INTRODUCTORY

GENETICS
COURSE: MOLBIO210 (BS 1st SEMESTER)
Dr. Madeeha Afzal
Learning objectives
What is the structure of DNA, and in what form is the genetic
information stored?
What features of the structure of DNA facilitate the accurate
transmission of genetic information from generation to generation?
Recommended reading material
Principles of
GENETICS
S I X T H E D I T I O N

D. Peter Snustad
University of Minnesota

Michael J. Simmons
University of Minnesota

John Wiley & Sons, Inc.

NATURE OF THE CHEMICAL SUBUNITS IN DNA
AND RNA
Nucleic acids, are macromolecules composed of repeating subunits called nucleotides.
Each nucleotide is composed of (1) a phosphate group, (2) a five-carbon sugar, or
pentose, and (3) a cyclic nitrogen-containing compound called a base (Figure 9.5).
In DNA, the sugar is 2-deoxyribose (thus the name deoxyribonucleic acid); in RNA, the
sugar is ribose (thus ribonucleic acid).
Four different bases commonly are found in DNA: adenine (A), guanine (G), thymine (T),
and cytosine (C). RNA also usually contains adenine, guanine, and cytosine but has a
different base, uracil (U), in place of thymine. Adenine and guanine are double-ring
bases called In DNA, the sugar is 2-deoxyribose (thus the name deoxyribonucleic acid); in
RNA, the sugar is ribose (thus ribonucleic acid). Four different bases commonly are found
in DNA: adenine (A), guanine (G), thymine (T), and cytosine (C). RNA also usually
contains adenine, guanine, and cytosine but has a different base, uracil (U), in place of
thymine. Adenine and guanine are double-ring bases called purines; cytosine, thymine,
and uracil are single-ring bases called pyrimidines. Both DNA and RNA, therefore,
contain four different subunits, or nucleotides: two purine nucleo- tides and two
pyrimidine nucleotides (Figure 9.6).
base, uracil (U), in place of thymine. Adenine and guanine are double-ring bases called

Nucleic acids are composed of repeating subunits called nucleotides.

Each nucleotide is composed of three units.

(1) O
A
phosphate O P O
group:
O

(a) In RNA: (b) In DNA:

Ribose 2-Deoxyribose
The Structures of DNA an
OH OH
(2)
A 5 CH2 O OH 5 CH2 O OH
five-carbon Pyrimidine nucleotides Purine nucleotides
C 4 1 C C 4 1 C
sugar or H H H H
pentose: H H H H O
H C3 CH
2 H C3 2
CH
O N N
H
OH OH OH H No hydroxyl group 6 N
H N N1 7
4 CH3 H N1
6 5
N3 5 N3
4
5 7
H 2 9
8 H
5 8 H 4
2 4 9
N
3 N
(a) In RNA only (b) In both RNA (c) In DNA only 2 6 2 6 3 N N
1
H 1
H H N O
O O N O O N O H
(with rare exceptions): and DNA: (with rare exceptions):
OPOCH
O NH2 O OPOCH OPOCH OPOCH 2 O
5
5
2 O 5
2 O
5
2 O
(3) O 4 1
C C C O 4 1 O 4 1 O 4 1
A 4 4 4
H N3 5C H N3 5C H H N3 5C CH3 3 2
cyclic, 3 2 3 2 3 2
nitrogen- O C2 6
C H O C2 6
C H O C2 6
C H
1 1 1 OH
containing N N N OH OH OH
base:
H H H
Deoxythymidine Deoxycytidine Deoxyadenosine Deoxyguanosine
Uracil Cytosine Thymine
monophosphate, dTMP monophosphate, dCMP monophosphate, dAMP monophosphate, dGMP
Pyrimidines
! FIGURE 9.6 Structures of the four common deoxyribonucleotides present in DNA. The carbons and nitrogens
NH2 in the rings of the bases are numbered 1 through 6 (pyrimidines) and 1 through 9 (purines). Therefore, the carbons
in the sugars of nucleotides are numbered 1! through 5! to distinguish them from the carbons in the bases.
C N
6
N1 5C
7
8
C H

