description of translation in both prokaryotes and eukaryotes and the components required for translation and also co translation tranlocation,post translation translocation and also inhibitors of translation in both prokaryotes and eukaryotes

1. TRANSLATION
D.INDRAJA

2. • Translation is the process of protein synthesis in which the genetic
information encoded in mRNA is translated into a sequence of amino acids
in a polypeptide chain
• Proteins are made up from a set of 20 amino acids called standard amino
acids. Each of the 20 amino acids is specified by specific codons
• Polypeptide synthesis proceeds from N-terminus to C-terminus and
ribosome read in 5’-3’ direction
LOCATION
• The translation takes place on ribosome in cytoplasm of the cell. It is
simultaneous in prokaryotic transcription, while required processing mRNA
in eukaryotes

3. COMPONENTS REQUIRED FOR
TRANSLATION
RIBOSOMES
• In prokaryotes ribosomes are distributed through out the cells
• In eukaryotes ribosomes are located in the cytoplasm frequently on the
extensive intra cellular membrane network of the endoplasmic reticlum
• The ribosomes of eukaryotes are larger, usually about 80S how ever size
varies from species to species
• The ribosome present in the mitochondria and chloroplast of eukaryotic cells
are smaller usually about 60S
• Ribosomes are approximately half protein and half RNA

4. • A ribosome is composed of two halves, a large and a small subunit. During
translation, ribosomal subunits assemble together like a sandwich on the
strand of mRNA
• Each subunit is composed of RNA molecules and proteins
• The small subunit binds to the mRNA
• The large subunit has binding sites for tRNAs and also catalyzes peptide
bonds between amino acids
TRANSFER RNAs
• The translation of a coded mRNA message into a sequence of amino acids in
a poly peptide requires tRNA molecule
• Atleast one specific type of tRNA is required per amino acid. Also a single
tRNA may recognize two or three codons all specifying one single amino
acid

5. • Anti codon arm of tRNA contain a triplet nucleotide sequence, which is
complementary to and base pairs with the codon sequence in mRNA during
translation
• Because of tRNAs ability to both carry a specific amino acid and to
recognize the codon for that amino acid, tRNAs are also known as adaptor
molecule
tRNA binding sites on ribosomes
a) A or amino acyl site  binds the incoming aminoacyl tRNA, the tRNA
carrying the next amino acid to be added to the growing polypeptide chain
b) P or peptidyl site binds the tRNA to which the growing polypeptide is
attached
c) E or exit site binds the departing uncharged tRNA

6. Messenger RNA
• The specific mRNA required as a template for the synthesis of the desired
polypeptide chain must be present .
Amino acids
• All amino acids that appear in the finished protein must be present at the
time of protein synthesis.
ATP and GTP
• ATP and GTP are required as the source of energy.
Protein factors
• Initiation, elongation, termination/release factors are required for peptide
synthesis.

7. STEPS IN TRANSLATION
• Activation of aminoacid/charging of tRNA
• Polypeptide chain Initiation
• Chain elongation
• Chain termination

8. Activation of Amino acid
• The attachment of amino acids to tRNAs is the function of the group of
enzymes called aminoacyl -tRNA synthetases (also known as aminoacyl
tRNA ligase)
• aminoacyl -tRNA synthetases activate the amino acids by covalently linking
them to tRNAs
• When a tRNA is chared with the amino acid corresponding to its anti codon
it is called aminoacyl- tRNA
• Amino acylation reaction is performed by two step process
1. Amino acids are activated by ATP forming an intermediate amino acyl
adenylate
2. Amino acid is transferred to the 3’ end of the tRNA
Amino acid attachment site
The amino acids are attached to the tRNAs by high energy bond (ester bond)
between the carboxyl group of the aminoacids and 3’ hydroxyl termini of the
tRNA

