Biol 205 Ø 14

Lecture Note # 2

Mr. S. ARCHIE HNE TOOMEY BSc,

MSc.

Bioinformatician & Genomicist

Lecturer:
DEPARTMENT OF BIOLOGICAL SCIENCES
T.J.R. FAULKNER COLLEGE OF SCIENCE & TECHNOLOGY
UNIVERSITY OF LIBERIA
 STRUCTURE AND COMPONENTS OF DNA

 DNA (deoxyribonucleic acid) is a hereditary material commonly found in the nucleus

of a cell. It is also present in mitochondria, which is called mitochondrial DNA

(mtDNA).

 DNA is a polymer of the many mono-deoxy ribonucleotides, covalently linked by 3′-

5′ phosphodiester bonds. It is a double-stranded molecule in which two strands wind

around each other and form a double helix.

 Whereas some viruses like Parvovirus have a single-stranded DNA molecule.

 STRUCTURE AND COMPONENTS OF DNA

 DNA consists of deoxyribose sugar, nitrogenous bases (purine and

pyrimidine), and phosphoric acid. Information is encoded in the DNA as the
sequences of ATGC.

 Adenine (A) pairs with thymine (T) with the double hydrogen bonds,
whereas guanine (G) pairs with cytosine (C) with the triple hydrogen bonds.

 The arrangement of the nucleotides (ATGC) in two strands gives rise to the
spiral structure of DNA, commonly known as the double helix.
STRUCTURE AND COMPONENTS OF DNA
 COMPONENTS OF DNA

• The essential components of DNA are:

• acid (phosphoric acid),

• pentose sugar (deoxyribose sugar),

• and nitrogen bases; purine (adenine and guanine) and pyrimidine

(cytosine and thymine).
COMPONENTS OF DNA
 COMPONENTS OF DNA

 Phosphoric acid: It contains the three monovalent hydroxyl groups and one
divalent oxygen atom linked to the pentavalent phosphorus atom. The

molecular formula of phosphoric acid is H 3PO4.

 Pentose sugar: Deoxyribose sugar is the pentose sugar present in the DNA.
Since it lacks one oxygen atom in carbon-2, it is known as deoxyribose.
Pentose sugar forms the ester with phosphoric acid and forms the 3’-5′
phosphodiester bond.
 COMPONENTS OF DNA

 3′-5′ phosphodiester bonds: Phoshpodiester bond is present between the 5’-hydroxyl

group and the 3’-hydroxyl group of the deoxypentose of the nucleotides. The phosphate group

joins these hydroxyl groups in the adjacent nucleotides. In the DNA, the sequences are

encoded in the 5′ end to the 3′ end of the chain. E.g., 5’-ATGC-3′

 Nitrogenous bases: There are two types of nitrogenous bases: purine and pyrimidines. The
purine derivatives present in the DNA are adenine (A) and guanine (G). The pyrimidine

derivatives present in the DNA are thymine (T) and cytosine ( C). In the case of the RNA,

thymine (T) is absent, which is replaced by the uracil (U).

 BASE-COMPOSITIONS OF DNA (CHARGAFF
RULE)

 The Chargaff rule was given by Erwin Chargaff and his colleagues in the 1940s and
has given the following conclusions:

 The base composition of DNA generally varies from one species to another.

 DNA specimens isolated from the different tissues of the same species have the
same base composition.

 The base composition of DNA in a given species does not change with the
organism’s age, nutritional state, or changing environment.
 BASE-COMPOSITIONS OF DNA (CHARGAFF
RULE)

• The number of adenine is equal to thymine (A=T), and guanine is equal to

cytosine (G=C), i.e., A+G=T+C.

• Proportion of the nitrogenous bases in human and E.coli are:

• Human: A-30.9 T-29.4 G-19.9 C-19.8

• E.coli: A-24.7 T-23.6 G-26.0 C-25.7

 PRIMARY STRUCTURE OF DNA

 The primary structure of DNA consists of the linear sequence of nucleotides

linked together by phosphodiester bonds.

 Nucleotides is composed of three components; nitrogenous bases, 5-

carbon (pentose) sugar, and phosphate groups.
 SECONDARY STRUCTURE OF DNA

 The secondary structure of DNA is a set of interactions between the bases, i.e.,
two linear strands bound to each other by phosphodiester bonds forming the
double helical structure of the DNA.

 The secondary structure is responsible for maintaining the shape of the nucleic
acid.
 TERTIARY STRUCTURE OF DNA

 The tertiary structure of DNA is the most common double helix structure which
includes the 3-forms of the DNA; A, B, and Z form.

