Topics covered are: 1. History and Characteristics of Genetic codes 2. Wobble hypothesis 3. Stages (Initiation, Elongation and Termination) of translation in Prokaryotes and Eukaryotes with enzymes and their functions 4. Post-translation modification such as Glycosylation, Lipidation, Phosphorylation, Acetylation, Methylation (lysine and arginine methylation) and Ubiquitination

1. TRANSLATION
By:
Aslesha Golwankar

2. THE GENETIC CODE
 The genetic code is a triplet code, in which three
nucleotides code for each amino acid in a protein called
as codon
 There are 64 codons (43 = 64) which specifies 20 amino
acids.
 3 codons do not represent the amino acids and causes
termination of translation

3. EXPERIMENT OF MARSHALL NIRENBERG AND
JOHANN HEINRICH MATTHAEI
 They created synthetic RNAs by using an enzyme called
polynucleotide phosphorylase
 Polynucleotide phosphorylase randomly links together
any RNA nucleotides
 The synthetic mRNAs were homopolymers
 polynucleotide phosphorylase was added to a solution
of uracil nucleotides that consisted entirely of uracil
nucleotides and thus contained only UUU codons

4.  These poly(U) RNAs were then added to 20 tubes, each
containing a cell-free protein-synthesizing system and
the 20 different amino acids, one of which was
radioactively labeled.
 Translation took place in all 20 tubes, but radioactive
protein appeared in only one of the tubes—the one
containing labeled phenylalanine

6.  They created synthetic RNAs containing two or three
different bases (known as random copolymers)
 determining the frequency of incorporation of particular
amino acids, it was possible to determine the composition
of the codon for many amino acids
 Problems: the theoretical calculations depended on the
random incorporation of bases which did not always occur,
and sometimes several different codons specify the same
amino acid

7.  In 1964, Nirenberg and Philip Leder developed another
technique that used ribosome-bound tRNAs
 They found that a very short sequence of mRNA—even
one consisting of a single codon—would bind to a
ribosome
 The codon on the short mRNA would then base pair
with the matching anticodon on a tRNA that carries the
amino acid specified by the codon
 The ribosome-bound mRNA was mixed with tRNAs and
amino acids and this mixture was passed through a
nitrocellulose filter

8.  The tRNAs paired with the ribosome-bound mRNA stuck
to the filter, whereas unbound tRNAs passed through
 They then isolated the ribosome-bound tRNAs and
determined which amino acids were present on the
bound tRNAs
 Using this method, Nirenberg and his colleagues were
able to determine the amino acids encoded by more
than 50 codons
 A total of 61 codons were shown to code for amino acids
and there were three stop codons

11. CHARACTERISTICS OF GENETIC CODE
1. The genetic code consists of a sequence of nucleotides in
DNA or RNA. There are four letters in the code,
corresponding to the four bases—A, G, C, and U (T in DNA).
2. The genetic code is a triplet code. Each amino acid is
encoded by a sequence of three consecutive nucleotides,
called a codon.
3. The genetic code is degenerate—there are 64 codons but
only 20 amino acids in proteins. Some codons are
synonymous, specifying the same amino acid.
4. Isoaccepting tRNAs are tRNAs with different anticodons that
accept the same amino acid; wobble allows the anticodon on
one type of tRNA to pair with more than one type of codon
on mRNA.

12. 5. The code is generally non-overlapping; each nucleotide
in an mRNA sequence belongs to a single reading
frame.
6. The reading frame is set by an initiation codon, which
is usually AUG.
7. When a reading frame has been set, codons are read
as successive groups of three nucleotides.
8. Any one of three termination codons (UAA, UAG, and
UGA) can signal the end of a protein; no amino acids
are encoded by the termination codons.
9. The code is almost universal.

