Translation and Genetic code

Topic: Translation and the genetic code:

Polypeptides and proteins

Synthesis of polypeptide chain;

Nonsense mutation and suppressor mutation;

The genetic code

Wobble hypothesis

Post-translational modification of protein

Faculty : Monika Sultana

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 Translation and Genetic code

Genetic code
The full set of relationships between codons and amino acids (or stop

signals) is called the genetic code. It refers to the instructions contained

in a gene that tell a cell how to make a specific protein.

For example, the sequence AUG is a codon that specifies the amino

acid methionine.

Codon: a specific sequence of three consecutive nucleotides that is part

of the genetic code and that specifies a particular amino acid in a

protein

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There are 64 possible codons, three of which do not code for amino acids but

indicate the end of a protein. The remaining 61 codons specify the 20 amino

acids that make up proteins.

Here are some features of codons:

 Most codons specify an amino acid

 Three "stop" codons mark the end of a protein

 One "start" codon, AUG, marks the beginning of a protein and also encodes

the amino acid methionine

Because most of the 20 amino acids are coded for by more than one codon,

the code is called degenerate.

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Translation/ Synthesis of polypeptide chain

Translation is the process by which the genetic code contained within a

messenger RNA (mRNA) molecule is decoded to produce a specific

sequence of amino acids in a polypeptide chain.

Two types of molecules with key roles in translation are tRNAs and

ribosomes.

Transfer RNA (tRNA)

It is an RNA molecule that assists in protein synthesis. Its unique shape

contains an amino acid attachment site on one end of the molecule and an

anticodon region on the opposite end.

 The anticodon region of tRNA recognizes a specific area on mRNA

called a codon. The tRNA molecule forms base pairs with its

complementary codon sequence on the mRNA molecule.

 Each tRNA has its corresponding amino acid attached to its end. When

a tRNA recognizes and binds to its corresponding codon in the

ribosome, the tRNA transfers the appropriate amino acid to the end of

the growing amino acid chain.

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Ribosomes
 serves as the site for protein synthesis.

 They are made up of ribosomal proteins and ribosomal RNA (rRNA).

 It is composed of two subunits – smaller and larger. The smaller

subunit is where the mRNA binds and is decoded, and in the larger

subunit, the amino acids get added. The two subunits are joined to each

other by interactions between the rRNAs in one subunit and proteins in

the other subunit.

The ribosome provides a set of handy slots where tRNAs can find their

matching codons on the mRNA template and deliver their amino acids. These

slots are called the A, P, and E sites.

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Translation occurs in the cytoplasm following DNA transcription and has

three stages: initiation, elongation, and termination.

Initiation

For translation to begin, the start codon (5’AUG) must be recognised. This

codon is specific to the amino acid methionine, which is nearly always the

first amino acid in a polypeptide chain.

At the 5’ cap of mRNA, the small 40s subunit of the ribosome binds.

Subsequently, the larger 60s subunit binds to complete the initiation

complex. The next step (elongation) can now commence.

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Elongation

Elongation is the stage where the amino acid chain gets longer. In elongation,

the mRNA is read one codon at a time, and the amino acid matching each

codon is added to a growing protein chain.

Each time a new codon is exposed:

 A matching tRNA binds to the codon

 The existing amino acid chain (polypeptide) is linked onto the amino acid of

the tRNA via a chemical reaction

 The mRNA is shifted one codon over in the ribosome, exposing a new codon

for reading

During elongation, tRNAs move through the A, P, and E sites of the

ribosome, as shown above. This process repeats many times as new codons
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are read and new amino acids are added to the chain.

Termination

Translation ends during the termination stage. Termination takes place

when a nonsense or stop codon (UAA, UAG, or UGA) enters the A site.

Release factors recognize these nonsense codons and signal the

hydrolysis of the bond between the tRNA and the P site polypeptide

chain. This releases the newly made protein, which needs to be folded to

function.