 The handedness (left or right) of the DNA, length of helix turn, and the number
of bases per turn are the basis for the different forms.

 It is the location of the atom in the 3-dimensional space.

 TERTIARY STRUCTURE OF DNA

 A-DNA  B-DNA  Z-DNA

 The size of the A-DNA  The size of the B-DNA  The size of the Z-DNA
is about 26 Å. is about 20 Å. is about 18 Å.

 It is a right-handed  It is a right-handed  It is a left-handed

double helix. double helix. double helix.

 It contains 11 base  It contains 10 base  It contains 12 base

pairs per helical turn. pairs per helical turn. pairs per helical turn.
TERTIARY STRUCTURE OF DNA
DOUBLE HELIX: WATSON AND CRICK’S
MODEL

 Watson and Crick’s model of double helical DNA was postulated by James D.
Watson and Francis H.C. Crick in 1953.

 According to this model, the two helical DNA chains are wound around each
other in the same axis of symmetry.
DOUBLE HELIX: WATSON AND CRICK’S
MODEL
 DOUBLE HELIX: WATSON AND CRICK’S
MODEL

 The purine and the pyrimidine bases in both the strands are hydrophobic and stacked
inside the double helix. Deoxyribose and phosphate groups are the backbone of the

DNA outside the double helix, which are hydrophilic.

 When these two helices are wound around each other, two types of grooves are
formed: major groove and the minor groove.

 Major groove: width-12 nm, depth-8.5 nm

 Minor groove: width-6 nm, depth-7.5 nm

 DOUBLE HELIX: WATSON AND CRICK’S
MODEL

 The diameter of the helix is 20 Å (Angstrom). The bases are 3.4 Å apart on the
helix axis. The length of each helical turn is 34 Å. In each of the complete
turns of the double helix, 10 base pairs are present in it.

 The hydrogen bond present in the double helix confers stability in the DNA. There is a
double hydrogen bond between adenine and guanine, whereas triple hydrogen bonds
are present between cytosine and thymine.

 The B-form of DNA (Watson-Crick structure of DNA) is the most stable form of
DNA.
THE DIFFERENCE BETWEEN DOUBLE-
STRANDED DNA AND SINGLE-
STRANDED DNA
 Although double stranded and single stranded DNA has same composition,
these have different strand (single stranded has one and double stranded has
two) aligned in different shapes.

 Likewise, the A/T and G/C ratio also differs. A detailed difference is given
below:
THE DIFFERENCE BETWEEN DOUBLE-
STRANDED DNA AND SINGLE-
STRANDED DNA
 FUNCTIONS OF DNA

 The DNA carries and transfers the genetic material from the parent cell to its
offspring during replication.

 DNA also carries all the genetic codes for synthesizing RNA.

 The RNA then codes proteins essential for the growth, development, and
proper functioning of any cell.

 So, DNA can be termed an instruction manual for cells.

 RNA (RIBONUCLEIC ACID)

 Similar to structure of DNA

○ sugar + phosphate + base

○ sugar is a ribose (instead of deoxyribose)

 Bases: ○ Adenine (A) ○ Guanine (G)○ Cytosine (C)○ Uracil (instead of

Thymine T)

 RNA is single-stranded
 RNA (RIBONUCLEIC ACID)

 ● Messenger mRNA  ● And many others …

○ Represents transcript of a gene from DNA that will be ○ miRNA - gene

translated onto protein (see transcription) expression regulation

 ● Transfer tRNA ○ siRNA - RNA

interference
○ carries amino-acids to ribosomes (see translation)
○ snRNA - splicing
 ● Ribosomal rRNA

○ includes major constituents of ribosomes (see

translation)
 ASSIGNMENT

 Write a term paper by group as will be indicated on the topics below in not less
then ten (10) pages. Prepare not more than 20 PowerPoint slides from the term
paper produced by each group. The assignment will be presented after the
midterm on a stipulated time indicated in the course syllabus.

 Group 1 topics: Phosphorylation, Glycosylation, Ubiquitination, Acetylation,

Methylation and Hydroxylation

 Group 2 topics: Sumoylation, Prenylation, Palmitoylation, Proteolytic

Cleavage, Disulfide Bond Formation and Lipidation
 Definition and Importance of
Genome Organization
 Genome organization refers to the arrangement and structure of DNA
within a cell.