10. • There are 20 aminoacyl-tRNA synthetases for 20 amino acids. These fall
into two distinct groups class I &class II
Class I  these attach the aminoacid to the free 2’or 3’ hydroxyl groups of the
adenosine at the 3’ terminus of tRNA molecules by ATP requiring
reaction.these are generally monomeric.
Class II these attach to the 3’OH group .these are generally dimeric or
multimeric

11. Translation in Prokaryotes

12. Polypeptide chain initiation
• Initiation involves binding of small ribosomal subunit to mRNA and then is
joined by the 50S subunit .it involves the reactions that precede the
formation of the peptide bond between the first two amino acids of the
protein
Major factors that are needed for initiation
Initiating amino acid and initiating codon
• The synthesis of all proteins starts with the same amino acid Methionine in
E.coli and in other Eubacteria the first amino acid in any newly synthesized
polypeptide is N-formyl methionine
• In eubacteria such as E.coli, AUG and GUG and on rare occasions UUG,
serve as initiation codons these are present in the initiating positions and
these are recognized by N-formyl met tRNA
• so first amino acid appeared is formyl methionine
• The meaning of AUG and GUG codons depends on their context.
• AUG
•  (Initiating position formyl methionine, coding region methionine)

13. • GUG
•  (Initiating position formyl methionine, coding region Valine)
Initiating tRNA
• In prokaryotes the initiator tRNA carries a formylated methionine residue
that initiates the protein synthesis.it recognize the initiating codons
AUG,GUG,UUG
• Conserved feautures of initiator tRNA distinguish them from elongator
tRNA
• Absence of base pairing between the bases 1 and 72 in acceptor arm
• Presence of three consecutive GC base pairs in anticodon arm(these
base pairs are required to allow the initiator tRNA to be inserted
directly in to the P-site

14. Initiation factors
• IF-1  binds over the A site of small ribosomal subunit and is thought to
prevent the initiator tRNA from binding to the A-site
• IF-2  directs the initiator tRNA to its correct position in the initiation
complex.it has ribosome dependent GTPase activity. The GTP is hydrolyzed
when the 50S subunit joins to generate a complete ribosome
• IF-3  binds to E site of 30S subunits and prevent premature reassociation
of the large and small subunits of the ribosome and also controls the ability
of 30S subunits to bind to mRNA and also selects the initiator tRNA for use
in initiation
Shine Dalgarno sequence
• The 30S subunit of the ribosome contains 16SrRNA
• The 3’ end of the 16SrRNA contains a consensus sequence called shine
dalgarno sequence and it is complementary to the 5’end sequence present in
the mRNA
• When they are in contact with the each other correct positioning of mRNA is
done

15. Steps involved in initiation
 Binding of IF-3 to the E site this prevents the
premature binding of 50S subunit to the 30S subunit
Binding of IF-1 to the A site this prevents premature
reassociation amino acyl tRNA to the A site
mRNA gets associated with the 30S subunit of the
ribosome. Correct positioning is said that when shine
dalgarno sequence of 16S rRNA binds to the 5’ region of
the mRNA
GTP bound IF-2 recruits the f met tRNA to the P site
of the 30S subunit of the ribosome
GTP hydrolysis occurs and removal of all factors have
been done
Joining of the 50S subunit and form 70S initiation
complex

16. Chain Elongation
• Elongation is a cyclic process on the ribosome in which one aminoacid at a
time is added to the nascent peptide chain
• Elongation rate in E.coli is roughly 15 amino acids per second
• Major factors that are needed for initiation:
 EF-Tu: Directs the next tRNA to its correct position in the ribosome.
 EF-Ts: Regenerates EF-Tu after the hydrolysis of attached GTP
molecule
 EF-G: Mediates Translocation
• Elongation takes place in 3 stages
– Decoding: In this case the ribosome selects and binds an amino acyl
tRNA whose anti codon is complementary to the mRNA codon in the A
site
– Transpeptidation: During tranpeptidation the peptidyl group on the P
site of tRNA is transferred to the amino acyl group in the A site through
the formation of peptide bond
– Translocation: In translocation, A and P site tRNAs are respectively
transferred to the P site and E site accompanied by their bound mRNA

