DNA, Chromosomes, and

Genomes
DNA, Chromosomes, and Genomes

Ø DNA structure and function

Ø Chromosomal DNA and its packaging in the chromatin fiber

Ø The regulation of chromatin structure

Ø The global structure of chromosomes

Ø How genomes evolve

47
DNA, Chromosomes, and Genomes
Ø DNA structure and function

Ø Chromosomal DNA and its packaging in the chromatin fiber

Ø The regulation of chromatin structure

Ø The global structure of chromosomes

Ø How genomes evolve

48
 THE STRUCTURE AND FUNCTION OF DNA

< A DNA Molecule Consists of Two Complementary Chains of

Nucleo�des

< The Structure of DNA Provides a Mechanism for Heredity

< In Eukaryotes, DNA Is Enclosed in a Cell Nucleus

A DNA Molecule Consists of Two Complementary Chains of Nucleo�des

DNA and its building blocks.

DNA is made of four types of nucleotides, which are
linked covalently into a polynucleotide chain (a DNA
strand) with a sugar-phosphate backbone from which
the bases (A, C, G, and T) extend. A DNA molecule is
composed of two antiparallel DNA strands held
together by hydrogen bonds between the paired
bases. The arrowheads at the ends of the DNA
strands indicate the polarities of the two strands. In the
diagram at the bottom left of the figure, the DNA
molecule is shown straightened out; in reality, it is
twisted into a double helix, as shown on the right.
 Deoxyribonucleic acid (DNA)
< Deoxyribonucleic acid (DNA) consists of nitrogenous bases
linked to a sugar–phosphate backbone
< DNA has a deoxyribose sugar (2’–H); RNA has a ribose sugar
(2’–OH).
< DNA contains the four bases adenine, guanine, cytosine, and
thymine; RNA has uracil instead of thymine.
< DNA is a double helix consis�ng of two polynucleo�de chains
that run an�parallel, with base pairs on the inside and the
sugar-phosphate backbone on the outside
Bases: the basic
(for RNA)

(for DNA)
 nucleoside

glycosidic
bon d
nucleotide

Adenosine 3’(2’),5’-bisphosphate (PAP) (not shown): Chen H et al. 2011. A nucleo�de

metabolite regulates stress-responsive gene expression and plant development. PLoS ONE
6(10): e26661.
 CH3

-CH3 , N6-Methyladenosine (m6A) modifica�on (prokaryo�c DNA or eukaryo�c mRNA) (replace one –H)
 CH3

(RNA) Methyla�on
Deamina�on
The Base Paring
Chargaff’s Experiment on nucleo�de base composi�on
The Structure of DNA Provides a Mechanism for Heredity

Complementary base pairs in the DNA double helix.

The shapes and chemical
structures of the bases allow
hydrogen bonds to form
efficiently only between A and T
and between G and C, because
atoms that are able to form
hydrogen bonds can then be
brought close together without
distorting the double helix. As
indicated, two hydrogen bonds
form between A and T, while
three form between G and C.
The bases can pair in this way
only if the two polynucleotide
chains that contain them are
antiparallel to each other.
 twist 36°/bp;
10 bp/turn 3.4 Å

34 Å

m = 10 Angstroms (Å) 20 Å The DNA Double Helix

The Structure of DNA Provides a Mechanism for Heredity

The DNA double helix.

