Lecture 1 1st Stage/ College of Pharmacy Human Biology

Basics of molecular biology

The central dogma in molecular biology can be described as "DNA makes RNA
and RNA makes protein," a positive statement which was originally termed the
sequence hypothesis by Crick (Figure 1). However, this simplification does not
make it clear that the central dogma as stated by Crick does not preclude the
reverse flow of information from RNA to DNA, only ruling out the flow from pro
tein to RNA or DNA.

Figure 1. The central dogma of molecular biology.

Some characteristics of the human DNA

The proteins coded by the DNA in our cells determine the structures and
functions of the cells. If there is a mutation in the DNA, it can change the
structure and function of the protein, which can have consequences on the
function of the cell and can lead to diseases.

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The backbone of the DNA strand is made from alternating phosphate and sugar
residues (Figure 1). The sugar in DNA is 2-deoxyribose, which is a pentose
(five-carbon) sugar.  The sugars are joined together by phosphate groups that
form phosphodiester bonds between the third and fifth carbon atoms of adjacent
sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In a
double helix the direction of the nucleotides in one strand
is opposite to their direction in the other strand: the strands are antiparallel.
The asymmetric ends of DNA strands are called the 5′ (five prime) and 3′ (three
prime) ends, with the 5′ end having a terminal phosphate group and the 3′ end a
hydroxyl group. One major difference between DNA and RNA is the sugar,
with the 2-  in DNA being  replaced by the alternative pentose sugar ribose in
RNA. The four bases found in DNA are adenine (abbreviated A), cytosine(C),
guanine (G) and thymine (T). These four bases are attached to the
sugar/phosphate to form the complete nucleotide, as shown for adenosine
monophosphate. The nucleobases are classified into two types: the purines, A
and G, being fused five- and six-membered heterocyclic compounds, and the
pyrimidines, the sixmembered rings C and T. A fifth pyrimidine nucleobase,
uracil (U), usually takes the place of thymine in RNA and differs from thymine
by lacking a methyl group
on its ring. Uracil is not usually found in
DNA, occurring only as a breakdown
product of cytosine.

.Figure 2 Structure of the DNA

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In a DNA double helix, each type of nucleobase on one strand bonds with just
one type of nucleobase on the other strand. This is called complementary base
pairing. Here, purines form hydrogen bonds to pyrimidines, with adenine
bonding only to thymine in two hydrogen bonds, and cytosine bonding only to
guanine in three hydrogen bonds. 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. The two strands of DNA in a double helix can therefore be pulled apart
like a zipper, either by a mechanical force or high temperature.
As a result of this complementarity, all the information in the double-stranded
sequence of a DNA helix is duplicated on each strand, which is vital in DNA
replication. Indeed, this reversible and specific interaction between
complementary base pairs is critical for all the functions of DNA in living
organisms.
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. Both sense and antisense
sequences can exist on different parts of the same strand of DNA (i.e. both
strands can contain both sense and antisense sequences).
In human cells DNA is in two compartments. Nuclear DNA, or nuclear
deoxyribonucleic acid (nDNA), is DNA contained within a nucleus of the cell.
Nuclear DNA encodes for the majority of the genome, with DNA located in
mitochondria coding for the rest. Nuclear DNA adheres to Mendelian
inheritance, with information coming from two parents, one male and
one female. The other DNA containing compartment is the mitochondria.
Mitochondria are cellular organelles within eukaryotic cells that convert
chemical energy from food into a form that cells can use, adenosine triphosphate
(ATP).

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In most multicellular organisms, including humans the mitochondrial DNA

(mtDNA) is inherited from the mother (maternally inherited).
Nuclear DNA and mitochondrial DNA differ in many ways. The structure
of nuclear DNA chromosomes is linear with open ends and includes 46
chromosomes containing more than 3 billion nucleotides (3.38*109).
Mitochondrial DNA chromosomes have closed, circular structures, and
contain 16,569 nucleotides. Nuclear DNA is located within the nucleus of
eukaryote cells and usually has two copies per cell while mitochondrial DNA is
located in the mitochondria and contains 100-1,000 copies per cell. Nuclear DN
A contains more than 20 thousands protein coding and more than 23 thousands n
on-coding genes. The mitochondrial DNA contains 37 genes. Of the 37 genes 13
are protein coding, 2 rRNA and 22 tRNA coding genes. The mutation rate for
nuclear DNA is less than 0.3% while that of mitochondrial DNA is generally
higher.

