Transcription

andTranslation

TIrc genctic aodc speahs t

"Tipkt haseseqaence RNA,I am;
of messenger
in character;
Uniatrsal,Eeqific,non-oaefkry** degqnerata
Faithfullyworhunderthedictansof DNA :
Tbexecute for prowinqntllesis,"
orders
tn! master's

-f. h" conventionalconceptof centraldogma of

I lif e whic h i n e s s e n c ei s " D N A ma k e s R N A
makes protein" is an oversimplification of
m olec ular b i o l o g y . W i th th e a d v a n c e sin cel l
biology an d ra p i d d e v e l o p me n ts i n bi o-
informatics, the terms genome, transcriptome rr'i,
ilil'*5 i:5i !SjTL]1'll:
and proteome are in current use to represent I
t he c ent r a l d o g ma o f mo l e c u l a r bi ol ogy
ITranslation
1Fig.25.l). Some information on the new
lpl+orr'.or,nL-]
c onc ept san d te rmi n o l o g yi s g i v e n h e re u nder.
Conventional concept concept
Current
(pre-bioinformatics
era) (bioinformatics
era)
GENOME
Fiq,25.1: Thecentraldogmaof life (or molecular
The total DNA (genetic information) biology)representedin the formof conventional
contained in an organism or a cell is regardedas and currentconcepts.
the genome.Thus, the genome is the storehouse
of biologi c a l i n fo rma ti o n . l t i n c l u d es the structuralmotifsand completeproteinstructures.
c hr om os om e si n th e n u c l e u s a n d th e D N A i n Comparative genomics involves the study of
m it oc hond ri a a
, n d c h l o ro p l a s ts . comparativegene function and phylogeny.

Genomics : The study of the structureand

TRANSCBIPTOME
function of genome is genomics. The term
functional genomics is used to represent the The RNA copies of the active protein
gene expressionand relationshipof genes with coding genes represent transcriptome. Thus,
gene products. Structural genomics refersto the transcri ptomei s the i ni ti al product of gene

542
Ghapten 25 : TFANSCRIPTION
AND THANSLATION 543

expression which directs the synthesis of

proteins.

Transcriptomics: The study of transcriptome q

that involvesall the RNA moleculesmade by a
cell, tissueor an organism is transcriptomics.

PROTEOIIE
The cell's repertoi re (reposito rylstorehou se) of
proteins with their nature and biological
functions is regarded as proteome. Thus,
proteome representsthe entire range of proteins
and t hei r b i o l o g i c a lfu n c ti o n si n a c e l l . Fig. 25.2 : RNApolymerase of E. coli.

Proteomics : The study of the proteome.

some selectedregionsof DNA. For certain other
Metabolomics : The use of genome sequence
regions of DNA, there may not be any
analysisfor determiningthe capability of a cell,
transcription at all. The exact reason for the
tissue or an organism to synthesize small
selectivetranscriptionis not known. This may be
molecules(metabolites)is metabolomics.
due to some i nbui l t si gnal s i n the D N A
Whether the central dogma of life is mol ecul e.
representedin the conventionalor more recent
form, replication, transcription and translation The productformed in transcriptionis referred
are the key or core processesthat ultimately to as primary transcript. Most often, the primary
control life. Reolication of DNA has been RNA transcripts are inactive. They undergo
described in Chapter 24, while transcriptionand certain alterations(splicing,terminal additions,
translationare discussedin this chapter. base modifications etc.) commonly known as
post-transcriptional modifications, to produce
functionally active RNA molecules.

There exist certain differences in the

transcriptionbetweenprokaryotesand eukaryotes.
Transcriptionis a processin which ribo- The RNA synthesisin prokaryotesis given in some
nucleic acid (RNA) is synthesizedfrom DNA. detail. This is followed by a brief discussionon
The word gene refersto the functional unit of eukaryotictranscription.
the DNA that can be transcribed.Thus, the
geneticinformationstoredin DNA is expressed TRANSCRIPTION IN PROKARYOTES
throughRNA. For this purpose,one of the two
strandsof DNA servesas a template(non-coding A single enzyme-DNA dependent RNA
strand or sensestrand)and produces working polymerase or simply RNA polymerase-
copiesof RNAmolecules. TheotherDNA strand synthesizesall the RNAs in prokaryotes.RNA
which does not participatein transcriptionis polymeraseof E. coli is a complex holoenzyme
referredto as codingstrandor antisensestrand (mol wt. 465 kDa) with five polypeptide
(frequentlyreferredto as coding strandsince subunits-2c, 1p and 1p' and one sigma(s)factor
with the exceptionof T for U, primarymRNA (Fi9.25,2).The enzyme without sigma factor is
containscodonswith the samebasesequence). referred to as core enzyme (ozpp').
An overview of RNA synthesisis depicted in
Transeription is selective
Fig,25.3. Transcription involves three different
Theentiremoleculeof DNA is not expressed stages-initiation, elongation and termination
RNAsare synthesized
in transcription. only for (Fig.25.4.
452 BIOCHEMISTRY

I. Essayquestions
1. Describethe role of second messengers
in hormonal action.
2. Write an account of the anterior pituitary hormones.
3. Discussin detail the synthesisand biochemicalfunctionsof thyroid hormones.
4. Describethe hormonesof adrenalcortex with special referenceto glucocorticoids.
5. Write briefly on the synthesisand biochemicalfunctionsof sex hormones.

II. Short notes

(a)'C'-Proteins, (b) Inositol triphosphate,(c) Hypothalamic hormones, (d) ACTH, (e) Goiter,
(fl Epinephrine,(g) Cortisol, (h) Castrin, (i) ADH, (j) Aldosterone.

III. Fill in the blanks

1. The enzyme that catalysesthe formation of cAMP from ATP is
2. The inorganicion that can act as a secondmessenger
for certainhormonesis
3. The endocrineorgan responsiblefor the synthesisof trophic hormonesis
4. The compounds that produce opiate-like effects on the central nervous system are

5. The enzyme that convertsiodide (l-) to active iodine (l+)

6. The most predominantmineralocorticoidsynthesizedby adrenalcortex
7. The major urinary excretoryproduct of catecholamines
8. The male sex hormone, testosterone, is converted to a more active form, namely

9. The precursorfor the synthesisof steroid hormones

10. The gastrointestinalhormone that increasesthe flow of bile from the gall bladder

IV. Multiple choice questions

11. lmpairmentin the synthesis
of dopamineby the brain is a majorcausative
factorfor the disorder
(a) Parkinson'sdisease(b) Addison'sdisease(c) Cushing,ssyndrome(d) Coiter.
12. One of the following hormonesis an amino acid derivative
(a) Epinephrine(b) Norepinephrine (c) Thyroxine(d) All of them.
13. The most activemineralocorticoid
hormoneis
(a) Cortisol (b) Aldosterone(c) 11-Deoxycorticosterone
(d) Corticosterone.
14. Name the hormone,predominantlyproducedin responseto fight, fright and flight
(a) Thyroxine (b) Aldosterone(c) Epinephrine(d) ADH.
15. The hormoneessentiallyrequiredfor the implantationof fertilizedovum and maintenanceof
pregnancy
(a) Progesterone
(b) Estrogen(c) Cortisol (d) Prolactin.
544 BIOCHEMISTRY

