UNIT 6.

PROTEINS SYNTHES
 GENETIC CODE

• A gene is a sequence of nucleotides that forms part of a DNA molecule that codes for a
specific polypeptide.
• The genetic code is the set of rules by which information encoded in genetic material
(DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells
using ribosome machinery.
• With four different nucleotides (A, C, G, U), a three-letter code (codon) can give 64
different possible codons (4 × 4 × 4 = 64). These 64 possible codons are more than enough
to code for the 20 amino acids found in living cells
 THE CHARACTERISTICS OF GENETIC CODE

• 1. The Genetic Code is a Triplet Codon: A codon consists of a group of three

nucleotides. And each codon codes for a specific amino acid in a polypeptide chain with
some exceptions
• 2. The Genetic Code is Used without Comma: The three nucleotides in a codon are
read in a continuous fashion without any comma. Examples: AUG, UAG, UGA and
UAA
• 3. The Genetic Code is Non-overlapping: The codons in the m-RNA sequence are
read successively without overlapping.
 CONT’D

• 4. The Genetic Code is Almost Universal: For many long years, it was thought that the
genetic code is universal, which led us into believing that all living organisms have the
same genetic code.
• 5. The Genetic Code is “Degenerate”: A codon is thought to code for a particular amino
acid. That is one codon for one amino acid. But more than one codon can code for a
particular amino acid, with two exceptions of AUG and UGG.
• This multiple coding by a single codon is called the degeneracy or redundancy of the
code.
 CONT’D

• 6. The Genetic Code has Start and Stop Codons: Out of 64 codons, only 61 codons are
called sense codons.
• The other three codons are called nonsense codons or stop codons or chain-terminating
codons.
• These three codons are UAG, UAA, and UGA; they do not specify any amino acid, and there
are no t-RNAs to carry the appropriate anticodons.
• The AUG codon, which code for methionine, is most of the time the start codon
or initiation codon for protein synthesis in both eukaryotes and prokaryotes
IMPORTANCE OF THE GENETIC CODE IN DETERMINING THE
STRUCTURE OF A PROTEIN

• DNA is Extremely Stable and Replicates Accurately

• According to central dogma concept, m-RNA is copied from DNA and m-RNA is then translated to
form proteins.
• The stability of DNA is a property critical to the maintenance of the integrity of the gene
• DNA molecule is a stable structure and replicates accurately in order to avoid any mutation or change
in nucleotides sequences in DNA. The stability of DNA can be attributed to important factors —
Hydrogen Bonds and Base Stacking
 COMPONENTS OF PROTEIN
SYNTHETIC MACHINERY

• Amino-acids
• DNA
• Non-genetic ribonucleic acids (RNAs: mRNA,
tRNA, rRNA)
• Ribosomes, and
• Enzymes
 1. AMINO-ACIDS

Proteins are the polymers of amino-acids; their

synthetic process requires the amino-acids as
the row material

These amino-acids occur in the matrix forming an

amino-acid pool.
 2. DNA

DNA is the master macromolecule of the cell;

Its immediate function is the determination of the kind of the

protein which a cell to manufacture.

DNA initiates, guides, regulates and controls the Protein

synthesis.
 3. NON-GENETIC RIBONUCLEIC
ACID

All the three kinds of RNA (rRNA,

mRNA and tRNA) take an active
part in protein synthesis
• mRNA carries coded information for protein synthesis,
from DNA to the site of protein synthesis (=Ribosomes)

• tRNAs transport amino acids from ‘amino-acid pool’ to the

site of protein synthesis.

• rRNA is thought having no specific function like mRNA

and tRNA, but it is a component of Ribosomes where
proteins are synthesized
 4. RIBOSOMES

Ribosomes are Protein-Synthesizing Machinery of the

cell.
The ribosomal surface is the site for mRNA and tRNA
binding. During protein synthesis, the ribosomes mediate
their Codon-Anticodon between the mRNA and tRNA
molecules
The ribosomes also permit the formation of peptide
bonds between the amino-acids
 5. ENZYMES

They catalyze all the steps of Protein Biosynthesis:

