Genetic Code,
tRNA
Translation
S.Karthikumar
AP/Biotechnology
KCET

Genetic Code
A
G U
A C
G
U
A
C
G
U
A
C
G
U
A
C
G
U
A
C
G
U
A
C
G
U
A
C
G
U
A
C
G
U A
C G
U A
C
G
U
A
C
G
U
A
C
G
U
A
C
G
C
C
A
G
C
C
A
G
A
G
A
G
A
G
C
C
G A
G
C
C
A
U
U
U
U
U
U
U
U

Terms
 Amino Acid - The building block of proteins.
 Genetic Code - The series of codons that make up an organism's DNA
 Codon - A three-nucleotide sequence in an mRNA sequence. Used to
specify an amino acid.
 Reading frame - mRNA sequence yield an amino acid sequence.
 Degenerate - Term used to describe the genetic code. Means that
more than one codon can specify for a single amino acid.
 Stop codon - A codon that is not recognized by a tRNA molecule. One
of three codons: UAA, UAG, or UGA. Signals the termination of DNA
translation.
 Synonyms - Codons that code for the same amino acid.

 Mutation - An error in the genetic code caused most often by a the incorrect
substitution, insertion, or deletion of a nucleotide.
 Frameshift mutation - One class of genetic code mutation that results from
the insertion or deletion of a nucleotide to an mRNA sequence. Results in a new
reading frame.
 Missense mutation - One class of genetic code mutation that results from the
substitution of one base group for another in a codon. Results in the change of
the amino acid for which the codon specifies.
 Nonsense mutation - One class of genetic code mutation that results from the
substitution of one base group for another in a codon. Results in a stop codon, a
codon that can no longer be recognized by tRNA molecules.
 Silent Mutation - A substitution base mutation that changes a codon, but
because of degeneracy does not change the amino acid that codon specifies.
 Suppressor mutation - A type of genetic code mutation that alters the result of
a different mutation.. It suppresses the effect of first mutation. ( Aminoacid
Sequence will be same but nt sequence may vary)
 True reversion - One type of suppression mutation that leads to the
restoration of the natural genetic code sequence. (Amino acid Sequence as
well as nucleotide sequences will be retained.)

The genetic code: how do nucleotides specify 20
amino acids?
 4 different nucleotides (A, G, C, U)
 Possible codes:
 1 letter code  4 AAs <20
 2 letter code  4 x 4 = 16 AAs <20
 3 letter code  4 x 4 x 4 = 64 AAs >>20
 Three letter code with 64 possibilities for 20 amino acids
suggests that the
 genetic code is degenerate (i.e., more than one codon
specifies the same amino acid).

UAG (Amber),
UAA (Ochre),
UGA (Opal)

Characteristics of the genetic
code (written as in mRNA, 5’ to 3’):
 Code is triplet. Each 3 nucleotide codon in mRNA specifies
1 amino acid.
 Code is comma free. mRNA is read continuously, 3 bases
at a time without skipping bases
(Some time, translational frameshifting is known to occur).
 Code is non-overlapping. Each nucleotide is part of only
one codon and is read only once.
 Code is almost universal. Most codons have the same
meaning in different organisms (Except for mitochondria of
mammals).

 Code is degenerate. 18 of 20 amino acids are coded by
more than one codon. Met and Trp are the only
exceptions.
 Code has start and stop signals. AUG codes for Met
and is the usual start signal.
UAA, UAG, and UGA are stop codons and specify the
the end of translation of a polypeptide.
UAG (Amber), UAA (Ochre), UGA (Opal)
 Wobble occurs in the tRNA anti-codon. 3rd base is less
constrained and pairs less specifically.

tRNA

Function
Carry amino acids during protein synthesis

tRNA cloverleaf structure
 All tRNA molecules are
small, ssRNA ranging
from 73-93 nts
 1st tRNA discovered –
tRNAAla
 Due to Intra base pairing
– cloverleaf structure

Structure
1. The 5'-terminal phosphate group.
2. The acceptor stem is a 7-bp stem made
by the base pairing of the 5'-terminal
nucleotide with the 3'-terminal
nucleotide (which contains the CCA 3'-
terminal group used to attach the
amino acid).
3. The CCA tail is a CCA sequence at the
3' end of the tRNA molecule. This
sequence is important for the
recognition of tRNA by enzymes critical
in translation.

 4. The D arm is a 4 bp stem ending
in a loop that often contains
dihydrouridine.
 5. The anticodon arm is a 5-bp stem
whose loop contains the anticodon.
 6. The T arm is a 5 bp stem
containing the sequence TΨC where
Ψ is a pseudouridine.
 7. Bases that have been modified,
especially by methylation. The first
anticodon base is sometimes
modified to inosine (derived from
adenine) or pseudouridine (derived
from uracil).