Initiation for RNA polymerase and, further,this enzyme

doesnot possessendo-or exonuclease activity.
The bindingof the enzymeRNA polymerase
Due to lack of the latter function (proof-reading
to DNA is the prerequisite for the transcription
to
activity),RNApolymerase hasno abilityto repair
start.The specificregionon the DNA wherethe
the mistakesin the RNA synthesized. This is in
enzyme binds is known as promoter region.
contrastto DNA replication which is carriedout
There are two base sequenceson the coding
with high fidelity.lt is, however,fortunatethat
DNA strandwhich the sigma factor of RNA
mistakesin RNA synthesis are lessdangerous,
polymerasecan recognizefor initiation of
since they are not transmitted to the daughter
transcription(Fig.2|.A.
cells.
1. Pribnowbox (TATAbox) : Thisconsistsof
Thedoublehelicalstructure of DNA unwinds
6 nucleotidebases(TATAAT), locatedon the left
as the transcription goes otr, resulting in
side about 10 basesaway (upstream) from the
supercoils.The problem of supercoils is
startingpoint of transcription. (more details in
overcomeby topoisomerases
2. The '-35' sequence: This is the second Chapter 24).
recognition sitein the promoterregionof DNA.
It containsa basesequence TTCACA,which is Termination
locatedabout 35 bases(upstream,hence-35) The process of transcription stops by
away on the left side from the site of terminationsignals.Two typesof terminationare
transcriptionstart. identified.
Elongation 1. Rho(p) dependent termination: A specific
protein,namedp factor,binds to the growing
As the holoenzyme, RNA polymerase RNA (andnot to RNA polymerase) or weaklyto
recognizes the promoterregion,the sigmafactor
DNA, and in the bound stateit acts as ATPase
is releasedand transcriptionproceeds.RNA is and releases RNA.
and terminates transcription
synthesizedfrom 5' end to 3' end (5'-+3') The p factor is also responsiblefor the
antiparallel to the DNA template. RNA of RNA polymerase from DNA.
dissociation
polymerase utilizesribonucleotide
triphosphates
(ATP,CTP, CTP and UTP)for the formationof 2. Rho (p) independenttermination : The
RNA.Forthe additionof eachnucleotide to the termination in this caseis broughtaboutby the
growing chain, a pyrophosphatemoiety is formation ol hairpinsof newly synthesized RNA.
released. This occurs due to the presence
of palindromes.
A palindromeis a word that readsalikeforward
The sequenceof nucleotidebasesin the and backwarde.g. madam,rotor.The presence
mRNA is complementary to the templateDNA of palindromes in the basesequenceof DNA
strand.lt is however,identicalto that of coding template(samewhen readin oppositedirection)
strandexceptthat RNAcontainsU in placeof T in thetermination regionis known,As a resultof
in DNA (Fig.2s.6). this, the newly synthesized RNA folds to form
RNA polymerase differs from DNA hairpins(due to complementary base pairing)
polymerase No primeris required that causeterminationof transcription.
in two aspects.
Tranecrlptlon
unlt If
o
a
DNA template N
3
-I]
za
C)
ll
T

z
3' z
5',
o
-1
fl

z
a
h>
-.1
d
z

9l
s
9l
546 BIOCHEMISTF|Y

-35
Sequence
Coding 5' -TTGAC
strand
Template a,
strand

Startof
transcription
Fiq.25.5: Promoterregionsof DNAin prokaryotes.

3' Codingstrand
5' Templatestrand
RNA----------------+s'..--..A
U G C A U G G C A........3',

Fig. 25.6 : nanscription-Complementary base pair relationship.

TRANSGRIPTION IN EUKARYOTES 2. RNA polymerase ll synthesizes the

precursorsfor mR N A s and smal l nucl earR N A s.
RNA synthesisin eukaryotesis a much more
complicated process than the transcription 3. RNA polymerase lll participates in the
describedabove for prokaryotes.As such, all the formation of tRNAs and small ribosomal RNAs.
details of eukaryotic transcription (particularly Besidesthe three RNA polymerasesfound in
about termination)are not clearly known. The the nucleus, there also exists a mitochondrial
salientfeaturesof availableinformationare given RNA polymerase in eukaryotes. The latter
hereunder. resembles prokaryotic RNA polymerase in
structureand function.
RNA po l y n te ra s e s
The nuclei of eukaryotic cells possessthree Promoter sites
distinct RNA polymerases(Fi9.25.7). ln eukaryotes,a sequenceof DNA bases-
1. RNA polymeraseI is responsiblefor the which is almost identical to pribnow box of
synthesisof precursorsfor the large ribosomal prokaryotes-is identified (Fig.25.A. This
RNA s . sequence,known as Hognessbox (or TATA box),

s', 3',
DNA
3', 5'
I II I
RNApolymerase
I RNApolymerase
ll RNApolymerase
I
+
II
+
I
+
e.
r\ q'l
r- { a-1
CJ
tl

)t-r<
I/ C)
Ribosomal Messenger Transfer
RNA
RNAs RNA
Fig. 25.7 : An oveNiew of transciption in eukaryotes.
 Chapter 25 : THANSCRIPTION
AND TRANSLATTON 547

CMT box
Non-coding
strand
Coding
strand
-70 bases -25 bases
^'
Codingregionof gene J

is located on the left about 25 nucleotides away Heterogeneous nuclear

(upstream) from the starting site of mRNA RNA (hnRNA)
synthesis. There also exists another site of
recognition between 70 and 80 nucleotides The primary mRNA transcript produced by
upstream from the start of transcription.This RNApolymerase ll in eukaryotes
is oftenreferred
second site is referred to as CAAT box. One of to as heterogeneous nuclearRNA(hnRNA). This
these two sites (or sometimes both) helps RNA is then processedto producemRNA neededfor
polymerase ll to recognize the requisite proteinsynthesis.
sequenceon DNA for transcription.
POST.TRAl{SCRIPTIONAL
MODIFICATIONS
Initiation of transcription
The moleculareventsrequiredfor the The RNAsproducedduringtranscription are
called primarytranscripts.
They undergo many
initiation of transcription in eukaryotes are
complex, and broadly involve three stages.
alterations-terminal base additions, base
modifications, splicing etc., which are
1. Chromatin containing the promoter collectively referredto as post-transcriptional
sequence made accessibleto the transcription modifications. Thisprocessis requiredto convert
machinery. the RNAs into the active forms. A group of
enzymes/namelyribonucleases, are responsible
2. Binding of transcription factors (TFs) to
for the processingof tRNAs and rRNAsof both
DNA sequencesin the promoter region.
prokaryotesand eukaryotes.
3. Stimulationof transcriptionby enhancers.
The prokaryoticmRNA synthesizedin trans-
A farge number of transcription factors criptionis almostsimilarto thefunctionalmRNA.
interact with eukaryotic promoter regions. In In contrast,eukaryoticmRNA (i.e. hnRNA)
humans, about six transcription factors have undergoes extens
ive post-transcri
ptionalchanges.
been identified(TFllD,TFllA, TFllB,TFllF,TFllE,
TFIIH).lt is postulatedthat the TFs bind to each
An outline of the post-transcriptional
modificationsis given in Fig.21.g,and some
other, and in turn to the enzyme RNA
polymerase.
highlightsare described.

Enhancercan increasegene expressionby Messenger RNA

about100fold.Thisis madepossibleby binding
of enhancersto transcriptionfactors to forri tn: primarytranscriptof mRNAis the hnRNA
.
in eukaryotes,which is subjected to many
activators.ltis believedthatthe chromatinforms
changesbeforefunctionalmRNA is produced'
a loop that allowsthe promoterand enhance'
to be close together in space to facilitate l. The 5, capping: The 5, end of mRNA is
transcription. cappedwith z-methylguanosine by an unusual
 BIOCHEMISTFIY

hnRNA(preRNA)

End Chemical
modifications

E
Cap Poly(A)tail Introns Cutpieces New chemical groups added
removed
Flg. 25.9: An outlineof post-transcriptional
modificationsof RNA(hnRNA-Heterogeneous
nuclearRNA).