Replication
DNA replication is the process of producing two identical replicas from one
original DNA molecule. This biological process occurs in all living organisms and
is the basis for biological inheritance. DNA is made up of two strands and each
strand of the original DNA molecule serves as a template for the production of the
complementary strand, a process referred to as semiconservative replication.
Cellular proofreading and error-checking mechanisms ensure near perfect fidelity
for DNA replication. DNA polymerases are a family of enzymes that carry out all
forms of DNA replication (Figure 3).

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Figure 3 DNA polymerases add nucleotides to the 3' end of a strand of DNA. If a
mismatch is accidentally incorporated, the polymerase is inhibited from further extension.
Proofreading removes the mismatched nucleotide and extension continues.

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Transcription
Transcription is the first step of gene expression, in which a particular segment
of DNA is copied into RNA (messenger RNA or mRNA) by the enzyme RNA
polymerase. RNA polymerase, and therefore the initiation of transcription,
requires the presence of a core promoter sequence in the DNA. Promoters are
regions of DNA that promote transcription and, in eukaryotes, are found at -30, -
75, and -90 base pairs upstream from the transcription start site.
Transcription factors are proteins that bind to these promoter
sequences and facilitate the binding of RNA polymerase.
One strand of the DNA, the template strand (also noncoding or antisense strand),
used as a template for RNA synthesis. As transcription proceeds, RNA
polymerase traverses the template strand and uses base pairing complementarity
with the DNA template to create an RNA copy. Although RNA polymerase
traverses the template strand from 3' → 5', the coding
(non-template or sense) strand and newly formed RNA can also be used as
reference points, so transcription can be described as occurring 5' → 3'. This
produces an RNA molecule from 5' → 3', an exact copy of the coding strand
(except that thymines are replaced with uracils, and the nucleotides are composed
of a ribose (5-carbon) sugar.

The genetic code

The genetic code is the set of rules by which information encoded within
genetic material (DNA or mRNA sequences) is translated into proteins by living
cells. Biological decoding is accomplished by the ribosome, which links amino
acids in an order specified by mRNA, using transfer RNA (tRNA) molecules
to carry amino acids and to read the mRNA three nucleotides at a time. The
genetic code is highly similar among all organisms and can be expressed in a
simple table with 64 entries.

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The code defines how sequences of these nucleotide triplets, called

codons, specify which amino acid will be added next during protein
synthesis. With some exceptions, a three-nucleotide codon in a nucleic
acid sequence specifies a single amino acid. Because the vast majority of
genes are encoded with exactly the same code, this particular code is of
ten referred to as the canonical or standard genetic code, or simply the
genetic code, though in fact some variant codes have evolved. For
example, protein synthesis in human mitochondria relies on a
genetic code that differs from the standard genetic code.

Translation starts with a chain initiation codon or start codon. The most
common start codon is AUG, which is read as methionine.

The three stop codons have been given names: UAG is amber, UGA is opal
(sometimes also called umber), and UAA is ochre. Stop codons are also
called "termination" or "nonsense" codons. They signal release of the
nascent polypeptide from the ribosome because there is no cognate tRNA
that has anticodons complementary to these stop signals, and so a release
factor binds to the ribosome instead.

Degeneracy is the redundancy of the genetic code. The genetic code has
redundancy but no ambiguity. For example, although codons GAA and
GAG both specify glutamic acid (redundancy), neither of them specifies
any other amino acid (no ambiguity).

Translation
In translation, mRNA is decoded by a ribosome to produce a specific
amino acid chain, or polypeptide. The polypeptide later folds into an active
protein and performs its functions in the cell. The ribosome facilitates
decoding by inducing the binding of complementary transfer RNA (tRNA)

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anticodon sequences to mRNA codons. The tRNAs carry specific amino

acids that are chained together into a polypeptide as the mRNA passes
through and is "read" by the ribosome (Figure 1.3). The entire process is a
part of gene expression.

Figure 4 Translation.

After the translation some proteins are modified through a process called
post-translational modification. Post-translational modification refers to
the covalent and generally enzymatic modification of proteins during or after
protein biosynthesis. Posttranslational modifications can occur on the amino
acid side chains or at the protein's C- or N- termini.

They can extend the chemical repertoire of the 20 standard amino acids
by introducing new functional groups such as phosphate, acetate, amide
groups, or methyl groups.

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Other forms of post-translational modification consist of cleaving peptide

bonds, as in processing a propeptide to a mature form or removing the
initiator methionine residue. The formation of disulfide bonds from cysteine
residues may also be referred to as a posttranslational modification. For
instance, the peptide hormone insulin is cut twice after disulfide bonds are
formed, and a propeptide is removed from the middle of the chain;
the resulting protein consists of two polypeptide chains connected by
disulfide bonds.

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