H C 2
3
4
C
9
N H purines; cytosine, thymine, and uracil are single-ring bases called pyrimidines. Both DNA
N and RNA, therefore, contain four different subunits, or nucleotides: two purine nucleo-
Adenine
tides and two pyrimidine nucleotides (! Figure 9.6). In polynucleotides such as DNA
O
and RNA, these subunits are joined together in long chains (! Figure 9.7). RNA usually
C
6
N exists as a single-stranded polymer that is composed of a long sequence of nucleotides.
H N1 5C
7
C H
8
DNA has one additionaland very importantlevel of organization: it is usually
9
a double-stranded molecule.
4
NH2 C2 3 C N H 5 end
N
NH2
Guanine
Purines DNA STRUCTURE: THE DOUBLE HELIX N1
6
5
N
7
8 Adenine
2 4 9
! FIGURE 9.5 Structural components of nucleic acids. The standard numbering systems One of the most exciting breakthroughs in the history of biology occurred 3
N
N
for the carbons in pentoses and the carbons and nitrogens in the ring structures of the in 1953 when James Watson and Francis Crick (! Figure 9.8) deduced the O
bases are shown in (2) and (3), respectively. Single-ring bases are called pyrimidines, and
double-ring-bases are purines. correct structure of DNA. Their double-helix model of the DNA molecule 5
O P OCH2 O
immediately suggested an elegant mechanism for the transmission of genetic O 4 1
information (see A Milestone in Genetics: The Double Helix on the Student O
 exists as a single-stranded polymer that is composed of a long sequence of nucleotides.
DNA has one additionaland very importantlevel of organization: it is usually

Phosphodiester linkage,
a double-stranded molecule. 5 end
NH2

DNA STRUCTURE: THE DOUBLE HELIX N1

6
5
N
7
8 Adenine

and 5 3 ends
2 4 9
One of the most exciting breakthroughs in the history of biology occurred 3
N
N
in 1953 when James Watson and Francis Crick (! Figure 9.8) deduced the O
correct structure of DNA. Their double-helix model of the DNA molecule 5
O P OCH2 O
immediately suggested an elegant mechanism for the transmission of genetic O 4 1
information (see A Milestone in Genetics: The Double Helix on the Student O
H 3 2
H
Companion site). Watson and Cricks double-helix structure was based on two 4 CH3
H HN 3
major kinds of evidence: 5
5
Thymine
In polynucleotides such as
1. When D NA aChargaff
nd RNA,
andthese subunits
colleagues analyzed are
2 6
1
Erwin the composition of O
O N

joined together in long chains (Figure).

DNA from many different organisms, they found that the concentra- O P OCH2
5

O
tion of thymine was always equal to the concentration of adenine and O
Structure of a polynucleotide chain.ofThe
the concentration tetranucleotide
cytosine was always equal to chain
the concentration of
4

3 2
1
NH2
H H
guanine (Table 9.1). Their results strongly suggested that thymine and
shown is a DNA chainadenine containing the sugar 2-deoxyribose.
as well as cytosine and guanine were present in DNA in some fixed H N3
4
5
Cytosine
RNA chains contain the sugar ribose.
interrelationship. Their data also showed that the total concentration of
O
O
2

N
1
6

pyrimidines (thymine plus cytosine) was always equal to the total concentration of
The nucleotides in polynucleotide purines (adenine pluschains are
guanine; see joined
Table 9.1).by O P OCH2 O
5

phosphodiester (C2.O WhenPXOrays C) arelinkages. Notefibers

focused through thatofthepurified molecules, the rays O 4 1

are deflected by the atoms of the molecules in specific patterns, called diffrac- H 3 2
H
polynucleotide showntion haspatterns,
a 5 (top) to 3 (bottom) chemical
which provide information about the organization of the com- H O
polarity because each ponents phosphodiester
of the molecules.linkage
These joins the 5 carbon
X-ray diffraction patterns can be recorded on
HN 1
6 N
X-ray-sensitive film just as patterns of light can be recorded with a camera and 5 7
Guanine
of 2-deoxyribose in one nucleotide
light-sensitive film.to the 3and
Watson carbon of 2-
Crick used X-ray diffraction data on DNA H2N
2
3
4 9
N
8