13. WOBBLE
 Many synonymous codons differ only in the third
position
 For example, alanine is encoded by the codons GCU,
GCC, GCA, and GCG, all of which begin with GC.
 When the codon on the mRNA and the anticodon of the
tRNA join the first (5′) base of the codon pairs with the
third base (3′) of the anticodon (A with U; C with G).
 Next, the middle bases of codon and anticodon pair.
 After these pairs have hydrogen bonded, the third bases
pair weakly— there may be flexibility, or wobble, in their
pairing

14.  In 1966, Francis Crick
developed the wobble
hypothesis, which proposed
that some nonstandard
pairings of bases could occur
at the third position of a
codon.
 For example, a G in the
anticodon may pair with
either a C or a U in the third
position of the codon

15. BINDING OF AMINO ACIDS TO TRANSFER RNA
 A cell has 30 to 50 different tRNAs and these tRNAs are
attached to the 20 different amino acids.
 Each tRNA is specific for a particular kind of amino acid
 All tRNAs have the sequence CCA at the 3′ end.
 The carboxyl group (COO⁻) of the amino acid is attached
to the 2′- or 3′- hydroxyl group of the adenine nucleotide
at the end of the tRNA

16.  Aminoacyl-tRNA synthetases- Enzyme which recognizes
a particular amino acids and all tRNAs that accept that
amino acid
 A cell has 20 different aminoacyl-tRNA synthetases, one
for each of the 20 amino acids.
 tRNA charging- Attachment of tRNA to its appropriate
amino acid.

17. The resulting aminoacetylated tRNA is written as:
Ala-tRNAAla – amino acid alanine (Ala) is attached to
it tRNA (tRNAAla)

18.  Stages of translation:
1. Initiation
2. Elongation
3. Termination

19. INITIATION IN PROKARYOTES
 Initiation comprises three major steps.
1. mRNA binds to the small subunit of the ribosome.
 A functional ribosome exists as two subunits, the small
30S subunit and the large 50S subunit
 Initiation factor 3 (IF-3) binds to the small subunit of the
ribosome and prevents the large subunit from binding
during initiation

20.  The Shine-Dalgarno sequence:
 Also known as ribosome binding site
 It is complementary to a sequence of nucleotides at the
3 end of 16S rRNA

21. 2. Next, the initiator fMet-tRNAfMet attaches to the
initiation codon.
 Initiation factor 2 (IF-2) forms a complex with GTP.
 Initiation factor 1 (IF-1) enhances the dissociation of the
large and small ribosomal subunits.
3. In the final step of initiation, IF-3 dissociates from the
small subunit, allowing the large subunit of the
ribosome to join the initiation complex.
 The molecule of GTP is hydrolyzed to guanosine
diphosphate (GDP), and IF-1 and IF-2 depart

23. INITIATION IN EUKARYOTES
 There is no Shine–Dalgarno sequence
 Kozak proposed a scanning hypothesis in which the 40S
subunit, already containing the initiator tRNA, attaches
to the 5′-end of the mRNA and scans along the mRNA
until it finds an appropriate AUG
 The initiator tRNA joins to make a complex of three
components (ternary complex) of the initiator tRNA,
eIF2 and GTP

24.  The ternary complex then forms part of a multifactor
complex (MFC) containing eIF1, eIF2-GTP-tRNAi, eIF3
and eIF5
 The binding of the MFC to a free 40S subunit is assisted
by eIF1A and the resulting complex is called the 43S pre-
initiation complex
 The second major step occurs when the 43S pre-
initiation complex has bound to the mRNA complex via
the interactions between eIF4G and eIF3.
 In the third step, ATP is used as the mRNA is scanned to
find the AUG start codon

25.  In the fourth step, to allow the 60S subunit to bind,
eIF5B must displace eIF1, eIF2, eIF3 and eIF5 and GTP is
hydrolyzed.
 eIF1A and eIF5B are released when the latter has
assisted 60S subunit binding to form the complete 80S
initiation complex.
 The released eIF2.GDP complex is recycled by eIF2B and
the rate of recycling (and hence the rate of initiation of
protein synthesis) is regulated by phosphorylation of the
α-subunit of eIF2

27. INITIATION FACTORS
Prokaryotes Eukaryotes Functions
IF1, IF3 eIF1, eIF1A, eIF3,
eIF5/eIF2, elF2B
Binding to small
subunit/initiator tRNA
delivery
IF2 eIF4B, eIF4F, elF4H
eIF5B
Binding to mRNA
Displacement of other
factors and large
subunit recruitment

28. ELONGATION IN PROKARYOTES
 A ribosome has three sites that can be occupied by
tRNAs; the aminoacyl or A site, the peptidyl or P site and
the exit or E site
 The initiator tRNA immediately occupies the P site but
all other tRNAs first enter the A site.
 After initiation, the ribosome is attached to the mRNA,
and fMet-tRNAfMet is positioned over the AUG start
codon in the P site; the adjacent A site is unoccupied