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Wobble hypothesis
There are more than one codon for one amino acid. This is called degeneracy

of genetic code. To explain the possible cause of degeneracy of codons, in

1966, Francis Crick proposed “the Wobble hypothesis”.

The Wobble Hypothesis Statement

 The first two bases of the codon make normal H-bond pairs with the 2nd

and 3rd bases of the anticodon.

 At the remaining position, less stringent rules apply and non-canonical

pairing may occur. The wobble hypothesis thus proposes a more flexible

set of base-pairing rules at the third position of the codon.

 A wobble base pair is a pairing between two nucleotides in RNA

molecules that does not follow Watson-Crick base pair rules.

 The relaxed base-pairing requirement, or “wobble,” allows the anticodon

of a single form of tRNA to pair with more than one triplet in mRNA.

 The four main wobble base pairs are guanine-uracil (G-U), hypoxanthine-

uracil (I-U), hypoxanthine-adenine (I-A), and hypoxanthine-cytosine (I-C)

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Nonsense mutation

Nonsense mutations that generate termination codons in the coding region of

a gene cause premature termination of protein synthesis. Nonsense mutations

can be suppressed by mutant tRNAs that can read termination codons as

sense codons, restoring the synthesis of an active gene product.

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Post-translational Modification
Posttranslational modifications (PTMs) refer to amino acid side chain

modification in some proteins after their biosynthesis.

Forms of PTM

There are many types of PTM that modify proteins in a variety of ways

and enable proteins to have functions in metabolism and regulation. Listed

below are common PTMs:

o Phosphorylation

o Methylation

o Acetylation

o Sumoylation

o Ubiquitination

o Lipidation

o Glycosylation

o ADP ribosylation (ADPr)

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Protein phosphorylation

It is a reversible modification in which an amino acid residue

is phosphorylated by a protein kinase by the addition of a covalently bound

phosphate group. Phosphorylation alters the structural conformation of a

protein, causing it to become activated, deactivated, or otherwise modifying

its function.

Protein ubiquitination

Ubiquitin is a small protein – approximately 8kDa in size – that can bind to a

substrate protein in a process known as ubiquitination, a type of modification

that serves to regulate a protein's function or mark it for degradation.

Ubiquitination occurs in three sequential steps that are catalyzed by three

groups of enzymes.

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Protein methylation

In protein methylation, enzymes known as methyltransferases add a methyl

group to specific amino acids on a protein molecule, such as the lysine and

arginine residues. Protein methylation can have effects on:

 Protein stability

 Protein subcellular localization

 Protomer binding affinity

 Protein-protein interactions

 Other protein modification events

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Protein acetylation

It is a common post-translational modification in eukaryotes and involves the

addition of an acetyl group to nitrogen via reversible and irreversible

processes. If lysine is acetylated, it is no longer positively charged. In turn,

the binding of DNA to the histone is relaxed, which facilitates the

transcription of genes.

Protein Glycosylation

It involves the covalent addition of a carbohydrate moiety to an amino acid,

forming a glycoprotein catalyzed by various different enzymes, which attach

specific glycans to specific amino acids. Glycoproteins are vital for a wide

range of biological processes including: transporting molecules, production

of enzymes, acting as cell attachment-recognition sites, etc. The varying

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types and structures of glycoproteins allow them to adapt to these diverse

function.

 alanine - ala - A
 arginine - arg - R
 asparagine - asn - N
 aspartic acid - asp - D
 cysteine - cys - C
 glutamine - gln - Q
 glutamic acid - glu - E
 glycine - gly - G
 histidine - his - H
 isoleucine - ile - I
 leucine - leu - L
 lysine - lys - K
 methionine - met - M
 phenylalanine - phe - F
 proline - pro - P
 serine - ser - S
 threonine - thr - T
 tryptophan - trp - W
 tyrosine - tyr - Y
 valine - val - V

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Sometimes it is not possible two differentiate two closely related amino acids,
therefore we have the special cases:

 asparagine/aspartic acid - asx - B

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