(A) A space-filling model of 1.5 turns of the DNA double helix. Each turn of
DNA is made up of 10.4 nucleotide pairs, and the center-to-center distance
between adjacent nucleotide pairs is 0.34 nm. The coiling of the two strands
around each other creates two grooves in the double helix: the wider groove
is called the major groove, and the smaller the minor groove, as indicated.
(B) A short section of the double helix viewed from its side, showing four
base pairs. The nucleotides are linked together covalently by
phosphodiester bonds that join the 3′-hydroxyl (–OH) group of one sugar to
the 5′-hydroxyl group of the next sugar. Thus, each polynucleotide strand
has a chemical polarity; that is, its two ends are chemically different. The 5′
end of the DNA polymer is by convention often illustrated carrying a
phosphate group, while the 3′ end is shown with a hydroxyl.
Models of the B, A, and Z forms of DNA. The sugar–
phosphate backbone of each chain is on the outside
in all structures (one purple and one green) with the
bases (silver) oriented inward. Side views are shown at
the top, and views along the helical axis at the bo�om. (a
The B form of DNA, the usual form found in cells, is
characterized by a helical turn every 10 base pairs (3.4
nm); adjacent stacked base pairs are 0.34 nm apart. The
major and minor grooves are also visible. (b) The more
compact A form of DNA has 11 bp per turn and shows a
large �lt of the base pairs with respect to the helix axis. In
addi�on, the A form has a central hole (bo�om). The A-
DNA conforma�on is favored when DNA is dehydrated.
This helical form is also adopted by RNA–DNA and RNA–
RNA helices. (c) Z DNA is a le�-handed helix and has a
zigzag (hence “Z”) appearance. The Z-DNA conforma�on
is favored in certain G/C-rich sequences.
 Figure 4–6 DNA as a template for its own duplica�on.

Because the nucleo�de A successfully pairs only with T, and G pairs with C, each
strand of DNA can act as a template to specify the sequence of nucleo�des in its
complementary strand. In this way, double-helical DNA can be copied precisely,
with each parental DNA helix producing two iden�cal daughter DNA helices
 Summary on DNA Structure

DNA structure varies with the sequence and the varia�on

can be recognized by cognate proteins

The stability of double helix comes from a combina�on of

mul�ple H-bonds, base stacking, and hydrophobic force.

The structure suggests a mechanism for replica�on and

transmission of gene�c informa�on that can be
experimentally tested

Profound implica�ons to all areas of molecular biology,

including the development of DNA methodology
RNA
< Ribose (2’-OH)
< Uracil instead of thymine
< (made) Single stranded
< Varied structures
Transesterifica�on and RNA hydrolysis
Examples of
RNA Folding
DNA and RNA: addi�onal implica�ons

DNA RNA

ds stores gene�c info ssRNA stores info

Stable, high fidelity Unstable, lower fidelity
Genome size unlimited For small genomes

SS - DNA damage DS interference, gene silencing,

infec�on, etc

More ac�ve:
cataly�c ac�vity
metal binding
structures
epigene�cs
Is it possible
for RNA to
encode a
eukaryo�c
genome?
WT

? hth
The rela�onship between gene�c informa�on carried in DNA and
proteins.
 The nucleo�de sequence of the human β-globin gene.

By conven�on, a nucleo�de sequence is wri�en from its 5ʹ end to

its 3ʹ end, and it should be read from le� to right in successive lines
down the page as though it were normal English text. This gene
carries the informa�on for the amino acid sequence of one of the
two types of subunits of the hemoglobin molecule; a different
gene, the α-globin gene, carries the informa�on for the other.
(Hemoglobin, the protein that carries oxygen in the blood, has four
subunits, two of each type.) Only one of the two strands of the
DNA double helix containing the β-globin gene is shown; the other
strand has the exact complementary sequence. The DNA
sequences highlighted in yellow show the three regions of the gene
that specify the amino acid sequence for the β-globin protein. We
shall see in Chapter 6 how the cell splices these three sequences
together at the level of messenger RNA in order to synthesize a
full-length β-globin protein.
Search for sequence and gene informa�on:
h�ps://www.ncbi.nlm.nih.gov/

Select a database, find all the informa�on about your gene of interest, e.g., ‘human β-globin gene’. Some of
the databases are:

Gene, Protein, BLAST (sequence comparison), PubMed (literatures), OMIM (gene�c diseases), etc.
In Eukaryotes, DNA Is Enclosed in a Cell Nucleus
A cross-sec�onal view of a typical cell nucleus.
(A) Electron micrograph of a thin sec�on through the nucleus of a human fibroblast.
(B) Schema�c drawing, showing that the nuclear envelope consists of two
membranes, the outer one being con�nuous with the endoplasmic re�culum (ER)
membrane (see also Figure 12–7). The space inside the endoplasmic re�culum (the
ER lumen) is colored yellow; it is con�nuous with the space between the two
nuclear membranes. The lipid bilayers of the inner and outer nuclear membranes
are connected at each nuclear pore. A sheetlike network of intermediate filaments
(brown) inside the nucleus forms the nuclear lamina (brown), providing mechanical
support for the nuclear envelope. The dark-staining heterochroma�n contains
specially condensed regions of DNA that will be discussed later.
 Summary
< Gene�c informa�on is carried in the linear sequence of
nucleo�des in DNA

< Each molecule of DNA is a double helix formed from two

complementary strands of nucleo�des held together by
hydrogen bonds between G-C and A-T base pairs

< The gene�c informa�on stored in an organism's DNA

contains the instruc�ons for all the proteins the organism
will ever synthesize. In eukaryotes, DNA is contained in
the cell nucleus

78
DNA, Chromosomes, and Genomes
Ø DNA structure and Function

Ø Chromosomal DNA and its packaging in the chromatin fiber

Ø The regulation of chromatin structure

Ø The global structure of chromosomes

Ø How genomes evolve

79
CHROMOSOMAL DNA AND ITS PACKAGING IN THE CHROMATIN FIBER
< Eukaryo�c DNA Is Packaged into a Set of Chromosomes
< Chromosomes Contain Long Strings of Genes
< The Nucleo�de Sequence of the Human Genome Shows How Our
Genes Are Arranged
< Each DNA Molecule That Forms a Linear Chromosome Must Contain a
Centromere, Two Telomeres, and Replica�on Origins
< DNA Molecules Are Highly Condensed in Chromosomes
< Nucleosomes Are a Basic Unit of Eukaryo�c Chromosome Structure
< The Structure of the Nucleosome Core Par�cle Reveals How DNA Is
Packaged
< Nucleosomes Have a Dynamic Structure, and Are Frequently Subjected
to Changes Catalyzed by ATP-Dependent Chroma�n Remodeling
Complexes
< Nucleosomes Are Usually Packed Together into a Compact Chroma�n
Fiber
Eukaryo�c DNA Is Packaged into a Set of Chromosomes

The complete set of human chromosomes.

81
These chromosomes, from a female, were isolated from a cell undergoing nuclear
division (mitosis) and are therefore highly compacted. Each chromosome has been
“painted” a different color to permit its unambiguous iden�fica�on under the
fluorescence microscope, using a technique called “spectral karyotyping.”
Chromosome pain�ng can be performed by exposing the chromosomes to a large
collec�on of DNA molecules whose sequence matches known DNA sequences
from the human genome. The set of sequences matching each chromosome is
coupled to a different combina�on of fluorescent dyes. DNA molecules derived
from chromosome 1 are labeled with one specific dye combina�on, those from
chromosome 2 with another, and so on. Because the labeled DNA can form base
pairs, or hybridize, only to the chromosome from which it was derived, each
chromosome becomes labeled with a different combina�on of dyes. For such
experiments, the chromosomes are subjected to treatments that separate the two
strands of double-helical DNA in a way that permits base-pairing with the single-
stranded labeled DNA, but keeps the overall chromosome structure rela�vely
intact. (A) The chromosomes visualized as they originally spilled from the lysed
cell. (B) The same chromosomes ar�ficially lined up in their numerical order. This
arrangement of the full chromosome set is called a karyotype.
Figure 4–11 The banding pa�erns of human chromosomes.

