Molecular basis of

inheritance

Dr Rana El Hajj
[email protected]
Molecular biology
 Is the branch of biology that deals with the molecular
basis of biological activity.
 This field overlaps with other areas of biology and
chemistry, particularly genetics and biochemistry.
 Molecular biology chiefly concerns itself with
understanding the interactions between the various
systems of a cell, including the interactions between the
different types of DNA, RNA and protein biosynthesis
as well as learning how these interactions are regulated.
 The field of molecular biology studies macromolecules and
the macromolecular mechanisms found in living things, such
as the molecular nature of the gene and its mechanisms of
gene replication, mutation, and expression.
 The genome
 The totality of genetic
information that is
encoded in the DNA or
RNA for some viruses.
All living things are grouped into
three domains:
Eukaryotes
Prokaryotes
Archaea
Eukaryotic cell
A eukaryotic cell is generally more advanced than a
prokaryotic cell.
 has a nucleus, which is separated from the rest of the
cell by a membrane. The nucleus contains
chromosomes, which are the carrier of the genetic
material.
 The genetic material is distributed among multiple
chromosomes.
 Eukaryotic DNA is linear and complexed with
proteins called histones.
 Components of the nucleus of eukaryotic cells

• Nuclear envelope: a highly regulated membrane barrier that separates

the nucleus from the cytoplasm in eukaryotic cells. It contains a large
number of different proteins that have been implicated in chromatin
organization and gene regulation.
• Nucleoplasm: stores DNA and facilitate an isolated environment
where controlled transcription and gene regulation is enabled. The
nucleoplasm contains several non-membrane bound substructures,
such as nuclear bodies.
• Nucleolus: concerned with producing and assembling the
cell's ribosomes. Following assembly, ribosomes are transported to
the cell cytoplasm where they serve as the sites for protein synthesis.
• Nuclear pores: large complex of proteins that allows small
molecules and ions to freely pass, or diffuse, into or out of the
nucleus.
Prokaryotic cell
 Prokaryotes are single-celled
organisms
 Without nucleus, no nuclear
membrane.
 DNA is naked, without
histones,
 Archaea are prokaryotes
(without nucleus) but some
aspects similar to
Eukaryotes.
 Deoxyribonucleic acid (DNA)
 The genetic instructions used in the
development and functioning of all
known living organisms and some
viruses.
 Deoxyribonucleic acid is a molecule
composed of two polynucleotide
chains that coil around each other to
form a double helix carrying genetic
instructions for the development,
functioning, growth and reproduction
of all known organisms and many
viruses.
 The main role of DNA
molecule is the long-term storage of information.
 DNA is often compared to a set of blueprints or a recipe,
or a code, since it contains the instructions needed to
construct other components of cells, such as proteins and
RNA molecules.
The chromosome
 The storage placeof
all genetic
information.
 The number of
chromosomevaries
from one speciesto
another.
The genes
 The DNA segments
that carry this genetic
information are called
genes.
Building Blocks - Nucleotides
 A nucleotide is composed of three parts: sugar (
Ribose in RNA and Deoxy ribose in DNA), base and
phosphate group. If all phosphate groups are
removed, a nucleotide becomes anucleoside.
 The four bases found in DNAare:
 Adenine (A),
 Cytosine (C),
 Guanine (G) and
 Thymine (T).
 A fifth pyrimidine base, called uracil (U), usually takes the
place of thymine in RNA and differs from thymine by
lacking a methyl group on its ring.
 These bases are classified
into two types; adenine and
guanine are fused five- and
six-membered heterocyclic
compounds called purines,
 while cytosine and thymine
are six-membered rings
called pyrimidines.
• In living organisms, DNA does not usually exist as a single
molecule, but instead as a pair of molecules that are held tightly
together. These two long strands have the shape of a double
helix.

• In a double helix the direction of the nucleotides in one strand

is opposite to their direction in the other strand: the strands are
antiparallels with asymmetric ends.

