Chapter 17 FROM GENE TO PROTEIN

How is the message of a gene translated by cells into a specific trait, such as brown hair or type
A blood?
In 1909, Archibald Garrod was the first to suggest that gene dictate phenotypes through
enymes that catalye specific chemical reactions in the cell!
"iochemists accumulate e#idence that showed that cells degrade organic molecules in a series
of steps, each catalyed by an enyme!
George Beadle and Edward Tatum $19%0s& suggested that a single gene specifies each
protein!
'hey wor(ed with fungus )eurospora crassa!
)eurospora is a haploid organism!
One gene - one protein hypothesis!
*esearchers realied that not all proteins are enymes!
'hey shifted from one gene + one enyme to one gene - one protein!
In the mid 19,0-s it became e#ident that the genetic information in .)A contains the code for all
the proteins needed by the cell!
/ost of the basic wor( was done with bacterial .)A!
'he information encoded in .)A is used to specify the se0uences of amino acids in proteins!
BAI! PRIN!IP"E OF TRAN!RIPTION AN# TRAN"ATION
1enes pro#ide the instructions for ma(ing specific proteins!
*)A or ribonucleic acid ser#es as an intermediary between .)A and protein!
.)A pro#ides the template for the se0uence of *)A nucleotides in the same way it pro#ides the
template for a new .)A strand!
.)A 2 *)A 2 protein
Tran$cription is the synthesis of *)A under the direction of .)A! 'his ta(es place in the
nucleus of the cell!
'he immediate product of transcription is the pre-me$$enger RNA, and RNA
proce$$ing yields the finished m*)A!
'he initial product of transcription including the *)A sections that are not translated into
proteins is called a primar% tran$cript!
Tran$lation is the synthesis of the polypeptide under the instructions of the m*)A! 'his occurs
in the cytoplasm of the cell with the help of ribosomes!
GENETI! !O#E
'he genetic code is the se0uence of nucleotides in .)A that specify for amino acids!
Triplet$ of nucleotides code for or specify all 30 the amino acids that ma(e proteins!
.uring transcription, the gene determines the base se0uence along the length of the *)A
4or each gene, only one of the two .)A strands is transcribed! !
4or each gene, one .)A strand functions as a template for transcription, the synthesis of a
complementary *)A molecule! 'his molecule of *)A is called a me$$enger RNA or mRNA!
'he *)A molecule is complementary to the .)A template rather than identical!
'he *)A bases are assembled according the base pairing rules e5cept that 6 pairs with A in
the .)A, and ribose replaces deo5yribose!
'he *)A strand is synthesied li(e a new .)A strand during replication, in an antiparallel
direction!
7-+ACC+,- $in .)A& 2 ,-+611+7- $in *)A&
'he genetic code is defined at the m*)A le#el!
/arshall )iremberg and his colleagues were the first to decipher a codon in the early
1980s! 'hey used the multiple copies of the triplet 666 $uracil& to ma(e a poly+uracil!
'his strand of repetitious 666 synthesies a polypeptide containing only the amino
acid phenylalanine!
'he base triplets are called codon$!
'he genetic code is made of continuous nono#erlapping triplets o& ba$e$! 'his is called the
reading &rame!
'here are '( codon$9 81 code for amino acids and 7 ser#e as stop signals!
'he start codon is A61, which also specifies the amino acid methionine!
Codons are read in a ,-27- direction along the m*)A, e! g! ,-+A61+7-
2
'he code is uni)er$al9 all organisms use the same code, e! g! CC1 is translated in A::
organisms as the AA proline!
A61 stands for the amino acid methionine, /et, and also functions as the $tart $ignal for
ribosomes to begin translating the m*)A at that point!
'hree of the 8% codons function as $top $ignal$, mar(ing the end of a genetic message!
;5ception to the uni#ersality of the genetic code are found in a few protooans li(e <aramecium
#ary in their translation system, and in some mitochondria and chloroplasts that transcribe and
translate their small .)A!
'he genetic code is redundant= with the e5ception of methionine and tryptophan, more than
one codon designates each amino acid, e! g! 1AA and 1A1 code for glutamic acid, 1lu!