17. Steps involved in Elongation:
EF-Tu with GTP mediates the entry of amino-acyl-tRNA into the A site and
forms EF-Tu GTP complex and this binds with the tRNA. next hydrolysis
of GTP of the complex to GDP helps drive the binding of amino-acyl tRNA
to the A site at which EF-Tu is released and it becomes inactivated and it is
activated by EF-Ts
The carboxyl end of the polypeptide chain is uncoupled from the tRNA
molecule in the P site and joined by a peptide bond to the amino acid linked
to the tRNA molecule in the A site. This reaction of protein synthesis is
catalyzed by a peptidyl transferase. The primary activity of peptidile
transfer however is a ribozyme activity encoded in the 23S rRNA of larger
sub unit
The t RNA present in the A site moves to the P site and the tRNA present in
the P site moves to E site. This is performed by EF-G (Also called
Translocase) with GTP by hydrolysing into GDP

19. Thirdstepinelongation

20. Proofreading
• Two fundamental different proofreading mechanisms are used in the cell.
Both are active process
I) Chemical proofreading
• This is carried out by amino acyl tRNA synthetases which recognizes an
incorrect amino acid attached to its tRNA molecule and remove it by
hydrolysis
• When incorrect amino acid binds to synthetases and form non cognate tRNA
adenylate then the wrong amino acid is added to the tRNA, is then
recognized as incorrect as incorrect by its structure in the tRNA binding site,
and so is hydrolyzed and released.
II) kinetic proofreading
• An incorrect tRNA molecule forms a smaller number of codon-anticodon
hydrogen bonds than a correct one, it there fore binds more weakly to the
ribosomes and is more likely to dissociate during the period where
elongation EF-G hydrolyses its GTP
• The elongation factor thereby introduces a short delay between codon-
anticodon basepairing and polypeptide chain elongation, which provides an
opportunity for the bound tRNA molecule to exit from the ribosome
• Thus the delay introduced by the elongation factor causes most incorrectly
bound tRNA molecules to leave the ribosome with out being used for protein
synthesis.

21. Chain Elongation

22. Chain termination
• Protein syhthesis ends when one of the three termination (stop) codons
(UAA,UAG,UGA) is reached.
Major factors that are needed for termination
• To terminate the polypeptide chain we need release factors(RF) and they are
classsified into class I(RF1&RF2) and class II(RF3)
• RF-1  recognizes the termination codons 5’-UAA-3’ and 5’-UAG-3’
• RF-2  recognizes 5’-UAA-3’ and 5’-UGA-3’
• RF-3  stimulates dissociation of RF-1 and RF-2 from the ribosome after
termination
Steps involved in termination
• The A site is now entered not by a tRNA, but by a protein release factor
• RF-1 and RF-2 recognizes the stop codons and activate the ribosome to
hydrolyze the bond between tRNA and polypeptide release through a
GGQ(Gly-Gly-Gln) motif which acts as peptide anticodon
• RF-3 stimulates release of RF-1 or RF-2 from the ribosome after termination
in a reaction requiring energy from the hydrolysis of GTP

23. Chain termination
•Now the RRF(ribosomal release factor )along with GTP and EFG binds to the
A site and acts as translocation and release the uncharged tRNA in the E site
•Once E site becomes free automatically IF3 binds to the E site and results in
dissociation of the larger subunit and all the products are released.

25. EUKARYOTIC TRANSLATION

26. Polypeptide chain initiation
• Eukaryotic initiation takes place in two different ways
1. Cap dependent initiation
2. Cap independent initiation
EXAMPLE : Cap dependent initiation  majority of eukaryotes go through cap
dependent initiation
EXAMPLE : Cap independent initiation  this generally go through IRES(internal
ribosome entry site) ,generally viruses in eukaryotes go through this mechanism
and also in cellular stress, when overall translation is reduced. Examples include
factors responding to apoptosis and stress-induced responses.
Cap dependent initiation Cap independent
initiation
•Circulization of mRNA •No circulization of mRNA
•5’ cap of mRNA is presnt •5’ cap of mRNA is absent
•Poly A tail is present •Poly A tail is absent
•Scanning of mRNA takes place •No scanning of mRNA takes place