 It is crucial for gene expression, regulation, and overall cellular

function.
 Overview of the Genome

 Composed of DNA, which includes both

coding regions (genes) and non-coding
regions (regulatory elements).

 Genome size varies widely across

organisms; for example, humans have
about 3 billion base pairs.
 Chromatin Structure

 Chromatin is the complex of DNA and

proteins (histones) that forms
chromosomes.

 Two types: euchromatin (active in

transcription) and heterochromatin
(more condensed, less active).
 Nucleosome Formation

 Nucleosomes consist of DNA wrapped around

histone proteins, resembling "beads on a
string."

 Their positioning affects gene accessibility and

expression.
Higher-Order Chromatin Structure

 Chromatin can form loops and domains that

bring distant regions of DNA into proximity,
influencing gene regulation.

 Scaffolding proteins play a role in maintaining

these structures.
Chromosome Structure

 Chromosomes are thread-like structures

composed of chromatin.

 Types include metacentric, acrocentric, and

telocentric based on centromere location.
 Genome Architecture

 Prokaryotic genomes are typically circular, while eukaryotic genomes

are linear and housed within a nucleus.

 Eukaryotic genomes often contain introns and exons, while prokaryotes

usually do not.
 Genomic Regions

 Coding regions (exons) are interspersed with non-coding regions

(introns).

 Functional elements include promoters, enhancers, and silencers that

regulate gene expression.
 Gene Clusters and Operons

 Genes with related functions can be clustered together, often

regulated as a unit (operons in prokaryotes).

 This organization allows for coordinated expression.

 Telomeres and Centromeres

 Telomeres protect chromosome ends from degradation and are

essential for cellular aging.

 Centromeres play a critical role in chromosome segregation during cell

division.
 Genome Mapping Techniques

 Techniques like Fluorescence In Situ Hybridization (FISH) and whole-

genome sequencing help visualize and understand genome structure.
 Comparative Genomics

 Studying genome similarities and differences

across species reveals evolutionary
relationships and functional conservation.
Epigenetic Modifications

 Chemical modifications (e.g., methylation) that do

not change DNA sequence but affect gene
expression.

 These changes can be influenced by environmental

factors and can be heritable.
 Transposable Elements

 DNA sequences that can move within the genome, contributing to

genetic diversity and evolution.

 Types include retrotransposons and DNA transposons.

 Role of Non-Coding RNA

 Non-coding RNAs (like miRNA and lncRNA) play crucial roles in

regulating gene expression and chromatin structure.
 Genome Evolution

 Mechanisms like duplication, deletion,

and rearrangement drive genome
evolution.

 Example: Gene duplication can lead to

new functions or specializations.
 Organellar Genomes

 Mitochondrial and chloroplast genomes

are distinct from nuclear genomes and
are circular in structure.

 They provide insights into

endosymbiotic theory and evolution.
 Human Genome Organization

 The human genome consists of 23 pairs of chromosomes, with a complex

structure that includes a variety of functional elements.

 The Human Genome Project has provided valuable insights into genetic
diseases and human biology.
Genome Stability and Repair

 Maintenance of genome integrity is vital; various repair mechanisms

(e.g., base excision repair) correct DNA damage.
 Implications in Disease

 Abnormalities in genome organization can

lead to diseases such as cancer and genetic
disorders.

 Understanding these mechanisms is key to

developing therapies.
 Advances in Genome Research

 New technologies (like CRISPR and single-cell sequencing) are

revolutionizing our understanding of genome organization and
function.

 These advances hold promise for personalized medicine and

biotechnological applications.
 DEFINITION OF DNA REPLICATION
 DNA replication is the biological process by which a cell duplicates its
DNA, ensuring that each daughter cell receives an identical copy of the
genetic material during cell division.

 This process is vital for growth, development, and maintenance of all

living organisms.

 The mechanism of replication is semiconservative, because to each

of the former DNA strands a new complementary strand is
synthesized. The process is also bidirectional since it occurs in
opposite directions.
SCHEME OF SEMICONSERVATIVE
REPLICATION OF DNA
 ENZYMES INVOLVED IN DNA
REPLICATION
 Helicase: Unwinds the DNA double helix, creating two single strands
for replication. Formation of the replication bubble.

 Single-Strand Binding Proteins (SSBPs): Stabilize the unwound

DNA strands to prevent them from re-annealing.

 Topoisomerase: Relieves torsional strain ahead of the replication fork

by cutting and re-joining the DNA strands.