A code ne#er codes for more than one amino acid= there is no ambiguit%!
1enetic information is encoded as a se0uence of nono#erlapping base triplets, or
codons, each of which is translated into a specific amino acid during protein synthesis!
'here are a few e5ceptions to the uni#ersality of the genetic code9
>ome unicellular eu(aryotes and organelle genes!
>ome pro(aryotes ha#e can translate stop codons into AA not found in most organisms!
TRAN!RIPTION
Tran$cription is the synthesis of *)A from a .)A template!
'ranscription means ?copying@!
*)A is a polymer of nucleotides!
RNA #NA
>ingle stranded .ouble stranded heli5
*ibose .eo5yribose
6racil 'hymine
'hree (inds of *)A are transcribed from .)A9 ribosomal *)A $rRNA&, transfer *)A $tRNA&,
and messenger *)A $mRNA&!
Me$$enger RNA or mRNA carries the specific information for ma(ing proteins!
*+ Initiation+
'ranscription begins when an *)A polymerase II binds to a .)A se0uence (nown as the
promoter+
RNA pol%mera$e II can initiate transcription but .)A polymerase cannot initiate translation=
it needs an *)A primer!
'he promoter e5tends se#eral doen nucleotide pairs from the start point towards the ,A end
of the .)A strand!
'he promoter determines which .)A strand is to be transcribed and is the point of
attachment of the *)A polymerase II!
'he .)A unwinds and the enyme initiates *)A synthesis at the start point on the template
strand!
'he se0uence that signals the end of transcription is called the terminator!
'he stretch of .)A that is transcribed is called a tran$cription unit!
,+ Elongation+
RNA pol%mera$e II binding and initiation o& tran$cription+
In pro(aryotes, *)A polymerase II binds directly to the promoter!
'here are se#eral (inds of *)A polymerases in eu(aryotes, each with a specialied function!
*)A polymerases are comple5es= each comple5 containing about 13 subunits or polypeptides!
In eu(aryotes, a group of at least se#en proteins called tran$cription &actor$ contribute to the
binding of *)A polymerase II to the promoter!
'hese enymes are present in all cells and ha#e many similarities to the .)A polymerases!
;u(aryotic promoters include a 'A'A bo5, a nucleotide se0uence containing 'A'A, about 3,
nucleotides upstream from the transcriptional start point!
'he 'A'A bo5es are gi#en as they occur in the non+transcribing .)A strand!
A transcription factor that recognies the 'A'A bo5 must bind to the .)A before *)A
polymerase II can attach!
Additional transcription factors become attached to the promoter and form together with *)A
polymerase II the tran$cription initiation comple-!
Bnce the transcription initiation comple5 is in place, the double heli5 unwinds and synthesis
begins at the start point!
As the *)A polymerase II mo#es, the .)A continues to unwind e5posing 10 to 30 bases at a
time for pairing with *)A nucleotides!
In the wa(e of the ad#ancing *)A synthesis, the double heli5 re+forms and the *)A molecule
Cust synthesied peels away from the .)A template strand!
'he *)A polymerase II uses nucleotides with three phosphate groups as substrates!
'hey remo#e two phosphates as the subunits are co#alently lin(ed to the 7- end of the growing
*)A molecule!
'hese reactions are strongly e5ergonic!
/essenger *)A contains the base se0uence that codes for proteins!
*)A synthesis does not re0uire a primer, but other proteins are needed!
'he first nucleotide at the ,- end retains its three+phosphate group! 'his is called the ./ cap,
and has a protecti#e function!
'he last nucleotide to be incorporated has an e5posed 7- DBH group!
'he termination of transcription is controlled by a specific base se0uence!
.ifferent genes may ha#e different promoter se0uences upstream from the protein+coding
se0uence!
Bnce the *)A polymerase II has recognied the promoter, it unwinds the heli5 and begins
transcription!
'he .)A is read in a 7-+to+,- direction!
0p$tream means toward the ,- end!
#own$tream means toward the 7- end!