27. Cap dependent initiation
• Initiation in eukaryotes involves different steps
• The main difference between translation in eubacteria and in
eukaryotes occur during the initiation phase. Eukaryotic cells require
more initiation factors than eubacteria (12 factors required for
initiation)

28. 43S pre initiation complex
• In the first step the EIF3 binds to the E site of the 40S subunit so that it can
prevent the premature reasocciation of 60S subunit
• EIF1 binds to the A site of the 40S subunit so that P site is free and the
initiator tRNA can directly enter in to it
• EIF2 along with GTP binds to the initiator tRNA and forms ternary complex
and bring the tRNA to the P site of the 40S ribosome(but the tRNA is not
properly placed in the P site due to the absence of mRNA
43S pre initiation complex

29. 48S pre initiation complex(attachment of mRNA)
• In eukaryotes mRNA has 5’ cap and 3’ poly A tail and also some secondary
structures at 5’ end the mRNA also have contiguous nucleotide sequence of
5’-GCC(A or G)CCAUGG3’ this sequence is required for optimal initiation
translation in eukaryotes which is called kozak’s rule/kozak’s sequence
• For the attachment of mRNA to the 43S complex it requires EIF4
complex.(it is a heterotrimeric complex containing EIF4A,EIF4G,EIF4E)
• EIF4E(acts as cap binding protein) binds to the 7 met guanosine which is a
cap region at 5’ end and next EIF4A(acts as helicase) binds to the secondary
structure at 5’ end and helps in removing the secondary structures
• EIF4G binds to the EIF4E and in turn PABP (poly A binding protein ) binds
to the EIF4G. This leads to the circulization of poly A tail takes place
• Now we have both mRNA bind initiation factors and 43S initiation complex
they both come and contact with each other and now it start to scan for the
kozak sequence in the mRNA
• Scanning takes place with the help of Dhx29 and Ddx3 proteins on the
mRNA

30. • Once it finds the start codon proper placing of the tRNA takes place(forms
complete 48S initiation complex) by hydrolyzing the GTP bound to EIF2 to
EIF-GDP(this is again utilized in GTP form and this conversion takes place
with the help of EIF2B)

31. 48S pre initiation complex

32. • 80S pre initiation complex(assembly of
larger subunit)
• Larger subunit 60S along with EIF5 and GTP comes and binds that removes
all the factors present in the complex later GTP that is present withEIF5 also
gets hydrolyzed and forms complete 80S complex
80S initiation complex

33. Chain Elongation
• Elongation is a cyclic process on the ribosome in which one aminoacid at a
time is added to the nascent peptide chain
• The eukaryotic elongation cycle closely resembles that of prokaryotes
factors that act similar as in prokaryotic elongation factors are
• EF-Tu eEF1A
• EF-Ts eEF1b
• EF-G  eEF-2
• Elongation takes place in 3 stages
– Decoding: In this case the ribosome selects and binds an amino acyl
tRNA whose anti codon is complementary to the mRNA codon in the A
site
– Transpeptidation: During tranpeptidation the peptidyl group on the P
site of tRNA is transferred to the amino acyl group in the A site through
the formation of peptide bond
– Translocation: In translocation, A and P site tRNAs are respectively
transferred to the P site and E site accompanied by their bound mRNA
In Prokaryotes In Eukaryotes

34. Steps involved in chain elongation
• eEF1A along with GTP brings the incoming tRNA to the A site and once it brings
there GTP gets hydrolyzed to GDP and again it should convert in to GTP. This is
done by the complex of (EFIB,EFIG,EF1D)
• Next step is to add peptide bond it is done with the help of the enzyme
peptidyl transferase which is performed by the rRNA of the larger
ribosome.