 Primase: Synthesizes a short RNA primer complementary to the DNA

template, providing a starting point for DNA polymerases.
 ENZYMES INVOLVED IN DNA
REPLICATION
 DNA Polymerase: Main enzyme that synthesizes new DNA strands by
adding nucleotides. Different types include:

 DNA Polymerase III (prokaryotes): Primary enzyme for

elongation.

 DNA Polymerase α, δ, ε (eukaryotes): Involved in synthesizing

both leading and lagging strands.

 DNA Ligase: Joins Okazaki fragments on the lagging strand, sealing

nicks in the sugar-phosphate backbone.
 ESSENCE OF DNA REPLICATION
 DNA replication is essential for:

 Genetic Continuity: Ensures that genetic information is accurately passed from

one generation to the next.

 Cell Division: Facilitates cell division processes such as mitosis and meiosis,
allowing growth, development, and tissue repair.

 Genetic Diversity: Allows for mutations, which can lead to variation and
evolution over time.

 The processes of DNA replication in prokaryotes and eukaryotes differ

significantly due to differences in their cellular structures, DNA organization, and
regulatory mechanisms.
 STRANDS AND ORIENTATION OF DNA
REPLICATION
During DNA replication, the two strands of the DNA molecule are:

1.Leading Strand: Orientation: 5' to 3‘, The leading strand is synthesized

continuously in the direction of the replication fork, following the unwinding of the
DNA.

2.Lagging Strand: Orientation: 3' to 5‘, The lagging strand is synthesized

discontinuously in short segments known as Okazaki fragments. This occurs in
the opposite direction to the movement of the replication fork. Each Okazaki
fragment is synthesized from 5' to 3' but overall is assembled in the 3' to 5'
direction relative to the template strand.
SCHEME OF DNA REPLICATION
 STEPS IN DNA REPLICATION
 Prokaryotic DNA Replication:

1.Initiation:

1.Begins at the origin of replication (oriC).

2.Helicase unwinds the DNA; SSBPs stabilize the strands.

2.Primer Synthesis:

1.Primase synthesizes an RNA primer complementary to the DNA

template.
 STEPS IN DNA REPLICATION
3. Elongation:

1.DNA Polymerase III adds nucleotides in a 5' to 3' direction.

2.Leading strand is synthesized continuously, while the lagging

strand is synthesized in Okazaki fragments.

4. Termination:

3.Replication forks meet at the termination site.

4.DNA ligase joins Okazaki fragments, completing the new DNA

strand.
 STEPS IN DNA REPLICATION
 Eukaryotic DNA Replication:
1. Initiation:
1. Multiple origins of replication are established along linear
chromosomes.
2. The Minichromosome Maintenance (MCM) complex acts as
helicase, unwinding the DNA.
2. Primer Synthesis:
3. Primase synthesizes RNA primers at various locations on both
strands.
 STEPS IN DNA REPLICATION
3. Elongation:
1. DNA Polymerase δ synthesizes the lagging strand, while DNA
Polymerase ε synthesizes the leading strand.
2. Okazaki fragments are formed on the lagging strand and are later
joined by DNA ligase.

4. Termination:
3. Replication forks converge or reach specific termination
sequences.
4. Telomeres are replicated by the enzyme telomerase to prevent
loss of genetic material.
 SPEED AND ACCURACY
 Prokaryotic replication is relatively fast, with rates of up to 1000
nucleotides per second.

 The fidelity of replication is maintained by proofreading mechanisms of

DNA polymerases.
 Eukaryotic replication is slower than prokaryotic, averaging about 50-
100 nucleotides per second.
 Eukaryotic cells also have more extensive proofreading and repair
mechanisms to maintain high fidelity.
 KEY DIFFERENCES
 Location: Prokaryotic replication occurs in the cytoplasm; eukaryotic
replication occurs in the nucleus.

 Origins: Prokaryotes have a single origin; eukaryotes have multiple

origins.

 Chromosome Structure: Prokaryotic DNA is circular; eukaryotic DNA

is linear and associated with histones.

 Enzymes: Different DNA polymerases are involved in prokaryotic and

eukaryotic systems.
 KEY DIFFERENCES
 Telomere Replication
 Prokaryotes:

 Telomeres: Not applicable, as prokaryotic DNA is circular and does not

have telomeres.

 Eukaryotes:

 Telomeres: Telomeres are specialized structures at the ends of linear

chromosomes that protect against degradation and loss of genetic
material. The enzyme telomerase helps to maintain telomere length.
Manual practical demonstration of DNA Replication on the marker board!