Chapter 17: Outline
DNA
Mutation
Chromosomes and
Variations
Chromatin
Supercoiling Genome Structure
RNA
Transfer, Ribosomal, Messenger
Heterogeneous and Small Nuclear
Viruses
17-1
Definitions
DNA stands for deoxyribonucleic acid.
It is the genetic code molecule for most
organisms.
RNA stands for ribonucleic acid. RNA
molecules are involved in converting
the genetic information in DNA into
proteins. In retroviruses, RNA is the
genetic material.
17-2
17.1 Nucleic Acids, DNA
DNA and RNA are polymers whose
monomer units are called
nucleotides
A nucleotide itself consists of:
1. a nitrogen containing
heterocyclic base
2. a ribose or deoxyribose sugar
ring
3. a phosphoric acid unit
17-3
Nucleobases
The bases found in nucleic acids are
derived from either the purine or the
pyrimidine ring systems.
Examples follow on the next screen.
N
HC
H
C
N
CH N
CH HC
pyrimidine
H
C
N
C
C N
N
H
purine
CH
17-4
Major Purine Bases
NH2
C
N1
HC
2
6
C
5
O
N
7
9
3 4C
N
8 CH
N
H
adenine
in DNA and RNA
C
HN
C
C
C
H2N
N
N
CH
N
H
guanine
in DNA and RNA
17-5
Major Pyrimidine Bases
O
O
NH2
C
CH
C
C
3 HN
CH
N3 4 5CH HN C
2 1 6
C CH
C CH C CH
O N
O N
O N
H
H
H
cytosine
in DNA
and RNA
thymine
in DNA
and some RNA
uracil
in RNA
17-6
Some less common bases
O
NH2
C CH3 HN C CH
N C
2
C CH2
C CH
O N
O N
H
H
5-methylcytosine
HN
HC
O
C
N
5,6-dihydrouracil
hypoxanthine
C
CH
C N
N
H
17-7
Nucleosides
A nucleoside is a
NH2
base
compound in
C
which the
N
C
N
DNA/RNA base
CH
forms a
C
H
C
N
glycosidic link to
N glycosidic
the sugar
H
O
CH
2 link
5'
molecule. The
O
sugar molecule is
1'
4' H
H
numbered with
3' 2'
H
primed numbers.
H
deoxyribose sugar OH H
17-8
Nucleotides-1
A nucloetide is the
NH2
base
repeating unit of the
C
DNA or RNA
N
phosphate N
C
polymer. The
CH
ester
nitrogen base is
C N
HC
attached b to the
N
2ribose (RNA) or
O3PO CH2
O
deoxyribose (DNA)
ring. The sugar is
H
H
phosphorylated at
H
H
carbon 5’
OH H
deoxyribose sugar
17-9
Nucleotides-2
Nucleotides are named after the parent
nucleoside. Examples follow.
NH2
C CH3
C
HN
C
C
N
O
2O3PO CH2
O
Deoxythymidine
H
H
5’-monophosphate
H
H
OH H
17-10
Nucleotides-3
NH2
NH2
N
C
C
N
C N
N
O P O CH2
O
O
H
H
H
H
OH H
O
N
CH
HC
O
O
O P O CH2
O
H
2-deoxy
Deoxyadenosine
5’-monophosphate
C
C
N
CH
CH
O
H
H
H
OH
H
Deoxycytidine
5’-monophosphate
17-11
Nucleotides-4
HN
O
2O3PO CH2
H
H
C
O
O
C
C
N
O
CH
HN
CH
C
H2N
2-
H
H
C
N
CH
C N
N
O3PO CH2
H
O
H
H
Uridine OH H
H
5’-monophosphate
OH H
Guanosine 5’-monophosphate
17-12
DNA/RNA Chains
When nucleotides polymerize, the 5’
phosphate on one unit esterifies to the
3’ OH on another unit. The terminal 5’
unit retains the phosphate. An
example of a three nucleotide DNA
product is shown on the next slide .
