BCHM 113 Biochemistry

Nucleic 2nd Semester AY 2021-22

Acids-2
Natural Science Department
College of Arts and Sciences
Our Lady of Fatima University
 The Central Dogma of Molecular
Biology
• The central dogma of molecular biology states that genetic
information contained in the DNA is transferred to RNA molecules
and then expressed in the structure of synthesized proteins.
• Genes are segments of DNA that contain the information needed
for the synthesis of proteins.
• Each protein in the body corresponds to a DNA gene.
 There are two steps in the flow of genetic
information:

– transcription — in eukaryotes, the DNA

Transcription, containing the stored information is in the
nucleus of the cell, and protein synthesis
Translation, occurs in the cytoplasm. The information
stored in the DNA must be carried out of the
and nucleus by mRNA.

Information – translation — mRNA serves as a template

on which amino acids are assembled in the
Flow sequence necessary to produce the correct
protein. The code carried by mRNA is
translated into an amino acid sequence by
tRNA.

• The communicative relationship

between mRNA nucleotides and
amino acids in a protein is called
the genetic code.
Transcription, Translation, and Information
Flow
Transcription: RNA Synthesis
Transcription: RNA Synthesis
mRNA synthesis
Under the influence of Ribonucleotides are
the enzyme RNA occurs in the 3′ to 5′
linked along the
polymerase, the DNA direction along the
DNA strand in a
double helix unwinds DNA strand (in the
sequence
at a point near the 5′ to 3′ direction
determined by the
gene that is being along the RNA
transcribed (the base pairing of the
strand) until the
initiation sequence). DNA and
termination
Only one strand of the ribonucleotide
sequence is
DNA is transcribed. bases (A::U, G:::C).
reached.

The newly-synthesized
mRNA strand moves Synthesis of tRNA
away from the DNA, and rRNA is similar
which rewinds into to this.
the double helix.
 Introns and Exons

In prokaryotes, each gene is a continuous segment along a

DNA molecule. Transcription of the gene produces mRNA
that is translated into a protein almost immediately,
because there is no nuclear membrane separating the
DNA from the cytoplasm.

In eukaryotes, the gene segments of DNA that code for

proteins (exons) are interrupted by segments that do not
carry an amino acid code (introns).

• Both exon and intron segments are transcribed,

producing heterogenous nuclear RNA (hnRNA).
• A series of enzymes cut out the intron segments and splice
the exon segments together to produce mRNA.
Introns and Exons
Genetic Code

Once the 3D structure of DNA was known, it was clear that the sequence
of the bases along the backbone in some way directed the order in
which amino acids were stacked to make proteins.

In 1961, Marshall Nirenberg and his coworkers began to unravel the

connection between the base sequence in DNA and the amino acid
sequence in proteins.

The genetic code uses a sequence of three bases (a triplet code) to

specify each amino acid. (A triplet code gives 43=64 possible
combinations, which is more than enough to specify the 20 amino acids.)

Each base triplet sequence that represents a code word on mRNA

molecules is called a codon.
Genetic Code
 Characteristics of the Genetic Code
The genetic code applies almost universally: with minor
exceptions, the same amino acid is represented by the
same codon(s) in all species.

Most amino acids are represented by more than one codon

(a feature known as degeneracy).

• Only methionine and tryptophan are represented by a single codon.

• Leucine, serine, and arginine are represented by six codons.
• No codon codes for more than one amino acid.

Only 61 of the 64 possible triplets represent amino acids. The

other three are used as signals for chain termination (a
“stop” signal).

The AUG codon (which also codes for methionine) functions

as a “start” signal, but only when it occurs as the first codon
in a sequence.
Characteristics of the Genetic Code
 Characteristics of the Genetic Code
• DNA is considered a universal genetic code because
every known living organism has genes made of
DNA. Bacteria, fungi, cats, plants, and you: every
organism uses DNA to store genetic information. All
organisms also use DNA to transcribe RNA, and then
they translate that RNA into proteins.

What are three important features of the universal

genetic code?
• Groups of three bases form codons, and each codon stands
for one amino acid (or start or stop). The codons are read in
sequence following the start codon until a stop codon is
reached. The genetic code is universal, unambiguous, and
redundant.
 Translation and Protein Synthesis
Step 1: Initiation of the polypeptide chain.
• mRNA and a small ribosomal subunit join; the initiating
codon (AUG) is aligned with P (peptidyl) site of the subunit.
• tRNA brings in methionine (eukaryotes) or N-
formylmethionine (prokaryotes).
• The resulting complex binds to the large ribosomal subunit
to form a unit called the initiation complex.
 Translation and Protein Synthesis
Step 2: Elongation of the chain.
• The next incoming tRNA with an anticodon that is
complementary to the mRNA codon bonds at the A
(aminoacyl) site on the mRNA.
• A peptide bond is formed between the amino acid segments,
(catalyzed by peptidyl transferase), which releases the amino
acid chain from the P site.
 Translation and Protein Synthesis
Step 2: Elongation of the chain, cont.
• The “empty” tRNA released, and the whole ribosome
moves one codon along the mRNA towards the 3’ end
(translocation).
• Another tRNA attaches to the A site, and the elongation
process is repeated.
 Translation and Protein Synthesis
Step 3: Termination of polypeptide synthesis.
• Elongation continues until the ribosome complex reaches a
stop codon (UAA, UAG, or UGA).
• A termination factor protein binds to the stop codon, and
separates the protein from the final tRNA.
• The ribosome can then synthesize another protein molecule.
Translation and Protein Synthesis
• There are 3 STOP
codons in the
genetic code -
UAG, UAA, and
UGA.
• These codons signal
the end of the
polypeptide chain
during translation.
• These codons are
also known as
nonsense codons or
termination codons
as they do not
code for an amino
acid.
Translation and
Protein Synthesis
 Several ribosomes can
move along a single
strand of mRNA,
producing several
identical proteins
simultaneously. These
complexes are called
polyribosomes or
polysomes.
 The growing
polypeptide chain
emerging from the
end of the ribosome
spontaneously folds
into the characteristic
3D shape of that
protein.
 Mutations are any changes resulting in an
incorrect base sequence on DNA.