• Transcription within the cell nucleus is catalyzed by
some specific enzymes
• Translation steps (Initiation, Elongation and
Termination) require a large variety of ribosomal
enzymes
Mechanisms of protein
biosynthesis
The coded information in
DNA is converted into the
amino acid sequences of
proteins by a multistep
process
1- CENTRAL DOGMA

DNA Transcription
RNA Translation
Proteins

2- Central Dogma reverse

2
Transcription 3

DNA Inverse
transcription RNA Translation
Proteins
1
1. Transcription of proteins-coding genes
and formation of functional mRNA
 This is the process by which information in DNA is used to code for the synthesis of
messenger RNA (mRNA). It occurs in the nucleus of the cell.
A gene = unit of DNA that contains the information to specify synthesis of a single
polypeptide chain or functional RNA

The vast majority of genes carry information to build protein molecules, and

It is the RNA copies of such protein-coding genes that constitute the
mRNA molecules of cells.
 TRANSCRIPTION…

• Initiation
• further divided into discrete
phases of DNA binding and
Transcription
initiation of RNA synthesis,
• Elongation, and

• Termination phases.
 A- Initiation
Transcription is initiated at a particular site of the DNA double strand
known as a promoter, near the protein-coding sequence.
• The DNA sequence at the promoter is recognized by specific proteins
 INITIATION
• A TATA box is a DNA sequence that indicates where reading of the genetic sequence
can start.
• The TATA box has lots of As and lots of Ts, which makes it easy to pull the strands of
DNA apart.
• It is part of the promoter sequence, which specifies to the transcription factors where
transcription begins.
• The TATA box is named for its conserved DNA sequence, which is mostly common
TATAA.
• Protein called TATA-binding protein (TBP) and other transcription factors bind to TATA
box and recruit an enzyme RNA polymerase, which synthesizes RNA from DNA.
 B_ELONGATION
• This is the second step after the initiation phase.
• Basically, is the stage when the RNA strands gets longer via the addition
of new nucleotides.
• During elongation, RNA polymerase “walks” along one strand, known as
the template strand, in the 3’ to 5’ direction. For each nucleotide in the
template, RNA polymerase adds a matching (complementary) RNA
nucleotide to the 3’ end of the RNA strand.
• The RNA transcript is nearly identical to the non-template, or coding,
strand of DNA. However, RNA strands have the base uracil (U) in place of
thymine (T), as well as a slightly different sugar in the nucleotide.
 C_TERMINATION

• RNA polymerase will keep transcribing until it gets

signals to stop.
• The process of ending transcription is
called termination, and it happens once the
polymerase transcribes a sequence of DNA known as
a terminator.
 RNA Processing (post transcription) in Eukaryotes

• In prokaryotes:
 RNA transcripts are ready to be translated right after transcription, and no further processing.

• In Eukaryotes:
 RNA transcripts are not yet ready to be translated
 RNA made from protein-encoding genes is called a pre-mRNA or primary RNA transcript
 The pre-mRNA needs extensive RNA processing in order to yield mature mRNA ready for
translation.
 RNA Processing in Eukaryotes….
RNA processing reactions involve:

Capping the 5’ end of the mRNA,

Polyadenylation: extending the 3’ end of the

molecule by the process called polyadenylation
and RNA splicing.
 CAPPING THE 5’ END OF THE MRNA

1. First, a triphosphatase removes the terminal phosphate from the 5’ triphosphate

end of the mRNA.
2. Next, a guanyltransferase transfers a GMP unit from GTP to the remaining 5’
diphosphate. These two reactions create a 5’–5’ triphosphate linkage between
two nucleotides.
3. Finally, methyltransferases add a methyl group to the guanine and to the 2’ OH
group of ribose residues
 CAPPING THE 5’ END OF THE MRNA…

The cap protects the 5’ end of the primary

transcript against attack by exoribonucleases
Exoribonucleases = enzymes that degrade RNA by
removing terminal nucleotides from either the 5’ end or
3’ end of the RNA molecule that have specificity for 3’ 5’
phosphodiester bonds and so cannot hydrolyze the 5’
5’ bond in the cap structure
 3’ PROCESSING: CLEAVAGE AND POLYADENYLATION

Cleavage of the RNA at its 3’ end and the addition of up to 250

A residues to form a poly(A) tail.

The poly(A) tail immediately binds several copies of a poly(A)

binding protein.