17-13
Segment of DNA Chain
5’-end
N
O
C
C N
C N
C
H2N
N
-2
O3PO CH2
O
H
H
H
H
H
O
guanine
CH
N
C
O
C
O
N
O P O CH2
O
O
H
H
H
H
H
O
3’-5’
link
CH3
C
CH
NH2
C
N
CH
C
CH
O
N
O P O CH2
O
O
H
H
H
H
OH H
3’-end
thymine
cytosine
17-14
Abbreviated DNA
DNA and RNA chains are abbreviated
using a structure where vertical lines
represent the sugars, diagonal lines
with P at the midpoint represent the
3,5-phosphodiester bonds, and
horizontal lines the ends of the chain.
The structures are always written with
the 5’ end to the left.
Single letter abbreviations are also used.
17-15
Abbreviated DNA-2
dG dT dC 3'
OH
5'
P P
P
Or: pdGpdTpdC
Or: pd(GTC)
RNA abbreviations lack the d (for deoxy)
17-16
DNA-Secondary Structure
The most common form of DNA is the B
form . Its structure was determined by
Watson and Crick in 1953.
This DNA consists of two chains of
nucleotides coiled around one another
in a right handed double helix.
The chains run antiparallel and are held
together by hydrogen bonding between
complimentary base pairs: A=T, G=C.
17-17
DNA-Secondary Structure: 2
H
Hydrogen
CH3
N H||||||||||| O
N
HC
bonding
C C
C C
N C
CH between A and T
N|||||||||||H N
C N
or
G
and
C
helps
N CH
A
TO
to hold the
H
chains
in
the
O
|||||||||||
N
N
H
HC C C
C CH double helix
N C
N H ||||||||||| N
CH
The strands are
N C
C N
said to be
N H ||||||||||| O
G
C
complimentary
H
17-18
DNA-Secondary Structure: 3
In addition to hydrogen bonding
between bases, other important
noncovalent interactions contribute to
helical stability.
2. Hydrophobic interactions among the
bases.
3. Base stacking results in weak van der
Waals attractions
2+
4. Electrostatic interactions with Mg ,
histones, etc.
17-19
DNA: Mutations
H
H
If tautomers
N H H N
form during
N
HC
C
C
C
replication,
N
N
N C
base
C
N CH
mispairing
O
can occur.
A
H
H
E. g. purine
N ||||||||||| H N
N
for purine: HC C C
C
a transition
N H ||||||||||| N
N C
mutation
C
N CH
O
CH
CH
N
C
CH
CH
N
17-20
DNA: Mutations-2
Hydrolysis of purine-sugar
O
H
bond can occur and purine
N C
base is lost.
N
O C
C CH
Bases can spontaneously
CH3
deaminate.
O
H
(cytosine  uracil)
N C
N
Ionizing radiation can cause O C
C CH
strand breaking and base
CH3
modifications, esp. thymine
dimers.
17-21
Xenobiotics
1. Base analogues
Caffeine can pair with guanine causing
a transition mutation.
2. Alkylating agents
Adenine and guanine are especially
liable to alkylation (e. g.
methylation).
Transversion mutations (purine for
pyrimidine or reverse) are possible.
17-22
Xenobiotics-2
3. Nonalkylating agents
Nitrous acid deaminates bases.
Polyaromatic hydrocarbons are
mutagenic and prevent base pairing.
4. Intercalating agents
Some planar molecules can insert
between base pairs. Adjacent pairs
may be deleted or new ones inserted
resulting in a frame-shift mutation.
17-23
DNA: Variations on a Theme
The Watson-Crick form of DNA (B-DNA)
is not the only one possible. A and Z
forms also exist.
The forms differ in helical conformation.
17-24
B DNA segment
Chain 2
Sugar-phosphate
backbone
Chain 1
Hydrogen bonded
base pairs in the
core of the helix17-25
B DNA: 2
Major groove
Outside diameter, 2 nm
Interior diameter, 1.1 nm
Minor groove
Length of one turn of helix
is 3.4 nm and contains 10
base pairs.
17-26
A DNA and Z DNA
A second form of DNA is the A form.