5'-+5' triphosphate linkage. S-Adenosyl- A diagrammatic representation of the

m et h i o n i n ei s th e d o n o r o f me th yl group. Thi s relationship between eukaryotic chromosomal
cap is requiredfor translation,besidesstabilizing DNA and mRNA is depicted in Fig,25,ll.
the structureof mRNA.
l';?tEremt rnHf*As produceei
2. Poly-A tail : A large number of eukaryotic
[:y al ternate spl i ci ng
mRNAs possessan adenine nucleotidechain at
t he 3 ' -e n d . T h i s p o l y -A ta i l , a s such, i s not Alternatepatternsof hnRNA splicing result in
produced during transcription.lt is later added different mRNA molecules which can produce
to stabilizemRNA. However, poly-A chain gets
reduced as the mRNA enterscvtosol.

3. Introns and their removal : Intronsare tne

int erv e n i n g n u c l e o ti d e s e q u e n ces i n mR N A Exon1 Intron Exon2
which do not code for proteins. On the
other hand, exons of mRNA possess genetic
code and are responsible for protein
synthesis. The splicingand excisionof introns is
illustratedin Fi9.25.10.The removalof intronsis
promoted by small nuclear ribonucleo-
protein particles(snRNPs).snRNPs(pronounced
as snurps) in turn, are formed by the
as s o c i a ti o no f s m a l l n u c l e a r R N A (snR N A )w i th
pr ote i n s .

The term spliceosome is used to represent

t he s n R N P a s s o c i a ti o nw i th h n R N A at the (r
,i
ex on -i n tro nj u n c ti o n . + 1,/
Exon 1 Exon2 Excised
Post-transcriptional
modifications of mRNA intron
occur in the nucleus. The mature RNA then Flg.25.10: Formationof matureRNAfromeukaryotic
enters the cytosol to perform its function mFNA (SnRNPs-Small nuclear
(translation). ribonucleoprotelnpaft icles).
 Ghapter 25 : TFANSCFIPTION
AND TBANSLATION 549

conversion of CAA codon in mRNA (of

apoprotein B gene) to UAA by the enzyme
cytidine deaminase.As a result,originatingfrom
1 .5x 1 o Bbp the same gene, the liver synthesizesa 100-kDa
protein (apoB 100) while the intestinal cells
synthesize 48-kDa protein (apoB 48). This
happensdue to formationof a terminationcodon
(UAA) from CAA in RNA editing.
1. 5x 106bp

Transfer RNA
All the tRNAs of prokaryotesand eukaryotes
undergopost-transcriptionalmodification.These
Onegene(with8 exonsand 2.5 x 104 bp include trimming, convertingthe existing bases
7 introns)I
I into unusual ones, and addition of CCA
+ nucleotidesto 3' terminal end of tRNAs.
8x1o3nt
Primarytranscript Ribosonral RNA
I
+ The preribosomalRNAsoriginallysynthesized
2x103nt are converted to ribosomal RNAs by a seriesof
mRNA post-transcriptionalchanges.

Fig. 25.11: A diagrammatic

representation
of the Inhibitors of transcription
relationshipbetweeneukaryoticchromosomalDNAand
mRNA(bp-Basepair; nt-Nucleotides). The synthesisof RNA is inhibited bv certain
anti bi oti csand toxi ns.
Actinomycin D : This is also known as
different proteins. Alternate splicing results in
dactinomycin. lt is synthesizedby Streptomyces.
mRNA heterogeneity.In fact, the processingof
Actinomycin D binds with DNA templatestrand
hnRNA molecules becomes a site for the
and blocks the movement of RNA polymerase.
regulationof gene expression.
This was the very first antibiotic used for the
Faultysplicingcan causediseases: Splicingof treatmentof tumors.
hnRNA has to be performedwith precision to
Rifampin : lt is an antibiotic widely used for
produce functional mRNA. Faulty splicing may
the treatment of tuberculosis and leprosy.
A good example is one type of
resultin diseases.
p-thalassemiain humans. This is due to a Rifampinbinds with the p-subunitof prokaryotic
RNA polymeraseand inhibits its activity.
mutationthat resultsin a nucleotidechangeat an
exon-intronjunction. The result is a diminished a-Amanitin : lt is a toxin produced by
or lack of synthesisof p-chain of hemoglobin, mushroom,Amanita phalloides.This mushroom
and consequentlythe diseasep-thalassemia. i s del i ci ous i n taste but poi sonousdue to the
toxin o-amanitin which tightly binds with RNA
mRNA editing polymerase ll of eukaryotes and inhibits
transcri pti on.
T he s equenc e i n th e D N A d e te rm i n e sth e
co ding s equence i n mR N A , a n d fi n a l l y th e
CELLULAR RNA CONTENTS
amino acid sequencein the protein. However,
in recent years, changes in the coding A typi cal bacteri um normal l y contai ns
information by editing of mRNA have been 0.05-0.10pg of RNA which contributesto about
reported.lt is estimatedthat about 0.01% of the 6Toof the total weight. A mammaliancell, being
mRNAs undergoesediting. One example is the larger in size, contains20-30 pg RNA, and this
550 B IOC H E MIS TRY

Fig, 25.12: A diagrammaticreprcsentationof RNAcontentof a cell (Note; FN,4srepressntedin

black are found in all organisms; RNAsin colour and exclusivelypresent in eukaryotesonly;
hnRNA-Heterogeneous nuclear RNA; rt
snRNA-Small nuclear RNA: snoRNA-Small

represents only 1% of the . cell weight. protein.The mRNA can be utilized as a template
Transcriptome,representingthe RNA derived for the synthesis of double-stranded comple-
from protein coding genes actually constitutes mentary DNA (cDNA) by using the enzyme
only 4o/",while the remaining 96oh is the non- This cDNA can be used as
reversetranscriptase.
coding RNA (F8.25.1A. The different non- a probe to identify the sequence of DNA in
coding RNAs are ribosomal RNA, transferRNA, 8enes.
s m a l l n u c l e a r R N A, s ma l l n u c l eol ar R N A and
small cytoplasmic RNA. The functions of
different RNAs are described in Chapter 2
(Refer Table 2.3\.
The genetic information stored in DNA is
passedon to RNA (through transcription),and
ultimatelyexpressedin the languageof proteins.
The biosynthesis of a protein or a polypeptide in
a living cell is referredto as translation.The term
Some of the viruses-known as rctrcviruses- translationis used to representthe biochemical
possess RNA as the genetic material. These translation of four-letter language information
virusescause cancers in animals, hence known from nucleic acids (DNA and then RNA) to 20
as oncogenic. They are actually found in the letter language of proteins. The sequence of
transformedcells of the tumors.
The enzyme RNA dependent DNA
polymerase -or simply reverse transcriptase- 5'Viral RNA
is responsible for the formation ol DNA from
s',-
Primer
RNA (Fig,25.13).This DNA is complementary
(cDNA) to viral RNA and can be transmittedinto
host DNA.
Synthesisof cDNA from mRNA : As already s', 5' R NA
described, the DNA expresses the genetic c 3' D NA
informationin the form of RNA. And the mRNA of RNAvirus.
Fiq.25.13: Reversetranscription
determines the amino acid sequence in a
Chapter 25 : THANSCRIPTION
AND TRANSLATION 551