Even though the base-pairing mechanism

provides a nearly perfect way of copying
DNA, on average one out of every 1010
bases are copied incorrectly.
Mutations • This leads to a change in the amino acid sequence
in a protein, or causes the protein not to be made at
all.

Mutations occur naturally during

replication. They can also be induced by
environmental factors:

• ionizing radiation (X-rays, UV, gamma rays).

• mutagens, which are chemical agents.
 Mutations may be beneficial to an
organism by making it more capable of
surviving in its environment, ultimately
(over millions of years of accumulating
changes) leading to the evolution of
new species.

Since much of an organism’s DNA does

Mutations not code for anything, mutations in
these regions are neutral.

Other mutations can be harmful, either

producing genetic diseases or other
debilitating conditions.
Recombinant DNA
 Recombinant DNA is produced when segments of
DNA from one organism are introduced into the
genetic material of another organism.
 “Genetic engineering” of E. coli to include the gene
for the production of human insulin enables large
quantities of insulin to be made available for the
treatment of diabetes.
Restriction Enzymes
• Restriction enzymes, found in a wide variety of bacterial cells,
catalyze the cleaving of DNA molecules, except for a few specific
types.
• These enzymes are normally part of a mechanism that protects
certain bacteria from invasion by foreign DNA (such as that in
viruses).
• In these bacteria, some of the bases in their DNA have methyl
groups attached.
• The methylated DNA of these bacteria is left untouched by the
restriction enzymes, but foreign DNA that lacks these bases
undergoes rapid cleavage and is rendered nonfunctional.
 Restriction Enzymes
• Restriction enzymes act at sites on DNA called palindromes,
where two strands have the same sequence but run in
opposite directions:

• Restriction enzymes are used to break DNA up into

fragments of known size and nucleotide sequence, which
can then be spliced (join/connect) together with DNA
ligases.
Plasmids

• The introduction of a new DNA segment (gene) into a

bacterial cell requires a DNA carrier called a vector,
which is often a circular piece of doublestranded DNA
called a plasmid.
• Plasmids range from 2000 to several hundred
thousand nucleotides, and are found in the
cytoplasm of bacterial cells.
• Plasmids function as accessories to chromosomes
by carrying genes for the inactivation of antibiotics
and the production of toxins. They are also able to
replicate independently of chromosomal DNA.
• A plasmid is isolated from a bacterium, and a restriction
enzyme is added, which cleaves it at a specific site:

• When the circular DNA is cut, two “sticky ends” are

produced, which have unpaired bases.
• The “sticky ends” are provided with complementary
sections for pairing from a human chromosome to which
the same restriction enzyme has been used:
 The Formation of Recombinant DNA
• The breaks in the strands are joined using DNA ligase, and the
plasmid becomes a circular piece of double-stranded,
recombinant DNA.
 replicate all
When the bacteria reproduce, they
of the genes, including the new
recombinant DNA plasmids.
The Formation
of
Recombinant
DNA

Because bacteria multiply quickly,

there are soon a large number of
bacteria containing the modified
plasmid, which are capable of
manufacturing the desired protein.
Production of Insulin
 Basic virus particle is called a
“virion” – intact and infective
virus particle

Viruses Components: Nucleic Acid (DNA or

RNA), Protein coat (capsid) made of
individual protein subunits called
capsomeres. Some may have and outer
envelope, a membrane, derived from
the host cell. The envelope can have
specific spikes of protein (H and N spikes
of Influenza) that aid in attachment and
makes them sensitive to chemical
actions of disinfectants.
 Viruses
• Types of viruses based on “morphology” – shape;
structure
• Helical (like TMV or Ebola) Polyhedral (adeno and polio)
Enveloped (flu) and Complex (bacteriophage)
 Preparation of gene maps.

In revealing details of various infections,

diseases such as "inborn errors of metabolism."

Finding out the complete nucleotide sequence

Applications of of genome of an organism and identification
of genes.
Recombinant Detecting cytogenetic abnormalities e.g.
DNA Down's syndrome, multifactorial disorders,
atherosclerosis, coronary artery disease etc.

Preventing various genetic disorders e.g.

inherited haemoglobin disorders,
phenylketonuria, retinoblastoma etc.

Understand a molecular event is biological

processes like growth, differentiation, ageing
etc.
 Applications of Recombinant DNA

Replacement or correction of deleterious mutation by transfer of clone

gene in a patient.

Production of genetically modified organisms (GMOs) or transgenic

organisms for providing particular product and nutrient.

Gene Therapy: Removal and replacement of defective genes with normal

healthy functional genes is known as gene therapy e.g. Sickle cell anemia,
Severe Combined Immuno-Deficiency (SCID). SCID is due to a defect in the
gene for the enzyme adenosine deaminase (ADA) in 25 per cent of the
cases.
 The end
Nucleic Acids-2
CHEM 113 Biochemistry
2nd Semester AY 2020-21

Natural Science Department

College of Arts and Sciences
Our Lady of Fatima University