• The asymmetric ends of DNA strands are called the 5′ and 3′

ends, with the 5' end having a terminal phosphate group and
the 3' end a terminal hydroxyl group.
 Base pairing
Each type of base on one strand forms a bond with
just one type of base on the other strand. This is called
complementary base pairing. Here, purines form
hydrogen bonds to pyrimidines, with A bonding only
to T, and C bonding only to G.

This arrangement of two nucleotides binding together

across the double helix is called a base pair. As
hydrogen bonds are not covalent, they can be
broken and rejoined relatively easily.
• Due to the specific base pairing, DNA's two strands are
complementary to each other. Hence, the nucleotide sequence
of one strand determines the sequence of another strand. For
example, the sequence of the two strands can be written as
• 5' -ACT- 3'
• 3' -TGA- 5'
• Note that they obey the (A:T) and (C:G) pairing rule. If we
know the sequence of one strand, we can deduce the sequence
of another strand. For this reason, a DNA database needs to
store only the sequence of one strand. By convention, the
sequence in a DNA database refers to the sequence of the 5' to
3' strand (left to right).
Sense and antisense
A DNA sequence is called "sense" if its sequence is the
same as that of a messenger RNA copy that is translated
into protein. The sequence on the opposite strand is called
the "antisense" sequence.
 Supercoiling
DNA can be twisted like a rope in a process called
DNA supercoiling. With DNA in its "relaxed" state, a
strand usually circles the axis of the double helix
once every 10.4 base pairs.
If the DNA is twisted in the direction of the helix
(counterclockwise), this is positive supercoiling,
and the bases are held more tightly together.
If they are twisted in the opposite direction, this is
negative supercoiling, and the bases come apart
more easily.
In nature, most DNA has slight negative supercoiling
that is introduced by enzymes called
topoisomerases.
• Negative supercoiling has an important biological function of facilitating local-
and global-strand separation of DNA molecules such as these occurring during
transcription and replication, respectively.
• Negative supercoiling would be advantageous in replication because it is easier to unwind
whereas positive supercoiling is more condensed and would make separation difficult.
Topoisomerases unwind helix to do DNA transcription and DNA replication.
DNA binding proteins
 Interactions with proteins

All the functions of DNA depend on interactions with

proteins. These protein interactions can be non-specific, or
the protein can bind specifically to a single DNA
sequence. Enzymes can also bind to DNA for example the
polymerases that copy the DNA sequence in transcription
and DNA replication.
• DNA-binding proteins
Within chromosomes, DNA is held in complexes with
structural proteins. These proteins organize the DNA into a
compact structure called chromatin. In eukaryotes this
structure involves DNA binding to a complex of small basic
proteins called histones, while in prokaryotes multiple types
of proteins are involved.
The histones form a disk-shaped complex called a
nucleosome. These non- specific interactions are formed
through basic residues in the histones making ionic bonds to
the acidic sugar- phosphate backbone of the DNA.
A nucleosome is the basic structural unit of DNA packaging in eukaryotes.
The structure of a nucleosome consists of a segment of DNA wound
around eight histone proteins
 Chromatin
Chromatin is the complex combination of DNA and
protein that makes up chromosomes. It is found inside
the nuclei of eukaryotic cells. The major components of
chromatin are DNA and histone proteins. The functions of
chromatin are to package DNA into a smaller volume to
fit in the cell.
• Chromatin is the substance which becomes visible
chromosomes during cell division. Its basic unit is
nucleosome, composed of 146 bp DNA and eight histone
proteins. The structure of chromatin is dynamically
changing, at least in part, depending on the need of
transcription. In the metaphase of cell division, the
chromatin is condensed into the visible chromosome. At
other times, the chromatin is less condensed.
Scaffold:
regions of DNA
matrix
attachment
regions
• Histones are the proteins closely associated with DNA
molecules.
• The function of histones is:
1- they play a role in the structure of chromatin
2- they play important roles in the regulation of gene
expression.