29.  Elongation occurs in three steps.
 The first step is the delivery of a charged tRNA to the A site.
 EF-Tu joins with GTP and then binds to a charged tRNA to
form a three-part complex.
 This three-part complex enters the A site of the ribosome,
where the anticodon on the tRNA pairs with the codon on
the mRNA.
 After the charged tRNA is in the A site, GTP is cleaved to
GDP, and the EF-Tu–GDP complex is released

31.  The second step is the creation of a peptide bond
between the amino acids that are attached to tRNAs in
the P and A sites.
 The formation of this peptide bond releases the amino
acid in the P site from its tRNA. The activity responsible
for peptidebond formation in the ribosome is referred to
as peptidyl transferase

32.  The third step in elongation is translocation
 This step positions the ribosome over the next codon
and requires elongation factor G (EF-G) and the
hydrolysis of GTP to GDP.
 Because the tRNAs in the P and A site are still attached
to the mRNA through codon– anticodon pairing, they do
not move with the ribosome as it translocates
 Consequently, the ribosome shifts so that the tRNA that
previously occupied the P site now occupies the E site,
from which it moves into the cytoplasm where it may be
recharged with another amino acid.

34. ELONGATION FACTORS
Prokaryotes Eukaryotes Functions
EF-Tu eEF1 Aminoacyl tRNA
delivery to ribosome
EF-Ts eEF1 Recycling of EF-Tu or
eEF1
EF-G eEF2 Translocation

35. TERMINATION IN PROKARYOTES
 Protein synthesis terminates when the ribosome
translocates to a termination codon as there are no
tRNAs with anticodons complementary to the
termination codons, no tRNA enters the A site of the
ribosome when a termination codon is encountered
 E. coli has three release factors—RF1, RF2, and RF3.
 Release factor 1 recognizes the termination codons UAA
and UAG
 RF2 recognizes UGA and UAA.
 Release factor 3 forms a complex with GTP and binds to
the ribosome.

36.  The release factors then promote the cleavage of the
tRNA in the P site from the polypeptide chain; in the
process, the GTP that is complexed to RF3 is hydrolyzed
to GDP.
 Additional factors help bring about the release of the
tRNA from the P site, the release of the mRNA from the
ribosome, and the dissociation of the ribosome

38. TERMINATION FACTORS
Prokaryotes Eukaryotes Functions
RF1
eRF
Polypeptide chain
reactionRF2
RF3

39. POST TRANSLATIONAL MODIFICATIONS

40. GLYCOSYLATION
 This is the addition of a carbohydrate or sugar to
proteins.
 Glycosylations are often required for correct peptide
folding and can increase protein stability and solubility
and protect against degradation.
 Sugars are added to Threonine, tyrosine and Serine
through O-linkage, and Asparagine and Arginine through
N-linkage.

41. GLYCOSYLATION

42. LIPIDATION
 Lipidation attaches a lipid group, such as a fatty acid,
covalently to a protein.
 In general, lipidation helps in membrane localization and
targeting signals
 Myristoylation plays a role in membrane targeting

43. EXAMPLE: MERISTOYLATION OF N-TERMINAL
GLYCINE

44. PHOSPHORYLATION
 Phosphorylation is the addition of a phosphate (PO4)
group to a serine, tyrosine or threonine residue in a
peptide chain
 It plays an important role in regulating many important
cellular processes such as cell cycle, growth and
apoptosis (programmed cell death).

46. N-ACETYLATION
 It has both reversible and irreversible mechanisms.
 Acetylation helps in protein stability, protection of the
N-terminus and the regulation of protein-DNA
interactions in the case of histones.

47. HAT – histone acetyletransferase
HAD – histone deacetylase

48. METHYLATION
 Protein methylation typically takes place on arginine or
lysine amino acid residues in the protein sequence.
 Methylation of histones, a type of DNA binding protein,
can regulate DNA transcription.

50. UBIQUITINATION
 Ubiquitination is a pathway in which small proteins
called ubiquitin (Ub) is linked to substrate protein
 The last amino acid of Ub is linked to lysine residue of
substrate protein through an isopeptide linkage
between C-terminal glycine of Ub and the amino group
of lysine
 Poly-ubiquitinated proteins are targeted for destruction
which leads to component recycling and the release of
ubiquitin.

52. THANK
YOU…