The poly(A) tail protects the 3’ end of the final mRNA against
exoribonucleases digestion and hence stabilizes the mRNA.
 RNA SPLICING
Pre-mRNA contains:

The protein coding-information stretches called exons (expressed sequences)

Over 90% of a gene’s total length being non-coding stretches called introns
(intervening sequences) that break up the code

 The introns must be removed from the pre-mRNA before the mRNA is translated.

 Removal of introns is done during the process called RNA splicing.

 The exons remain in the finished mRNA and are expressed in the final
protein.
 RNA splicing………..

 SPLICING IS CARRIED OUT BY A SPLICEOSOME, A COMPLEX OF

FIVE SMALL RNA MOLECULES (CALLED SNRNAS, FOR SMALL
NUCLEAR RNAS) TOGETHER WITH A HUNDREDS OF PROTEINS
WHICH RECOGNIZE INTRON/EXON JUNCTION.
 WHY DO GENES INCLUDE INTRONS?
 Introns typically comprise over 90% of a gene’s total length, which means that a lot of RNA must be
transcribed and then discarded.

 A cell must spend energy to synthesize the RNA and proteins that make up the spliceosome and that
destroy intronic RNA and incorrectly spliced transcripts.

 Finally, the complexity of the splicing process creates many opportunities for things to go wrong: A
majority of mutations linked to inherited diseases involve defective splicing.

What is the advantage of arranging a gene

as a set of exons separated by introns?
 What is the advantage of arranging a gene as a set of exons
separated by introns?
 Splicing allows cells to increase variation in gene expression through alternative splicing.

Variation may result from:

 Selecting alternative sequences to serve as 5’ or 3’ splice sites, or

 Skipping an exon.

Thus, certain exons present in the gene may or may not be included in
the mature RNA transcript.

As a result of alternative splicing, a given gene can generate more than one
protein product, and expression of one gene can be finely tailored to suit
different needs of different types of cells.
 Transcription termination….

A TYPICAL HAIRPIN STRUCTURE FORMED BY THE 3’ END OF AN RNA MOLECULE DURING

TERMINATION OF TRANSCRIPTION.
 TRANSLATION

•Is the process by which the information of the sequence of bases in messenger RNA is converted into a
sequence of amino acids in a polypeptide chain. The process of translation takes place on ribosomes in the
cytoplasm. It involves another form of RNA called transfer RNA which is found in the cytoplasm
•Translation is divided into three steps: initiation, elongation, and termination.
 During initiation, the components of the translational apparatus come together with an mRNA, and a
tRNA carrying the first amino acid binds to the start codon.
 During elongation, amino acids are brought to the mRNA by tRNA and are added, one by one, to a
growing polypeptide chain.
 During termination, a stop codon in the mRNA is recognized by a protein release factor, and the
translational apparatus comes apart, releasing a completed polypeptide
• The transfer RNA combines with specific amino acids in the cytoplasm and transfer them to
the ribosomes (amino acid activation).
• The three unpaired bases called anti-codons combine with their corresponding codons on
messenger RNA.
 CONT’D

• Amino acids are therefore aligned in a sequence depending on bases on

messenger RNA.
• The first codon on messenger RNA is called the start codon ,on strand of
mRNA the first codon is AUG. The transfer RNA with Anti-codons UAC is
the one with the first amino acid of polypeptide chain.
• This is the first amino acid to be brought to a ribosome.
CONT’D

• More amino acids continue to be brought to ribosomes in this way and peptide
bonds are then established between them forming a long polypeptide chain.
• Some codons do not code for any amino acid, these are called Non-sense
codons or stop codons(UAG, UAA,UGA).
• When ribosomes reach the stop codons formation of polypeptide chain stops
and the completed chain peels off, the tRNA molecule is released from
ribosome to the cytoplasm.
 RIBOSOME

 A ribosome has an mRNA binding sites and three tRNA binding sites known as the A
site, P site and E site.
 A site (Aminoacyl-tRNA binding site):Holds the tRNA carrying the next amino acid to
be added to the polypeptide chain.
 P site (Peptidyl-tRNA binding site): Holds the tRNA carrying the growing polypeptide
chain.
 E site (Exit site): Site from which tRNA that has lost its amino acid is discharged.
BINDING SITE OF A RIBOSOME
STRUCTURE OF A TRANSFER RNA
THE EFFECT OF CHANGE IN GENETIC CODE ON THE
STRUCTURE OF PROTEIN DURING PROTEIN
SYNTHESIS