It has 11 base pairs per turn of the helix
and the bases lie at an angle of about
20o relative to the helix axis. It, too, is
a right hand double helix.
A third form of DNA is the Z form. It is a
left handed helix.
A picture of A DNA is on the next slide.
17-27
A DNA segment
Base pairs not
perpendicular to
helix axis. 11 pairs
per turn.
17-28
DNA, Higher Order Structure
Examples of higher order structures
include cruciforms, triple helices, and
supercoils.
Cruciforms are cross-like structures
likely to form when the DNA sequence
contains a palindrome, a sequence
providing the same information read
forward or backward.
E. g. MADAM I’M ADAM
17-29
Cruciforms
Inverted repeats form palindromes
within DNA. Palindromes play an
important role in the function of
restriction enzymes.
ATATCGACTCCGATAT
TATAGCTGAGGCTATA
T
C
C
A
CGATAT
ATATCG
GCTATA
TATAGC
G
A
G
T
17-30
Triple Helix
A polypurine strand hydrogen-bonded to
a poly pyrimidine strand can form a
triple helix (H-DNA) involving Hoogsteen
base pairing.
17-31
Supercoiling
Prokaryotic DNA is circular. If the
circular loop of right-handed DNA is
twisted in a left-handed manner the
DNA is said to be negatively
supercoiled. Cruciforms and H-DNA
can result.
Extra right-handed twists results in a
positively supercoiled loop of DNA.
This is found when DNA coils around a
protein core to form a supercoil.
17-32
Chromosomes (Prokaryote)
In the nucloid the E. coli chromosome
(circular DNA) is attached to a protein
core in at least 40 places.
The protein HU binds DNA. Polyamines
(+ charge) bound to DNA help
neutralize DNA charge for denser
packing of the DNA.
A diagram of the E. coli chromosome is
on the next slide.
17-33
The E. coli Chromosome
Fig 17.16
17-34
Chromosomes (Eukaryote)
Eukaryotic chromosomes have two
unique structural elements:
Centromere: AT-rich, associated with
nonhistome protein to form
kinetochore which interacts with
spindle fibers during cell division.
Telomeres: CCCA repeats at the end of
DNA that postpone loss of coding on
replication.
17-35
Chromosomes (Eukaryote)-2
Each chromosome has one linear DNA
complexed with histone proteins to
form nucleosomes. Histones regulate
access to DNA of transcription factors.
Cells not undergoing cell division have
partially decondensed chromosomes
called chromatin which looks like a
beaded chain.
As chromatin packs to form chromosomes, 30nm and 200 nm fibers
appear. Chromosomes have multiple
levels of supercoiling.
17-36
Chromosomes (Eukaryote)-3
The figure below shows
levels of coiled structure
for nuclear chromatin.
17-37
Genome
The genome of each living organism is
the full set of inherited instructions
required to sustain all living processes.
Size varies: 1x106 to 1x1010 base pairs
Eukaryotes have larger and more
complex information-coding capacity
than prokaryotes.
17-38
Genome: Prokaryotes
1. Size. Most prokaryotic genomes are
smaller: E. g. E. coli 4.6 Mb, 4300
genes.
2. Coding capacity. Genes are compact
and continuous. Little, if any,
noncoding DNA.
3. Gene expression. Higher percentage
of operons, sets of linked genes.
Prokaryotes often contain plasmids,
nonchromosome DNA.
17-39
Genome: Eukaryotes
1. Genomic size. Larger than
prokaryotes but many have vast
amounts of noncoding DNA.
2. Coding capacity. Enormous capacity
but only about 1.5% codes for
proteins.
3. Coding continuity. Most are discontinuous and contain noncoding
introns.
17-40
Genome: Eukaryotes-2
About 45% of human genome is
“repeated sequences.”
Tandem repeats (satellite DNA) have
multiple copies arranged next to each
other and can vary from 10 to 2000 bp
repeating to 105 to 107 bp.
Interspersed genome-wide repeats are
scattered in the genome. Many result
from transposition whereby DNA
sequences are duplicated and moved
in the genome.
17-41