Five types of histones have been identified: H1 (or H5),

H2A, H2B, H3 and H4.
• H1 and its homologous protein H5 are involved in
higher-order structures of chromatin. The other four
types of histones associate with DNA to form
nucleosomes.
 Histones (H1, H2A, H2B, H3, H4, and H5) organized into
two super classes as follows: Core histones – H2A, H2B,
H3 and H4 and linker histones – H1 and H5.
 Histones contain a high proportion of basic amino acids
(arginine and lysine) that facilitate binding to the
negatively charged DNA molecule.

Linker histones bind to the

DNA that enters and exits
the nucleosome and
facilitate the shift in equi-
librium of chromatin
towards more condensed,
higher order forms
 Two of each of the core histones (H2A, H2B, H3 and H4)
assemble to form one nucleosome core particle by
wrapping 146 base pairs of DNA around the protein spool
in 1.65 left-handed super-helical turn. The linker histone
H1 binds the nucleosome and the entry and exit sites of
the DNA, thus locking the DNA into place and allowing
the formation of higher order structure.
 Chromosomes
 A chromosome is an organized structure of DNA and
protein that is found in cells. It is a single piece of
coiled DNA containing many genes, regulatory
elements and other nucleotide sequences.
Chromosomes also contain DNA-bound proteins,
which serve to package the DNA and control its
functions.
• Chromosomes in prokaryotes

The prokaryotes – bacteria and archaea – typically have a

single circular chromosome, but many variations do
exist. Most bacteria have a single circular chromosome
that can range in size from only 160,000 base pairs in the
endosymbiotic bacterium Candidatus Carsonella ruddii, to
12,200,000 base pairs in the soil-dwelling bacterium
Sorangium cellulosum. Spirochaetes of the genus Borrelia
are a notable exception to this arrangement, with bacteria
such as Borrelia burgdorferi, containing a single linear
chromosome.
 Overview of Gene Expression
 An organism may contain many types of somatic cells,
each with distinct shape and function. However, they all
have the same genome. The genes in a genome do not
have any effect on cellular functions until they are
"expressed". Different types of cells express different sets
of genes, thereby exhibiting various shapes and functions.
Essential steps involved in the expression of
the genes.
 Gene expression
Is the process by which information from a gene is
used in the synthesis of a functional gene product. These
products are often proteins, but in non-protein coding
genes such as ribosomal RNA (rRNA), transfer RNA
(tRNA) or small nuclear RNA (snRNA) genes, the
product is a functional RNA.
Steps of gene expression
Several steps in the gene expression
process may be modulated, including
 Transcription
 RNA splicing
 Translation
 Post-translational modification of a
protein.
Transcription
A DNA strand is used as a template to synthesize a
complementary RNA strand, which is called the primary
transcript.
Schematic illustration of transcription. (a) DNA before transcription. (b)
During transcription, the DNA should unwind so that one of its strand can
be used as template to synthesize a complementary RNA.
 RNA splicing

RNA splicing, is a form of RNA processing in which a newly made precursor messenger RNA
(pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). During splicing,
introns (non-coding regions) are removed and exons (coding regions) are joined together.

The poly-A tail makes the RNA molecule more stable and prevents its degradation. Additionally,
the poly-A tail allows the mature messenger RNA molecule to be exported from the nucleus
and translated into a protein by ribosomes in the cytoplasm.
 Translation

Translation is the process in which ribosomes in the cytoplasm or endoplasmic

reticulum synthesize proteins after the process of transcription of DNA to RNA
in the cell's nucleus.
Post-translational modification PTM

Protein post-translational modifications increase the

functional diversity of the proteome by the covalent addition
of functional groups or proteins, proteolytic cleavage of
regulatory subunits, or degradation of entire proteins.