• Mutations are changes in genetic codons caused by changes in nucleotide bases. Some
mutations do not have much effect.
• Mutations occur in two ways:
A. A base-pair substitution: It is a change from one base pair to another base pair in
DNA.
B. Base-pair insertions or deletions: It is a change in which a base-pair is either
incorrectly inserted or deleted in a codon.
 (A) A BASE-PAIR SUBSTITUTION

• Consider the following changes in the DNA from

• This change in base pair brings changes in the m-RNA codon from one purine to the other
purine.
• In this case, the m-RNA codon is changed from 5’-AAA-3’ (lysine) to 5’-GAA-3’
(glutamic acid).
• This is missense mutation.
 (B) BASE-PAIR INSERTIONS OR DELETIONS

• Insertion or deletion of one or two bases changes the reading frame from the point of
insertion or deletion.
• Insertion or deletion of three or its multiple bases insert or delete one or multiple
codon hence one or multiple amino acids and reading frame remains unaltered from
that point onwards, mutations are referred to as frame-shift insertion or deletion
mutations.
EXAMPLES
EFFECTS OF ALTERATION OF NUCLEOTIDE SEQUENCE
• Change in Nucleotide (Mutation) Sequence Leads to Change in
Polypeptides
• Amino acids (proteins) are the ultimate product of the nucleotide
sequence present in genes (DNA).
• Thus, any change in the nucleotide sequence of a gene can result
into producing wrong or different polypeptide chain.
• One of the best examples is Sickle-cell anaemia. In this disease, the
nucleotide “T” in the DNA sequence is replaced by “A” nucleotide.
• The minor substitution in the nucleotide sequence is transcribed as a mutant codon
on the m-RNA.
• And during translation, due to mutant codon on the m-RNA, valine is synthesized
instead of glutamic acid.
 ALBINISM
• Albinism occurs due to mutation in the gene for tyrosinase, an enzyme which
converts tyrosine to DOPA (dihydroxyphenylalanine).
• Melanin, skin pigment, is derived from DOPA. Melanin absorbs light in the
ultraviolet (UV) range and protects the skin against harmful UV radiation from
the sun. People with albinism produce no melanin.
• Therefore, they have white skin, white hair, eyes with red iris, and they are very
sensitive to light.
 SICKLE CELL ANAEMIA

• Sickle-cell anaemia is a genetic disease that affects haemoglobin molecules.

• Haemoglobin is a protein found in red blood cells, and is responsible for the
transportation of oxygen through the body.
• Haemoglobin, the molecule affected in sickle-cell anaemia, consists of four
polypeptide chains: Two alpha-globin polypeptides and two betta-globin
polypeptides-each of which is associated with a haeme group (a non-protein
chemical group involved in oxygen binding and added to each polypeptide
after the polypeptide is synthesized).
 CAUSE
• The mutation causing sickle cell anaemia is a single nucleotide substitution (A to T) in the
DNA of haemoglobin coding gene.
• The change in a single nucleotide is transcribed as a codon for valine amino acid (GUG) on
the m-RNA instead of glutamic acid (GAG).
• Eventually, due to change in the codon, valine amino acid is translated instead of glutamic
acid at the 6th position from N-terminus of the haemoglobin polypeptide chain.
• This defective form of haemoglobin in persons with sickle cell anaemia is referred to as
HbS.
• The amino acid valine makes the haemoglobin molecules stick together, forming long
fibres which convert the normal disc-shape of red blood cells into sickle-shaped red
blood cells.
 SYMPTOMS
 The sickled red blood cells are fragile and break easily, resulting in the anaemia.
 Normal red blood cells normally squeeze and pass through blood capillaries smoothly.
 However, sickled cells are not flexible and therefore have the tendency to get clogged in capillaries.
 As a result, blood circulation is impaired and tissues become deprived of oxygen.
 Oxygen deprivation occurs at the extremities, the heart, lungs, brain, kidneys, gastrointestinal tract,
muscles, and joints.