;5ample9
)ontranscribed .)A strand .1 2 A 2 T 2 G 2 A 2 ! 2 T 2 31
'ranscribed .)A strand $template& 31 2 T 2 A 2 ! 2 T 2 G 2 A 2 .1
*)A P 2 P 2 P2 .1 2 A 20 2 G 2 A 2 ! 2 0 2 31 2 O4

'ranscription progresses at a rate of about 80 nucleotides per second!
/essenger *)A contains additional base se0uences that do not code for proteins!
'he leader $e5uence at its ,- end contains recognition signals for ribosome binding, which
allow the ribosomes to be properly positioned to translate the message!
3+ Termination+
At the end of the coding se0uence there is a special termination or $top codon!
6AA, 61A, or 6A1 are termination codons!
Ehen the *)A polymerase II transcribes a stop codon, transcription stops!
:eader se0uence coding se0uence termination codon!
'he stretch of .)A that is transcribed into an *)A molecule is called a transcription unit!
Termination o& Tran$cription
In pro6ar%ote$, transcription proceeds through a terminator se0uence in the .)A!
'he transcribed terminator in the *)A functions as the termination signal, causing the
polymerase to detach from the .)A and release the transcript!
In eu6ar%ote$, the pre+m*)A is clea#ed from the growing *)A chain while *)A polymerase II
continues to transcribe the .)A!
'he *)A polymerase II continues for hundreds of nucleotides past the termination signal!
'he termination signal in the .)A codes for what is called the pol%aden%lation signal
$AA6AAA& in pre+m*)A molecule!
About 10 to 7, nucleotides past the AA6AAA, the *)A is cut fee from the polymerase enyme!
'he polymerase detaches from the .)A by a mechanism that is not understood!
E07AR8OTI! !E"" MO#IF8 RNA AFTER TRAN!RIPTION
Alteration o& mRNA end$+
'he newly synthesied pre+m*)A is modified before it goes to the cytoplasm!
'he ,A end is capped off with a modified form of a guanine nucleotide $unusual nucleotide, 7+
methyl guanylate&!
1. It helps to protect the m*)A from degradation by hydrolytic enymes!
2. 'he ,A cap signal the place of attachment of the m*)A to the ribosomes!
'he 7A end is capped with poly$A& tail consisting of some ,0 to 3,0 adenine nucleotides!
'he function of the poly$A& tail is similar to that of the ,A cap9 protecti#e and attachment to
ribosomes! 'he 7A also facilitates the e5port of the m*)A from the nucleus to the cytoplasm!
;5ample of a capped pre+m*)A9
G 2 P 2 P 2 P2 0TR 2 $tart codon 2 .1 2 A 20 2 G 2 A 2 ! 2 0 2 0TR9AA0AAA: 2 31 2 AAAA+++AAAAA
'here are sections of the *)A besides the polyA tail and the ,- cap that will not be translated!
'hese regions at the ,- and 7- ends are called 6'* for untran$lated region$
Tran$lation modi&ication$; noncoding and coding $e5uence$
/ost eu(aryotic genes and their *)A transcripts ha#e long noncoding se0uences of
nucleotides!
'hese noncoding stretches of nucleotides do get translated!
'he noncoding regions are called intron$ $inter#ening se0uences&!
'he coding regions are called e-on$ $e5pressing se0uences&!
1enes may ha#e multiple introns and e5ons!
'he entire gene is transcribed and it contains both introns and e5ons! 'his is called precur$or
mRNA or pre-mRNA!
Introns must be remo#ed and the e5ons spliced together for the m*)A to become functional!
1. 'he pre+m*)A combines with $mall nuclear ribonucleoprotein$ $$nRNP$& and other
proteins to form a molecular comple5 called a $pliceo$ome!
2. Eithin the spliceosome, sn*)<s base pairs with nucleotides at the ends of the intron!
3. 'he *)A transcript is cut and the intron is released, and e5ons are spliced together! 'hen
the spliceosome is released!
Ribo<%me$+
*)A is capable of catalying some reactions!
In a few cases, the splicing of e5ons occurs without the assistance of enymes9 the intron
catalyes its own e5cision!
*iboymes are catalytic *)A molecules!
Function$ o& intron$+
>ome introns seem to control gene acti#ity!
>ome genes gi#e rise to two or more polypeptides by alternati)e RNA $plicing!