35. • In the next it is translocated three nucleotides in 5’ to 3’ direction with the
help of Eef-2

36. Chain Elongation

37. • Co-translational translocation
• Most proteins that are secretory, membrane-bound, or reside in
the endoplasmic reticulum (ER), golgi or endosomes use the co-translational
translocation pathway.
• This process begins with the N-terminal signal peptide of the protein being
recognized by a signal recognition particle (SRP) while the protein is still
being synthesized on the ribosome.
• The synthesis pauses while the ribosome-protein complex is transferred to
an SRP receptor on the ER in eukaryotes.
• There, the nascent protein is inserted into the translocon, a membrane-
bound protein conducting channel composed of the Sec61 translocation
complex in eukaryotes.
• In secretory proteins and type I transmembrane proteins, the signal sequence
is immediately cleaved from the nascent polypeptide once it has been
translocated into the membrane of the ER (eukaryotes) by signal peptidase.
• The signal sequence of type II membrane proteins and some polytopic
membrane proteins are not cleaved off and therefore are referred to as signal
anchor sequences

38. • Within the ER, the protein is first covered by a chaperone protein to protect
it from the high concentration of other proteins in the ER, giving it time
to fold correctly.
• Once folded, the protein is modified as needed (for example,
by glycosylation), then transported to the Golgi for further processing and
goes to its target organelles or is retained in the ER by various ER
retention mechanisms

39. Post-translational translocation
• Even though most secretory proteins are co-translationally translocated,
some are translated in the cytosol and later transported to the ER/plasma
membrane by a post-translational system.
• This pathway is facilitated by Sec62 and Sec63, two membrane-bound
proteins. The Sec63 complex is embedded in the ER membrane.
• The Sec63 complex causes hydrolysis of ATP, which allows chaperone
proteins to bind to an exposed peptide chain and slide the polypeptide into
the ER lumen.
• Once in the lumen the polypeptide chain can be folded properly. This occurs
in only unfolded proteins that are in the cytosol.
• In addition, proteins targeted to other destinations, such
as mitochondria, chloroplasts, or peroxisomes, use specialized post-
translational pathways. Also, proteins targeted for the nucleus are
translocated post-translation. They pass through the nuclear
envelope via nuclear pores.

40. `

41. Chain termination
• Two types specific protein release factors have been discovered
a) eRF1(eukaryotic release factor 1)  it acts by binding to the ribosomal A
site and recognizing stop codons directly
b) eRF3  it is GTP binding protein .The eRF3-GTP acts along with eRF1
to promote clevage of the peptidyl tRNA thus releasing the completed
protein chain
• eRF3 GTPase monitors the correct recognition of a stop codon by eRF1
• Hydrolysis of eRF3-GTP to eRF3-GDP assumes correct termination of
translation.

42. Chain Termination

43. Inhibitors Function
Chloramphenicol Inhibits peptidyl transferase on larger
subunit in prokaryote
Cyclohexamide Inhibits peptidyl transferase on larger
subunit in eukaryote
Erythromycin Inhibits translocation in prokaryote
Paromomycin Increase ribosomal error rate
Puromycin It is a Amino acyl tRNA analogue
(premature chain termination in
both prokaryotes and eukaryotes)
Streptomycin mRNA misreading and inhibits chain
initiation in prokaryotes
Tetracyclin Inhibits binding of amino acyl tRNA
to smaller subunit in prokaryote
Inhibitors of Protein Synthesis

44. Inhibitor Function
Diptheria Inactivates eEF2 by ADP ribosylation
Ricin/Abrin/Sarcin- (Fungal protein) •Ricin and Abrin are poisinous plant
glycosidases inactivate eukaryotic
large subunit by depurinating the
28SrRNA located in sarcin-ricin loop
that is useful for ribosomal factors
binding centre
•Sarcin cleaves phosphodiesterase
bond in sarcin-ricin loop
Fusidic acid Inhibits protein synthesis by targeting
ribosome bound EG-G in both
translocation and ribosome recycling
factor or release factor in prokaryotes