N
deoxyribose in the adjacent nucleotide. Therefore, the chain has
! FIGURE 9.7 Structure of a polynucleotide chain. The tetranucleotide chain shown is a
O
5
O P OCH2
a 5 carbon terminus DNA at the
chaintop and the
containing a 3sugar
carbon terminus
2!-deoxyribose. at the
RNA chains contain the sugar ribose.
O
O
The nucleotides in polynucleotide chains are joined by phosphodiester (C O P O C) 4 1

bottom. linkages. Note that the polynucleotide shown has a 5! (top) to 3! (bottom) chemical polarity H 3 2 H
because each phosphodiester linkage joins the 5! carbon of 2!-deoxyribose in one nucleo- H
3 OH
tide to the 3! carbon of 2!-deoxyribose in the adjacent nucleotide. Therefore, the chain has
a 5! carbon terminus at the top and a 3! carbon terminus at the bottom. 3 end
DNA STRUCTURE: THE DOUBLE HELIX
One of the most exciting breakthroughs in the history of biology occurred in 1953 when James
Watson and Francis Crick deduced the correct structure of DNA.
Their double-helix model of the DNA molecule immediately suggested an elegant mechanism for
the transmission of genetic information
Watson and Cricks double-helix structure was based on two major kinds of evidence:
1. When Erwin Chargaff and colleagues analyzed the composition of DNA from many different
organisms, they found that the concentration of thymine was always equal to the concentration of
adenine and
the concentration of cytosine was always equal to the concentration of guanine. Their results
strongly suggested that thymine and adenine as well as cytosine and guanine were present in DNA
in some fixed interrelationship. Their data also showed that the total concentration of pyrimidines
(thymine plus cytosine) was always equal to the total concentration of purines (adenine plus
guanine)(known as Chargaff rule)
2. When X rays are focused through fibers of purified molecules, the rays are deflected by the atoms
of the molecules in specific patterns, called diffraction patterns, which provide information about
the organization of the com- ponents of the molecules. These X-ray diffraction patterns can be
recorded on X-ray-sensitive film just as patterns of light can be recorded with a camera and light-
sensitive film. Watson and Crick used X-ray diffraction data on DNA structure provided by Maurice
Wilkins, Rosalind Franklin, and their coworkers. These data indicated that DNA was a highly
ordered, two-stranded structure with repeating substructures spaced every 0.34 nanometer along
the axis of the molecule.
 On the basis of Chargaffs chemical data, Wilkins and Franklins X-ray
diffraction data, and inferences from model building, Watson and
Crick proposed that DNA exists as a right- handed double helix in
which the two poly- nucleotide chains are coiled about one another
in a spiral. Watson, Crick, and Wilkins shared the 1962 Nobel Prize in
Physiology or Medicine for their work on the double-helix model.
Unfortunately, Franklin died prematurely (age 37) in 1958, and Nobel
Prizes cannot be awarded posthumously.
 Each of the two polynucleotide chains in a double helix consists of a
sequence of nucleotides linked together by phosphodiester bonds,
joining adjacent deoxyribose moieties.
The two polynucleotide strands are held together in their helical
configuration by hydrogen bonding between bases in opposing
strands; the resulting base pairs are stacked between the two chains
perpendicular to the axis of the molecule like the steps of a spiral
staircase. The base-pairing is specific: adenine is always paired with
thymine, and guanine is always paired with cytosine. Thus, all base
pairs consist of one purine and one pyrimidine.
 202 Chapter 9 DNA and the Molecular Structure of Chromosomes

Diagram of a DNA double helix,

Opposite polarity of the two strands Hydrogen bonding in A-T and G-C base pairs

5 3 H

illustrating the opposite chemical Thymine

H
C
H

polarity (see Figure) of the two

P OH
H C O
+
A T
S S C6 5
4C
H H

strands and the hydrogen bonding

N
P N1 2
3
N Adenine
P Sugar C H+ C

between thymine (T) and adenine

N
T A 3

N1 6
5 C 7
S
8 C H
S O 2 4 9

(A) and between cytosine (C) and

C 3 C N
P H N Sugar
P

guanine (G). 5 S
G C
S
5
P
The base-pairing in DDiagram
! FIGURE 9.11NA, ofTa DNA
with
doubleA
helix,
P

S
A T
S
Cytosine
H
H
C
H
N
+

and C with G, iillustrating

s g9.7)
overned band y tthehe C6 H
5
the opposite chemical polarity (see 4 C

3 P O
Figure of the two strands hydrogen P 1 3 +
Guanine
hydrogen-bonding potential of the
N 2 N
bonding between thymine (T) and adenine C G Sugar C H C N
S N1 6
C
(A) and between cytosine (C) and guanine S 5 7

bases. S: the s(G).ugar 2-deoxyribose; O

+ 8 C H
The base-pairing in DNA, T with A and C P

C
2 4
C
9
HO H 3 N
with G, is governed by the hydrogen-bonding N N Sugar

P: a phosphate group.
potential of the bases. S ! the sugar
2-deoxyribose; P ! a phosphate group. 3 5 H

