INTRODUCTION TO MOLECULAR BIOLOGY
SALWA HASSAN TEAMA
Molecular biology; the study of gene structure and functions at the
molecular level to understand the molecular basis of hereditary,
genetic variation,….. and the expression patterns of genes.
The Molecular biology study the flow of information from DNA to
RNA to protein.
The Molecular biology field overlaps with other areas, particularly
genetics and biochemistry.
The Molecular biology allows the laboratory to be predictive in
nature; events that occur in the future.
The totality of genetic information within one mature cell of an
Encoded in the DNA (or, for some viruses, RNA).
The diploid genome of the typical human cells contains
approx.7x10⁹ base pairs that are divided into 23 chromosomes.
THE GENOME DATABASE
Organized in six major organism groups:
THREE DOMAIN OF LIFE
Eukaryotes are generally more advanced than prokaryotes
Eukaryotic cells are found in animals, plants, fungi and protists
Cell with a true nucleus, where the genetic material is surrounded
by a membrane;
Eukaryotic genome is more complex than that of prokaryotes and
distributed among multiple chromosomes;
Eukaryotic DNA is linear;
Eukaryotic DNA is complexed with proteins called histones;
Numerous membrane-bound organelles;
Complex internal structure;
Cell division by mitosis.
Prokaryotic Cell; Unicellular organisms, found in all
environments. These include bacteria and archaea;
Without a nucleus; no nuclear membrane (genetic material
dispersed throughout the cytoplasm;
No membrane-bound organelles;
Cell contains only one circular DNA molecule contained in the
DNA is naked (no histone);
Simple internal structure; and
Cell division by simple binary fission.
Archaea is prokaryotes;
organisms without nucleus
but some aspects of their
molecular biology are
more similar to those of
Modified from Strachan and Read . Source: http://geneticssuite.net/node/33
Jane Ades. Source: National Human Genome Research Institute
In normal human cell DNA contained in the nucleus, arranged in 23
pairs of chromosomes.
The Chromosome: the storage place for all genetic information, the
number of chromosomes varies from one species to another.
Human chromosome: Twenty three pairs of chromosomes: Twenty
two pairs of chromosomes (autosomes); One pair (sex chromosome)
determines the sex of individual (female) (XX) or (male) (XY).
Source: National Human Genome Research Institute
Most of the genes consist of;
short coding sequences or
exons are interrupted by a
longer intervening noncoding
sequence or introns; although
a few genes in the human
genome have no introns.
The basic units of inheritance.
It is a segment within a very long strand of DNA with specific
instruction for the production of one specific protein.
Located on chromosome on it's place or locus.
Allele: A variant of the DNA sequence at a given locus. Each
allele inherited from a different parent.
CENTRAL DOGMA OF MOLECULAR BIOLOGY
DNA molecules serve as templates for either complementary DNA strands during the
process of replication or complementary RNA during the process of transcription.
RNA molecules serve as a template for ordering amino acids by ribosomes during
GENERAL STRUCTURE OF NUCLEIC ACID
DNA and RNA are long chain polymers of small compounds called
DNA: Four different types of nucleotides differ in nitrogenous base:
A is for adenine; G is for guanine; C is for cytosine and T is for
thymine. RNA: thymine base replaced by uracil base.
Nitrogenous base: these bases are classified based on their chemical
structures into two groups: Purine: Double ringed structure
(Adenine and Guanine) and Pyrimidine: Single ring structures
(cytosine, thymine or uracil).
Each nucleotide is composed of a nitrogen base; five carbon
sugar (ribose in RNA or deoxyribose in DNA) and a phosphate
group. The phosphate joins the sugars in a DNA or RNA chain
through their 5' - and 3' - hydroxyl group by phosphodiester
DEOXYRIBONUCLEIC ACID (DNA)
The gigantic molecule which is used to encode genetic
information for all life on Earth.
The genetic material of all cellular organisms and most viruses.
DNA molecule is incredibly long. It is tightly packed.
DNA forms: A Form, B Form and Z Form,…B-DNA is the
naturally occurring form of DNA inside cells.
DNA DOUBLE HELIX
The structure of DNA was described by British Scientists
Watson and Crick as long double helix shaped structure.
Linked as a twisted ladder.
The curving sides of the ladder represent the sugar-
phosphate backbone of the two DNA strands; the rungs
are the base pairs.