.ifferent segments of the *)A can be treated as introns or e5ons!
>ome proteins ha#e structural and functional sections that perform two functions, e! g! catalytic
and attachment to the membrane! 'hese areas are called domain$!
.omains are coded for by different e5ons!
Introns increase the probability of crossing o#er between genes without interfering with coding
se0uences!
It increases the chances of recombination between two alleles and of crossing o#er between
homologous chromosomes! )ew and potentially useful proteins could arise in this way!
'his re$hu&&ling of e5ons may contribute to the e#olution of protein di#ersity!
PROTEIN 8NT4EI
Tran$lation is protein synthesis!
.uring translation the m*)A is decoded
'he four+base m*)A is con#erted into a 30+amino acid polymer!
Tran$&er RNA
Tran$&er RNA is the decoding molecule in the translation process!
'ransfer *)A is made in the nucleus and tra#el to the cytoplasm where it ta(es an amino acid
and deli#ers it to the ribosome to be incorporated into a protein!
'he t*)A is used repeatedly in both pro(aryotes and eu(aryotes!
;ach t*)A is specific for one amino acid!
'he cell (eeps a stoc( of amino acids in its cytoplasm!
At one end of the t*)A molecule there is a three-ba$e anticodon= which is complementary to a
three-ba$e codon in the m*)A!
At the other end of the t*)A, an amino acid is attached!
'he AA becomes attached to the t*)A before becoming incorporated into a polypeptide!
'he carbo5yl group of an AA becomes attached to the 7- end of a t*)A!!
'he amino group is left free to participate in peptide bond formation!
>pecialied regions of the t*)A9
Anticodon complementary to a m*)A codon!
>ite for amino acid binding!
>ite for ribosomal recognition!
>ite for the aminoacyl+t*)A synthetase recognition!
>obble h%pothe$i$
'here are 81 codons but the usual number of t*)A is %,! >ome cells ha#e only %0 different
t*)A to pair with 81 codons!
'he third base $,- end& on the anticodon is sometimes capable of forming hydrogen bonds with
more than one (ind of nucleotide of a m*)A codon $7- end&!
>ome t*)A can recognie up to three different codons!
Aminoac%l-tRNA $%ntheta$e$!
A t*)A that binds to an m*)A codon specifying a particular amino acid must carry only that
amino acid to the ribosome!
'here has to be a correct match between the t*)A and the amino acid!
Amino acids are attached to their respecti#e t*)A by specific enymes called aminoac%l-tRNA
$%ntheta$e$
'he aminoacyl+t*)A synthetase is specific for each amino acid! 'here are 30 of these
enymes!
'he binding of the t*)A and amino acid is an endergonic process that occurs at the e5pense of
A'<!
'he result is an acti#ated amino acid called aminoac%l tRNA!
'he resulting comple5 is called aminoac%l-tRNA$ bind to the messenger *)A coding
se0uence!
Ribo$ome$
Ribo$ome$ ha#e a catal%tic function and a $tructural function, to hold the m*)A, the
aminoacyl+t*)A and the growing polypeptide chain!
*ibosomes couple the t*)As to their proper codons on the m*)A and facilitate the formation of
peptide bond between amino acids!
;ach ribosome is made of a large and small subunit= each subunit contains one molecule of
ribosomal *)A and large amount of proteins!
In eu(aryotes, the subunits are made in the nucleolus!
;ach ribosome has three depressions called the A and P sites after the word aminoac%l-tRNA
$ite and peptid%l-tRNA $ite, and the E site for e-it $ite!
'he t*)A holding the polypeptide chain occupies the < site!
'he t*)A bringing the ne5t amino acid to be incorporated into the chain occupies the A site!
'he ribosome holds the t*)A and the m*)A close together and positions the new amino acid
for addition to the carbo5yl end of the growing polypeptide! 'hen the formation of the peptide
bond is catalyed and formed!
"efore translation begins, the ribosomal subunits are dissociated!
<rotein synthesis is di#ided into three stages9 initiation, elongation and termination!
Initiation
Initiation begins when the m*)A, a t*)A with the first amino acid of the peptide, and the two
subunits of the r*)A come together!