amino acids in the protein synthesized is The codons AUG-and, sometimes, GUG-
determinedby the nucleotidebase sequenceof are the chain initiating codons.
m RNA.
Other characteristics of
Variability of cells in translation genetic code
There are wide variations in the cells with The genetic code is universal,specific, non-
respectto the quality and quantity of proteins overlappingand degenerate.
synthesized.This largely depends on the need 1. Universality : The same codons are used
and abifity of the cells. Erythrocy4es(red blood to code for the sameamino acids in all the living
c ells ) la c k th e m a c h i n e ry fo r tra n sl ati on,and organisms. Thus, the genetic code has been
therefore cannot synthesize proteins. conservedduring the courseof evolution.Hence
genetic code is appropriately regarded as
I n g e n e ra l ,th e g ro w i n g a n d d i v i di ng cel l s
produce larger quantities of proteins. Some of universal.There are, however, a few exceptions.
the cells continuously synthesizeproteins for For instance,AUA is the codon for methionine
export. For instance,liver cells produce albumin in mitochondria.The same codon (AUA) codes
and blood clotting factors for export into the for isoleucine in cytoplasm. With some
exceptionsnoted, the genetic code is universal.
blood f o r c i rc u l a ti o n .T h e n o rma l Ii v e r cel l s are
very rich in the protein biosyntheticmachinery, 2. Specificity : A particular codon always
and thus the liver may be regarded asthe protein codes for the same amino acid, hence the
factory in the human body. genetic code is highly specific or unambiguous
e.g. UGG is the codon for tryptophan.
GENETIC CODE 3. Non-overlapping: The geneticcode is read
The fhree nucleotide (triplet) base sequences from a fixed point as a continuousbasesequence.
in nRNA that act as code words for amino acids It is non-overlapping, commalessand without any
in protein constitutethe geneticcode or simply punctuations.For instance,UUUCUUACACGC
codons.The genetic code may be regardedas a is read as UUU/CUU/ACA/GCG. Addition or
dictionary of nucleotidebases(A, C, C and U ) deletionof one or two baseswill radicallychange
that determinesthe seouenceof amino acids in the messagesequencein mRNA. And the protein
oroteins. synthesizedfrom such mRNA will be totally
different. This is encountered in frameshift
The codons are composed of the four mutations which cause an alteration in the
nucleotide bases,namely the purines-adenine readingframe of mRNA.
( A ) and g u a n i n e (C ), a n d th e p y r i mi di nes-
cytosine (C) and uracil (U). These four bases 4. Degenerate: Most of the amino acids have
produce 64 different combinations(43) of three more than one codon. The codon is degenerate
base codons, as depicted in Table 25.1. The or redundant, since there are 6l codons
nucleotidesequenceof the codon on mRNA is available to code for only 20 amino acids. For
wriften from the S'-end to 3' end. Sixty one instance,glycine has four codons. The codons
codons code for the 20 amino acids found in that designatethe same amino acid are called
protein. synonyms. Most of the synonyms differ only in
the third (3' end) base of the codon.
The three codons UAA, UAG and UCA do
not code for amino acids. They act as stop The Wobble hypothesis explains codon
signalsin protein synthesis.Thesethree codons degeneracy(describedlater).
are collectively known as termination codons or
Godosr.antEcodon recognition
non-sensecodons. The codons UAC, UAA and
UCA are often referred to, respectively, as The codon of the mRNA is recognizedby the
amber, ochre and opal codons. anticodon of IRNA (Fig.25.14). They pair with
 BIOCHEMISTRY

each other in antiparalleldirection (5'+ 3' of complementary base in the anticodon (5'-base).
mRNA with 3' -) 5' of IRNA). The usual Wobbling is attributed to the difference in the
conventional complementary base paiiing spatial arrangement of the 5'-end of the
(A=U, C=C) occurs between the first two bases anticodon.The possiblepairingof 51end baseof
of codon and the last two bases of anticodon. anticodon (of IRNA) with the 3'-end base of
The third base of the codon is rather lenient or codon (mRNA) is given
flexible with regardto the complementarybase.
Anticodon Codon
The anticodon region of IRNA consists of seven
nucleotides and it recognizes the three letter c- Gr
basepairing
A_ [ ] Conventional
codon in mRNA.
U_ G orA Non-conventional
1
base
Wobble hypothesis G_ pairing
U or C J (coloured)
putforthby Crick,is the
Wobblehypothesis, Wobble hypothesisexplainsthe degeneracyof
phenomenon in which a single IRNA can the geneticcode, i.e. existenceof multiple codons
recognize more than one codon. This is due to for a single amino acid. Although there are 61
the fact that the third base (3'-base)in the codonsfor amino acids,the number of tRNAs is
codon often fails to recognizethe specific far less(around40) which is due to wobbling.

Second base (middle one) fhird base

3'end
.I
UCU UAU UGUI U
lrry lcvs
ucc uAc_l uccI c
UCA UAA Stop UGA Stop A
UCG UAG Stop UGG Trp G
ccu CGU U
ccc cGc c
Pro Arg
ccA CGA A
ccG c G G iG
. . . . . . , , , i . , . . . , , -, . . . --. . . -. . . --------
i-"---""""-"--'---"' a:

i ACU AAU AGUI

lSer
i
i
U
i

i Acc AAC]*. AGcl i c

i Thr
i ACA AAA

i t99 MG ]',
GCU
GCC GGC c
Ala Glv
GCA GGA A
GCG
*AuG ,r*r, as initiating
Mon, besi(tes in prcteinsyntresis;
residue
Ming lot neffiionine uAA,UAGandt)GAcalted
as nonsense
cofuns,are responsible of proteinspthesis.
fortermination
 AND TRANSLATION
Ghapter 25 : TFANSCRIPTION 553

fMet
3'e nd A-
fhe protein synthesis which involves the
translation of nucleotide base sequence of
mRNA into the languageof amino acid sequence
may be divided into the following sfagesfor the
convenienceof understanding.
l. Requirementof the components

Anticodon ll. Activation of amino acids

lll. Protein synthesisproper
lV. Chaperonesand protein folding
ililltl
V. Post-translational
modifications.
5' AUG M 3' m RNA
tI I. R E QU IR E ME N T OF TI{E
Codon GOMPONENTS

Fig. 25.14 : Complementary binding of codon

The protein synthesismay be consideredas a
(of nRNA) and anticodon (ot iRNA). biochemicalfactory operatingon the ribosomes.
As a factory is dependent on the supply of raw
materials to give a final product, the protein
Mutations and genetic code synthesisalso requiresmany components.
Mutations result in the change of nucleotide 1. Amino acids : Proteins are polymers of
sequencesin the DNA, and consequentlyin the amino acids. Of the 20 amino acids found in
RNA. The different types of mutations are protein structure, half of them (10) can be
described in Chapter 24. The ultimate effect of synthesized by man. About lO essentialamino
mutations is on the translation through the acids have to be provided through the diet.
alterationsin codons.Some of the mutationsare Protein synthesiscan occur only when all the
harmful. amino acids neededfor a particularprotein are
available. lf there is a deficiency in the dietary
The occurrence of the disease sickle-cell
supply of any one of the essentialamino acids,
anemia due to a single base alteration
(CTC+ CAC in DNA, and CAG + GUC in the translationstops. lt is, therefore,necessary
that a regular dietary supply of essentialamino
RNA) is a classicalexampleof the seriousness of
acids, in sufficientquantities,is maintained,as it
mutations.The result is that glutamateat the 6th
positionof B-chainof hemoglobinis replacedby is a prerequisitefor protein synthesis.
valine. This happens since the altered codon As regards prokaryotes, there is no
GUG of mRNA codes for valine instead of requirementof amino acids, since all the 20 are
glutamate(coded by CAC in normal people). synthesizedfrom the inorganic components.