Chromosomes 1–22 are numbered in approximate

order of size. A typical human 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 red line represents the posi�on of the
centromere (see Figure 4–19), which appears as a
constric�on on mito�c chromosomes. The red
knobs on chromosomes 13, 14, 15, 21, and 22
indicate the posi�ons of genes that code for the
large ribosomal RNAs. These banding pa�erns are
obtained by staining chromosomes with Giemsa
stain, and they can be observed under the light
microscope.
A human karyotype

The human X chromosome

can be divided into dis�nct
p: short arm regions by its pa�ern of
q: long arm staining bands
The cytogene�c loca�on of genes on chromosomes
The CFTR (cys�c fibrosis transmembrane conductance regulator) gene is located on the long arm of
chromosome 7 at posi�on 7q31.2.
Chromosomes Contain Long Strings of Genes
The arrangement of genes in the genome of S. cerevisiae compared to humans.
(A) S. cerevisiae is a budding yeast widely used for brewing and
baking. The genome of this single-celled eukaryote is distributed
over 16 chromosomes. A small region of one chromosome has been
arbitrarily selected to show its high density of genes. (B) A region of
the human genome of equal length to the yeast segment in (A). The
human genes are much less densely packed and the amount of
interspersed DNA sequence is far greater. Not shown in this sample
of human DNA is the fact that most human genes are much longer
than yeast genes.
The Eukaryo�c Chromosome: it takes three to…
 Origin of Replica�on of Chromosome

< Bacterial chromosome has a single ORC – point of regula�on

< Mul�ple ORC in eukaryotes
< In humans, there are ~ 10,000 origins of replica�on (yeast ~400).
< Each bidirec�onal replica�on is called a replicon.
< Origins of replica�on are sca�ered throughout the chroma�n, 30 –
300 kb apart.
 Centromere

< A constricted region of a chromosome, the site of

attachment (the kinetochore) to the mitotic or
meiotic spindle
< Consisting of repetitive DNA sequences of 5-300
bases in length and special H3 variants (cenH3/
CENP-A).
< Centromere functions:1) hold sister chromatids
together, 2) kinetochore attachment that helps
chromosome movement
An Example of Cell Division
microtubules a�ach the centeromere through kinetochore
Centromeres Contain a Centromeric Histone H3
Variant and Repetitive DNA
Development of human ar�ficial chromosomes (HACs)
that bypass centromeric DNA removes a key barrier
limi�ng mammalian synthe�c genome efforts.

< Seeding CENP-A nucleosome assembly induces

centromere forma�on

< Seeding centromeric chroma�n bypasses sequence

elements in repe��ve centromere DNA

< Non-repe��ve HAC templates ease ini�al construc�on

and downstream genomic analyses
Haploid Arabidopsis thaliana produced by
crossing plants expressing altered CENH3 to wild
type

a, GFP–CENH3 and GFP–tailswap transgenes used in

this study. HFD, C-terminal histone fold domain. b, c,
Chromosome spreads from mito�c telophase in
diploid and haploid A. thaliana, respec�vely. d, e,
Chromosome spreads from late diplotene in diploid
and haploid A. thaliana, respec�vely. In d and e,
chromosomes 2 and 4 are joined at their nucleolar
organizer regions independent of homologue pairing
(arrows). f, Haploids (right) have narrower rose�e
leaves than diploids. g, Haploids (right) have smaller
flowers than diploids. Scale bars: 0.5 µm for b and c;
1 µm for d and e.

Nature 464: 615 (2010); see also Science 331: 876 (2011)
Telomeres
< Telomere is required for chromosome stability.
< Telomere consists of a simple repeat
< Telomerase maintains the telomere length, uses the 3′–
OH of the G+T telomeric strand to prime synthesis of
tandem TTGGGG repeats.
< The RNA component of telomerase has a sequence that
pairs with the C+A-rich repeats.
< One of the protein subunits is a reverse transcriptase that
uses the RNA as template to synthesis the G+T-rich
sequence.
Telomeres Seal the Chromosome Ends
< The telomere-binding protein TRF2 catalyzes a reaction
in which the 3′ repeating unit of the G+T-rich strand forms
a loop at an upstream region of the telomere.

A loop forms at the end of

chromosomal DNA
Telomeres Are Essential for Survival
< Telomerase is expressed in
actively dividing cells and is
not expressed in quiescent
cells.
< Loss of telomeres results in
senescence.
< Escape from senescence
can occur if telomerase is
reactivated, or via unequal
homologous recombination
to restore telomeres.
Muta�on in telomerase causes telomeres
to shorten in each cell division