Attachment of an amino acid
to tRNA molecule
 Each aminoacid will attach to specific tRNA by
specific aminoacyl synthetase enzyme
 Aminoacid is attached with tRNA – called Aminoacylated
or Charged tRNA
 Example seryl-tRNA or tRNASer
 If mischarged; serine is attached with Leu-tRNA - Seryl-
tRNALeu
 Attachment is by two steps
 1. Activation (aa + ATP -> Aminoacyl AMP)
 2. Transfer (Aminoacyl AMP + tRNA -> Aminoacyl tRNA
+ AMP)

Charging of tRNA
 charged by attachment of a
specific amino acid to their 3’-
end to become aminoacyl-tRNA ,
 Aminoacylation of aminoacid
First, the aminoacyl-tRNA
synthetase attaches adenosine
monophosphate(AMP) to the –
COOH group of the amino acid
to creat an aminoacyl adenylate
intermediate.
 Aminoacyl-tRNA synthetases
The synthetase enzymes contact
their cognate tRNA by the inside
of its L-shaped and use certain
parts of the tRNA, called identity
elements, to distinguish these
similar molecules from one
another.

Animation – tRNA charging

Codon-Anti codon Interaction
 61 out of 64 possible codons represent 20 aminoacids
 It was expected that 61 distinct tRNA molecules
 But ~ 40 tRNA molecules available
 (Then How 40 tRNA moleculaes recognize 61 codons?)
 Only first two bases of codon and anti-codon interact, the 3rd letter
doesn’t pair / match
 Usually Inosine is present at 3rd position in anticodon
 Inosine can pair with either A / U / C
 Thus a single tRNA molecule can pair with more than one codons, i.e its
synanyms
 This concept called – Wobble hyphothesis – proposed by Francis Crick -
1965

 Acceptor site - A three-nucleotide position in a ribosome that
binds to an aminoacyl tRNA, a tRNA molecule bearing an
amino acid.
 Acceptor stem - One secondary structural feature of tRNA.
Contains the sequence CCA and has a free 3' –OH. Binds to
the amino acid.
 Adenylylation - The first step in tRNA charging. Involves the
"activation" of an amino acid so that the acid can be bound to a
tRNA molecule. The process of activation involves the transfer
of an AMP group from ATP to the amino acid.
 Aminoacyl tRNA - A tRNA molecule that has been charged. It
is loaded with an amino acid and is ready to participate in
translation at the ribosome, where it binds to the acceptor site.
 Aminoacyl-tRNA synthase - The enzyme that catalyzes the
bond between specific tRNA and amino acid, to form aminoacyl
tRNA.

 Anticodon arm - A secondary structural feature of tRNA. Contains the
anticodon that base pairs with an mRNA codon during translation.
 Carboxyl group - A chemical functional group made up of a carbon double-
bonded to an oxygen and single-bonded to an –OH group.
 Charging - The two-step process in which an amino acid is "loaded" onto a
tRNA. The first step is adenylylation; the second is the binding of tRNA and
amino acid into an aminoacyl tRNA.
 Charged tRNA - Term used to describe a tRNA molecule that has been
loaded with an amino acid and is ready to participate in translation.
 Dihydrouridine - One of the unusual bases found in tRNA. Contains two
additional hydrogens in place of the double bond that is usually found in
uracil.
 Dihydrouridine arm - A secondary structural feature of tRNA. Contains a
number of dihydrouridines.

Ribosomes

 Multicomponent particles involved in protein
synthesis
 Having proteins and small rRNA (different length)
 Both prokaryotes & Eukaryotes are having
1 small sub unit and 1 large sub unit

Eukaryotic cytoplasmic ribosomes are larger and more
complex than prokaryotic ribosomes. Mitochondrial and
chloroplast ribosomes differ from both examples shown.
Ribosome
Source
Whole
Ribosome
Small
Subunit
Large
Subunit
Prokaryot
e
70S 30S
16S RNA
21 proteins
50S
23S & 5S
RNAs
31 proteins
Eukaryote 80S 40S
18S RNA
33 proteins
60S
28S, 5.8S, &5S
RNAs
49 proteins
Ribosome Composition (S = sedimentation coefficient)

Prokaryotic Ribosomes
•50 s and 30 s subunits association and dissociation is
• based on the conc. Of MgCl2.
•At high Con. – Association
•At Low Conc. – Dissociation
Small Sub Unit – Binding of mRNA
large sub Unit – Binding of tRNA

Translation - Direction
Movement of Ribosome on mRNA is 5’ to 3’ end
Synthesis of protein peptide from Amino terminal to Carboxyl terminal

Translation….