Frameshift mutations are caused by deletion 2. Ribosomes: The functionally active ribo-
or insertion of nucleotides in the DNA that somes are the centres or factories for protein
generatealteredmRNAs.As the readingframe of synthesis.Ribosomesmay also be considered as
mRNA is continuous, the codons are read in workbenchesof translation.Ribosomesare huge
continuation,and amino acids are added. This complex structures(70S for prokaryotesand 80S
results in proteins that may contain several for eukaryotes)of proteinsand ribosomalRNAs.
altered amino acids, or sometimesthe protein Eachribosomeconsistsof two subunits-one big
synthesismay be terminatedprematurely. and one small. The functional ribosomehas two
5s4 B IOC H E MIS TR Y

protein
synthesized
Completely

Fig. 25.15: A polyribosomein proteinsynthesis.

sites-A site and P site. Eachsite covers both the 5. Energy sources z Both ATP and GTP are
subunits.A siteis for binding of aminoacyltRNA required for the supply of energy in protein
and P sife is for binding peptidyl IRNA, during synthesis.Some of the reactions involve the
the courseof translation.Some authorsconsider breakdown of ATP or CTP, respectively,to AMP
A site as acceptor site, and P site as donor site. and GMP with the liberationof pyrophosphate.
In caseof eukaryotes,there is anothersite called Each one of these reactionsconsumestwo high
exif site or Esife. Thus, eukaryotescontain three energy phosphates(equivalentto 2 ATP).
sites (A, P and E) on the ribosomes.'
6. Proteinfactors : The processof translation
The ribosomes are located in the cytosomal involves a number of protein factors.Theseare
fractionof the cell. They are found in association neededfor initiation,elongationand termination
with rough endoplasmicreticulum (RER)to form of protein synthesis. The protein factors are
clusters RER-ribosomes, where the protein more complex in eukaryotes compared to
synthesis occurs. The term polyribosome prokaryotes.
(polysome) is used when several ribosomes
s im ulta n e o u s l ytra n s l a te o n a s i n gl e mR N A il. ACTTVATTONOF AMr{O ACTDS
(Fig.2s.rA.
Amino acids are activated and attached to
3. Messenger RNA (mRNA) : The specific tRNAs in a two step reaction. A group of
informationrequiredfor the synthesisof a given enzymes-namely aminoacyltnNn synthetases-
protein is presenton the mRNA. The DNA has are required for this process.These enzymes are
passedon the genetic information in the form of highly specific for the amino acid and the
codons to mRNA to translate into a protein correspondingtRNA.
sequence.
The amino acid is first attachedto the enzyme
4. Transfer RNAs (tRNAs) : They carry the utilizing ATP to form enzyme-AMP-aminoacid
amino acids,and hand them over to the growing complex. The amino acid is then transferredto
pept id e c h a i n . T h e a mi n o a c i d i s coval entl y the 3' end of the IRNA to form aminoacvl IRNA
bound to IRNA at the 3'-end. Each IRNA has a (Fig.2s.t6).
three nucleotide base sequence-the anticodon,
which is responsibleto recognize the codon III. PROTEIN SYNTI{ESIS PROPER
(complementary bases) of mRNA for protein
The protein or polypeptide synthesisoccurs
svnthesis.
on the ribosomes (rather polyribosomes).The
In man, there are about 50 different tRNAs nRNA is read in the 5'-+3' direction and the
whereasin bacteriaaround 40 tRNAs are found. polypeptide synthesis proceeds from N-terminal
Some amino acids (particularly those with end to C-terminal end. Translation is directional
multiple codons) have more than one IRNA. and col l i nearw i th mR N A .
 Ghapter 25 : THANSCRIPTION AND TFANSLATION JJJ

Aminoacid

-AMP-Aminoacid

tRNA

Fiq.25.16 : Formationof aminocacyl IRNA (AA-Amino acid; E-Enzyme).

The prokaryotic mRNAs are polycistronic, protein biosynthesis in eukaryotes is better

s inc e a s ingl e mR N A h a s m a n y c o d i n g re gi ons understoodnow.
that code for different polypeptides.In contrast,
Translation in eukaryotes is briefly descrihed
eukaryotic mRNA is monocistronic, since it
here, along with some relevdnt features of
codes for a single polypeptide.
prokaryotic protein biosynthesis. Translation
In caseof prokaryotes,translationcommences proper is divided into three stages-initiation,
beforethe transcriptionof the gene is completed. el ongati on and termi nati on (as i t i s done for
T hus , s im ult a n e o u tra
s n s c ri p ti o na n d tra n s l ati on transcription).
are possible.This is not so in case of eukaryotic
or ganis m s s i n c e tra n s c ri p ti o n o c c u rs i n the
,NITIATION OF TRANSLAT'ON
nucleus whereas translationtakes place in the
cytosol. Further,the primary transcript(hnRNA) The initiation of translationin eukaryotesis
formed from DNA has to undergo several complex, involving at least ten eukaryotic
modificationsto generatefunctional mRNA. initiation factors (etFs).Some of the elFs contain
Protein synthesisis comparativelysimple in multiple (3-8)subunits.The processof translation
case of prokaryotes compared to eukaryotes. initiation can be divided into four steps
Further, many steps in eukaryotic translation (Fig.25.1V.
were not understoodfor ouite sometime. For 1 . Ribosomaldissociation.
these reasons,majority of the textbooksearlier
used to describe translation in prokaryotesin 2. Formationof 43S preinitiationcomplex.
detail, and give most important and relevant
3. Formationof 48S initiation complex.
informationfor eukaryotictranslation.With the
advancesin molecular biology, the processof 4. Formationof 80S initiation complex.
 BIOGHEMISTRY