'he se0uence of nucleotides at either end of the m*)A molecule helps to bind the molecule to
the ribosomal subunit!
In all organisms the codon for the initiation of protein synthesis is A61, which codes for the
amino acid methionine! 'his is called the initiation tRNA!
1! /essenger *)A binds to the small ribosomal subunit! 'he subunit binds attaches to the
,A end of the m*)A!
3! 'he initiation tRNA binds to a specific codon called the $tart codon9
the t*)A anticodon 6AC binds to the start codon A61! 'his t*)A carries the amino
acid methionine!
7! 'he large ribosomal subunit then binds to the small one creating a functional ribosome!
<roteins called initiation &actor$ bring all these components together!
%! Ehen the initiation process is completed, the initiator r*)A sits in the < site of the
ribosome, and the #acant A site is ready for the ne5t aminoacyl t*)A!
'he synthesis of peptides is initiated at its amino end, which is called the )+terminus!
'he other end is called the C+terminus= C for the carbo5yl end!
Elongation
'he initiator t*)A is bound to the < site of the ribosome!
'he A site is unoccupied!
Amino acids are added one by one to the polypeptide chain!
1! Codon recognition! 'he anticodon of an incoming aminoacyl+t*)A carrying an amino acid
binds to the codon of the m*)A in the A site! 'he bonds are hydrogen bonds!
;longation factors bring the t*)A to the A site!
'his reaction re0uires energy, which is pro#ided by 3 molecules of 1'<, guanosine
triphosphate!
3! Peptide bond formation! 'he polypeptide separates from the t*)A to which it was bound $in
the < site& and attaches by a peptide bond to the amino acid carried by the t*)A in the A site!
'he amino group of the AA at the A site is aligned with the carbo5yl of the AA in the
< site!
'he ribosome catalyes the reaction! 'he enyme is called peptid%l tran$&era$e, a
component the large ribosomal subunit!
*)A catalysts are called ribo<%me$!
7! Translocation! 'he t*)A at the < site now lea#es the ribosome and ribosome translocates
$mo#es& the t*)A in the A site, carrying the growing peptide chain, to the < site! 'he m*)A
mo#es with it!
'he codon and anticodon remain bonded and the m*)A and t*)A mo#e as a unit!
'he ne5t m*)A codon is brought in to the A site!
;nergy is supplied by 1'<!
'ranslocation occurs in a ,-+to+7- direction of the m*)A!
Termination9
1. 'ranslocation is repeated many times until a $top codon reaches the ribosome A site!
2. 'he codons 6AA, 6A1 and 61A do not code for amino acids but signal to stop translation!
3. A protein called relea$e &actor binds directly to the stop codon in the A site!
4. 'he release factor causes the addition of a water molecule instead of an amino acid to the
polypeptide chain!
5. 'his reaction hydrolyes the complete polypeptide from the t*)A that is in the < site, freeing
the polypeptide from the t*)A that is in the < site!
6. 'he ribosomes dissociate into the two subunits, which can then be used to form a new
ribosome!
A single ribosome can ma(e an a#erage sie polypeptide in less than a minute!
Pol%ribo$ome$
A pol%ribo$ome or polysome, is a comple5 of one m*)A and many ribosomes!
Bnce the ribosome mo#es past the initiation code, a second ribosome can attach to the m*)A
and start its own translation of a new polypeptide!
A m*)A is generally translates simultaneously by se#eral ribosomes!
<olyribosomes occur in both pro(aryotic and eu(aryotic cells!
POTTRAN!RIPTION MO#IFI!ATION IN E07AR8OTE+
'he basic features of transcription and translation are the same in pro(aryotes and eu(aryotes!
;u(aryotic m*)A molecules undergo specific po$t-tran$criptional modi&ication and
proce$$ing before they become competent for transport and translation!
After synthesis, the polypeptide begins to fold forming a functional protein, a three dimensional
protein with its secondary and tertiary structure!
A gene determines the primary structure
'he primary structure in turn, determines conformation!
Certain amino acids may become modified by the attachment of sugars, lipids, phosphate
groups, or other molecules!
>ome amino acids may be remo#ed from the leading end of the polypeptide!