Possess antiparallel polarity.
Stabilized by hydrogen bonds between the bases.
Within the structure of DNA, the number of thymine is always equal
to the number of adenine, and the number of cytosine is always equal
The bases pair in a specific way: Adenine A with thymine T (two
hydrogen bonds) and guanine G with cytosine C (three hydrogen
These forms are distinguished by:
The number of base pair
The angle between each base
The helical diameter of the
Right or left hand direction of
double helix B Form
The nucleus of eukaryotic cells contains DNA, histones, and non-
histone proteins. These three elements combine to form the
chromatin fibers of the nucleus.
Four histones, H2A, H2B, H3 and H4, combine by twos to form the
core particle of nucleosomes, the basic structural units of chromatin,
which have a core of histones around which the DNA winds.
The remaining histone, H1, ties DNA to the nucleosome and possibly
also sets up linkages that wind nucleosome chains into chromatin
DNA The molecule of life carry all the instruction that provide
almost all information necessary for a living organism to grow
DNA responsible for preserving, copying and transmitting
information within cells and from generation to generation..
RNA is a polymer of purine and pyrimidine ribonucleotides linked
together by phosphodiester bridgs analogous to those in DNA. RNA
possesses several specific difference:
RNA: Sugar moiety is ribose rather than the 2' deoxyribose of the
Pyrimidine components contains uracil instead of thymine in DNA.
RNA exists as a single strand, however, the single strand is capable
of folding back on itself like hairpin thus acquiring double strand
Since RNA molecule exist as single strand, its guanine content does
not necessarily equal to its uracil content.
THREE MAJOR CLASSES OF RNA:
Transfer (tRNA) and
Minor classes of RNA include:
Small nuclear RNA,
Small nucleolar RNA,
Transcripts of structural genes that encode all the information
necessary for the synthesis of a polypeptide/s of protein.
Intermediate carrier of genetic information; deliver genetic
information to the cytoplasm where protein synthesis takes place.
The 5' terminus is capped by 7 methyguanosine triphosphate.
Synthesis of the poly (A) tail involves cleavage of its 3' end and
then the addition of about 200 adenine residues.
Small molecules consisting approx. 70-80 nucleotides.
All tRNAs share a common secondary structure represented
by a coverleaf.
They have four- base paired stems defining three stem loops
(the D loop, anticodon loop, and T loop) and the acceptor
stem to which amino acids are added in the charging step.
tRNA molecules serves as an adaptor for translation of
information in the sequence of the mRNA into specific
The RNA component of the ribosome.
Provide a mechanism for decoding mRNA into amino
acids and interacts with tRNAs during translation by
providing peptidyl transferase activity.
Factory for protein synthesis.
Composed of ribosomal RNA and ribosomal proteins; known as a
Translate messenger RNA (mRNA) to build polypeptide chains using
amino acids delivered by transfer RNA (tRNA).
Most mRNA are translated by
more than one ribosome at a
time; the result, a structure in
which many ribosomes
translate a mRNA in tandem, is
called a polysomes.
THE GENETIC CODE
The purine and pyrimidine bases
of the DNA molecule are the
letters or alphabet of the genetic
Series of codons in part of a
mRNA molecule. Each codon
consists of three nucleotides.
The sequence of codons in the
mRNA defines the primary
structure of the final protein.
The triplet sequence of mRNA that specify certain amino acid.
64 different combination of bases ; 61 of them code for 20 amino acid
(AA); the last 3 codon (UAG,UGA,UAA) don not code for amino acids ,
they are termination codons.
More than on triplet codon specify the same amino acid
They are mainly different in the third base. The base pairing between the
last nuleotide with the corresponding anticodon is not strict this is called
Each codon specifies a particular amino acid, the codon ACG codes for the
amino acid threonine, and only threonine.
Universal: It is the same for all species i.e. plants, animals with the exception of
This means that successive triplets are read in order. Each nucleotide is part
of only one triplet codon.
THE GENETIC CODE
The basic building materials of a cell, made by cell itself; the
final product of most genes.
Chain like polymers of a few or many thousands of amino
Proteins can be composed of one or more polypeptide chains.
FOUR LEVELS OF PROTEIN STRUCTURE
Primary structure: Formed by joining the amino acid sequence into a
Secondary structure: Different conformation that can be taken by the
polypeptide: alpha helix and strands of beta sheet.
