5.

DNA Structure
Carbohydrates, nucleotides, double helix.
6. Chromosomes
Nucleosomes, chromosome structure, cell cycle.
BIOPOLYMERS
Two types of nucleic acid

DNA deoxyribonucleic acid

RNA ribonucleic acid

 Nucleic Acid Function
Nucleic acids are the cell's information molecules.
There are two kinds of nucleic acids:

• Deoxyribonucleic acid, or DNA,

• Ribonucleic acid, or RNA.
DNA makes up the cell's inherited library of
information, the genes. DNA carries instructions for
building all the proteins that carry out cell activities.
RNA acts as an intermediary in the protein-making
process. DNA's information is transcribed into RNA,
which is then translated into the primary structure of
proteins. This is known as the central dogma.
The central dogma of molecular biology
 DNA and RNA composition
Pyrimidines
NH2 O O

N NH NH

N O N O N O
H H H

Cytosine Thymine Uracil

C T U
NH 2 O

N N
N NH

N N
H N H N NH2

Adenine Guanine
HO
A G O
OH HO
OH
O
H H
Purines H H
H H
H H
OH H
OH OH

Deoxyribose Ribose
(DNA) (RNA)
 Nucleic acid nomenclature
Phosphorylated nucleosides are called nucleotides
NH2

Purine or pyrimidine base

N
N
O

-O N
P O O O O N
O

O- H H -O P O P O P O
O
H H
O- O- H H
OH OH -O

H H
OH OH

Adenosine 5´-monophosphate (AMP)

Adenosine 5´-diphosphate (ADP)

Adenosine 5´-triphosphate (ATP)

Primary Structure
The connection between nucleotides in a
DNA strand is referred to as a
phosphodiester linkage.

The linkage of the sugar-phosphate

backbone of a single DNA strand is such
that there is a directionality. That is, the
phosphate on the 5' carbon of deoxyribose is
linked to the 3' carbon of the next
deoxyribose. This lends a directionality to a
DNA strand which is said to have a 5' to 3'
direction.

DNA in the cell adopts a double-stranded

helical conformation.
 Watson and Crick

Dr. Francis Crick, left, and Dr.

James D. Watson at Cambridge in
the 1950's, after they discovered the
double helix. The two have
continued to drive the genetic
revolution.
Dr. Crick died recently. Dr.
Watson worked at Harvard and is
now president of the Cold Spring
Harbor Laboratory.
 Watson-Crick Model of DNA
Francis Crick and James Watson proposed a
model of DNA structure in 1953.

DNA is a double-stranded helix twisted to the right

Bases pair in a complementary manner (A-T, C-G)

internally with respect to the sugar-phosphate backbone of
the molecule

Two strands of DNA are held together by hydrogen bonds

between the bases
 The DNA duplex
DNA consists of two strands of
nucleotides that twist around one
another, forming a double helix.

The strands are held together by

hydrogen bonds between pairs of
nitrogenous bases.

The base A always pairs with T,

and C always pairs with G. the two
strands are complementary and
antiparallel

The two strands of a DNA double

helix are arranged in opposite
directions and are said to be anti-
parallel in that one strand is 5' - 3' and
the complementary strand is 3' - 5'.
05_02_DNA.jpg
Base pairs

A-T and G-C base pairing results in

strand complementarity, with one strand
of the double helix forming a sequence of
bases complementary in hydrogen
bonding to that of the other strand.
05_06_compl_pairs.jpg
05_08_major_minor_gr.jpg
05_06_compl_pairs.jpg
 Watson/Crick Model of DNA
Two strands are antiparallel

The orientation of phosphodiester bond is from 3’ to 5’ on one

strand and from 5’ to 3’ on the other strand

5'-CAGCTAGAGTCATCG-3'
3'-GTCGATCTCAGTAGC-5'

Molecule makes a complete turn of the helix every 3.4 nm

There are 10.4 base pairs per turn
Major grooves alternate with minor grooves
Molecule is 20 Å in diameter and of equal width along its entire
length.
B Form DNA

Minor Groove

Major Groove
Other forms of DNA
On the left are shown the three known
conformers of double stranded DNA, A-, Z-, and
B-DNA

Although B-DNA is the primary in vivo

conformation, DNA-RNA hybrid molecules adopt
the A conformation in cells, and Z-DNA may
arise in GC rich stretches of chromosomal DNA.
Whereas A- and B-DNA are right handed
helices, Z-DNA is left handed. A-DNA forms
under non-physiological conditions when B-DNA
is dehydrated.

There are large differences in the depths of the

grooves in the three conformers.
B-DNA has major and minor grooves of similar
depths,
A-DNA has a cavernous major groove and a
minor groove that is quite shallow.
Z-DNA has the opposite arrangement, with a
deep minor groove and a major groove into
which the bases are extruded.
 Differences between A, B and Z DNA
Helix
DNA Helix Major Minor
Bp/turn diameter
Conformation Handedness Groove groove
(nm)

Wide Narrow and

B Right 10.5 ~2
and deep deep

Narrow Wide and

A Right 11.0 ~2
and deep shallow

Narrow and
Z Left 2.0 ~ 1.8 Flat
deep
 Quiz
On the diagram of a small portion of
a DNA molecule, match the labels
below to the numbered label lines.
(a) Base
(b) Sugar
(c) Phosphate
(d) Hydrogen bond
(e) 5′ end
(f) 3′ end
 The problem of packing DNA
Chromosomal DNA is long in relation to eukaryotic nuclei and
bacteria.
E. coli chromosome around 1.5mm long
in a <1 micrometer diameter cell.