Met

Met

48SinitiationcomPlex

['iTl+[-gl +P i

80S initiation comPlex

Ghapter 25 : THANSCRIPTION
AND TFANSLATION JJ/

Ribosomal dissociation Formation of 8OS initiation complex

The 80S ribosomedissociates to form 40S and 48S initiationcomplex binds to 605 ribosomal
605 subunits.Two initiating factors namely elF- subunit to form 80S initiation complex. The
3 and elF-lA bind to the newly formed 40S binding involvesthe hydrolysisof CTP (boundto
subunit,and therebyblock its reassociation with elF-2).This step is facilitatedby the involvement
605 subunit.For this reason,some workersname of el F-5.
elF-3 as anti-association factor.
As the 80S complex is formed, the initiation
factors bound to 48S initiation complex are
Formation of 43S preinitiation released,and recycled. The activation of elF-2
complex requi res el F-2B (al so cal l ed as guani ne
A ternary complex containingmet-tRNArand nucleotide exchange factor) and CTP. The
elF-2 bound to CTP attachesto 40S ribosomal activatedelF:2 (i.e. bound to CTP) requireselF-
subunit to form 43S preinitiationcomplex. The 2C to form the ternary complex.
pr es enc e o f e l F -3 a n d e l F -1 A s ta b i li zesthi s
Regulatidnof initiation
complex (Nofe .' Met-tRNA is specifically
involved in binding to the initiation condon The elF-4F, a complex formed by the
AUGs; hence the superscript'is used in met- assembly of three initiation factors controls
t RNA l. initiation, and thus the translationprocess.elF-
4E, a component of elF-4F is primarily
Formation ol 48S initiation complex responsiblefor the recognition of mRNA cap.
And this step is the rate-limitingin translation.
T he bi n d i n g o f mR N A to 4 3 S p re i ni ti ati on
complex resultsin the formationof 48S initiation elF-2 which is involved in the formation of
complex through the intermediate43S initiation 43S preinitiationcomplex also controls protein
complex. This, however, involves certain biosynthesisto some extent.
interactions between some of the elFs and
activationof mRNA. Initiation of translation
in prokaryotes
elF-4F complex is formed by the association
of elF-4C, elF-4A with elF-4E. The so formed The formation of translation initiation
elF-4F(referredto as cap binding protein)binds complex in prokaryotes is less complicated
to the cap of mRNA. Then elF-4A and elF-48 compared to eukaryotes. The 30S ribosomal
bind to mRNA and reduce its complex structure. subunit is bound to initiation factor 3 (lF-3)and
This mRNA is then transferredto 43S complex. attached to ternary complex of lF-2, formyl met-
For the appropriate association of 43S IRNA and CTP. Another initiationfactor namely
preinitiationcomplex with mRNA, energy has to lF-l also participates in the formation of
be supplied by ATP. preinitiation complex. The recognition of
i ni ti ati on codon A U G i s done through S hi ne-
Recognition of initiation codon : The
Dalgarnosequence.A 50S ribosomeunit is now
ribosomal initiation complex scans the mRNA
bound with the 30S unit to produce 70S
for the identification of appropriate initiation
initiation complex in prokaryotes.
codon. S'-AUG is the initiation codon and its
recognitionis facilitatedby a specific sequence
ELONGATION OF TRANSLATTON
of nucleotides surrounding it. This marker
sequencefor the identificationof AUC is called Ribosomeselongatethe polypeptidechain by
as Kozak consensus sequences. In case of a sequenti aladdi ti onof ami no aci ds.The ami no
prokaryotes the recognition sequence of acid sequenceis determinedby the order of the
initiation codon is.referredto as Shine-Dalgarno codons in the specific mRNA. Elongation, a
sequence. cyclic process involving certain elongation
558 BIOCHEMISTRY

factors(EFs),may be dividedinto threesteps In case of prokaryotes,the elongation factors

(Fig.2s.tA. are different, and they are EF-Tu,EF-Ts(in place
1. Binding of aminoacyl I-RNA to A-site. of of EF-1a)and EF-G (insteadof EF-2).

2. Peptide bond formation.

Incorporation of amino acids
3. Translocation.
thataboutsixaminoacidsper
It is estimated
second are incorporated during the course of
Binding of aminoacyl-tRNA to
elongation of translation in eukaryotes. In case
A-site
of prokaryotes,as many as 20 amino acids can
The 8OS initiation complex contains met- be incorporated per second. Thus the processof
tRNAi in the P-site,and the A-site is free. Another protein/polypeptide synthesis in translation
aminoacyl-tRNA is placed in the A-site. This occurs with great speed and accuracy.
requiresproper codon recognitionon the mRNA
and the involvement of elongation factor 1a TEBil,,INATTONOF TBANSLATTON
(EF-la)and supply of energy by GTP. As the
Terminationis a simple processwhen
aminoacyl-tRNAis placed in the A-site, EF-1d,
compared to initiation and elongation. After
and CDP are recycled to bring another
severalcyclesof elongation,incorporatingamino
aminoacyl-tRNA.
acids and the formation of the specific protein/
polypeptide molecule, one of the stop or
Peptide bond formation
termination signals (UAA, UAG and UCA)
The enzyme peptidyltransferase catalyses the terminates the growing polypeptide. The
formation of peptide bond (Fi9.25.19). The terminationcodons which act as stop signalsdo
activity of this enzyme lies on 28S RNA of 605 not have specific tRNAs to bind. As the
ribosomal subunit. lt is therefore the rRNA (and termination codon occupies the ribosomal
not protein) referred to as ribozyme that .A-site, the releasefactor namely eRF recognizes
catalyses the peptide bond formation. As the the stop signal.eRF-CTPcomplex, in association
amino acid in the aminoacyl-tRNA is already with the enzyme peptidyltransferase,cleavesthe
activated, no additional energy is required for peptide bond between the polypeptide and the
peptide bond formation. IRNA occupying P-site.ln this reaction,a water
molecule, instead of an amino acid is added.
The net result of peptide bond formation is
This hydrolysis releasesthe protein and tRNA
the attachment of the growing peptide chain to
from the P-site.The 80S ribosome dissociatesto
the IRNA in the A-site.
form 40S and 605 subunitswhich are recycled.
The mRNA is also released.
Translocation
As the peptide bond formation occurs, the ,N']TBITOBS OF PROTEIN
ribosome moves to the next codon of the mRNA svtTttEsrs
(towards 3'-end). This process called
Translationis a complex processand it has
translocation,basically involves the movement
become a favourite target for inhibition by
of growing peptide chain from A-site to P-site.
antibiotics. Antibiotics are the substances
TranslocationrequiresEF-2 and GTP. GTP gets
produced by bacteriaor fungi which inhibit the
hydrolysedand suppliesenergyto move mRNA.
growth of other organisms. Majority of the
EF-2 and CTP complex recycles for
antibiotics interfere with the bacterial protein
translocation
synthesisand are harmlessto higher organisms.
ln recent years, another site namely exit site This is due to the fact that the process of
(E-site) has been identified in eukaryotes. The translationsufficiently d iffersbetweenprokaryotes
deacylated IRNA moves into the E-site, from and eukaryotes.The action of a few important
where it leavesthe ribosome. antibioticson translationis describednext.
 AND TBANSLATION
25: TBANSCRIPTION

Met
I
AAr
I
AAz
l-
AAr
I
Met 4Az

Peptidyltransferase
@
,z- PePtidebond

f$et
I
l
AAr
I
AAz
Translocation
i
AAr
I'
I

Ain
@
mRNA Peptide
synthesized

Hg. E.l8 con|;d. nort Golumn

560 BIOCHEMISTFIY

Peptidyltransferase

3'mRNA

Ribosome

Flg. 25.19: Formationof peptidebondin translation(P-site - PeptidylIRNAsite;A-site- AminoacylIRNAsite).

Streptomycin : Initiation of protein synthesis IV. GI{APERONES AND

is inhibitedby streptomycin.lt causesmisreading PROTEIN FOLDING
of mRNA and interfereswith the normal pairing
The three dimensional conformation of
between codons and anticodons.
proteins is important for their biological
Tetracycline : lt inhibits the binding of functions. Some of the proteins can
aminoacyl IRNA to the ribosomal complex. In spontaneouslygeneratethe correct functionally
fact, tetracycline can also block eukaryotic active conformation e.g. denatured pancreatic
protein synthesis. This, however, does not ribonuclease. However, a vast majority
happen since eukaryotic cell membrane is not of proteins can attain correct conformation,
permeableto this drug. only through the assistance of certain
Puromycin: This has a structuralresemblance proteins referredto as chaperones.Chaperones
to aminoacylIRNA. Puromycinentersthe A site are heat shock proteins (originally discovered
and gets incorporated into the growing peptide in response to heat shock). They facilitate
chain and causes its release. This antibiotic and favour the interactions on the
prevents protein synthesis in both prokaryotes polypeptide surfaces to finally give the
and eukaryotes. specific conformation of a protein.
Chaperones can reversibly bind to
Chloramphenicol : lt acts as a competitive
hydrophobic regions of unfolded proteins and
inhibitor of the enzyme peptidyltransferase and
folding intermediates. They can stabilize
thus interfereswith elongationof peptide chain.
intermediates, prevent formation of
Erythromycin : lt inhibits translocation by incorrect intermediates, and also prevent
binding with 50S subunit of bacterialribosome. undesirableinteractionswith other proteins.All
Diphtheria toxin : lt preventstranslocation in these activities of chaperoneshelp the protein to
eukaryotic protein synthesis by inactivating attain compact and biologically active
elongation factor eEF2. conformation.
Ghapten 2s : TFANSCRIPTION
AND THANSLATION 561