Tertiary structure: Result from folding the secondary structure
components of the polypeptide into three-dimensional configuration.
Quaternary structure: complex of several protein molecules or
polypeptide chains, usually called protein subunits, which function as
part of the larger assembly or protein complex.
George Rice. Montana State University.Source: http://serc.carleton.edu/microbelife/research_methods/genomics/replication.html
POST-REPLICATIVE MODIFICATION OF DNA
Methylation; one of the major post- replicative reactions.
Site of methylation of eukaryotic DNA is always on cytosine
residues in CG dinucleotide.
DNA methylation plays an important role for epigenetic gene
regulation in development and disease.
Mitochondria is a membrane enclosed organelle found in most
eukaryotic cells. These organelles range from 1-10 micrometers
(μm) in size.
Mitochondria generates most of the cell's supply of adenosine
Mitochondria is involved in a range of other processes, such as
signaling, cellular differentiation, cell death, as well as the control
of the cell cycle and cell growth.
Mitochondria has been implicated in several human diseases,
including mental disorders, cardiac dysfunction, and may play a
role in the aging process.
Mitochondria has its own DNA.
Human cells have hundreds of mitochondria, each containing a
number of copies of a small circular molecule, mitochondrial
The mitochondrial DNA is only 16 kb in length (less than
0.03 % of the length of the smallest nuclear chromosome) and
encodes only a few dozen genes. Although the products of these
genes function in mitochondria, the majority of proteins
found in mitochondria, in fact, product of nuclear genes.
Mitochondrial genes exhibit exclusively maternal inheritance.
Gene expression process by which a gene product (an RNA or
polypeptide ) is made.
From DNA to Protein
RNA polymerase makes a copy of information in the gene (complementary RNA)
complementary to one strands of DNA.
It occurs on ribosomes, messenger RNA decoded or translated to determine the
sequence of amino acid in the protein being synthesized.
TYPES OF CONTROL IN EUKARYOTES
Transcriptional, prevent transcription, prevent mRNA from being
Posttranscriptional, control mRNA after it has been produced.
Translational, prevent translation; involve protein factors needed for
Posttranslational, after the protein has been produced.
DNA DAMAGE/DNA REPAIR
Salwa Hassan Teama
Nucleic acid fractionation
Polymerase chain reaction
Vector, Molecular cloning
Nucleic acid enzymes
Electrophoretic separation of nucleic acid
• DNA: Southern blotting
• RNA: Northern blotting
• Protein: Western blotting
Molecular cytogenetic analysis
COMMON TOOLS AND TECHNIQUES OF MOLECULAR BIOLOGY
HUMAN GENOME PROJECT
The human genome project is an attempt to sequence
of the 3 billion chemical base pairs that make up
human DNA, store this information in databases,
Improve tools for data analysis, transfer related
technologies to the private sector, and
Address the ethical, legal, and social issues (ELSI)
that may arise from the project.
HUMAN GENOME PROJECT
1990, American geneticists started an ambitious quest to map and
sequence the entire human genome.
1999, the final draft of human chromosome 22.
2000, the final draft of human chromosome 21.
2001, working draft of the whole human genome.
2004, the finished sequence of the euchromatic part of human
FUNCTIONAL GENOMICS AND OTHER TECHNOLOGIES
Genomics: Involves the sequencing of the complete genome, including structural gene,
regulatory sequences and noncoding DNA segments in the chromosome of an organism and
the interpretation of all the structural and functional implications of these sequences and of
many transcripts and proteins the genome encode. Genomic information offers new
therapies and diagnostic methods for treatment of many diseases.
Transcriptomics: is the systematic and quantitative analysis of all the transcript present in a
cell or a tissue under a defined set of conditions (the transcriptome).
Proteomics: is the total set of proteins expressed from the genome of cell via transcriptome.
It is the quantitative study of the proteome.
Metabolomics: is the study of all the small molecules, including metabolic intermediates
(amino acids, nucleotides ,sugars,…) that exist within a cell. The metabolome provides a
senstive indicator of the physiological status of a cell and has potential uses in monitoring
disease and its management.
Source: European Bioinformatics Institute. http://www.ebi.ac.uk/microarray/biology_intro.html
APPLICATION OF MOLECULAR BIOLOGY