Structure of DNA and RNA

Part 1:
DNA Structure
(Deoxyribonucleic acid = DNA)
Formation of nucleotide
The bases of the DNA
Naming Bases, Nucleosides, Nucleotides
DNA is composed of polynucleotide chains
- DNA is composed of two polynucleotide chains
twisted around each other in the form of a double
helix;
- The sugar-phosphate backbones of the
polynucleotide chains coil around the outside of the
helix, and the nitrogenous bases (G, C, A, T) point
toward the center;
- Two polynucleotide chains (DNA strands) are held
together by hydrogen bonds between the paired
bases;
- Two DNA strands run antiparallel to each other in
the DNA molecule
Sugar-Phosphate Backbone of DNA
- Phosphodiester linkage: the phosphoryl group
between the two nucleotide has one sugar esterified
to it through a 3-hydroxyl and a second sugar
esterified to it through a 5-hydroxyl.
- Phosphodiester linkages create the repeating, that
is sugar-phosphate backbone of the
polynucleotide chain.
- DNA chains have a free 5-phosphate at one end
and free 3-hydroxyl at the other end. The
convention is to write DNA sequences from the 5
end to the 3-end
Base pairs of DNA
1
6
3
4
1
2
6
3
4
2
DNA is double helix: Watson-Crick model (1953)
James D. Watson and Francis H. Crick
(1953)
The double-helical structure of DNA
was built based on Chargaffs rules
and Franklin and Wilkins X-ray
diffraction studies.
The key features of DNA structure
Complementary base pairing:
- G pairs with C by forming three hydrogen
bonds
- A pairs with T by forming two hydrogen
bonds
- Every base pair consists of one purine (G
or A) and one pyrimidine (C or T)
- It is a double-stranded helix
- It has a uniform diameter
- It is right-handed (It twists to the right)
- It is antiparallel (the two strand run in opposite
directions)
- The sugar-phosphate backbones of the
polynucleotide chains coil around the outside of
the helix, and the nitrogenous bases point toward
the center
The helical structure of DNA
The double helix has minor and major grooves
Nonpolar hydrogen
Hydrogen bond acceptor
Hydrogen bond donor
Methyl group
-The major groove is rich in
chemical information.
- Chemical groups in the
major groove specifies the
identity of the base pairs.
These patterns are important
because they allow proteins
recognize and bind to DNA
The double helix exits in multiple conformations
10 bases/ helical turn
11 bases/ helical turn
Left-handed helix
Some DNA molecules are circles
The chromosomes of eukaryotic cells each contain a single (extremely long) DNA
molecule. However, most bacterial chromosomes are circular.
Circular DNA
Many bacteria have small autonomously replicating genetic elements know as
plasmid, which are generally circular DNA molecules.
Topological states of covalently closed, circular DNA
Mitochondrial DNA
Summary: DNA structure
Part 2:
RNA Structure
(Ribonucleic acid = RNA)
Ribose is five-carbon sugar (pentose) in RNA
The bases of the RNA
in DNA
RNA contains Ribose and Uracil and usually
single-stranded
RNA chains fold back on themselves to form local
regions of double helix similar to A-form DNA
Double helical characteristics of RNA:
various stem-loop structures
Hairpin
Bulge
Loop
Pseudoknot: The pseudoknot structure is formed by base pairing
between noncontiguous complementary sequences
Base pairs of RNA
G:U
Non-Watson-Crick base pair
RNA molecules can form intramolecular base
pairs and fold into specific structures
Several types of RNA are produced in cells
tRNA
mRNA
rRNA
Some RNAs are enzymes
Summary: RNA structure
Question 1:
One strand of DNA has the sequence 5-ATTCCG-3. The
complementary strand for this is

a) 5- TAAGGC-3
b) 5-ATTCCG-3
c) 5-ACCTTA-3
d) 5-CGGAAT-3
e) 5-GCCTTA-3
Question 2:
In human DNA, 30% of the nucleotides are
adenine. What are the percentages of the other
nucleotides?
Chromosome, Chromatin and the
Nucleosome
Packing of DNA into chromosomes
-A human cell contains: 3x 10
9
bp/ haploid
set of chromosomes
- The thickness of each base pair: 3.4
- Total length of DNA: 10
10
= 1 m/
haploid set of chromosomes
- DNA length: 2 m/ diploid cell
- Diameter of human cell nucleus: 10-15 m

DNA must be compacted
DNA packs into chromosomes
Chromosome can be circular or linear
Comparison of typical prokaryotic and
eukaryotic cells
-Prokaryotic cells typically have only
one complete copy of their chromosome
that is packed in a structure called
nucleoid.
- Prokaryotes also carry one or more
smaller independent circular DNAs,
called plasmids.

- The majority of eukaryotic cells are
diploid (contain 2 copies of each
chromosome)
- Two copies of a given chromosome are
called homologs
- Eukaryotic chromosomes are always
contained within a membrane- bound
organell called the nucleus
Human chromosomes
The chromosomes as visualized as they
originally spilled from the lysed cell
The same chromosomes artificially lined
up in order
- A display of the full set of 46 human chromosomes is called the human karyotype.