base-pairing results from the hydrogen-bonding capacities of the bases in their

normal configurations (! Figure 9.11). In their common structural configurations,
adenine and thymine form two hydrogen bonds, and guanine and cytosine form three
hydrogen bonds. Hydrogen bonding is not possible between cytosine and adenine or
 The Structures of DNA and RNA 201
The Structures of DNA and RNA 201
structure (! Figure 9.9) provided by Maurice
3' 5'
e 9.9) provided by Maurice Wilkins, Rosalind Franklin (see Figure 9.8),
and their coworkers. These data indicated 3' 5' S
Franklin (see Figure 9.8), P
C G S
ers. These data indicated that DNA was a highly ordered, two-stranded
S
C G S S G C
P
P S
ghly ordered, two-stranded structure with repeating substructures
S G
spaced
C
P
P
S
eating substructures spaced every 0.34 nanometer (1 nm ! 10"9 meter) P S C GP
S
eter (1 nm ! 10"9 meter) along the axis of the molecule.
S C GP
S S
P
he molecule. S S
On the basis of Chargaffs chemical P
S
data, S P
T A S
Chargaffs chemical data, Wilkins and Franklins X-ray diffraction
S P data, P
T A S
ns X-ray diffraction data, and inferences from model building, Watson P S G C
S
S P
model building, Watson and Crick proposed that DNA exists S Gas a right-C P P
C G S
that DNA exists as a right- P
handed double helix in which the StwoC poly- G S
S
P
in which the two poly- nucleotide chains are coiled about one another P S T A
S
S T A P
e coiled about one another in a spiral (! Figure 9.10). Watson, Crick, P
S
S P
S P
re 9.10). Watson, Crick, S P
and Wilkins shared the 1962 Nobel Prize in S P P S
the 1962 Nobel Prize in P ! SFIGURE 9.9 Photograph of the S G
! FIGURE 9.9 Photograph Physiology
of the or Medicine for their work on S the G
X-ray diffraction pattern obtained
3.4 nm P
cine for their work on the X-ray diffraction pattern obtained 3.4 nm P S
double-helix model. Unfortunately,S Franklin with
S DNA. The central cross-shaped P
T A S
Unfortunately, Franklin with DNA. The central cross-shaped P
T A
died prematurely (age 37) in 1958, and Nobel P
Photograph of the X-ray diffraction pattern obtained with DNA.
e 37) in 1958, and Nobel pattern indicates that the DNA
rded posthumously. Prizes cannot be awarded
S G
posthumously.
C
S
pattern
P
molecule
indicates that the DNA
has a helical structure, and
S G C
P
S
molecule has a helical structure, and P S
The central cross-shaped pattern indicates that the DNA
polynucleotide chains in a the dark bands at the top and bottom
double
Each of
helix
the two
consists
polynucleotide
of a sequence
S T
of
chains
A P
S in a

nucleotides
S
the dark
indicate
bands
that the
at the top and bottom
bases are stacked
S T
S
AP

of a sequence of nucleotides indicate that the bases are stacked P

molecule has a helical structure, and the dark bands at the top
osphodiester bonds, joining perpendicular to the axislinked
of the together
mol- by phosphodiester S C
P
bonds,
S
G
joining perpendicular
ecule with a
to the axis of the mol-
periodicity of 0.34 nm.
S C
S
G S
moieties (Table 9.2). The ecule with a periodicity adjacent
of 0.34 nm. deoxyribose moieties (Table 9.2 ). S The
and bottom indicate that the bases are stacked perpendicular to
trands are held together in two polynucleotide strands are held S
together
G C
P
in S S G C
P
S
P
P
their helical configuration by hydrogen bonding (Table 9.2) between bases in opposing
the axis of the molecule with a periodicity of 0.34 nm.
ation by hydrogen bonding (Table 9.2) between bases in opposing
strands;
base pairs are stacked between the two chains perpendicular to the the resulting
0.34
base
nm
pairs are
P
S
stacked
C
between
G
the
S
two chains perpendicular to the
0.34 nm P
S
C G S