Types of chaperones get glycosylatedor transported.Therefore,CFTR

gets degraded.
Chaperonesare categorizedinto two major
Sroups C ertai nneurol ogi caldi seasesw hi ch are due
to cel l ul ar accumul ati on of aggregatesof
1. Hs p 7 0 s y s te m : T h i s ma i n l y c o nsi stsof
mi sfol ded protei ns or thei r parti al l y degraded
Hsp70 (70-kDa fieat shock protein) and Hsp40
products have been identified.The term prions
( 40- k Da H rp ). T h e s e p ro te i n s c a n bi nd
(proteinous infectious agents) is used to
(p ro te i n a
indiv idua l l yto th e s u b s tra te ) n d hel p i n
col l ecti vel yrepresentthem.
the correct formation of protein folding.
P ri onsexhi bi t the characteri sti cs
of vi ral or
2. Chaperonin system : This is a large
microbial pathogensand have been implicated
oligomericassemblywhich forms a structureinto
i n many di seases.e.g. mad cow di sease,
which the folded proteins are inserted. The
Creutzfeldt-Jacob disease,Alzheimer's disease,
c haper on i ns y s te mm a i n l y h a s H s p 6 0a n d H spl 0
Huntington'sdisease(Refer Chapter 2).
i. e. 60 k D a H s p a n d 1 0 k D a H s p . C h a p eroni ns
are requiredat a later part of the protein folding
V. POST.TRANSLATIONAL
process/ and often work in association with
MOD IFIC A TION S OF P R OTE IN S
Hsp70 system.
The proteinssynthesizedin translationare, as
P r ot ein m i s fo l d i n g and diseases such, not functi onal .Many changestake pl ace
The failure of a protein to fold properly in the polypeptidesafter the initiation of their
generally leads to its rapid degradation.Cystic synthesisor, most frequently, after the protein
fibrosis (CF) is a common autosomal recessrve synthesis is completed. These modifications
disease.Some casesof CF with mutationsthat i ncl ude protei n fol di ng (descri bed al ready),
result in altered protein (cystic fibrosis tri mmi ng by proteol yti c degradati on, i ntei n
transmembrane conductance regulator or in spl i ci ng and coval ent changes w hi ch are
short CFTR)have been reported.Mutated CFTR col l ecti vel y know n as post-translational
cannot fold properly, besidesnot being able to modifications (Fig.25.20).

BIOM=DIGAL,/ CUilICilL DOISGEPIE

re Faulty splicing oJ hnRNA may result in certq.in diseaese.g. ftthalassemia.

Inhibitors of transcription are used os therapeutic agents. Thus, actinomgcin D was the
first antibiotic used in the treatment ot' tumors. Rifampin is employed to treat
tuberculosisand leprosy.
i9 Retrouiruses(RNA ts the genetic material) are oncogenic i.e. cause cancers.
l,9 Seueralantibiotics selectiuelyblock bacterial translation, and thus inhibit their growth
e.g. streptomycin,tetracqcline,puromycin.
Protein mislolding often results in the t'ormation of prions (proteinous inlectious
agents)which houe been implicated in mang diseosese.g. mad cow disese,Alzheimer's
diseose.
t:t Lebers' hereditary optic neuropathy is caused by mutation in mtDNA in males. The
uictims become blind due fo loss of central uision os a result of neuroretinol
degeneration.
562 BIOGHEMISTF|Y

Polypeptide

Intein Chemical(covalent)
splicing modifications

removed intein

Ftq,25.20: An outlineof post-translational of proteins.

modifications

Proteolytic degradation group of enzymescalledprotein kinasescatalyse

phosphorylation while proteinphosphatasesare
Many proteins are synthesized as the (removalof
responsiblefor dephosphorylation
precursorswhich are much bigger in size than
phosphate group).Many enzymesthat undergo
the functional proteins. Some portions of
phosphorylation areknown
or dephosphorylation
precursormoleculesare removed by proteolysis
in metabolisms (e.g.glycogensynthase).
to liberate active proteins. This process is
commonly referred to as trimming. The 2. Hydroxylation: During the formationof
formation of insulin from preproinsulin, collagen,the aminoacidsprolineand lysineare
conversion of zymogens (inactive digestive respectivelyconvertedto hydroxyprolineand
enzymes e.g. trypsinogen)to the active enzymes hydroxylysine. occursin the
This hydroxylation
are some examplesof trimming. endoplasmic reticulumand requiresvitaminC.
3. Glycosylation: The aftachmentof carbo-
lntein splicing
hydratemoiety is essentialfor someproteinsto
Inteinsareinterveningsequences in certain perform their functions. The complex
proteins. These are comparable to introns in carbohydrate moiety is attachedto the amino
mRNAs. lnteins have to be removed, and exteins acids, serine and threonine(O-linked)or to
ligated in the appropriateorder for the protein to asparagine(N-linked), of
leadingto the synthesis
become active. glycoproteins.
Vitamin K dependent carboxylation of
Govalent modifications glutamicacid residuesin certainclottingfactors
The proteins synthesizedin translation are is alsoa post-translational
modification.
subjectedto many covalent changes.By these
fn the lable 25.2, selectedexamplesof post-
modificationsin the amino acids, the proteins
translationalmodificationof proteinsthrough
may be converted to active form or inactive
their aminoacidsare given.
form. Selected examples of covalent
modificationsare describedbelow.
1 . Phosphorylation : The hydroxyl group
containing amino acids of proteins, namely
serine, threonine and tyrosine are subjectedto The eukaryoticproteins(tensof thousands)
phosphorylation.The phosphorylationmay either are distributed between the cytosol, plasma
increaseor decreasethe activityof the proteins.A membraneand a numberof cellularorganelles
 Ghapter 25: TBANSCRIPTION
AND TBANSLATION s63