- The homologous chromosomes are numbered and arranged in pairs .
- The only non-homologous chromosome pair is the sex chromosome in male, where a
Y chromosome is inherited from the father and an X chromosome from the mother.
Genome size is related to the complexity of the organism
Species Genome size (Mb) Approximate
number of genes
Gene density
(genes/ Mb)
PROKARYOTES (bacteria)
Mycoplasma genitalium 0.58 500 860
Streptococus pneumonia 2.2 2,300 1,600
Escherichia coli 4.6 4,400 950
EUKARYOTES
Fungi: Saccharomyces cerevisiae 12 5,800 480
Invertebrates: Caenorhabditis elegans 97 19,000 200
Invertebrates: Drosophila melanogaster 180 13,700 80
Vertebrate: Homo sapiens 2,900 27,000 9.3
Vertebrate: Mus musculus 2,500 29,000 12
Plants: Arabidopsis thaliana 125 25,500 200
Plants: Oryza sativa (rice) 430 >45,000 >100
* Genome: the whole of the genetic information of an organism (one haploid set
of chromosomes in eukaryotes.
* Genome size: The length of DNA associated with one haploid complement of
chromosome
More complex organisms have decreased gene density
-Increases in gene size and increases in the DNA between genes, called
intergenic sequences.
- Individual genes are longer because of two reasons: 1) increase in regionss of
DNA required to direct and regulate transcription, called regulatory sequenes;
2) protein-encoding genes in eukaryotes frequently have discontinuous protein-
coding regions. These interspersed non-protein-encoding regions is called
introns.
Species Gene density
(genes/ Mb)
Average number of
introns per gene
Percentage of DNA
that is repetive
PROKARYOTES (bacteria)
Escherichia coli 950 0 <1
EUKARYOTES
Fungi: Saccharomyces cerevisiae 480 0.04 3.4
Invertebrates: Caenorhabditis elegans 200 5 6.3
Invertebrates: Drosophila melanogaster 80 3 12
Vertebrate: Homo sapiens 9.3 6 46
Contribution of introns and repeated sequences to
different genomes
The organization of genes on a typical vertebrate
chromosome
Replication and segregation of chromosomes occur
through cell cycle
During interphase chromosomes are replicated, and during mitosis
they become highly condensed and then are separated and distributed
to the two daughter nuclei. The highly condensed chromosomes in a
dividing cell are known as mitotic chromosomes
Different levels of chromosome structure can be observed
by microscopy
Interphase M phase
Eukaryotic chromosomes require centromeres, telomere, and
origins of replication to be maintained during cell division
Origins of replication
- Origins of replication are the
sites at which DNA replication
machinery assembles to initiate
replication.
-Each chromosome has multiple
origins of replication. They are
found some 30-40 kb apart
throughout the length of each
eukaryotic chromosome.
- Prokaryotic chromosomes
typically have only single site of
replication initiation.
- Origins of replication are found
in non-coding reagions.
Centromeres are requires for the correct segregation of
chromosomes after DNA replication
- The primary motif comprising the
heterochromatin of primate
centromeres is the satellite DNA,
which consists of tandem array of a
171bp repeating unit.
- Kinetochore: a specialized assembly
of proteins that bind to centromere and
also attach to microtubules growing
out from centromeres during mitosis.
- The kinetochore interacts with the
machinery that pulls the daughter
chromosomes away from one another
and into the two daughter cells
- Each chromosome has one and only
one centromere
Centromere size and composition varies dramatically between
different organisms
Telomeres seal the end of chromosomes
- Telomeres are located at the two ends of
chromosomes. Telomeres are bound by a number of
proteins
- Telomeric proteins distinguish the natural ends of
the chromosome from sites of chromosome
breakage and other DNA breaks in the cell.
- Telomeres act as a specialized origin of replication
that allows the cell to replicate the ends of
chromosomes. Telomeres facilitate end replication
through the recruitment of an unusual DNA
polymerase, called Telomerase.
- Most telomeres have a simple repeating sequences
that varies from organism to organism. This repeat
is typically a short TG-rich repeat.
The repeat sequence (from human cell)
The eukaryotic mitotic cell cycle
Prepare for cell division
Prepare for chromosome
segregation
S phase
- DNA synthesis occurs during the S phase resulting in the duplication of
chromosome. The duplicated pair is called sister chromatids.
- Sister chromatids are held together after duplication through the action of a
molecule called cohensin. The process that holds them together is called sister
chromatid cohension
M phase
- Each pair of sister chromatids is bound to a structure called the mitotic spindle. The
structure is composed of long protein fibers called microtubules that are attached to one of
the two microtubule organizing centers. Chromarid attachment is mediated by the
kinetochore assembled at each centromere.
- The cohension between the chromatids is dissolved (cohensin cleavege)
- Sister chromatid separation: the chromatids are rapidly pulled toward opposite poles of
the mitotic spindle.
