater
than 5X this).
 Chloroplasts are ~120
kb and have ~120 genes.
DNA in ORGANELLES

30. DNA Can Undergo Reversible Strand Separation
Denaturation or “melting,”(unwinding and separation
of DNA strands), can be induced by increasing the
temperature of a solution of DNA.
 Denaturation and renaturation of DNA are the basis
of nucleic acid hybridization.
 Loss of the multiple weak interactions holding the
strands together along the entire length of the DNA
molecules lead to an abrupt change in the
absorption of ultraviolet (UV) light.
 The melting temperature (Tm ) at which DNA strands
will separate depends on several factors:
a. When the ion concentration is low, shielding of
negatively charged phosphate groups in the two
strands by positively charged ions is decreased,
thus increasing the repulsive forces between the
strands and reducing the Tm.

31. b. A greater proportion of G-C pairs require higher
temperatures to denature.
c. pH extremes denature DNA at low temperature. At low
pH, the bases become positively charged, repelling each
other. At high pH, the bases become negatively
charged, again repelling each other because of the
similar charge.
d. Agents that destabilize hydrogen bonds, such as
formamide or urea, also lower the Tm.

32. Through the analysis of DNA renaturation studies, the large sizes
of eukaryotic genomes reveal large amounts of repeated DNA.
These undergo a complex pattern of re-annealing which reveals
a large amount of repeated DNA sequences (fast annealing) and
unique, non-repeated DNA (slow annealing).