Certain glycoproteins are targeted to reach

lysosomes, as the lysosomal proteins can
recognize the glycosidic compounds e.g.
N-acetylglucosami ne phosphate.
Amino acid Post-translational For the transport of secretory proteins, a
modification(s) speciaf mechanism is operative.A signatrpeptide
Amino-terminal Glycosylation,
acetylation, containing 'l 5-35 amino acids, located at the
aminoacid myristoylation,
formylation. amino terminal end of the secretory proteins
Carboryterminal ADP-ribosylation facilitates the transport.
Methylation,
3.TIe_.99iq..................
Arginine Methylation Protein targeting to mitochondria
Aspartic
acid Phosphorylation,
hydroxylation Most of the proteins of mitochondria are
(-SH)
Cysteine (-S-S-) tormation,
Cystine synthesizedin the cytosol, and their transport to
formation,
selenocysteine mitochondria is a complex process.Majority of
glycosylation. the proteins are synthesizedas larger preproteins
Glutamicacid ycarboxylation.
Methylation, with N-terminal presequencesfor the entry of
Histidine phosphorylation,
Methylation, these proteins into mitochondria. fhe fiansport
Lysine Acetylation,
methylation, of unfolded proteins is often facilitated by
hydrorylation,
biotinylation. chaperones.
Methionine formation.
Sulfoxide One protein namely mitochondrial matrix
Phenylalanine hydrorylation,
Glycosylation, targetingsignaf involved in protein targetinghas
Proline glycosylation.
Hydrorylation, been identified. This protein can recognize
Serine glycosylation.
Phosphorylation, mitochondrial receptor and transport certain
Threonine Phosphorylation,
methylalion proteinsfrom cytosolto mitochondria.This is an
glycosylation. energy-dependentprocess.
Tryptophan Hydrorylatron.
Tyrosine phosphorylation,
Hydrorylation, Protdin targeting to
iodnation.
sulfonylation, other organelles
Specificsignalsfor the transportof proteinsto
(nucleus,mitochondria, reticulum organellessuch as nuclei and peroxisomeshave
endoplasmic
places, perform been identified.
etc.). At the appropriate they
their functions. The smaller proteinscan easily passthrough
The proteins,synthesized in translation,have nuclear pores. However, for larger proteins,
to reach their destination to exhibit their nuclear localization signals are needed to
biological activities. This is carried out by a facilitate their entrv into nucleus.
process called protein targeting or protein
sorting or protein localization. The protefns
move from one compartment to another by
multiplemechanisms.
The protein transportfrom the endoplasmic
reticulum through the Golgi apparatus,and The mitochondrial DNA (mtDNA) has
beyondusescarriervesicles.lt may be, however, structural and functional resemblanceswith
notedthat onfy the correctly folded proteinsare prokaryotic DNA. This fact supports the view
recognizedas the cargo for transport. Protein that mitochondria are derivativesof prokaryotes.
targeting and post-translationalmodifications mtDNA is circular in nature and containsabout
occur in a well coordinated manner. 16,000 nucleotidebases.
564 B IOC H E MIS TR Y

A vast majority of structuraland functional mtDNA is inherited from the mother.

proteinsof the mitochondriaare synthesizedin Mitochondrial DNA is subjected high rate of
to
t he c v to s o l .u n d e rth e i n fl u e n c eo f n u cl earD N A . mutati ons(about 10 ti mes more than nucl e ar
However, certain proteins(around 13), most of DNA) that causesinherited defectsin oxidative
them being the componentsof electrontransport phosphorylation.The best known among them
c hain , a re s y n th e s i z e di n th e m i to c h ondri a(e.9. are certain mitochondrial myopathies and
c y t oc h ro m eb o f c o m p l e x l l l , tw o subuni tsof Leber'shereditaryoptic neuropathy.The latter is
ATP synthase).Transcriptiontakes place in the mostly found in males and is characterizedby
m it oc h o n d ri al e a d i n gto th e s y n th e s i of
s mR N A s, bl i ndnessdue to l ossof centralvi si on as a result
tRNAs and rRNAs.Two typesof rRNA and about of neuroretinal degeneration. Leber's hereditary
22 speciesof IRNA have been so far identified. optic neuropathy is a consequence of single
Transcriptionis followed by translationresulting basemutati oni n mtD N A . D ue to thi s,the amino
in pr o te i n s y n th e s i s . aci d hi sti di ne, i n pl ace of argi ni ne, is
T he mi to c h o n d ri ao f th e s p e rm cel l do not incorporatedinto the enzyme NADH coenzyme
ent er th e o v u m d u ri n g fe rti l i z a ti on,therefore, Q reductase.

1. Tronscription is the processin which RNA is synthesizedfrom DNA, urhich is carried

out in 3 stoges-initiation,elongationand termination.
2. In case of prokaryotes, a single enzyme synthesizesall the RNAs. ln eukaryotes,RNA
polymerase l, Il and III respectiuelgcatalyse the lormotion o/ rRNAs, mRNAs ond
fRNAs.
3. The primary mRNA transcript(i.e. hnRNA) undergoespost-transcriptionalmodifications
e.g. base modifications,splicing etc.
4. Reuersetranscription is the proce.sso/ synfhesizing DNA t'rom RNA by the enzyme
reuersetranscriptase.
6 Biosynlhesisof a protein or a polypeptide is known os tronslation. The amino ocid
sequenceof a protein is determined by the triplet nucleosidebosesequencesof mRNA,
arranged os codons.
6. The genetic code (codons)-<omposedof A, G, C and U-is uniuersol, specific, non-
ouerlappingand degenerote.Of the 64 codons,three (UAA, UAG, UGA) are termination
codons while the rest code lor amino acids.
7. Ribosomesore the t'actoriesof protein biosgnfhesis.Translation inuoluesactiuation of
omino acids,protein synfhesisproper (initiation,elongotionand termination),protein
lolding and post-translational modit'ications.
8. The post-translationalmodifications include proteolytic degradation, intein splicing and
couolent modit'icotions (phosphorylation, hydroxylation, glycosylation etc.). These
modificotionsare required to moke the proteins biologicallyactiue.
9. The proteins synthesizedin translation reach the destinotion to exhibit their biological
actiuitg. This is csrried out by a processcalled protein targeting or protein sorting.
10. The mitochondriopossessindependentDNA with the machineryfor transcriptionand
translation. Howeuer,only a few proteins (around 73) are actually synthesizedin the
mitochondria.
Ghapter 25: TRANSCFIIPTEN
AND TRANSLATION 565

I. Essay questions

1. Give an account of transcription.Compare the RNA synthesisbetween prokaryotesand

eukaryotes.
(translation).
2. Describeproteinbiosynthesis
3. Discussthe inhibitorsof transcriptionand translation.
4. Cive an account of post-transcriptional
and post-translational
modifications.
5. What is geneticcode? Describethe characteristicsof geneticcode. Add a note on the effects
of mutationson genetic code.

II. Short notes

(a) Cenome,(b) Heterogeneous nuclearRNA (hnRNA),(c) EukaryoticRNA polymerases, (d) Introns
and exons, (e) Reversetranscription,(0 Wobble hypothesis,(g) Anticodon, (h) Shine-Dalgarno
(j) Chaperones,(k) Proteintargeting.
sequence,(i) Peptidyltransferase,

III. Fill in the blanks

1. The total DNA (Beneticinformation)contained in an organism (or a cell) is referredto as

2. Th e p ri m a ry tra n s c ri p tp ro d u cedbyR N A po| ymerasel | i seukaryotes-.

3. The interveningnucleotidesequencesin mRNA that do not code for proteins
4. The synthesisof complementary DNA (cDNA) from mRNA is catalysedby the enzyme

5. A singleIRNA is capableof recognizingmore than one codon, and this phenomenonis referred
to as
6. The factoriesfor protein biosynthesisare
7. The enzymepeptidyltransferase calalysesthe formationof peptidebond during translation.The
chemicalnatureof this enzymeis
8. The proteins that facilitate the formation of specific conformation of proteins are

9. The common term used for the diseasesdue to misfoldingof proteins

10. The processof delivery of proteins in a cell to the site their biological activity is

IV. Multiple choice questions

11. The codon(s)that terminate(s)protein biosynthesis

(a) UAA (b) UAG (c) UCA (d) All of them.
12. The nitrogenousbasethat is never found in the geneticcode
(a) Adenine(b) Cuanine(c) Thymine(d) Cytosine.
13. The total DNA (geneticinformation)contained in a living cell (or organism)is regardedas
(a) Cenome (b) Transciptome(c) Proteome(d) Cene.
14. The enzyme responsiblefor the synthesisof mRNAs in eukaryoticcells
(a) RNA polymerase| (b) RNA polymerasell (c) RNA polymerasellt (d) RNA polymerasea,.
15. MitochondrialDNA is inheritedfrom
(a) Mother only (b) Fatheronly (c) Both of them (d) Eithermother or father.