Mitosis maintains the
parental chromosome
number
Meiosis reduces the
parental chromosome
number
Nucleosomes are the building blocks of chromosomes
-The nucleosome composed of a core of 8 histone
proteins (histone octamer)- two molecules each of
histone H2A, H2B, H3, H4- and the DNA
warapped around them.
- The DNA between each nucleosome is called
linker DNA (20-60 bp).
- the DNA most tightly associated with the
nucleosome is called core DNA (146 bp)
Histones are positively-charged proteins
Structure of core histones
- A conserved region found in every core
histone , called the histone-fold domain.
- Histone fold is composed of three
helical regions separated by two short
unstructured loops (fig. B)
- The core histonea each have an N-terminal
extension, called N-terminal tail because
it lacks a defined structure and is accessible
within the intact nucleosome.
The assembly of a nucleosome
- H3 and H4 histones first form
heterodimers that then come together to
form a tetramer with two molecules
each of H3 and H4.
- H2A and h2B form heterodimers
- H3-H4 tetramer binds to DNA, then
two H2A-H2B dimers join the H3-H4-
DNA complex to form final nuleosome
The structure of a nucleosome
- The nucleosome has an approximately two-fold axis of symetry, called dyad axis.
- Of the 146 bp of DNA included in the structure, the histion fold region of H3-H4 tetramer
interact with central 60 bp. The N-terminal region of H3 interacts with the final 13bp at
each end of the bound DNA. The two H2A-H2B dimers each associate with approximately
30bp od DNA on either side of the central 60bp of DNA bound by H3 and H4.
The sites of contact between the histones and the DNA
- AT rich sequences in the minor groove are easier to compress than GC rich sequences,
each histone octamer tends to position itself on the DNA so as to maximize AT rich minor
grooves on the inside of the DNA coil.
- The association of DNA with nucleosome is mediated by large number of of hydrogen
bonds between the histone and the DNA (hydrogen bonds between the proteins and the
oxygen atoms in the phosphate diester backbone near the minor groove of the DNA)
The histone N-terminal tails stabilized DNA wrapping around
the octamer
- H2B and H3 tails emerge from between
the two DNA helices
- H4 and H2A tails emerge from either
the top or bottom face of the
octamer
- Histone tails serve as the grooves of a
screw, directing the DNA to wrap around
the histone octamer disc in a left-handed
manner
Histone H1 induces tighter DNA wrapping around
the nucleosome
Histone H1 interacts with the with the linker DNA between nucleosomes, further
tightening the association of the DNA with the nucleosome.
Nucleosome arrays can form more complex structures:
the 30nm fiber
The histone N-terminal tails are requires for the
formation of of the 30-nm fiber
* The role of N-terminal tail is to stabilize the 30-nm fiber by interacting with
adjacent nucleosomes.
e.g: the H4 terminus make multiple hydrogen bonds with H2A and H2B on the
surface of an adjacent nucleosome
Electron micrographs show chromatin structures
30-nm fiber
Unpacked
chromatin
Electron micrographs show zigzag model
The higher-order structure of chromatin
Nucleosome remodeling complexes
- Nucleosome remodeling complexes:
protein machines that use the energy of
ATP hydrolysis to change the structure
of nuclesomes
- Different nucleosome remodeling
complexes disrupt and re-form
nucleosome, to allow increased access
to the DNA. The DNA-binding protein
could be involved in gene expression,
DNA replication, or DNA repair.
Some prominent types of covalent amino acid side-chain
modifications found on nucleosomal histones
Modification of the N-terminal tails of the histones
alters the function of chromatin
Me
Ac
P
Phosphate group
Acetyl group
Methyl group
Modification of the N-terminal tails of the histones
alters the function of chromatin
Nucleosomes are assembled immediately after
DNA replication
Summary
DNA organized into large structures called chromosome
Chromosome can be either circular or linear
Each chromosome must have one or more origins of replication. In eukaryote cells,
centromere play a critical role in the segregation of chromosomes and telomere help to
protect and replicate the ends of linear chromosomes
The combination of eukaryotic DNA and its associated proteins is referred to as
chromatin. The fundamental unit of chromatin is the nucleosome, which is made up of
two copies each of core histones (H2A, H2B, H3 and H4) and approximatly 147 bp of
DNA
Once DNA is packaged into nucleosome, it has the ability to form more complex
structures. This process id facilitated by H1 histone. A more compact form of chromatin,
30-nm fiber, is readily formed by array of H1-bound nucleosomes
The interaction of the DNA with the histones in nucleosome is dynamic, allowing DNA-
binding proteins intermittent access to the DNA. Nucleosome remodeling complexes
increase the accessibility of DNA incorporated into nucleosomes by increasing the
mobility of nucleosomes.
Modification of the histone N-terminal tails also alters the accessibility of chromatin.
The types of modification include acetylation and methylation of Lys and
phosphorylation of Ser.
Nucleosomes are assembled immediately after the DNA replicated. Histone H3-H4
tetramer and H2A-H2B dimer are randomly distributed to one or the other daughter
molecules. On average, each new DNA molecule receives half old and half new
histones.