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Protein Synthesis (1)

The document outlines the process of protein synthesis, emphasizing the central dogma of molecular biology, which describes how genetic information is translated into proteins. It details the genetic code, the role of mRNA and tRNA, and the stages of translation including activation, initiation, elongation, termination, and post-translational processing. Key concepts such as reading frames, codon-anticodon pairing, and the structure of tRNA are also discussed.

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6 views

Protein Synthesis (1)

The document outlines the process of protein synthesis, emphasizing the central dogma of molecular biology, which describes how genetic information is translated into proteins. It details the genetic code, the role of mRNA and tRNA, and the stages of translation including activation, initiation, elongation, termination, and post-translational processing. Key concepts such as reading frames, codon-anticodon pairing, and the structure of tRNA are also discussed.

Uploaded by

sajjtam
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Protein Synthesis

CHEM 125: Physical & Bioorganic Chemistry


Objective - The Central Dogma
Translation and Protein
Biosynthesis

Protein life cycle in eukaryotes


The genetic code for proteins
consists of triplets of
nucleotides
• There are 20 common, genetically encoded amino
acids
• A four-letter code in groups of two is insufficient (16)
• A four-letter code in groups of three IS sufficient (64)
• Living organisms use non-overlapping mRNA code
with no punctuation
Overlapping vs Non-overlapping
code
Reading Frames

• Reading frame is set at the initiation of translation process


• In almost every case, only one reading frames will produce a functional protein
• This reading frame is known as open reading frame
Features of the genetic code
• The code is written in the 5’  3’ direction
• Third base is less important in binding to tRNA
• First codon establishes the reading frame
• If reading frame is thrown off by a base or two, all
subsequent codons are out of order
• 61/64 codons code for amino acids
• Three are termination codons
• UAA, UGA, UAG
• AUG = initiation codon (as well as Met codon)
Nucleotide Code Dictionary
Genetic code is degenerate
• 4 nucleotides; 43=64 codons possible
• 3 sequences for stop codon, 1 for start (also
Met)
• 61 different codons to specify only 20 amino
acids
• Only Met and Trp have unique codons
• Either each amino acid is specified by >1
tRNA or tRNAs can bind to more than one
codon (Both occur)
Genetic Code
• Amino acid sequence of protein is constructed
through the translation of information encoded
in mRNA
• Amino acids are specified by mRNA codons
consisting of nucleotide triplets. Translation
requires adapter molecules, the tRNAs, that
recognize codons and insert amino acids at
the correct position in the protein
Genetic code (cont.)
• AUG signals initiation, and UAA, UAG, and UGA signal
termination
• Genetic code is degenerate—multiple code words for almost
every amino acid
• Standard genetic code words are universal for almost every
species
• Third position in each codon is less specific than the first two
Adapter (tRNA) brings amino
acid to mRNA
Molecular Recognition of
Codons in mRNA by tRNA
• The codon sequence is complementary with the
anticodon sequence
• The codon in mRNA base pairs with the anticodon in
mRNA via hydrogen bonding
• The alignment of two RNA segments is antiparallel
Structure and characteristic features of
tRNA
• sRNA of 73–93 nucleotides in both
bacteria and eukaryotes
• Cloverleaf structure in 2-D
• “Twisted L” shape in 3-D
• Amino acid arm
• Has amino acid esterified via
carboxyl group
Structure and characteristic features of
tRNA
• Anticodon arm
Have modified bases
Methylated bases, etc.
• D arm
Contains dihydrouridine (D)
Contributes to folding
• TC arm
Contains pseudouridine ()―has bonding
between base and ribose
Helps in folding
Wobble base-pairing in
anticodon
• When different codons specify one amino acid, the difference lies at the
third position of the codon (5’ end of tRNA anticodon)
• Wobble or flexibility at this site allows the tRNA anti-codon to read multiple
codon sequences
• Minimum of 32 tRNAs are required to translate all 61 codons (31 for amino
acids and 1 for initiation with fMet)
“Wobble” pairings in tRNA
with mRNA can occur in
the third base
• The third base of a codon can form non-canonical base
pairs with its complement (anticodon) in tRNA
• Some tRNAs contain Inosinate (I), which can H-bond
with U,C, and A
• These H-bonds are weaker and were named by Crick as
“wobble” base pairs
• Example: In yeast, CGA, GCU, and CGC all bind to tRNAArg,
which has the anticodon 3’-GCI-5’
• Although sequences are usually written 5’3’, the anticodon here is
written 3’5’ to illustrate its bonding to the mRNA codons
Anticodon containing inosinate (G or A)
can pair with any of 3 codon sequences
Ribosome and
polypeptide synthesis
• 2 Subunits of ribosome
• “Small” subunit involved in the recognition of
the mRNA and tRNA sequences
• “Large” subunit attaches the amino acid to
form a polypeptide chain

• Ribosome is a large protein synthesis machine


• It finds the specific start site that sets the reading frame
• As the ribosome moves along the mRNA, it translates codons to amino acids using tRNA
• At the end, stop codon, it releases protein to cytoplasm and detach itself
Five stages of protein synthesis

1) Activation of amino acids


• tRNA is aminoacylated
2) Initiation of translation
• mRNA and aminoacylated tRNA bind to ribosome
3) Elongation
• Cycles of aminoacyl-tRNA binding and peptide bond
formation…until a STOP codon is reached
4) Termination and ribosome recycling
• mRNA and protein dissociate, ribosome recycled
5) Folding and post-translational processing
• Catalyzed by a variety of enzymes
Overview of protein
synthesis

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