In some cases, the polypeptide may be cut in two or more pieces, or two polypeptides that ha#e
been synthesied separately may be Coined to form the 0uaternary structure of a functional
protein!
ignal mechani$m &or targeting protein$ to the ER+
4ree ribosomes are suspended in the cytosol and ma(e proteins that dissol#e and function in
the cytosol!
"ound ribosomes are attached to the cytosol side of the ;* membrane!
'hey ma(e proteins of the endomembrane system $nuclear en#elope, ;*, 1olgi apparatus,
lysosomes, #acuoles, and plasma membrane& and protein that are secreted by the cell!
<olypeptide synthesis begins in the cytosol!
A se0uence called $ignal peptide, made of about 30 amino acids near the leading amino end
of the polypeptide is recognied by a protein+*)A comple5 called the $ignal-recognition
particle, RP, as it emerges from the ribosome!
'he >*< binds to a receptor protein in the ;* membrane!
'he receptor is part of a protein comple5 that has a pore and a signal+clea#ing enyme!
'he >*< lea#es and the polypeptide resumes growing emerging into the cisternal space of the
;*, through the protein pore!
'he signal peptide is remo#ed by an enyme!
'he finished polypeptide is released into the cistern or remains partially embedded in the ;*
membrane if it is destined to that structure!
T%pe$ o& RNA in a eu6ar%otic cell+
1! /essenger *)A, t*)A and r*)A!
3! <rimary transcript or pre+m*)A9 direct product of transcription= contains introns and e5ons!
7! >mall nuclear *)A $sn*)A&9 part of the spliceosomes, the comple5es of protein and *)A
that splice pre+m*)A in the nucleus!
%! >*< *)A9 part of the signal recognition of polypeptides destined to the ;*!
,! >mall interfering *)A, si*)A, and micro*)A, mi*)A, ha#e been recently disco#ered and
are in#ol#ed in regulating which genes get e5pressed!
8! >mall nucleolar *)A, sno*)A, aid s in processing pre+r*)A transcripts in the nucleolus!
M0TATION
A gene is a &unctional unit!
Mutation$ are disruptions on the structure of a chromosome or changes in a single base pair of
nucleotides!
Point mutation$ are chemical changes in one base pair of a gene!
Ba$e-pair $ub$titution in the .)A results in a different base pair that will be transcribed into
an altered m*)A!
"ase+pair substitutions could be!!!
Mi$$en$e mutation$ result in the replacement of one amino acid for another= this
replacement may or ma(e not ma(e Fsense!F
Non$en$e mutation$ con#ert an amino acid specifying codon into a termination codon!
In$ertion$ and deletion$ are additions or losses of nucleotide pairs in a gene!
In a &rame$hi&t mutation one or two nucleotides are inserted or deleted from the .)A!
As a result, the codons downstream of the insertion specify an entirely new se0uence of amino
acids!
/utations can be produced by errors in .)A replication, by physical agents $radiation& or by
chemicals called mutagen$!
"ase analogues a re similar to normal .)A bases but pair incorrectly during .)A
replication!
Chemicals that insert themsel#es in the .)A and distort the double heli5!
Chemicals that change the structure of the bases and their chemical properties!
>hat i$ a gene?
A region of the .)A encoding a polypeptide or an *)A molecule, as their final products!
0MMAR8 OF T4E !4ARA!TERITI! OF T4E GENETI! !O#E
/essenger *)A consists of only four bases, A, 1, C, and 6, forming chains of #arious
lengths and se0uences!
m*)A codon that specifies a gi#en AA is a triplet of three nucleotides!
;ach codon is translated in a continuous se0uence, three successi#e nucleotides at a time!
'he code is nono#erlapping!
'he codon se0uence complements an anticodon se0uence in the adapter t*)A!
'he code is uni#ersal! All li#ing organisms share the codons that specify the same AA!
'he same codon does not specify two or more AA! 'here are no ambiguities!
;5cept for methionine and tryptophan, all AA are designated by more than one codon! 8%
codons specify 30 AA and chain termination!
.egeneracy in the third codon position!
>obble h%pothe$i$9 the third nucleotide of the t*)A anticodon can form hydrogen bonds with
more than one (ind of base in the third position of a codon!