Eukaryotic chromosomes are around meters

long, but stored in nuclei that are less than a
micrometer across.
Tertiary structure of DNA

Right handed (negative) Relaxed circular Left handed (positive)

Topoisomerases supercoil DNA
 Bacterial chromosomes
Genes encoded in large circular
genome - 4.6 x 106 bp

Genome forms a compact structure

called the nucleoid
DNA organized in 50-100 loops
(domains)
The ends of loops are constrained
by binding to protein structure
which is in contact with cell
membrane
 Bacterial chromosome structure
Supercoiled DNA is generated by DNA topoisomerase

Bacterial DNA is much less structured than eukaryotic DNA

Circular molecule is compacted by association with:

Polyamines (spermine and spermidine, +ve charge),
HU proteins (small, basic, +ve, dimeric) and H-NS (monomeric,
neutral) DNA binding proteins
and by supercoiling
Eukaryotic Chromosome Structure
DNA is packaged into chromosomes

Chromosomes

Attachment of loops of chromatin fibres to

nonhistone protein complexes = scaffold

Nucleosome fibres condense more into 30 nm

chromatin fibre.

Duplex DNA winds around histone octamers to

form nucleosomes = 11 nm histone fiber

Primary structure of DNA = double helix = 2nm

duplex DNA
 Histones
The packaging of DNA involves complexing the DNA with basic proteins called
histones to form a complex fibre called chromatin which is made up of a repeating
unit known as the nucleosome.
Nucleosome structure
DNA HI
Each Nucleosome:
Contains 4 dimers (i.e. 2 each.
of H2A, H2B, H3, H4) with
146 nucleotide pairs of DNA Nucleosome
in 2 full turns around protein
(histone octamer).
Histone Octamer
20 additional nucleotide pairs
and histone H1 holds
nucleosome together.

Histone H1
helps ‘clamp’ the DNA onto
the nucleosome
participates in higher-order
chromatin folding
 Histone octamer crystal structure
H2a, H2b, H3 & H4 dimer Histone tails

DNA
30 nm chromatin fiber
The 30nm fiber or solenoid
 DNA domains
Contain ≈100kbp
loops, anchored to
nuclear scaffold by
AT-rich sequences.
05_24_Chromatin pack.jpg
 Number of chromosomes per cell
Humans have 46 chromosomes
Typically cells are diploid and have 23
pairs
44 of them are called autosomes and
are numbered 1 through 22.
Chromosome 1 is the longest, 22 is the
shortest.
The other 2 chromosomes are the sex
chromosomes: the X and Y
chromosomes.
Males have and X and a Y; females
have 2 Xs.
Prokaryotic cell
division
or binary fission
Single circular DNA is
replicated
Bacterium grows to
twice normal size
Cell divides into two
daughter cells
Each daughter cell with
an identical copy of
DNA
Rapid process, taking as
little as 20 minutes.
 Eukaryotic Cell Cycle
Sequence of events from the time a cell is formed, until the cell
divides once again.
Before cell division, the cell must:
Copy genetic material (DNA)
Roughly double its cytoplasm
Synthesize organelles, membranes, proteins, and other
molecules.
Cell cycle is divided into two main phases:
Interphase: the stage between cell divisions
Mitotic Phase: the stage when cell is dividing
05_17_cell cycle.jpg
Cell Cycle: ordered sequence of events in which a cell
duplicates its chromosomes and divides into two.

Significance: loss of the cell cycle control ultimately leads to

cancer

The Nobel Prize in Physiology or Medicine for 2001 was

awarded to Leland H. Hartwell, R. Timothy (Tim) Hunt and
Paul M. Nurse for their discoveries of “key regulators of the
cell cycle”
The Life Cycle of a Eukaryotic Cell:
Interphase: Time between cell divisions.
Most cells spend about 90% of their time in interphase.
Cells actively synthesize materials they need to grow.
Chromosomes are duplicated.
Interphase can be divided into three stages:
1. G1 phase: Just after cell division.
Cell grows in size, increases number of organelles, and makes
proteins needed for DNA synthesis.
2. S phase: DNA replication.
Single chromosomes are duplicated so they contain two sister
chromatids.
3. G2 phase: Just before cell division.
Protein synthesis increases in preparation for cell division.
 The Cell Cycle

G1
“Gap” - cell growth before
DNA replication
S
“Synthesis” - DNA
replication
G2
“Second Gap” - preparation
for division
05_18_mitosis.jpg
 Chromosomes
• Chromosomes exist in 2 different states:
• Before replication, chromosomes have one chromatid.
• After replication, chromosomes have 2 sister chromatids, held together at
the centromere.
• Each chromatid is one piece of DNA with its supporting proteins.
• In mitosis, the two chromatids of each chromosome separate, with each
chromatid going into a daughter cell.
 Centromere

Contains an unique sequence, usually (but not

always) at the midpoint of the chromosome.

The attachment site for spindle fibers in MITOSIS.

spindle fiber
 Chromosome Structure
Euchromatin - comprises most of the
genome, transcriptionally active,

Heterochromatin - highly condensed

inactive chromatin located at centromeres
and telomeres

Centromere - attachment point for sister

chromatids and spindle fibers Metaphase chromosome

Telomere - Telomeres at ends of

chromosome are TTAGGG sequence
repeats (500-3000 times), maintained by
telomerases. Telomere shortening is
important in ageing.
 Mitosis is Used for Growth and Repair
Mitosis produces 2 identical cells with the same number of chromosomes.

DNA duplicates and there is a single division, giving each cell 23 pairs of
chromosomes.

Some tissues are be repaired often: lining of gut, white blood cells, skin- cells
have a lifespan of only a few days.

Other cells do not divide at all after birth: nerve and muscle.

Red blood cells intermediate with a life-span of ~ 120 days.

DNA duplicates to form 2 sister chromatids.

Chromosomes attach to spindle and separate.

Used for growth, repair and in single-cell organisms, reproduction.