3' 5' 3' 5'

axis of the ismolecule like the steps of a spiral staircase (Figure 9.10). The base-pairing is
ke the steps of a spiral staircase (Figure 9.10). The base-pairing
ways paired with thymine, and guanine is always paired with cyto-
specific: adenine is always paired with thymine, and guanine is always paired with cyto-
FIGURE 9.10 Diagram of the double-helix ! FIGURE 9.10 Diagram of the double-helix
airs consist of one purine and one pyrimidine. The specificity
sine. Thus, of all!base pairs consist of one purine and one pyrimidine. The specificity of
structure of DNA. structure of DNA.
 The specificity of base-pairing results from the hydrogen-bonding
capacities of the bases in their normal configurations. In their common
structural configurations, adenine and thymine form two hydrogen bonds,
and guanine and cytosine form three hydrogen bonds. Hydrogen bonding is
not possible between cytosine and adenine or thymine and guanine when
they exist in their common structural states.
Once the sequence of bases in one strand of a DNA double helix is known,
the sequence of bases in the other strand is also known because of the
specific base-pairing.The two strands of a DNA double helix are thus said to
be complementary. This property, the complementarity of the two strands
of the double helix, makes DNA uniquely suited to store and transmit
genetic information from generation to generation .
PROBLEM: CALCULATING BASE CONTENT OF
DNA
Double-stranded genomic DNA was isolated from the bacterium
Mycobacterium tuberculosis, and chemical analysis showed that 33
percent of the bases in the DNA were guanine residues. Given this
information, is it possible to determine what percent of the bases in
the DNA of M. tuberculosis were adenine residues?
Single-stranded genomic DNA was isolated from bacteriophage
X174, and chemical analysis showed that 22 percent of the bases in
the X174 DNA were cytosines. Based on this information, is it
possible to determine what percent of the bases in the DNA pack-
aged in the X174 virion were adenines?
 The base pairs in DNA are stacked about 0.34 nm apart, with 10 base pairs per turn
(360) of the double helix . The sugar-phosphate backbones of the two complementary
strands are antiparallel. Unidirectionally along a DNA double helix, the phosphodiester
bonds in one strand go from a 3 carbon of one nucleotide to a 5 carbon of the adjacent
nucleotide, whereas those in the complementary strand go from a 5 carbon to a 3
carbon. This opposite polarity of the complementary strands of a DNA double helix
plays an important role in DNA replication, transcription, and recombination.
The stability of DNA double helices results in part from the large number of hydrogen
bonds between the base pairs (even though each hydrogen bond by itself is weak, much
weaker than a covalent bond) and in part from the hydrophobic bonding (or stacking
forces) between adjacent base pairs.
The planar sides of the base pairs are relatively nonpolar and thus tend to be
hydrophobic (water-insoluble). Because of this insolubility in water, the hydrophobic core
of stacked base pairs contributes considerable stability to DNA molecules present in the
aqueous protoplasms of living cells. The space-filling drawing also shows that the two
grooves of a DNA double helix are not identical; one, the major groove, is much wider
than the other, the minor groove. The difference between the major groove and the
minor groove is important when one examines the interactions between DNA and
proteins that regulate gene expression. Some proteins bind to the major groove; others
bind to the minor groove.
DNA STRUCTURE: NEGATIVE SUPERCOILS IN
VIVO
All the functional DNA molecules present in living cells display one
other very important level of organizationthey are supercoiled.
The DNA molecules of almost all organisms, from the smallest viruses
to the largest eukaryotes, exhibit negative supercoiling in vivo, and
many of the bio- logical functions of chromosomes can be carried out
only when the participating DNA molecules are negatively
supercoiled. (The DNA of some viruses that infect Archaea is
positively supercoiled.) Considerable evidence indicates that negative
supercoiling is involved in replication, recombination, gene
expression, and regulation of gene expression. Similar amounts of
negative supercoiling exist in the DNA molecules present in bacterial
chromosomes and eukaryotic chromosomes.
Difference between RNA and DNA structure
Uracil instead of thymine
Ribose instead of
Deoxyribose
DNA is double stranded, RNA
is usually single stranded,
may exist in double stranded
forms
Therefore, in DNA purines
are always equal to
pyramidines, but not in RNA
TYPES OF RNA MOLECULES
Five major types of RNAmRNA, tRNA, rRNA, snRNA (small nuclear
RNA), and miRNA (Micro-RNA)are produced by transcription.
Unlike mRNAs, which specify polypeptides, the final products of
tRNA, rRNA, snRNA, and miRNA genes are RNA molecules. Transfer
RNA, ribosomal RNA, snRNA, and miRNA molecules are not
translated.